Miracle-dz/UniFAR-FTUs huggingface dataset:
A Combination of Topic Models with Max-margin Learning for Relation Detection

This paper proposes a novel application of a supervised topic model to do entity relation detection (ERD). We adapt Maximum Entropy Discriminant Latent Dirichlet Allocation (MEDLDA) with mixed membership for relation detection. The ERD task is reformulated to fit into the topic modeling framework. Our approach combines the benefits of both, maximum-likelihood estimation (MLE) and max-margin estimation (MME), and the mixed membership formulation enables the system to incorporate heterogeneous features. We incorporate different features into the system and perform experiments on the ACE 2005 corpus. Our approach achieves better overall performance for precision, recall and Fmeasure metrics as compared to SVM-based and LLDA-based models.
Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site

Significance Protein biosynthesis is most tightly controlled during translation initiation that involves numerous initiation factors and regulatory proteins. This complexity confounds conventional biochemical methods. Single-molecule approaches are ideally suited to address such questions. However, their application is hindered by the lack of fluorescently labeled components of the eukaryotic translation machinery. Here, we demonstrate an approach to label human 40S ribosomal subunits. As an extension of this approach, we used single-molecule fluorescence to demonstrate that 40S ribosomal subunits are recruited to the hepatitis C virus mRNA in a single-step process, and that components of a translational extract regulate the conformation of this complex. Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data support a single-step model of HCV IRES recruitment to 40S subunits, irreversible on the initiation time scale. We furthermore demonstrated that after binding, the 40S:HCV IRES complex is conformationally dynamic, undergoing slow large-scale rearrangements. Addition of translation extracts suppresses these fluctuations, funneling the complex into a single conformation on the 80S assembly pathway. These findings show that 40S:HCV IRES complex formation is accompanied by dynamic conformational rearrangements that may be modulated by initiation factors.
The Greek version of the Gagging Assessment Scale in children and adolescents: psychometric properties, prevalence of gagging, and the association between gagging and dental fear

BACKGROUND No studies assessing the association between gagging and dental fear are available in pediatric samples. AIM To assess the psychometric properties of the Greek version of the Gagging Assessment Scale (GAS), to explore the prevalence of gagging, and to evaluate the relationship between gagging and dental fear in a pediatric sample. DESIGN A total of 849 8- and 14-year-old children filled out a questionnaire consisting of demographic items, the Greek version of the GAS, and the Greek Children's Fear Survey Schedule Dental Subscale (CFSS-DS); the older children also completed the Greek version of the Modified Dental Anxiety Scale (MDAS). The short form of dentist part of the Gagging Problem Assessment (GPA-de-c/SF) was used to objectively assess gagging. RESULTS A total of 51 children (6.0%) demonstrated gagging on the GPA-de-c/SF. Children rated as gaggers on the GPA-de-c/SF had significantly higher GAS scores. There were no relationships between GPA-de-c/SF and the CFSS-DS or MDAS. The GAS ratings were significantly correlated with the CFSS-DS (rho = 0.420, P < 0.001) and MDAS (rho = 0.429, P < 0.001). The internal consistency was good (Cronbach's alpha = 0.697). CONCLUSIONS The GAS demonstrated good psychometric properties. Dental fear was correlated with the self-report gagging assessment, but not with the objective gagging assessment.
Impact of esophageal cancer staging on overall survival and disease-free survival based on the 2010 AJCC classification by lymph nodes

This retrospective study investigated the effect of modifications presented in the seventh edition of the American Joint Committee on Cancer (AJCC) Manual for staging esophageal cancer on the characterization of the effectiveness of post-operative chemotherapy and/or radiotherapy, as measured by overall and disease-free survival. The seventh edition of the AJCC Manual classifies the number of lymph nodes (N) positive for regional metastasis into three subclasses. We used the AJCC classification system to characterize the cancers of 413 Chinese patients with esophageal cancer who underwent radical resection plus regional lymph node dissection over a 10-year period. The 10-year survival rate was 14.3% for stage N1 patients and 6.1% for stage N2 patients. Only one stage N3 patient was followed >4 years (53.4 months). The 10-year disease-free rate was 13.6% for stage N1 patients. Patients with stage N2 or N3 cancer were more likely to have tumor recurrences, metastases or death than patients with stage N1 cancer. Post-operative radiotherapy provided no survival benefit, and may have had a negative effect on survival. In this study, the N stage of esophageal cancer was an independent factor affecting overall and disease-free survival. Our results did not clarify whether or not radiotherapy after radical esophagectomy offers any survival benefit to patients with esophageal cancer.
Mechanisms of immune escape in viral hepatitis

