Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Active Learning for Named Entity Recognition

Deep neural networks have advanced the state of the art in named entity recognition. However, under typical training procedures, advantages over classical methods emerge only with large datasets. As a result, deep learning is employed only when large public datasets or a large budget for manually labeling data is available. In this work, we show otherwise: by combining deep learning with active learning, we can outperform classical methods even with a significantly smaller amount of training data.
Elastomer biaxial characterization using bubble inflation technique. I: Experimental investigations

The biaxial rheological behavior of materials such as elastomers or polymers can be obtained using a bubble-inflation-technique. A circular membrane is clamped at the rim and expanded under gas pressure. The inflation of the circular membrane is recorded using a CCD video camera and the blowing pressure by a pressure sensor. Then, from elongation and curvature radius measurements at the pole of the bubble, one can deduce equibiaxial stress-strain data. This study describes the optimization of a bubble-inflation rheometer. The most sensitive point of the technique is the estimation of the elongation at the bubble pole, deduced from video camera measurements. A direct measurement of the bubble thickness was performed using a magnetic probe in order to validate rheometer results. Such a validation has evidently never been carried out before. Results of quasi-static equibiaxial characterization of elastomers are presented and analyzed.
Concrete Durability Improvement in a Sulfate Environment Using Bacteria

AbstractUsing carbonate-producing bacteria is a promising novel technique to improvement of concrete characteristics. Durability of concrete in harsh environments such as sulfate exposure has been constantly an important issue. The intention of the current study is evaluation of durability improvement of concrete containing bacteria exposed to sulfate environment. To do so, seven groups of 70-mm concrete prisms were made using two different bacterial strains accompanied with mixing water; the effects of sulfate solution exposure on durability properties of tested specimens including mass variation, volume variation, water absorption, and compressive strength were then determined. Furthermore, seven groups of concrete discs with 100 mm diameter and thickness of 50 mm were prepared from the aforementioned batches to investigate the chloride permeability of bacterial concrete by rapid chloride permeability test (RCPT). The results indicated that bacteria incorporation in concrete reduces mass variation, volu.
Impact of tropical land convection on the water vapour budget in the tropical tropopause layer

Abstract. The tropical deep overshooting convection is known to be most intense above continental areas such as South America, Africa, and the maritime continent. However, its impact on the tropical tropopause layer (TTL) at global scale remains debated. In our analysis, we use the 8-year Microwave Limb Sounder (MLS) water vapour (H2O), cloud ice-water content (IWC), and temperature data sets from 2005 to date, to highlight the interplays between these parameters and their role in the water vapour variability in the TTL, and separately in the northern and southern tropics. In the tropical upper troposphere (177 hPa), continents, including the maritime continent, present the night-time (01:30 local time, LT) peak in the water vapour mixing ratio characteristic of the H2O diurnal cycle above tropical land. The western Pacific region, governed by the tropical oceanic diurnal cycle, has a daytime maximum (13:30 LT). In the TTL (100 hPa) and tropical lower stratosphere (56 hPa), South America and Africa differ from the maritime continent and western Pacific displaying a daytime maximum of H2O. In addition, the relative amplitude between day and night is found to be systematically higher by 5–10% in the southern tropical upper troposphere and 1–3% in the TTL than in the northern tropics during their respective summer, indicative of a larger impact of the convection on H2O in the southern tropics. Using a regional-scale approach, we investigate how mechanisms linked to the H2O variability differ in function of the geography. In summary, the MLS water vapour and cloud ice-water observations demonstrate a clear contribution to the TTL moistening by ice crystals overshooting over tropical land regions. The process is found to be much more effective in the southern tropics. Deep convection is responsible for the diurnal temperature variability in the same geographical areas in the lowermost stratosphere, which in turn drives the variability of H2O.
The Efficacy of a Short Education Program and a Short Physiotherapy Program for Treating Low Back Pain in Primary Care: A Cluster Randomized Trial

