Miracle-dz/UniFAR-FTUs huggingface dataset:
Primary Infection by a Human Immunodeficiency Virus with Atypical Coreceptor Tropism

ABSTRACT The great majority of human immunodeficiency virus type 1 (HIV-1) strains enter CD4+ target cells by interacting with one of two coreceptors, CCR5 or CXCR4. Here we describe a transmitted/founder (T/F) virus (ZP6248) that was profoundly impaired in its ability to utilize CCR5 and CXCR4 coreceptors on multiple CD4+ cell lines as well as primary human CD4+ T cells and macrophages in vitro yet replicated to very high titers (>80 million RNA copies/ml) in an acutely infected individual. Interestingly, the envelope (Env) glycoprotein of this clade B virus had a rare GPEK sequence in the crown of its third variable loop (V3) rather than the consensus GPGR sequence. Extensive sequencing of sequential plasma samples showed that the GPEK sequence was present in virtually all Envs, including those from the earliest time points after infection. The molecularly cloned (single) T/F virus was able to replicate, albeit poorly, in cells obtained from ccr5 Δ32 homozygous donors. The ZP6248 T/F virus could also infect cell lines overexpressing the alternative coreceptors GPR15, APJ, and FPRL-1. A single mutation in the V3 crown sequence (GPEK->GPGK) of ZP6248 restored its infectivity in CCR5+ cells but reduced its ability to replicate in GPR15+ cells, indicating that the V3 crown motif played an important role in usage of this alternative coreceptor. These results suggest that the ZP6248 T/F virus established an acute in vivo infection by using coreceptor(s) other than CCR5 or CXCR4 or that the CCR5 coreceptor existed in an unusual conformation in this individual.
A Production Oriented Approach for Vandalism Detection in Wikidata - The Buffaloberry Vandalism Detector at WSDM Cup 2017

Wikidata is a free and open knowledge base from the Wikimedia Foundation, that not only acts as a central storage of structured data for other projects of the organization, but also for a growing array of information systems, including search engines. Like Wikipedia, Wikidata's content can be created and edited by anyone; which is the main source of its strength, but also allows for malicious users to vandalize it, risking the spreading of misinformation through all the systems that rely on it as a source of structured facts. Our task at the WSDM Cup 2017 was to come up with a fast and reliable prediction system that narrows down suspicious edits for human revision. Elaborating on previous works by Heindorf et al. we were able to outperform all other contestants, while incorporating new interesting features, unifying the programming language used to only Python and refactoring the feature extractor into a simpler and more compact code base.
The Rees-Eysenck body index and Sheldon's somatotype system.

The objections of Parnell to the Rees-Eysenck Index of body build have been examined and found to be based on erroneous premises. A critique has been offered of Sheldon's system of somatotyping which was stated by Parnell to be superior to the Rees-Eysenck Index. Finally, a comparison was made between the two systems in terms of their ability to account for certain empirical findings reported by Parnell and his associates with respect to the relation ship between body build and temperament. It was concluded that Sheldon's system was unnecessarily complicated, statistically inadequate, and theoretically not well founded. It was demonstrated that the Rees-Eysenck Index could embody the established empirical findings without apparent loss of information, despite its simplicity.
The Military in New Times

Thinking through the end of the Cold War, James Burk armed force and armed forces in a turbulent world, James N. Rosenau the future of transitional warfare, William R. Thompson the shifting threat and American national security - sources and consequences of change, Donald M. Snow a farewell to arms? the military and the nation-state in a changing world, Christopher Dandecker the postmodern military, Charles C. Moskos and J. Burk multinational peacekeeping operations - background and effectiveness, David R. Segal and Robert J. Waldman the challenge of nonviolence in the new world order, Robert L. Holmes.
Activity of herpes simplex virus type 1 latency-associated transcript (LAT) promoter in neuron-derived cells: evidence for neuron specificity and for a large LAT transcript

