Miracle-dz/UniFAR-FTUs huggingface dataset:
Allosteric gating mechanism underlies the flexible gating of KCNQ1 potassium channels

KCNQ1 (Kv7.1) is a unique member of the superfamily of voltage-gated K+ channels in that it displays a remarkable range of gating behaviors tuned by coassembly with different β subunits of the KCNE family of proteins. To better understand the basis for the biophysical diversity of KCNQ1 channels, we here investigate the basis of KCNQ1 gating in the absence of β subunits using voltage-clamp fluorometry (VCF). In our previous study, we found the kinetics and voltage dependence of voltage-sensor movements are very similar to those of the channel gate, as if multiple voltage-sensor movements are not required to precede gate opening. Here, we have tested two different hypotheses to explain KCNQ1 gating: (i) KCNQ1 voltage sensors undergo a single concerted movement that leads to channel opening, or (ii) individual voltage-sensor movements lead to channel opening before all voltage sensors have moved. Here, we find that KCNQ1 voltage sensors move relatively independently, but that the channel can conduct before all voltage sensors have activated. We explore a KCNQ1 point mutation that causes some channels to transition to the open state even in the absence of voltage-sensor movement. To interpret these results, we adopt an allosteric gating scheme wherein KCNQ1 is able to transition to the open state after zero to four voltage-sensor movements. This model allows for widely varying gating behavior, depending on the relative strength of the opening transition, and suggests how KCNQ1 could be controlled by coassembly with different KCNE family members.
Disruption of Type I Interferon Induction by HIV Infection of T Cells

Our main objective of this study was to determine how Human Immunodeficiency Virus (HIV) avoids induction of the antiviral Type I Interferon (IFN) system. To limit viral infection, the innate immune system produces important antiviral cytokines such as the IFN. IFN set up a critical roadblock to virus infection by limiting further replication of a virus. Usually, IFN production is induced by the recognition of viral nucleic acids by innate immune receptors and subsequent downstream signaling. However, the importance of IFN in the defense against viruses has lead most pathogenic viruses to evolve strategies to inhibit host IFN induction or responses allowing for increased pathogenicity and persistence of the virus. While the adaptive immune responses to HIV infection have been extensively studied, less is known about the balance between induction and inhibition of innate immune defenses, including the antiviral IFN response, by HIV infection. Here we show that HIV infection of T cells does not induce significant IFN production even IFN I Interferon production. To explain this paradox, we screened HIV proteins and found that two HIV encoded proteins, Vpu and Nef, strongly antagonize IFN induction, with expression of these proteins leading to loss of expression of the innate immune viral RNA sensing adaptor protein, IPS-1 (IFN-β promoter stimulator-1). We hypothesize that with lower levels of IPS-1 present, infected cells are defective in mounting antiviral responses allowing HIV to replicate without the normal antiviral actions of the host IFN response. Using cell lines as well as primary human derived cells, we show that HIV targeting of IPS-1 is key to limiting IFN induction. These findings describe how HIV infection modulates IFN induction providing insight into the mechanisms by which HIV establishes infection and persistence in a host.
Natural Language Processing for Enhancing Teaching and Learning

Advances in natural language processing (NLP) and educational technology, as well as the availability of unprecedented amounts of educationally-relevant text and speech data, have led to an increasing interest in using NLP to address the needs of teachers and students. Educational applications differ in many ways, however, from the types of applications for which NLP systems are typically developed. This paper will organize and give an overview of research in this area, focusing on opportunities as well as challenges.
Controlling respiratory mechanical impedance; an analysis of proportional assist ventilation

A new type of breath delivery was introduced to critical care life support called proportional assist ventilation (PAV). Unlike AC and PSV, the successful operation of PAV depends on an impedance model that closely matches true impedance and accurate estimation of model parameters. The original concept of PAV introduced by Younes assumes the simple RC model of the lung. Since the lung is actually much more complex than the RC model.
Physiological value-based efficient usable security solutions for body sensor networks

