bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Difference in Facial Movement Between the Medial and the Lateral Midface: A 3-Dimensional Skin Surface Vector Analysis
Authors: Freytag David L , Alfertshofer Michael G , Frank Konstantin , Melnikov Dmitry V , Moellhoff Nicholas , Swift Arthur , Heisinger Stephan , Gotkin Robert H , Ehrl Denis , Cotofana Sebastian 
Published: March 2021

Abstract

Background
Our understanding of the functional anatomy of the face is constantly improving. To date, it is unclear whether the anatomic location of the line of ligaments has any functional importance during normal facial movements such as smiling.

Objectives
The authors sought to identify differences in facial movements between the medial and lateral midface by means of skin vector displacement analyses derived from 3-dimensional (3D) imaging and to further ascertain whether the line of ligaments has both a structural and functional significance in these movements.

Methods
The study sample consisted of 21 healthy volunteers (9 females and 12 males) of Caucasian ethnic background with a mean age of 30.6 (8.3) years and mean BMI of 22.57 (2.5) kg/m2. 3D images of the volunteers’ faces in repose and during smiling (Duchenne type) were taken. 3D imaging-based skin vector displacement analyses were conducted.

Results
The mean horizontal skin displacement was 0.08 (2.0) mm in the medial midface (lateral movement) and was −0.08 (1.96) mm in the lateral midface (medial movement) (P = 0.711). The mean vertical skin displacement (cranial movement of skin toward the forehead/temple) was 6.68 (2.4) mm in the medial midface, whereas it was 5.20 (2.07) mm in the lateral midface (P = 0.003).

Conclusions
The results of this study provide objective evidence for an antagonistic skin movement between the medial and lateral midface. The functional boundary identified by 3D imaging corresponds to the anatomic location of the line of ligaments.

Level of Evidence: 4
PrecisionProDB: improving the proteomics performance for precision medicine
Authors: Cao Xiaolong , Xing Jinchuan 
Published: March 2021

Abstract

Summary
As the next-generation sequencing technology becomes broadly applied, genomics and transcriptomics are becoming more commonly used in both research and clinical settings. However, proteomics is still an obstacle to be conquered. For most peptide search programs in proteomics, a standard reference protein database is used. Because of the thousands of coding DNA variants in each individual, a standard reference database does not provide perfect match for many proteins/peptides of an individual. A personalized reference database can improve the detection power and accuracy for individual proteomics data. To connect genomics and proteomics, we designed a Python package PrecisionProDB that is specialized for generating a personized protein database for proteomics applications. PrecisionProDB supports multiple popular file formats and reference databases, and can generate a personized database in minutes. To demonstrate the application of PrecisionProDB, we generated human population-specific reference protein databases with PrecisionProDB, which improves the number of identified peptides by 0.34% on average. In addition, by incorporating cell line-specific variants into the protein database, we demonstrated a 0.71% improvement for peptide identification in the Jurkat cell line. With PrecisionProDB and these datasets, researchers and clinicians can improve their peptide search performance by adopting the more representative protein database or adding population and individual-specific proteins to the search database with minimum increase of efforts.

Availabilityand implementation
PrecisionProDB and pre-calculated protein databases are freely available at https://github.com/ATPs/PrecisionProDB and https://github.com/ATPs/PrecisionProDB_references.

Supplementary information
Supplementary data are available at Bioinformatics online.
Protein contact map refinement for improving structure prediction using generative adversarial networks
Authors: Maddhuri Venkata Subramaniya Sai Raghavendra , Terashi Genki , Jain Aashish , Kagaya Yuki , Kihara Daisuke 
Published: March 2021

Abstract

Motivation
Protein structure prediction remains as one of the most important problems in computational biology and biophysics. In the past few years, protein residue–residue contact prediction has undergone substantial improvement, which has made it a critical driving force for successful protein structure prediction. Boosting the accuracy of contact predictions has, therefore, become the forefront of protein structure prediction.

