Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Levels of HIV Unspliced RNA from Patients on Combination Antiretroviral Therapy with Undetectable Plasma Viremia Predict the Therapy Outcome

Background Combination antiretroviral therapy (cART), the standard of care for HIV-1 infection, is considered to be successful when plasma viremia remains below the detection limit of commercial assays. Yet, cART fails in a substantial proportion of patients after the apparent success. No laboratory markers are known that are predictive of cART outcome in initial responders during the period of undetectable plasma viremia. Methodology/Principal Findings Here, we report the results of a retrospective longitudinal study of twenty-six HIV-infected individuals who initially responded to cART by having plasma viremia suppressed to <50 copies/ml. Eleven of these patients remained virologically suppressed, whereas fifteen experienced subsequent cART failure. Using sensitive methods based on seminested real-time PCR, we measured the levels of HIV-1 proviral (pr) DNA, unspliced (us) RNA, and multiply spliced RNA in the peripheral blood mononuclear cells (PBMC) of these patients at multiple time points during the period of undetectable plasma viremia on cART. Median under-therapy level of usRNA was significantly higher (0.43 log10 difference, P = 0.0015) in patients who experienced subsequent cART failure than in successfully treated patients. In multivariate analysis, adjusted for baseline CD4+ counts, prior ART experience, and particular cART regimens, the maximal usRNA level under therapy was the best independent predictor of subsequent therapy failure (adjusted odds ratio [95% CI], 24.4 [1.5–389.5], P = 0.024). The only other factor significantly associated with cART failure was prior ART experience (adjusted odds ratio [95% CI], 12.3 [1.1–138.4], P = 0.042). Levels of usRNA under cART inversely correlated with baseline CD4+ counts (P = 0.0003), but did not correlate with either baseline usRNA levels or levels of prDNA under therapy. Conclusion Our data demonstrate that the level of HIV-1 usRNA in PBMC, measured in cART-treated patients with undetectable plasma viremia, is a strong predictive marker for the outcome of therapy.
Aspartate inhibits LPS-induced MAFbx and MuRF1 expression in skeletal muscle in weaned pigs by regulating Akt, AMPKα and FOXO1

Infection and inflammation can result in the rapid loss of muscle mass and myofibrillar proteins (muscle atrophy). In addition, aspartate (Asp) is necessary for protein synthesis in mammalian cells. We hypothesized that Asp could attenuate LPS-induced muscle atrophy in a piglet model. Twenty-four weaning piglets were allotted to four treatments, including non-challenged control, LPS challenged control, LPS+0.5% Asp and LPS+1.0% Asp. On d 21, the piglets were injected with i.p. injection of LPS (100 ug/kg BM) or saline. At 4 h post-injection, blood, gastrocnemius and longissimus dorsi muscles samples were collected for biochemical and molecular analyses. Asp decreased the concentrations of cortisol and glucagon in plasma. In addition, Asp increased protein and RNA contents in muscles, and decreased mRNA expression of muscle atrophy F-box (MAFbx) and muscle RING finger 1 (MuRF1). Moreover, Asp decreased phosphorylation of AMPKα but increased phosphorylation of Akt and Forkhead Box O (FOXO) 1 in the muscles. Our results indicate that Asp suppresses LPS-induced MAFbx and MuRF1 expression via activation of Akt signaling, and inhibition of AMPKα and FOXO1 signaling.
Transmission pattern selection for relay communication with distributed space-time codes

We propose an efficient space-time coded cooperative relay communications scheme that employs linear precoding and transmission-pattern selection. If effectively exploited, distributed spatial diversity and the cooperative nature of multihop communications could significantly increase the coverage area of a wireless network that consists of a number of power-limited relay nodes. We build upon an existing block linear precoding technique for conventional multiple-input multiple-output systems studied in to improve the diversity performance of a multihop relay network. We propose a distributed-relay-selection algorithm to maximize the signal-to-noise ratio at the receiver. We show, via simulation, that the proposed pattern-selection scheme with precoding outperforms the conventional space-time coded relay system using quasi-orthogonal space-time block codes by over 2 dB at a bit error rate of 10-3.
Procedural justice and workplace deviance: the mediating role of perceived normative conflict in work groups

