Miracle-dz/UniFAR-FTUs huggingface dataset:
A High-Protein Diet With Resistance Exercise Training Improves Weight Loss and Body Composition in Overweight and Obese Patients With Type 2 Diabetes

OBJECTIVE To evaluate the effects of two low-fat hypocaloric diets differing in the carbohydrate-to-protein ratio, with and without resistance exercise training (RT), on weight loss, body composition, and cardiovascular disease (CVD) risk outcomes in overweight/obese patients with type 2 diabetes. RESEARCH DESIGN AND METHODS A total of 83 men and women with type 2 diabetes (aged 56.1 ± 7.5 years, BMI 35.4 ± 4.6 kg/m2) were randomly assigned to an isocaloric, energy-restricted diet (female subjects 6 MJ/day, male subjects 7 MJ/day) of either standard carbohydrate (CON; carbohydrate:protein:fat 53:19:26) or high protein (HP; 43:33:22), with or without supervised RT (3 days/week) for 16 weeks. Body weight and composition, waist circumference (WC), and cardiometabolic risk markers were assessed. RESULTS Fifty-nine participants completed the study. There was a significant group effect (P ≤ 0.04) for body weight, fat mass, and WC with the greatest reductions occuring in HP+RT (weight [CON: −8.6 ± 4.6 kg, HP: −9.0 ± 4.8 kg, CON+RT: −10.5 ± 5.1 kg, HP+RT: −13.8 ± 6.0 kg], fat mass [CON: −6.4 ± 3.4 kg, HP: −6.7 ± 4.0 kg, CON+RT: −7.9 ± 3.7 kg, HP+RT: −11.1 ± 3.7 kg], and WC [CON: −8.2 ± 4.6 cm, HP: −8.9 ± 3.9 cm, CON+RT: −11.3 ± 4.6 cm, HP+RT: −13.7 ± 4.6 cm]). There was an overall reduction (P < 0.001) in fat-free mass (−2.0 ± 2.3 kg), blood pressure (−15/8 ± 10/6 mmHg), glucose (−2.1 ± 2.2 mmol/l), insulin (−4.7 ± 5.4 mU/l), A1C (−1.25 ± 0.94%), triglycerides (−0.47 ± 0.81 mmol/l), total cholesterol (−0.67 ± 0.69 mmol/l), and LDL cholesterol (−0.37 ± 0.53 mmol/l), with no difference between groups (P ≥ 0.17). CONCLUSIONS An energy-restricted HP diet combined with RT achieved greater weight loss and more favorable changes in body composition. All treatments had similar improvements in glycemic control and CVD risk markers.
Ultrawideband MIMO/Diversity Antennas With a Tree-Like Structure to Enhance Wideband Isolation

A compact printed ultrawideband (UWB) multiple-input multiple-output (MIMO)/diversity antenna system (of two elements) with a size of 35 × 40 mm2 operating at a frequency range of 3.110. 6 GHz is proposed. The wideband isolation can be achieved through a tree-like structure on the ground plane. The effectiveness of the tree-like structure is analyzed. Measured S-parameters show that the isolation is better than -16 dB (-20 dB in most of the band) across the UWB of 3.110. 6 GHz. The radiation patterns, gain, and envelope correlation coefficient are also measured. The proposed antenna is suitable for some portable MIMO/diversity applications.
Interception Probability and Proximity Effects: Implications in Shielding Design Against Lightning

The effects of a neighboring object on the interception probability distribution of an air terminal are investigated through scale model experiments. The discharge interception probability of an earthed rod is influenced by the presence of a neighboring shorter one when both inserted in a rod-plane gap. This depends on the polarity of the impulse voltage, the height of the earthed rods and their displacement with respect to the energized rod. The experimental results are interpreted in terms of the breakdown mechanism and electric field calculations; their possible extension to shielding design is discussed. Proximity effects may result in a reduction in the striking distance and interception radius of an air terminal, especially at the lower interception probabilities. A new approach for shielding design is introduced, which considers, besides lightning parameters and height of the prospective struck objects, interception probability and proximity effects.
Mechanisms of the Depot Specificity of Peroxisome Proliferator–Activated Receptor γ Action on Adipose Tissue Metabolism

