bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cultural Responsiveness in Child Protection: Stakeholders and Parental Perceptions of Working Children and Culture-appropriate Assessment in Ghana
Authors: Adonteng-Kissi Obed 
Published: July 2022

AbstractThere is a need to understand cultural responsiveness in the field of child protection and accommodate best interests of the child to local contexts. This research addresses cultural responsiveness in social work interventions as part of child protection services in cases of ‘child labour’ in rural and urban Ghana. The sample size of this study is sixty participants (thirty men and thirty women), and it is made up of social workers and other child welfare practitioners in government agencies; non-governmental organisations; and parents whose children were involved in child labour as well as parents whose children were not. Using semi-structured interviews, focus group discussions and participant observation as methods of data collection, participants included parents (ten), stakeholders (ten), focus groups (thirty people); and parental interviews in participant observation (ten) were conducted to gather the needed data with purposive sampling across rural and urban communities in Ghana. Applying a framework approach as the main qualitative data analysis approach, interviews were recorded and transcribed. Overall, the research finds that professionals need to immerse themselves in different cultural practices and communication whilst considering different working definitions for parenting and creating a mission and vision statement that embraces different cultures.
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics
Authors: Almeida Tiago , Antunes Rui , F. Silva João , Almeida João R , Matos Sérgio 
Published: July 2022

AbstractThe identification of chemicals in articles has attracted a large interest in the biomedical scientific community, given its importance in drug development research. Most of previous research have focused on PubMed abstracts, and further investigation using full-text documents is required because these contain additional valuable information that must be explored. The manual expert task of indexing Medical Subject Headings (MeSH) terms to these articles later helps researchers find the most relevant publications for their ongoing work. The BioCreative VII NLM-Chem track fostered the development of systems for chemical identification and indexing in PubMed full-text articles. Chemical identification consisted in identifying the chemical mentions and linking these to unique MeSH identifiers. This manuscript describes our participation system and the post-challenge improvements we made. We propose a three-stage pipeline that individually performs chemical mention detection, entity normalization and indexing. Regarding chemical identification, we adopted a deep-learning solution that utilizes the PubMedBERT contextualized embeddings followed by a multilayer perceptron and a conditional random field tagging layer. For the normalization approach, we use a sieve-based dictionary filtering followed by a deep-learning similarity search strategy. Finally, for the indexing we developed rules for identifying the more relevant MeSH codes for each article. During the challenge, our system obtained the best official results in the normalization and indexing tasks despite the lower performance in the chemical mention recognition task. In a post-contest phase we boosted our results by improving our named entity recognition model with additional techniques. The final system achieved 0.8731, 0.8275 and 0.4849 in the chemical identification, normalization and indexing tasks, respectively. The code to reproduce our experiments and run the pipeline is publicly available.Database URLhttps://github.com/bioinformatics-ua/biocreativeVII_track2
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID
Authors: Langnickel Lisa , Darms Johannes , Heldt Katharina , Ducks Denise , Fluck Juliane 
Published: July 2022

Abstract
preVIEW is a freely available semantic search engine for Coronavirus disease (COVID-19)-related preprint publications. Currently, it contains &gt;43 800 documents indexed with &gt;4000 semantic concepts, annotated automatically. During the last 2 years, the dynamic situation of the corona crisis has demanded dynamic development. Whereas new semantic concepts have been added over time—such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest—the service has been also extended with several features improving the usability and user friendliness. Most importantly, the user is now able to give feedback on detected semantic concepts, i.e. a user can mark annotations as true positives or false positives. In addition, we expanded our methods to construct search queries. The presented version of preVIEW also includes links to the peer-reviewed journal articles, if available. With the described system, we participated in the BioCreative VII interactive text-mining track and retrieved promising user-in-the-loop feedback. Additionally, as the occurrence of long-term symptoms after an infection with the virus SARS-CoV-2—called long COVID—is getting more and more attention, we have recently developed and incorporated a long COVID classifier based on state-of-the-art methods and manually curated data by experts. The service is freely accessible under https://preview.zbmed.de
Distinct cardiovascular phenotypes are associated with prognosis in systemic sclerosis: a cardiovascular magnetic resonance study
Authors: Knight Daniel S , Karia Nina , Cole Alice R , Maclean Rory H , Brown James T , Masi Ambra , Patel Rishi K , Razvi Yousuf , Chacko Liza , Venneri Lucia , Kotecha Tushar , Martinez-Naharro Ana , Kellman Peter , Scott-Russell Ann M , Schreiber Benjamin E , Ong Voon H , Denton Christopher P , Fontana Marianna , Coghlan J Gerry , Muthurangu Vivek 
Published: July 2022

