bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth
Authors: Li Zhen , Wang Xinyue , Yang Kebin , Zhu Chenglei , Yuan Tingting , Wang Jiongliang , Li Ying , Gao Zhimin 
Published: December 2021

Abstract
Background
Xylan is one of the most abundant hemicelluloses and can crosslink cellulose and lignin to increase the stability of cell walls. A number of genes encoding glycosyltransferases play vital roles in xylan biosynthesis in plants, such as those of the GT43 family. However, little is known about glycosyltransferases in bamboo, especially woody bamboo which is a good substitute for timber.

Results
A total of 17 GT43 genes (PeGT43–1 ~ PeGT43–17) were identified in the genome of moso bamboo (Phyllostachys edulis), which belong to three subfamilies with specific motifs. The phylogenetic and collinearity analyses showed that PeGT43s may have undergone gene duplication, as a result of collinearity found in 12 pairs of PeGT43s, and between 17 PeGT43s and 10 OsGT43s. A set of cis-acting elements such as hormones, abiotic stress response and MYB binding elements were found in the promoter of PeGT43s. PeGT43s were expressed differently in 26 tissues, among which the highest expression level was found in the shoots, especially in the rapid elongation zone and nodes. The genes coexpressed with PeGT43s were annotated as associated with polysaccharide metabolism and cell wall biosynthesis. qRT–PCR results showed that the coexpressed genes had similar expression patterns with a significant increase in 4.0 m shoots and a peak in 6.0 m shoots during fast growth. In addition, the xylan content and structural polysaccharide staining intensity in bamboo shoots showed a strong positive correlation with the expression of PeGT43s. Yeast one-hybrid assays demonstrated that PeMYB35 could recognize the 5′ UTR/promoter of PeGT43–5 by binding to the SMRE cis-elements.

Conclusions
PeGT43s were found to be adapted to the requirement of xylan biosynthesis during rapid cell elongation and cell wall accumulation, as evidenced by the expression profile of PeGT43s and the rate of xylan accumulation in bamboo shoots. Yeast one-hybrid analysis suggested that PeMYB35 might be involved in xylan biosynthesis by regulating the expression of PeGT43–5 by binding to its 5′ UTR/promoter. Our study provides a comprehensive understanding of PeGT43s in moso bamboo and lays a foundation for further functional analysis of PeGT43s for xylan biosynthesis during rapid growth.
Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
Authors: Liang Ying , Wei Kunhua , Wei Fan , Qin Shuangshuang , Deng Chuanhua , Lin Yang , Li Mingjie , Gu Li , Wei Guili , Miao Jianhua , Zhang Zhongyi 
Published: December 2021

Abstract
Background
Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood.

Results
To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs.

Conclusion
This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.
Burden of kidney failure from atheroembolic disease and association with survival in people receiving dialysis in Australia and New Zealand: a multi-centre registry study
Authors: Scott Tahira , Ethier Isabelle , Hawley Carmel , Pascoe Elaine M. , Viecelli Andrea K. , Ng Arnold , Cho Yeoungjee , Johnson David W. 
Published: December 2021

Abstract
Background
Cardiovascular disease is a leading cause of mortality in kidney failure (KF). Patients with KF from atheroembolic disease are at higher risk of cardiovascular disease than other causes of KF. This study aimed to determine survival on dialysis for patients with KF from atheroembolic disease compared with other causes of KF.

Methods
All adults (≥ 18 years) with KF initiating dialysis as the first kidney replacement therapy between 1 January 1990 and 31 December 2017 according to the Australia and New Zealand Dialysis and Transplant registry were included. Patients were grouped into either: KF from atheroembolic disease and all other causes of KF. Survival outcomes were assessed by the Kaplan-Meier method and Cox regression analysis adjusted for patient-related characteristics.

Results
Among 65,266 people on dialysis during the study period, 334 (0.5%) patients had KF from atheroembolic disease. A decreasing annual incidence of KF from atheroembolic disease was observed from 2008 onwards. Individuals with KF from atheroembolic disease demonstrated worse survival on dialysis compared to those with other causes of KF (HR 1.80, 95% confidence interval [CI] 1.61–2.03). The respective one- and five-year survival rates were 77 and 23% for KF from atheroembolic disease and 88 and 47% for other causes of KF. After adjustment for patient characteristics, KF from atheroembolic disease was not associated with increased patient mortality (adjusted HR 0.93 95% CI 0.82–1.05).

