Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Culture Time and Media in an In Vitro Testis Organ Culture System.

BACKGROUND The complexity of spermatogenesis makes development of appropriate in vitro testis models challenging. A novel in vitro mouse testis culture system has been reported but not yet evaluated as an alternative model for male reproductive toxicity testing. We assessed the effects of media composition on sperm differentiation and testis morphology of cultured mouse testis fragments. METHODS Testes from postnatal day 5 B6:CBA-Tg(Acrv1-EGFP)2727Redd/J male mice were cultured in knockout serum replacement (KSR) or Albumax I (Albumax) medium. Enhanced green fluorescent protein (EGFP) expression was examined on days 35, 42, 45, and 49 of culture. Histology and flow cytometry were performed for testis morphology and spermatid differentiation. RESULTS EGFP signals were first observed in round spermatids on day 22 of culture (corresponding to postnatal day 27) and were observed until the end of culture, indicating testis-specific protein expression. A-kinase anchor protein 4 expression, a marker of elongated spermatid (step 15-16) occurred earlier in explants cultured in KSR than Albumax medium (typically day 35 and after day 42 of culture, respectively). The percentage of seminiferous tubules with elongated spermatid was higher in Albumax than KSR medium from days 45 to 49 of culture. CONCLUSION Albumax medium may facilitate or support better morphology and spermatid production than KSR medium. Further studies need to improve spermatid production and refinement of this in vitro testis culture system that may be useful as a supplement to current male reproductive toxicity testing or an alternative model in cases where in vivo testing may be unfeasible. Birth Defects Research 109:465-474, 2017. © 2017 Wiley Periodicals, Inc.
The Sloan Digital Sky Survey: The Cosmic Spectrum and Star Formation History

We present a determination of the "cosmic optical spectrum" of the universe, i.e., the ensemble emission from galaxies, as determined from the red-selected Sloan Digital Sky Survey main galaxy sample, and compare it with previous results of the blue-selected 2dF Galaxy Redshift Survey. Broadly, we find good agreement in both the spectrum and the derived star formation histories. If we use a power-law star formation history model in which the star formation rate is ∝(1 + z)β out to z = 1, then we find that a β of 2-3 is still the most likely model and that there is no evidence for current surveys to be missing large amounts of star formation at high redshift. In particular, "fossil cosmology" of the local universe gives measures of star formation history that are consistent with direct observations at high redshift. Using the photometry of the Sloan Digital Sky Survey, we are able to derive the cosmic spectrum in absolute units (i.e., units of W Å-1 Mpc-3) at 2-5 Å resolution and find good agreement with published broadband luminosity densities. For a Salpeter initial mass function, the best-fit stellar mass-to-light ratio is 3.7-7.5 M☉/L☉ in the r band (corresponding to Ωstarsh = 0.0025-0.0055), and from both the stellar emission history and the Hα luminosity density independently we find a cosmological star formation rate of 0.03-0.04 h M☉ yr-1 Mpc-3 today.
BFS-4K: An Efficient Implementation of BFS for Kepler GPU Architectures

Breadth-first search (BFS) is one of the most common graph traversal algorithms and the building block for a wide range of graph applications. With the advent of graphics processing units (GPUs), several works have been proposed to accelerate graph algorithms and, in particular, BFS on such many-core architectures. Nevertheless, BFS has proven to be an algorithm for which it is hard to obtain better performance from parallelization. Indeed, the proposed solutions take advantage of the massively parallelism of GPUs but they are often asymptotically less efficient than the fastest CPU implementations. This paper presents BFS-4K, a parallel implementation of BFS for GPUs that exploits the more advanced features of GPU-based platforms (i.e., NVIDIA Kepler) and that achieves an asymptotically optimal work complexity. The paper presents different strategies implemented in BFS-4K to deal with the potential workload imbalance and thread divergence caused by any actual graph non-homogeneity. The paper presents the experimental results conducted on several graphs of different size and characteristics to understand how the proposed techniques are applied and combined to obtain the best performance from the parallel BFS visits. Finally, an analysis of the most representative BFS implementations for GPUs at the state of the art and their comparison with BFS-4K are reported to underline the efficiency of the proposed solution.
Bulk-induced boundary perturbations

