Miracle-dz/UniFAR-FTUs huggingface dataset:
DTP in low income countries: improved child survival or survival bias?

EDITOR—We proposed that BCG and measles vaccine have non-specific beneficial effects, whereas diphtheria-tetanus-pertussis (DTP) vaccination might have no beneficial effect.1 In response, the World Health Organization commissioned several studies.2–4 A WHO expert task force found substantial evidence against a deleterious effect of DTP; all studies showed DTP to be associated with reduced mortality. A negative DTP effect was found only in Guinea-Bissau, and this was presumed to be due to a country specific issue or a peculiarity of the data.5 In our survival analysis, vaccination status was a …
Counting hard-to-count populations: the network scale-up method for public health

Estimating sizes of hidden or hard-to-reach populations is an important problem in public health. For example, estimates of the sizes of populations at highest risk for HIV and AIDS are needed for designing, evaluating and allocating funding for treatment and prevention programmes. A promising approach to size estimation, relatively new to public health, is the network scale-up method (NSUM), involving two steps: estimating the personal network size of the members of a random sample of a total population and, with this information, estimating the number of members of a hidden subpopulation of the total population. We describe the method, including two approaches to estimating personal network sizes (summation and known population). We discuss the strengths and weaknesses of each approach and provide examples of international applications of the NSUM in public health. We conclude with recommendations for future research and evaluation.
Preference judgements involve a network of structures within frontal, cingulate and insula cortices

Environmental stimuli constantly compete for human attention and in many cases decisions are made based on the affective meaning they convey. Although the network of structures involved in processing affective value has been well described, the specific contribution of these structures to the process by which affective value guides decision making is less well understood and is the focus of the present study. Thus, subjects read descriptions of individually tailored holidays, varying in incentive value and then made preference judgements, cognitive judgements or no decision. Choices made from an affective perspective, compared with those made from a cognitive perspective, activated a region of the anterior insula/operculum and also the anterior cingulate cortex. Furthermore, activity in perigenual, anterior cingulate cortex was correlated with subjective ratings of incentive value. In contrast, medial orbitofrontal cortex (OFC) and a region of posterior ventrolateral prefrontal cortex (PFC), bordering on the insula, were found to be more active when affective stimuli guided response selection than when no selection was made. However, only the activity in the ventrolateral PFC was specific to response selection based on affective compared with cognitive judgements. It is proposed that the necessary introspection required to make subjective preference judgements is provided by the insula and cingulate cortices, while the medial OFC and posterior ventrolateral PFC/insula cortices contribute to stimulus evaluation and motivational aspects of response selection, respectively.
Why the FLMP should not be applied to McGurk data ...or how to better compare models in the Bayesian framework

We come back on two criticisms addressed to the “Fuzzy-Logical Model of Perception” (FLMP): its assumed ability to fit any data, and the choice of a “fitting all” procedure rather than a “predicting AV from A and V” approach. We confirm the FLMP ability to fit random data in the “McGurk region”, that is in all conditions including conflicting stimuli, thanks to the “0/0 trick”. This is associated to a high instability of the rmse value in the optimal region. Then we introduce a Bayesian approach replacing fit by global likelihood. In this sounder framework, rmse instabilities decrease likelihood, hence the 0/0 trick is problematic for the FLMP. We conclude by indicating when the FLMP can be used in sound conditions: apart from the “McGurk” region.
Performance of Genomic Bordering Elements at Predefined Genomic Loci

ABSTRACT Eukaryotic DNA is organized into chromatin domains that regulate gene expression and chromosome behavior. Insulators and/or scaffold-matrix attachment regions (S/MARs) mark the boundaries of these chromatin domains where they delimit enhancing and silencing effects from the outside. By recombinase-mediated cassette exchange (RMCE), we were able to compare these two types of bordering elements at a number of predefined genomic loci. Flanking an expression vector with either S/MARs or two copies of the non-S/MAR chicken hypersensitive site 4 insulator demonstrates that while these borders confer related expression characteristics at most loci, their effect on chromatin organization is clearly distinct. Our results suggest that the activity of bordering elements is most pronounced for the abundant class of loci with a low but negligible expression potential in the case of highly expressed sites. By the RMCE procedure, we demonstrate that expression parameters are not due to a potential targeting action of bordering elements, in the sense that a linked transgene is directed into a special class of loci. Instead, we can relate the observed transcriptional augmentation phenomena to their function as genomic insulators.
Cooperative multithreading in dynamically reconfigurable systems