Deviant workplace behavior (DWB) constitutes a frequent and costly problem for organizations. This study examines the relationship between procedural justice, a specific type of organizational justice perception that reflects how fairly the organizational procedures are designed, and deviant workplace behavior in its two categories of organizational (DWBO) and interpersonal (DWBI) deviances. The model tested suggests that perceptions of procedural justice affect DWB by influencing the employees’ sense of a normative conflict (PNC) in their work groups, which in turn prompts them to reciprocate with both DWBO and DWBI. SEM results show that procedural justice (PJ) is an antecedent of PNC that fully mediates the relationship of PJ and both types of the mentioned workplace deviance. Data were collected from 270 teachers of a Spanish public university. Implications of the results for the prediction and supervising of workplace deviance are discussed and future research directions are offered.
Colony‐morphology screening uncovers a role for the Pseudomonas aeruginosa nitrogen‐related phosphotransferase system in biofilm formation

Pseudomonas aeruginosa is an opportunistic human pathogen whose survival is aided by forming communities known as biofilms, in which cells are encased in a self‐produced matrix. We devised a mutant screen based on colony morphology to identify additional genes with previously unappreciated roles in biofilm formation. Our screen, which identified most known biofilm‐related genes, also uncovered PA14_16550 and PA14_69700, deletions of which abrogated and augmented biofilm formation respectively. We also identified ptsP, which encodes enzyme I of the nitrogen‐regulated phosphotransferase (PTSNtr) system, as being important for cyclic‐di‐GMP production and for biofilm formation. Further experiments showed that biofilm formation is hindered in the absence of phosphotransfer through the PTSNtr, but only in the presence of enzyme II (PtsN), the putative regulatory module of the PTSNtr. These results implicate unphosphorylated PtsN as a negative regulator of biofilm formation and establish one of the first known roles of the PTSNtr in P. aeruginosa.
Molecular Cloning, Characterization and Functional Analysis of the Genes Encoding DXR and DXS, the Two Enzymes in the MEP Pathway, from Amomum villosum Lour.

Amomum villosum Lour. (officinal name Fructus Amomi) is one of the most well-known and authentic herbs in South China. Monoterpenes in its volatile oil are the main medicinal compounds. The condensation of pyruvate with D-glyceraldhyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) catalyzed by DXP synthase (DXS, EC: 2.2.1.7) and the conversion of DXP to 2-C-methyl-D-erythritol-4-phosphate (MEP), catalyzed by DXP reductoisomerase (DXR, EC:1.1.1.267), are the initial steps of the MEP pathway for isoprenoid biosynthesis. A DXR gene, AvDXR (GenBank accession no. FJ459894), and a DXS gene, AvDXS (FJ455512), were isolated from the leaves of Amomum villosum. The 1749-bp full-length cDNA of AvDXR contained a 1416-bp open reading frame (ORF) encoding a peptide of 472 amino acids, and the 2347-bp full-length cDNA of AvDXS contained a 2148-bp ORF encoding a peptide of 715 amino acids. The deduced amino acid sequences of the AvDXR and AvDXS proteins shared high homology with DXRs and DXSs from other plant species, respectively, and the AvDXS belonged to class 1 plant DXS. Chloroplast transit peptides were found in the N-terminal region of AvDXR and AvDXS. A proline-rich region, two highly conserved NADPH-binding domains and two substrate-binding domains consistent with the enzymatic functions of DXR were found in AvDXR. AvDXS contained a TPP-binding domain and a DRAG domain related to the catalysis of DXS. The functional color assay in Escherichia coli with pAC-BETA implied that AvDXR and AvDXS encoded functional proteins that manipulate the biosynthesis of isoprenoid precursors. Both AvDXR and AvDXS were expressed extensively in the leaves, stems, roots, pericarps and seeds of A. villosum. AvDXS expression was similar in all tissues investigated, whereas higher levels of AvDXR were observed in the fruits, the main part for the accumulation of volatile oil in A. villosum, which suggested that AvDXR might play a more influential role in monoterpene precursor biosynthesis than AvDXS. The role of AvDXS in other isoprenoid biosynthesis, especially the primary isoprenoid biosynthesis remained to be investigated.
Hydroclimatic association of the monthly summer monsoon rainfall over India with large‐scale atmospheric circulations from tropical Pacific Ocean and the Indian Ocean region

