bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test–retest reliability of RC21X: a web-based cognitive and neuromotor performance measurement tool
Authors: Saganis Xanthia , Goreczny Anthony J , Kondraske George , Berman Masha , Comnick Ian , Allen Tyler , Nussbaum Paul D 
Published: August 2020

Abstract

Objective
As computerized cognitive testing becomes increasingly popular in clinical and research settings, conducting studies on efficacy and psychometric properties is essential. One such program is RC21X, a web-based brain performance measurement tool. Based on empirically supported neurocognitive and neuromotor tasks, the 12-min test consists of 15 modules measuring memory, motor coordination, processing speed, and executive functioning. Because individuals may use RC21X repeatedly to track changes in cognitive performance, establishing reliability of the program is imperative. The current study examined test–retest reliability of RC21X within a 2-week period.

Method
The sample consisted of 222 individuals: 192 (86.5%) were male, and 30 (13.5%) were female. Average age was 44.06 years (SD = 17.76), with ages ranging from 7 to 82 years. We computed Pearson’s correlation coefficients for module and composite scores to determine reliability between performance at times 1 and 2.

Results
All correlations were statistically significant (p &lt; .001). The 2-week test–retest reliability for composite score was 0.72, with subtest coefficients ranging from 0.54 on an auditory memory recognition task to 0.89 on a finger tapping task. We replicated these analyses with participants’ (n = 43) test sessions 3 and 4; we found similar results to those from test 1 and test 2 analyses, suggesting stability of results over multiple administrations.

Conclusions
Results for RC21X were comparable to existing literature that supports moderate to high reliability of other computer-based tests. Although future research needs to investigate validity of RC21X, our findings support potential applications in research, clinical use, and personal brain performance measurement.
HaploGrouper: a generalized approach to haplogroup classification
Authors: Jagadeesan Anuradha , Ebenesersdóttir S Sunna , Guðmundsdóttir Valdis B , Thordardottir Elisabet Linda , Moore Kristjan H S , Helgason Agnar 
Published: August 2020

Abstract

Motivation
We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.

Results
HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species—given an extant annotated phylogenetic tree defined by sequence variants.

Availability and implementation
The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Machine Learning-Based Model to Evaluate Readability and Assess Grade Level for the Web Pages
Authors: Pantula Muralidhar , Kuppusamy K S 
Published: August 2020

AbstractEvaluating readability of web documents has gained attention due to several factors such as improving the effectiveness of writing and to reach a wider spectrum of audience. Current practices in this direction follow several statistical measures in evaluating readability of the document. In this paper, we have proposed a machine learning-based model to compute readability of web pages. The minimum educational standards required (grade level) to understand the contents of a web page are also computed. The proposed model classifies the web pages into highly readable, readable or less readable using specified feature set. To classify a web page with the aforementioned categories, we have incorporated the features such as sentence count, word count, syllable count, type-token ratio and lexical ambiguity. To increase the usability of the proposed model, we have developed an accessible browser extension to perform the assessments of every web page loaded into the browser.
Cronkhite–Canada syndrome: from clinical features to treatment
Authors: Wu Ze-Yu , Sang Li-Xuan , Chang Bing 
Published: August 2020

AbstractCronkhite–Canada syndrome (CCS) is a rare acquired polyposis with unknown etiology. To date, &gt;500 cases have been reported worldwide. CCS is typically characterized by gastrointestinal symptoms, such as diarrhea and skin changes (e.g. alopecia, pigmentation, and nail atrophy). Endoscopic features include diffuse polyps throughout the entire gastrointestinal tract, except for the esophagus. Pathological types of polyps in CCS mainly include inflammatory, hyperplastic, hamartomatous, and adenomatous polyps. CCS can be complicated by many diseases and has a canceration tendency with a high mortality rate. Moreover, there is no uniform standard treatment for CCS. A review of the reported cases of CCS is presented herein, with the goal of improving our understanding of this disease.
Health reform and Indigenous health policy in Brazil: contexts, actors and discourses
Authors: de M Pontes Ana Lucia , Santos Ricardo Ventura 
Published: August 2020

