Miracle-dz/UniFAR-FTUs huggingface dataset:
Regional skeletal muscle measurement: evaluation of new dual-energy X-ray absorptiometry model.

Although there is growing interest in studying muscle distribution, regional skeletal muscle (SM) mass measurement methods remain limited. The aim of the present study was to develop a new dual-energy X-ray absorptiometry (DEXA) model for estimating regional adipose tissue-free skeletal muscle mass (AT-free SM). Relationships were derived from Reference Man data between tissue-system- level components (i.e., AT-free SM, AT, skeleton, and skin) and molecular-level components including fat-free soft tissue, fat, and bone mineral. The proposed DEXA-SM model was evaluated by multiscan computerized axial tomography (CT). Twenty-seven male subjects [age, 36 +/- 12 (SD) yr; body mass, 73.2 +/- 12.4 kg; 20 were healthy, and 7 had acquired immunodeficiency syndrome] completed DEXA and CT studies. Identical landmarks for DEXA and CT measurements were selected in three regions, including calves, thighs, and forearms. There was a strong correlation for AT-free SM estimates between the new DEXA and CT methods (e.g., sum of three regions, r = 0.86, P < 0.001). Regional AT-free SM measured in the 27 subjects by DEXA and CT, respectively, were 3.44 +/- 0.60 and 3. 47 +/- 0.55 kg (difference 0.9%, P > 0.05) for calves, 10.49 +/- 1. 77 and 10.05 +/- 1.79 kg (difference 4.4%, P < 0.05) for thighs, 1. 36 +/- 0.49 and 1.20 +/- 0.41 kg (difference 13.3%, P < 0.01) for forearms, and 15.29 +/- 2.33 and 14.72 +/- 2.33 kg (difference 3.9%, P < 0.05) for the sum all three regions. Although the suggested DEXA-SM model needs minor refinements, this is a promising in vivo approach for measurement of regional SM, because DEXA is widely available, relatively inexpensive, and radiation exposure is low.
Seven‐up facilitates insect counter‐defense by suppressing cathepsin B expression

When challenged by the dietary soybean cysteine protease inhibitor scN, the cowpea bruchid (Callosobruchus maculatus) adapts to the inhibitory effects by readjusting the transcriptome of its digestive system, including the specific activation of a cathepsin B‐like cysteine protease CmCatB. To understand the transcriptional regulation of CmCatB, we cloned a portion of its promoter and demonstrated its activity in Drosophila cells using a chloramphenicol acetyltransferase reporter system. EMSAs detected differential DNA‐binding activity between nuclear extracts of scN‐adapted and ‐unadapted midguts. Two tandem chicken ovalbumin upstream promoter (COUP) elements were identified in the CmCatB promoter that specifically interacted with a protein factor unique to nuclear extracts of unadapted insect guts, where CmCatB expression was repressed. Seven‐up (Svp) is a COUP‐TF‐related transcription factor that interacted with the COUP responsive element. Polyclonal anti‐(mosquito Svp) serum abolished the specific DNA‐binding activity in cowpea bruchid midgut extracts, suggesting that the protein factor is an Svp homolog. Subsequent cloning of a cowpea bruchid Svp (CmSvp) indicated that it shares a high degree of amino acid sequence similarity with COUP‐TF/Svp orphan nuclear receptor family members from varied species. The protein was more abundant in scN‐unadapted insect guts than scN‐adapted guts, consistent with the observed DNA‐binding activity. Furthermore, CmCatB expression was repressed when CmSvp was transiently expressed in Drosophila cells, most likely through COUP binding. These findings indicate that CmSvp may contribute to insect counter‐defense, in part by inhibiting CmCatB expression under normal growth conditions, but releasing the inhibition when insects are challenged by dietary protease inhibitors.
Modelling and simulation of complex repetitive construction operations

