Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Antioxidant Intake in Relation to Semen Quality Parameters in Infertile Men: a Cross-Sectional Study

The objective of this study was to assess the association between dietary antioxidant intake and semen quality parameters in infertile men. In this cross-sectional study, dietary antioxidant intake was evaluated in 175 infertile Iranian men by a validated dish-based 106-item semi-quantitative food frequency questionnaire. Men were asked to abstain from ejaculation for at least 72 hours before sample collection. Semen parameters were assessed by a sperm counting chamber and Terminal deoxynucleotidyl transferase dUTP nick end labeling assay methods. Linear quantile regression was used to determine the associations between antioxidant nutrient intake and semen quality parameters (including total sperm count, sperm density, total motility, DNA damage and DNA fragmentation). Mean age of study participants was 32.19 ± 2.34 years. Compared with the lowest quartile, men in the highest quartile of dietary β-carotene and vitamin C intake had lower sperm DNA fragmentation index (Ptrend = 0.042 and Ptrend = 0.03, respectively). Also, dietary intake of beta-cryptoxanthin had a positive association with sperm density (Ptrend = 0.02), and dietary lutein was associated with total sperm count (Ptrend = 0.045). Dietary intake of other antioxidants did not significantly correlate with the indicators related to the quantity and quality of sperm (p > 0.05). These data suggest that dietary intake of some of the antioxidants is associated with semen related parameters.
BthTX-I from Bothrops jararacussu induces apoptosis in human breast cancer cell lines and decreases cancer stem cell subpopulation

ABSTRACT Background: Breast cancer is the neoplasm with both the highest incidence and mortality rate among women worldwide. Given the known snake venom cytotoxicity towards several tumor types, we evaluated the effects of BthTX-I from Bothrops jararacussu on MCF7, SKBR3, and MDAMB231 breast cancer cell lines. Methods: BthTX-I cytotoxicity was determined via MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazoliumbromide assay. Cell death was measured by a hypotonic fluorescent solution method, annexin-V-FITC/propidium iodide staining and by apoptotic/autophagic protein expression. Cancer stem cells (CSCs) were quantified by flow cytometry using anti-CD24-FITC and anti-CD44-APC antibodies and propidium iodide. Results: BthTX-I at 102 µg/mL induced cell death in all cell lines. The toxin induced apoptosis in MCF7, SKBR3, and MDAMB231 in a dose-dependent manner, as confirmed by the increasing number of hypodiploid nuclei. Expression of pro-caspase 3, pro-caspase 8 and Beclin-1 proteins were increased, while the level of the antiapoptotic protein Bcl-2 was diminished in MCF7 cells. BthTX-I changed the staining pattern of CSCs in MDAMB231 cells by increasing expression of CD24 receptors, which mediated cell death. Conclusions: BthTX-I induces apoptosis and autophagy in all breast cancer cell lines tested and also reduces CSCs subpopulation, which makes it a promising therapeutic alternative for breast cancer.
Epidemiology of Clavicle Fractures Among US High School Athletes, 2008-2009 Through 2016-2017

