Miracle-dz/UniFAR-FTUs huggingface dataset:
Somatic Populations of PGT135–137 HIV-1-Neutralizing Antibodies Identified by 454 Pyrosequencing and Bioinformatics

Select HIV-1-infected individuals develop sera capable of neutralizing diverse viral strains. The molecular basis of this neutralization is currently being deciphered by the isolation of HIV-1-neutralizing antibodies. In one infected donor, three neutralizing antibodies, PGT135–137, were identified by assessment of neutralization from individually sorted B cells and found to recognize an epitope containing an N-linked glycan at residue 332 on HIV-1 gp120. Here we use next-generation sequencing and bioinformatics methods to interrogate the B cell record of this donor to gain a more complete understanding of the humoral immune response. PGT135–137-gene family specific primers were used to amplify heavy-chain and light-chain variable-domain sequences. Pyrosequencing produced 141,298 heavy-chain sequences of IGHV4-39 origin and 87,229 light-chain sequences of IGKV3-15 origin. A number of heavy and light-chain sequences of ∼90% identity to PGT137, several to PGT136, and none of high identity to PGT135 were identified. After expansion of these sequences to include close phylogenetic relatives, a total of 202 heavy-chain sequences and 72 light-chain sequences were identified. These sequences were clustered into populations of 95% identity comprising 15 for heavy chain and 10 for light chain, and a select sequence from each population was synthesized and reconstituted with a PGT137-partner chain. Reconstituted antibodies showed varied neutralization phenotypes for HIV-1 clade A and D isolates. Sequence diversity of the antibody population represented by these tested sequences was notably higher than observed with a 454 pyrosequencing-control analysis on 10 antibodies of defined sequence, suggesting that this diversity results primarily from somatic maturation. Our results thus provide an example of how pathogens like HIV-1 are opposed by a varied humoral immune response, derived from intrinsic mechanisms of antibody development, and embodied by somatic populations of diverse antibodies.
The UPV at GeoCLEF 2007

In this work we attempted to determine the relative importance of the geographical and WordNet-extracted terms with respect to the remainder of the query. Our system is based on Lucene and uses LingPipe for Named Entity recognition. Geographical terms are expanded with WordNet holonyms and synonyms and indexed separately. We checked the relative importance of the terms by boosting them with reduction factors (0.75, 0.5 and 0.25). The comparison to the clean system (using only Lucene) shows that it is possible to improve the mean average precision if the importance of geographical terms is equal or less than the half with respect to the content words in the query. We also observed that WordNet holonyms may help in improving the recall but the term expansion is sensible to ambigue place names. As a further work, we will need to implement a toponym disambiguation method in order to reduce the impact of this kind of ambiguity.
Enabling OpenVX support in mW-scale parallel accelerators

mW-scale parallel accelerators are a promising target for application domains such as the Internet of Thing (IoT), which require a strong compliance with a limited power budget combined with high performance capabilities. An important use case is given by smart sensing devices featuring increasingly sophisticated vision capabilities, at the cost of an increasing amount of near-sensor computation power. OpenVX is an emerging standard for the embedded vision, and provides a C-based application programming interface and a runtime environment. OpenVX is designed to maximize functional and performance portability across diverse hardware platforms. However, state-of-the-art implementations rely on memory-hungry data structures, which cannot be supported in constrained devices. In this paper we propose an alternative and novel approach to provide OpenVX support in mW-scale parallel accelerators. Our main contributions are: (i) an extension to the original OpenVX model to support static management of application graphs in the form of binary files; (ii) the definition of a companion run-time environment providing a lightweight support to execute binary graphs in a resource-constrained environment. Our approach achieves 68% memory footprint reduction and 3× execution speed-up compared to a baseline implementation. At the same time, data memory bandwidth is reduced by 10% and energy efficiency is improved by 2×.
General packet radio service in GSM

