Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of branched-chain volatile fatty acids by certain anaerobic bacteria

Net production of isobutyric acid, isovaleric acid, and 2-methylbutyric acid by cultures of Bacteroides ruminicola and Megasphaera elsdenii on media that contained Trypticase or casein hydrolysate continued (up to 5 days) after growth had ceased. Only trace quantities of these acids were produced in a medium that contained a mixture of amino acids that did not include the branched-chain amino acids. M. elsdenii produced increased quantities of the branched-chain fatty acids in a medium that contained Trypticase when glucose was reduced or eliminated from the culture medium. However, B. ruminicola produced increased quantities of branched-chain fatty acids and of phenylacetic acid from Trypticase when glucose was supplied at 3 mg/ml rather than at 1 mg/ml. Single strains of Streptococcus bovis, Selenomonas ruminantium, Bacteroides amylophilus, and Butyrivibrio fibrisolvens did not produce branched-chain fatty acids.
Cardioprotective Effects of Erythropoietin in Rats Subjected to Ischemia–Reperfusion Injury: Assessment of Infarct Size with 99mTc-Annexin V

Administration of erythropoietin (EPO) during or immediately after myocardial ischemia can reduce subsequent myocardial apoptosis, a key phenomenon in myocardial ischemia–reperfusion injury. In this study, we assessed the effect of EPO on 99mTc-annexin V myocardial uptake and whether the accumulation of 99mTc-annexin V can predict cardiac remodeling and functional deterioration. Methods: Eighteen rats with left coronary artery (LCA) occlusion were randomized to receive either an intravenous injection of EPO (EPO group) or saline (nontherapy [nT] group) immediately after release of the occlusion. After 20 min of LCA occlusion and 30 min of reperfusion, the rats were injected with 99mTc-annexin V. One hour after 99mTc-annexin V injection, the LCA was reoccluded and 201Tl was injected intravenously, and the rats were sacrificed 1 min later. The heart was removed and sectioned, and dual-tracer autoradiography was performed to evaluate the distribution of the area at risk (defined on the thallium autoradiograph) and the area of apoptosis (defined on the annexin autoradiograph). Adjacent histologic specimens had deoxyuridine triphosphate nick-end labeling (TUNEL) staining to confirm the presence of apoptosis and were compared with autoradiography. Another 16 rats were randomized to EPO and nT groups and underwent echocardiography immediately after release of the LCA occlusion and at 2 and 4 wk after surgery. Results: The areas of 99mTc-annexin V accumulation in the EPO group were smaller than those in the nT group, though the 201Tl defect areas of these 2 groups were comparable (area ratio, 0.318 ± 0.038 vs. 0.843 ± 0.051, P < 0.001, for annexin and 24.8 ± 2.1 vs. 25.9 ± 2.6 mm2, P = NS, for thallium). 99mTc-annexin V accumulation correlated with the density of TUNEL-positive cells (r = 0.886, P < 0.001). In the nT group, left ventricular end-diastolic dimension (Dd) increased from baseline at 2 wk by 34.7% ± 3.8% and remained stable at 34.9% ± 5.0% at 4 wk after coronary occlusion. In the EPO group, Dd increased by 8.5% ± 2.1% (P < 0.01 vs. nT at 2 wk) and 13.2% ± 2.8% (P < 0.01 vs. nT at 4 wk). In the nT group, the left ventricular percentage of fractional shortening decreased by 42.2% ± 3.4% and 52.9% ± 3.4% at 2 and 4 wk, respectively, whereas in the EPO group it decreased 9.0% ± 1.9% at 2 wk (P < 0.01 vs. nT at 2 wk) and 11.1% ± 6.7% at 4 wk (P < 0.01 vs. nT at 4 wk). Conclusion: This study demonstrated that a single treatment with EPO immediately after release of coronary ligation suppressed cardiac remodeling and functional deterioration. 99mTc-annexin V autoradiographs and TUNEL staining confirm that this change is due to a decrease in the extent of myocardial apoptosis in the ischemic/reperfused region.
Comparative study of mathematically modelled High Electron Mobility Transistors and silicon nanowire transistors

