bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test-Retest-Reliability of Computer-Based Metamorphopsia Measurement in Macular Diseases
Authors: Claessens Daniela , Schuster Alexander K. , Krüger Ronald V. , Liegl Marian , Singh Laila , Kirchhof Bernd 
Published: December 2020

AbstractIn this study, the test-retest-reliability as one aspect of reliability of metamorphopsia measurements using a computer-based measuring method was determined in patients with macular diseases. Metamorphopsia amplitude, position, and area were quantified using AMD – A Metamorphopsia Detector software (app4eyes GmbH & Co. KG, Germany) in patients with diabetic, myopic, or uveitic macular edema, intermediate or neovascular age-associated macular degeneration, epiretinal membrane, vitelliform maculopathy, Irvine-Gass syndrome, or macular edema due to venous retinal occlusion. The intraclass correlation coefficient (ICC) was calculated in order to determine the repeatability of two repeated measurements and was used as an indicator of the reliability of the measurements. In this study, metamorphopsia measurements were conducted on 36 eyes with macular diseases. Metamorphopsia measurements made using AMD – A Metamorphopsia Detector software were highly reliable and
repeatable in patients with maculopathies. The intraclass correlation coefficient of all indices was excellent (0.95 – 0.97). For diseases of the vitreoretinal interface or macular diseases with intra- or subretinal edema, this metamorphopsia measurement represents a supplement for visual function testing in the clinic, as well as in clinical studies.
Dental and Medical Students’ Knowledge and Attitude toward COVID-19: A Cross-Sectional Study from Pakistan
Authors: Ali Saqib , Alam Beenish Fatima , Farooqi Faraz , Almas Khalid , Noreen Sara 
Published: December 2020

Abstract
Objective The aims of this study were to investigate the awareness, knowledge, and attitudes of Pakistani medical and dental undergraduate students toward COVID-19 during the surge of its outbreak.
Materials and Methods The multicentered, cross-sectional study was carried out nationwide among undergraduate medical and dental students. A convenience sampling technique was used. A self-developed online questionnaire was pretested to be completed by the participants. It was distributed using social media. The survey was comprised of questions related to demographics, health status, general hygiene perception, understanding, and the learning attitudes of the students. Comparisons of the knowledge scores and the attitude responses with the demographic information were done using the independent t-test, one-way ANOVA, and Chi-square, as appropriate.
Results Of the 937 total respondents, 353 (38%) were males and 582 (62%) were females; two students did not mark their gender. Of these, 680 (73%) were dental students and 257 (27%) were medical students. The mean knowledge score of the female dental students (5.15 ± 1.08) was significantly higher than that of the male students (4.87 ± 1.09). Overall, the mean knowledge score was statistically higher among the medical students in comparison to the dental students (5.21 ± 1.15, 5.05 ± 1.09; p = 0.054), respectively.
Conclusion The medical and dental students were both aware of the importance of the use of a mask. The medical students had a greater awareness regarding the mode of transmission, symptoms, and origin of COVID-19. However, the dental students showed better understanding of the use of surgical masks and the correct protocol for hand washing. Social media was considered the main source for COVID-19 related information.
Discipline-Specific Perspectives on Caring for Babies with Trisomy 13 or 18 in the Neonatal Intensive Care Unit
Authors: Torbert Nicholas , Neumann Marie , Birge Nicole , Perkins Donnetta , Ehrhardt Elizabeth , Weaver Meaghann S. 
Published: December 2020

Objective Care offerings vary across medical settings and between families for babies with trisomy 13 or 18. The purpose of this qualitative descriptive study was to explore nurse, advanced practice practitioner, and neonatologist perspectives on care for babies with trisomy 13 or 18 in the intensive care unit.
Study Design Voice-recorded qualitative interviews occurred with 64 participants (41 bedside nurses, 14 advance practice practitioners, and 9 neonatologists) from two neonatal intensive care units (NICU) in the midwestern United States. Consolidated Criteria for Reporting Qualitative Research guidelines were followed. Content analyses occurred utilizing MAXQDA (VERBI Software, 2020).
Results Over half of NICU staff perceived care for babies with trisomy 13 or 18 as different from care for other babies with critical chronic illness. Qualitative themes included internal conflict, variable presentation and prognosis, grappling with uncertainty, family experiences, and provision of meaningful care. Neonatologists emphasized the variability of presentation and prognosis, while nurses emphasized provision of meaningful care. Phrases “hard/difficult” were spoken 31 times; primarily describing the comorbidities, complexities, and prognostic uncertainty.
Conclusion Care for babies with these genetic diagnoses reveals need for a shared dialogue not only with families but also across staff disciplines. While perspectives differ, participants depicted striving to offer compassionate, family-centered care while also balancing biomedical uncertainty about interventions for children with trisomy 13 and 18.
Key Points
Cortical tension overrides geometrical cues to orient microtubules in confined protoplasts
Authors: Colin Leia , Chevallier Antoine , Tsugawa Satoru , Gacon Florian , Godin Christophe , Viasnoff Virgile , Saunders Timothy E. , Hamant Olivier 
Published: December 2020