Study Design. Cluster randomized clinical trial. Objective. To assess the efficacy of a short education program and short physiotherapy program for treating low back pain (LBP) in primary care. Summary of Background Data. There is sparse evidence on the effectiveness of education and physiotherapy programs that are short enough to be feasible in primary care. Methods. Sixty-nine primary care physicians were randomly assigned to 3 groups and recruited 348 patients consulting for LBP; 265 (79.8%) were chronic. All patients received usual care, were given a booklet and received a consistent 15 minutes group talk on health education, which focused on healthy nutrition habits in the control group, and on active management for LBP in the “education” and “education + physiotherapy” groups. Additionally, in the “education + physiotherapy” group, patients were given a second booklet and a 15-minute group talk on postural hygiene, and 4 one-hour physiotherapy sessions of exercise and stretching which they were encouraged to keep practicing at home. The main outcome measure was improvement of LBP-related disability at 6 months. Patients' assessment and data analyses were blinded. Results. During the 6-month follow-up period, improvement in the “control” group was negligible. Additional improvement in the “education” and “education + physiotherapy” groups was found for disability (2.0 and 2.2 Roland Morris Questionnaire points, respectively), LBP (1.8 and 2.10 Visual Analogue Scale points), referred pain (1.3 and 1.6 Visual Analogue Scale points), catastrophizing (1.6 and 1.8 Coping Strategies Questionnaire points), physical quality of life (2.9 and 2.9 SF-12 points), and mental quality of life (3.7 and 5.1 SF-12 points). Conclusion. The addition of a short education program on active management to usual care in primary care leads to small but consistent improvements in disability, pain, and quality of life. The addition of a short physiotherapy program composed of education on postural hygiene and exercise intended to be continued at home, increases those improvements, although the magnitude of that increase is clinically irrelevant.
Use of Supplementary Cementing Materials to Increase the Resistance to Chloride Ion Penetration of Concretes Cured at Elevated Temperatures

It has long been known that elevated curing temperatures, while accelerating the early strength gain of concrete, reduce the ultimate strength. Recent research has shown that elevated curing temperatures can also reduce the resistance to chloride diffusion of plain portland cement concretes. This paper describes an investigation of the chloride penetration of 0.40 and 0.50 water-cement ratio (w/c) concretes containing either 5 percent silica fume or 30 percent blast furnace slag (substitution by mass) cured at elevated temperatures. Plain portland cement concretes were used as controls. The concretes were cured at constant temperatures of 23, 50, or 70 deg C to a degree of hydration of approximately 70 percent. Supplemental tests were performed on concretes cured overnight using a steam-curing regime. Both the silica fume and slag concretes performed better than the controls in these tests.
Stability Analysis of Sliding–Grazing Phenomenon in Dry-Friction Oscillator Using Takagi–Sugeno Fuzzy Approach

Dry-friction oscillators are mechanical systems with dry friction and stick-slip vibrations. In the context of control theory, the stability analysis of this type of dynamical systems is important since they exhibit non-smooth bifurcations, or most famously a sliding-grazing bifurcation inducing abrupt chaos. This paper develops a Lyapunovbased framework to study the so-called structural stability of the system, predicting the onset of such unique bifurcations. To achieve this, the non-linear system is first represented as a non-smooth Takagi-Sugeno (TS) fuzzy model, and the structural stability is then formulated as Linear Matrix Inequalities (LMI) feasibility problems with less conservative formulation. Solving the resulting LMI problem, the onset of sliding-grazing bifurcation can be accurately predicted.
Comparison of European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Etest Methods with the CLSI Broth Microdilution Method for Echinocandin Susceptibility Testing of Candida Species

