Miracle-dz/UniFAR-FTUs huggingface dataset:
Janus-kinase-2 relates directly to portal hypertension and to complications in rodent and human cirrhosis

Objective Angiotensin II (AngII) activates via angiotensin-II-type-I receptor (AT1R) Janus-kinase-2 (JAK2)/Arhgef1 pathway and subsequently RHOA/Rho-kinase (ROCK), which induces experimental and probably human liver fibrosis. This study investigated the relationship of JAK2 to experimental and human portal hypertension. Design The mRNA and protein levels of JAK2/ARHGEF1 signalling components were analysed in 49 human liver samples and correlated with clinical parameters of portal hypertension in these patients. Correspondingly, liver fibrosis (bile duct ligation (BDL), carbon tetrachloride (CCl4)) was induced in floxed-Jak2 knock-out mice with SM22-promotor (SM22Cre+-Jak2f/f). Transcription and contraction of primary myofibroblasts from healthy and fibrotic mice and rats were analysed. In two different cirrhosis models (BDL, CCl4) in rats, the acute haemodynamic effect of the JAK2 inhibitor AG490 was assessed using microsphere technique and isolated liver perfusion experiments. Results Hepatic transcription of JAK2/ARHGEF1 pathway components was upregulated in liver cirrhosis dependent on aetiology, severity and complications of human liver cirrhosis (Model for End-stage Liver disease (MELD) score, Child score as well as ascites, high-risk varices, spontaneous bacterial peritonitis). SM22Cre+- Jak2f/f mice lacking Jak2 developed less fibrosis and lower portal pressure (PP) than SM22Cre−-Jak2f/f upon fibrosis induction. Myofibroblasts from SM22Cre+-Jak2f/f mice expressed less collagen and profibrotic markers upon activation. AG490 relaxed activated hepatic stellate cells in vitro. In cirrhotic rats, AG490 decreased hepatic vascular resistance and consequently the PP in vivo and in situ. Conclusions Hepatic JAK2/ARHGEF1/ROCK expression is associated with portal hypertension and decompensation in human cirrhosis. The deletion of Jak2 in myofibroblasts attenuated experimental fibrosis and acute inhibition of JAK2 decreased PP. Thus, JAK2 inhibitors, already in clinical use for other indications, might be a new approach to treat cirrhosis with portal hypertension.
Single top quark production at the fermilab tevatron : Threshold resummation and finite-order soft gluon corrections

I present a calculation of threshold soft-gluon corrections to single top-quark production in pp collisions via all partonic processes in the t and s channels and via associated top quark and W boson production. The soft-gluon corrections are formally resummed to all orders, and finite-order expansions of the resummed cross section are calculated through next-to-next-to-next-to-leading-order (NNNLO) at next-to-leading logarithmic (NLL) accuracy. Numerical results for single top-quark production at the Tevatron are presented, including the dependence of the cross sections on the top-quark mass and on the factorization and renormalization scales. The threshold corrections in the t channel are small while in the s channel they are large and dominant. Associated tW production remains relatively minor due to the small leading-order cross section even though the K factors are large.
An Effective Neural Network Model for Graph-based Dependency Parsing

Most existing graph-based parsing models rely on millions of hand-crafted features, which limits their generalization ability and slows down the parsing speed. In this paper, we propose a general and effective Neural Network model for graph-based dependency parsing. Our model can automatically learn high-order feature combinations using only atomic features by exploiting a novel activation function tanhcube. Moreover, we propose a simple yet effective way to utilize phrase-level information that is expensive to use in conventional graph-based parsers. Experiments on the English Penn Treebank show that parsers based on our model perform better than conventional graph-based parsers.
CD5 expression identifies a subset of splenic marginal zone lymphomas with higher lymphocytosis: a clinico-pathological, cytogenetic and molecular study of 24 cases

