Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal bone histopathology study on cochlear otosclerosis: A memoir for the cochlear 
implant surgeon

The aim of this study was to describe the pathologic changes in temporal bones with cochlear otosclerosis that may have implications for cochlear implantation. Fifteen human temporal bones with otosclerosis were used for this study. In each temporal bone was studied: (1) medial wall of the middle ear and in particular the horizontal segment of the facial nerve canal; (2) the round window niche and the corresponding part of the scala tympani; (3) the area of the labyrinthine segment and first genu of the facial nerve. Six temporal bones revealed otosclerotic pathology spanning the otic capsule between the cochlear endosteum and the facial nerve canal. The labyrinthine facial nerve was enveloped by otosclerosis in two cases, while the horizontal segment was involved in four temporal bones. Complete obstruction of the round window niche was observed in three cases, while round window niche obstruction was observed in four temporal bones. Otosclerosis presents difficulties for implant candidates. These otosclerotic changes with obstruction are usually present at the round window or at the scala tympani. The histology described underpins the need to counsel patients regarding the possibility of facial nerve stimulation and difficult implantation. Key words: Cochlear otosclerosis, histopathology, round window, obstruction.
Comparative efficacy and safety and dolutegravir and lamivudine in treatment naive HIV patients

Objective: Compare the efficacy and safety of the 2-drug antiretroviral therapy regimen dolutegravir + lamivudine (DTG + 3TC) with traditional 3-drug regimens in treatment-naive patients with HIV-1. Design: Data from double-blind, randomized controlled trials of at least 48 weeks’ duration in treatment-naive patients with HIV-1 identified by systematic review were evaluated using a Bayesian network meta-analysis methodology. Methods: The primary outcome was virologic suppression at Week 48 for 3-drug regimens versus DTG + 3TC (also analyzed in patient subgroup with baseline viral load >100 000 RNA copies/ml). Secondary outcomes included CD4+ cell count change from baseline and safety (adverse events, serious adverse events, and drug-related adverse events) at Week 48. Results: The network contains 14 unique regimens from 14 randomized controlled trials based on data from 10 043 patients. The proportional difference for viral suppression at 48 weeks for DTG + 3TC versus the other 13 regimens included in the network ranged from −2.7% (−11.0, 5.6%) versus DTG + tenofovir alafenamide/emtricitabine (FTC) to 7.3% (0.6, 13.8%) versus efavirenz + tenofovir disoproxil fumarate/FTC. DTG + 3TC was found to be significantly better than efavirenz + tenofovir disoproxil fumarate/FTC and similar to all other regimens analysed in terms of viral suppression at 48 weeks. With regard to other outcomes (CD4+, adverse event, serious adverse event, drug-related adverse events) at 48 weeks, DTG+3TC was broadly similar to all regimens analysed. Conclusion: This network meta-analysis demonstrates similar efficacy and safety outcomes over 48 weeks with DTG + 3TC compared with traditional 3-drug antiretroviral therapy regimens.
Coping Strategy, Religiosity, and Chronic Elderly’s Life Satisfaction

Decrease in physical or biological conditions that occur in the elderly will result in disruption of various organs of the body so that it can cause chronic disease in the elderly. Chronic diseases can have an impact on increasing stress and life satisfaction in the elderly. This study aims to analyze the effect of coping strategies and religiosity on the life satisfaction of elderly men and women with chronic disease. The design used in this study is a cross sectional study at Medika Dramaga Hospital, Bogor Regency. Examples in the study amounted to 60 people who had chronic diseases, had suffered for more than six months and were selected by accidental sampling technique. The results showed no difference between coping strategies, religiosity, and life satisfaction of elderly men and women with chronic disease. The duration of an elderly person suffering from a disease is positively related to coping strategies. Religiosity and the duration of the elderly suffer from diseases are significantly positively related to life satisfaction. Elderly people who are still working in old age will reduce their life satisfaction. The longer the elderly suffer from chronic diseases and the higher the religiosity of the elderly, the life satisfaction of the elderly will increase.
Understanding and predicting method-level source code changes using commit history data

