Miracle-dz/UniFAR-FTUs huggingface dataset:
Idiopathic Male Infertility Is Strongly Associated with Aberrant Promoter Methylation of Methylenetetrahydrofolate Reductase (MTHFR)

Background Abnormal germline DNA methylation in males has been proposed as a possible mechanism compromising spermatogenesis of some men currently diagnosed with idiopathic infertility. Previous studies have been focused on imprinted genes with DNA methylation in poor quality human sperms. However, recent but limited data have revealed that sperm methylation abnormalities may involve large numbers of genes or shown that genes that are not imprinted are also affected. Methodology/Principal Findings Using the methylation-specific polymerase chain reaction and bisulfite sequencing method, we examined methylation patterns of the promoter of methylenetetrahydrofolate reductase (MTHFR) gene (NG_013351: 1538–1719) in sperm DNA obtained from 94 idiopathic infertile men and 54 normal fertile controls. Subjects with idiopathic infertility were further divided into groups of normozoospermia and oligozoospermia. Overall, 45% (41/94) of idiopathic infertile males had MTHFR hypermethylation (both hemimethylation and full methylation), compared with 15% of fertile controls (P<0.05). Subjects with higher methylation level of MTHFR were more likely to have idiopathic male infertility (P-value for trend = 0.0007). Comparing the two groups of idiopathic infertile subjects with different sperm concentrations, a higher methylation pattern was found in the group with oligozoospermia. Conclusions Hypermethylation of the promoter of MTHFR gene in sperms is associated with idiopathic male infertility. The functional relevance of hypermathylation of MTHFR to male fertility warrants further investigation.
Benthic Dinitrogen Fixation Traversing the Oxygen Minimum Zone Off Mauritania (NW Africa)

Despite its potential to provide new nitrogen (N) to the environment, knowledge on benthic dinitrogen (N2) fixation remains relatively sparse and its contribution to the marine N budget, is regarded as minor. Benthic N2 fixation is often observed in organic-rich sediments coupled to heterotrophic metabolisms, such as sulfate reduction. In the present study, benthic N2 fixation together with sulfate reduction and other heterotrophic metabolisms were investigated at six station between 47 and 1108 m water depth along the 18°N transect traversing the highly productive upwelling region known as Mauritanian oxygen minimum zone (OMZ). Bottom water oxygen concentrations ranged between 30 and 138 µM. Benthic N2 fixation determined by the acetylene reduction assay was detected at all stations with highest rates (0.15 mmol m-2 d-1) on the shelf (47 and 90 m water depth) and lowest rates (0.08 mmol m-2 d-1) below 412 m water depth. The biogeochemical data suggest that part of the N2 fixation could be linked to sulfate- and iron-reducing bacteria. Molecular analysis of the key functional marker gene for N2 fixation, nifH, confirmed the presence of sulfate- and iron-reducing diazotrophs. High N2 fixation further coincided with bioirrigation activity caused by burrowing macrofauna, both of which showed high rates at the shelf sites and low rates in deeper waters. However, statistical analyses proved that none of these processes and environmental variables were significantly correlated with benthic diazotrophy, which lead to the conclusion that either the key parameter controlling benthic N2 fixation in Mauritanian sediments remains unidentified or that a more complex interaction of control mechanisms exists. N2 fixation rates in Mauritanian sediments were 2.7 times lower than those from the anoxic Peruvian OMZ.
Does Usage of an eHealth Intervention Reduce the Risk of Excessive Gestational Weight Gain? Secondary Analysis From a Randomized Controlled Trial

