Friday, February 28, 2020

Iris Publishers-Open access Journal of Civil & Structural Engineering | Effect of Garment Wastes on Swell-Consolidation Characteristics of Expansive Soil



Authored by Md Shariful Islam*



Introduction

Expansive clays are considered as a problematic due to high shrinkage and swelling potential. Expansive clays swell considerably when water is added to them and then shrink with the loss of water. Many civil constructions and foundations are subjected to large uplifting forces caused by swelling and shrinkage problems. These forces impact heaving, cracking and the breakup of both building foundation and slab-on-grade members. Expansive clays cover large parts of the United States, South America, Africa, Australia, India and a little portion of Bangladesh. There are little amount in research and investigation on swelling and shrinkage problems of expansive clay which are performed in Bangladesh. For Bangladesh it can be considered as a great significant data study due to its engineering significance, it has drawn attentions to many researchers and designers. Many innovative techniques are developed to counteract the problems posed by expansive soils by transformation of soil index properties with the addition of chemicals such as cement, fly ash, lime or combination of these, often alter the physical and chemical properties of the soil including the cementation of the soil particles. Especially use of lime or sand admixture has proved to have a great potential as an economical method for improving the geotechnical properties of expansive soils. These methods are quite effective in controlling the volumetric changes in expansive soils. Apart from the above techniques, geosynthetic inclusions as a technique of random reinforcement have also been found quite effective in controlling swelling and shrinkage [1]. Compacted expansive soils, reinforced with polypropylene fibres, have exhibited reduced tension cracking and controlled volumetric changes due to swelling and shrinkage [2]. Shen SL, et al. [3,4] observed that fibre inclusions increased the tensile strength. A combination of fly ash and polypropylene fibres has also been found to reduce the swelling and shrinkage characteristics of expansive soils [5-7]. Yilmaz I, et al. [8] observed that an increase in fiber content led to a reduction in the swelling potential of lime-stabilized clayey soil. Al-Muhaidib et al. [9] investigated the effect of two types of fibres (natural and synthetic) on the swelling properties of clayey soils. Jamsawang P [10] presented that the swell-consolidation characteristics of remoulded expansive clay specimens reinforced with randomly distributed nylon fiber. The secondary consolidation characteristics of both unreinforced and fiber-reinforced specimens also studied. It should be mentioned here that there are quite a few differences between the work done by [9].
In this paper, two types of soil samples been considered, and soil has been collected from two different locations of Bangladesh. One is Ghodagari in Rajshahi that is the north part of Bangladesh and another is Gazipur in Dhaka that is the east part of Bangladesh. The main objectives of this paper is to evaluate the swellingconsolidation and unconfined compression characteristic of fiberreinforced of two different remolded expansive soils. This paper presents that the effective in controlling the volumetric changes in two expansive soils by using polysynthetic (Garment waste). This fiber chooses due to locally available and economical in Bangladesh. This fiber also uses as a recycling purpose. It also presents the comparison the swell-consolidation and unconfined compression characteristics of two different types of remoulded expansive clays specimens reinforced with randomly disturbed of polysynthetic (Garment waste). The odeometer test (one-degree consolidation test) of both unreinforced and reinforced specimens were observed. It should be mentioned that there is a little bit difference between the work done by Jamsawang P [10]. The fibre content presented in Jamsawang P [10] ranges from 0% to 0.3% that time nylon fibre was considered whereas this paper presents that one type of fibre (polysynthetic (Garment waste) and the ranges from 0% to 2%. The aspect ratios(l/d) considered in this paper were only 15 which is similar to Jamsawang P [10].

Swelling potential and swelling pressure

The term swelling potential is generally used to indicate the amount of vertical swell (expressed as percentage of initial sample thickness) obtained under a particular surcharge (usually 1psi).
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Where, Sp = swelling potential in percentage
δh = amount of vertical swell
h = initial height

The swelling pressure is defined as the vertical pressure required to prevent volume change of laterally confined sample when it is allowed to take in water. Percent expansion decreases with increase in confining pressure for a given initial moisture content and density.




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Iris Publishers-Open access Journal of Civil & Structural Engineering | Stability Performance Assessment of Pipelines under Hydrostatic Pressure




Authored by Tadeh Zirakian*


Introduction

Subsea pipelines are externally loaded by a constant source of hydrostatic pressure. Local buckling can occur at pressures much lower than that required for critical buckling (Pcr), and after one region has been compromised, the zone of damage may begin to expand along the length of the pipe leading to eventual collapse of the pipeline [1,2]. During buckling and the ensuing propagation of damage, significant changes are found to occur in the cross section of the pipe geometry. An analysis of post-buckling behavior prior to total collapse should be considered in order to better understand the gradual failure mechanisms of these structures in both the radial as well as longitudinal directions [3-6]. As depicted in Figure 1, the phenomenon of buckling tends to flatten the pipeline in cross section locally, while propagation of this damage longitudinally may be characterized by three zones: the near-end buckled and far-end unbuckled regions, and a transition of pipe length between the two (Figure 1). After buckling initiation, damage propagation reaches a steady state for which the external hydrostatic pressure is constant. Buckling propagation stops when the external hydrostatic pressure is lower than the buckle propagation pressure [7]. According to the elastic stability theory, deformation of pipeline occurs in two stages: pre-buckling and post-buckling [8]. Research has shown that in loads lower than the buckling load, deformation of pipeline is based on a stable pre-buckling path [9,10,12]. As pressure increases, the pipeline section starts to develop plastic hinges and then begins to fail. With the continual increase in pressure, the pipeline undergoes further deformation in the radial direction until the onset of pipeline buckling at a certain external pressure, i.e. the critical buckling load Pcr. Beyond this point, the pipeline behavior is described by the post-buckling path, which may be unstable for pipelines with elasto-plastic materials. The pipeline deformation diagram is portrayed in Figure 2 Illustrated in Figure 3 is also the development of yield lines with buckling propagation along the pipeline section (Figure 2 & 3).

