Miracle-dz/UniFAR-FTUs huggingface dataset:
Ran modulates spindle assembly by regulating a subset of TPX2 and Kid activities including Aurora A activation

Ran, a GTPase in the Ras superfamily, is proposed to be a spatial regulator of microtubule spindle assembly by maintaining key spindle assembly factors in an active state close to chromatin. RanGTP is hypothesized to maintain the spindle assembly factors in the active state by binding to importin β, part of the nuclear transport receptor complex, thereby preventing the inhibitory binding of the nuclear transport receptors to spindle assembly factors. To directly test this hypothesis, two putative downstream targets of the Ran spindle assembly pathway, TPX2, a protein required for correct spindle assembly and Kid, a chromokinesin involved in chromosome arm orientation on the spindle, were analyzed to determine if their direct binding to nuclear transport receptors inhibited their function. In the amino-terminal domain of TPX2 we identified nuclear targeting information, microtubule-binding and Aurora A binding activities. Nuclear transport receptor binding to TPX2 inhibited Aurora A binding activity but not the microtubule-binding activity of TPX2. Inhibition of the interaction between TPX2 and Aurora A prevented Aurora A activation and recruitment to microtubules. In addition we identified nuclear targeting information in both the amino-terminal microtubule-binding domain and the carboxy-terminal DNA binding domain of Kid. However, the binding of nuclear transport receptors to Kid only inhibited the microtubule-binding activity of Kid. Therefore, by regulating a subset of TPX2 and Kid activities, Ran modulates at least two processes involved in spindle assembly.
The ice-breaker effect: singing mediates fast social bonding

It has been proposed that singing evolved to facilitate social cohesion. However, it remains unclear whether bonding arises out of properties intrinsic to singing or whether any social engagement can have a similar effect. Furthermore, previous research has used one-off singing sessions without exploring the emergence of social bonding over time. In this semi-naturalistic study, we followed newly formed singing and non-singing (crafts or creative writing) adult education classes over seven months. Participants rated their closeness to their group and their affect, and were given a proxy measure of endorphin release, before and after their class, at three timepoints (months 1, 3 and 7). We show that although singers and non-singers felt equally connected by timepoint 3, singers experienced much faster bonding: singers demonstrated a significantly greater increase in closeness at timepoint 1, but the more gradual increase shown by non-singers caught up over time. This represents the first evidence for an ‘ice-breaker effect’ of singing in promoting fast cohesion between unfamiliar individuals, which bypasses the need for personal knowledge of group members gained through prolonged interaction. We argue that singing may have evolved to quickly bond large human groups of relative strangers, potentially through encouraging willingness to coordinate by enhancing positive affect.
Design of Dependable Task Scheduling Algorithm in Cloud Environment

Cloud computing is a very emerging technology now a days and has a lot of research in various areas like resource allocation, virtual machine (VM) allocation, task scheduling, security, privacy, etc. A large number of requests arrive in cloud every time; it is necessary to manage these requests which contains some independent and some dependent tasks. Dependent tasks causes delay in execution to other tasks so requires a heuristic approach for scheduling. In this paper we have proposed a new heuristic algorithm for dependable task scheduling which will reduce the period of scheduling and compared the results with Bounded Number of Processors (BNP) class of scheduling algorithms- Modified Critical Path (MCP), Earliest Time First (ETF) and Dynamic Level Scheduling (DLS). The results show less makespan, high speedup and low scheduling length ratio.
The Effect of Cooling Rate on the Microstructure Configuration of Continuously Cast Steel Slabs

This research work is another step for increasing the efficiency and productivity of the steel making process by enhancing both quality and quantity of the steel produced by the Continuous Casting process. When steels cool from a high temperature, austenite transforms into other phase configurations according to the austenite composition and cooling rate. As result of phase transformation, the steel crystal structure and, consequently, both the shape and the lattice parameter of the unit cell, change. These changes may introduce dilatational strains into the microstructure, which result in the creation of residual stress concentration zones within the microstructure. These stress concentration zones are vulnerable regions to the formation of microcracks or growth of the flaws in these regions. The main objective of this dissertation is to develop a method to define the optimum cooling rate for cooling continuously as-cast steel on industrial level. An FEM algorithm developed with the ANSYS codes is introduced in this dissertation to simulate the cooling of as-cast steel from any temperature below the solidification temperature. The algorithm is capable of being customized to simulate the thermodynamic behavior of as-cast steel microstructure with any chemical composition and any casting geometry imposed to desired cooling method. The phase transformation simulations were based on the CCT diagram and, therefore, they were quasi-real models. The models predict, analytically, the generation of the stress concentration regions due to the thermodynamic strains during cooling a sample from the austenite temperature range with different cooling rates. Another series of FEM models presented in this dissertation and post non-destructive tests (NDT) ultrasonic image analysis tests suggested in this work, can be used in the discussion of the effect of the cooling rate on the altering of the soundness of the tested steel. A combination of the suggested FEM algorithm and post image processing of NDT ultrasonic images along with laboratory cooling experiments and microstructural analysis provide a guideline to find the cooling rate for each grade of steel in the casting steel industry. Results of JMATPRO software also are deployed to increase the accuracy of the experimental set up and to obtain the required input data to run the proposed numerical algorithm cooling simulation.
Oracle estimation of adaptive cosine packet transforms for underdetermined audio source separation