In the Global System for Mobile Communications (GSM) Phase 2+ development, one major activity is to specify the general packet radio service (GPRS). The standardization is expected to be completed at the end of 1997. The purpose of GPRSI like other packet data services, is to efficiently accommodate data sources that are bursty in nature. Another important goal of the technology is to make it possible for GSM license holders to share physical resources on a dynamic, flexible basis between packet data services and other GSM services. The authors present a detailed description of the GPRS system, emphasizing the radio link protocol, and demonstrate its performance. The performance measures have been obtained from the WINLAB GPRS simulator.
Exploring ‘near’: Characterizing the spatial extent of drinking place influence on crime

The important role of facilities in understanding crime patterns is widely recognized. Studies have demonstrated a connection between the presence of facilities such as bars, parks, schools and fast food restaurants and higher crime rates. Typically, these studies use a single distance threshold. Areas within the threshold are assumed to be related to the facility and those outside the threshold unrelated. But the choice of threshold in each study is usually an ad hoc decision based on the expertise of the researcher. Until recently, there has been no systematic evaluation of the methodology used to define those thresholds. This paper evaluates two methods for determining an empirically-based answer to the question ‘How close is “near”? ’ The results of an example analysis testing the association of drinking places and crime in Seattle, Washington are reported. The two most common facility-based measures, Euclidean distance buffers and Street distance buffers are compared across two levels of aggregation and 18 separate distances. Findings indicate the geographic extent of increased crime around drinking places varies based on the type of buffer (Euclidean vs. Street distance) and the width of the distance bands (street block vs. 402 meter (quarter mile) increments). The geographic extent of the influence of drinking places on crime is best captured by street distance measures across street block distances (122 meter bands). Implications of these findings for theory and practice are discussed.
Integrating Fragmented Objects into a CORBA Environment

The design of distributed applications based on a fragmented object model has many benefits. Unlike traditional middleware with a RPC-based client-server interaction, the implementation of a fragmented object may be distributed over an arbitrary number of fragments, without restrictions on internal structure or interaction, while maintaining a transparent, standardized interface on the outside. In this paper we describe a middleware system that integrates the concept of fragmented objects into a CORBA environment. Our fragmented objects support implicit binding using the ORB’s marshalling mechanism by defining customized IOR profiles, while full interoperability with traditional CORBA applications is maintained. Furthermore, we show that a broad range of tasks in distributed systems can be solved elegantly using a fragmented object approach. Our own CORBA middleware AspectIX implements the described functionality.
Elites Tweet to Get Feet Off the Streets: Measuring Regime Social Media Strategies During Protest

As non-democratic regimes have adapted to the proliferation of social media, they have began actively engaging with Twitter to enhance regime resilience. Using data taken from the Twitter accounts of Venezuelan legislators during the 2014 anti-Maduro protests in Venezuela, we fit a topic model on the text of the tweets and analyze patterns in hashtag use by the two coalitions. We argue that the regime’s best strategy in the face of an existential threat like the narrative developed by La Salida and promoted on Twitter was to advance many competing narratives that addressed issues unrelated to the opposition’s criticism. Our results show that the two coalitions pursued different rhetorical strategies in keeping with our predictions about managing the conflict advanced by the protesters. This article extends the literature on social media use during protests by focusing on active engagement with social media on the part of the regime. This approach corroborates and expands on recent research on inferring regime strategies from propaganda and censorship.
Immediate early gene expression in medial prefrontal cortex and hippocampus as a function of aging

