Miracle-dz/UniFAR-FTUs huggingface dataset:
The Evolutionary Origin And Elaboration Of Sociality In The Aculeate Hymenoptera: Maternal Effects, Sib‐social Effects, And Heterochrony

We discuss the evolutionary origin and elaboration of sociality using an indirect genetic effects perspective. Indirect genetic effects models simultaneously consider zygotic genes, genes expressed in social partners (especially mothers and siblings), and the interactions between them. Incorporation of these diverse genetic effects should lead to more realistic models of social evolution. We first review haplodiploidy as a factor that promotes the evolution of eusociality. Social insect biologists have doubted the importance of relatedness asymmetry caused by haplodiploidy and focused on other predisposing factors such as maternal care. However, indirect effects theory shows that maternal care evolves more readily in haplodiploids, especially with inbreeding and despite multiple mating. Because extended maternal care is believed to be a precondition for the evolution of eusociality, the evolutionary bias towards maternal care in haplodiploids may result in a further bias towards eusociality in these groups. Next, we compare kin selection and parental manipulation and then briefly review additional hypotheses for the evolutionary origin of eusociality. We present a verbal model for the evolutionary origin and elaboration of sib‐social care from maternal care based on the modification of the timing of expression of maternal care behaviors. Specifically, heterochrony genes cause maternal care behaviors to be expressed prereproductively towards siblings instead of postreproductively towards offspring. Our review demonstrates that both maternal effect genes (expressed in a parental manipulation manner) and direct effect zygotic genes (expressed in an offspring control manner) are likely involved in the evolution of eusociality. We conclude by describing theoretical and empirical advances with indirect genetic effects and sociogenomics, and we provide specific quantitative genetic and genomic predictions from our heterochrony model for the evolutionary origin and elaboration of eusociality.
Shape manipulation using physically based wire deformations

This paper develops an efficient, physically based shape manipulation technique. It defines a 3D model with profile curves, and uses spine curves generated from the profile curves to control the motion and global shape of 3D models. Profile and spine curves are changed into profile and spine wires by specifying proper material and geometric properties together with external forces. The underlying physics is introduced to deform profile and spine wires through the closed form solution to ordinary differential equations for axial and bending deformations. With the proposed approach, global shape changes are achieved through manipulating spine wires, and local surface details are created by deforming profile wires. A number of examples are presented to demonstrate the applications of our proposed approach in shape manipulation. Copyright © 2010 John Wiley & Sons, Ltd.
Spectral and temporal modulation features for phonetic recognition

Recently, the modulation spectrum has been proposed and found to be a useful source of speech information. The modulation spectrum represents longer term variations in the spectrum and thus implicitly requires features extracted from much longer speech segments compared to MFCCs and their delta terms. In this paper, a Discrete Cosine Transform (DCT) analysis of the log magnitude spectrum combined with a Discrete Cosine Series (DCS) expansion of DCT coefficients over time is proposed as a method for capturing both the spectral and modulation information. These DCT/DCS features can be computed so as to emphasize frequency resolution or time resolution or a combination of the two factors. Several variations of the DCT/DCS features were evaluated with phonetic recognition experiments using TIMIT and its telephone version (NTIMIT). Best results obtained with a combined feature set are 73.85% for TIMIT and 62.5% for NTIMIT. The modulation features are shown to be far more important than the spectral features for automatic speech recognition and far more noise robust.
HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis

The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq) technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq) techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Here we present HBS-tools, a set of command line based tools for the preprocessing, mapping, methylation calling, and summarizing of genome-wide hairpin-BS-Seq data. It accepts paired-end hairpin-BS-Seq reads to recover the original (pre-bisulfite-converted) sequences using global alignment and then calls the methylation statuses for cytosines on both DNA strands after mapping the original sequences to the reference genome. After applying to hairpin-BS-Seq datasets, we found that HBS-tools have a reduced mapping time and improved mapping efficiency compared with state-of-the-art mapping tools. The HBS-tools source scripts, along with user guide and testing data, are freely available for download.
Autobiographical Remembering and Individual Differences in Emotional Intelligence