AbstractGiven the challenges related to reducing socio-economic and health inequalities, building specific health system approaches for Indigenous peoples is critical. In Brazil, following constitutional reforms that led to the universalization of health care in the late 1980s, a specific health subsystem was created for Indigenous peoples in 1999. In this paper, we use a historical perspective to contextualize the creation of the Indigenous Health Subsystem in Brazil. This study is based on data from interviews with Indigenous and non-Indigenous subjects and document-based analysis. In the 1980s, during the post-dictatorship period in Brazil, the emergence of Indigenous movements in the country and the support for pro-Indigenous organizations helped establish a political agenda that emphasized a broad range of issues, including the right to a specific health policy. Indigenous leaders established alliances with participants of the Brazilian health reform movement, which resulted in broad debates about the specificities of Indigenous peoples, and the need for a specific health subsystem. We highlight three main points in our analysis: (1) the centrality of a holistic health perspective; (2) the emphasis on social participation; (3) the need for the reorganization of health care. These points proved to be convergent with the development of the Brazilian health reform and were expressed in documents of the Indigenist Missionary Council (CIMI) and the Union of Indigenous Nations (UNI). They were also consolidated in the final report of the First National Conference on the Protection of Indigenous Health in 1986, becoming the cornerstone of the national Indigenous health policy declared in 1999. Our analysis reveals that Indigenous people and pro-Indigenous groups were key players in the development of the Indigenous Health Subsystem in Brazil.
Predictors of nursing leadership in Uganda: a cross-sectional study
Authors: Nanyonga Rose Clarke , Bosire Edna N , Heller David J , Bradley Elizabeth , Reynolds Nancy R 
Published: August 2020

Abstract
Evidence regarding the role of nurses-in-leadership and how to engage nurses in policy decisions is minimal in sub-Saharan Africa. The purpose of this study was: (1) to assess the leadership practices of nurses-in-leadership in Uganda (by self-report) and from the perspective of ‘followers’ (direct-report, peers, co-workers, other); and (2) to determine factors (positively) associated with leadership practices. We surveyed 480 nurses, 120 in leadership roles (Response Rate 57%) and 360 ‘followers’ (Response Rate 60%), who were recruited from five hospitals in Kampala, Uganda. We used the Leadership Practice Inventory (Self and Observer), a project-specific demographic questionnaire and Denison’s Organizational Culture Survey (DOCS). Sixty-three per cent of the respondents held a registered nursing certificate; 79% had received formal leadership training; 47% were based in private for-profit (PFP) hospitals, 28% in private not-for-profit (PNFP) and 25% in public hospitals. Among the five leadership practices, nurses-in-leadership used the practice of Model the Way (M = 8.27, SD = 1.30), Challenge the Process (M = 8.12, SD = 1.30) and Encourage the Heart (M = 8.04, SD = 1.51) more frequently (on a 10-point Likert Scale). Inspire a Shared Vision (M = 7.82, SD = 1.57) and Enable Others to Act (M = 7.62, SD = 1.66) practices were used less frequently. The same rank order was true for leadership scores from the perception of followers. However, leadership scores by followers were significantly lower (P &lt; 0.01) than the nurse leader self-reported scores across all sub-scales. Leadership practice scores were higher in public than private hospitals (P &lt; 0.0001). Organizational culture (OC) was associated (P &lt; 0.001) with leadership practices. Although overall leadership practice scores were generally high, the less frequent use of Inspire and Enable practices suggests opportunities for targeted improvement. Moreover, differences between self-reported and leadership scores by followers suggest perception gaps between leaders and their followers. The positive relationship between public hospital settings and self-reported leadership practices among nurses-in-leadership suggests that important nursing leadership practices are possible even in a low-resource clinical setting.
Molecular dynamics simulations informed by membrane lipidomics reveal the structure–interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii
Authors: Jiang Xukai , Yang Kai , Yuan Bing , Han Meiling , Zhu Yan , Roberts Kade D , Patil Nitin A , Li Jingliang , Gong Bin , Hancock Robert E W , Velkov Tony , Schreiber Falk , Wang Lushan , Li Jian 
Published: August 2020

Abstract

Background
MDR bacteria represent an urgent threat to human health globally. Polymyxins are a last-line therapy against life-threatening Gram-negative ‘superbugs’, including Acinetobacter baumannii. Polymyxins exert antimicrobial activity primarily via permeabilizing the bacterial outer membrane (OM); however, the mechanism of interaction between polymyxins and the OM remains unclear at the atomic level.

