Miracle-dz/UniFAR-FTUs huggingface dataset:
The structure of communities in scale‐free networks

Scale‐free networks are often used to model a wide range of real‐world networks, such as social, technological, and biological networks. Understanding the structure of scale‐free networks evolves into a big data problem for business, management, and protein function prediction. In the past decade, there has been a surge of interest in exploring the properties of scale‐free networks. Two interesting properties have attracted much attention: the assortative mixing and community structure. However, these two properties have been studied separately in either theoretical models or real‐world networks. In this paper, we show that the structural features of communities are highly related with the assortative mixing in scale‐free networks. According to the value of assortativity coefficient, scale‐free networks can be categorized into assortative, disassortative, and neutral networks, respectively. We systematically analyze the community structure in these three types of scale‐free networks through six metrics: node embeddedness, link density, hub dominance, community compactness, the distribution of community sizes, and the presence of hierarchical communities. We find that the three types of scale‐free networks exhibit significant differences in these six metrics of community structures. First, assortative networks present high embeddedness, meaning that many links lying within communities but few links lying between communities. This leads to the high link density of communities. Second, disassortative networks exhibit great hubs in communities, which results in the high compactness of communities that nodes can reach each other via short paths. Third, in neutral networks, a big portion of links act as community bridges, so they display sparse and less compact communities. In addition, we find that (dis)assortative networks show hierarchical community structure with power‐law‐distributed community sizes, while neutral networks present no hierarchy. Understanding the structure of communities from the angle of assortative mixing patterns of nodes can provide insights into the network structure and guide us in modeling information propagation in different categories of scale‐free networks. Copyright © 2016 John Wiley & Sons, Ltd.
Efficacy and safety of daily use of tadalafil in treatment of patients with premature ejaculation: A randomised placebo‐controlled clinical trial

The study aimed to evaluate the efficacy and safety of the once‐daily use of 5 mg tadalafil in the treatment of patients with premature ejaculation (PE). In a single‐blind placebo‐controlled clinical study, it was carried out on 100 patients with PE. All patients were randomised equally divided into two groups (50 patients each). Group 1 was given placebo in the form of oral multivitamin tablet once a day for 6 weeks. Group 2 was given 5 mg tadalafil once a day for 6 weeks. All patients were asked to complete Arabic Index of Premature Ejaculation (AIPE) before and after the treatment. This study showed that there were no statistically significant differences between patients in the placebo and tadalafil groups regarding the mean values of the seven questions and total scores of the AIPE questionnaire before treatment (p value >.05). The mean values of the seven questions and total scores of AIPE questionnaire in the tadalafil group were significantly higher than the placebo group after treatment (p value = .001). This study concluded that once‐daily use of 5 mg tadalafil for 6 weeks was effective and well tolerated in the treatment of patients with PE.
The Phylogenetic Relationships of the Chinese and Vietnamese Waterfall frogs of the genus Amolops

Ranid frogs of the genus Amolops occur in Southeast Asia and are typically found near waterfalls. Their phylogenetic relationships have not been resolved. We include 2,213 aligned nucleotide sites of the 12S, 16S and tRNA(val) gene regions of the mitochondrial DNA genome from 43 individuals of Chinese and Vietnamese Amotops, Huia, Hylarana, Meristogenys, Odorrana and Rana. The outgroup species were from the genera Chaparana, Limnonectes, Nanorana, and Paa. The data were analyzed within the framework of a refutationist philosophy using maximum parsimony. Four clades of waterfall frogs were resolved. Meristogenys was not resolved as the sister group to either Huia nor Amolops. The hypothesis Of evolutionary relationships placed Amolops chapaensis and Huia nasica in the genus Odorrana.
Complexity Increases Predictability in Allometrically Constrained Food Webs