Behavior of pipelines in response to external pressure has been the subject of numerous studies, which have shown that length of the pipe and ratio of its diameter to the wall thickness play a decisive role in the pipe’s resistance against buckling. According to Bresse [13], the stability of pipelines under hydrostatic pressure as based on small deflection theory, the critical buckling pressure Pcr can be obtained using the following equation:
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In Eq. (1), R is the pipeline radius, E is the Young’s modulus of elasticity of the pipeline material and I is the moment of inertia of the pipeline cross-section. A similar formula has been developed by Bryan [14], i.e. Eq. (2), for a freestanding long pipeline subjected to hydrostatic pressure. The difference between Bryan’s and Bresse’s formulae is the replacement of E with E/(1-ν2). This accounts for plane strain conditions in computing the buckling pressure of infinitely long pipes.
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In the above equation, D is the mean diameter of the pipeline, E is the Young’s modulus of elasticity of the pipeline material, t is the mean thickness of the pipe wall, and ν is Poisson’s ratio. The first research introducing the buckling propagation in pipelines was the work of Mesloh et al. [15] followed closely by Palmer and Martin’s study [16]. In the latter study, it was claimed that the propagation pressure can be determined using the strain energy of the collapsed cross-section of the pipe with an equation proposed for this purpose. In this research, the experimental values obtained with low diameter-to-thickness ratios (D⁄t) were greater than the predicted results. This issue is expected in deep water conditions considering the effects of plastic deformation [7]. The studies of Johns et al. & Mesloh et al. [1,15], took an experimental approach to this subject and determined the adequacy of different arrestor geometries for stopping the buckling propagation. These studies resulted in the empirical formula of propagation pressure Ppr based on diameter, thickness, and yield stress (σY).
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Palmer & Martin [16] proposed the following formula for predicting the buckling propagation pressure in pipelines Ppr. This equation is based on the assumption that the material is rigid and perfectly plastic. In their model, four plastic hinges govern the collapse mechanism during buckling propagation based on an energy balance.
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Barlow’s formula [17], i.e. Eq. (5), is used for calculating the hoop stress in thin-walled cylinders with D0/t>20, in which D0 is the outer diameter and t is the wall thickness.
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Where, Pi is the internal pressure and Pe is the external pressure applied on the pipe as shown in Figure 4, and H σ is the hoop stress in this equation. It is noted that the use of this equation is limited to thin-walled pipes [18].

Internal and external pressures induce hoop stress, which results in expansion of the pipe’s circular cross-section. On this basis, while studying the fully- or partially-anchored pipelines, one can expect to observe the Poisson effect, i.e. the expansion or compression of material in one direction due to an external force which entails compression or expansion reaction in the other direction [19,20]. Thus, because of the Poisson effect, the hoop stress in an anchored pipeline creates longitudinal stress. Pressure-induced longitudinal stresses in an anchored pipeline can be obtained from the following equation:




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Thursday, February 27, 2020

Iris Publishers-Open access Journal of Ophthalmology & Vision Research | Eye Regeneration and Healing with Amniotic Membrane




Authored by Carmen Álvarez*


Complementary

If a person has suffered some tumor, ulcers, epithelial defects of the cornea and the conjunctiva, the treatment with amniotic membrane (MA) provides very satisfactory results to achieve the healing and reconstruction of the ocular surface in the short and long term. It is possible to opt for the use of the amniotic membrane, a medical-surgical procedure that is also used to increase the chances of success in some corneal surgeries, when there are cases with problems of tissue regeneration or scarring in the postoperative period. The amniotic membrane is used since the 40s in ophthalmology and is the innermost layer of the placenta, which is obtained in deliveries performed by elective cesarean sections. Prior to obtaining the placenta - the written authorization of the mother is needed and the same protocol for the donation of other tissues is carried out. “It is an essential requirement to avoid possible transmission of infectious diseases in the recipient and other complications” .. MA deflates and heals.
The amniotic membrane (MA) It is a resistant tissue, transparent, thin and rich in collagen that lines the placenta, in the period of fetal development, very similar to the skin. It is formed by three layers: epithelial, basal membrane and stromal matrix. “The basement membrane facilitates the migration of the epithelial cells responsible for the differentiation and proliferation of cells of the corneal surface and inhibits their death.” Amnio is of fetal origin and becomes the inner layer. Its outer surface is composed of connective tissue and epithelial cells. “Amnio alone does not provide stem cells, but allows proper reproduction and migration of epithelial cells, meaning that the amniotic membrane acts to promote reepithelialization of the cornea and releases substances with great anti-inflammatory power, promotes healing, reduces the production of fibrosis and the formation of new vessels on the ocular surface “.

How does it work?

The use of the amniotic membrane can heal in two ways
• As a graft, that is to say placing the basement membrane upwards to produce a growth of the epithelial tissue above the MA, restoring the ocular surface.
• By coating placing the basement membrane down to reduce the inflammatory process, favor re-epithelialization and decrease the healing process under the membrane.
It is currently used successfully in ocular surface surgeries.
Corneal reconstruction
Recurrent corneal erosions, corneal ulcers, perforations, bullous keratopathy and persistent epithelial defects.
Conjunctival lesions
pterygium, epithelial tumors, damaged blisters in glaucoma surgery.
Healing ocular lesions


Symbéfaron, deficiency of stem cells, scleromalacia, reconstruction of the cul-de-sac, band keratopathy, temporary coating and in the treatment of chemical ocular burns.