Preemptive multitasking, a popular technique for timesharing of computational resources in software-based systems, faces considerable difficulties when applied to partially reconfigurable hardware. In this paper, we propose a cooperative scheduling technique for reconfigurable hardware threads as a feasible compromise between computational efficiency and implementation complexity. We have implemented this mechanism for the multithreaded reconfigurable operating system ReconOS and evaluated its overheads and performance on a prototype.
Consumer Satisfaction

Supported employment has been demonstrated to be a successful rehabilitation model for individuals with severe disabilities. This study was conducted to evaluate the effectiveness of this employment model from the perspective of the individuals with severe disabilities whom it serves. A Consumer Satisfaction Survey, developed by individuals with disabilities and found to be a valid and reliable instrument, was administered to 110 persons with disabilities in Virginia through face-to-face interviews. The results indicated that the majority of consumers like their jobs. Most are happy with supported employment services and would use them again if they lost their job or decided to change jobs. Close to half of the consumers would like to change some aspect of their job to make it better, and more than half feel that their current job is not the career they would like to have permanently. The findings suggest the need to increase consumer involvement in all phases of supported employment service delivery. Strategies to ensure consumer choice and respond to desires to change parts of consumers' jobs or pursue career advancement opportunities are discussed.
Recursive fermion system in Cuntz algebra. I---Embeddings of fermion algebra into Cuntz algebra

Embeddings of the CAR (canonical anticommutation relations) algebra of fermions into the Cuntz algebra ${\cal O}_2$ (or ${\cal O}_{2d}$ more generally) are presented by using recursive constructions. As a typical example, an embedding of CAR onto the U(1)-invariant subalgebra of ${\cal O}_2$ is constructed explicitly. Generalizing this construction to the case of ${\cal O}_{2^p}$, an embedding of CAR onto the U(1)-invariant subalgebra of ${\cal O}_{2^p}$ is obtained. Restricting a permutation representation of the Cuntz algebra, we obtain the Fock representation of CAR. We apply the results to embed the algebra of parafermions of order $p$ into ${\cal O}_{2^p}$ according to the Green's ansatz.
Proteomics as a research tool in clinical and experimental ophthalmology

It is estimated that 37 million people worldwide suffer from blindness and 124 million people have impaired vision. While the relatively recently developed therapies, antivascular endothelial growth factor inhibitors for the treatment of age‐related macular degeneration, and prostaglandin analogues for the treatment of glaucoma are beneficial for some patients, there are many individuals with sight‐threatening diseases for whom no effective pharmacological therapy is available. For many of these diseases, the molecular mechanisms remain to be comprehensively elucidated, thus precluding the design of successful therapies against specific pathological targets. The current review summarises recent attempts to elucidate molecular mechanisms of ocular diseases, including diabetic retinal disease, age‐related macular degeneration and inherited blindness using proteomic methodologies. A novel hypothesis can be generated from global protein expression analysis of disease tissue, which can then be addressed with cellular and in vivo functional studies. For example, the identification of extracellular carbonic anhydrase from the vitreous of diabetic retinopathy patients using MS based proteomics led to the elucidation of a new pathway involved in intraretinal edema, which could be inhibited by a number of agents targeting different proteins in this pathway in relevant animal models. The potential of protein biomarkers for diagnosis and the identification of novel disease mechanisms are also discussed.
Myocardial Motion Analysis for Determination of Tei-Index of Human Heart

