bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling
Authors: Thomas Stacy , Lichtenberg Tara , Dang Kristen , Fitzsimons Michael , Grossman Robert L. , Kundra Ritika , Lavery Jessica A. , Lenoue-Newton Michele L. , Panageas Katherine S. , Sawyers Charles , Schultz Nikolaus D. , Sirintrapun Sahussapont J. , Topaloglu Umit , Welch Angelica , Yu Thomas , Zehir Ahmet , Gardos Stuart 
Published: August 2020

PURPOSE As data-sharing projects become increasingly frequent, so does the need to map data elements between multiple classification systems. A generic, robust, shareable architecture will result in increased efficiency and transparency of the mapping process, while upholding the integrity of the data. MATERIALS AND METHODS The American Association for Cancer Research’s Genomics Evidence Neoplasia Information Exchange (GENIE) collects clinical and genomic data for precision cancer medicine. As part of its commitment to open science, GENIE has partnered with the National Cancer Institute’s Genomic Data Commons (GDC) as a secondary repository. After initial efforts to submit data from GENIE to GDC failed, we realized the need for a solution to allow for the iterative mapping of data elements between dynamic classification systems. We developed the Linked Entity Attribute Pair (LEAP) database framework to store and manage the term mappings used to submit data from GENIE to GDC. RESULTS After creating and populating the LEAP framework, we identified 195 mappings from GENIE to GDC requiring remediation and observed a 28% reduction in effort to resolve these issues, as well as a reduction in inadvertent errors. These results led to a decrease in the time to map between OncoTree, the cancer type ontology used by GENIE, and International Classification of Disease for Oncology, 3rd Edition, used by GDC, from several months to less than 1 week. CONCLUSION The LEAP framework provides a streamlined mapping process among various classification systems and allows for reusability so that efforts to create or adjust mappings are straightforward. The ability of the framework to track changes over time streamlines the process to map data elements across various dynamic classification systems.
Understanding Geospatial Factors Associated With Cervical Cancer Screening Uptake in Amazonian Peruvian Women
Authors: Barrett Benjamin W. , Paz-Soldan Valerie A. , Mendoza-Cervantes Diana , Sánchez Graciela Meza , Córdova López Jhonny J. , Gravitt Patti E. , Rositch Anne F. ,   on behalf of the Proyecto Precancer Study Group
Published: August 2020

PURPOSECervical cancer (CC) is the most common and second-most deadly cancer among Peruvian women. Access to services is strongly associated with CC screening uptake. This study investigated geospatial features contributing to utilization of screening. We used geolocated data and screening information from a Knowledge, Attitudes, and Practice (KAP) survey implemented in Iquitos, Peru in 2017.MATERIALS AND METHODSThe KAP collected cross-sectional CC screening history from 619 female interviewees age 18-65 years within 5 communities of varying urbanization levels. We used spatial statistics to determine if screened households tended to cluster together or cluster around facilities offering screening in greater numbers than expected, given the underlying population density.RESULTSOn the basis of K-functions, screened households displayed greater clustering among each other as compared with clustering among unscreened households. Neighborhood-level factors, such as outreach, communication, or socioeconomic condition, may be functioning to generate pockets of screened households. Cross K-functions showed that screened households are generally located closer to health facilities than unscreened households. The significance of facility access is apparent and demonstrates that travel and time barriers to seeking health services must be addressed.CONCLUSIONThis study highlights the importance of considering geospatial features when determining factors associated with CC screening uptake. Given the observed clustering of screened households, neighborhood-level dynamics should be further studied to understand how they may be influencing screening rates. In addition, results demonstrate that accessibility issues must be carefully considered when designing an effective cancer screening program that includes screening, follow-up, and treatment.
Patients With MEN1 Are at an Increased Risk for Venous Thromboembolism
Authors: Lee Maya E , Ortega-Sustache Yashira M , Agarwal Sunita K , Tepede Aisha , Welch James , Mandl Adel , Bansal Rashika , Tirosh Amit , Piaggi Paolo , Cochran Craig , Simonds William F , Weinstein Lee S , Blau Jenny E 
Published: August 2020

Abstract

Background
Multiple endocrine neoplasia type 1 (MEN1) is a rare inherited disorder predisposing the development of multiple functional and nonfunctional neuroendocrine tumors (NETs). Only uncommon MEN1-associated functional NETs such as glucagonomas (&lt;1%) and adenocorticotropic hormone-producing tumors (&lt;5%) are known to be associated with hypercoagulability. It is unknown if patients with MEN1 generally have an increased risk of venous thromboembolism (VTE).

