Miracle-dz/UniFAR-FTUs huggingface dataset:
Using neighborhood cohesiveness to infer interactions between protein domains

MOTIVATION In recent years, large-scale studies have been undertaken to describe, at least partially, protein-protein interaction maps, or interactomes, for a number of relevant organisms, including human. However, current interactomes provide a somehow limited picture of the molecular details involving protein interactions, mostly because essential experimental information, especially structural data, is lacking. Indeed, the gap between structural and interactomics information is enlarging and thus, for most interactions, key experimental information is missing. We elaborate on the observation that many interactions between proteins involve a pair of their constituent domains and, thus, the knowledge of how protein domains interact adds very significant information to any interactomic analysis. RESULTS In this work, we describe a novel use of the neighborhood cohesiveness property to infer interactions between protein domains given a protein interaction network. We have shown that some clustering coefficients can be extended to measure a degree of cohesiveness between two sets of nodes within a network. Specifically, we used the meet/min coefficient to measure the proportion of interacting nodes between two sets of nodes and the fraction of common neighbors. This approach extends previous works where homolog coefficients were first defined around network nodes and later around edges. The proposed approach substantially increases both the number of predicted domain-domain interactions as well as its accuracy as compared with current methods.
Simuun: A simulation Environment for Undulatory Locomotion

Abstract This paper presents SIMUUN, a block-based simulation environment, which has been developed on top of Matlab/Simulink™, in order to facilitate research into various aspects of undulatory locomotion in biology and robotics.Simulations of snake-like mechanisms are set up in this environment by connecting customizable SIMUUN body segment modules via appropriate joint blocks, which are activated either by explicit or by neuromuscular joint control modules, to propagate a travelling wave along the mechanism.Several force models are included in SIMUUN to characterize the interaction with the locomotion environment, and to emulate crawling, walking, and swimming.The simulation tools developed were used to study anguilliform swimming in robotics and in biology, and assess the effect of different body configurations on gait generation. Related simulation results are presented to illustrate the versatility of these tools and the potential of their use in a variety of domains.
Social recommendation across multiple relational domains

Social networks enable users to create different types of personal items. In dealing with serious information overload, the major problems of social recommendation are sparsity and cold start. In existing approaches, relational and heterogeneous domains can not be effectively utilized for social recommendation, which brings a challenge to model users and multiple types of items together on social networks. In this paper, we consider how to represent social networks with multiple relational domains and alleviate the major problems in an individual domain by transferring knowledge from other domains. We propose a novel Hybrid Random Walk (HRW), which can integrate multiple heterogeneous domains including directed/undirected links, signed/unsigned links and within-domain/cross-domain links into a star-structured hybrid graph with user graph at the center. We perform random walk until convergence and use the steady state distribution for recommendation. We conduct experiments on a real social network dataset and show that our method can significantly outperform existing social recommendation approaches.
Central gain of the cardiac sympathetic afferent reflex in dogs with heart failure.