By using chloramphenicol acetyltransferase (CAT) assays in neuron-derived cell lines, we show here that promoter activity associated with the herpes simplex virus type 1 latency-associated transcript (LAT) had neuronal specificity. Promoter activity in these transient CAT assays coincided with a DNA region containing excellent RNA polymerase II promoter consensus sequences. Primer extension analysis in a LAT promoter-CAT plasmid construct placed the start of transcription about 28 nucleotides from the first T in the consensus TATA box sequence. Neuronal specificity of this promoter was suggested by examining the effect of sequences upstream of the promoter on CAT activity in neuronal versus nonneuronal cells. In nonneuronal cells, promoter activity was decreased 3- to 12-fold with the addition of upstream sequences. In contrast, in neuron-derived cells, the addition of upstream sequences did not decrease promoter activity. The LAT promoter predicted by our transient CAT assays was located over 660 nucleotides upstream from the 5' end of the previously mapped 2-kilobase (kb) LAT. This unusual location was explained by in situ and Northern (RNA) blot hybridization analyses that suggested that LAT transcription began near the promoter detected in our CAT assays, rather than near the 5' end of the 2-kb LAT. In situ hybridization with neurons from latently infected rabbits detected small amounts of LAT RNA within 30 nucleotides of the consensus TATA box sequence. This suggested that LAT transcription began near this TATA box. Northern blot hybridization of RNA from ganglia of latently infected rabbits revealed a faint 8.3-kb band of the same sense as LAT. We conclude that (i) the LAT promoter has neuronal specificity, (ii) the LAT promoter is located over 660 nucleotides upstream of the 5' end of the previously characterized stable 2-kb LAT, (iii) LAT transcription begins about 28 nucleotides from the first T of the consensus TATA box sequence and extends to near the first available polyadenylation site approximately 8.3 kb away, and (iv) this 8.3-kb RNA may be an unstable precursor of the more stable 2- and 1.3-kb LATs.
Models of biological effects of radiation in the Geant4 Toolkit

A project, named Geant4-DNA, is in progress to extend the Geant4 simulation toolkit to model the effects of radiation with biological systems at cellular and DNA level. The first component implemented in the first development cycle of the project describes the fractional survival of a population of cells irradiated with photons or charged particles. The software system developed provides the user the option to choose among a small set of alternative models for the calculation of mammalian cell survival after irradiation. The flexible design adopted makes the system open to further extension to implement other cell survival models available in literature. The preliminary design of a prototype of the cell survival models implemented and preliminary results in some selected cell lines are described.
Clipping Noise Mitigation in Optical OFDM Systems

This letter describes a new non-linear algorithm for clipping noise mitigation in intensity modulation/direct detection dc biased optical orthogonal frequency division multiplexing (DCO-OFDM) systems. Clipping noise is often the major limitation in DCO-OFDM. In this letter, we show that extra information about the clipped signal can be extracted using a non-linear process and then used to mitigate the clipping noise. The effectiveness of the new algorithm is demonstrated by simulation and in an optical wireless experiment.
Introduction: Uveal melanoma

The iris, ciliary body and choroid constitute the uveal tract. The uveal tract is embryologically derived from the mesoderm and neural crest. It is a highly vascularized structure composed of melanocytes, supporting connective tissue with fibroblasts and blood vessels and peripheral nerves. Histopathologically there are four different types of uveal melanoma (UM) identified: spindle cell, epithelioid, mixed and necrotic. Approximately 5% of all UM arise in ocular and adnexal structures (Chang et al. 1998). Most ocular melanomas (85%) are uveal in origin, whereas primary conjuctival and orbital melanomas are very rare (Chang et al. 1998; Singh & Topham 2003). Approximately 90% of all UM develop in the choroid, 7% in the ciliary body and 3% in the iris (Damato 2001). UM is the most common primary intraocular malignant tumor (Strickland & Lee 1981) with an annual incidence, which has remained stable for the last 50 years, of 8.4–11.7 cases per million in whites (Bergman et al. 2002).
Practical recommendations for exercise training in patients with COPD

The aim of this article was to provide practical recommendations to healthcare professionals interested in offering a pulmonary rehabilitation programme for patients with chronic obstructive pulmonary disease (COPD). The latest research findings were brought together and translated into clinical practice. These recommendations focus on the description of useful assessment tests and of the most common exercise modalities for patients with COPD. We provide specific details on the rationale of why and especially how to implement exercise training in patients with COPD, including the prescription of training mode, intensity and duration, as well as suggestions of guidelines for training progression.
Thai Multi-Document Summarization: Unit Segmentation, Unit-Graph Formulation, and Unit Selection

