bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation of the rice AN1‐type zinc‐finger protein gene ASL4 causes chloroplast development defects and seedling lethality
Authors: Lin D. Z. , Pan Q. W. , Wang X. M. , Chen Y. , Pan X. B. , Dong Y. J. 
Published: November 2021

Abstract

Plant zinc‐finger proteins play a crucial role in biosynthesis and plant development. However, it is not known whether certain zinc‐finger proteins play a role in rice chloroplast development.

In this study, a novel rice zinc‐finger protein mutant asl4 (albino seedling lethality4), which exhibits an albino lethal phenotype at the seedling stage, was used. Chlorophyll fluorescence analysis and TEM were used to investigate features of the asl4 mutant. The genetic behaviour and function of ASL4 gene were then analysed thorough map‐based cloning, transgenic complement and subcellular localization.

The albino lethal phenotype was caused by a single nucleotide (G*) deletion mutation on the exon of the ASL4 (LOC_Os09g21710) gene. The ASL4 gene encoded a novel zinc‐finger protein containing two ZnF‐AN1 domains, which was localized to the nucleocytoplasm. The ASL4 transcripts were highly expressed in all leaves but relatively less in other tissues, suggesting its tissue‐specific expression. The transcript levels of associated genes for Chl biosynthesis, photosynthesis and chloroplast development were severely suppressed in asl4 mutants.

In conclusion, the absence of ASL4 function caused a defect in chloroplast development and seedling lethality. This is the first published report on the importance of the ZnF‐AN1 type zinc‐finger protein gene in chloroplast development in rice.
Harnessing root architecture to address global challenges
Authors: Lynch Jonathan P. 
Published: November 2021

SUMMARYRoot architecture can be targeted in breeding programs to develop crops with better capture of water and nutrients. In rich nations, such crops would reduce production costs and environmental pollution and, in developing nations, they would improve food security and economic development. Crops with deeper roots would have better climate resilience while also sequestering atmospheric CO2. Deeper rooting, which improves water and N capture, is facilitated by steeper root growth angles, fewer axial roots, reduced lateral branching, and anatomical phenotypes that reduce the metabolic cost of root tissue. Mechanical impedance, hypoxia, and Al toxicity are constraints to subsoil exploration. To improve topsoil foraging for P, K, and other shallow resources, shallower root growth angles, more axial roots, and greater lateral branching are beneficial, as are metabolically cheap roots. In high‐input systems, parsimonious root phenotypes that focus on water capture may be advantageous. The growing prevalence of Conservation Agriculture is shifting the mechanical impedance characteristics of cultivated soils in ways that may favor plastic root phenotypes capable of exploiting low resistance pathways to the subsoil. Root ideotypes for many low‐input systems would not be optimized for any one function, but would be resilient against an array of biotic and abiotic challenges. Root hairs, reduced metabolic cost, and developmental regulation of plasticity may be useful in all environments. The fitness landscape of integrated root phenotypes is large and complex, and hence will benefit from in silico tools. Understanding and harnessing root architecture for crop improvement is a transdisciplinary opportunity to address global challenges.
Oxidative stress response and programmed cell death guided by NAC013 modulate pithiness in radish taproots
Authors: Hoang Nam V. , Park Suhyoung , Park Chulmin , Suh Hannah , Kim Sang‐Tae , Chae Eunyoung , Kang Byoung‐Cheorl , Lee Ji‐Young 
Published: November 2021

