LLukas22/scidocs huggingface dataset:
High-resolution array CGH defines critical regions and candidate genes for microcephaly, abnormalities of the corpus callosum, and seizure phenotypes in patients with microdeletions of 1q43q44

Microdeletions of 1q43q44 result in a recognizable clinical disorder characterized by moderate to severe intellectual disability (ID) with limited or no expressive speech, characteristic facial features, hand and foot anomalies, microcephaly (MIC), abnormalities (agenesis/hypogenesis) of the corpus callosum (ACC), and seizures (SZR). Critical regions have been proposed for some of the more prominent features of this disorder such as MIC and ACC, yet conflicting data have prevented precise determination of the causative genes. In this study, the largest of pure interstitial and terminal deletions of 1q43q44 to date, we characterized 22 individuals by high-resolution oligonucleotide microarray-based comparative genomic hybridization. We propose critical regions and candidate genes for the MIC, ACC, and SZR phenotypes associated with this microdeletion syndrome. Three cases with MIC had small overlapping or intragenic deletions of AKT3, an isoform of the protein kinase B family. The deletion of only AKT3 in two cases implicates haploinsufficiency of this gene in the MIC phenotype. Likewise, based on the smallest region of overlap among the affected individuals, we suggest a critical region for ACC that contains ZNF238, a transcriptional and chromatin regulator highly expressed in the developing and adult brain. Finally, we describe a critical region for the SZR phenotype which contains three genes (FAM36A, C1ORF199, and HNRNPU). Although ~90% of cases in this study and in the literature fit these proposed models, the existence of phenotypic variability suggests other mechanisms such as variable expressivity, incomplete penetrance, position effects, or multigenic factors could account for additional complexity in some cases.
Workshop on teaching ethics in software engineering programmes

To operate effectively in today¿s volatile software industry, graduates from Software Engineering programmes need to be equipped with knowledge of both real world situations and best Software Engineering practice. This knowledge should include relevant aspects of ethical, professional, and legal issues and there should be recognition that facing ethical dilemmas is highly likely to be an integral part of the graduate¿s eventual career.
Bag-of-Words Image Representation: Key Ideas and Further Insight

In the context of object and scene recognition, state-of-the-art performances are obtained with visual Bag-of-Words (BoW) models of mid-level representations computed from dense sampled local descriptors (e.g., Scale-Invariant Feature Transform (SIFT)). Several methods to combine low-level features and to set mid-level parameters have been evaluated recently for image classification. In this chapter, we study in detail the different components of the BoW model in the context of image classification. Particularly, we focus on the coding and pooling steps and investigate the impact of the main parameters of the BoW pipeline. We show that an adequate combination of several low (sampling rate, multiscale) and mid-level (codebook size, normalization) parameters is decisive to reach good performances. Based on this analysis, we propose a merging scheme that exploits the specificities of edge-based descriptors. Low and high contrast regions are pooled separately and combined to provide a powerful representation of images. We study the impact on classification performance of the contrast threshold that determines whether a SIFT descriptor corresponds to a low contrast region or a high contrast region. Successful experiments are provided on the Caltech-101 and Scene-15 datasets. M. T. Law (B) · N. Thome · M. Cord LIP6, UPMC—Sorbonne University, Paris, France e-mail: Marc.Law@lip6.fr N. Thome e-mail: Nicolas.Thome@lip6.fr M. Cord e-mail: Matthieu.Cord@lip6.fr B. Ionescu et al. (eds.), Fusion in Computer Vision, Advances in Computer 29 Vision and Pattern Recognition, DOI: 10.1007/978-3-319-05696-8_2, © Springer International Publishing Switzerland 2014
Effect of triple-h prophylaxis on global end-diastolic volume and clinical outcomes in patients with aneurysmal subarachnoid hemorrhage.

BACKGROUND
Although prophylactic triple-H therapy has been used in a number of institutions globally to prevent delayed cerebral ischemia (DCI) after subarachnoid hemorrhage (SAH), limited evidence is available for the effectiveness of triple-H therapy on hemodynamic variables. Recent studies have suggested an association between low global end-diastolic volume index (GEDI), measured using a transpulmonary thermodilution method, and DCI onset. The current study aimed at assessing the effects of prophylactic triple-H therapy on GEDI.


METHODS
This prospective multicenter study included aneurysmal SAH patients admitted to 9 hospitals in Japan. The decision to administer prophylactic triple-H therapy and the management protocols were left to the physician in charge (physician-directed therapy) of each participating institution. The primary endpoints were the changes in the hemodynamic variables as analyzed using a generalized linear mixed model.


RESULTS
Of 178 patients, 62 (34.8 %) received prophylactic triple-H therapy and 116 (65.2 %) did not. DCI was observed in 35 patients (19.7 %), with no significant difference between the two groups [15 (24.2 %) vs. 20 (17.2 %), p = 0.27]. Although a greater amount of fluid (p < 0.001) and a higher mean arterial pressure (p = 0.005) were observed in the triple-H group, no significant difference was observed between the groups in GEDI (p = 0.81) or cardiac output (p = 0.62).


CONCLUSIONS
Physician-directed prophylactic triple-H administration was not associated with improved clinical outcomes or quantitative hemodynamic indicators for intravascular volume. Further, GEDI-directed intervention studies are warranted to better define management algorithms for SAH patients with the aim of preventing DCI.
An Experimental Test of the Impact of Overconfidence and Gender on Trading Activity

We perform an asset market experiment in order to investigate whether overconfidence induces trading. We investigate three manifestations of overconfidence: calibration-based overconfidence, the better-than-average effect and illusion of control. Novelly, the measure employed for calibration-based overconfidence is task-specific in that it is designed to influence behavior. We find that calibration-based overconfidence does engender additional trade, though the better-than-average also appears to play a role. This is true both at the level of the individual and also at the level of the market. There is little evidence that gender influences trading activity. JEL Classification: G10, G11, G12, G14 The authors gratefully acknowledge the co-editor’s valuable suggestions in improving the paper’s exposition and two anonymous referrers’ valuable comments. In addition, the authors would like to thank the very helpful comments of Lucy Ackert, Ben Amoako-Adu, Bruno Biais, Tim Cason, Narat Charupat, Günter Franke, Simon Gervais, Markus Glaser, Patrik Guggenberger, Michael Haigh, Joachim Inkmann, Marhuenda Joaquin, Alexander Kempf, Brian Kluger, Roman Kraeussl, Bina Lehmann, Tao Lin, Harald Lohre, Greg Lypny, Elizabeth Maynes, Moshe Milevsky, Dean Mountain, Gordon Roberts, Chris Robinson, Stefan Rünzi, Gideon Saar, Dirk Schiereck, Harris Schlesinger, Chuck Schnitzlein, Michael Schröder, Betty Simkins, Brian Smith, Issouf Soumare, Yisong Tian, Chris Veld, Boyce Watkins, Martin Weber and Stephan Wiehler, along with seminar participants from American Finance Association 2005 (Philadelphia), the Economic Science Association 2004 (Amsterdam), the Financial Management Association 2004 (New Orleans), the Financial Management Association European Meeting 2004 (Zurich), European Financial Management Association 2004 (Basle), the Northern Finance Association (St. John’s, Newfoundland), the 2004 Symposium for Experimental Finance at the Aston Centre for Experimental Finance (Aston Business School), the 2005 Federal Reserve Bank of Atlanta Experimental Finance Conference, the University of Köln, the University of Konstanz, McMaster University, the University of Tilburg, Wilfred Laurier University and York University. Valuable technical assistance was provided by Harald Lohre, Amer Mohamed and John O’Brien. Generous financial assistance from ZEW, Institut de Finance Mathématiques de Montréal and SSHRC is gratefully acknowledged. Any views expressed represent those of the authors only and not necessarily those of McKinsey & Company, Inc. C © The Authors 2008. Published by Oxford University Press on behalf of the European Finance Association. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 556 RICHARD DEAVES, ERIK LÜDERS, AND GUO YING LUO
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing

Summary
CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss.


Availability and implementation
CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine.


Contact
jkoca@ceitec.cz.


Supplementary information
Supplementary data are available at Bioinformatics online.
Efficacy and safety of single fecal microbiota transplantation for Japanese patients with mild to moderately active ulcerative colitis

The clinical utility of fecal microbiota transplantation (FMT) in patients with ulcerative colitis (UC) is still controversial. We investigated the efficacy and safety of single FMT for patients with mild to moderately active UC in a Japanese population. Fifty-seven patients were evaluated for eligibility, and 16 patients were excluded. Forty-one patients with UC refractory to standard medical therapy were treated with single FMT by colonoscopic administration. Changes in the fecal microbiota were assessed by 16S ribosomal DNA based terminal restriction fragment length polymorphism analysis. At 8 weeks after FMT, no patient achieved clinical remission, and 11 of 41 patients (26.8 %) showed clinical response. The full Mayo score and the Mayo clinical score significantly decreased at week 8 [full Mayo score 5.5 ± 2.4 (mean ± standard deviation) at initiation and 4.6 ± 2.2 at week 8, P < 0.004; Mayo clinical score 4.0 ± 2.0 at initiation and 3.0 ± 1.9 at week 8, P < 0.001], but there were no statistically significant effects on the Mayo endoscopic score. No adverse events occurred after FMT or during the follow-up period of 8 weeks. The proportion of Bifidobacterium was significantly higher in the donor feces used for responders than in the donor feces used for nonresponders. The proportion of Lactobacillales and Clostridium cluster IV were significantly higher in the donor feces used for nonresponders. Single FMT by colonoscopy was performed safely in all patients, but sufficient clinical efficacy and microbial restoration were not confirmed in patients with mild to moderately active UC.
Seven Theories of Human Nature

INTRODUCTION: RIVAL THEORIES AND CRITICAL ASSESSMENTS 1. Confucianism: the Way of the Sages by David Haberman 2. Upanishadic Hinduism: Quest for Ultimate Knowledge by David Haberman 3. Buddhism: In the Footsteps of the Buddha by David Haberman 4. Plato: the Rule of Reason 5. Aristotle: the Ideal of Human Fulfilment 6. The Bible: Humanity in relation to God HISTORICAL INTERLUDE 7. Kant: Reasons and Causes, History and Religion 8. Marx: The Economic Basis of Human Nature 9. Sartre: Atheistic Existentialism 10. Darwinian Theories of Human Nature CONCLUSION: TOWARDS A SYNTHESIS OF THE THEORIES?
Comparison of in-hospital and longer-term outcomes of hybrid and Norwood stage 1 palliation of hypoplastic left heart syndrome.

OBJECTIVES
The hybrid approach for the initial management of hypoplastic left heart syndrome shifts the risks of major open surgery from the vulnerable neonatal period to an older age. This study determined differences between the hybrid and the standard Norwood procedures in postoperative in-hospital mortality, renal failure, and survival to at least 2 years of age.


METHODS
Data from the Pediatric Health Information System, a detailed hospital discharge database of 43 freestanding children's hospitals, were analyzed. The Pediatric Health Information System includes demographic information, diagnosis, and procedure and clinical service data. Instrumental variable regression techniques were used to estimate the predicted probability of in-hospital mortality, renal failure, and survival to 24 months of age for infants with hypoplastic left heart syndrome who received a hybrid or Norwood procedure. The statistical models controlled for demographics and comorbid chromosomal anomalies.


RESULTS
A total of 3654 infants with hypoplastic left heart syndrome underwent intervention from 1998 to 2012. Of these, 242 underwent the hybrid approach and the remainder underwent the Norwood procedure. Instrumental variable models showed significantly reduced odds of patients who underwent the hybrid approach being diagnosed with renal failure (adjusted risk ratio [ARR], 0.48; 95% confidence interval [CI], 0.26-0.89); increased odds of surviving initial hospitalization (ARR, 1.28; 95% CI, 1.06-1.55); increased odds of survival, indicated by readmissions more than 6 months after initial hospitalization (ARR, 1.53; 95% CI, 1.05-2.22); and a decrease in length of stay by 20 days for the initial surgical hospitalization (95% CI, -27.4 to -13.9).


CONCLUSIONS
The short term hospital-based outcomes and longer-term survival outcomes of the hybrid approach for hypoplastic left heart syndrome may be better than those of the Norwood procedure.
Human Resource Management System

The paper titled “HUMAN RESOURCE MANAGEMENT SYSTEM” is basically concerned with managing the Administrator of HUMAN RESOURCE Department in a company. A Human Resource Management System (HRMS), refers to the systems and processes at the intersection between human resource management (HRM) and information technology. It merges HRM as a discipline and in particular its basic HR activities and processes with the information technology field, whereas the programming of data processing systems evolved into standardized routines and packages of enterprise resource planning (ERP) software[1]. The main objective of this paper is to reduce the effort of Administrator to keep the daily events such as attendance, projects, works, appointments, etc. This paper deals with the process of identifying the employees, recording their attendance hourly and calculating their effective payable hours or days. This paper should maintain the records of each and every employee and their time spend in to company, which can be used for performance appraisal. Based on that transfer, removal, promotion can be done. Keyword: Human Resource, Administrator, Employee
Branch technical position on the use of expert elicitation in the high-level radioactive waste program

AlESTRACT The U.S. Department of Energy (DOE) is conducting a program of site characterization to gather enough information, about the Yucca Mountain (Nevada) site, to be able to evaluate the waste isolation capabilities of a potential geologic repository. Should the site be found suitable, DOE will apply to the U.S. Nuclear Regulatory Commission for permission to construct and then operate a proposed geologic repository for the disposal of spent nuclear fuel and other high-level radioactive waste at Yucca Mountain. In deciding whether to grant or deny DOE's license application for a geologic repository, NRC will closely examine the facts and expert judgment set forth in any potential DOE license application. NRC expects that subjective judgments of individual experts and, in some cases, groups of experts, will be used by DOE to interpret data obtained during site characterization and to address the many technical issues and inherent uncertainties associated with predicting the performance of a repository system for thousands of years. NRC has traditionally accepted, for review, expert judgment to evaluate and interpret the factual bases of license applications and is expected to give appropriate consideration to the judgments of DOE's experts regarding the geologic repository. Such consideration, however, envisions DOE using expert judgments to complement and supplement other sources of scientific and technical information, such as data collection, analyses, and experimentation. In this document, the NRC staff has set forth technical positions that: (1) provide general guidelines on those circumstances that may warrant the use of a formal process for obtaining the judgments of more than one expert (i.e., expert elicitation); and (2) describe acceptable procedures for conducting expert elicitation when formally elicited judgments are used to support a demonstration of compliance with NRC's geologic disposal regulation, currently set forth in 10 CFR Part 60. In this NUREG, the staff also provides an expanded definition of "peer review" over that provided earlier in NUJREG-1297. FOREWORD This Branch Technical Position (BTP) was developed only for application to the high-level waste program, as part of the staff's Iterative Performance Assessment efforts. The technical positions contained here reflect staff experience gained from both monitoring the U.S. Department of Energy's site characterization program at Yucca Mountain, Nevada, and developing the U.S. Nuclear Regulatory Commission's independent regulatory capability. Although there are several examples of the use of expert elicitation in a nuclear regulatory context, no formal Agency guidance on this subject exists. Thus, in developing …
Open problems on k-orbit polytopes

Abstract We present 35 open problems on combinatorial, geometric and algebraic aspects of k -orbit abstract polytopes. We also present a theory of rooted polytopes that has appeared implicitly in previous work but has not been formalized before.
Types of arcs in a fuzzy graph

Article history: Received 31 December 2007 Received in revised form 12 December 2008 Accepted 3 January 2009
Is the brain really a small-world network?

It is commonly assumed that the brain is a small-world network (e.g., Sporns and Honey 2006). Indeed, one of the present authors claimed as much 15 years ago (Hilgetag et al. 2000). The small-worldness is believed to be a crucial aspect of efficient brain organization that confers significant advantages in signal processing (e.g., LagoFernández et al. 2000). Correspondingly, the small-world organization is deemed essential for healthy brain function, as alterations of small-world features are observed in patient groups with Alzheimer’s disease (Stam et al. 2007), autism (Barttfeld et al. 2011) or schizophrenia spectrum diseases (Liu et al. 2008; Wang et al. 2012; Zalesky et al. 2011). While the colloquial idea of a small, interconnected world has a long tradition (e.g., Klemperer 1938), the present concept of small-world features of networks is frequently associated with the Milgram experiment (Milgram 1967) that demonstrated surprisingly short paths across social networks (‘six degrees of separation’). The concept was formalized by Watts and Strogatz (1998), who derived small-world networks from regular networks by including a small proportion of random network shortcuts. Such an organization results in short paths across the whole network—almost as small as in random networks—combined with local ‘cliquishness’ (or clustering) of neighboring nodes, due to dense local interconnections. These features can be mathematically summarized by the smallworld coefficient (Humphries et al. 2006), which is defined as the clustering coefficient of a given network (normalized by the clustering coefficient of a same-size random network) divided by the network’s normalized average shortest pathlength. While any network that has a smallworld coefficient larger than one is formally a small-world network, for many researchers, the term has become associated with the specific Watts and Strogatz model that is based on the partial random rewiring of a regular network (Fig. 1a). Indeed, the estimation of the rewiring probability has been used to directly associate real-world networks with the Watts and Strogatz model (Humphries and Gurney 2008). Incidentally, the small-world coefficient might not faithfully capture the small-world property as originally described by Watts and Strogatz (1998). Therefore, an alternative coefficient has been proposed that compares the clustering of the network to a lattice instead of a random network (Telesford et al. 2011). A large number of empirical network data conform to the small-world features of short paths combined with high clustering, including many neural networks—but do these Electronic supplementary material The online version of this article (doi:10.1007/s00429-015-1035-6) contains supplementary material, which is available to authorized users.
Velo: A Knowledge-Management Framework for Modeling and Simulation

Velo is a reusable, domain-independent knowledge-management infrastructure for modeling and simulation. Velo leverages, integrates, and extends Web-based open source collaborative and data-management technologies to create a scalable and flexible core platform tailored to specific scientific domains. As the examples here describe, Velo has been used in both the carbon sequestration and climate modeling domains.