bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data
Authors: Lee Young-Lim , Bosse Mirte , Takeda Haruko , Moreira Gabriel Costa Monteiro , Karim Latifa , Druet Tom , Oget-Ebrad Claire , Coppieters Wouter , Veerkamp Roel F. , Groenen Martien A. M. , Georges Michel , Bouwman Aniek C. , Charlier Carole 
Published: May 2023

Abstract
Background
Structural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and translocations. The genomics revolution enabled the discovery of sub-microscopic SVs via array and whole-genome sequencing (WGS) data, paving the way to unravel the functional impact of SVs. Recent human expression QTL mapping studies demonstrated that SVs play a disproportionally large role in altering gene expression, underlining the importance of including SVs in genetic analyses. Therefore, this study aimed to generate and explore a high-quality bovine SV catalogue exploiting a unique cattle family cohort data (total 266 samples, forming 127 trios).

Results
We curated 13,731 SVs segregating in the population, consisting of 12,201 deletions, 1,509 duplications, and 21 multi-allelic CNVs (> 50-bp). Of these, we validated a subset of copy number variants (CNVs) utilising a direct genotyping approach in an independent cohort, indicating that at least 62% of the CNVs are true variants, segregating in the population. Among gene-disrupting SVs, we prioritised two likely high impact duplications, encompassing ORM1 and POPDC3 genes, respectively. Liver expression QTL mapping results revealed that these duplications are likely causing altered gene expression, confirming the functional importance of SVs. Although most of the accurately genotyped CNVs are tagged by single nucleotide polymorphisms (SNPs) ascertained in WGS data, most CNVs were not captured by individual SNPs obtained from a 50K genotyping array.

Conclusion
We generated a high-quality SV catalogue exploiting unique whole genome sequenced bovine family cohort data. Two high impact duplications upregulating the ORM1 and POPDC3 are putative candidates for postpartum feed intake and hoof health traits, thus warranting further investigation. Generally, CNVs were in low LD with SNPs on the 50K array. Hence, it remains crucial to incorporate CNVs via means other than tagging SNPs, such as investigation of tagging haplotypes, direct imputation of CNVs, or direct genotyping as done in the current study. The SV catalogue and the custom genotyping array generated in the current study will serve as valuable resources accelerating utilisation of full spectrum of genetic variants in bovine genomes.
Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses
Authors: Yan Jun , Su Peisen , Meng Xianyong , Liu Pingzeng 
Published: May 2023

Abstract
Background
The receptor-like kinase (RLK) gene families in plants contains a large number of members. They are membrane proteins with an extracellular receptor domain and participate in biotic and abiotic stress responses.

Results
In this study, we identified RLKs in 15 representative plant genomes, including wheat, and classified them into 64 subfamilies by using four types of phylogenetic trees and HMM models. Conserved exon‒intron structures with conserved exon phases in the kinase domain were found in many RLK subfamilies from Physcomitrella patens to Triticum aestivum. Domain distributions of RLKs were also diagrammed. Collinearity events and tandem gene clusters suggested that polyploidization and tandem duplication events contributed to the member expansions of T. aestivum RLKs. Global expression pattern analysis was performed by using public transcriptome data. These analyses were involved in T. aestivum, Aegilops tauschii and Brachypodium distachyon RLKs under biotic and abiotic stresses. We also selected 9 RLKs to validate the transcriptome prediction by using qRT‒PCR under drought treatment and with Fusarium graminearum infection. The expression trends of these 9 wheat RLKs from public transcriptome data were consistent with the results of qRT‒PCR, indicating that they might be stress response genes under drought or F. graminearum treatments.