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Iris Publishers-Open access Journal of Ophthalmology & Vision Research | Corneal Transplantation Today. Giving Patients A Better Quality of Life




Authored by Cesar Gomezperalta*


Complementary

Corneal transplant has been around for many years, the first one done more than a 100 years ago. Although the principle is the same, exchanging unhealthy, distorted, opaque or decompensated tissue for a healthy one, thanks to the evolution, knowledge in Medicine, higher technology and the need for more successful results, corneal transplant has reached a very specialized status.
With Penetrating Keratoplasty or Lamellar Keratoplasty the cornea can be exchanged in a partial or total way depending on the patient‘s pathology. In developed countries lamellar surgery is the gold standard for corneal transplant and in developing countries penetrating keratoplasty is still done in large numbers. The full thickness exchange of the cornea, the penetrating keratoplasty, is performed for pathologies in which most or all of the cornea is altered being opaque, scared or decompensated. It is a very good procedure, although endothelial rejection and open eye surgery complications can occur. Also, as endothelium is replaced, durability is an issue and a new transplantation may be necessary years after.
On the other hand, partial thickness exchange, lamellar keratoplasty, can be performed anteriorly or posteriorly. Anterior Lamellar Keratoplasty, removes scars, alterations in shape such as Keratoconus and transparency issues. You can remove up to 95% of the anterior tissue. It can be done manually, with microkeratomes or femtosecond lasers. It gives great visual results, has no endothelial rejection and the graft can last a lifetime. Posterior Lamellar Keratoplasty or Endothelial Keratoplasty was developed to remove only the abnormal or deficient endothelium. Different techniques have been presented and aimed for minimal invasive surgery, damage less and less the grafted tissue and fast visual recovery. It may also have endothelial rejection and other complications.

In many countries of the world corneal transplant still has social and religious considerations. There is still tabu about receiving someone else’s part of the eye and donation issues are still complicated. What it is a fact, is that patients that have been transplanted they recover functionality, quality of vision and what it is more important, quality of life. Patients with low vision due to corneal pathology stop working, stop doing daily life activities and has a very negative impact on their lives. In a study done at our clinic (Vision Percepcion - Mexico City, Mexico), one hundred transplanted patients for Keratoconus that depended 100% in glasses or contact lenses to function and partially do their life, work and activities, recovered not only good vision much less dependent on the use of a correction, but most of them without glasses could do their work, hobbies and normal life. Corneal transplant is not a surgery to remove glasses but when restoring corneal architecture other procedures may be performed to help patients see without them. This corrective procedure includes laser, phacoemulsification and intraocular lenses on their various modalities (Figure 1).




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Wednesday, February 26, 2020

Iris Publishers-Open access Online Journal of Dentistry & Oral Health| Orthotropics Technique in Orthodontics










Authored by Rohit Kulshrestha*



Short Communication

Orthotropics is a wellness strategy that enables children to develop straight teeth and good dental and jaw alignment. However, equally important, the orthotropic approach also improves facial appearance and positively impacts a child’s health through airway development and better posture. Ideally active orthotropic treatment begins between the ages 6-8 and finishes long before most traditional orthodontic treatment would even begin. It addresses the underlying causes of bad bites and misaligned teeth utilizing removable dental appliances as opposed to braces. If begun at the ideal age, Orthotropics negates the need for the extraction of adult teeth or jaw surgery and minimizes or eliminates the need for fixed braces during adolescence [1].
Traditional orthodontics focuses primarily on straightening misaligned teeth. The main goal is to create a great smile with perfect tooth alignment, and a proper bite (occlusion). Braces and wires, or aligners such as Invisalign® are the preferred way of aligning the teeth. In cases of severe crowding, some teeth may be extracted. Poor jaw relationship is corrected by using various mechanics and appliances, such as elastics, headgear, Herbst, etc. Severe discrepancy in jaw relationship is usually resolved by jaw surgery in adulthood, when all growth is complete. Orthotropics is a philosophy and treatment focused on proper and harmonious facial development. Its primary objective is the correction of unfavorable growth pattern of both jaws (usually excessive vertical growth and lack of horizontal growth). Such adverse growth has both an aesthetic and a functional impact on the patient. It produces longer, narrower, flatter faces with larger noses and sagging tissue later in life; and with lack of proper forward growth of the face, airway may be compromised.
New evidence shows that in growing children, adequate airway flow plays a crucial role in somatic, cognitive and behavioral development. Orthotropic treatment helps develop better facial features and wider airways. It is more face centered than tooth centered. As such, it does not produce perfect tooth alignment - but it does significantly improve crowding, Tooth alignment can be done later, if desired, with braces or with non-brace aligners (phase II treatment). Orthotropics may prevent the need for jaw surgery later in life [2].
Orthotropics utilizes the concepts of aesthetics, function, structural and neurological balance and airway maximization for diagnosis and treatment-planning for both children and adults. Extensive research, and continuous development allows the orthodontist to use Orthotropics to determine the most meaningful and efficient course of treatment that addresses all individual concerns.

 In order to maintain good oral posture, it’s succeeded by having your tongue rest on your top palate. And you need enough room for it, for both width and length. Orthotropics can help you grow your mid-face, which means to grow more room for your top palate, so you can maintain better oral posture and it allows your tongue to have more room to rest. Traditional orthodontics do not really provide growth guidance or vertical appliances. They may provide expanders to expand the width and space between your teeth, but their traditional idea is that it only works for those who are beneath a certain age. For example, until age 16, you cannot have an expander because you reached full growth. This is not true. Orthodontics is primarily concerned with the creation of well-aligned, attractive teeth. Both children and adults can successfully improve dental aesthetic and functional challenges with orthodontic care. Utilizing fixed braces and beginning typically after all adult teeth are erupted, age 11-13, orthodontic treatment does not manage the underlying causes of malocclusion and thus after active treatment, long term wear of retainers is necessary to prevent relapse [3]. In addition, without adjunctive jaw surgery, orthodontics has minimal impact on facial appearance and long-term general health.





