Miracle-dz/UniFAR-FTUs huggingface dataset:
Advanced Structural and Functional Brain MRI in Multiple Sclerosis

Abstract Conventional magnetic resonance imaging (MRI) of the central nervous system is crucial for an early and reliable diagnosis and monitoring of patients with multiple sclerosis (MS). Focal white matter (WM) lesions, as detected by MRI, are the pathological hallmark of the disease and show some relation to clinical disability, especially in the long run. Gray matter (GM) involvement is evident from disease onset and includes focal (i.e., cortical lesions) and diffuse pathology (i.e., atrophy). Both accumulate over time and show close relation to physical disability and cognitive impairment. Using advanced quantitative MRI techniques such as magnetization transfer imaging (MTI), diffusion tensor imaging (DTI), proton MR spectroscopy (1H-MRS), and iron imaging, subtle MS pathology has been demonstrated from early stages outside focal WM lesions in the form of widespread abnormalities of the normal appearing WM and GM. In addition, studies using functional MRI have demonstrated that brain plasticity is driven by MS pathology, playing adaptive or maladaptive roles to neurologic and cognitive status and explaining, at least in part, the clinicoradiological paradox of MS.
Immune activation and paediatric HIV-1 disease outcome

Purpose of reviewThe paediatric HIV epidemic is changing. Over the past decade, new infections have substantially reduced, whereas access to antiretroviral therapy (ART) has increased. Overall this success means that numbers of children living with HIV are climbing. In addition, the problems observed in adult infection resulting from chronic inflammation triggered by persistent immune activation even following ART mediated suppression of viral replication are magnified in children infected from birth. Recent findingsFeatures of immune ontogeny favour low immune activation in early life, whereas specific aspects of paediatric HIV infection tend to increase it. A subset of ART-naïve nonprogressing children exists in whom normal CD4+ cell counts are maintained in the setting of persistent high viremia and yet in the context of low immune activation. This sooty mangabey-like phenotype contrasts with nonprogressing adult infection which is characterized by the expression of protective HLA class I molecules and low viral load. The particular factors contributing to raised or lowered immune activation in paediatric infection, which ultimately influence disease outcome, are discussed. SummaryNovel strategies to circumvent the unwanted long-term consequences of HIV infection may be possible in children in whom natural immune ontogeny in early life militates against immune activation. Defining the mechanisms underlying low immune activation in natural HIV infection would have applications beyond paediatric HIV.
Converting Enzyme Inhibition Normalizes QT Interval in Spontaneously Hypertensive Rats

We quantified the repolarization time (so-called QT interval) in a rat, an animal species that does not show a well-characterized T wave on surface ECG. We used spontaneously hypertensive rats (SHR) and converting enzyme inhibition to demonstrate a reversible increase in QT interval in pressure-overloaded hearts in the absence of ischemia. An implanted telemetry system recording ECG data in freely moving rats was used to automatically calculate the RR interval. The QT duration was manually determined by use of a calibrated gauge, and a time-frequency domain analysis was used to evaluate heart rate variability. Left ventricular mass was sequentially assessed by echocardiography. Before treatment, 12-month-old SHR had higher left ventricular mass, QT and RR intervals, and unchanged heart rate variability compared with age-matched Wistar rats. A 2-month converting enzyme inhibition treatment with trandolapril reduces systolic blood pressure, left ventricular mass, and QT interval. The RR interval and heart rate variability remains unchanged. There is a positive correlation between the QT interval and left ventricular mass. The SHR is suitable for longitudinal studies on the QT interval. Thus, the detection of the QT interval reflects the phenotypic changes that occur during mechanical overload and, on the basis of these criteria, allows an in vivo determination of the adaptational process.
Spatial linkages between coral proxies of terrestrial runoff across a large embayment in Madagascar

Abstract. Coral cores provide vital climate reconstructions for site-specific temporal variability in river flow and sediment load. Yet, their ability to record spatial differences across multiple catchments is relatively unknown. Here, we investigate spatial linkages between four coral proxies of terrestrial runoff and their relationships between sites. Coral cores were drilled in and around Antongil Bay, the largest bay in Madagascar, and individually analysed for fifteen years of continuous luminescence (G / B), Ba / Ca, δ18Osw and δ13C data. Each coral core was drilled close to individual river mouths (≥ 7 km), and proxy data were compared to modelled river discharge and sediment runoff data for the three corresponding catchments. A reasonable agreement between terrestrial runoff proxies with modelled river discharge and sediment yield was observed. Some inconsistencies between proxy and modelled data are likely linked to proxy behaviour, watershed size and local environmental physiochemical parameters. In general, the further a coral resided from its river source, the weaker the proxy relationship was with modelled data and other corals, due to mixing gradients and currents. Nevertheless, we demonstrate that two coral Ba / Ca and luminescence (G / B) records influenced by the same watershed are reproducible. Furthermore, a strong Ba / Ca relationship was observed between two cores from distant watersheds, with baseline averages in agreement with modelled sediment runoff data. As humic acids behave conservatively in the water column, luminescence (G / B) data gave the highest regional correlations between cores, and showed the most consistent relationship with site specific modelled discharge. No statistical relationship was observed between cores in terms of interannual δ18Osw and δ13C, meaning corals were recording a localised signal at their respective sites, confounded by vital effects. Comparing proxy baseline averages and mean seasonal cycles provided a good overview of the runoff dynamics of the bay system.
Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data