AbstractAimsCardiovascular involvement in systemic sclerosis (SSc) is heterogeneous and ill-defined. This study aimed to: (i) discover cardiac phenotypes in SSc by cardiovascular magnetic resonance (CMR); (ii) provide a CMR-based algorithm for phenotypic classification; and (iii) examine for associations between phenotypes and mortality.Methods and resultsA retrospective, single-centre, observational study of 260 SSc patients who underwent clinically indicated CMR including native myocardial T1 and T2 mapping from 2016 to 2019 was performed. Agglomerative hierarchical clustering using only CMR variables revealed five clusters of SSc patients with shared CMR characteristics: dilated right hearts with right ventricular failure (RVF); biventricular failure dilatation and dysfunction (BVF); and normal function with average cavity (NF-AC), normal function with small cavity (NF-SC), and normal function with large cavity (NF-LC) sizes. Phenotypes did not co-segregate with clinical or antibody classifications. A CMR-based decision tree for phenotype classification was created. Sixty-three (24%) patients died during a median follow-up period of 3.4 years. After adjustment for age and presence of pulmonary hypertension (PH), independent CMR predictors of all-cause mortality were native T1 (P &lt; 0.001) and right ventricular ejection fraction (RVEF) (P = 0.0032). NF-SC and NF-AC groups had more favourable prognoses (P≤0.036) than the other three groups which had no differences in prognoses between them (P &gt; 0.14). Hazard ratios (HR) were statistically significant for RVF (HR = 8.9, P &lt; 0.001), BVF (HR = 5.2, P = 0.006), and NF-LC (HR = 4.9, P = 0.002) groups. The NF-LC group remained significantly predictive of mortality after adjusting for RVEF, native T1, and PH diagnosis (P = 0.0046).ConclusionWe identified five CMR-defined cardiac SSc phenotypes that did not co-segregate with clinical data and had distinct outcomes, offering opportunities for a more precision-medicine based management approach.
Tumor necrosis factor-α-inducing protein of Helicobacter pylori promotes epithelial-mesenchymal transition and cancer stem-like cells properties via activation of Wnt/β-catenin signaling pathway in gastric cancer cells
Authors: Guo Kaiyun , Duan Jie , Lu Jingwen , Xiao Lingqiao , Han Liang , Zeng Shasha , Tang Xin , Li Wenjing , Huang Lijun , Zhang Yan 
Published: July 2022

ABSTRACT
Tumor necrosis factor-α-inducing protein (Tipα) is a newly identified toxin that promotes the inflammation and carcinogenesis caused by Helicobacter pylori. However, its mechanism of pathogenesis is still unclear. To investigate the carcinogenic mechanisms of Tipα, SGC7901 cells and SGC7901-derived cancer stem-like cells (CSCs) were stimulated by recombinant Tipα with or without Wnt/β-catenin signaling inhibitor XAV939. qRT-PCR and Western blotting were employed to detect expression of epithelial-mesenchymal transition (EMT), CSCs markers and downstream target genes of this signaling pathway. The cell migration ability was measured by wound healing assay and transwell assay. Our results indicated that Tipα promoted CSC properties of SGC7901 spheroids, including increased expression of CSC specific surface markers CD44, Oct4 and Nanog and an increased capacity for self-renewal. Tipα activated Wnt/β-catenin signaling in both SGC7901 cells or CSCs. Furthermore, Tipα induced the EMT and increased the expressions of downstream target genes of this signaling, including c-myc, cyclin D1 and CD44. However, XAV939 pretreatment inhibited Tipα-induced EMT and CSC properties in SGC7901 cells or CSCs. These results suggest that Tipα promotes EMT and CSC-like properties in gastric cancer cells through activation of Wnt/β-catenin signaling pathway, thereby accelerating the progression of gastric cancer.
Replication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes
Authors: Malhotra Nitish , Seshasayee Aswin Sai Narain 
Published: July 2022

