Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of possible sites for posttranslational modifications in human gamma crystallins: Effect of glycation on the structure of human gamma‐b‐crystallin as analyzed by molecular modeling

Crystallins are recognized as one of the long‐lived proteins of lens tissue that might serve as the target for several posttranslational modifications leading to cataract development. We have studied several such sites present in the human γ‐crystallins based either on PROSITE pattern search results or earlier experimental evidences. Their probabilities were examined on the basis of the database analysis of the γ‐crystallin sequences and on their specific locations in the constructed homology models. An N‐glycosylation site in human γD‐crystallin and several phosphorylation sites in all four human γ‐crystallins were predicted by the PROSITE search. Some of these sites were found to be strongly conserved in the γ‐crystallin sequences from different sources. An extensive analysis of these sites was performed to predict their probabilities as potential sites for protein modifications. Glycation studies were performed separately by attaching sugars to the human γB‐crystallin model, and the effect of binding was analyzed. The studies showed that the major effect of αD‐glucose (αD‐G) and αD‐glucose‐6‐phosphate (αD‐G6P) binding was the disruption of charges not only at the surface but also within the molecule. Only a minor alteration in the distances of sulfhydryl groups of cysteines and on their positions in the three‐dimensional models were observed, leading us to assume that glycation alone is not responsible for intra‐ and intermolecular disulfide bond formation. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Addition of Blood Pressure and Weight Transmissions to Standard Remote Monitoring of Implantable Defibrillators and its Association with Mortality and Rehospitalization

Background— Among patients with implantable defibrillators (ICD), use of remote patient monitoring (RPM) is associated with lower risk of death and rehospitalization. Standard ICD RPM can be supplemented with weight and blood pressure data. It is not known whether standard RPM plus routine weight and blood pressure transmission (RPM+) is associated with better outcomes. Methods and Results— RPM+ patients (n=4106) were compared with patients who only transmitted standard ICD RPM data (n=14 183). Logistic regression models identified patient, physician, and hospital characteristics associated with RPM+ utilization. Mortality and rehospitalization were examined using landmark analyses at 180 days after ICD implant in Medicare fee-for-service patients. In these analyses, we examined the independent association between RPM+ utilization and times to events up to 3 years after device implantation with Cox regression models. We further examined whether the association between RPM+ and outcomes varied by frequency or type of transmissions. Determinants of RPM+ utilization included impaired ejection fraction, cardiac resynchronization therapy, and institutional practice. The risk of mortality of RPM+ patients was similar to standard ICD RPM patients (hazard ratio, 1.06; 95% confidence interval, 0.94–1.19; P=0.34). RPM+ patients also had similar risks of all-cause hospitalization (subdistribution hazard ratio, 1.03; 95% confidence interval, 0.94–1.14; P=0.52), cardiovascular hospitalization (subdistribution hazard ratio, 0.92; 95% confidence interval, 0.83–1.02; P=0.15), or heart failure hospitalizations (subdistribution hazard ratio, 0.90; 95% confidence interval, 0.78–1.05; P=0.18). RPM+ transmission frequency was not associated with outcomes. Conclusions— In patients using standard ICD RPM, the added transmission of weight and blood pressure data was not associated with improved outcomes.
FPGA based design of Generic Multilevel Built In Test Equipment for radars

Built In Test Equipments are used to simulate targets to check functionality of different subsystems and the performance (like ECCM) of the radar as a whole. We present an Field Programmable Gate Array (FPGA) based design of a Generic Multilevel Built In Test Equipment (BITE) capable of simulating target echo at Intermediate Frequency (IF), Radio Frequency (RF) levels and at Field. The design also closely simulates the target behavior, like motion in range and azimuth, different doppler, different modulation codes and multiple targets. The implementation solution presented utilizes the efficient FPGA resources so as to meet the timings in crucial applications. The work highlights the features of the design with real implementation and test in a radar system.
Flexible Nonhomogeneous Markov Models for Panel Observed Data