We address the problem of instantaneous, underdetermined audio source separation by time-frequency masking. Using oracle estimators, we determine experimental upper performance bounds, by assuming that we have reference sources available, and that we know, or have estimated, the mixing structure. Oracle estimation of four musical sources from two-channel mixtures demonstrates a potential for SDR improvements of up to 12.7 dB, compared to semi-blind methods. We also show that using adaptive cosine packet transforms, rather than fixed-basis STFTs, can improve performance by up to 2.2 dB. Finally, by allowing more than one non-zero source coefficient per time-frequency index, improvements of up to 7.7 dB could be possible.
Identifying enterotype in human microbiome by decomposing probabilistic topics into components

Discovering the global structures of microbial community using large-scale metagenomes is a significant challenge in the era of post-genomics. Data-driven methods such as dimension reduction have shown to be useful when they applied on a metagenomics profile matrix which summarize the abundance of functional or taxonomic categorizations in metagenomic samples. Analogously, model-driven method such as probability topic model (PTM) has been used to build a generative model to simulate the generating of a microbial community based on metagenomic profiles. Data-driven methods are direct and simple, they provide intuitive visualization and understanding of metagenomic profiles. Model-driven methods are often complicated but give a generative mechanism of microbial community which is helpful in understanding the generating process of complex microbial ecology. However, results from model-driven methods are usually hard to visualize and there is less an intuitive understanding of them. We developed a new computational framework to incorporate the strength of data-driven methods into model-based methods and applied the framework to discover and interpret enterotype in human microbiome.
Qualitative systematic review: barriers and facilitators to smoking cessation experienced by women in pregnancy and following childbirth.

AIM To explore barriers and facilitators to smoking cessation experienced by women during pregnancy and postpartum by undertaking a synthesis of qualitative studies. BACKGROUND The majority of pregnant women are aware that smoking in pregnancy compromises maternal and infant health. Despite this knowledge, quit rates among pregnant women remain low, particularly among women in disadvantaged circumstances; disadvantage also increases the chances of living with a partner who smokes and returning to smoking after birth. A deeper understanding of what hinders and what helps pregnant smokers to quit and remain ex-smokers postpartum is needed. DESIGN A synthesis of qualitative research using meta-ethnography. DATA SOURCES Five electronic databases (January 1990-May 2013) were searched comprehensively, updating and extending the search for an earlier review to identify qualitative research related to the review's aims. REVIEW METHODS Following appraisal, 38 studies reported in 42 papers were included and synthesized following the principles of meta-ethnography. Over 1100 pregnant women were represented, the majority drawn from disadvantaged groups. RESULTS Four factors were identified that acted both as barriers and facilitators to women's ability to quit smoking in pregnancy and postpartum: psychological well-being, relationships with significant others, changing connections with her baby through and after pregnancy; appraisal of the risk of smoking. CONCLUSION The synthesis indicates that barriers and facilitators are not fixed and mutually exclusive categories; instead, they are factors with a latent capacity to help or hinder smoking cessation. For disadvantaged smokers, these factors are more often experienced as barriers than facilitators to quitting.
Consensus acceleration in multiagent systems with the Chebyshev semi-iterative method

We consider the fundamental problem of reaching consensus in multiagent systems. To date, the consensus problem has been typically solved with decentralized algorithms based on graph Laplacians. However, the convergence of these algorithms is often too slow for many important multiagent applications, and thus they are increasingly being combined with acceleration methods. Unfortunately, state-of-the-art acceleration techniques require parameters that can be optimally selected only if complete information about the network topology is available, which is rarely the case in practice. We address this limitation by deriving two novel acceleration methods that can deliver good performance even if little information about the network is available. The first is based on the Chebyshev semi-iterative method and maximizes the worst-case convergence speed given that only rough bounds on the extremal eigenvalues of the network matrix are available. It can be applied to systems where agents use unreliable communication links, and its computational complexity is similar to those of simple Laplacian-based methods. This algorithm requires synchronization among agents, so we also propose an asynchronous version that approximates the output of the synchronous algorithm. Mathematical analysis and numerical simulations show that the convergence speed of the proposed acceleration methods decrease gracefully in scenarios where the sole use of Laplacian-based methods is known to be impractical.
Spatio-Temporal Connectivity in Dynamic Tropical Fragmented Landscapes