Methods
We queried a prospective natural history study of germline mutation-positive MEN1 patients (n = 286) between 1991 and 2019 for all lifetime events of VTE. The search terms were: DVT, thromb, embol, PE, pulmonary embolism, clot, hematology consult, anticoagulant, coumadin, lovenox, xarelto, warfarin, aspirin, rivaroxaban, and apixaban. Incidence rates were calculated, accounting for age and sex. Comparisons were made to published incidence rates in healthy populations, different types of cancer, and Cushing’s syndrome.

Results
Thirty-six subjects (median age 45 years, range 16–75) experienced a VTE event, yielding a prevalence rate of 12.9%. The age–sex adjusted incidence rate of VTE is 9.11 per 1000 patient-years, with a sex-adjusted lifetime incidence rate of 2.81 per 1000 patient-years. MEN1-associated lifetime incidence rates are ~2-fold higher than the estimated annual incidence rate in the general population and are comparable to the known risk in the setting of various types of cancer. Approximately 80% of patients who had a VTE were diagnosed with pancreatic NETs, of which 24% were insulinomas. Fourteen patients (42%) experienced perioperative VTE events.

Conclusions
MEN1 patients have an increased risk of VTE. Further mechanistic investigation and validation from other MEN1 cohorts are needed to confirm the increased prevalence of VTE in MEN1.
Whole exome sequencing reveals a homozygous nonsense mutation in HEXA gene leading to Tay-Sachs disease in Saudi Family
Authors: Naseer Muhammad Imran , Abdulkareem Angham Abdulrahman , Jan Mohammed Mohammed , Chaudhary Adeel G. , Al-Qahtani Mohammad H. 
Published: August 2020

Objective: To study the causative variants in affected member of a Saudi family with Tay-Sachs disorder. This disorder includes paralysis, decreasing in attentiveness, seizures, blindness, motor deterioration progresses rapidly leading to a completely unresponsive state and a cherry-red spot visible on the eye.
Methods: Whole exome sequencing (WES) and Sanger sequencing was performed to study the variant leading to the disease.
Results: WES data analysis and Sanger sequencing validation, identifies a homozygous nonsense mutation c.1177C>T, p.Arg393Ter as a result in protein change. This mutation was also studied in 100 unrelated healthy controls.
Conclusions: We detected homozygous mutation in HEXA gene that may lead to cause Tay-Sachs disorder. Moreover, explain the possibility that HEXA gene may play important role for multiple aspects of normal human neurodevelopment.
doi: https://doi.org/10.12669/pjms.36.6.2579
How to cite this:Naseer MI, Abdulkareem AA, Jan MM, Chaudhary AG, Al-Qahtani MH. Whole exome sequencing reveals a homozygous nonsense mutation in HEXA gene leading to Tay-Sachs disease in Saudi Family. Pak J Med Sci. 2020;36(6):1425-1428. doi: https://doi.org/10.12669/pjms.36.6.2579
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Morphological and genetic evaluation of the thumbprint emperor, Lethrinus harak (Forsskål, 1775) in the Pacific and Indian Oceans
Authors: Afrisal Muhammad , Iwatsuki Yukio , Burhanuddin Andi Iqbal 
Published: August 2020