Summary Methods for fitting nonhomogeneous Markov models to panel‐observed data using direct numerical solution to the Kolmogorov Forward equations are developed. Nonhomogeneous Markov models occur most commonly when baseline transition intensities depend on calendar time, but may also occur with deterministic time‐dependent covariates such as age. We propose transition intensities based on B‐splines as a smooth alternative to piecewise constant intensities and also as a generalization of time transformation models. An expansion of the system of differential equations allows first derivatives of the likelihood to be obtained, which can be used in a Fisher scoring algorithm for maximum likelihood estimation. The method is evaluated through a small simulation study and demonstrated on data relating to the development of cardiac allograft vasculopathy in posttransplantation patients.
The “Small World” of Private Equity Funds

The authors explore the structure of the network of relationships between 225 private equity firms arranging “club deals” between 2000 and 2017 with different private equity firms. After using the tools of social network analysis to assess this structure and the prominence of the players within it, they find that the network is dominated by few central players, suggesting the existence of a “small world” of relationships. Some players are found to act as a brokers of relationships between other players, despite having a lower number of connections, increasing the resources exchanged in the network. Network centrality is shown to have the largest economic effect on the likelihood of club deal formation. This finding supports the idea that the establishment of private equity consortiums is not merely for capital constraint motivations or portfolio diversification, but also to increase social capital and ensure future deal flow.
Evacuation analysis of a hospital based on FDS+Evac software

Recently trample and other disasters concerning mass crowd frequently happened in public places and the public evacuation safety draws the whole society's attention. Hospital is such a special public place that the evacuation study on it is rare. So this paper chooses a hospital as the object of study and resets the velocity of pedestrians in the software FDS+Evac by means of collecting data related to real velocities of different pedestrian groups in hospital, and investigates how the parameters such as velocity and exit familiarity influence the evacuation results. The results show that large velocity difference leads to intermittent flow. However, the influence of exit familiarity is weakened by the following behavior, but it is essential to the people who lagged behind in the evacuation.
Long-term psychosocial outcome of adults with tetralogy of Fallot and transposition of the great arteries: a historical comparison

Abstract Objective: To make a historical comparison on the long-term psychosocial outcome of cardiothoracic surgery during childhood. Methods: Adult patients operated for tetralogy of Fallot or transposition of the great arteries between 1980 and 1990 (recent sample) were compared with patients who underwent surgery and were investigated 10 years earlier (historical sample). In addition, atrial switch and arterial switch patients within the recent sample were compared. Psychosocial functioning was measured using standardised, validated psychological questionnaires. Results: Although the recent sample of patients overall shows a favourable quality of life, impairments were found in income, living conditions, relationships, offspring, and occupational level. Compared with the historical sample, the recent sample showed no significant improvements on psychosocial functioning, except for a better educational level. The amount of educational problems, such as learning difficulties, was still high compared with normative data. Recently operated patients with transposition of the great arteries (arterial switch) scored significantly better on the Short Form-36 vitality scale (p = 0.02) compared with historical patients with transposition of the great arteries (atrial switch). Conclusions: Despite improvements in medical treatment over the past few decades, hardly any change was found in the psychosocial outcome of the recent patient sample compared with the historical patient sample. In particular, the percentage of patients needing special education and showing learning problems remained high, whereas income was low compared with normative data.
Suppression of zebrafish VEGF gene by cytomegalovirus promoter-driven short hairpin constructs induces vascular development defects and down regulation NRP1 expression

The usage of RNA interference for gene knockdown in zebrafish through expression of the small interfering RNA mediators from DNA vectors has created a lot of excitement in the research community. In this work, the ability of human cytomegalovirus immediate early promoter (CMV promoter)-driven short hairpin RNA (shRNA) expression vector to induce shRNA against vascular endothelial growth factor (VEGF) gene in zebrafish was tested, and its effects on VEGF-mediated vasculogenesis and angiogenesis were evaluated. Altogether four vectors targeting various locations of VEGF gene were constructed, and pSI-V4 was proven to be the most effective one. Microinjection of pSI-V4 into the zebrafish embryos resulted in defective vascular formation and down regulation of VEGF expression. In situ hybridization analysis indicated that silencing VEGF gene expression by pSI-V4 resulted in down regulation of neuropilin-1 (NRP1), a potent VEGF receptor. Knockdown of VEGF expression by morpholino gave the same result. This provided evidence that the VEGF-mediated angiogenesis in zebrafish was in part dependent on NRP1 expression. The results contributed to a better understanding of molecular mechanisms of cardiovascular development and provided a potential promoter for making inducible knockdown in zebrafish.
Two Conserved Residues Govern the Salt and pH Dependencies of the Binding Reaction of a PDZ Domain*

PDZ domains are protein-protein interaction modules found in hundreds of human proteins. Their binding reactions are sensitive to variations in salt and pH but the basis of the respective dependence has not been clear. We investigated the binding reaction between PSD-95 PDZ3 and a peptide corresponding to a native ligand with protein engineering in conjunction with stopped-flow and equilibrium fluorimetry and found that the two conserved residues Arg-318 and His-372 were responsible for the salt and pH dependencies, respectively. The basis of the salt-dependent variation of the affinity was explored by mutating all charged residues in and around the peptide-binding pocket. Arg-318 was found to be crucial, as mutation to alanine obliterated the effect of chloride on the binding constants. The direct interaction of chloride with Arg-318 was demonstrated by time-resolved urea denaturation experiments, where the Arg-318 → Ala mutant was less stabilized by addition of chloride as compared with wild-type PDZ3. We also demonstrated that protonation of His-372 was responsible for the increase of the equilibrium dissociation constant at low pH. Both chloride concentration and pH (during ischemia) vary in the postsynaptic density, where PSD-95 is present, and the physiological buffer conditions may thus modulate the interaction between PSD-95 and its ligands through binding of chloride and protons to the “molecular switches” Arg-318 and His-372, respectively.
Molecular Detection of Avian Influenza Virus but not West Nile Virus in Wild Birds in Northern Turkey

In this study, a total of 402 samples (173 cloacal swab samples, 169 tracheal swab samples and 60 organ pools including the lung, spleen, liver, trachea and brain) obtained from 27 different wild avian species from Kizilirmak delta and the adjacent wetlands in northern Turkey were surveyed for the presence of RNA from Avian influenza virus (AIV) and West Nile virus (WNV) by Taqman‐based real‐time reverse transcriptase‐polymerase chain reaction assay. No WNV genomic RNA was detected in any sample. In contrast, AIV RNA was found in two of 402 samples (0.49%).
Pyruvate-induced Long-term Maintenance of Glutathione S-Transferase in Rat Hepatocyte Cultures

The addition of pyruvate to the culture medium has been reported to improve the maintenance of P450-dependent enzyme expression in primary rat hepatocyte cultures. In this study, the effects of 30mM pyruvate on cell morphology, albumin secretion and glutathione S-transferase (GST) expression were investigated as a function of the time in culture. The effect of triiodothyronine (T3) exposure on GST expression was also measured in pyruvate-treated cultures. Transmission electron microscopy showed that untreated hepatocytes deteriorated after culture for 7 days, whereas the morphology of the pyruvate-treated cells was similar to that observed in intact liver tissue. The albumin secretion rate was significantly higher in rat hepatocytes exposed to pyruvate than in control cells. In the presence of pyruvate, μ and α class GST activities were well maintained, whereas GST π activity was increased over the entire culture period. HPLC analysis revealed that the complement of GST subunits present in hepatocytes is altered during culture with pyruvate: μ class proteins remained relatively constant, whereas a decrease in the a class content was accompanied by a strong increase in GST subunit P1 (GSTP1). The induction of GSTP1 was confirmed at the mRNA level. In control cultures, π class GST activity was increased, but total, μ, and α class GST activities continuously declined as a function of culture time and became undetectable beyond 7 days in culture. At the protein and mRNA levels, a much smaller increase in GSTP1 was observed than in the pyruvate cultures. When the pyruvate-treated cell cultures were exposed to T3, an inhibitory effect on GST activities and proteins was found. These results indicate that this simple culture model could be useful for studying the expression and regulation of GST.
Construction of Asymmetric Type-2 Fuzzy Membership Functions and Application in Time Series Prediction

