Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk Factors for Anastomotic Leakage after Laparoscopic Rectal Resection

Purpose The anastomotic leakage rate after rectal resection has been reported to be approximately 2.5-21 percent, but most results were associated with open surgery. The aim of this study was to identify risk factors and their relationship to the experience of the surgeon for anastomotic leakage after laparoscopic rectal resection. Methods Between March 2003 and December 2008, 156 patients underwent a laparoscopic rectal resection without a diverting ileostomy. The patients' characteristics, the details of treatment, the intraoperative results, and the postoperative results were recorded prospectively. Univariate and multivariate analyses were applied to identify risk factors for anastomotic leakage. Results The majority of operations were performed for malignant disease (n = 150; 96.2%), and 96 patients (61.5%) were males. Conversion to open surgery occurred in 1 case (0.6%). The anastomotic leak rate was 10.3% (16/156), and there were no mortalities. In the univariate analysis, tumor location, anastomotic level, intraoperative events, and operation time were associated with increased anastomotic leakage rate. In the multivariate analysis, anastomotic level (odds ratio [OR], 6.855; 95% confidence interval [CI], 1.271 to 36.964) and operation time (OR, 8.115; 95% CI, 1.982 to 33.222) were significantly associated with anastomotic leakage. Conclusion The important risk factors for anastomotic leakage after laparoscopic rectal resection without a diverting ileostomy were low anastomosis and long operation time. An additional procedure, such as diverting stoma, may reduce the anastomotic leakage if it is selectively applied in cases with these risk factors.
Highly Configurable and Extensible Code Clone Detection

Code clone detection is an enabling technology for plenty of applications, each having different requirements to a clone detector. We present a generic pipeline model of the code clone detection process. Based on this model we developed the JCCD code clone detection API for implementing custom clone detectors. By combining and parameterizing predefined API components as well as by adding new components, the pipeline model does not only facilitate to build new clone detectors, but also to parallelize the detection process.
Deep Speech: Scaling up end-to-end speech recognition

We present a state-of-the-art speech recognition system developed using end-to-end deep learning. Our architecture is significantly simpler than traditional speech systems, which rely on laboriously engineered processing pipelines; these traditional systems also tend to perform poorly when used in noisy environments. In contrast, our system does not need hand-designed components to model background noise, reverberation, or speaker variation, but instead directly learns a function that is robust to such effects. We do not need a phoneme dictionary, nor even the concept of a "phoneme. " Key to our approach is a well-optimized RNN training system that uses multiple GPUs, as well as a set of novel data synthesis techniques that allow us to efficiently obtain a large amount of varied data for training. Our system, called Deep Speech, outperforms previously published results on the widely studied Switchboard Hub5'00, achieving 16.0% error on the full test set. Deep Speech also handles challenging noisy environments better than widely used, state-of-the-art commercial speech systems.
Bacterial Infection in Chronic Obstructive Pulmonary Disease in 2000: a State-of-the-Art Review

SUMMARY Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States. The precise role of bacterial infection in the course and pathogenesis of COPD has been a source of controversy for decades. Chronic bacterial colonization of the lower airways contributes to airway inflammation; more research is needed to test the hypothesis that this bacterial colonization accelerates the progressive decline in lung function seen in COPD (the vicious circle hypothesis). The course of COPD is characterized by intermittent exacerbations of the disease. Studies of samples obtained by bronchoscopy with the protected specimen brush, analysis of the human immune response with appropriate immunoassays, and antibiotic trials reveal that approximately half of exacerbations are caused by bacteria. Nontypeable Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae are the most common causes of exacerbations, while Chlamydia pneumoniae causes a small proportion. The role of Haemophilus parainfluenzae and gram-negative bacilli remains to be established. Recent progress in studies of the molecular mechanisms of pathogenesis of infection in the human respiratory tract and in vaccine development guided by such studies promises to lead to novel ways to treat and prevent bacterial infections in COPD.
Role of Ring Finger Protein 213 in Moyamoya Disease