Normal aging is accompanied by cognitive decline that differs from other aging-related pathological states like Alzheimer's disease. With an increasing proportion of the world population falling in an age group of 65 years and above, a preventive gerontological approach would improve the quality of life in the elderly. Especially important in this regard is the early detection of cognitive decline, so that appropriate measures can be taken to prevent development of cognitive deficits. Impairment in cognitive flexibility, the ability to modify a previously learnt behavior, is one such measure of impairment across species in aged animals. Previous work from our lab has demonstrated that a cognitive flexibility deficit, as measured by extinction of conditioned fear, first emerges in middle-aged animals. Extinction of conditioned fear requires coordinated activity of infralimbic (IL) and prelimbic (PL) subregions of prefrontal cortex, dorsal and ventral hippocampus, and various amygdala sub nuclei. Of these, prefrontal cortex-and hippocampus-dependent behaviors are impaired during aging, indicating that aging-related impairments within these structures could underlie extinction deficits during iii aging. One way to measure region-specific neuronal activation is through analysis of immediate early gene (IEG) expression. IEG expression at rest is not random but reflects ongoing memory consolidation. The role of IEGs as markers of neuronal plasticity and their critical role in memory consolidation make them ideal markers for investigating early cognitive decline. The current study investigated aging-related changes in the expression of IEGs, Zif-268 and Arc in the IL and PL subregions of the mPFC in addition to dorsal and ventral hippocampus. Specifically, the current study used western blotting and immunohistochemistry to investigate region-specific expression of the IEGs Zif-268 and Arc in naive adult, middle-aged and aged animals. We found that Zif-268 expression was reduced in IL, PL, CA1 and DG of dorsal hippocampus and DG of ventral hippocampus starting middle-age. In addition, Arc expression was reduced in IL but not PL in aged rodents. Within hippocampus, Arc expression was reduced within dorsal but not ventral subregion starting middle age. These data indicate that IEG expression changes are region-specific, can be evident starting middle age and may contribute to behavioral deficits during the aging process.
All voucher specimens are not created equal: a cautionary tale involving North American pleurocerid gastropods

Although the now routine use of DNA sequences has revolutionized biodiversity research, the taxonomic reliability of these data is a concern, because a significant percentage of sequences in public DNA databases may be misidentified (Bridge et al., 2003). This problem can be minimized through the use of sequences generated from voucher-based taxonomic studies. However, voucher-based reference systems may occasionally fail. Here we document a recent such case and propose two precautionary steps that may help minimize this problem for malacologists in the future. A recent research note (Lee et al., 2006) presented robust nuclear and mitochondrial phylogenetic evidence that the western North American pleurocerid gastropod, Juga hemphilli (Henderson, 1935), belongs to the eastern genus Elimia and is, according to the nuclear marker, sister to Elimia livescens (Menke, 1830). The analysed specimens came from two Florida Museum of Natural History lots collected at the type locality of J. hemphilli dallesensis (Henderson, 1935). One (FLMNH 267703) consisted of dried adult shells unsuitable for genotyping and the other (FLMNH 280708) was composed of
Social and private valuations of commercial photovoltaic systems in Australia

Commercial distributed PV systems present different economic values for each stakeholders in the electricity industry. While societal valuations are driven by PV performance and environmental cost, the private value depend on commercial arrangements between participants and PV policies. These estimations can play an important role helping to tailor PV policies that maximize PV benefits for industry participants. In this paper we assess the current and future social and private value of a particular commercial PV system for the society, retailers, DNSPs and PV customers using different pricing arrangements and carbon cost scenarios. Our results show that the economic value varies considerably for stakeholders, that the system is socially beneficial and that payback periods for PV owners range from 8 to 10 years.
The price formation of substitute markets : Theory and empirical application