Abstract
Bacterial genome organization is primarily driven by chromosomal replication from a single origin of replication. However, chromosomal rearrangements, which can disrupt such organization, are inevitable in nature. Long DNA repeats are major players mediating rearrangements, large and small, via homologous recombination. Since changes to genome organization affect bacterial fitness—and more so in fast-growing than slow-growing bacteria—and are under selection, it is reasonable to expect that genomic positioning of long DNA repeats is also under selection. To test this, we identified identical DNA repeats of at least 100 base pairs across ∼6,000 bacterial genomes and compared their distribution in fast- and slow-growing bacteria. We found that long identical DNA repeats are distributed in a non-random manner across bacterial genomes. Their distribution differs in the overall number, orientation, and proximity to the origin of replication, between fast- and slow-growing bacteria. We show that their positioning—which might arise from a combination of the processes that produce repeats and selection on rearrangements that recombination between repeat elements might cause—permits less disruption to the replication-dependent genome organization of bacteria compared with random suggesting it as a major constraint to positioning of long DNA repeats.
Assessing patterns of change in lifestyle behaviours by parity: a longitudinal cohort study
Authors: Makama Maureen , Earnest Arul , Lim Siew , Skouteris Helen , Hill Briony , Teede Helena , Boyle Jacqueline A , Brown Wendy J , Hodge Allison M , Moran Lisa J 
Published: July 2022

Abstract

Background
The time constraints and reprioritization of personal health associated with having children may lead women to adopt less healthy lifestyles. We assessed the patterns of change in weight and lifestyle behaviours associated with having children and whether these differ between primiparous and multiparous women.

Methods
Data were from Surveys 3 and 5 of the 1973–1978 birth cohort of the Australian Longitudinal Study on Women’s Health. In women who were nulliparous at Survey 3, we assessed changes in weight, energy intake, diet (diet quality, macronutrients and micronutrients), physical activity and sitting time by parity status at Survey 5 using one-way analysis of covariance.

Results
Of 4927 eligible women, 2503 gave birth (1090 primiparous and 1413 multiparous) by Survey 5. Women who had given birth 6 years later increased weight (1.0 kg; 95% CI 0.5, 1.5), energy intake (833.9 kJ/day; 95% CI 706.7, 961.1) and diet quality (1.5 units; 95% CI 0.8, 2.1), but decreased physical activity [–405.0 Metabolic Equivalent of Task.min/week; 95% CI –464.2, –345.8] and sitting time (–1.8 h/day; 95% CI –1.9, –1.6) (adjusted mean differences) relative to those who remained nulliparous. In subgroup analysis involving further stratification by parity, the increase in diet quality was only seen in women who became primiparous and the decrease in sitting time was more marked in multiparous women.

Conclusion
Childbearing is associated with increased weight and energy intake, decreased physical activity, increased diet quality and decreased sitting time. More research targeting weight, energy intake and physical activity for improvement in women during the childbearing years is warranted.
Monitoring of Adverse Events in Recipients of the 2-Dose Ebola Vaccine Regimen of Ad26.ZEBOV Followed by MVA-BN-Filo in the UMURINZI Ebola Vaccination Campaign
Authors: Nyombayire Julien , Ingabire Rosine , Magod Ben , Mazzei Amelia , Mazarati Jean-Baptiste , Noben Jozef , Katwere Michael , Parker Rachel , Nsanzimana Sabin , Wall Kristin M , Sayinzoga Felix , Tichacek Amanda , Robinson Cynthia , Hammoud Niina , Priddy Frances , Allen Susan , Karita Etienne 
Published: July 2022

Abstract

Background
From 2019 to 2021, Rwandan residents of the border with the Democratic Republic of the Congo were offered the Ad26.ZEBOV (adenovirus type 26 vector vaccine encoding Ebola virus glycoprotein) and MVA-BN-Filo (modified vaccinia virus Ankara vector vaccine, encoding glycoproteins from Ebola, Sudan, Marburg, and nucleoprotein from Tai Forest viruses) Ebola vaccine regimen.

Methods
Nonpregnant persons aged ≥2 years were eligible. Unsolicited adverse events (UAEs) were reported through phone calls or visits, and serious adverse events (SAEs) were recorded per International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use guidelines.