Background Classically, splenic marginal zone B-cell lymphoma is characterized by the absence of CD5 expression. Cases of apparent splenic marginal zone B-cell lymphoma showing CD5 expression, as diagnosed by blood studies, have been described; however, in the absence of histological evidence, the correct diagnosis of these cases is controversial because of possible confusion with other CD5-positive small B-cell neoplasms. Design and Methods We report a series of 24 CD5-positive, t(11;14)-negative cases of splenic marginal zone B-cell lymphoma diagnosed by flow cytometry studies of blood and histologically proven on spleen sections. Clinical data as well as morphological, immunological, cytogenetic and molecular characteristics were assessed to evaluate the similarities and differences of these cases with those of classical CD5-negative splenic marginal zone B-cell lymphoma. Results The CD5 expression detected in blood by flow cytometry was confirmed in most cases by immunohistochemistry on spleen sections. In general, cases of CD5-positive and CD5-negative splenic marginal zone B-cell lymphoma did not appear different and, in particular, they showed similar karyotypic changes such as 7q deletion, trisomy 3, trisomy 18 and biased IGHV usage (i.e. VH1-2). The main differences were a higher lymphocyte count at diagnosis (8.15×109/L versus 3.90×109/L; P=0.005) and more frequent diffuse bone marrow infiltration (34% versus 8%; P=0.03) in the CD5-positive group. A tendency to a more mutated IGHV status in the CD5 positive cases was observed (80% versus 54.5%; (P=0.11). No significant differences in outcome were found in relation to CD5 expression. Conclusions This study confirms the existence of cases of CD5-positive splenic marginal zone B-cell lymphoma and shows that these cases are closely related to classical splenic marginal zone lymphoma. Whether or not CD5-positive splenic marginal zone B-cell lymphoma constitutes a true subset obviously requires the study of more cases.
Modulation of Spontaneous Brain Activity during Mental Imagery

Magnetic measurements of average power of human alpha and beta activity over the occipital and parietal areas of the scalp reveal spatially selective suppression of the activity of the occipital cortex when abstract figures are briefly presented visually and subjects simply indicate that they saw the figure. However, the duration of the suppression increases markedly when subjects must indicate whether or not they had previously seen the figure. The reaction time is similarly prolonged during the search of visual memory, and is commensurate with the duration of selective suppression of brain activity. It is also demonstrated that alpha activity is not replaced by beta activity during this suppression, but that power in the beta band is also diminished during memory search. Low correlations between the scalp distributions of power in the beta and alpha bands indicate that partly different neuronal populations give rise to activity of these different frequency bands. Since magnetic fields are negligibly affected by intervening bone tissues, dramatic asymmetries in the distribution of alpha activity across the scalps of individuals and the differences in distribution between individuals cannot be ascribed to differences in skull thickness but are due instead to differences in underlying brain anatomy or function. Nevertheless, a common pattern of suppression of alpha activity is observed across subjects during well-controlled cognitive tasks. This implies that the visual system is involved in mental imagery.
Cost analysis of the use of emergency departments for primary care services in Charlotte, North Carolina.

BACKGROUND Patients often inappropriately seek emergency services for ambulatory care-sensitive conditions (ACSCs). The unnecessary use of emergency departments (EDs) is an expensive burden on hospitals and payers. Here, we identify factors influencing ED visits for ACSCs and analyze the costs of such visits for EDs and primary care clinics. METHODS Age, race, sex, and insurance data from 2007 for 3 primary care safety net clinics and 4 EDs in Charlotte, North Carolina, were analyzed using the New York University (NYU) algorithm to identify ACSC diagnoses. Cost analyses used hospital charge data and net margins as surrogates for payer and hospital system costs. RESULTS A total of 113,730 (59.4%) of 191,622 ED visits were for ACSCs. Factors that increased the number of ACSC-related visits included lack of insurance coverage; receipt of Medicaid insurance; age of less than 2 years; African American, Hispanic, or Native American race or ethnicity; and female sex. Charges in the EDs were 320%-728% higher than those in the primary care clinics, allowing for a potential savings of 69%-86% had ACSCs been treated in primary care clinics instead of in EDs. LIMITATIONS The NYU algorithm may have inherent weaknesses in the categorization of ACSC-related visits and the accuracy of cost assignment, especially for vulnerable patients, such as those with comorbidities or those aged less than 2 years. CONCLUSION The majority of conditions treated during outpatient ED visits are treatable in primary care clinics or even preventable. Some groups are at higher risk for inappropriate use of EDs. Solutions to this complex problem will require payers and hospital systems to design and invest in novel targeted interventions.
The origin and evolution of genomic imprinting and viviparity in mammals