Methods
We constructed a lipid A-based OM model of A. baumannii using quantitative membrane lipidomics data and employed all-atom molecular dynamics simulations with umbrella sampling techniques to elucidate the structure–interaction relationship and thermodynamics governing the penetration of polymyxins [B1 and E1 (i.e. colistin A) representing the two clinically used polymyxins] into the OM.

Results
Polymyxin B1 and colistin A bound to the A. baumannii OM by the initial electrostatic interactions between the Dab residues of polymyxins and the phosphates of lipid A, competitively displacing the cations from the headgroup region of the OM. Both polymyxin B1 and colistin A formed a unique folded conformation upon approaching the hydrophobic centre of the OM, consistent with previous experimental observations. Polymyxin penetration induced reorientation of the headgroups of the OM lipids near the penetration site and caused local membrane disorganization, thereby significantly increasing membrane permeability and promoting the subsequent penetration of polymyxin molecules into the OM and periplasmic space.

Conclusions
The thermodynamics governing the penetration of polymyxins through the outer leaflet of the A. baumannii OM were examined and novel structure–interaction relationship information was obtained at the atomic and membrane level. Our findings will facilitate the discovery of novel polymyxins against MDR Gram-negative pathogens.
Rules and validation processes for interoperable BIM data exchange
Authors: Lee Yong-Cheol , Eastman Charles M , Solihin Wawan 
Published: August 2020

Abstract
Diverse industries have recognized the significance of a neutral data standard for seamless building information modeling (BIM) data exchanges and adopted commonly agreed schemes such as the industry foundation classes (IFC) schema for enhancing BIM data interoperability. To selectively employ domain-specific data exchange requirements, the AEC-FM (the Architecture, Engineering, Construction, and Facility Management) industries have developed their own schema with a subset of the IFC schema, named a model view definition (MVD). However, because of latent human errors, inadequate MVD definitions, and error-prone data mapping problems, the adoption of IFC for exchanging and sharing BIM data is frequently limited with severe data integrity issues. This challenging situation requires the detailed examination of the limitations of the heterogeneous IFC translation processes of the current BIM authoring and application tools. To accomplish this objective, the authors thoroughly investigated the two MVDs, the Coordination View Version 2.0 and the Construction Operations Building Information Exchange, broadly used as an international standard for developing the IFC translation processes, and then identified their intrinsic requirements/rules and developed rule-based data validation processes. These new intrinsic knowledge of the two MVD specifications will be fundamental foundations to create coherent BIM data exchange systems that are currently scattered and dispersed in heterogeneous IFC translation processes and structures. Newly revealed rules pertaining to these two MVDs have been executed with IfcDoc, which is the IFC documentation tool. This BIM data validation process is expected to not only accurately evaluate the translation processes between BIM native data and IFC ones but also help industry professionals ensure the integrity and the accuracy of their BIM data according to the BIM data exchange standards using the two MVDs. In addition, the outcomes of this research study are expected to bolster the interoperable BIM adoption and offer the values of greater consistency of BIM data exchange.
Stereotactic body radiation therapy using CyberKnife for T1N0M0 lung cancer patients with severe pulmonary dysfunction
Authors: Abe Takanori , Ryuno Yasuhiro , Saito Satoshi , Aoshika Tomomi , Igari Mitsunobu , Hirai Ryuta , Kumazaki Yu , Kaira Kyoichi , Kagamu Hiroshi , Ishida Hironori , Noda Shin-ei , Kato Shingo 
Published: August 2020