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Iris Publishers-Open access Online Journal of Dentistry & Oral Health| Rotated Upper Central Incisor Complicated by Pathological Migration with Crowding in Upper and Lower Anterior Teeth Treated by Clear Aligners



Authored by Cecilia Young*


Background

Pathological tooth migration increased between 2.95 to 7.97 times as bone loss increased [1], it is difficult to treat, and the multidisciplinary approach is usually needed [2-4]. The combination of periodontal and orthodontic treatment is being used to improve the periodontal conditions and esthetics [2-6]. Most of the case reports were related to tipping or intrusion of the central incisors [2-6]. Fixed appliances make brushing and flossing more difficult. Oral hygiene practices during clear aligner treatment can be easily maintained. A Meta-analysis concluded that clear aligners were better for periodontal health than fixed appliances [7]. Another systematic review showed a significant improvement of the periodontal health indexes was revealed, in particular when clear aligner treatment was compared to fixed appliances [8], no periodontal adverse effects were observed in the studies using clear aligner treatment [8].
Yunyan et al concluded that clear aligners had advantage in segmented movement of teeth and shortened treatment duration in a systematic review [9], the eight relevant studies used Invisalign [9]. Rossini et al. stated that clear aligner treatment aligns and levels the arches; it is effective in controlling anterior intrusion but not anterior extrusion; it is effective in controlling posterior buccolingual inclination but not anterior buccolingual inclination; it is effective in controlling upper molar bodily movements of about 1.5mm; and it is not effective in controlling rotation, of rounded teeth in particular [10]. The devices applied in the 11 relevant studies were Invisalign [10].

Case Report

A 48-year-old lady with mobile rotated and overerupted upper right central incisor visited the dental clinic (Figure 1). She noticed that the tooth became longer and very mobile and wanted to improve the esthetics. She had no complaint with the profile (Figure 2). The upper and lower anterior teeth were crowded (Figure 3).


Diagnosis


It was difficult to estimate the original position of the tooth since the upper anterior teeth were crowded, whether it was pathologically migrated or the tooth was originally in an imbalance position that could not be controlled by the lip and finally over erupted and then started the periodontal problem, to help the discussion for the treatment goals, the operator requested the photos in her young age. The 11 was rotated but on the occlusal plane when she was 20 years old (figure 4). Pre-op OPG showed that there was generalised bone loss (figure 5). Pre-op tracing showed slightly retruded Maxilla and Mandible (Figure 6). 11 was rotated (figure 3) and overerupted (figure 3) with mobility.



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Tuesday, February 25, 2020

Iris Publishers- Open access Journal of Urology & Nephrology | Evaluation of the 29 MHz Micro-Ultrasound Imaging for Prostate Cancer Diagnosis and Treatment



Authored by Whitney Stanton*


Introduction

Prostate cancer is the most common form of malignancy and the second leading cause of cancer death in men in the United States. In 2019, approximately 174,650 cases of prostate cancer will be diagnosed [1]. Although a serious disease, most men will not die from prostate cancer. The use of the prostate specific antigen (PSA) blood test and trans-rectal ultrasound guided (TRUS) biopsy have resulted in over-diagnosis and overtreatment of clinically insignificant prostate cancer while also missing high-risk clinically significant tumors [2]. Clinically significant prostate cancer is defined as a lesion with high-grade prostate cancer (Gleason Score ≥ 7) or volume ≥ 0.5 cc. Therefore, it is important to identify men who have clinically significant prostate cancer who would benefit from treatment as well as identify men with low-risk tumors who would benefit from a more conservative approach such as active surveillance.
The use of multiparametric magnetic resonance imaging (mpMRI) in conjunction with the Prostate Imaging and Reporting Data System version 2 (PIRADS v2) allows physicians to target lesions in the prostate for biopsy [2]. PIRADS v2 assigns one composite score that indicates risk of clinically significant prostate cancer on mpMRI. A PIRADS score of 3, 4, or 5 designates intermediate, high, or very high risk of clinically significant prostate cancer, respectively. Men with a PIRADS score ≥ 3 are recommended for prostate biopsy, but a PIRADS score ≤ 2 cannot rule out clinically significant prostate cancer. Conventionally, a patient undergoes mpMRI and the urologist uses the mpMRI report to guide prostate biopsies in-office using a real-time urologic ultrasound, which operates at 6-9 MHz. The ExactVu™ Micro-Ultrasound system (ExactVu™ Micro-Ultrasound, Exact Imaging, Markham, Canada) is a new 29 MHz prostate imaging technique which provides a realtime imaging of cancer lesions at a high resolution of 70 microns [3]. In a study comparing high resolution micro-ultrasound imaging to mpMRI, micro-ultrasound imaging provided similar sensitivity to clinically significant prostate cancer as mpMRI. Micro-ultrasound imaging provides a real-time, high-resolution ultrasound platform and can be used to guide prostate biopsies in-office with improved imaging resolution compared to conventional urologic ultrasound, making it more time and cost effective. Herein, we describe our findings of micro-ultrasound imaging compared to preoperative mpMRI for the diagnosis of cancer lesions. Micro-ultrasound was employed as an adjunct in addition to standard-of-care TRUS in four men undergoing primary and salvage cryotherapy.

Discussion

This study received institutional review board approval under COMIRB #19-139. Four patients underwent cryotherapy for treatment of non-metastatic prostate cancer. Each patient had confirmatory TRUS biopsy pathology, three of the four men had prior mpMRI, and all men had micro-ultrasound before, during, and after cryotherapy in addition to the standard-of-care transrectal ultrasound. All cases were performed according to the same surgical protocol and by the same surgeon. Two freeze thaw cycles were completed and were monitored via ultrasound. The entire prostate gland was treated. The cryotherapy probes were placed through the cryotherapy template under ultrasound guidance [4].
Case 1
This patient was a 73-year-old male with no family history of prostate cancer. He had previous cyberknife radiotherapy in 2011 for Gleason grade group 3 (4 + 3 = 7) prostate cancer involving seven out of 26 biopsy cores. Cyberknife radiotherapy is a form of imageguided stereotactic body radiation therapy [5]. After cyberknife radiotherapy, his PSA nadired to 0.4 ng/ml, but slowly increased to 2.6 ng/ml prompting a PET-CT scan in August 2018. The PETCT revealed a centrally located focus of increased tracer uptake within the inferior prostate, likely compatible with malignancy. There was no evidence of bony metastases. In September 2018, the patient underwent a 20-core TRUS biopsy and was found to have Gleason grade group 3 (4 + 3 =7) in 1 of 20 cores and Gleason grade group 2 (3 + 4 = 7) in 1 of 20 cores involving 15 and 30% of each core, respectively. The mpMRI demonstrated a 1.6 cm diffusion restricting early enhancing lesion in the central gland near the apex and was concerning for disease recurrence. The prostate volume was 32 cc. During his cryotherapy procedure, three probes were used: two on the left and one on the right. The prostate volume was 49.7 g. The micro-ultrasound identified suspicious lesions bilaterally at the apex, consistent with the mpMRI.
Case 2