Background: Little is known about the epidemiology of clavicle fractures in United States (US) high school athletes. Sports participation among high school students has increased steadily, placing increased numbers at risk of sports-related injury. Purpose: To describe the epidemiology of clavicle fractures among high school athletes, including injury rates by sex, sport, and type of play and trends in operative versus nonoperative treatment. Study Design: Descriptive epidemiology study. Methods: The study data set included all athlete-exposure (AE) and clavicle fracture data collected from 2008-2009 through 2016-2017 from a large sample of US high schools as part of the National High School Sports-Related Injury Surveillance Study for students participating in boys’ football, boys’/girls’ soccer, boys’/girls’ basketball, boys’/girls’ volleyball, boys’ wrestling, boys’ baseball, girls’ softball, girls’ field hockey, boys’ ice hockey, boys’/girls’ lacrosse, boys’/girls’ swimming and diving, boys’/girls’ track and field, girls’ gymnastics, girls’ cheerleading, boys’/girls’ tennis, and boys’/girls’ cross-country. Results: Overall, 567 clavicle fractures were reported during 31,520,765 AEs, an injury rate of 1.80 per 100,000 AEs. Injury rates varied by sport, with the highest rates in the boys’ full-contact sports of ice hockey (5.27), lacrosse (5.26), football (4.98), and wrestling (2.21). Among girls’ sports, the highest rates were in soccer (0.92), lacrosse (0.26), and basketball (0.25). In sex-comparable sports, injury rates were still significantly higher among boys (1.03) than girls (0.35) (rate ratio, 2.91; 95% CI, 1.97-4.30). Injury rates were significantly higher in competition (4.58) as compared with practice (0.87) (rate ratio, 5.27; 95% CI, 4.44-6.26). Most injuries were treated conservatively (82.7%) rather than operatively (17.3%). Time to return to sports varied, with a greater proportion of medical disqualifications among those treated operatively (40.0%) as compared with those treated conservatively (22.6%) (injury proportion ratio, 1.77; 95% CI, 1.31-2.39). Conclusion: Although clavicle fracture rates are relatively low, they vary by sport, sex, and activity. Understanding such differences should drive more effective, targeted injury prevention efforts. Increased time loss from sports with surgical versus conservative treatment may have been influenced by factors including injury severity and its timing relative to the season’s progress.
Zebrafish as a Smart Model to Understand Regeneration After Heart Injury: How Fish Could Help Humans

Myocardial infarction (MI) in humans is a common cause of cardiac injury and results in irreversible loss of myocardial cells and formation of fibrotic scar tissue. This fibrotic tissue preserves the integrity of the ventricular wall but undermines pump function, leading to congestive heart failure. Unfortunately, the mammalian heart is unable to replace cardiomyocytes, so the life expectancy for patients after an episode of MI is lower than for most common types of cancers. Whereas, humans cannot efficiently regenerate their heart after injury, the teleost zebrafish have the capability to repair a “broken” heart. The zebrafish is probably one of the most important models for developmental and regenerative biology of the heart. In the last decades, the zebrafish has become increasingly important for scientific research: it has many characteristics that make it a smart model for studying human disease. Moreover, adult zebrafish efficiently regenerate their hearts following different forms of injury. Due to these characteristics, and to the availability of genetic approaches, and biosensor zebrafish lines, it has been established useful for studying molecular mechanisms of heart regeneration. Regeneration of cardiomyocytes in zebrafish is not based on stem cells or transdifferentiation of other cells but on the proliferation of preexisting cardiomyocytes. For this reason, future studies into the zebrafish cardiac regenerative mechanisms could identify specific molecules able to regulate the proliferation of preexisting cardiomyocytes; these factors may be studied in order to understand regulation of myocardial plasticity in cardiac repair processes after injury and, in particular, after MI in humans.
Pluripotent Stem Cells for Brain Repair: Protocols and Preclinical Applications in Cortical and Hippocampal Pathologies

Brain injuries causing chronic sensory or motor deficit, such as stroke, are among the leading causes of disability worldwide, according to the World Health Organization; furthermore, they carry heavy social and economic burdens due to decreased quality of life and need of assistance. Given the limited effectiveness of rehabilitation, novel therapeutic strategies are required to enhance functional recovery. Since cell-based approaches have emerged as an intriguing and promising strategy to promote brain repair, many efforts have been made to study the functional integration of neurons derived from pluripotent stem cells (PSCs), or fetal neurons, after grafting into the damaged host tissue. PSCs hold great promises for their clinical applications, such as cellular replacement of damaged neural tissues with autologous neurons. They also offer the possibility to create in vitro models to assess the efficacy of drugs and therapies. Notwithstanding these potential applications, PSC-derived transplanted neurons have to match the precise sub-type, positional and functional identity of the lesioned neural tissue. Thus, the requirement of highly specific and efficient differentiation protocols of PSCs in neurons with appropriate neural identity constitutes the main challenge limiting the clinical use of stem cells in the near future. In this Review, we discuss the recent advances in the derivation of telencephalic (cortical and hippocampal) neurons from PSCs, assessing specificity and efficiency of the differentiation protocols, with particular emphasis on the genetic and molecular characterization of PSC-derived neurons. Second, we address the remaining challenges for cellular replacement therapies in cortical brain injuries, focusing on electrophysiological properties, functional integration and therapeutic effects of the transplanted neurons.
Alignment of Rutaceae Genomes Reveals Lower Genome Fractionation Level Than Eudicot Genomes Affected by Extra Polyploidization

Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, and the genome of one close relative in the Rutaceae family, atalantia (Atalantia buxifolia), has also been sequenced. Here, we show a family-level comparative analysis of Rutaceae genomes. By using grape as the outgroup and checking cross-genome gene collinearity, we systematically performed a hierarchical and event-related alignment of Rutaceae genomes, and produced a gene list defining homologous regions based on ancestral polyploidization or speciation. We characterized genome fractionation resulting from gene loss or relocation, and found that erosion of gene collinearity could largely be described by a geometric distribution. Moreover, we found that well-assembled Rutaceae genomes retained significantly more genes (65–82%) than other eudicots affected by recursive polyploidization. Additionally, we showed divergent evolutionary rates among Rutaceae plants, with sweet orange evolving faster than others, and by performing evolutionary rate correction, re-dated major evolutionary events during their evolution. We deduced that the divergence between the Rutaceae family and grape occurred about 81.15–91.74 million years ago (mya), while the split between citrus and atalantia plants occurred <10 mya. In addition, we showed that polyploidization led to a copy number expansion of key gene families contributing to the biosynthesis of vitamin C. Overall, the present effort provides an important comparative genomics resource and lays a foundation to understand the evolution and functional innovation of Rutaceae genomes.
ARE ANTIBIOTICS OF ANY USE IN THE MANAGEMENT OF GRANULOMA ANNULARE IN CHILDREN?

Background: Granuloma annulare (GA) is a benign inflammatory dermatosis of unknown cause, of which generalised granuloma annulare (GGA) is a subtype that tends to be resistant to treatment. Various antibiotics have been used to treat GGA, the most recent being combination therapy with rifampicin, ofloxacin and minocycline (ROM). This study aims to explore the efficacy of antibiotics in treating GGA, and whether antibiotics may be useful in children with GGA. Materials and Methods: A systematic review of literature published from 1947 to 2017 was undertaken in order to evaluate the use of antibiotics in treating GGA. Data on characteristics of children with GGA were extracted and eligible studies were then qualitatively analysed. Results: Seven hundred and ninety (790) potential studies were identified, of which 16 were eligible for inclusion in the final analysis. Of these 16 studies, majority were case studies (n=9, 56.3%), with 2 case series (12.5%), 2 retrospective studies (12.5%) and 3 open-label prospective studies (18.8%). Main antibiotic treatments reported were either monthly combination therapy of rifampicin, ofloxacin and minocycline (ROM), or monotherapy with dapsone or doxycycline. Out of a total of 158 patients with GA, 72 patients (45.6%) were treated with antibiotics. Of the 72, 48.6% (n=35) of these patients had GGA while 4 were children; two with GA (2 with GGA), all of whom were treated with dapsone. Conclusion: There is paucity of evidence to support the use of antibiotics in the treatment of GGA in children. Although ROM has shown promising results in adults, more studies are needed to validate these findings in children.
Anatomical and Neuromuscular Determinants of Strength Change in Previously Untrained Men Following Heavy Strength Training