The Tei index, an important indicator of heart function, lacks a direct method to compute because it is difficult to directly evaluate the isovolumic contraction time (ICT) and isovolumic relaxation time (IRT) from which the Tei index can be obtained. In this paper, based on the proposed method of accurately measuring the cardiac cycle physical phase, a direct method of calculating the Tei index is presented. The experiments based on real heart medical images show the effectiveness of this method. Moreover, a new method of calculating left ventricular wall motion amplitude is proposed and the experiments show its satisfactory performance.
Evolutionary changes in the orbits and palatal openings of early tetrapods, with emphasis on temnospondyls

ABSTRACT Open palates with large interpterygoid vacuities are a diagnostic characteristic of temnospondyl amphibians, the most species-rich group of early tetrapods. Aside from their functional roles, several other aspects of such vacuities, such as their variation and spatial relationships relative to the orbits, have received only scarce attention. The present work examines patterns of shape and size changes in the orbits and vacuities of temnospondyls using a time-calibrated phylogeny of 69 temnospondyl taxa and 13 additional early tetrapod ‘outgroups' (colosteids, an embolomere, ‘microsaurs' and nectrideans). Orbit and vacuity outlines are quantified in a comparative framework using standard eigenshape analyses. In addition, we employ a series of ratios of linear measurements of both orbits and vacuities, and subject them to a phylogenetic principal component analysis in order to evaluate their proportional changes relative to the skull and to one another. Finally, we examine rates of evolutionary change and their associated shifts for shape and size for both structures, and assess the strength and significance of the correlations between these two variables using phylogenetic generalised least squares analyses. Although orbits and vacuities have fairly simple outlines, they both reveal complex models of proportional change across the temnospondyl phylogeny. These changes exhibit strong phylogenetic signal, that is, trait covariance among taxa is predicted by tree topology. We discuss the hypothesis that, early in tetrapod evolution, the functional role of the vacuities was related to the accommodation of the anterior jaw muscles. Only later in evolution did such vacuities serve to accommodate the eye muscles only.
Ethylenediaminetetraacetic Acid and 65Zn Binding by Intestinal Digesta, Intestinal Mucosa and Blood Plasma 1

Summary The mechanisms of zinc absorption and the effect of EDTA (ethylenediaminetetraacetic acid) on zinc absorption were studied at the intestinal digesta, intestinal mucosa, and blood plasma levels. Dialytic and gel nitration studies showed complexing of 65Zn with free amino acids or EDTA-14C in the intestinal digesta. The EDTA-14C:65Zn complex was bound to a zinc binding protein in the intestinal mucosa (mol wt 14,000-18,000) and to a plasma protein (mol wt 65,000-70,000), that had a greater affinity for zinc than the mucosal protein. The ratios obtained for the cpm EDTA-14C:cpm 65Zn in the main peaks eluted from gel filtration columns (1.10 in intestinal digesta preparation, 1.26 in mucosa soluble fractions, and 1.26 in blood plasma) indicated strong binding of the EDTA-zinc complex. When EDTA was not present in the diet, 65Zn complexed with amino acids in the intestinal digesta and with the same mucosal and blood proteins.
Comparison of high ribavirin induction versus standard ribavirin dosing, plus peginterferon-α for the treatment of chronic hepatitis C in HIV-infected patients: the PERICO trial.

