Miracle-dz/UniFAR-FTUs huggingface dataset:
From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents.

Hystricognath rodents include Old World Phiomorpha and New World Caviomorpha. These two groups have an enigmatic biogeographical history. Using a nuclear marker, the exon 28 of the von Willebrand Factor gene (vWF), we reconstructed the phylogenetic relationships among 23 Hystricognathi species. These taxa encompass the complete familial diversity of the Hystricognathi. Our results indicate a basal trifurcation of hystricognaths leading to Hystricidae, Phiomorpha s.s. (Bathyergidae, Thryonomyidae, and Petromuridae), and Caviomorpha. The monophyly of caviomorphs is robustly supported, confirming a single colonization event of South America by hystricognaths. Caviomorpha are divided into four lineages: Cavioidea, Erethizontoidea, Chinchilloidea, and Octodontoidea. Furthermore, we suggest that (1) Chinchillidae and Dinomyidae are sister clades, (2) Abrocomidae is a true Octodontoidea, and (3) Capromyidae, Echimyidae, and Myocastoridae cluster together. Surprisingly, Erethizontidae does not appear to be the most diverged caviomorph lineage. The molecular results are discussed in the light of previous paleontological and morphological observations. Local molecular clocks are used to estimate divergence dates among hystricognath lineages. An Asian origin is suggested for Caviomorpha, and a colonization route through Australia and Antarctica is indicated as an alternative to the hypothesis of a transatlantic migration of Caviomorpha from Africa to South America.
Proteus mirabilis MR/P fimbriae: molecular cloning, expression, and nucleotide sequence of the major fimbrial subunit gene

Proteus mirabilis, a cause of serious urinary tract infection and acute pyelonephritis, produces several putative virulence determinants, among them, fimbriae. Principally, two fimbrial types are produced by this species: mannose-resistant/Proteus-like (MR/P) fimbriae and mannose-resistant/Klebsiella-like (MR/K) fimbriae. To isolate MR/P fimbrial gene sequences, a P. mirabilis cosmid library was screened by immunoblotting and by hybridization with an oligonucleotide probe based on the N-terminal amino acid sequence of the isolated fimbrial polypeptide, ADQGHGTVKFVGSIIDAPCS. One clone, pMRP101, reacted strongly with a monoclonal antibody specific for MR/P fimbriae and with the DNA probe. This clone hemagglutinated both tannic acid-treated and untreated chicken erythrocytes with or without 50 mM D-mannose and was shown to be fimbriated by transmission electron microscopy. A 525-bp open reading frame, designated mrpA, predicted a 175-amino-acid polypeptide including a 23-amino-acid hydrophobic leader peptide. The unprocessed and processed polypeptides are predicted to be 17,909 and 15,689 Da, respectively. The N-terminal amino acid sequence of the processed fimbrial subunit exactly matched amino acid residues 24 to 43 predicted by the mrpA nucleotide sequence. The MrpA polypeptide shares 57% amino acid sequence identity with SmfA, the major fimbrial subunit of Serratia marcescens mannose-resistant fimbriae.
Differences between Patterns of Brain Activity Associated with Semantics and Those Linked with Phonological Processing Diminish with Age

It is widely believed that language function tends to show little age-related performance decline. Indeed, some older individuals seem to use compensatory mechanisms to maintain a high level of performance when submitted to lexical tasks. However, how these mechanisms affect cortical and subcortical activity during semantic and phonological processing has not been extensively explored. The purpose of this study was to look at the effect of healthy aging on cortico-subcortical routes related to semantic and phonological processing using a lexical analogue of the Wisconsin Cart-Sorting Task. Our results indicate that while young adults tend to show increased activity in the ventrolateral prefrontal cortex, the dorsolateral prefrontal cortex, the fusiform gyrus, the ventral temporal lobe and the caudate nucleus during semantic decisions and in the posterior Broca's area (area 44), the temporal lobe (area 37), the temporoparietal junction (area 40) and the motor cortical regions during phonological decisions, older individuals showed increased activity in the dorsolateral prefrontal cortex and motor cortical regions during both semantic and phonological decisions. Furthermore, when semantic and phonological decisions were contrasted with each other, younger individuals showed significant brain activity differences in several regions while older individuals did not. Therefore, in older individuals, the semantic and phonological routes seem to merge into a single pathway. These findings represent most probably neural reserve/compensation mechanisms, characterized by a decrease in specificity, on which the elderly rely to maintain an adequate level of performance.
Workplace as an origin of health inequalities.