ABSTRACT The antifungal broth microdilution (BMD) method of the European Committee on Antibiotic Susceptibility Testing (EUCAST) and the Etest agar diffusion method were compared with the Clinical and Laboratory Standards Institute (CLSI) BMD method M27-A3 for anidulafungin, caspofungin, and micafungin susceptibility testing of 133 clinical isolates of Candida species. The isolates were characterized for the presence or absence of fks1 and/or fks2 gene mutations and included 34 isolates of C. glabrata (4 mutant strains), 32 of C. albicans (1 mutant strain), 25 of C. parapsilosis, 19 of C. guilliermondii, 12 of C. tropicalis (2 mutant strains), and 11 of C. krusei. Excellent essential agreement (EA; within 2 dilutions) between the CLSI and EUCAST and CLSI and Etest MIC results was observed. The overall EA between the EUCAST and CLSI results ranged from 89.5% (caspofungin) to 99.2% (micafungin), whereas the EA between the Etest and CLSI results ranged from 90.2% (caspofungin) to 93.2% (anidulafungin). The categorical agreement (CA) between methods for each antifungal agent was assessed using previously determined epidemiological cutoff values (ECVs). Excellent CA (>90%) was observed for all comparisons between the EUCAST and CLSI results with the exceptions of C. glabrata and caspofungin (85.3%) and C. krusei and caspofungin (54.5%). The CA between the Etest and CLSI results was also excellent for all comparisons, with the exception of C. krusei and caspofungin (81.8%). All three methods were able to differentiate wild-type (WT) strains from those with fks mutations. With anidulafungin as the test reagent, the CLSI method identified 5 of 7 mutant strains, whereas the EUCAST method and the Etest identified 6 of 7 mutant strains. With either caspofungin or micafungin as the test reagent, the CLSI method identified all 7 mutant strains and the EUCAST method identified 6 of 7 mutant strains. The Etest identified all 7 mutant strains using caspofungin as the reagent. All three test methods showed a high level of agreement and of ability to distinguish fks mutant strains of Candida species from WT strains using each of the echinocandins.
pS2 (TFF1) expression in prostate carcinoma: correlation with steroid receptor status  

pS2 or TFF1 is a member of the trefoil factor family, which is distributed throughout the gastrointestinal tract in both normal and diseased tissues. It is also considered to be one of the major estrogen‐regulated proteins and an indicator of estrogen receptor (ER) functionality. pS2 has previously been investigated in benign and malignant prostate lesions with little information about its relationship to steroid receptor status. Our purpose was to correlate pS2 expression with steroid receptor status (ER alpha and progesterone receptor (PR)) and other pathologic variables in prostate carcinoma. 15 benign prostate hyperplasia (BPH) and 47 prostate carcinoma cases were investigated by means of immunohistochemistry for pS2, ER and PR expression. 80% of BPH showed pS2 cytoplasmic immunoreactivity in hyperplastic acini and about half of these cases also exhibited nuclear staining decorating basal or both basal and luminal nuclei. pS2 was highly expressed in prostate carcinoma (91.4%) with both cytoplasmic and nuclear patterns of staining. The latter pattern was significantly associated with carcinoma having a low Gleason score (p=0.02). pS2 lacked any significant correlation with steroid receptor status, stage or grade. Univariate survival analysis revealed a significant impact of stage (p=0.03) and nodal status (p<0.0001) on patient outcome. The diagnostic value of pS2 expression in prostate carcinoma validated 74.19% accuracy, 91.48% sensitivity and 78.18% positive predictive value. The high sensitivity of pS2 expression in prostate carcinoma could make it a suitable marker for diagnosis of prostate carcinoma, especially in metastatic cases of unknown origin. The absence of correlation and dissimilarity in immunolocalization between pS2 and ER alpha leads to the assumption that ER alpha could not be the regulatory protein for pS2 and may raise questions about the functionality of ER alpha in prostate. The nuclear pattern of pS2 immunoreactivity either in benign or malignant prostatic lesions is similar to the published data on ER beta distribution and could also identify a subset of carcinoma patients with a favorable prognosis.
Age-related loss of the responsiveness of the tuberoinfundibular dopaminergic neurons to prolactin in the female rat.

