Miracle-dz/UniFAR-FTUs huggingface dataset:
Undiagnosed tuberculosis in a community with high HIV prevalence: implications for tuberculosis control.

BACKGROUND Although failure of tuberculosis (TB) control in sub-Saharan Africa is attributed to the HIV epidemic, it is unclear why the directly observed therapy short-course (DOTS) strategy is insufficient in this setting. We conducted a cross-sectional survey of pulmonary TB (PTB) and HIV infection in a community of 13,000 with high HIV prevalence and high TB notification rate and a well-functioning DOTS TB control program. METHODS Active case finding for PTB was performed in 762 adults using sputum microscopy and Mycobacterium tuberculosis culture, testing for HIV, and a symptom and risk factor questionnaire. Survey findings were correlated with notification data extracted from the TB treatment register. RESULTS Of those surveyed, 174 (23%) tested HIV positive, 11 (7 HIV positive) were receiving TB therapy, 6 (5 HIV positive) had previously undiagnosed smear-positive PTB, and 6 (4 HIV positive) had smear-negative/culture-positive PTB. Symptoms were not a useful screen for PTB. Among HIV-positive and -negative individuals, prevalence of notified smear-positive PTB was 1,563/100,000 and 352/100,000, undiagnosed smear-positive PTB prevalence was 2,837/100,000 and 175/100,000, and case-finding proportions were 37 and 67%, respectively. Estimated duration of infectiousness was similar for HIV-positive and HIV-negative individuals. However, 87% of total person-years of undiagnosed smear-positive TB in the community were among HIV-infected individuals. CONCLUSIONS PTB was identified in 9% of HIV-infected individuals, with 5% being previously undiagnosed. Lack of symptoms suggestive of PTB may contribute to low case-finding rates. DOTS strategy based on passive case finding should be supplemented by active case finding targeting HIV-infected individuals.
SAM and the Particle Physics Data Grid

The D0 experiment’s data and job management system software, SAM, is an operational prototype of many of the concepts being developed for Grid computing. We explain how the components of SAM map into the Data Grid architecture. We discuss the future use of Grid components to either replace existing components of SAM or to extend its functionality and utility; work being carried out as part of the Particle Physics Data Grid (PPDG) project.
RFID-Based Production Process Monitoring Solutions

The keys to success in the implementation of RFID are the utilization of the data collected using the RFID technology and the establishment of an RFID implementation strategy for the future. These two issues necessitate a step-by-step implementation of RFID with a firm future perspective as well as of the technologies that supports it. As a practical means for enabling the above proposals NEC offers an RFID-Based Production Process Monitoring Solution backed by the RFID implementation and pilot expertise of the NEC Group. This paper introduces the RFID technologies backing the solution and its future deployment perspectives.
Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA.

The crystal structure of a ternary complex of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) heterodimer (p66/p51), a 19-base/18-base double-stranded DNA template-primer, and a monoclonal antibody Fab fragment has been determined at 3.0 A resolution. The four individual subdomains of RT that make up the polymerase domains of p66 and p51 are named fingers, palm, thumb, and connection [Kohlstaedt, L. A. , Wang, J., Friedman, J. M. , Rice, P. A. & Steitz, T. A. (1992) Science 256, 1783-1790]. The overall folding of the subdomains is similar in p66 and p51 but the spatial arrangements of the subdomains are dramatically different. The template-primer has A-form and B-form regions separated by a significant bend (40-45 degrees). The most numerous nucleic acid interactions with protein occur primarily along the sugar-phosphate backbone of the DNA and involve amino acid residues of the palm, thumb, and fingers of p66. Highly conserved regions are located in the p66 palm near the polymerase active site. These structural elements, together with two alpha-helices of the thumb of p66, act as a clamp to position the template-primer relative to the polymerase active site. The 3'-hydroxyl of the primer terminus is close to the catalytically essential Asp-110, Asp-185, and Asp-186 residues at the active site and is in a position for nucleophilic attack on the alpha-phosphate of an incoming nucleoside triphosphate. The structure of the HIV-1 RT/DNA/Fab complex should aid our understanding of general mechanisms of nucleic acid polymerization. AIDS therapies may be enhanced by a fuller understanding of drug inhibition and resistance emerging from these studies.
Impact of Diabetes Care by Pharmacists as Part of Health Care Team in Ambulatory Settings: A Systematic Review and Meta-analysis