Previous studies from our laboratory have shown that the cardiac sympathetic afferent reflex is enhanced in dogs with experimental heart failure. The aim of the present study was to determine if the central gain of the cardiac sympathetic afferent reflex was also enhanced in dogs with heart failure. Fifteen dogs with pacing-induced heart failure were used in this study. Seventeen sham-operated dogs served as control. At the time of the acute experiment the dogs were anesthetized with alpha-chloralose. Arterial blood pressure, heart rate, and renal sympathetic nerve activity were recorded. After sinoaortic denervation and cervical vagotomy, a thoracotomy was performed in the second intercostal space. The left stellate ganglion was identified, and the left cardiac sympathetic nerves were cut. The central end of the left cardiac sympathetic nerves was placed on bipolar stimulating electrodes. The renal sympathetic nerve activity responses to electrical stimulation (30 Hz, 1 ms with varying voltages from 1 to 10 V; or 10 V, 1 ms with varying frequencies from 1 to 30 Hz) of the afferent cardiac sympathetic nerves were compared between sham and heart failure groups. Reflex renal sympathetic nerve activity responses to stimulation of the cardiac sympathetic nerves were significantly greater in the heart failure group compared with that in the sham group (21.4 +/- 3.2 vs. 9.8 +/- 2.9% at 10 V, 30 Hz and 27.7 +/- 4.5 vs. 9.9 +/- 3.4% at 30 Hz, 10 V, heart failure vs. sham group, respectively; for both relationships, P < 0.05). This enhanced central gain of the cardiac sympathetic afferent reflex in the heart failure group was significantly attenuated after intravenous and cerebroventricular injection of the angiotensin II receptor antagonist losartan (5 mg/kg i.v. and 0.125 mg/kg in 0.1 ml i.c.v.). These data suggest that the central gain of the cardiac sympathetic afferent reflex is enhanced in dogs with heart failure and central angiotensin II plays an important role in this enhanced response.
Low Prevalence of Liver Disease but Regional Differences in HBV Treatment Characteristics Mark HIV/HBV Co-Infection in a South African HIV Clinical Trial

Background Hepatitis B virus (HBV) infection is endemic in South Africa however, there is limited data on the degree of liver disease and geographic variation in HIV/HBV coinfected individuals. In this study, we analysed data from the CIPRA-SA ‘Safeguard the household study’ in order to assess baseline HBV characteristics in HIV/HBV co-infection participants prior to antiretroviral therapy (ART) initiation. Methods 812 participants from two South African townships Soweto and Masiphumelele were enrolled in a randomized trial of ART (CIPRA-SA). Participants were tested for hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and HBV DNA. FIB-4 scores were calculated at baseline. Results Forty-eight (5.9%) were HBsAg positive, of whom 28 (58.3%) were HBeAg positive. Of those with HBV, 29.8% had an HBV DNA<2000 IU/ml and ALT<40 IU/ml ; 83.0% had a FIB-4 score <1.45, consistent with absent or minimal liver disease. HBV prevalence was 8.5% in Masiphumelele compared to 3.8% in Soweto (relative risk 2.3; 95% CI: 1.3–4.0). More participants in Masiphumelele had HBeAg-negative disease (58% vs. 12%, p = 0.002) and HBV DNA levels ≤2000 IU/ml, (43% vs. 6% p<0.007). Conclusion One third of HIV/HBV co-infected subjects had low HBV DNA levels and ALT while the majority had indicators of only mild liver disease. There were substantial regional differences in HBsAg and HbeAg prevalence in HIV/HBV co-infection between two regions in South Africa. This study highlights the absence of severe liver disease and the marked regional differences in HIV/HBV co-infection in South Africa and will inform treatment decisions in these populations.
A Multi-Omics Approach to Evaluate the Quality of Milk Whey Used in Ricotta Cheese Production

In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to several whey samples used for Ricotta production to evaluate the microbial community composition in depth using both RNA and DNA as templates for NGS library construction. Whey samples demonstrating a high microbial and aerobic spore load contained mostly Firmicutes; although variable, some samples contained a relevant amount of Gammaproteobacteria. Several lots of whey acquired as raw material for Ricotta production presented defective organoleptic properties. To define the volatile compounds in normal and defective whey samples, a headspace gas chromatography/mass spectrometry (GC/MS) analysis was conducted. The statistical analysis demonstrated that different microbial communities resulted from DNA or cDNA library sequencing, and distinguishable microbiota composed the communities contained in the organoleptic-defective whey samples.
Studies on copper, silver and zinc concentrations in muscle and liver of Barbus plebejus, Cyprinus carpio and Leuciscus cephalus from Kilickaya Reservoir in Turkey

