Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting airway remodeling in COPD and emphysema using low-dose CT imaging

In this study, we quantitatively characterize lung airway remodeling caused by smoking-related emphysema and Chronic Obstructive Pulmonary Disease (COPD), in low-dose CT scans. To that end, we established three groups of individuals: subjects with COPD (n=35), subjects with emphysema (n=38) and healthy smokers (n=28). All individuals underwent a low-dose CT scan, and the images were analyzed as described next. First the lung airways were segmented using a fast marching method and labeled according to its generation. Along each airway segment, cross-section images were resampled orthogonal to the airway axis. Next 128 rays were cast from the center of the airway lumen in each crosssection slice. Finally, we used an integral-based method, to measure lumen radius, wall thickness, mean wall percentage and mean peak wall attenuation on every cast ray. Our analysis shows that both the mean global wall thickness and the lumen radius of the airways of both COPD and emphysema groups were significantly different from those of the healthy group. In addition, the wall thickness change starts at the 3rd airway generation in the COPD patients compared with emphysema patients, who display the first significant changes starting in the 2nd generation. In conclusion, it is shown that airway remodeling happens in individuals suffering from either COPD or emphysema, with some local difference between both groups, and that we are able to detect and accurately quantify this process using images of low-dose CT scans.
Evaluation of Antimicrobial Activity of Anogeissus leiocarpus and Terminalia avicennioides against Infectious Diseases Prevalent in Hospital Environments in Nigeria

The crude methanol extracts of the two plants selected on the basis of ethnobotanical uses were phytochemically screened and found to contain saponins, steroids, tannins, terpenes, anthraquinone and carbohydrates. The crude methanolic extracts exhibited broad growth inhibition against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Sal- monella typhi, Escherichia coli, Pseudomonas aeruginosa, Neisseria gonorrhoea and Candida albicans. The Minimum Inhibition Concentration (MIC) of Anogeissus leiocarpus methanol extract was found to be 0.4 mg/mL against S. aureus, St. pyogenes, P. aeruginosa and N. gonorrhoea, while B. subtilis has the MIC of 0.3 mg/mL. The rest of the microorganisms were resistant to Anogeissus leiocarpus methanol extract. Terminalia avicennioides methanol extract has the MIC of 0.4 mg/mL on S. aureus, S. typhi, E. coli, P. aeruginosa, N. gonorrhoea and C. albicans. Both S. pyogenes and B. subtilis have the MIC of 0.3 mg/mL against Terminalia avicennioides methanol extract. The rest of the microorganisms were resistant. Both Corynebacterium ulcerans and Klebsiella pneumoniae were resistant to the two plant extracts. The present investigation justify the use of these extracts in the treatment of infectious diseases particularly those caused by S. pyogenes having the highest zone of inhibition as well as the lowest MIC (0.3 mg/mL) for the two plants. Further purification of the most prom- ising extracts is currently being undertaken.
Amplified Fragment Length Polymorphism Assessment of Genetic Diversity in Pacific Lampreys

Abstract This study is the first to document genetic differences among Pacific lampreys Lampetra tridentata across much of their range. We examined collections of migrating adult Pacific lampreys from the Naka River, Japan; Moose River, Alaska; and six Pacific Northwest locations (North Fork Toutle, Willamette, Deschutes, John Day, Rogue, and Klamath rivers) based on variation at 180 polymorphic loci among the 556 amplified fragment length polymorphism loci generated by seven primer combinations. Despite the large geographical distances separating the samples, the different collections were characterized by a high proportion of shared bands, which indicated significant levels of historical gene flow across the range of the species. Analysis of molecular variance across three geographical regions—the Pacific Northwest, Alaska, and Japan—showed divergence among samples (genetic differentiation index FST = 0.106, P < 0.001) and significant differences among regions (regional differentiation FRT = 0.014; P < .
Endogenous Fatty Acids Are Essential Signaling Factors of Pancreatic β-Cells and Insulin Secretion