SUMMARYRadish, Raphanus sativus L., is an important root crop that is cultivated worldwide. Owing to its evolutionary proximity to Arabidopsis thaliana, radish can be used as a model root crop in research on the molecular basis of agronomic traits. Pithiness is a significant defect that reduces the production of radish with commercial value; however, traditional breeding to eliminate this trait has thus far been unsuccessful. Here, we performed transcriptomics and genotype‐by‐sequencing (GBS)‐based quantitative trait locus (QTL) analyses of radish inbred lines to understand the molecular basis of pithiness in radish roots. The transcriptome data indicated that pithiness likely stems from the response to oxidative stress, leading to cell death of the xylem parenchyma during the root‐thickening process. Subsequently, we narrowed down a list of candidates responsible for pithiness near a major QTL and found polymorphisms in a radish homologue of Arabidopsis ANAC013 (RsNAC013), an endoplasmic reticulum bound NAC transcription factor that is targeted to the nucleus to mediate the mitochondrial retrograde signal. We analysed the effects of polymorphisms in RsNAC013 using Arabidopsis transgenic lines overexpressing RsNAC013 alleles as well as in radish inbred lines bearing these alleles. This analysis indicated that non‐synonymous variations within the coding sequence result in different levels of RsNAC013 activities, thereby providing a genetic condition for root pithiness. The elevated oxidative stress or hypoxia that activates RsNAC013 for mitochondrial signalling enhances this process. Collectively, this study serves as an exemplary case of translational research taking advantage of the extensive information available from a model organism.
Comparison between the Mission Plus device and gold standard methods for measuring hemoglobin concentrations and packed cell volumes in cattle
Authors: Heller Luciana M. , Zapa Dina M. B. , Melo‐Junior Rubens D. , Cavalcante Alliny S. A. , Couto Luiz F. M. , Ferreira Lorena L. , Soares Vando E. , Martins Danieli B. , Camargo Fabrício , Iara Ítalo H. N. , Arnhold Emmanuel , Rodrigues Daniel C. , Leme Fabíola O. P. , Lopes Welber D. Z. 
Published: November 2021

BackgroundA point‐of‐care device that can provide immediate and reliable hemoglobin (Hb) concentrations and packed cell volumes (PCVs) would be useful in veterinary medicine.ObjectivesWe aimed to compare the use of a human device (Mission Plus; MP) with a gold standard (GS) method for measuring Hb concentrations and PCVs in cattle blood.MethodsBlood samples from clinically healthy cattle (n = 122) were collected with or without an anticoagulant (K2EDTA). The GS and MP methods were compared with correlation coefficients. Passing‐Bablok regression analyses were also performed, and the acceptability judgment was completed using Bland‐Altman plots.ResultsThe CVmax for Hb values obtained using the GS method, the MP device without K2EDTA, and the MP device with K2EDTA were approximately 2.70%, 1.70%, and 2.0%, respectively, whereas the CVmax for PCVs was 0.90%, 1.83%, and 2.05%, respectively. A positive correlation (97.5% confidence interval) was observed between the Hb concentrations and PCV values detected using the MP and GS techniques in blood with and without K2EDTA. Bland‐Altman plots showed agreement between the MP and GS methods. For Hb using blood collected with or without the addition of K2EDTA, the mean differences were −0.87 g/dL (95% CI: 1.35; −3.96) and 0.08 g/dL (95% CI: 2.16, −1.99), respectively. For PCVs using blood collected with or without the addition of K2EDTA, the mean differences were −3.75% (95% CI: 0.61. −8.12) and −0.88% (95% CI: 2.86, −4.62), respectively.ConclusionsThe MP device can be used to analyze Hb concentrations and PCVs in bovine blood to assist in field diagnoses.
Nursing interventions to improve care of people with dementia in hospital: a mixed methods systematic review protocol
Authors: Moody Elaine , Weeks Lori E. , Belliveau Anne , Bilski Trish , Rothfus Melissa , McDougall Heather , Jamieson Hannah 
Published: November 2021

ABSTRACT

Objective:
This review will focus on the effectiveness of, and experience with, nursing interventions to improve the care of people with dementia in hospital.

Introduction:
Acute care for people with dementia has been identified as an area for improvement. Admission to hospital can be upsetting and difficult for people with dementia and can be associated with negative outcomes. Nurses play a significant role in shaping the experience of hospitalization and are the focus of many related interventions.

Inclusion criteria:
This mixed methods review will examine literature on improving acute care for people with dementia. The quantitative component will consider studies that evaluate nursing interventions to improve care of people with dementia, comparing the intervention with usual care, other therapies, or no comparator. Outcomes will include behavioral, health, and health system indicators. The qualitative component will consider studies that explore the experience of nursing interventions from the perspective of people with dementia, their family- or friend-caregivers, and nurses.

Methods:
This review will be conducted in accordance with JBI methodology for mixed methods systematic reviews. Twelve databases and gray literature sources will be searched for published and unpublished studies. Titles, abstracts, and full-text selections will be screened by two or more independent reviewers and assessed for methodological validity using the standard JBI critical assessment tools. This review will follow a convergent segregated approach to data synthesis and integration.