The hydroclimatic association between the monthly Indian summer monsoon rainfall and a proposed monthly composite index (MCI) of large‐scale atmospheric circulations from the Pacific Ocean and Indian Ocean regions is established. The spatial variability of this association is also checked. The predictability of the monthly Indian summer monsoon rainfall using the MCI is also investigated and is seen to be encouraging. Copyright © 2006 Royal Meteorological Society
Cebus Phylogenetic Relationships: A Preliminary Reassessment of the Diversity of the Untufted Capuchin Monkeys

The untufted, or gracile, capuchin monkeys are currently classified in four species, Cebus albifrons, C. capucinus, C. olivaceus, and C. kaapori, with all but C. kaapori having numerous described subspecies. The taxonomy is controversial and their geographic distributions are poorly known. Cebus albifrons is unusual in its disjunct distribution, with a western and central Amazonian range, a separate range in the northern Andes in Colombia, and isolated populations in Trinidad and west of the Andes in Ecuador and northern Peru. Here we examine previous morphological and molecular hypotheses of the taxonomy and phylogeny of Cebus. We construct a time‐calibrated phylogeny based upon mitochondrial DNA sequences from 50 Cebus samples from across their range. Our data indicate that untufted capuchins underwent a radiation at about 2 Ma, and quickly diversified in both the Andes and the Amazon. We provide a provisional reassessment for the taxonomy of untufted capuchins in the Amazon, the Llanos, the Andes, Trinidad, and Central America, splitting currently paraphyletic taxa into several species, including: at least two Amazonian species (C. yuracus and C. unicolor); a species from the Guiana Shield (most likely the same as Humboldt's C. albifrons); two northern Andean species, C. versicolor, C. cesarae; C. brunneus (with trinitatis a junior synonym) on the Venezuelan coast, and C. adustus in the region of Lake Maracaibo; C. capucinus in northwestern Ecuador and Colombia, and Panama; C. imitator in Central America; C. olivaceus and C. castaneus occupying a large part of the Guiana Shield; and C. kaapori in the eastern Amazon, south of the Rio Amazonas. More intensive and extensive geographic sampling is needed, including that for some subspecies not represented here. Taxa from the southwestern Amazon (yuracus, cuscinus, and unicolor) and the phylogenetic position of Humboldt's Simia albifrons from the Orinoco remain particularly poorly defined. Am. J. Primatol. 74:381–393, 2012. © 2012 Wiley Periodicals, Inc.
Eu-ist Integrated Project (ip) Ist-2003-506826 Sekt D3.1.1.b State-of-the-art on Ontology Evolution Sekt Consortium

EU-IST Integrated Project (IP) IST-2003-506826 SEKT Deliverable D3.1. 1.b (WP3.1) This document is an informal deliverable provided to SEKT partners. The main aim of this document is to provide an overview of existing research results and ongoing research in the are of ontology evolution. It further identifies relevant open research questions with respect to ontology evolution that will be addressed within the SEKT project.
Fuzzy Controlled Individual Cell Equalizers for Lithium-Ion Batteries

A fuzzy logic control battery equalizing controller (FLCBEC) is adopted to control the cell voltage balancing process for a series connected Li-ion battery string. The proposed individual cell equalizer (ICE) is based on the bidirectional Cuk converter operated in the discontinuous capacitor voltage mode (DCVM) to reduce the switching loss and improve equalization efficiency. The ICE with the proposed FLCBEC can reduce the equalizing time, maintain safe operations during the charge/discharge state and increase the battery string capacity.
α2-Antiplasmin, Plasminogen Activator Inhibitor (PAI) and Dilute Blood Clot Lysis Time in Selected Disease States

