Miracle-dz/UniFAR-FTUs huggingface dataset:
Ca2+ channels from the sea urchin sperm plasma membrane

Ca2+ influx across the sea urchin sperm plasma membrane is a necessary step during the egg jelly-induced acrosome reaction. There is pharmacological evidence for the involvement of Ca2+ channels in this influx, but their presence has not been directly demonstrated because of the small size of this cell. Sea urchin sperm Ca2+ channels are being studied by fusing isolated plasma membranes into planar lipid bilayers. With this strategy, a Ca2+ channel has been detected with the following characteristics: (a) the channel exhibits a high mainstate conductance (gamma MS) of 172 pS in 50 mM CaCl2 solutions with voltage- dependent decaying to smaller conductance states at negative Em; (b) the channel is blocked by millimolar concentrations of Cd2+, Co2+, and La3+, which also inhibit the egg jelly-induced acrosome reaction; (c) the gamma MS conductance sequence for the tested divalent cations is the following: Ba2+ greater than Sr2+ greater than Ca2+; and (d) the channel discriminates poorly for divalent over monovalent cations (PCa/PNa = 5.9). The sperm Ca2+ channel gamma MS rectifies in symmetrical 10 mM CaCl2, having a maximal slope conductance value of 94 pS at +100 mV applied to the cis side of the bilayer. Under these conditions, a different single-channel activity of lesser conductance became apparent above the gamma MS current at positive membrane potentials. Also in 10 mM Ca2+ solutions, Mg2+ permeates through the main channel when added to the cis side with a PCa/PMg = 2.9, while it blocks when added to the trans side. In 50 mM Ca2+ solutions, the gamma MS open probability has values of 1.0 at voltages more positive than - 40 mV and decreases at more negatives potentials, following a Boltzmann function with an E0.5 = -72 mV and an apparent gating charge value of 3.9. These results describe a novel Ca2(+)-selective channel, and suggest that the main channel works as a single multipore assembly.
Directed Dependency Graph based Concurrency Control for Persistent Systems

Persistent stores abstract over all aspects of storage including the distinction between primary and secondary storage. One consequence of this abstraction is that the store appears to the user to be free from failure. Since computers are vulnerable to failure, persistent systems typically provide mechanisms to support this appearance of a failure-free store. These allow the system to recover automatically from store failure to a self-consistent state, exhibiting a property called stability.
Distance-based interference coordination for device-to-device communications in cellular networks

In this paper, a two-step scheme is proposed to deal with the mutual interference between cellular networks and D2D communications. First, in order to mitigate the interference from D2D transmission to cellular communication, we propose an efficient power control scheme to obtain the upper bound of D2D transmit power. Next, to control the interference from cellular user to D2D receiver, an improved distance-based resource allocation scheme is proposed. Simulation results show that by applying our method the reliability of D2D communication improves significantly without degrading the performance of the cellular connection.
Variational segmentation framework in prolate spheroidal coordinates for 3D real-time echocardiography

This paper presents a new formulation of a deformable model segmentation in prolate spheroidal coordinates for segmentation of 3D cardiac echocardiography data. The prolate spheroidal coordinate system enables a representation of the segmented surface with descriptors specifically adapted to the "ellipsoidal" shape of the ventricle. A simple data energy term, based on gray-level information, guides the segmentation. The segmentation framework provides a very fast and simple algorithm to evolve an initial ellipsoidal object towards the endocardial surface of the myocardium with near real-time deformations. With near real-time performance, additional constraints on landmark points, can be used interactively to prevent leakage of the surface.
A Structural Split in the Human Genome