Results
Following Ad26.ZEBOV, UAEs were reported by 0.68% of 216 113 vaccinees and were more common in younger children (aged 2–8 years, 1.2%) compared with older children (aged 9–17 years, 0.4%) and adults (aged ≥18 years, 0.7%). Fever and headache were the most reported symptoms. All 17 SAEs related to vaccine were in children aged 2–8 years (10 postvaccination febrile convulsions ± gastroenteritis and 7 fever and/or gastroenteritis). The incidence of febrile seizures was 8 of 26 062 (0.031%) prior to initiation of routine acetaminophen in December 2020 and 2 of 15 897 (0.013%) thereafter. Nonobstetric SAEs were similar in males and females. All 20 deaths were unrelated to vaccination. Young girls and adult women with UAEs were less likely to receive the second dose than those without UAEs. Seven unrelated SAEs occurred in 203 267 MVA-BN-Filo recipients.

Conclusions
Postvaccination febrile convulsions in young children were rare but not previously described after Ad26.ZEBOV and were reduced with routine acetaminophen. The regimen was otherwise safe and well-tolerated.
Long-Axis Rotation of Jaws of Bamboo Sharks (Chiloscyllium plagiosum) During Suction Feeding
Authors: Scott Bradley R , Brainerd Elizabeth L , Wilga Cheryl A D 
Published: July 2022

SynopsisLong-axis rotation (LAR) of the jaws may be an important component of vertebrate feeding mechanisms, as it has been hypothesized to occur during prey capture or food processing across diverse vertebrate groups including mammals, ray-finned fishes, and sharks and rays. LAR can affect tooth orientation as well as muscle fiber direction and therefore muscle power during feeding. However, to date only a handful of studies have demonstrated this LAR in vivo. Here, we use XROMM to document LAR of the upper and lower jaws in white-spotted bamboo sharks, Chiloscyllium plagiosum, during suction feeding. As the lower jaw begins to depress for suction expansion, both the upper jaw (palatoquadrate) and lower jaw (Meckel's cartilage) evert, such that their toothed surfaces move laterally, and then they invert with jaw closing. Eversion has been shown to tense the dental ligament and erect the teeth in some sharks, but it is not clear how this tooth erection would contribute to suction feeding in bamboo sharks. Two recent XROMM studies have shown LAR of the lower jaws during mastication in mammals and stingrays and our study extends LAR to suction feeding and confirms its presence in shark species. Examples of LAR of the jaws are becoming increasingly widespread across vertebrates with unfused mandibular symphyses. Unfused lower jaws are the plesiomorphic condition for most vertebrate lineages and therefore LAR may be a common component of jaw mechanics unless the mandibular symphysis is fused.
Stimulatory effects of TGFα in granulosa cells of bovine small antral follicles
Authors: Lundberg Allie L , Jaskiewicz Nicole M , Maucieri Abigail M , Townson David H 
Published: July 2022

Abstract
Intraovarian growth factors play a vital role in influencing the fate of ovarian follicles. They affect proliferation and apoptosis of granulosa cells (GC) and can influence whether small antral follicles continue their growth or undergo atresia. Transforming growth factor-alpha (TGFα), an oocyte-derived growth factor, is thought to regulate granulosa cell function; yet its investigation has been largely overshadowed by emerging interest in TGF-beta superfamily members, such as bone morphogenetic proteins (BMP) and anti-Mullerian hormone (AMH). Here, effects of TGFα on bovine GC proliferation, intracellular signaling, and cytokine-induced apoptosis were evaluated. Briefly, all small antral follicles (3–5 mm) from slaughterhouse specimens of bovine ovary pairs were aspirated and the cells were plated in T25 flasks containing DMEM/F12 medium, 10% FBS, and antibiotic-antimycotic, and incubated at 37 °C in 5% CO2 for 3 to 4 d. Once confluent, the cells were sub-cultured for experiments (in 96-, 12-, or 6-well plates) in serum-free conditions (DMEM/F12 medium with ITS). Exposure of the bGC to TGFα (10 or 100 ng/mL) for 24 h stimulated cell proliferation compared to control (P &lt; 0.05; n = 7 ovary pairs). Proliferation was accompanied by a concomitant increase in mitogen-activated protein kinase (MAPK) signaling within 2 h of treatment, as evidenced by phosphorylated ERK1/2 expression (P &lt; 0.05, n = 3 ovary pairs). These effects were entirely negated, however, by the MAPK inhibitor, U0126 (10uM, P &lt; 0.05). Additionally, prior exposure of the bGC to TGFα (100 ng/mL) failed to prevent Fas Ligand (100 ng/mL)-induced apoptosis, as measured by caspase 3/7 activity (P &lt; 0.05, n = 7 ovary pairs). Collectively, the results indicate TGFα stimulates proliferation of bGC from small antral follicles via a MAPK/ERK-mediated mechanism, but this action alone fails to prevent apoptosis, suggesting that TGFα may be incapable of promoting their persistence in follicles during the process of follicular selection/dominance.
Insights from two independent transcriptomic studies of the bovine corpus luteum during pregnancy
Authors: Hughes Camilla H K , Mezera Megan A , Wiltbank Milo C , Pate Joy L 
Published: July 2022

