Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of the effects of grain size on the mechanical properties of nanocrystalline copper using molecular dynamics simulation with initial realistic samples

Abstract Molecular dynamics simulations have been performed to study the mechanical properties of a columnar nanocrystalline copper with a mean grain size between 9.0 and 24 nm. A melting–cooling method has been used to generate the initial samples: this method produces realistic samples that contain defects inside the grains such as dislocations and vacancies. The results of uniaxial tensile tests applied to these samples reveal the presence of a critical mean grain size between 16 and 20 nm, for which there is an inversion of the conventional Hall–Petch relation. The principal mechanisms of deformation present in the samples correspond to a combination of dislocations and grain boundary sliding. In addition, this analysis shows the presence of sliding planes generated by the motion of perfect edge dislocations that are absorbed by grain boundaries. It is the initial defects present inside the grains that lead to this mechanism of deformation. An analysis of the atomic configurations further shows that nucleation and propagation of cracks are localised on the grain boundaries especially on the triple grains junctions.
Immediate and punitive impact of mechanosensory disturbance on olfactory behaviour of larval Drosophila

ABSTRACT The ability to respond to and to learn about mechanosensory disturbance is widespread among animals. Using Drosophila larvae, we describe how the frequency of mechanosensory disturbance (‘buzz’) affects three aspects of behaviour: free locomotion, innate olfactory preference, and potency as a punishment. We report that (i) during 2–3 seconds after buzz onset the larvae slowed down and then turned, arguably to escape this situation; this was seen for buzz frequencies of 10, 100, and 1000 Hz, (ii) innate olfactory preference was reduced when tested in the presence of the buzz; this effect was strongest for the 100 Hz frequency, (iii) after odour-buzz associative training, we observed escape from the buzz-associated odour; this effect was apparent for 10 and 100, but not for 1000 Hz. We discuss the multiple behavioural effects of mechanosensation and stress that the immediate effects on locomotion and the impact as punishment differ in their frequency-dependence. Similar dissociations between immediate, reflexive behavioural effects and reinforcement potency were previously reported for sweet, salty and bitter tastants. It should be interesting to see how these features map onto the organization of sensory, ascending pathways.
Test and development of efficient blades for use in VTOL aircraft

The Phoenix LR Type 2 mod 1system shows the necessity for further testing using a variety of set ups wth respect to blade and gears. Further, during the course of writing this report, numerous design changes to the blade to lighten the structure was developed which will help with the required performance of the rotor. By limiting the weight of the components, the blade would have to lift less weight and thus draw less power from the power supply to remain airborne. However, making a craft too light and sacrificing strength is also not advisable as well as there is a possibility of blade failure before the full lift capacity of the blade has been tested. These interplay of factors contribute to making the design of a high efficient long endurance aircraft an especially difficult task. This of course has not factored in the added complexity of balancing energy supply weight and airframe integrity. This balancing act is important as carrying more energy in the form of batteries increases the weight of the aircraft while requiring the blades to generate more lift. This added required lift again requires more energy to overcome the generated corresponding drag. Therefore, finding the most optimal layout and settings is crucial in this particular problem.
Uremic Toxins Inhibit Transport by Breast Cancer Resistance Protein and Multidrug Resistance Protein 4 at Clinically Relevant Concentrations

