Miracle-dz/UniFAR-FTUs huggingface dataset:
RAPID DIVERSIFICATION, INCOMPLETE ISOLATION, AND THE “SPECIATION CLOCK” IN NORTH AMERICAN SALAMANDERS (GENUS PLETHODON): TESTING THE HYBRID SWARM HYPOTHESIS OF RAPID RADIATION

Abstract The history of life has been marked by several spectacular radiations, in which many lineages arise over a short period of time. A possible consequence of such rapid splitting in the recent past is that the intrinsic barriers that prevent gene flow between many species may have too little time to develop fully, leading to extensive hybridization among recently evolved lineages. The salamander genus Plethodon in eastern North America has been proposed as a possible example of this scenario, but without explicit statistical tests. In this paper, we present a nearly comprehensive phylogeny for the 45 extant species of eastern Plethodon, based on DNA sequences of mitochondrial (two genes, 1335 base pairs) and nuclear genes (two genes, up to 3481 base pairs). We then use this phylogeny to examine rates and patterns of diversification and hybridization. We find significantly rapid diversification within the glutinosus species group. Examining patterns of natural hybridization in light of the phylogeny shows considerable hybridization within this clade, including introgression between species that are morphologically distinct and distantly related. Reproductive isolation increases over time and may be very weak among the most recently diverged species. These results suggest that the origin of species and the evolution of intrinsic reproductive isolating mechanisms, rather than being synonymous, may be decoupled in some cases (i.e., rapid origin of lineages outstrips the “speciation clock”). In contrast to the conclusions of a recent review of adaptive radiation and hybridization, we suggest that extensive hybridization sometimes may be a consequence, rather than a cause, of rapid diversification.
Local smoothing for manifold learning

We propose methods for outlier handling and noise reduction using weighted local linear smoothing for a set of noisy points sampled from a nonlinear manifold. Weighted PCA is used as a building block for our methods and we suggest an iterative weight selection scheme for robust local linear fitting together with an outlier detection method based on minimal spanning trees to further improve robustness. We also develop an efficient and effective bias-reduction method to deal with the "trim the peak and fill the valley" phenomenon in local linear smoothing. Synthetic examples along with several image data sets are presented to show that manifold learning methods combined with weighted local linear smoothing give more accurate results.
Pre‐transplant predictors of one yr weight gain after kidney transplantation

Clinically useful predictors of weight gain could be used to reduce the epidemic of post‐kidney transplant obesity and resulting co‐morbidities. The purpose of this study was to identify predictors of weight gain at 12 months following kidney transplant in a cohort of 96 recipients. Demographic, clinical, and environmental data were obtained at transplant and 12 months. Descriptive, correlational, and Bayesian network analysis were used to identify predictors. For the 52 (55.9%) recipients who gained weight, the average amount gained was 9.18 ± 6.59 kg. From the 15 baseline factors that met inclusion criteria, Bayesian network modeling identified four baseline predictors for weight gain: younger age, higher carbohydrate consumption, higher trunk fat percentage, and higher perception of mental health quality of life. Three are modifiable through either pre‐ or immediate post‐transplant clinical intervention programs.
A new 82-kD barbed end-capping protein (radixin) localized in the cell- to-cell adherens junction: purification and characterization

An 82-kD protein has been purified from the undercoat of the adherens junction isolated from the rat liver. The purification scheme includes low salt extraction followed by DEAE-cellulose ion exchange, DNase I- actin affinity, and carboxyl methyl-cellulose ion exchange chromatographies. The purified 82-kD protein was essentially free of contaminants as judged by SDS-PAGE combined with silver staining. The substoichiometric 82-kD protein largely inhibited the actin filament assembly; when the molar ratio of the 82-kD protein to G-actin was 1:1,000, the viscosity was reduced to 28% of the control value. Direct electron microscopic studies revealed that the 82-kD protein selectively inhibited monomer addition at the barbed ends of actin filaments. By use of the antibody raised against the 82-kD protein, this protein was shown by immunofluorescence microscopy to be localized at the cell-to-cell adherens junction in various types of cells. In contrast, the 82-kD protein was not concentrated at the cell-to- substrate adherens junctions (focal contacts). These findings have led us to conclude that the 82-kD protein is a barbed end-capping protein which is associated with the undercoat of the cell-to-cell adherens junction. Hence, we have tentatively designated the 82-kD protein as radixin (from the Latin word radix meaning root).
Viewpoint Dependence in Human Spatial Memory