SignificanceIn plants, microtubules largely determine the direction of cell expansion and the orientation of cell division planes. However, what processes orient the microtubules has remained debated. Here, we used microfabricated wells to confine and deform wallless plant cells in a controlled way to analyze the response of microtubules to cell geometry and surface tension. We demonstrate that microtubules align with cell geometry by default, whereas when surface tension increases (e.g. when turgor pressure increases), they align with the direction of maximal tension. Not only does this explain many observations in plant tissues, but it also provides a simple mechanism at the core of plant morphogenesis, in which microtubules can spontaneously align with tension, in a typical self-organized system.
Estimating literary translators’ earnings penalty
Authors: Mirsafian Leila , Pirnajmuddin Hossein , Nejadansari Dariush 
Published: December 2020

Abstract
Seeking to fill the gap in economics-related research in the subfield of translator studies, this article aims to identify
the best approach to estimate the earnings penalty and forgone income of Iranian professional literary translators. The data were collected
through interviews with 118 Iranian professional literary translators. A multiple regression analysis done to estimate the translators’
annual income equation shows that male Tehran-based literary translators who have no other jobs and spent less time on higher education earn
more than their colleagues who are female, do not live in Tehran, have other jobs, and spent more time on higher education. However, the
multiple regression analysis for estimating the average forgone income equation of the interviewees indicates that the more experience and
the fewer award jury/editorial board memberships female non-Tehran-based literary translators have, the more they suffer from earnings
penalties. Building on these findings, the article highlights the implications of cultural economics research for translator studies.
Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols
Authors: Illing Björn , Severati Andrea , Hochen Justin , Boyd Paul , Raison Paulin , Mather Rachel , Downie Adam T , Rummer Jodie L , Kroon Frederieke J , Humphrey Craig 
Published: December 2020

AbstractIn fishes, swimming performance is considered an important metric to measure fitness, dispersal and migratory abilities. The swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g. connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water quality parameters and flow velocity. In this study, we automated the control of multi-lane swimming chambers for small fishes by developing an open-source algorithm. This automation allowed us to execute repeatable flow scenarios and reduce operator interference and inaccuracies in flow velocity typically associated with manual control. Furthermore, we made structural modifications to a prior design to reduce the areas of lower flow velocity. We then validated the flow dynamics of the new chambers using computational fluid dynamics and particle-tracking software. The algorithm provided an accurate alignment between the set and measured flow velocities and we used it to test whether faster critical swimming speed (Ucrit) protocols (i.e. shorter time intervals and higher velocity increments) would increase Ucrit of early life stages of two tropical fish species [4–10-mm standard length (SL)]. The Ucrit of barramundi (Lates calcarifer) and cinnamon anemonefish (Amphiprion melanopus) increased linearly with fish length, but in cinnamon anemonefish, Ucrit started to decrease upon metamorphosis. Swimming protocols using longer time intervals (more than 2.5 times increase) negatively affected Ucrit in cinnamon anemonefish but not in barramundi. These species-specific differences in swimming performance highlight the importance of testing suitable Ucrit protocols prior to experimentation. The automated control of flow velocity will create more accurate and repeatable data on swimming performance of larval fishes. Integrating refined measurements into individual-based models will support future research on the effects of environmental change.
Impact of medication adherence to dual antiplatelet therapy on the long-term outcome of drug-eluting or bare-metal stents
Authors: Choi J.H , Choi J.M , Lee S.H , Jang Y.J , Kang M , Lee J.M , Park T.K , Yang J.H , Song Y.B , Choi K.H , Hahn J.Y , Choi S.H , Gwon H.C , Lee S.H 
Published: December 2020

Abstract

Objective
In percutaneous coronary intervention, drug-eluting stent (DES) showed better clinical outcome compared to bare-metal stent (BMS) but mostly with different DAPT durations. This study investigated the clinical superiority of DES over BMS with regard to the medication adherence to dual antiplatelet therapy (DAPT).

Methods
We retrospectively enrolled all Koreans PCI patients in year 2011 (n=47,291). Medication adherence to DAPT was assessed by proportion of days covered (PDC) per 6 months. Analysis adjusted with the clinical propensity for receiving DES or BMS and DAPT PDC of the first 6 month was performed. Primary outcome was the 5-year major adverse clinical event (MACE) risk consisting all-cause death, revascularization, shock, or stroke.