The secretion of insulin from β-cells depends on extracellular factors, in particular glucose and other small molecules, some of which act on G-protein–coupled receptors. Fatty acids (FAs) have been discussed as exogenous secretagogues of insulin for decades, especially after the FA receptor GPR40 (G-protein–coupled receptor 40) was discovered. However, the role of FAs as endogenous signaling factors has not been investigated until now. In the present work, we demonstrate that lowering endogenous FA levels in β-cell medium by stringent washing or by the application of FA-free (FAF) BSA immediately reduced glucose-induced oscillations of cytosolic Ca2+ ([Ca2+]i oscillations) in MIN6 cells and mouse primary β-cells, as well as insulin secretion. Mass spectrometry confirmed BSA-mediated removal of FAs, with palmitic, stearic, oleic, and elaidic acid being the most abundant species. [Ca2+]i oscillations in MIN6 cells recovered when BSA was replaced by buffer or as FA levels in the supernatant were restored. This was achieved by recombinant lipase–mediated FA liberation from membrane lipids, by the addition of FA-preloaded FAF-BSA, or by the photolysis of cell-impermeant caged FAs. Our combined data support the hypothesis of FAs as essential endogenous signaling factors for β-cell activity and insulin secretion.
Leptin attenuates cardiac apoptosis after chronic ischaemic injury.

AIMS We have previously shown that activation of leptin signalling in the heart reduces cardiac morbidity and mortality after myocardial infarction (MI). In the present study, we tested the hypothesis that leptin signalling limits cardiac apoptosis after MI through activation of signal transducer and activator of transcription (STAT)-3 responsive anti-apoptotic genes, including B-cell lymphoma (bcl)-2 and survivin, that serve to downregulate the activity of caspase-3. METHODS AND RESULTS Hearts from C57BL/6J and three groups of leptin-deficient Ob/Ob mice (food-restricted, ad libitum, and leptin-repleted) were examined 4 weeks after permanent left coronary artery ligation or sham operation. Inflammatory and apoptotic cell number was determined in cardiac sections by immunostaining. Expression of cardiac bcl-2, survivin, and pro and active caspase-3 was determined and correlated with in vitro caspase-3 activity. In the absence of MI, both lean and obese leptin-deficient mice exhibited increased cardiac apoptosis compared with wild-type mice. After MI, the highest rates of apoptosis were seen in the infarcted tissue of lean and obese Ob/Ob mice. Further, leptin-deficient hearts, as well as hearts from wild-type mice treated with the STAT-3 inhibitor WP1066, exhibited blunted anti-apoptotic bcl-2 and survivin gene expression, and increased caspase-3 protein expression and activity. The increased caspase-3 activity and apoptosis in hearts of leptin-deficient mice after MI was significantly attenuated in Ob/Ob mice replete with leptin, reducing apoptosis to levels comparable to that observed in wild-type mice after MI. CONCLUSION These results demonstrate that intact leptin signalling post-MI acts through STAT-3 to increase anti-apoptotic bcl-2 and survivin gene expression and reduces caspase-3 activity, consistent with a cardioprotective role of leptin in the setting of chronic ischaemic injury.
Dynamic visualization of expressed gene networks

Cellular biochemical machineries, what we call pathways, consist of dynamically assembling and disassembling macromolecular complexes. While our models for the organization of biochemical machines are derived largely from in vitro experiments, do they reflect their organization in living cells? We have developed a general experimental strategy that addresses this question by allowing the quantitative probing of molecular interactions in intact living cells. The experimental strategy is based on protein fragment complementation assays (PCA), a method whereby protein interactions are coupled to refolding of enzymes from cognate fragments where reconstitution of enzyme activity acts as the detector of a protein interaction. A biochemical machine or pathway is defined by grouping interacting proteins into those that are perturbed in the same way by common factors (hormones, metabolites, enzyme inhibitors, etc). In this review, we describe how we go from descriptive to quantitative representations of biochemical networks at an individual to whole genome level and how our approach will lead ultimately to better descriptions of the biochemical machineries that underlie living processes. J. Cell. Physiol. 196: 419–429, 2003. © 2003 Wiley‐Liss, Inc.
A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291T = LMG 9904T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976T).
Delivery and activity of antimicrobial drugs released from human fibrin sealant.

