Miracle-dz/UniFAR-FTUs huggingface dataset:
Structured Prediction via Learning to Search under Bandit Feedback

We present an algorithm for structured prediction under online bandit feedback. The learner repeatedly predicts a sequence of actions, generating a structured output. It then observes feedback for that output and no others. We consider two cases: a pure bandit setting in which it only observes a loss, and more fine-grained feedback in which it observes a loss for every action. We find that the fine-grained feedback is necessary for strong empirical performance, because it allows for a robust variance-reduction strategy. We empirically compare a number of different algorithms and exploration methods and show the efficacy of BLS on sequence labeling and dependency parsing tasks.
Prophylactic Antibiotics for Endoscopy-Associated Peritonitis in Peritoneal Dialysis Patients

Introduction Continuous ambulatory peritoneal dialysis (CAPD) peritonitis may develop after endoscopic procedures, and the benefit of prophylactic antibiotics is unclear. In the present study, we investigated whether prophylactic antibiotics reduce the incidence of peritonitis in these patients. Patients and methods We retrospectively reviewed all endoscopic procedures, including esophagogastroduodenoscopy (EGD), colonoscopy, sigmoidoscopy, cystoscopy, hysteroscopy, and hysteroscopy-assisted intrauterine device (IUD) implantation/removal, performed in CAPD patients at Chang Gung Memorial Hospital, Taiwan, between February 2001 and February 2012. Results Four hundred and thirty-three patients were enrolled, and 125 endoscopies were performed in 45 patients. Eight (6.4%) peritonitis episodes developed after the examination. Antibiotics were used in 26 procedures, and none of the patients had peritonitis (0% vs. 8.1% without antibiotic use; p = 0.20). The peritonitis rate was significantly higher in the non-EGD group than in the EGD group (15.9% [7/44] vs. 1.2% [1/81]; p<0.005). Antibiotic use prior to non-EGD examinations significantly reduced the endoscopy-associated peritonitis rate compared to that without antibiotic use (0% [0/16] vs. 25% [7/28]; p<0.05). Peritonitis only occurred if invasive procedures were performed, such as biopsy, polypectomy, or IUD implantation, (noninvasive procedures, 0% [0/20] vs. invasive procedures, 30.4% [7/23]; p<0.05). No peritonitis was noted if antibiotics were used prior to examination with invasive procedures (0% [0/10] vs. 53.8% [7/13] without antibiotic use; p<0.05). Although not statistically significant, antibiotics may play a role in preventing gynecologic procedure-related peritonitis (antibiotics, 0% [0/4] vs. no antibiotics, 55.6% [5/9]; p = 0.10). Conclusion Antibiotic prophylaxis significantly reduced endoscopy-associated PD peritonitis in the non-EGD group. Endoscopically assisted invasive procedures, such as biopsy, polypectomy, IUD implantation/removal, and dilatation and curettage (D&C), pose a high risk for peritonitis. Prophylactic antibiotics for peritonitis prevention may be required in colonoscopic procedures and gynecologic procedures.
Role of Bovine Albumin in a Serum-free Suspension Cell Culture Medium

Summary A serum-free culture medium, supplemented with 1% bovine serum albumin, supported the growth of both primary and continuous suspension-type cultures of various mammalian tumor cells. The role of albumin added to the medium was also studied. Defatted albumin failed to support cell growth, unless reconstituted with its lipid extract. Similarly, defatted albumin, when combined with oleic and linoleic acids, also supported cell growth. Therefore, albumin-bound fatty acids play an important growth-promoting role in serum-free medium. We thank the Nissui Saiyaku Company for supplying the fatty acids. This work was partly supported by a Grant-in-Aid from the Educational Ministry of Japan.
Comparing summarisation techniques for informal online reviews

In this paper we evaluate three methods for summarising game reviews written in a casual style. This was done in order to create a review summarisation system to be used by clients of deltaDNA. We look at one well-known method based on natural language processing, and describe two statistical methods that could be used for summarisation: one based on TF-IDF scores another using supervised latent Dirichlet allocation. We find, due to the informality of these online reviews, that natural language based techniques work less well than they do on other types of reviews, and we recommend using techniques based on the statistical properties of the words' frequencies. In particular, we decided to use a TF-IDF score based system in the final system.
Selective Reduction of Blood Flow to White Matter During Hypercapnia Corresponds With Leukoaraiosis