This patient was a 67-year-old male with history of a urethral stricture. An elevated PSA of 6.77 ng/ml prompted a TRUS biopsy that revealed Gleason grade group 3 (4 + 3 = 7) prostate cancer with multifocal perineural invasion. He had a negative CT of the abdomen and there was no evidence of metastatic disease in the abdomen or pelvis. A mpMRI of the prostate revealed a PIRADS 4 nodule (9 mm hypointense) in the lateral left peripheral zone in the mid aspect of the gland with acute restriction and a PIRADS 3 nodule (2.3 cm) in the anterior left transition zone from mid to base that predominantly had well-circumscribed boundaries, but demonstrated asymmetric enhancement with acute restriction. During his cryotherapy procedure, seven probes were used: four on the left and three on the right. The prostate volume was 50.3 g. The micro-ultrasound clearly visualized seminal vesicle invasion and extra-prostatic extension on left side, consistent with his biopsy findings.



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Iris Publishers- Open access Journal of Urology & Nephrology | Role of Retrograde Intrarenal Surgery in Management of Renal Stones: 3 Years Experience



Authored by Yadav Rajinder*


Introduction

The incidence of urinary stone disease is increasing all over the world due to environmental conditions in association with improving health services and diagnostic modalities [1,2]. The management of renal stones has evolved due to technological advancements in last few decades from open to percutaneous to very minimally invasive procedures. The success of these minimally invasive modalities has made open surgery for renal stone disease rare. PCNL (percutaneous nephrolithotomy) became the procedure of choice after its first description in 1976 for management of large burden renal stones and as a treatment option for small renal calculi [3]. Although PCNL had a good stone clearance rate, it is associated with a potential morbidity of bleeding which may need angioembolisation (0.6-1.4%) Michel MS, et al. [4] and so has limitations in patients with bleeding diathesis. Also, PCNL is technically more demanding and is a morbid procedure associated with longer hospitalization, postoperative pain, longer bed rest, and longer time to return to work etc. With rapid advances in technology, miniaturization of endoscopes, improvement in fiberoptic technology, availability of holmium: YAG laser and other ancilliary instruments have rendered RIRS (Retrograde Intrarenal Surgery) a better opportunity for management of renal and ureteric stones. Also, RIRS is associated with low complication rate, minimal morbidity and early return to work
We started flexible ureteroscopy in 2003 with the availability of 30 Watts Holmium laser. Initially we used to do diagnostic ureteroscopy and used to remove small stones left over after fragmentation by ESWL and PCNL and broken stents. With the availability of first flexible ureteroscope we could perform only 30 cases successfully. It was not possible to buy another flexible ureteroscope as it was costly. We borrowed the flexible laryngoscope and performed another 25 cases of removal of small stones from ureter and kidney. Both the scopes were from stortz. With the availability of baskets and flexible ureteroscope we performed RIRS in another 100 cases of upper ureteric and renal stones of up to 2 cm. size. More than 2 cm. size renal stones were treated by PCNL till 2013. With rapid advances in technology, miniaturization of endoscope and video endoscope and improvement in fiber-optic technology, availability of Holmium: YAG laser and other ancillary instruments has rendered RIRS (Retrograde intrarenal surgery) a better opportunity for management of renal and ureteric stones. Also, RIRS is associated with low complication rate, minimal morbidity and early return to work. At present RIRS is limited to patients where PCNL/ESWL are contraindicated because of presence of bleeding diathesis, patients with morbid obesity, malrotated kidney, malpositioned kidney and stone size up to 2 cm [5]. We have evaluated the feasibility and efficacy of RIRS for management of stones including those of stone size > 2cm (including partial and complete staghorn). Staged RIRS is performed for patients with large stone burden (partial and complete staghorn stones) as an alternative to PCNL [6].

Materials and Methods

A prospective study was done from August 2013 to June 2016. 274 patients with renal and upper ureteric stones including stone size > 2 cm to multiple, bilateral including even partial and staghorn stones underwent RIRS at our institution. RIRS was considered the first choice for management of renal stones coming to our hospital irrespective of stone size. Patients were pre-informed about staged procedure if they had bilateral large renal stones. Preoperatively, Stone size and laterality were assessed on NCCT KUB, X-ray KUB films or CT urography. All the patients were investigated for comorbidity. All the patients had urine culture and sensitivity done before the procedure and RIRS was carried out only after urine culture was sterile. Most of the patients were admitted on the same day in the morning and those who were suspected to have infection or obstructed system were pre-stented and treated for a week with appropriate antibiotics to clear the infection and improve renal function in those cases where renal functions were deranged. Almost all patients were operated under general anesthesia except for few cases who were not fit for GA, were done under spinal anesthesia. We did not routinely pre stent the patient. Cystoscopy was performed in all patients to rule out any urethral obstruction or bladder abnormality and to assess the compliance of ureteric orifices. We used video-endoscopes and flexible ureteroscope from Storz and Olympus with double deflection.
All the patients were ureteroscoped by semi-rigid ureteroscope of size 7/8.5 Fr. and guidewire was inserted into the kidney and the ureteroscope was passed up to the renal pelvis. There was no need to dilate ureteric orifice in patients in whom ureteroscope could be passed till renal pelvis and 14/12 Fr. was easily negotiated up to PUJ without any difficulty. We used new ureteroscopic sheath in all patients except in pre-stented patients, where old sheaths were reused. Those patients in whom ureteroscope could not be negotiated, dilatation of orifice was done with balloon dilator. Few of the patients had stricture in ureter, which did not allow urteroscopic dilatation and underwent balloon dilatation. During these procedures, if the patient had pyonephrosis or turbid infected urine, we did not proceed further, and patient was left with the stent and RIRS was done at a second stage. Double guide wire was rarely used. All these procedures were carried out under C-arm guidance.
RGP was not done in most of the cases except in few where the calyces were in awkward position, just to guide the ureteroscope into a particular calyx. Sometimes to access a stone in a difficult calyx, the table was tilted towards right or left depending on the side of the stone or by placing a sandbag under the renal angle. In 9 cases where access sheath could not be negotiated, flexible ureteroscope was guided over flexible biwire into the renal pelvis. We did not reposition the stones from calyces in most cases (except in 4 cases). If calyx was not negotiable, we divided the infundibulum, diverticular or calyceal neck with laser wherever needed, particularly in lower calyx to fragment the stones. We used 200-micron laser fiber in lower calyces and middle calyx stone and 365 microns in upper calyx and pelvic stones. Our energy setting was 0.2 Joules and 10 Hertz. We used painting and popcorn effect in all patients to fragment the stones. We did not used drilling technique. By painting technique, we powdered the stone by keeping the laser fiber 1-2 mm. away from the stone. In most of the cases painting was started from one of the margins and continued on the margins only. At the end of fragmentation, the stone was fragmented by popcorn effect where laser beam was focused in the center of the calyx and fragments flew like popcorns coming in contact with laser and get hit by laser fiber to become tiny fragments. Fragments were not removed except for taking few pieces for chemical analysis.

