bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stratified randomization for platform trials with differing experimental arm eligibility
Authors: Selukar Subodh , May Susanne , Law Dave , Othus Megan 
Published: August 2021

Background: Platform trials facilitate efficient use of resources by comparing multiple experimental agents to a common standard of care arm. They can accommodate a changing scientific paradigm within a single trial protocol by adding or dropping experimental arms—critical features for trials in rapidly developing disease areas such as COVID-19 or cancer therapeutics. However, in these trials, efficacy and safety issues may render certain participant subgroups ineligible to some experimental arms, and methods for stratified randomization do not readily apply to this setting. Methods: We propose extensions for conventional methods of stratified randomization for platform trials whose experimental arms may differ in eligibility criteria. These methods balance on a prespecified set of stratification variables observable prior to arm assignment that remains the same across experimental arms. To do so, we suggest modifying block randomization by including experimental arm eligibility as a stratifying variable, and we suggest modifying the imbalance score calculation in dynamic balancing by performing pairwise comparisons between each eligible experimental arm and standard of care arm participants eligible to that experimental arm. Results: We provide worked examples to illustrate the proposed extensions. In addition, we also provide a formula to quantify the relative efficiency loss of platform trials with varying eligibility compared with trials with non-varying eligibility as measured by the size of the common standard of care arm. Conclusions: This article presents important extensions to conventional methods for stratified randomization in order to facilitate the implementation of platform trials with differing experimental arm eligibility.
Manual joint mobilisation techniques, supervised physical activity, psychological treatment, acupuncture and patient education for patients with tension-type headache. A systematic review and meta-analysis
Authors: Krøll Lotte Skytte , Callesen Henriette Edemann , Carlsen Louise Ninett , Birkefoss Kirsten , Beier Dagmar , Christensen Henrik Wulff , Jensen Mette , Tómasdóttir Hanna , Würtzen Hanne , Høst Christel Vesth , Hansen Jakob Møller 
Published: August 2021

AbstractBackgroundTension-type headache (TTH) has been ranked the second most prevalent health condition worldwide. Non-pharmacological treatments for TTH are widely used as a supplement or an alternative to medical treatment. However, the evidence for their effects are limited. Therefore, the aim of this study was to review the evidence for manual joint mobilisation techniques, supervised physical activity, psychological treatment, acupuncture and patient education as treatments for TTH on the effect of headache frequency and quality of life.MethodsA systematic literature search was conducted from February to July 2020 for clinical guidelines, systematic reviews, and individual randomised controlled trials (RCT). The primary outcomes measured were days with headache and quality of life at the end of treatment along with a number of secondary outcomes. Meta-analyses were performed on eligible RCTs and pooled estimates of effects were calculated using the random-effect model. The overall certainty of evidence was evaluated using the Grading of Recommendations, Assessment, Development, and Evaluation approach (GRADE). In addition, patient preferences were included in the evaluation.ResultsIn all, 13 RCTs were included. Acupuncture might have positive effects on both primary outcomes. Supervised physical activity might have a positive effect on pain intensity at the end of treatment and headache frequency at follow-up. Manual joint mobilisation techniques might have a positive effect on headache frequency and quality of life at follow-up. Psychological treatment might have a positive effect on stress symptoms at the end of treatment. No relevant RCTs were identified for patient education. The overall certainty of evidence was downgraded to low and very low. No serious adverse events were reported. A consensus recommendation was made for patient education and weak recommendations for the other interventions.ConclusionBased on identified benefits, certainty of evidence, and patient preferences, manual joint mobilisation techniques, supervised physical activity, psychological treatment, acupuncture, and patient education can be considered as non-pharmacological treatment approaches for TTH. Some positive effects were shown on headache frequency, quality of life, pain intensity and stress symptoms. Few studies and low sample sizes posed a challenge in drawing solid conclusions. Therefore, high-quality RCTs are warranted.
Coronavirus disease-19 and headache; impact on pre-existing and characteristics of de novo: a cross-sectional study
Authors: Al-Hashel Jasem Youssef , Abokalawa Fathi , Alenzi Maram , Alroughani Raed , Ahmed Samar Farouk 
Published: August 2021

Abstract
Background
Coronavirus disease-19 is caused by the severe acute respiratory syndrome coronavirus 2 Headache is a common symptom during and after Coronavirus disease-19. We aimed to study headache character in relation to COVID-19.

