Miracle-dz/UniFAR-FTUs huggingface dataset:
Feasibility of MR-Based Body Composition Analysis in Large Scale Population Studies

Introduction Quantitative and accurate measurements of fat and muscle in the body are important for prevention and diagnosis of diseases related to obesity and muscle degeneration. Manually segmenting muscle and fat compartments in MR body-images is laborious and time-consuming, hindering implementation in large cohorts. In the present study, the feasibility and success-rate of a Dixon-based MR scan followed by an intensity-normalised, non-rigid, multi-atlas based segmentation was investigated in a cohort of 3,000 subjects. Materials and Methods 3,000 participants in the in-depth phenotyping arm of the UK Biobank imaging study underwent a comprehensive MR examination. All subjects were scanned using a 1.5 T MR-scanner with the dual-echo Dixon Vibe protocol, covering neck to knees. Subjects were scanned with six slabs in supine position, without localizer. Automated body composition analysis was performed using the AMRA Profiler™ system, to segment and quantify visceral adipose tissue (VAT), abdominal subcutaneous adipose tissue (ASAT) and thigh muscles. Technical quality assurance was performed and a standard set of acceptance/rejection criteria was established. Descriptive statistics were calculated for all volume measurements and quality assurance metrics. Results Of the 3,000 subjects, 2,995 (99.83%) were analysable for body fat, 2,828 (94.27%) were analysable when body fat and one thigh was included, and 2,775 (92.50%) were fully analysable for body fat and both thigh muscles. Reasons for not being able to analyse datasets were mainly due to missing slabs in the acquisition, or patient positioned so that large parts of the volume was outside of the field-of-view. Discussion and Conclusions In conclusion, this study showed that the rapid UK Biobank MR-protocol was well tolerated by most subjects and sufficiently robust to achieve very high success-rate for body composition analysis. This research has been conducted using the UK Biobank Resource.
Roles of nitrate, nitrite and ammonium ion in phytochrome regulation of nitrate reductase gene expression in maize

The influence of nitrate and its metabolites on the nitrate reductase (NR) gene expression and its relationship with phytochrome (Pfr) regulation of NR in etiolated maize leaves is examined. Nitrate induction and Pfr stimulation are brought about by independent signalling phenomena. Phorbol myristate acetate (PMA), a stimulator of protein kinase C (PKC), mimicked the effect of red light but could not replace the nitrate requirement for the induction of NR transcript accumulation. This suggests that while PKC‐type enzymes may be involved in mediating the Pfr signal, nitrate may follow an independent signalling mechanism. Experiments with 5‐hydroxytryptamine (5HT) and lithium ions (Li+), which are known to modulate phosphoinositide (PI) turnover, indicated that in addition to generating Pfr‐induced second messengers for PKC activation, PI cycle may also generate other signals which mediate nitrate induction of NR gene expression in the dark. The products of nitrate reduction ie, nitrite and ammonium ion had inhibitory and stimulatory effects respectively, on NR transcript accumulation. They work mainly at the level of nitrate induction.
An intelligent editor for multi-presentation user interfaces

In ubiquitous computing, interactive applications are shipped with different variations of its user interface depending on the constraints imposed by the context in which they are running, such as the user, the computing platform and environment. A multi-presentation user interface is composed of a series of interconnected user interfaces for the same task to be carried out in different contexts of use. When access to software applications must be guaranteed in more than one context of use, it is necessary to automatically adapt the interface in order to preserve their usability when context switching occurs, for instance, a switch from a desktop to a pocket computer. To achieve this goal, this paper proposes a model and a visualization technique to express and manipulate the plasticity domains of a multi-presentation user interface. The plasticity domain denotes the set of contexts of use it is able to cover while preserving its usability. This paper focuses primarily on one aspect of the context of use: the computing platform and its screen size: when the dimensions of a graphical user interface change, the multi-presentation interface automatically switches to the presentation which is the most adapted to this screen. The model supports the definition of this plasticity domain in terms of window size and location. The visualization technique helps in both making observable the set of presentations that fit the available space, and perceiving which operations could help in switching from one presentation to another one. The model has been integrated into a user interface description language and is supported by an intelligent editor, because it infers from plasticity domains all the constraints and conditions required for context switching.
Energy-delay tradeoffs in a load-balanced router