OBJECTIVE: To investigate the effect of the workplace on the socioeconomic gradient of sickness absence. DESIGN: Comparison of the relation between socioeconomic status and employee sickness absence in three different towns. SETTINGS: The towns of Raisio, Valkeakoski, and Nokia in Finland. They are equal in size and regional social deprivation indices, located in the neighbourhood of a larger city, and produce the same services to the inhabitants. SUBJECTS: All permanent local government employees from Raisio (n = 887), Valkeakoski (n = 972), and Nokia (n = 934) on the employer's registers during 1991 to 1993. MAIN OUTCOME MEASURES: Rates of short (1-3 days) and long (> 3 days) spells of sickness absence, irrespective of cause, and separately for infection, musculoskeletal disorder, and trauma. RESULTS: In blue collar male and female workers, compared with the same sex higher grade white collar workers, the age adjusted numbers of long sick leaves were 4.9 (95% CI 4.2, 5.8) and 2.8 (2.6, 3.1) times higher, respectively. The risk varied significantly between the towns, in men in relation to long sick leaves irrespective of cause and resulting from musculoskeletal disorders, and in women in relation to long leaves resulting from infection. The numbers of long sick leaves were 3.9 (95% CI 2.8, 5.4) times higher in blue collar male workers than in higher grade white collar male workers in Raisio, 4.9 (95% CI 3.8, 6.3) times higher in Valkeakoski, and 5.8 (95% CI 4.5, 7.5) times higher in Nokia. Sickness absence of blue collar employees differed most between the towns. The rates of long sick leaves in blue collar men were 1.46 times greater (95% CI 1.25, 1.72) in Valkeakoski and 1.85 times greater (95% CI 1.58, 2.16) in Nokia than in Raisio. In men, no significant differences were found between the towns as regards the numbers of long sick leaves of higher grade white collar male workers. The socioeconomic gradients differed more between the towns in men who had worked for four years or more in the same employment than in men who had worked for shorter periods. No consistent health gradients of socioeconomic status were evident for short sick leaves among either sex. CONCLUSIONS: In men and to a lesser extent in women, the workplace is significantly associated with health inequalities as reflected by medically certified sickness absence and the corresponding socioeconomic gradients of health.
Bayesian Nonparametrics for Microphone Array Processing

Sound source localization and separation from a mixture of sounds are essential functions for computational auditory scene analysis. The main challenges are designing a unified framework for joint optimization and estimating the sound sources under auditory uncertainties such as reverberation or unknown number of sounds. Since sound source localization and separation are mutually dependent, their simultaneous estimation is required for better and more robust performance. A unified model is presented for sound source localization and separation based on Bayesian nonparametrics. Experiments using simulated and recorded audio mixtures show that a method based on this model achieves state-of-the-art sound source separation quality and has more robust performance on the source number estimation under reverberant environments.
Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

As shown by Jarzynski, free energy differences between equilibrium states can be expressed in terms of the statistics of work carried out on a system during non-equilibrium transformations. This exact result, as well as the related Crooks fluctuation theorem, provide the basis for the computation of free energy differences from fast switching molecular dynamics simulations, in which an external parameter is changed at a finite rate, driving the system away from equilibrium. In this article, we first briefly review the Jarzynski identity and the Crooks fluctuation theorem and then survey various algorithms building on these relations. We pay particular attention to the statistical efficiency of these methods and discuss practical issues arising in their implementation and the analysis of the results.
Pressure pain thresholds in volunteers and herniorrhaphy patients