Results
We show a novel contact map refinement method, ContactGAN, which uses Generative Adversarial Networks (GAN). ContactGAN was able to make a significant improvement over predictions made by recent contact prediction methods when tested on three datasets including protein structure modeling targets in CASP13 and CASP14. We show improvement of precision in contact prediction, which translated into improvement in the accuracy of protein tertiary structure models. On the other hand, observed improvement over trRosetta was relatively small, reasons for which are discussed. ContactGAN will be a valuable addition in the structure prediction pipeline to achieve an extra gain in contact prediction accuracy.

Availability and implementation
https://github.com/kiharalab/ContactGAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Unexpected population genetic structure in two closely related euphaeid damselflies from the Yaeyama and Taiwan Islands (Odonata: Euphaeidae)
Authors: Kanke Emi , Suzuki Kohei , Sekiné Kazuki , Suzuki Tomoya , Hatta Kokichi , Yang Man-Miao , Tojo Koji 
Published: March 2021

Abstract
In general, population genetics theory predicts that a fragmented smaller population will contain relatively less genetic diversity than a larger population, and so will have a higher rate of genetic fixation due to random genetic drift or inbreeding. However, in this study, having analysed the genetic structure of the mitochondrial DNA COI region between two closely related euphaeid damselflies, we obtained unexpected results which contradict the theoretically expected patterns. Despite their geographical proximity, Euphaea yayeyamana was clearly genetically isolated on Ishigaki and Iriomote Islands, and no haplotype crossovers were observed. Even within each island, several diverse haplotypes were observed, indicating a significantly high haplotype intra-island diversity. However, the genetic diversity within Taiwan’s population of Euphaea formosa was significantly lower than that within either Ishigaki or Iriomote Island, even though Taiwan is significantly larger, with high mountain ranges that reach c. 4000 m a.s.l. and an abundance of habitats, all factors that should contribute to high genetic diversity. The current low diversity status for Taiwan’s population may be due to genetic bottleneck effects. In contrast, despite the very small population sizes of Ishigaki and Iriomote Islands coupled with the effects of glacial and interglacial geological events, they have maintained markedly high genetic diversity.
SEARCH Human Immunodeficiency Virus (HIV) Streamlined Treatment Intervention Reduces Mortality at a Population Level in Men With Low CD4 Counts
Authors: Kamya Moses R , Petersen Maya L , Kabami Jane , Ayieko James , Kwariisima Dalsone , Sang Norton , Clark Tamara D , Schwab Joshua , Charlebois Edwin D , Cohen Craig R , Bukusi Elizabeth A , Peng James , Jain Vivek , Chen Yea-Hung , Chamie Gabriel , Balzer Laura B , Havlir Diane V 
Published: March 2021

Abstract

Background
We tested the hypothesis that patient-centered, streamlined human immunodeficiency virus (HIV) care would achieve lower mortality than the standard treatment model for persons with HIV and CD4 ≤ 350/uL in the setting of population-wide HIV testing.

Methods
In the SEARCH (Sustainable East Africa Research in Community Health) Study (NCT01864603), 32 communities in rural Uganda and Kenya were randomized to country-guided antiretroviral therapy (ART) versus streamlined ART care that included rapid ART start, visit spacing, flexible clinic hours, and welcoming environment. We assessed persons with HIV and CD4 ≤ 350/uL, ART eligible in both arms, and estimated the effect of streamlined care on ART initiation and mortality at 3 years. Comparisons between study arms used a cluster-level analysis with survival estimates from Kaplan-Meier; estimates of ART start among ART-naive persons treated death as a competing risk.

Results
Among 13 266 adults with HIV, 2973 (22.4%) had CD4 ≤ 350/uL. Of these, 33% were new diagnoses, and 10% were diagnosed but ART-naive. Men with HIV were almost twice as likely as women with HIV to have CD4 ≤ 350/uL and be untreated (15% vs 8%, respectively). Streamlined care reduced mortality by 28% versus control (risk ratio [RR] = 0.72; 95% confidence interval [CI]: .56, .93; P = .02). Despite eligibility in both arms, persons with CD4 ≤ 350/uL started ART faster under streamlined care versus control (76% vs 43% by 12 months, respectively; P &lt; .001). Mortality was reduced substantially more among men (RR = 0.61; 95% CI: .43, .86; P = .01) than among women (RR = 0.90; 95% CI: .62, 1.32; P = .58).