The collection of immunoglobulin genes in an individual’ germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of the several hundred known V alleles. Furthermore, this set of known V alleles is both incomplete (particularly for non-European samples), and contains a significant number of spurious alleles. The resulting uncertainty as to which immunoglobulin alleles are present in any given sample results in inaccurate B cell receptor sequence annotations, and in particular inaccurate inferred naive ancestors. In this paper we first show that the currently widespread practice of aligning each sequence to its closest match in the full set of IMGT alleles results in a very large number of spurious alleles that are not in the sample’s true set of germline V alleles. We then describe a new method for inferring each individual’s germline gene set from deep sequencing data, and show that it improves upon existing methods by making a detailed comparison on a variety of simulated and real data samples. This new method has been integrated into the partis annotation and clonal family inference package, available at httpS://github.com/psathyrella/partis, and is run by default without affecting overall run time. Author Summary Antibodies are an important component of the adaptive immune system, which itself determines our response to both pathogens and vaccines. They are produced by B cells through somatic recombination of germline DNA, which results in a vast diversity of antigen binding affinities across the B cell repertoire. We typically learn about the development of this repertoire, and its history of interaction with antigens, by sequencing large numbers of the DNA sequences from which antibodies are derived. In order to understand such data, it is necessary to determine the combination of germline V, D, and J genes that was rearranged to form each such B cell receptor sequence. This is difficult, however, because the immunoglobulin locus exhibits an extraordinary level of diversity across individuals – encompassing both allelic variation and gene duplication, deletion, and conversion – and because the locus’s large size and repetitive structure make germline sequencing very difficult. In this paper we describe a new computational method that avoids this difficulty by inferring each individual’s set of immunoglobulin germline genes directly from expressed B cell receptor sequence data.
Exposure to Road, Railway, and Aircraft Noise and Arterial Stiffness in the SAPALDIA Study: Annual Average Noise Levels and Temporal Noise Characteristics

Background: The impact of different transportation noise sources and noise environments on arterial stiffness remains unknown. Objectives: We evaluated the association between residential outdoor exposure to annual average road, railway, and aircraft noise levels, total noise intermittency (IR), and total number of noise events (NE) and brachial-ankle pulse wave velocity (baPWV) following a cross-sectional design. Methods: We measured baPWV (meters/second) in 2,775 participants (49–81 y old) at the second follow-up (2010–2011) of the Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults (SAPALDIA). We assigned annual average road, railway, and aircraft noise levels (Ldensource), total day- and nighttime NEtime and IRtime (percent fluctuation=0%, none or constant noise; percent fluctuation=100%, high fluctuation) at the most exposed façade using 2011 Swiss noise models. We applied multivariable linear mixed regression models to analyze associations. Results: Medians [interquartile ranges (IQRs)] were baPWV=13.4 (3.1) m/s; Ldenair (57.6% exposed)=32.8 (8.0) dB; Ldenrail (44.6% exposed)=30.0 (8.1) dB; Ldenroad (99.7% exposed): 54.2 (10.6) dB; NEnight=123 (179); NEday=433 (870); IRnight=73% (27); and IRday=63.8% (40.3). We observed a 0.87% (95% CI: 0.31, 1.43%) increase in baPWV per IQR of Ldenrail, which was greater with IRnight>80% or with daytime sleepiness. We observed a nonsignificant positive association between Ldenroad and baPWV in urban areas and a negative tendency in rural areas. NEnight, but not NEday, was associated with baPWV. Associations were independent of the other noise sources and air pollution. Conclusions: Long-term exposure to railway noise, particularly in an intermittent nighttime noise environment, and to nighttime noise events, mainly related to road noise, may affect arterial stiffness, a major determinant of cardiovascular disease. Ascertaining noise exposure characteristics beyond average noise levels may be relevant to better understand noise-related health effects. https://doi.org/10.1289/EHP1136
A tube concept in rubber viscoelasticity