Software development and software maintenance require a large amount of source code changes to be made to a software repositories. Any change to a repository can introduce new resource needs which will cost more time and money to the repository owners. Therefore it is useful to predict future code changes in an effort to help determine and allocate resources. We are proposing a technique that will predict whether elements within a repository will change in the near future given the development history of the repository. The development history is collected from source code management tools such as GitHub and stored local in a PostgreSQL. The predictions are developed using the machine learning approaches Support Vector Machine and Random Forest. Furthermore, we will investigate what factors have the most impact on the performance of predicting using either Support Vector Machines or Random Forest with future code changes using commit history. Visualizations were used as part of the approach to gain a deeper understanding of each repository prior to making predictions. To validate the results we analyzed open source Java software repositories including; acra, storm, fresco, dagger, and deeplearning4j.
SLAUGHTER QUALITY OF BLACK SLAVONIAN PIG – ENDANGERED BREED AND ITS CROSS-BREDS WITH SWEDISH LANDRACE WHILE KEEPING THEM OUTDOOR

Black Slavonian pig is an autochtonuous Croatian breed derived by crossing Mangulitza, Berkshire and Polandchina at the end of 19 century. It belongs to the group of endangered breeds. Because of its pronounced resistance, pigmented skin and ability of consuming high amounts of roughage (pasture), it is very convenient for keeping it outdoors, especially for organic production within low-input traditional technology. The investigation was conducted on 10 Black Slavonian pigs and 10 crossbreds between Black Slavonian pig (BS) and Swedish Landrace boars (SL). The pigs were fed until weighed approx. 135 kg. They were slaughtered at 12 months age and Black Slavonian pigs at 18 months. The pigs were kept outdoors in a natural low-lying pasture. The pasture area per animal was 0.05 ha. A traditional lowinput technology was applied. Apart from pasture. the pigs consumed food found on stubbles after cereals had been harvested (wheat, barley, corn) and were given small amount of corn (0.15 kg/head/day). Dissection of cooled (+4C ) right pig carcasses was done by the modified method (Weniger et.al., 1963). The meat quality was investigated on a sample of long back muscle (Muscullus longissimus dorsi – MLD) taken between 13 and 14 rib. Outdoor keeping system and low inputs technology resulted in trunks of very significantly (P 0.05) were determined between analyzed pig genotypes. Crossbreds meat, compared to Black Slavonian pig meat, was known for very significantly (P<0.01) higher share of water (71.99% : 71.65%) and lower share of fat (5.30% : 5.90%).
Validation of a smartphone-based, computer-assisted sperm analysis system compared with laboratory-based manual microscopic semen analysis and computer-assisted semen analysis

Purpose This study aimed to evaluate the clinical efficacy of a portable smartphone-based system for computer-assisted semen analysis (CASA) compared with the results of manual microscopic semen analysis (SA) and laboratory-based CASA for self-evaluation of semen parameters by a male partner. Materials and Methods From July 2017 to February 2018, a total of 28 samples were analyzed for concentration and motility with a smartphone-based CASA system and the results compared with those from laboratory-based CASA and manual microscopic SA with a Makler Counting Chamber (SEFI Medical Instruments, Israel). Results Sperm concentration and motility measured with the smartphone-based CASA system were positively correlated with the microscopic-based results. Likewise, sperm motility calculated with smartphone-based CASA was positively correlated with the laboratory-based CASA results. These results suggest that the smartphone-based CASA system can be used for clinical semen diagnosis. Conclusions A portable smartphone-based CASA system can play a role in motivating infertile males to visit clinics, thus resulting in early diagnosis and treatment with cost-effectiveness. The device can be used for easy follow-up on a screening basis by the male partner before visiting a clinic for fertility evaluation or by infertile males after receiving medical management. Additionally, future software advancements and post-marketing consumer surveys will make possible wider applications, including assessment of sperm morphology, in the coming future.
Activin receptor-like kinase5 inhibition suppresses mouse melanoma by ubiquitin degradation of Smad4, thereby derepressing eomesodermin in cytotoxic T lymphocytes

