Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduction of Oxidative Stress Attenuates Lipoapoptosis Exacerbated by Hypoxia in Human Hepatocytes

Chronic intermittent hypoxia, a characteristic of obstructive sleep apnea (OSA), is associated with the progression of simple hepatic steatosis to necroinflammatory hepatitis. We determined whether inhibition of a hypoxia-induced signaling pathway could attenuate hypoxia-exacerbated lipoapoptosis in human hepatocytes. The human hepatocellular carcinoma cell line (HepG2) was used in this study. Palmitic acid (PA)-treated groups were used for two environmental conditions: Hypoxia (1% O2) and normoxia (20% O2). Following the treatment, the cell viability was determined by the 3,4-(5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium salt (MTS) assay, and the mechanism of lipoapoptosis was evaluated by Western blotting. Hypoxia exacerbated the suppression of hepatocyte growth induced by palmitic acid via activation of mitochondrial apoptotic pathways as a result of endoplasmic reticulum (ER) and oxidative stresses. Ammonium pyrrolidine dithiocarbamate, a scavenger of reactive oxygen species, attenuated the hypoxia-exacerbated lipoapoptosis in hepatocytes, whereas glycerol, which reduces ER stress, did not. This may have been because inhibition of oxidative stress decreases the expression of pro-apoptotic proteins, such as caspase 9 and cytochrome c. These results suggested that modulation of apoptotic signaling pathways activated by oxidative stress can aid in identifying novel therapeutic strategies for the treatment of nonalcoholic steatohepatitis (NASH) with OSA. Further in vivo studies are necessary to understand the pathophysiologic mechanism of NASH with OSA and to prove the therapeutic effect of the modulation of the signaling pathways.
Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis

The advent and widespread application of next-generation sequencing (NGS) technologies to the study of microbial genomes has led to a substantial increase in the number of studies in which whole genome sequencing (WGS) is applied to the analysis of microbial genomic epidemiology. However, microorganisms such as Mycobacterium tuberculosis (MTB) present unique problems for sequencing and downstream analysis based on their unique physiology and the composition of their genomes. In this study, we compare the quality of sequence data generated using the Nextera and TruSeq isolate preparation kits for library construction prior to Illumina sequencing-by-synthesis. Our results confirm that MTB NGS data quality is highly dependent on the purity of the DNA sample submitted for sequencing and its guanine-cytosine content (or GC-content). Our data additionally demonstrate that the choice of library preparation method plays an important role in mitigating downstream sequencing quality issues. Importantly for MTB, the Illumina TruSeq library preparation kit produces more uniform data quality than the Nextera XT method, regardless of the quality of the input DNA. Furthermore, specific genomic sequence motifs are commonly missed by the Nextera XT method, as are regions of especially high GC-content relative to the rest of the MTB genome. As coverage bias is highly undesirable, this study illustrates the importance of appropriate protocol selection when performing NGS studies in order to ensure that sound inferences can be made regarding mycobacterial genomes.
Fungal contaminations of indoor and outdoor air of buildings of the University of Cape Coast, Ghana

The presence of microscopic spores in the air affects the quality of air inhaled by animals including humans. Microbial contamination of air impacts the well-being of occupants of an indoor environment, sometimes with dire consequences. The study investigated fungal contaminations of indoor and outdoor air of the Hospital, Library and Senior Common Room (SCR) of the University of Cape Coast, Ghana. Indoor and outdoor air was sampled using the Koch’s sedimentation method. Colony forming units per cubic meter of air (cfu/m) were determined with the Omeliansky formula. The isolated fungi were identified based on morphological and growth characteristics. For indoor air, the least colony counts were recorded in the SCR for both morning and afternoon samples, whilst the Hospital air had the highest colony counts. For outdoor air, the colony counts were lower in SCR and the Library for both morning and afternoon samples compared to the Hospital. The results further indicated that indoor concentrations of fungi, for morning and afternoon, ranged between 4.0x10 and 2.1x10 cfu/m, whereas outdoor concentrations of fungi ranged between 1.1x10 and 3.0x10 cfu/m, revealing an overall higher levels of contamination of outdoor air than indoor air at all the three buildings. Consequently, estimated indoor/outdoor (I/O) concentration ratios of fungi revealed an exogenous source of indoor contaminations at all the three buildings sampled. Fungi isolated from indoor and outdoor air were of the genera Aspergillus, Curvularia, Cylindrocarpon, Fusarium, Mucor, Neurospora, Penicillium and Rhodotorula. We conclude that indoor and outdoor air of the buildings sampled were contaminated with airborne fungi; however, based on estimated I/O ratios, the indoor ambient conditions of the buildings were good. The implication of findings of this study is that the presence of airborne fungal contaminants of indoor and outdoor workplace environment may pose serious occupational health consequences, hence low productivity.
Evidence for an ecological cost of enhanced herbicide metabolism in Lolium rigidum