Objective: To conduct a comprehensive systematic review and meta-analyses examining the impact of pharmacist interventions as part of health care teams on diabetes therapeutic outcomes in ambulatory care settings. Data Sources: PubMed/MEDLINE, EMBASE, Cochrane Library, International Pharmaceutical Abstracts, Web of Science, Scopus, WHO’s Global Health Library, ClinicalTrials.gov, and Google Scholar were searched (1995 to February 2017). Search terms included pharmacist, team, and diabetes. Study Selection: Full-text articles published in English with comparative designs, including randomized controlled trials, nonrandomized controlled trials, and pretest-posttest studies evaluating hemoglobin A1C (A1C), were assessed. Data Extraction and Synthesis: Two reviewers independently screened for study inclusion and extracted data. Quality of the studies was assessed using tools developed based on the framework of the Cochrane Collaboration’s recommendations. Data Synthesis: A total of 1908 studies were identified from the literature and reference searches; 42 studies were included in the systematic review (n = 10 860) and 35 in the meta-analyses (n = 7417). Mean age ranged from 42 to 73 years, and 8% to 100% were male. The overall standardized mean difference (SMD) for A1C for pharmacist care versus comparison was 0.57 (P < 0.01), a moderate effect representing a mean difference of 1.1% (95% CI = 0.88-1.27). The effects for systolic blood pressure and low-density lipoprotein cholesterol were between small and moderate (SMD = 0.31 and 0.32; P < 0.01). The heterogeneity was high for all outcomes (>83%), indicating functional differences among the studies. No publication bias was detected. Conclusion: Pharmacists’ interventions as part of the patient’s health care team improved diabetes therapeutic outcomes, substantiating the important role of pharmacists in team-based diabetes management.
Prospective Randomized Multicenter Trial of Empirical Antitachycardia Pacing Versus Shocks for Spontaneous Rapid Ventricular Tachycardia in Patients With Implantable Cardioverter-Defibrillators: Pacing Fast Ventricular Tachycardia Reduces Shock Therapies (PainFREE Rx II) Trial Results

Background—Successful antitachycardia pacing (ATP) terminates ventricular tachycardia (VT) up to 250 bpm without the need for painful shocks in implantable cardioverter-defibrillator (ICD) patients. Fast VT (FVT) >200 bpm is often treated by shock because of safety concerns, however. This prospective, randomized, multicenter trial compares the safety and utility of empirical ATP with shocks for FVT in a broad ICD population. Methods and Results—We randomized 634 ICD patients to 2 arms—standardized empirical ATP (n=313) or shock (n=321)—for initial therapy of spontaneous FVT. ICDs were programmed to detect FVT when 18 of 24 intervals were 188 to 250 bpm and 0 of the last 8 intervals were >250 bpm. Initial FVT therapy was ATP (8 pulses, 88% of FVT cycle length) or shock at 10 J above the defibrillation threshold. Syncope and arrhythmic symptoms were collected through patient diaries and interviews. In 11±3 months of follow-up, 431 episodes of FVT occurred in 98 patients, representing 32% of ventricular tachyarrhythmias and 76% of those that would be detected as ventricular fibrillation and shocked with traditional ICD programming. ATP was effective in 229 of 284 episodes in the ATP arm (81%, 72% adjusted). Acceleration, episode duration, syncope, and sudden death were similar between arms. Quality of life, measured with the SF-36, improved in patients with FVT in both arms but more so in the ATP arm. Conclusions—Compared with shocks, empirical ATP for FVT is highly effective, is equally safe, and improves quality of life. ATP may be the preferred FVT therapy in most ICD patients.
Genomic mixing to elucidate the genetic system of complex traits.