This study examined whether changes in strength following a moderate-duration strength training program were associated with changes in specific combinations of anatomical and neuromuscular variables. 36 men (18–40 y) completed 10 weeks of lower-limb heavy resistance (6-RM) strength training. Measurements included cross-sectional area (CSA), fascicle length (lf) and fascicle angle (θf) from proximal, middle and distal regions of the four quadriceps components; agonist (EMG:M), antagonist (EMG) muscle activities and percent voluntary quadriceps activation (%VA; interpolated twitch technique); patellar tendon moment arm distance; and maximal isometric, concentric and eccentric (60° s–1) torque. Multiple regression models were developed to quantify the relationship between the change in maximum torque and the changes in combinations of anatomical and neuromuscular variables. The best model for each contraction mode was determined using Akaike’s Information Criterion (AICc), an information-theoretic approach for model selection. Strength increased significantly following training (mean range = 12.5–17.2%), and moderate relationships were observed between modeled data (using best-fit prediction models) and the change in torque for each contraction mode. The change in isometric torque was best (although weakly) predicted by the linear combination of the change in proximal-region vastus lateralis (VL) CSA and fascicle angle (R2 = 0.27, p < 0.05; AICcwi = 0.52, i.e., the probability the model would be selected as the “best model”). The models best predicting the change in concentric and eccentric torque both included the combination of the change in quadriceps (i.e., mean of all muscles) EMG:M and the change in vastus intermedius fascicle angle combined with either a change in proximal-region VL (R2 = 0.40, p < 0.001; AICcwi = 0.15) or whole quadriceps (R2 = 0.41, p < 0.001; AICcwi = 0.30) CSA (concentric and eccentric, respectively). Models incorporating the change in proximal CSA typically received substantial support (AICC < 2) for concentric torque prediction models, and the change in % VA and pre-training moment arm distance had substantial support for use in eccentric torque prediction models. In conclusion, adaptations varied between individuals, however strength training programs targeted to improve a group of variables that particularly includes agonist muscle activation might yield the greatest improvements in concentric and eccentric knee extension strength, whereas proximal muscle size and fascicle angle appear most important for isometric torque improvements.
Long Non-coding RNAs as Communicators and Mediators Between the Tumor Microenvironment and Cancer Cells

Long non-coding RNAs (lncRNAs) are a class of more than 200 nucleotides RNA transcripts which have limited protein coding capacity. They regulate numerous biological processes in cancers through diverse molecular mechanisms. Aberrant expression of lncRNAs has been frequently associated with human cancer. Furthermore, the tumor microenvironment (TME) is composed of different cells such as cancer-associated fibroblasts (CAFs), endothelial cells and infiltrated immune cells, and all of which participate in communication with tumor cells affecting the progression of tumor. LncRNAs are directly and indirectly involved in the crosstalk between stromal cells and tumor cells and dysregulated lncRNAs expression in these cells could drive tumorigenesis. In this review, we explore the influence of aberrantly expressed lncRNAs in tumor progression, clarify the critical roles of lncRNAs in the TME, summarize findings on crosstalk between infiltrated immune cells, CAFs, endothelial cells, and tumor cells via lncRNAs, and discuss the promise of lncRNAs as tumor diagnostic markers and therapeutic targets.
Does the Nucleoid Determine Cell Dimensions in Escherichia coli?

Bacillary, Gram-negative bacteria grow by elongation with no discernible change in width, but during faster growth in richer media the cells are also wider. The mechanism regulating the change in cell width W during transitions from slow to fast growth is a fundamental, unanswered question in molecular biology. The value of W that changes in the divisome and during the division process only, is related to the nucleoid complexity, determined by the rates of growth and of chromosome replication; the former is manipulated by nutritional conditions and the latter—by thymine limitation of thyA mutants. Such spatio-temporal regulation is supported by existence of a minimal possible distance between successive replisomes, so-called eclipse that limits the number of replisomes to a maximum. Breaching this limit by slowing replication in fast growing cells results in maximal nucleoid complexity that is associated with maximum cell width, supporting the notion of Nucleoid-to-Divisome signal transmission. Physical signal(s) may be delivered from the nucleoid to assemble the divisome and to fix the value of W in the nascent cell pole.
Adaptive Temporal Sampling for Volumetric Path Tracing of Medical Data

