bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cross-sectional cohort study of the activity and turnover of neutrophil granulocytes in juvenile idiopathic arthritis
Authors: Backlund Malin , Venge Per , Berntson Lillemor 
Published: June 2021

Abstract
Background
The inflammatory process in juvenile idiopathic arthritis (JIA) involves both the innate and the adaptive immune system. The turnover and activity of neutrophil granulocytes may be reflected by proteins secreted from primary or secondary granules and from the cytoplasm of sequestered cells. Our primary aim was to compare the levels of the secondary neutrophil granule protein human neutrophil lipocalin (HNL), in JIA patients and controls, and to explore a possible priming of neutrophils through parallel analyses in plasma and serum. A secondary aim was to relate the levels of HNL to two other well-studied leukocyte proteins, S100A8/A9 and myeloperoxidase (MPO), as well as to clinical aspects of JIA.

Methods
The concentrations of the three biomarkers in serum, two of them also in plasma, were measured using enzyme-linked immunosorbent assay in 37 children with JIA without medical treatment, in high disease activity based on juvenile arthritis disease activity score 27 (JADAS27), 32 children on medical treatment, mainly in lower disease activity, and 16 healthy children. We assessed for differences between two groups using the Mann-Whitney U test, and used the Kruskal-Wallis test for multiple group comparisons. Spearman rank correlation, linear and multiple regression analyses were used for evaluation of associations between biomarker concentrations and clinical scores.

Results
The concentrations of HNL and MPO in serum were significantly increased in children with JIA (p < 0.001, p = 0.002) compared with healthy children, but we found no difference in the plasma levels of HNL and MPO between children with JIA and controls. The serum concentrations of MPO and HNL were unaffected by medical treatment, but S100A8/A9 was reduced by medical treatment and correlated with JADAS27 in both univariate (r = 0.58, p < 0.001) and multivariate (r = 0.59, p < 0.001) analyses.

Conclusions
Neutrophil granulocytes in children with JIA are primed to release primary and secondary granule proteins, without relation to medical treatment, whereas signs of increased turnover and sequestration of neutrophil granulocytes are reduced by treatment. Levels of neutrophil-originating proteins in serum most likely reflect underlying disease activities of JIA.
Assessment of transition readiness in adolescents in Thailand with rheumatic diseases: a cross-sectional study
Authors: Kittivisuit Sirinthip , Lerkvaleekul Butsabong , Soponkanaporn Sirisucha , Ngamjanyaporn Pintip , Vilaiyuk Soamarat 
Published: June 2021

Abstract
Background
Most childhood-onset rheumatic diseases are chronic health conditions, which need long-term care throughout adulthood. A well-organized transition care is challenging and patient assessment of transition skills is needed for transfer preparation to an adult care setting. The Transition Readiness Assessment Questionnaire (TRAQ) is used to assess transition skills in chronically ill patients. Currently, limited transition skill assessment data exist in pediatric patients with rheumatic diseases, especially in Asian countries. This study aimed to determine the transition readiness skills in patients with rheumatic diseases and ascertain predictive factors contributing to high transition readiness skills.

Methods
This is a cross-sectional study. All patients with rheumatic diseases aged 15–20 years were recruited. The TRAQ was cross-culturally adapted into the Thai language with good internal consistency and reliability. Patients completed the Thai TRAQ at the recent clinic visit and took the retest at a 2-week interval. Demographic data, baseline characteristics, clinical manifestations, and disease status were collected. Descriptive and logistic regression analyses were performed.

Results
A total of 111 patients with a mean age of 17.4 ± 1.8 years were included. Median (IQR) disease duration was 6.4 (3.2–9.0) years. The most common rheumatic disease was juvenile idiopathic arthritis (48.6%), followed by systemic lupus erythematosus (35.1%). The mean TRAQ score was 3.85 ± 0.69. Independent visits (OR 4.35, 95% CI 1.23–15.37) was a predictor of a high TRAQ score. Furthermore, dependent visits (OR 7.84, 95% CI 2.41–25.50) was a predictor of low TRAQ score in the “appointment keeping” domain, whereas inactive disease (OR 4.54, 95% CI 1.25–16.55) was a predictor of a low TRAQ score in “tracking health issues” domain. Lack of knowledge and skills on health insurance coverage, financial management, appointment arrangement, and coping with their illness were issues causing lower TRAQ score.