A Body Sensor Network (BSN) is a network of economically powered, wireless, wearable, and implanted health monitoring sensors, designed to continually collect and communicate health information from the host they are deployed on. Due to the sensitive nature of the data collected, securing BSNs is important for privacy preservation and protecting the host from bodily harm. In this article, we present Physiological Value-based Security (PVS), a usable and efficient way of securing intersensor communication schemes for BSNs. The PVS scheme distributes the key used for securing a particular message along with the message itself, by hiding it using physiological values. In this way, it not only eliminates the need for any explicit key distribution, but also reduces the number of keys required at each node to meet all its secure communication requirements. We further demonstrate the use of the PVS scheme in securing cluster topology formation in BSNs. Traditional protocols for cluster formation do not consider security and are therefore susceptible to malicious attacks. We present a PVS-based cluster formation protocol which mitigates these attacks. Performance analysis of the protocol shows that compared to cluster formation protocols secured with non-PVS-based key distribution schemes, it performs efficiently.
Dynamic Voltage Restorer Based on Flying Capacitor Multilevel Converters Operated by Repetitive Control

This paper presents the control system based on the so-called repetitive control for a five-level flying-capacitor dynamic voltage restorer (DVR). This DVR multilevel topology is suitable for medium-voltage applications and operated by the control scheme developed in this paper. It is able to mitigate power-quality disturbances, such as voltage sags, harmonic voltages, and voltage imbalances simultaneously within a bandwidth. The control structure has been divided into three subsystems; the first one improves the transient response of the filter used to eliminate the modulation high-frequency harmonics, the second one deals with the load voltage; and the third is charged with maintaining balanced voltages in the flying capacitors. The well-developed graphical facilities available in PSCAD/EMTDC are used to carry out all modelling aspects of the repetitive controller and test system. Simulation results show that the control approach performs very effectively and yields excellent voltage regulation.
Opposite Regulation of Insulin Sensitivity by Dietary Lipid Versus Carbohydrate Excess

To understand the mechanisms in lipid-induced insulin resistance, a more physiological approach is to enhance fatty acid (FA) availability through the diet. Nine healthy men ingested two hypercaloric diets (in 75% excess of habitual caloric intake) for 3 days, enriched in unsaturated FA (78 energy % [E%] fat) (UNSAT) or carbohydrates (80 E% carbohydrate) (CHO) as well as a eucaloric control diet (CON). Compared with CON, the UNSAT diet reduced whole-body and leg glucose disposal during a hyperinsulinemic-euglycemic clamp, while decreasing hepatic glucose production. In muscle, diacylglycerol (DAG) and intramyocellular triacylglycerol were increased. The accumulated DAG was sn-1,3 DAG, which is known not to activate PKC, and insulin signaling was intact. UNSAT decreased PDH-E1α protein content and increased inhibitory PDH-E1α Ser300 phosphorylation and FA oxidation. CHO increased whole-body and leg insulin sensitivity, while increasing hepatic glucose production. After CHO, muscle PDH-E1α Ser300 phosphorylation was decreased, and glucose oxidation increased. After UNSAT, but not CHO, muscle glucose-6-phosphate content was 103% higher compared with CON during the clamp. Thus, PDH-E1α expression and covalent regulation, and hence the tricarboxylic acid cycle influx of pyruvate-derived acetyl-CoA relative to β-oxidation–derived acetyl-CoA, are suggested to impact on insulin-stimulated glucose uptake. Taken together, the oxidative metabolic fluxes of glucose and FA are powerful and opposite regulators of insulin action in muscle.
Tunable dispersion and dispersion slope compensator using novel Gires-Tournois Bragg grating coupled-cavities

We report on the first realization of lattice-coupled all-fiber Gires-Tournois etalons for chromatic dispersion (CD) compensation. CD tunability is obtained by cascading two fiber Bragg grating superstructures. We show that the use of one superstructure with lattice-coupled cavities leads to a 60% tunability increase compared to single cavity designs. Dispersion slope compensation is proposed and demonstrated using a temperature gradient.
Oncologic Impact of Fewer Than 12 Lymph Nodes in Patients Who Underwent Neoadjuvant Chemoradiation Followed by Total Mesorectal Excision for Locally Advanced Rectal Cancer