In an effort to improve productivity and optimise resource use, a simplified activity-on-arrow (AOA) approach is used in this paper to model and simulate real-world repetitive construction operations of high-rise buildings. The objective of the paper is to use simulation to find the optimum combination of construction resources to improve construction productivity and minimise operational cost. In order to achieve the goals of the study, a simulation model for typical floor finishes activities of a high-rise building project was developed. The model was validated through a predefined construction operation. Several model runs were then conducted using different resource combinations. The results were tabulated to arrive at the optimum combination that improves productivity and reduces the operational cost. In addition, the developed model was used to experiment with different resource alternatives and overtime options for one floor and for repetitive floors in order to arrive at the best resource alternatives that provide the optimum solution. The potential of using this approach for resource optimisation of large infrastructure networks is investigated, and possible future extensions to the present study are discussed.
Characterization of Nerve Growth Factor (NGF) Release from Hippocampal Neurons: Evidence for a Constitutive and an Unconventional Sodium‐dependent Regulated Pathway

We investigated the mechanism of neuronal nerve growth factor (NGF) release with regard to the potential function of NGF as a mediator of neuronal plasticity in the CNS. The analysis was performed in hippocampal slices and in primary cultures of hippocampal neurons, transiently transfected with an NGF cDNA construct to increase the level of NGF expression. In both systems there was activity‐dependent NGF release initiated by high potassium (KCl), veratridine, glutamate or carbachol. Replacement of 90% of sodium in the medium with N‐methyl‐glucamine strongly reduced this release. The KCl‐ and veratridine‐initiated NGF release was suppressed by tetrodotoxin; release by glutamate was less sensitive to tetrodotoxin but was sodium‐dependent. The glutamate effect could be inhibited by GYK152644, an antagonist of α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole propionic acid receptors, but not by MK‐801, an antagonist of NMDA receptors. The activity‐dependent release of NGF did not depend on extracellular Ca2+, but was sensitive to the intracellular Ca2+ chelator bis‐(o‐aminophenoxy)‐ethane‐N,N,N',N'‐tetraacetic acid tetra(acetoxymethyl)‐ester, and to depletion of intracellular calcium stores. Conversely, mobilization of Ca2+ from intracellular stores with caffeine and thapsigargin mimicked the effect of depolarization. Basal NGF release could be reduced by either temperature block (15°C) or tetrodotoxin to ˜50%. The combination of both treatments reduced NGF release to below the detection limit, suggesting that basal release has constitutive and regulated components, the latter presumably resulting from spontaneous activity of interconnected neurons.
A Comparative Exposure Assessment of Campylobacter in Ontario, Canada

To inform source attribution efforts, a comparative exposure assessment was developed to estimate the relative exposure to Campylobacter, the leading bacterial gastrointestinal disease in Canada, for 13 different transmission routes within Ontario, Canada, during the summer. Exposure was quantified with stochastic models at the population level, which incorporated measures of frequency, quantity ingested, prevalence, and concentration, using data from FoodNet Canada surveillance, the peer‐reviewed and gray literature, other Ontario data, and data that were specifically collected for this study. Models were run with @Risk software using Monte Carlo simulations. The mean number of cells of Campylobacter ingested per Ontarian per day during the summer, ranked from highest to lowest is as follows: household pets, chicken, living on a farm, raw milk, visiting a farm, recreational water, beef, drinking water, pork, vegetables, seafood, petting zoos, and fruits. The study results identify knowledge gaps for some transmission routes, and indicate that some transmission routes for Campylobacter are underestimated in the current literature, such as household pets and raw milk. Many data gaps were identified for future data collection consideration, especially for the concentration of Campylobacter in all transmission routes.
Fast, exact linkage analysis for categorical traits on arbitrary pedigree designs