During chronic kidney disease (CKD), there is a progressive accumulation of toxic solutes due to inadequate renal clearance. Here, the interaction between uremic toxins and two important efflux pumps, viz. multidrug resistance protein 4 (MRP4) and breast cancer resistance protein (BCRP) was investigated. Membrane vesicles isolated from MRP4- or BCRP-overexpressing human embryonic kidney cells were used to study the impact of uremic toxins on substrate specific uptake. Furthermore, the concentrations of various uremic toxins were determined in plasma of CKD patients using high performance liquid chromatography and liquid chromatography/tandem mass spectrometry. Our results show that hippuric acid, indoxyl sulfate and kynurenic acid inhibit MRP4-mediated [3H]-methotrexate ([3H]-MTX) uptake (calculated Ki values: 2.5 mM, 1 mM, 25 µM, respectively) and BCRP-mediated [3H]-estrone sulfate ([3H]-E1S) uptake (Ki values: 4 mM, 500 µM and 50 µM, respectively), whereas indole-3-acetic acid and phenylacetic acid reduce [3H]-MTX uptake by MRP4 only (Ki value: 2 mM and IC50 value: 7 mM, respectively). In contrast, p-cresol, p-toluenesulfonic acid, putrescine, oxalate and quinolinic acid did not alter transport mediated by MRP4 or BCRP. In addition, our results show that hippuric acid, indole-3-acetic acid, indoxyl sulfate, kynurenic acid and phenylacetic acid accumulate in plasma of end-stage CKD patients with mean concentrations of 160 µM, 4 µM, 129 µM, 1 µM and 18 µM, respectively. Moreover, calculated Ki values are below the maximal plasma concentrations of the tested toxins. In conclusion, this study shows that several uremic toxins inhibit active transport by MRP4 and BCRP at clinically relevant concentrations.
ShARe/CLEF eHealth 2013 Named Entity Recognition and Normalization of Disorders Challenge

Objective: There are abundant mentions of clinical conditions, anatomical sites, medications and procedures in clinical documents. This paper describes use of a cascade of machine learners to automatically extract mentions of named entities about disorders from clinical notes. Tasks: A Conditional Random Field (CRF) machine learner has been used for named entity recognition and to capture more complex (multiple word) named entities we have used Support Vector Machines (SVM). Firstly, the training data was converted to the CRF format. Different feature sets were ap- plied using 10-fold cross validation to find the best feature set for the machine learning model. Secondly, the identified named entities were passed to the SVM to find any relation among the identified disorder mentions to decide whether they are a part of a complex disorder. Approach: Our approach was based on a novel supervised learning model which incorporates two machine learning algorithms (CRF and SVM). Evalua- tion of each step included precision, recall and F-score metrics. Resources: We have used several tools which are created in our lab includ- ing TTSCT (Text to SNOMED CT) service, Lexical Management System (LMS) and Ring-fencing approach. A set of gazetteers was created from the training data and employed in analysis as well. Results: Evaluation results produced a precision of 0.766, recall of 0.726 and F-score of 0.746 for named entity recognition based on 10-fold cross vali- dation; and precision, recall and F-measure of 0.927 for relation extraction based on 5-fold cross validation on the training data. On the official test data on strict mode a precision of 0.686, recall of 0.539 and F-score of 0.604 was achieved. Based on the results our team was the 11 th out of 25 participating teams. In the relaxed mode a precision of 0.912, recall of 0.701 and F-score of 0.793 was recorded and our team was the 12 th . A multi stage supervised ma- chine learning method with mixed computational strategies seems to provide a reasonable strategy for automated extraction of disorders.
Hereditary Hyperbilirubinemias: A Molecular and Mechanistic Approach

Heme from senescent erythrocytes is degraded to bilirubin in the spleen and in the hepatic Kupffer cells. Heme from heme-containing enzymes in the liver is converted to bilirubin in the hepato~ytes. ~ In the circulation, bilirubin is bound tightly to albumin. In the liver, the bilirubin-albumin complex passes through the endothelial fenestrae and bilirubin comes into contact with the sinusoidal membrane of the hepatocyte. Free bilirubin is taken up in the cell via a membrane carrier-pro-The role of albumin in this process is unclear; mutant analbuminemic rats are not jaundiced and in these animals the rate of disappearance of bilirubin from the circulation is n ~ r m a l . ~ However, albumin may play a role in delivery of bilirubin to the liver and prevent diffusion to peripheral tissues. Within the
The DPP4 Inhibitor Linagliptin Protects from Experimental Diabetic Retinopathy