1 In some cases, evaluation of resource competitive interactions between herbicide resistant vs. susceptible weed ecotypes provides evidence for the expression of fitness costs associated with evolved herbicide‐resistant gene traits. Such fitness costs impact in the ecology and evolutionary trajectory of resistant populations. 2 Neighbourhood experiments were performed to quantify competitive effects and responses between herbicide‐susceptible (S) and resistant (R) Lolium rigidum individuals in which resistance is due to enhanced herbicide metabolism mediated by cytochrome P450. 3 In two‐way competitive interactions between the S and R phenotypes, individuals of the S phenotype were the stronger effect competitors on both a per capita and per unit‐size basis. The S phenotype also exhibited a stronger competitive response to wheat plants than did the R phenotype, displaying significantly greater (30%) above‐ground biomass at the vegetative stage. When subjected to competition from wheat, R individuals produced significantly fewer reproductive tillers and allocated fewer resources to reproductive traits than individuals of the S phenotype. 4 The role of potential mechanisms underlying this resistance cost driven by traits such as plant size and tolerance to low resource availability, as well as the evolutionary implications of the results are discussed. 5 Synthesis. Evolved herbicide resistance due to enhanced‐herbicide metabolism mediated by cytochrome‐P450 in L. rigidum has been shown to be accompanied with an impaired ability to compete for resources. These results are consistent with the resource‐based theory that predicts a negative trade‐off between growth and plant defence.
Object behavior analysis

Object Behavior Analysis nalysis is the study and modeling of a given problem domain, within the context of stated goals and objectives. It focuses on what a system is supposed to do, rather than how it is supposed to do it (which we consider the design aspects). In addition , it must embody the rule of traceability (why), which justifies the existence of a given result by tying it back to the stated goals and objectives. The components of the problem domain can be described as anything that end users of the system, both humans and machines, view as part of the problem context. This may include technical issues, if the users view such issues as part of the problem. • • • • • • • • • • • • • • • • We want the analysis process to be carried out in a predictable and controllable manner. In taking an object-oriented approach to analysis , our goal on completion is that we have a clear understanding of the behaviors exhibited by the system , the objects that exhibit these behaviors, the relationships among the objects, and how the objects interact with one another (the system dynamics). This must all be specified in a clear and well-defined language of object and behavior names, chosen from the problem domain. In addition, any implementation code must be traceable back to the results of the analysis. This means that the vocabulary and structures apparent in the design and implementation must clearly reflect the vocabulary and structures that result from the analysis. Object-oriented analysis endeavors to model a situation in terms of a collection of interacting entities, each of which provides a well-defined set of behaviors and attributes. Most published approaches describe conceptually similar definitions , although they adopt alternate terminologies [2, 3, 10]. There is a high degree of agreement on the desired structure of the end result; we differ in how to get to the end result. Many approaches recommend first searching for the tangible objects , notably seeking the nouns in a requirements specification and any applicable verbs and adjectives. With nouns as the objects, the message interface is determined from the verbs, and the logical properties are derived from the adjectives. Although this basic approach may work for small systems, it is our experience that it simply will not scale up. First, it assumes that a complete, …
Minimization Problems Based on Relative  $\alpha $ -Entropy I: Forward Projection

