Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic and Transcriptional Modifications in Repetitive Elements in Petrol Station Workers Exposed to Benzene and MTBE

Benzene, a known human carcinogen, and methyl tert-butyl ether (MTBE), not classifiable as to its carcinogenicity, are fuel-related pollutants. This study investigated the effect of these chemicals on epigenetic and transcriptional alterations in DNA repetitive elements. In 89 petrol station workers and 90 non-occupationally exposed subjects the transcriptional activity of retrotransposons (LINE-1, Alu), the methylation on repeated-element DNA, and of H3K9 histone, were investigated in peripheral blood lymphocytes. Median work shift exposure to benzene and MTBE was 59 and 408 µg/m3 in petrol station workers, and 4 and 3.5 µg/m3, in controls. Urinary benzene (BEN-U), S-phenylmercapturic acid, and MTBE were significantly higher in workers than in controls, while trans,trans-muconic acid (tt-MA) was comparable between the two groups. Increased BEN-U was associated with increased Alu-Y and Alu-J expression; moreover, increased tt-MA was associated with increased Alu-Y and Alu-J and LINE-1 (L1)-5′UTR expression. Among repetitive element methylation, only L1-Pa5 was hypomethylated in petrol station workers compared to controls. While L1-Ta and Alu-YD6 methylation was not associated with benzene exposure, a negative association with urinary MTBE was observed. The methylation status of histone H3K9 was not associated with either benzene or MTBE exposure. Overall, these findings only partially support previous observations linking benzene exposure with global DNA hypomethylation.
Sublingual administration of 2-hydroxyethyl methacrylate enhances antibody responses to co-administered ovalbumin and Streptococcus mutans

Abstract Objective: The oral mucosa of patients undergoing dental procedures is often exposed to residual monomers leaking from incompletely cured acrylic resins. We investigated whether 2-hydroxyethyl methacrylate (HEMA) monomers applied to the sublingual mucosa in mice modulate the antibody responses towards co-administered ovalbumin (OVA) or live oral bacteria. Material and methods: OVA, live mouse oral commensal Lactobacillus murinus or live human oral commensal Streptococcus mutans were administered sublingually with or without HEMA to BALB/c mice on four weekly occasions. One week after the last administration, the experiment was terminated and serum antibody levels were analyzed using ELISA. Results: Significantly increased IgG and IgE anti-OVA antibody activity was found in the sera from mice immunized with OVA together with HEMA, as compared to mice immunized with OVA alone. Likewise, S. mutans together with HEMA induced an IgG anti-S. mutans antibody response that was significantly higher than the antibody response detected after application of S. mutans alone. No IgG anti-L. murinus antibody response was detected in mice immunized with L. murinus together with HEMA, as compared to the background activity. Conclusions: We report that HEMA monomers have adjuvant properties when sublingually administered in combination with OVA or S. mutans.
The Functional Oligomeric State of Tegument Protein GP41 Is Essential for Baculovirus Budded Virion and Occlusion-Derived Virion Assembly

ABSTRACT gp41, one of the baculovirus core genes, encodes the only recognized tegument (O-glycosylated) protein of the occlusion-derived virion (ODV) phenotype so far. A previous study using a temperature-sensitive Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) mutant showed that GP41 plays a crucial role in budded virion (BV) formation. However, the precise function of GP41 in the baculovirus replication cycle remains unclear. In this study, AcMNPV GP41 was found to accumulate around the ring zone (RZ) region within the infected nucleus and finally assembled into both BVs and ODVs. Deletion of gp41 from the AcMNPV genome showed that BVs were no longer formed and ODVs were no longer assembled, suggesting the essential role of this gene in baculovirus virion morphogenesis. In infected cells, besides the 42-kDa monomers, dimers and trimers were detected under nonreducing conditions, whereas only trimeric GP41 forms were selectively incorporated into BVs or ODVs. Mutations of all five cysteines in GP41 individually had minor effects on GP41 oligomer formation, albeit certain mutations impaired infectious BV production, suggesting flexibility in the intermolecular disulfide bonding. Single mutations of key leucines within two predicted leucine zipper-like motifs did not interfere with GP41 oligomerization or BV and ODV formation, but double leucine mutations completely blocked oligomerization of GP41 and progeny BV production. In the latter case, the usual subcellular localization, especially RZ accumulation, of GP41 was abolished. The above findings clearly point out a close correlation between GP41 oligomerization and function and therefore highlight the oligomeric state as the functional form of GP41 in the baculovirus replication cycle. IMPORTANCE The tegument, which is sandwiched between the nucleocapsid and the virion envelope, is an important substructure of many enveloped viruses. It is composed of one or more proteins that have important functions during virus entry, replication, assembly, and egress. Unlike another large DNA virus (herpesvirus) that encodes an extensive set of tegument components, baculoviruses very likely exploit the major tegument protein, GP41, to execute functions in baculovirus virion morphogenesis and assembly. However, the function of this O-glycosylated baculovirus tegument protein remains largely unknown. In this study, we identified trimers as the functional structure of GP41 in baculovirus virion morphogenesis and showed that both disulfide bridging and protein-protein interactions via the two leucine zipper-like domains are involved in the formation of different oligomeric states. This study advances our understanding of the unique viral tegument protein GP41 participating in the life cycle of baculoviruses.
Intensive care nurses' experiences of providing end-of-life care after treatment withdrawal: a qualitative study.