The stones were observed under C-arm and larger fragments were fragmented if visible. The fragments were basketed by tipless basket or by engage basket for chemical analysis. All the patients were stented after passing a guidewire through the sheath and the sheath was withdrawn under ureteroscopic guidance to see any injury to ureter. The stents were inserted over the guidewire into the collecting system without Ureteroscope and cystoscope by pusher under C-arm guidance. Patient was catheterized for next 24 hours. Most of the patients were discharged after 24 hours and allowed to resume normal work after 2-3 days. All the patients were advised to come for follow-up after 1 week to see the progress. They were advised to get X-ray KUB done after 3 weeks prior to stent removal. If any fragments of stone were found in kidney or ureter, they were relooked and removed during stent removal.

Results


Our case series has the largest study populations in adults published in literature until now. We had in total 274 patients, 185 patients being males and 89 females. 83 patients had single stone, 96patients had multiple stones, 54 patients had partial staghorn stone and 16 patients had staghorn stone. According to stone size 68 patients had < 1cm stone size, 99 patients had stone size 1-2 cm and 107 patients had > 2 cm stone size. 87 patients had unilateral renal stones, 85 patients had bilateral renal stones, 77 patients had renal with ureteric stones and 25 patients had upper ureteric stones (FIgure 1&2).


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Monday, February 24, 2020

Iris Publishers- Open access Journal of Biostatistics & Biometric Applications | Absolute Dpcr Quantification of Micrornas by Absolute Dpcr for the Diagnostic Screening of Colon Cancer


Authored by Farid E Ahmed*

Introduction

Colorectal cancer (CRC) is the third most common malignancy worldwide, with an estimated one million new cases and half million deaths yearly. Screening for CRC allows early stage diagnosis of malignancy and potentially reduces disease mortality. The convenient and inexpensive fecal occult blood test (FOBT) screening test has low sensitivity and requires dietary restriction, which impedes compliance. Although colonoscopy. Is the golden screening standard for the for this cancer, the invasive nature, abdominal pain and high cost have hampered worldwide application of this procedure. A noninvasive sensitive screen for colon cancer (CC) requiring no dietary restriction is a more convenient test. CC is more abundant in the USA than rectal cancer (RC).

The discovery of small non-coding protein sequences, 17- 27 nucleotides long RNAs (such as microRNAs), has opened new opportunities for a non-invasive test for early diagnosis of many cancers. MiRNA functions seem to regulate development and apoptosis, and specific miRNAs are critical in oncogenesis, effective in classifying solid and liquid tumors, and serve as oncogenes or suppressor genes. MiRNA genes are frequently located at fragile sites, as well as minimal regions of loss of heterozygosity, or amplification of common break-point regions, suggesting their involvement in carcinogenesis. Profiles of miRNA expression differ between normal tissues and tumor types, and evidence suggests that miRNA expression profiles can cluster similar tumor types together more accurately than expression profiles of protein-coding mRNA genes. Although exosomal RNA are missed, a parallel carried out on stool miRNAs to compare the extent of loss when colonocytes are only used can be carried out, and an appropriate corrections for exsosomal loss can be made. To ascertain the validity of a miRNA screening test for CC, it must be validated in a study, using a nested case control epidemiology design and employing a prospective specimen collection, retrospective blind evaluation (PRoBE) of control subjects and test colon cancer patients, as delineated by NCI’s Early Detection Research Network (EDRN) http://edrn.nci. nih.gov. Immunoparamagnetic are employed to capture colonocytes from harsh stool environment, whose extracted fragile total small RNA is stabilized shortly after stool excretion by commercial kits so it does not ever fragment, followed by standardized analytical quantitative miRNA dPCR-chip profiling in noninvasive stool samples, to develop a panel of few stable miRNAs for absolute quantitative diagnostic screening of early sporadic colon cancer (stage 0-1), more economically and with higher sensitivity and specificity than other CC screening test on the market today.

