Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Gating Modifier Toxins on Membrane Thickness: Implications for Toxin Effect on Gramicidin and Mechanosensitive Channels

Various gating modifier toxins partition into membranes and interfere with the gating mechanisms of biological ion channels. For example, GsMTx4 potentiates gramicidin and several bacterial mechanosensitive channels whose gating kinetics are sensitive to mechanical properties of the membrane, whereas binding of HpTx2 shifts the voltage-activity curve of the voltage-gated potassium channel Kv4.2 to the right. The detailed process by which the toxin partitions into membranes has been difficult to probe using molecular dynamics due to the limited time scale accessible. Here we develop a protocol that allows the spontaneous assembly of a polypeptide toxin into membranes in atomistic molecular dynamics simulations of tens of nanoseconds. The protocol is applied to GsMTx4 and HpTx2. Both toxins, released in water at the start of the simulation, spontaneously bind into the lipid bilayer within 50 ns, with their hydrophobic patch penetrated into the bilayer beyond the phosphate groups of the lipids. It is found that the bilayer is about 2 Å thinner upon the binding of a GsMTx4 monomer. Such a thinning effect of GsMTx4 on membranes may explain its potentiation effect on gramicidin and mechanosensitive channels.
Cocreation and Evaluation of Inclusive and Accessible Open Educational Resources: A Mapping Toward the IMS Caliper

The aim of this paper is to introduce a model to cocreate and evaluate inclusive and accessible open educational resources (IA-OERs) toward the perspective of the IMS caliper analytics framework. The model was applied by 72 teachers of primary and secondary schools who cocreated and evaluated IA-OERs in the context of the validation phase of the inclusive learning project. The evaluation of the IA-OERs covered two aspects: Web accessibility and quality. Moreover, an accessibility dashboard was developed to display the graphics of the results obtained from the Web accessibility evaluation.
On the Complexity of the Balanced Vertex Ordering Problem

We consider the problem of finding a balanced ordering of the vertices of a graph. More precisely, we want to minimise the sum, taken over all vertices v, of the difference between the number of neighbours to the left and right of v. This problem, which has applications in graph drawing, was recently introduced by Biedl et al. [Discrete Applied Math. 148:27―48, 2005]. They proved that the problem is solvable in polynomial time for graphs with maximum degree three, but NP-hard for graphs with maximum degree six. One of our main results is to close the gap in these results, by proving NP-hardness for graphs with maximum degree four. Furthermore, we prove that the problem remains NP-hard for planar graphs with maximum degree four and for 5-regular graphs. On the other hand, we introduce a polynomial time algorithm that determines whetherthere is a vertex ordering with total imbalance smaller than a fixed constant, and a polynomial time algorithm that determines whether a given multigraph with even degrees has an 'almost balanced' ordering.
Subspace Regularized Sparse Multitask Learning for Multiclass Neurodegenerative Disease Identification

The high feature-dimension and low sample-size problem is one of the major challenges in the study of computer-aided Alzheimer's disease (AD) diagnosis. To circumvent this problem, feature selection and subspace learning have been playing core roles in the literature. Generally, feature selection methods are preferable in clinical applications due to their ease for interpretation, but subspace learning methods can usually achieve more promising results. In this paper, we combine two different methodological approaches to discriminative feature selection in a unified framework. Specifically, we utilize two subspace learning methods, namely, linear discriminant analysis and locality preserving projection, which have proven their effectiveness in a variety of fields, to select class-discriminative and noise-resistant features. Unlike previous methods in neuroimaging studies that mostly focused on a binary classification, the proposed feature selection method is further applicable for multiclass classification in AD diagnosis. Extensive experiments on the Alzheimer's disease neuroimaging initiative dataset showed the effectiveness of the proposed method over other state-of-the-art methods.
Perceived Ethnic Discrimination and Depressive Symptoms Among Biethnic Adolescents in South Korea

