Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Stable, Soluble Trimers Containing Complete Ectodomains of Human Immunodeficiency Virus Type 1 Envelope Glycoproteins

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins function as a membrane-anchored trimer of three gp120 exterior glycoproteins and three gp41 transmembrane glycoproteins. Previously, we reported three approaches to stabilize soluble trimers containing parts of the gp41 ectodomains: addition of GCN4 trimeric helices, disruption of the cleavage site between gp120 and gp41, and introduction of cysteines in the gp41 coiled coil to form intersubunit disulfide bonds. Here, we applied similar approaches to stabilize soluble gp140 trimers including the complete gp120 and gp41 ectodomains. A combination of fusion with the GCN4 trimeric sequences and disruption of the gp120-gp41 cleavage site resulted in relatively homogeneous gp140 trimers with exceptional stability. The gp120 epitopes recognized by neutralizing antibodies are intact and exposed on these gp140 trimers. By contrast, the nonneutralizing antibody epitopes on the gp120 subunits of the soluble trimers are relatively occluded compared with those on monomeric gp120 preparations. This antigenic similarity to the functional HIV-1 envelope glycoproteins and the presence of the complete gp41 ectodomain should make the soluble gp140 trimers useful tools for structural and immunologic studies.
Empowerment Online: Feminist Adult Learning Strategies

The purpose of this is to investigate how adult female learners constitute their perceptions of self and learning behavior in an internet learning environment—weblog. Based on previous qualitative research method and literature review, this study intended to develop and validate a feminist adult learning strategy scale (FALSS) to understand the women’s learning strategy by applying weblogs. 417 valid data from the participants in two studies (exploratory and confirmatory factor analysis) were analyzed for the purpose. The results of these studies supported a 15-item, 4-factor FALSS: Empowerment Attempt, Sharing Expe- riences, Participatory Learning, and Critical Thinking and Open-Mindedness.
Distracted While Reading? Changing to a Hard-to-Read Font Shields against the Effects of Environmental Noise and Speech on Text Memory

The purpose of this study was to investigate the distractive effects of background speech, aircraft noise and road traffic noise on text memory and particularly to examine if displaying the texts in a hard-to-read font can shield against the detrimental effects of these types of background sounds. This issue was addressed in an experiment where 56 students read shorter texts about different classes of fictitious creatures (i.e., animals, fishes, birds, and dinosaurs) against a background of the aforementioned background sounds respectively and silence. For half of the participants the texts were displayed in an easy-to-read font (i.e., Times New Roman) and for the other half in a hard-to-read font (i.e., Haettenschweiler). The dependent measure was the proportion correct answers on the multiple-choice tests that followed each sound condition. Participants’ performance in the easy-to-read font condition was significantly impaired by all three background sound conditions compared to silence. In contrast, there were no effects of the three background sound conditions compared to silence in the hard-to-read font condition. These results suggest that an increase in task demand—by displaying the text in a hard-to-read font—shields against various types of distracting background sounds by promoting a more steadfast locus-of-attention and by reducing the processing of background sound.
Development and validation of a positive and negative affect scale

The aim of this study was to construct a positive and negative affect scale (AS) and to search for validity evidence. The participants were 850 undergraduate students from southern Brazil, 57% female, with a mean age of 21 years (SD=3). A factor analysis extracted two factors: positive affect (PA) and negative affect (NA). The first one presented an eigenvalue of 5.1 explaining 25.6% of the total variance; the second factor presented an eigenvalue of 2,6 explaining 12.8% of the total variance. The internal consistency for PA was . 83, and . 77 for NA. High correlations between the two factors of the AS and PANAS were observed: . 73 for PA and . 74 for NA. It was also observed that PA had positive correlations with life satisfaction, hope, optimism, and self-esteem while NA presented negative correlations with those variables. These results indicate evidences of construct validity and appropriate psychometric properties.
Deterministic packet marking for max-min flow control