Pressure algometry is a method to estimate pressure pain sensitivity in tissues. The aim of the present study was to evaluate the reproducibility of pressure pain thresholds (PPT) in the abdominal integument and to evaluate the use of pressure algometry as a measure of wound tenderness following surgery. PPT was determined in 20 healthy volunteers on two separate examinations, and in 14 patients at the incisional site before and following inguinal herniotomy. In volunteers, PPT was higher for men than for women, and no difference was observed between the first and second day of examination. In surgical patients a significant decrease in PPT was observed following operation. Morphine 0.07 mg/kg caused a slight but significant increase in PPT. Pressure algometry may be useful to study nociceptive mechanisms and the dynamics of wound pain in surgical patients.
Mesenchymal stem cells in the colorectal tumor microenvironment: Recent progress and implications

Mesenchymal stem cells (MSCs) are nonhematopoietic multipotent adult stem cells. They have been shown to have a natural tropism for many tumors types, including colorectal, and are capable of escaping host immune surveillance. MSCs are known to engraft at tumors and integrate into their architecture, potentially as carcinoma‐associated fibroblasts. In contrast with other malignancies, our understanding of the interactions between colorectal cancer cells and MSCs remains limited. Considering the established importance of inflammation in the colorectal cancer primary tumor microenvironment and the role of stromal cells in this process, there is a potential wealth of information to be gleaned from further investigation of interactions between these cell populations. Epithelial–mesenchymal transition is central to colorectal cancer progression and MSCs have also been implicated in this process. This review explores the current knowledge (both in vitro and in vivo) of interactions between colorectal cancer cells and MSCs. It highlights potential effects of cell source, number and ratio on outcome of in vivo studies and explores strategies to more accurately explore their role in the primary tumor microenvironment. As our understanding of the underlying molecular processes in colorectal cancer develops, elucidation of these interactions will be central to development of novel therapeutic strategies for this prevalent disease.
The prognostic significance of combined androgen receptor, E-Cadherin, Ki67 and CK5/6 expression in patients with triple negative breast cancer

Background Triple Negative Breast Cancer (TNBC) represents a heterogeneous group of tumors with poor prognosis owing to aggressive tumor biology and lack of targeted therapies. No clear prognostic biomarkers have been identified to date for this subgroup. Materials and Methods In this retrospective study we evaluated the prognostic role of 4 different molecular determinants, including androgen receptor (AR), E-cadherin (CDH1), Ki67 index, and basal cytokeratins (CKs) 5/6, in a cohort of 99 patients with TNBC. All patients received neo/adjuvant chemotherapy (mostly anthracycline/taxane-based). Immunohistochemistry (IHC) was performed in formalin-fixed paraffin-embedded primary tumor samples. CDH1 expression was considered positive as ≥ 30% of the membrane cells staining. AR positivity was defined as > 10% of positive tumor cells. High Ki67 was defined as ≥20% positive tumor cells. CK5/6 expression was judged positive if the score was ≥1. Results The absence of AR expression was significantly associated with highly undifferentiated tumors. Univariate analyses showed that lack of expression of CDH1, tumor size and nodal status were significantly correlated with worse RFS and OS (p< 0.05). AR expression and low Ki67 showed a trend towards better RFS and OS. Patients with absent CK5/6 expression in univariate and multivariate analyses had poorer RFS (p=0.02 and p=0.002, respectively) and OS (p=0.05 and p=0.02, respectively). Multivariate analysis showed an independent association between CDH1 expression and better RFS and OS (p< 0.05) beyond tumor size, nodal status, and grade. The Kaplan-Meier curves showed that patients with AR and CDH1 negative expression and high Ki-67 levels have a significant correlation with poor outcome. Conclusions Our study supports the use of IHC expression of AR, CDH1, Ki67, and CK5/6 as prognostic markers in TNBCs and suggests a link between their expression and prognosis and may help to stratify TNBC patients in different prognostic classes.
Fostering Work Engagement through State and Trait Trust: Evidence from Irish University Research Centres