Knowledge of the molecular virology of the hepatitis viruses and the responses they elicit has emphasised the importance of host immunity in resolving infection and mediating liver damage. Many viruses cause cytolytic infections in which viral replication occurs at the expense of host cell viability. However this is a shortsighted strategy for the virus as it provides a clear “danger signal”1 that alerts the host’s innate and adaptive immune defences to eliminate the virus and terminate the infection. Such a life cycle requires a high rate of transmission from host to host, causes acute tissue damage and is unlikely to result in persistent infection. In order to cause chronic infection viruses must use strategies that enable them to evade or modify host immune responses sufficiently to prevent clearance. Of the hepatitis viruses only hepatitis B (HBV) and hepatitis C (HCV) viruses cause chronic infections and in order to do so they must evade host immune responses. Neither hepatitis A virus nor hepatitis E virus cause chronic infection and must be assumed to lack the ability to escape immune responses. Understanding the mechanisms used by HBV and HCV to evade host immunity is central to understanding their pathogenicity and necessary for the development of effective therapeutic strategies. Although knowledge of the mechanisms of immune escape by hepatitis viruses is increasing, considerable insight has come from the study of other viruses, some of which can cause hepatitis such as Epstein-Barr virus (EBV), HIV, and model systems such as murine lymphocytic choriomeningitis virus (LCMV), as well as transgenic mouse models of HBV infection. In both acute HBV and HCV infection a vigorous antiviral T lymphocyte response is associated with viral clearance. In chronic hepatitis B and hepatitis C virus specific T lymphocyte responses are weak or absent. The mechanisms leading to ineffectual …
Bond of Reinforcement in High-Strength Concrete

This paper describes an examination of the development of tension lap splices in high-strength concrete and the applicability of the restriction in the ACI 318 code where the values of √fc′ used to calculate development length shall not exceed 100 psi. The focus is on the development of splices with Grade 60 epoxy-coated and uncoated bars in normalweight concrete. A summary of the behavior of bond is presented to provide context for the study. It is followed by a literature review to analyze the relevant previous experimental work in this area. Based on the analysis of those data, a modification to the current code limitation is proposed. The main conclusion of this paper is that the limit of 100 psi (0.689 MPa) on the square root of the specified compressive strength in Section 12.1. 2 of ACI 318-11 (Section 25.4.1.4 of 318-14) may be extended to 120 psi (0.827 MPa) based on the analysis of available data without significant modifications to the current provisions for concrete strengths up to 16,000 psi (110 MPa).
Retinal neuronal death induced by intraocular administration of a nitric oxide donor and its rescue by neurotrophic factors in rats.

PURPOSE To investigate the neurotoxic outcome in the rat retina exposed to nitric oxide (NO) released from an NO donor and to evaluate the effects of neurotrophic factors on the survival of NO-damaged retinal cells. METHODS An NO releasing compound, N-ethyl-2-(1-ethyl-2-hydroxy-2-nitrosohydrazino) ethanamine (NOC 12), was intravitreously injected into a rat's right eye. The influences of NOC 12 on retinal neurons and the neuroprotective effects of ciliary neurotrophic factor (CNTF) or brain-derived neurotrophic factor (BDNF) on NOC 12-mediated damage were estimated by counting cells in the ganglion cell layer (GCL) and by measuring the thickness of retinal layers. The exact count of retinal ganglion cells (RGCs) was also confirmed by means of retrograde labeling with a fluorescent tracer. RESULTS Morphometric analyses of retinal damage in the NOC 12-exposed eyes demonstrated a significant and dose-dependent decrease in cell density in the GCL and a reduction in thickness of the inner plexiform layer and inner nuclear layer, but not of the outer nuclear layer. TdT-dUTP terminal nick-end labeling of retinal sections after intravitreous injection of NOC 12 demonstrated that NO could trigger apoptotic cell death. The counting of the RGCs labeled with a fluorescent tracer suggested that a decrease in GCL cell density induced by NOC 12 reflects a loss in RGCs. Treatment with CNTF (1 microg) or BDNF (1 microg) before the intravitreous injection of NOC 12 (400 nmol) demonstrated that these trophic factors have protective effects against NO-induced neuronal cell death in the retina. CONCLUSIONS Exogenous NO induces retinal neurotoxicity, suggesting that NO plays a pathogenic role in degenerative retinal diseases. BDNF and CNTF protect retinal neurons from NO-mediated neurotoxicity.
Characteristics of Outpatient Clinical Decision Support Systems: A Taxonomic Description