Concentrations of Ag, Cu and Zn were studied in muscle and liver of Barbus plebejus, Cyprinus carpio and Leuciscus cephalus from Kilickaya Reservoir. The heavy metal analysis of samples were carried out by using a flame atomic absorption spectrophotometer. The mean heavy metal concentrations of Ag, Cu and Zn were obtained as 1.47±3.44, 1.65±3.31 and 2.89±4.52 µg/g in muscle and 1.78±4.19, 2.07±3.28 and 10.58±3.88 µg/g respectively in liver for Barbus plebejus, the corresponding figures were 9.67±1.36, 3.53±4.56 and 11.64±21.79 µg/g in muscle and 10.06±1.14, 5.10±4.94 and 55.28±40.77 µg/g in liver for Cyprinus carpio and 8.54±1.55, 1.58±2.93 and 3.16±4.52 µg/g in muscle and 8.15±3.14, 3.35±5.13 and 13.73±11.82 µg/g in liver for Leuciscus cephalus. Zinc concentrations differed significantly between the two tissues (p
Broken Heart Syndrome in a Patient on Maintenance Hemodialysis

Context:Broken heart syndrome or Takotsubo cardiomyopathy (TC) is a disorder characterized by transient left ventricular apical ballooning that almost invariably precedes emotional or physical stress. Although the patients with chronic kidney disease on hemodialysis have shown to exhibit sustained activity of sympathetic nervous system, the presentation of TC in these patients is a rare entity with few case reports in the literature. Case Report: A 75-year-old female with past medical history of end-stage renal disease presented with chest pressure and heaviness that started during her maintenance hemodialysis session. Electrocardiogram showed ST elevation and T wave inversion in V3-V6 leads. Emergent left heart catheterization was done that showed normal coronaries and akinesis of apical left ventricle wall consistent with TC. She was started on maximal medical management and underwent hemodialysis the next day without recurrence of the symptoms. Conclusion: TC may an underdiagnosed entity in patients on hemodialysis. However, it should be considered in the differential diagnosis in hemodialysis patients, particularly who presents with chest pain and/or symptoms.
Methods for determining the parameters and characteristics of PMSM

Determination of parameters is required for modeling and performance analysis of electrical machines. As permanent magnet synchronous machines (PMSMs) do not have a plethora of literature, standards and patents for parameter determination, this paper presents a comprehensive study of the available methods in literature for parameter determination along with novel methods of d- and q-axis inductance measurement proposed by the authors. Besides, the presented methods for measurement and calculation of armature resistance, flux linkage constant, leakage inductance, and d- and q-axis inductances are applied to a laboratory PMSM and evaluation of the proposed methods based on their complexity and accuracy is performed according to the experimental results.
A Physical and Functional Interaction between Yeast Pol4 and Dnl4-Lif1 Links DNA Synthesis and Ligation in Nonhomologous End Joining*

Genetic studies have implicated theSaccharomyces cerevisiae POL4 gene product in the repair of DNA double-strand breaks by nonhomologous end joining. Here we show that Pol4 preferentially catalyzes DNA synthesis on small gaps formed by the alignment of linear duplex DNA molecules with complementary ends, a DNA substrate specificity that is compatible with its predicted role in the repair of DNA double-strand breaks. Pol4 also interacts directly with the Dnl4 subunit of the Dnl4-Lif1 complex via its N-terminal BRCT domain. This interaction stimulates the DNA synthesis activity of Pol4 and, to a lesser extent, the DNA joining activity of Dnl4-Lif1. Notably, the joining of DNA substrates that require the combined action of Pol4 and Dnl4-Lif1 is much more efficient than the joining of similar DNA substrates that require only ligation. Thus, the physical and functional interactions between Pol4 and Dnl4-Lif1 provide a molecular mechanism for both the recruitment of Pol4 to in vivo DNA double-strand breaks and the coupling of the gap filling DNA synthesis and DNA joining reactions that complete the microhomology-mediated pathway of nonhomologous end joining.
An Official Journal of the American Heart Association Pulmonary Arterial Pulse Wave Velocity and Impedance in Man