Conclusions
Survival outcomes on dialysis are worse for individuals with KF from atheroembolic disease compared to those with other causes of KF, probably due to patient demographics and higher comorbidity.
Reduction of metal artifacts from knee tumor prostheses on CT images: value of the single energy metal artifact reduction (SEMAR) algorithm
Authors: Zhang Fang-ling , Li Ruo-cheng , Zhang Xiao-ling , Zhang Zhao-hui , Ma Ling , Ding Lei 
Published: December 2021

Abstract
Background
To evaluate the effect of the single energy metal artifact reduction (SEMAR) algorithm with a multidetector CT (MDCT) for knee tumor prostheses.

Methods
First, a phantom of knee tumor prosthesis underwent a MDCT scan. The raw data was reconstructed by iterative reconstruction (IR) alone and IR plus SEMAR. The mean value of the CT number and the image noise were measured around the prosthesis at the stem level and articular level. Second, 95 consecutive patients with knee tumor prostheses underwent MDCT scans. The raw data were also reconstructed by the two methods. Periprosthetic structures were selected at the similar two levels. Four radiologists visually graded the image quality on a scale from 0 to 5. Additionally, the readers also assessed the presence of prosthetic complication and tumor recurrence on a same scale.

Results
In the phantom, when the SEMAR was used, the CT numbers were closer to normal value and the noise of images using soft and sharper kernel were respectively reduced by up to 77.1% and 43.4% at the stem level, and by up to 82.2% and 64.5% at the articular level. The subjective scores increased 1 ~ 3 points and 1 ~ 4 points at the two levels, respectively. Prosthetic complications and tumor recurrence were diagnosed in 66 patients. And the SEMAR increased the diagnostic confidence of prosthetic complications and tumor recurrence (4 ~ 5 vs. 1 ~ 1.5).

Conclusions
The SEMAR algorithm can significantly reduce the metal artifacts and increase diagnostic confidence of prosthetic complications and tumor recurrence in patients with knee tumor prostheses.
Time to regain birth weight - a marker to predict the severity of retinopathy of prematurity?
Authors: Anvekar Ajay , Athikarisamy Sam , Rao Shripada , Gill Andy , Nathan Elizabeth , Doherty Dorota , Lam Geoffrey 
Published: December 2021

Abstract
Background
Poor weight gain in the first few weeks of life has been studied as a predictor of retinopathy of prematurity (ROP). Our aim was to assess whether time taken to regain birthweight (BW) be used as an additional marker to identify infants with type 1 ROP.

Methods
In this retrospective study, preterm infants (< 27 weeks gestational age at birth) born during the period from 1/1/2010–31/12/2015 at a tertiary neonatal intensive care unit in Australia were included. Twenty-seven preterm infants with Type 1 ROP were identified. Controls (No ROP or ROP other than type 1) were matched with cases on gestational age at birth and BW (1:4 ratio). Data were collected from the database and medical records.

Results
The median (IQR) gestational age for Type 1 ROP and control groups were 24 (24–26) and 25 (24–26) weeks respectively and median (IQR) BW for Type 1 ROP and control groups were 675 (635–810) and 773 (666–884) grams respectively. Preterm infants with Type 1 ROP were more likely to be small for gestational age (SGA) (18.5% vs 3.7%, p = 0.015) and had increased weeks on oxygen therapy (median 11.9 vs 9.1, p = 0.028). Time to regain BW was longer in preterm infants with type 1 ROP than controls but did not reach statistical significance (median 9 vs 7 days, OR 1.08, 95% CI 1.00–1.17, p = 0.059) adjusted for SGA and duration of oxygen therapy. The area under the curve from the time to regain BW model with adjustment for SGA and duration of oxygen therapy was 0.73 (95% CI 0.62–0.83).

Conclusion
We hypothesize that time to regain BW has potential to aid prediction of Type 1 ROP and this warrants further investigation in a larger prospective study.
Association of COVID-19 mortality with politics and on-demand testing in 217 U.S. counties
Authors: Robertson Leon S. 
Published: December 2021

Abstract
Background
Previous research found increased COVID-19 spread associated with politics and on-demand testing but not in the same study. The objective of this study is to estimate the contribution of each corrected for the other and a variety of known risk factors.

Methods
Using data from 217 U.S. counties of more than 50,000 population where testing data were available in April, 2021, the associations of COVID-19 deaths with politics, testing and other risk factors were examined by Poisson and least squares regression.

Results
Statistical controls for 15 risk factors failed to eliminate the association of COVID mortality risk with percent of vote for Donald Trump in 2016 or negative tests per population. Each is independently predictive of increased mortality.