Abstract
We retrospectively investigated the efficacy and safety of stereotactic body radiotherapy (SBRT) for T1N0M0 lung cancer using CyberKnife (CK) among 13 patients with severe pulmonary dysfunction which was defined as forced expiratory volume in 1 s (FEV1.0) of &lt;1 L. The prescribed dose was 54 Gy in 3 fractions but adjusted for some patients if their tumors were in close proximity to the organs at risk (54 Gy/3 fractions: n = 11; 50 Gy/5 fractions: n = 1; 60 Gy/8 fractions: n = 1). During follow up (median follow-up: 27 months), we evaluated local control, overall survival and toxicity, using diagnostic imaging and laboratory tests. The patients’ median FEV1.0 was 0.84 L. Of the 13 patients, 3 were diagnosed as having lung cancer histologically and 10 diagnosed clinically. Their 2-year rates for overall survival and local control were 89 and 100%, respectively. So far, we have seen no adverse effects of grade 2 or higher. We concluded that CK-SBRT is effective and well tolerated for T1N0M0 lung cancer, even in patients with severe pulmonary dysfunction, but should be further evaluated with a larger cohort and longer follow-up periods.
Familial adenomatous polyposis: a case study
Authors: Yorke Joseph , Yamoah Francis Akwaw , Awoonor-Williams Ronald , Konney Thomas Okpoti , Acheampong Emmanuel , Adjei Ernest , Ababio Kwabena Acheamfour , Aning Daniel Gyawu , Afful-Yorke Dennis , Aidoo Freda Manu , Assim Claudia Gyamfua , Gyamfi Frank Enoch , Assim Raphael Owusu Sekyere , Konadu Saabea Owusu , Kuwornu David Elikplim , Acheampong Emmanuella Nsenbah 
Published: August 2020

Abstract
Familial adenomatous polyposis (FAP) is an inherited syndrome characterized by several adenomatous polyps of the gastrointestinal (GI) mucosa. If treatment is not provided, an average individual with classic FAP will develop colorectal carcinoma around the age of 40 years. The incidence rate of FAP in developing countries like Ghana is unknown compared to advanced countries. We present the first FAP case of a 22-year-old Ghanaian female who presented with massive lower GI bleeding and underwent surgical management after a thorough investigation. The initial assumption that colonic polyps are scarce in native Africans may be more than what is perceived. This highlights the need for the availability of endoscopic services in Ghana.
Travel-related hepatitis E: a two-decade GeoSentinel analysis
Authors: Nicolini Laura Ambra P , Stoney Rhett J , Della Vecchia Andrea , Grobusch Martin , Gautret Philippe , Angelo Kristina M , van Genderen Perry J J , Bottieau Emmanuel , Leder Karin , Asgeirsson Hilmir , Leung Daniel T , Connor Bradley , Pandey Prativa , Toscanini Federica , Gobbi Federico , Castelli Francesco , Bassetti Matteo , Hamer Davidson H 
Published: August 2020

Abstract

Background
Hepatitis E virus (HEV) is widely distributed worldwide and is endemic in developing countries. Travel-related HEV infection has been reported at national levels, but global data are missing. Moreover, the global availability of HEV diagnostic testing has not been explored so far. The aim of this study is to describe the epidemiology of HEV infections in returning travellers and availability of HEV diagnostic testing in the GeoSentinel surveillance network.

Methods
This was a multicentre retrospective cross-sectional study. All confirmed and probable HEV travel-related infections reported in the GeoSentinel Network between 1999 and 2018 were evaluated. GeoSentinel sites were asked to complete a survey in 2018 to assess the availability and accessibility of HEV diagnostic procedures (i.e. serology and molecular tests) throughout the study period.

Results
Overall, 165 travel-related HEV infections were reported, mainly since 2010 (60%) and in tourists (50%). Travellers were exposed to hepatitis E in 27 countries; most travellers (62%) were exposed to HEV in South Asia. One patient was pregnant at the time of HEV infection and 14 had a concomitant gastrointestinal infection. No deaths were reported. In the 51% of patients with information available, there was no pre-travel consultation. Among 44 GeoSentinel sites that responded to the survey, 73% have access to HEV serology at a local level, while 55% could perform (at a local or central level) molecular diagnostics.