Summary This paper is an attempt to assess the relevance of the inhibitors of fibrinolysis for clot lysis in selected disease states and to discuss the mechanisms leading to acquired abnormal levels of such inhibitors. When compared to 20 control subjects the 30 hypertriglyceridemic patients (14 with type IIb and 16 with type IV) displayed significantly (p <0.001) increased plasma plasminogen activator inhibitor (PAI) activity (221 ± 88% and 290 ± 104% respectively; mean ± SD), moderately (p <0.01) increased α2 antiplasmin (α2AP) level (112 ± 11% and 115 ± 16%) and accordingly an obviously prolonged dilute blood clot lysis time (DBCLT). Neither PAI activity and α2AP level nor DBCLT were significantly different from controls in the 10 patients with hyperlipoproteinemia type IIa. The 18 patients with severe hepatic cirrhosis had low α2AP level (59 ± 19.7%) and accelerated clot lysis, while mean PAI activity (160 ± 87%) was slightly (p <0.05) increased. In the 17 nephrotic patients α2AP was increased (115 ±12%) while PAI activity was similar to controls and DBCLT rather shorter. Two liver secretion enzymes, namely serum Cholinesterase and plasma protein C, were found to be decreased in cirrhotic patients, similar to control values in hyperlipoproteinemia type Ha and obviously increased in nephrotic patients as well as in hypertriglyceridemic subjects. The relevance of PAI and α2AP for clot lysis was considered in relation to data in the literature concerning the behaviour of t-PA and factor XIII. Enhanced hepatic synthesis of protease inhibitors and factor XIII as a possible cause of delayed clot lysis in hypertriglyceridemia was envisaged.
The Basic Helix-Loop-Helix Transcription Factor NeuroD1 Facilitates Interaction of Sp1 with the Secretin Gene Enhancer

ABSTRACT The basic helix-loop-helix transcription factor NeuroD1 is required for late events in neuronal differentiation, for maturation of pancreatic β cells, and for terminal differentiation of enteroendocrine cells expressing the hormone secretin. NeuroD1-null mice demonstrated that this protein is essential for expression of the secretin gene in the murine intestine, and yet it is a relatively weak transcriptional activator by itself. The present study shows that Sp1 and NeuroD1 synergistically activate transcription of the secretin gene. NeuroD1, but not its widely expressed dimerization partner E12, physically interacts with the C-terminal 167 amino acids of Sp1, which include its DNA binding zinc fingers. NeuroD1 stabilizes Sp1 DNA binding to an adjacent Sp1 binding site on the promoter to generate a higher-order DNA-protein complex containing both proteins and facilitates Sp1 occupancy of the secretin promoter in vivo. NeuroD-dependent transcription of the genes encoding the hormones insulin and proopiomelanocortin is potentiated by lineage-specific homeodomain proteins. The stabilization of binding of the widely expressed transcription factor Sp1 to the secretin promoter by NeuroD represents a distinct mechanism from other NeuroD target genes for increasing NeuroD-dependent transcription.
Florian et al_ICMCSSE 2012_3

We here propose improved version of elastic graph matching (EGM) as a face detector, called the multi -scale EGM (MS-EGM). In this improvement, Gabor wavelet-based pyramid reduces computational complexity for the feature re presentation often used in the conventional EGM, but preserving a crit ical amount of information about an image. The MS-EGM gives us hig her detection performance than Viola-Jones object detection algor ithm of the AdaBoost Haar-like feature cascade. We also show ra pid detection speeds of the MS-EGM, comparable to the Viola-Jones m thod. We find fruitful benefits in the MS-EGM, in terms of t opological feature representation for a face. Keywords—Face Detection, Gabor Wavelet Based Pyramid, Elastic Graph Matching, Topological Preservation, R edundancy of Computational Complexity.
Full-duplex self-backhauling for small-cell 5G networks

We consider in-band self-backhauling for small cell 5G systems. In-band self-backhauling enables efficient usage of frequency resources. When coupled with a flexible frame format, it also enables efficient time-division duplexing of uplink, downlink, and backhaul transmissions. Self-backhauling is particularly efficient when coupled with FD relaying. Antenna design, as well as cancellation in radio frequency and digital domains at an FD relay enables reuse of the same resources for backhaul and access hops. The use of radio resources in the self-backhauling and access hops can be coordinated to maximize end-to-end performance. We evaluate FD in-band self-backhauling in indoor 5G scenarios, targeting mobile broadband and ultrareliable communication use cases. Self-backhauling shows considerable promise for reaching 5G targets in these scenarios.
A microcosm study to support aquatic risk assessment of nickel: Community‐level effects and comparison with bioavailability‐normalized species sensitivity distributions