In this study, we aimed to establish the mechanisms whereby peroxisome proliferator–activated receptor γ (PPARγ) agonism brings about redistribution of fat toward subcutaneous depots and away from visceral fat. In rats treated with the full PPARγ agonist COOH (30 mg · kg−1 · day−1) for 3 weeks, subcutaneous fat mass was doubled and that of visceral fat was reduced by 30% relative to untreated rats. Uptake of triglyceride-derived nonesterified fatty acids was greatly increased in subcutaneous fat (14-fold) and less so in visceral fat (4-fold), with a concomitant increase, restricted to subcutaneous fat only, in mRNA levels of the uptake-, retention-, and esterification-promoting enzymes lipoprotein lipase, aP2, and diacylglycerol acyltransferase 1. Basal lipolysis and fatty acid recycling were stimulated by COOH in both subcutaneous fat and visceral fat, with no frank quantitative depot specificity. The agonist increased mRNA levels of enzymes of fatty acid oxidation and thermogenesis much more strongly in visceral fat than in subcutaneous fat, concomitantly with a stronger elevation in O2 consumption in the former than in the latter. Mitochondrial biogenesis was stimulated equally in both depots. These findings demonstrate that PPARγ agonism redistributes fat by stimulating the lipid uptake and esterification potential in subcutaneous fat, which more than compensates for increased O2 consumption; conversely, lipid uptake is minimally altered and energy expenditure is greatly increased in visceral fat, with consequent reduction in fat accumulation.
Whisker maps of neuronal subclasses of the rat ventral posterior medial thalamus, identified by whole‐cell voltage recording and morphological reconstruction

Whole‐cell voltage recordings were made in vivo in the ventral posterior medial nucleus (VPM) of the thalamus in urethane‐anaesthetised young (postnatal day 16–24) rats. Receptive fields (RFs) on the whisker pad were mapped for 31 neurones, and 10 cells were recovered for morphological reconstruction of their dendritic arbors. Most VPM neurones had antagonistic subthreshold RFs that could be divided into excitatory and inhibitory whiskers. VPM cells comprised different classes, the most frequently occurring being single‐whisker excitation (SWE) and multi‐whisker excitation (MWE) cells. In SWE cells (36 % of VPM neurones), only principal whisker (PW) deflection evoked an EPSP and was followed by a single action potential (AP) or remained subthreshold. The depolarisation was terminated by a large, delayed IPSP. A stimulus evoked on average 0.74 ± 0.46 APs (mean ±s.d.) with short latency (8.1 ± 1.0 ms) and small temporal scatter (0.31 ± 0.23 ms dispersion of 50 % of the first APs). In MWE cells (29 % of VPM neurones), deflection of several whiskers evoked EPSPs. PW responses were either subthreshold EPSPs or consisted of an EPSP followed by one or several APs (0.96 ± 0.99 APs per stimulus). AP responses were often associated with putative low‐threshold calcium‐dependent regenerative potentials and were followed by a small delayed IPSP. AP responses had a longer latency (12.3 ± 2.6 ms) and larger temporal scatter (2.5 ± 1.6 ms) than responses of SWE cells. MWE cells had a lower input resistance than SWE cells. The elongation of dendritic arbors along the representation fields of rows and arcs in VPM barreloids was weakly correlated with the subthreshold RF elongation along whisker rows and arcs, respectively. Evoked EPSP‐AP responses exhibited a sharper directional tuning than subthreshold EPSPs, which in turn exhibited a sharper directional tuning than IPSPs. In conclusion, we document two main classes of VPM neurones. SWE cells responded with a precisely timed single AP to the deflection of the PW. In contrast, MWE cell RFs were more broadly tuned and the temporally dispersed multiple AP responses of these cells represented the degree of collective deflection of the PW and several adjacent whiskers.
ALMA OBSERVATIONS OF THE ORION PROPLYDS