AIMS AND OBJECTIVES To explore the experiences of intensive care nurses who provided end-of-life care to adult patients and their families after a decision had been taken to withdraw treatment. BACKGROUND End-of-life care following treatment withdrawal is a common phenomenon in intensive care. Less is known about nurses' experiences of providing care for the dying patient and their family in this context, when compared to specialist palliative care. DESIGN Descriptive exploratory qualitative study. METHODS A purposive sample of 13 intensive care nurses participated in a semistructured face-to-face interview. Transcribed data were analysed using the principles of interpretative phenomenological analysis. RESULTS The essence of nurses' experiences of providing end-of-life care after the withdrawal of treatment was interpreted as 'doing the best to facilitate a comfortable and dignified death'. Four master themes included the following: caring for the dying patient and their family; providing and encouraging presence; reconnecting the patient and family; and dealing with emotions and ambiguity. Uncertainties were evident on processes and actions involved in treatment withdrawal, how to reconnect patients and their family effectively and how to reduce the technological environment. CONCLUSIONS Providing end-of-life care after a decision has been taken to withdraw treatment was a common aspect of intensive care. It was evident that nurses were doing their utmost to support patients and families at the end of life, despite the multiple challenges they faced. RELEVANCE TO CLINICAL PRACTICE The interpretive findings from this study should assist intensive care unit nurses to better understand and develop their role in providing high-quality end-of-life care after treatment withdrawal. Practice guidelines should be developed to reduce ambiguity and support the delivery of high-quality care for adults as they approach the final stages of life in intensive care units.
The solar neighborhood age-metallicity relation - Does it exist?

We test the hypothesis that the spread in the age-metallicity plot of the solar neighborhood is due to a mixture of stars belonging to kinematically different sub-populations of the Galactic disk, i.e., the thin and the thick disk. We use a kinematic subsample of similar to 600 stars from a sample of similar to 6000 dwarf and subgiant stars from the Hipparcos catalog. All of these stars have a full set of stellar parameters determined, including good ages. We find that a significant spread in [Me/H] is present in both kinematic populations, especially at large stellar ages. This implies that a simple one-to-one relation between ages and metallicities is not possible. In fact, there are stars that are-truly old and at the same time have [Me/H] > 0.2 dex. (Less)
Effects of different amylose to amylopectin ratios on rumen fermentation and development in fattening lambs

Objective The objective of this experiment was to examine the effects of different amylose/amylopectin ratios on rumen fermentation and development of fattening lambs. Methods Forty-eight 7-day-old male Small-tailed Han sheep×Northeast fine wool sheep were randomly assigned to four treatments of dietary amylose/amylopectin ratios (0.12, 0.23, 0.24, and 0.48 in tapioca starch, corn starch, wheat starch and pea starch diets, respectively). Three lambs from each treatment were slaughtered at 21, 35, 56, and 77 days of age to determine the rumen fermentation and development. Results Compared with tapioca starch diet, the pea starch diet significantly increased the concentration of ammonia nitrogen in the ruminal fluid of lambs but significantly decreased the bacterial protein content. At 56 and 77 d, the rumen propionate concentration tended to be greatest in the tapioca starch group than in other groups. The rumen butyrate concentration was the greatest in lambs fed on pea starch compared with those fed on other starch diets. Furthermore, the pea starch diet significantly stimulated rumen development by increasing the papillae height, width and surface area in the rumen ventral or dorsal locations in lambs. However, different amylose/amylopectin ratios diets did not significantly affect the feed intake, body weight, average daily gain, the relative weight and capacity of the rumen in lambs with increasing length of trial periods. Conclusion Lambs early supplemented with a high amylose/amylopectin ratio diet had favourable morphological development of rumen epithelium, which was not conducive to bacterial protein synthesis.
The Field Validity of Static-99/R Sex Offender Risk Assessment Tool in California