Background and Purpose— Age-related white matter disease (leukoaraiosis) clusters in bands in the centrum semiovale, about the occipital and frontal horns of the lateral ventricles, in the corpus callosum, and internal capsule. Cerebrovascular anatomy suggests that some of these locations represent border zones between arterial supply territories. We hypothesized that there are zones of reduced cerebrovascular reserve (susceptible to selective reductions in blood flow, ie, steal phenomenon) in the white matter of young, healthy subjects, the physiological correlate of these anatomically defined border zones. Furthermore, we hypothesized that these zones spatially correspond with the regions where the elderly develop leukoaraiosis. Methods— Twenty-eight healthy volunteers underwent functional MR mapping of the cerebrovascular response to hypercapnia. We studied 18 subjects by blood oxygen level-dependent MRI and 10 subjects by arterial spin labeling MRI. We controlled both end-tidal pco2 and po2. All functional data was registered in Montreal Neurological Institute space and generated composite blood oxygen level-dependent MR and arterial spin labeling MR maps of cerebrovascular reserve. We compared these maps with frequency maps of leukoaraiosis published previously. Results— Composite maps demonstrated significant (90% CI excluding the value zero) steal phenomenon in the white matter. This steal was induced by relatively small changes in end-tidal pco2. It occurred precisely in those locations where elderly patients develop leukoaraiosis. Conclusions— This steal phenomenon likely represents the physiological correlate of the previously anatomically defined internal border zones. Spatial concordance with white matter changes in the elderly raises the possibility that this steal phenomenon may have a pathogenetic role.
GCOE Discussion Paper Series Global COE Program Human Behavior and Socioeconomic Dynamics

Political coalition formation games can describe the formation and dissolution of nations, as well as the creation of coalition governments, the establishment of political parties, and other similar phenomena. These games have been studied from a theoretical perspective, but the models have not been used extensively in empirical work. This paper presents a method of estimating political coalition formation models with many-player coalitions, and then applies this method to the recent heisei municipal amalgamations in Japan to estimate structural coefficients that describe the behaviour of municipalities. The method enables counterfactual analysis, which in the Japanese case shows that the national government could increase welfare via a counter-intuitive policy involving transfers to richer municipalities conditional on their participation in a merger.
The TIGER 700 RMRS Bank: RMRS Construction from Dependencies

We present a treebank conversion method by which we construct an RMRS bank for HPSG parser evaluation from the TIGER Dependency Bank. Our method effectively performs automatic RMRS semantics construction from functional dependencies, following the semantic algebra of Copestake et al. (2001). We present the semantics construction mechanism, and focus on some special phenomena. Automatic conversion is followed by manual validation. First evaluation results yield high precision of the automatic semantics construction rules.
Subunit 1 of cytochrome oxidase from Neurospora crassa: nucleotide sequence of the coding gene and partial amino acid sequence of the protein.

A partial protein sequence (223 residues) of cytochrome oxidase subunit 1 from Neurospora crassa has been established. The nucleotide sequence of a cloned mitochondrial DNA segment, including the structural gene coding for the mature subunit 1 (CO I locus) was determined. In contrast to the situation in yeast, the CO I locus in N. crassa is not interrupted by long intervening sequences. A polypeptide of 555 residues with a mol. wt. of 61 000 has been deduced from the reading frame established by protein sequencing. With the exception of the C‐terminal part of the polypeptide, the proposed sequences for subunit 1 of N. crassa, yeast, and man are largely homologous. Protein sequencing reveals that a region of low homology close to the C‐terminal portion belongs to the structural gene in N. crassa. The DNA sequence coding for the prepiece, which characterizes the polypeptide precursor of the N. crassa subunit 1, has not yet been localized. A RNA species of approximately 6.8 kb has been identified as the CO I transcript. There is no indication of splicing of this large transcript.
Spleen lymphocyte function modulated by a cocoa‐enriched diet