All ecosystems are subjected to chronic disturbances, such as harvest, pollution, and climate change. The capacity to forecast how species respond to such press perturbations is limited by our imprecise knowledge of pairwise species interaction strengths and the many direct and indirect pathways along which perturbations can propagate between species. Network complexity (size and connectance) has thereby been seen to limit the predictability of ecological systems. Here we demonstrate a counteracting mechanism in which the influence of indirect effects declines with increasing network complexity when species interactions are governed by universal allometric constraints. With these constraints, network size and connectance interact to produce a skewed distribution of interaction strengths whose skew becomes more pronounced with increasing complexity. Together, the increased prevalence of weak interactions and the increased relative strength and rarity of strong interactions in complex networks limit disturbance propagation and preserve the qualitative predictability of net effects even when pairwise interaction strengths exhibit substantial variation or uncertainty.
Real-time recognition of suicidal behavior using an RGB-D camera

Inmates in solitary confinement may attempt to harm themselves in many ways, resulting in trivial to mortal injuries. In this context, suicide by hanging is one of the major causes of death among the incarcerated. The Rapid detection of suicide can reduce the mortality rate. Recently, several technologies have been developed to detect suicide by hanging attempts, but most of them use bulky devices, or they are greatly depending on human attention. In this paper, we propose a computer vision based system to automatically detect suicide by hanging attempts. Our method is based on modeling suicidal actions using pose and motion features, by exploiting the body joints' positions. The proposed video surveillance system analyses depth images provided by an RGB-D camera to detect the event of interest in real-time, regardeless of illumination conditions. The experimental results obtained on a realistic dataset demonstrated the high precision of our system in detecting suicide by hanging.
Insulin-stimulated glucose uptake in skeletal muscle, adipose tissue and liver: a positron emission tomography study

Objective Insulin resistance is reflected by the rates of reduced glucose uptake (GU) into the key insulin-sensitive tissues, skeletal muscle, liver and adipose tissue. It is unclear whether insulin resistance occurs simultaneously in all these tissues or whether insulin resistance is tissue specific. Design and methods We measured GU in skeletal muscle, adipose tissue and liver and endogenous glucose production (EGP), in a single session using 18F-fluorodeoxyglucose with positron emission tomography (PET) and euglycemic–hyperinsulinemic clamp. The study population consisted of 326 subjects without diabetes from the CMgene study cohort. Results Skeletal muscle GU less than 33 µmol/kg tissue/min and subcutaneous adipose tissue GU less than 11.5 µmol/kg tissue/min characterized insulin-resistant individuals. Men had considerably worse insulin suppression of EGP compared to women. By using principal component analysis (PCA), BMI inversely and skeletal muscle, adipose tissue and liver GU positively loaded on same principal component explaining one-third of the variation in these measures. The results were largely similar when liver GU was replaced by EGP in PCA. Liver GU and EGP were positively associated with aging. Conclusions We have provided threshold values, which can be used to identify tissue-specific insulin resistance. In addition, we found that insulin resistance measured by GU was only partially similar across all insulin-sensitive tissues studied, skeletal muscle, adipose tissue and liver and was affected by obesity, aging and gender.
TREATMENT OF FULL THICKNESS ARTICULAR CARTILAGE DEFECTS WITH MICROFRACTURE

Microfracture is a stem cell stimulation technique to promote the healing of full thickness articulate cartilage defects Sixty-six patients have undergone microfracture for full thickness articulate cartilage defects over a five year period. All procedures were performed by one surgeon following the technique of Steadman. All patients were under 46, had an isolated chondral lesion, had a stable well aligned knee and were a minimum of one year post surgery. Patients were evaluated with a preoperative and follow up IKDC score, WOMAC score, KOOS Score, Tegner activity level and SF 36, VAS pain scores and overall knee function score. Failure was determined by the need for a secondary chondral procedure. Nine patients failed. Thus the overall success rate was 86%. The failure rate was higher with larger lesions. There was a significant improvement in IKDC score, WOMAC score, KOOS Score, Tegner activity level and SF 36, VAS pain scores and overall knee function score. Microfracture has a good success rate in the short to medium term with isolated full thickness articular cartilage lesions in the stable well aligned knee.
Effective Footstep Planning for Humanoids Using Homotopy-Class Guidance

