Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of the Munc18c/Syntaxin4 N-peptide complex defines universal features of the N-peptide binding mode of Sec1/Munc18 proteins

Sec1/Munc18 proteins (SM proteins) bind to soluble NSF attachment protein receptors (SNAREs) and play an essential role in membrane fusion. Divergent modes of regulation have been proposed for different SM proteins indicating that they can either promote or inhibit SNARE assembly. This is in part because of discrete modes of binding that have been described for various SM/SNARE complexes. One mode suggests that SM proteins bind only to Syntaxins (Stx) preventing SNARE assembly, whereas in another they facilitate SNARE assembly and bind to SNARE complexes. The mammalian cell surface SM protein Munc18c binds to an N-peptide in Stx4, and this is compatible with its interaction with SNARE complexes. Here we describe the crystal structure of Munc18c in complex with the Stx4 N-peptide. This structure shows remarkable similarity with a yeast complex indicating that the mode of binding, which can accommodate SNARE complexes, is highly conserved throughout evolution. Modeling reveals the presence of the N-peptide binding mode in most but not all yeast and mammalian SM/Stx pairs, suggesting that it has coevolved to fulfill a specific regulatory function. It is unlikely that the N-peptide interaction alone accounts for the specificity in SM/SNARE binding, implicating other contact surfaces in this function. Together with other data, our results support a sequential two-state model for SM/SNARE binding involving an initial interaction via the Stx N-peptide, which somehow facilitates a second, more comprehensive interaction comprising other contact surfaces in both proteins.
Evaluation of F1 calves sired by Brahman, Boran, and Tuli bulls for birth, growth, size, and carcass characteristics.

Birth (n = 308), weaning (n = 291), feedlot and carcass (n = 142), and yearling heifer traits (n = 139) were evaluated in F1 calves sired by Brahman (BR), Boran (BO), and Tuli (TU) bulls and born to multiparous Hereford and Angus cows. Calves sired by BR were heaviest (P < .05) at birth and largest (P < .05) for cannon bone length. Tuli crosses were smaller (P < .05) for birth weight and cannon bone length than BR and BO crosses. No significant differences were observed for gestation length among sire breeds. Brahman crosses had larger (P < .05) weaning weight, hip height, and preweaning ADG than calves sired by BO and TU. Similar trends were observed for feedlot traits. Carcasses of BR crosses were heavier (P < .05) and had less (P < .05) internal fat than those of BO and TU crosses. Tuli crosses averaged greater (P < .05) skeletal maturity than BO crosses. Tuli crosses averaged greater marbling (P < .05) than BR crosses and less (P < .05) Warner-Bratzler shear force than BO crosses. No differences were observed in longissimus muscle area, fat thickness, or yield grade among sire breeds. Heifers sired by BR were heaviest (P < .05) and tallest (P < .05) at yearling measurement. Brahman F1 heifers had larger (P < .05) pelvic height and pelvic area, due to larger skeletal frame size, than BO and TU F1 heifers. These results indicate large differences in growth and skeletal size exist among calves sired by these three breeds. Several important differences also exist for carcass quality traits, but not for carcass yield traits, among these three breeds.
The effect of the different teflon films on anisotropic conductive adhesive film (ACF) bonding

New interconnect materials are always necessary as a result of evolving packaging technologies and increasing performance and environmental demands on electronic systems. Polymer-based conductive-adhesive materials have become widely used in many electronic packaging interconnect applications. Among all the conductive-adhesive materials, the anisotropic conductive adhesives (ACA) (or anisotropic conductive adhesive films, ACF) have gained popularity as a potential replacement for solder interconnects. For ACF interconnection, thermo-compression (T/C) bonding is the most common method. In this study, the effects of the some important processing parameters, including the increasing rate of bonding temperature and different Teflon films, on the reliability of the ACF joints were investigated. Results show that the performances of the ACF joints were affected by the distribution of conductive particles and the curing degree of the ACF, which was determined by the bonding temperature ramp rates. The bonding strengths of ACF joints are different for the different Teflon filmpsilas thickness and kinds.
Slits Loaded Circularly Polarized Universal UHF RFID Reader Antenna