Background: The Lethrinidae (emperors) include many important food fish species. Accurate determination of species and stocks is important for fisheries management. The taxonomy of the genus Lethrinus is problematic, for example with regards to the identification of the thumbprint emperor Lethrinus harak. Little research has been done on L. harak diversity in the Pacific and Indian Oceans. This study aimed to evaluate the morphometric and genetic characters of the thumbprint emperor, L. harak (Forsskål, 1775) in the Pacific and Indian Oceans. Methods: This research was conducted in the Marine Biology Laboratory, Faculty of Marine Science and Fisheries, Hasanuddin University, and Division of Fisheries Science, University of Miyazaki. Morphometric character measurements were based on holotype character data, while genetic analysis was performed on cytochrome oxidase subunit I (COI) sequence data. Morphometric data were analysed using principal component analysis (PCA) statistical tests in MINITAB, and genetic data were analysed in MEGA 6. Results: Statistical test results based on morphometric characters revealed groupings largely representative of the Indian and Pacific Oceans. The Seychelles was separated from other Indian Ocean sites and Australian populations were closer to the Pacific than the Indian Ocean group. The genetic distance between the groups was in the low category (0.000 - 0.042). The phylogenetic topology reconstruction accorded well with the morphometric character analysis, with two main L. harak clades representing Indian and Pacific Ocean, and Australia in the Pacific Ocean clade. Conclusions: These results indicate that geographical and environmental factors can affect the morphometric and genetic characteristics of L. harak.
Poor eating habits and predictors of weight gain during the COVID-19 quarantine measures in Kuwait: a cross sectional study
Authors: AlMughamis Nouf , AlAsfour Shaimaa , Mehmood Shariq 
Published: August 2020

Background: Despite the public health importance of documenting the burden of physical inactivity and weight gain, there is a paucity of such data in Kuwait during the lockdown for Covid-19 pandemic. Therefore, this survey was designed to estimate: the burden of poor eating habits particularly binge eating habits, fluctuations in weight and its predictors among the Kuwaiti public. Methods: This cross-sectional survey was conducted from 2nd to 12th April 2020 among the general public in Kuwait. All data were collected through a social media platform (WhatsApp groups), through convenience and snowball sampling methods. The survey comprised three sections: a) demographic characteristics of respondents, b) eating habits particularly binge eating, consumption of snacks and beverages c) subjective feelings of anxiety and d) weight before and during the pandemic. All data were analyzed using SPSS (v.25). Results: There was a total of 522 valid respondents, with a mean age of 41.78 (11.75) years. There was a significant increase in weight of respondents during the quarantine (mean difference= -1.13, SD 5.39, t= -4.52, p < 0.001). Those with reporting unhealthy diets were 4.5 times more likely to report an increase in weight. Those reporting having anxiety throughout the day were 2.45 times more likely and those consuming snacks excessively were associated with 3.27 times higher odds of increase in weight than those not consuming it. Conclusions: We recommend that authorities develop a strategic plan to counter harmful effects of this pandemic on health that are originating from sedentary lifestyle, unhealthy eating patterns and psychological issues.
Utilizing passive sensing data to provide personalized psychological care in low-resource settings
Authors: Byanjankar Prabin , Poudyal Anubhuti , Kohrt Brandon A , Maharjan Sujen Man , Hagaman Ashley , van Heerden Alastair 
Published: August 2020

Background: With the growing ubiquity of smartphones and wearable devices, there is an increased potential of collecting passive sensing data in mobile health. Passive data such as physical activity, Global Positioning System (GPS), interpersonal proximity, and audio recordings can provide valuable insight into the lives of individuals. In mental health, these insights can illuminate behavioral patterns, creating exciting opportunities for mental health service providers and their clients to support pattern recognition and problem identification outside of formal sessions. In the Sensing Technologies for Maternal Depression Treatment in Low Resource Settings (StandStrong) project, our aim was to build an mHealth application to facilitate the delivery of psychological treatments by lay counselors caring for adolescent mothers with depression in Nepal. Methods: This paper describes the development of the StandStrong platform comprising the StandStrong Counselor application, and a cloud-based processing system, which can incorporate any tool that generates passive sensing data. We developed the StandStrong Counselor application that visualized passively collected GPS, proximity, and activity data. In the app, GPS data displays as heat maps, proximity data as charts showing the mother and child together or apart, and mothers’ activities as activity charts. Lay counselors can use the StandStrong application during counseling sessions to discuss mothers’ behavioral patterns and clinical progress over the course of a five-week counseling intervention. Awards based on collected data also can be automatically generated and sent to mothers. Additionally, messages can be sent from counselors to mother’s personal phones through the StandStrong platform. Discussion: The StandStrong platform has the potential to improve the quality and effectiveness of psychological services delivered by non-specialists in diverse global settings.
Children and young people's experiences of living with developmental coordination disorder/dyspraxia: study protocol for a qualitative evidence synthesis
Authors: O'Dea Áine , Coote Susan , Robinson Katie 
Published: August 2020

