Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular mechanism for depolarization-induced modulation of Kv channel closure

Voltage-dependent potassium (Kv) channels provide the repolarizing power that shapes the action potential duration and helps control the firing frequency of neurons. The K+ permeation through the channel pore is controlled by an intracellularly located bundle-crossing (BC) gate that communicates with the voltage-sensing domains (VSDs). During prolonged membrane depolarizations, most Kv channels display C-type inactivation that halts K+ conduction through constriction of the K+ selectivity filter. Besides triggering C-type inactivation, we show that in Shaker and Kv1.2 channels (expressed in Xenopus laevis oocytes), prolonged membrane depolarizations also slow down the kinetics of VSD deactivation and BC gate closure during the subsequent membrane repolarization. Measurements of deactivating gating currents (reporting VSD movement) and ionic currents (BC gate status) showed that the kinetics of both slowed down in two distinct phases with increasing duration of the depolarizing prepulse. The biphasic slowing in VSD deactivation and BC gate closure was strongly correlated in time and magnitude. Simultaneous recordings of ionic currents and fluorescence from a probe tracking VSD movement in Shaker directly demonstrated that both processes were synchronized. Whereas the first slowing originates from a stabilization imposed by BC gate opening, the subsequent slowing reflects the rearrangement of the VSD toward its relaxed state (relaxation). The VSD relaxation was observed in the Ciona intestinalis voltage-sensitive phosphatase and in its isolated VSD. Collectively, our results show that the VSD relaxation is not kinetically related to C-type inactivation and is an intrinsic property of the VSD. We propose VSD relaxation as a general mechanism for depolarization-induced slowing of BC gate closure that may enable Kv1.2 channels to modulate the firing frequency of neurons based on the depolarization history.
A local prescription for the softening length in self-gravitating gaseous discs

In 2D-simulations of self-gravitating gaseous discs, the potential is often computed in the framework of “softened gravity” initially designed for N-body codes. In this special context, the role of the softening length λ is twofold: i) to avoid numerical singularities in the integral representation of the potential (i.e., arising when the separation |r − r � |→ 0); and ii) to account for stratification of matter in the direction perpendicular to the disc mid-plane. So far, most studies have considered λ as a free parameter and various values or formulae have been proposed without much mathematical justification. In this paper, we demonstrate by means of a rigorous calculus that it is possible to define λ such that the gravitational potential of a flat disc coincides at order zero with that of a geometrically thin disc of the same surface density. Our prescription for λ, valid in the local, axisymmetric limit, has the required properties i) and ii). It is mainly an analytical function of the radius and disc thickness, and is sensitive to the vertical stratification. For mass density profiles considered (namely, profiles expandable over even powers of the altitude), we find that λ: i) is independant of the numerical mesh, ii) is always a fraction of the local thickness H; iii) goes through a minimum at the singularity (i.e., at null separation); and iv) is such that 0.13 < λ/H < 0.29 typically (depending on the separation and on density profile). These results should help us to improve the quality of 2D- and 3D-simulations of gaseous discs in several respects (physical realism, accuracy, and computing time).
The neuromagnetic brain activation patterns of induced compassion in advanced Zen meditation practitioners

The concept of compassion is complex, where religious and philosophical writings are abundant but scientific publications remain sparse. The surge in neuroscientific publications related to prosocial behaviors, spirituality, and Buddhist-based meditation practices has sparked a growing interest in issues once considered foreign to the scientific arena. There is currently a strong need to develop neuroscientific methods that incorporate subjective trait and state measures. In addition, the use of powerful new technologies such as high density whole head magnetoencephalography (MEG) provides novel methods for mapping brain states over time in a way never before thought possible. The current proposal will attempt to use MEG in combination with both state and trait scales to better understand how mind and brain are related to the production of induced compassion. The sample for investigation will include high level Zen Buddhist practitioners with many years of intensive religious practice within a Buddhist framework that requires the cultivation of compassion. The hope is that these findings may one day shed light on an array of psychiatric disorders where certain forms of social impairments could benefit from practices traditionally sequestered within only religious contexts. Dedicated to all those who have suffered at the hands of those who have chosen hate as their mode of being, may grace come to victim and perpetrator alike, and may the ignorance of hate one day fully give way to compassionate embrace. TABLE OF CONTENTS Page ABSTRACT iii LIST OF TABLES viii LIST OF FIGURES ix ACKNOWLEDGEMENTS x Chapter I. REVIEW OF THE LITERATURE
All I really need to know about pair programming I learned in kindergarten