This paper proposes a method to construct asymmetric fuzzy membership functions (MFs) for improving performance of type-2 fuzzy logic systems. The effect of asymmetric type-2 fuzzy MFs for fuzzy logic systems is discussed by illustration examples. Each asymmetric MF is constructed by four Gaussian functions to introduce the properties of uncertain mean and uncertain variance. Based on the gradient method, the corresponding learning algorithm is derived. This modification improves the approximation accuracy and reduces the computational complexity. Simulation results of nonlinear systems identification and chaotic time-series prediction are shown to demonstrate the effectiveness.
Simultaneous occurrence of fumonisin B1 and other mycotoxins in moldy corn collected from the People's Republic of China in regions with high incidences of esophageal cancer

A total of 31 corn samples collected from households in the counties of Cixian and Linxian of the People's Republic of China, where high incidences of esophageal cancer have been reported, were analyzed for fumonisin B1 (FB1), aflatoxin, and total trichothecene mycotoxins. High levels of FB1 (18 to 155 ppm; mean, 74 ppm) were found in 16 of the samples that showed heavy mold contamination. FB1, at lower levels (20 to 60 ppm; mean, 35.3 ppm), was also found in 15 samples, collected from the same households, that did not show any visible mold contamination. The levels of aflatoxin in the samples were low (1 to 38.4 ppb; mean, 8.61 ppb). High levels of total type-A trichothecenes were also found in the moldy corn samples (139 to 2,030 ppb; mean, 627 ppb). Immunochromatography of selected samples revealed that these samples contained T-2 toxin, HT-2 toxin, iso-neosolaniol, monoacetoxyscirpenol, and several other type-A trichothecenes. The concentration of total type-B trichothecenes in 15 moldy corn samples was in the range of 470 to 5,826 ppb (mean, 2,359 ppb). High levels (3.7 to 5.0 mg/g) of FB1 were produced in corn in the laboratory by five Fusarium moniliforme strains isolated from the moldy corn. These fungi were also capable of forming various nitrosamines (5 to 16 micrograms per flask) in the presence of nitrate and precursor amines. (ABSTRACT TRUNCATED AT 250 WORDS)
Two immediate-early pathogen-responsive members of the AtCMPG gene family in Arabidopsis thaliana and the W-box-containing elicitor-response element of AtCMPG1

The Arabidopsis thaliana genome contains at least 50 predicted AtCMPG genes. The encoded protein family is defined by a common domain possessing four strictly conserved amino acid residues [Cys, Met, Pro, and Gly (CMPG)] that designate the family. Two members, AtCMPG1 and AtCMPG2, with high sequence similarity to the previously described, immediate-early pathogen-responsive PcCMPG1 gene from Petroselinum crispum were selected for analysis of their expression modes and defense-related promoter elements. Among the most striking similarities with PcCMPG1 were immediate-early transcriptional activation on infection or treatment with a pathogen-derived elicitor and the functional importance of a W-box-containing AtCMPG1 promoter element. Remarkably, this strongly pathogen/elicitor-responsive element, F, did not respond to wounding, in contrast to the AtCMPG1 promoter itself. Comparative analysis, both within the A. thaliana genome and across species, provided further insight into the large structural diversity of W-box-containing elements. Possible roles of AtCMPG proteins in regulatory processes are discussed with reference to a large variety of family members, partly with assigned functions, from plants as well as animals.
Fluorescent detection of cyanobacterial DNA using bacterial magnetic particles on a MAG-microarray.