Computer-based clinical decision support systems (CDSSs) have been championed for their potential to improve health-care quality. However, there has been no systematic study of the types of CDSSs that have been developed. In previous work, we developed the CDSS Taxonomy for comprehensively describing the technical, workflow, and contextual characteristics of CDSSs. We now use the CDSS Taxonomy to describe outpatient CDSSs evaluated in randomized controlled trials published between 1998 and 2002. 31 studies comprising 42 CDSS systems were included in our analysis. The majority of systems used rule-based reasoning engines to "push" explicit, individualized recommendations concerning non-urgent decisions to clinicians or patients, but not both. 71% of the systems required someone to manually enter data into the system or to process the system output for use by the target decision maker. The average kappa for coding agreement was > 0.6. Our findings demonstrate that outpatient CDSSs vary greatly in design and function. Many impose a data entry or output-processing burden on clinic staff. More complete reporting of CDSS characteristics is needed in the literature.
Accuracy of Six Commercially Available Systems for Identification of Members of the Family Vibrionaceae

ABSTRACT Six commercially available bacterial identification products were tested with Vibrio alginolyticus (12 strains), V. cholerae (30 strains), Photobacterium (Vibrio) damselae (10 strains), V. fluvialis (10 strains), V. furnissii (4 strains), V. hollisae (10 strains), V. metschnikovii (9 strains), V. mimicus (10 strains), V. parahaemolyticus (30 strains), and V. vulnificus (10 strains) to determine the accuracy of each system for identification. The products included API 20E, Crystal E/NF, MicroScan Neg ID2 and Rapid Neg ID3, and Vitek GNI+ and ID-GNB. Each product was tested only with those species that were listed in its database. Overall, the systems correctly identified 63.9, 80.9, 63.1, 73.6, 73.5, and 77.7% of the isolates to species level, respectively. Error rates ranged from 0.8% for the API 20E to 10.4% for the Rapid Neg ID3. The API 20E gave “no identification” for 13.1% of the isolates, while the Neg ID2, GNI+, ID-GNB, and Crystal were unable to identify 1.8, 2.9, 5.0, and 6.9%, respectively. For V. cholerae, specifically, accuracy ranged from 50.0 to 96.7%, with the API 20E having the worst performance and Crystal having the best. V. fluvialis presented the biggest challenge for the API 20E and the GNI+, with probabilities averaging 10%, while V. mimicus was a major problem with the Crystal E/NF, which identified none of the strains correctly. With the Neg ID2, correct answers were often obtained only after a modified inoculation of the panel with a bacterial suspension prepared with 0.85% NaCl. Additional tests required for identification often included growth in the absence of NaCl, which is not readily available in most clinical laboratories. The only product to correctly identify at least 90% of V. cholerae strains was the Crystal E/NF, and only three of the six products, the API 20E and both of the Vitek cards, correctly identified more than 90% of the V. parahaemolyticus strains. Thus, extreme care must be taken in the interpretation of answers from these six commercially available systems for the identification of Vibrio species.
Control-Flow Bending: On the Effectiveness of Control-Flow Integrity

Control-Flow Integrity (CFI) is a defense which prevents control-flow hijacking attacks. While recent research has shown that coarse-grained CFI does not stop attacks, fine-grained CFI is believed to be secure. We argue that assessing the effectiveness of practical CFI implementations is non-trivial and that common evaluation metrics fail to do so. We then evaluate fullyprecise static CFI -- the most restrictive CFI policy that does not break functionality -- and reveal limitations in its security. Using a generalization of non-control-data attacks which we call Control-Flow Bending (CFB), we show how an attacker can leverage a memory corruption vulnerability to achieve Turing-complete computation on memory using just calls to the standard library. We use this attack technique to evaluate fully-precise static CFI on six real binaries and show that in five out of six cases, powerful attacks are still possible. Our results suggest that CFI may not be a reliable defense against memory corruption vulnerabilities. We further evaluate shadow stacks in combination with CFI and find that their presence for security is necessary: deploying shadow stacks removes arbitrary code execution capabilities of attackers in three of six cases.
Assessment of the prognostic impact of the Epstein–Barr virus-encoded latent membrane protein-1 expression in Hodgkin's disease