Two related issues are seldom jointly addressed in the cross market price discovery literature: i) a model that focuses on non-price parameter, ii) testing a non-price parameter model against a price parameter model. We have two objectives in this paper. First, develop a joint trade direction model (JTDM) from the single market model in Madhavan, Richardson and Roomans (1997). Second, estimate and test the JTDM against the Gonzalo and Granger (1995) VECM measure of price discovery. By doing so, we test the relevance of trade direction against quote change in cross-market price formation. The estimation of 20 Chinese twin-board rms reveal i) VECM and JTDM generate consistent ranking in 4 out of 10 A-H rms and 2 out of 10 A-B rms, all of which provide strong evidence of price discovery by the H or B boards; ii) Where VECM and JTDM generate con icting rankings in 6 A-H rms, the Wald test and/or J-test rejects VECM in favor of JTDM; iii) Where VECM and JTDM generate con icting rankings in 8 A-B rms, the Wald test and J-test rejects VECM (JTDM) in favor of JTDM (VECM) for 2(3) rms; neither model nor model selection tests are able to decide which board is more informative in 3 A-B rms. The less consistent results in the A-B sample group is not surprising given that the A and B boards were implicitly merged in 2001-2002. JEL classi cation: G14, G15.
Building Combined Classifiers

This chapter covers different approaches that may be taken when building an ensemble method, through studying specific examples of each approach from research conducted by the authors. A method called Negative Correlation Learning illustrates a decision level combination approach with individual classifiers trained co-operatively. The Model level combination paradigm is illustrated via a tree combination method. Finally, another variant of the decision level paradigm, with individuals trained independently instead of co-operatively, is discussed as applied to churn prediction in the telecommunications industry.
Research Methods in the Social Sciences

With its clear presentation and integration of detailed real-world examples, the acclaimed "Research Methods in the Social Sciences "accessibly illustrates the relevance of social sciences research without sacrificing key content. The eighth edition includes engaging new studies and examples that explore the use of Twitter feeds in social sciences research, the effect of climate change on human conflict, the use of rational intuition in explaining the Chelyabinsk meteor explosion, and much more. The eighth edition also includes new and expanded coverage of conducting qualitative research, as well as conducting research in our digital age, including the use of the Internet and various computer software packages for retrieving, cleaning, coding, and analyzing "big data. "
Investigating the Role of Mitochondrial Haplogroups in Genetic Predisposition to Meningococcal Disease

Background and Aims Meningococcal disease remains one of the most important infectious causes of death in industrialized countries. The highly diverse clinical presentation and prognosis of Neisseria meningitidis infections are the result of complex host genetics and environmental interactions. We investigated whether mitochondrial genetic background contributes to meningococcal disease (MD) susceptibility. Methodology/Principal Findings Prospective controlled study was performed through a national research network on MD that includes 41 Spanish hospitals. Cases were 307 paediatric patients with confirmed MD, representing the largest series of MD patients analysed to date. Two independent sets of ethnicity-matched control samples (CG1 [N = 917]), and CG2 [N = 616]) were used for comparison. Cases and controls underwent mtDNA haplotyping of a selected set of 25 mtDNA SNPs (mtSNPs), some of them defining major European branches of the mtDNA phylogeny. In addition, 34 ancestry informative markers (AIMs) were genotyped in cases and CG2 in order to monitor potential hidden population stratification. Samples of known African, Native American and European ancestry (N = 711) were used as classification sets for the determination of ancestral membership of our MD patients. A total of 39 individuals were eliminated from the main statistical analyses (including fourteen gypsies) on the basis of either non-Spanish self-reported ancestry or the results of AIMs indicating a European membership lower than 95%. Association analysis of the remaining 268 cases against CG1 suggested an overrepresentation of the synonym mtSNP G11719A variant (Pearson's chi-square test; adjusted P-value = 0.0188; OR [95% CI] = 1.63 [1.22–2.18]). When cases were compared with CG2, the positive association could not be replicated. No positive association has been observed between haplogroup (hg) status of cases and CG1/CG2 and hg status of cases and several clinical variants. Conclusions We did not find evidence of association between mtSNPs and mtDNA hgs with MD after carefully monitoring the confounding effect of population sub-structure. MtDNA variability is particularly stratified in human populations owing to its low effective population size in comparison with autosomal markers and therefore, special care should be taken in the interpretation of seeming signals of positive associations in mtDNA case-control association studies.
Effect of Number of Options on Recall of Information Supporting Different Decision Strategies