Conclusion
Apparently, many people who test negative for the SARS-CoV-2 virus engage in activities that increase their risk, a problem likely to increase with the availability of home tests. There is no association of negative tests with the Trump vote but, according to polling data, Trump voters’ past resistance to public health recommendations has been extended to resistance to being vaccinated, threatening the goal of herd immunity.
Barriers and facilitators to facility HIV self-testing in outpatient settings in Malawi: a qualitative study
Authors: Mphande Misheck , Campbell Paula , Hoffman Risa M. , Phiri Khumbo , Nyirenda Mike , Gupta Sundeep K. , Wong Vincent , Dovel Kathryn 
Published: December 2021

AbstractBackgroundFacility HIV self-testing (HIVST) within outpatient departments can increase HIV testing coverage by facilitating HIVST use in outpatient waiting spaces while clients wait for routine care. Facility HIVST allows for the majority of outpatients to test with minimal health care worker time requirements. However, barriers and facilitators to outpatients’ use of facility HIVST are still unknown.MethodsAs part of a cluster randomized trial on facility HIVST in Malawi, we conducted in-depth interviews with 57 adult outpatients (> 15 years) who were exposed to the HIVST intervention and collected observational journals that documented study staff observations from facility waiting spaces where HIVST was implemented. Translated and transcribed data were analyzed using constant comparison analysis in Atlas.ti.ResultsFacility HIVST was convenient, fast, and provided autonomy to outpatients. The strategy also had novel facilitators for testing, such as increased motivation to test due to seeing others test, immediate support for HIVST use, and easy access to additional HIV services in the health facility. Barriers to facility HIVST included fear of judgment from others and unwanted status disclosure due to lack of privacy. Desired changes to the intervention included private, separate spaces for kit use and interpretation and increased opportunity for disclosure and post-test counseling.ConclusionsFacility HIVST was largely acceptable to outpatients in Malawi with novel facilitators that are unique to facility HIVST in OPD waiting spaces.Trial registrationThe parent trial is registered withClinicalTrials.gov,NCT03271307, and Pan African Clinical Trials, PACTR201711002697316.
Results of the home mechanical ventilation national program among adults in Chile between 2008 and 2017
Authors: Maquilón César , Antolini Mónica , Valdés Nicolás , Andrade Marianela , Canales Krishnna , Rabec Claudio , Olave Cristian , Aguayo Miguel , Rivas Patricia , Andrade Carmen , Venegas Ángela , Zapata Sandra , Torres María Elena , Cabrera Osvaldo , Villalobos Jorge 
Published: December 2021

Abstract
Background
Home mechanical ventilation (HMV) is a viable and effective strategy for patients with chronic respiratory failure (CRF). The Chilean Ministry of Health started a program for adults in 2008.

Methods
This study examined the following data from a prospective cohort of patients with CRF admitted to the national HMV program: characteristics, mode of admission, quality of life, time in the program and survival.

Results
A total of 1105 patients were included. The median age was 59 years (44–58). Women accounted for 58.1% of the sample. The average body mass index (BMI) was 34.9 (26–46) kg/m2. A total of 76.2% of patients started HMV in the stable chronic mode, while 23.8% initiated HMV in the acute mode. A total of 99 patients were transferred from the children's program. There were 1047 patients on non-invasive ventilation and 58 patients on invasive ventilation. The median baseline PaCO2 level was 58.2 (52–65) mmHg. The device usage time was 7.3 h/d (5.8–8.8), and the time in HMV was 21.6 (12.2–49.5) months. The diagnoses were COPD (35%), obesity hypoventilation syndrome (OHS; 23.9%), neuromuscular disease (NMD; 16.3%), non-cystic fibrosis bronchiectasis or tuberculosis (non-CF BC or TBC; 8.3%), scoliosis (5.9%) and amyotrophic lateral sclerosis (ALS; 5.24%). The baseline score on the Severe Respiratory Insufficiency questionnaire (SRI) was 47 (± 17.9) points and significantly improved over time. The lowest 1- and 3-year survival rates were observed in the ALS group, and the lowest 9-year survival rate was observed in the non-CF BC or TB and COPD groups. The best survival rates at 9 years were OHS, scoliosis and NMD. In 2017, there were 701 patients in the children's program and 722 in the adult´s program, with a prevalence of 10.4 per 100,000 inhabitants.

Conclusion
The most common diagnoses were COPD and OHS. The best survival was observed in patients with OHS, scoliosis and NMD. The SRI score improved significantly in the follow-up of patients with HMV. The prevalence of HMV was 10.4 per 100,000 inhabitants.
Trial registration This study was approved by and registered at the ethics committee of North Metropolitan Health Service of Santiago, Chile (N° 018/2021).
Management of septic arthritis of the hip joint in adults. A systematic review of the literature
Authors: Balato Giovanni , de Matteo Vincenzo , Ascione Tiziana , de Giovanni Roberto , Marano Ernesto , Rizzo Maria , Mariconda Massimo 
Published: December 2021

Abstract
Background
The septic arthritis of the hip is a complex condition characterized by a variety of clinical presentations, a challenging diagnosis and different surgical treatment options, including arthroscopy, resection arthroplasty and one and two-stage total hip replacement. Each technique reports variable results in terms of infection eradication rate. The aim of this systematic review is to compare the most relevant studies available in current literature and to assess if a better treatment outcome can be predicted based on the microbiology, history, and type of infection (active vs quiescent) of each case.