This letter proposes a deterministic packet marking scheme that estimates the maximum link price on a communication path. The proposed scheme is simple and IP-compatible because it uses two-bit explicit congestion notification (ECN) field and IP identification (IPid) field in the standard IP header for the estimation. Through simulations using real IP packet traces, we show that our scheme indeed works as designed with small estimation errors, and thus enables existing max-min flow control algorithms to serve their purpose without the need of separate out-of-band control packets to carry link prices.
Characterizing context‐dependent differential firing activity in the hippocampus and entorhinal cortex

The rat hippocampus and entorhinal cortex have been shown to possess neurons with place fields that modulate their firing properties under different behavioral contexts. Such context‐dependent changes in neural activity are commonly studied through electrophysiological experiments in which a rat performs a continuous spatial alternation task on a T‐maze. Previous research has analyzed context‐based differential firing during this task by describing differences in the mean firing activity between left‐turn and right‐turn experimental trials. In this article, we develop qualitative and quantitative methods to characterize and compare changes in trial‐to‐trial firing rate variability for sets of experimental contexts. We apply these methods to cells in the CA1 region of hippocampus and in the dorsocaudal medial entorhinal cortex (dcMEC), characterizing the context‐dependent differences in spiking activity during spatial alternation. We identify a subset of cells with context‐dependent changes in firing rate variability. Additionally, we show that dcMEC populations encode turn direction uniformly throughout the T‐maze stem, whereas CA1 populations encode context at major waypoints in the spatial trajectory. Our results suggest scenarios in which individual cells that sparsely provide information on turn direction might combine in the aggregate to produce a robust population encoding. © 2014 Wiley Periodicals, Inc.
Glycosylation of Wall Teichoic Acid in Staphylococcus aureus by TarM*

Wall teichoic acid (WTA) glycopolymers are major constituents of cell envelopes in Staphylococcus aureus and related Gram-positive bacteria with important roles in cell wall maintenance, susceptibility to antimicrobial molecules, biofilm formation, and host interaction. Most S. aureus strains express polyribitol phosphate WTA substituted with d-alanine and N-acetylglucosamine (GlcNAc). WTA sugar modifications are highly variable and have been implicated in bacteriophage susceptibility and immunogenicity, but the pathway and enzymes of staphylococcal WTA glycosylation have remained unknown. Revisiting the structure of S. aureus RN4220 WTA by NMR analysis revealed the presence of canonical polyribitol phosphate WTA bearing only α-linked GlcNAc substituents. A RN4220 transposon mutant resistant to WTA-dependent phages was identified and shown to produce altered WTA, which exhibited faster electrophoretic migration and lacked completely the WTA α-GlcNAc residues. Disruption of a gene of unknown function, renamed tarM, was responsible for this phenotype. Recombinant TarM was capable of glycosylating WTA in vitro in a UDP-GlcNAc-dependent manner, thereby confirming its WTA GlcNAc-transferase activity. Deletion of the last seven amino acids from the C terminus abolished the activity of TarM. tarM-related genes were found in the genomes of several WTA-producing bacteria, suggesting that TarM-mediated WTA glycosylation is a general pathway in Gram-positive bacteria. Our study represents a basis for dissecting the biosynthesis and function of glycosylated WTA in S. aureus and other bacteria.
Ultrasound-Guided Steroid Injections for Two Painful Neuromas in the Stump of a Below-Elbow Amputee.

From the Department of Physical Medicine & Rehabilitation, Keelung Hospital, Ministry of Health and Welfare, Keelung, Taiwan (Y-HH); Department of Physical Medicine and Rehabilitation, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan (C-HW, T-GW); and Department of Physical Medicine and Rehabilitation, Hacettepe University Medical School, Ankara, Turkey (LÖ).
Work-Efficient Parallel and Incremental Graph Connectivity