Varieties of transforming growth factor-b (TGF-b) antagonists have been developed to intervene with excessive TGF-b signalling activity in cancer. Activin receptor-like kinase5 (ALK5) inhibitors antagonize TGF-b signalling by blocking TGF-b receptor-activated Smad (R-Smad) phosphorylation. Here we report the novel mechanisms how ALK5 inhibitors exert a therapeutic effect on a mouse B16 melanoma model. Oral treatment with a novel ALK5 inhibitor, EW-7197 (2.5 mg/kg daily) or a representative ALK5 inhibitor, LY-2157299 (75 mg/kg bid) suppressed the progression of melanoma with enhanced cytotoxic T-lymphocyte (CTL) responses. Notably, ALK5 inhibitors not only blocked R-Smad phosphoryla-tion, but also induced ubiquitin-mediated degradation of the common Smad, Smad4 mainly in CD8 þ T cells in melanoma-bearing mice. Accordingly, T-cell-specific deletion of Smad4 was sufficient to suppress the progression of melanoma. We further identified eomesodermin (Eomes), the T-box transcription factor regulating CTL functions, as a specific target repressed by TGF-b via Smad4 and Smad3 in CD8 þ T cells. Thus, ALK5 inhibition enhances anti-melanoma CTL responses through ubiquitin-mediated degradation of Smad4 in addition to the direct inhibitory effect on R-Smad phosphorylation. OPEN ACCESS TRANSPARENT PROCESS SOURCE DATA ALK5 inhibitors degrade Smad4 to derepress CTLs 1720 ß 2013 The Authors. Published by John Wiley and Sons, Ltd on behalf of EMBO. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Raf‐1 kinase, a potential regulator of intracellular pH in Xenopus oocytes

Xenopus laevis oocytes undergo an increase in intracellular pH (pHi) from 7.2 to 7.7 due to the upregulation of Na+/H+ antiporters in their plasma membrane during oocyte meiotic maturation. Up‐regulation of Na+/H+exchangers (NHE) found in other cell systems appears to be controlled, in some cases, by direct phosphorylation of the exchanger. A number of active protein kinases can be found in maturing Xenopus oocytes. These include, c‐mos kinase, Raf‐1 kinase, mitogen‐activated kinase kinase (MAPKK), MAPK, ribosomal S6 kinase (RSK), and histone H‐1 kinase. Our previous study indicated that c‐mos kinase, was involved in regulating the increase in oocyte pHi. In the current study, we show that when mRNA coding for a constitutively active form of Raf‐1 kinase (ΔN‐Raf‐1) was microinjected into oocytes, the protein product induced an increase in oocyte pHi. On the contrary, the injection of mRNA coding for wild‐type Raf‐1 (WT‐Raf‐1) or a kinase‐deficient form of Raf‐1 (KD‐Raf‐1) had no effect on the recipient oocyte pHi. 8‐Br‐cAMP and forskolin blocked the increase in pHi during oocyte meiotic maturation, but had no effect on the Raf‐1‐induced increase in oocyte pHi. Studies using antisense c‐mos oligos demonstrated that Raf‐1 was not working via a feedback loop to endogenous c‐mos mRNA within the recipient oocytes. Experiments using the selective MAPKK inhibitor, PD 98059, indicated that the Raf‐1 effect on oocyte pHi was not mediated by the downstream kinase, MAPKK. Therefore, Raf‐1 appears to act independently of c‐mos kinase in a pathway, not involving MAPKK, leading to the up‐regulation of the Na+/H+ antiporters in Xenopus oocytes.
The Effects of High Temperature on Blood Serum Parameters and the Egg Productivity Characteristics of Japanese Quails (Coturnix coturnix japonica)

In this study, it was aimed to determine the effects of higher temperatures on the blood serum values, egg productivity, egg weight and the thickness of eggshell of the Japanese quails. By this purpose, two temperature groups were arranged by consisting of control (18-24 C) and trial (35 C) groups. In the end o o of the research, it was observed that the higher temperature increased some of the blood serum values such as glucose, Na, triglyceride (P<0.05), cholesterol (P<0.01) and uric acid (P<0.001) levels but reduced the blood serum protein (P<0.01), albumin (P<0.001), P (P<0.05), K (P<0.01) and ALP (P<0.05) levels. Even if the higher temperature has led a decrease in the egg productivity in all ages during the trial period, the difference that was observed in all ages except the seventh week was found important (P<0.05). The values of the egg weight in both control and trial groups were found as 10.53 and 9.93g (P<0.01); the values of eggshell thickness as 0.23 and 0.20 mm (P<0.001).
Étude de la répartition de Lymnaea truncatola dans le nord-ouest algérien et de sa réceptivité a Fasciola hepatica