Background Excessive gestational weight gain (GWG) contributes to the development of obesity in mother and child. Internet-based interventions have the potential for delivering innovative and interactive options for prevention of excessive GWG to large numbers of people. Objective The objective of this study was to create a novel measure of Internet-based intervention usage patterns and examine whether usage of an Internet-based intervention is associated with reduced risk of excessive GWG. Methods The website featured blogs, local resources, articles, frequently asked questions (FAQs), and events that were available to women in both the intervention and control arm. Weekly reminders to use the website and to highlight new content were emailed to participants in both arms. Only intervention arm participants had access to the weight gain tracker and diet and physical activity goal-setting tools. A total of 1335 (898 intervention and 437 control) relatively diverse and healthy pregnant women were randomly assigned to the intervention arm or control arm. Usage patterns were examined for both intervention and control arm participants using latent class analysis. Regression analyses were used to estimate the association between usage patterns and three GWG outcomes: excessive total GWG, excessive GWG rate, and GWG. Results Five usage patterns best characterized the usage of the intervention by intervention arm participants. Three usage patterns best characterized control arm participants’ usage. Control arm usage patterns were not associated with excessive GWG, whereas intervention arm usage patterns were associated with excessive GWG. Conclusions The control and intervention arm usage pattern characterization is a unique methodological contribution to process evaluations for self-directed Internet-based interventions. In the intervention arm some usage patterns were associated with GWG outcomes. ClinicalTrial ClinicalTrials.gov; Clinical Trials Number: NCT01331564; https://clinicaltrials.gov/ct2/show/NCT01331564 (Archived by WebCite at http://www.webcitation/6nI9LuX9w)
Second Harmonic Generation Reveals Subtle Fibrosis Differences in Adult and Pediatric Nonalcoholic Fatty Liver Disease

Objectives Investigate subtle fibrosis similarities and differences in adult and pediatric nonalcoholic fatty liver disease (NAFLD) using second harmonic generation (SHG). Methods SHG/two-photon excitation fluorescence imaging quantified 100 collagen parameters and determined qFibrosis values by using the nonalcoholic steatohepatitis (NASH) Clinical Research Network (CRN) scoring system in 62 adult and 36 pediatric NAFLD liver specimens. Results Six distinct parameters identified differences among the NASH CRN stages with high accuracy (area under the curve, 0835-0.982 vs 0.885-0.981, adult and pediatric). All portal region parameters showed similar changes across early stages 0, 1C, and 2, in both groups. Parameter values decreased in adults with progression from stage 1A/B to 2 in the central vein region. In children, aggregated collagen parameters decreased, but nearly all distributed collagen parameters increased from stage 1A/B to 2. Conclusions SHG analysis accurately reproduces NASH CRN staging in NAFLD, as well as reveals differences and similarities between adult and pediatric collagen deposition not captured by currently available quantitative methods.
V2V Radio Channel Performance Based on Measurements in Ramp Scenarios at 5.9 GHz

This paper focuses on vehicle-to-vehicle (V2V) radio channel properties under ramp scenarios with different structures. Ramps are categorized according to different construction structures into: 1) viaduct ramp with soundproof walls in an urban area and 2) a general ramp without soundproof walls in a suburban region. Furthermore, considering whether the line of sight is available, the entire propagation process of the radio signal is divided into various propagation zones. Propagation characteristics, including the distribution of fading, fading depth (FD), level crossing rate, average fade duration, Root-Mean-Square (rms) delay spread, propagation path loss, and shadow fading, have been estimated and extracted. In particular, the radio channel properties in different types of ramp scenarios are compared and some interesting findings are obtained: 1) an abrupt fluctuation of the received signal level (RSL) in the urban viaduct ramp scenario indicates the nonignorable impact of soundproof walls on V2V radio channel and 2) continuous changes of RSL and different FD values in various propagation zones can be observed in suburban ramp scenarios. Furthermore, the statistical characteristics of RMS delay spread are fitted using a generalized extreme value model with a good fit. Furthermore, propagation path loss is modeled, demonstrating the difference of path loss values in the transition region owing to the impact of soundproof walls. Overall, the research results emphasize the significance of the V2V radio channel modeling under ramp scenarios.
Melatonin Cytotoxicity Is Associated to Warburg Effect Inhibition in Ewing Sarcoma Cells