Results
Patients with DES (n=46,356) showed higher PDC (78% versus 60%, p&lt;0.001) and lower MACE risk (39% versus 56%, p&lt;0.001) compared to patients with BMS (n=935). In the propensity-matched 1,868 patients, MACE risk was lower with DES than BMS (46% versus 54%, HR=0.80, 95% CI: 0.70–0.91, p&lt;0.001). Patients with good medication adherence (PDC ≥80%) showed much lower MACE risk compared to patients with PDC &lt;80% regardless of DES or BMS (HR=0.36, 95% CI: 0.30–0.44; HR=0.40, 95% CI: 0.33–0.48, p&lt;0.001, all). Patients with DES and PDC &lt;80% showed higher MACE risk compared to BMS with and PDC ≥80% (HR=1.30, 95% CI: 1.03–1.64, p=0.027).

Conclusions
Good medication adherence to DAPT in the first 6 month was prerequisite for better clinical outcome in both DES and BMS. DES with poor adherence to DAPT showed worse outcome compared with BMS with good adherence.
Impact of medication adherence to dual antiplatelet therapy.

Funding Acknowledgement
Type of funding source: None
File-based localization of numerical perturbations in data analysis pipelines
Authors: Salari Ali , Kiar Gregory , Lewis Lindsay , Evans Alan C , Glatard Tristan 
Published: December 2020

Abstract

Background
Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear.

Method
We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computational conditions. Spot leverages system-call interception through ReproZip to reconstruct and compare provenance graphs without pipeline instrumentation.

Results
By applying Spot to the structural pre-processing pipelines of the Human Connectome Project, we found that linear and non-linear registration are the cause of most numerical instabilities in these pipelines, which confirms previous findings.
A methodological approach to correlate tumor heterogeneity with drug distribution profile in mass spectrometry imaging data
Authors: Prasad Mridula , Postma Geert , Franceschi Pietro , Morosi Lavinia , Giordano Silvia , Falcetta Francesca , Giavazzi Raffaella , Davoli Enrico , Buydens Lutgarde M C , Jansen Jeroen 
Published: December 2020

Abstract

Background
Drug mass spectrometry imaging (MSI) data contain knowledge about drug and several other molecular ions present in a biological sample. However, a proper approach to fully explore the potential of such type of data is still missing. Therefore, a computational pipeline that combines different spatial and non-spatial methods is proposed to link the observed drug distribution profile with tumor heterogeneity in solid tumor. Our data analysis steps include pre-processing of MSI data, cluster analysis, drug local indicators of spatial association (LISA) map, and ions selection.

Results
The number of clusters identified from different tumor tissues. The spatial homogeneity of the individual cluster was measured using a modified version of our drug homogeneity method. The clustered image and drug LISA map were simultaneously analyzed to link identified clusters with observed drug distribution profile. Finally, ions selection was performed using the spatially aware method.

Conclusions
In this paper, we have shown an approach to correlate the drug distribution with spatial heterogeneity in untargeted MSI data. Our approach is freely available in an R package 'CorrDrugTumorMSI'.
Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation
Authors: Yuan Dengyue , Chen Xuehui , Gu Haoran , Zou Ming , Zou Yu , Fang Jian , Tao Wenjing , Dai Xiangyan , Xiao Shijun , Wang Zhijian 
Published: December 2020

Abstract

Background
Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to high-elevation environments is largely unknown. Triplophysa bleekeri, an endemic fish inhabiting high-altitude regions, is an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of T. bleekeri, with a size of ∼628 Mb (contig and scaffold N50 of 3.1 and 22.9 Mb, respectively). We investigated the origin and environmental adaptation of T. bleekeri based on 21,198 protein-coding genes in the genome.

Results
Compared with fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the T. bleekeri genome. Genes involved in DNA repair exhibit positive selection for T. bleekeri, Triplophysa siluroides, and Triplophysa tibetana, indicating that adaptive convergence in Triplophysa species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from 3 populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations.

Conclusions
These results will help us expand our understanding of environmental adaptation and genetic diversity of T. bleekeri and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as T. bleekeri.
iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Authors: Palatnick Aspyn , Zhou Bin , Ghedin Elodie , Schatz Michael C 
Published: December 2020

Abstract

Background
Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is on a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available.

Results
iGenomics is the first comprehensive mobile genome analysis application, with capabilities to align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets of viral and bacterial genomes and show that iGenomics has performance comparable to the popular BWA-MEM/SAMtools/IGV suite, without necessitating a laptop or server cluster.

