Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic genetic interaction studies identify histone demethylase Utx as potential target for ameliorating Huntington’s disease

Huntington’s Disease (HD) is a dominantly inherited neurodegenerative disease caused by alterations in the huntingtin gene (htt). Transcriptional dysregulation is an early event in HD progression. Protein acetylation and methylation particularly on histones regulates chromatin structure thereby preventing or facilitating transcription. Although protein acetylation has been found to affect HD symptoms, little is known about the potential role of protein methylation in HD pathology. In recent years, a series of proteins have been described that are responsible for methylating and demethylating histones as well as other proteins. We carried out systematic genetic interaction studies testing lysine and arginine methylases and demethylases in a Drosophila melanogaster HD model. We found that modulating methylation enzymes that typically affect histone positions H3K4, H3K36 or H3K79 had varying effects on HD pathology while modulating ones that typically affect constitutive heterochromatin marks at H3K9 and H4K20 generally had limited impact on HD pathology. In contrast, modulating enzymes acting on the facultative heterochromatin mark at H3K27 had specific effects on HD pathology, with reduction of the demethylase Utx rescuing HTT induced pathology while reducing PRC2 complex core methylase components led to more aggressive pathology. Further exploration of the mechanism underlying the methylation-specific interactions suggest that these lysine and arginine methylases and demethylases are likely exerting their influence through non-histone targets. These results highlight a novel therapeutic approach for HD in the form of Utx inhibition.
Improved Xylose Metabolism by a CYC8 Mutant of Saccharomyces cerevisiae

ABSTRACT Engineering Saccharomyces cerevisiae for the utilization of pentose sugars is an important goal for the production of second-generation bioethanol and biochemicals. However, S. cerevisiae lacks specific pentose transporters, and in the presence of glucose, pentoses enter the cell inefficiently via endogenous hexose transporters (HXTs). By means of in vivo engineering, we have developed a quadruple hexokinase deletion mutant of S. cerevisiae that evolved into a strain that efficiently utilizes d-xylose in the presence of high d-glucose concentrations. A genome sequence analysis revealed a mutation (Y353C) in the general corepressor CYC8, or SSN6, which was found to be responsible for the phenotype when introduced individually in the nonevolved strain. A transcriptome analysis revealed altered expression of 95 genes in total, including genes involved in (i) hexose transport, (ii) maltose metabolism, (iii) cell wall function (mannoprotein family), and (iv) unknown functions (seripauperin multigene family). Of the 18 known HXTs, genes for 9 were upregulated, especially the low or nonexpressed HXT10, HXT13, HXT15, and HXT16. Mutant cells showed increased uptake rates of d-xylose in the presence of d-glucose, as well as elevated maximum rates of metabolism (Vmax) for both d-glucose and d-xylose transport. The data suggest that the increased expression of multiple hexose transporters renders d-xylose metabolism less sensitive to d-glucose inhibition due to an elevated transport rate of d-xylose into the cell. IMPORTANCE The yeast Saccharomyces cerevisiae is used for second-generation bioethanol formation. However, growth on xylose is limited by pentose transport through the endogenous hexose transporters (HXTs), as uptake is outcompeted by the preferred substrate, glucose. Mutant strains were obtained with improved growth characteristics on xylose in the presence of glucose, and the mutations mapped to the regulator Cyc8. The inactivation of Cyc8 caused increased expression of HXTs, thereby providing more capacity for the transport of xylose, presenting a further step toward a more robust process of industrial fermentation of lignocellulosic biomass using yeast.
Kv1.1 channelopathy abolishes presynaptic spike width modulation by subthreshold somatic depolarization