AbstractA minimum of 12 harvested lymph nodes (hLNs) are recommended in colorectal cancer. However, a paucity of hLNs is frequently presented after preoperative chemoradiation (pCRT) in rectal cancer and the significance of this is still uncertain. The aim of this study is to analyze the impact of hLNs on long-term oncologic outcomes.A total of 302 patients with locally advanced rectal cancer who underwent pCRT and curative resection between 1989 and 2009 were reviewed. Patients were categorized into 2 groups according to the number of hLNs: <12 versus ≥12 LN. The 2 groups were compared with respect to 5-year disease-free and overall survival. The optimal number or ratio of hLNs was investigated in subgroup analysis according to LN status.The median follow-up was 57 months. Patient characteristics other than age did not differ between the 2 groups. The group with <12 LNs had more favorable ypTNM and ypN stage than those with ≥12 LNs. However, the long-term oncologic outcomes were not significantly different between the 2 groups. In subgroup analysis of ypN(−), the group with <5 hLNs had the most favorable oncologic outcomes. In ypN(+) cases, a higher LN ratio tended to be associated with poorer 5-year overall survival.The paucity of hLNs in locally advanced rectal cancer after chemoradiation did not imply poor oncologic outcomes in this study. In addition, <5 hLNs in ypN(−) patients could reflect a good tumor response rather than suboptimal radicality.
Distributed Algorithms for Minimum Cost Multicast With Network Coding

Network coding techniques are used to find the minimum-cost transmission scheme for multicast sessions with or without elastic rate demand. It is shown that in wireline networks, solving for the optimal coding subgraphs in network coding is equivalent to finding the optimal routing scheme in a multicommodity flow problem. A set of node-based distributed gradient projection algorithms are designed to jointly implement congestion control/routing at the source node and ¿virtual¿ routing at intermediate nodes. The analytical framework and distributed algorithms are further extended to interference-limited wireless networks where link capacities are functions of the signal-to-interference-plus-noise ratio (SINR). To achieve minimum-cost multicast in this setting, the transmission powers of links must be jointly optimized with coding subgraphs and multicast input rates. Node-based power allocation and power control algorithms are developed for the power optimization. The power algorithms, when iterated in conjunction with the congestion control and routing algorithms, converge to the jointly optimal multicast configuration. The scaling matrices required in the gradient projection algorithms are explicitly derived and are shown to guarantee fast convergence to the optimum from any initial condition.
An efficient feature selection paradigm using PCA-CFS-Shapley values ensemble applied to small medical data sets

The precise diagnosis of patient profiles into categories, such as presence or absence of a particular disease along with its level of severity, remains to be a crucial challenge in biomedical field. This process is realized by the performance of the classifier by using a supervised training set with labeled samples. Then based on the result obtained, the classifier is allowed to predict the labels of new samples. Due to presence of irrelevant features it is difficult for standard classifiers from obtaining good detection rates. Hence it is important to select the features which are more relevant and by with good classifiers could be constructed to obtain a good accuracy and efficiency. This study is aimed to classify the medical profiles, and is realized by feature extraction (FE), feature ranking (FR) and dimension reduction methods (Shapley Values Analysis) as a hybrid procedure to improve the classification efficiency and accuracy. To appraise the success of the proposed method, experiments were conducted across 6 different medical data sets using J48 decision tree classifier. The experimental results showed that using the PCA-CFS-Shapley Values analysis procedure improves the classification efficiency and accuracy compared with individual usage.
An experimental test of frequency-dependent selection on male mating strategy in the field