A preliminary global microarray expression analysis using an exfoliated colonocytes enrichment strategy, which employed control subjects and various stages (0-4) of CC, using Affymetrix Gene Chip miRNA 2.0 Array, showed 180 preferentially expressed miRNA genes that were either increased (124 miRNAs), or reduced (56 miRNAs) in expression in stool samples from CC patients. This allowed careful selection of 14 miRNAs (12 Up-Regulated, miR-19a, miR-20a, miR-21, miR-31, miR-34a, miR-96, miR-106a, miR-133a, miR-135b, miR-206, miR-224 and miR-302; and 2 Down-Regulated, miR-143 and miR-145) Table 1 for further PCR analysis (Table 1).
Then analysis carried out using absolute miRNAs expression by a chip-based digital PCR by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions; some of which contain the target molecule (positive), while others do not (negative). A single molecule can be amplified a million-fold or more. During amplification, TaqMan chemistry with dye-labeled probes is used to detect sequence-specific targets. When no target sequence is present, no signal accumulates. Following dPCR analysis, the fraction of negative reactions is used to generate an absolute count of the number of target molecules in the sample, without the need for standards or endogenous controls. In conventional qPCR, the signal from wild-type sequences dominates and obscures the signal from rare sequences. By minimizing the effect of competition between targets, dPCR overcomes the difficulties inherent to amplifying rare sequences and allows for sensitive & precise absolute quantification of the selected miRNAs. Applied Biosystem Quant Studio™ 3D instrument only performs the imaging and primary analysis of the digital chips. The chips themselves must be cycled offline on a Dual Flat Block Gene Amp® 9700 PCR System or the ProFlex™ 2x Flat PCR System. The Quant Studio™ 3D Digital PCR System (Figure 1) can read the digital chip in less than 1 minute, following thermal cycling (Figure 1).

1. Chip Case Lid- The lid used to seal the Digital PCR 20K Chip for thermal cycling and imaging on the Quant StudioTM 3D Instrument.
2. Digital PCR 20K Chip- The 10-mm2 consumable that contains the 20,000 reaction wells, which suspend the individual PCR reactions for thermal cycling and imaging.
3. Quant StudioTM 3D Digital PCR Chip Case- The thermal -conductive base that secures and protects the Digital PCR 20K Chip during all phases of use.
4. Chip ID- A label applies to the Quant StudioTM 3D Digital PCR chip Case Lid that can be used to uniquely identify the chip to which it is applied.
5. Fill Port- The aperture within the Chip Case Lid through which immersion Fluid is injected on to the Chip.
6. Reaction Wells- The 20,000 physical holes within the Digital PCR 20K Chip that suspend the individual PCR reaction.
The current Quant Studio™ 3D Digital PCR Chip allows for one sample per chip; although, duplexing allows for analysis of two targets per chip. Sample prep for digital PCR is no different than for real-time PCR, when using the Quant Studio™ 3D Digital PCR System. The concentration of cDNA stock can be estimated by including all of the necessary dilution factors into the Analysis Suite™ software, which gives the copies/μL in the stock. A critical step in dPCR, is sample partitioning [i.e., division of each sample into thousands of discrete subunits prior to amplification by PCR, each ideally containing either zero or one (or at most, a few) template molecules]. Each partition behaves as an individual PCR reaction –as with real-time PCR—fluorescent FAM probes [or others, as VIC fluorescence. Samples containing amplified products are considered positive (1, fluorescence), and those without product –with little or no fluorescence are negative (0, fluorescence). The ratio of positives to negatives in each sample is the basis of amplification. Unlike real-time qPCR, dPCR does not rely on the number of amplification cycles to determine the initial amount of template nucleic acid in each sample, but it relies on Poisson Statistics to determine the absolute template quantity. The unique sample partitioning step of dPCR, coupled with Poisson Statistics, allows for higher precision than both traditional and qPCR methods; permitting for analysis of rare miRNA targets. The use of a nanofluidic chip provides a convenient mechanism to run thousands of PCR reactions in parallel. Each well is loaded with a mixture of sample, master mix, and Applied Biosystems TaqMan Assay reagents are individually analyzed to detect the presence (positive) or absence (negative) of an endpoint signal. To account for wells that may have received more than one molecule of the target sequence, a correction factor is applied using the Poisson model. It features a filter set that is optimized for the FAM™, VIC®, and ROX™ dyes, available from Life Technologies.

Absolute quantification of the 14 miRNAs is shown in Table 2, and Table 3 is a representation of SDs and R2 for the 14 miRNAs tested by absolute digital PCR. (Figure 2) is Workflow of a digital miRNA’s PCR for colon cancer profiling in human colon tissue or stool samples. (Figure 3). is a graphical representation of the absolute quantification of the 12 up- or 2 down-regulated miRNAs in Human Stool by the QuantStudioTM 3D Digital PCR Chip System. Digital PCR, however, needs a rough estimate of the concentration of miRNAs of interest to carry out first , in order to make appropriate dilutions; Non-template controls and a RT negative control must be set up for each miRNA, when using a “primer pool method” for retro-transcription; a chip-based dPCR method requires less pipetting steps, which reduces potential PCR contamination, and Quant StudioTM 3D chip has 20,000 fixed reaction wells, which reduces variability of dPCR results (Figure 2 & 3 and Table 2 & 3).

To avoid bias and ensure that biomarker selection and outcome assessment will not influence each other, a prospective specimen collection retrospective blinded evaluation (PRoBE) design randomized selection could be employed. An enrichment and exfoliation strategy of colonocytes from stool for miRNA profiling using Dynal superparamagnetic polystyrene beads coated with a mouse IgG1 monoclonal antibody (Ab) Ber-Ep4, specific for an epitope on the protein moiety of the glycopolypeptide membrane antigen Ep-CAM, which is expressed on the surface of colonocytes and colon carcinoma cells, can be used. Comparing the Agilent electrophoretic (18S and 28S) patterns to those obtained from total RNA extracted from stool, and differential lysis of colonocytes by RT lysis buffer (Quagen), could be construed as a validation that the electrophoretic pattern observed in stool (18S and 28S) is truly due to the presence of human colonocytes, and not due to stool contamination with Escherichia coli (16S and 23S). While some exsosomal RNA can be released from purified colonocytes into stool, correction for that effect can be made. Hence, for CRC screening, miRNA markers are more comprehensive and preferable to a DNA-, epigenetic-, mRNA- or a protein-based marker. An added advantage of the use of the stable, nondegradable miRNAs by PCR expression, or chip-based methods is being automatable, making them more economical and acceptable by laboratory personnel performing these assays.