Significance Synaptic transmission depends on all-or-none action potentials. However, subthreshold membrane potential fluctuations at the cell body spread passively along the axon and affect the shape of presynaptic action potentials, calcium influx, and neurotransmitter release. Here we apply a superresolution method to identify small presynaptic terminals for patch clamp. Subthreshold modulation of action potentials is abolished by a mutation in the potassium channel Kv1.1 associated with the neurological channelopathy episodic ataxia type 1. Surprisingly, pharmacological or genetic ablation of Kv1.1 fails to prevent subthreshold modulation. Kv1.1 deletion and mutation have distinct effects on the composition and voltage sensitivity of presynaptic channels and consequently on modulation of neurotransmitter release. Although action potentials propagate along axons in an all-or-none manner, subthreshold membrane potential fluctuations at the soma affect neurotransmitter release from synaptic boutons. An important mechanism underlying analog–digital modulation is depolarization-mediated inactivation of presynaptic Kv1-family potassium channels, leading to action potential broadening and increased calcium influx. Previous studies have relied heavily on recordings from blebs formed after axon transection, which may exaggerate the passive propagation of somatic depolarization. We recorded instead from small boutons supplied by intact axons identified with scanning ion conductance microscopy in primary hippocampal cultures and asked how distinct potassium channels interact in determining the basal spike width and its modulation by subthreshold somatic depolarization. Pharmacological or genetic deletion of Kv1.1 broadened presynaptic spikes without preventing further prolongation by brief depolarizing somatic prepulses. A heterozygous mouse model of episodic ataxia type 1 harboring a dominant Kv1.1 mutation had a similar broadening effect on basal spike shape as deletion of Kv1.1; however, spike modulation by somatic prepulses was abolished. These results argue that the Kv1.1 subunit is not necessary for subthreshold modulation of spike width. However, a disease-associated mutant subunit prevents the interplay of analog and digital transmission, possibly by disrupting the normal stoichiometry of presynaptic potassium channels.
Glyph-Based Data Augmentation for Accurate Kanji Character Recognition

In this paper, we address a problem of data augmentation for character recognition. Particularly, we focus on incorporating variation in glyph into data augmentation of character images, which is a simple approach for data augmentation. Generally, existing methods increase data size by distorting images, whereas the proposed method applies noise injection into glyphs, resulting in data with radical variation in glyph. The proposed method exploits public database of glyphs for kanji and augments glyphs by injecting noise into glyphs. Then, we generate images of kanji automatically by deploying stroke images on the augmented glyphs. We carried out experiments for kanji character recognition using augmented data. The results show the effectiveness of the proposed method.
Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilms on Stainless Steel

ABSTRACT Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, facilitating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilms on stainless steel served as a model system for surface sampling, to test the performance of a sonicating swab in comparison with a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both types of swabs were examined using scanning electron microscopy, to visualize biofilms and surface structures (i.e., polishing grooves and scratches). Laser scanning confocal microscopy was used to image and to quantitate the biofilms remaining after sampling with each swab type. The total viable counts were significantly higher (P ≤ 0.05) with the sonicating swab than with the standard swab in each trial. The sonicating swab was more consistent in cell recovery than was the standard swab, with coefficients of variation ranging from 8.9% to 12.3% and from 7.1% to 37.6%, respectively. Scanning electron microscopic imaging showed that biofilms remained in the polished grooves of the coupons sampled with the standard swab but were noticeably absent with the sonicating swab. Percent area measurements of biofilms remaining on the stainless steel coupons showed significantly (P ≤ 0.05) less biofilm remaining when the sonicating swab was used (median, 1.1%), compared with the standard swab (median, 70.4%). The sonicating swab provided greater recovery of cells, with more consistency, than did the standard swab, and it is employs sonication, suction, and scrubbing. IMPORTANCE Inadequate surface sampling can result in foodborne illness outbreaks from biotransfer, since verification of sanitization protocols relies on surface sampling and recovery of microorganisms for detection and enumeration. Swabbing is a standard method for microbiological sampling of surfaces. Although swabbing offers portability and ease of use, there are limitations, such as high user variability and low recovery rates, which can be attributed to many different causes. This study demonstrates some benefits that a sonicating swab has over a standard swab for removal and collection of microbiological samples from a surface, to provide better verification of surface cleanliness and to help decrease the potential for biotransfer of pathogens into foods.
Electrochemical Quantification of Extracellular Local H2O2 Kinetics Originating from Single Cells