The relationship between individual differences in Emotional Intelligence (EI) and self-reported arousal from remembering an autobiographical emotional or neutral event was examined. Participants (N = 235; 75 men; M age = 18.7 yr., SD = 0.9, range = 18–22) were required to complete the Japanese version of the Emotional Skills and Competence Questionnaire to assess EI. Participants were then asked to recall personal episodes from autobiographical memory, and then completed the Memory Characteristics Questionnaire (MCQ). A group with high EI-rated, emotionally neutral episodes higher than did a group with low EI on several MCQ subscales: sound, participants, overall memory, and doubt/certainty. However, differences in ratings between the two groups were not observed for emotionally positive episodes. These results suggest that high EI is related to more effective use of weak retrieval cues when recalling neutral autobiographical memories.
Differential Response to DNA Damage May Explain Different Cancer Susceptibility Between Small and Large Intestine

Although large intestine (LI) cancer is the second-leading cause of cancer-related deaths in the United States, small intestine (SI) cancer is relatively rare. Because oxidative DNA damage is one possible initiator of tumorigenesis, we investigated if the SI is protected against cancer because of a more appropriate response to oxidative DNA damage compared with the LI. Sixty rats were allocated to three treatment groups: 3% dextran sodium sulfate (DSS, a DNA-oxidizing agent) for 48 hrs, withdrawal (DSS for 48 hrs + DSS withdrawal for 48 hrs), or control (no DSS). The SI, compared with the LI, showed greater oxidative DNA damage (P < 0.001) as determined using a quantitative immunohistochemical analysis of 8-oxodeoxyguanosine (8-oxodG). The response to the DNA adducts in the SI was greater than in the LI. The increase of TdT–mediated dUTP-biotin nick end labeling (TUNEL)-positive apoptosis after DSS treatment was greater in the SI compared with the LI (P < 0.001), and there was a positive correlation (P = 0.031) between DNA damage and apoptosis in the SI. Morphologically, DSS caused an extensive loss of crypt structure shown in lower crypt height (P = 0.006) and the number of intact crypts (P = 0.0001) in the LI, but not in the SI. These data suggest that the SI may be more protected against cancer by having a more dynamic response to oxidative damage that maintains crypt morphology, whereas the response of the LI makes it more susceptible to loss of crypt architecture. These differential responses to oxidative DNA damage may contribute to the difference in cancer susceptibility between these two anatomic sites of the intestine.
On Transmission Mode Selection in D2D-Enhanced Small Cell Networks

We consider a small cell network enhanced with the possibility of D2D communications. In such networks, there are two possible transmission modes: 1) two-hop or indirect transmission via a small cell base station (SBS) and 2) one-hop or direct transmission. Transmission via an SBS is performed on a channel allocated by the SBS, and hence it is interference-free. Direct transmission, in contrast, is performed only if a primary channel is idle, and is impaired by the interference resulted from the lack of coordination. Despite being interference-free, the indirect mode might be inefficient due to high radio resource consumption, latency, and complexity. Since implementing a central controller as well as obtaining channel/network knowledge is costly, users need to choose the optimal transmission mode in a distributed manner given no prior information. In this letter, we first characterize the utility of each transmission mode. We then solve the mode selection problem using a bandit model.
Merchant Vessel Classification Based on Scattering Component Analysis for COSMO-SkyMed SAR Images