Understanding the genetic basis of complex traits has become one of the major issues in genetics, but recent advances in this field are still faced with a difficulty, the so-called "missing heritability. " It is speculated that missing heritability mainly stems from a large number of variants of small effect that are poorly detected by currently available methods. In order to overcome this problem, many recent genetic studies of complex traits have actively used outbred stocks of mice. However, most of the available outbred stocks have a limited amount of genetic variation, because many stocks originate from Swiss mouse colonies. We have repeatedly shown that wild-derived strains are a useful mouse resource since there is a large genetic diversity among these strains. Here, we give an overview of mouse resources produced by crossing different founder mice. Finally, we propose an advantage of new attempts to conduct selective breeding using heterogeneous stocks created by mixing genomes of wild-derived inbred strains of mice when studying complex traits.
AdaRTE: Adaptable Dialogue Architecture and Runtime Engine. A New Architecture for Health-Care Dialogue Systems

Spoken dialogue systems have been increasingly employed to provide ubiquitous automated access via telephone to information and services for the non-Internet-connected public. In the health care context, dialogue systems have been successfully applied. Nevertheless, speech-based technology is not easy to implement because it requires a considerable development investment. The advent of VoiceXML for voice applications contributed to reduce the proliferation of incompatible dialogue interpreters, but introduced new complexity. As a response to these issues, we designed an architecture for dialogue representation and interpretation, AdaRTE, which allows developers to layout dialogue interactions through a high level formalism that offers both declarative and procedural features. AdaRTE aim is to provide a ground for deploying complex and adaptable dialogues whilst allows the experimentation and incremental adoption of innovative speech technologies. It provides the dynamic behavior of Augmented Transition Networks and enables the generation of different backends formats such as VoiceXML. It is especially targeted to the health care context, where a framework for easy dialogue deployment could reduce the barrier for a more widespread adoption of dialogue systems.
Synthesis of Large‐Area MoS2 Atomic Layers with Chemical Vapor Deposition

Large-area MoS(2) atomic layers are synthesized on SiO(2) substrates by chemical vapor deposition using MoO(3) and S powders as the reactants. Optical, microscopic and electrical measurements suggest that the synthetic process leads to the growth of MoS(2) monolayer. The TEM images verify that the synthesized MoS(2) sheets are highly crystalline.
Modification of Cyclic Nucleotide–Gated Ion Channels by Ultraviolet Light

We irradiated cyclic nucleotide–gated ion channels in situ with ultraviolet light to probe the role of aromatic residues in ion channel function. UV light reduced the current through excised membrane patches from Xenopus oocytes expressing the α subunit of bovine retinal cyclic nucleotide–gated channels irreversibly, a result consistent with permanent covalent modification of channel amino acids by UV light. The magnitude of the current reduction depended only on the total photon dose delivered to the patches, and not on the intensity of the exciting light, indicating that the functionally important photochemical modification(s) occurred from an excited state reached by a one-photon absorption process. The wavelength dependence of the channels' UV light sensitivity (the action spectrum) was quantitatively consistent with the absorption spectrum of tryptophan, with a small component at long wavelengths, possibly due to cystine absorption. This spectral analysis suggests that UV light reduced the currents at most wavelengths studied by modifying one or more “target” tryptophans in the channels. Comparison of the channels' action spectrum to the absorption spectrum of tryptophan in various solvents suggests that the UV light targets are in a water-like chemical environment. Experiments on mutant channels indicated that the UV light sensitivity of wild-type channels was not conferred exclusively by any one of the 10 tryptophan residues in a subunit. The similarity in the dose dependences of channel current reduction and tryptophan photolysis in solution suggests that photochemical modification of a small number of tryptophan targets in the channels is sufficient to decrease the currents.
Dissecting the roles of E1A and E1B in adenoviral replication and RCAd-enhanced RDAd transduction efficacy on tumor cells

