bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SEQC2 epigenomics quality control (EpiQC) study
Authors: Foox Jonathan , Nordlund Jessica , Lalancette Claudia , Gong Ting , Lacey Michelle , Lent Samantha , Langhorst Bradley W. , Ponnaluri V. K. Chaithanya , Williams Louise , Padmanabhan Karthik Ramaswamy , Cavalcante Raymond , Lundmark Anders , Butler Daniel , Mozsary Christopher , Gurvitch Justin , Greally John M. , Suzuki Masako , Menor Mark , Nasu Masaki , Alonso Alicia , Sheridan Caroline , Scherer Andreas , Bruinsma Stephen , Golda Gosia , Muszynska Agata , Łabaj Paweł P. , Campbell Matthew A. , Wos Frank , Raine Amanda , Liljedahl Ulrika , Axelsson Tomas , Wang Charles , Chen Zhong , Yang Zhaowei , Li Jing , Yang Xiaopeng , Wang Hongwei , Melnick Ari , Guo Shang , Blume Alexander , Franke Vedran , Ibanez de Caceres Inmaculada , Rodriguez-Antolin Carlos , Rosas Rocio , Davis Justin Wade , Ishii Jennifer , Megherbi Dalila B. , Xiao Wenming , Liao Will , Xu Joshua , Hong Huixiao , Ning Baitang , Tong Weida , Akalin Altuna , Wang Yunliang , Deng Youping , Mason Christopher E. 
Published: December 2021

AbstractBackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq
Authors: Missarova Alsu , Jain Jaison , Butler Andrew , Ghazanfar Shila , Stuart Tim , Brusko Maigan , Wasserfall Clive , Nick Harry , Brusko Todd , Atkinson Mark , Satija Rahul , Marioni John C. 
Published: December 2021

AbstractscRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.
Evaluating the efficacy, impact, and feasibility of community-based house screening as a complementary malaria control intervention in southern Africa: a study protocol for a household randomized trial
Authors: Sangoro Onyango P. , Fillinger Ulrike , Saili Kochelani , Nkya Theresia Estomih , Marubu Rose , Masaninga Freddie , Trigo Sonia Casimiro , Tarumbwa Casper , Hamainza Busiku , Baltazar Candrinho , Mberikunashe Joseph , Chisanga Brian , Menale Kassie , Chanda Emmanuel , Mutero Clifford Maina 
Published: December 2021

Abstract
Background
Concerted effort to control malaria has had a substantial impact on the transmission of the disease in the past two decades. In areas where reduced malaria transmission is being sustained through insecticide-based vector control interventions, primarily long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS), non-insecticidal complementary tools will likely be needed to push towards malaria elimination. Once interruption in local disease transmission is achieved, insecticide-based measures can be scaled down gradually and eventually phased out, saving on costs of sustaining control programs and mitigating any unintended negative health and environmental impacts posed by insecticides. These non-insecticidal methods could eventually replace insecticidal methods of vector control.
House screening, a non-insecticidal method, has a long history in malaria control, but is still not widely adopted in sub-Saharan Africa. This study aims to add to the evidence base for this intervention in low transmission settings by assessing the efficacy, impact, and feasibility of house screening in areas where LLINs are conventionally used for malaria control.

Methods
A two-armed, household randomized clinical trial will be conducted in Mozambique, Zambia, and Zimbabwe to evaluate whether combined the use of house screens and LLINs affords better protection against clinical malaria in children between 6 months and 13 years compared to the sole use of LLINs. Eight hundred households will be enrolled in each study area, where 400 households will be randomly assigned the intervention, house screening, and LLINs while the control households will be provided with LLINs only. Clinical malaria incidence will be estimated by actively following up one child from each household for 6 months over the malaria transmission season. Cross-sectional parasite prevalence will be estimated by testing all participating children for malaria parasites at the beginning and end of each transmission season using rapid diagnostic tests.
CDC light traps and pyrethrum spray catches (PSC) will be used to sample adult mosquitoes and evaluate the impact of house screening on indoor mosquito density, species distribution, and sporozoite rates.

Discussion
This study will contribute epidemiological data on the impact of house screening on malaria transmission and assess the feasibility of its implementation on a programmatic scale.