Ship classification in high-resolution synthetic aperture radar (SAR) satellite images is a hotspot and a continuing problem in SAR applications. The scattering components of ships are the strong scatter of objects in SAR images, and these can represent the superstructure of different ship types. Based on analyses of different scattering components of bulk carriers, oil tankers, and container ships, we propose a new classification method for these three ship types in COSMO-SkyMed SAR images. First, morphological preprocessing is applied to suppress sidelobes. Second, based on Hough transform (HT), the orientation of the principal axis is extracted, and the modified minimum enclosing rectangle (MER) of the ship is obtained and rotated along the principal axis. Finally, the ship type is decided according to the width ratio of MER between the HT line, the ratio of ship and nonship points on the principal axis, and the scattering density. The results show that this method has good performance in ship classification, with an overall accuracy of over 80%.
SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision

UNLABELLED Many time-consuming analyses of next -: generation sequencing data can be addressed with modern cloud computing. The Apache Hadoop-based solutions have become popular in genomics BECAUSE OF: their scalability in a cloud infrastructure. So far, most of these tools have been used for batch data processing rather than interactive data querying. The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next-generation sequencing data. SparkSeq is a general-purpose, flexible and easily extendable library for genomic cloud computing. It can be used to build genomic analysis pipelines in Scala and run them in an interactive way. SparkSeq opens up the possibility of customized ad hoc secondary analyses and iterative machine learning algorithms. This article demonstrates its scalability and overall fast performance by running the analyses of sequencing datasets. Tests of SparkSeq also prove that the use of cache and HDFS block size can be tuned for the optimal performance on multiple worker nodes. AVAILABILITY AND IMPLEMENTATION Available under open source Apache 2.0 license: https://bitbucket.org/mwiewiorka/sparkseq/.
The Drosophila Kctd‐family homologue Kctd12‐like modulates male aggression and mating behaviour

In Drosophila, serotonin (5‐HT) regulates aggression, mating behaviour and sleep/wake behaviour through different receptors. Currently, how these various receptors are themselves regulated is still not completely understood. The KCTD12‐family of proteins, which have been shown to modify G‐protein‐coupled receptor (GPCR) signalling in mammals, are one possibility of auxiliary proteins modulating 5‐HT receptor signalling. The KCTD12‐family was found to be remarkably conserved and present in species from C. elegans to humans. The Drosophila KCTD12 homologue Kctd12‐like (Ktl) was highly expressed in both the larval and adult CNS. By performing behavioural assays in male Drosophila, we now reveal that Ktl is required for proper male aggression and mating behaviour. Previously, it was shown that Ktl is in a complex with the Drosophila 5‐HT receptor 5‐HT7, and we observed that both Ktl and the 5‐HT1A receptor are required in insulin‐producing cells (IPCs) for proper adult male behaviour, as well as for hyperaggressive activity induced by the mammalian 5‐HT1A receptor agonist 8‐hydroxy‐2‐dipropylaminotetralin‐hydrobromide. Finally, we show that Ktl expression in the IPCs is necessary to regulate locomotion and normal sleep/wake patterns in Drosophila, but not the 5‐HT1A receptor. Similar to what was observed with mammalian KCTD12‐family members that interact physically with a GPCR receptor to regulate desensitization, in Drosophila Ktl may function in GPCR 5‐HT receptor pathways to regulate their signalling, which is required for proper adult male behaviour.
Factors Influencing Blind Collision Risk in En Route Sectors Under Free-Flight Conditions