Background Children with developmental coordination disorder (DCD) face significant challenges to deal with everyday activities due to underlying motor proficiency difficulties. These challenges affect children and young people’s participation; that is, involvement in daily life situations. A small body of qualitative research has explored the experiences of children and young people with DCD from their own perspective. Therfore, understanding what it is like to live with DCD is not well conceptualised in the literature. There is a pressing need to synthesise the findings of discrete qualitative studies to advance the conceptual understanding of living with DCD, to inform health service delivery and the development and implementation of complex interventions. Aim This study aims to systematically review and synthesise qualitative literature regarding children and young people’s experiences and views of everyday life and living with DCD. Methods The method of qualitative evidence synthesis that will be followed in this review is a meta-ethnography. The eMERGe and PRISMA reporting guidelines will be adhered to. Ten databases will be searched; Academic Search Complete, AMED, CINAHL, ERIC, MEDLINE, PsychArticles, PsychInfo, EMBASE, SPORTDiscus, and Web of Science. The Joanna Briggs Institute Checklist will be used by two independent reviewers to appraise all included papers. Discussion The findings of this meta-ethnography will endeavour to inform future research, policy and practice. In particular, the results will help to inform the design of future complex interventions to meet the needs of children and young people with DCD. Dissemination will involve the publication of the results in a peer-reviewed journal. Increasingly researchers and policymakers are calling for services to be informed by the perspective and voice of children with DCD. Therefore, a policy brief will be published so that the findings are widely available. Registration: PROSPERO registration number CRD42019129178; registered on 09 July 2019.
Mapping the use of Group-Based Trajectory Modelling in medication adherence research: A scoping review protocol
Authors: Walsh Caroline A. , Mucherino Sara , Orlando Valentina , Bennett Kathleen E. , Menditto Enrica , Cahir Caitriona 
Published: August 2020

The use of group-based trajectory modelling (GBTM) within the medication adherence literature is rapidly growing. Researchers are adopting enhanced methods to analyse and visualise dynamic behaviours, such as medication adherence, within ‘real-world’ populations. Application of GBTM based on longitudinal adherence behaviour allows for the identification of adherence trajectories or groups. A group is conceptually thought of a collection of individuals who follow a similar pattern of adherence behaviour over a period of time. A common obstacle faced by researchers when implementing GBTM is deciding on the number of trajectory groups that may exist within a population. Decision-making can introduce subjectivity, as there is no ‘gold standard’ for model selection criteria. This study aims to examine the extent and nature of existing evidence on the application of GBTM for medication adherence assessment, providing an overview of the different GBTM techniques used in the literature. The methodological framework will consist of five stages: i) identify the research question(s); ii) identify relevant studies; iii) select studies; iv) chart the data and finally, v) collate, summarise and report the results. Original peer-reviewed articles, published in English, describing observational and interventional studies including both concepts and/or sub-concepts of GBTM and medication adherence or any other similar terms, will be included. The following databases will be queried: PubMed/MEDLINE; Embase (Ovid); SCOPUS; ISI Web of Science and PsychInfo. This scoping review will utilise the PRISMA extension for Scoping Reviews (PRISMA-ScR) tool to report results. This scoping review will collect and schematise different techniques in the application of GBTM for medication adherence assessment available in the literature to date, identifying research and knowledge gaps in this area. This review can represent an important tool for future research, providing methodological support to researchers carrying out a group-based trajectory analysis to assess medication adherence in a real-world context.
Microsecond pulse-mode operation of a micro-integrated high-power external-cavity tapered diode laser at 808  nm
Authors: Chi Mingjun , Müller André , Hansen Anders K. , Jensen Ole B. , Petersen Paul M. , Sumpf Bernd 
Published: August 2020