Objective: The aim of this study was to help people comprehensively understand the research advances related to ring finger protein 213 (RNF213) in moyamoya disease (MMD) and to understand the disease at the molecular level to provide a new perspective of the diagnosis of the disease. Data Sources: This review was based on data in articles published between 2005 and 2015 that were retrieved from the PubMed database. The search terms included RNF213, MMD, intracranial major artery stenosis/occlusion (ICASO), genotype, phenotype, mutant and variants, and the combinations of these terms. Study Selection: Articles related to MMD and RNF213 were selected for review, and we also reviewed publications related to ICASO. Results: RNF213 is not only associated with MMD but also associated with intracranial major artery stenosis. In addition, RNF213 variants exhibit apparent ethnic diversity; specifically, the c.14576G>A variant is mainly detected in Korean, Chinese, and Japanese populations, particularly the latter population. The genotypes of RNF213 correlate with the phenotypes of MMD; for example, the homozygous c.14576G>A variant is associated with early-onset, severe symptoms, and an unfavorable prognosis. Furthermore, the RNF213 c.14576G>A variant should be considered during the diagnosis of MMD because no patients with quasi-MMD have been reported to carry the RNF213 c.14576G>A variant whereas 66 of 78 patients with definite MMD have been found to carry this variant. Conclusions: The growing literature demonstrates that MMD is primarily caused by the synergy of genetic and environmental factors, and unknown genetic modifiers might play roles in the etiology of MMD. Further research should be conducted to clarify the pathogenic mechanism of MMD.
Session 2: How is Europe coping with the current phase of the crisis? "North-South Asymmetry in the eurozone"

The paper examines the developments in a number of key macroeconomic indicators in the Eurozone countries both before and after the Economic and Monetary Union (EMU) in order to assess how economic fluctuations, the level of per capita income and the external balances across member-states have been affected by the adoption of the Single Currency in 1999. The examination stops before the global crisis of 2008, so that the asymmetries cannot be considered as a byproduct of the recent deterioration of macroeconomic performance for several Eurozone countries. In fact, the paper aims to show that the seeds of the current malaise in the Eurozone were fully present well before the crisis, although very little attention was paid to them.
Relative work and family role centralities: Predicting changes in marriage and family beliefs

Abstract How might anticipated role priorities (centrality) influence changes in beliefs about marriage and family that can influence to the transition to adulthood? The current longitudinal study of 149 young adults investigated changes in the relative role centralities of anticipated adult roles and the predictability of the centralities of changes in marriage and family beliefs. Using parallel procedures from Hall and Willoughby (2016), five distinct relative centrality profiles were created: Child Centered, Marriage Centered, Marriage and Child, Career Centered, and Family and Career. Fifty-four percent of the sample shifted into different relative centrality groups over the course of one year; women were more likely to become more marriage and more parenthood oriented. Relative role centrality at time 1 predicted changes in beliefs related to being child-focused, marital permanence, and marital readiness. It is argued that relative role centrality has implications for young adults’ intentions and decisions that influence the transition to adulthood.
Minimum Energy Cooperative Path Routing in Wireless Networks: An Integer Programming Formulation

We study the problem of minimum energy cooperative path (MECP) routing in wireless networks. The joint problem of cooperative routing in wireless networks that combines route selection and the transmit diversity was recently presented in A. Khandani et al. (2003). Several heuristic algorithms were also proposed in A. Khandani et al. (2003) to approximate the minimum energy cooperative path, while it has not been possible to judge the quality of the solutions with respect to the optimal. In this paper, we present an integer programming formulation of the MECP problem towards an optimal solution for a network where the locations of the nodes are known a priori and fixed
Towards Unsupervised Training of Speaker Independent Acoustic Models

Can we automatically discover speaker independent phonemelike subword units with zero resources in a surprise language? There have been a number of recent efforts to automatically discover repeated spoken terms without a recognizer. This paper investigates the feasibility of using these results as constraints for unsupervised acoustic model training. We start with a relatively small set of word types, as well as their locations in the speech. The training process assumes that repetitions of the same (unknown) word share the same (unknown) sequence of subword units. For each word type, we train a whole-word hidden Markov model with Gaussian mixture observation densities and collapse correlated states across the word types using spectral clustering. We find that the resulting state clusters align reasonably well along phonetic lines. In evaluating cross-speaker word similarity, the proposed techniques outperform both raw acoustic features and language-mismatched acoustic models.
Stroke, Depression, and Functional Health Outcomes Among Adults in the Community