Monte‐Carlo path tracing techniques can generate stunning visualizations of medical volumetric data. In a clinical context, such renderings turned out to be valuable for communication, education, and diagnosis. Because a large number of computationally expensive lighting samples is required to converge to a smooth result, progressive rendering is the only option for interactive settings: Low‐sampled, noisy images are shown while the user explores the data, and as soon as the camera is at rest the view is progressively refined. During interaction, the visual quality is low, which strongly impedes the user's experience. Even worse, when a data set is explored in virtual reality, the camera is never at rest, leading to constantly low image quality and strong flickering. In this work we present an approach to bring volumetric Monte‐Carlo path tracing to the interactive domain by reusing samples over time. To this end, we transfer the idea of temporal antialiasing from surface rendering to volume rendering. We show how to reproject volumetric ray samples even though they cannot be pinned to a particular 3D position, present an improved weighting scheme that makes longer history trails possible, and define an error accumulation method that downweights less appropriate older samples. Furthermore, we exploit reprojection information to adaptively determine the number of newly generated path tracing samples for each individual pixel. Our approach is designed for static, medical data with both volumetric and surface‐like structures. It achieves good‐quality volumetric Monte‐Carlo renderings with only little noise, and is also usable in a VR context.
On‐Site Example‐Based Material Appearance Acquisition

We present a novel example‐based material appearance modeling method suitable for rapid digital content creation. Our method only requires a single HDR photograph of a homogeneous isotropic dielectric exemplar object under known natural illumination. While conventional methods for appearance modeling require prior knowledge on the object shape, our method does not, nor does it recover the shape explicitly, greatly simplifying on‐site appearance acquisition to a lightweight photography process suited for non‐expert users. As our central contribution, we propose a shape‐agnostic BRDF estimation procedure based on binary RGB profile matching. We also model the appearance of materials exhibiting a regular or stationary texture‐like appearance, by synthesizing appropriate mesostructure from the same input HDR photograph and a mesostructure exemplar with (roughly) similar features. We believe our lightweight method for on‐site shape‐agnostic appearance acquisition presents a suitable alternative for a variety of applications that require plausible “rapid‐appearance‐modeling”.
Keep Your Host Language Object and Also Query it: A Case for SQL Query Support in RDBMS for Host Language Objects

As a result of prolific growth in data science and machine learning applications, modern relational database management systems (RDBMS) are experimenting with various approaches to facilitate advanced analytical computations, in addition to the relational operations that they traditionally support. The most common approach has been to integrate an embedded high level language (HLL) interpreter into the RDBMS along with any additional libraries that specialize in numerical computations. Such implementations, e.g., user defined functions (UDFs), follow generally a black-box setup, and for many complex workflows that require datasets to be passed and processed back-and-forth between the query execution engine and the embedded HLL interpreter, optimization opportunities are not fully explored yet. In this paper, we propose and implement the concept of virtual tables that can be used to expose data set objects maintained by the embedded HLL interpreter to the query engine for executing relational operations. Unlike prevalent solutions, our approach minimizes the need for performing data copies and conversions, performing them lazily when required. It also facilitates better optimization opportunities for the execution of SQL queries as the RDBMS is able to analyze the data characteristics of the HLL objects before producing an execution plan. The approach is also programmer friendly, allowing for a more intuitive implementation of computational workflows. We perform evaluations over a variety of workloads which demonstrate the performance and programming benefits of virtual tables.
DV8: Automated Architecture Analysis Tool Suites

This paper present our tool suite called DV8. The objective of DV8 is to measure software modularity, detect architecture anti-patterns as technical debts, quantify the maintenance cost of each instance of an anti-pattern, and enable return on investment analyses of architectural debts. Different from other tools, DV8 integrates data from both source code and revision history. We now elaborate on each of DV8's capabilities