Planning the motion for humanoid robots is a computationally-complex task due to the high dimensionality of the system. Thus, a common approach is to first plan in the low-dimensional space induced by the robot’s feet—a task referred to as footstep planning. This low-dimensional plan is then used to guide the full motion of the robot. One approach that has proven successful in footstep planning is using search-based planners such as A* and its many variants. To do so, these search-based planners have to be endowed with effective heuristics to efficiently guide them through the search space. However, designing effective heuristics is a time-consuming task that requires the user to have good domain knowledge. Thus, our goal is to be able to effectively plan the footstep motions taken by a humanoid robot while obviating the burden on the user to carefully design local-minima free heuristics. To this end, we propose to use user-defined homotopy classes in the workspace that are intuitive to define. These homotopy classes are used to automatically generate heuristic functions that efficiently guide the footstep planner. We compare our approach for footstep planning with a standard approach that uses a heuristic common to footstep planning. In simple scenarios, the performance of both algorithms is comparable. However, in more complex scenarios our approach allows for a speedup in planning of several orders of magnitude when compared to the standard approach.
Learning Probabilistic Relational Models with (Partially Structured) Graph Databases

Probabilistic Relational Models (PRMs) such as Directed Acyclic Probabilistic Entity Relationship (DAPER) models are probabilistic models dealing with knowledge representation and relational data. Existing literature dealing with PRM and DAPER relies on well structured relational databases. In contrast, a large portion of real-world data is stored in Nosql databases specially graph databases that do not depend on a rigid schema. This paper builds on the recent work on DAPER models, and describes how to learn them from partially structured graph databases. Our contribution is twofold. First, we present how to extract the underlying ER model from a partially structured graph database. Then, we describe a method to compute sufficient statistics based on graph traversal techniques. Our objective is also twofold: we want to learn DAPERs with less structured data, and we want to accelerate the learning process by querying graph databases. Our experiments show that both objectives are completed, transforming the structure learning process into a more feasible task even when data are less structured than an usual relational database.
Faster Secure Two-Party Computation Using Garbled Circuits

Secure two-party computation enables two parties to evaluate a function cooperatively without revealing to either party anything beyond the function’s output. The garbled-circuit technique, a generic approach to secure two-party computation for semi-honest participants, was developed by Yao in the 1980s, but has been viewed as being of limited practical significance due to its inefficiency. We demonstrate several techniques for improving the running time and memory requirements of the garbled-circuit technique, resulting in an implementation of generic secure two-party computation that is significantly faster than any previously reported while also scaling to arbitrarily large circuits. We validate our approach by demonstrating secure computation of circuits with over 10 9 gates at a rate of roughly 10 ms per garbled gate, and showing order-of-magnitude improvements over the best previous privacy-preserving protocols for computing Hamming distance, Levenshtein distance, Smith-Waterman genome alignment, and AES.
Sensitive and less invasive confirmatory diagnosis of visceral leishmaniasis in Sudan using loop-mediated isothermal amplification (LAMP)