The objective was to determine the association between stroke and depression, the co-occurrence of stroke and depression, and functional health outcomes among adults in the US population. Data were drawn from the Midlife Development in the United States Study (MIDUS) (N = 3032), a nationally representative sample of adults age 25 to 74. Multiple logistic regression analyses were used to determine the association between stroke (past 12-month prevalence), depression (past 12-month prevalence), and functional health outcomes (past 12 months) and to determine whether there is an interaction between depression and stroke in predicting impairment in functioning. Almost one third (29.2%) of adults with stroke in the past year also had depression in the past year (odds ratio 3.5, 95% confidence interval 1.4, 8.9). The co-occurrence of stroke and depression was associated with significantly greater limitations in walking and climbing stairs and poorer general physical functioning than that associated with either without the other. There was evidence of interaction between depression and stroke in predicting limitations, specifically with a statistically significant effect in walking short distances (P = .045). These findings are consistent with previous clinical data and extend those data by suggesting that the co-occurrence of depression and stroke is associated with even poorer functional health outcomes, compared with each alone, and that there may be synergism between the two disorders related to this effect.
Interleukin-10 Family and Tuberculosis: An Old Story Renewed

The interleukin-10 (IL-10) family of cytokines consists of six immune mediators, namely IL-10, IL-19, IL-20, IL-22, IL-24 and IL-26. IL-10, IL-22, IL-24 and IL-26 are critical for the regulation of host defense against Mycobacterium tuberculosis infections. Specifically, IL-10 and IL-26 can suppress the antimycobacterial immunity and promote the survival of pathogen, while IL-22 and IL-24 can generate protective responses and inhibit the intracellular growth of pathogen. Knowledge about the new players in tuberculosis immunology, namely IL-10 family, can inform novel immunity-based countermeasures and host directed therapies against tuberculosis.
“Is the friendship worth keeping:” Gender differences in communicating forgiveness in friendships

Although forgiveness plays an integral role in friendship maintenance, interpersonal communication scholarship has largely overlooked how transgressions and forgiveness are negotiated between friends. This study focuses on gender differences to develop a typology of relational transgressions in friendships. Two hundred and thirty survey respondents (116 women and 114 men) described relational transgressions in their friendships, the perceived severity of these transgressions, and strategies used to communicate forgiveness. A combination of MANCOVA and inductive analyses reveals gender differences. While male transgressions typically involve encroaching on other intimate relationships and theft, female transgressions emphasize disclosing personal communication beyond the friendship’s boundaries. Conflicts between male friends could escalate from verbal to physical aggression, whereas female friends were likely to sabotage other close relationships that threatened the friendship. Finally, males preferred to communicate forgiveness using the minimizing strategy, while female friends generally favored the discussion and conditional forgiveness strategies. Overall, the perceived severity of a transgression was positively related to use of the discussion and conditional forgiveness strategies, and negatively related to the minimizing strategy. The implications of these findings are discussed.
Observation – A Part of Kindergarten Teachers' Professional Skill Set

Knowledge and skills in observation form part of the qualifications a kindergarten teacher needs to become a professional. In this article, I will focus on the theme of observation in kindergarten teacher education (KTE) in Norway. One of the largest educational institutions in the country is used as reference for this study. By means of document analysis, the intended learning outcomes in observation are studied at a societal and institutional level. The purpose of the study is to gain insight into the rationale for observation in the educational context, to identify which observational methods are emphasized, and what students should focus on in their observation work. The results reveal that the intended learning outcomes in observation vary depending on the disciplinary profiles the students have chosen. The study also reveals shortcomings between the societal and institutional levels, as well as a need for discussion and clarification of key observation methods in a profession-oriented education, in line with recent perspectives on children, where children are seen as participants. The results might raise questions about the organization of KTE and whether the theme of observation is research-based and profession-oriented.
Somatic Sensation of Hand-Object Interactive Movement Is Associated with Activity in the Left Inferior Parietal Cortex

Manipulation of objects and tool-use are known to be controlled by a network of frontal motor and parietal areas. Here, we investigate which of these areas are associated with the somatic sensation of hand-object interactive movement using functional magnetic resonance imaging. To dissociate the sensation of movement from the motor control commands, we used a new kinesthetic illusion. Twelve blindfolded right-handed participants placed the palm of their right or left hand on an object (a ball). Simultaneously, we vibrated the tendon of the wrist extensor muscle. This elicited the illusion that the wrist is flexing and the touched object is also moving along with the hand (hand-object illusion). As controls, we vibrated the skin surface over the nearby bone, which does not elicit any illusions, or we vibrated the tendon when the hand did not touch the object, which only generates the illusory flexion of the hand. We found that the hand-object illusion specifically activated the left inferior parietal lobule (IPL) (supramarginal gyrus and parietal operculum, including cytoarchitectonic areas ip1 and op1) and area 44. The left IPL was activated both during the hand-object illusions with the right and left hands, and the activity was greater than in the right corresponding parietal region, suggesting a dominant role of the left hemisphere. We conclude that the left IPL is involved in the somatic perception of hand-object interactive movement and suggest that the underlying mechanism is the somatic integration of internal information about the body and external information about the object.
Steroid prophylaxis for prevention of nerve function impairment in leprosy: randomised placebo controlled trial (TRIPOD 1)