Objectives This study investigated the association between perceived ethnic discrimination and depressive symptoms among biethnic adolescents in South Korea. Methods We performed a cross-sectional study of 4141 biethnic adolescents using data from the 2012 National Survey of Multicultural Families. Perceived ethnic discrimination was measured using the question “Have you ever been discriminated against or ignored because either of your parents is not a Korean? ” with an assessment of depressive symptoms over the past 12 months. Logistic regression was applied to examine potential associations between perceived ethnic discrimination and depressive symptoms. Results Among 4141 biethnic adolescents, 558 (13.5%) reported having experienced ethnic discrimination. The most common discriminatory perpetrators were friends (n=241, 5.8%), followed by strangers (n=67, 1.6%). Depressive symptoms were related to experience of ethnic discrimination (odds ratio [OR], 3.80; 95% confidence interval [CI], 2.89 to 4.98) after adjusting for potential confounders. In an analysis focusing on the perpetrators of discrimination, depressive symptoms were found to be associated with perceived ethnic discrimination from friends (OR, 3.95; 95% CI, 2.75 to 5.68), teachers (OR, 4.53; 95% CI, 2.16 to 9.51), family members and relatives (OR, 3.89; 95% CI, 1.59 to 9.48), neighbors (OR, 2.48; 95% CI, 1.14 to 5.38), and strangers (OR, 2.49; 95% CI, 1.30 to 4.79). Furthermore, the OR for depressive symptoms among those exposed to 1, 2, or 3 or more discriminatory perpetrators were 3.61 (95% CI, 2.49 to 5.24), 3.61 (95% CI, 1.68 to 7.74), and 6.69 (95% CI, 2.94 to 15.22), respectively. Conclusions According to our findings, friends were the most common perpetrators of discrimination and the experience of ethnic discrimination was associated with depressive symptoms among biethnic adolescents in South Korea.
Active smoking and secondhand smoke increase breast cancer risk: the report of the Canadian Expert Panel on Tobacco Smoke and Breast Cancer Risk (2009)

Four authoritative reviews of active smoking and breast cancer have been published since 2000, but only one considered data after 2002 and conclusions varied. Three reviews of secondhand smoke (SHS) and breast cancer (2004–2006) each came to different conclusions. With 30 new studies since 2002, further review was deemed desirable. An Expert Panel was convened by four Canadian agencies, the Ontario Tobacco Research Unit, the Public Health Agency of Canada, Physicians for a Smoke-Free Canada and the Canadian Partnership Against Cancer to comprehensively examine the weight of evidence from epidemiological and toxicological studies and understanding of biological mechanisms regarding the relationship between tobacco smoke and breast cancer. This article summarises the panel's full report (http://www.otru.org/pdf/special/expert_panel_tobacco_breast_cancer.pdf). There are 20 known or suspected mammary carcinogens in tobacco smoke, and recognised biological mechanisms that explain how exposure to these carcinogens could lead to breast cancer. Results from the nine cohort studies reporting exposure metrics more detailed than ever/never and ex/current smoker show that early age of smoking commencement, higher pack-years and longer duration of smoking increase breast cancer risk 15% to 40%. Three meta-analyses report 35% to 50% increases in breast cancer risk for long-term smokers with N-acetyltransferase 2 gene (NAT2) slow acetylation genotypes. The active smoking evidence bolsters support for three meta-analyses that each reported about a 65% increase in premenopausal breast cancer risk among never smokers exposed to SHS. The Panel concluded that: 1) the association between active smoking and breast cancer is consistent with causality and 2) the association between SHS and breast cancer among younger, primarily premenopausal women who have never smoked is consistent with causality.
Better bounds for matchings in the streaming model

In this paper we present improved bounds for approximating maximum matchings in bipartite graphs in the streaming model. First, we consider the question of how well maximum matching can be approximated in a single pass over the input when O(n) space is allowed, where n is the number of vertices in the input graph. Two natural variants of this problem have been considered in the literature: (1) the edge arrival setting, where edges arrive in the stream and (2) the vertex arrival setting, where vertices on one side of the graph arrive in the stream together with all their incident edges. The latter setting has also been studied extensively in the context of on-line algorithms, where each arriving vertex has to either be matched irrevocably or discarded upon arrival. In the online setting, the celebrated algorithm of Karp-Vazirani-Vazirani achieves a 1--1/e approximation by crucially using randomization (and using O(n) space). Despite the fact that the streaming model is less restrictive in that the algorithm is not constrained to match vertices irrevocably upon arrival, the best known approximation in the streaming model with vertex arrivals and O(n) space is the same factor of 1--1/e. We show that no (possibly randomized) single pass streaming algorithm constrained to use O(n) space can achieve a better than 1--1/e approximation to maximum matching, even in the vertex arrival setting. This leads to the striking conclusion that no single pass streaming algorithm can get any advantage over online algorithms unless it uses significantly more than O(n) space. Additionally, our bound yields the best known impossibility result for approximating matchings in the edge arrival model (improving upon the bound of 2/3 proved by Goel at al[SODA'12]). Second, we consider the problem of approximating matchings in multiple passes in the vertex arrival setting. We show that a simple fractional load balancing approach achieves approximation ratio
Instruction of haematopoietic lineage choices, evolution of transcriptional landscapes and cancer stem cell hierarchies derived from an AML1-ETO mouse model