Genomic imprinting is widespread in eutherian mammals. Marsupial mammals also have genomic imprinting, but in fewer loci. It has long been thought that genomic imprinting is somehow related to placentation and/or viviparity in mammals, although neither is restricted to mammals. Most imprinted genes are expressed in the placenta. There is no evidence for genomic imprinting in the egg-laying monotreme mammals, despite their short-lived placenta that transfers nutrients from mother to embryo. Post natal genomic imprinting also occurs, especially in the brain. However, little attention has been paid to the primary source of nutrition in the neonate in all mammals, the mammary gland. Differentially methylated regions (DMRs) play an important role as imprinting control centres in each imprinted region which usually comprises both paternally and maternally expressed genes (PEGs and MEGs). The DMR is established in the male or female germline (the gDMR). Comprehensive comparative genome studies demonstrated that two imprinted regions, PEG10 and IGF2-H19, are conserved in both marsupials and eutherians and that PEG10 and H19 DMRs emerged in the therian ancestor at least 160 Ma, indicating the ancestral origin of genomic imprinting during therian mammal evolution. Importantly, these regions are known to be deeply involved in placental and embryonic growth. It appears that most maternal gDMRs are always associated with imprinting in eutherian mammals, but emerged at differing times during mammalian evolution. Thus, genomic imprinting could evolve from a defence mechanism against transposable elements that depended on DNA methylation established in germ cells.
Modulation of Brain Activity after Learning Predicts Long-Term Memory for Words

The acquisition and maintenance of new language information, such as picking up new words, is a critical human ability that is needed throughout the life span. Most likely you learned the word “blog” quite recently as an adult, whereas the word “kipe,” which in the 1970s denoted stealing, now seems unfamiliar. Brain mechanisms underlying the long-term maintenance of new words have remained unknown, albeit they could provide important clues to the considerable individual differences in the ability to remember words. After successful training of a set of novel object names we tracked, over a period of 10 months, the maintenance of this new vocabulary in 10 human participants by repeated behavioral tests and magnetoencephalography measurements of overt picture naming. When naming-related activation in the left frontal and temporal cortex was enhanced 1 week after training, compared with the level at the end of training, the individual retained a good command of the new vocabulary at 10 months; vice versa, individuals with reduced activation at 1 week posttraining were less successful in recalling the names at 10 months. This finding suggests an individual neural marker for memory, in the context of language. Learning is not over when the acquisition phase has been successfully completed: neural events during the access to recently established word representations appear to be important for the long-term outcome of learning.
Deterministic Simulation of Flat-Fading MIMO Wireless Channels Under Non-Isotropic Scattering Conditions

This paper describes a simple methodology for the simulation of flat-fading multiple-input multiple-output (MIMO) wireless propagation channels under non-isotropic scattering conditions. The proposed channel simulator is based on the sum- of-sinusoids (SOS) principle and has been developed under the framework of the geometrical one-ring scattering model. All the simulation parameters are computed in a purely deterministic manner, which results in an ergodic channel simulator. By considering that the angle of arrival (AOA) of the received signal follows the von Mises distribution, we will show that the proposed simulator satisfactorily approximates the channel's time and spatial correlation functions.
Carrier relaxation time modelling of monolayer black phosphorene

Phosphorene as an innovative structure that can be exfoliated similarly to the graphene with a direct, inherent and suitable bandgap presents exceptional prospects for future generations of electronic devices. Phosphorene possess high carrier mobility, therefore, in this work its carrier statistics in the form of monolayer phosphorene in the non-degenerate limit is analytically modelled and the mobility relation with carrier relaxation time is investigated. Energy dispersion relation is used to develop and calculate the required parameters for carrier relaxation time model which is an important parameter in conduction theory. On the other hand, the dependency of carrier velocity and mobility to voltage, normalised Fermi energy and temperature are modelled. Finally, the carrier relaxation time as a function of carrier mobility is modelled and its dependency towards temperature and normalised Fermi energy is discussed. It is shown that the relaxation time is strongly dependent on the carrier mobility which increases by increasing the mobility.
Supplementary Information Supplementary Methods