This work concentrates on the mathematical modeling of High Electron Mobility Transistors (HEMTs). Fermi-Dirac distribution characteristics of HEMTs and Silicon Nano-wire Transistors (SNWTs) were compared. Our mathematical modelling involves study of V-I characteristics, Electric field versus Drift velocity characteristics, ID electron density versus position characteristics, transconductance versus gate-source voltage characteristics, unity gain cut off frequency versus gate-length characteristics, mobility versus temperature characteristics and Density of states versus position characteristics. According to this model, Transferred Electron Devices (TEDs) has better drift velocity versus electric field characteristics compared to GaAs Metal Semiconductor Field Effect Transistors (MESFETs), and SNWTs have better V-I characteristics compared to HEMT. GaAs/AlGaAs HEMTs have better transconductance and unity gain cut-off frequency than GaAs HEMTs. HEMTs modelled using ballistic mobility method have better V-I characteristics compared to SNWTs. GaN HEMTs have high mobility compared to GaAs HEMTs. SNWTs have better density of states characteristics compared to GaN HEMTs.
Lipid Lowering Effect of Punica granatum L. Peel in High Lipid Diet Fed Male Rats

Many herbal medicines have been recommended for the treatment of dyslipidemia. The antilipidemic effect of hydroethanolic extract of pomegranate peel (Punica granatum L.) was investigated in high lipid diet fed male rats. Intraperitoneally administration of pomegranate peel extract (50, 100, 200, and 300 mg/kg body weight) for 23 days on the levels of serum cholesterol, triglycerides, LDL, HDL, alkaline phosphatase (AP), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) in high lipid diet fed male rats was evaluated. Treatment of pomegranate extract decreased body weight in treated rats, significantly. Administration of the plant extract significantly decreased serum total cholesterol, triglycerides, LDL-C, alkaline phosphatise, AST, and ALT levels, whereas it increased serum HDL-C in high lipid diet fed rats in comparison to saline control group. Also, histopathological study showed that treatment of pomegranate peel extract attenuates liver damage in high lipid diet fed rats in comparison to saline group. It is concluded that the plant should be considered as an excellent candidate for future studies on dyslipidemia.
Evolution and diversity of floral scent chemistry in the euglossine bee-pollinated orchid genus Gongora

•Background and Aims Animal-pollinated angiosperms have evolved a variety of signalling mechanisms to attract pollinators. Floral scent is a key component of pollinator attraction, and its chemistry modulates both pollinator behaviour and the formation of plant–pollinator networks. The neotropical orchid genus Gongora exhibits specialized pollinator associations with male orchid bees (Euglossini). Male bees visit orchid flowers to collect volatile chemical compounds that they store in hind-leg pouches to use subsequently during courtship display. Hence, Gongora floral scent compounds simultaneously serve as signalling molecules and pollinator rewards. Furthermore, because floral scent acts as the predominant reproductive isolating barrier among lineages, it has been hypothesized that chemical traits are highly species specific. A comparative analysis of intra- and inter-specific variation of floral scent chemistry was conducted to investigate the evolutionary patterns across the genus. •Methods Gas chromatography–mass spectrometry (GC-MS) was used to analyse the floral scent of 78 individuals belonging to 28 different species of Gongora from two of the three major lineages sampled across the neotropical region. Multidimensional scaling and indicator value analyses were implemented to investigate the patterns of chemical diversity within and among taxonomic groups at various geographic scales. Additionally, pollinator observations were conducted on a sympatric community of Gongora orchids exhibiting distinct floral scent phenotypes. •Key Results A total of 83 floral volatiles, mainly terpenes and aromatic compounds, were detected. Many of the identified compounds are common across diverse angiosperm families (e.g. cineole, eugenol, β-ocimene, β-pinene and terpinen-4-ol), while others are relatively rare outside euglossine bee-pollinated orchid lineages. Additionally, 29 volatiles were identified that are known to attract and elicit collection behaviour in male bees. Floral scent traits were less variable within species than between species, and the analysis revealed exceptional levels of cryptic diversity. Gongora species were divided into 15 fragrance groups based on shared compounds. Fragrance groups indicate that floral scent variation is not predicted by taxonomic rank or biogeographic region. •Conclusions Gongora orchids emit a diverse array of scent molecules that are largely species specific, and closely related taxa exhibit qualitatively and quantitatively divergent chemical profiles. It is shown that within a community, Gongora scent chemotypes are correlated with near non-overlapping bee pollinator assemblies. The results lend support to the hypothesis that floral scent traits regulate the architecture of bee pollinator associations. Thus, Gongora provides unique opportunities to examine the interplay between floral traits and pollinator specialization in plant–pollinator mutualisms.
Modern health services utilization and associated factors in North East Ethiopia