Conclusions
Patients, who had independent visits, had a higher chance to obtain higher TRAQ scores, whereas patients, who had an inactive disease or dependent visits, had less transition readiness skills. Physicians and parents should prepare to transfer patients to adult care settings, mainly encouraging independent living skills.
HIVIntact: a python-based tool for HIV-1 genome intactness inference
Authors: Wright Imogen A. , Bale Michael J. , Shao Wei , Hu Wei-Shau , Coffin John M. , Van Zyl Gert U. , Kearney Mary F. 
Published: June 2021

AbstractThe characterisation of the HIV-1 reservoir, which consists of replication-competent integrated proviruses that persist on antiretroviral therapy (ART), is made difficult by the rarity of intact proviruses relative to those that are defective. While the only conclusive test for the replication-competence of HIV-1 proviruses is carried out in cell culture, genetic characterization of genomes by near full-length (NFL) PCR and sequencing can be used to determine whether particular proviruses have insertions, deletions, or substitutions that render them defective. Proviruses that are not excluded by having such defects can be classified as genetically intact and, possibly, replication competent. Identifying and quantifying proviruses that are potentially replication-competent is important for the development of strategies towards a functional cure. However, to date, there are no programs that can be incorporated into deep-sequencing pipelines for the automated characterization and annotation of HIV genomes. Existing programs that perform this work require manual intervention, cannot be widely installed, and do not have easily adjustable settings. Here, we present HIVIntact, a python-based software tool that characterises genomic defects in NFL HIV-1 sequences, allowing putative intact genomes to be identified in-silico. Unlike other applications that assess the genetic intactness of HIV genomes, this tool can be incorporated into existing sequence-analysis pipelines and applied to large next-generation sequencing datasets.
Influence of perceived stress on prenatal depression in Surinamese women enrolled in the CCREOH study
Authors: Gokoel Anisma R. , Abdoel Wahid Firoz , Zijlmans Wilco C. W. R. , Shankar Arti , Hindori-Mohangoo Ashna D. , Covert Hannah H. , MacDonald-Ottevanger Meerte-Sigrid , Lichtveld Maureen Y. , Harville Emily W. 
Published: June 2021

Abstract
Background
Prenatal depression may have adverse health effects on mothers and their offspring. Perceived stress is an important risk factor for depression during pregnancy. Studies have shown that both perceived stress and depression may negatively influence birth outcomes. While 20% of pregnancies in Suriname, a middle-income Caribbean country located in northern South America, results in adverse birth outcomes, data on prenatal depression and its risk factors are lacking. This study aimed to assess the influence of perceived stress on depression during pregnancy in Surinamese women.

Methods
Survey data were used from 1143 pregnant women who participated in the Caribbean Consortium for Research in Environmental and Occupational Health-MeKiTamara prospective cohort study that addresses the impact of chemical and non-chemical environmental exposures in mother/child dyads in Suriname. The Edinburgh Depression Scale and Cohen Perceived Stress Scale were used to screen for probable depression (cut-off ≥ 12) and high stress (cut-off ≥ 20), respectively. The association between perceived stress and depression was examined using bivariate and multiple logistic regression analyses, adjusted for social support (including resilience) and maternal demographics.

Results
The prevalence of high perceived stress during the first two trimesters and the third trimester were 27.2% and 24.7% respectively. 22.4% of the participants had probable depression during first or second trimester and 17.6% during the third trimester. Women experiencing high stress levels during the first two trimesters had 1.92 increased odds (95% CI 1.18–3.11, p = 0.008) of having probable depression during the third trimester of pregnancy than those with low stress levels. Pregnant women with low individual resilience during early pregnancy (52.1%) had 1.65 (95% CI 1.03–2.63, p = 0.038) increased odds of having probable depression during later stages of pregnancy compared to those with high individual resilience. Low educational level (p = 0.004) and age of the mother (20–34 years) (p = 0.023) were significantly associated with probable depression during the third trimester.