Conclusion
In this study, we identified, classified, evolved, and expressed RLKs in wheat and related plants. Thus, our results will provide insights into the evolutionary history and molecular mechanisms of wheat RLKs.
Effects of HDAC inhibitors on neuroblastoma SH-SY5Y cell differentiation into mature neurons via the Wnt signaling pathway
Authors: Choi Jiyun , Hwang Jinsu , Ramalingam Mahesh , Jeong Han-Seong , Jang Sujeong 
Published: May 2023

AbstractHistone deacetylase (HDAC) inhibitors affect cell homeostasis, gene expression, and cell cycle progression and promote cell terminal differentiation or apoptosis. However, the effect of HDAC inhibition on SH-SY5Y cells, which are neuroblastoma cells capable of differentiating into neurons under specific conditions, such as in the presence of retinoic acid (RA), is unknown. In this study, we hypothesized that HDAC inhibitors induced the neuronal differentiation of SH-SY5Y cells. To test this hypothesis, we used phase contrast microscopy, immunocytochemistry (ICC), qPCR, and western blotting analysis. MS-275 and valproic acid (VPA), two HDAC inhibitors, were selected to evaluate neuronal differentiation. It was confirmed that cells treated with MS-275 or VPA differentiated into mature neurons, which were distinguished by bipolar or multipolar morphologies with elongated branches. In addition, the mRNA expression of neuronal markers (Tuj1 and NEFH) and the oligodendrocyte marker (CNP) was significantly increased with MS-275 or VPA treatment compared to that with RA treatment. In addition, the protein expression of the other neuronal markers, Tuj1 and NeuN, was highly increased with HDAC inhibitor treatments compared to that with RA treatment. Furthermore, we confirmed that noncanonical Wnt signaling was upregulated by HDAC inhibitors via MAPK signaling and the Wnt/JNK pathway. Therefore, both MS-275 and VPA promoted the differentiation of SH-SY5Y cells into mature neurons via the Wnt signaling pathway.
Role of tillage measures in mitigating waterlogging damage in rapeseed
Authors: Tian Xiaoqin , Li Zhuo , Liu Yonghong , Li Wei 
Published: May 2023

Abstract
Background
Tillage measures have been effectively adopted for mitigating waterlogging damage in field crops, yet little is known about the role of tillage measures in crop responses to waterlogging. A field experiment was performed to investigate the effect of conventional planting (CK), small ridge planting (SR), big ridge planting (BR) and film side planting (FS) on soil available nutrients and enzymatic activity, chlorophyll contents, leaf nutrients, soluble protein, soluble sugar, nitrate reductase, antioxidant enzyme activity, lipid peroxidation, agronomic traits and yield of rapeseed under waterlogging stress conditions.

Results
Tillage measures remarkably improved rapeseed growth and yield parameters under waterlogging stress conditions. Under waterlogging conditions, rapeseed yield was significantly increased by 33.09 and 22.70% in the SR and BR groups, respectively, compared with CK. Correlation analysis showed that NO3−-N, NH4+-N, and urease in soils and malonaldehyde (MDA), superoxide dismutase (SOD), and nitrate reductase in roots were the key factors affecting rapeseed yield. The SR and BR groups had significantly increased NO3−-N by 180.30 and 139.77%, NH4+-N by 115.78 and 66.59%, urease by 41.27 and 26.45%, SOD by 6.64 and 4.66%, nitrate reductase by 71.67 and 26.67%, and significantly decreased MDA content by 14.81 and 13.35% under waterlogging stress, respectively, compared with CK. In addition, chlorophyll and N content in leaves, soluble sugar and POD in roots, and most agronomic traits were also significantly enhanced in response to SR and BR under waterlogging conditions.

Conclusion
Overall, SR and BR mitigated the waterlogging damage in rapeseed mainly by reducing the loss of soil available nitrogen, decreasing the MDA content in roots, and promoting urease in soils and SOD and nitrate reductase in roots. Finally, thorough assessment of rapeseed parameters indicated that SR treatment was most effective followed by BR treatment, to alleviate the adverse effects of waterlogging stress.
Severe cardiogenic shock and cardiac arrest due to fulminant cardiac sarcoidosis: a case report
Authors: Chakrala Teja , Prakash Roshni O. , Jain Anshul , Vautier R. Ashton , Prasada Sahil , Al-Ani Mohammed , Ahmed Mustafa M. 
Published: May 2023

Abstract
Background
Cardiac sarcoidosis is found to occur in approximately 5% of patients with sarcoidosis. Its presentation can typically range from complete heart block to ventricular arrhythmias. This condition can rarely present with severe heart failure and cardiogenic shock requiring aggressive and timely management strategies. Advanced imaging techniques are usually required to assist with its diagnosis.