Methods
This was a cross-sectional study. Patients who had Coronavirus disease-19, confirmed by reverse transcription polymerase chain reaction technique and presented to the headache clinic within 3 months after the onset of infections were identified to the study. Study included patients diagnosed as primary headache disorders according to The International Classification of Headache Disorders, 3rd edition. Participants were grouped into categories according to having previous or de novo headache. Descriptive data, paired sample t-test and the chi-squared test (X2) were used for statistical analyses of the data.

Results
A total of 121 patients were included in this study. Their mean age was 35.29 + 9.54 and most of them were females (83.5%). Prior to Coronavirus disease-19 infections, 78 (64.5%) had migraine and 11(9.1%) experienced a tension-type headache while 32 (26.4) reported de novo headache post Coronavirus disease-19. Patient had significant increase in headache days 11.09 ± 8.45 post Coronavirus disease-19 compared with 8.66 ± 7.49 headache days before Coronavirus disease-19 infection (p < 0.006). Post Coronavirus disease-19, the usage of analgesic increased significantly by the patient with migraine (2.31 ± 1.65 vs 3.05 ± 2.09, p = 0.002) while the patient with tension type headache had statistically significant increase in severity (5.556 ± 1.86 vs 7 ± 2.25, p = 0.033) and frequency (7 ± 6.29 vs 12.72 ± 7.96, p = 0.006) of headache attacks. Bi-frontal and temporal headache are the most reported (40.6% each) headache site among de novo headache group. Patients younger than 40 years had longer duration of the headache attack (18.50 ± 16.44 vs 5.5 ± 9.07, p = 0.045) post COVID-19. Male patients compared to females (8.66 ± 1.15 versus 5.93 ± 2.01 p = 0.04) had more severe headache post Coronavirus disease-19. De novo headache resolved within 1 month in most of patients (65.3%).

Conclusion
Primary headache get worse after Coronavirus disease-19. De novo primary headache is frequent post Coronavirus disease-19 and resolve within 1 month. Headaches related to Coronavirus disease-19 are severe, present as migraine phenotype. Young male patients with Coronavirus disease-19 tend to have worse headache.
Solar-Driven Photoelectrochemical Performance of Novel ZnO/Ag2WO4/AgBr Nanorods-Based Photoelectrodes
Authors: Mustafa Elfatih , Adam Rania E. , Rouf Polla , Willander Magnus , Nur Omer 
Published: August 2021

Abstract
Highly efficient photoelectrochemical (PEC) water oxidation under solar visible light is crucial for water splitting to produce hydrogen as a source of sustainable energy. Particularly, silver-based nanomaterials are important for PEC performance due to their surface plasmon resonance which can enhance the photoelectrochemical efficiency. However, the PEC of ZnO/Ag2WO4/AgBr with enhanced visible-light water oxidation has not been studied so far. Herein, we present a novel photoelectrodes based on ZnO/Ag2WO4/AgBr nanorods (NRs) for PEC application, which is prepared by the low-temperature chemical growth method and then by successive ionic layer adsorption and reaction (SILAR) method. The synthesized photoelectrodes were investigated by several characterization techniques, emphasizing a successful synthesis of the ZnO/Ag2WO4/AgBr heterostructure NRs with excellent photocatalysis performance compared to pure ZnO NRs photoelectrode. The significantly enhanced PEC was due to improved photogeneration and transportation of electrons in the heterojunction due to the synergistic effect of the heterostructure. This study is significant for basic understanding of the photocatalytic mechanism of the heterojunction which can prompt further development of novel efficient photoelectrochemical-catalytic materials.