Trial registration
ClinicalTrials.gov PACTR202008524310568. Registered on August 11, 2020.
The COPE-Trial—Communicating prognosis to parents in the neonatal ICU: Optimistic vs. PEssimistic: study protocol for a randomized controlled crossover trial using two different scripted video vignettes to explore communication preferences of parents of preterm infants
Authors: Forth Fiona A. , Hammerle Florian , König Jochem , Urschitz Michael S. , Neuweiler Philipp , Mildenberger Eva , Kidszun André 
Published: December 2021

AbstractBackgroundOne of the numerous challenges preterm birth poses for parents and physicians is prognostic disclosure. Prognoses are based on scientific evidence and medical experience. They are subject to individual assessment and will generally remain uncertain with regard to the individual. This can result in differences in prognostic framing and thus affect the recipients’ perception. In neonatology, data on the effects of prognostic framing are scarce. In particular, it is unclear whether parents prefer a more optimistic or a more pessimistic prognostic framing.ObjectiveTo explore parents’ preferences concerning prognostic framing and its effects on parent-reported outcomes and experiences. To identify predictors (demographic, psychological) of parents’ communication preferences.Design, setting, participantsUnblinded, randomized controlled crossover trial (RCT) at the Division of Neonatology of the University Medical Center Mainz, Germany, including German-speaking parents or guardians of infants born preterm between 2010 and 2019 with a birth weight < 1500 g. Inclusion of up to 204 families is planned, with possible revision according to a blinded sample size reassessment.InterventionEmbedded in an online survey and in pre-specified order, participants will watch two video vignettes depicting a more optimistic vs. a more pessimistic framing in prognostic disclosure to parents of a preterm infant. Apart from prognostic framing, all other aspects of physician-parent communication are standardized in both videos.Main outcomes and measuresAt baseline and after each video, participants complete a two-part online questionnaire (baseline and post-intervention). Primary outcome is the preference for either a more optimistic or a more pessimistic prognostic framing. Secondary outcomes include changes in state-anxiety (STAI-SKD), satisfaction with prognostic framing, evaluation of prognosis, future optimism and hope, preparedness for shared decision-making (each assessed using customized questions), and general impression (customized question), professionalism (adapted from GMC Patient Questionnaire) and compassion (Physician Compassion Questionnaire) of the consulting physician.DiscussionThis RCT will explore parents’ preferences concerning prognostic framing and its effects on physician-parent communication. Results may contribute to a better understanding of parental needs in prognostic disclosure and will be instrumental for a broad audience of clinicians, scientists, and ethicists.Trial registrationGerman Clinical Trials Register DRKS00024466. Registered on April 16, 2021.
Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system
Authors: Jiang Xu , Ma Hui , Zhao Qing-lei , Yang Jun , Xin Cai-yun , Chen Bocong 
Published: December 2021

AbstractAs an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.
Surgical resection for patients with recurrent or metastatic gastrointestinal stromal tumors: a protocol for a systematic review and meta-analysis update
Authors: Cai Zhaolun , Xin Chunyu , Jiang Zhiyuan , Liu Chunyu , Shen Chaoyong , Zhao Guozhen , Yin Yuan , Yin Xiaonan , Zhao Zhou , Mu Mingchun , Zhang Bo 
Published: December 2021

Abstract
Background
There are limited data on the clinical benefits of adding surgical resection in patients with recurrent or metastatic gastrointestinal stromal tumors (GISTs). This protocol outlines the planned scope and methods for a systematic review and meta-analysis update that will compare the clinical outcomes of surgical resection combined with tyrosine kinase inhibitor (TKI) with TKI treatment alone in patients with recurrent or metastatic GISTs.

Methods
This review will update a previously published systematic review by our team. This protocol is presented in accordance with the PRISMA-P guideline. PubMed, Embase, and Cochrane Central Register of Controlled Trials will be systematically searched and supplemented by a secondary screening of the references of all included studies. We will include randomized controlled trials (RCTs) and non-randomized studies (NRS) in this review update. The outcomes evaluated will be overall survival and progression-free survival. Two reviewers will independently screen and select studies, extract data from the included studies, and assess the risk of bias of the included studies. Data extracted from RCTs and NRS will be analysed and reported separately. Preplanned subgroup analyses and sensitivity analyses are detailed within this protocol. The strength of the body of evidence will be assessed using GRADE.