Melatonin kills or inhibits the proliferation of different cancer cell types, and this is associated with an increase or a decrease in reactive oxygen species, respectively. Intracellular oxidants originate mainly from oxidative metabolism, and cancer cells frequently show alterations in this metabolic pathway, such as the Warburg effect (aerobic glycolysis). Thus, we hypothesized that melatonin could also regulate differentially oxidative metabolism in cells where it is cytotoxic (Ewing sarcoma cells) and in cells where it inhibits proliferation (chondrosarcoma cells). Ewing sarcoma cells but not chondrosarcoma cells showed a metabolic profile consistent with aerobic glycolysis, i.e. increased glucose uptake, LDH activity, lactate production and HIF-1α activation. Melatonin reversed Ewing sarcoma metabolic profile and this effect was associated with its cytotoxicity. The differential regulation of metabolism by melatonin could explain why the hormone is harmless for a wide spectrum of normal and only a few tumoral cells, while it kills specific tumor cell types.
Alkali-Silica Reaction in a Form of Chemical Shrinkage

The current approach of ASR testing and mitigating damaging ASR heavily depends on accelerated mortar-bar tests (AMBT) and concrete prism tests (CPT). Although these approaches have resulted significant advances in avoidance of ASR damage in concrete, it was found to have limitations and drawbacks. Therefore, there is a growing demand for an ASR test method to overcome the above issues. A chemical approach that simulates aggregate-pore solution reaction that exists in concrete has been proposed in this study while as-received aggregates were immersed in alkaline solution (i.e., 1N NaOH + Ca(OH)2) and allowed to react at a relatively high temperature (i.e., 80 o C). The approach measures solution volume change in a form of chemical shrinkage over time as the reaction between aggregates and solution proceed. Highly reactive borosilicate glass balls were tested first to validate the proposed approach before any aggregate testing. The tested aggregates were categorized based on the measured chemical shrinkage. The aggregates that are failed by AMBT but passed by CPT and vice versa were identified by this method, and an ASR mechanism in terms of chemical shrinkage was proposed. The results indicate that the proposed test measures solution volume contraction due to ASR and has the potential to predict aggregate alkali reactivity in a short period of time.
Viable bacteria persist on antibiotic spacers following two‐stage revision for periprosthetic joint infection

Treatment in periprosthetic joint infection (PJI) remains challenging. The failure rate of two‐stage revision and irrigation and debridement with component retention in PJI suggests that biofilm cells have a high tolerance to antibiotic chemotherapy. Previous work has demonstrated that biofilm cells have high antibiotic tolerance in vitro, but there is little clinical evidence to support these observations. The aim of this study was to determine if retrieved antibiotic spacers from two‐stage revision total knee arthroplasty for PJI have evidence of remaining viable bacteria. Antibiotic poly (methyl methacrylate) (PMMA) spacers from two‐stage revision total knee arthroplasty for PJI were prospectively collected and analyzed for bacterial 16s rRNA using polymerase chain reaction (PCR), reverse transcription (RT)‐PCR, quantitative RT‐PCR (qRT‐PCR), and single genome analysis (SGA). PCR and RT‐PCR identified bacterial species on 53.8% (7/13) of these samples. When initial culture negative cases are excluded, 68% (6/9) samples were identified with bacterial species. A more rigorous qRT‐PCR analysis showed a strong positive signal for bacterial contamination in 30.7% (4/13) of cases. These patients did not show any clinical evidence of PJI recurrence after 15 months of follow‐up. Because the half‐life of bacterial rRNA is approximately a few days, the identification of bacteria rRNA on antibiotic PMMA spacers suggests that viable bacteria were present after conclusion of antibiotic therapy. This study provides evidence for the high tolerance of biofilm cells to antibiotics in vivo and the important role of bacterial persisters in PJI. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:452–458, 2018.
A spatially explicit estimate of the prewhaling abundance of the endangered North Atlantic right whale