Minimization problems with respect to a one-parameter family of generalized relative entropies are studied. These relative entropies, which we term relative α-entropies (denoted Iα), arise as redundancies under mismatched compression when cumulants of compressed lengths are considered instead of expected compressed lengths. These parametric relative entropies are a generalization of the usual relative entropy (Kullback-Leibler divergence). Just like relative entropy, these relative α-entropies behave like squared Euclidean distance and satisfy the Pythagorean property. Minimizers of these relative α-entropies on closed and convex sets are shown to exist. Such minimizations generalize the maximum Rényi or Tsallis entropy principle. The minimizing probability distribution (termed forward Iα-projection) for a linear family is shown to obey a power-law. Other results in connection with statistical inference, namely subspace transitivity and iterated projections, are also established. In a companion paper, a related minimization problem of interest in robust statistics that leads to a reverse Iα-projection is studied.
A Discriminative Approach to Japanese Abbreviation Extraction

This paper addresses the difficulties in recognizing Japanese abbreviations through the use of previous approaches, examining actual usages of parenthetical expressions in newspaper articles. In order to bridge the gap between Japanese abbreviations and their full forms, we present a discriminative approach to abbreviation recognition. More specifically, we formalize the abbreviation recognition task as a binary classification problem in which a classifier determines a positive (abbreviation) or negative (nonabbreviation) class, given a candidate of abbreviation definition. The proposed method achieved 95.7% accuracy, 90.0% precision, and 87.6% recall on the evaluation corpus containing 7,887 (1,430 abbreviations and 6,457 non-abbreviation) instances of parenthetical expressions.
The minimal seed of turbulent transition in the boundary layer

Abstract This paper describes a scenario of transition from laminar to turbulent flow in a spatially developing boundary layer over a flat plate. The base flow is the Blasius non-parallel flow solution; it is perturbed by optimal disturbances yielding the largest energy growth over a short time interval. Such perturbations are computed by a nonlinear global optimization approach based on a Lagrange multiplier technique. The results show that nonlinear optimal perturbations are characterized by a localized basic building block, called the minimal seed, defined as the smallest flow structure which maximizes the energy growth over short times. It is formed by vortices inclined in the streamwise direction surrounding a region of intense streamwise disturbance velocity. Such a basic structure appears to be a robust feature of the base flow since it is practically invariant with respect to the initial energy of the perturbation, the target time, the Reynolds number and the dimensions of the computational domain. The minimal seed grows very rapidly in time while spreading, and it triggers nonlinear effects which bring the flow to turbulence in a very efficient manner, through the formation of a turbulence spot. This evolution of the initial optimal disturbance has been studied in detail by direct numerical simulations. Using a perturbative formulation of the Navier–Stokes equations, each linear and nonlinear convective term of the equations has been analysed. The results show the fundamental role of the streamwise inclination of the vortices in the process. The nonlinear coupling of the finite amplitude disturbances is crucial to sustain such streamwise inclination, as well as to generate dislocations within the flow structures, and local inflectional velocity distributions. The analysis provides a picture of the transition process characterized by a sequence of structures appearing successively in the flow, namely, $ \mrm{\Lambda} $ vortices, hairpin vortices and streamwise streaks. Finally, a disturbance regeneration cycle is conceived, initiated by the fast nonlinear amplification of the minimal seed, providing a possible scenario for the continuous regeneration of the same fundamental flow structures at smaller space and time scales.
Channeling Fisher: Randomization Tests and the Statistical Insignificance of Seemingly Significant Experimental Results*

I follow R. A. Fisher'sThe Design of Experiments (1935), using randomization statistical inference to test the null hypothesis of no treatment effects in a comprehensive sample of 53 experimental papers drawn from the journals of the American Economic Association. In the average paper, randomization tests of the significance of individual treatment effects find 13% to 22% fewer significant results than are found using authors’ methods. In joint tests of multiple treatment effects appearing together in tables, randomization tests yield 33% to 49% fewer statistically significant results than conventional tests. Bootstrap and jackknife methods support and confirm the randomization results.
The Impact of a Mindfulness Based Program on Perceived Stress, Anxiety, Depression and Sleep of Incarcerated Women