Pair programming is a practice in which two programmers work side-by-side at one computer, continuously collaborating on the same design, algorithm, code, or test. This method has been demonstrated to improve productivity and the quality of software products. Moreover, a recent survey (hereafter referred to as "the pair programming survey") found that programmers were universally more confident in their solutions when programming in pairs as opposed to working alone. Likewise, 96% agreed they enjoy their jobs more when pair programming [12].
Characterization of Intestinal Microbiomes of Hirschsprung’s Disease Patients with or without Enterocolitis Using Illumina-MiSeq High-Throughput Sequencing

Hirschsprung-associated enterocolitis (HAEC) is a life-threatening complication of Hirschsprung’s disease (HD). Although the pathological mechanisms are still unclear, studies have shown that HAEC has a close relationship with the disturbance of intestinal microbiota. This study aimed to investigate the characteristics of the intestinal microbiome of HD patients with or without enterocolitis. During routine or emergency surgery, we collected 35 intestinal content samples from five patients with HAEC and eight HD patients, including three HD patients with a history of enterocolitis who were in a HAEC remission (HAEC-R) phase. Using Illumina-MiSeq high-throughput sequencing, we sequenced the V4 region of bacterial 16S rRNA, and operational taxonomic units (OTUs) were defined by 97% sequence similarity. Principal coordinate analysis (PCoA) of weighted UniFrac distances was performed to evaluate the diversity of each intestinal microbiome sample. The microbiota differed significantly between the HD patients (characterized by the prevalence of Bacteroidetes) and HAEC patients (characterized by the prevalence of Proteobacteria), while the microbiota of the HAEC-R patients was more similar to that of the HAEC patients. We also observed that the specimens from different intestinal sites of each HD patient differed significantly, while the specimens from different intestinal sites of each HAEC and HAEC-R patient were more similar. In conclusion, the microbiome pattern of the HAEC-R patients was more similar to that of the HAEC patients than to that of the HD patients. The HD patients had a relatively distinct, more stable community than the HAEC and HAEC-R patients, suggesting that enterocolitis may either be caused by or result in a disruption of the patient’s uniquely adapted intestinal flora. The intestinal microbiota associated with enterocolitis may persist following symptom resolution and can be implicated in the symptom recurrence.
System-Wide Effectiveness of Active Learning in Collaborative Filtering

The accuracy of a collaborative-filtering system largely depends on two factors: the quality of the recommendation algorithm and the number and quality of the available product ratings. In general, the more ratings are elicited from the users, the more effective the recommendations are. However, not all the ratings are equally useful and specific techniques, which are defined as rating elicitation strategies, can be used to selectively choosing the items to be presented to the user for rating. In this paper we consider several rating elicitation strategies and we evaluate their system utility, i.e., how the overall behavior of the system changes when new ratings are added. We discuss the pros and cons of different strategies with respect to several metrics (MAE, precision, NDCG and coverage). It is shown that different strategies can improve different aspects of the recommendation quality.
Attention all mobile users !

The ongoing convergence between the telecommunications industry and the information technology industry leads to new products and services for the enduser. Products based on Wireless Application Protocol (WAP ) technology bring the world of Internet into our pockets, where the services provided may be wireless and accessed from anywhere. There are high expectations to these new services provided by products like the next generation of mobile phones, Personal Digital Assistants (PDAs), handheld computers and so on. The leading telecom industries expect services like banking transactions and mobile electronic commerce (ecommerce) to be widely used by the adopters. Based on our empirical research, we claim that system developers of such mobile services who do not realize that there is a major fundamental difference between stationary computing services and mobile computing services will see the whole concept of mobile e-commerce challenged. Designing services and applications to be used with mobile devices requires a new way of thinking. In this article we elucidate one aspect we believe to be important, namely attention. We have observed that existing mobile devices demand too much attention from the user, actually more attention than the user is willing to give.
Sidechain harmonic enhancement of noise corrupted speech for hearing impaired listeners

This work presents a single channel speech enhancement approach aimed at improving speech clarity for hearing impaired listeners under challenging listening conditions. The proposed method applies nonlinear distortions to speech components isolated from the observed noisy signal using aggressive speech enhancement. The enhanced components are then mixed back into the noisy signal. The results show that the proposed approach significantly improves speech clarity in noise.
Understanding TCP dynamics in a di erentiated services internet