There have been several challenges in summarization of Thai multiple documents since Thai language itself lacks of explicit word/phrase/sentence boundaries. This paper gives definition of Thai Elementary Discourse Unit (TEDU) and then presents our three-stage summarization process. Towards implementation of this process, we propose unit segmentation using TEDUs and their derivatives, unit-graph formation using iterative unit weighting and cosine similarity, and unit selection using highest-weight priority, redundancy removal, and post-selection weight recalculation. To examine performance of the proposed methods, a number of experiments are conducted using fifty sets of Thai news articles with their manually constructed reference summary. By three common evaluation measures of ROUGE-1, ROUGE-2, and ROUGE-SU4, the results evidence that (1) our TEDU-based summarization outperforms paragraph-based summarization, (2) our iterative weighting is superior to traditional TF-IDF, (3) the highest-weight priority without centroid preference and unit redundancy consideration helps improving summary quality, and (4) post-selection weight recalculation tends to raise summarization performance under some certain circumstances.
Contact-induced cross-dialectal phonetic variability in an endangered Iranian language: The case of Taleshi

Khalili, Niloofar Nathalie (Ph.D., Linguistics, Department of Linguistics]) Contact-induced cross-dialectal phonetic variability in an endangered Iranian language: The case of Taleshi Thesis directed by Professor David Rood This work presents the first large-scale empirical analysis of vowel variation in the three dialects (Northern, Central, Southern) of the spoken Iranian Taleshi. The vowel system of this minority language is underdocumented. My data provide unique and important insight, therefore, into this contracting language variety. Acoustic analyses are conducted on 6252 realizations of the Taleshi central vowels /ə/ and /ɨ/ in the spontaneous and controlled speech of 142 men and women living in Iran, in order to explore the impact centuries of contact with Farsi and other languages has had (and continues to have) on Taleshi. Fine-grained analyses in the F2 vowel formant reveal subtle permutations of the Taleshi sound system suggestive of convergence with neighboring languages (Farsi, Turkish). Specifically, this work identifies convergence between schwa /ə/ (a vowel in Taleshi) and /o/ (a vowel in Farsi) as well as the convergence between /ɨ/ (a vowel also in Taleshi) and /u/ (again in Taleshi and Farsi) in the three dialects of Taleshi. The impact of language contact is evident in significant F2 differences between speakers of the Central dialect, who have geographically less contact with other languages (Farsi, Turkish, etc.) vs. those speaking the Northern and the Southern dialects who have more contact with other languages. Statistical analyses controlling for internal factors (the target words’ phonetic environment) and external factors (speaker age, education, settlement, and gender) known to contribute to formant variation, identify factors driving variation. Furthermore, the influence of language contact becomes evidenced in enhanced phonological convergence (F2 differences) in words that overlap phonologically, orthographically, and semantically (cognates and loanwords) with Farsi compared to words that do not share such interlingual similarity. Lastly, the degree of language activation in different speech settings would also support a contact explanation, in that convergence is most apparent in the speech reflecting increased activation of the contact language (as measured by percentage of language use in different speech settings during data collection). These comparisons demonstrate the role that convergence plays in the sound variations that are already inherent in Taleshi and contribute new data to the field of language contact. The paper argues that the sound variations in Taleshi are a consequence of both long-term language contact as well as more general social factors.
Uptake, distribution, depletion, and in ovo transfer of isomers of hexabromocyclododecane flame retardant in diet‐exposed American kestrels (Falco sparverius)