The North Atlantic right whale (NARW) (Eubalaena glacialis) is one of the world's most threatened whales. It came close to extinction after nearly a millennium of exploitation and currently persists as a population of only approximately 500 individuals. Setting appropriate conservation targets for this species requires an understanding of its historical population size, as a baseline for measuring levels of depletion and progress toward recovery. This is made difficult by the scarcity of records over this species’ long whaling history. We sought to estimate the preexploitation population size of the North Atlantic right whale and understand how this species was distributed across its range. We used a spatially explicit data set on historical catches of North Pacific right whales (NPRWs) (Eubalaena japonica) to model the relationship between right whale relative density and the environment during the summer feeding season. Assuming the 2 right whale species select similar environments, we projected this model to the North Atlantic to predict how the relative abundance of NARWs varied across their range. We calibrated these relative abundances with estimates of the NPRW total prewhaling population size to obtain high and low estimates for the overall NARW population size prior to exploitation. The model predicted 9,075–21,328 right whales in the North Atlantic. The current NARW population is thus <6% of the historical North Atlantic carrying capacity and has enormous potential for recovery. According to the model, in June–September NARWs concentrated in 2 main feeding areas: east of the Grand Banks of Newfoundland and in the Norwegian Sea. These 2 areas may become important in the future as feeding grounds and may already be used more regularly by this endangered species than is thought.
Application of the 2013 American College of Cardiology/American Heart Association Cholesterol Guideline to the Korean National Health and Nutrition Examination Surveys from 1998 to 2012

Background The 2013 American College of Cardiology/American Heart Association (ACC/AHA) guideline for the treatment of blood cholesterol recommends statin therapy for individuals at high risk of atherosclerotic cardiovascular disease (ASCVD). The aim of this study was to investigate serial trends in the percentages of Korean adults considered eligible for statin therapy according to the new ACC/AHA cholesterol guideline. Methods Data from the Korean National Health and Nutrition Examination Survey (KNHANES) I (1998, n=7,698), II (2001, n=5,654), III (2005, n=5,269), IV (2007 to 2009, n=15,727), and V (2010 to 2012, n=16,304), which used a stratified, multistage, probability sampling design, were used as representative of the entire Korean population. Results The percentage of adults eligible for statin therapy according to the ACC/AHA cholesterol guideline increased with time: 17.0%, 19.0%, 20.8%, 20.2%, and 22.0% in KNHANES I, II, III, IV, and V, respectively (P=0.022). The prevalence of ASCVD was 1.4% in KNHANES I and increased to 3.3% in KNHANES V. The percentage of diabetic patients aged 40 to 75 years with a low density lipoprotein cholesterol levels of 70 to 189 mg/dL increased from 4.8% in KNHANES I to 6.1% in KNHANES V. People with an estimated 10-year ASCVD risk ≥7.5% and aged 40 to 75 years accounted for the largest percentage among the four statin benefit groups: 9.1% in KNHANES I and 11.0% in KNHANES V. Conclusion Application of the 2013 ACC/AHA guideline has found that the percentage of Korean adults in the statin benefit groups has increased over the past 15 years.
Differential diagnosis between newly diagnosed asthma and COPD using exhaled breath condensate metabolomics: a pilot study

Asthma and chronic obstructive pulmonary disease (COPD) are heterogeneous diseases with high pathological burden and healthcare costs [1–3]. In outpatient clinical practice, an accurate differential diagnosis is often very difficult, particularly in adult smokers, requiring specific lung function tests [4, 5]. Since nuclear magnetic resonance (NMR)-based metabolomics of exhaled breath condensate (EBC) discriminates adults with COPD [6–8] or asthma [9] from healthy subjects, we hypothesised that it is also able to differentiate asthma and COPD patients of different severities. NMR profiling of EBC discriminates between asthma and COPD and this may help clinicians with differential diagnosis http://ow.ly/cNGI30hWYAE
Key point localization for 3d model generation from facial illustrations using SURF and color features

This paper proposes a novel scheme to improve localization accuracy of facial key points in facial illustrations. The proposed scheme estimates the location of facial key points considering global structure of facial key points evaluated by RANSAC like scheme where local evaluation is performed with SURF and color features. Experimental results using a data set composed of facial illustrations show that the estimation error can be reduced to about 8.93 pixels per a key point.
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation

Abstract Motivation Protein–protein interactions (PPI) play a crucial role in our understanding of protein function and biological processes. The standardization and recording of experimental findings is increasingly stored in ontologies, with the Gene Ontology (GO) being one of the most successful projects. Several PPI evaluation algorithms have been based on the application of probabilistic frameworks or machine learning algorithms to GO properties. Here, we introduce a new training set design and machine learning based approach that combines dependent heterogeneous protein annotations from the entire ontology to evaluate putative co-complex protein interactions determined by empirical studies. Results PPI annotations are built combinatorically using corresponding GO terms and InterPro annotation. We use a S.cerevisiae high-confidence complex dataset as a positive training set. A series of classifiers based on Maximum Entropy and support vector machines (SVMs), each with a composite counterpart algorithm, are trained on a series of training sets. These achieve a high performance area under the ROC curve of ≤0.97, outperforming go2ppi—a previously established prediction tool for protein-protein interactions (PPI) based on Gene Ontology (GO) annotations. Availability and implementation https://github.com/ima23/maxent-ppi Supplementary information Supplementary data are available at Bioinformatics online.
Abrus Agglutinin, a type II ribosome inactivating protein inhibits Akt/PH domain to induce endoplasmic reticulum stress mediated autophagy‐dependent cell death

Abrus agglutinin (AGG), a type II ribosome‐inactivating protein has been found to induce mitochondrial apoptosis. In the present study, we documented that AGG‐mediated Akt dephosphorylation led to ER stress resulting the induction of autophagy‐dependent cell death through the canonical pathway in cervical cancer cells. Inhibition of autophagic death with 3‐methyladenine (3‐MA) and siRNA of Beclin‐1 and ATG5 increased AGG‐induced apoptosis. Further, inhibiting apoptosis by Z‐DEVD‐FMK and N‐acetyl cysteine (NAC) increased autophagic cell death after AGG treatment, suggesting that AGG simultaneously induced autophagic and apoptotic death in HeLa cells. Additionally, it observed that AGG‐induced autophagic cell death in Bax knock down (Bax‐KD) and 5‐FU resistant HeLa cells, confirming as an alternate cell killing pathway to apoptosis. At the molecular level, AGG‐induced ER stress in PERK dependent pathway and inhibition of ER stress by salubrinal, eIF2α phosphatase inhibitor as well as siPERK reduced autophagic death in the presence of AGG. Further, our in silico and colocalization study showed that AGG interacted with pleckstrin homology (PH) domain of Akt to suppress its phosphorylation and consequent downstream mTOR dephosphorylation in HeLa cells. We showed that Akt overexpression could not augment GRP78 expression and reduced autophagic cell death by AGG as compared to pcDNA control, indicating Akt modulation was the upstream signal during AGG's ER stress mediated autophagic cell death. In conclusion, we established that AGG stimulated cell death by autophagy might be used as an alternative tumor suppressor mechanism in human cervical cancer. © 2016 Wiley Periodicals, Inc.
Inhibition of Glutamine Synthetase Triggers Apoptosis in Asparaginase-Resistant Cells

The resistance to L-asparaginase (ASNase) has been associated to the overexpression of asparagine synthetase (AS), although the role played by other metabolic adaptations has not been yet defined. Both in ASNase-sensitive Jensen rat sarcoma cells and in ARJ cells, their ASNase-resistant counterparts endowed with a five-fold increased AS activity, ASNase treatment rapidly depletes intracellular asparagine. Under these conditions, cell glutamine is also severely reduced and the activity of glutamine synthetase (GS) is very low. After 24h of treatment, while sensitive cells have undergone massive apoptosis, ARJ cells exhibit a marked increase in GS activity, associated with overexpression of GS protein but not of GS mRNA, and a partial restoration of glutamine and asparagine. However, when ARJ cells are treated with both ASNase and L-methionine-sulfoximine (MSO), an inhibitor of GS, no restoration of cell amino acids occurs and the cell population undergoes a typical apoptosis. No toxicity is observed upon MSO treatment in the absence of ASNase. The effects of MSO are not referable to depletion of cell glutathione or inhibition of AS. These findings indicate that, in the presence of ASNase, the inhibition of GS triggers apoptosis. GS may thus constitute a target for the suppression of ASNase-resistant phenotypes.