Conclusions
Early detection and management of stress and depression during pregnancy are important. Health education programs, targeting the reduction of stress during pregnancy, may help to reduce depression and its potential adverse health effects on the mother and child.
Male–female concordance in reported involvement of women in contraceptive decision-making and its association with modern contraceptive use among couples in rural Maharashtra, India
Authors: Dixit Anvita , Johns Nicole E. , Ghule Mohan , Battala Madhusudana , Begum Shahina , Yore Jennifer , Saggurti Niranjan , Silverman Jay G. , Reed Elizabeth , Benmarhnia Tarik , Averbach Sarah , Raj Anita 
Published: June 2021

Abstract
Objective
Women’s involvement in contraceptive decision-making increases contraceptive use and reduces unmet need, but study of this has been limited to women’s self-reports. Less research is available examining couple concordance and women’s involvement in contraceptive decision-making as reported by both men and women.

Study design
We carried out a cross-sectional study using data from rural India (N = 961 young married couples). Using multivariable regression we examined the association between concordance or discordance in spousal reports of wife’s involvement in contraceptive decision-making and modern contraceptive use, adjusting for demographics, intimate partner violence, and contraceptive use discussion.

Results
More than one third (38.3%) of women reported current modern contraceptive use. Report of women’s involvement in contraceptive decision-making showed 70.3% of couples agreed that women were involved, jointly or alone (categorized as Concordant 1), 4.2% agreed women were not involved (categorized at Concordant 2), 13.2% had women report involvement but men report women were uninvolved (categorized as Discordant 1), and 12.2% had women report uninvolvement but men report that women were involved (categorized as Discordant 2). Discordant 2 couples had lower odds of modern contraceptive use relative to Concordant 1 couples (adjusted RR = 0.61, 95% CI 0.45–0.83). No other significant differences between Concordant 1 couples and other categories were observed.

Conclusion
One in four couples indicated discordance on women’s involvement in contraceptive decision making, with Discordant 2 category having lower odds of contraceptive use. Couples’ concordance in women’s involvement in contraceptive decision-making offers a target for family planning research and interventions to better meet their needs.
Trial registration ClinicalTrial.gov, NCT03514914. https://clinicaltrials.gov/ct2/show/NCT03514914
Sequential motor learning transfers from real to virtual environment
Authors: Takeo Yuhi , Hara Masayuki , Shirakawa Yuna , Ikeda Takashi , Sugata Hisato 
Published: June 2021

Abstract
Background
Skill acquisition of motor learning between virtual environments (VEs) and real environments (REs) may be related. Although studies have previously examined the transfer of motor learning in VEs and REs through the same tasks, only a small number of studies have focused on studying the transfer of motor learning in VEs and REs by using different tasks. Thus, detailed effects of the transfer of motor skills between VEs and REs remain controversial. Here, we investigated the transfer of sequential motor learning between VEs and REs conditions.

Methods
Twenty-seven healthy volunteers performed two types of sequential motor learning tasks; a visually cued button-press task in RE (RE task) and a virtual reaching task in VE (VE task). Participants were randomly assigned to two groups in the task order; the first group was RE task followed by VE task and the second group was VE task followed by RE task. Subsequently, the response time in RE task and VE task was compared between the two groups respectively.

Results
The results showed that the sequential reaching task in VEs was facilitated after the sequential finger task in REs.