Hexabromocyclododecane (HBCDD) is a flame retardant and a global contaminant, yet the toxicokinetics of HBCDD diastereoisomers remains unknown in wildlife species. The present study examined in captive American kestrels (Falco sparverius) (diastereo) isomer‐specific HBCDD uptake, depletion, tissue distribution, and transfer to eggs in a dietary dosing study with an HBCDD technical mixture (HBCDD‐TM). Adult tissue and plasma collections were from separate cohorts of unpaired individual males (n = 10) and females (n = 10) exposed for 21 d to 800 ng/g wet weight of HBCDD‐TM (in safflower oil and injected into their cockerel [brain] diet), followed by a 25‐d depuration period. A separate cohort of 12 males only was used for control adult tissue and plasma collections. For egg collections, separate cohorts of 11 control pairs (n = 22 birds) and 20 HBCDD‐exposed pairs (n = 40 birds) were allowed to breed, and their eggs were collected (n = 19 exposed eggs and n = 10 control eggs). The sum (Σ) HBCDD concentrations were near or below detection (<0.01–0.1 ng/g wet wt) in all control samples but quantifiable in all samples from exposed birds (no differences [p > 0.05] between males and females). Arithmetic mean ΣHBCDD concentrations were highest in fat >> eggs > liver > plasma. The mean ΣHBCDD depletion rate in plasma between the uptake and depuration periods was estimated to be 0.22 ng/g/d with a half‐life of approximately 15 d. The γ‐HBCDD diastereoisomer was >60% of the ΣHBCDD in plasma after the uptake period and similar to the HBCDD‐TM (∼80%). After the depuration period, α‐HBCDD was >70% of the HBCDD in plasma, fat, liver, and eggs; and this α‐HBCDD domination indicated isomer‐specific accumulation as a result of selective metabolism, uptake, protein binding, and/or in ovo transport. Environ Toxicol Chem 2015;34:1103–1112. © 2015 SETAC
Estimating and communicating prognosis in advanced neurologic disease

Prognosis can no longer be relegated behind diagnosis and therapy in high-quality neurologic care. High-stakes decisions that patients (or their surrogates) make often rest upon perceptions and beliefs about prognosis, many of which are poorly informed. The new science of prognostication—the estimating and communication “what to expect”—is in its infancy and the evidence base to support “best practices” is lacking. We propose a framework for formulating a prediction and communicating “what to expect” with patients, families, and surrogates in the context of common neurologic illnesses. Because neurologic disease affects function as much as survival, we specifically address 2 important prognostic questions: “How long? ” and “How well? ” We provide a summary of prognostic information and highlight key points when tailoring a prognosis for common neurologic diseases. We discuss the challenges of managing prognostic uncertainty, balancing hope and realism, and ways to effectively engage surrogate decision-makers. We also describe what is known about the nocebo effects and the self-fulfilling prophecy when communicating prognoses. There is an urgent need to establish research and educational priorities to build a credible evidence base to support best practices, improve communication skills, and optimize decision-making. Confronting the challenges of prognosis is necessary to fulfill the promise of delivering high-quality, patient-centered care.
Early model-driven timing validation of IoT-compliant use cases

Several IoT platforms, with support for a rich set of device libraries, facilitate rapid development of embedded IoT applications. But, none of the approaches deal with the analysis of performance characteristics. An example is the early timing validation of IoT use cases in specialized timing analysis tools. Addressing this gap, a generic workflow for a quick, early model-driven, system-level timing validation of IoT compliant hand-written code in specialized timing analysis tools, such as SymTA/S, is proposed in this paper. A prototype implementation of the workflow and its experimental evaluation in a novel, IoT-compliant real-time emission monitoring use case is presented. The main benefit of the proposed workflow is the early feedback regarding performance characteristics of the embedded IoT application, under varying timing constraints.
Hormonal treatment reduces psychobiological distress in gender identity disorder, independently of the attachment style.

