Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagosomes can support Yersinia pseudotuberculosis replication in macrophages

Yersinia pseudotuberculosis is able to replicate inside macrophages. However, the intracellular trafficking of the pathogen after its entry into the macrophage remains poorly understood. Using in vitro infected bone marrow‐derived macrophages, we show that Y. pseudotuberculosis activates the autophagy pathway. Host cell autophagosomes subverted by bacteria do not become acidified and sustain bacteria replication. Moreover, we report that autophagy inhibition correlated with bacterial trafficking inside an acidic compartment. This study indicates that Y. pseudotuberculosis hijacks the autophagy pathway for its replication and also opens up new opportunities for deciphering the molecular basis of the host cell signalling response to intracellular Yersinia infection.
The Structural Neural Substrates of Persistent Negative Symptoms in First-Episode of Non-Affective Psychosis: A Voxel-Based Morphometry Study

Objectives: An important subset of patients with schizophrenia present clinically significant persistent negative symptoms (PNS). Identifying the neural substrates of PNS could help improve our understanding and treatment of these symptoms. Methods: This study included 64 non-affective first-episode of psychosis (FEP) patients and 60 healthy controls; 16 patients displayed PNS (i.e., at least one primary negative symptom at moderate or worse severity sustained for at least six consecutive months). Using voxel-based morphometry (VBM), we explored for gray matter differences between PNS and non-PNS patients; patient groups were also compared to controls. All comparisons were performed at p < 0.05, corrected for multiple comparisons. Results: PNS patients had smaller gray matter in the right frontal medial–orbital gyrus (extending into the inferior frontal gyrus) and right parahippocampal gyrus (extending into the fusiform gyrus) compared to non-PNS patients. Compared to controls, PNS patients had smaller gray matter in the right parahippocampal gyrus (extending into the fusiform gyrus and superior temporal gyrus); non-PNS patients showed no significant differences to controls. Conclusion: Neural substrates of PNS are evident in FEP patients. A better understanding of the neural etiology of PNS may encourage the search for new medications and/or alternative treatments to better help those affected.
AR(infty) estimation and nonparametric stochastic complexity

Let H* be the transfer function of a linear stochastic system such that H* and its inverse are in H/sup infinity /(D). Writing the system as an AR( infinity ) system, the best AR (k) approximation of the system is estimated using the method of least squares. A useful representation theorem for the parameter estimation error is presented. The effect of undermodeling and parameter uncertainty (due to estimation) on honest prediction, and the optimal choice of k, are questioned. This question is answered and the result is applied to the AR approximation of ARMA systems. The excess of the mean of the nonparametric stochastic complexity with respect to the AR class of an ARMA system with zeros less than 1/ beta in moduli is found asymptotically to be less than sigma /sup 2/log/sup 2/N/log beta after N samples. >
“I Suck at Everything”: Crime, Arrest, and the Generality of Failure

ABSTRACT In this article, we advance the idea that getting arrested amounts to “failing at crime. ” And akin to the notion of the generality of deviance—where those who engage in any given form of criminal behavior are also likely to engage in a wide array of other problematic behaviors—we examine whether failing at crime (getting arrested) is associated with other forms of life failure. Using data from multiple waves of the National Longitudinal Study of Adolescent to Adult Health, our results reveal that, independent of one’s level of self-reported criminal behavior and other key potential confounders (IQ and self-control), being arrested is a significant predictor of a host of life failures related to education, employment, relationships, and health. The key implication of our study is that it highlights the need to develop a theory of the “generality of failure. ”
Application-level isolation and recovery with solitude

When computer systems are compromised by an attack, it is difficult to determine the precise extent of the damage caused by the attack because the state changes made by an attacker and those made by regular users can be closely intertwined. This problem occurs due to implicit sharing in operating systems, and it can be especially severe for persistent state. In particular, the file system provides a single namespace that when compromised can have cascading effects on the entire system, making intrusion analysis and recovery a time-consuming and error-prone process. In this paper, we present Solitude, an application-level isolation and recovery system that is designed to both limit the effects of attacks and simplify the post-intrusion recovery process. Solitude uses a copy-on-write filesystem to provide a transparent, restricted privilege isolation environment for running untrusted applications, and it uses an explicit file sharing mechanism across the isolation environments that limits attack propagation without compromising functionality. Solitude provides two modes of recovery. If a sandboxed application proves to be untrustworthy, a course-grained recovery method allows easily removing the footprint of the software. However, if a user mistakenly moves malicious files to the trusted environment via explicit file sharing, then Solitude uses data dependency tracking to allow fine-grained recovery.
Romanized Berber and Romanized Arabic Automatic Language Identification Using Machine Learning