Graphic Abstract
High-Performance Multifunctional Photodetector and THz Modulator Based on Graphene/TiO2/p-Si Heterojunction
Authors: Wei Miaoqing , Zhang Dainan , Zhang Lei , Jin Lichuan , Zhang Huaiwu 
Published: August 2021

Abstract
In this paper, we have reported a multifunctional device from graphene/TiO2/p-Si heterojunction, followed by its systematical analysis of optical response in a device under ultraviolet–visible-infrared band and transmission changes of terahertz waves in the 0.3–1.0 THz band under different bias voltages. It is found that photodetector in the “back-to-back” p-n-p energy band structure has a seriously unbalanced distribution of photogenerated carriers in the vertical direction when light is irradiated from the graphene side. So this ensures a higher optical gain of the device in the form of up to 3.6 A/W responsivities and 4 × 1013 Jones detectability under 750 nm laser irradiation. Besides, the addition of TiO2 layer in this terahertz modulator continuously widens the carrier depletion region under negative bias, thereby realizing modulation of the terahertz wave, making the modulation depth up to 23% under − 15 V bias. However, almost no change is observed in the transmission of terahertz wave when a positive bias is applied. A similar of an electronic semiconductor diode is observed that only allows the passage of terahertz wave for negative bias and blocks the positive ones.

Graphic Abstract
Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice
Authors: Ma Yamei , Zhao Junliang , Fu Hua , Yang Tifeng , Dong Jingfang , Yang Wu , Chen Luo , Zhou Lian , Wang Jian , Liu Bin , Zhang Shaohong , Edwards David 
Published: August 2021

AbstractBackgroundDirect seeding is an efficient rice cultivation practice. However, its application is often limited due to O2deficiency following submergence, leading to poor seed germination, seedling establishment, and consequently yield loss. Identification of genes associated with tolerance to submergence and understanding their regulatory mechanisms is the fundamental way to address this problem. Unfortunately, the molecular mechanism of rice response to submergence stress is still not well understood.ResultsHere, we have performed a genome-wide identification of FCS-like zinc finger (FLZ) proteins and assessed their involvement in submergence response in rice. We identified 29 FLZ genes in rice, and the expression analysis revealed that several genes actively responded to submergence stress. Eight OsFLZ proteins interact with SnRK1A. As a case study, we demonstrated that OsFLZ18 interacted with SnRK1A and inhibited the transcriptional activation activity of SnRK1A in modulating the expression of its target geneαAmy3, a positive regulator in rice flooding tolerance. In line with this,OsFLZ18-overexpression lines displayed retarded early seedling growth and shorter coleoptile following submergence.ConclusionsThese data provide the most comprehensive information ofOsFLZgenes in rice, and highlight their roles in rice submergence response.
airpg: automatically accessing the inverted repeats of archived plastid genomes
Authors: Mehl Tilman , Gruenstaeudl Michael 
Published: August 2021

AbstractBackgroundIn most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations.ResultsWe introduce , a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using , followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations.ConclusionThe number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index athttp://pypi.python.org/pypi/airpg.
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Authors: Vernale Amélie , Prünster Maria Mandela , Marchianò Fabio , Debost Henry , Brouilly Nicolas , Rocher Caroline , Massey-Harroche Dominique , Renard Emmanuelle , Le Bivic André , Habermann Bianca H. , Borchiellini Carole 
Published: August 2021

Abstract
Background
The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on animals. For this reason, several transcriptomic, genomic, histological, physiological and biochemical studies focused on sponge epithelia. Nevertheless, the complete and precise protein composition of cell–cell junctions and mechanisms that regulate epithelial morphogenetic processes still remain at the center of attention.

Results
To get insights into the early evolution of epithelial morphogenesis, we focused on morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis. Homoscleromorpha are a sponge class with a typical basement membrane and adhaerens-like junctions unknown in other sponge classes. We took advantage of the dynamic context provided by cell dissociation-reaggregation experiments to explore morphogenetic processes in epithelial cells in a non-bilaterian lineage by combining fluorescent and electron microscopy observations and RNA sequencing approaches at key time-points of the dissociation and reaggregation processes.

Conclusions
Our results show that part of the molecular toolkit involved in the loss and restoration of epithelial features such as cell–cell and cell–matrix adhesion is conserved between Homoscleromorpha and Bilateria, suggesting their common role in the last common ancestor of animals. In addition, sponge-specific genes are differently expressed during the dissociation and reaggregation processes, calling for future functional characterization of these genes.
Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development
Authors: Li Ting , Wang Yapeng , Shi Yaqin , Gou Xiaonan , Yang Bingpeng , Qu Jianzhou , Zhang Xinghua , Xue Jiquan , Xu Shutu 
Published: August 2021

Abstract
Background
Maize kernel filling, which is closely related to the process of double fertilization and is sensitive to a variety of environmental conditions, is an important component of maize yield determination. Silk is an important tissue of maize ears that can discriminate pollen and conduct pollination. Therefore, investigating the molecular mechanisms of kernel development and silk senescence will provide important information for improving the pollination rate to obtain high maize yields.