Abstract Aims: H2O2 is produced by all eukaryotic cells under physiological and pathological conditions. Due to its enormous relevance for cell signaling at low concentrations and antipathogenic function at high concentrations, precise quantification of extracellular local hydrogen peroxide concentrations ([H2O2]) originating from single cells is required. Results: Using a scanning electrochemical microscope and bare platinum disk ultramicroelectrodes, we established sensitive long-term measurements of extracellular [H2O2] kinetics originating from single primary human monocytes (MCs) ex vivo. For the electrochemical techniques square wave voltammetry, cyclic and linear scan voltammetry, and chronoamperometry, detection limits for [H2O2] were determined to be 5, 50, and 500 nM, respectively. Following phorbol ester stimulation, local [H2O2] 5–8 μm above a single MC increased by 3.4 nM/s within the first 10 min before reaching a plateau. After extracellular addition of H2O2 to an unstimulated MC, the local [H2O2] decreased on average by 4.2 nM/s due to degradation processes of the cell. Using the scanning mode of the setup, we found that H2O2 is evenly distributed around the producing cell and can still be detected up to 30 μm away from the cell. The electrochemical single-cell measurements were validated in MC populations using electron spin resonance spectroscopy and the Amplex® UltraRed assay. Innovation and Conclusion: We demonstrate a highly sensitive, spatially, and temporally resolved electrochemical approach to monitor dynamics of production and degradation processes for H2O2 separately. Local extracellular [H2O2] kinetics originating from single cells is quantified in real time. Antioxid. Redox Signal. 29, 501–517.
Tumor‐associated APE1 variant exhibits reduced complementation efficiency but does not promote cancer cell phenotypes

Base excision repair (BER) is the major pathway for coping with most forms of endogenous DNA damage, and defects in the process have been associated with carcinogenesis. Apurinic/apyrimidinic endonuclease 1 (APE1) is a central participant in BER, functioning as a critical endonuclease in the processing of noncoding abasic sites in DNA. Evidence has suggested that APE1 missense mutants, as well as altered expression or localization of the protein, can contribute to disease manifestation. We report herein that the tumor‐associated APE1 variant, R237C, shows reduced complementation efficiency of the methyl methanesulfonate hypersensitivity and impaired cell growth exhibited by APE1‐deficient mouse embryonic fibroblasts. Overexpression of wild‐type APE1 or the R237C variant in the nontransformed C127I mouse cell line had no effect on proliferation, cell cycle status, steady‐state DNA damage levels, mitochondrial function, or cellular transformation. A human cell line heterozygous for an APE1 knockout allele had lower levels of endogenous APE1, increased cellular sensitivity to DNA‐damaging agents, impaired proliferation with time, and a distinct global gene expression pattern consistent with a stress phenotype. Our results indicate that: (i) the tumor‐associated R237C variant is a possible susceptibility factor, but not likely a driver of cancer cell phenotypes, (ii) overexpression of APE1 does not readily promote cellular transformation, and (iii) haploinsufficiency at the APE1 locus can have profound cellular consequences, consistent with BER playing a critical role in proliferating cells. Environ. Mol. Mutagen. 58:84–98, 2017. © 2017 Wiley Periodicals, Inc.
Effect of Hazardous Alcohol Use During Pregnancy on Growth Outcomes at Birth: Findings from a South African Cohort Study