The Load-Balanced Router architecture has received a lot of attention because it does not require centralized scheduling at the internal switch fabrics. In this paper we reexamine the architecture, motivated by its potential to turn off multiple components and thereby conserve energy in the presence of low traffic. We perform a detailed analysis of the queue and delay performance of a Load-Balanced Router under a simple random routing algorithm. We calculate probabilistic bounds for queue size and delay, and show that the probabilities drop exponentially with increasing queue size or delay. We also demonstrate a tradeoff in energy consumption against the queue and delay performance.
Neural Basis of Adaptive Response Time Adjustment during Saccade Countermanding

Humans and macaque monkeys adjust their response time adaptively in stop-signal (countermanding) tasks, responding slower after stop-signal trials than after control trials with no stop signal. We investigated the neural mechanism underlying this adaptive response time adjustment in macaque monkeys performing a saccade countermanding task. Earlier research showed that movements are initiated when the random accumulation of presaccadic movement-related activity reaches a fixed threshold. We found that a systematic delay in response time after stop-signal trials was accomplished not through a change of threshold, baseline, or accumulation rate, but instead through a change in the time when activity first began to accumulate. The neurons underlying movement initiation have been identified with stochastic accumulator models of response time performance. Therefore, this new result provides surprising new insights into the neural instantiation of stochastic accumulator models and the mechanisms through which executive control can be exerted.
Lexical Tone Recognition with an Artificial Neural Network

Objectives: Tone production is particularly important for communicating in tone languages such as Mandarin Chinese. In the present study, an artificial neural network was used to recognize tones produced by adult native speakers. The purposes of the study were (1) to test the sensitivity of the neural network to speaker variation typically in adult speaker groups, (2) to evaluate two normalization procedures to overcome the effects of speaker variation, and (3) to compare tone recognition performance of the neural network with that of the human listeners. Design: A feedforward multilayer neural network was used. Twenty-nine adult native Mandarin Chinese speakers were recruited to record tone samples. The F0 contours of the vowel part of the 1044 monosyllabic words recorded were extracted using an autocorrelation method. Samples from the F0 contours were used as inputs to the neural network. The efficacy of the neural network was first tested by varying the number of inputs and the number of neurons in the hidden layer from 1 to 16. The sensitivity of the neural network to speaker variation was tested by (1) using the raw F0 data from speech tokens of a number of randomly drawn speakers that varied from 1 to 29, (2) using the raw F0 data from speech tokens of either male-only or female-only speakers, and (3) using two sets of normalized F0 data (i.e., tone 1-based normalization and first-order derivative) from speech tokens from a number of randomly drawn speakers that varied from 1 to 29. The recognition performance of the neural network under several experimental conditions was compared with the corresponding recognition performance of 10 normal-hearing, native Mandarin Chinese speaking adult listeners. Results: Three inputs and four hidden neurons were found to be sufficient for the neural network to perform at about 85% correct using speech samples without normalization. The performance of the neural network was affected by variation across speakers particularly between genders. Using the tone 1-based normalization procedure, the performance of the neural network improved significantly. The recognition accuracy of the neural network as a whole or for each tone was comparable with that of the human listeners. Conclusions: The neural network can be used to evaluate the tone production of Mandarin Chinese speaking adults with human listener-like recognition accuracy. The tone 1-based normalization procedure improves the performance of the neural network to human listener-like accuracy. The success of our neural network in recognizing tones from multiple speakers supports its utility for evaluating tone production. Further testing of the neural network with hearing-impaired speakers might reveal its potential use for clinical evaluation of tone production.
Fibre Bragg grating sensing and finite element analysis of the biomechanics of the mandible

This paper describes the application of fibre Bragg grating (FBG) sensors to measure strains at the outer surface of a mandible. The strains were correlated to identical ones obtained with a numerical finite element model. For this purpose, a synthetic mandible was used and 4 Bragg sensors were glued to the mandible. Strain patterns were assessed for different load configurations which included the forces of the masseter and temporal muscles and occlusion loads on different tooth (incisor, canine and molar). Overall the strains obtained using different measuring methods were identical, namely for the case of symmetric loading. When loading was non-symmetric, strain differences were observed at one sensor.
Comparative studies need to rely both on sound natural history data and on excellent statistical analysis