The influence of closed string moduli on the D-brane moduli space is studied from a worldsheet point of view. Whenever a D-brane cannot be adjusted to an infinitesimal change of the closed string background, the corresponding exactly marginal bulk operator ceases to be exactly marginal in the presence of the brane. The bulk perturbation then induces a renormalization group flow on the boundary whose end-point describes a conformal D-brane of the perturbed theory. We derive the relevant renormalization group equations in general and illustrate the phenomenon with a number of examples, in particular the radius deformation of a free boson on a circle. At the self-dual radius we can give closed formulae for the induced boundary flows which are exact in the boundary coupling constants.
Fast Inference with Min-Sum Matrix Product

The MAP inference problem in many graphical models can be solved efficiently using a fast algorithm for computing min-sum products of n × n matrices. The class of models in question includes cyclic and skip-chain models that arise in many applications. Although the worst-case complexity of the min-sum product operation is not known to be much better than O(n3), an O(n2.5) expected time algorithm was recently given, subject to some constraints on the input matrices. In this paper, we give an algorithm that runs in O(n2 log n) expected time, assuming that the entries in the input matrices are independent samples from a uniform distribution. We also show that two variants of our algorithm are quite fast for inputs that arise in several applications. This leads to significant performance gains over previous methods in applications within computer vision and natural language processing.
High Proportion of HIV-HCV Coinfected Patients with Advanced Liver Fibrosis Requiring Hepatitis C Treatment in Haiphong, Northern Vietnam (ANRS 12262)

Rationale and Aims Screening and treatment for chronic hepatitis C are very limited in Vietnam and clinical data on HCV-related liver disease in HIV-coinfected people are almost inexistent. This study aimed to assess the severity of liver fibrosis and its risk factors in HIV-HCV coinfected patients in Haiphong, Northern Vietnam. Methods A cross-sectional study was conducted at a HIV outpatient clinic. Consecutive HIV treated adults with positive HCV serology completed a standardised epidemiological questionnaire and had a comprehensive liver assessment including hepatic elastography (Fibroscan®, Echosens). Results From February to March 2014, 104 HIV-HCV coinfected patients receiving antiretroviral therapy (ART) were prospectively enrolled (99 males, median age: 35.8 (32.7–39.6) years, median CD4 count: 504 (361–624) /mm3. Of them, 93 (89.4%) had detectable HCV RNA (median 6.19 (4.95–6.83 Log10 IU/mL). Patients were mainly infected with genotypes 1a/1b (69%) and genotypes 6a/6e (26%). Forty-three patients (41.3%) had fibrosis ≥F2 including 24 patients (23.1%) with extensive fibrosis (F3) and/or cirrhosis (F4). In univariate analysis, excessive alcohol consumption, estimated time duration from HCV infection, nevirapine and lopinavir-based ARV regimen and CD4 nadir were associated factors of extensive fibrosis/cirrhosis. Alcohol abuse was the only independent factor of extensive fibrosis in multivariate analysis. Using Fibroscan® as a gold standard, the high thresholds of AST-to-platelet ratio index (APRI) and fibrosis-4 score (FIB-4) had very good performances for the diagnosis of extensive fibrosis/cirrhosis (Se: 90 and 100%, Sp:84 and 81%, AUROCs = 0.93, 95%CI: 0.86–0.99 and 0.96 (0.92–0.99), respectively). Conclusion In this study, nearly 25% of HIV-HCV coinfected patients successfully treated with ART have extensive fibrosis or cirrhosis, and therefore require urgently HCV treatment.
Heterogeneous HIV Testing Preferences in an Urban Setting in Tanzania: Results from a Discrete Choice Experiment