Previous studies have shown the down‐regulating in vitro effect of cocoa flavonoids on lymphocyte and macrophage activation. In the present paper, we report the capacity of a long‐term rich cocoa diet to modulate macrophage cytokine secretion and lymphocyte function in young rats. Weaned rats received natural cocoa (4% or 10% food intake), containing 32 mg flavonoids/g, for 3 weeks. Spleen immune function was then evaluated through the analysis of lymphocyte composition, their proliferative response and their ability to secrete cytokines and Ig. In addition, the status of activated peritoneal macrophages was established through tumour necrosis factor (TNF)‐α secretion. The richest cocoa diet (10%) caused a reduction of TNF‐α secretion by peritoneal macrophages showing anti‐inflammatory activity. Similarly, although a 10% cocoa diet increased lymphocyte proliferation rate, it down‐regulated T helper 2 (Th2)‐related cytokines and decreased Ig secretion. These changes were accompanied by an increase in spleen B cell proportion and a decrease in Th cell percentage. In summary, these results demonstrate the functional activity of a cocoa‐high dosage in down‐regulating the immune response that might be beneficial in hypersensitivity and autoimmunity.
The sea urchin sperm receptor for egg jelly is a modular protein with extensive homology to the human polycystic kidney disease protein, PKD1

During fertilization, the sea urchin sperm acrosome reaction (AR), an ion channel-regulated event, is triggered by glycoproteins in egg jelly (EJ). A 210-kD sperm membrane glycoprotein is the receptor for EJ (REJ). This conclusion is based on the following data: purified REJ binds species specifically to EJ dotted onto nitrocellulose, an mAb to REJ induces the sperm AR, antibody induction is blocked by purified REJ, and purified REJ absorbs the AR-inducing activity of EJ. Overlapping fragments of REJ cDNA were cloned (total length, 5,596 bp). The sequence was confirmed by microsequencing six peptides of mature REJ and by Western blotting with antibody to a synthetic peptide designed from the sequence. Complete deglycosylation of REJ followed by Western blotting yielded a size estimate in agreement with that of the mature amino acid sequence. REJ is modular in design; it contains one EGF module and two C-type lectin carbohydrate-recognition modules. Most importantly, it contains a novel module, herein named the REJ module (700 residues), which shares extensive homology with the human polycystic kidney disease protein (PKD1). Mutations in PKD1 cause autosomal dominant polycystic kidney disease, one of the most frequent genetic disease of humans. The lesion in cellular physiology resulting from mutations in the PKD1 protein remains unknown. The homology between REJ modules of the sea urchin REJ and human PKD1 suggests that PKD1 could be involved in ionic regulation.
Using Implicit Association Tests in Age-Heterogeneous Samples: The Importance of Cognitive Abilities and Quad Model Processes

Implicit association tests (IATs) are increasingly used to indirectly assess people’s traits, attitudes, or other characteristics. In addition to measuring traits or attitudes, IAT scores also reflect differences in cognitive abilities because scores are based on reaction times (RTs) and errors. As cognitive abilities change with age, questions arise concerning the usage and interpretation of IATs for people of different age. To address these questions, the current study examined how cognitive abilities and cognitive processes (i.e., quad model parameters) contribute to IAT results in a large age-heterogeneous sample. Participants (N = 549; 51% female) in an age-stratified sample (range = 12–88 years) completed different IATs and 2 tasks to assess cognitive processing speed and verbal ability. From the IAT data, D2-scores were computed based on RTs, and quad process parameters (activation of associations, overcoming bias, detection, guessing) were estimated from individual error rates. Substantial IAT scores and quad processes except guessing varied with age. Quad processes AC and D predicted D2-scores of the content-specific IAT. Importantly, the effects of cognitive abilities and quad processes on IAT scores were not significantly moderated by participants’ age. These findings suggest that IATs seem suitable for age-heterogeneous studies from adolescence to old age when IATs are constructed and analyzed appropriately, for example with D-scores and process parameters. We offer further insight into how D-scoring controls for method effects in IATs and what IAT scores capture in addition to implicit representations of characteristics.
Draft Genome Sequence of Paenisporosarcina sp. Strain TG-14, a Psychrophilic Bacterium Isolated from Sediment-Laden Stratified Basal Ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica

ABSTRACT The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments.
Generalized spike-and-slab priors for Bayesian group feature selection using expectation propagation

We describe a Bayesian method for group feature selection in linear regression problems. The method is based on a generalized version of the standard spike-and-slab prior distribution which is often used for individual feature selection. Exact Bayesian inference under the prior considered is infeasible for typical regression problems. However, approximate inference can be carried out efficiently using Expectation Propagation (EP). A detailed analysis of the generalized spike-and-slab prior shows that it is well suited for regression problems that are sparse at the group level. Furthermore, this prior can be used to introduce prior knowledge about specific groups of features that are a priori believed to be more relevant. An experimental evaluation compares the performance of the proposed method with those of group LASSO, Bayesian group LASSO, automatic relevance determination and additional variants used for group feature selection. The results of these experiments show that a model based on the generalized spike-and-slab prior and the EP algorithm has state-of-the-art prediction performance in the problems analyzed. Furthermore, this model is also very useful to carry out sequential experimental design (also known as active learning), where the data instances that are most informative are iteratively included in the training set, reducing the number of instances needed to obtain a particular level of prediction accuracy.
Security applications of distributed arithmetic coding

Distributed arithmetic coding (DAC) has recently been proposed for compression in the Slepian-Wolf setting. With respect to syndrome coding, DAC allows to easily adapt to non-stationary statistics of the signal to be coded, and works well for short and medium block lengths. In this paper we develop security applications of DAC in the field of biometric authentication. We show that DAC can be used for authentication by employing the codeword as secure hash, and using the outcome of DAC decoding for authentication. Moreover, we introduce a second powerful security feature, namely the randomization of the DAC intervals. This allows to protect the hash from attacks. We assess the authentication performance of the proposed scheme with respect to template matching and turbo codes.
Incidence and Determinants of Tuberculosis among Adults Initiating Antiretroviral Therapy – Mozambique, 2004–2008

Background In Mozambique, tuberculosis (TB) is thought to be the most common cause of death among antiretroviral therapy (ART) enrollees. Monitoring proportions of enrollees screened for TB, and incidence and determinants of TB during ART can help clinicians and program managers identify program improvement opportunities. Methodology/Principal Findings We conducted a retrospective cohort study among a nationally representative sample of the 79,500 adults (>14 years old) initiating ART during 2004–2007 to estimate clinician compliance with TB screening guidelines, factors associated with active TB at ART initiation, and incidence and predictors of documented TB during ART follow-up. Of 94 sites enrolling >50 adults on ART, 30 were selected using probability-proportional-to-size sampling; 2,596 medical records at these sites were randomly selected for abstraction and analysis. At ART initiation, median age of patients was 34, 62% were female, median baseline CD4+ T-cell count was 153/µL, and 11% were taking TB treatment. Proportions of records with TB screening documentation before ART initiation improved from 31% to 66% during 2004–2007 (p<0.001). TB screening compliance varied widely by ART clinic [n = 30, 2%–98% (p<0.001)] and supporting non-Governmental Organization (NGO) [n = 7, 27%–83% (p<0.001)]. Receiving TB treatment at ART enrollment was associated with male sex (p<0.001), weight <45 kg (p<0.001) and CD4<50/µL (p = 0.001). Isoniazid preventive therapy (IPT) was prescribed to <1% of ART enrollees not taking TB treatment. TB incidence during ART was 2.32 cases per 100 person-years. Factors associated with TB incidence included adherence to ART <95% (AHR 2.06; 95% CI, 1.32–3.21). Conclusion Variations in TB screening by clinic and NGO may reflect differing investments in TB screening activities. Future scale-up should target under-performing clinics. Scale-up of TB screening at ART initiation, IPT, and ART adherence interventions could significantly reduce incident TB during ART.
A METHOD FOR DERIVING AEROSOL OPTICAL DEPTH FROM METEOROLOGICAL SATELLITE DATA