A simple structure circularly polarized (CP) UHF (ultrahigh frequency) RFID (radio frequency identification) reader antenna that operates within the universal RFID bands (840-960 MHz) is investigated. Here, the technique of loading a corner truncated square patch antenna into an L-shaped ground plane is initially studied to achieve good impedance matching with broad CP bandwidth. To further enhance both the impedance bandwidth and CP bandwidth, a novel technique of loading three narrow slits into the corner truncated square patch is proposed. By meticulously arranging these three slits in a certain manner, from the experimental results, besides achieving a gain level of approximately 8.6 dBic, the proposed antenna can also yield an impedance bandwidth from 685 to 1125 MHz, while good CP bandwidth between 836 and 986 MHz is also demonstrated.
Exonic Splicing Enhancer-Dependent Selection of the Bovine Papillomavirus Type 1 Nucleotide 3225 3′ Splice Site Can Be Rescued in a Cell Lacking Splicing Factor ASF/SF2 through Activation of the Phosphatidylinositol 3-Kinase/Akt Pathway

ABSTRACT Bovine papillomavirus type 1 (BPV-1) late pre-mRNAs are spliced in keratinocytes in a differentiation-specific manner: the late leader 5′ splice site alternatively splices to a proximal 3′ splice site (at nucleotide 3225) to express L2 or to a distal 3′ splice site (at nucleotide 3605) to express L1. Two exonic splicing enhancers, each containing two ASF/SF2 (alternative splicing factor/splicing factor 2) binding sites, are located between the two 3′ splice sites and have been identified as regulating alternative 3′ splice site usage. The present report demonstrates for the first time that ASF/SF2 is required under physiological conditions for the expression of BPV-1 late RNAs and for selection of the proximal 3′ splice site for BPV-1 RNA splicing in DT40-ASF cells, a genetically engineered chicken B-cell line that expresses only human ASF/SF2 controlled by a tetracycline-repressible promoter. Depletion of ASF/SF2 from the cells by tetracycline greatly decreased viral RNA expression and RNA splicing at the proximal 3′ splice site while increasing use of the distal 3′ splice site in the remaining viral RNAs. Activation of cells lacking ASF/SF2 through anti-immunoglobulin M-B-cell receptor cross-linking rescued viral RNA expression and splicing at the proximal 3′ splice site and enhanced Akt phosphorylation and expression of the phosphorylated serine/arginine-rich (SR) proteins SRp30s (especially SC35) and SRp40. Treatment with wortmannin, a specific phosphatidylinositol 3-kinase/Akt kinase inhibitor, completely blocked the activation-induced activities. ASF/SF2 thus plays an important role in viral RNA expression and splicing at the proximal 3′ splice site, but activation-rescued viral RNA expression and splicing in ASF/SF2-depleted cells is mediated through the phosphatidylinositol 3-kinase/Akt pathway and is associated with the enhanced expression of other SR proteins.
Antiviral therapy of symptomatic HCV‐associated mixed cryoglobulinemia: Meta‐analysis of clinical studies

Hepatitis C virus (HCV) infection may be associated with extra‐hepatic illness including mixed cryoglobulinemia. Evidence on HCV‐related mixed cryoglobulinemia in the non‐transplantation setting exists even if its appropriate management remains unclear. The cornerstone of treatment for symptomatic HCV‐associated mixed cryoglobulinemia is antiviral therapy but little is known about its activity. A systematic review of the literature with a meta‐analysis of clinical studies was performed in order to assess efficacy and safety of combination antiviral therapy for symptomatic HCV‐associated mixed cryoglobulinemia in non‐immunosuppressed individuals. The random effects model of DerSimonian and Laird was used, with heterogeneity and sensitivity analyses. The primary outcome was sustained virological response (as a measure of efficacy), and the secondary outcome was the rate of patients stopping (or dose reducing) antiviral agents (as a measure of tolerability). Ten clinical studies (300 unique patients) were identified; the rate of baseline kidney involvement ranged between 4% and 39%. The summary estimate of frequency of sustained viral response was 0.42 with a 95% confidence interval (CI) of 0.31; 0.54 (random effects model). Significant heterogeneity occurred (P = 0.00001; I2 = 77.6%). Stratified analysis showed higher efficacy in those studies using combination therapy with pegylated—than conventional IFN; the summary estimate of sustained viral response being 0.52 (95% CI, 0.40; 0.63) and 0.32 (95% CI, 0.15; 0.49), respectively. There was good association between viral and clinical response, weighted K 0.634 (95% CI, 0.455; 0.814), by a meta‐analysis at individual level on a subset of reports (n = 3; 74 unique patients). The summary estimate of frequency of patients stopping (or dose reducing) antiviral agents was 0.15 (95% CI, 0.08; 0.21); no heterogeneity occurred (P = 0.05; I2 = 51%). In summary, combination antiviral therapy (pegylated IFN plus ribavirin) gives satisfactory response in more than the half of patients with symptomatic mixed cryoglobulinemia associated with HCV. HCV‐related mixed cryoglobulinemia is uncommon in developed countries and this clearly hampers randomized controlled clinical trials aimed to evaluate efficacy and safety of antiviral therapy in non‐immunosuppressed individuals. J. Med. Virol. 85: 1019–1027, 2013. © 2013 Wiley Periodicals, Inc.
Developing a success model of Research Information Management System for research affiliated institutions