The aquatic risk assessment for nickel (Ni) in the European Union is based on chronic species sensitivity distributions and the use of bioavailability models. To test whether a bioavailability‐based safe threshold of Ni (the hazardous concentration for 5% of species [HC5]) is protective for aquatic communities, microcosms were exposed to 5 stable Ni treatments (6–96 μg/L) and a control for 4 mo to assess bioaccumulation and effects on phytoplankton, periphyton, zooplankton, and snails. Concentrations of Ni in the periphyton, macrophytes, and snails measured at the end of the exposure period increased in a dose‐dependent manner but did not indicate biomagnification. Abundance of phytoplankton and snails decreased in 48 μg Ni/L and 96 μg Ni/L treatments, which may have indirectly affected the abundance of zooplankton and periphyton. Exposure up to 24 μg Ni/L had no adverse effects on algae and zooplankton, whereas the rate of population decline of the snails at 24 μg Ni/L was significantly higher than in the controls. Therefore, the study‐specific overall no‐observed‐adverse‐effect concentration (NOAEC) is 12 μg Ni/L. This NOAEC is approximately twice the HC5 derived from a chronic species sensitivity distribution considering the specific water chemistry of the microcosm by means of bioavailability models. Thus, the present study provides support to the protectiveness of the bioavailability‐normalized HC5 for freshwater communities. Environ Toxicol Chem 2016;35:1172–1182. © 2015 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc. on behalf of SETAC.
Artery Wall Imaging and Effects of Postmenopausal Estrogen Therapy

Background: Estrogen therapy that is started at the time of menopause seems to protect against the development of atherosclerosis and cardiovascular diseases, in contrast to the initial increased cardiovascular risk when hormone therapy is initiated in older women. With increased aging and degree of atherosclerosis, the thickness of the artery intima increases and that of the media decreases. These changes can be noninvasively estimated using high-frequency ultrasound. Methods and results: The thickness of carotid and femoral artery intima and media was assessed, using noninvasive high-frequency ultrasound (25 MHz). Long-term estrogen users (mean treatment duration 20 years) had a significantly thinner mean carotid intima layer (-25%; P=0.0002), a thicker media layer (+74%; P=0.0002) and a substantially lower intima/media thickness ratio (-54%; P < 0.0001) than 17 age-matched nonusers, with values closer to those in 20 premenopausal women. Similar but less pronounced differences between the postmenopausal groups were found for the femoral artery. Conclusions: A preserved thin artery wall intima and a low intima/media thickness ratio, at values close to those in young women might be partially responsible for the beneficial cardiovascular effects of estrogen therapy when it is initiated at the time of menopause.
Importance of Inheritance and Interface in OOP Paradigm Measure through Coupling Metrics

A large numbers of metrics have been proposed for measuring properties of object-oriented software such as size, inheritance, cohesion and coupling. The coupling metrics presented in this paper exploring the difference between inheritance and interface programming. This paper presents a measurement to measure coupling between object (CBO), number of associations between classes (NASSocC), number of dependencies in metric (NDepIN) , number of dependencies out metric (NDepOut) , Number of children (NOC) and Depth of Inheritance Tree (DIT) in object oriented programming. A measurement is done for C# inheritance and interface programs. The metric values of class inheritance and interface prove which program is good to use and beneficial for C# developers.
Data Mining to Recognize Fail Parts in Manufacturing Process

In many manufacturing processes, some key process parameters have very strong relationship with the normal or various faulty products of finished products. The abnormal changes of these process parameters could result in various categories of faulty products. In this paper, a data mining model is developed for on-line intelligent monitoring and diagnosis of the manufacturing processes. In the proposed model, an Apriori learning rules developed for monitoring the manufacturing process and recognizing faulty quality of the products being produced. In addition, this algorithm is developed to discover the causal relationship between manufacturing parameters and product quality. These extracted rules are applied for diagnosis of the manufacturing process; provide guidelines on improving the product quality. Therefore, the data mining system provides abnormal warnings, reveals assignable cause(s), and helps operators optimally set the process parameters. The proposed model is successfully applied to an assembly line in hard disk drive process, which improves the product quality and saves manufacturing cost.
An intelligent readout circuit for infrared multispectral remote sensing

Over the years infrared imaging technology has enabled many critical applications such as thermal and spectral imaging, medical diagnostics, and remote sensing. The growth in infrared imaging technology has been made possible by dramatic technical advances in infrared sensor manufacturing, as well as improvements in algorithms for image processing. However, the most powerful existing infrared imaging systems are still far behind their biological counterparts in many aspects including energy efficiency, computational capabilities, and performance. Inspired by biological imaging systems, in this paper we present an intelligent readout circuit based upon spectrally tunable infrared nanostructure sensors, which can revolutionize multispectral remote sensing systems.