We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of protoplanetary disks (“proplyds”) in the Orion Nebula Cluster. We imaged five individual fields at 856 μm containing 22 Hubble Space Telescope (HST)-identified proplyds and detected 21 of them. Eight of those disks were detected for the first time at submillimeter wavelengths, including the most prominent, well-known proplyd in the entire Orion Nebula, 114–426. Thermal dust emission in excess of any free–free component was measured in all but one of the detected disks, and ranged between 1 and 163 mJy, with resulting disk masses of 0.3–79 Mjup. An additional 26 stars with no prior evidence of associated disks in HST observations were also imaged within the 5 fields, but only 2 were detected. The disk mass upper limits for the undetected targets, which include OB stars, θ1 Ori C, and θ1 Ori F, range from 0.1 to 0.6 Mjup. Combining these ALMA data with previous Submillimeter Array observations, we find a lack of massive (≳3 Mjup) disks in the extreme-UV-dominated region of Orion, within 0.03 pc of θ1 Ori C. At larger separations from θ1 Ori C, in the far-UV-dominated region, there is a wide range of disk masses, similar to what is found in low-mass star forming regions. Taken together, these results suggest that a rapid dissipation of disk masses likely inhibits potential planet formation in the extreme-UV-dominated regions of OB associations, but leaves disks in the far-UV-dominated regions relatively unaffected.
Designing Visual Interfaces

The expertise of graphic designers is n o t very well understood in the software community. Only a small fraction of the commercial software development community (mostly the big players) hire the services of graphic designers and/or human interface designers. Though developments like World Wide Web has spawned offa sudden demand for graphic design services, the bulk of Web pages or graphical user interfaces for that matter, are in reality designed by the technical team members. Graphic design is often viewed as an 'artistic' profession that provides a quick face-lift to make software look 'user-friendly'. Generally speaking, the software engineering community seldom appreciated n o r acknowledged the fact that certain sound visual principles govern the graphic design of user interfaces.
On Structural Analysis of Large Networks

Containing much valuable information, networks such as the World Wide Web, social networks and metabolic networks draw increasingly attention in scientific communities. Network clustering (or graph partitioning) is the discovery of underlying clusters of related vertices in networks. But beyond organizing vertices into clusters of peers is the question of what role each vertex play in the network. This paper presents some new ways of uncovering underlying structures, including the roles that vertices play in the network. Identifying vertex roles is useful for applications such as viral marketing and epidemiology. For example, hubs are responsible for spreading ideas or disease. We applied our algorithm to analyze some real networks. The results demonstrate a superior performance over other methods such as modularity-based algorithms.
Time to Detection of Mycobacterium tuberculosis Using the MGIT 320 System Correlates with Colony Counting in Preclinical Testing of New Vaccines

ABSTRACT Clinical studies have suggested that the enumeration of mycobacteria by using automated liquid systems is a faster and simpler alternative to quantitative cultures. Here, we show that the time to detection of M. tuberculosis growth as measured with the MGIT 320 liquid culture system inversely correlates with CFU determinations from culture on solid media and that mycobacterial quantification using the MGIT system is faster and easier to perform than CFU plating.
Genome-Wide and Functional Annotation of Human E3 Ubiquitin Ligases Identifies MULAN, a Mitochondrial E3 that Regulates the Organelle's Dynamics and Signaling