Conclusions
iGenomics is available open source (https://github.com/stuckinaboot/iGenomics) and for free on Apple's App Store (https://apple.co/2HCplzr).
Continued Statural Growth in Older Adolescents and Young Adults With Crohn’s Disease and Ulcerative Colitis Beyond the Time of Expected Growth Plate Closure
Authors: Gupta Neera , Liu Chunyan , King Eileen , Sylvester Francisco , Lee Dale , Boyle Brendan , Trauernicht Anna , Chen Shiran , Colletti Richard ,   ImproveCareNow Network, Adler Jeremy , Ali Sabina A , Al-Nimr Amer , Ayers Travis D , Baron Howard I , Beasley Genie L , Benkov Keith J , Cabrera Jose M , Cho-Dorado Michele E , Dancel Liz D , Di Palma Joan S , Dorsey Jill M , Gulati Ajay S , Hellmann Jennifer A , Higuchi Leslie M , Hoffenberg Edward , Israel Esther J , Jester Traci W , Kiparissi Fevronia , Konikoff Michael R , Leibowitz Ian , Maheshwari Anshu , Moulton Dedrick E , Moses Jonathan , Ogunmola Nicholas A , Palmadottir Johanna G , Pandey Akash , Pappa Helen M , Pashankar Dinesh S , Pasternak Brad A , Patel Ashish S , Quiros J Anthony , Rountree Carl B , Samson Charles M , Sandberg Kelly C , Schoen Bess , Steiner Steven J , Stephens Michael C , Sudel Boris , Sullivan Jillian S , Suskind David L , Tomer Gitit , Tung Jeanne , Verstraete Sofia G 
Published: December 2020

Abstract

Background
Cessation of statural growth occurs with radiographic closure of the growth plates, radiographically defined as bone age (BA) 15 years in females and 17 in males.

Methods
We determined the frequency of continued growth and compared the total height gain beyond the time of expected growth plate closure and the chronological age at achievement of final adult height in Crohn’s disease (CD) vs ulcerative colitis (UC) and described height velocity curves in inflammatory bowel disease (IBD) compared with children in the National Health and Nutrition Examination Survey (NHANES). We identified all females older than chronological age (CA) 15 years and males older than CA 17 years with CD or UC in the ImproveCareNow registry who had height documented at ≥3 visits ≥6 months apart.

Results
Three thousand seven patients (48% female; 76% CD) qualified. Of these patients, 80% manifested continued growth, more commonly in CD (81%) than UC (75%; P = 0.0002) and in females with CD (83%) than males with CD (79%; P = 0.012). Median height gain was greater in males with CD (1.6 cm) than in males with UC (1.3 cm; P = 0.0004), and in females with CD (1.8 cm) than in females with UC (1.5 cm; P = 0.025). Height velocity curves were shifted to the right in patients with IBD vs NHANES.

Conclusions
Pediatric patients with IBD frequently continue to grow beyond the time of expected growth plate closure. Unexpectedly, a high proportion of patients with UC exhibited continued growth, indicating delayed BA is also common in UC. Growth, a dynamic marker of disease status, requires continued monitoring even after patients transition from pediatric to adult care.
Universal Healthcare Coverage Does Not Ensure Adherence to Initial Colorectal Cancer Screening Guidelines
Authors: McEvoy Christian S , Shah Nina G , Roberts Sarah E , Carroll Anna M , Platz Timothy A , Oxner Christopher R , Butler Ralph E , Ricca Robert L 
Published: December 2020

Abstract

Introduction
Colorectal cancer is the second leading cause of cancer deaths in the USA, and screening tests are underutilized. The aim of this study was to determine the proportion of individuals at average risk who utilized a recommended initial screening test in a universal healthcare coverage system.

Materials and Methods
This is a retrospective cohort study of active duty and retired military members as well as civilian beneficiaries of the Military Health System. Individuals born from 1960 to 1962 and eligible for full benefits on their 50th birthday were evaluated. Military rank or rank of benefits sponsor was used to determine socioeconomic status. Adherence to the U.S. Preventive Services Task Force guidelines for initial colorectal cancer screening was determined using “Current Procedural Terminology” and “Healthcare Common Procedure Coding System” codes for colonoscopy, sigmoidoscopy, fecal occult blood test, and fecal immunohistochemistry test. Average risk individuals who obtained early screening ages 47 to 49 were also identified.

Results
This study identified 275,665 individuals at average risk. Of these, 105,957 (38.4%) adhered to screening guidelines. An additional 19,806 (7.2%) individuals were screened early. Colonoscopy (82.7%) was the most common screening procedure. Highest odds of screening were associated with being active duty military (odds ratio [OR] 3.63, 95% confidence interval [CI] 3.43 to 3.85), having highest socioeconomic status (OR 2.37, 95% CI 2.31 to 2.44), and having managed care insurance (OR 4.36, 95% CI 4.28 to 4.44).

Conclusions
Universal healthcare coverage does not ensure initial colorectal cancer screening utilization consistent with guidelines no does it eliminate disparities.