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Iris Publishers- Open access Journal of Biostatistics & Biometric Applications | Digital Signal Processing for Analytics in Biostatistics & Biometric Applications



Authored by Ehsan Sheybani*

Abstract

All the biostatistics and biometric applications suffer from the effects of added noise due to their data dependency. The quality of data and impurities due to noise could affect the decisions made based on these datasets. Detecting anomalies caused by noisy datasets requires special preprocessing techniques that do not hurt the integrity of data. The authors have developed computationally low power, low bandwidth, and low-cost filters (DMAW) that will remove the noise, compress the dataset, and decompose the dataset so that a decision can be made by looking at different layers of data. This wavelet-based method is guaranteed to converge to a stationary point for both uncorrelated and correlated data. Presented here is the theoretical background with examples showing the performance and merits of this novel approach compared to other alternatives.
Keywords:Biostatistics; Biometric; Discrete wavelet transform; Discrete meyer mdaptive wavelet
Abbreviations:FFT: Fast-Fourier Transform; IFFT: Inverse Fast-Fourier Transform; FT: Fourier transform; CWT: Continuous Wavelet Transform; DWT: Discrete Wavelet Transform; MWT: Multi-Resolution Wavelet Transform; DMAW: Discrete Meyer Adaptive Wavelet

Introduction

Biostatistics and biometric (bio-systems) are exciting fields that try to answer a broad range of questions in the interface of medicine, science, statistics, and engineering. It is hard to imagine where medicine and science would be today without advanced bio-systems, wireless sensor networks, robotics, 3D printers, nanoparticles, and big date analytics, to name a few. Technology has had a dramatic effect on the trend of biostatistics and biometric, producing what may be the most challenging period in the history of human beings. One form of the convergence of technology in science and medicine is advanced bio-systems. Bio-systems provide alternative means for analysis and visualization of the scientific and medical information and services, providing patients and researchers with an extraordinary new range of options.
Traditionally, standard methods such as Fast-Fourier Transform (FFT) and Inverse Fast-Fourier Transform (IFFT) have been used to process datasets for medical and scientific purposes. Due to non-parametric features of these methods and their resolution limitations and observation time dependence, use of spectral estimation and signal pre and post-processing techniques based on wavelets to process data has been proposed. Multi-resolution wavelet transforms and advanced spectral estimation techniques have proven to offer efficient solutions to this problem [1]. This paper discusses innovative wavelet-based filter banks designed to enhance the analysis of dataset using parametric spectral methods and signal classification algorithms.
Finally, the volume, depth, and breadth of data acquired from advance imaging systems has resulted in the recent out of bounds growth of data, thus, requiring modern processing and visualization techniques to extract useful information for decisionmaking. Finding correlation among thousands of variables in big datasets to determine their relative importance is not a simple task. Advanced analysis and scientific data visualization have proven to be effective techniques in discerning information from big datasets. Using proven, fast, and sophisticated filtering techniques, this article also aims at extracting information, showing patterns, and allowing mining of big datasets in real-time for faster and more effective decision making. Given the unique challenges of scientific big data visualization, the research presented in this paper covers some potential solutions and offers a means of setting standards for this new and evolving field.

Discussion

This study aims at reducing the dimensionality of dataset to reduce computational load in further processing [2]. The proposed method ranks features for learning a distance function in order to capture the semantics of the dataset [3]. It also uses the orthogonality properties of wavelets to decompose the dataset into spaces of coarse and detailed signals. Depending on whether a given function is analyzed in all scales and translations or a subset of them, the continuous (CWT), discrete (DWT), or multi-resolution wavelet transform (MWT) can be applied. The DWT can be used to suppress noise and reduce order of data in a wireless sensor network. Due to its ability to extract information in both time and frequency domain, DWT is considered a very powerful tool. The approach consists of decomposing the signal of interest into its detailed and smoothed components (high-and low-frequency).
The detailed components of the signal at different levels of resolution localize the time and frequency of the event. Therefore, the DWT can extract the coarse features of the signal (compression) and filter out details at high frequency (noise). DWT has been successfully applied to system analysis for removal of noise and compression [4]. DWT-based filters can be used to localize abrupt changes in signals in time and frequency. The invariance to shift in time (or space) in these filters makes them unsuitable for compression problems. Therefore, creative techniques have been implemented to cure this problem [5]. These techniques range in their approach from calculating the wavelet transforms for all circular shifts and selecting the “best” one that minimizes a cost function [6], to using the entropy criterion [7] and adaptively decomposing a signal in a tree structure so as to minimize the entropy of the representation. In this paper a new approach to cancellation of noise and compression of data has been proposed. The discrete Meyer adaptive wavelet (DMAW) is both translationand scale-invariant and can represent a signal in a multi-scale format. While DMAW is not the best fit for entropy criterion, it is well suited for the proposed compression and cancellation purposes [8-10].

Conclusion

As expected, the DMAW filters perform well under noisy conditions in an imaging environment. The decomposed signal could be easily freed up from noise and reduced down to its coarse component only. This could be reduction by several orders of magnitude in some cases. Future plans include the application of these filters to fused datasets and comparison between different approaches. Additionally, the results of these study can be used in the decision making stage to realize the difference this approach can make in speed and efficiency of this process. Future work will address issues such as characterizing the parameters for simulation and modeling of the proposed filter; showing how complex examples with correlated data will be filtered for redundancy; comparing the proposed approach with other similar approaches and giving comparative results to support the claimed advantages, both theoretically and experimentally.

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Iris Publishers- Open access Journal of Agriculture and Soil Science | Effects of Seed Rate and Nitrogen Fertilizer Rate on Growth and Biomass Yield of Oat (Avena Sativa L.)

  Authored by  Yidersal Erega *, Abstract The present study was conducted to assess seed rate (SR) and nitrogen rate (NR) effects on biomass...