Background/aims Dipeptidyl peptidase 4 (DPP4) inhibitors improve glycemic control in type 2 diabetes, however, their influence on the retinal neurovascular unit remains unclear. Methods Vasculo- and neuroprotective effects were assessed in experimental diabetic retinopathy and high glucose-cultivated C. elegans, respectively. In STZ-diabetic Wistar rats (diabetes duration of 24 weeks), DPP4 activity (fluorometric assay), GLP-1 (ELISA), methylglyoxal (LC-MS/MS), acellular capillaries and pericytes (quantitative retinal morphometry), SDF-1a and heme oxygenase-1 (ELISA), HMGB-1, Iba1 and Thy1.1 (immunohistochemistry), nuclei in the ganglion cell layer, GFAP (western blot), and IL-1beta, Icam1, Cxcr4, catalase and beta-actin (quantitative RT-PCR) were determined. In C. elegans, neuronal function was determined using worm tracking software. Results Linagliptin decreased DPP4 activity by 77% and resulted in an 11.5-fold increase in active GLP-1. Blood glucose and HbA1c were reduced by 13% and 14% and retinal methylglyoxal by 66%. The increase in acellular capillaries was diminished by 70% and linagliptin prevented the loss of pericytes and retinal ganglion cells. The rise in Iba-1 positive microglia was reduced by 73% with linagliptin. In addition, the increase in retinal Il1b expression was decreased by 65%. As a functional correlate, impairment of motility (body bending frequency) was significantly prevented in C. elegans. Conclusion Our data suggest that linagliptin has a protective effect on the microvasculature of the diabetic retina, most likely due to a combination of neuroprotective and antioxidative effects of linagliptin on the neurovascular unit.
A wavelet constrained POCS supperresolution algorithm for high resolution image reconstruction from video sequence

Research interest in multi-frame supperresolution has risen substantially in recent years. Most methods developed deal with operations working directly in the image domain. This paper presents a wavelet-domain superresolution method based on the projection on to convex set (POCS) technique. An iterative procedure is utilized to extract information hidden in a group of video frames to update the wavelet coefficients. Since these coefficients correspond to the high frequency information in the spatial domain, the extracted fine features from other frames augment the individual low-resolution image to a superresolution image. The effectiveness of the algorithm is demonstrated by experimental results.
Optimization and Characterization of the Friction Stir Welded Sheets of AA 5754-H111: Monitoring of the Quality of Joints with Thermographic Techniques

Friction Stir Welding (FSW) is a solid-state welding process, based on frictional and stirring phenomena, that offers many advantages with respect to the traditional welding methods. However, several parameters can affect the quality of the produced joints. In this work, an experimental approach has been used for studying and optimizing the FSW process, applied on 5754-H111 aluminum plates. In particular, the thermal behavior of the material during the process has been investigated and two thermal indexes, the maximum temperature and the heating rate of the material, correlated to the frictional power input, were investigated for different process parameters (the travel and rotation tool speeds) configurations. Moreover, other techniques (micrographs, macrographs and destructive tensile tests) were carried out for supporting in a quantitative way the analysis of the quality of welded joints. The potential of thermographic technique has been demonstrated both for monitoring the FSW process and for predicting the quality of joints in terms of tensile strength.
Bidirectional links between HIV and intimate partner violence in pregnancy: implications for prevention of mother-to-child transmission

Prevention of mother‐to‐child transmission (PMTCT) has the potential to eliminate new HIV infections among infants. Yet in many parts of sub‐Saharan Africa, PMTCT coverage remains low, leading to unacceptably high rates of morbidity among mothers and new infections among infants. Intimate partner violence (IPV) may be a structural driver of poor PMTCT uptake, but has received little attention in the literature to date.
Virtual Reality Training Versus Blended Learning of Laparoscopic Cholecystectomy

AbstractThis study compared virtual reality (VR) training with low cost-blended learning (BL) in a structured training program.Training of laparoscopic skills outside the operating room is mandatory to reduce operative times and risks.Laparoscopy-naïve medical students were randomized in 2 groups stratified for sex. The BL group (n = 42) used E-learning for laparoscopic cholecystectomy (LC) and practiced basic skills with box trainers. The VR group (n = 42) trained basic skills and LC on the LAP Mentor II (Simbionix, Cleveland, OH). Each group trained 3 × 4 hours followed by a knowledge test concerning LC. Blinded raters assessed the operative performance of cadaveric porcine LC using the Objective Structured Assessment of Technical Skills (OSATS). The LC was discontinued when it was not completed within 80 min. Students evaluated their training modality with questionnaires.The VR group completed the LC significantly faster and more often within 80 min than BL (45% v 21%, P = .02). The BL group scored higher than the VR group in the knowledge test (13.3 ± 1.3 vs 11.0 ± 1.7, P < 0.001). Both groups showed equal operative performance of LC in the OSATS score (49.4 ± 10.5 vs 49.7 ± 12.0, P = 0.90). Students generally liked training and felt well prepared for assisting in laparoscopic surgery. The efficiency of the training was judged higher by the VR group than by the BL group.VR and BL can both be applied for training the basics of LC. Multimodality training programs should be developed that combine the advantages of both approaches.
Counting Structures in Grid Graphs, Cylinders and Tori Using Transfer Matrices: Survey and New Results