Background Promoter-associated CpG islands (PCIs) mediate methylation-dependent gene silencing, yet tend to co-locate to transcriptionally active genes. To address this paradox, we used data mining to assess the behavior of PCI-positive (PCI+) genes in the human genome. Results PCI+ genes exhibit a bimodal distribution: (1) a ‘housekeeping-like’ subset characterized by higher GC content and lower intron length/number, and (2) a ‘pseudogene paralog’ subset characterized by lower GC content and higher intron length/number (p<0.001). These subsets are functionally distinguishable, with the former gene group characterized by higher expression levels and lower evolutionary rate (p<0.001). PCI-negative (PCI-) genes exhibit higher evolutionary rate and narrower expression breadth than PCI+ genes (p<0.001), consistent with more frequent tissue-specific inactivation. Conclusions Adaptive evolution of the human genome appears driven in part by declining transcription of a subset of PCI+ genes, predisposing to both CpG→TpA mutation and intron insertion. We propose a model of evolving biological complexity in which environmentally-selected gains or losses of PCI methylation respectively favor positive or negative selection, thus polarizing PCI+ gene structures around a genomic core of ancestral PCI- genes.
Dysbiosis in the Pathogenesis of Pediatric Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBDs) are chronic inflammatory conditions of the gastrointestinal tract that occur in genetically susceptible individuals. Crohn's disease (CD) and ulcerative colitis (UC) are two major types of IBD. In about 20–25% of patients, disease onset is during childhood and pediatric IBD can be considered the best model for studying immunopathogentic mechanisms. The fundamentals of IBD pathogenesis are considered a defective innate immunity and bacterial killing with overaggressive adaptive immune response. A condition of “dysbiosis”, with alterations of the gut microbial composition, is regarded as the basis of IBD pathogenesis. The human gastrointestinal (GI) microbial population is a complex, dynamic ecosystem and consists of up to one thousand different bacterial species. In healthy individuals, intestinal microbiota have a symbiotic relationship with the host organism and carry out important metabolic, “barrier,” and immune functions. Microbial dysbiosis in IBD with lack of beneficial bacteria, together with genetic predisposition, is the most relevant conditions in the pathogenesis of the pediatric IBD.
Altered patterns of brain activity during transient anger among young males with alcohol use disorders: A preliminary study

The aim of the study was to investigate the neural substrates associated with processing anger among young males with alcohol use disorders (AUDs) using functional magnetic resonance imaging (fMRI). Eighteen individuals with AUD and 15 demographically similar non-abusers participated in the study. Participants were scanned on their brain functioning while they viewed an audio-visual film clip that was previously designed specifically to induce anger emotion, followed by anpsychological assessment. Greater brain activities were detected in the left inferior frontal gyrus (IFG) and dorsal anterior cingulate cortex (dACC) among subjects with AUD compared to the controls during the exposure to anger-provoking stimuli. Despite the same level of subjective anger during anger induction, the greater activations both in the IFG and dACC regions may suggestthat individuals with AUD have a greater propensity to undergo cognitive control and self-regulation while experiencing anger.
Second-order theory for nonlinear phase noise in coherent fiber-optic system based on phase shift keying

A second-order perturbation technique is used to develop analytical expressions for the phase variance in a nonlinear fiber optic system based on phase-shift keying. Typically, in short-haul fiber optic communication system, the nonlinear effects are smaller than dispersive effect, and it is found that the difference between the first and second-order solution is negligible. However, when the transmission distance is long and/or lunch power is large, nonlinearity becomes a stronger perturbation, and the first-order theory is not adequate to describe the phase fluctuations. Coupling between fiber non-linearity and amplitude noise leads to a random walk of the signal phase, which degrades the transmission performance of phase-shift keying system. An analytical expression has been obtained based on a second-order perturbation technique for the variance of nonlinear phase noise, which is found to be in good agreement with numerical simulation.
Effects of Eye Images and Norm Cues on Charitable Donation

Laboratory and field experiments have shown that people are more likely to be prosocial in the presence of watching eyes images. This “watching eyes effect” may be explained by the reputation-based partner choice model or a norm-compliance model suggesting that eye images elicit conformity to locally specific behavioral norms. A previous laboratory study that investigated the effects of local norms on charitable donations by using watching eye images and manipulating money visible in a collection box found that the presence of eye images significantly increased overall donations; however, the images did not make people more likely to conform to the apparent local norm. Here, we report the results of a field study examining the effects of watching eyes and the amount of money in transparent collection boxes on charitable giving in an izakaya (a Japanese-style tavern) setting. Contrary to the previous study, we found that the amount donated increased more under the large- than the small-norm treatment. The presence of eye images increased the overall amount donated but was more salient under the small-norm treatment. We found that participants were more likely to increase the amount of money in the box than to conform to the local norm of a small donation when the eye images were present. The results of this study suggest that an appropriate combination of eye images and normative information can alter people’s behavior without changing their economic incentives.
Testing the connection between the X-ray and submillimetre source populations using Chandra