We investigate microsecond pulse-mode operation of a micro-integrated high-power diode laser based on volume Bragg grating external-cavity feedback around 808 nm. The laser system contains a tapered amplifier consisting of a ridge-waveguide section and a tapered section with separated electrical contacts. Thus, the diode laser system can be pulsed by modulating the injected current either to the ridge waveguide section (

I

R
W

) or to the tapered amplifier section (

I

T
A

). With a trigger signal of a 50 µs pulse width and a 10 kHz repetition rate, comparing the modulation depth, peak output power, beam propagation factor, and spectral bandwidth, we conclude that the pulse-mode operation achieved by modulating the

I

T
A

gives better results than by modulating the

I

R
W

due to the decreased thermal effect. At a constant

I

R
W

of 0.2 A and a modulated

I

T
A

of 6.0 A, 4.3 W of peak output power is obtained with an emission spectral bandwidth with an upper bound of 0.2 nm, and a beam propagation factor in the slow axis,

M

s
l
o
w

2

, of 2.6 (

1

/

e

2

). The modulation depth is almost 100%. The results show that the tapered diode laser system may be a good candidate for microsecond pulse-mode solid-state lasers.
Single-shot ultrafast burst imaging using an integral field spectroscope with a microlens array
Authors: Nemoto Hirofumi , Suzuki Takakazu , Kannari Fumihiko 
Published: August 2020

To fully utilize the functions of a center-wavelength-sweeping pulse train generated by a free-space angular-chirp-enhanced delay optical layout for a probe laser pulse in sequentially timed all-optical mapping photography (STAMP), we introduced an integral field spectroscopy (IFS) method using a microlens array (MLA) to produce hyperspectral images, referring to the technique as lens array (LA)-STAMP. Compared with the previous STAMP utilizing spectral filtering where a bandpass filter generated hyperspectral images, LA-STAMP achieved much higher optical throughput. In a prototype setup, we used a

60

×

60

MLA and demonstrated single-shot burst imaging of a femtosecond laser-induced ablation process on a glass surface with 300 ps frame intervals in a 1.8 ns time window. Each frame image was constructed by assembling spectrally dispersed

36

×

36

monochromatic segments distributed by each lenslet on

5

×

5

pixels of a CCD camera. The spatial resolution was

∼

4.4

µ

m

, which was determined by the MLA’s pitch and the magnification of the microscope lens. We limited the number of frames to seven in this prototype setup, although it can be scaled to

∼

24

with a spatial resolution of

∼

1

µ

m

by designing IFS with a fine pitch MLA.
5D data iteration in a multi-wavelength OFDM-PON using the hyperchaotic system
Authors: Li Mingye , Liu Bo , Ullah Rahat , Ren Jianxin , Mao Yaya , Han Shun , Zhao Jianye , Tang Rong , Chen Shuaidong , Ling Jing 
Published: August 2020

In this Letter, a novel five-dimensional (5D) data-iteration-based encryption model is proposed at physical layer for multi-wavelength optical frequency division multiplexing passive optical network (OFDM-PON) by using a hyperchaotic system. The proposed scheme can generate five chaotic sequences at a time. The sensitivity of

10

−
18

can be achieved, along with a key space of

10

95

. In addition, we use a multi-wavelength channel to transmit the information, and the optical network unit can freely choose the wavelength. The probability shaping technology has greatly improved the bit error rate performance. A

16

G
b

/

s

/

λ

data is successfully transmitted across 25 km standard single-mode fiber in the experimental verifications. Therefore, it will have a positive impact in the future security optical network.