Background Efforts to reduce Human Immunodeficiency Virus (HIV) transmission through treatment rely on HIV testing programs that are acceptable to broad populations. Yet, testing preferences among diverse at-risk populations in Sub-Saharan Africa are poorly understood. We fielded a population-based discrete choice experiment (DCE) to evaluate factors that influence HIV-testing preferences in a low-resource setting. Methods Using formative work, a pilot study, and pretesting, we developed a DCE survey with five attributes: distance to testing, confidentiality, testing days (weekday vs. weekend), method for obtaining the sample for testing (blood from finger or arm, oral swab), and availability of HIV medications at the testing site. Cluster-randomization and Expanded Programme on Immunization (EPI) sampling methodology were used to enroll 486 community members, ages 18–49, in an urban setting in Northern Tanzania. Interviewer-assisted DCEs, presented to participants on iPads, were administered between September 2012 and February 2013. Results Nearly three of five males (58%) and 85% of females had previously tested for HIV; 20% of males and 37% of females had tested within the past year. In gender-specific mixed logit analyses, distance to testing was the most important attribute to respondents, followed by confidentiality and the method for obtaining the sample for the HIV test. Both unconditional assessments of preferences for each attribute and mixed logit analyses of DCE choice patterns suggest significant preference heterogeneity among participants. Preferences differed between males and females, between those who had previously tested for HIV and those who had never tested, and between those who tested in the past year and those who tested more than a year ago. Conclusion The findings suggest potentially significant benefits from tailoring HIV testing interventions to match the preferences of specific populations, including males and females and those who have never tested for HIV.
Lentinan protects pancreatic β cells from STZ‐induced damage

Pancreatic β‐cell death or dysfunction mediated by oxidative stress underlies the development and progression of diabetes mellitus (DM). In this study, we evaluated the effect of lentinan (LNT), an active ingredient purified from the bodies of Lentinus edodes, on pancreatic β‐cell apoptosis and dysfunction caused by streptozotocin (STZ) and the possible mechanisms implicated. The rat insulinoma cell line INS‐1 were pre‐treated with the indicated concentration of LNT for 30 min. and then incubated for 24 hrs with or without 0.5 mM STZ. We found that STZ treatment causes apoptosis of INS‐1 cells by enhancement of intracellular reactive oxygen species (ROS) accumulation, inducible nitric oxide synthase (iNOS) expression and nitric oxide release and activation of the c‐jun N‐terminal kinase (JNK) and p38 mitogen‐activated protein kinase (MAPK) signalling pathways. However, LNT significantly increased cell viability and effectively attenuated STZ‐induced ROS production, iNOS expression and nitric oxide release and the activation of JNK and p38 MAPK in a dose‐dependent manner in vitro. Moreover, LNT dose‐dependently prevented STZ‐induced inhibition of insulin synthesis by blocking the activation of nuclear factor kappa beta and increasing the level of Pdx‐1 in INS‐1 cells. Together these findings suggest that LNT could protect against pancreatic β‐cell apoptosis and dysfunction caused by STZ and therefore may be a potential pharmacological agent for preventing pancreatic β‐cell damage caused by oxidative stress associated with diabetes.
The effect of low-level laser therapy on the healing of hard palate mucosa and the oxidative stress status of rats.

OBJECTIVE The biostimulation effects of low-level laser therapy (LLLT) have been demonstrated recently. This study investigated the effects of LLLT on palatal mucoperiosteal wound healing and oxidative stress status in rats. MATERIAL AND METHOD Forty-two male Wistar rats weighing 250-300 g were used in this study. A standardized full-thickness wound was created in the mucoperiosteum of the hard palates of the rats using a 3-mm-diameter biopsy punch. Treatment using a GaAlAs laser at a wavelength of 940 nm and a dose of 10 J/cm(2) was initiated after surgery and repeated on the 2nd, 4th, and 6th days post-surgery. Seven animals from each group were sacrificed on the 7th, 14th, and 21st days after surgery. Total antioxidant status and total oxidative status were measured in serum. RESULTS The histopathological findings revealed reduced numbers of inflammatory cells on the 7th day, increased mitotic activity of fibroblasts on the 14th and 21st day, and the same degree of collagen synthesis and vascularization on the days 7, 14, and 21 in the LLLT group compared with the control group. No significant differences in total oxidative status and total antioxidant status were observed between the groups. CONCLUSION LLLT using a GaAlAs laser at a wavelength of 940 nm and a dose of 10 J/cm(2) elicited a positive healing effect on palatal mucoperiosteal wounds likely via the induction of fibroblasts. The oxidative stress status was not affected by LLLT.
Chlamydia pneumoniae Is Genetically Diverse in Animals and Appears to Have Crossed the Host Barrier to Humans on (At Least) Two Occasions