We have examined expression of the Epstein–Barr virus (EBV) latent membrane protein-1 (LMP1) in the malignant Hodgkin and Reed–Sternberg (HRS) cells of Hodgkin's disease (HD) and its impact on response to treatment and on survival. Paraffin tissue from 100 adult immunocompetent patients with HD were analysed using immunohistochemistry to identify LMP1 expression. According to the Rye classification, 8% of patients had lymphocyte predominance (LP) subtype, 48% had nodular sclerosis (NS) disease, 37% were of the mixed cellularity (MC) subtype and 7% were of the lymphocyte depletion (LD) subtype. During the five year follow-up period 27 patients died and 74 patients achieved a complete remission. Patients with LD subtype were older (P = 0.03), less frequently achieved complete remission (P = 0.01), had shorter disease-free survival (P = 0.01) and overall survival (P = 0.002) compared with the other subtypes of HD. LMP1 expression was found in the tumour cells of 26% of cases of HD. LMP1 expression was less common in NS disease than in the other subtypes (P = 0.05), whereas an association between MC subtype and LMP1 expression was not found (P = 0.22). Using the log-rank test there were no differences in overall survival or disease-free survival based on EBV status either when all patients were analysed or when LD and LP subtypes were excluded. However, the presence of EBV was associated with significantly longer disease-free survival in the subgroup of patients ≤ 30 years old (P = 0.02) and in those patients ≤ 34 years old (P = 0.05). In contrast, there was a trend for shorter disease-free survival for EBV-positive patients in the subgroup > 35 years old, but this difference was not statistically significant (P = 0.11). A similar trend was observed in patients > 50 years old. Analysis of the impact of LMP1 expression in patients who had different stage and B symptoms status showed that expression of EBV was associated with longer disease-free survival (P = 0.019) in early stage (1 + 2) patients without B symptoms. Significant differences in the other subgroups based on EBV status was not found. Factors adversely affecting the likelihood to achieve a complete remission were: absence of LMP1 expression (OR 6.4, 95% Cl 1.07–38.5, P = 0.04), age (OR 1.68, 95%Cl 1.15–2.5, P = 0.007) and subtype of HD (OR 3.32, 95%Cl 1.11–9.94, P = 0.03). Age and subtype of HD had an independent impact on overall survival (P = 0.01). We conclude that expression of LMP1 in HRS cells has a favourable impact on prognosis for HD patients, but that this effect may be restricted to young adult patients and those with early stage disease. © 2001 Cancer Research Campaign http://www.bjcancer. com
Targeting proteins to distinct subcellular compartments reveals unique requirements for MHC class I and II presentation

Peptides derived from exogenous proteins are presented by both MHC class I and II. Despite extensive study, the features of the endocytic pathway that mediate cross-presentation of exogenous antigens on MHC class I are not entirely understood and difficult to generalize to all proteins. Here, we used dendritic cells and macrophages to examine MHC class I and II presentation of hen egg-white lysozyme (HEL) in different forms, soluble and liposome encapsulated. Soluble HEL or HEL targeted to a late endosomal compartment only allowed for MHC class II presentation, in a process that was blocked by chloroquine and a cathepsin S (CatS) inhibitor; brefeldin A (BFA) also blocked presentation, indicating a requirement for nascent MHC class II. In contrast, liposome-encapsulated HEL targeted to early endosomes entered the MHC class I and II presentation pathways. Cross-presentation of HEL in early endosomal liposomes had several unique features: it was markedly increased by BFA and by blockade of the proteasome or CatS activity, it occurred independently of the transporter associated with antigen processing but required an MHC class I surface-stabilizing peptide, and it was inhibited by chloroquine. Remarkably, chloroquine facilitated MHC class I cross-presentation of soluble HEL and HEL in late endosomal liposomes. Altogether, MHC class I and II presentation of HEL occurred through pathways having distinct molecular and proteolytic requirements. Moreover, MHC class I sampled antigenic peptides from various points along the endocytic route.
Effects of a School-Based Instrumental Music Program on Verbal and Visual Memory in Primary School Children: A Longitudinal Study

This study examined the effects of a school-based instrumental training program on the development of verbal and visual memory skills in primary school children. Participants either took part in a music program with weekly 45 min sessions of instrumental lessons in small groups at school, or they received extended natural science training. A third group of children did not receive additional training. Each child completed verbal and visual memory tests three times over a period of 18 months. Significant Group by Time interactions were found in the measures of verbal memory. Children in the music group showed greater improvements than children in the control groups after controlling for children’s socio-economic background, age, and IQ. No differences between groups were found in the visual memory tests. These findings are consistent with and extend previous research by suggesting that children receiving music training may benefit from improvements in their verbal memory skills.
A dynamic framework for strengthening women's social capital: strategies for community development in rural Bangladesh

There is considerable evidence in the literature that social capital contributes to poverty alleviation, but evidence of how development actors can strengthen the productive social capital for poor people remains scarce. This article describes strategies to strengthen social capital developed by an NGO and poor women as part of a development programme, undertaken in Jessore District, rural Bangladesh, during 2006–2012. The NGO and the women leveraged bonding (familial), bridging (peers), and linking (vertical links to powerholders) social capital to improve the livelihoods of women and their families, simultaneously changing gender relations within households and communities. Against a background of local norms and ethics, the NGO and the women employed strategies that created opportunities for women to meet and exchange, and develop their social skills, know-how, self-worth and capacity to act. Drawing on these strategies, the article presents a dynamic framework for strengthening social capital for community development, providing theoretical insights into the mechanisms for doing so.