Incarcerated women enter the prison setting with remarkable histories of trauma, mental health and substance abuse issues. Given the stress of incarceration and separation from their children, families, and significant others, it is not surprising that many women experience increased anxiety, depression, and problems with sleep. Due to these negative outcomes, it is imperative to find efficient non-pharmacological interventions. This pilot study examined the impact of a 12-week mindfulness based program on the stress, anxiety, depression and sleep of women with a total of 33 completing the study. In one group, women’s perceived stress, anxiety and depression were all significantly lower following the intervention compared to prior to the intervention. Challenges with implementing the pilot study are addressed. Despite challenges and limitations, the low-cost non-pharmacological intervention has potential for a reducing the symptoms of anxiety and depression.
Lactose-over-Glucose Preference in Bifidobacterium longum NCC2705: glcP, Encoding a Glucose Transporter, Is Subject to Lactose Repression

ABSTRACT Analysis of culture supernatants obtained from Bifidobacterium longum NCC2705 grown on glucose and lactose revealed that glucose utilization is impaired until depletion of lactose. Thus, unlike many other bacteria, B. longum preferentially uses lactose rather than glucose as the primary carbon source. Glucose uptake experiments with B. longum cells showed that glucose transport was repressed in the presence of lactose. A comparative analysis of global gene expression profiling using DNA arrays led to the identification of only one gene repressed by lactose, the putative glucose transporter gene glcP. The functionality of GlcP as glucose transporter was demonstrated by heterologous complementation of a glucose transport-deficient Escherichia coli strain. Additionally, GlcP exhibited the highest substrate specificity for glucose. Primer extension and real-time PCR analyses confirmed that expression of glcP was mediated by lactose. Hence, our data demonstrate that the presence of lactose in culture medium leads to the repression of glucose transport and transcriptional down-regulation of the glucose transporter gene glcP. This may reflect the highly adapted life-style of B. longum in the gastrointestinal tract of mammals.
Krebs von den Lungen‐6 (KL‐6) is a prognostic biomarker in patients with surgically resected nonsmall cell lung cancer

By immunizing mice with a lung adenocarcinoma cell line, we previously established a murine IgG1 monoclonal antibody that recognizes a sialylated sugar chain designated Krebs von den Lungen‐6 (KL‐6). KL‐6 is a high–molecular‐weight glycoprotein classified as a human MUC1 mucin. The aim of this study was to determine whether KL‐6 expression in tumors correlates with circulating KL‐6 levels and whether circulating KL‐6 has any prognostic value in patients with surgically resected non‐small cell lung cancer (NSCLC). Immunohistochemical analysis of KL‐6 expression was performed on 103 NSCLC tissues, and its associations with serum KL‐6 levels and survival were examined. We also evaluated whether KL‐6 expression patterns and/or serum KL‐6 levels could predict prognosis in these NSCLC patients. Immunohistochemical analysis of KL‐6 in NSCLC tissues showed that a depolarized KL‐6 expression pattern was associated with a high level of circulating KL‐6 and a poor prognosis in NSCLC patients who underwent curative surgery. Furthermore, a high circulating KL‐6 level was associated with both poorer progression‐free survival (PFS) and overall survival (OS), and multivariate analyses confirmed its independent prognostic value for both PFS and OS (p = 0.041 and 0.023, respectively). Our data suggest that preoperative serum KL‐6 level reflects KL‐6 expression patterns in NSCLC tissue, and can serve as a useful prognostic biomarker in NSCLC patients who undergo curative surgery.
Isolated Weakness of Middle, Ring, and Little Fingers due to a Small Cortical Infarction in the Medial Precentral Gyrus