Background Ethiopia is one of the developing countries with the poorest health status and the health services utilization is generally low with different patterns in different regions of the country. Therefore, the aim of this study was to assess utilization of modern health services and associated factors in Dessie, Ethiopia. Methods A cross sectional study design was employed from January to March, 2015 in Dessie City. The total sample was 420 adults. Adults were selected by stratified random sampling. The strata were made using residence as urban and rural residents. The data was collected using pre-tested, interviewer administered questionnaire. The data was entered into Epi infoTM7 software and exported to Statistical Package for Social Sciences (SPSS) version 20 Software for analysis. Binary logistic regression was used to evaluate independent effect of each variable on modern health service utilization by controlling the effect of others. The strength of association between dependent variable and independent variables was expressed by odds ratio with 95% confidence interval. Results The overall modern health services utilization rate was 41.8%. Being Female sex, annual income greater than poverty line, poor perception of health status, high perceived severity of illness, two or more than two number of illnesses in the last 12 months prior to the survey and presence of chronic health problem were found to have a significant association with utilization of modern health services. Conclusion Modern health services utilization was found to be low. Being female sex, annual income above poverty line, having poor perceived health status, having two or more than two illnesses, severe perceived severity of illness and having chronic health problem were found to have a statistically significant association with utilization. Therefore, efforts have to be made to increase utilization of modern health services through establishing systems like health extension workers and health development army.
Activation of an Immunoregulatory and Antiviral Gene Expression Program in Poly(I:C)-Transfected Human Neutrophils1

Neutrophils, historically known for their involvement in acute inflammation, are also targets for infection by many different DNA and RNA viruses. However, the mechanisms by which they recognize and respond to viral components are poorly understood. Polyinosinic:polycytidylic acid (poly(I:C)) is a synthetic mimetic of viral dsRNA that is known to interact either with endosomal TLR3 (not expressed by human neutrophils) or with cytoplasmic RNA helicases such as melanoma differentiation-associated gene 5 (MDA5) and retinoic acid-inducible gene I (RIG-I). In this study, we report that intracellularly administered poly(I:C) stimulates human neutrophils to specifically express elevated mRNA levels encoding type I IFNs, immunoregulatory cytokines, and chemokines, such as TNF-α, IL-12p40, CXCL10, CXCL8, CCL4, and CCL20, as well as classical IFN-responsive genes (IRG), including IFIT1 (IFN-induced protein with tetratricopeptide repeats 1)/IFN-stimulated gene (ISG)56, G1P2/ISG15, PKR (dsRNA-dependent protein kinase), and IFN-regulatory factor (IRF)7. Investigations into the mechanisms whereby transfected poly(I:C) promotes gene expression in neutrophils uncovered a crucial involvement of the MAPK-, PKR-, NF-κB-, and TANK (TNF receptor-associated NF-κB kinase)-binding kinase (TBK1)/IRF3-signaling transduction pathways, as illustrated by the use of specific pharmacological inhibitors. Consistent with the requirement of the cytoplasmic dsRNA pathway for antiviral signaling, human neutrophils were found to constitutively express significant levels of both MDA5 and RIG-I, but not TLR3. Accordingly, neutrophils isolated from MDA5-deficient mice had a partial impairment in the production of IFN-β and TNF-α upon infection with encephalomyocarditis virus. Taken together, our data demonstrate that neutrophils are able to activate antiviral responses via helicase recognition, thus acting at the frontline of immunity against viruses.
Hash-AV: fast virus signature scanning by cache-resident filters

