Strategies for whole-exome sequencing analysis in a case series study of familial male infertility

Background: Infertility is one of the common health issues around the world. The prevalence of male factor infertility among infertile couples is approximately 30%- 35%, of which genetic factors account for 15%. The family-based whole-exome sequencing (WES) approach can accurately detect novel variants. However, selecting an appropriate sample for data generation using WES has proven to be challenging in familial male infertility studies. The aim of this study was to identify types of pathogenic male infertility in cases of familial asthenozoospermia. Case: Two families with multiple cases were recruited for the purpose of WES. The study population included two affected cases in pedigree I and three affected cases in pedigree II. Two different variant callers (SAMtools and GATK) with a single-sample calling strategy (SSCS) and a multiple-sample calling strategy (MSCS), were applied to identify variant sites. Conclusion: In this study, we represented the results for variant prioritization of WES data without sequencing fertile siblings in the same pedigree by applying two different pipelines (homozygosity and linkage-based strategy). Using the aforementioned strategies, we prioritized annotated variants and generated a logical shortlist of private variants for each pedigree. Key words: Male infertility, Whole-exome sequencing, GATK, SAMtools

Demonstration of the etching cobalt oxide grown on the stainless steel as a base metal surface using F2/He dielectric barrier discharge plasma in atmospheric pressure

Metal surface cleaning or etching techniques using reactive plasma are emerging as one of the dry processing techniques for surface contaminants with high bond energy, especially for cleaning and decontamination of nuclear components and equipment. In this study, the plasma reaction due to the discharge of a dielectric barrier of a mixture of 95% helium and 5% fluorine with cobalt oxide film grown on the surface of stainless steel 304 was studied experimentally. Experimental results show that cobalt oxide becomes a powder after plasma irradiation and is easily separated from the surface of the base metal. The optimal plasma generating conditions of the dielectric barrier discharge (DBD) used in this experimental study were obtained at atmospheric pressure, voltage 4.5 kV, and frequency 25 kHz with a etching rate of 10.875 {\mu}mol/min. The samples were analyzed before and after plasma irradiation, using Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX) and the purification rate was performed using a sequential weighting of the samples with scales 10^(-4) grams accurately obtained. The results show the ability of this method to effectively remove the surface contamination of cobalt from the surface of stainless steel 304

Réponses morphologiques, physiologiques et biochimiques au déficit en eau chez les jeunes plants de trois populations de poiriers sauvages (Pyrus boisseriana)

Water shortage limits production of fruit orchards, like pear, in arid and semi-arid regions. The identification of wild pear germplasm for potential use as rootstock would be valuable for pear cultivation in semi-arid regions. Relative drought tolerance of wild pear germplasm (Pyrus boisseriana) from three different populations distributed along an elevational gradient (semi-arid 1000, semi-wet 1350 and semi-wet 1600 populations) was evaluated in a greenhouse trial. Established container-grown seedlings were exposed to 18 days of simulated drought, or not, followed by a seven day recovery. Biomass allocation and accumulation, physiological (stomatal conductance, photosynthesis, transpiration, xylem water potential) and biochemical parameters (leaf pigments, free proline, malondialdehyde and hydrogen peroxide production) were evaluated. Although all populations were able to recover from water shortage, thereby being relatively drought tolerant, some differences among populations were detected for gas exchange parameters, biomass accumulation and proline concentration in favor of the semi-arid 1000 elevation population, which was more drought tolerant; it had the most rapid and complete recovery of physiological activity (stomatal conductance and carbon fixation). In addition, all populations increased carotenoids in leaves. Overall, we showed that plants from semi-arid 1000 elevation greater tolerance to drought than those from higher elevations. Although the initial drought resistance response of the 1000 elevation source was promising, additional field studies are needed to confirm the greenhouse results and the benefit of a more drought resistant rootstock to commercial scions.En régions arides et semi-arides, la disponibilité en eau est le facteur limitant des vergers de production, comme en culture de poirier, par exemple. À cet égard, l’évaluation d’une collection de poiriers sauvages pourrait mettre en évidence du matériel potentiellement utilisable comme porte-greffe et tolérant à la sécheresse dans ces régions. Des poiriers sauvages (Pyrus boisseriana) originaires de trois populations différentes selon leur répartition en altitude (populations « semi-aride 1 000 m », « semi-humide 1350 m » et « semi-humide 1 600 m ») ont été évalués pour leur tolérance à la sécheresse dans un essai en serre. Des semis cultivés en pots ont été soumis à 18 jours de sécheresse, puis à une reprise de sept jours de croissance en conditions normales d’irrigation. La répartition et l’accumulation de la biomasse, les paramètres physiologiques (conductance stomatique, photosynthèse, transpiration, potentiel hydrique du xylème) et biochimiques (teneurs en pigments des feuilles, proline libre et malondialdéhyde ; production de peroxyde d’hydrogène) ont été évalués par rapport à des témoins non soumis au stress hydrique. Bien que toutes les populations de poirier aient pu se rétablir après la période sans irrigation et présentent de ce fait une certaine tolérance à la sécheresse, certaines différences de comportement entre celles-ci ont été détectées pour ce qui concerne les échanges gazeux, l’accumulation de la biomasse et la concentration de la proline dont les valeurs étaient en faveur de la population établie en zone semi-aride à une altitude de 1000 m. Celle-ci a d’ailleurs montré une reprise plus rapide et plus complète de son activité physiologique (conductance stomatique et fixation du carbone). À noter que le taux de caroténoïdes dans les feuilles a augmenté dans toutes les populations soumises au stress hydrique. De manière générale, nous avons montré que les plantes appartenant à la population établie en zone semi-aride à 1 000 m d’altitude présentaient une plus grande tolérance à la sécheresse que celles appartenant aux populations des altitudes plus élevées (populations semi-humides). Ces plantes constituent donc un matériel prometteur comme candidats porte-greffe pour les greffons commerciaux de poiriers destinés à la culture dans les régions soumises fréquemment à des déficits hydriques.Fil: Zarafshar, Mehrdad. Tarbiat Modares University. Faculty of Natural Resources and Marine Sciences. Department of Forestry; IránFil: Akbarinia, Moslem. Tarbiat Modares University. Faculty of Natural Resources and Marine Sciences. Department of Forestry; IránFil: Askari, Hossein. Shahid Beheshti University, G.C. Faculty of New Technologies and Energy Engineering. Biotechnology Department; IránFil: Hosseini, Seyed Mohsen. Tarbiat Modares University. Faculty of Natural Resources and Marine Sciences. Department of Forestry; IránFil: Rahaie, Mehdi. University of Tehran. Faculty of New Science and Technology. Department of Life Science Engineering; IránFil: Struve, Daniel. Ohio State University. Department of Horticulture and Crop Science.; Estados UnidosFil: Striker, Gustavo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentin

Economic Feasibility of the Profitability of Insurances Related to Oil and Gas Wells

Insurance is among the most important tools that have been devised to prepare readiness for dealing with threats. These valuable man-made tools with their capabilities have controlled many undesirable effects of unforeseen events. In each country, growth and development of insurance industry is considered as an indicator for evaluating the level of development. From the perspective of insurers, the risks of energy, especially the oil and gas industry, are known as high risks. Economic feasibility of the profitability of insurance related to oil and gas wells is the aim of this study that was performed through damage coefficient indicators and profit margin with scenario planning using engineering economics method. The results of this research indicate that the damage coefficient of this field of insurance is much lower than the whole insurance industry and have a suitable and very high profit margin. Therefore, due to the low damage coefficient and high profit margin and the stability of these types of insurance, their profitability is confirmed economically and investment and providing insurance coverage is adequately justifiable for these types of risk

Economic Feasibility of the Profitability of Insurances Related to Oil and Gas Wells

Insurance is among the most important tools that have been devised to prepare readiness for dealing with threats. These valuable man-made tools with their capabilities have controlled many undesirable effects of unforeseen events. In each country, growth and development of insurance industry is considered as an indicator for evaluating the level of development. From the perspective of insurers, the risks of energy, especially the oil and gas industry, are known as high risks. Economic feasibility of the profitability of insurance related to oil and gas wells is the aim of this study that was performed through damage coefficient indicators and profit margin with scenario planning using engineering economics method. The results of this research indicate that the damage coefficient of this field of insurance is much lower than the whole insurance industry and have a suitable and very high profit margin. Therefore, due to the low damage coefficient and high profit margin and the stability of these types of insurance, their profitability is confirmed economically and investment and providing insurance coverage is adequately justifiable for these types of risk

Abscisic acid interplays with PPARγ receptors and ameliorates diabetes-induced cognitive deficits in rats

Objective: This study intended to evaluate if central administration of abscisic acid (ABA) alone or in combination with GW9662, a peroxisome proliferator–activated receptor γ (PPAR-γ) antagonist, could modulate learning and memory as well as hippocampal synaptic plasticity in a rat model of streptozotocin (STZ)–induced diabetes. Materials and Methods: Intraperitoneal injection of STZ (65 mg/kg) was used to induce diabetes. Diabetic rats were than treated with intracerebroventricular (i.c.v.) administration of ABA (10, 15 and 20 µg/rat), GW9662 (3 µg/rat) or GW9662 (3 µg/rat) plus ABA (20 µg/rat).Animals’ spatial and passive avoidance learning and memory performances were assessed by Morris water maze (MWM) and shuttle box tasks, respectively. Further, in vivo electrophysiological field recordings were assessed in the CA1 region. Results: STZ diabetic rats showed diminished learning and memory in both MWM and shuttle box tasks.  The STZ-induced memory deficits were attenuated by central infusion of ABA (10 and 20 µg/rat). Besides, STZ injection impaired long-term potentiation induction in CA1 neurons that was attenuated by ABA at 20 μg/rat. Central administration of GW9662 (3 µg/rat) alone did not modify STZ-induced spatial and passive avoidance learning and memory performances of rats. Further, GW9662 prevented ABA capacity to restore learning and memory in behavioral and electrophysiology trials. Conclusion: Altogether, ABA ameliorates cognitive deficits in rats via activation of PPAR-γ receptor in diabetic rats