Une etude preliminaire sur les habitats de Lymnaea truncatula Muller dans le nord-ouest de l’Algerie a permis de denombrer 33 gites positifs representes par des oueds, des sources, des marecages et des canaux d’irrigation. Malgre un polymorphisme de la coquille et un polymorphisme enzymatique, les limnees de huit de ces stations se sont averees experimentalement receptives a Fasciola hepatica L.
Ultrastructure of human blastocyst – endometrial interactions in vitro U

The morphology of endometrial–trophoblast interactions during early implantation varies among species (Wimsatt, 1975). However, different species appear to pass through common phases during implantation. The process of implantation has been divided into well-defined sequences to facilitate comparisons among species (Falck Larsen, 1974; Schlafke and Enders, 1975; Enders, 1976). Apposition describes the orientation of the blastocyst towards the endometrial surface epithelium. This phase varies among species (Wimsatt, 1975) and there are no available data on apposition in humans. Adhesion is a common stage for all mammals. It comprises the first cellular contacts between the blastocyst and the endometrium (Enders and Schlafke, 1969). The only morphological indications of adhesion observed ultrastructurally in different species in vivo consist of intimate apposition between apical plasma membranes of trophoblastic and endometrial epithelial cells. No membrane specializations that could imply junction formation have been observed in guinea-pigs, ferrets, armadillos, bats, rats or rhesus monkeys (Enders and Schlafke, 1967, 1969; Enders et al., 1980, 1983). Penetration of the uterine surface epithelium also varies among species. Comparative studies by Schlafke and Enders (1975) on animal models have distinguished three types of penetration: (i) displacement implantation, which is characterized by apoptosis of the uterine epithelium before invasion into the stroma starts (Parr et al., 1987), and is observed in mice (Potts, 1968) and rats (Enders and Schlafke, 1967; Welsh and Enders, 1991); (ii) fusion implantation, in which syncytial trophoblasts fuse with maternal epithelial cells during penetration, and is found in rabbits (Falck Larsen, 1961; Enders and Schlafke, 1971); and (iii) intrusive implantation, in which trophoblastic cytoplasmic extensions penetrate between apparently intact epithelial cells, and which occurs in ferrets (Enders and Schlafke, 1972), rhesus monkeys (Reinius et al., 1973; Enders et al., 1983) and marmoset monkeys (Moore et al., 1985; Enders and Lopata, 1999). In humans, the processes of adhesion and penetration have not been elucidated. The only report of attachment and penetration seems to be two photographs taken by light microscopy (Shettles, 1960), which may indicate intrusive implantation (O’Rahilly, 1973; for review see Lopata, 1996). Notable differences, even between closely related species, indicate that great care should be taken when animals are used as models for humans, although individual phases might display similar mechanisms. Therefore, we developed a three-dimensional cell culture model of the human Journal of Reproduction and Fertility (2000) 120, 337–350
Human phenylalanine monooxygenase and thioether metabolism

Objectives The substrate specificity of wild‐type human phenylalanine monooxygenase (wt‐hPAH) has been investigated with respect to the mucoactive drug, S‐carboxymethyl‐L‐cysteine and its thioether metabolites. The ability of wt‐hPAH to metabolise other S‐substituted cysteines was also examined.
Ruminal parameters and ruminal degradability of feedlot sheep fed safflower grains