In the old female rat the previous findings of a sustained reduction of the secretory activity of the hypothalamic tuberoinfundibular dopaminergic (TIDA) neurons associated with a persistent hyperprolactinemia as well as the observation of a failure of the prolactin (PRL) short-loop feedback mechanism have been suggestive of an age-related loss of the responsiveness of the TIDA neurons to the stimulatory action of PRL. Yet the existence of significant impairments in the capacity of the neurons to respond to PRL could not be demonstrated in an earlier study using multiparous old rats in constant estrus compared to young nulliparous estrous rats. In the present study we have readdressed the issue using nulliparous old rats (24-26 months) compared to virgin young rats (4-5 months); two sets of old rats were studied which displayed distinct senile reproductive states, namely persistent diestrus or repetitive pseudopregnancy, and they were compared to young rats in diestrus or in repetitive pseudopregnancy, respectively. The secretory activity of the TIDA neurons was evaluated by measurement of dopamine biosynthesis in the neurons (DOPA accumulation in the median eminence after decarboxylase inhibition) and dopamine release into hypophysial portal blood, and PRL influence on the activity of the TIDA neurons was studied after repeated s.c. administrations of ovine PRL (oPRL) or the solvent vehicle. A reduced activity of the TIDA neurons was observed in both groups of nulliparous aged rats compared to their respective young control group. (ABSTRACT TRUNCATED AT 250 WORDS)
Genome-wide functional characterization of putative peroxidases in the head blight fungus Fusarium graminearum.

Reactive oxygen species (ROS) are associated with various developmental processes and host-pathogen interactions in pathogenic fungi. Peroxidases are a group of ROS-detoxifying enzymes that are involved in the oxidative stress response and in a variety of physiological processes. In this study, we performed a genome-wide functional characterization of putative peroxidase genes in Fusarium graminearum, a head blight pathogen of cereal crops. We identified 31 putative peroxidase genes and generated deletion mutants for these genes. Twenty-six of the deletion mutants showed developmental phenotypes indistinguishable from that of the wild-type, and five deletion mutants exhibited phenotypic changes in at least one phenotypic category. Four deletion mutants, fca6, fca7, fpx1 and fpx15, showed increased sensitivity to extracellular H2 O2 . Deletion mutants of FCA7 also exhibited reduced virulence and increased trichothecene production compared with those of the wild-type strain, suggesting that Fca7 may play an important role in the host-pathogen interaction in F. graminearum. To identify the transcription factors (TFs) regulating FCA6, FCA7, FPX1 and FPX15 in response to oxidative stress, we screened an F. graminearum TF mutant library for growth in the presence of H2 O2 and found that multiple TFs co-regulated the expression of FCA7 under oxidative stress conditions. These results demonstrate that a complex network of transcriptional regulators of antioxidant genes is involved in oxidative stress responses in this fungus. Moreover, our study provides insights into the roles of peroxidases in developmental processes and host-pathogen interactions in plant-pathogenic fungi.
Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection

Abstract Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high-depth whole-genome sequencing data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean ×68 depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats. Among the 9342 RIPs, 4828 were located in gene regions and 5 were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but an approximately neutral selection for Alu elements based on the frequency spectrum of RIPs. SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population, and it should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof of concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms.
Wet-season spatial variability in N 2 O emissions from a tea field in subtropical central China