The identification of the language of text/speech input is the first step to be able to properly do any language-dependent natural language processing. The task is called Automatic Language Identification (ALI). Being a well-studied field since early 1960’s, various methods have been applied to many standard languages. The ALI standard methods require datasets for training and use character/word-based n-gram models. However, social media and new technologies have contributed to the rise of informal and minority languages on the Web. The state-of-the-art automatic language identifiers fail to properly identify many of them. Romanized Arabic (RA) and Romanized Berber (RB) are cases of these informal languages which are under-resourced. The goal of this paper is twofold: detect RA and RB, at a document level, as separate languages and distinguish between them as they coexist in North Africa. We consider the task as a classification problem and use supervised machine learning to solve it. For both languages, character-based 5-grams combined with additional lexicons score the best, F-score of 99.75% and 97.77% for RB and RA respectively.
Research on Multi-Carrier PWM Modulation Strategies of Three-Level Inverter

Three-level inverter is widely used in high voltage and high power occasions. In this paper, different modulation strategies used in three-level inverter are studied and analyzed. The harmonic characteristics of different modulation strategies were compared, and the respective relationship of harmonic characteristic, modulation degree and total harmonic distortion in different modulation strategies was obtained. The conclusion is validated by the results of simulation and experimentation.
Malaria “Diagnosis” and Diagnostics in Afghanistan

In many malaria-endemic areas, including Afghanistan, overdiagnosis of malaria is common. Even when using parasite-based diagnostic tests prior to treatment, clinicians commonly prescribe antimalarial treatment following negative test results. This practice neglects alternative causes of fever, uses drugs unnecessarily, and might contribute to antimalarial drug resistance. We undertook a qualitative study among health workers using different malaria diagnostic methods in Afghanistan to explore perceptions of malaria diagnosis. Health workers valued diagnostic tests for their ability to confirm clinical suspicions of malaria via a positive result, but a negative result was commonly interpreted as an absence of diagnosis, legitimizing clinical diagnosis of malaria and prescription of antimalarial drugs. Prescribing decisions reflected uncertainty around tests and diagnosis, and were influenced by social- and health-system factors. Study findings emphasize the need for nuanced and context-specific guidance to change prescriber behavior and improve treatment of malarial and nonmalarial febrile illnesses.
Adaptation-Level Phenomena and the Prevalence of Cooperation*

We conducted a computer simulation study to examine the relation between an individual-level decision process and the prevalence of self-sacrificial cooperation in large groups of interacting "individuals. " In each simulated interaction, two randomly paired individuals played a single round of the prisoner's dilemma. Individual decisions about whether or not to cooperate were made on the basis of a simple rule known as "win-stay, lose-change. " For each individual, wins and losses were defined in relation to a simulated adaptation level. The rate of adaptation was varied systematically, and we made a distinction between "upward" adaptation to gains and "downward" adaptation to losses. We found that the overall prevalence of cooperation was determined mainly by the rate of downward adaptation, whereas the rate of upward adaptation had very little effect. Moreover, we found a strongly negative relation between the prevalence of cooperation and the rate of downward adaptation. This latter finding is particularly significant in view of evidence that people generally adapt to losses slowly, for it suggests that slow downward adaptation at the individual level may fuel the
The Increased Sex Differences in Susceptibility to Emotional Stimuli during Adolescence: An Event-Related Potential Study