Background Confirmatory diagnosis of visceral leishmaniasis (VL), as well as diagnosis of relapses and test of cure, usually requires examination by microscopy of samples collected by invasive means, such as splenic, bone marrow or lymph node aspirates. This causes discomfort to patients, with risks of bleeding and iatrogenic infections, and requires technical expertise. Molecular tests have great potential for diagnosis of VL using peripheral blood, but require well-equipped facilities and trained personnel. More user-friendly, and field-amenable options are therefore needed. One method that could meet these requirements is loop-mediated isothermal amplification (LAMP) using the Loopamp Leishmania Detection Kit, which comes as dried down reagents that can be stored at room temperature, and allows simple visualization of results. Methodology/Principal findings The Loopamp Leishmania Detection Kit (Eiken Chemical Co., Japan), was evaluated in the diagnosis of VL in Sudan. A total of 198 VL suspects were tested by microscopy of lymph node aspirates (the reference test), direct agglutination test-DAT (in house production) and rK28 antigen-based rapid diagnostic test (OnSite Leishmania rK39-Plus, CTK Biotech, USA). LAMP was performed on peripheral blood (whole blood and buffy coat) previously processed by: i) a direct boil and spin method, and ii) the QIAamp DNA Mini Kit (QIAgen). Ninety seven of the VL suspects were confirmed as cases by microscopy of lymph node aspirates. The sensitivity and specificity for each of the tests were: rK28 RDT 98.81% and 100%; DAT 88.10% and 78.22%; LAMP-boil and spin 97.65% and 99.01%; LAMP-QIAgen 100% and 99.01%. Conclusions/Significance Due to its simplicity and high sensitivity, rK28 RDT can be used first in the diagnostic algorithm for primary VL diagnosis, the excellent performance of LAMP using peripheral blood indicates that it can be also included in the algorithm for diagnosis of VL as a simple test when parasitological confirmatory diagnosis is required in settings that are lower than the reference laboratory, avoiding the need for invasive lymph node aspiration.
The RNA Helicase Rm62 Cooperates with SU(VAR)3-9 to Re-Silence Active Transcription in Drosophila melanogaster

Gene expression is highly dynamic and many genes show a wide range in expression over several orders of magnitude. This regulation is often mediated by sequence specific transcription factors. In addition, the tight packaging of DNA into chromatin can provide an additional layer of control resulting in a dynamic range of gene expression covering several orders of magnitude. During transcriptional activation, chromatin barriers have to be eliminated to allow an efficient progression of the RNA polymerase. This repressive chromatin structure has to be re-established quickly after it has been activated in order to tightly regulate gene activity. We show that the DExD/H box containing RNA helicase Rm62 is targeted to a site of rapid induction of transcription where it is responsible for an increased degree of methylation at H3K9 at the heat shock locus after removal of the heat shock stimulus. The RNA helicase interacts with the well-characterized histone methyltransferase SU(VAR)3-9 via its N-terminus, which provides a potential mechanism for the targeting of H3K9 methylation to highly regulated genes. The recruitment of SU(VAR)3-9 through interaction with a RNA helicase to a site of active transcription might be a general mechanism that allows an efficient silencing of highly regulated genes thereby enabling a cell to fine tune its gene activity over a wide range.
Synaptic Granger Causality: A New Approach to Untangling Excitatory and Inhibitory Connectivities

Interactions between brain signals are often measured in terms of information flow. However, when solving the inverse problem -characterizing the structure behind a specific functional link- there are many possibilities with very different consequences. Excitation and inhibition, for instance, may each produce a causal dependence by coordinating neuronal populations, but inhibitory connections do not transmit information packages. Here, we introduce the concept of synaptic Granger causality (sGC), an extension of the well-known Granger causality approach that quantifies the ratio of excitatory/inhibitory projections involved in a functional link on the basis of the analysis of time series constructed using autoregressive models. The method is validated by using the membrane potential obtained from numerical simulations of neuronal motifs that mimic extracellular brain activity, similar to the experimentally measured local field potential. When excitatory and inhibitory synapses are not mixed, the method correctly predicts the type of synapses that participate in the signaling. Moreover, when both inputs project on the same neuron or population, the sGC estimates the proportion of both types of interaction. Our results suggest that sGC allows for a better inference on the anatomical structure underlying effective connectivity and its role in the information process.
Identification and expression profiling of Pht1 phosphate transporters in wheat in controlled environments and in the field