Small cortical strokes can produce predominant isolated weakness in a particular group of fingers: radial or ulnar. The traditional views are of point-to-point representations of each finger to neurons located in the precentral gyrus of the motor cortex such that the neurons of the radial fingers are located laterally and those of the ulnar fingers are located medially. We present a case of isolated weakness of middle, ring, and little fingers due to a small cortical infarction in the medial precentral gyrus.
Review on Molecular Typing Methods of Pathogens

This paper presents several common molecular typing methods, Pulsed-Field Gel Electrophoresis (PFGE), Restriction Fragment Length Polymorphisma (RFLP), Random Amplified Polymorphic DNA (RAPD), Automatic Ribotyping, rep-PCR, Multi-Locus Sequence Typing (MLST), in which the application and progress of molecular typing of pathgens for these methods are described. These methods played an important role in pathgens source tracking, knowing the source(s) of bacteria in pharmaceutical, preventing and controlling the diarrhea and food-poisoning outbreaks, which have great value in the remediation and prevention of further bacterial contamination.
Endothelial permeability is increased by the supernatant of peripheral blood mononuclear cells stimulated with HLA Class II antibody

BACKGROUND: The generation of inflammatory mediators from monocytes activated by HLA Class II antibodies is thought to play important roles in the etiology of nonhemolytic transfusion reactions. Increased permeability of endothelial cells contributes to the pathogenesis of rash, urticaria, angioedema, and pulmonary edema, which are symptoms of transfusion reactions.
Preclinical Profile of BI 224436, a Novel HIV-1 Non-Catalytic-Site Integrase Inhibitor

ABSTRACT BI 224436 is an HIV-1 integrase inhibitor with effective antiviral activity that acts through a mechanism that is distinct from that of integrase strand transfer inhibitors (INSTIs). This 3-quinolineacetic acid derivative series was identified using an enzymatic integrase long terminal repeat (LTR) DNA 3′-processing assay. A combination of medicinal chemistry, parallel synthesis, and structure-guided drug design led to the identification of BI 224436 as a candidate for preclinical profiling. It has antiviral 50% effective concentrations (EC50s) of <15 nM against different HIV-1 laboratory strains and cellular cytotoxicity of >90 μM. BI 224436 also has a low, ∼2.1-fold decrease in antiviral potency in the presence of 50% human serum and, by virtue of a steep dose-response curve slope, exhibits serum-shifted EC95 values ranging between 22 and 75 nM. Passage of virus in the presence of inhibitor selected for either A128T, A128N, or L102F primary resistance substitutions, all mapping to a conserved allosteric pocket on the catalytic core of integrase. BI 224436 also retains full antiviral activity against recombinant viruses encoding INSTI resistance substitutions N155S, Q148H, and E92Q. In drug combination studies performed in cellular antiviral assays, BI 224436 displays an additive effect in combination with most approved antiretrovirals, including INSTIs. BI 224436 has drug-like in vitro absorption, distribution, metabolism, and excretion (ADME) properties, including Caco-2 cell permeability, solubility, and low cytochrome P450 inhibition. It exhibited excellent pharmacokinetic profiles in rat (clearance as a percentage of hepatic flow [CL], 0.7%; bioavailability [F], 54%), monkey (CL, 23%; F, 82%), and dog (CL, 8%; F, 81%). Based on the excellent biological and pharmacokinetic profile, BI 224436 was advanced into phase 1 clinical trials.
XMM—Newton observations of the Perseus cluster — II. Evidence for gas motions in the core

The 5–9 keV spectrum of the inner ∼100 kpc of the Perseus cluster measured by XMM–Newton can be well described by an optically thin plasma emission model as predicted by the apec code, without any need for invoking a strong Ni overabundance or the effects of resonant scattering. For the strongest 6.7-keV line of He-like iron, the optical depth of the cluster, calculated using observed density, temperature and abundance profiles, is of the order of 3. The lack of evidence for resonant scattering effects implies gas motion in the core with a range in velocities of at least half of the sound velocity. If this motion has the character of small-scale turbulence, then its dissipation would provide enough energy to compensate for radiative cooling of the gas. The activity of the supermassive black hole at the centre of the cluster may be the driving force of the gas motion.