On an evolving graph that is continuously updated by a high-velocity stream of edges, how can one efficiently maintain if two vertices are connected? This is the connectivity problem, a fundamental and widely studied problem on graphs. We present the first shared-memory parallel algorithm for incremental graph connectivity that is both provably work-efficient and has polylogarithmic parallel depth. We also present a simpler algorithm with slightly worse theoretical properties, but which is easier to implement and has good practical performance. Our experiments show a throughput of hundreds of millions of edges per second on a $20$-core machine.
Using Bayesian Networks for Candidate Generation in Consistency-based Diagnosis

Consistency-based diagnosis relies heavily on the assumption that discrepancies between model predictions and sensor observations can be detected accurately. When sources of uncertainty like sensor noise and model abstraction exist robust schemes have to be designed to make a binary decision on whether predictions are consistent with observations. This risks the occurrence of false alarms and missed alarms when an erroneous decision is made. Moreover when multiple sensors (with differing sensing properties) are available the degree of match between predictions and observations can be used to guide the search for fault candidates. In this paper we propose a novel approach to handle this problem using Bayesian networks. In the consistency- based diagnosis formulation, automatically generated Bayesian networks are used to encode a probabilistic measure of fit between predictions and observations. A Bayesian network inference algorithm is used to compute most probable fault candidates.
Estimation and Inference for Di ¤ erence-InDi ¤ erence Regressions with Persistent Errors

This paper is concerned with estimation and inference for di¤erence-in-di¤erence regressions with errors that exhibit high serial dependence, including near unit roots, unit roots and linear trends. We propose a couple of solutions based on a parametric formulation of the error covariance. First stage estimates of autoregressive structures are obtained by using the Han, Phillips and Sul (2011, 2013a) X-di¤erencing transformation. The X-di¤erencing method is simple to implement and is unbiased in large N settings. Compared to similar parametric methods, the approach is computationally simple and requires fewer restrictions on the permissible parameter space of the error process. Simulations suggest that our methods perform well in the nite sample across a wide range of panel dimensions and dependence structures. KeyWords: Treatment E¤ects, Di¤erence-in-Di¤erence Estimation, Serial Dependence, X-di¤erencing, Cochrane-Orcutt Transformation JEL Classi cation: C33 This paper is written for the presentation at the 14th Advances in Econometrics Conference in honor of Peter C.B. Phillips at Southern Methodist University on November 1-3, 2013. We thank Tom Fomby for organizing the conference and Yoosoon Chang and Joon Y. Park for preparing the conference program. We also thank Badi Baltagi for helpful comments.
Modeling neuroendocrine stress reactivity in salivary cortisol: adjusting for peak latency variability

Abstract In this report, we present growth curve modeling (GCM) with landmark registration as an alternative statistical approach for the analysis of time series cortisol data. This approach addresses an often-ignored but critical source of variability in salivary cortisol analyses: individual and group differences in the time latency of post-stress peak concentrations. It allows for the simultaneous examination of cortisol changes before and after the peak while controlling for timing differences, and thus provides additional information that can help elucidate group differences in the underlying biological processes (e.g. intensity of response, regulatory capacity). We tested whether GCM with landmark registration is more sensitive than traditional statistical approaches (e.g. repeated measures ANOVA – rANOVA) in identifying sex differences in salivary cortisol responses to a psychosocial stressor (Trier Social Stress Test –TSST) in healthy adults (mean age 23). We used plasma ACTH measures as our “standard” and show that the new approach confirms in salivary cortisol the ACTH finding that males had longer peak latencies, higher post-stress peaks but a more intense post-peak decline. This finding would have been missed if only saliva cortisol was available and only more traditional analytic methods were used. This new approach may provide neuroendocrine researchers with a highly sensitive complementary tool to examine the dynamics of the cortisol response in a way that reduces risk of false negative findings when blood samples are not feasible.
I. Problems and Designs of Cross-Validation 1

THE term &dquo;cross-validation&dquo; is often loosely applied to any one of several distinct, though closely related, experimental designs. Before we get lost in a swamp of semantic confusion, it may be well to identify each of these, to point out their similarities and differences and to make clear the objectives which it serves. What name we give to each is secondary, although for convenience I shall attach a different name to each.
Validation of Ultrastructural Analysis of Mitochondrial Deposits in Cardiomyocytes as a Method of Detecting Early Acute Myocardial Infarction in Humans *