Conclusions
These findings suggested that the sequential reaching task in VEs can be facilitated by a motor learning task comprising the same sequential finger task in REs, even when a different task is applied.
Increased extracellular fluid is associated with white matter fiber degeneration in CADASIL: in vivo evidence from diffusion magnetic resonance imaging
Authors: Yu Xinfeng , Yin Xinzhen , Hong Hui , Wang Shuyue , Jiaerken Yeerfan , Zhang Fan , Pasternak Ofer , Zhang Ruiting , Yang Linglin , Lou Min , Zhang Minming , Huang Peiyu 
Published: June 2021

Abstract
Background
White matter hyperintensities (WMHs) are one of the hallmarks of cerebral small vessel disease (CSVD), but the pathological mechanisms underlying WMHs remain unclear. Recent studies suggest that extracellular fluid (ECF) is increased in brain regions with WMHs. It has been hypothesized that ECF accumulation may have detrimental effects on white matter microstructure. To test this hypothesis, we used cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) as a unique CSVD model to investigate the relationships between ECF and fiber microstructural changes in WMHs.

Methods
Thirty-eight CADASIL patients underwent 3.0 T MRI with multi-model sequences. Parameters of free water (FW) and apparent fiber density (AFD) obtained from diffusion-weighted imaging (b = 0 and 1000 s/mm2) were respectively used to quantify the ECF and fiber density. WMHs were split into four subregions with four levels of FW using quartiles (FWq1 to FWq4) for each participant. We analyzed the relationships between FW and AFD in each subregion of WMHs. Additionally, we tested whether FW of WMHs were associated with other accompanied CSVD imaging markers including lacunes and microbleeds.

Results
We found an inverse correlation between FW and AFD in WMHs. Subregions of WMHs with high-level of FW (FWq3 and FWq4) were accompanied with decreased AFD and with changes in FW-corrected diffusion tensor imaging parameters. Furthermore, FW was also independently associated with lacunes and microbleeds.

Conclusions
Our study demonstrated that increased ECF was associated with WM degeneration and the occurrence of lacunes and microbleeds, providing important new insights into the role of ECF in CADASIL pathology. Improving ECF drainage might become a therapeutic strategy in future.
Evaluating implementation of International Health Regulations core capacities: using the Electronic States Parties Self-Assessment Annual Reporting Tool (e-SPAR) to monitor progress with Joint External Evaluation indicators
Authors: Razavi Ahmed , Collins Samuel , Wilson Anne , Okereke Ebere 
Published: June 2021

Abstract
Background
The International Health Regulations (IHR) are a legally binding instrument designed to improve Global Health Security by limiting the cross boarder spread of health risks. All 196 signatories to the IHR (2005) are required to report progress towards IHR core capacity implementation through an annual multi-sectoral self-assessment process known as the State Parties Self-Assessment Annual Reporting (SPAR). This mandatory process sits alongside the voluntary, external, peer-reviewed Joint External Evaluations (JEE) as two core components of the IHR monitoring and evaluation framework. JEEs are intended to occur once every 4–5 years following a voluntary request from the member state. This means that interim monitoring of IHR core capacity compliance, can be challenging and additional data sources are required. The outputs of the SPAR process represent one such source. Although the JEE and SPAR tools are intended to be complimentary, there has been no publicly available mapping of JEE indicators to SPAR indicators in order to inform progress on IHR compliance.

Results
This paper mapped JEE indicators to SPAR indicators and found a high level of correlation suggesting the SPAR process offers a method for countries and technical assistance programmes to monitor progress on IHR compliance and identify gaps in between JEE visits. However, coverage was not complete, and several gaps were identified most notably in antimicrobial resistance (AMR) and vaccinations.

Conclusion
Enhancing alignment between JEE and SPAR could offer a more consistent and complete way of assessing compliance with IHR.
Protocol development for somatic embryogenesis, SSR markers and genetic modification of Stipagrostis pennata (Trin.) De Winter
Authors: Asadi-Aghbolaghi Masoumeh , Dedicova Beata , Ranade Sonali Sachi , Le Kim-Cuong , Sharifzadeh Farzad , Omidi Mansoor , Egertsdotter Ulrika 
Published: June 2021

Abstract
Background
Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.