The central aim of this research was to examine the impact of state and trait trust on employees’ levels of work engagement. More specifically, in this study, the three forms of state trust - trust in top management, trust in direct supervisor and trust in team members, as well as trait trust (trust propensity) - were hypothesised as antecedents of work engagement. Furthermore, it was proposed that organizational identification, affective commitment to the supervisor and team psychological safety will mediate the effects of trust in top management, trust in direct supervisor and trust in team members on work engagement respectively. Finally, the relationship of work engagement with a variety of work outcomes such as, in-role job performance, innovative work behaviour, feedback seeking, error communication and organizational commitment, as well as the mediating effects of learning goal orientation on these relationships were investigated. Using survey data from 152 research scientists, drawn from six university science research centres operating in Ireland, the hypotheses were tested through hierarchical multiple regression analyses. The results of this study showed that as hypothesised, organizational identification, affective commitment to the supervisor, and team psychological safety fully mediated the effects of trust in top management, trust in direct supervisor, and trust in team members on work engagement respectively. Moreover, the findings of this study indicated that trust propensity was also positively and significantly related to work engagement. Additionally, it was found that learning goal orientation partially mediated the effects of work engagement on in-role job performance, innovative work behaviour, feedback seeking and error communication, while it did not mediate the relationship between work engagement and organizational commitment. On the basis of these findings, recommendations were made for the management of research centres and for future research directions.
Microstructure control of medium carbon steel joints by low-temperature linear friction welding

Medium carbon steel sheets of 2.6 mm thick were successfully welded by linear friction welding at various frequencies and applied pressures. The welding temperature decreased with the decreasing frequency, but unexpectedly with the increasing applied pressure. A medium carbon steel joint with no martensitic transformation could be obtained at a welding temperature below the A1 point under the conditions of low frequency and high applied pressure. Moreover, the welding temperature evolution was found to be correlated with the behaviour of the flash expelling at the welding interface. It was revealed that the welding temperature can be determined as the temperature at which the ultimate tensile strength of the interface material decreased below the applied pressure.
Disruption of neural systems of visual attention in schizophrenia.

BACKGROUND Patients with schizophrenia show attention deficits. The frontal P2a and posterior N2b event-related potential components are early indices of activity in neural systems supporting attention and they are reduced in schizophrenia in auditory tasks. However, the auditory P300 is reduced as well. Thus, the P2a and N2b reductions may simply reflect a general event-related potential amplitude reduction. The visual P300, however, is often spared in schizophrenia. If neural systems supporting attention are specifically disrupted in schizophrenia, the attention-sensitive P2a and N2b should be differentially reduced in patients, compared with the P300, in a visual attention task. METHODS We analyzed 64-channel event-related potentials from 14 schizophrenic patients and 14 control subjects in a visual object-spatial attention task. We examined the amplitude of the P2a, N2b, and P300 components in the target minus standard difference wave to see if there was a differential reduction of the P2a and N2b compared with the P300. RESULTS Both the P2a and N2b waveforms were reduced in the patient group (81% [control mean, 1.99 microV; patient mean, 0.38 microV] and 95% [control mean, 0.55 microV; patient mean, 0.03 microV], respectively) while the P300 was not reduced. Measured at the peak of the frontal P2a, the N2b was larger dorsally in the spatial task and larger ventrally in the object task in the control group. CONCLUSIONS The spatial distribution of the P2a and N2b was consistent with activity in the prefrontal cortex and modality-specific posterior cortex, respectively. The differential reduction of the P2a and N2b waveforms supports the hypothesis of specific disruption in neural systems of visual attention in schizophrenia.
Adaptive MIMO-OFDM based on partial channel state information

Relative to designs assuming no channel knowledge at the transmitter, considerably improved communications become possible when adapting the transmitter to the intended propagation channel. As perfect knowledge is rarely available, transmitter designs based on partial (statistical) channel state information (CSI) are of paramount importance not only because they are more practical but also because they encompass the perfect- and no-knowledge paradigms. In this paper, we first provide a partial CSI model for orthogonal frequency division multiplexed (OFDM) transmissions over multi-input multi-output (MIMO) frequency-selective fading channels. We then develop an adaptive MIMO-OFDM transmitter by applying an adaptive two-dimensional (2-D) coder-beamformer we derived recently on each OFDM subcarrier, along with an adaptive power and bit loading scheme across OFDM subcarriers. Relying on the available partial CSI at the transmitter, our objective is to maximize the transmission rate, while guaranteeing a prescribed error performance, under the constraint of fixed transmit-power. Numerical results confirm that the adaptive 2-D space-time coder-beamformer (with two basis beams as the two "strongest" eigenvectors of the channel's correlation matrix perceived at the transmitter) combined with adaptive OFDM (power and bit loaded with M-ary quadrature amplitude modulated (QAM) constellations) improves the transmission rate considerably.
Privacy–Security Trade-Offs in Biometric Security Systems—Part I: Single Use Case