Abstract: In the present study, ultrastructural analysis of mitochondrial deposits (black dots within mitochondria) as a method for the detection of early acute myocardial infarction (AMI) was evaluated. In 24 patients with AMI and six controls, analysis was performed in the heart of infarcted patients and noninfarcted controls. In the infarction area in lactate dehydrogenase (LDH)‐diagnosed AMI, the percentage of positive mitochondria was significantly higher compared to corresponding heart tissue in control patients and compared to noninfarcted areas within these patients. Also in patients with a clinically diagnosed AMI but no LDH decoloration, a significant higher percentage of positive mitochondria was found in the left ventricle compared to controls and noninfarcted areas. In patients with AMI, an increase in mitochondria with deposits was found in the infarction area compared to controls and noninfarcted tissue within the same patient, suggesting that electron microscopical changes in mitochondria can be used for the diagnosis of AMI less than 3 h old.
The Universal Welfare State: Theory and the Case of Sweden

In the existing literature on welfare state typologies, the concept of the universal welfare state is not defined precisely enough to allow for comparisons of universality over time and between countries. In this paper, I discuss some problems with the way the term ‘the universal welfare state’ has been used and I suggest possible solutions. Among other things, I propose that the term ‘universality’ be used to describe the provision of a specific welfare benefit independently of individual income and/or other individual characteristics. It should also be used to describe the coverage of welfare benefits rather than their size. Based on the theoretical discussion, a number of possible indicators of universality are applied to the case of Sweden in the 1990s. The conclusion is that, despite its economic crisis, universality in Sweden did not decrease.
Dual processes, evolution and rationality

In this fascinating book, Keith Stanovich combines two big ideas: the selfish gene hypothesis of Dawkins (1976) and a strong form of the dual process theory of reasoning (see Evans, 2003). The consequence is an intriguing argument that, while Dawkins is generally correct in arguing that organisms act as mere vehicles of their replicators (genes), humans alone have to ability to break out from this ‘‘evolutionary rationality’’ and to pursue their own goals. Dual process theory is the key here. Stanovich believes that an analytic system of thinking evolved uniquely in humans and at a ‘‘long leash’’ from the genes. Hence, we alone can think and act for ourselves. The thesis is illustrated early in the book by the following thought experiment. Suppose (in some future world) that you decide to have your body frozen for 300 years in the hope that a cure for death will have been found. How should you arrange for your body to be looked after in the meantime? You could have it located in a secure institution protected by current laws. But a lot can happen in 300 years. It might be damaged by war or accident, or demolished by some developer who succeeds in getting the law changed. Perhaps it would be safer to build a robot to carry your body around: it would be programmed to keep you safe at all times. Now the problem is that you cannot anticipate all the difficulties that the robot may encounter. Hence, you program the robot with general reasoning and problem-solving abilities so that it can deal with novel problems and keep you safe. Of course, you expect the robot to sacrifice itself if necessary to protect you. However, there is a difficulty in this scenario. You have made the robot so smart that it can think for itself. What if it decides to pursue its own goals rather than yours? What if the robot rebels? In reality, of course, you are the robot and the genes the designer.
MIMO FIR feedforward design for zero error tracking control

This paper discusses a multi-input multi-output (MIMO) finite impulse response (FIR) feedforward design. The design is intended for systems that have (non-)minimum phase zeros in the plant description. The zeros of the plant (either minimum or non-minimum phase) are used in the shaping of the reference signals whereas the poles of the plant are used in constructing feedforward forces. The FIR coefficients themselves are obtained from data-based optimizations which are the result of iterative machine measurements on an industrial wafer scanner. The resulting experimental results demonstrate the ability to obtain zero error tracking.
Self-Assessment and Reflection: Tools for Promoting Teacher Changes Toward Learner-Centered Practices