Systematic review registration number:
PROSPERO CRD42021230951
A trans-national examination of the impact of the COVID-19 pandemic on abortion requests through a telemedicine service
Authors: van Ooijen Liën Trudi , Gemzell-Danielsson Kristina , Waltz Mitzi , Gomperts Rebecca 
Published: November 2021

BackgroundThe COVID-19 pandemic is limiting access to reproductive healthcare worldwide. Substantial research gaps remain regarding the impact of the pandemic on access to abortion care.MethodsWe performed a cohort analysis of abortion requests made through the telemedicine abortion service Women on Web (WoW) between 18 March 2020 and 4 May 2020. We used binary logistic regression analyses to test the association between COVID-19 as a reason for the help request and reporting having had an ultrasound to determine gestation and/or use of contraception. A subanalysis of Italy, Argentina, Malaysia and the United Arab Emirates (UAE) was executed to explore differences between countries.ResultsOf requests made during the study period, 43.5% (n=1972) were COVID-19-related. A negative association was found with having had an ultrasound to determine gestation length and COVID-19-related requests. Italy had the highest percentage (66.5%, n=117) of COVID-19-related requests in the subanalysis, followed by Argentina (55.3%, n=68), Malaysia (51.9%, n=41) and the UAE (44.4%, n=75).ConclusionsAlmost half the women and pregnant people having an abortion through WoW reported experiencing obstacles to abortion care because of COVID-19. Abortion guidelines should be updated to permit abortion services via telemedicine. This is especially urgent during the ongoing pandemic.
Home monitoring with technology-supported management in chronic heart failure: a randomised trial
Authors: Rahimi Kazem , Nazarzadeh Milad , Pinho-Gomes Ana-Catarina , Woodward Mark , Salimi-Khorshidi Gholamreza , Ohkuma Toshiaki , Fitzpatrick Raymond , Tarassenko Lionel , Denis Mike , Cleland John 
Published: November 2021

ObjectivesWe aimed to investigate whether digital home monitoring with centralised specialist support for remote management of heart failure (HF) is more effective in improving medical therapy and patients’ quality of life than digital home monitoring alone.MethodsIn a two-armed partially blinded parallel randomised controlled trial, seven sites in the UK recruited a total of 202 high-risk patients with HF (71.3 years SD 11.1; left ventricular ejection fraction 32.9% SD 15.4). Participants in both study arms were given a tablet computer, Bluetooth-enabled blood pressure monitor and weighing scales for health monitoring. Participants randomised to intervention received additional regular feedback to support self-management and their primary care doctors received instructions on blood investigations and pharmacological treatment. The primary outcome was the use of guideline-recommended medical therapy for chronic HF and major comorbidities, measured as a composite opportunity score (total number of recommended treatment given divided by the total number of opportunities the treatment should have been given, with a score 1 indicating 100% adherence to recommendations). Co-primary outcome was change in physical score of Minnesota Living with Heart Failure questionnaire.Results101 patients were randomised to ‘enhanced self-management’ and 101 to ‘supported medical management’. At the end of follow-up, the opportunity score was 0.54 (95% CI 0.46 to 0.62) in the control arm and 0.61 (95% CI 0.52 to 0.70) in the intervention arm (p=0.25). Physical well-being of participants also did not differ significantly between the groups (17.4 (12.4) mean (SD) for control arm vs 16.5 (12.1) in treatment arm; p for change=0.84).ConclusionsCentral provision of tailored specialist management in a multi-morbid HF population was feasible. However, there was no strong evidence for improvement in use of evidence-based treatment nor health-related quality of life.Trial registration numberISRCTN86212709
Synergistic antitumor activity of pan-PI3K inhibition and immune checkpoint blockade in bladder cancer
Authors: Zhu Shaoming , Ma A-Hong , Zhu Zheng , Adib Elio , Rao Ting , Li Na , Ni Kaiyuan , Chittepu Veera Chandra Sekhar Reddy , Prabhala Rao , Garisto Risco Juan , Kwiatkowski David , Mouw Kent , Sonpavde Guru , Cheng Fan , Pan Chong-xian 
Published: November 2021