Tlie differential pressure method of Womersley and McDonald was used to measure instantaneous blood flow in the main pulmonary artery in ten human subjects. Three subjects had normal pulmonary arterial pressures and flows, seven had mitral stenosis and pulmonary hypertension. The spectrum of input impedance versus frequency was similar to that previously reported for the dog and rabbit, with the modulus decreasing from relatively high values at zero frequency to a minimum between 2 and 5 cycles/sec. Characteristic impedance and phase velocity were lower in the normal subjects than in those with pulmonary hypertension (averages, 23 dyne sec crrr' and 1.68 m/sec in the normals; 46 dyne sec cnr ' and 4.77 m/sec in the hypertensives). Hydraulic energy dissipated per unit time by pulsations in the pulmonary bed was usually higher in the hypertensive than in the normal cases, because of the greater stiffness of the pulmonary arteries in the subjects with pulmonary hypertension. The elasticity of the pulmonary arterial tree appears to be as important as the state of the arterioles and capillaries in determining the energy required for pulsatile pulmonary blood flow. ADDITIONAL
Minimizing Electricity Cost: Optimization of Distributed Internet Data Centers in a Multi-Electricity-Market Environment

The study of Cyber-Physical System (CPS) has been an active area of research. Internet Data Center (IDC) is an important emerging Cyber-Physical System. As the demand on Internet services drastically increases in recent years, the power used by IDCs has been skyrocketing. While most existing research focuses on reducing power consumptions of IDCs, the power management problem for minimizing the total electricity cost has been overlooked. This is an important problem faced by service providers, especially in the current multi-electricity market, where the price of electricity may exhibit time and location diversities. Further, for these service providers, guaranteeing quality of service (i.e. service level objectives-SLO) such as service delay guarantees to the end users is of paramount importance. This paper studies the problem of minimizing the total electricity cost under multiple electricity markets environment while guaranteeing quality of service geared to the location diversity and time diversity of electricity price. We model the problem as a constrained mixed-integer programming and propose an efficient solution method. Extensive evaluations based on real-life electricity price data for multiple IDC locations illustrate the efficiency and efficacy of our approach.
Aversion to carbon dioxide

conducted at the University of British Colombia. These studies have used the gradual fill methods proposed by the American Veterinary Medical Association (AVMA) in an attempt to further clarify aversion associated with carbon dioxide. We have contacted the authors of this work and understand that they will also be responding to Dr Wood’s letter. Therefore, we will leave the discussion of these proposed methods and their findings to them. Finally, in the absence of conclusive evidence in Dr Wood’s letter, we are not convinced that he is correct in concluding (stated as his belief) that euthanasia of laboratory rodents with carbon dioxide is humane. We feel that this conclusion fails to take into account the wealth of literature supporting the aversiveness of carbon dioxide. We refer to the use of carbon dioxide as an ‘accepted’ pain stimulus in pain studies involving humans and other species (Thürauf et al. 1991, Komai & Bryant 1993, Peppel & Anton 1993, Danneman et al. 1997). Therefore, when all of this information is taken into account, the balance of evidence does seem to indicate that carbon dioxide is not a humane method of euthanasia. We also feel that until conclusive experimental evidence can be provided that carbon dioxide can be used humanely, the only humane action is to stop using carbon dioxide to induce unconsciousness and death in animals in the currently accepted protocols.
Covalent Coupling of Vitamin D3 to the Major Cat Allergen Fel d 1 Improves the Effects of Allergen-Specific Immunotherapy in a Mouse Model for Cat Allergy