Results
In this study, transcript profiles were determined in an elite maize inbred line (KA105) to investigate the molecular mechanisms functioning in self-pollinated and unpollinated maize kernels and silks. A total of 5285 and 3225 differentially expressed transcripts (DETs) were identified between self-pollinated and unpollinated maize in a kernel group and a silk group, respectively. We found that a large number of genes involved in key steps in the biosynthesis of endosperm storage compounds were upregulated after pollination in kernels, and that abnormal development and senescence appeared in unpollinated kernels (KUP). We also identified several genes with functions in the maintenance of silk structure that were highly expressed in silk. Further investigation suggested that the expression of autophagy-related genes and senescence-related genes is prevalent in maize kernels and silks. In addition, pollination significantly altered the expression levels of senescence-related and autophagy-related genes in maize kernels and silks. Notably, we identified some specific genes and transcription factors (TFs) that are highly expressed in single tissues.

Conclusions
Our results provide novel insights into the potential regulatory mechanisms of self-pollinated and unpollinated maize kernels and silks.
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
Authors: Christiansen Henrik , Heindler Franz M. , Hellemans Bart , Jossart Quentin , Pasotti Francesca , Robert Henri , Verheye Marie , Danis Bruno , Kochzius Marc , Leliaert Frederik , Moreau Camille , Patel Tasnim , Van de Putte Anton P. , Vanreusel Ann , Volckaert Filip A. M. , Schön Isa 
Published: August 2021

AbstractBackgroundGenome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.ResultsIn an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.ConclusionsPrior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant
Authors: Khasin Maya , Bernhardson Lois F. , O’Neill Patrick M. , Palmer Nathan A. , Scully Erin D. , Sattler Scott E. , Funnell-Harris Deanna L. 
Published: August 2021

Abstract
Background
As effects of global climate change intensify, the interaction of biotic and abiotic stresses increasingly threatens current agricultural practices. The secondary cell wall is a vanguard of resistance to these stresses. Fusarium thapsinum (Fusarium stalk rot) and Macrophomina phaseolina (charcoal rot) cause internal damage to the stalks of the drought tolerant C4 grass, sorghum (Sorghum bicolor (L.) Moench), resulting in reduced transpiration, reduced photosynthesis, and increased lodging, severely reducing yields. Drought can magnify these losses. Two null alleles in monolignol biosynthesis of sorghum (brown midrib 6-ref, bmr6-ref; cinnamyl alcohol dehydrogenase, CAD; and bmr12-ref; caffeic acid O-methyltransferase, COMT) were used to investigate the interaction of water limitation with F. thapsinum or M. phaseolina infection.

Results
The bmr12 plants inoculated with either of these pathogens had increased levels of salicylic acid (SA) and jasmonic acid (JA) across both watering conditions and significantly reduced lesion sizes under water limitation compared to adequate watering, which suggested that drought may prime induction of pathogen resistance. RNA-Seq analysis revealed coexpressed genes associated with pathogen infection. The defense response included phytohormone signal transduction pathways, primary and secondary cell wall biosynthetic genes, and genes encoding components of the spliceosome and proteasome.

Conclusion
Alterations in the composition of the secondary cell wall affect immunity by influencing phenolic composition and phytohormone signaling, leading to the action of defense pathways. Some of these pathways appear to be activated or enhanced by drought. Secondary metabolite biosynthesis and modification in SA and JA signal transduction may be involved in priming a stronger defense response in water-limited bmr12 plants.
Giant right atrium, what does it hide? Case presentation
Authors: Martín Talavera María , Valverde Pérez Israel , Manso García Begoña 
Published: August 2021

Abstract
Background
Malformation of the right atrium is a rare cardiac abnormality and is usually reported as isolated malformation in the literature.

Case presentation
Prenatal giant atrial dilatation in an asymptomatic infant was treated surgically at 18 months of age, due to potential risk of thrombosis and arrhythmias. Post-surgical echocardiographic images illustrate residual atrial elevated pressure.

Conclusions
Sometimes, as seems in our case, right atrial dilatation hides an associated restrictive right ventricle.