We summarize two lines of research that investigated whether human spatial memories are viewpoint dependent (e.g., viewer-centered reference frames) viewpoint independent (e.g., scene-centered reference frames). In one series of experiments, participants made judgments of relative direction after viewing a Sl~ti~_ I layout from one or two perspectives. The findings indicated that multiple views of a spatial layout produced multiple viewpoint dependent representations in memory. These findings were corroborated by the results of experiments on scene recognition. These experiments showed, again, that multiple views of a scene produced multiple viewpoint dependent representations in memory, and that a novel view of a familiar scene was recognized by normalizing it to the most similar view in memory. A preliminary computational model of scene recognition formalizes several of these concepts. When people learn a new spatial environment, they must encode the locations of objects in memory with respect to one or more frames of reference. Reference frames may be determined by the location of the viewer with respect to the space. An example of such a viewpoint dependent reference frame is one that specifies location in terms of retinal coordinates, which change from view to view. Alternatively, reference frames may be determined independently of the viewer’s perspective. Fixed axes centered on the scene itself constitute one example of a viewpoint independent reference frame. The goal of the research described below is to determine whether spatial memories are viewpoint dependent or viewpoint independent. We have taken two approaches to this problem. In one line of research, we have examined people’s abilities to retrieve and to transform in imagination their knowledge of a spatial layout. In the other line of research, we have examined people’s abilities to recognize scenes that they have recently learned. Each of these projects will be described in turn. In addition, we will describe a preliminary computational model of human scene recognition.
Intelligent barge-in in conversational systems

In this paper we present novel solutions to problems re-lated to barge-in in telephony-based conversational systems. In particular we address recovery from falsely detected barge-in events and a method for signaling to the user that barge-in is disallowed at a particular dialogue state. The mechanisms and signals used to manage turn taking are similar to those in human-human conversation, which makes them easy to understand for users without explanation or prior training.
Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1*

Background: ETS family transcription factors recognize DNA via structurally conserved DNA-binding domains that share limited amino acid homology. Results: DNA recognition by the ETS domains of Ets-1 and PU.1, two extreme sequence-divergent paralogs, was compared. Conclusion: Preferential hydration differentiates DNA recognition by Ets-1 and PU.1. Significance: Preferential hydration represents a potential mechanism for PU.1 regulation and its activity as a pioneer transcription factor in vivo. ETS family transcription factors regulate diverse genes through binding at cognate DNA sites that overlap substantially in sequence. The DNA-binding domains of ETS proteins (ETS domains) are highly conserved structurally yet share limited amino acid homology. To define the mechanistic implications of sequence diversity within the ETS family, we characterized the thermodynamics and kinetics of DNA site recognition by the ETS domains of Ets-1 and PU.1, which represent the extremes in amino acid divergence among ETS proteins. Even though the two ETS domains bind their optimal sites with similar affinities under physiologic conditions, their nature of site recognition differs strikingly in terms of the role of hydration and counter ion release. The data suggest two distinct mechanisms wherein Ets-1 follows a “dry” mechanism that rapidly parses sites through electrostatic interactions and direct protein-DNA contacts, whereas PU.1 utilizes hydration to interrogate sequence-specific sites and form a long-lived complex relative to the Ets-1 counterpart. The kinetic persistence of the high affinity PU.1·DNA complex may be relevant to an emerging role of PU.1, but not Ets-1, as a pioneer transcription factor in vivo. In addition, PU.1 activity is critical to the development and function of macrophages and lymphocytes, which present osmotically variable environments, and hydration-dependent specificity may represent an important regulatory mechanism in vivo, a hypothesis that finds support in gene expression profiles of primary murine macrophages.
The Dynamic Response and Vibration of Functionally Graded Carbon Nanotube-Reinforced Composite (FG-CNTRC) Truncated Conical Shells Resting on Elastic Foundations