Background: Allergen-specific immunotherapy (SIT) is currently the only curative treatment for allergy but the treatment needs to be improved. We hypothesize that covalent coupling of immunomodulating vitamin D3 to the major cat allergen Fel d 1 can enhance the beneficial effects of SIT to cat allergy. Methods: We treated mice sensitized to Fel d 1 with subcutaneous injections of two doses of recombinant Fel d 1 coupled to 1α,25-dihydroxyvitamin D3 (rFel d 1:VD3) and compared to treatment with the same doses of rFel d 1 in a mouse model for cat allergy. Airway hyperresponsiveness (AHR), cytokines and cells in bronchoalveolar lavage (BAL), in vitro activation of splenocytes to rFel d 1, and Fel d 1-specific immunoglobulins were evaluated. Results: Treatment with both doses of rFel d 1:VD3 decreased AHR, cellular influx and Th2 cytokines in BAL compared to untreated mice. High- and low-dose rFel d 1 treatment also decreased AHR and BAL Th2 cytokines, with less decrease for the low-dose treatment. Importantly, the total number of cells and eosinophils in BAL was markedly reduced at both high- and low-dose rFel d 1:VD3 compared to treatment with rFel d 1 alone. Finally, treatment with both rFel d 1 and rFel d 1:VD3 induced Fel d 1-specific serum IgG. Conclusion: Our results indicate a beneficial therapeutic effect of rFel d 1:VD3 on airway inflammation, AHR and rFel d 1-specific immune responses and thus suggest that this novel immunomodulatory candidate may improve both the efficacy and safety of SIT.
Scoping the common antecedents of job stress and job satisfaction for nurses (2000-2013) using the job demands-resources model of stress.

AIM To identify core antecedents of job stress and job satisfaction, and to explore the potential of stress interventions to improve job satisfaction. BACKGROUND Decreased job satisfaction for nurses is strongly associated with increased job stress. Stress management strategies might have the potential to improve job satisfaction. EVALUATION Comparative scoping review of studies (2000-2013) and location of their outcomes within the 'job demands-job resources' (JD-R) model of stress to identify commonalities and trends. DISCUSSION Many, but not all, antecedents of both phenomena appeared consistently suggesting they are common mediators. Others were more variable but the appearance of 'emotional demands' as a common antecedent in later studies suggests an evolving influence of the changing work environment. The occurrence of 'shift work' as a common issue in later studies points to further implications for nurses' psychosocial well-being. CONCLUSIONS Job satisfaction problems in nursing might be co-responsive to stress management intervention. Improving the buffering effectiveness of increased resilience and of prominent perceived job resource issues are urgently required. IMPLICATIONS FOR NURSING MANAGEMENT Participatory, psychosocial methods have the potential to raise job resources but will require high-level collaboration by stakeholders, and participative leadership and facilitation by managers to enable better decision-latitude, support for action planning and responsive changes.
Semi-supervised tuning from temporal coherence

Recent works demonstrated the usefulness of temporal coherence to regularize supervised training or to learn invariant features with deep architectures. In particular, enforcing a smooth output change while presenting temporally-closed frames from video sequences, proved to be an effective strategy. In this paper we prove the efficacy of temporal coherence for semi-supervised incremental tuning. We show that a deep architecture, just mildly trained in a supervised manner, can progressively improve its classification accuracy, if exposed to video sequences of unlabeled data. The extent to which, in some cases, a semi-supervised tuning allows to improve classification accuracy (approaching the supervised one) is somewhat surprising. A number of control experiments pointed out the fundamental role of temporal coherence.
Computational mechanics modelling of nanoparticle-reinforced composite materials across the length scales

Currently, research work modelling of interface phenomena of nanoparticle-reinforced composite materials, notably Carbon Nanotubes (CNT)-epoxy composites are investigated across the length scales. This paper describes the kinematics of nanoparticle-reinforced composite materials as a continuum media, the formulation of governing equations (fundamentals) and the statement of boundary conditions for multi-scale modelling of the material. The identification problem for the non-classical parameters of the model has been solved by experimental results and a method of conjugated gradients. The model has been validated to predict some basic mechanical properties of a polymeric matrix reinforced with nanoscale particles/fibres/tubes (including CNT) as a function of size and also dispersion of nanoparticles. The outcome of this paper is expected to have wide-ranging technical benefits with direct relevance to industry in the areas of transportation (aerospace, automotive, rail, maritime) and civil infrastructure development.