Expanding human occupation on the planet reduces and fragments native habitats, threatening biodiversity, ecosystem functioning, and services. Tropical regions have recently been experiencing unprecedented amounts of forest conversion and fragmentation. As tropical forests harbor a large fraction of the world’s biodiversity, their loss and fragmentation has spearheaded the sixth mass extinction. Nevertheless, the tropical regions experience unique low intensity land-use and bioclimatic characteristics that result in highly dynamic forested landscapes. These dynamical landscapes, when subjected to the current scenario of intense global change, poses particular challenges for biodiversity conservation in human-modified landscapes. This thesis provides insights towards (i) the development of new metrics to quantify landscape dynamics; (ii) the assessment of the effects of land-use intensification on spatio-temporal dynamics and connectivity; and (iii) the quantification of potential drivers of these changes in the spatial dynamics. In the first part of my thesis, I developed a graph-theoretical method that incorporates the spatial dynamics of the landscape in the evaluation of landscape connectivity. I tested this method using a large set of Atlantic Forest landscapes of Brazil. In the second part of the thesis, I evaluated the effects of different drivers of landscape spatial dynamics, particularly focusing on land-use intensification alongside its economic and social drivers. My results pointed to the fact that land-use intensification reduces spatio-temporal dynamics of landscapes, as a large fraction
Dead Reckoning, Landmark Learning, and the Sense of Direction: A Neurophysiological and Computational Hypothesis

Behavioral and neurophysiological evidence strongly suggests that, within certain limits, rodents and humans can keep track of their directional heading relative to an inertial, and hence allocentric coordinate system. This sense of direction appears to involve the integration of angular velocity signals that arise primarily in the vestibular system. A hypothesis is proposed in which the integration process, an operation that may be difficult for neurons to implement, is replaced by a linear associative mapping, an operation that is at least theoretically easy to implement with neurons. The proposed system makes use of a set of linearly independent vectors representing the combination of the current head direction, and head angular velocity representations to recall the resulting head direction. It is then proposed that visual landmarks become incorporated into the directional system, enabling both the correction of cumulative error and, ultimately, the computation of novel, optimal trajectories between locations. According to the hypothesis, this occurs through the association of hippo-campal local-view cells (i.e., direction selective place cells) with head-direction cells located downstream in the dorsal presubiculum. The possible neurophysiological and neuroan-atomical bases for the proposed system are discussed.
Permeability of Iris germanica’s multiseriate exodermis to water, NaCl, and ethanol

The exodermis of Iris germanica roots is multiseriate. Its outermost layer matures first with typical Casparian bands and suberin lamellae. But as subsequent layers mature, the Casparian band extends into the tangential and anticlinal walls of their cells. Compared with roots in which the endodermis represents the major transport barrier, the multiseriate exodermis (MEX) was expected to reduce markedly radial water and solute transport. To test this idea, precocious maturation of the exodermis was induced with a humid air gap inside a hydroponic chamber. Hydraulic conductivity (Lppc) was measured on completely submerged roots (with an immature exodermis) and on air-gap-exposed root regions (with two mature exodermal layers) using a pressure chamber. Compared with regions of roots with no mature exodermal layers, the mature MEX reduced Lppc from 8.5×10−8 to 3.9×10−8 m s−1 MPa−1. Puncturing the MEX increased Lppc to 19×10−8 m s−1 MPa−1, indicating that this layer constituted a substantial hydraulic resistance within the root (75% of the total). Alternatively, a root pressure probe was used to produce pressure transients from which hydraulic conductivity was determined, but this device measured mainly flow through the endodermis in these wide-diameter roots. The permeability of roots to NaCl and ethanol was also reduced in the presence of two mature MEX layers. The data are discussed in terms of the validity of current root models and in terms of a potential role for I. germanica MEX during conditions of drought and salt stress.
Enhancing Software Testing by Judicious Use of Code Coverage Information

Recently, tools for the analysis and visualization of code coverage have become widely available. At first glance, their value in assessing and improving the quality of automated test suites seems to be obvious. Yet, experimental studies as well as experience from projects in industry indicate that their use is not without pitfalls. We found these tools in a number of recent projects quite beneficial. Therefore, we set out to gather code coverage information from one of these projects. In this experience report, first the system under scrutiny as well as our methodology is described. Then, four major questions concerning the impact and benefits of using these tools are discussed. Furthermore, a list of ten lessons learned is derived. The list may help developers judiciously use code coverage tools, in order to reap a maximum of benefits.
Chemotactic response with a constant delay-time mechanism in Ciona spermatozoa revealed by a high time resolution analysis of flagellar motility