Methods
A systematic review of the literature was performed in accordance with the PRISMA guidelines, including the studies dealing with the treatment of hip septic arthritis in adult patients. Electronic databases, namely the MEDLINE, Scopus, and Web of Science, were reviewed using a combination of following keywords “septic arthritis” AND “hip joint” OR “hip” AND “adult”.

Results
The total number of patients included in this review was 1236 (45% of which females), for 1238 hips. The most common pathogen isolated was Staphylococcus aureus in its Methicillin-sensitive variant ranging from 2 to 37% of cases. Negative cultures were the second most common finding. It was also differentiated the type of infection of the hip, 809 and 417 patients with active and quiescent hip infection, respectively, were analyzed. Eradication rates for two-stage revision arthroplasty ranged between 85 and 100%, for one-stage approach between 94 and 100%, while for arthroscopic debridement/lavage between 89 and 100%.

Conclusion
Staphylococcus aureus is the most common microorganism isolated followed by culture negative infections. Arthroscopic, one and two stage procedures can be effective in the treatment of hip septic arthritis when the indication is consistent with the type of infection retrieved.

Level of evidence
IV, therapeutic study.
Healthcare professionals’ perceptions of impacts of the Covid-19-pandemic on outpatient care in rural areas: a qualitative study
Authors: Hoerold Madlen , Gottschalk Marc , Debbeler Carla Maria , Heytens Heike , Ehrentreich Saskia , Braun-Dullaeus Ruediger C. , Apfelbacher Christian 
Published: December 2021

Abstract
Background
Measures to manage the COVID-19 pandemic have led to impacts on healthcare systems and providers worldwide. Outpatient healthcare professionals (HCPs) provide the majority of patient care. Insight into their experiences during a pandemic is rare. Therefore, we explored how primary and secondary care HCPs in a rural area in Germany experienced their work during the pandemic and what health-related outcomes they perceived in their patients. In this context, we also examined the impact on access to and utilization of healthcare and working conditions.

Methods
We conducted a qualitative interview study with outpatient HCPs. We recruited by e-mail, telephone, professional networks and personal contacts. Data were collected between August 2020 and January 2021. All interviews were audio recorded, transcribed, and analysed using qualitative content analysis.

Results
Our sample consisted of 28 HCPs (15 family physicians, 7 cardiologists, and 6 non-physician assistants, 12 female) from Saxony-Anhalt, Germany. HCPs experienced fewer consultations as well as cancellations by hospitals and secondary care physicians, especially at the beginning of the Covid-19-pandemic, while they continued throughout to provide outpatient care. They quickly adopted changes in practice organisation and healthcare provision. There was a shift towards telephone consultations, home visits as well as unconventional consultations e.g. through the practice window. Family physicians used personal relationships to support utilization of healthcare and to avoid health-related effects. Social tension and burden seemed to interact with a perceived lack of preparedness, the pandemic-related changes in their working condition as well as access to and utilization of healthcare. Chronic disease monitoring was postponed, which could have consequences in the course of disease of patients. HCPs experienced effects on patients’ psychological well-being.

Conclusion
Our study demonstrates the impacts of Covid-19-pandemic on outpatient care in rural areas and emphasizes its importance. HCPs experienced impacts on access to and utilization of healthcare, working conditions and health-related outcomes. Health policy should create a framework for healthcare to support outpatient care in rural areas with a looming undersupply of primary and secondary care in order to maintain healthcare and reduce pandemic impacts.
Daily rhythms in gene expression of the human parasite Schistosoma mansoni
Authors: Rawlinson Kate A. , Reid Adam J. , Lu Zhigang , Driguez Patrick , Wawer Anna , Coghlan Avril , Sankaranarayanan Geetha , Buddenborg Sarah K. , Soria Carmen Diaz , McCarthy Catherine , Holroyd Nancy , Sanders Mandy , Hoffmann Karl F. , Wilcockson David , Rinaldi Gabriel , Berriman Matthew 
Published: December 2021

Abstract
Background
The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis.

Results
Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host’s active phase and a ‘peak in metabolic activity’ during the host’s resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity.

Conclusions
There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis.