Miracle-dz/UniFAR-FTUs huggingface dataset:
The exosome of Trypanosoma brucei

The yeast exosome is a complex of at least 10 essential 3′–5′ riboexonucleases which is involved in 3′‐processing of many RNA species. An exosome‐like complex has been found or predicted to exist in other eukaryotes but not in Escherichia coli. The unicellular parasite Trypanosoma brucei diverged very early in eukaryotic evolution. We show here that T.brucei contains at least eight exosome subunit homologs, but only a subset of these associate in a complex. Accordingly, the T.brucei exosome is smaller than that of yeast. Both free and complex‐associated homologs are essential for cell viability and are involved in 5.8S rRNA maturation. We suggest that the exosome was present in primitive eukaryotes, and became increasingly complex during subsequent evolution.
Permeable surfaces hypersonic aircraft optimal heat protection mathematical modeling

The problems of intended for the atmosphere entry hypersonic aircraft surfaces optimal effusion heat protection mathematical modeling are considered. The physico-chemical processes (the dissociation and the ionization) in laminar boundary layer of compressible gas are appreciated. The Groups theory approach to distributed parameters systems optimization is applied. An optimal control in the first approximation in analytical form is obtained. Some possibilities of special blow laws use for hypersonic aircraft surfaces heat protection nearing to optimal are considered. Computation experiments numerical results are discussed.
Emission patterns and emission rates of MVOC and the possibility for predicting hidden mold damage?

UNLABELLED Laboratory trials were performed in order to search for the variety of the production of microbial volatile organic compounds (MVOC), which could be used as indicators for hidden mold damage. Concerning MVOC production the experiments showed a dependency on the mold genus/species, the different strains used and the building materials used as substrate. It could be proved that the production of certain MVOC is not consistent at all times. On the whole low emission rates in terms of microg/h/m2 of the MVOC were found. Extrapolating the emissions rates from the laboratory trails to an indoor air situation results in concentrations below the analytical detection limit in most cases. According to these results only heavy or very large fungal contaminations might be detected by this method in indoor air. The studies were performed at the Institute of Hygiene and Environmental Medicine, Charite, Germany. PRACTICAL IMPLICATIONS Microorganisms like bacteria and molds produce a huge variety of substances, and a part of them are released into the environment. Some compounds like, e.g. alcohols or ketones are volatile, therefore found in the air and called MVOC. Those compounds were considered helpful to track especially hidden mold damage. The study presented here showed, that the emission pattern varies from genus to genus and sometimes even from fungal strain to fungal strain. The results concerning the emission rates from different infested building materials proved, that the concentrations produced are much too low to be detected in indoor air, especially considering the dilution because of ventilation. Therefore, we conclude that MVOC should not be used as predictors for mold damage in indoor environments.
The venous stasis syndrome after deep venous thrombosis or pulmonary embolism: a population-based study.

OBJECTIVES To estimate the incidence and determine predictors of venous stasis syndrome and venous ulcers after deep venous thrombosis and pulmonary embolism. PATIENTS AND METHODS This population-based retrospective cohort study reviewed medical records of 1527 patients with incident deep venous thrombosis or pulmonary embolism between 1966 and 1990. We recorded baseline characteristics, event type (deep venous thrombosis with or without pulmonary embolism or pulmonary embolism alone), leg side and site of deep venous thrombosis (proximal with or without distal deep venous thrombosis vs distal deep venous thrombosis alone), and venous stasis syndrome and venous ulcer. RESULTS Two hundred forty-five patients developed venous stasis syndrome. One-year, 5-year, 10-year, and 20-year cumulative incidence rates were 7.3%, 14.3%, 19.7%, and 26.8%, respectively. By 20 years the cumulative incidence of venous ulcers was 3.7%. Patients with deep venous thrombosis with or without pulmonary embolism were 2.4-fold (95% confidence interval, 1.7-fold-3.2-fold) more likely to develop venous stasis syndrome than patients with pulmonary embolism and no diagnosed deep venous thrombosis. In patients aged 40 years or younger with proximal compared with distal-only deep venous thrombosis, venous stasis syndrome was 3.0-fold more likely (95% confidence interval, 1.6-fold-4.7-fold). In patients with unilateral leg deep venous thrombosis, venous stasis syndrome usually developed in the concordant leg (P < .001). There was a 30% (95% confidence interval, 2%-62%) increased risk for venous ulcer per decade of age at the incident venous thromboembolism. CONCLUSIONS The cumulative incidence of venous stasis syndrome continues to increase for 20 years after venous thromboembolism. Pulmonary embolism alone is less likely to cause venous stasis syndrome.
Evaluation of aneuploidy and DNA damage in human spermatozoa: applications in field studies