Specificity of protein ubiquitylation is conferred by E3 ubiquitin (Ub) ligases. We have annotated ∼617 putative E3s and substrate-recognition subunits of E3 complexes encoded in the human genome. The limited knowledge of the function of members of the large E3 superfamily prompted us to generate genome-wide E3 cDNA and RNAi expression libraries designed for functional screening. An imaging-based screen using these libraries to identify E3s that regulate mitochondrial dynamics uncovered MULAN/FLJ12875, a RING finger protein whose ectopic expression and knockdown both interfered with mitochondrial trafficking and morphology. We found that MULAN is a mitochondrial protein – two transmembrane domains mediate its localization to the organelle's outer membrane. MULAN is oriented such that its E3-active, C-terminal RING finger is exposed to the cytosol, where it has access to other components of the Ub system. Both an intact RING finger and the correct subcellular localization were required for regulation of mitochondrial dynamics, suggesting that MULAN's downstream effectors are proteins that are either integral to, or associated with, mitochondria and that become modified with Ub. Interestingly, MULAN had previously been identified as an activator of NF-κB, thus providing a link between mitochondrial dynamics and mitochondria-to-nucleus signaling. These findings suggest the existence of a new, Ub-mediated mechanism responsible for integration of mitochondria into the cellular environment.
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2

Computational models are increasingly important for studying complex neurophysiological systems. As scientific tools, it is essential that such models can be reproduced and critically evaluated by a range of scientists. However, published models are currently implemented using a diverse set of modeling approaches, simulation tools, and computer languages making them inaccessible and difficult to reproduce. Models also typically contain concepts that are tightly linked to domain-specific simulators, or depend on knowledge that is described exclusively in text-based documentation. To address these issues we have developed a compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format. We describe how LEMS underpins the latest version of NeuroML and show that this framework can define models of ion channels, synapses, neurons and networks. Unit handling, often a source of error when reusing models, is built into the core of the language by specifying physical quantities in models in terms of the base dimensions. We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines. LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties.
HABITS: a Bayesian filter approach to indoor tracking and location

Using Wi-Fi signals is an attractive and reasonably affordable option to deal with the currently unsolved problem of widespread tracking in an indoor environment. History aware-based indoor tracking system (HABITS) models human movement patterns by applying a discrete Bayesian filter to predict the areas that will, or will not, be visited in the future. We outline here the operation of the HABITS real-time location system (RTLS) and discuss the implementation in relation to indoor Wi-Fi tracking with a large wireless network. Testing of HABITS shows that it gives comparable levels of accuracy to those achieved by doubling the number of access points. We conclude that HABITS improves on standard real-time location systems in term of accuracy (overcoming blackspots), latency (giving position fixes when others cannot), cost (less APs are required than are recommended by standard RTLS systems) and prediction (short, medium and longer-term predictions are available from HABITS).
Nanoemulsion Formulations of Fungicide Tebuconazole for Agricultural Applications

Tebuconazole (TBZ) nanoemulsions (NEs) were formulated using a low energy method. TBZ composition directly affected the drop size and surface tension of the NE. Water fraction and the organic-to-surfactant-ratio (RO/S) were evaluated in the range of 1–90 and 1–10 wt %, respectively. The study was carried out with an organic phase (OP) consisting of an acetone/glycerol mixture containing TBZ at a concentration of 5.4 wt % and Tween 80 (TW80) as a nonionic and Agnique BL1754 (AG54) as a mixture of nonionic and anionic surfactants. The process involved a large dilution of a bicontinuous microemulsion (ME) into an aqueous phase (AP). Pseudo-ternary phase diagrams of the OP//TW80//AP and OP//AG54//AP systems at T = 25 °C were determined to map ME regions; these were in the range of 0.49–0.90, 0.01–0.23, and 0.07–0.49 of OP, AP, and surfactant, respectively. Optical microscope images helped confirm ME formation and system viscosity was measured in the range of 25–147 cP. NEs with drop sizes about 9 nm and 250 nm were achieved with TW80 and AG54, respectively. An innovative low-energy method was used to develop nanopesticide TBZ formulations based on nanoemulsion (NE) technology. The surface tension of the studied systems can be lowered 50% more than that of pure water. This study’s proposed low-energy NE formulations may prove useful in sustainable agriculture.
Vector-based and landmark-guided navigation in desert ants of the same species inhabiting landmark-free and landmark-rich environments