A large number of Internet applications are sensitive to overload conditions in the network. While these applications have been designed to adapt somewhat to the varying conditions in the Internet, they can beneet greatly from an increased level of predictability in network services. We propose minor extensions to the packet queueing and discard mechanisms used in routers, coupled with simple control mechanisms at the source that enable the network to guarantee minimal levels of throughput to diierent sessions while sharing the residual network capacity in a cooperative manner. The service realized by the proposed mechanisms is an interpretation of the controlled-load service being standardized by the ietf. Although controlled-load service can be used in conjunction with any transport protocol, our focus in this paper is on understanding its interaction with tcp. Speciically, we study the dynamics of tcp traac in an integrated services network that simultaneously supports both best-eeort and controlled-load sessions. In light of this study, we propose and experiment with several variations to tcp's control mechanisms with the objective of ne-tuning them for an integrated services environment. We then investigate the eeect of network transients, such as changes in traac load and in service levels, on the performance of controlled-load as well as best-eeort connections. To capture the evolution of integrated services in the Internet, we also consider situations where only a selective set of routers are capable of providing service diierentiation between best-eeort and controlled-load traac. Finally, we show how the service mechanisms proposed here can be embedded within more elaborate packet and link scheduling frameworks in a fully-evolved integrated services Internet.
A LysR-Type Transcriptional Regulator in Burkholderia cenocepacia Influences Colony Morphology and Virulence

ABSTRACT Burkholderia cenocepacia strain K56-2 typically has rough colony morphology on agar medium; however, shiny colony variants (shv) can appear spontaneously. These shv all had a minimum of 50% reduction in biomass formation and were generally avirulent in an alfalfa seedling infection model. Three shv—K56-2 S15, K56-2 S76, and K56-2 S86—were analyzed for virulence in a chronic agar bead model of respiratory infection and, although all shv were able to establish chronic infection, they produced significantly less lung histopathology than the rough K56-2. Transmission electron microscopy revealed that an extracellular matrix surrounding bacterial cells was absent or reduced in the shv compared to the rough wild type. Transposon mutagenesis was performed on the rough wild-type strain and a mutant with an insertion upstream of ORF BCAS0225, coding for a putative LysR-type regulator, exhibited shiny colony morphology, reduced biofilm production, increased N-acyl homoserine lactone production, and avirulence in alfalfa. The rough parental colony morphotype, biofilm formation, and virulence in alfalfa were restored by providing BCAS0225 in trans in the BCAS0225::pGSVTp-luxCDABF mutant. Introduction of BCAS0225 restored the rough morphotype in several shv which were determined to have spontaneous mutations in this gene. In the present study, we show that the conversion from rough wild type to shv in B. cenocepacia correlates with reduced biofilm formation and virulence, and we determined that BCAS0225 is one gene involved in the regulation of these phenotypes.
LKB1 and Notch Pathways Interact and Control Biliary Morphogenesis

Background LKB1 is an evolutionary conserved kinase implicated in a wide range of cellular functions including inhibition of cell proliferation, regulation of cell polarity and metabolism. When Lkb1 is inactivated in the liver, glucose homeostasis is perturbed, cellular polarity is affected and cholestasis develops. Cholestasis occurs as a result from deficient bile duct development, yet how LKB1 impacts on biliary morphogenesis is unknown. Methodology/Principal Findings We characterized the phenotype of mice in which deletion of the Lkb1 gene has been specifically targeted to the hepatoblasts. Our results confirmed that lack of LKB1 in the liver results in bile duct paucity leading to cholestasis. Immunostaining analysis at a prenatal stage showed that LKB1 is not required for differentiation of hepatoblasts to cholangiocyte precursors but promotes maturation of the primitive ductal structures to mature bile ducts. This phenotype is similar to that obtained upon inactivation of Notch signaling in the liver. We tested the hypothesis of a functional overlap between the LKB1 and Notch pathways by gene expression profiling of livers deficient in Lkb1 or in the Notch mediator RbpJκ and identified a mutual cross-talk between LKB1 and Notch signaling. In vitro experiments confirmed that Notch activity was deficient upon LKB1 loss. Conclusion LKB1 and Notch share a common genetic program in the liver, and regulate bile duct morphogenesis.
Multiple-channel detection of a Gaussian time series over frequency-flat channels

This work addresses the problem of deciding whether a set of realizations of a vector-valued time series with unknown temporal correlation are spatially correlated or not. Specifically, the spatial correlation is induced by a colored source over a frequency-flat single-input multiple-output (SIMO) channel distorted by independent and identically distributed noises with temporal correlation. The generalized likelihood ratio test (GLRT) for this detection problem does not have a closed-form expression and we have to resort to numerical optimization techniques. In particular, we apply the successive convex approximations approach which relies on solving a series of convex problems that approximate the original (non-convex) one. The proposed solution resembles a power method for obtaining the dominant eigenvector of a matrix, which changes over iterations. Finally, the performance of the proposed detector is illustrated by means of computer simulations showing a great improvement over previously proposed detectors that do not fully exploit the temporal structure of the source.
Mechanosensitvity of isolated myenteric neuronal networks