Evolutionary biologists aim to determine why a particular trait evolved. Detailed studies of single species can identify fitness benefits of specific traits and why those traits evolved, but these results might be rather species specific. Thus, to reach general conclusions about which ecological factors favour the evolution of a specific trait, comparative studies in several taxa are needed. Currently, comparative studies arising from databases summarizing many field studies are flourishing and provide important insights for our understanding of social evolution [1–3]. Large, diverse datasets require detailed specialist knowledge in a wide variety of systems or taxa that is very rare, making it difficult to assess the quality of such databases. Referees of papers submitted to assess these comparative studies should review the part of the database for which they do have specialized knowledge. In some cases, studies with large databases could benefit from one additional referee that focuses only on the database itself, just as the views of specialized referees are often sought on aspects of statistical analysis or of animal ethics. In sum, the quality of a study depends on the quality of the data, and this is also the case for comparative studies. A recently published comparative study in Royal Society Open Science about cooperative breeding in mammals [4] used a database previously used in a comparative study of the evolution of monogamy in the same taxa [5]. It had already been shown that for the third largest mammalian order, the Eulipotyphla, the information in this database is, to a large extent, inadequate [6]. In the supplement to their earlier publication on the evolution of social monogamy [5], Lukas & Clutton-Brock state that the database is the result of a systemic literature review on ‘mammalian species…collecting …
Diagnosis, prevention and treatment of accidental and perioperative hypothermia

Abstract Accidental hypothermia and its variant, perioperative hypothermia, is a rather common clinical phenomenon in patients. This is surprising because the negative effects on clinical outcomes are well described and effective patient-warming devices are available today. The aim of this paper is to describe the physiologic background of accidental and perioperative hypothermia, the clinical relevance and existing prophylaxis and treatment options. Patient warming techniques will be discussed in detail. Remaining technical and clinical challenges and the need for further research will be addressed. We will present existing guidelines and standards and analyse the impact of accidental and perioperative hypothermia on cost effectiveness.
A NOVEL APPROACH OF ADAPTIVE SOCIALLY AWARE ROUTING ALGORITHM IN DELAY TOLERANT NETWORKS

Original scientific paper Under the delay tolerant network, high mobility of the node and the transmission distance make it impossible to keep a durable and regular data routing path between two nodes. As a result, such failure affects the function of packet routing mechanism. Therefore, in order to improve the efficacy of data transmission, conventional delay tolerant routing adopts more packet replication, or makes opportunistic on-line with encountered nodes and selects advantageous ones to increase packet arrival rate or reduce transmission delay rate. However, excessive increase of packet replication or excessive records for selected transmission nodes may result in internet traffic or a waste of resources. It may also lead to a lower level of the routing protocol or a complicated operation. Thus, conventional delay tolerant routing is not satisfying. This research intends to design an optimized forward strategy on the basis of different routing algorithm. This strategy is based on adaptive socially aware and aims at improving solving problems of delay tolerant networks routing.
Molecular Epidemiology of Metallo-β-Lactamase-Producing Pseudomonas aeruginosa in the Calgary Health Region: Emergence of VIM-2-Producing Isolates

ABSTRACT A study was designed to describe the molecular epidemiology of carbapenem-resistant (CR) Pseudomonas aeruginosa in a large well-defined geographical region with a centralized laboratory system serving one pediatric and three large adult hospitals (acute care centers I, II, and III). Molecular characterization was done using PCR with sequencing of the integron-associated gene cassettes. Pulsed-field gel electrophoresis (PFGE) using a modified combined Stenotrophomas maltophilia and Streptococcus pneumoniae protocol with SpeI was performed on CR P. aeruginosa strains isolated in the Calgary Health Region during 2002-2006. The majority (96%) of metallo-β-lactamase (MBL)-producing isolates produced VIM-2 with gene cassettes aacC1 and aacA4, while 4% produced IMP-7 with gene cassettes aacC4 and aacC1. Eighty-six percent of VIM-2 producers belonged to a cluster (MBLV) that was responsible for nosocomial outbreaks during 2003 (intensive care unit) and 2004 (bone marrow transplant unit) at acute care center I. Environmental isolates from these units also belonged to MBLV. The majority of strains from cluster MBLVR (related to MBLV) were present in acute care center III. Isolates producing IMP-7 belonged to a different cluster (MBLI) and were related to strains described during the 1990s. PFGE of the MBL-negative CR strains showed that 37% belonged to a closely related cluster, NMBL, whose members were predominantly isolated from acute care center II. Our findings suggest that CR and dissemination of MBL clusters among P. aeruginosa populations in large geographic healthcare regions are dynamic processes that require continuous molecular surveillance.
A Case of Potential Treatment of Remote Pain After Sacral Nerve Stimulation for Chronic Urinary Retention