Background Cohort studies have noted associations between hazardous alcohol use during pregnancy and infant growth outcomes, but many have not controlled for potential psychosocial confounders. To assess the unique contribution of hazardous alcohol use, we examined its effect on infant growth outcomes while controlling for maternal psychosocial stressors and hazardous tobacco and drug use in a cohort of 986 pregnant South African women enrolled into the Drakenstein Child Health Study between 2012 and 2015. Methods Data on psychosocial stressors and maternal risk behaviors were collected between 28 and 32 weeks of gestation. Participants were categorized as hazardous alcohol users if they obtained moderate or high scores (>10) on the Alcohol, Smoking and Substance Involvement Screening Test at this assessment or retrospectively reported drinking at least 2 drinks weekly during any trimester of pregnancy. Infant growth outcomes were recorded at delivery. Multivariable regression models examined correlates of hazardous alcohol use and associations between hazardous alcohol use and birth outcomes. Results Overall, 13% of mothers reported hazardous alcohol use. Recent exposure to intimate partner violence (adjusted odds ratio (aOR) = 2.08; 95% confidence interval (CI): 1.37, 3.18) and hazardous tobacco use (aOR = 5.03; 95% CI: 2.97, 8.52) were significant correlates of hazardous alcohol use. After controlling for potential psychosocial confounders, hazardous alcohol use remained associated with lower infant weight‐for‐age (B = −0.35, 95% CI: −0.56, −0.14), height‐for‐age (B = −0.46, 95% CI: −0.76, −0.17), and head‐circumference‐for‐age z‐scores (B = −0.43, 95% CI: −0.69, −0.17). Conclusions Interventions to reduce hazardous alcohol use among pregnant women in South Africa are needed to prevent alcohol‐related infant growth restrictions. As these growth deficits may lead to neurodevelopmental consequences, it is critical to identify alcohol‐related growth restrictions at birth and link exposed infants to early interventions for neurodevelopment.
A Digital Offset Reduction Method for Dynamic Comparators Based on Phase Measurement

This paper presents a low-cost technique to reduce offset voltage of a dynamic comparator. The proposed method is based on output-data phase measuring. A full-digital implementation is used to measure phase without impacting offset accuracy. Simulation and measured results show that the eye-diagram at the compartor input can be shifted up to 245mV due to offset, achieving a successful correction, and making the technique suitable for high-speed applications. The technique requires less than 500ns to achieve convergence and calibration. In this way, there is not need to break the communication link associated to the comparator. The circuit has been implemented in a 130nm TSMC standard CMOS process and detailed experimental results are shown along this document.
Interaction between Nonsteroidal Anti-inflammatory Drugs and Low-fat Dietary Intervention on Colorectal Cancer Incidence; the Women's Health Initiative (WHI) Dietary Modification Trial

ABSTRACT Background: The Women's Health Initiative (WHI) Dietary Modification (DM) trial did not show that reductions in dietary fat accompanied by increases in vegetable and fruit consumption decrease the incidence of colorectal cancer. Secondary analyses suggested that aspirin use may modify the intervention effects of DM on colorectal cancer development, although a recent reanalysis including the postintervention period confirmed no main effect of the intervention on reducing colorectal cancer incidence Methods: We analyzed data from 48,834 postmenopausal women who were randomized into the low-fat DM (N = 19,540) or comparison (N = 29,294) group for an average 8.1 years and followed for an additional 9.4 years through August 31, 2014. Exposure to specific class(es) or strength(s) of nonsteroidal anti-inflammatory drugs (NSAIDs) was modeled at baseline and as time-dependent use through the 9-year clinic visit. A Cox proportional hazard model was employed to assess the association of the DM, medication use, and their interaction with colorectal cancer events. Results: A total of 906 incident cases of colorectal cancer were identified during the intervention and postintervention periods. By both exposure models, we found that colorectal cancer incidence was not different in the DM from the comparison group among any type of NSAID users. None of the interactions with any category of NSAID use was statistically significant; however there was most modest evidence for an interaction (p = 0.07) with aspirin use at baseline (hazard ratio [HR] = 0.81, 95% confidence interval [CI], 0.60–1.11 for users; HR = 1.12, 95% CI, 0.97–1.30 for nonusers). Strength and duration of aspirin use at baseline did not alter the associations. Conclusion: Extended follow-up of women in the WHI DM trial did not confirm combined protective effects of aspirin and low-fat diet on colorectal cancer risk among the postmenopausal women.
Centralized Optimization for Dec-POMDPs Under the Expected Average Reward Criterion