Abstract Phosphorus (P) is an important macronutrient with critical functions in plants. Phosphate (Pi) transporters, which mediate Pi acquisition and Pi translocation within the plant, are key factors in Pi deficiency responses. However, their relevance for adaptation to long‐term Pi limitation under agronomic conditions, particularly in wheat, remains unknown. Here, we describe the identification of the complete Pi transporter gene family (Pht1) in wheat (Triticum aestivum). Gene expression profiles were compared for hydroponic and field‐grown plant tissues of wheat at multiple development stages. Cis‐element analysis of selected Pht1 promoter regions was performed. A broad range of expression patterns of individual TaPht1 genes was observed in relation to tissue specificity and the nutrient supply in the soil or in liquid culture, as well as an influence of the experimental system. The expression patterns indicate the involvement of specific transporters in Pi uptake, and in Pi transport and remobilisation within the plant, at different growth developmental stages. Specifically, the influence of Pi nutrition indicates a complex regulatory pattern of TaPht1 gene transcript abundances as a response to low Pi availability in different culture systems, correlating with the existence of different cis‐acting promoter elements.
Outside-Host Growth of Pathogens Attenuates Epidemiological Outbreaks

Opportunist saprotrophic pathogens differ from obligatory pathogens due to their capability in host-independent growth in environmental reservoirs. Thus, the outside-host environment potentially influences host-pathogen dynamics. Despite the socio-economical importance of these pathogens, theory on their dynamics is practically missing. We analyzed a novel epidemiological model that couples outside-host density-dependent growth to host-pathogen dynamics. Parameterization was based on columnaris disease, a major hazard in fresh water fish farms caused by saprotrophic Flavobacterium columnare. Stability analysis and numerical simulations revealed that the outside-host growth maintains high proportion of infected individuals, and under some conditions can drive host extinct. The model can show stable or cyclic dynamics, and the outside-host growth regulates the frequency and intensity of outbreaks. This result emerges because the density-dependence stabilizes dynamics. Our analysis demonstrates that coupling of outside-host growth and traditional host-pathogen dynamics has profound influence on disease prevalence and dynamics. This also has implications on the control of these diseases.
Thyroid Status in Patients with Type 2 Diabetes Attending a Tertiary Care Hospital in Eastern India

Objective: Type 2 diabetes mellitus and thyroid dysfunction (TD) are two major public health endocrine problem, but the prevalence of TD and iodine status in patients with T2 DM in India is less studied. The study objective was to explore the prevalence of TD and to evaluate iodine health in type 2 diabetes patients attending a tertiary care center in Eastern India. Methods: Consecutive 100 patients with diabetes attending outpatient department were evaluated clinically and biochemically (thyrotropin [TSH], free thyroxine, anti-TPO antibody, and urinary iodine). We excluded pregnant women or patients taking drugs that can alter thyroid function. Subclinical hypothyroid and overt hypothyroidism were diagnosed as per standard definitions. Results: Out of 100 patients were analyzed, 51 (51%) were male. Mean (±standard deviation) age was 45.4 ± 11.2 years, body mass index 24.1 ± 4.28 kg/m2, and duration of diabetes 7.76 ± 5.77 years. The prevalence of subclinical hypothyroidism and overt hypothyroidism was 23/100 (23%) and 3/100 (3%), respectively. Thyroid autoantibody was positive in 13 (13.1%) patients. All patients were iodine sufficient. A trend toward increased neuropathy (r = 0.45) and nephropathy (r = −0.29) was associated with rising TSH. Conclusion: Almost one in four people living with diabetes are suffering from TD. Thus, routine screening should be implemented. Salt iodination program is a huge success in this part of the country.
Relationship between speaking English as a second language and agitation in people with dementia living in care homes: Results from the MARQUE (Managing Agitation and Raising Quality of life) English national care home survey

As not speaking English as a first language may lead to increased difficulties in communication with staff and other residents, we (1) tested our primary hypotheses that care home residents with dementia speaking English as a second language experience more agitation and overall neuropsychiatric symptoms, and (2) explored qualitatively how staff consider that residents' language, ethnicity, and culture might impact on how they manage agitation.