Teachers need self-assessment and reflection tools to help them assess fundamental beliefs and assumptions about learning, learners, and teaching, as well as differences between their perceptions of practice and those held by students in their classroom. A process of reflection will help to identify the personal characteristics and practices that must change to improve motivation and achievement for each student.
Naming or defining? On the necessity of reduction in religious studies

Although debate continues over the place of reductionist and non‐reductionist approaches within the academic study of religion, much of the debate falters due to a failure to appreciate the necessity of ‘understanding’ for the effectiveness of ‘explaining’ cultural phenomena. This article addresses this very problem, reassessing the role of the insider within a methodological reductionist approach within religious studies. Assessing the delimitation of critical analysis to ‘knowable knowledge’ construction, teasing out theoretical problems with verification, and recognising the role of data construction in first‐order description prior to second‐order theorisation, this article will argue that the insider’s perspective is indeed an essential aspect of the critical analytical approach. Unlike phenomenological or irreductive approaches, however, the insider's perspective is limited to the stage of data construction (‘understanding’). At the secondary level of theorisation, the relative relations bringing together data within an analytical study takes precedence (‘explanation’). Thus, within a methodological reductionist approach (distinguished from ontological reductionism), there can be no explanation without understanding.
Tomlinson–Harashima Precoding for Multiuser MIMO Systems With Quantized CSI Feedback and User Scheduling

This paper studies the sum rate performance of a low complexity quantized CSI-based Tomlinson-Harashima (TH) precoding scheme for downlink multiuser MIMO transmission, employing greedy user selection. The asymptotic distribution of the output-signal-to-interference-plus-noise ratio of each selected user and the asymptotic sum rate as the number of users K grows large are derived by using extreme value theory. For fixed finite signal-to-noise ratios and a finite number of transmit antennas nT, we prove that as K grows large, the proposed approach can achieve the optimal sum rate scaling of the MIMO broadcast channel. We also prove that, if we ignore the precoding loss, the average sum rate of this approach converges to the average sum capacity of the MIMO broadcast channel. Our results provide insights into the effect of multiuser interference caused by quantized CSI on the multiuser diversity gain.
Stimulation of FcγRI on Primary Sensory Neurons Increases Insulin-Like Growth Factor-I Production, Thereby Reducing Reperfusion-Induced Renal Injury in Mice

Biological role(s) of FcγRI on mouse primary sensory neurons are not fully understood. Sensory neuron stimulation increases insulin-like growth factor-I (IGF-I) production, thereby reducing ischemia/reperfusion (I/R)-induced tissue injury in mice. In this study, we examined whether the Fc fragment of IgG (IgGFc) increases IGF-I production through sensory neuron stimulation, thereby reducing I/R-induced renal injury in mice. IgGFc increased the calcitonin-gene–related peptide (CGRP) release and cellular cAMP levels in dorsal root ganglion neurons isolated from wild-type (WT) mice, whereas, native IgG did not. Pretreatment with anti-FcγRI Ab, a protein kinase A inhibitor KT5710, and a phospholipase A2 inhibitor 4-bromophenylacyl bromide inhibited these effects induced by IgGFc. Administration of IgGFc enhanced increases of renal tissue levels of CGRP and IGF-I and reduced I/R-induced renal injury in WT mice. Increases of renal tissue level of caspase-3, renal accumulation of neutorphils, and renal tubular apoptosis were inhibited by administration of IgGFc in WT mice subjected to renal I/R. Pretreatment with anti–IGF-I Ab completely reversed these effects induced by IgGFc in WT mice. Administration of native IgG did not show any effects in WT mice subjected to renal I/R. None of the effects observed in WT mice was seen after IgGFc administration in CGRP-knockout mice and denervated WT mice. These observations suggest that activation of FcγRI by IgGFc may stimulate sensory neurons, thereby promoting IGF-I production, contributing to reduction of the reperfusion-induced renal injury via attenuation of inflammatory responses in mice.