nils-herrmann/clean_scirepeval huggingface dataset:
Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta analysis of genome wide association studies
Venue: The Lancet Neurology
Year: 2019

Genome wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease.  We did a meta analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation.  Between Oct 1, 2017, and Aug 9, 2018, we analysed 7*8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does) and 1*4 million controls. We identified 90 independent genome wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16 36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow up functional studies. Tissue specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate adjusted p=0*0035 for intracranial volume, p=0*024 for putamen volume) smoking status (p=0*024) and educational attainment (p=0*038) Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8*00 x 10 7) INTERPRETATION These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed up with more diverse data.
Unethical conduct among professionals in the construction industry
Year: 2008

Construction industry is a very challenging and complex sector. The ability to control and communicate with various stages, process and parties to meet the project objectives are not an easy job and these responsibilities are on the professionals shoulders. Besides that, the professionals are also facing their own crisis and dilemma as an ethical professional. This study is focusing on three group of professionals; engineers, architects and quantity surveyors. The objectives of this study are: to identify the elements of unethical conducts; the characteristics and responsibilities needed to avoid unethical conducts; and also trying to identify ways to reduce these problems. 100 sets of questionnaire surveys were distributed to the professionals in Johor and Selangor. From this study, the political and social behavior elements is identified as the most common element of unethical conducts with 90% agreement by the professionals. A total of six characteristics that are listed as important to the professionals which include integrity; accountability; trust; being responsible; self discipline; communications skills and certain personality traits. For the responsibilities needed, including: to protect the interests and welfare of the client; to be loyal and not to engage in conflicts; and the professional as advisor to a client were the highest agreement between the professionals. A successful code of ethics is when the professionals perceive that it was created to guide the behavior of the professionals besides reinforce a company's shared value. The professionals agreed that this method is the best solution to the ethic's problems. The finding of the study can also be used by the industry to increase the level of ethics among the professional in Malaysia.
A tutorial on decomposition methods for network utility maximization
Venue: IEEE Journal on Selected Areas in Communications
Year: 2006

A systematic understanding of the decomposability structures in network utility maximization is key to both resource allocation and functionality allocation. It helps us obtain the most appropriate distributed algorithm for a given network resource allocation problem, and quantifies the comparison across architectural alternatives of modularized network design. Decomposition theory naturally provides the mathematical language to build an analytic foundation for the design of modularized and distributed control of networks. In this tutorial paper, we first review the basics of convexity, Lagrange duality, distributed subgradient method, Jacobi and Gauss Seidel iterations, and implication of different time scales of variable updates. Then, we introduce primal, dual, indirect, partial, and hierarchical decompositions, focusing on network utility maximization problem formulations and the meanings of primal and dual decompositions in terms of network architectures. Finally, we present recent examples on: systematic search for alternative decompositions; decoupling techniques for coupled objective functions; and decoupling techniques for coupled constraint sets that are not readily decomposable
Per oral endoscopic myotomy for esophageal diverticula with or without esophageal motility disorders.
Venue: Clinics and research in hepatology and gastroenterology
Year: 2019

Mid esophageal and epiphrenic diverticula (MED) can be associated with esophageal motility disorders. Per oral endoscopic myotomy (POEM) is an established treatment for esophageal motility disorders that has also been introduced for the treatment of MED.  Data were prospectively collected from patients with MED treated with POEM at our institution. When esophageal motility disorders were present, myotomy was performed extending the myotomy to the lower esophageal sphincter (LES) to treat the motility dysfunction associated with the diverticulum. In the absence of esophageal motility disorder, POEM was performed without including the LES in the myotomy to achieve diverticulotomy.  Four patients were treated with POEM for MED between April 2017 and March 2018. The patients suffered from distal esophageal spasm, jackhammer esophagus or esophago gastric junction outflow obstruction. One patient had no esophageal motility disorder. Diverticulum size was 3 cm in one case and 6 cm in the others. Preoperative Eckardt scores ranged from 6 to 8. No life threatening complications were reported. Intraoperative pneumoperitoneum was described in two cases and one patient experienced aspiration pneumonia. The patients with motility disorders were asymptomatic at 6 8 months follow up. The patient without documented underlying esophageal motility disorder had an Eckardt score of 3 at 9 months follow up. Two cases of gastro esophageal reflux were successfully managed with proton pump inhibitors.  In the case of MED and esophageal motility disorder, POEM permitted treatment of the underlying cause of the diverticulum, achieving favorable early clinical outcomes. In the absence of motility disorder, POEM was feasible with promising early outcomes, and could be a valid alternative to surgical diverticulectomy in selected patients.
CEUS Net: Lesion Segmentation in Dynamic Contrast Enhanced Ultrasound with Feature Reweighted Attention Mechanism
Venue: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)
Year: 2020