Clinical Report Multiple Cutaneous Inverted Papilloma in a German shepherd Dog

Abstract Case Description-In this clinical report, occurrence of a rare case of canine cutaneous inverted papilloma was discussed. A 4-year-old, intact, male German shepherd dog was presented with multiple skin lesions, located on the inguinal region near the root of penis, which have been progressively growing since two months ago. In close examination of the lesions multiple, firm, painful, and cup-shaped nodules in different sizes with a central pore filled with keratin were observed. Treatment and Outcome-Surgical excision and histological evaluation was done. Histologically this tumor was characterized by endophytic projections of the epidermis extending into dermis.Cytopathic effects included ballooning degeneration of keratinocytes, koilocytosis, irregularity of keratohyalin granules, and margination of nuclear chromatin. Numerous eosinophilic intranuclear inclusions were present within keratinocytes of endophytic lesion. Immunohistochemically, the tumor cells were intensely positive for pancytokeratin. On the basis of histopathological and clinical findings, the tumor was diagnosed as multiple cutaneous inverted papilloma. There was no recurrence or any other complications in post operative monitoring. Clinical Relevance-Inverted papillomas are relatively uncommon in dogs; whereas, the incidence of this tumor in the inguinal region is uncommon. Treatment of inverted papilloma was completed by surgical excision in ablating the tumor masses and preventing re-growth. 92 Case Description A 4-year-old, intact, male German shepherd dog was presented for treatment of multiple skin lesions, located on the inguinal region near the root of penis. The owner declared that the masses have been growing up rapidly through two months prior to presentation. On clinical examination; all vital signs (heart Rate, respiratory rate and rectal temperature) were in the normal range. On dermatological examination, multiple, firm, painful, and cup-shaped nodules in different sizes with a central pore filled with keratin were observed and the masses had well-demarcated border Treatment and Outcome Based on the clinical examination, cutaneous neoplasia was suspected and complete surgical excision of the masses was recommended. The dog was premedicated with 0/05 mg/kg acepromazine (KELA Laboratoria) intramusculary and anesthesia intravenously was induced with 10 mg/kg thiopental sodium (Sandoz) and was maintained with halothane 2% (Halothane BP, Nicholas Piramal). An elliptical incision was made in the skin around the lesion and the masses were dissected from subcutaneous tissues. The skin was sutured with Nylon (Monofil Polyamid, Supa) USP: 2/0 in interrupted suture pattern. Postoperative care included Cefazoline (Exir Pharmaceutrical Co.) at 20 mg/kg intramuscularly, every 12 hours for 3 days. The removed masses were fixed in 10% neutral buffered formalin, processed routinely, embedded in paraffin, sectioned at 5 µm thickness, stained with hematoxylin and eosin, and studied with a routine light microscope. Immunohistochemistry of additional section was performed with Avidin-Biotin complex method by using monoclonal antibodies for pancytokeratin antibody (1/500). Microscopic examination at the nodules revealed cupshaped epidermal proliferation with centripetal papillary projections into dermi

Globotriaosylsphingosine Accumulation and Not Alpha-Galactosidase-A Deficiency Causes Endothelial Dysfunction in Fabry Disease

BACKGROUND: Fabry disease (FD) is caused by a deficiency of the lysosomal enzyme alpha-galactosidase A (GLA) resulting in the accumulation of globotriaosylsphingosine (Gb3) in a variety of tissues. While GLA deficiency was always considered as the fulcrum of the disease, recent attention shifted towards studying the mechanisms through which Gb3 accumulation in vascular cells leads to endothelial dysfunction and eventually multiorgan failure. In addition to the well-described macrovascular disease, FD is also characterized by abnormalities of microvascular function, which have been demonstrated by measurements of myocardial blood flow and coronary flow reserve. To date, the relative importance of Gb3 accumulation versus GLA deficiency in causing endothelial dysfunction is not fully understood; furthermore, its differential effects on cardiac micro- and macrovascular endothelial cells are not known. METHODS AND RESULTS: In order to assess the effects of Gb3 accumulation versus GLA deficiency, human macro- and microvascular cardiac endothelial cells (ECs) were incubated with Gb3 or silenced by siRNA to GLA. Gb3 loading caused deregulation of several key endothelial pathways such as eNOS, iNOS, COX-1 and COX-2, while GLA silencing showed no effects. Cardiac microvascular ECs showed a greater susceptibility to Gb3 loading as compared to macrovascular ECs. CONCLUSIONS: Deregulation of key endothelial pathways as observed in FD vasculopathy is likely caused by intracellular Gb3 accumulation rather than deficiency of GLA. Human microvascular ECs, as opposed to macrovascular ECs, seem to be affected earlier and more severely by Gb3 accumulation and this notion may prove fundamental for future progresses in early diagnosis and management of FD patients