INTRODUCTION Gender identity disorder may be a stressful situation. Hormonal treatment seemed to improve the general health as it reduces psychological and social distress. The attachment style seemed to regulate distress in insecure individuals as they are more exposed to hypothalamic-pituitary-adrenal system dysregulation and subjective stress. AIM The objectives of the study were to evaluate the presence of psychobiological distress and insecure attachment in transsexuals and to study their stress levels with reference to the hormonal treatment and the attachment pattern. METHODS We investigated 70 transsexual patients. We measured the cortisol levels and the perceived stress before starting the hormonal therapy and after about 12 months. We studied the representation of attachment in transsexuals by a backward investigation in the relations between them and their caregivers. MAIN OUTCOME MEASURES We used blood samples for assessing cortisol awakening response (CAR); we used the Perceived Stress Scale for evaluating self-reported perceived stress and the Adult Attachment Interview to determine attachment styles. RESULTS At enrollment, transsexuals reported elevated CAR; their values were out of normal. They expressed higher perceived stress and more attachment insecurity, with respect to normative sample data. When treated with hormone therapy, transsexuals reported significantly lower CAR (P < 0.001), falling within the normal range for cortisol levels. Treated transsexuals showed also lower perceived stress (P < 0.001), with levels similar to normative samples. The insecure attachment styles were associated with higher CAR and perceived stress in untreated transsexuals (P < 0.01). Treated transsexuals did not expressed significant differences in CAR and perceived stress by attachment. CONCLUSION Our results suggested that untreated patients suffer from a higher degree of stress and that attachment insecurity negatively impacts the stress management. Initiating the hormonal treatment seemed to have a positive effect in reducing stress levels, whatever the attachment style may be.
Lot-release criteria, postlicensure quality control, and the Haemophilus influenzae type b conjugate vaccines.

In the United States, vaccines are licensed by the Center for Biologics Evaluation and Research (CBER) of the Food and Drug Administration on the basis of their demonstrated safety and efficacy and the demonstrated ability of the manufacturer to produce a consistent product. After licensure, vaccines are generally released to the market on a lot-by-lot basis, following CBER's review of lot-release testing results. A lot is released only if it meets all predefined specifications. A discussion of US vaccine regulation was published recently by Parkman and Hardegree.1 See also p 849. As reported in this issue ofTHE Journal,2during studies of the interchangeability of licensedHaemophilus influenzaetype b (Hib) polysaccharide-protein conjugate vaccines, Anderson et al found that a lot of Hib vaccine with the capsular polysaccharide conjugated to the meningococcal outer membrane protein complex (PedvaxHib, Merck and Co, West Point, Pa) produced lower than expected immune
Caspase-dependent Cleavage of Signaling Proteins during Apoptosis

Caspases are activated during apoptosis and cleave specific proteins, resulting in the irreversible commitment to cell death. The signal transduction proteins MEKK1, p21-activated kinase 2, and focal adhesion kinase are caspase substrates that contribute to the cell death response when cleaved. Thirty additional signaling proteins were screened for their ability to be cleaved during apoptosis. Twenty-two of these proteins were not affected in Jurkat cells stimulated to undergo apoptosis by Fas ligation, exposure to ultraviolet-C or incubation with etoposide. Ras GTPase-activating protein was found to be a caspase substrate whose cleavage followed the same time course as that for activation of caspase activity and the cleavage of MEKK1 and focal adhesion kinase. Four additional proteins, Cbl, Cbl-b, Raf-1, and Akt-1, were cleaved later in the apoptotic response. These signaling proteins were similarly cleaved in U937 cells undergoing apoptosis. Cleavage of the proteins was blocked by caspase inhibitors in Jurkat cells or in U937 cells expressing BclxL, demonstrating that the cleavage was dependent on caspase activation. Cleavage of Raf-1 and Akt correlated with the loss of extracellular signal-regulated kinase and Akt activities in apoptotic cells. Neither c-Jun N-terminal kinase nor p38 mitogen-activated protein kinase was cleaved in cells undergoing apoptosis, and the activation of the c-Jun N-terminal kinase and p38 mitogen-activated protein kinase pathways was not compromised in apoptotic cells. These results indicate that caspase-dependent cleavage of specific proteins induces the turn off of survival pathways, such as the extracellular signal-regulated kinase and phosphatidylinositol-3 kinase/Akt pathways, that could otherwise interfere with the apoptotic response.
A new public key system based on Polynomials over finite fields GF(2)

In this paper a new public key system based on polynomials over fields GF (2) is developed. The security of the system is based on the difficulty of finding discrete logarithms over GF (2) with sufficiently large k. The presented system has all features of ordinary public key schemes such as public key encryption and digital signatures. The security and implementation aspects of the presented system are also introduced along with comparison with other well known public key systems.