There is a very large literature devoted to counting structures, e.g., spanning trees, Hamiltonian cycles, independent sets, acyclic orientations, in the n×m grid graph G(n,m). In particular the problem of counting the number of structures in fixed height graphs, i.e., fixing m and letting n grow, has been, for different types of structures, attacked independently by many different authors, using a transfer matrix approach. This approach essentially permits showing that the number of structures in G(n,m) satisfies a fixed-degree constant-coefficient recurrence relation in n. In contrast there has been surprisingly little work done on counting structures in grid-cylinders (where the left and right, or top and bottom, boundaries of the grid are wrapped around and connected to each other) or in grid-tori (where the left edge of the grid is connected to the right and the top edge is connected to the bottom one). The goal of this paper is to demonstrate that, with some minor modifications, the transfer matrix technique can also be easily used to count structures in fixed height grid-cylinders and tori.
Temperature dependence of the gain in p-doped and intrinsic 1.3 μm InAs/GaAs quantum dot lasers

The gain of p-doped and intrinsic InAs∕GaAs quantum dot lasers is studied at room temperature and at 350K. Our results show that, although one would theoretically expect a higher gain for a fixed carrier density in p-doped devices, due to the wider nonthermal distribution of carriers amongst the dots at T=293K, the peak net gain of the p-doped lasers is actually less at low injection than that of the undoped devices. However, at higher current densities, p doping reduces the effect of gain saturation and therefore allows ground-state lasing in shorter cavities and at higher temperatures.
Drug-Gene Interactions of Antihypertensive Medications and Risk of Incident Cardiovascular Disease: A Pharmacogenomics Study from the CHARGE Consortium

Background Hypertension is a major risk factor for a spectrum of cardiovascular diseases (CVD), including myocardial infarction, sudden death, and stroke. In the US, over 65 million people have high blood pressure and a large proportion of these individuals are prescribed antihypertensive medications. Although large long-term clinical trials conducted in the last several decades have identified a number of effective antihypertensive treatments that reduce the risk of future clinical complications, responses to therapy and protection from cardiovascular events vary among individuals. Methods Using a genome-wide association study among 21,267 participants with pharmaceutically treated hypertension, we explored the hypothesis that genetic variants might influence or modify the effectiveness of common antihypertensive therapies on the risk of major cardiovascular outcomes. The classes of drug treatments included angiotensin-converting enzyme inhibitors, beta-blockers, calcium channel blockers, and diuretics. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, each study performed array-based genome-wide genotyping, imputed to HapMap Phase II reference panels, and used additive genetic models in proportional hazards or logistic regression models to evaluate drug-gene interactions for each of four therapeutic drug classes. We used meta-analysis to combine study-specific interaction estimates for approximately 2 million single nucleotide polymorphisms (SNPs) in a discovery analysis among 15,375 European Ancestry participants (3,527 CVD cases) with targeted follow-up in a case-only study of 1,751 European Ancestry GenHAT participants as well as among 4,141 African-Americans (1,267 CVD cases). Results Although drug-SNP interactions were biologically plausible, exposures and outcomes were well measured, and power was sufficient to detect modest interactions, we did not identify any statistically significant interactions from the four antihypertensive therapy meta-analyses (Pinteraction > 5.0×10−8). Similarly, findings were null for meta-analyses restricted to 66 SNPs with significant main effects on coronary artery disease or blood pressure from large published genome-wide association studies (Pinteraction ≥ 0.01). Our results suggest that there are no major pharmacogenetic influences of common SNPs on the relationship between blood pressure medications and the risk of incident CVD.
A Weak-Type Estimate for Commutators