Conclusion
Reported access to HEV diagnostic testing is suboptimal among sites that responded to the survey; this could negatively affect diagnosing HEV. Pre-travel consultations before travel to South Asia and other low-income and high-prevalence areas with a focus on food and water precautions could be helpful in preventing hepatitis E infection. Improved HEV diagnostic capacity should be implemented to prevent and correctly diagnose travel-related HEV infection.
COVID-19 Pandemic Once Again Exposes the Weakest Link in Laboratory Services: Specimen Delivery
Authors: Lapić Ivana , Komljenović Sven , Knežević Josip , Rogić Dunja 
Published: August 2020

Abstract

Objective
Reorganization of the emergency department (ED) during the COVID-19 pandemic implied closure of the ED-dedicated laboratory and manual transport of all specimens to the dislocated central laboratory. The impact of such reorganization on laboratory turnaround time (TAT) was examined.

Methods
The TAT from blood sampling to specimen reception (TAT1), from specimen reception to test reporting (TAT2), and from sampling to test reporting (TAT3) were compared between the pandemic peak month in 2020 and the same month in 2019. We evaluated whether TAT2 fulfills the recommended 60-minute criteria.

Results
A statistically significant difference was observed for all comparisons (P &lt;.001), with TAT1 prominently contributing to TAT3 prolongation (from 48 minutes to 108 minutes) and exceeding the recommended 60-minute criteria. The TAT2 was extended from 33 minutes to 49 minutes.

Conclusion
An ED reorganization compromised the usual laboratory services for patients in the ED, with manual specimen delivery being the main cause for TAT prolongation.
Steve Reich’s Signature Rhythm and an Introduction to Rhythmic Qualities
Authors: Yust Jason 
Published: August 2020

AbstractThe rhythm of Steve Reich’s Clapping Music (1972) features in so many of his pieces that it can be understood as a rhythmic signature. A theory of rhythmic qualities allows us to identify the signature rhythm’s significant features and relate it to other cyclic rhythms like the Central/West African “standard pattern,” from which it probably originates. Rhythmic qualities derive from the discrete Fourier transform, whose mathematical properties make the theory particularly robust. One property, described by the convolution theorem, predicts the effects of Reich’s diverse rhythmic canons. I apply the theory to Music for Pieces of Wood (1973) and Nagoya Marimbas (1994).
Economic Costs of Diseases and Deaths Attributable to Tobacco Use in India, 2017–2018
Authors: John Rijo M , Sinha Praveen , Munish Vineet Gill , Tullu Fikru T 
Published: August 2020

AbstractIntroductionAbout 28.6% of Indian adults use tobacco. This study estimates the economic burden of deaths and diseases attributable to smoking and smokeless tobacco (SLT) use for persons aged ≥35 years.MethodsThe National Sample Survey data on healthcare expenditures, the Global Adult Tobacco Survey data on tobacco use prevalence, and relative risks of all-cause mortality from tobacco use were used to estimate the economic burden of diseases and deaths attributable to tobacco use in India, using a prevalence-based attributable-risk approach. Costs are estimated under the following heads: (1) direct medical and nonmedical expenditures; (2) indirect morbidity costs; and (3) indirect mortality costs of premature deaths.ResultsTotal economic costs attributable to tobacco use from all diseases and deaths in India in the year 2017–2018 for persons 35 years or older amount to INR 1773.4 billion (US $27.5 billion), of which 22% is direct and 78% is indirect cost. Men bear 91% of the total costs. Smoking contributed 74% and SLT use contributed 26% of the costs.ConclusionsThe economic costs of tobacco use amount to approximately 1.04% of India’s gross domestic product (GDP), while the excise tax revenue from tobacco in the previous year was only 12.2% of its economic costs. The direct medical costs alone amount to 5.3% of total health expenditure. The enormous costs imposed on the nation’s health care system due to tobacco use could potentially stress the public health care system and strain the economy and it warrants massive scaling up of tobacco control efforts in India.ImplicationsThe study finds that the economic burden from tobacco constitutes more than 1% of India’s GDP, and the direct health expenditures on treating tobacco-related diseases alone accounts for 5.3% of the total private and public health expenditures in India in a year. It shows that, for every INR 100 that is received as excise taxes from tobacco products, INR 816 of costs is imposed on society through its consumption. It establishes that tobacco consumption is a major resource drain on the national exchequer, and its effective regulation through comprehensive fiscal and non-fiscal policies is highly warranted.