Based on the classical shell theory, the linear dynamic response of functionally graded carbon nanotube-reinforced composite (FG-CNTRC) truncated conical shells resting on elastic foundations subjected to dynamic loads is presented. The truncated conical shells are reinforced by single-walled carbon nanotubes (SWCNTs) that vary according to the linear functions of the shell thickness. The motion equations are solved by the Galerkin method and the fourth-order Runge–Kutta method. In numerical results, the influences of geometrical parameters, elastic foundations, natural frequency parameters, and nanotube volume fraction of FG-CNTRC truncated conical shells are investigated. The proposed results are validated by comparing them with those of other authors.
Implementation of the Chebyshev structure with minimum storage

The Chebyshev structure, which is one of the implementation techniques for the McClellan transform, has good efficiency and a good roundoff noise. Its drawback is the increase of the required storage space. A method is presented to reduce the storage needed for the Chebyshev structure, and an efficient systolic cell with minimum storage is obtained. The hardware complexity of each cell is 1/N that of the filters. >
Coxiella Detection in Ticks from Wildlife and Livestock in Malaysia

Abstract Recent studies have shown that ticks harbor Coxiella-like bacteria, which are potentially tick-specific endosymbionts. We recently described the detection of Coxiella-like bacteria and possibly Coxiella burnetii in ticks found from rural areas in Malaysia. In the present study, we collected ticks, including Haemaphysalis bispinosa, Haemaphysalis hystricis, Dermacentor compactus, Dermacentor steini, and Amblyomma sp. from wildlife and domesticated goats from four different locations in Malaysia. Coxiella 16s rRNA genomic sequences were detected by PCR in 89% of ticks tested. Similarity analysis and phylogenetic analyses of the 16s rRNA and rpoB partial sequences were performed for 10 representative samples selected based on the tick species, sex, and location. The findings here suggested the presence of C. burnetii in two samples, each from D. steini and H. hystricis. The sequences of both samples clustered with published C. burnetii sequences. The remaining eight tick samples were shown to harbor 16s rRNA sequences of Coxiella-like bacteria, which clustered phylogenetically according to the respective tick host species. The findings presented here added to the growing evidence of the association between Coxiella-like bacteria and ticks across species and geographical boundaries. The importance of C. burnetii found in ticks in Malaysia warrants further investigation.
Aggregate-Query Processing in Data Warehousing Environments

In this paper we introduce generalized projections (G P an extension of duplicateeliminating projections, that capture aggregations, groupbys, duplicate-eliminating projections (distinctand duplicate-preserving projections in a common unified framework. Using G P s we extend well known and simple algorithms for SQL queries that use distinct projections to derive algorithms for queries using aggregations like sum, max, min, count, and avg. We develop powerful query rewrite rules for aggregate queries that unify and extend rewrite rules previously known in the literature. We then illustrate the power of our approach by solving a very practical and important problem in data warehousing: how to answer an aggregate query on base tables using materialized aggregate views (summary
Growth inhibition of pancreatic cancer cells by histone deacetylase inhibitor belinostat through suppression of multiple pathways including HIF, NFkB, and mTOR signaling in vitro and in vivo