Fast virus scanning is becoming increasingly important in today's Internet. While Moore's law continues to double CPU cycle speed, virus scanning applications fail to ride on the performance wave due to their frequent random memory accesses. This paper proposes Hash-AV, a virus scanning "booster" technique that aims to take advantage of improvements in CPU performance. Using a set of hash functions and a bloom filter array that fits in CPU second-level (L2) caches, Hash-AV determines the majority of "no-match" cases without accesses to main memory. Experiments show that Hash-AV improves the performance of the open-source virus scanner Clam-AV by a factor of 2.5 to 10. The key to Hash-AV's success lies in a set of "bad but cheap" hash functions that are used as initial hashes. The speed of Hash-AV makes it well suited for "on-access" virus scanning, providing greater protections to the user. Through intercepting system calls and wrapping glibc libraries, we have implemented an "on-access" version for Hash-AV+Clam-AV. The on-access scanner can examine input data at a throughput of over 200 Mb/s, making it suitable for network-based virus scanning.
Bestrophin expression and function in the human pancreatic duct cell line, CFPAC‐1

Pancreatic duct epithelial cells (PDECs) have been shown to express calcium activated chloride channels (CaCCs) and there is evidence for their involvement in fluid secretion from these cells. The molecular identity of the CaCC in PDECs remains unknown. Recently, the bestrophin family of proteins have been proposed as a potential molecular candidate for CaCCs. Expression of bestrophins is strongly correlated with the function of CaCCs in a variety of tissues. In the present study, the expression of bestrophins has been investigated in the cystic fibrosis pancreatic duct cell line, CFPAC‐1. Iodide efflux analysis was used to characterise native CaCCs in CFPAC‐1 cell monolayers. Efflux was induced with the addition of UTP (100 μm, 10.2 ± 1.5 nmol min−1), which was blocked by the chloride channel blockers niflumic acid (81%) and DIDS (90%). The UTP‐stimulated iodide efflux was shown to be Ca2+ dependent and cAMP independent. RT‐PCR analysis of RNA isolated from CFPAC‐1 cells demonstrated positive identification of all four human bestrophin mRNAs. Western blot of CFPAC‐1 cell protein isolates with antibodies specific to human bestrophin 1 (hBest1) showed that hBest1 protein was expressed in this cell line. HBest1 was present on the cell surface, demonstrated using biotinylation and confocal imaging, as well as in the cytoplasm. SiRNA‐mediated silencing of hBest1 in CFPAC‐1 cells reduced the UTP‐stimulated iodide efflux by around 40%. This study provides evidence that the bestrophins are expressed in pancreatic duct cells and, more specifically, that hBest1 plays a role in the CaCCs found in these cells.
Towards User Personality Profiling from Multiple Social Networks

The exponential growth of online social networks has inspired us to tackle the problem of individual user attributes inference from the Big Data perspective. It is well known that various social media networks exhibit different aspects of user interactions, and thus represent users from diverse points of view. In this preliminary study, we make the first step towards solving the significant problem of personality profiling from multiple social networks. Specifically, we tackle the task of relationship prediction, which is closely related to our desired problem. Experimental results show that the incorporation of multi-source data helps to achieve better prediction performance as compared to single-source baselines.
Peptidoglycan Induces Nuclear Factor-κB Activation and Cyclooxygenase-2 Expression via Ras, Raf-1, and ERK in RAW 264.7 Macrophages*

In this study, we investigated the signaling pathway involved in cyclooxygenase-2 (COX-2) expression caused by peptidoglycan (PGN), a cell wall component of the Gram-positive bacterium Staphylococcus aureus, in RAW 264.7 macrophages. PGN caused dose- and time-dependent increases in COX-2 expression, which was attenuated by a Ras inhibitor (manumycin A), a Raf-1 inhibitor (GW 5074), and an MEK inhibitor (PD 098059). Treatment of RAW 264.7 macrophages with PGN caused time-dependent activations of Ras, Raf-1, and ERK. The PGN-induced increase in Ras activity was inhibited by manumycin A. Raf-1 phosphorylation at Ser-338 by PGN was inhibited by manumycin A and GW 5074. The PGN-induced increase in ERK activity was inhibited by manumycin A, GW 5074, and PD 098059. Stimulation of cells with PGN activated IκB kinase α/β (IKKα/β), IκBα phosphorylation, IκBα degradation, and κB-luciferase activity. Treatment of macrophages with an NF-κB inhibitor (pyrrolidine dithiocarbamate), an IκBα phosphorylation inhibitor (Bay 117082), and IκB protease inhibitors (l-1-tosylamido-2-phenylethyl chloromethyl ketone and calpain inhibitor I) all inhibited PGN-induced COX-2 expression. The PGN-mediated increase in the activities of IKKα/β and κB-luciferase were also inhibited by the Ras dominant negative mutant (RasN17), manumycin A, GW 5074, and PD 098059. Further studies revealed that PGN induced the recruitment of p85α and Ras to Toll-like receptor 2 in a time-dependent manner. Our data demonstrate for the first time that PGN activates the Ras/Raf-1/ERK pathway, which in turn initiates IKKα/β and NF-κB activation, and ultimately induces COX-2 expression in RAW 264.7 macrophages.
An Interior-Point Method for Large-Scale  $\ell_1$-Regularized Least Squares