Discussion
This systematic review and meta-analysis update will provide a current assessment of the evidence for the role of surgery in patients with recurrent or metastatic advanced GISTs. These findings will be used by the Chinese Society of Clinical Oncology (CSCO) GIST guideline recommendations on surgical treatment for recurrent or metastatic advanced GIST patients in China.

Systematic review registration
This protocol was prospectively registered in the Open Science Framework Registry (https://osf.io/xus7m).
Projecting onto rectangular matrices with prescribed row and column sums
Authors: Bauschke Heinz H. , Singh Shambhavi , Wang Xianfu 
Published: December 2021

AbstractIn 1990, Romero presented a beautiful formula for the projection onto the set of rectangular matrices with prescribed row and column sums. Variants of Romero’s formula were rediscovered by Khoury and by Glunt, Hayden, and Reams for bistochastic (square) matrices in 1998. These results have found various generalizations and applications.In this paper, we provide a formula for the more general problem of finding the projection onto the set of rectangular matrices with prescribed scaled row and column sums. Our approach is based on computing the Moore–Penrose inverse of a certain linear operator associated with the problem. In fact, our analysis holds even for Hilbert–Schmidt operators, and we do not have to assume consistency. We also perform numerical experiments featuring the new projection operator.
Impact of COVID-19 pandemic on African indigenous vegetables value chain in Kenya
Authors: Ogada Maurice Juma , Justus Ochieng’ , Paul Maina , Omondi Sikei Geophrey , Juma Adero Nashon , Taracha Evans , Ahmed Hassan 
Published: December 2021

Abstract
Background
African indigenous vegetables are important for food security and nutrition, and income of the poor farm households. In the era of COVID-19, they are critical for boosting people’s immunity. Unfortunately, both production of and trade in these vegetables is likely to be severely affected by the pandemic.

Methods
This study examined potential effects of COVID-19 pandemic on production and trade of African indigenous vegetables using a cross-sectional survey of 244 farmers and 246 traders from different regions in Kenya.

Results
COVID-19 has a negative impact on production and trading of AIVs in Kenya. Findings indicate that 75% of the farmers are experiencing declining production due to reduced access to input, farm labour and output market. Secondly, about 98% of the traders have recorded a drop in sales volumes due to containment measures implemented by the government and personal safety precautions. In particular, farmers’ production and traders’ sales volumes declined by 39 and 65%, respectively, during the first phase of the pandemic.

Conclusion
The findings indicate that the sub-sector requires targeted interventions which may include input support, careful reopening and control of the open-air markets, reduced taxation and facilitated access to urban markets.
Long-term and combined effects of N-[2-(nitrooxy)ethyl]-3-pyridinecarboxamide and fumaric acid on methane production, rumen fermentation, and lactation performance in dairy goats
Authors: Li Zongjun , Lei Xinjian , Chen Xiaoxu , Yin Qingyan , Shen Jing , Yao Junhu 
Published: December 2021

Abstract
Background
In recent years, nitrooxy compounds have been identified as promising inhibitors of methanogenesis in ruminants. However, when animals receive a nitrooxy compound, a high portion of the spared hydrogen is eructated as gas, which partly offsets the energy savings of CH4 mitigation. The objective of the present study was to evaluate the long-term and combined effects of supplementation with N-[2-(nitrooxy)ethyl]-3-pyridinecarboxamide (NPD), a methanogenesis inhibitor, and fumaric acid (FUM), a hydrogen sink, on enteric CH4 production, rumen fermentation, bacterial populations, apparent nutrient digestibility, and lactation performance of dairy goats.