Multi‐symptom diseases without a consistent continuous measurement of severity may be best understood with a categorical interpretation. In this paper, we present LOCate v.2, a fast, exact algorithm for linkage analysis of all types of categorical traits, both ordinal and nominal. Our method is able to incorporate missing data and analyze complex genealogical structure, including inbreeding loops. LOCate v.2 computes exact likelihoods efficiently through an elimination algorithm, similar to that used by Superlink for binary traits. We compare LOCate v.2 to LOT and QTLlink, two existing methods of linkage analysis for ordinal traits. We find that LOCate v.2 outperforms both methods when used to analyze simulated nominal traits. In addition, LOCate v.2 performs as well as QTLlink on simulated ordinal traits, and better than LOT due to the necessity of cutting large pedigrees for analysis in LOT. To demonstrate the versatility of LOCate v.2, we conduct an ordinal and nominal linkage analysis of ventricular arrhythmias in a large, inbred pedigree of German Shepherd dogs. We find that a trichotomous ordinal or nominal interpretation strengthens the evidence in favor of linkage to a region on chromosome 6, and provides new evidence of linkage to a region on chromosome 11. LOCate v.2 is a unified, fast, and robust method for linkage analysis of ordinal and nominal traits which will be valuable to researchers interested in investigating any type of categorical trait. Genet. Epidemiol. 2011. © 2011 Wiley‐Liss, Inc. 35:371‐380, 2011
What is the effect of additional physiotherapy on sitting balance following stroke compared to standard physiotherapy treatment: a systematic review

Background: Sitting balance dysfunction is commonly experienced following stroke. Physiotherapists utilize interventions to address this problem but it is unclear whether treatment type, target or practice intensity may affect outcomes. Objective: To compare the effects of standard physiotherapy to standard physiotherapy plus an additional physiotherapy treatment after stroke. Data Sources: The databases of Cochrane Library, CINAHL, Embase, Ovid Medline, AMED, and the Physiotherapy Evidence Database (PEDro) up to December 2014 were searched. Study Selection: Randomized controlled trials in English reported in peer-reviewed journals regarding the effect of additional physiotherapy on sitting balance were retrieved. Data Extraction: The PEDro scale was used to assess study quality. Results: Eleven studies met inclusion criteria. Nine targeted the ICF (International Classification of Function, Disability and Health) domain of Activity. The Trunk control test (TCT) was used as a primary outcome measure in five studies, and the Trunk Impairment Scale (TIS) was used in four. There was a significant effect (mean difference = 1.67, 95% CI = 0.54–2.80) favoring intervention, as measured by the TIS. There was no evidence to support the effect of additional treatment on sitting balance as measured by the TCT (mean difference = − 1.53, 95% CI = − 9.37 to 6.32). Conclusion:The current evidence supports strategies that target deficits at the activity level and increase total treatment time. The TIS is most responsive as a measure of treatment efficacy. Further research is required using recommended outcome measures to facilitate generation of a minimum data set and data pooling.
Algebraic decoding of (71, 36, 11), (79, 40, 15), and (97, 49, 15) quadratic residue codes

Recently, a new algebraic decoding algorithm for quadratic residue (QR) codes was proposed by Truong et al. Using that decoding scheme, we now develop three decoders for the QR codes with parameters (71, 36, 11), (79, 40, 15), and (97, 49, 15), which have not been decoded before. To confirm our results, an exhaustive computer simulation has been executed successfully.
Epitope Mapping of Neutralizing Botulinum Neurotoxin A Antibodies by Phage Display

ABSTRACT Single-chain antibodies neutralize activity and bind nonoverlapping epitopes of botulinum A neurotoxin. Two phage display epitope libraries were constructed from the 1.3 kb of binding domain cDNA. The minimal epitopes selected against the single-chain Fv-Fc antibodies correspond to conformational epitopes with amino acid residues 1115 to 1223 (S25), 1131 to 1264 (3D12), and 889 to 1294 (C25).
High-resolution protein complexes from integrating genomic information with molecular simulation

Bacteria use two-component signal transduction systems (TCS) extensively to sense and react to external stimuli. In these, a membrane-bound sensor histidine kinase (SK) autophosphorylates in response to an environmental stimulus and transfers the phosphoryl group to a transcription factor/response regulator (RR) that mediates the cellular response. The complex between these two proteins is ruled by transient interactions, which provides a challenge to experimental structure determination techniques. The functional and structural homolog of an SK/RR pair Spo0B/Spo0F, however, has been structurally resolved. Here, we describe a method capable of generating structural models of such transient protein complexes. By using existing structures of the individual proteins, our method combines bioinformatically derived contact residue information with molecular dynamics simulations. We find crystal resolution accuracy with existing crystallographic data when reconstituting the known system Spo0B/Spo0F. Using this approach, we introduce a complex structure of TM0853/TM0468 as an exemplary SK/RR TCS, consistent with all experimentally available data.
The Determinants of Corporate Debt Maturity: A Study of Indian Firms