Conclusions
After population-based HIV testing, streamlined care reduced population-level mortality among persons with HIV and CD4 ≤ 350/uL, particularly among men. Streamlined HIV care models may play a key role in global efforts to reduce AIDS deaths.
Average of Patient Deltas: Patient-Based Quality Control Utilizing the Mean Within-Patient Analyte Variation
Authors: Cembrowski George S , Xu Qian , Cervinski Mark A 
Published: March 2021

Abstract

Background
Because traditional QC is discontinuous, laboratories use additional strategies to detect systematic error. One strategy, the delta check, is best suited to detect large systematic error. The moving average (MA) monitors the mean patient analyte value but cannot equitably detect systematic error in skewed distributions. Our study combines delta check and MA to develop an average of deltas (AoD) strategy that monitors the mean delta of consecutive, intrapatient results.

Methods
Arrays of the differences (delta) between paired patient results collected within 20–28 h of each other were generated from historical data. AoD protocols were developed using a simulated annealing algorithm in MatLab (Mathworks) to select the number of patient delta values to average and truncation limits to eliminate large deltas. We simulated systematic error by adding bias to arrays for plasma albumin, alanine aminotransferase, alkaline phosphatase, amylase, aspartate aminotransferase, bicarbonate, bilirubin (total and direct), calcium, chloride, creatinine, lipase, sodium, phosphorus, potassium, total protein, and magnesium. The average number of deltas to detection (ANDED) was then calculated in response to induced systematic error.

Results
ANDED varied by combination of assay and AoD protocol. Errors in albumin, lipase, and total protein were detected with a mean of 6 delta pairs. The highest ANDED was calcium, with a positive 0.6-mg/dL shift detected with an ANDED of 75. However, a negative 0.6-mg/dL calcium shift was detected with an ANDED of 25.

Conclusions
AoD detects systematic error with relatively few paired patient samples and is a patient-based QC technique that will enhance error detection.
Influence of sex on intracellular calcium homoeostasis in patients with atrial fibrillation
Authors: Herraiz-Martínez Adela , Tarifa Carmen , Jiménez-Sábado Verónica , Llach Anna , Godoy-Marín Hector , Colino-Lage Hildegard , Nolla-Colomer Carme , Casabella-Ramon Sergi , Izquierdo-Castro Paloma , Benítez Iván , Benítez Raul , Roselló-Díez Elena , Rodríguez-Font Enrique , Viñolas Xavier , Ciruela Francisco , Cinca Juan , Hove-Madsen Leif 
Published: March 2021

Abstract

Aims
Atrial fibrillation (AF) has been associated with intracellular calcium disturbances in human atrial myocytes, but little is known about the potential influence of sex and we here aimed to address this issue.

Methods and results
Alterations in calcium regulatory mechanisms were assessed in human atrial myocytes from patients without AF or with long-standing persistent or permanent AF. Patch-clamp measurements revealed that L-type calcium current (ICa) density was significantly smaller in males with than without AF (−1.15 ± 0.37 vs. −2.06 ± 0.29 pA/pF) but not in females with AF (−1.88 ± 0.40 vs. −2.21 ± 0.0.30 pA/pF). In contrast, transient inward currents (ITi) were more frequent in females with than without AF (1.92 ± 0.36 vs. 1.10 ± 0.19 events/min) but not in males with AF. Moreover, confocal calcium imaging showed that females with AF had more calcium spark sites than those without AF (9.8 ± 1.8 vs. 2.2 ± 1.9 sites/µm2) and sparks were wider (3.0 ± 0.3 vs. 2.2 ± 0.3 µm) and lasted longer (79 ± 6 vs. 55 ± 8 ms), favouring their fusion into calcium waves that triggers ITIs and afterdepolarizations. This was linked to higher ryanodine receptor phosphorylation at s2808 in women with AF, and inhibition of adenosine A2A or beta-adrenergic receptors that modulate s2808 phosphorylation was able to reduce the higher incidence of ITI in women with AF.