SUMMARY This study aimed to evaluate the rumen degradability of dry matter (DM), disappearance of neutral detergent fiber (NDF) of Tifton 85 hay, and fermentation parameters (pH and ruminal ammonia nitrogen) of sheep fed diets with inclusion of safflower grains (0, 7.50 and 15%). Three mixed breed lambs with average body weight of 35.50± 1.50 kg were used. The rumen degradability of dry matter and NDF of the Tifton 85 haywas analyzedby the disappearance of DM and NDF, and the kinetic parameters adjusted according to the first order asymptotic model. The samples were incubated in the rumen in descending order (96, 48, 24, 12, 6, 3, 0 hours). The determination of ruminal pH and ruminal ammonia nitrogen (RAN) was performed before feeding and 2, 4, 6 and 8 hours after feeding. Data of ruminal fermentation were tested by analysis of variance with repeated measures in time, at 5% probability. Ruminal pH values were not statistically different. When evaluating the RAN, there was a significant difference between the times and treatments for the diet with 15% safflower. The diets presented low effective degradability of DM and NDF with mean values of 18.02% and 47.40%, respectively. The safflower grain can be used up to 7.50% in the diets without altering the degradability and ruminal fermentation.
Especies nocturnas de Scarabaeoidea (Coleoptera: Polyphaga) en el norte de Sinaloa, México

Abundance and richness of nocturnal species of Scarabaeoidea in northern Sinaloa, were recorded by mean of light traps operated during July to December, 2008. Samples were obtained in cultivated lands, tropical deciduous forest and xeric scrub of eight localities of municipalities of Ahome and El Fuerte, located between 8 and 84 m of elevation. A total of 38,619 specimens belonging to 29 species of the genera Phyllophaga, Diplotaxis, Paranomala, Pelidnota, Cyclocephala, Dyscinetus, Strategus, Oxygrylius, Megasoma, Dichotomius, Copris, Digitonthophagus and Hybosorus were collected. Phyllophaga was the richest genus, with 10 species, among them Phyllophaga opaca was predominant. The most abundant species were: Cyclocephala sinaloae (45.06%), Oxygrylius ruginasus (28.66%), Phyllophaga opaca (25.03%) and Ph. cristagalli (0.24%). The highest number of scarab beetles (51.38%) was collected during July, coinciding with beginning of the rainy season. The locality with the greatest scarab richness was Cerro de las Microondas, where 17 species were collected. Phyllophaga yaqui, Diplotaxis ambigua, Dyscinetus picipes and Xyloryctes corniger, are recorded for the first time in the state of Sinaloa.
Molecular Phylogeny of the Genus Cronius Stimpson, 1860, with Reassignment of C. tumidulus and Several American Species of Portunus to the Genus Achelous De Haan, 1833 (Brachyura: Portunidae)

As currently recognized by most taxonomists, the genus Cronius Stimpson, 1860, encompasses only two species, both distributed in tropical and subtropical waters. Cronius ruber (Lamarck, 1818) is reported from both the Pacific and Atlantic American coastlines, as well as the eastern Atlantic, and C. tumidulus (Stimpson, 1871) is reported to occur exclusively in the tropical western Atlantic. We examine potential differences between allopatric populations assigned to C. ruber, test hypothesized monophyly of the genus, and resolve the phylogenetic position of its members within the Portunidae. In so doing, we also revisit taxonomic classification of American species currently assigned to the genus Portunus. New 16S mtDNA sequences were obtained from representatives of the genera Charybdis, Cronius, Lupella, Lupocyclus, Polybius, Portunus, and Thalamita for examination along with sequences from GenBank. Slight but consistent genetic differences were found among populations assigned to Cronius ruber from the Pacific American coastline, the Atlantic American coastline, and the eastern Atlantic coastline (West Africa). The name C. edwardsii (Lockington, 1877) is resurrected for specimens from the eastern Pacific, but further analyses are needed to determine if additional taxonomic revisions may be required to more narrowly restrict use of the name C. ruber among a complex of Atlantic populations. Presently assigned members of Cronius do not form a monophyletic group. The well-defined clade representing C. ruber (including the resurrected C. edwardsii) is placed in a weakly supported grouping with representatives of Laleonectes, Thalamita, and Charybdis. In contrast, Cronius tumidulus forms a well-supported cluster with several present American representatives of the genus Portunus, which themselves are well separated from P. pelagicus, type species of that genus. Thus, we propose a revised taxonomy with placement of C. tumidulus in the resurrected genus Achelous De Haan 1833, an assignment that we also propose for nine American species currently treated under Portunus.