Objective:A case is presented in which a 58-year-old man developed a potential unintended and durable treatment of pain at remote sites (cervical region and low back) after sacral nerve stimulation for chronic urinary retention. Methods:Proper placement of the electrodes in the S3 foramen was confirmed by physiological response and fluoroscopy. Results:Potential causality was shown by recurrent pain with the stimulators turned off and abatement of pain with the stimulators turned on. Discussion:The current case presents a potential example of neurological crosstalk and highlights the inherent complexity in human neural physiology. Further research may reveal novel treatment strategies for patients with voiding dysfunction and chronic pain syndromes.
Amniocentesis in HIV Pregnant Women: 16 Years of Experience

The iatrogenic risk of HIV vertical transmission, calculated in initial epidemiologic studies, seemed to counterindicate invasive prenatal diagnosis (PND) procedures. The implementation of highly active antiretroviral therapy (HAART) represented a turning point in PND management, owing to a rapid and effective reduction of maternal viral load (VL). In the present study, we identified cases of vertical transmission in HIV-infected pregnant women who did amniocentesis in the second trimester of pregnancy (n = 27), from 1996 to 2011. We divided our sample into Group A—women under HAART when submitted to amniocentesis (n = 20) and Group B—women without antiretroviral therapy before amniocentesis (n = 7). We had 1 case of vertical transmission in Group B. Preconceptional or early first trimester HIV serology is essential to avoid performing an amniocentesis without antiretroviral therapy or viral suppression. When there is an indication for amniocentesis in an HIV-infected pregnant woman, it should be done if the patient is on HAART and, if possible, when VL is undetectable. Nowadays, with combined first trimester screening test to select pregnancies with high risk of aneuploidies, advanced maternal age is a less frequent indication to perform PND invasive procedures, representing an outstanding gain in prenatal diagnosis of this population.
Digital Commons@Becker

Background: Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. Results: We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥ 2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw reads against the entire genome using Novoalign
Risk of Gastric Pouch Enlargement With Adjustable Gastric Banding in Premenopausal Women: Sex Hormones May Play a Role

Objective: To examine the influence of age and gender on the development of proximal gastric pouch distension (PPD) after laparoscopic adjustable gastric banding (LAGB) surgery. Background: PPD is the most common reason for revision with adjustable gastric banding surgery. Maintaining the anatomical integrity of bariatric surgery is a key to long-term success. It is therefore important to understand risk factors for complications. Methods: We extracted details of 3000 consecutive individuals who underwent primary LAGB procedures at a single center between February 2005 and May 2011. Contemporaneous details of all complications were recorded in a database. The characteristics of those that subsequently required revision surgery for PPD were assessed and compared with those that did not. Results: There were 132 cases for PPD requiring surgical intervention before September 2011. Incident PPD occurred in 5.1% and 1.3% of women and men, respectively. The mean age of those with PPD was 39.9 ± 9.25 compared with 43.9 ± 11.0 for those without it. The age and gender effects were independent, and the age effect was restricted to women. The adjusted odds ratios were 0.971 (95% CI [confidence interval], 0.954–0.986, P < 0.001) for age and 0.26 (95% CI, 0.12–0.56, P = 0.001) for male gender and younger women were more likely to have asymmetrical distension. Conclusions: Younger women are at higher risk of PPD after LAGB surgery than men and women older than 50 years. Sex hormones may play a role in predisposing to gastric stretch after surgery. These findings may apply more broadly to the gastric “restrictive” component of other bariatric procedures.
Learning Multi-View Neighborhood Preserving Projections

We address the problem of metric learning for multi-view data, namely the construction of embedding projections from data in different representations into a shared feature space, such that the Euclidean distance in this space provides a meaningful within-view as well as between-view similarity. Our motivation stems from the problem of cross-media retrieval tasks, where the availability of a joint Euclidean distance function is a prerequisite to allow fast, in particular hashing-based, nearest neighbor queries. We formulate an objective function that expresses the intuitive concept that matching samples are mapped closely together in the output space, whereas non-matching samples are pushed apart, no matter in which view they are available. The resulting optimization problem is not convex, but it can be decomposed explicitly into a convex and a concave part, thereby allowing efficient optimization using the convex-concave procedure. Experiments on an image retrieval task show that nearest-neighbor based cross-view retrieval is indeed possible, and the proposed technique improves the retrieval accuracy over baseline techniques.