The present study investigated how pubertal development and sex interact to influence humans’ emotion susceptibility during adolescence. Event-related potentials were recorded for highly emotional, mildly emotional and neutral stimuli in positive and negative blocks, when 73 adolescents (36 pre-/early pubertal students, 19 boys, 10–12 years old; 37 mid-/late pubertal students, 18 boys, 11–13 years old) performed an implicit emotion task. Behavioral analysis showed higher positive mood ratings for pre-/early compared to mid-/late pubertal subjects, irrespective of sex and block. ERP analysis demonstrated increasing Late Positive Potential (LPP) amplitudes from neutral, Mildly Positive (MP) to Highly Positive (HP) stimuli in pre-/early pubertal, but not in mid-/late pubertal adolescents. However, girls exhibited higher P3a amplitudes during mid-/late relative to pre-/early puberty for negative stimuli irrespective of intensity; while this puberty effect was absent in boys. In addition, girls compared to boys exhibited a more pronounced LPP enhancement effect for Highly Negative (HN) stimuli and a lower threshold of responding to negative stimuli in P3b amplitudes, regardless of puberty. These results suggest that, though there is a puberty-independent sensitivity to negative stimuli in girls relative to boys, puberty selectively intensifies girls’ attention bias for negative stimuli and reduces experiential sensitivity to positive stimuli in both sexes. The implication of these results for the sex-related psychopathology during adolescence were discussed.
Micromachined CPW-fed suspended patch antenna for 77 GHz automotive radar applications

A new approach to high performance patch antenna at millimeter wave, especially 77 GHz of frequency for automotive applications, is introduced. The proposed antenna is composed of coplanar waveguide (CPW) feed line, a feeding post, supporting posts, and a radiating patch. The performance of antenna was improved by elevating the radiating patch in the air while remaining feed network on the high dielectric constant substrate. A 2 /spl times/ 1 array antenna was also designed with a simple feed network. The fabricated antenna showed broadband characteristics and high radiation efficiency. Measured -10 dB bandwidths were about 9.0 GHz (11.8 %) from 73.3 GHz to 82.3 GHz in single patch antenna and about 10.0 GHz (12.7 %) from 73.9 GHz to 83.9 GHz in 2 /spl times/ 1 patch array antenna. Simulated radiation efficiencies were 94 % for single patch antenna and 93 % for 2 /spl times/ 1 patch array antenna respectively.
Correction: Identification and treatment of the Staphylococcus aureus reservoir in vivo

Vol. 213, No. 7, June 27, 2016. Pages [1141–1151][1]. The authors regret that in their original paper, the y axis labels in Fig. 5 h were reversed. The corrected figure appears below. The online HTML and PDF versions of this article have been corrected. The error only remains in the print version
CONCURRENCY AND COMPUTATION : PRACTICE AND EXPERIENCE Concurrency Computat

This paper describes a technique to reliably and securely identify individual integrated circuits (ICs) based on the precise measurement of circuit delays and a simple challenge–response protocol. This technique could be used to produce key-cards that are more difficult to clone than ones involving digital keys on the IC. We consider potential venues of attack against our system, and present candidate implementations. Experiments on Field Programmable Gate Arrays show that the technique is viable, but that our current implementations could require some strengthening before it can be considered as secure. Copyright c © 2004 John Wiley & Sons, Ltd.
Design and Expression of a Dimeric Form of Human Immunodeficiency Virus Type 1 Antibody 2G12 with Increased Neutralization Potency

ABSTRACT The antigen-binding fragment of the broadly neutralizing human immunodeficiency virus type 1 (HIV-1) antibody 2G12 has an unusual three-dimensional (3D) domain-swapped structure with two aligned combining sites that facilitates recognition of its carbohydrate epitope on gp120. When expressed as an intact immunoglobulin G (IgG), 2G12 formed typical IgG monomers containing two combining sites and a small fraction of a higher-molecular-weight species, which showed a significant increase in neutralization potency (50- to 80-fold compared to 2G12 monomer) across a range of clade A and B strains of HIV-1. Here we show that the higher-molecular-weight species corresponds to a 2G12 dimer containing four combining sites and present a model for how intermolecular 3D domain swapping could create a 2G12 dimer. Based on the structural model for a 3D domain-swapped 2G12 dimer, we designed and tested a series of 2G12 mutants predicted to increase the ratio of 2G12 dimer to monomer. We report a mutation that effectively increases the 2G12 dimer/monomer ratio without decreasing the expression yield. Increasing the proportion of 2G12 dimer compared to monomer could lead to a more potent reagent for gene therapy or passive immunization.
A Reverse Approach to Named Entity Extraction and Linking in Microposts