BACKGROUND Ribavirin (RBV) exposure seems to be critical to maximize treatment response in human immunodeficiency virus (HIV)-positive patients with chronic hepatitis C virus (HCV) infection. METHODS HIV/HCV-coinfected individuals naive to interferon were prospectively randomized to receive peginterferon-α-2a (180 μg/d) plus either RBV standard dosing (1000 or 1200 mg/d if <75 or ≥ 75 kg, respectively) or RBV induction (2000 mg/d) along with subcutaneous erythropoietin β (450 IU/kg/wk), both during the first 4 weeks, followed by standard RBV dosing until completion of therapy. Early stopping rules at weeks 12 and 24 were applied in patients with suboptimal virological response. RESULTS A total of 357 patients received ≥ 1 dose of the study medication. No differences in main baseline characteristics were found when comparing treatment arms. Sustained virological response (SVR) was attained by 160 (45%) patients, with no significant differences between RBV induction and standard treatment arms (SVR in 72 of 169 patients [43%] vs 88 of 188 [47%], respectively). At week 4, undetectable HCV RNA (29% vs 25%) and mean RBV trough concentration (2.48 vs 2.14 μg/mL) were comparable in both arms, whereas mean hemoglobin decay was less pronounced in the RBV induction plus erythropoietin arm than in the RBV standard dosing arm (-1.7 vs -2.3 mg/dL; P < .005). Treatment discontinuation occurred in 91 (25%) patients owing to nonresponse and in 29 (8%) owing to adverse events. HCV relapse occurred in 34 patients (10%). Univariate and multivariate analyses identified HCV genotype 2 or 3 (odds ratio [OR], 10.3; 95% confidence interval [CI], 2.08-50.2; P = .004), IL28B CC variants (OR, 2.92; 95% CI, 1.33-6.41; P = .007), nonadvanced liver fibrosis (OR, 2.27; 95% CI, 1.06-5.01; P = .03), and rapid virological response (OR, 40.3; 95% CI, 5.1-314.1; P < .001) as predictors of SVR. CONCLUSIONS A 4-week course of induction therapy with high RBV dosing along with erythropoietin does not improve SVR rates in HIV/HCV-coinfected patients. Preemptive erythropoietin might blunt the benefit of RBV overdosing by enhancing erythrocyte uptake of plasma RBV.
Use of antithrombotic measures for stroke prevention in atrial fibrillation

OBJECTIVE To evaluate appropriateness of antithrombotic use to prevent stroke in atrial fibrillation. DESIGN, PATIENTS 344 patients with atrial fibrillation, stratified by age, were assessed clinically for contraindications to anticoagulation and stroke risk. The use of warfarin and aspirin was compared with recommendations for anticoagulation derived from pooled clinical trial data. RESULTS Low risk of stroke was seen in 47 (14%) patients, moderate risk in 213 (62%), and high risk in 84 (24%) patients included in the sample (mean (SD) age 68.4 (17.2) years, 42% men). The proportion of patients requiring anticoagulation varied from 258/344 (75%) to 72/344 (21%) depending upon criteria used, of whom 86/258 (33%) and 36/72 (50%) were receiving warfarin, respectively. Warfarin or aspirin were not being used in 124/297 (42%) patients with moderate to high risk, whereas anticoagulation was being undertaken in 13/47 (27%) patients at low risk of stroke. Antithrombotic use (warfarin or aspirin) was significantly less common in patients over 75 years of age, regardless of absence of contraindications and eligibility according to various criteria (p < 0.001). CONCLUSIONS A clear need for anticoagulation using clinical criteria existed in about 25% of patients in atrial fibrillation presenting to medical clinics who were at high risk of stroke. Of these, only 50% of eligible patients were being anticoagulated. Appropriate anticoagulation needs to be based on risk assessment rather than age. Consensus is therefore needed on appropriate antithrombotic use in clinical practice.
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Identification of Yeasts Is Contingent on Robust Reference Spectra