A constitutive model is derived for the time-dependent response of particle-reinforced elastomers at finite strains. An amorphous rubbery polymer is treated as a network of long chains linked by permanent junctions (chemical crosslinks, entanglements and filler particles). A strand between two neighboring junctions is thought of as a sequence of mers whose motion is restricted to some tube by surrounding macromolecules. Unlike the conventional approach that presumes the cross-section of the tube to be constant, we postulate that its radius strongly depends on the longitudinal coordinate. This implies that a strand may be modeled as a sequence of segments whose thermal motion is totally frozen by the environment (bottle-neck points of the tube) bridged by threads of mers which go through all possible configurations during the characteristic time of a test. Thermal fluctuations affect the tube's radius, which results in freezing and activation of regions with high molecular mobility (RHMs). The viscoelastic response of an elastomer is associated with thermally activated changes in the number of RHMs in strands. Stress-strain relations for a rubbery polymer at finite strains and kinetic equations for the concentrations of RHMs are developed by using the laws of thermodynamics. At small strains these relations are reduced to the conventional integral constitutive equation in linear viscoelasticity with a novel scaling law for relaxation times. The governing equation is determined by 5 adjustable parameters which are found by fitting experimental data in tensile dynamic tests on a carbon black filled natural rubber vulcanizate.
Optimization of multi-stage amplifiers in deep-submicron CMOS using a distributed/parallel genetic algorithm

This paper presents a framework for time-domain optimization of amplifiers employing a parallel genetic algorithm based on a message passing interface. This methodology achieves a considerable reduction in the optimization time (up to 19 times faster than a serial implementation). Increasing the processing capacity allows searching within a larger design space using complex transistors models, yielding more accurate results. The optimization, based on transient simulations, is possible due to the integration of a genetic algorithm optimizer together with the open-source simulator NGSPICE source-code.
High incidence of plasmid-mediated quinolone resistance genes among ciprofloxacin-resistant clinical isolates of Enterobacteriaceae at a tertiary care hospital in Puducherry, India

Background. Plasmid-mediated quinolone resistance (PMQR) has received considerable attention recently. Data analysis in Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER) revealed 75% of the Enterobacteriaceae isolates to be ciprofloxacin-resistant in 2012. Few reports regarding the prevalence of PMQR are available from India. Hence, the present study was carried out to ascertain the prevalence of PMQR genes among clinical isolates of ciprofloxacin-resistant Enterobacteriaceae in JIPMER. Methods. The study included 642 ciprofloxacin-resistant clinical Enterobacteriaceae isolates. JIPMER hospital’s annual consumption data for fluoroquinolones were retrieved from the Department of Pharmacy. The test isolates were screened for the presence of qnr A, B, D, S and aac(6′)-Ib-cr genes. PMQR-positive isolates alone were tested for the presence of class I (intI1) and class II (intI2) integrons. Randomly selected PCR amplicons were sequenced and analysed using MEGA software. A total of 30 PMQR strains chosen at random were assessed for the transferability of the PMQR genes. Results. A majority of the strains exhibited high MIC values with 106 strains exhibiting MIC values >256 µg/mL. The aac(6′)-Ib-cr gene had the highest prevalence at 64% (414) while, qnrB and qnrS genes were present in 15% (97) and 10% (64) of the isolates respectively. None of the strains were positive for qnrA and qnrD. All PMQR-positive isolates were screened for class I (intI1) and class II (intI2) integrons. Class I integron was found to be predominant among the test isolates with a few of them carrying both the classes of integrons. Transferability of PMQR genes to transconjugants was identified. Conclusion. The incidence of PMQR genes in the tertiary-care setup of the JIPMER hospital was found to be high which could be probably due to the increased prescription of fluoroquinolones. Thus, there is a need for rational usage of fluoroquinolones.
Learning Hierarchical Task Models By Demonstration

Acquiring a domain-specific ’task model’ is an essential and notoriously challenging aspect of building knowledge-based systems. This paper presents machine learning techniques which are built into an interface that eases this knowledge acquisition task. These techniques infer hierarchical models, including parameters for non-primitive actions, from partially-annotated demonstrations. Such task models can be used for plan recognition, intelligent tutoring, and other collaborative activities. Among the contributions of this work are a sound and complete learning algorithm and empirical results that measure the utility of possible annotations.
A General Factor of Personality From Multitrait–Multimethod Data and Cross–National Twins