Measurement site and instrumentation All the measurements were done at the Mace Head atmospheric research station on the west coast of Ireland (53°19' N, 9°54'W) in August-October 2013. Mace Head is known for the strong tidal changes and presence of iodine emitting macroalgae beds consisting of e.g. kelps such as different Laminaria species 14 and other brown algae such as Ascophyllum nodosum and Fucus vesiculosus 34. Mace Head represents of typical North Atlantic rocky shores in terms of the macroalgae exposure times. Instrumentation at the station contained both ion and neutral cluster detecting devices and multiple particle counters. The smallest particles or clusters in the 1.5−3 nm range were detected with two particle size magnifiers (PSM, Airmodus A11, ref. 35). The PSM utilizes supersaturated diethylene glygol vapor to grow even the smallest particles or clusters to a detectable sizes for the condensation particle counter (CPC, Airmodus A20). During this campaign one PSM was set to scan continuously from 1.5 to 3 nm and the other one was set to a constant cut off size of 1.5 nm (based on calibration by negatively charged ammonium sulphate particles). Due to extremely intense new particle formation events, the sample had to be diluted by a factor of up to 50 for the PSM so that the CPC optical counter was able to count the particles accurately. A Neutral cluster and Air Ion Spectrometer (NAIS) was used for measuring total concentration and size distributions of clusters and particles between 2.5 and 40 nm. Naturally-charged ions were detected with an atmospheric pressure interface-time of flight (APi-TOF) mass spectrometer (Tofwerk A.G., ref. 36) that was run in the negative polarity mode detecting negatively charged ions. The APi-TOF inlet flow was set to a constant ~7.5 liters min −1 , from which a 0.8 liters min −1 sample was then introduced to the mass spectrometer through an orifice and two ion guiding quadrupoles. The ions were detected in the high vacuum of the TOF and separated according to their time-of-flights and reported as mass-to-charge (m/z) ratios. The elemental composition of neutral molecules and clusters was analyzed with a CI-APi-TOF (chemical ionization-APi-TOF) that was equipped with a nitrate ion (NO 3 −) based chemical ionization inlet prior to the APi-TOF. The original design of the inlet that minimized wall losses of the sample is described in ref. 37 and the CI-APi-TOF used here for acidic cluster detection is …
Interaction of IL1B and IL1RN polymorphisms, smoking habit, gender, and ethnicity with aggressive and chronic periodontitis susceptibility

Background: Although the interleukin-1 (IL-1) plays a critical role in the pathogenesis of periodontitis, associations between IL1 gene cluster polymorphisms and the disease remains unclear. Aims: To investigate the importance of IL1B-511C>T (rs16944), IL1B +3954C>T (rs1143634), and IL1RN intron 2 variable number tandem repeat (VNTR) (rs2234663) polymorphisms, individually or in combination, as the risk factors of periodontitis in a Southeastern Brazilian population with a high degree of miscegenation. Subjects and Methods: A total of 145 individuals, with aggressive (aggressive periodontitis [AgP], n = 43) and chronic (chronic periodontitis [CP], n = 52) periodontitis, and controls (n = 50) were genotyped by polymerase chain reaction (PCR) (IL1RN intron 2 VNTR) or PCR-restriction fragment length polymorphism (PCR-RFLP) (IL1B-511 C>T and IL1B + 3954C>T) techniques. Statistical Analysis: The independent t-test, Chi-square, and Fisher′s exact tests were used. The SNPStats program was used for haplotype estimation and multiplicative interaction analyses. Results: The IL1B +3954T allele represented risk for CP (odds ratio [OR] = 2.84), particularly in smokers (OR = 4.43) and females (OR = 6.00). The minor alleles IL1RNFNx012 and FNx013 increased the risk of AgP (OR = 2.18), especially the IL1RNFNx012FNx012 genotype among white Brazilians (OR = 7.80). Individuals with the combinations of the IL1B + 3954T and IL1RNFNx012 or FNx013-containing genotypes were at increased risk of developing CP (OR = 4.50). Considering the three polymorphisms (rs16944, rs1143634, and rs2234663), the haplotypes TC2 and CT1 represented risk for AgP (OR = 3.41) and CP (OR = 6.39), respectively. Conclusions: Our data suggest that the IL1B +3954C>T and IL1RN intron 2 VNTR polymorphisms are potential candidates for genetic biomarkers of periodontitis, particularly in specific groups of individuals.
XRD and Photoluminescence Properties of CaSO4:Dy Phosphor Synthesized by New Co-Precipitation Method