The myenteric neurons, sandwiched between two muscles layers, are constantly under mechanical stress. Their mechanosensitive properties are poorly understood. This study elucidates new features of primary cultured myenteric neurons and the mechanical stimulus modality exciting them. It also reveals that myenteric neurons are mechanosensitive along entire neurites and the soma. Normal stress rather than shear stress is their adequate stimulus. These data will help to understand the complex process of enteric mechanotransduction under physiological and pathophysiological conditions.
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

Motivation: Identification and characterization of protein–protein interactions (PPIs) is one of the key aims in biological research. While previous research in text mining has made substantial progress in automatic PPI detection from literature, the need to improve the precision and recall of the process remains. More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction. Results: We developed an interaction detection method and explored the usefulness of various features in automatically identifying PPIs in text. The results show that our approach outperforms other systems using the AImed dataset. In the tests where our system achieves better precision with reduced recall, we discuss possible approaches for improvement. In addition to test datasets, we evaluated the performance on interactions from five human-curated databases—BIND, DIP, HPRD, IntAct and MINT—where our system consistently identified evidence for ∼60% of interactions when both proteins appear in at least one sentence in the PubMed abstract. We then applied the system to extract articles from PubMed to annotate known, high-throughput and interologous interactions in I2D. Availability: The data and software are available at: http://www.cs. utoronto.ca/∼juris/data/BI09/. Contact: yniu@uhnres.utoronto.ca; juris@ai.utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
A New Approach to the Sensitivity Conjecture

One of the major outstanding foundational problems about boolean functions is the sensitivity conjecture, which (in one of its many forms) asserts that the degree of a boolean function (i.e. the minimum degree of a real polynomial that interpolates the function) is bounded above by some fixed power of its sensitivity (which is the maximum vertex degree of the graph defined on the inputs where two inputs are adjacent if they differ in exactly one coordinate and their function values are different). We propose an attack on the sensitivity conjecture in terms of a novel two-player communication game. A strong enough lower bound on the cost of this game would imply the sensitivity conjecture. To investigate the problem of bounding the cost of the game, three natural (stronger) variants of the question are considered. For two of these variants, protocols are presented that show that the hoped for lower bound does not hold. These protocols satisfy a certain monotonicity property, and (in contrast to the situation for the two variants) we show that the cost of any monotone protocol satisfies a strong lower bound.
CFM: A Fitness-Model-Based Topology Control Algorithm for Wireless Sensor Networks

Abstract The main objective of wireless sensor network design is to maximize network lifetime. The network topology, which is the important foundation of upper layer protocols, serves as the supportive groundwork for this goal. We constructed the model of sensor networks, and investigated the property of topology with complex network theory. Three statistical parameters were used to describe the network structure, and then some ideal characteristics were concluded for topology. The characteristics of topology can be achieved by fitness model, so we designed an approximate clustering algorithm based on fitness model, which is distributed. CFM is composed of three phases: links generation phase, heads selection phase and cluster division phase. The performance of CFM algorithm was analyzed through simulation experiments, which indicated a well-constructed topology and effectively prolonged network lifetime.
Transcriptomes and Proteomes Define Gene Expression Progression in Pre-meiotic Maize Anthers

Plants lack a germ line; consequently, during reproduction adult somatic cells within flowers must switch from mitotic proliferation to meiosis. In maize (Zea mays L.) anthers, hypoxic conditions in the developing tassel trigger pre-meiotic competence in the column of pluripotent progenitor cells in the center of anther lobes, and within 24 hr these newly specified germinal cells have patterned their surrounding neighbors to differentiate as the first somatic niche cells. Transcriptomes were analyzed by microarray hybridization in carefully staged whole anthers during initial specification events, after the separation of germinal and somatic lineages, during the subsequent rapid mitotic proliferation phase, and during final pre-meiotic germinal and somatic cell differentiation. Maize anthers exhibit a highly complex transcriptome constituting nearly three-quarters of annotated maize genes, and expression patterns are dynamic. Laser microdissection was applied to begin assigning transcripts to tissue and cell types and for comparison to transcriptomes of mutants defective in cell fate specification. Whole anther proteomes were analyzed at three developmental stages by mass spectrometric peptide sequencing using size-fractionated proteins to evaluate the timing of protein accumulation relative to transcript abundance. New insights include early and sustained expression of meiosis-associated genes (77.5% of well-annotated meiosis genes are constitutively active in 0.15 mm anthers), an extremely large change in transcript abundances and types a few days before meiosis (including a class of 1340 transcripts absent specifically at 0.4 mm), and the relative disparity between transcript abundance and protein abundance at any one developmental stage (based on 1303 protein-to-transcript comparisons).