Policies that differentially apply to sexual offenders at different risk levels require defensible procedures for classifying offenders into risk categories. The current study examines the reliability and validity of Static-99 and Static-99R sexual offender risk assessment tools as implemented in the State of California. California is a valuable case study because it is a large jurisdiction that has devoted considerable resources to the implementation of risk tools. In Study 1, 55 corrections and probation officers scored Static-99R for 14 common cases. Overall, rater reliability was acceptable (intraclass correlation [ICC] .78), with higher reliability found for experienced scorers (ICC .85) than less experienced scorers (ICC .71). In the second study, the predictive ability of Static-99 and Static-99R was examined in a prospective study of 475 randomly selected adult males released in 2006 –2007 and followed for 5 years. Static-99/R scores were strongly related to subsequent sexual recidivism (areas under the curve .80). As well, there was acceptable fit between the expected and observed recidivism rates. These results suggest that it is possible to implement empirically derived risk assessment tools in large jurisdictions without degrading predictive accuracy.
Design of strictly positive real, fixed-order dynamic compensators

The authors present sufficient conditions for the design of strictly positive real (SPR), fixed-order dynamic compensators. The primary motivation for designing SPR compensators is for application to positive real (PR) plants. When an SPR compensator is connected to a PR plant in a negative feedback configuration, the closed loop is guaranteed stable for arbitrary plant variations as long as the plant remains PR. Equations that are a modified form of the optimal projection equations, with the separation principle not holding in either the full- or reduced-order case, are given. A solution to the design equations is shown to exist when the plant is PR (or just stable). Finally, the closed-loop system consisting of a PR plant and an SPR compensator is shown to be S-structured Lyapunov stable. <<ETX>>
Modeling Evolving Behaviors in Ant Colonies

Modeling societies of individuals is a challenging task increasingly attracting the interest of the Machine Learning community. In ant colonies, individuals have the same physical attitudes and, in principle, can assume any role the social environment requires. For he biologist understanding the complex dynamics ruling a colony is hard due to the difficulty of collecting and classifying long term ant activities. Here we present a novel approach for analyzing activity logs from an ant colony using an RFID environment. A semi-automated algorithm for segmenting traces and discovering the role played by each individual during the observation phase is described. A Structured Hidden Markov Model was used to build the model of single individual activities. Then, the global profile of the colony was traced during the emigration from one nest to another. The method provided significant information concerning the social dynamics of ant colonies.
Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains

Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo. Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo. Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH–S-transferase–C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST–C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems.
The emerging role of the intestine in metabolic diseases

The intestine is an important metabolic organ that has gained attention in recent years for the newly identified role that it plays in the pathophysiology of various metabolic diseases including obesity, insulin resistance and diabetes. Recent insights regarding the role of enteroendocrine hormones, such as GIP, GLP-1, and PYY in metabolic diseases, as well as the emerging role of the gut microbial community and gastric bypass bariatric surgeries in modulating metabolic function and dysfunction have sparked a wave of interest in understanding the mechanisms involved, in an effort to identify new therapeutics and novel regulators of metabolism. This review summarizes the current evidence that the gastrointestinal tract has a key role in the development of obesity, inflammation, insulin resistance and diabetes and discusses the possible players that can be targeted for therapeutic intervention.
Monetary Policy Activism and Price Responsiveness to Aggregate Shocks under Rational Inattention

This paper presents a general equilibrium model that is consistent with recent empirical evidence showing that the U.S. price level and inflation are much more responsive to aggregate technology shocks than to monetary policy shocks. The model of this paper builds on recent work by Mackowiak and Wiederholt (2009), who show that models of endogenous attention allocation deliver prices to be more responsive to more volatile shocks as, everything else being equal, firms pay relatively more attention to more volatile shocks. In fact, according to the U.S. data, aggregate technology shocks are more volatile than monetary policy shocks inducing in this paper, firms to pay more attention to the former than to the latter. However, most important, this work adds to the literature by showing that the ability of the model of this paper to account for observed price dynamics crucially depends on monetary policy. In particular, this paper shows how interest rate feedback rules affect the incentives faced by firms in allocating attention. A policy rate responding more actively to expected inflation and output fluctuations induces firms to pay relatively more attention to more volatile shocks. This new mechanism of transmission of monetary policy helps rationalizing the observed behavior of prices in response to technology and monetary policy shocks, and implies novel predictions about the impact of changes in Taylor rules coefficients on economic fluctuations.
Prostate stem cell antigen gene is expressed in islets of pancreas