This paper presents the luminescence properties of dysprosium (Dy) doped calcium sulfate (CaSO4) phosphor material produced by co-precipitation technique with 0.1 - 0.5 mol% concentration of dopant. The crystallinity of the produced powder was studied using x-ray powder diffraction (XRD). The XRD spectrum shows high purity anhydrite CaSO4 phosphor material produced. The average crystallite size of 74 nm with orthorhombic crystal system was obtained. The luminescence behavior of produced CaSO4: Dy was studied using a photoluminescence (PL) spectrometer. The excitation and emission spectrum peaks associated with defects and vacancies of the phosphor material at claimed crystalline phase. The mixed peaks of excitation and emission that corresponds to micro and nano sized particle was shown for the produced powders. These properties show that the produced powders have wide range of luminescence detection with many electron traps ready for thermoluminescence (TL) information storage.
Semantics for a useful fragment of the situation calculus

In a recent paper, we presented a new logic called ES for reasoning about the knowledge, action, and perception of an agent. Although formulated using modal operators, we argued that the language was in fact a dialect of the situation calculus but with the situation terms suppressed. This allowed us to develop a clean and workable semantics for the language without piggybacking on the generic Tarski semantics for first-order logic. In this paper, we reconsider the relation between ES and the situation calculus and show how to map sentences of ES into the situation calculus. We argue that the fragment of the situation calculus represented by ES is rich enough to handle the basic action theories defined by Reiter as well as Golog. Finally, we show that in the full second-order version of ES, almost all of the situation calculus can be accommodated.
Analysis of LOXL1 polymorphisms in a United States population with pseudoexfoliation glaucoma

Purpose To identify if recently described LOXL1 (lysyl oxidase-like 1) polymorphisms are associated with pseudoexfoliation glaucoma (XFG) in a United States (U.S.) Caucasian patient population. Methods Individuals with XFG were identified using standard clinical examination techniques. TaqMan allelic discrimination assays were used to genotype 13 single nucleotide polymorphisms (SNPs) that tag LOXL1 in Caucasian individuals. The coding region of exon 1 that includes the previously associated SNP, rs1048661, was sequenced. Allele and genotype frequencies were compared between cases and unrelated controls. Results Fifty affected individuals and 235 control individuals were recruited into this study. We replicated the previously reported association of three SNPs (rs1048661, rs2165241, and rs3825942) in our independent XFG population (single SNP p-values were 0.001-0.02). The risk alleles at these three and several other intragenic SNPs are part of an extended XFG-associated LOXL1 haplotype with a frequency of 32.0% in XFG patients and 21.6% in controls. Conclusions We have performed an analysis of LOXL1 and XFG in a United States patient population and have confirmed the strong association previously reported for Icelandic and Swedish samples. However, due to the high frequency of risk alleles in non-XFG individuals, this association should not form the basis of a diagnostic test for XFG. It is likely that additional genetic or environmental factors modulate the penetrance of LOXL1 susceptibility alleles.
Predicting Students Drop Out: A Case Study

The monitoring and support of university freshmen is considered very important at many educational institutions. In this paper we describe the results of the educational data mining case study aimed at predicting the Electrical Engineering (EE) students drop out after the first semester of their studies or even before they enter the study program as well as identifying success-factors specific to the EE program. Our experimental results show that rather simple and intuitive classifiers (decision trees) give a useful result with accuracies between 75 and 80%. Besides, we demonstrate the usefulness of cost-sensitive learning and thorough analysis of misclassifications, and show a few ways of further prediction improvement without having to collect additional data about the students.