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of diseases. Since the first isolation of C. pneumoniae TWAR in 1965, all human isolates have been essentially clonal, providing little evolutionary insight. To address this gap, we investigated the genetic diversity of 30 isolates from diverse geographical locations, from both human and animal origin (amphibian, reptilian, equine and marsupial). Based on the level of variation that we observed at 23 discreet gene loci, it was clearly evident that the animal isolates were more diverse than the isolates of human origin. Furthermore, we show that C. pneumoniae isolates could be grouped into five major genotypes, A-E, with A, B, D and E genotypes linked by geographical location, whereas genotype C was found across multiple continents. Our evidence strongly supports two separate animal-to-human cross species transfer events in the evolutionary history of this pathogen. The C. pneumoniae human genotype identified in the USA, Canada, Taiwan, Iran, Japan, Korea and Australia (non-Indigenous) most likely originated from a single amphibian or reptilian lineage, which appears to have been previously geographically widespread. We identified a separate human lineage present in two Australian Indigenous isolates (independent geographical locations). This lineage is distinct and is present in Australian amphibians as well as a range of Australian marsupials.
Cooperative Multi-Cell Networks: Impact of Limited-Capacity Backhaul and Inter-Users Links

Cooperative technology is expected to have a great impact on the performance of cellular or, more generally, infrastructure networks. Both multicell processing (cooperation among base stations) and relaying (cooperation at the user level) are currently being investigated. In this presentation, recent results regarding the performance of multicell processing and user cooperation under the assumption of limited-capacity interbase station and inter-user links, respectively, are reviewed. The survey focuses on related results derived for non-fading uplink and downlink channels of simple cellular system models. The analytical treatment, facilitated by these simple setups, enhances the insight into the limitations imposed by limited-capacity constraints on the gains achievable by cooperative techniques.
Fibrinolytic Deficit and Platelet Activation in Atrial Fibrillation and Their Postablation Modulation

This study aims to examine the effects of atrial fibrillation (AF) on the expression of the cellular mediators plasminogen activator inhibitor 1 (PAI-1) and CD40 ligand (CD40-L). Additionally, the effect of catheter ablation on the levels of the aforementioned biomarkers was also examined. In this prospective study, plasma samples were collected from patients with AF at baseline prior to ablation and at 1 and 3 months postablation. There was a statistically significant increase in CD40-L at baseline in patients with AF compared to control (P = .0034). There was a statistically significant decrease in CD40-L levels postablation at both 1 month (P < .0001) and 3 months (P < .0001) compared to baseline. Baseline levels of PAI-1 were elevated compared to the control group (mean 19.55 ± 2.17 ng/mL vs 4.85 ± 0.41 ng/mL) and a statistically significant decrease in circulating PAI-1 levels 1 month postablation (P = .05) was noted compared to preablation levels. These data suggest that inflammation plays an important role in the pathogenesis of AF and that these cellular mediators are modulated by catheter ablation.
Treadmill Exercise Activates Subcortical Neural Networks and Improves Walking After Stroke: A Randomized Controlled Trial

Background and Purpose— Stroke often impairs gait thereby reducing mobility and fitness and promoting chronic disability. Gait is a complex sensorimotor function controlled by integrated cortical, subcortical, and spinal networks. The mechanisms of gait recovery after stroke are not well understood. This study examines the hypothesis that progressive task-repetitive treadmill exercise (T-EX) improves fitness and gait function in subjects with chronic hemiparetic stroke by inducing adaptations in the brain (plasticity). Methods— A randomized controlled trial determined the effects of 6-month T-EX (n=37) versus comparable duration stretching (CON, n=34) on walking, aerobic fitness and in a subset (n=15/17) on brain activation measured by functional MRI. Results— T-EX significantly improved treadmill-walking velocity by 51% and cardiovascular fitness by 18% (11% and −3% for CON, respectively; P<0.05). T-EX but not CON affected brain activation during paretic, but not during nonparetic limb movement, showing 72% increased activation in posterior cerebellar lobe and 18% in midbrain (P<0.005). Exercise-mediated improvements in walking velocity correlated with increased activation in cerebellum and midbrain. Conclusions— T-EX improves walking, fitness and recruits cerebellum-midbrain circuits, likely reflecting neural network plasticity. This neural recruitment is associated with better walking. These findings demonstrate the effectiveness of T-EX rehabilitation in promoting gait recovery of stroke survivors with long-term mobility impairment and provide evidence of neuroplastic mechanisms that could lead to further refinements in these paradigms to improve functional outcomes.
Determination of muscle architecture and fiber characteristics of the superficial and deep digital flexor muscles in the forelimbs of adult horses.