Background Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for yeast identification is limited by the requirement for protein extraction and for robust reference spectra across yeast species in databases. We evaluated its ability to identify a range of yeasts in comparison with phenotypic methods. Methods MALDI-TOF MS was performed on 30 reference and 167 clinical isolates followed by prospective examination of 67 clinical strains in parallel with biochemical testing (total n = 264). Discordant/unreliable identifications were resolved by sequencing of the internal transcribed spacer region of the rRNA gene cluster. Principal Findings Twenty (67%; 16 species), and 24 (80%) of 30 reference strains were identified to species, (spectral score ≥2.0) and genus (score ≥1.70)-level, respectively. Of clinical isolates, 140/167 (84%) strains were correctly identified with scores of ≥2.0 and 160/167 (96%) with scores of ≥1.70; amongst Candida spp. (n = 148), correct species assignment at scores of ≥2.0, and ≥1.70 was obtained for 86% and 96% isolates, respectively (vs. 76.4% by biochemical methods). Prospectively, species-level identification was achieved for 79% of isolates, whilst 91% and 94% of strains yielded scores of ≥1.90 and ≥1.70, respectively (100% isolates identified by biochemical methods). All test scores of 1.70–1.90 provided correct species assignment despite being identified to “genus-level”. MALDI-TOF MS identified uncommon Candida spp. , differentiated Candida parapsilosis from C. orthopsilosis and C. metapsilosis and distinguished between C. glabrata, C. nivariensis and C. bracarensis. Yeasts with scores of <1.70 were rare species such as C. nivariensis (3/10 strains) and C. bracarensis (n = 1) but included 4/12 Cryptococcus neoformans. There were no misidentifications. Four novel species-specific spectra were obtained. Protein extraction was essential for reliable results. Conclusions MALDI-TOF MS enabled rapid, reliable identification of clinically-important yeasts. The addition of spectra to databases and reduction in identification scores required for species-level identification may improve its utility.
Climatically Driven Changes in the Supply of Terrigenous Sediment to the East China Sea

We examine the paleoceanographic record over the last ∼400 kyr derived from major, trace, and rare earth elements in bulk sediment from two sites in the East China Sea drilled during Integrated Ocean Drilling Program Expedition 346. We use multivariate statistical partitioning techniques (Q‐mode factor analysis, multiple linear regression) to identify and quantify five crustal source components (Upper Continental Crust (UCC), Luochuan Loess, Xiashu Loess, Southern Japanese Islands, Kyushu Volcanics), and model their mass accumulation rates (MARs). UCC (35–79% of terrigenous contribution) and Luochuan Loess (16–55% contribution) are the most abundant end‐members through time, while Xiashu Loess, Southern Japanese Islands, and Kyushu Volcanics (1–22% contribution) are the lowest in abundance when present. Cycles in UCC and Luochuan Loess MARs may indicate continental and loess‐like material transported by major rivers into the Okinawa Trough. Increases in sea level and grain size proxy (e.g., SiO2/Al2O3) are coincident with increased flux of Southern Japanese Islands, indicating localized sediment supply from Japan. Increases in total terrigenous MAR precede minimum relative sea levels by several thousand years and may indicate remobilization of continental shelf material. Changes in the relative contribution of these end‐members are decoupled from total MAR, indicating compositional changes in the sediment are distinct from accumulation rate changes but may be linked to variations in sea level, riverine and eolian fluxes, and shelf‐bypass processes over glacial‐interglacials, complicating accurate monsoon reconstructions from fluvial dominated sediment.
Detecting Emails Containing Requests for Action

Automatically finding email messages that contain requests for action can provide valuable assistance to users who otherwise struggle to give appropriate attention to the actionable tasks in their inbox. As a speech act classification task, however, automatically recognising requests in free text is particularly challenging. The problem is compounded by the fact that typical emails contain extraneous material that makes it difficult to isolate the content that is directed to the recipient of the email message. In this paper, we report on an email classification system which identifies messages containing requests; we then show how, by segmenting the content of email messages into different functional zones and then considering only content in a small number of message zones when detecting requests, we can improve the accuracy of message-level automated request classification to 83.76%, a relative increase of 15.9%. This represents an error reduction of 41% compared with the same request classifier deployed without email zoning.
Consequences of HIV for children: avoidable or inevitable?

Abstract The HIV/AIDS epidemic has many serious consequences for children. These consequences are, however, rarely inevitable. Families can provide a protective barrier that deflects blows, or minimises their impact and a supportive nurturing environment that can help children recover from harm. If strong enough, and with sufficient access to quality services and support from communities, families can reduce the impacts of HIV/AIDS on children to negligible levels in most areas of impact. It is apparent that the impacts felt by children are not simply unfortunate, inevitable consequences of this epidemic. A strong and supported family with good access to quality services can deflect almost all of the impact. It is as a result of an interaction of the context of poverty, which weakens families, and a failure to adequately respond, that impacts are felt by children.