The t(8;21) chromosomal translocation activates aberrant expression of the AML1‐ETO (AE) fusion protein and is commonly associated with core binding factor acute myeloid leukaemia (CBF AML). Combining a conditional mouse model that closely resembles the slow evolution and the mosaic AE expression pattern of human t(8;21) CBF AML with global transcriptome sequencing, we find that disease progression was characterized by two principal pathogenic mechanisms. Initially, AE expression modified the lineage potential of haematopoietic stem cells (HSCs), resulting in the selective expansion of the myeloid compartment at the expense of normal erythro‐ and lymphopoiesis. This lineage skewing was followed by a second substantial rewiring of transcriptional networks occurring in the trajectory to manifest leukaemia. We also find that both HSC and lineage‐restricted granulocyte macrophage progenitors (GMPs) acquired leukaemic stem cell (LSC) potential being capable of initiating and maintaining the disease. Finally, our data demonstrate that long‐term expression of AE induces an indolent myeloproliferative disease (MPD)‐like myeloid leukaemia phenotype with complete penetrance and that acute inactivation of AE function is a potential novel therapeutic option.
Properties of Intermediate-Frequency Vacuum Arc Under Axial Magnetic Field

This paper presents an experimental study of the intermediate-frequency (400-800 Hz) vacuum arc under axial magnetic field (AMF). Arc-voltage noise at the first current semi-wave is inconspicuous even if the current is not interrupted successfully. This fact is attributed to the application of a sufficiently strong AMF provided by the current flowing through a short vacuum gap. The influence of the current frequency on peak arc voltage and the rate of rise of the arc voltage are investigated. Interrupting ability of a vacuum interrupter (VI) with cup-type AMF contacts made from CuCr50 is examined. It is found that the upper limit of current interruption is inversely proportional for frequencies in the range from 400 to 800 Hz. Phase shift of AMF is studied by the finite-element method based on a simplified symmetric model. The results show that the phase-shift angle increases with the current frequency and influences intermediate-frequency current interruption of VI with AMF contacts.
Advanced glycation end products in diabetic patients with optimized glycaemic control and their effects on endothelial reactivity: possible implications in venous graft failure

Diabetic patients exhibit an increased risk of saphenous graft occlusion after coronary bypass. Advanced glycation end products (AGEs) are ubiquitous signalling proteins that are associated with vascular and neurological complication of diabetes. The aim of this study is to verify whether AGE levels may promote endothelial cell alterations responsible for vein graft failure.
Propagation Characteristics of BSISO Indices

The spatial structure and propagation of tropical intraseasonal convection anomalies diagnosed with the outgoing longwave radiation‐based Madden‐Julian Oscillation index are examined in the boreal summer and winter seasons. It is shown that the outgoing longwave radiation‐based Madden‐Julian Oscillation index represents both northward and eastward propagation in summer and eastward propagation in winter in a manner consistent with Madden‐Julian Oscillation and Boreal Summer Intraseasonal Oscillation propagation as diagnosed in many previous studies. The outgoing longwave radiation‐based Madden‐Julian Oscillation index and three other widely used indices for tracking the Boreal Summer Intraseasonal Oscillation are then compared in their lag correlation structure over selected reference areas, cross‐correlation coefficients of the two principal component time series, and time‐dependent phase angle composites. The outgoing longwave radiation anomalies from these different indices propagate differently according to these diagnostics. One of them exhibits little propagation at all, even though one would expect good propagation based on composites of the phases separately. This illustrates the general point that while composites of individual phases, presented in a sequence, are generally taken to imply that the phases tend to occur in that sequence in time, that need not be the case. It is suggested that propagation characteristics are relevant to the application of the indices and that smoother propagation is desirable.
Development and Validation of a Short Version of the Seattle Angina Questionnaire

Background—Clinical trials and national performance measures increasingly mandate reporting patients’ perspectives of their health status: their symptoms, function, and quality of life. Although the Seattle Angina Questionnaire (SAQ) is a validated disease-specific health status instrument for coronary artery disease (CAD) with high test–retest reliability, predictive power, and responsiveness, its use in routine clinical practice has been limited, in part, by its length (19 items). Methods and Results—Using data from 10 408 patients with CAD from 5 multicenter registries, we derived and validated a shortened version of the SAQ (SAQ-7) among patients presenting with stable CAD, undergoing percutaneous coronary intervention, and after acute myocardial infarction. We examined the psychometric properties of the SAQ-7 as compared with the full SAQ. Seven items from the Physical Limitation, Angina Frequency, and Quality of Life domains were identified for the SAQ-7, with high levels of concordance (0.88–1.00) with each original SAQ domain. The SAQ-7 demonstrated good construct validity (compared with Canadian Cardiovascular Society class for angina), with a correlation of 0.62 and 0.38 for patients with stable CAD and undergoing percutaneous coronary intervention, respectively. It was highly reproducible in patients with stable CAD (intraclass correlation, ≥0.78) and exhibited excellent responsiveness in patients after percutaneous coronary intervention (≥18 points in each SAQ domain). Finally, the SAQ-7 was predictive of 1-year mortality and readmission. Conclusions—To increase the feasibility of measuring patient-reported outcomes in patients with CAD, we developed and validated a shortened 7-item SAQ instrument for use in clinical trials and routine care.
Unsupervised Statistical Method for Edgel Clustering With Applications to Shape Localization