Conclusion
Perturbations of the calcium homoeostasis in AF is sex-dependent, concurring with increased spontaneous SR calcium release-induced electrical activity in women but not in men, and with diminished ICa density in men only.
Biological Control of Hemlock Woolly Adelgid: Implications of Adult Emergence Patterns of TwoLeucopisspp. (Diptera: Chamaemyiidae) andLaricobius nigrinus(Coleoptera: Derodontidae) Larval Drop
Authors: Dietschler Nicholas J , Bittner Tonya D , Trotter R Talbot , Fahey Timothy J , Whitmore Mark C 
Published: March 2021

AbstractThe hemlock woolly adelgid (Hemiptera: Adelgidae Adelges tsugae Annand) poses a serious threat to hemlocks in eastern North America, and ongoing research is focused on the identification and development of biological controls to protect and manage hemlock resources. Three predators native to the Pacific Northwest of North America that have been the focus of much research are Leucopis argenticollis (Zetterstedt), Leucopis piniperda (Malloch) (Diptera: Chamaemyiidae), and Laricobius nigrinus (Fender) (Coleoptera: Derodontidae). This study addresses the knowledge gap of adult Leucopis spp. emergence patterns, with comparisons to the timing of larval La. nigrinus drop for pupation. Adult Leucopis spp. emergence was observed in the lab from field-collected, adelgid-infested foliage from Washington state in 2019 and 2020. Adult Leucopis spp. were collected daily as they emerged from foliage collections and identified to species using morphological features; a subset was validated using DNA barcoding. Accumulated heating degree days were calculated to compare a standardized emergence timing across collections made at different locations and temperature regimes. The abundance of the two Leucopis spp. and of the combined Leucopis spp. and La. nigrinus varied among sites and years, and no species was consistently more abundant than the other. Evaluations of seasonal emergence trends of the three species determine the predator complex behaves in a temporally stratified and predictable way. Emergence of adult Le. argenticollis was observed first, followed by La. nigrinus larval drop, with Le. piniperda emerging at the end of larval drop, and finally a second emergence of Le. argenticollis.
Chinese stroke survivors’ perceptions of participation in exercise or sitting Tai Chi
Authors: Zhao Jie , Zang Yuli , Chau Janita Pak Chun , He Rong , Thompson David R 
Published: March 2021

Abstract

Aims
Exercise promotes functional recovery among stroke survivors and is recommended to be commenced as soon as is feasible. However, little is known about stroke survivors’ perception of participation in exercise or sitting Tai Chi, a more culturally appropriate and popular movement in China. To explore Chinese stroke survivors’ perceptions of participation in exercise or sitting Tai Chi.

Methods and results
Face-to-face semi-structured interviews and content analysis of transcripts were conducted with a purposive sample of 30 stroke survivors. The qualitative study explored perceptions of post-stroke participation in exercise or sitting Tai Chi. The consolidated criteria for reporting qualitative research checklist was used to report findings. Perceived facilitators of exercise participation were healthcare professionals’ encouragement and recommendations, family and peer support and survivors’ motivation, intention, and self-perceived benefits. Perceived barriers were fear of falling, physical discomfort, and challenges in standing. Despite some reservations, most participants were willing to try sitting Tai Chi.

Conclusions
Encouragement and support, motivation, and perceived benefits were important for exercise participation after stroke. With the premise that all medical and nursing students in China are trained in Tai Chi, for stroke survivors with no access to formal exercise programmes, sitting Tai Chi may offer an appropriate alternative.
Toward Understanding Everyday Lives of Older Adults: A Methodological Exploration
Authors: Shin Jung-hye , Her-Xiong Youhung , Tredinnick Ross , Ponto Kevin 
Published: March 2021

Abstract

Background and Objectives
Emerging trends in aging in place and increasing needs for home health care highlight the importance of researching older adults’ daily lives as they unfold within their residential environments. However, studies that examine how older adults interact with their home environments are scarce as homes are fluid and private spaces and do not render themselves easily to the researcher’s eyes. This article explores a new investigational method combining 3D-scanning and biomarker tracking technology with in-depth qualitative interviews in situ to explore older adults’ daily interactions with their home environments.

Research Design and Methods
We employed a unique approach that combined spatial, locational, and physiological tracking technology with in-depth qualitative in-home interviews with older adults aged 62–89 who received home modifications as a means to successfully age in place. We explored multiple data sets both individually and collectively, using various data analysis, visualization, and integration methods to test the feasibility and utility of our approach.