The tendency to use an optinizing decision strategy (try to choose the best option) was hypothesized to be stronger when there is a small number of options and the tendency to use a satisficing strate gy (try to choose a good option) to be stronger when there is a large number of options. The tendency to think about aspects of the options on which the chosen option is the best was hypothesized to be stronger when an optimizing strategy was used and the tendency to think about aspects on which the chosen option is satisfactory to be stronger when a satisficing strategy was used. From these hypotheses it was predicted that recall of information about aspects on which the chosen option was the best but not good will be greater following a choice from a small number of options and recall of information about aspects on which the chosen option was good but not the best will be greater following a choice from a large number of options. An experiment confirmed these predictions.
Putative Psychotic Symptoms in the Mexican American Population: Prevalence and Co-Occurrence With Psychiatric Disorders

It is reported that Latin Americans describe culturally normative experiences or express putative psychotic symptoms in medical and mental health treatment settings that complicate the diagnostic process. Previous research reported that Latinos were more likely than European Americans and African Americans to have their diagnoses changed from schizophrenia to other disorders. This study describes the prevalence and likelihood of putative psychotic symptoms being expressed independent of any psychiatric disorder or co-occurring with common disorders such as depression or anxiety within a Mexican American population sample. Epidemiologic data of the Mexican American Prevalence and Services Survey (N = 3012) were used to contrast rates and patterns of putatively psychotic features among adults by demographic variables and diagnostic status using DSM-III-R criteria and receipt of treatment. Putative psychotic symptoms were reported by 17% of US-born and 7% of immigrants without disorders, and by 38% of US-born and 28% of immigrants with lifetime disorders, totaling 18% lifetime prevalence for the entire study population of Mexican Americans. First-rank Schneiderian symptoms were higher in those with a disorder compared with those without a disorder for both sexes. The results of this study indicate that putative psychotic symptoms are common among Mexican Americans, and their presence is a strong precautionary signal for evaluating clinicians to correctly distinguish whether putative psychotic symptoms are indicators of nonorganic psychoses or other psychiatric disorders, or are simply cultural expressions. Research is needed to identify the determinants of misdiagnosis in clinical practice, and guidelines are needed to assist clinicians.
Statistical and Similarity Methods for Classifying Emotion in Suicide Notes

In this paper we report on the approaches that we developed for the 2011 i2b2 Shared Task on Sentiment Analysis of Suicide Notes. We have cast the problem of detecting emotions in suicide notes as a supervised multi-label classification problem. Our classifiers use a variety of features based on (a) lexical indicators, (b) topic scores, and (c) similarity measures. Our best submission has a precision of 0.551, a recall of 0.485, and a F-measure of 0.516.
Vessel wall imaging for intracranial vascular disease evaluation

Accurate and timely diagnosis of intracranial vasculopathies is important owing to the significant risk of morbidity with delayed and/or incorrect diagnosis both from the disease process and inappropriate therapies. Conventional luminal imaging techniques for analysis of intracranial vasculopathies are limited to evaluation of changes in the vessel lumen. Vessel wall MRI techniques can allow direct characterization of pathologic changes of the vessel wall. These techniques may improve diagnostic accuracy and improve patient outcomes. Extracranial carotid vessel wall imaging has been extensively investigated in patients with atherosclerotic disease and has been shown to accurately assess plaque composition and identify vulnerable plaque characteristics that may predict stroke risk beyond luminal stenosis alone. This review provides a brief history of vessel wall MRI, an overview of the intracranial vessel wall MRI techniques, its applications, and imaging findings of various intracranial vasculopathies pertinent to the neurointerventionalist, neurologist, and neuroradiologist. We searched MEDLINE, PubMed, and Google for English publications containing any of the following terms: ‘intracranial vessel wall imaging’, ‘intracranial vessel wall’, and ‘intracranial vessel wall MRI’.