Pancreatic ductal adenocarcinoma is a devastating disease with few therapeutic options. Histone deacetylase inhibitors are a novel therapeutic approach to cancer treatment; and two new pan‐histone deacetylase inhibitors (HDACi), belinostat and panobinostat, are undergoing clinical trials for advanced hematologic malignancies, non‐small cell lung cancers and advanced ovarian epithelial cancers. We found that belinostat and panobinostat potently inhibited, in a dose‐dependent manner, the growth of six (AsPc1, BxPc3, Panc0327, Panc0403, Panc1005, MiaPaCa2) of 14 human pancreatic cancer cell lines. Belinostat increased the percentage of apoptotic pancreatic cancer cells and caused prominent G2/M growth arrest of most pancreatic cancer cells. Belinostat prominently inhibited PI3K‐mTOR‐4EBP1 signaling with a 50% suppression of phorphorylated 4EBP1 (AsPc1, BxPc3, Panc0327, Panc1005 cells). Surprisingly, belinostat profoundly blocked hypoxia signaling including the suppression of hypoxia response element reporter activity; as well as an approximately 10‐fold decreased transcriptional expression of VEGF, adrenomedullin, and HIF1α at 1% compared to 20% O2. Treatment with this HDACi decreased levels of thioredoxin mRNA associated with increased levels of its endogenous inhibitor thioredoxin binding protein‐2. Also, belinostat alone and synergistically with gemcitabine significantly (P = 0.0044) decreased the size of human pancreatic tumors grown in immunodeficiency mice. Taken together, HDACi decreases growth, increases apoptosis, and is associated with blocking the AKT/mTOR pathway. Surprisingly, it blocked hypoxic growth related signals. Our studies of belinostat suggest it may be an effective drug for the treatment of pancreatic cancers when used in combination with other drugs such as gemcitabine. © 2014 Wiley Periodicals, Inc.
Entropy Production of Composites with Elliptical Inclusions for Bone Analysis

The prediction of the effective mechanical behavior of composites is not always a problem with a straightforward solution. Generally, this has influences from the geometrical arrangement, shape and size of the composite aggregate. Several micromechanical methods can be found, where it is attempted to predict the effective properties of composite materials, among them are The Mori & Tanaka method [1], the self-consistent method [2,3], and the differential scheme [4].
Wake me when it’s over – Bacterial toxin–antitoxin proteins and induced dormancy

Toxin–antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. During normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. Intense investigations have revealed a multitude of mechanisms for both regulation and activation of toxin–antitoxin systems, which are abundant in pathogenic microorganisms. This minireview provides an overview of the current knowledge regarding type II toxin–antitoxin systems along with their clinical and environmental implications.
WDFY1 mediates TLR3/4 signaling by recruiting TRIF

Toll‐like receptors (TLRs) are pattern recognition receptors that sense a variety of pathogens, initiate innate immune responses, and direct adaptive immunity. All TLRs except TLR3 recruit the adaptor MyD88 to ultimately elicit inflammatory gene expression, whereas TLR3 and internalized TLR4 use TIR‐domain‐containing adaptor TRIF for the induction of type I interferon and inflammatory cytokines. Here, we identify the WD repeat and FYVE‐domain‐containing protein WDFY1 as a crucial adaptor protein in the TLR3/4 signaling pathway. Overexpression of WDFY1 potentiates TLR3‐ and TLR4‐mediated activation of NF‐κB, interferon regulatory factor 3 (IRF3), and production of type I interferons and inflammatory cytokines. WDFY1 depletion has the opposite effect. WDFY1 interacts with TLR3 and TLR4 and mediates the recruitment of TRIF to these receptors. Our findings suggest a crucial role for WDFY1 in bridging the TLR–TRIF interaction, which is necessary for TLR signaling.
Simultaneous Single Unit Recording in vitro with a Photoetched Laser Deinsulated Gold Multimicroelectrode Surface

Flat photoetched gold conductors 12 ¿m wide and 2 ¿m thick, situated on a glass plate and deinsulated at their tips with single 8 ns UV laser pulses, have been utilized to record single unit extra-cellular activity from brain ganglia of the snail Helix pomatia. A fixed array of 36 such conductors, terminating in six rows and six columns in a 0.5 mm x 1 mm area, is capable of monitoring simultaneous single unit activity from numerous neurons. Spike amplitudes of 300¿500 ¿V are generally observed from the predominant 40 ¿m diameter cells of these ganglia. Giant neurons usually produce signal amplitudes of over 3 mV that are simultaneously seen by many electrodes. Signals can be monitored by merely resting a locally desheathed ganglion on the recording area under its own weight in a shallow pool of Ringer. A 10 ¿m diameter crater in a 3¿4 ¿m thick insulation layer has an impedance of 2¿4 M¿at 1 kHz. The capacitance of this metal electrolyte interface is about 0.5 pF/¿m2, suggesting that the UV laser produces a partially colloidal gold surface. With this recessed tip design, simultaneous single unit recording from small neurons appears ensured if electrode impedances are below 4 M¿, shunt impedances are above 30 M¿, and glia cells are not allowed to reinsulate the end of the gold conductor.
Impact of Diabetes on Long-Term Prognosis in Patients With Unstable Angina and Non–Q-Wave Myocardial Infarction: Results of the OASIS (Organization to Assess Strategies for Ischemic Syndromes) Registry