Results
A review of individual data sets allowed unique insights into different aspects of the daily lives of this sample of older adults. When combined, the data sets and subsequent analysis allowed an in-depth understanding of participants’ well-being and adaptive behaviors.

Discussion and Implications
This study provides a strong methodology for studying the home environment and its impact on the participants’ health and well-being. Insights obtained through this method can inform research, policy, and practice at all levels for professionals to continue exploring ways to support older adults aged 65 and older aging at home.
Smoking, Radiation Therapy, and Contralateral Breast Cancer Risk in Young Women
Authors: Reiner Anne S , Watt Gordon P , John Esther M , Lynch Charles F , Brooks Jennifer D , Mellemkjær Lene , Boice John D , Knight Julia A , Concannon Patrick , Smith Susan A , Liang Xiaolin , Woods Meghan , Shore Roy , Malone Kathleen E , Bernstein Leslie ,   The WECARE Study Collaborative Group, Bernstein Jonine L 
Published: March 2021

Abstract
Evidence is mounting that cigarette smoking contributes to second primary contralateral breast cancer (CBC) risk. Whether radiation therapy (RT) interacts with smoking to modify this risk is unknown. In this multicenter, individually matched, case-control study, we examined the association between RT, smoking, and CBC risk. The study included 1521 CBC cases and 2212 controls with unilateral breast cancer, all diagnosed with first invasive breast cancer between 1985 and 2008 aged younger than 55 years. Absorbed radiation doses to contralateral breast regions were estimated with thermoluminescent dosimeters in tissue-equivalent anthropomorphic phantoms, and smoking history was collected by interview. Rate ratios (RRs) and 95% confidence intervals (CIs) for CBC risk were estimated by multivariable conditional logistic regression. There was no interaction between any measure of smoking with RT to increase CBC risk (eg, the interaction of continuous RT dose with smoking at first breast cancer diagnosis [ever/never]: RR = 1.00, 95% CI = 0.89 to 1.14; continuous RT dose with years smoked: RR = 1.00, 95% CI = 0.99 to 1.01; and continuous RT dose with lifetime pack-years: RR = 1.00, 95% CI = 0.99 to 1.01). There was no evidence that RT further increased CBC risk in young women with first primary breast cancer who were current smokers or had smoking history.
Pain and QOL in Pediatric Sickle Cell Disease: Buffering by Resilience Processes
Authors: Wright Laura A , Cohen Lindsey L , Gise Jensi , Shih Sharon , Sil Soumitri , Carter, Sierra 
Published: March 2021

AbstractObjectiveSickle cell disease (SCD) is a group of inherited blood disorders. The central feature of this chronic condition is pain. Several identified risk factors exacerbate the impact of pain on quality of life (QOL) in SCD; however, there are relatively fewer investigations of strengths-based resilience variables that might buffer the influence of pain on living with SCD. The purpose of this study was to examine strength-based resilience processes in youth with SCD and their parents. Grounded in an ecological resilience-risk model, we evaluated whether adolescent and parent protective factors (pain acceptance, mindfulness, and psychological flexibility) moderated the relation between adolescent-reported pain burden and QOL.MethodsNinety-three 12- to 18-year-old adolescents with SCD and their parents participated. Adolescents completed assessments of pain characteristics, pain acceptance, mindfulness, and QOL. Parents completed instruments measuring demographic and disease variables and parent psychological flexibility.ResultsPain variables were associated with protective factors in predicted directions. Adolescent acceptance and mindfulness were positively correlated with QOL. Parent psychological flexibility and adolescent QOL were not related. After controlling for demographic, pain, and disease variables, moderation analyses indicated that adolescent pain acceptance buffered the relation between SCD pain burden and QOL. Moderation analyses were not significant for adolescent mindfulness or parent psychological flexibility.ConclusionsResults suggest that strengths-based factors may play an important role for adolescents’ QOL within the context of SCD pain. Interventions that enhance teenagers’ ability to accept pain might be particularly useful to improve QOL in adolescents living with SCD pain.