Case presentation
A 70-year-old woman with a history of pulmonary sarcoidosis presented with non-ST elevation myocardial infarction, congestive hepatopathy, and acute renal failure. Left heart catheterization showed evidence of non-obstructive coronary artery disease, and right heart catheterization revealed severely elevated filling pressures and depressed cardiac index. She underwent aggressive diuresis and placement of an intra-aortic balloon pump in addition to initiation of inotropic and vasopressor support. While in the cardiac intensive care unit, she experienced frequent episodes of ventricular tachycardia and went into cardiac arrest requiring cardiopulmonary resuscitation. High clinical suspicion for cardiac sarcoidosis was confirmed by cardiac magnetic resonance imaging findings. After starting immunosuppressive therapy for cardiac sarcoidosis, she demonstrated clinical improvement.

Conclusion
Patients with cardiac sarcoidosis may remain asymptomatic or present with conduction abnormalities and arrhythmias. They rarely present with severe biventricular heart failure and cardiogenic shock, and in such cases, they require timely initiation of pharmacologic and device therapies, along with implementation of mechanical circulatory support.
Randomised clinical trial: 3-year interim analysis results of the VISION trial to evaluate the long-term safety of vonoprazan as maintenance treatment in patients with erosive oesophagitis
Authors: Haruma Ken , Kinoshita Yoshikazu , Yao Takashi , Kushima Ryoji , Akiyama Junichi , Aoyama Nobuo , Kanoo Tatsuhiro , Miyata Kouji , Kusumoto Naomi , Uemura Naomi 
Published: May 2023

Abstract
Background
VISION is a randomised, phase 4, open-label, parallel-group, multicentre study conducted in 33 centres in Japan. The aim of this study was to assess the long-term safety of vonoprazan for maintenance treatment of healed erosive oesophagitis versus lansoprazole.

Methods
Patients with endoscopically diagnosed erosive oesophagitis were randomised 2:1 to once-daily vonoprazan 20 mg or lansoprazole 30 mg, for a 4- to 8-week healing phase. Patients with endoscopically confirmed healing entered a 260-week maintenance phase with a once-daily starting dose of vonoprazan 10 mg or lansoprazole 15 mg. Primary endpoint was change in gastric mucosal histopathology.

Results
Of 208 patients (vonoprazan, n = 139; lansoprazole, n = 69) entering the healing phase, 202 entered the maintenance phase (vonoprazan, n = 135; lansoprazole, n = 67). At 3 years, 109 vonoprazan-treated and 58 lansoprazole-treated patients remained on treatment. Histopathological evaluation of gastric mucosa showed that hyperplasia of parietal, foveolar and G cells was more common with vonoprazan than lansoprazole at week 156 of the maintenance phase. There was no marked increase in the occurrence of parietal, foveolar and G cell hyperplasia among patients in the vonoprazan group from week 48 to week 156. Histopathological evaluation of the gastric mucosa also showed no neoplastic changes in either group. No new safety issues were identified.