This is the first part of a two-part paper on the information theoretic study of biometric security systems. In this paper, the design of single-use biometric security systems is analyzed from an information theoretic perspective. A fundamental trade-off between privacy, measured by the normalized equivocation rate of the biometric measurements, and security, measured by the rate of the key generated from the biometric measurements, is identified. The privacy-security region, which characterizes the above-noted trade-off, is derived for this case. The scenario in which an attacker of the system has side information is then considered. Inner and outer bounds on the privacy-security region are derived in this case. Finally, biometric security systems with perfect privacy are studied, which is shown to be possible if and only if common randomness can be generated from two biometric measurements.
Cellular components and signals required for the cardiac outflow tract assembly in Drosophila

Specification of cardiac primordia and formation of the Drosophila heart tube is highly reminiscent of the early steps of vertebrate heart development. We previously reported that the final morphogenesis of the Drosophila heart involves a group of nonmesodermal cells called heart-anchoring cells and a pair of derived from the pharyngeal mesoderm cardiac outflow muscles. Like the vertebrate cardiac neural crest cells, heart-anchoring cells migrate, interact with the tip of the heart, and participate in shaping the cardiac outflow tract. To better understand this process, we performed an in-depth analysis of how the Drosophila outflow tract is formed. We found that the most anterior cardioblasts that form a central outflow tract component, the funnel-shaped heart tip, do not originate from the cardiac primordium. They are initially associated with the pharyngeal cardiac outflow muscles and join the anterior aorta during outflow tract assembly. The particular morphology of the heart tip is disrupted in embryos in which heart-anchoring cells were ablated, revealing their critical role in outflow tract morphogenesis. We also demonstrate that Slit and Robo are required for directed movements of heart-anchoring cells toward the heart tip and that the cell–cell contact between the heart-anchoring cells and the ladybird-expressing cardioblasts is critically dependent on DE-cadherin Shotgun. Our observations suggest that the similarities between Drosophila and vertebrate cardiogenesis extend beyond the early developmental events.
Combining maximal regularity and energy estimates for time discretizations of quasilinear parabolic equations

We analyze fully implicit and linearly implicit backward difference formula (BDF) methods for quasilinear parabolic equations, without making any assumptions on the growth or decay of the coefficient functions. We combine maximal parabolic regularity and energy estimates to derive optimal-order error bounds for the time-discrete approximation to the solution and its gradient in the maximum norm and energy norm.
Running title : Botrytis fragariae a new species infecting strawberry 4 5

27 Botrytis cinerea causes preand postharvest decay of many fruit and vegetable crops. A survey in 28 German strawberry fields revealed Botrytis strains that differed from B. cinerea in diagnostic 29 PCR markers and growth appearance. Phylogenetic analyses showed these strains to belong to an 30 undescribed species in Botrytis clade 2, named Botrytis fragariae sp. nov. Isolates of B. fragariae 31 were detected in strawberry fields throughout Germany, sometimes at similar frequencies as B. 32 cinerea, and in the Southeastern United States. B. fragariae was isolated from overwintering 33 strawberry tissue, but not from freshly infected fruit. B. fragariae invaded strawberry tissues with 34 similar or lower efficiency than B. cinerea but showed poor colonization of inoculated non-host 35 AEM Accepted Manuscript Posted Online 24 February 2017 Appl. Environ. Microbiol. doi:10.1128/AEM.00269-17 Copyright © 2017 American Society for Microbiology. All Rights Reserved. on O cber 6, 2017 by gest ht://aem . sm . rg/ D ow nladed fom