Oncolytic viruses have recently received widespread attention for their potential in innovative cancer therapy. Many telomerase promoter-regulated oncolytic adenoviral vectors retain E1A and E1B. However, the functions of E1A and E1B proteins in the oncolytic role of replication-competent adenovirus (RCAd) and RCAd enhanced transduction of replication defective adenoviruses (RDAd) have not been addressed well. In this study, we constructed viruses expressing E1A alone, E1A plus E1B-19 kDa, and E1A plus E1B-19 kDa/55 kDa. We then tested their roles in oncolysis and replication of RCAd as well as their roles in RCAd enhanced transfection rate and transgene expression of RDAd in various cancer cells in vitro and in xenografted human NCI-H460 tumors in nude mice. We demonstrated that RCAds expressing E1A alone and plus E1B-19 kDa exhibited an obvious ability in replication and oncolytic effects as well as enhanced RDAd replication and transgene expression, with the former showed more effective oncolysis, while the latter exhibited superior viral replication and transgene promotion activity. However, RCAd expressing both E1A and E1B-19 kDa/55 kDa was clearly worst in all these abilities. The effects of E1A and E1B observed through using RCAd were further validated by using plasmids expressing E1A alone, E1A plus E1B-19 kDa, and E1A plus E1B-19 kDa/55 kDa proteins. Our study provided evidence that E1A was essential for inducing replication and oncolytic effects of RCAd as well as RCAd enhanced RDAd transduction, and expression of E1B-19 kDa other than E1B-55 kDa could promote these effects. E1B-55 kDa is not necessary for the oncolytic effects of adenoviruses and somehow inhibits RCAd-mediated RDAd replication and transgene expression.
No Correlations Involved: Decision Making Under Uncertainty in a Conservative Sparse Information Space

This letter is concerned with decision making under uncertainty in problems involving high dimensional state spaces. Inspired by conservative information fusion techniques, we propose a novel paradigm where decision making is performed over a conservative rather than the original information space. The key idea is that regardless of the sparsity pattern of the latter, one can always calculate a sparse conservative information space, which admits computationally efficient decision making. In this letter, we take this concept to the extreme and consider a conservative approximation that decouples the state variables, leading to a conservative diagonal information matrix. As a result, the computational complexity involved with evaluating impact of a candidate action is reduced to O(n), for an n-dimensional state, as the calculations do not involve any correlations. Importantly, we show that for measurement observation models involving arbitrary single state variables, this concept yields exactly the same results compared to using the original information matrix. We demonstrate applicability of this concept to a sensor deployment problem.
The neural architecture of age-related dual-task interferences

In daily life elderly adults exhibit deficits when dual-tasking is involved. So far these deficits have been verified on a behavioral level in dual-tasking. Yet, the neuronal architecture of these deficits in aging still remains to be explored especially when late-middle aged individuals around 60 years of age are concerned. Neuroimaging studies in young participants concerning dual-tasking were, among others, related to activity in middle frontal (MFG) and superior frontal gyrus (SFG) and the anterior insula (AI). According to the frontal lobe hypothesis of aging, alterations in these frontal regions (i.e., SFG and MFG) might be responsible for cognitive deficits. We measured brain activity using fMRI, while examining age-dependent variations in dual-tasking by utilizing the PRP (psychological refractory period) test. Behavioral data showed an increasing PRP effect in late-middle aged adults. The results suggest the age-related deteriorated performance in dual-tasking, especially in conditions of risen complexity. These effects are related to changes in networks involving the AI, the SFG and the MFG. The results suggest that different cognitive subprocesses are affected that mediate the observed dual-tasking problems in late-middle aged individuals.
A biochemical pathway for a cellular behaviour: pHi, phosphorylcreatine shuttles, and sperm motility

Sperm motility and respiration are tightly coupled processes, both activated by an increased intracellular pH (pHi). As the sperm pHi increases, the flagellar motor driving motility is activated, leading to ATP consumption. Energy for motility is provided by mitochondrial respiration; energy transport from sperm mitochondrion to tail involves distinct isozymes of creatine kinase that effect a phosphorylcreatine shuttle. The activation of sperm motility and respiration can be described as a linked series of biochemical reactions that form a cell behavioural pathway analogous to the reaction sequences of intermediary metabolism.
Phase II study of procarbazine, CCNU, and vincristine combination chemotherapy in the treatment of malignant brain tumors