Abstract In three studies, a General Factor of Personality (GFP) was found to occupy the apex of the hierarchical structure. In Study 1, a GFP emerged independent of method variance and accounted for 54% of the reliable variance in a multitrait–multimethod assessment of 391 Italian high school students that used self-, teacher-, and parent-ratings on the Big Five Questionnaire — Children. In Study 2, a GFP was found in the seven dimensions of Cloninger's Temperament and Character Inventory as well as the Big Five of the NEO PI-R, with the GFPtci correlating r = . 72 with the GFPneo. These results indicate that the GFP is practically the same in both test batteries, and its existence does not depend on being extracted using the Big Five model. The GFP accounted for 22% of the total variance in these trait measures, which were assessed in 651 pairs of 14- to 30-year-old Japanese twins. In Study 3, a GFP accounted for 32% of the total variance in nine scales derived from the NEO PI-R, the Humor Styles Questionnaire, and the Trait Emotional Intelligence Questionnaire assessed in 386 pairs of 18- to 74-year-old Canadian and U.S. twins. The GFP was found to be 50% heritable with high scores indicating openness, conscientiousness, sociability, agreeableness, emotional stability, good humor and emotional intelligence. The possible evolutionary origins of the GFP are discussed.
Perceived Risk and the Internet Shopping Experience in Online Purchasing Behaviour

This paper reports the findings of a Web-based survey of 700 New Zealand Internet users. The survey was designed to explore the importance of perceived consumer risk and the Internet shopping experience in the online purchasing behaviour of Internet users. Both perceived consumer risk and loss of social interaction in Internet shopping were found to be negatively associated with the amount of online purchases made. The results of the study suggest that electronic retailing Web sites could usefully include features that reduce perceived consumer risk and enhance online customer service.
The Numerical Solution of Separably Stiff Systems by Precise Partitioning

Most codes for solving stiff systems of ordinary &fferentlal equations spend most of their time solving systems of linear equations with coefficient matrix I hflJ, where J is the Jacobian matrix of the system The precise partltmning method solves these systems approxamately by partitioning the Jaeobian into stiff and nonstiff parts The method resembles a method proposed by Enright and Kamel [ACM Transactmns on Mathemattcal Software 5, 4(Dec. 1979), 374-385], bu t chffers in tha t the partition of the Jacobmn matrix is more precise In this paper the method is implemented by revising a popular code. Numermal results inchcate tha t for systems of more than about ten equations with few stiff eigenvalues, the precise partitmning method can save CPU time compared to the unmodified code.
SPORC: Group Collaboration using Untrusted Cloud Resources

Cloud-based services are an attractive deployment model for user-facing applications like word processing and calendaring. Unlike desktop applications, cloud services allow multiple users to edit shared state concurrently and in real-time, while being scalable, highly available, and globally accessible. Unfortunately, these benefits come at the cost of fully trusting cloud providers with potentially sensitive and important data. To overcome this strict tradeoff, we present SPORC, a generic framework for building a wide variety of collaborative applications with untrusted servers. In SPORC, a server observes only encrypted data and cannot deviate from correct execution without being detected. SPORC allows concurrent, low-latency editing of shared state, permits disconnected operation, and supports dynamic access control even in the presence of concurrency. We demonstrate SPORC's flexibility through two prototype applications: a causally-consistent key-value store and a browser-based collaborative text editor. Conceptually, SPORC illustrates the complementary benefits of operational transformation (OT) and fork* consistency. The former allows SPORC clients to execute concurrent operations without locking and to resolve any resulting conflicts automatically. The latter prevents a misbehaving server from equivocating about the order of operations unless it is willing to fork clients into disjoint sets. Notably, unlike previous systems, SPORC can automatically recover from such malicious forks by leveraging OT's conflict resolution mechanism.
Effect of Probiotic and Population Density on the Growth Performance and Carcass Characteristics in Broiler Chickens

In order to assess the effect of a probiotic and population density on the growth performance and the carcass characteristics in broiler chickens, an experiment was conducted involving 208 1-day-old Peterson brand chicks. They were fed a corn and soy paste diet with 23 and 20 percent crude protein at the first and last stage respectively and 3.2 Mcal ME/kg. A completely randomized design with a 2 x 2 factorial arrangement, with two probiotics levels: 0 y 0.1% and two population density levels: 10 and 16 birds/m , with 2 four repetitions per treatment. The evaluation centered on growth performance: weight gain, feed consumption, food conversion and carcass variables: hot and chilled carcass weight, as well as breast, leg and thigh output. The growth performance was not affected (P>0.05) by probiotic and population density. The greatest yields (P<0.05) in the hot carcass weight was reported from the interaction between 0.1% probiotic and 10 birds/m . The probiotic increased (P<0.05) the lean leg meat. The density of 16 birds/m showed the 2 2 highest yield (P<0.05) in leg fat versus 10 birds/m . The results of this study indicated that, 0.1% probiotic 2 increased the lean leg meat yield and the population density of 16 birds/m generates a higher fat deposit 2 in broiler chickens.