Results
Twenty-four primiparous dairy goats were used in a randomized complete block design with a 2 × 2 factorial arrangement of treatments: supplementation without or with FUM (32 g/d) or NPD (0.5 g/d). All samples were collected every 3 weeks during a 12-week feeding experiment. Both FUM and NPD supplementation persistently inhibited CH4 yield (L/kg DMI, by 18.8% and 18.1%, respectively) without negative influence on DMI or apparent nutrient digestibility. When supplemented in combination, no additive CH4 suppression was observed. FUM showed greater responses in increasing the molar proportion of propionate when supplemented with NPD than supplemented alone (by 10.2% vs. 4.4%). The rumen microbiota structure in the animals receiving FUM was different from that of the other animals, particularly changed the structure of phylum Firmicutes. Daily milk production and serum total antioxidant capacity were improved by NPD, but the contents of milk fat and protein were decreased, probably due to the bioactivity of absorbed NPD on body metabolism.

Conclusions
Supplementing NPD and FUM in combination is a promising way to persistently inhibit CH4 emissions with a higher rumen propionate proportion. However, the side effects of this nitrooxy compound on animals and its residues in animal products need further evaluation before it can be used as an animal feed additive.
In Vivo Metabolic Roles of G Proteins of the Gi Family Studied With Novel Mouse Models
Authors: Wess Jürgen 
Published: December 2021

Abstract
G protein–coupled receptors (GPCRs) are the target of ~30% to 35% of all US Food and Drug Administration–approved drugs. The individual members of the GPCR superfamily couple to 1 or more functional classes of heterotrimeric G proteins. The physiological outcome of activating a particular GPCR in vivo depends on the pattern of receptor distribution and the type of G proteins activated by the receptor. Based on the structural and functional properties of their α-subunits, heterotrimeric G proteins are subclassified into 4 major families: Gs, Gi/o, Gq/11, and G12/13. Recent studies with genetically engineered mice have yielded important novel insights into the metabolic roles of Gi/o-type G proteins. For example, recent data indicate that Gi signaling in pancreatic α-cells plays a key role in regulating glucagon release and whole body glucose homeostasis. Receptor-mediated activation of hepatic Gi signaling stimulates hepatic glucose production, suggesting that inhibition of hepatic Gi signaling could prove clinically useful to reduce pathologically elevated blood glucose levels. Activation of adipocyte Gi signaling reduces plasma free fatty acid levels, thus leading to improved insulin sensitivity in obese, glucose-intolerant mice. These new data suggest that Gi-coupled receptors that are enriched in metabolically important cell types represent potential targets for the development of novel drugs useful for the treatment of type 2 diabetes and related metabolic disorders.
Low-Concentration Norepinephrine Infusion for Major Surgery: A Safety and Feasibility Pilot Randomized Controlled Trial
Authors: Aykanat Verna M. , Myles Paul S. , Weinberg Laurence , Burrell Aidan , Bellomo Rinaldo 
Published: December 2021

BACKGROUND:
Prevention of hypotension during the intra- and postoperative period is an important goal. Peripheral administration of low-concentration norepinephrine may be a safe and effective strategy to reduce the risk of hypotension.

METHODS:
We conducted a 2-center, randomized pilot feasibility trial, with a target of 60 adult patients undergoing major noncardiac surgery. We randomized patients to receive a peripheral low-concentration (10 µg/mL) norepinephrine or placebo (saline 0.9%) infusion. The study drug infusion was titrated to achieve a minimum systolic blood pressure target, preselected within 10% of baseline value and within the range limit 100 to 120 mm Hg during surgery and for up to 4 or 24 hours postoperatively.

RESULTS:
We achieved a high consent rate (84%), successful study drug administration throughout surgery (98% of patients) and absence of unblinding. There were no important study drug-related adverse events. The average intraoperative systolic blood pressure was 120 ± 12.6 mm Hg in the norepinephrine group and 115 ± 14.9 mm Hg in the placebo group. The mean difference between the intraoperative systolic blood pressure achieved less the preselected minimum systolic blood pressure target was 10.0 ± 12.7 mm Hg in the norepinephrine group and 2.9 ± 14.7 mm Hg in the placebo group; difference in means, 7.1 (95% confidence interval, 0.2–14.0) mm Hg.

CONCLUSIONS:
A future large trial evaluating the effectiveness and safety of peripheral administration of low-concentration norepinephrine during the perioperative period is feasible, and likely to achieve a minimum systolic blood pressure threshold.