We developed a simulation model of the flight of aircraft through an en route sector. We used the model in two experiments. The first studied the effect of directional clumping on risk. The second was a full factorial design with replication, which simulated a large number of scenarios to assess the impact of key input factors on free flight risk measures. We measured risk for a given flight by the mean distance of closest approach to other aircraft and the mean number of approaches closer than a specified distance. Using analysis of variance and regression analysis, we determined the most important influences on blind collision risk. The most important factors were time of entry into the sector and number of aircraft. Also influential were certain orientations of flight paths and the distribution of airspeeds. The least important factor was altitude. The relationship between number of aircraft and the two risk measures could be quantified in regression relationships. 3 Overview The airspace over the US is congested, with a high and growing volume of traffic. In the interests of safety, the congestion is made worse by the constraint that aircraft be routed through a series of pre-established airways where they can be subject to the positive control of air traffic controllers. One proposal to mitigate the congestion problem is free flight. There are several variants of free flight, but all give pilots additional authority to fly directly from one point to another without restricting their movements to the established airways. In principle, free flight should save time and fuel. But extra freedom to navigate carries with it an increased risk that aircraft will pass dangerously close to each other, creating a conflict that might become a midair collision. This analysis addressed the risks of free flight. In particular, the research aimed to better understand the relative importance of several risk factors. We did not consider the effects of actions by pilots and controllers to avoid or resolve conflicts between two aircraft wanting to use the same airspace at the same time. That is, we considered only blind conflicts. To progress from blind conflicts to actual conflicts will require analysis of all the clever technologies and control actions that keep the skies safe and is the ultimate goal of a complete safety analysis. Our more modest goal here was to understand in a quantitative way the background conditions that lead to risk. …
Perturbation of Maize Phenylpropanoid Metabolism by an AvrE Family Type III Effector from Pantoea stewartii1[OPEN]

The virulence activity of an effector protein belonging to the widely conserved AvrE family is linked to its ability to cause system-wide reprogramming of phenylpropanoid metabolism in susceptible maize seedlings. AvrE family type III effector proteins share the ability to suppress host defenses, induce disease-associated cell death, and promote bacterial growth. However, despite widespread contributions to numerous bacterial diseases in agriculturally important plants, the mode of action of these effectors remains largely unknown. WtsE is an AvrE family member required for the ability of Pantoea stewartii ssp. stewartii (Pnss) to proliferate efficiently and cause wilt and leaf blight symptoms in maize (Zea mays) plants. Notably, when WtsE is delivered by a heterologous system into the leaf cells of susceptible maize seedlings, it alone produces water-soaked disease symptoms reminiscent of those produced by Pnss. Thus, WtsE is a pathogenicity and virulence factor in maize, and an Escherichia coli heterologous delivery system can be used to study the activity of WtsE in isolation from other factors produced by Pnss. Transcriptional profiling of maize revealed the effects of WtsE, including induction of genes involved in secondary metabolism and suppression of genes involved in photosynthesis. Targeted metabolite quantification revealed that WtsE perturbs maize metabolism, including the induction of coumaroyl tyramine. The ability of mutant WtsE derivatives to elicit transcriptional and metabolic changes in susceptible maize seedlings correlated with their ability to promote disease. Furthermore, chemical inhibitors that block metabolic flux into the phenylpropanoid pathways targeted by WtsE also disrupted the pathogenicity and virulence activity of WtsE. While numerous metabolites produced downstream of the shikimate pathway are known to promote plant defense, our results indicate that misregulated induction of phenylpropanoid metabolism also can be used to promote pathogen virulence.
Effects of changes in hemoglobin level on quality of life and cognitive function in inflammatory bowel disease patients

Background: Anemia commonly complicates inflammatory bowel disease (IBD). In patients with chronic renal failure, the treatment of anemia with iron ± erythropoietin improves both quality of life (QOL) and cognitive function (CF). The same drugs are effective in treating severe anemia in IBD, but there is no evidence to direct the treatment of mild anemia. Concern exists that the use of iron may exacerbate inflammation in patients with IBD. The present study examined the association between changes in hemoglobin (Hb) in a population of IBD patients and changes in QOL and CF independent of change in disease activity (DA). Subsidiary aims were to assess whether the use of iron was associated with worsening DA. Methods: A cohort of 50 patients with IBD (29 Crohn's disease and 21 ulcerative colitis) took part. Iron replacement was given to 21 patients with low Hb. Measures of QOL, CF, DA, and Hb were recorded at baseline and at 6 months. Results: The iron‐treated group had lower Hb and higher DA scores compared with the non‐iron‐treated group at baseline. In a hierarchical regression model, changes in DA accounted for 13% (P = 0.17) and changes in Hb accounted for 18% (P = 0.005) of the variance in change in SF‐36 and 12% (P = 0.23) and 17% (P = 0.009) in the Inflammatory Bowel Disease Questionnaire. In this pilot study, although no associations were identified between changes in Hb or DA and CF, increases in Hb improved QOL scores in IBD patients independent of changes in DA. We found no similar effect with CF, but again, the sample size was small. We found no evidence that iron therapy causes worsening of DA. Conclusions: Treatment of IBD‐associated anemia with iron may lead to improvement in patients' QOL.
Stability of Wireless and Wireline Networked Control Systems