Research Information Management System (RIMS) is essential for any research institutes and universities. RIMS should have some effective usability features or success components of its strategic information access and display. The success or failure of the implementation of RIMS is highly dependent on the level of success and user acceptance. The measurement of IS success remains a top concern for researchers, practitioners and managers. Thus, the evaluation of RIMS success is vital. Therefore, the main objective of this paper is to propose a success model of RIMS implementation based on an extensive literature review that shows inter-relationship among IS success factors. Results from the literature review shows that several IS success studies have used and extended DeLone & McLean model in different context such as E-Learning, Learning Management System (LMS), Banking, Project Management, Health Management etc. Prior studies have extended the generic framework of DeLone & McLean model. However, few have extended it to different dimensions such as technological, organization and human perspective. Hence, to fill this gap the proposed model is used to describe the multidimensional factors that influence the success and user acceptance of RIMS. Three important aspects of IS success such as human, organization and technology are studied. Outcomes of this study can be used as a guideline for research institutions' management, RIMS designers and researchers when implementing and using RIMS.
Software Architecture Selection Framework Based on Quality Attributes

Software Architectures are generally designed with particular functional and nonfunctional requirements. Organizations often need to choose Software Architecture for future development from several competing candidate architectures. The various Stakeholders' quality requirements need to be considered collectively to describe the quality requirements of the envisioned system and therefore build the basis for the comparison and selection criteria. Choosing Software Architecture for any system still remains a difficult task as many different stake holders are involved in the selection process. Stakeholders view on quality requirements is different and at times they can also be conflicting in nature. Existing software architecture selection methods [1, 2, 3, 4] have been analyzed to identify their limitations. To overcome the limitations and challenges, a selection framework has been proposed and validated based on multiattribute decision making using Hypothetical Equivalents [7]. The proposed framework provides the rationale for an architecture selection process by comparing the fitness of competing candidate architectures for the envisioned system based on the quality requirements of different Stakeholders.
Graphene Nanoribbon Tunnel Field-Effect Transistor via Segmented Edge Saturation