Abstract. Tea fields emit large amounts of nitrous oxide (N2O) to the atmosphere. Obtaining accurate estimations of N2O emissions from tea-planted soils is challenging due to strong spatial variability. We examined the spatial variability in N2O emissions from a red-soil tea field in Hunan Province, China, on 22 April 2012 (in a wet season) using 147 static mini chambers approximately regular gridded in a 4.0 ha tea field. The N2O fluxes for a 30 min snapshot (10:00–10:30 a.m.) ranged from −1.73 to 1659.11 g N ha−1 d−1 and were positively skewed with an average flux of 102.24 g N ha−1 d−1. The N2O flux data were transformed to a normal distribution by using a logit function. The geostatistical analyses of our data indicated that the logit-transformed N2O fluxes (FLUX30t) exhibited strong spatial autocorrelation, which was characterized by an exponential semivariogram model with an effective range of 25.2 m. As observed in the wet season, the logit-transformed soil ammonium-N (NH4Nt), soil nitrate-N (NO3Nt), soil organic carbon (SOCt) and total soil nitrogen (TSNt) were all found to be significantly correlated with FLUX30t (r = 0.57–0.71, p
Fronto‐temporal connectivity predicts cognitive empathy deficits and experiential negative symptoms in schizophrenia

Impaired cognitive empathy is a core social cognitive deficit in schizophrenia associated with negative symptoms and social functioning. Cognitive empathy and negative symptoms have also been linked to medial prefrontal and temporal brain networks. While shared behavioral and neural underpinnings are suspected for cognitive empathy and negative symptoms, research is needed to test these hypotheses. In two studies, we evaluated whether resting‐state functional connectivity between data‐driven networks, or components (referred to as, inter‐component connectivity), predicted cognitive empathy and experiential and expressive negative symptoms in schizophrenia subjects. Study 1: We examined associations between cognitive empathy and medial prefrontal and temporal inter‐component connectivity at rest using a group‐matched schizophrenia and control sample. We then assessed whether inter‐component connectivity metrics associated with cognitive empathy were also related to negative symptoms. Study 2: We sought to replicate the connectivity‐symptom associations observed in Study 1 using an independent schizophrenia sample. Study 1 results revealed that while the groups did not differ in average inter‐component connectivity, a medial‐fronto‐temporal metric and an orbito‐fronto‐temporal metric were related to cognitive empathy. Moreover, the medial‐fronto‐temporal metric was associated with experiential negative symptoms in both schizophrenia samples. These findings support recent models that link social cognition and negative symptoms in schizophrenia. Hum Brain Mapp 38:1111–1124, 2017. © 2016 Wiley Periodicals, Inc.
Regulation of a human cytomegalovirus immediate-early gene (US3) by a silencer-enhancer combination

The US3 open reading frame of human cytomegalovirus (HCMV) is transcribed at immediate-early (IE) times after infection. Upstream of the US3 promoter, between -84 and -259 bp relative to the transcription start site, there are five copies of an 18-bp repeat, referred to as 5R2. Between -340 and -560 bp there are seven copies of a 10-bp dyad repeat, referred to as 7R1. We investigated the roles of these repeats in transcription from the US3 promoter in human foreskin fibroblast or HeLa cells. In transient transfection assays, the region containing 5R2 up-regulated transcription and was responsive to the p65 subunit of NF-kappa B. The DNA region containing 7R1 down-regulated transcription from either the US3 promoter or a heterologous promoter in a position- and orientation-independent manner. Mutational analysis and transient transfections indicated that DNA containing the 10-bp dyad or one-half of the dyad was sufficient to cause repression of downstream gene expression. DNA probes containing one or more copies of the pentanucleotide sequence TGTCG specifically bound cellular proteins, as demonstrated by electrophoretic mobility shift assays and cold-competition electrophoretic mobility shift assays. Two different DNA-protein complexes were detected with DNA probes containing one or two copies of the pentanucleotide. In HCMV-infected cell nuclear extracts, one of the DNA-protein complexes was present in amounts inversely proportional to the amount of US3 transcription. Its formation was affected by dephosphorylation of the DNA-binding protein(s). Transient dephosphorylation of the cellular repressor protein may occur during HCMV infection. Repression of US3 transcription may relate to the number of pentanucleotides and the cellular proteins that bind to it. Twenty-one copies of a TRTCG motif (R = purine) were found clustered upstream of the US3 gene and also in the modulator upstream of the HCMV IE1 and IE2 genes.