In this paper, the decentralized partially observable Markov decision process (Dec-POMDP) systems with discrete state and action spaces are studied from a gradient point of view. Dec-POMDPs have recently emerged as a promising approach to optimizing multiagent decision making in the partially observable stochastic environment. However, the decentralized nature of the Dec-POMDP framework results in a lack of shared belief state, which makes the decision maker impossible to estimate the system state based on local information. In contrast to the belief-based policy, this paper focuses on optimizing the decentralized observation-based policy, which is easily to be applied and does not have the sharing problem. By analyzing the gradient of the objective function, we have developed a centralized stochastic gradient policy iteration algorithm to find the optimal policy on the basis of gradient estimates from a single sample path. This algorithm does not need any specific assumption and can be applied to most practical Dec-POMDP problems. One numerical example is provided to demonstrate the effectiveness of the algorithm.
TRPV1 channels in human skeletal muscle feed arteries: implications for vascular function

What is the central question of this study? We sought to determine whether human skeletal muscle feed arteries (SFMAs) express TRPV1 channels and what role they play in modulating vascular function. What is the main finding and its importance? Human SMFAs do express functional TRPV1 channels that modulate vascular function, specifically opposing α‐adrenergic receptor‐mediated vasocontraction and potentiating vasorelaxation, in an endothelium‐dependent manner, as evidenced by the α1‐receptor‐mediated responses. Thus, the vasodilatory role of TRPV1 channels, and their ligand capsaicin, could be a potential therapeutic target for improving vascular function. Additionally, given the ‘sympatholytic’ effect of TRPV1 activation and known endogenous activators (anandamide, reactive oxygen species, H+, etc.), TRPV1 channels might contribute to functional sympatholysis during exercise.
Novel mechanism for the generation of human xeno-autoantibodies against the nonhuman sialic acid N-glycolylneuraminic acid

The nonhuman sialic acid N-glycolylneuraminic acid (Neu5Gc) is metabolically incorporated into human tissues from certain mammalian-derived foods, and this occurs in the face of an anti-Neu5Gc “xeno-autoantibody” response. Given evidence that this process contributes to chronic inflammation in some diseases, it is important to understand when and how these antibodies are generated in humans. We show here that human anti-Neu5Gc antibodies appear during infancy and correlate with weaning and exposure to dietary Neu5Gc. However, dietary Neu5Gc alone cannot elicit anti-Neu5Gc antibodies in mice with a humanlike Neu5Gc deficiency. Other postnatally appearing anti-carbohydrate antibodies are likely induced by bacteria expressing these epitopes; however, no microbe is known to synthesize Neu5Gc. Here, we show that trace exogenous Neu5Gc can be incorporated into cell surface lipooligosaccharides (LOS) of nontypeable Haemophilus influenzae (NTHi), a human-specific commensal/pathogen. Indeed, infant anti-Neu5Gc antibodies appear coincident with antibodies against NTHi. Furthermore, NTHi that express Neu5Gc-containing LOS induce anti-Neu5Gc antibodies in Neu5Gc-deficient mice, without added adjuvant. Finally, Neu5Gc from baby food is taken up and expressed by NTHi. As the flora residing in the nasopharynx of infants can be in contact with ingested food, we propose a novel model for how NTHi and dietary Neu5Gc cooperate to generate anti-Neu5Gc antibodies in humans.
Preparation and characterization of poly(ethylene oxide)/lithium montmorillonite composites

Poly(ethylene oxide)/lithium montmorillonite (PEO/L iMMT) composites were prepared by mixing and ultrasonication PEO and LiMMT in water. Characterization of PEO/LiMMT composites was performed by differential scanning c(DSC), Fourier transform infrared spectroscopy (FT-IR) and non-isothermal th ermogravimetry (TGA). DSC and TGA reveal that higher loadings of LiMMT significantly influence the crystallinity, melting temperatures and thermal stability of PEO, respecti vely. Glass transition temperatures of PEO do not change with addition of LiMMT. FT-IR ana lysis shows that the helical structure of PEO chains is distorted in PEO/LiMMT composites. Changes of activation energy in composites compared to pure PEO indicate possible c hanges in the mechanism of the nonisothermal degradation of PEO due to addition of Li MMT.