Conclusions
In this interim analysis of VISION, no new safety concerns were identified in Japanese patients with healed erosive oesophagitis receiving vonoprazan or lansoprazole as maintenance treatment for 3 years. (CT.gov identifier: NCT02679508; JapicCTI-163153; Japan Registry of Clinical Trials: jRCTs031180040).
Clinical features and images of malignant lymphoma localized in the pancreatic head to differentiate from pancreatic ductal adenocarcinoma: a case series study
Authors: Kato Naohiro , Yamaguchi Atsushi , Sugata Syuhei , Hamada Takuro , Furuya Nao , Mizumoto Takeshi , Tamaru Yuzuru , Kusunoki Ryusaku , Kuwai Toshio , Kouno Hirotaka , Tazuma Sho , Sudo Takeshi , Kido Miki , Ito Takuo , Kuraoka Kazuya , Kohno Hiroshi 
Published: May 2023

Abstract
Background
Pathological examination by endoscopic ultrasonography–guided fine-needle aspiration (EUS-FNA) has been reported to be useful in diagnosing pancreatic malignant lymphoma (ML), but some ML cases are difficult to be differentiated from pancreatic ductal adenocarcinoma (PDAC).

Methods
This retrospective study included 8 patients diagnosed with ML that had a pancreatic-head lesion at initial diagnosis and 46 patients with resected PDAC in the pancreatic head between April 2006 and October 2021 at our institute. ML and PDAC were compared in terms of patients’ clinical features and imaging examinations.

Results
The median tumor size was larger in ML than in PDAC (45.8 [24–64] vs. 23.9 [8–44] mm), but the median diameter of the caudal main pancreatic duct (MPD) was larger in PDAC (2.5 [1.0–3.5] vs. 7.1 [2.5–11.8] mm), both showing significant differences between these malignancies (both, P < 0.001). In the analysis of covariance, MLs showed a smaller caudal MPD per tumor size than PDACs, with a statistical difference (P = 0.042). Sensitivity and specificity using sIL-2R ≥ 658 U/mL plus CA19-9 < 37 U/mL for the differentiation of ML from PDAC were 80.0% and 95.6%, respectively.

Conclusions
Diagnosing pancreatic ML using cytohistological examination through EUS-FNA can be difficult in some cases. Thus, ML should be suspected if a patient with a pancreatic tumor has a small MPD diameter per tumor size, high serum sIL-2R level, normal CA19-9 level. If the abovementioned features are present and still cannot be confirmed as PDAC, re-examination should be considered.
Barriers and facilitators to the transplant process among patients living with polycystic kidney disease: a qualitative Approach
Authors: Smith Juliana , Harris Orlando O. , Adey Deborah , Park Meyeon 
Published: May 2023

Abstract
Background
Kidney transplant is the gold standard for renal replacement therapy in patients with autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. Despite the medical and economic benefits of preemptive kidney transplant over dialysis before transplant, only 9–21% of qualifying patients receive preemptive transplants. Given the low rates of preemptive transplant, the aim of this study was to determine perceived facilitators and barriers to preemptive transplant among ADPKD patients using a qualitative approach.

Methods
Data were collected between July 2021 and January 2022 from virtual individual semi-structured interviews of 16 adult participants with ADPKD. Qualitative analysis of the recorded interviews was conducted to generate themes.

Results
Our findings revealed two themes specific for facilitators to preemptive transplant (social support and patient agency) and three themes specific to barriers for preemptive transplant (inadequate social support, gaps in knowledge, and institutional and systemic policies). The results also include various subthemes and the application of these themes to the social ecological model.

Conclusions
These findings suggest that increasing social support and patient agency, such as through patient navigator programs and encouraging effective communication between health care providers and patients, can facilitate the transplant process. Increasing dissemination of transplant knowledge from institutions and systems to patients through paired kidney exchange education and live donor outreach can also increase timely access to preemptive kidney transplants for patients with ADPKD. Our findings are limited by our single site study in the US, which may not apply to individuals experiencing different social, cultural, and health access conditions.
The effect of COVID-19 on women’s experiences of pregnancy, birth and postpartum in Indonesia: a rapid online survey
Authors: McGowan Linda , Astuti Andari , Hafidz Firdaus , Pratiwi Cesa , Yulian Vinami , Hughes Elizabeth , Pratiwi Arum , Indomo Emi Nurjasmi , Fu Yu 
Published: May 2023

Abstract
Background
The interrelationship of psychological and social factors in the current COVID-19 pandemic has been highlighted in research mainly focused on the global north. The impact of lockdowns can exacerbate psychological distress and affect access to services. Less is known about the psychosocial impact on women in the context of lower-middle income countries (LMICs); the aim of this study was to capture the impact of COVID-19 on women’s experiences of pregnancy, birth and postpartum in Indonesia.