We provide field-based experimental evidence for the frequency-dependent nature of the fitness of alternative mating strategies. We manipulated the frequency of genetically determined phenotypic strategies in six wild populations of the side-blotched lizard, Uta stansburiana. The within-population pattern of mating was assessed using nine microsatellite loci to assign paternity. Within populations of the side-blotched lizard exist three colour morphs (orange, blue and yellow) associated with male mating strategy. The frequency of these morphs has previously been found to oscillate over a 4- to 5-year period. We found, as predicted, that the common phenotype lost fitness to its antagonist. The mating patterns of all six populations adhered to a priori predictions that were derived from previous empirical and theoretical observations on this system. We found that the frequency-dependent nature of male fitness could be accounted for by the composition of their competitors at a small local population level, driven by associations within a focal female's social neighbourhood.
Structure of bacterial LigD 3′-phosphoesterase unveils a DNA repair superfamily

The DNA ligase D (LigD) 3′-phosphoesterase (PE) module is a conserved component of the bacterial nonhomologous end-joining (NHEJ) apparatus that performs 3′ end-healing reactions at DNA double-strand breaks. Here we report the 1.9 Å crystal structure of Pseudomonas aeruginosa PE, which reveals that PE exemplifies a unique class of DNA repair enzyme. PE has a distinctive fold in which an eight stranded β barrel with a hydrophobic interior supports a crescent-shaped hydrophilic active site on its outer surface. Six essential side chains coordinate manganese and a sulfate mimetic of the scissile phosphate. The PE active site and mechanism are unique vis à vis other end-healing enzymes. We find PE homologs in archaeal and eukaryal proteomes, signifying that PEs comprise a DNA repair superfamily.
Use of Semantic Relation Between Words in Text Clustering

In traditional document clustering methods, a document is considered a bag of words. The fact that the words may be semantically relateda crucial information for clusteringis not taken into account. The feature vector representing the document is constructed from the frequency count of document terms. To improve results, weights calculated from techniques like Inverse Document Frequency (IDF) and Information Gain (IG) are applied to the frequency count. These weights also are essentially statistical parameters and do not make use of any semantic information.
A faster implementation of the Goemans-Williamson clustering algorithm

We give an implementation of the Goemans-Williamson clustering procedure which is at the core of several approximation algorithms including those for Generalized Steiner Trees, Prize Collecting Travelling Salesman, 2-Edge Connected Subgraph etc. On a graph with <i>n</i> nodes and <i>m</i> edge, our implementation gives <i>&Ogr;</i> (<i>k</i>(<i>n</i> + <i>m</i>) <i>log</i><sup>2</sup> <i>n</i>) time approximation algorithms for all these problems at the expense of a slight additive degradation of 1/n<sup><i>k</i></sup> in the approximation factor, for any constant <i>k</i>.
Transmural changes in fibre helix angle in normal and failing canine ventricles

Fibre orientation relative to the base-apex axis (the helix angle) varies across the ventricular wall. The aim of this study was to examine the consistency of transmural helix angle in 6 normal canine hearts, and 3 canines with heart failure from the Johns Hopkins DT-MRI dataset.
What should students learn in their first (and often only) software engineering course?

The questions that are proposed as the basis for academy panel sessions are important ones to ask. In the aggregate, they cover an enormous expanse of the software engineering landscape. The reality of undergraduate computing education is that the vast majority of students do not go through software engineering curricula where there is time to address the academy questions in some depth. Instead, they are in computer science or computer engineering programs, and receive their software engineering education in a single course. What students should really learn in this first, and often only, software engineering course is important because the majority of computing students will not see any other software engineering. The course designer will need to make judicious choices in selecting the material for this course because all of software engineering will not fit in just one course even if you try by using one of the classic software engineering tomes as the textbook. I do not know the right answer to the question I pose in the title of this position paper. I suspect that there is no one set of software engineering topics that should be included, but rather a range of topics to select from based on the purpose and perspective of the course. The answer to this question is important to everyone who has responsibility for providing the software engineering education for the next generation of computing students.
Employing Active-Learning Techniques and Metacognition in Law School: Shifting Energy from Professor to Student