Let K be a smooth Calderón-Zygmund convolution kernel on R and suppose we are given a function a ∈ L∞. The two-dimensional commutator Tf(x) = ∫ K(x− y)f(y) ∫ [x,y] a(z) dz dy was shown to be bounded on L(R), p > 1 by Christ and Journé [1]. In this article, we show that this operator is also of weak type (1, 1).
Eikonal rendering: efficient light transport in refractive objects

We present a new method for real-time rendering of sophisticated lighting effects in and around refractive objects. It enables us to realistically display refractive objects with complex material properties, such as arbitrarily varying refractive index, inhomogeneous attenuation, as well as spatially-varying anisotropic scattering and reflectance properties. User-controlled changes of lighting positions only require a few seconds of update time. Our method is based on a set of ordinary differential equations derived from the eikonal equation, the main postulate of geometric optics. This set of equations allows for fast casting of bent light rays with the complexity of a particle tracer. Based on this concept, we also propose an efficient light propagation technique using adaptive wavefront tracing. Efficient GPU implementations for our algorithmic concepts enable us to render a combination of visual effects that were previously not reproducible in real-time.
Subsidization Competition: Vitalizing the Neutral Internet

Unlike telephone operators, which pay termination fees to reach the users of another network, Internet content providers (CPs) do not pay the Internet service providers (ISPs) of users they reach. While the consequent cross subsidization to CPs has nurtured content innovations at the edge of the Internet, it reduces the investment incentives for the access ISPs to expand capacity. As potential charges for terminating CPs' traffic are criticized under the net neutrality debate, we propose to allow CPs to voluntarily subsidize the usage-based fees induced by their content traffic for end-users. We model the regulated subsidization competition among the CPs under a neutral network and show how deregulation of subsidization could increase an access ISP's utilization and revenue, strengthening its investment incentives. Our results suggest that subsidization competition will increase the competitiveness and welfare of the Internet content market. However, regulators might need to: 1) regulate access prices if the access ISP market is not competitive enough; and 2) regulate subsidies if network is highly congested. We envision that subsidization competition could become a viable net-neutral model for the future Internet.
Molecular Characterisation and Three-Dimensional Structural Analysis of Mutations in 21 Unrelated Families with Inherited Factor VII Deficiency

Summary Factor VII (FVII) is a four-domain glycoprotein that plays a critical role in the initiation of blood coagulation. Hereditary deficiencies of this plasma protein results in a bleeding diathesis that varies in severity amongst affected patients. We have analysed the FVII gene in 27 patients with FVII deficiency from 21 unrelated families predominantly of Middle-Eastern extraction. A total of 19 different mutations were identified, of which 12 were novel and 7 had been previously reported. Nine of the 12 novel mutations were missense mutations located in the Gla domain (Ser23Pro), the second epidermal growth factor domain (Cys135Arg) and the catalytic serine protease domain (Arg247Cys, Arg277Cys, Ser282Arg, Pro303Thr, Ser363Ile, Trp364Cys, Trp364Phe), of which five are homozygous. Three novel splice mutations were identified in intron 1a (IVS1a+5), intron 2 (IVS2+1) and intron 6 (IVS6+1). Of the seven previously reported mutations, five were missense mutations of which three are homozygous (Gln100Arg, Arg152Gln, Arg304Gln, Cys310Phe and Thr359Met), one was a 17 bp deletion (10585del17bp) and one was a splice site mutation within intron 7 (IVS7+7). This study has significantly extended the current database of FVII mutations, including the number of known homozygous mutations. Conformational analyses of crystal structures for FVIIa and the FVIIa-tissue factor complex provided likely explanations for the effect of the missense mutations on FVIIa secretion or function. In particular, since 23 missense mutations were located to the serine protease domain, mostly to the region between the catalytic triad and the contact surface with tissue factor, this showed that the orientation of the serine protease domain relative to bound tissue factor in the complex is crucial for functional activity.