Prostate stem cell antigen (PSCA) is a glycosylphosphatidylinositol-anchored cell surface antigen with an organ-dependent expression pattern in cancers; e.g., up-regulated in prostate cancer and down-regulated in gastric cancer. Previously it was reported that PSCA is not expressed in the normal pancreas but aberrantly expressed in pancreatic cancer. In this present study, we identified PSCA expression in islets of the pancreas by immunohistochemistry, which was co-localized with four islet-cell markers: insulin, glucagon, somatostatin and pancreatic polypeptide. In our investigation of the transcription start site of PSCA, we found a non-coding splicing variant of PSCA as well as authentic PSCA transcripts in mRNA samples from a normal pancreas. Both the transcripts were also identified in several pancreatic cancer cell lines. We previously reported that PSCA expression is correlated to the methylation status of the enhancer region in gastric and gallbladder cancer cell lines but not in pancreatic cancer cell lines, suggesting that PSCA expression is regulated in a diff erent mode in pancreatic cancer from that in gastric and gallbladder cancers.
Flexible word meaning in embodied agents

Learning the meanings of words requires coping with referential uncertainty – a learner hearing a novel word cannot be sure which aspects or properties of the referred object or event comprise the meaning of the word. Data from developmental psychology suggest that human learners grasp the important aspects of many novel words after just a few exposures, a phenomenon known as fast mapping. Traditionally, word learning is viewed as a mapping task, in which the learner has to map a set of forms onto a set of pre-existing concepts. We criticise this approach and argue instead for a flexible nature of the coupling between form and meanings as a solution to the problem of referential uncertainty. We implemented and tested the model in populations of humanoid robots that play situated language games about objects in their shared environment. Results show that the model can handle an exponential increase in uncertainty and allows scaling towards very large meaning spaces, while retaining the ability to grasp an operational meaning almost instantly for a great number of words. In addition, the model captures some aspects of the flexibility of form-meaning associations found in human languages. Meanings of words can shift between being very specific (names) and general (e.g. ‘small’). We show that this specificity is biased not by the model itself but by the distribution of object properties in the world.
The effect of purified Quercus cortex extract on biochemical parameters of organism and productivity of healthy broiler chickens

Aim: Modern methods of producing poultry meat without the use of antibiotics are known, and it is possible to achieve the desired conditions, including the use of herbal preparations. In addition, it is known that metabolites of medicinal plants are inhibitors of the quorum sensing system in bacteria. The aim of the present study was to determine the effect of Quercus cortex extract in a reduced dose on the productivity and body state of healthy chicken broilers. Materials and Methods: For the experiment, 120 heads of 7-day-old healthy broiler chickens were selected, and they were divided into four groups (n=30, 3 replicates of 10 birds in each group) by the analog method. The composition of diets of the experimental Groups I and II additionally included Q. cortex extract and Groups II and III included an enzyme preparation containing glucoamylase and concomitant cellulolytic enzymes. The following methods of study were used; gas chromatography–mass spectrometry, mass spectrometry and atomic emission spectrometry, and hematological analysis. Results: It was established that the increase in live weight of broiler chickens in experimental groups exceeded the analogous indicator in the control group by 3.1-16.6%, and feed intake within the entire experimental period increased by 2.6-15.4%, against a background of decreasing feed consumption for a weight gain of 1 kg of live weight (by 3.7-9.2%). There was an increase in iron concentration in blood of broiler chickens in Groups I and II (7.8-11.8%), in liver (23.7-92.4%, p≤0.05), and in spleen (53.9-77.7%, р≤0.05) against the background of a decrease in muscle tissue. A decreased content of monocytes and granulocytes was found, especially in experimental Group I. Conclusion: In the experiment, it was shown for the first time that the inclusion of Q. cortex extract in an enzyme-containing diet (anti-quarantine substances) was found to increase the productivity of poultry.
Import Demands For U.S. Fresh Grapefruit: Effect Of U.S. Promotion Programs And Trade Policies Of Importing Nations

Abstract This study estimated import demands for U.S. fresh grapefruit in Japan, France, Canada, and the Netherlands. Historically, these nations have imported about 90 percent of U.S. grapefruit exports. Four import demand functions were specified and estimated by joint generalized least squares based on the sample period 19691 to 1988IV. Results show that U.S. FOB price, per capita income of importing countries, exchange rates, price of substitutes, U.S. grapefruit promotion programs, and removal of trade restrictions have had an important effect on U.S. fresh grapefruit exports. Analyses suggest that U.S. producers can effectively promote fresh grapefruit in foreign markets, and that trade concessions have an important influence on grapefruit exports.