Forty‐eight patients with primary or metastatic malignant tumors of the central nervous system (CNS) were treated with combination chemotherapy, consisting of procarbazine (100 mg/m2 × 14 days), CCNU (75 mg/m2), and vincristine (1.4 mg/m2 × 2, 1 week apart) (PCV) every 4 weeks. Most patients had undergone initial resection of primary tumors, postoperative radiotherapy, and a post irradiation interval of 3 months or more. Other patients harbored unbiopsied, newly‐discovered primary or metastatic tumors. All patients were deteriorating neurologically when treatment began. Overall response rate for PCV combination therapy was 44%, no better than results obtained with single agent procarbazine or BCNU, the most effective drugs used alone in previous brain tumor chemotherapy studies.
The genetics of water-use efficiency and its relation to growth in maritime pine

To meet the increasing demand of wood biomass worldwide in the context of climate change, developing improved forest tree varieties for high productivity in water-limited conditions is becoming a major issue. This involves breeding for genotypes combining high growth and moderate water loss and thus high water-use efficiency (WUE). The present work provides original data about the genetics of intrinsic WUE (the ratio between net CO2 assimilation rate and stomatal conductance, also estimated by carbon isotope composition of plant material; δ13C) and its relation to growth in Pinus pinaster Ait. First, heritability for δ13C was estimated (0.29) using a 15-year-old progeny trial (Landes provenance), with no significant differences among three sites contrasting in water availability. High intersite correlations (0.63–0.91) and significant but low genotype–environment interactions were detected. Secondly, the genetic architectures of δ13C and growth were studied in a three-generation inbred pedigree, introducing the genetic background of a more-drought-adapted parent (Corsican provenance), at ages of 2 years (greenhouse) and 9 years (plantation). One of the quantitative trait loci (QTLs) identified in the field experiment, explaining 67% of the phenotypic variance, was also found among the QTLs detected in the greenhouse experiment, where it colocalized with QTLs for intrinsic WUE and stomatal conductance. This work was able to show that higher WUE was not genetically linked to less growth, allowing thus genetic improvement of water use. As far as is known, the heritability and QTL effects estimated here are based on the highest number of genotypes measured to date.
Polycyclic Aromatic Hydrocarbon–DNA Adducts and Breast Cancer: A Pooled Analysis

Abstract Polycyclic aromatic hydrocarbon (PAH)-DNA adducts have been associated with breast cancer in several small studies. The authors' pooled analysis included 873 cases and 941 controls from a population-based case-control study. Competitive enzyme-linked immunosorbent assay in peripheral mononuclear cells was conducted in 2 rounds, and results were pooled on the basis of round-specific quantiles. The odds ratio for breast cancer was elevated in relation to detectable PAH-DNA adducts (1.29 as compared with non-detectable adduct levels; 95% confidence interval = 1.05, 1.58), but there was no apparent dose-response relationship with increasing quantiles. No consistent pattern emerged when the results were stratified by PAH sources (e.g., active cigarette smoking or PAH-containing foods), or when the cases were categorized by stage of disease or hormone receptor status. These data provide only modest support for an association between PAH-DNA adducts and breast cancer development.
Data Driven Vessel Trajectory Forecasting Using Stochastic Generative Models

In this work, we propose a data driven trajectory forecasting algorithm that utilizes both recorded historical and streaming trajectory observations. The algorithm performs Bayesian inference on a directed graph the walks on which represent stochastic change point models of trajectory classes. Parameter distributions of these models are learnt from recorded trajectories. Forecasting is then made by calculating the class – or, walk– probabilities and corresponding predictive distributions for a given stream of location and velocity observations. This approach is tailored for the maritime domain and automatic identification system (AIS) data exploitation through the use of an Ornstein-Uhlenbeck process driven stochastic process model that captures vessel motion characteristics. We demonstrate the efficacy of this approach on a real data set.
Self-polarization effect in the middle point of an optical fiber

In this paper, we report both numerically and experimentally an unexpected phenomenon of self-polarization occurring in the middle point of an isotropic optical fiber when two uncorrelated partially polarized waves are simultaneously injected at the ends of the fiber. More precisely, we demonstrate that two counterpropagating waves of equal intensity exhibit a spontaneous organization of their polarization states around two pools of attraction just in the middle point of propagation, and then both recover a partially polarized state at their respective fiber outputs. The self-polarization effect then remains hidden within the optical fiber in the sense that no apparent sign of this process is detected at the fiber outputs. A geometric definition of the degree of polarization is used to measure the efficiency of the polarization phenomenon.