The powerful combination of the Chandra X-ray telescope, the SCUBA submillimetre-wave camera and the gravitational lensing effect of the massive galaxy clusters A2390 and A1835 has been used to place stringent X-ray flux limits on six faint submillimetre SCUBA sources and deep submillimetre limits on three Chandra sources which lie in fields common to both instruments. One further source is marginally detected in both the X-ray and submillimetre bands. For all the SCUBA sources our results are consistent with starburst-dominated emission. For two objects, including SMMJ 14011+0252 at z=2.55, the constraints are strong enough that they can only host powerful active galactic nuclei if they are both Compton-thick and any scattered X-ray flux is weak or itself absorbed. The lensing amplification for the sources is in the range 1.5–7, assuming that they lie at z≳1. The brightest detected X-ray source has a faint extended optical counterpart (I≈22) with colours consistent with a galaxy at z≃1. The X-ray spectrum of this galaxy is hard, implying strong intrinsic absorption with a column density of about 1023 cm−2 and an intrinsic (unabsorbed) 2–10 keV luminosity of 3×1044 erg s−1. This source is therefore a Type II quasar. The weakest detected X-ray sources are not detected in Hubble Space Telescope images down to I≃26.
The Developmental Basis for the Evolution of Muroid Dentition

Analysis of gene expression patterns and tooth morphogenesis in the mouse and sibling vole 3 Vanhemmilleni, Ilman heidän kannustustaan ja kiinnostustaan tuskin oltaisiin tässä " Nothing in biology makes sense except in light of evolution. " T. Dobzhansky 5 Contents Abbreviations 7 Abstract 9 Original publications 10 Introduction 11 Literature review 12 The problem of morphological evolution 12 Developmental biology in evolution research 13 Morphogenesis as a target for evolutionary processes 14 Morphogenesis is based on local differences in intercellular signaling 15 Lateral inhibition and dissociation in pattern formation 17 Serial homology and diversification 21 The tooth as a model system 22 The evolution of the mammalian dentition 25 The origin of teeth 25 The integration of occlusion in mammals 25 The evolution of molar cusp patterns 27 The evolution of specialized rodent dentition 28 The evolution of muroid teeth 29 The lower first molars of the mouse and sibling vole 31 The developmental biology of the teeth 32 Morphogenesis 32 Determination of positional identity and tooth morphogenesis 34 Molecular interactions in tooth morphogenesis 36 Signaling centers in tooth development 40 Aims 42 Results and discussion 43 The morphogenesis of mouse and vole teeth 43 The dentitions of the mouse and vole 43 Rudimentary tooth germs in mouse and sibling vole upper diastema regions 44 Morphogenesis of mouse and sibling vole first lower molars (M 1 s) 45 The basic developmental pathways are conserved in the teeth of the mouse and sibling vole 50 The gene sequences are conserved between the mouse and vole 50 The genes are expressed similarly in mouse and vole molars 52 Cross-species recombinations of mouse and vole tissues can produce a tooth 53 Epithelial signaling centers 54 Enamel knots as epithelial signaling centers 55 Early epithelial signaling centers 55 Conservation of signaling center programs 56 Early epithelium and dental formulas 57 Individual tooth germs develop from a continuous dental lamina 58 Early epithelium controls the positional identities of the tooth germs 58 Positional identity and tooth morphogenesis 60 Evolution of muroid dental formulas 60 Enamel knots and crown morphogenesis 62 The development of individual enamel knots 63 Molecular and mechanical models for enamel knot induction and function 65 Enamel knots and cusp patterns 68 6 The evolution of mouse and sibling vole molar cusp patterns 69 Crown size and cusp numbers 70 Orthogonal and diagonal cusp positions 71 The evolution of prismatism and hypselodonty in …
Qualidade de vida e a cirurgia em cancro da mama: revisão narrativa da literatura = Quality of life and breast cancer surgery: narrative literature review

Resumo: Este artigo tem o objectivo de realizar uma revisao nao sistematica e narrativa da literatura de estudos que comparam a qualidade de vida de mulheres com cancro da mama submetidas a diferentes tipos de cirurgia. Ao analisar os estudos, verificou-se que estes abordavam diversos aspectos, agrupados em tres dimensoes: a) Metodologia adoptada, se referindo aos instrumentos utilizados, o intervalo de avaliacao e o procedimento de recolha de dados; b) Variaveis sociodemograficas e psicoemocionais, que diz respeito a idade, escolaridade, estado civil, sexualidade e percepcao da imagem corporal; e c) Variaveis clinicas, relacionado ao tipo de tratamento e ao estadio da doenca. Os resultados levam-nos a reflectir sobre a importância de incluir a avaliacao da qualidade de vida no processo de tratamento e no seguimento das doentes, independente do tipo de cirurgia a que as mulheres sao submetidas. Palavras-chave: Cancro da mama; qualidade de vida; cirurgia; revisao narrativa. Abstract: This article aims to conduct a non-systematic and narrative review of the literature of studies comparing the quality of life in women with breast cancer undergoing different types of surgery. Analyzing the studies, they showed several aspects, grouped into three dimensions: a) Methodology adopted, referring to the instruments, the interval of evaluation, and the procedure of data collection; b) Sociodemographic and psychoemotional variables, related to age, educational level, marital status, sexuality and perception of body image; and c) Clinical variables, related to the type of treatment and the stage of the disease. Results leads us to reflect on the importance of including the assessment of quality of life in the treatment process and follow-up of patients, regardless of the type of surgery that women are submitted. Keywords: Breast cancer; quality of life; surgery; narrative review. Resumen: Este articulo tiene como objetivo realizar una revision no sistematica y narrativa de la literatura de estudios que comparan la calidad de vida de mujeres con cancer de mama sometidas a diferentes tipos de cirugia. Mediante el analisis de los estudios, se encontro diversos aspectos, agrupados en tres dimensiones: a) Metodologia utilizada, se refiere a los instrumentos, el intervalo de evaluacion, asi como el procedimiento de recoleccion de datos; b) Variables socio-demograficas y psico-emocionales, relativas a la edad, la educacion, el estado civil, la sexualidad y la percepcion de la imagen corporal; y c) Variables clinicas, relacionadas con el tipo de tratamiento y lo estadio de la enfermedad. Los resultados nos llevan a reflexionar sobre la importancia de incluir la evaluacion de la calidad de vida en el proceso de tratamiento y el seguimiento de los pacientes, sin importar el tipo de cirugia al que las mujeres son sometidas. Palabras clave: Cancer de mama; calidad de vida; cirugia; revision narrativa. DOI: http://dx.doi. org/10.21615/cesp.10. 1.3
Imaging panel skew correction and auto-focusing in radiotherapy cone beam imaging

Digital transducers, notably amorphous silicon panels, are being used in image guided radiotherapy. Using kilo-voltage X-ray sources panel transducers are providing cone beam volume reconstruction. Theoretical considerations show that even sub-degree skew can result in the wandering of projection points across many detector elements to produce serious blurring of the cone beam reconstruction away from the imaging isocentre. The importance of identifying and correcting transducer skew is highlighted and shown to be of potentially greater importance than mechanical flex. Radiographic imaging of a suspended radio-opaque test object is described for direct characterisation of skew. The results of skew correction by image processing are presented. The use of 'auto-focusing' grey level change detection algorithms in cone beam reconstruction images, following programmed incremental angular transformation of the projection profiles of a 'Rando' anthropomorphic phantom, is shown to have the potential for automating skew correction.
A Framework for Outsourcing of Secure Computation

We study the problem of how to efficiently outsource a sensitive computation on secret inputs to a number of untrusted workers, under the assumption that at least one worker is honest. In our setting there is a number of clients C_1,…,Cn with inputs x1,…,xn. The clients want to delegate a secure computation of f(x1,…,xn) to a set of untrusted workers W1,…,Wm. We want do so in such a way that as long at there is at least one honest worker (and everyone else might be actively corrupted) the following holds 1) the privacy of the inputs is preserved 2) the output of the computation is correct (in particular workers cannot change the inputs of honest clients). We propose a solution where the clients' work is minimal and the interaction pattern simple (one message to upload inputs, one to receive results), while at the same time reducing the overhead for the workers to a minimum. Our solution is generic and can be instantiated with any underlying reactive MPC protocol where linear operations are ``for free''. In contrast previous solutions were less generic and could only be instantiated for specific numbers of clients/workers.
University and Secondary School Students' Misconceptions about the Concept of "Aromaticity" in Organic Chemistry.

Aromaticity concept is given incorrect or incomplete to the student in secondary education and knowledge based on this basic concept has been caused to another misconception in future. How are the achievement levels relating to the comprehension of various characteristics of aromatic compounds for the first and third grade students attending Department of Chemistry in Faculty of Sciences and Arts, and Faculty of Education in Dicle University and eleventh (last) grade secondary students? Sample of this study consists of 140 students from Department of Chemistry in Faculty of Sciences and Arts, and Faculty of Education in Dicle University and 65 students randomly selected from secondary school students in Diyarbakır city center. Data were collected from the achievement test developed for aromaticity concept and features. According to the findings of this study, the average achievement scores difference between the students’ relating to cyclic properties, planer structure, conjugated double bond, the reactions of aromatic compounds and aromatic compounds obeying Huckel’s Rule has been found significant. It has been seen that the Aromaticity concept was given in a less amount in secondary school chemistry instruction program or even insufficient and misconceived form in some chemistry books by reviewing the last grade of secondary school chemistry text books. The findings of this study showed that the students have had misconceptions about this subject. So, the secondary school instruction program could be reviewed and given place about aromaticity concept on a large scale.
HYDROLOGICAL MODELING OF THE IROQUOIS RIVER WATERSHED USING HSPF AND SWAT 1

ABSTRACT: The performance of two popular watershed scale simulation models — HSPF and SWAT — were evaluated for simulating the hydrology of the 5,568 km2 Iroquois River watershed in Illinois and Indiana. This large, tile drained agricultural watershed provides distinctly different conditions for model comparison in contrast to previous studies. Both models were calibrated for a nine‐year period (1987 through 1995) and verified using an independent 15‐year period (1972 through 1986) by comparing simulated and observed daily, monthly, and annual streamflow. The characteristics of simulated flows from both models are mostly similar to each other and to observed flows, particularly for the calibration results. SWAT predicts flows slightly better than HSPF for the verification period, with the primary advantage being better simulation of low flows. A noticeable difference in the models' hydrologic simulation relates to the estimation of potential evapotranspiration (PET). Comparatively low PET values provided as input to HSPF from the BASINS 3.0 database may be a factor in HSPF's overestimation of low flows. Another factor affecting baseflow simulation is the presence of tile drains in the watershed. HSPF parameters can be adjusted to indirectly account for the faster subsurface flow associated with tile drains, but there is no specific tile drainage component in HSPF as there is in SWAT. Continued comparative studies such as this, under a variety of hydrologic conditions and watershed scales, provide needed guidance to potential users in model selection and application.
Stabilizing RED using a Fuzzy Controller

Active queue management (AQM) is an effective method to provide an early notification of network congestion by pro-actively dropping or marking packets. In this paper, we propose a novel algorithm called fuzzy control RED (FCRED) that overcomes the drawbacks of the original RED. FCRED uses a fuzzy controller to adjust the maximum drop probability to stabilize the average queue length around the target queue length. We demonstrate by simulation results that FCRED maintains its performance independent of traffic loads, round trip propagation delay, and bottleneck capacity. We also demonstrate that FCRED is robust to non-responsive UDP traffic and HTTP traffic, and it is effective for networks with multiple bottlenecks. Comparison with other well-known AQM algorithms like PI, REM and ARED demonstrates the superiority of FCRED in achieving faster convergence to queue length target, and smaller queue length jitter.