Abstract
Several recent studies have used transcriptomics to investigate luteal changes during the maternal recognition of the pregnancy period in ruminants. Although these studies have contributed to our understanding of luteal function during early pregnancy, few attempts have been made to integrate information across these studies and distinguish key luteal transcripts or functions that are repeatably identified across multiple studies. Therefore, in this study, two independent studies of the luteal transcriptome during early pregnancy were combined and compared. In the first study, corpora lutea (CL) from day 20 of pregnancy were compared with CL collected on day 14 of pregnancy, prior to embryonic signaling. The cattle were nonlactating. In the second study, CL from day 20 of pregnancy were compared with CL collected from day 20 cyclic cattle that had been confirmed as not yet undergoing luteal regression. These were lactating cattle. Three methods were used to compare these two datasets, to identify key luteal regulators. In the first method, all transcripts with Benjamini–Hochberg-adjusted P-value (Q value) &lt; 0.05 in both datasets were considered. This yielded 22 transcripts, including several classical interferon-stimulated genes, as well as regulators of transforming growth factor-beta (TGFB) and latent TGFB-binding proteins (LTBP)1 and 2. In the second, less conservative method, all transcripts with P &lt; 0.01 and changed in the same direction in both datasets were considered. This yielded an additional 20 transcripts that were not identified in the first analysis, for a total of 42 common transcripts. These transcripts were regulators of functions such as inflammatory balance and matrix remodeling. In the third method, transcripts with Q &lt; 0.10 were subject to pathway analysis, and common pathways were identified. Retinoic acid signaling and classical interferon signaling pathways were identified with this method. Finally, regulation by interferon tau (IFNT) was investigated. Among the 42 transcripts identified, 32 were regulated by IFNT in cultured luteal cells (Q &lt; 0.05). Among those not regulated by IFNT were LTBP1 and 2, which are TGFB-binding proteins. In summary, common transcripts from two studies of the luteal transcriptome during early pregnancy were combined and shared changes were identified. This not only generated a list of potential key luteal regulators, which were mostly IFNT regulated, but also included transcripts not regulated by IFNT, including LTBP1 and 2.
Ruminant conceptus-maternal interactions: interferon-tau and beyond
Authors: Mathew Daniel J , Peterson Katie D , Senn L Kirsten , Oliver Mary A , Ealy Alan D 
Published: July 2022

Abstract
Embryonic or fetal loss in cattle is associated with problems that occur during oocyte maturation, early embryonic development, conceptus elongation, maternal recognition of pregnancy (MRP), and/or placental attachment and implantation. Many of these problems manifest as inadequate or asynchronous communication between the developing conceptus and endometrium, resulting in pregnancy failure. This review will provide an overview of how various conceptus-endometrial paracrine signaling systems control the fate of early pregnancy in cattle and other ruminants. We begin by summarizing the actions of interferon-tau, the classic MRP signal in ruminates, and then explore how other secretory factors derived from either the conceptus or endometrium influence establishment and maintenance of pregnancy. Insight into how the endometrium responds to male vs. female conceptuses or conceptuses produced by in vitro methods will also be described. Specific focus will be placed on describing how “omic” technologies and other cutting-edge techniques have assisted with identifying novel conceptus and/or endometrial factors and their functions. Recent findings indicate that the endometrial transcriptome and histotroph are altered by conceptus sex, quality, and origin, suggesting that the endometrium is a sensor of conceptus biochemistry. Although the endometrium has a certain level of flexibility in terms of conceptus-maternal interactions, this interplay is not sufficient to retain some pregnancies. However, new information inspires us to learn more and will help develop technologies that mitigate early embryonic loss and reproductive failure in ruminants and other animals.