BackgroundAlthough unstable coronary artery disease is the most common reason for admission to a coronary care unit, the long-term prognosis of patients with this diagnosis is unknown. This is particularly true for patients with diabetes mellitus, who are known to have a high morbidity and mortality after an acute myocardial infarction. Methods and ResultsProspectively collected data from 6 different countries in the Organization to Assess Strategies for Ischemic Syndromes (OASIS) registry were analyzed to determine the 2-year prognosis of diabetic and nondiabetic patients who were hospitalized with unstable angina or non–Q-wave myocardial infarction. Overall, 1718 of 8013 registry patients (21%) had diabetes. Diabetic patients had a higher rate of coronary bypass surgery than nondiabetic patients (23% versus 20%, P <0.001) but had similar rates of catheterization and angioplasty. Diabetes independently predicted mortality (relative risk [RR], 1.57; 95% CI, 1.38 to 1.81;P <0.001), as well as cardiovascular death, new myocardial infarction, stroke, and new congestive heart failure. Moreover, compared with their nondiabetic counterparts, women had a significantly higher risk than men (RR, 1.98; 95% CI, 1.60 to 2.44; and RR, 1.28; 95% CI, 1.06 to 1.56, respectively). Interestingly, diabetic patients without prior cardiovascular disease had the same event rates for all outcomes as nondiabetic patients with previous vascular disease. ConclusionsHospitalization for unstable angina or non–Q-wave myocardial infarction predicts a high 2-year morbidity and mortality; this is especially evident for patients with diabetes. Diabetic patients with no previous cardiovascular disease have the same long-term morbidity and mortality as nondiabetic patients with established cardiovascular disease after hospitalization for unstable coronary artery disease.
Learning and optimization of an aspect hidden Markov model for query language model generation

The Relevance Model (RM) incorporates pseudo relevance feedback to derive query language model and has shown a good performance. Generally, it is based on uni-gram models of individual feedback documents from which query terms are sampled independently. In this paper, we present a new method to build the query model with latent state machine (LSM) which captures the inherent term dependencies within the query and the term dependencies between query and documents. Our method firstly splits the query into subsets of query terms (i.e., not only single terms, but different combinations of multiple query terms). Secondly, these query term combinations are then considered as weighted latent states of a hidden Markov Model to derive a new query model from the pseudo relevant documents. Thirdly, our method integrates the Aspect Model (AM) with the EM algorithm to estimate the parameters involved in the model. Specifically, the pseudo relevant documents are segmented into chunks, and different chunks are associated with different weights in relation to a latent state. Our approach is empirically evaluated on three TREC collections, and demonstrates statistically significant improvements over a baseline language model and the Relevance Model.
Phage therapy—constraints and possibilities

Abstract The rise of antibiotic-resistant bacterial strains, causing intractable infections, has resulted in an increased interest in phage therapy. Phage therapy preceded antibiotic treatment against bacterial infections and involves the use of bacteriophages, bacterial viruses, to fight bacteria. Virulent phages are abundant and have proven to be very effective in vitro, where they in most cases lyse any bacteria within the hour. Clinical trials on animals and humans show promising results but also that the treatments are not completely effective. This is partly due to the studies being carried out with few phages, and with limited experimental groups, but also the fact that phage therapy has limitations in vivo. Phages are large compared with small antibiotic molecules, and each phage can only infect one or a few bacterial strains. A very large number of different phages are needed to treat infections as these are caused by genetically different strains of bacteria. Phages are effective only if enough of them can reach the bacteria and increase in number in situ. Taken together, this entails high demands on resources for the construction of phage libraries and the testing of individual phages. The effectiveness and host range must be characterized, and immunological risks must be assessed for every single phage.