This paper provides a general framework for analyzing the stability of general nonlinear networked control systems (NCS) with disturbances in the setting of stability. Our presentation provides sharper results for both gain and maximum allowable transfer interval (MATI) than previously obtainable and details the property of uniformly persistently exciting scheduling protocols. This class of protocols was shown to lead to stability for high enough transmission rates and were a natural property to demand, especially in the design of wireless scheduling protocols. The property is used directly in a novel proof technique based on the notions of vector comparison and (quasi)-monotone systems. We explore these results through analytical comparisons to those in the literature, as well as through simulations and numerical comparisons that verify that the uniform persistence of excitation property of protocols is, in some sense, the ldquofinestrdquo property that can be extracted from wireless scheduling protocols.
The Influence of Estrogen on Hepatobiliary Osteopontin (SPP1) Expression in a Female Rodent Model of Alcoholic Steatohepatitis

Our recent studies suggest that higher neutrophil infiltration in females correlates with increased hepatobiliary expression of osteopontin (OPN) in alcoholic steatohepatitis (ASH). The objective of this study was to understand the role of alcohol in altering estrogen levels in females by examining the effect of ethanol (EtOH) on the estrous cycle and then investigate the potential relationship between estradiol (E2) and hepatobiliary OPN expression in a female rat ASH model. Ovariectomized (OVX) and E2-implanted OVX rats in the ASH group were evaluated for OPN mRNA and protein expression. Low doses of E2 resulted in significant down-regulation of OPN protein and mRNA as compared to the OVX group. However, with increasing doses of E2, there was up-regulation of both OPN mRNA and protein. Osteopontin was localized primarily to the biliary epithelium. Liver injury assessed by serum ALT and histopathology revealed a pattern similar to OPN expression. In all groups, hepatic neutrophilic infiltration correlated positively with OPN expression. Based on these data, we conclude that in our ASH model, low doses of E2 appear to be hepatoprotective, whereas the protective effect appears to diminish with increasing doses of E2, although additional cause and effect studies are needed for confirmation.
Buffering and Amplifying Effects of Relationship Commitment in Business-to-Business Relationships

Using an assimilation and contrast framework, the authors assess the buffering and amplifying effects of relationship commitment on organizational buyers’ intentions to switch suppliers when a relationship is strained by the incumbent's own misbehavior. The results of three studies show that both calculative and affective commitment buffer incumbent suppliers against minor incidences of their own misbehavior but that affective commitment also reliably amplifies the adverse effects of an incumbent supplier's flagrant opportunism. Process tests indicate that buyer perceptions of supplier conformance to normative standards account for (completely mediate) the observed buffering and amplification effects in a manner consistent with the underlying assimilation and contrast framework.
The Role of the Independent Neuropsychologist in Special Education

Neuropsychologists are playing an increasing role in special education. We explain steps that neuropsychologists can take to ethically and effectively approach the “quasi-forensic” role of independent evaluator. Because neuropsychologists may provide reports for treatment, school programming, and legal disputes, it is important that they are familiar with the school programming process and the unique litigation procedures available for children with disabilities in special education. We provide guidelines including determining referral questions, obtaining outside information, choosing assessments, considering the legal constructs of questions, reviewing discrepant results from other evaluations and Individual Education Plans and communicating ideas.