Abstract Objective To determine whether addition of low dose prednisolone to multidrug treatment can prevent reaction and nerve function impairment in leprosy. Design Multicentre, double blind, randomised, placebo controlled, parallel group trial. Setting Six centres in Bangladesh and Nepal. Participants 636 people with newly diagnosed multibacillary leprosy. Intervention Prednisolone 20 mg/day for three months, with tapering dose in month 4, plus multidrug treatment, compared with multidrug treatment alone. Main outcome measures Signs of reaction, impairment of sensory and motor nerve function, and nerve tenderness needing full dose prednisolone at four months and one year. Results Prednisolone had a significant effect in the prevention of reaction and nerve function impairment at four months (relative risk 3.9, 95% confidence interval 2.1 to 7.3), but this was not maintained at one year (relative risk 1.3, 0.9 to 1.8). Fewer events occurred in the prednisolone group at all time points up to 12 months, but the difference at 12 months was small. Subgroup analysis showed a difference in response between people with and without impairment of nerve function at diagnosis. Conclusions The use of low dose prophylactic prednisolone during the first four months of multidrug treatment for leprosy reduces the incidence of new reactions and nerve function impairment in the short term, but the effect is not sustained at one year. The presence of nerve function impairment at diagnosis may influence the response to low dose prednisolone.
Critical roles of mTOR Complex 1 and 2 for T follicular helper cell differentiation and germinal center responses

T follicular helper (Tfh) cells play critical roles for germinal center responses and effective humoral immunity. We report here that mTOR in CD4 T cells is essential for Tfh differentiation. In Mtorf/f-Cd4Cre mice, both constitutive and inducible Tfh differentiation is severely impaired, leading to defective germinal center B cell formation and antibody production. Moreover, both mTORC1 and mTORC2 contribute to Tfh and GC B cell development but may do so via distinct mechanisms. mTORC1 mainly promotes CD4 T cell proliferation to reach the cell divisions necessary for Tfh differentiation, while Rictor/mTORC2 regulates Tfh differentiation by promoting Akt activation and TCF1 expression without grossly influencing T cell proliferation. Together, our results reveal crucial but distinct roles for mTORC1 and mTORC2 in CD4 T cells during Tfh differentiation and germinal center responses. DOI: http://dx.doi. org/10.7554/eLife.17936. 001
Roles of the Two Active Sites of Somatic Angiotensin‐Converting Enzyme in the Cleavage of Angiotensin I and Bradykinin Insights From Selective Inhibitors

&NA; Somatic angiotensin‐converting enzyme (ACE) contains two homologous domains, each bearing a functional active site. The in vivo contribution of each active site to the release of angiotensin II (Ang II) and the inactivation of bradykinin (BK) is still unknown. To gain insights into the functional roles of these two active sites, the in vitro and in vivo effects of compounds able to selectively inhibit only one active site of ACE were determined, using radiolabeled Ang I or BK, as physiological substrates of ACE. In vitro studies indicated that a full inhibition of the Ang I and BK cleavage requires a blockade of the two ACE active sites. In contrast, in vivo experiments in mice demonstrated that the selective inhibition of either the N‐domain or the C‐domain of ACE by these inhibitors prevents the conversion of Ang I to Ang II, while BK protection requires the inhibition of the two ACE active sites. Thus, in vivo, the cleavage of Ang I and BK by ACE appears to obey to different mechanisms. Remarkably, in vivo the conversion of Ang I seems to involve the two active sites of ACE, free of inhibitor. Based on these findings, it might be suggested that the gene duplication of ACE in vertebrates may represent a means for regulating the cleavage of Ang I differently from that of BK. (Circ Res. 2003;93:148‐154.)
GeneOverlap: An R package to test and visualize gene overlaps

Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.