In this paper, segmented edge saturation (SES) is proposed as a novel method to design high-performance tunnel FETs (TFETs) using smooth graphene nanoribbon (GNR). When the edges of a smooth GNR are saturated by different elements in its different segments, the energy gaps (<inline-formula> <tex-math notation="LaTeX">${E}_{g})$ </tex-math></inline-formula> of these segments can be tuned. Therefore, the tunneling and blocking effects are achieved simultaneously by reducing and enlarging the <inline-formula> <tex-math notation="LaTeX">${E}_{g}$ </tex-math></inline-formula> of GNR in its specific regions. Both high on-to-off current (<inline-formula> <tex-math notation="LaTeX">${I}_{ \mathrm{\scriptscriptstyle ON}}/{I}_{ \mathrm{\scriptscriptstyle OFF}})$ </tex-math></inline-formula> ratio and large <inline-formula> <tex-math notation="LaTeX">${I}_{ \mathrm{\scriptscriptstyle ON}}$ </tex-math></inline-formula> are obtained. Simulation results show that the <inline-formula> <tex-math notation="LaTeX">$\mathrm {I}_{ \mathrm{\scriptscriptstyle OFF}}$ </tex-math></inline-formula> of the SES GNR TFET is below <inline-formula> <tex-math notation="LaTeX">$1 \times 10^{-4} ~\mu \text{A}/\mu \text{m}$ </tex-math></inline-formula> and the <inline-formula> <tex-math notation="LaTeX">${I}_{{ \mathrm{\scriptscriptstyle ON}}}$ </tex-math></inline-formula> reaches 2000 <inline-formula> <tex-math notation="LaTeX">$\mu \text{A}/\mu \text{m}$ </tex-math></inline-formula> at 0.4-V supply voltage. Detailed transport mechanisms of this TFET are investigated in comparisons with its uniform saturation counterparts. Dynamic performance and scaling ability analyzes are also carried out. The largest intrinsic delay and switching energy are only 0.17 ps and 0.09 fJ/<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula>. Meanwhile, it can maintain high <inline-formula> <tex-math notation="LaTeX">${I}_{{ \mathrm{\scriptscriptstyle ON}}}/{I}_{ \mathrm{\scriptscriptstyle OFF}}$ </tex-math></inline-formula> ratios when the channel length is scaled down to several nanometers. The discussions on GNR edge roughness suggest that the roughness should be avoided for better <inline-formula> <tex-math notation="LaTeX">${I}_{ \mathrm{\scriptscriptstyle ON}}$ </tex-math></inline-formula> behaviors. The good performance of the TFET highlights the capabilities of SES in the developments of GNR tunnel devices.
Sprint interval exercise elicits near maximal peak VO2 during repeated bouts with a rapid recovery within 2 minutes.

AIM We investigated the cardiorespiratory response during acute sprint interval exercise (SIE; 4 x 30 sec maximal efforts, each separated by 4 min recovery) vs. continuous endurance exercise (CEE; 30 min) at 70% VO2max. METHODS Oxygen consumption (VO2) and heart rate were measured in 8 males (age: 23±2.3 y, height: 181±6.4 cm, body mass: 78±8.6 kg, VO2max: 52±3.1 ml·kg-1·min-1, mean±SD). Pre-exercise diet was controlled. RESULTS AND CONCLUSION Total VO2 was greater with CEE vs. SIE (87.6±13.1 vs. 35.1±4.4 L O2) with small differences (P=0.06) in average heart rates (CEE: 157±10 bpm vs. SIE: 149±6 bpm) and peak heart rates (CEE: 166±10 vs. SIE: 173±6; P=0.14). VO2 increased during the sprint bouts (53-72% of VO2max) and attained near maximal values (84-96%) in the immediate recovery period (within 20 sec). Thereafter a rapid decrease occurred so that at 2 min of recovery VO2 was ~1.5 L/min (~38% VO2max). During the remaining 2 min of recovery VO2 declined more slowly to ~1.3 L/min or ~33% of VO2max. Similar heart rate responses with CEE and SIE and a greater VO2 during SIE suggest increased muscle oxygen extraction with SIE, which might explain the greater peripheral adaptations, observed previously with sprint vs. continuous training. The potential value of shorter recovery durations to SIE needs to be examined.
Correlation between ribosylation of pertussis toxin substrates and inhibition of peptidoglycan‐, muramyl dipeptide‐ and lipopolysaccharide‐induced mitogenic stimulation in B lymphocytes

Selective inhibition by pertussis toxin (PT) of mitogenic activation of mouse B lymphocytes by bacterial mitogens (peptidoglycan and lipopolysaccharide) and muramyl dipeptide (a synthetic analog of peptidoglycan fragment) was demonstrated. Mitogenic activation of B cells by protein kinase C activators and ionomycin was insensitive to PT. Also PT did not inhibit peptidoglycan‐ and lipopolysaccharide‐induced differentiation of B cells into Ig‐secreting cells, when it was added to the cultures after the proliferative stage of the response. B lymphocyte membranes contained two major PT substrates (40 and 41 kDa). The extent of PT‐mediated ADP ribosylation of these substrates correlated with the degree of PT‐mediated inhibition of mitogenic stimulation of B cells. B cell stimulation by all mitogens tested was not inhibited by cholera toxin at nontoxic concentrations that are known to cause maximal increase in cAMP in B cells. Since the only known substrates for PT‐mediated ADP ribosylation in mammalian cells are the α subunits of some G proteins, our data suggest that G proteins are present in B cell membranes and that they are involved in B cell activation induced by bacterial mitogens.
Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences

Ursids (bears) in general, and giant pandas in particular, are highly altricial at birth. The components of bear milks and their changes with time may be uniquely adapted to nourish relatively immature neonates, protect them from pathogens, and support the maturation of neonatal digestive physiology. Serial milk samples collected from three giant pandas in early lactation were subjected to untargeted metabolite profiling and multivariate analysis. Changes in milk metabolites with time after birth were analysed by Principal Component Analysis, Hierarchical Cluster Analysis and further supported by Orthogonal Partial Least Square-Discriminant Analysis, revealing three phases of milk maturation: days 1-6 (Phase 1), days 7-20 (Phase 2), and beyond day 20 (Phase 3). While the compositions of Phase 1 milks were essentially indistinguishable among individuals, divergences emerged during the second week of lactation. OPLS regression analysis positioned against the growth rate of one cub tentatively inferred a correlation with changes in the abundance of a trisaccharide, isoglobotriose, previously observed to be a major oligosaccharide in ursid milks. Three artificial milk formulae used to feed giant panda cubs were also analysed, and were found to differ markedly in component content from natural panda milk. These findings have implications for the dependence of the ontogeny of all species of bears, and potentially other members of the Carnivora and beyond, on the complexity and sequential changes in maternal provision of micrometabolites in the immediate period after birth.
Systematic review of the role of sedation in diagnostic spinal interventional techniques.

BACKGROUND There is ongoing controversy regarding the validity of controlled diagnostic blocks due to variability in sensitivity, specificity, and accuracy. Consequently, identification of false-positive rates, false-negative rates, and placebo responses is crucial. The reasons described for false-positive responses to diagnostic anesthetic blocks are many; however, sedation and psychological factors have been implied as causes. Further, there is no consensus with regards to sedation prior to controlled diagnostic blocks and their influence on the accuracy and validity of a diagnosis. STUDY DESIGN A systematic review of the literature evaluating the influence of sedation on diagnostic spinal interventional techniques. OBJECTIVES To systematically assess the quality of clinical studies evaluating the diagnostic accuracy of controlled diagnostic blocks in the diagnosis of chronic spinal pain. METHODS A comprehensive evaluation of the literature relating to sedation in diagnostic interventional techniques was performed. The methodologic quality assessment of the studies was carried out by utilizing Agency for Healthcare Research and Quality (AHRQ) methodologic quality criteria with scores of 50 or higher included in the assessment of the level of evidence. Level of evidence was based on the U.S. Preventive Services Task Force (USPSTF) criteria for the assessment of accuracy of diagnostic studies. LIMITATIONS All 3 of the studies were produced by one group of authors. Thus paucity of the literature on the subject of facet joint pain and the lack of literature on the subjects of discogenic pain and sacroiliac joint pain are major limitations. RESULTS Three studies were identified which met inclusion and methodologic assessment quality criteria. Sedation can be a confounding factor in a small population of patients specifically if fentanyl is employed and non-stringent criteria are followed. Based on the 3 randomized double-blind trials with stringent criteria utilizing 80% pain relief and the ability to perform prior painful movements without any significant pain following the diagnostic injection in evaluation of facet joint pain, the indicated evidence is Level II-1. CONCLUSION This systematic review provides no significant evidence of the influence of sedation either with midazolam or fentanyl in the evaluation of cervical and lumbar facet joint pain with controlled cervical and lumbar facet joint nerve blocks with an indicated evidence of Level II-1, with application of stringent criteria of at least 80% pain relief and the ability to perform previously painful movements after the diagnostic blocks.
Evaluation of an online shopping system under Preferences and Constraints

Designing interactive systems with graphic user interfaces is an important step in the development of online devices and websites. Online shopping systems and recommender applications have improved in the last decade and they are now widely used all over the world. However, it is important to understand online shoppers needs and preferences and to take them into account. In this regard, several online shopping systems rely on customer preference elicitation while others suggest products based on other customers recommendations. The focus of this paper is the interaction design of a system for Managing Preferences and Constraints (MPC) and Preferences Learning (PL). An evaluation method is utilized to obtain user feedback on how effective the system is and how easy it is to use, compared to other systems. The Volere requirements specification template was used with the six step framework to guide the evaluation.