In this paper, we present a statistical model for linking edgels, which yields two models for edgel clustering. The first model favors large clusters, whereas the second one favors small sub-clusters. We show how the first model can significantly help localizing a shape in an image. The second model might be useful for other applications, such as clustering edgels into objects.
Goal Recognition over POMDPs: Inferring the Intention of a POMDP Agent

Plan recognition is the problem of inferring the goals and plans of an agent from partial observations of her behavior. Recently, it has been shown that the problem can be formulated and solved using planners, reducing plan recognition to plan generation. In this work, we extend this model-based approach to plan recognition to the POMDP setting, where actions are stochastic and states are partially observable. The task is to infer a probability distribution over the possible goals of an agent whose behavior results from a POMDP model. The POMDP model is shared between agent and observer except for the true goal of the agent that is hidden to the observer. The observations are action sequences O that may contain gaps as some or even most of the actions done by the agent may not be observed. We show that the posterior goal distribution P(G|O) can be computed from the value function VG(b) over beliefs b generated by the POMDP planner for each possible goal G. Some extensions of the basic framework are discussed, and a number of experiments are reported.
Learning to Fish with Genetics: A Primer on the Vertebrate Model Danio rerio

In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of genetics and experimental embryology, significant inroads have been made into the regulation of embryonic axis formation, organogenesis, and the development of neural networks. Research with this model has also expanded into other areas, including the genetic regulation of aging, regeneration, and animal behavior. Zebrafish are a popular model because of the ease with which they can be maintained, their small size and low cost, the ability to obtain hundreds of embryos on a daily basis, and the accessibility, translucency, and rapidity of early developmental stages. This primer describes the swift progress of genetic approaches in zebrafish and highlights recent advances that have led to new insights into vertebrate biology.
Synchronization of the Cardiac Pacemaker with Repetitive Stimulation of the Carotid Sinus Nerve in the Dog

In anesthetized open-chest dogs, the right carotid sinus nerve was stimulated with brief bursts of electrical impulses. When a single burst was given with each heart beat, the reflexly induced change in heart rate depended on the time within the cardiac cycle that the stimulus was applied. The maximum response was obtained when the P-St interval (i.e., the time from the beginning of the P wave to the beginning of the stimulus burst) was approximately zero. At this P-St interval the cardiac cycle (P-P interval) was prolonged to a mean value of 583 ± 145 (SD) msec from a prestimulation control value of 408 ± 80 msec. The minimum response, a mean P-P interval 45 ± 20 msec less than the maximum, was obtained at a mean P-St interval of 322 ± 48 msec. As a consequence of this phase dependency, over a definite but small range of stimulation frequencies, the discharge of the cardiac pacemaker became synchronized with the neural activity in the baroreceptor reflex arc. Within this critical range of stimulation frequencies, the cardiac pacemaker responded paradoxically to carotid sinus nerve stimulation: a change in the frequency of stimulation evoked a parallel, rather than the well-known inverse, change in heart rate.
Assessment of traffic noise due to transverse rumble strips at residential areas

Transverse rumble strips (TRS) are commonly being installed to alert the drivers through sound and vibration effects. The sound produced affects the existing traffic noise level which caused noise annoyance to the nearby residents. This study aims to assess the traffic noise due to TRS at residential areas by determining the roadside noise levels, traffic and road characteristics and evaluating the relationship between these parameters. Middle overlapped (MO), middle layer overlapped (MLO) and raised rumbler (RR) TRS profiles with same thickness were selected. The measurements of roadside noise levels and skid resistance were conducted using sound level meter (SLM) and British pendulum tester (BPT) respectively. Traffic characteristics were evaluated using previous data measured using automatic traffic counter (ATC). In overall, MLO produced highest roadside noise levels with increase of 20.5dBA from baseline. Generally, the increase of roadside noise level due to TRS is strong with speed, weak to medium with skid resistance of TRS and no relationship with traffic volume. Based on three TRS profile types, MLO is not suitable to be installed on the roadways adjacent to the residential areas as the increase of roadside noise level is significant which is more than 5dBA compared to MO and RR.