Bacterial magnetic particles (BMPs) were used for the identification of cyanobacterial DNA. Genus-specific oligonucleotide probes for the detection of Anabaena spp. , Microcystis spp. , Nostoc spp. , Oscillatoria spp. , and Synechococcus spp. were designed from the variable region of the cyanobacterial 16S rDNA of 148 strains. These oligonucleotide probes were immobilized on BMPs via streptavidin-biotin conjugation and employed for magnetic-capture hybridization against digoxigenin-labeled cyanobacterial 16S rDNA. Bacterial magnetic particles were magnetically concentrated, spotted in 100-microm-size microwell on MAG-microarray, and the fluorescent detection was performed. This work details the development of an automated technique for the magnetic isolation, the concentration of hybridized DNA, and the detection of specific target DNA on MAG-microarray. The entire process of hybridization and detection was automatically performed using a magnetic-separation robot and all five cyanobacterial genera were successfully discriminated.
A general computational model of mitochondrial metabolism in a whole organelle scale

UNLABELLED A computational tool for mitochondrial systems biology has been developed as a simulation model of E-Cell2, a publicly available simulation system. The general model consists of 58 enzymatic reactions and 117 metabolites, representing the respiratory chain, the TCA cycle, the fatty acid beta-oxidation and the inner-membrane transport system. It is based on previously published enzyme kinetics studies in the literature; we have successfully integrated and packaged them into a single large model. The model can be easily extended and modified so that mitochondrial biologists/physiologists can integrate their own models and evaluate them in the context of the whole organelle metabolism. AVAILABILITY The mitochondrial model is bundled up with E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences. SUPPLEMENTARY INFORMATION All the kinetic data are available via http://www.e-cell.org
Reproductive success and effective population size in woodrats (Neotoma macrotis)

Discrepancies between the census size and the genetically effective size of populations (Ne) can be caused by a number of behavioural and demographic factors operating within populations. Specifically, strong skew in male reproductive success, as would be expected in a polygynous mating system, could cause a substantial decrease in Ne relative to census size. Because the mating system of Neotoma macrotis had previously been described as one nearing harem polygyny, I examined the distribution of reproductive success and genetic variation within a population of this species. Combining genetic data and three years of field observations, I show that variance in reproductive success does not deviate from poisson expectations within either sex and variance in success is similar between the sexes. Furthermore, both males and females had multiple partners across litters in addition to some evidence of multiple paternity within litters. Despite a lack of strong skew in reproductive success, an estimate of Ne based on a number of demographic parameters suggests that the ratio of Ne/N in this population is 0.48. Although the ratio of Ne/N suggests that the population is experiencing higher rates of genetic drift than would be expected based on census size alone, the population maintains high levels of genetic diversity. Estimates of neighbourhood size and patterns of recruitment to the study site suggest that immigration plays an important role in this population and may contribute to the maintenance of high levels of genetic diversity.
Stretch-Induced Uterine Myocyte Differentiation During Rat Pregnancy: Involvement of Caspase Activation1

Proliferation, differentiation, and apoptosis are three major processes by which the pregnant uterus maintains homeostasis to accommodate the growing fetus. We demonstrated previously that caspase activation in the pregnant rat myometrium at midgestation coincides with the transition from uterine hyperplasia to hypertrophy. We hypothesized that this transition was induced by stasis of myometrial blood flow (and subsequent hypoxia/ischaemia insult) resulting from acute myometrial stretch induced by a growing embryo. Therefore, we measured the expression of active caspase 3 and two hypoxia markers (transcription factor HIF1A and pimonidazole hydrochloride) in pregnant rat myometrium. To investigate the effect of gravidity we used unilaterally pregnant rats. Caspase 3 was activated only in the gravid horn of the unilaterally pregnant animals on Gestational Days 12–15. This activation was associated with high levels of HIF1A and pimonidazole immunostaining, which were limited to the circular myometrial layer of the gravid horn, indicative of hypoxia within this tissue. To isolate the effect of myometrial stretch applied by the growing fetus, we inserted an expandable polymer tube (intra-uterine expandable tube [IUET]) into the empty horn of Day 13 and Day 20 unilaterally pregnant rats. Tissue was collected 2, 14, and 24 h later. In the IUET-stretched empty horn, cleaved caspase 3 was activated at midgestation (Day 14), but not at late gestation (Day 21). We speculate that hypoxia resulting from mechanical stretch may activate caspase 3 within the pregnant myometrium only in the context of a specific endocrine environment.