BackgroundImmune checkpoint blockade (ICB) induces durable response in approximately 20% of patients with advanced bladder urothelial cancer (aUC). Over 50% of aUCs harbor genomic alterations along the phosphoinositide 3-kinase (PI3K) pathway. The goal of this project was to determine the synergistic effects and mechanisms of action of PI3K inhibition and ICB combination in aUC.MethodsAlterations affecting the PI3K pathway were examined in The Cancer Genome Atlas (TCGA) and the Cancer Dependency Map databases. Human and mouse cells withPtendeletion were used for in vitro studies. C57BL/6 mice carrying syngeneic tumors were used to determine in vivo activity, mechanisms of action and secondary resistance of pan-PI3K inhibition, ICB and combination.ResultsAlterations along the PI3K pathway occurred in 57% of aUCs in TCGA. CRISPR (clustered regularly interspaced short palindromic repeats) knockout ofPIK3CAinduced pronounced inhibition of cell proliferation (p=0.0046). PI3K inhibition suppressed cancer cell growth, migration and colony formation in vitro. Pan-PI3K inhibition, antiprogrammed death 1 (aPD1) therapy and combination improved the overall survival (OS) of syngeneic mice with PTEN-deleted tumors from 27 days of the control to 48, 37, and 65 days, respectively. In mice with tumors not containing a PI3K pathway alteration, OS was prolonged by the combination but not single treatments. Pan-PI3K inhibition significantly upregulated CD80, CD86, MHC-I, and MHC-II in dendritic cells, and downregulated the transforming growth factor beta pathway with a false discovery rate-adjusted q value of 0.001. Interferon alpha response was significantly upregulated with aPD1 therapy (q value: <0.001) and combination (q value: 0.027). Compared with the control, combination treatment increased CD8+T-cell infiltration (p=0.005), decreased Treg-cell infiltration (p=0.036), and upregulated the expression of multiple immunostimulatory cytokines and granzyme B (p<0.01). Secondary resistance was associated with upregulation of the mammalian target of rapamycin (mTOR) pathway and multipleSprrfamily genes.ConclusionsThe combination Pan-PI3K inhibition and ICB has significant antitumor effects in aUC with or without activated PI3K pathway and warrants further clinical investigation. This combination creates an immunostimulatory tumor milieu. Secondary resistance is associated with upregulation of the mTOR pathway andSprrfamily genes.
Study of radial motion phase advance during motion excitations in a Penning trap and accuracy of JYFLTRAP mass spectrometer
Authors: Nesterenko D. A. , Eronen T. , Ge Z. , Kankainen A. , Vilen M. 
Published: November 2021

AbstractPhase-imaging ion-cyclotron-resonance technique has been implemented at the Penning-trap mass spectrometer JYFLTRAP and is routinely employed for mass measurements of stable and short-lived nuclides produced at IGISOL facility. Systematic uncertainties that impose limitations on the accuracy of measurements are discussed. It was found out that the phase evolution of the radial motion of ions in a Penning trap during the application of radio-frequency fields leads to a systematic cyclotron frequency shift when more than one ion species is present in the trap during the cyclotron frequency measurement. An analytic expression was derived to correctly account for the shift. Cross-reference mass measurements with carbon-cluster ions have been performed providing the mass-dependent and residual uncertainties.
Are Households Willing to Finance the Cost of Individual Water Supply? Case Study in Central Tunisia
Authors: Favre Marine 
Published: November 2021

In developing countries, the Sustainable Development Goals (SDG) set by the United Nations and the expectations expressed by modern local populations call for universal water access through individual connections (IC), to be achieved by 2030. An ambitious target such as this presents the challenge of how best to achieve the goal of funding high-quality but expensive water supply systems, to serve populations with low incomes. This raises the question of the assessment of the relevant households’ willingness to pay (WTP) for improved water service in rural areas, in particular in the context of developing countries. This paper examines this issue using a case study in Tunisia. As with other developing countries, Tunisia faces difficult challenges: the increasing demand for water and the inherent cost that is involved must be met whilst climate change is likely to increase the pressure on already stressed resources. The approach applied in this paper is to assess the households’ WTP using a contingent valuation (CV) method in a dedicated field household survey in Central Tunisia. The particular governorate in which the survey was conducted was facing at the time of this study high social expectations, in particular, coming under increasing demand from inhabitants of rural communities to be individually connected to water supplies in the same way as their urban counterparts who were served by SONEDE, the national utility company. The results of the survey reveal that non-SONEDE-piped households were not willing to pay the amount required in order to have an individual connection (the average bid was USD 443 whereas the expected contribution is above USD 800). It was found that a household’s WTP for an individual connection had a direct relationship with its trust in the current water management model, alternative modes of supply, and its socio-economic characteristics. However, if already connected, households would be willing to pay more than their current water expenses, although the amount they were willing to pay was still lower than the sustainable water cost enabling long-term maintenance of the system. SONEDE-piped households stated a clear WTP the amount required to keep water services for the future (average bid of USD 14 to add to their current quarterly water bill of USD 14). Based on these results, this paper concludes by highlighting several policy implications.
Professional Pitchers Display Differences in UCL Morphology and Elbow Gapping During Moving Valgus Stress Testing After UCL Reconstruction
Authors: Kissenberth Michael J. , Thigpen Charles A. , Bailey Lane Brooks , Campbell Joel , Geist Derik J. , Schweppe Mark L. , Wyland Douglas J. , Hawkins Richard J. , Noonan Thomas J. , Shanley Ellen 
Published: November 2021