ABSTRACT During their chemotactic swimming toward eggs, sperm cells detect their species-specific chemoattractant and sense concentration gradients by unknown mechanisms. After sensing the attractant, sperm cells commonly demonstrate a series of responses involving different swimming patterns by changing flagellar beats, gradually approaching a swimming path toward the eggs, which is the source of chemoattractants. Shiba et al. observed a rapid increase in intracellular Ca2+ concentrations in Ciona spermatozoa after sensing chemoattractants; however, the biochemical processes occurring inside the sperm cells are unclear. In the present study, we focused on the timing and sensing mechanism of chemical signal detection in Ciona. One of the most crucial problems to be solved is defining the initial epoch of chemotactic responses. We adopted a high rate of video recording (600 Hz) for detailed analysis of sperm motion and a novel method for detecting subtle signs of beat forms and moving paths of sperm heads. From these analyses, we estimated a virtual sensing point of the attractant before initiation of motility responses and found that the time delay from sensing to motility responses was almost constant. To evaluate the efficiency of this constant delay model, we performed computer simulation of chemotactic behaviors of Ciona spermatozoa.
Large‐scale comparison of protein sequence alignment algorithms with structure alignments

Sequence alignment programs such as BLAST and PSI‐BLAST are used routinely in pairwise, profile‐based, or intermediate‐sequence‐search (ISS) methods to detect remote homologies for the purposes of fold assignment and comparative modeling. Yet, the sequence alignment quality of these methods at low sequence identity is not known. We have used the CE structure alignment program (Shindyalov and Bourne, Prot Eng 1998;11:739) to derive sequence alignments for all superfamily and family‐level related proteins in the SCOP domain database. CE aligns structures and their sequences based on distances within each protein, rather than on interprotein distances. We compared BLAST, PSI‐BLAST, CLUSTALW, and ISS alignments with the CE structural alignments. We found that global alignments with CLUSTALW were very poor at low sequence identity (<25%), as judged by the CE alignments. We used PSI‐BLAST to search the nonredundant sequence database (nr) with every sequence in SCOP using up to four iterations. The resulting matrix was used to search a database of SCOP sequences. PSI‐BLAST is only slightly better than BLAST in alignment accuracy on a per‐residue basis, but PSI‐BLAST matrix alignments are much longer than BLAST's, and so align correctly a larger fraction of the total number of aligned residues in the structure alignments. Any two SCOP sequences in the same superfamily that shared a hit or hits in the nr PSI‐BLAST searches were identified as linked by the shared intermediate sequence. We examined the quality of the longest SCOP‐query/ SCOP‐hit alignment via an intermediate sequence, and found that ISS produced longer alignments than PSI‐BLAST searches alone, of nearly comparable per‐residue quality. At 10–15% sequence identity, BLAST correctly aligns 28%, PSI‐BLAST 40%, and ISS 46% of residues according to the structure alignments. We also compared CE structure alignments with FSSP structure alignments generated by the DALI program. In contrast to the sequence methods, CE and structure alignments from the FSSP database identically align 75% of residue pairs at the 10–15% level of sequence identity, indicating that there is substantial room for improvement in these sequence alignment methods. BLAST produced alignments for 8% of the 10,665 nonimmunoglobulin SCOP superfamily sequence pairs (nearly all <25% sequence identity), PSI‐BLAST matched 17% and the double‐PSI‐BLAST ISS method aligned 38% with E‐values <10.0. The results indicate that intermediate sequences may be useful not only in fold assignment but also in achieving more complete sequence alignments for comparative modeling. Proteins 2000;40:6–22. © 2000 Wiley‐Liss, Inc.
What Does the Shipley-2 Measure for Children and Adolescents? Integrated and Conjoint Confirmatory Factor Analysis With the WISC-IV

We used integrated and conjoint confirmatory factor analysis of Shipley-2 and Wechsler Intelligence Scale for Children–Fourth Edition (WISC-IV) data to investigate constructs measured in the Shipley-2 for children and adolescents. We also estimated Shipley-2 composite reliability at the subtest level rather than the item level. The three Shipley-2 subtests for the most part measured what was described in the manual, although Block Patterns measured visual spatial ability in addition to fluid ability and Abstraction was best considered a measure of psychometric g. The g factors derived from the WISC-IV and Shipley-2 were similar but not identical. Internal reliability estimates for Shipley-2 composites that were based on correlations between the subtests were substantially lower than those based on the items. Last, based on WISC-IV derived g factors, 37% to 53% of the variance in Shipley-2 composites was explained by g. Some of the reliable variance in the Shipley-2 composites was due to something specific that the subtests had in common not explained by psychometric g.