Contrast enhanced ultrasound (CEUS) has been a popular clinical imaging technique for the dynamic visualization of the tumor microvasculature. Due to the heterogeneous intra tumor vessel distribution and ambiguous lesion boundary, automatic tumor segmentation in the CEUS sequence is challenging. To overcome these difficulties, we propose a novel network, CEUS Net, which is a novel U net network infused with our designed feature reweighted dense blocks. Specifically, CEUS Net incorporates the dynamic channel wise feature re weighting into the Dense block for adapting the importance of learned lesion relevant features. Besides, in order to efficiently utilize dynamic characteristics of CEUS modality, our model attempts to learn spatial temporal features encoded in diverse enhancement patterns using a multichannel convolutional module. The CEUS Net has been tested on tumor segmentation tasks of CEUS images from breast and thyroid lesions. It results in the dice index of 0.84, and 0.78 for CEUS segmentation of breast and thyroid respectively.
Horizons of modern molecular dynamics simulation in digitalized solid freeform fabrication with advanced materials
Year: 2020

Our ability to shape and finish a component by combined methods of fabrication including (but not limited to) subtractive, additive, and/or no theoretical mass loss/addition during the fabrication is now popularly known as solid freeform fabrication (SFF) Fabrication of a telescope mirror is a typical example where grinding and polishing processes are first applied to shape the mirror, and thereafter, an optical coating is usually applied to enhance its optical performance. The area of nanomanufacturing cannot grow without a deep knowledge of the fundamentals of materials and consequently, the use of computer simulations is now becoming ubiquitous. This article is intended to highlight the most recent advances in the computation benefit specific to the area of precision SFF as these systems are traversing through the journey of digitalization and Industry 4.0. Specifically, this article demonstrates that the application of the latest materials modelling approaches, based on techniques such as molecular dynamics, are enabling breakthroughs in applied precision manufacturing techniques.
Development of a National Physical Activity Plan for the United States.
Venue: Journal of physical activity health
Year: 2014

Efforts to increase population levels of physical activity are increasingly taking the form of strategic plans at national, state/regional, and local levels. The processes employed for developing such plans have not been described previously. The purpose of this article is to chronicle the processes employed in and lessons learned from developing the US National Physical Activity Plan (NPAP) METHODS The Coordinating Committee oversaw development of the NPAP. Key steps in the process included creating a private public coalition based in the private sector, organizing the NPAP around 8 societal sectors, reviewing the evidence base for promotion of physical activity in each sector, conducting a national conference to initiate development of the NPAP's core content, ensuring broad participation in developing and refining the NPAP, and launching the NPAP through a press event that attracted national attention.  The 3 year effort to develop the NPAP was guided by a private public collaborative partnership involving private sector organizations and government agencies. Launched in May 2010, the NPAP included more than 250 evidence based recommendations for changes to policy and practice at the national, state, and local levels across 8 societal sectors.
A Distributed Ambient Backscatter MAC Protocol for Internet of Things Networks
Venue: IEEE Internet of Things Journal
Year: 2020