OBJECTIVE To provide a quantitative description of the architecture of superficial digital flexor (SDF) and deep digital flexor (DDF) muscles in adult horses to predict muscle-tendon behavior and estimate muscle forces. SAMPLE POPULATION 7 forelimb specimens from 7 adult Thoroughbreds. PROCEDURE Muscle and tendon lengths and volumes were measured from 6 fixed forelimbs. After processing, fiber bundle and sarcomere lengths were measured. Optimal fascicle lengths and muscle length-to-fascicle length, muscle length-to-free tendon length, and fascicle length-to-tendon length ratios were calculated, as were tendon and muscle physiologic cross-sectional areas (PCSAs). Pennation angles were measured in 1 embalmed specimen. RESULTS The SDF optimal fascicle lengths were uniformly short (mean +/- SD, 0.8 +/- 0.1 cm), whereas DDF lengths ranged from 0.9 +/- 0.2 cm to 10.8 +/- 1.6 cm. The DDF humeral head had 3 architectural subunits, each receiving a separate median nerve branch, suggestive of neuromuscular compartmentalization. Pennation angles were small (10 degrees to 25 degrees). The PCSAs of the SDF and DDF muscle were 234 +/- 51 cm2 and 259 +/- 30 cm2, with estimated forces of 4,982 +/- 1148 N and 5,520 +/- 544 N, respectively. CONCLUSIONS AND CLINICAL RELEVANCE The SDF muscle appears to provide strong tendinous support with little muscle fascicular shortening and fatigue-resistance properties. The DDF muscle combines passive and dynamic functions with larger tension development and higher shortening velocities during digital motion. Architectural parameters are useful for estimation of forces and have implications for analysis of muscle-tendon function, surgical procedures involving muscle-tendon lengthening, and biomechanical modeling.
Augmented Expression of Atrial Natriuretic Polypeptide Gene in Ventricles of Spontaneously Hypertensive Rats (SHR) and SHR‐Stroke Prone

Tissue levels of atrial natriuretic polypeptide (ANP) and ANP messenger RNA (mRNA) in the atrium and ventricle were measured simultaneously in spontaneously hypertensive rats (SHR) and its substrain, SHR-stroke prone (SHRSP), and these levels were compared with those in control Wistar-Kyoto rats (WKY). At 27 weeks of age with established hypertension and ventricular hypertrophy, ANPmRNA levels in ventricles from SHR and SHRSP were markedly increased, and total contents of ventricular ANPmRNA in SHR and SHRSP were approximately 50% and 250%, respectively, of the corresponding atrial contents. However, levels and total contents of atrial ANPmRNA in SHR and SHRSP were similar to those of WKY, and the total content of ventricular ANPmRNA in WKY was only 6% of the content of atrial ANPmRNA. ANP concentrations in ventricles of SHR and SHRSP were increased in association with the augmentation of ANPmRNA levels. During the prehypertensive stage at 6 weeks of age, slight increases in levels and total contents of ANPmRNA and ANP in the ventricle were observed only in SHRSP. These results demonstrate that the expression of the ANP gene is markedly augmented in ventricles of SHR and SHRSP, especially of SHRSP, at the stage of established hypertension and ventricular hypertrophy, and they also suggest that these genetically hypertensive rats are one of the best animal models to investigate the biosynthesis, storage, and secretion of ventricular ANP.
Form Factors and Dyson-Schwinger Equations

A synopsis exemplifying the employment of Dyson-Schwinger equations in the calculation and explanation of hadron electromagnetic form factors and related phenomena. In particular the contribution: presents the pion form factor computed simultaneously at spacelike and timelike momenta; reports aspects of the evolution of the nucleon and Delta masses with current-quark mass and the correlation of their mass difference with that between scalar and axial-vector diquarks; describes an estimate of the s-quark content of a dressed u-quark and its impact on the nucleon's strangeness magnetic moment; and comments upon the domain within which a pseudoscalar meson cloud can materially contribute to hadron form factors.