Background: Ulnar collateral ligament (UCL) reconstruction (UCLR) of the elbow has received much attention given the rise in incidence among baseball pitchers. Stress ultrasonography has been demonstrated to be a critical evaluation tool of the UCL. No study has dynamically evaluated the ability of UCLR to restore normal kinematics. Purpose/Hypothesis: The purpose of this study was to compare ulnohumeral gapping during a moving valgus stress test as well as UCL thickness between professional pitchers with and without UCLR. We hypothesized that the ulnohumeral joint will display greater gapping and the UCL graft will be thicker in pitchers after UCLR compared with uninjured pitchers. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Ultrasonography was used to measure the medial ulnohumeral joint distance and the UCL thickness of 70 asymptomatic professional baseball pitchers; 6 of the participants had a history of UCLR. Images were captured of the dominant (D) and nondominant (ND) elbows at the maximal cocking position under 2 loaded conditions within the moving valgus stress test arc: (1) gravity stress and (2) 2.5 kg (5.5 lb) of valgus force using a dynamometer. Intra- and interrater reliability of the measurements was established with intraclass correlation coefficients (ICCs). Separate mixed-model analyses of variance (D side × UCL) were used to compare the D and ND elbow variables between pitchers with and without a history of UCLR. Results: All measurements displayed good reliability according to ICCs. Pitchers with a history of UCLR demonstrated less gapping (5.6 ± 2.9 vs 4.2 ± 1.2 mm; P = .002) and greater UCL graft thickness (0.17 ± 0.07 vs 0.11 ± 0.08 mm; P = .03) compared with the native ligament in pitchers without prior UCL injury. Conclusion: Our data demonstrated that the UCLR results in a thicker, stiffer construct with less medial elbow gapping than the anatomical UCL. Using ultrasound to evaluate the UCL was a reliable, efficient, and clinically feasible method to assess UCL thickness and joint gapping in players with a history of UCLR. Future studies may consider this approach to evaluate surgical techniques and graft types for UCLR.
FASTAFS: file system virtualisation of random access compressed FASTA files
Authors: Hoogstrate Youri , Jenster Guido W. , van de Werken Harmen J. G. 
Published: November 2021

Abstract
Background
The FASTA file format, used to store polymeric sequence data, has become a bioinformatics file standard used for decades. The relatively large files require additional files, beyond the scope of the original format, to identify sequences and to provide random access. Multiple compressors have been developed to archive FASTA files back and forth, but these lack direct access to targeted content or metadata of the archive. Moreover, these solutions are not directly backwards compatible to FASTA files, resulting in limited software integration.

Results
We designed a linux based toolkit that virtualises the content of DNA, RNA and protein FASTA archives into the filesystem by using filesystem in userspace. This guarantees in-sync virtualised metadata files and offers fast random-access decompression using bit encodings plus Zstandard (zstd). The toolkit, FASTAFS, can track all its system-wide running instances, allows file integrity verification and can provide, instantly, scriptable access to sequence files and is easy to use and deploy. The file compression ratios were comparable but not superior to other state of the art archival tools, despite the innovative random access feature implemented in FASTAFS.

Conclusions
FASTAFS is a user-friendly and easy to deploy backwards compatible generic purpose solution to store and access compressed FASTA files, since it offers file system access to FASTA files as well as in-sync metadata files through file virtualisation. Using virtual filesystems as in-between layer offers format conversion without the need to rewrite code into different programming languages while preserving compatibility.