Ambient backscatter communication enabling device to device (D2D) communications via the ambient radio frequency (RF) signal has revealed its numerous application potential in the Internet of Things (IoT) networks. However, the work on the link layer for the backscatter communication is in its infancy due to the constraints of ultralow power and cost in such a system, especially a channel access protocol in the backscatter communication system for IoT networks is rarely mentioned. In this article, a distributed multiple access control (MAC) protocol is presented, which allows multiple backscatter devices (BDs) to connect with each other by relying on the ambient RF signal. By combining an analog channel sensing strategy with the dual backoff mechanism, each BD can switch among the transmission, receiving, and energy harvesting (EH) states. Specifically, each BD starts a randomly designated time for EH once the channel is sensed to be busy. As the timer expires, the BD ceases the EH and continues its sensing and backoff procedures. With the consideration of the false alarm and the miss detection problems occurring while sensing, an enhanced 3 D Markov model is built to analyze the saturation throughput performance of the proposed MAC protocol. Extensive simulations verify the analysis and demonstrate the advantage of the proposed backscatter MAC protocol.
The Tom Oppe Lecture: Behavioural phenotypes and child psychiatry
Year: 2008

The concept of a behavioural phenotype was first introduced by Nyhan (1972) when he described a characteristic behaviour of self mutilation in Lesch Nyhan Syndrome. Later, Flint and Yule (1994) pointed out that a behavioural phenotype is a characteristic pattern of motor, cognitive, linguistic and social abnormalities that is consistently associated with a biological disorder. In some instances the behavioural phenotype may represent a psychiatric disorder, in others there may be behaviours that usually will not be regarded as a psychiatric disorder. Dykens (1995) added that a behavioural phenotype may best be described as the heightened probability that people with a given syndrome will be characterized by certain behavioural sequelae. The implications of this are (i) that there is a certain amount of within syndrome variability, (ii) that there is total vs. partial specificity of certain behaviours, (iii) that behavioural phenotypes relate to various behavioural domains, (iv) that behavioural phenotypes have indirect effects on the behaviour of caretakers, and (v) that developmental and contextual factors in addition to genetic factors contribute to behavioural phenotypes (Hodapp Dykens, 2007) The rather recent interest in the concept of behavioural phenotypes has renewed the interest of Child and Adolescent Psychiatry in intellectual disability issues that had been lost for decades. It also increased interest in the genetic origins of mental disorders and behavioural abnormalities with an interaction of two major recent scientific developments in the field. One of these trends is represented by the rapid progress in molecular biology that has led to a better understanding of the genetic mechanisms contributing to psychopathology. The other trend is based on the development of more and more refined instruments for the dimensional assessment of adaptive and maladaptive behaviours which have supplemented the classical categorical approach of assessment in child psychopathology. With this theoretical underpinning, the study of behavioural phenotypes has become an attractive research domain in child and adolescent psychiatry. In addition, there are also practical implications in terms of improving communication among experts and lay person both on assessment and counselling.
Black, Asian and Minority Ethnic groups in England are at increased risk of death from COVID 19: indirect standardisation of NHS mortality data
Venue: Wellcome open research
Year: 2020

International and UK data suggest that Black, Asian and Minority Ethnic (BAME) groups are at increased risk of infection and death from COVID 19. We aimed to explore the risk of death in minority ethnic groups in England using data reported by NHS England.  We used NHS data on patients with a positive COVID 19 test who died in hospitals in England published on 28th April, with deaths by ethnicity available from 1st March 2020 up to 5pm on 21 April 2020. We undertook indirect standardisation of these data (using the whole population of England as the reference) to produce ethnic specific standardised mortality ratios (SMRs) adjusted for age and geographical region.  The largest total number of deaths in minority ethnic groups were Indian (492 deaths) and Black Caribbean (460 deaths) groups. Adjusting for region we found a lower risk of death for White Irish (SMR 0.52; 95%CIs 0.45 0.60) and White British ethnic groups (0.88; 95%CIs 0.86 0.0.89) but increased risk of death for Black African (3.24; 95%CIs 2.90 3.62) Black Caribbean (2.21; 95%CIs 2.02 2.41) Pakistani (3.29; 95%CIs 2.96 3.64) Bangladeshi (2.41; 95%CIs 1.98 2.91) and Indian (1.70; 95%CIs 1.56 1.85) minority ethnic groups.  Our analysis adds to the evidence that BAME people are at increased risk of death from COVID 19 even after adjusting for geographical region, but was limited by the lack of data on deaths outside of NHS settings and ethnicity denominator data being based on the 2011 census. Despite these limitations, we believe there is an urgent need to take action to reduce the risk of death for BAME groups and better understand why some ethnic groups experience greater risk. Actions that are likely to reduce these inequities include ensuring adequate income protection, reducing occupational risks, reducing barriers in accessing healthcare and providing culturally and linguistically appropriate public health communications.
Just doing what I do: on the awareness of fluent agency
Year: 2017

Hubert Dreyfus has argued that cases of absorbed bodily coping show that there is no room for self awareness in flow experiences of experts. In this paper, I argue against Dreyfus' maxim of vanishing self awareness by suggesting that awareness of agency is present in expert bodily action. First, I discuss the phenomenon of absorbed bodily coping by discussing flow experiences involved in expert bodily action: merging into the flow; immersion in the flow; emergence out of flow. I argue against the claim that flow experience does not involve an awareness of agency for each of these features, while conceding that fluent agency does not involve self awareness in the thetic sense. I challenge the assumption that the awareness of fluent agency must be understood in terms of a thetic awareness of agency. Instead, I develop an Anscombean account of the awareness of fluent agency in terms of the phenomenal character of knowing one's aims. I respond to the challenge that if an Anscombean account of the awareness of agency is to succeed, then agents must be able to answer Anscombean questions. I consider the objection that awareness of agency is not a form of self awareness by outlining an account of self awareness as self synthesis that is distinct from self perception and self ascription, but which makes room for self awareness in expert bodily action.
A pedagogical evaluation of accessible settings in Google's Android and Apple's IoS mobile operating systems and native apps using the SAMR model of educational technology and an educational model of technical captial
Year: 2015

This article describes an investigation into the potential of mobile operating systems and native apps to transform educational inclusion for disabled students. It is framed by a philosophy of inclusive technology, which theorises that contemporary technologies, such as the World Wide Web, netbooks, tablets and smartphones, could possibly increase the social inclusion of people with disabilities, as these technologies are more portable, provide greater social access to institutional environments and communities, are more socially acceptable and allow greater social communication than traditional assistive technologies. By drawing reference to this philosophy, the article evaluates the accessible software available in Google's Android and Apple's iOS operating systems for tablets and smart phones. These systems were chosen as previous literature observes that they offer provision for students with disabilities, and their manufacturers have claimed that they are amongst the most accessible technologies on the market. Two instruments are used to evaluate these devices: (1) A sociological model of technical capital: This model is based on Bourdieu's theory of social capital, and is premised on the notion that access to technology, either through financial, geographical, intellectual or physical means, increases life chances and access to financial capital, social equality and access to higher levels of education; (2) The SAMR Model of Educational Technology: This model is premised on the theory that educational applications of technology are premised on the transformation or enhancement of traditional pedagogies, either through the substitution, augmentation, modification or redefinition of educational tasks. The evaluation of these mobile operating systems concentrates on their use in three staple study skills: (1) The making and sharing notes in written, audio and video formats; (2) The organisation of information in the form of text based, audio and video files; (3) The recording of still images, audio and video files. The evaluation finds that both operating systems have similarly effective accessible settings in terms of their ability to enlarge text, reverse colours and save and change the quality of audio and video files. However, it is found that Android has better native facilities for audio recording, organizing and sharing files, and Apple iOS has an advantage in terms of its ability to photograph in photo negative and create time lapse recordings. However, there are issues with both operating systems in terms of pricing, potential ease of use, and cultural diversity. The evaluation concludes that these mobile operating systems have the potential to be used for tasks discussed in the SAMR model, but both systems still need to improve a number of features in order to make their potential technical capital more socially accessible.