What is metacognition and why have your students engage in it? Metacognition is an instructional tool that "shifts energy from professor to student. " Researchers in fields of psychology and education have found metacognition to be an effective method to engage students in the learning process. Law students are diverse in their learning styles, according to assessments performed annually at St. John's University School of Law. Law professors are encouraged to engage students in active learning and metacognitive exercises. This article presents examples of teaching techniques involving active engagement and metacognition.
Synchronized Expression of Two Caspase Family Genes, ice-2 and ice-5, in Hydrogen Peroxide-Induced Cells of the Silkworm, Bombyx mori

Abstract Caspase family proteins play important roles in different stages of the apoptotic pathway. To date, however, functions of Bombyx mori L. (Lepidoptera: Bombycidae) caspase family genes are poorly known. This paper focuses on the morphology, mitochondrial membrane potential, and expression profiles of two novel B. mori caspase family genes (ice-2 and ice-5) in 3 µM hydrogen peroxide (H2O2) damaged B. mori cells, which were separated from the ovary of B. mori. In addition, comparisons were made between damage caused by H2O2 and by ultraviolet (UV) irradiation. The results showed that the potential change of the mitochondrial membrane occurred at 0.5 h after H2O2 stimulation, which was sooner than occurred in the UV treated model where the obvious decrease appeared at 6 h after stimulation. In addition, the total change in the potential of the mitochondrial membrane in H2O2 treated B. mori cells was larger than with UV treated cells during the whole process. Analysis of fluorescent quantitative real-time PCR demonstrated that ice-2 and ice-5 might be involved in both H2O2 and UV-induced apoptosis in B. mori cells. Notably, after exposure to H2O2, the expression patterns of ice-5 were remarkably higher than those of ice-2, while the result was the opposite after exposure to UV irradiation. The data indicate that apoptosis induced by H2O2 was directly related to the mitochondrial pathway. The two isoforms of B. mori ice may play different roles in the mitochondrion associated apoptotic pathway in B. mori cells, and the apoptotic pathway in H2O2 induced B. mori cells is different from the UV induced apoptotic pathway.
Feedback for coaches: Who coaches the coach?

The aim of this study was to investigate the feedback mechanisms that sport coaches utilized to enhance their coaching practice at various stages of their careers. Sport coaches (n = 21) were interviewed in-depth with the resulting information being analysed using HyperRESEARCH qualitative data analysis software package. Results suggested four distinct dimensions that characterized the sources of feedback used by coaches: networks, players/participants, critical thinking skills and support systems. Those more experienced coaches with established networks of like-minded coaches seemed to be more open to constructive feedback. Similarly, novice coaches appeared to accept feedback from non-reliable sources in lieu of more informed sources. A distinctive emerging feature was the lack of formal feedback mechanisms within groups of coaches at all levels of qualification.
Biological effects of simulated ultraviolet daylight: a new approach to investigate daily photoprotection

Background: The irradiance of standard ultraviolet daylight (UV‐DL) is representative of most frequently encountered UV exposure conditions and simulators of UV‐DL can now be used to properly investigate the biological effects of a non‐extreme UV radiation. One of the characteristics of the simulated UV‐DL used in this study is its dUVA to dUVB irradiance ratio, which amounts to 24, instead of close to 10, for the simulated zenithal UV radiation (UV‐SSR).
Runtime support for automatic wide area implementation management in legion

Computational grids have the potential to give programmersaccess to a much larger set and wider range of underlyingcomputing resources than currently possible. To be useful in this capacity, however, grids must address the problems of heterogeneity, multiple disjoint administrative domains, and scale. This paper describes the Legion implementationmodel, which prescribes how active objects are created and managed in the face of these problems. The Legion wide area metasystem maintains object executablesin architecture-specific binary format, and automaticallydownloads and executes the appropriate binary for theplatform on which the object is to run. The implementationmodel relieves the programmer from requiring an individualaccount on all the machines or domains on which herobjects may run, and from explicitly installing programsthroughout the metasystem. Instead, programmers have asingle account, register executables once, with Legion, andcan then potentially utilize all the machines in the system.