Recently, a lot of attention has been paid to regularization based methods for sparse signal reconstruction (e.g., basis pursuit denoising and compressed sensing) and feature selection (e.g., the Lasso algorithm) in signal processing, statistics, and related fields. These problems can be cast as -regularized least-squares programs (LSPs), which can be reformulated as convex quadratic programs, and then solved by several standard methods such as interior-point methods, at least for small and medium size problems. In this paper, we describe a specialized interior-point method for solving large-scale -regularized LSPs that uses the preconditioned conjugate gradients algorithm to compute the search direction. The interior-point method can solve large sparse problems, with a million variables and observations, in a few tens of minutes on a PC. It can efficiently solve large dense problems, that arise in sparse signal recovery with orthogonal transforms, by exploiting fast algorithms for these transforms. The method is illustrated on a magnetic resonance imaging data set.
Fluorescent leukocytes enter plaque on the microscope stage.

Atherosclerosis is a disease driven by lipid accumulation and leukocyte influx in the vessel wall.1 Because visualizing leukocyte behavior in vivo is the holy grail for those interested in understanding leukocyte migration, major progress has been made in developing intravital microscopy approaches to study leukocyte movement. Understanding how certain leukocytes, such as T cells, participate in various diseases including cancer2,3 has been one of intravital microscopy’s success stories. The technology has also proven beneficial for understanding basic processes of leukocyte biology, such as the patrolling behavior of monocytes,4 monocyte movement within the spleen,5 the existence of neutrophil slings,6 and the differentiation of hematopoietic stem cells to leukocytes in the bone marrow.7 These 3-dimensional methods that combine high temporal resolution, (sub)cellular spatial resolution, and multicolor encoding for multiple cells or proteins can inform on in vivo biology in unprecedented ways, including real-time interaction of cells with each other and the tissue environment. Article, see p 770 One of the major challenges in performing intravital microscopy in live animals is the need to control respiratory, peristaltic, and cardiovascular motion. The beating heart (and to a somewhat lesser degree, the arterial vasculature) in a live animal moves rapidly with a high amplitude of motion. Without sophisticated stabilization methods, cardiovascular motion makes it impossible to focus on a cell residing in tissue, let alone isolation and resolution …
Comparison of oral azithromycin with oral doxycycline in the treatment of acne vulgaris.

BACKGROUND Acne vulgaris is a common inflammatory disorder of the skin that involves pilosebaceous units. This study was conducted to compare the efficacy of oral azithromycin with oral doxycycline in the treatment of acne vulgaris in our population. METHODS This randomized controlled trial was conducted in the dermatology department of Lady Reading Hospital, Peshawar from January to December 2011. All male and female patients of age (14-30 years) having moderate acne vulgaris on face only were included in the study. Patients were randomly divided into two groups. Patients in first group were given azithromycin 500 mg daily before meal for 4 consecutive days monthly for 3 months while patients in second group were given doxycycline 100 mg daily after meals for 3 months. Patients were followed up after taking treatment for three months to see the response of each drug. Response was graded as excellent, good, moderate, mild and no response. RESULTS A total of 386 patients equally divided in azithromycin and doxycycline groups. Male to female ratio in azithromycin and doxycycline groups was 0.82:1.11 and 0.89:1.04 respectively. Mean age in both groups was 18.45 ± 2.91 years and 17.96 ± 2.59 years respectively. In azithromycin group, an excellent response was noted in 6 (3.1%), and good response was observed in 44 (22.8%) patients. In doxycycline group 22 (11.4%) patients had excellent and 107 (55.4%) patients had good response. The difference being statistically significant. CONCLUSION Doxycycline is a better option fdr treatment of acne vulgaris as compared to azithromycin.