The study examines the determinants of debt maturity structure decisions, using a sample of companies chosen from two broad indices, viz., the BSE 500 and the CNX 500 index. The study results suggest that collateralizable assets and leverage are the important determinants of debt maturity choice. Size and firm quality have the predicted effect on debt maturity; however, results are statistically significant only in the case of fixed effect firm and time model. It finds no evidence of the impact of effective tax rate, asset maturity, and growth prospects on debt maturity in the Indian context.
Particle swarm optimization based robust PID controller tuning scheme

A novel optimal tuning technique for robust PID controllers based on the augmented Lagrangian particle swarm optimization (ALPSO) is presented. To this aim, we first consider the problem on PID controller tuning satisfying Hinfin performance criteria. It suffers from computational intractability and conservatism when the existing methods are introduced. In the proposed approach, the ALPSO based optimal robust gain tuning technique for PID controllers is introduced in order to solve simply and directly such a design problem without using any complicated manipulations. The proposed scheme works without any conservative assumption required in the conventional methods, and also enables one to find a set of optimal gains by just solving the constrained optimization problem in a straightforward way. The numerical results demonstrate that our approach is not only computationally efficient but also considerably convenient to obtain a set of optimal PID controller parameters.
Cross Economic Determinants of Implied Volatility Smile Dynamics: Three Major European Currency Options

This paper examines the contemporaneous and lead–lag relationships between economic variables and implied volatility smiles for three major European currency options. We find that cross economic determinants are at least as important as own economic variables in explaining the dynamics of implied volatility smiles. Out‐of‐sample tests also suggest that cross economic variables are important in predicting an economy's currency option smile. These findings suggest that the price impact from cross economic determinants may help fill the gap between the theoretical and the practical implied volatility skews.
M2M Architecture: Can It Realize Ubiquitous Computing in Daily life?

Ubiquitous computing called pervasive one is based on the thought of pervading ability of computation in daily life applications. In other words, it aims to include computation in devices such as electronic equipment and automobiles. This has led to disengagement of computers from desktop form. Accordingly, the notice in ubiquitous computing being taken of a world steeped in remote and wireless computer-based-services. Handheld and wearable programmed devices such as sense and control appliances are such devices. This advancement is rapidly moving domestic tasks and life from device-and-human communication to the device-and-device model. This model called Machine to Machine (M2M) has led to acceleration of developments in sciences such as nano-science, bio-science, and information science. As a result, M2M led to appearance of applications in various fields such as, environment monitoring, agricultural, health care, logistics, and business. Since it is envisaged that M2M communications will play a big role in the future in all wireless applications and will be emerged as a progressive linkage for next-generation communications, this paper aims to consider how much M2M architectures can realize ubiquitous computing in daily life applications. This is carried out after acquainting and initiating readers with M2M architectures and arguments for M2M. Some of the applications was not achievable before but are becoming viable owing to emergence of M2M communications.
Application of Learning Using Privileged Information(LUPI): Botnet Detection

Traffic anomaly detection is primarily concerned with identifying malicious traffic patterns in a much larger stream of benign traffic. Traditionally, this is achieved by selecting a very specialized set of traffic-based features that are used for both training a model, as well as for detection at runtime. This paper introduces a novel method of anomaly detection that breaks the assumption that the same set of features should be used for both training and runtime detection. Building upon the concept of Learning Using Privileged Information (LUPI), this paper shows how to build a detection model that uses an extended set of features, some that are available only during training, and some also available at runtime, with results significantly superior to the traditional learning methods. We demonstrate the usage of the privileged features in detecting malicious botnet activities in a network, activities shown to be challenging to detect in past works.
Identification of a tyrosine‐phosphorylated 35 kDa carboxy‐terminal fragment (p35CagA) of the Helicobacter pylori CagA protein in phagocytic cells: Processing or breakage?