With the goal of incorporating measures of sperm nuclear integrity in an epidemiology study, semen samples from young Czech men were analysed for sperm aneuploidy and sperm chromatin structure in addition to routine measures of sperm production and quality. The exposure in question was to high seasonal air pollution containing reactive polyaromatic hydrocarbons potentially capable of affecting spermatogenesis and damaging sperm DNA. The sperm aneuploidy assay uses fluorescence in situ hybridization to label selected sperm chromosomes; as applied in this study, the sex chromosomes (X,Y) and chromosome 8 were targeted. The sperm chromatin structure assay detects sperm nuclei with increased susceptibility to denaturation, a feature that is associated with DNA damage. Logistically, these assays were relatively easy to incorporate into the study design. The aneuploidy assay provided information suggesting that exposure to high levels of air pollution may increase the risk of sperm aneuploidy and that it is important to control for exposure to cigarette smoke and/or alcohol in such studies. The sperm chromatin structure assay provided valuable baseline information about Czech semen donors and data suggestive of an adverse effect of smoking and air pollution on spermatozoa that merits further investigation.
Cutaneous mast cells are altered in normal healthy volunteers sitting in front of ordinary TVs/PCs – results from open‐field provocation experiments

Background: Considerable controversy has surrounded the question of possible biological responses to electromagnetic fields (EMFs) generated from visual display terminals (VDTs), such as personal computers (PCs) and ordinary television sets (TVs). The cellular and molecular mechanisms for such potential harmful health hazards have not yet been understood, although clues from the literature include mast cells and histamine. The aim of this study was therefore to investigate possible biological mast cell responses to TV/PC screens.
One-model speech recognition and synthesis based on articulatory movement HMMs

One-model speech recognition (SR) and speech synthesis (SS) based on a common articulatory movement model are described herein. The SR engine has an articulatory feature (AF) extractor and an HMM based classifier that models articulatory gestures. Experimental results of a phoneme recognition task show that the AF outperforms MFCC even if the training data are limited to a single speaker. In the SS engine, the same speaker-invariant HMM is applied to generate an AF sequence, and then, after converting AFs into vocal tract parameters, a speech signal is synthesized by a PARCOR filter, together with a residual signal. Phoneme-to-phoneme speech conversion, using AF exchange, is also described.
Identification of the Serine Biosynthesis Pathway as a Critical Component of BRAF Inhibitor Resistance of Melanoma, Pancreatic, and Non–Small Cell Lung Cancer Cells

Metastatic melanoma cells commonly acquire resistance to BRAF V600E inhibitors (BRAFi). In this study, we identified serine biosynthesis as a critical mechanism of resistance. Proteomic assays revealed differential protein expression of serine biosynthetic enzymes PHGDH, PSPH, and PSAT1 following vemurafenib (BRAFi) treatment in sensitive versus acquired resistant melanoma cells. Ablation of PHGDH via siRNA sensitized acquired resistant cells to vemurafenib. Inhibiting the folate cycle, directly downstream of serine synthesis, with methotrexate also displayed similar sensitization. Using the DNA-damaging drug gemcitabine, we show that gemcitabine pretreatment sensitized resistant melanoma cells to BRAFis vemurafenib and dabrafenib. We extended our findings to BRAF WT tumor cell lines that are intrinsically resistant to vemurafenib and dabrafenib. Pretreatment of pancreatic cancer and non–small cell lung cancer cell lines with sublethal doses of 50 and 5 nmol/L of gemcitabine, respectively, enhanced killing by both vemurafenib and dabrafenib. The novel aspects of this study are the direct identification of serine biosynthesis as a critical mechanism of BRAF V600E inhibitor resistance and the first successful example of using gemcitabine + BRAFis in combination to kill previously drug-resistant cancer cells, creating the translational potential of pretreatment with gemcitabine prior to BRAFi treatment of tumor cells to reverse resistance within the mutational profile and the WT. Mol Cancer Ther; 16(8); 1596–609. ©2017 AACR.
Predictive value of different estimated glomerular filtration rates on hospital adverse events following acute myocardial infarction.

AIM to assess whether different glomerular filtration rate (GFR) equations render different predictive value on hospital adverse events in patients hospitalised due to acute myocardial infarction. METHODS the study design is cross-sectional. Data from consecutive patients with acute myocardial infarction were analyzed. Three different estimated GFR equations, i.e. Cockroft-Gault (eGFRC-G), MDRD (eGFRMDRD) and CKD-EPI (eGFRCKD-EPI) were calculated. Hospital adverse events in these study patients were recorded. The predictive values of these eGFRs on hospital adverse events were compared with ROC curve. Univariate and multivariable analysis to assess which GFR equation as independent predictor for hospital adverse events were performed. RESULTS among 103 study patients, 49 patients (47.6%) experienced hospital adverse events. Proportion of hospital adverse events were significantly associated with eGFRMDRD (p<0.01) and eGFRCKD-EPI (p=0.02), but not with eGFRC-G (p=0.10). Hospital adverse events were better predicted by eGFRMDRD than by eGFRCKD-EPI (AUC, 0.698; 95%CI: 0.596-0.800, p<0.01 versus AUC, 0.693; 95%CI: 0.591-0.796, p<0.01). Multivariable analysis showed moderate (adjusted OR 3.50; 95%CI: 1.38-8.85, p<0.01) and severe (adjusted OR 8.13, 95%CI: 1.38-47.91, p=0.02) kidney dysfunctions based on eGFRMDRD were independent predictors for hospital adverse events. CONCLUSION an eGFR based on MDRD gave better predictive value than eGFR based on CKD-EPI on hospital adverse events among acute myocardial infarction. Moderate and severe kidney dysfunctions based on eGFRMDRD were independent predictors for hospital adverse events following acute myocardial infarction.
Estimate your dose: RADDOSE‐3D

We present the current status of RADDOSE‐3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X‐ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimize radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimize the use of their crystals. It also allows quantitative comparisons between different radiation damage studies, giving a universal “x‐axis” against which to plot various metrics.
Characterization of gene expression profiles in early bovine pregnancy using a custom cDNA microarray

Gene expression analysis comparing nonpregnant with pregnant bovine uteri, including placenta, was performed with a custom cDNA microarray containing 1,933 independent genes. These genes were classified into six categories according to biological function, as follows: cell and tissue structural dynamics (108 genes), intercellular communication (221), intracellular metabolism (265), cell cycle and apoptosis (26), regulation of gene expression (113), expressed sequence tag (EST) and function unknown (617), and uncomplemented genes (583 clones). This array possessed bovine placental/endometrial specificity, as it included many pregnancy‐specific molecules, such as pregnancy‐associated glycoprotein‐1 (PAGs), placental lactogen (PLs), and prolactin‐related protein‐1 (PRPs). A total of 77 genes were induced and 12 repressed in the placenta/endometrium. Our results point to a fundamental role for bovine placental‐specific genes such as PAGs, PLs, and PRPs, in implantation and placentogenesis, and document that cDNA microarray analysis from bovine placenta/endometrium is possible and is a specific tool for monitoring genome‐wide gene expression during the establishment and maintenance of pregnancy. Mol. Reprod. Dev. 65: 9–18, 2003. © 2003 Wiley‐Liss, Inc.
University of Groningen Bacterial fingerprints across Europe

Methicillin-resistant Staphylococcus aureus (MRSA) represents a serious threat for public health worldwide. Of particular concern is the emergence of community-acquired MRSA, which is often difficult to distinguish from nosocomial MRSA due to a lack of suitable typing methods for early detection. For example, the USA300 pulsed-field gel electrophoresis (PFGE) pattern includes both the classical community-acquired USA300 clone with spa-type t008 and an epidemiologically unrelated nosocomial clone with spa-type t024. Likewise, spa-typing cannot distinguish the classical USA300 from nosocomial MRSA with the spa-type t008. Since the fast and high-resolution distinction of these S. aureus types is important for infection prevention and surveillance, we investigated whether multiplelocus variable number tandem repeat (VNTR) fingerprinting (MLVF) can be applied to overcome these limitations. Indeed, MLVF correctly grouped 91 MRSA isolates belonging to the classical USA300 lineage, nosocomial MRSA isolates with the USA300 PFGE profile and spa-type t024, and nosocomial MRSA isolates with spa-type t008 into three distinct clusters. Importantly, several sub-clusters were also identified, reflecting epidemiological relationships between the respective isolates. We conclude that MLVF has the discriminatory power needed to rapidly distinguish very similar communityacquired and nosocomial MRSA isolates, and that MLVF-based sub-clustering of isolates is highly useful for epidemiological investigations, outbreak prevention and control.
Relationship between education and cardiovascular risk score.

369 (BMI) of 30 kg/m2 or higher. The level of education was classified as primary, secondary, and higher. Patients had their cardiovascular risk estimated using the SCORE algorithm, which is designed for risk assessment in primary prevention and can be applied to people without a diagnosed cardiovascular disease. In this model, the risk is defined as the probability of cardiovascular events within the following 10 years, culminating in death. A high-risk group included subjects without a clinical cardiovascular disease, whose SCORE was equal or above 5% or, in the case of diabetes, subjects with total cholesterol levels of 320 mg/dl (7 mmol/l) or higher, LDL cholesterol levels of 240 mg/dl (7 mmol/l) or higher, and blood pressure of 180/110 mmHg or higher.5
Overview of Proteome Analysis

This unit reviews the new discipline of proteomics, which includes any large‐scale protein‐based systematic analysis of the proteome or defined sub‐proteome from a cell, tissue, or entire organism. Proteomics originated in the mid‐1990s due to two key enabling advances, availability of complete genome sequences, and mass spectrometry advances that allowed high sensitivity identifications of proteins. Proteome analyses can be broadly categorized into three types of studies: quantitative protein profile comparisons, analysis of protein‐protein interactions, and compositional analysis of simple proteomes or subproteomes such as organelles or large protein complexes. The complexity of different types of proteomes, the merits of targeted versus global proteome studies, and the advantages of alternative separation and analysis technologies are discussed.
CD23+CD21highCD1dhigh B Cells in Inflamed Lymph Nodes Are a Locally Differentiated Population with Increased Antigen Capture and Activation Potential

CD23+CD21highCD1dhigh B cells in inflamed nodes (Bin cells) accumulate in the lymph nodes (LNs) draining inflamed joints of the TNF-α–transgenic mouse model of rheumatoid arthritis and are primarily involved in the significant histological and functional LN alterations that accompany disease exacerbation in this strain. In this study, we investigate the origin and function of Bin cells. We show that adoptively transferred GFP+ sorted mature follicular B (FoB) cells home preferentially to inflamed LNs of TNF-α–transgenic mice where they rapidly differentiate into Bin cells, with a close correlation with the endogenous Bin fraction. Bin cells are also induced in wild-type LNs after immunization with T-dependent Ags and display a germinal center phenotype at higher rates compared with FoB cells. Furthermore, we show that Bin cells can capture and process Ag-immune complexes in a CD21-dependent manner more efficiently than can FoB cells, and they express greater levels of MHC class II and costimulatory Ags CD80 and CD86. We propose that Bin cells are a previously unrecognized inflammation-induced B cell population with increased Ag capture and activation potential, which may facilitate normal immune responses but may contribute to autoimmunity when chronic inflammation causes their accumulation and persistence in affected LNs.
Monomial ideals and independence of IΣ 2 DRAFT