In this paper, we present a pipeline for named entity extraction and linking that is designed specifically for noisy, grammatically inconsistent domains where traditional named entity techniques perform poorly. Our approach leverages a large knowledge base to improve entity recognition, while maintaining the use of traditional NER to identify mentions that are not co-referent with any entities in the knowledge base
Electric Field Effects on Photoluminescence of CdSe Nanoparticles in a PMMA Film

External electric field effects on spectra and decay of photoluminescence (PL) as well as on absorption spectra were measured for CdSe nanoparticles in a poly(methyl methacrylate) (PMMA) film. Electrophotoluminescence (E-PL) spectra as well as electroabsorption spectra show a remarkable Stark shift which depends on the particle size, indicating a large electric dipole moment in the first exciton state. The E-PL spectra also show that PL of CdSe is quenched by application of electric fields, and the magnitude of the field-induced quenching becomes larger with increasing size. The PL decay profiles observed in the absence and presence of electric field show that the field-induced quenching of PL mainly originates from the field-induced decrease in population of the emitting state prepared through the relaxation from the photoexcited state.
CD4 Independence of Simian Immunodeficiency Virus Envs Is Associated with Macrophage Tropism, Neutralization Sensitivity, and Attenuated Pathogenicity

ABSTRACT To investigate the basis for envelope (Env) determinants influencing simian immunodeficiency virus (SIV) tropism, we studied a number of Envs that are closely related to that of SIVmac239, a pathogenic, T-tropic virus that is neutralization resistant. The Envs from macrophage-tropic (M-tropic) virus strains SIVmac316, 1A11, 17E-Fr, and 1100 facilitated infection of CCR5-positive, CD4-negative cells. In contrast, the SIVmac239 Env was strictly dependent upon the presence of CD4 for membrane fusion. We also found that the Envs from M-tropic virus strains, which are less pathogenic in vivo, were very sensitive to antibody-mediated neutralization. Antibodies to the V3-loop, as well as antibodies that block SIV gp120 binding to CCR5, efficiently neutralized CD4-independent, M-tropic Envs but not the 239 Env. However, triggering the 239 Env with soluble CD4, presumably resulting in exposure of the CCR5 binding site, made it as neutralization sensitive as the M-tropic Envs. In addition, mutations of N-linked glycosylation sites in the V1/V2 region, previously shown to enhance antigenicity and immunogenicity, made the 239 Env partially CD4 independent. These findings indicate that Env-based determinants of M tropism of these strains are generally associated with decreased dependence on CD4 for entry into cells. Furthermore, CD4 independence and M tropism are also associated with neutralization sensitivity and reduced pathogenicity, suggesting that the humoral immune response may exert strong selective pressure against CD4-independent M-tropic SIVmac strains. Finally, genetic modification of viral Envs to enhance CD4 independence may also result in improved humoral immune responses.
Genome-wide association study for pigmentation traits in Chinese Holstein population.

With the Illumina BovineSNP50K BeadChip, we performed a genome-wide association study (GWAS) for two pigmentation traits in a Chinese Holstein population: proportion of black (PB) and teat colour (TC). A case-control design was used. Cases were the cows with PB <0.30 (n = 129) and TC <2 points (n = 140); controls were those with PB >0.90 (n = 58) and TC >4 points (n = 281). The RM test of roadtrips (version 1.2) was applied to detect SNPs for the two traits with 42 883 and 42 741 SNPs respectively. A total of nine and 12 genome-wide significant (P < 0.05) SNPs associated with PB and TC respectively were identified. Of these, two SNPs for PB were located within the KIT and IGFBP7 genes, and the other four SNPs were 23~212 kb away from the PDGFRA gene on BTA6; nine SNPs associated with TC were located within or 21~78.8 kb away from known genes on chromosomes 4, 11, 22, 23 and 24. By combing through our GWAS results and the biological functions of the genes, we suggest that the KIT, IGFBP7, PDGFRA, MITF, ING3 and WNT16 genes are promising candidates for PB and TC in Holstein cattle, providing a basis for further investigation on the genetic mechanism of pigmentation formation.
Eomesoderminlo CTLA4hi Alloreactive CD8+ Memory T Cells Are Associated With Prolonged Renal Transplant Survival Induced by Regulatory Dendritic Cell Infusion in CTLA4 Immunoglobulin–Treated Nonhuman Primates