Aerosols are important agent of radiative forcing and climate disturbance, especially in a polluted environment. In general, the impact of aerosol on the climate depends on aerosol optical properties. One of important aerosol optical properties is aerosol optical depth (AOD). In general, AOD can be measured using ground-based sunphotometers. However, it is costly to deploy such instruments over a large area. Due to a lack of comprehensive measurement on a global scale, retrieval of aerosol information from some instruments on board satellites (e.g. MODIS and POLDER) has been developed. However, aerosol information from such satellites has relatively short historical records. In addition, such information is available only once or twice a day. Therefore, in this work, we propose a method for deriving AOD from meteorological geostationary satellite data. This is because geostationary satellites have advantage that they have longer historical data and their data are available on the hourly basis. According to the proposed method, a radiative transfer model, namely 6S, was used to construct series of look up tables (LUT) which contained pre-computed datasets including earth-atmospheric reflectivity, aerosol information and surface albedo. The satellite images in a visible channel were used to calculate the earth-atmospheric reflectivity data and these data were later employed as the main input of the method. In addition, the infrared images from the satellite were also used to identify cloud scene over the area. The value of AOD, which makes the value of the earth-atmospheric reflectivity from the LUT matching to the earth-atmospheric reflectivity obtained from the satellite data, will be considered as the true AOD. For the validation, the calculated AOD from this method was compared with the ground-based AOD measurements from NASA-AERONET. It was found that the measured and calculated AOD were in reasonable agreement.
Characterization of Soluble Hepatitis C Virus RNA-Dependent RNA Polymerase Expressed in Escherichia coli

ABSTRACT Production of soluble full-length nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) has been shown to be problematic and requires the addition of salts, glycerol, and detergents. In an effort to improve the solubility of NS5B, the hydrophobic C terminus containing 21 amino acids was removed, yielding a truncated NS5B (NS5BΔCT) which is highly soluble and monodispersed in the absence of detergents. Fine deletional analysis of this region revealed that a four-leucine motif (LLLL) in the hydrophobic domain is responsible for the solubility profile of the full-length NS5B. Enzymatic characterization revealed that the RNA-dependent RNA polymerase (RdRp) activity of this truncated NS5B was comparable to those reported previously by others. For optimal enzyme activity, divalent manganese ions (Mn2+) are preferred rather than magnesium ions (Mg2+), whereas zinc ions (Zn2+) inhibit the RdRp activity. Gliotoxin, a known poliovirus 3D RdRp inhibitor, inhibited HCV NS5B RdRp in a dose-dependent manner. Kinetic analysis revealed that HCV NS5B has a rather low processivity compared to those of other known polymerases.
The new method on gas-water two phase steady-state productivity of fractured horizontal well in tight gas reservoir

Based on a large number of tight gas exploration and development literature researches, it is found that the horizontal drilling technology and fracturing operation are usually used in the tight gas reservoir for its low permeability. Three tasks have been done in this paper. First, we described the characteristics and the ﬂow mechanism of the tight gas reservoirs which are different from the conventional ones and gave a new deﬁnition of two phase pseudo pressure. Second, formation stress sensitivity, starting pressure gradient and the interaction of fractures are considered. Equivalent ﬂow resistance was used to establish a model of tight gas steady ﬂow, and a new productivity formula of fractured horizontal well in tight gas reservoir derived by the new ﬂow model. Third, the productivity inﬂuence research has been done, which gives the inﬂuence degree of different parameters. It is signiﬁed that the productivity will increase with the addition of the permeability modulus and decrease with the increase of the water-gas volume ratio. The inﬂuence of starting pressure gradient was not very clear and the fractures parameters showed the opposite situation. Therefore optimization design of tight gas reservoir development mode can be improved by the productivity formula and research. Cited as : Li, X. , Liang, J., Xu, W. , et al. The new method on gas-water two phase steady-state productivity of fractured horizontal well in tight gas reservoir. Advances in Geo-Energy Research, 2017, 1(2): 105-111, doi: 10.26804/ager.2017. 02.06.