Engraftment and healing of native or cultured skin grafts depend on adherence, vascularization, and control of microbial contamination in the wound bed. Fibrin sealant is a biocompatible polymer that may be used to promote skin engraftment by serving as a delivery vehicle for antimicrobial drugs. Human fibrin sealant (25 mg/ml) was polymerized with antibacterial agents (mupirocin [32 micrograms/ml], nitrofurazone [0.02% wt/vol], polymyxin B [400 U/ml], or norfloxacin [20 micrograms/ml]) on nitrocellulose (nc) backing and was prepared as 6 mm diameter discs with skin punches. Discs (n = 6) were applied in the Wet Disc Assay to clinical isolates of Staphylococcus aureus (mupirocin, nitrofurazone) or Pseudomonas aeruginosa (polymyxin B, norfloxacin). Controls included drug applied to 6 mm paper discs (25 microliter) and nitrocellulose discs submerged in each drug, blotted, and applied to bacterial cultures on agar in petri dishes. Data were expressed as zone of clearing (mm diameter +/- SEM) after overnight incubation at 35 degrees C. Significant differences (ANOVA and Turkey's test, p < 0.05) were found for each drug released from the disc of fibrin sealant compared with other vehicles. Release from filter paper discs compared with nitrocellulose was significant for nitrofurazone and norfloxacin. Serial transfer of fibrin discs to fresh bacterial cultures after 24 hours showed no zones of clearing. The data show that fibrin sealant releases topical drugs with no inhibition of antimicrobial activity on burn organisms. Greater zones of clearing from fibrin sealant may result from passive fluid retention or from active binding to fibrin followed by protease digestion by burn organisms. (ABSTRACT TRUNCATED AT 250 WORDS)
Lethal Synergism between Influenza and Streptococcus pneumoniae

The devastating synergism of bacterial pneumonia with influenza viral infections left its mark on the world over the last century. Although the details of pathogenesis remain unclear, the synergism is related to a variety of factors including pulmonary epithelial barrier damage which exposes receptors that influence bacterial adherence and the triggering of an exaggerated innate immune response and cytokine storm, which further acts to worsen the injury. Several therapeutics and combination therapies of antibiotics, anti-inflammatories including corticosteroids and toll-like receptor modifiers, and anti-virals are being discussed. This mini review summarizes recent developments in unearthing the pathogenesis of the lethal synergism of pneumococcal co-infection following influenza, as well as addresses potential therapeutic options and combinations of therapies currently being evaluated.
Diversity and Stability in Communities Structured by Asymmetric Resource Allocation

MacArthur (1955) first proposed a hypothesis regarding the relationship between diversity and stability by claiming that diverse communities enhance ecosystem stability. This hypothesis was based on Odum’s (1953) qualitative notion that stability increases as the number of links in a food web increase. MacArthur reasoned that more choices lead to less dependence on a particular path and thus more stability. A variety of views on the diversity-stability hypothesis ranging from agreement to opposition have been argued from numerous theoretical (May 1972, 1973; Doak et al. 1998; Tilman 1999; Yachi and Loreau 1999; Lehman and Tilman 2000) and empirical (McNaughton 1993; Tilman 1994, 1996; Ives et al. 1999; McGrady-Steed and Morin 2000; Wootton 2001) perspectives. Although several studies support the claim that biodiversity regulates stability, no clear consensus on the validity of the hypothesis has yet been reached (Cottingham et al. 2001). Part of the controversy over the diversity-stability hypothesis stems from the multitude of meanings assigned to stability (Pimm 1984). Mikkelson (1999, p. 483) argued
Correcting for batch effects in case-control microbiome studies

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses. Author Summary Batch effects are obstacles to comparing results across studies. Traditional meta-analysis techniques for combining p-values from independent studies, like Fisher’s method, are effective but statistically conservative. If batch-effects can be corrected, then statistical tests can be performed on data pooled across studies, increasing sensitivity to detect differences between treatment groups. Here, we show how a simple, model-free approach corrects for batch effects in case-control microbiome datasets.
Temperature and Vibration Dependence of the Faraday Effect of Gd2O3 NPs-Doped Alumino-Silicate Glass Optical Fiber

All-optical fiber magnetic field sensor based on the Gd2O3 nano-particles (NPs)-doped alumino-silicate glass optical fiber was developed, and its temperature and vibration dependence on the Faraday Effect were investigated. Uniformly embedded Gd2O3 NPs were identified to form in the core of the fiber, and the measured absorption peaks of the fiber appearing at 377 nm, 443 nm, and 551 nm were attributed to the Gd2O3 NPs incorporated in the fiber core. The Faraday rotation angle (FRA) of the linearly polarized light was measured at 650 nm with the induced magnetic field by the solenoid. The Faraday rotation angle was found to increase linearly with the magnetic field, and it was about 18.16° ± 0.048° at 0.142 Tesla (T) at temperatures of 25 °C–120 °C, by which the estimated Verdet constant was 3.19 rad/(T∙m) ± 0.01 rad/(T∙m). The variation of the FRA with time at 0.142 T and 120 °C was negligibly small (−9.78 × 10−4 °/min). The variation of the FRA under the mechanical vibration with the acceleration below 10 g and the frequency above 50 Hz was within 0.5°.
Anomaly Detection with Partially Observed Anomalies

In this paper, we consider the problem of anomaly detection. Previous studies mostly deal with this task in either supervised or unsupervised manner according to whether label information is available. However, there always exists settings which are different from the two standard manners. In this paper, we address the scenario when anomalies are partially observed, i.e., we are given a large amount of unlabeled instances as well as a handful labeled anomalies. We refer to this problem as anomaly detection with partially observed anomalies, and proposed a two-stage method ADOA to solve it. Firstly, by addressing the difference between the anomalies, the observed anomalies are clustered, while the unlabeled instances are filtered to get potential anomalies and reliable normal instances. Then, with the above instances, a weight is attached to each instance according to the confidence of its label, and a weighted multi-class model is built, which will be further used to distinguish different anomalies to the normal instances. Experimental results show that in the aforementioned setting, existing methods behave unsatisfactorily and the proposed method performs significantly better than all these methods, which validates the effectiveness of the proposed approach.
Cheerleading and cynicism of effective mentoring in current empirical research

This article presents the results of a review of current empirical research of effective practices in teacher mentoring. Compiling literature published since 2000 in peer-reviewed journals, we examine arguments for mentoring practices to improve teacher candidate and novice teacher experiences and skills. The emergent “effective” mentoring practices can be grouped into these categories: (a) critical reflection and feedback, (b) modeling, (c) collaboration, and (d) knowledge about the needs of novice teachers. We consider these practices in light of larger arguments made in the literature about mentoring, including the purposes of mentoring and the qualities and professional development of mentors, and situated in our professional roles in teacher education. Finally, we argue the literature does not provide evidence to support mentoring of any sort, and how future research can address that lack of evidence and the divergent perspectives on effective mentoring practices.
Hyperuricemia Induces Wnt5a/Ror2 Gene Expression, Epithelial–Mesenchymal Transition, and Kidney Tubular Injury in Mice

Background Hyperuricemia contributes to kidney injury, characterized by tubular injury with epithelial–mesenchymal transition (EMT). Wnt5a/Ror2 signaling drives EMT in many kidney pathologies. This study sought to evaluate the involvement of Wnt5a/Ror2 in hyperuricemia-induced EMT in kidney tubular injury. Methods A hyperuricemia model was performed in male Swiss background mice (3 months old, 30–40 g) with daily intraperitoneal injections of 125 mg/kg body weight (BW) of uric acid. The mice were terminated on day 7 (UA7, n=5) and on day 14 (UA14, n=5). Allopurinol groups (UAl7 and UAl14, each n=5) were added with oral 50 mg/kg BW of allopurinol treatment. The serum uric acid level was quantified, and tubular injury was assessed based on PAS staining. Reverse transcriptase-PCR was done to quantify Wnt5a, Ror2, E-cadherin, and vimentin expressions. IHC staining was done for E-cadherin and collagen I. We used the Shapiro–Wilk for normality testing and one-way ANOVA for variance analysis with a P<0.05 as significance level using SPSS 22 software. Results The hyperuricemia groups had a higher uric acid level, which was associated with a higher tubular injury score. Meanwhile, the allopurinol groups had a significantly lower uric acid level and tubular injury than the uric acid groups. Reverse transcriptase-PCR revealed downregulation of the E-cadherin expression. While vimentin and collagen I expression are upregulated, which was associated with a higher Wnt5a expression. However, the allopurinol groups had reverse results. Immunostaining revealed a reduction in E-cadherin staining in the epithelial cells and collagen I positive staining in the epithelial cells and the interstitial areas. Conclusion Hyperuricemia induced tubular injury, which might have been mediated by EMT through the activation of Wnt5a.
Expression Fetal Liver of Asialoglycoprot emn Receptor in Human

Asialoglycoprotein (ASGP) receptor, which exists in hepatic parenchymal cells, plays important roles in the clearance of desialylated glycoproteins from the circulation. To study the expression of ASGP receptor in human fetal liver, specimens were obtained after therapeutic/ spontaneous abortion or at autopsy with informed consent. Reverse transcription polymerase chain reaction and immunohistochemical staining showed that ASGP receptor was present as early as 15 weeks of gestation in human fetal liver. In liver at 15 weeks-gestation it was stained uniformly in cytoplasm as seen in HepG2 cells. As gestation proceed the ASGP receptor was frequently observed on the cell surface and intracellular staining showed a spotted distribution. We conclude that the expression of ASGP receptor is an early event in the developmental process of fetal liver. Furthermore, the distribution of ASGP receptor changes as the liver develops.