Methods
We conducted a rapid cross-sectional online survey of women across all 34 provinces in Indonesia to capture participants’ experiences. Data were collected between 10th July to 9th August 2020 including demographics, effects on general and mental health and impact on service use. Descriptive statistics and thematic analysis were used to analyse responses, including those women who self-identified with a pre-existing mental health problem.

Results
Responses were obtained from 1137 women, this included pregnant women (n = 842) and postpartum women (n = 295). The majority of women (97%) had accessed antenatal care during their pregnancy, but 84% of women reporting feeling fearful and anxious about attending visits, resulting in some women not attending or changing provider. A small number (13%) were denied the presence of a birth companion, with 28% of women reporting that their babies had been removed at birth due to protocols or baby’s health. Feeling anxious was a common experience among women (62%) during their pregnancy, birth or postnatal period, with a small number (9%) feeling depressed. Lockdown measures led to tensions within personal and family relationships.

Conclusions
Women in Indonesia reported that the pandemic added an increased burden in pregnancy, birth and post-partum period: physically, psychologically, spiritually and financially. Maternity services were disrupted and health insurance cover lacked responsiveness, which either directly or indirectly impacted on women’s choices, and equal access to care. Given the longevity of the current pandemic there is a need to develop tailored supportive interventions for women and their families and develop bespoke training for midwives and other relevant health professionals.
The roles of multi-component interventions in reducing mistreatment of women and enhancing respectful maternity care: a systematic review
Authors: Kasaye Habtamu , Sheehy Annabel , Scarf Vanessa , Baird Kathleen 
Published: May 2023

Abstract
Background
Despite recognition of the adverse impacts of the mistreatment of women during pregnancy, labour and birth, there remains limited evidence on interventions that could reduce mistreatment and build a culture of respectful maternity care (RMC) in health facilities. The sustainability of effective individual interventions and their adaptability to various global contexts remain uncertain. In this systematic review, we aimed to synthesise the best available evidence that has been shown to be effective in reducing the mistreatment of women and/or enhancing RMC during women’s maternity care in health facilities.

Methods
We searched the online databases PubMed, CINAHL, EBSCO Nursing/Academic Edition, Embase, African Journals Online (AJOL), Scopus, Web of Science, and grey literature using predetermined search strategies. We included cluster randomized controlled trials (RCTs) and pre-and-post observational studies and appraised them using JBI critical appraisal checklists. The findings were synthesised narratively without conducting a meta-analysis. The certainty of evidence was assessed using GRADE criteria.

Results
From the 1493 identified records, 11 studies from six sub-Sahara African countries and one study from India were included: three cluster RCTs and nine pre- and post-studies. We identified diverse interventions implemented via various approaches including individual health care providers, health systems, and policy amendments. Moderate certainty evidence from two cluster RCTs and four pre- and post-studies suggests that multi-component interventions can reduce the odds of mistreatment that women may experience in health facilities, with odds of reduction ranging from 18 per cent to 66 per cent. Similarly, women’s perceptions of maternity care as respectful increased in moderate certainty evidence from two cluster RCTs and five pre- and post-studies with reported increases ranging from 5 per cent to 50 per cent.

Conclusions
Multi-component interventions that address attitudes and behaviors of health care providers, motivate staff, engage the local community, and alleviate health facility and system constraints have been found to effectively reduce mistreatment of women and/or increase respectful maternity care. Such interventions which go beyond a single focus like staff training appear to be more likely to bring about change. Therefore, future interventions should consider diverse approaches that incorporate these components to improve maternal care.