Helicobacter pylori is a very common bacterial pathogen that causes gastric disease by inducing the infiltration of immune cells as an initial event. Virulent H. pylori strains express a type IV secretion system composed of several virulence (Vir) proteins encoded by the cag pathogenicity island (cag PAI). During infection of phagocytic cells (U937, Josk‐M and J774A.1) we have detected a de novo tyrosine‐phosphorylated protein (p35p‐Tyr) with sizes of 30 kDa, 38 kDa or 40 kDa, depending on the H. pylori strain. p35p‐Tyr occurrence required functional virB4, virB7, virB10, virB11, virD4 and cagA (cytotoxin‐associated gene A) genes encoded by the cag PAI suggesting that p35p‐Tyr is a bacterial protein of variable size. We have biochemically purified p35p‐Tyr from infected U937 cells. Tryptic peptides of p35p‐Tyr determined by matrix‐assisted laser desorption/ionization‐mass spectrometry (MALDI‐MS) identified the carboxy (C)‐terminal part of the H. pylori CagA protein. Subsequent analysis by two‐dimensional electrophoresis (2‐DE) and immunoblotting using anti‐CagA antibodies revealed the presence of three stable CagA protein species in phagocytes: (i) 130–140 kDa full‐length CagA (p135CagA), (ii) a 100–105 kDa fragment (p100CagA) and (iii) a 30–40 kDa fragment (p35CagA). Unlike p135CagA, p35CagA and p100CagA were also detected in much lower amounts in H. pylori without host cell contact. Therefore, breakage or processing leads to the production of p35CagA and p100CagA, a process that is enhanced after translocation into host cells. MALDI‐MS data and the isoelectric point determined by both 2‐DE and sequence analysis suggested that p35CagA represents the C‐terminal part of CagA and p100CagA corresponds to the remaining amino (N)‐terminal fragment. The possible function of CagA in host signal transduction and development of gastric disease is discussed.
Credit Aggregates, Countercyclical Buffer: stylised facts

The relationship between Credit to private sector, Growth and investment is in a first step evaluated empirically through Error Correction model (ECM), using Credit Level for various national economies. The more important results are the following: the quality of estimation results for the relationship between Investment (with a separate analysis for Business and Households) and Credit is much better than for the relationship between GDP and Credit and in most cases it's the Investment cycle that explains the Credit cycle. In addition, specific results for United States are given, replacing Credit Level data by Credit Flow data. In this case, both cycles drive each other for Business, whereas for Households, it's the investment cycle that drives the Credit cycle.
Usefulness of dobutamine stress tests for detection of cardiac abnormalities in dogs with experimentally induced early left ventricular dysfunction.

OBJECTIVE To determine whether dobutamine stress tests (DST) can be used to detect cardiac dysfunction in dogs with early left ventricular dysfunction (ELVD) induced by rapid right ventricular pacing (RRVP). ANIMALS 7 adult male Beagles. PROCEDURE A pacemaker was surgically implanted in each dog at the level of the right ventricular apex. Electrocardiography, Doppler sphygmomanometry, and Doppler echocardiography were performed before and during a DST prior to activation of the pacemaker and every 3 to 4 days during the period of RRVP. Dobutamine stress tests were performed by infusing dobutamine at incremental dosages ranging from 12.5 to 42.5 microg/kg of body weight/min. RESULTS Clinical signs of congestive heart failure were not observed during the pacing period. However, all dogs developed ELVD associated with significant changes in values for most Doppler echocardiographic variables obtained prior to DST Adverse cardiac effects were not detected during DST. Most Doppler echocardiographic indices of cardiac function were significantly altered in response to dobutamine infusion during the pacing period, compared with prepacing values. However, a dobutamine-induced 2-fold increase in cardiac output was maintained. CONCLUSIONS AND CLINICAL RELEVANCE Dobutamine stress tests can be safely performed in dogs with experimentally induced ELVD. Dobutamine stress tests may be a sensitive, noninvasive diagnostic method, complementary to standard clinical examinations, for detection of early cardiac dysfunction in dogs asymptomatic for dilated cardiomyopathy.