We show that a miniaturised version of Maclagan’s theorem on monomial ideals is equivalent to 1−Con(IΣ2) and classify a phase transition threshold for this theorem. This work highlights the combinatorial nature of Maclagan’s theorem. Monomial ideals play an important role in commutative algebra and algebraic combinatorics. Maclagan’s theorem has several applications in computer algebra (See, for example, [8]), so the logical and combinatorial issues which surround it are of particular interest. We rst determine an upper bound for the miniaturised version of Maclagan’s theorem based on a very short proof of Maclagan’s theorem using Friedman’s adjacent Ramsey theorem. We apply known upper bounds for Friedman’s nite adjacent Ramsey theorem for this part. We provide lower bounds for the miniaturised Maclagan theorem. This proof of independence of IΣ2 is a cleaned up version of the proof in [9]. We nish by determining a sharp phase transition threshold for the miniaturised Maclagan’s theorem. These results complement the study by Aschenbrenner and Pong [3] and the determination of lower bounds in [9]. Furthermore this paper ts into the general ∗Partially supported by the Japan Society for the Promotion of Science (KAKENHI 23340020) and a JSPS postdoctoral fellowship for foreign researchers. This is the pre-peer reviewed version of an article which is in press at Mathematical Logic Quarterly
Antecedents of Employees' Information Security Awareness - Review, synthesis, and Directions for Future Research

Living in a digital age, where all kinds of information are accessible electronically at all times, organizations worldwide struggle to keep their information assets secure. Interestingly, the majority of organizational information systems security (ISS) incidents are the direct or indirect result of human errors. To explore how organizations can defend themselves against harmful ISS behaviour, employees’ information security awareness (ISA) has become a top-priority in research and practice. ISA is referred to as a state of consciousness and knowledge about security issues and is a strong predictor of security compliant behaviour. However, to date knowledge about the factors that are responsible for some employees having a higher level of ISA than others is limited and widely dispersed among multidisciplinary outlets. Therefore, our study provides an extensive review of the literature on ISA’s antecedents with the aim to synthesize the literature and to reveal areas for further research. We analysed 44 publications to discern various institutional, individual, and socio-environmental ISA ante-cedents. Identifying and understanding these factors will be useful for stakeholders interested in improving the effectiveness of awareness strategies, in increasing employees’ ISA and in ultimately lowering the substantial ISS threats for organizations and society.
Comparing primiparous and multiparous mothers in a nurse home visiting prevention program.

BACKGROUND An important yet overlooked feature of prominent prevention programs serving expectant mothers is the exclusion of women with children. This study examines mothers (n = 3,260) participating in a program without parity exclusion criteria, and compares demographic characteristics, risk status, service use, and child maltreatment outcomes. METHODS A longitudinal, prospective study comparing primiparous (n = 1,890) and multiparous (n = 1,370) mothers participating in a nurse home visiting program. Patient groups are compared using bivariate and multivariate methods. RESULTS Comparison by parity shows multiparous mothers had higher cumulative risk scores and individual risk factors related to maternal and child health, behavioral health, and violence exposure. Multiparous mothers were more likely to seek out services themselves and to initiate services later in the postnatal period. A significant trend exists among more children and greater caregiver stress, maternal depression, and child maltreatment. Multivariate models indicate infants of multiparous mothers have a higher risk (hazard ratio = 1.49) for later reports of child maltreatment. CONCLUSIONS As compared with primiparous mothers, multiparous mothers were at higher risk but had similar levels of service use. Programs limited to primiparous mothers are missing a critical opportunity for prevention. Programs serving multiparous mothers should incorporate strategies to directly address caregiver stress and postpartum depression.
DISENTANGLING GENETIC AND PRENATAL SOURCES OF FAMILIAL RESEMBLANCE ACROSS ONTOGENY IN A WILD PASSERINE

Cross‐fostering experiments are widely used by quantitative geneticists to study genetics and by behavioral ecologists to study the effects of prenatal investment. Generally, the effects of genes and prenatal investment are confounded and the interpretation given to such experiments is largely dependent on the interests of the researcher. Using a large‐scale well‐controlled experiment on a wild population of blue tits (Cyanistes caeruleus), we are able to partition variation in body mass across ontogeny into the effects of genes and the effects of between‐clutch variation in egg characteristics. We show that although egg effects are important early in ontogeny they quickly dissipate, suggesting that the genetic interpretation of cross‐fostering experiments may be preferable for many types of trait. However, the heritability of body mass is smaller than has previously been reported. Our results suggest that this is due to a combination of controlling postnatal environmental effects more carefully and accounting for viability selection operating early in ontogeny.