Background Memory T cells (Tmem), particularly those resistant to costimulation blockade (CB), are a major barrier to transplant tolerance. The transcription factor Eomesodermin (Eomes) is critical for Tmem development and maintenance, but its expression by alloactivated T cells has not been examined in nonhuman primates. Methods We evaluated Eomes and coinhibitory cytotoxic T lymphocyte antigen-4 (CTLA4) expression by alloactivated rhesus monkey T cells in the presence of CTLA4 immunoglobulin, both in vitro and in renal allograft recipients treated with CTLA4Ig, with or without regulatory dendritic cell (DCreg) infusion. Results In normal monkeys, CD8+ T cells expressed significantly more Eomes than CD4+ T cells. By contrast, CD8+ T cells displayed minimal CTLA4. Among T cell subsets, central Tmem (Tcm) expressed the highest levels of Eomes. Notably, EomesloCTLA4hi cells displayed higher levels of CD25 and Foxp3 than EomeshiCTLA4lo CD8+ T cells. After allostimulation, distinct proliferating EomesloCTLA4hi and EomeshiCTLA4lo CD8+ T cell populations were identified, with a high proportion of Tcm being EomesloCTLA4hi. CB with CTLA4Ig during allostimulation of CD8+ T cells reduced CTLA4 but not Eomes expression, significantly reducing EomesloCTLA4hi cells. After transplantation with CB and rapamycin, donor-reactive EomesloCTLA4hi CD8+ T cells were reduced. However, in monkeys also given DCreg, absolute numbers of these cells were elevated significantly. Conclusions Low Eomes and high CTLA4 expression by donor-reactive CD8+ Tmem is associated with prolonged renal allograft survival induced by DCreg infusion in CTLA4Ig-treated monkeys. Prolonged allograft survival associated with DCreg infusion may be related to maintenance of donor-reactive EomesloCTLA4hi Tcm.
RICE: rapid interconnect circuit evaluation using AWE

This paper describes the Rapid Interconnect Circuit Evaluator (RICE) software developed specifically to analyze RC and RLC interconnect circuit models of virtually any size and complexity. RICE focuses specifically on the passive interconnect problem by applying the moment-matching technique of Asymptotic Waveform Evaluation (AWE) and application-specific circuit analysis techniques to yield large gains in run-time efficiency over circuit simulation without sacrificing accuracy. Moreover, this focus of AWE on passive interconnect problems permits the use of moment-matching techniques that produce stable, pre-characterized, reduced-order models for RC and RLC interconnects. RICE is demonstrated to be as accurate as a transient circuit simulation with hundreds or thousands of times the efficiency. The use of RICE is demonstrated on several VLSI interconnect and off-chip microstrip models. >
Development of an Adaptive Tsetse Population Management Scheme for the Luke Community, Ethiopia

Abstract Since 1996, tsetse (Glossina spp.) control operations, using odor-baited traps, have been carried out in the Luke area of Gurage zone, southwestern Ethiopia. Glossina morsitans submorsitans Newstead was identified as the dominant species in the area, but the presence of Glossina fuscipes Newstead and Glossina pallidipes Austen also was recorded. Here, we refer to the combined number of these three species and report the work undertaken from October 2002 to October 2004 to render the control system more efficient by reducing the number of traps used and maintaining the previously reached levels of tsetse occurrence and trypanosomiasis prevalence. This was done by the design and implementation of an adaptive tsetse population management system. It consists first of an efficient community-participatory monitoring scheme that allowed us to reduce the number of traps used from 216 to 127 (107 monitoring traps and 20 control traps). Geostatistical methods, including kriging and mapping, furthermore allowed identification and monitoring of the spatiotemporal dynamics of patches with increased fly densities, referred to as hot spots. To respond to hot spots, the Luke community was advised and assisted in control trap deployment. Adaptive management was shown to be more efficient than the previously used mass trapping system. In that context, trap numbers could be reduced substantially, at the same time maintaining previously achieved levels of tsetse occurrences and disease prevalence.