Results
A protocol for plant regeneration from somatic embryos of S. pennata was developed. Somatic embryogenesis was induced on Murashige & Skoog (MS) medium supplemented with 3 mg·L–1 2,4-D subsequently shoots were induced on MS medium and supplemented with 5 mg·L–1 zeatin riboside. The highest shoots induction was obtained when embryogenic callus derived from mature embryos (96%) in combination with MS filter-sterilized medium was used from Khuzestan location. The genetic stability of regenerated plants was analysed using ten simple sequence repeats (SSR) markers from S. pennata which showed no somaclonal variation in regenerated plants from somatic embryos of S. pennata. The regenerated plants of S. pennata showed genetic stability without any somaclonal variation for the four pairs of primers that gave the expected amplicon sizes. This data seems very reliable as three of the PCR products belonged to the coding region of the genome.
Furthermore, stable expression of GUS was obtained after Agrobacterium-mediated transformation using a super binary vector carried by a bacterial strain LBA4404.

Conclusion
To our knowledge, the current work is the first attempt to develop an in vitro protocol for somatic embryogenesis including the SSR marker analyses of regenerated plants, and Agrobacterium-mediated transformation of S. pennata that can be used for its large-scale production for commercial purposes.
Semi-supervised few-shot learning approach for plant diseases recognition
Authors: Li Yang , Chao Xuewei 
Published: June 2021

Abstract
Background
Learning from a few samples to automatically recognize the plant leaf diseases is an attractive and promising study to protect the agricultural yield and quality. The existing few-shot classification studies in agriculture are mainly based on supervised learning schemes, ignoring unlabeled data's helpful information.

Methods
In this paper, we proposed a semi-supervised few-shot learning approach to solve the plant leaf diseases recognition. Specifically, the public PlantVillage dataset is used and split into the source domain and target domain. Extensive comparison experiments considering the domain split and few-shot parameters (N-way, k-shot) were carried out to validate the correctness and generalization of proposed semi-supervised few-shot methods. In terms of selecting pseudo-labeled samples in the semi-supervised process, we adopted the confidence interval to determine the number of unlabeled samples for pseudo-labelling adaptively.

Results
The average improvement by the single semi-supervised method is 2.8%, and that by the iterative semi-supervised method is 4.6%.

Conclusions
The proposed methods can outperform other related works with fewer labeled training data.
A low-cost automated growth chamber system for continuous measurements of gas exchange at canopy scale in dynamic conditions
Authors: Salvatori Nicole , Giorgio Alberti , Muller Onno , Rascher Uwe , Peressotti Alessandro 
Published: June 2021

Abstract
Background
Obtaining instantaneous gas exchanges data is fundamental to gain information on photosynthesis. Leaf level data are reliable, but their scaling up to canopy scale is difficult as they are acquired in standard and/or controlled conditions, while natural environments are extremely dynamic. Responses to dynamic environmental conditions need to be considered, as measurements at steady state and their related models may overestimate total carbon (C) plant uptake.

Results
In this paper, we describe an automatic, low-cost measuring system composed of 12 open chambers (60 × 60 × 150 cm; around 400 euros per chamber) able to measure instantaneous CO2 and H2O gas exchanges, as well as environmental parameters, at canopy level. We tested the system’s performance by simulating different CO2 uptake and respiration levels using a tube filled with soda lime or pure CO2, respectively, and quantified its response time and measurement accuracy. We have been also able to evaluate the delayed response due to the dimension of the chambers, proposing a method to correct the data by taking into account the response time ($${t}_{0}$$

t
0

) and the residence time (τ). Finally, we tested the system by growing a commercial soybean variety in fluctuating and non-fluctuating light, showing the system to be fast enough to capture fast dynamic conditions. At the end of the experiment, we compared cumulative fluxes with total plant dry biomass.

Conclusions
The system slightly over-estimated (+ 7.6%) the total C uptake, even though not significantly, confirming its ability in measuring the overall CO2 fluxes at canopy scale. Furthermore, the system resulted to be accurate and stable, allowing to estimate the response time and to determine steady state fluxes from unsteady state measured values. Thanks to the flexibility in the software and to the dimensions of the chambers, even if only tested in dynamic light conditions, the system is thought to be used for several applications and with different plant canopies by mimicking different environmental conditions.