SUMMARY The central Australian desert ant Melophorus bagoti lives in a visually cluttered semi-arid habitat dotted with grass tussocks, bushes and trees. Previously, it was shown that this species has a higher propensity to switch from vector-based navigation to landmark-guided navigation compared with the North African desert ant Cataglyphis fortis, which usually inhabits a visually bare habitat. Here, we asked whether different colonies of M. bagoti, inhabiting more and less cluttered habitats, show a similar difference. We compared ants from typically cluttered habitats with ants from an exceptional nest located in an open field largely devoid of vegetation. Ants from both kinds of nests were trained to forage from a feeder and were then displaced to a distant test site on the open field. Under these conditions, ants from cluttered habitats switched more readily from vector-based navigation to landmark-guided navigation than ants from the open field. Thus, intraspecific differences caused by the experience of particular landmarks encountered en route, or of particular habitats, influence navigational strategies in addition to previously found interspecific, inherited differences due to the evolutionary history of living in particular habitats.
Analysis and verification of the interaction model in software design

One essential aspect in software design and software quality insurance is the complexity of component interdependencies. More complex designs drive the cost of production and maintenance. This paper proposes a new methodology for the analysis and verification of the interaction model of the software design throughout the software development lifecycle. For the analysis, the interaction model is described in an interaction model description language. Analysis techniques are applied to identify critical parts of the software application and to anticipate potential scenarios of failure modes. Coupling, cohesion, and instability metrics are computed on different levels of design refinement. They guide the analysis during the risk assessment of failure modes. The interaction model allows for the verification of the model against the underlying implementation of the software application. We provide tool support for all activities.
Characterization of a recombinant humanized anti-cocaine monoclonal antibody and its Fab fragment

Variations of post-translational modifications are important for stability and in vivo behavior of therapeutic antibodies. A recombinant humanized anti-cocaine monoclonal antibody (h2E2) was characterized for heterogeneity of N-linked glycosylation and disulfide bonds. In addition, charge heterogeneity, which is partially due to the presence or absence of C-terminal lysine on the heavy chains, was examined. For cocaine overdose therapy, Fab fragments may be therapeutic, and thus, a simplified method of generation, purification, and characterization of the Fab fragment generated by Endoproteinase Lys-C digestion was devised. Both the intact h2E2 antibody and purified Fab fragments were analyzed for their affinities for cocaine and 2 of its metabolites, benzoylecgonine and cocaethylene, by fluorescence quenching of intrinsic antibody tyrosine and tryptophan fluorescence resulting from binding of these drugs. Binding constants obtained from fluorescence quenching measurements are in agreement with recently published radioligand and ELISA binding assays. The dissociation constants determined for the h2E2 monoclonal and its Fab fragment are approximately 1, 5, and 20 nM for cocaethylene, cocaine, and benzoylecgonine, respectively. Tryptophan fluorescence quenching (emission at 330 nm) was measured after either excitation of tyrosine and tryptophan (280 nm) or selective excitation of tryptophan alone (295 nm). More accurate binding constants are obtained using tryptophan selective excitation at 295 nm, likely due to interfering absorption of cocaine and metabolites at 280 nm. These quenching results are consistent with multiple tryptophan and tyrosine residues in or near the predicted binding location of cocaine in a previously published 3-D model of this antibody's variable region.
Delta extraction: An abstraction technique to comprehend why two objects could be related

In an execution of a large scale program, even a simple observable behavior may be generated by a wide range of the source code. To comprehend how such a behavior is implemented in the code, a debugger would be helpful. However, when using a debugger, developers often encounter several types of cumbersome tasks and are often confused by the huge and complicated runtime information. To support such a debugger-based comprehension task, we propose an abstraction technique of runtime information, named delta, and present a delta extraction and visualization tool. Basically, a delta is defined for two linked objects in an object-oriented program's execution. It intuitively represents the reason why these objects could be related in the execution, and it can hide the details of how these objects were related. We have conducted experiments on four subject tasks from two real-world systems to evaluate how appropriately an extracted delta can answer the `why' question and how long the tool can reduce the working time to answer the question. The results show that each delta can successfully answer the question and a tens-of-minutes to one-hour debugger-based task can be reduced by extracting a delta.