bluuebunny/crossref_metadata_2025_split huggingface dataset:
A plastid phylogenomic framework for the palm family (Arecaceae)
Authors: Yao Gang , Zhang Yu-Qu , Barrett Craig , Xue Bine , Bellot Sidonie , Baker William J. , Ge Xue-Jun 
Published: March 2023

Abstract
Background
Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research.

Results
Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support.

Conclusions
The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.
SRSF1 regulates primordial follicle formation and number determination during meiotic prophase I
Authors: Sun Longjie , Lv Zheng , Chen Xuexue , Wang Chaofan , Lv Pengbo , Yan Lu , Tian Shuang , Xie Xiaomei , Yao Xiaohong , Liu Jingjing , Wang Zhao , Luo Haoshu , Cui Sheng , Liu Jiali 
Published: March 2023

Abstract
Background
Ovarian folliculogenesis is a tightly regulated process leading to the formation of functional oocytes and involving successive quality control mechanisms that monitor chromosomal DNA integrity and meiotic recombination. A number of factors and mechanisms have been suggested to be involved in folliculogenesis and associated with premature ovarian insufficiency, including abnormal alternative splicing (AS) of pre-mRNAs. Serine/arginine-rich splicing factor 1 (SRSF1; previously SF2/ASF) is a pivotal posttranscriptional regulator of gene expression in various biological processes. However, the physiological roles and mechanism of SRSF1 action in mouse early-stage oocytes remain elusive. Here, we show that SRSF1 is essential for primordial follicle formation and number determination during meiotic prophase I.

Results
The conditional knockout (cKO) of Srsf1 in mouse oocytes impairs primordial follicle formation and leads to primary ovarian insufficiency (POI). Oocyte-specific genes that regulate primordial follicle formation (e.g., Lhx8, Nobox, Sohlh1, Sohlh2, Figla, Kit, Jag1, and Rac1) are suppressed in newborn Stra8-GFPCre Srsf1Fl/Fl mouse ovaries. However, meiotic defects are the leading cause of abnormal primordial follicle formation. Immunofluorescence analyses suggest that failed synapsis and an inability to undergo recombination result in fewer homologous DNA crossovers (COs) in the Srsf1 cKO mouse ovaries. Moreover, SRSF1 directly binds and regulates the expression of the POI-related genes Six6os1 and Msh5 via AS to implement the meiotic prophase I program.

Conclusions
Altogether, our data reveal the critical role of an SRSF1-mediated posttranscriptional regulatory mechanism in the mouse oocyte meiotic prophase I program, providing a framework to elucidate the molecular mechanisms of the posttranscriptional network underlying primordial follicle formation.
Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling
Authors: Ren Junxiao , Hu Zhengzheng , Li Quanlin , Gu Shuang , Lan Fangren , Wang Xiqiong , Li Jianbo , Li Junying , Shao Liwa , Yang Ning , Sun Congjiao 
Published: March 2023

Abstract
Background
Embryonic diapause (dormancy) is a state of temporary arrest of embryonic development that is triggered by unfavorable conditions and serves as an evolutionary strategy to ensure reproductive survival. Unlike maternally-controlled embryonic diapause in mammals, chicken embryonic diapause is critically dependent on the environmental temperature. However, the molecular control of diapause in avian species remains largely uncharacterized. In this study, we evaluated the dynamic transcriptomic and phosphoproteomic profiles of chicken embryos in pre-diapause, diapause, and reactivated states.

Results
Our data demonstrated a characteristic gene expression pattern in effects on cell survival-associated and stress response signaling pathways. Unlike mammalian diapause, mTOR signaling is not responsible for chicken diapause. However, cold stress responsive genes, such as IRF1, were identified as key regulators of diapause. Further in vitro investigation showed that cold stress-induced transcription of IRF1 was dependent on the PKC-NF-κB signaling pathway, providing a mechanism for proliferation arrest during diapause. Consistently, in vivo overexpression of IRF1 in diapause embryos blocked reactivation after restoration of developmental temperatures.

Conclusions
We concluded that embryonic diapause in chicken is characterized by proliferation arrest, which is the same with other spices. However, chicken embryonic diapause is strictly correlated with the cold stress signal and mediated by PKC-NF-κB-IRF1 signaling, which distinguish chicken diapause from the mTOR based diapause in mammals.
Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves
Authors: Guo Yang , Meng Lingfeng , Wang Minxiao , Zhong Zhaoshan , Li Denghui , Zhang Yaolei , Li Hanbo , Zhang Huan , Seim Inge , Li Yuli , Jiang Aijun , Ji Qianyue , Su Xiaoshan , Chen Jianwei , Fan Guangyi , Li Chaolun , Liu Shanshan 
Published: March 2023

AbstractBackgroundBivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution.ResultsWe present a hologenome ofConchocele bisecta(Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers ofC. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent inC. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance inC. bisecta.ConclusionsThus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.
Assessing the impacts of COVID-19 vaccination programme’s timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries
Authors: Liu Yang , Procter Simon R. , Pearson Carl A. B. , Montero Andrés Madriz , Torres-Rueda Sergio , Asfaw Elias , Uzochukwu Benjamin , Drake Tom , Bergren Eleanor , Eggo Rosalind M. , Ruiz Francis , Ndembi Nicaise , Nonvignon Justice , Jit Mark , Vassall Anna 
Published: March 2023

Abstract
Background
The COVID-19 vaccine supply shortage in 2021 constrained roll-out efforts in Africa while populations experienced waves of epidemics. As supply improves, a key question is whether vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.

Methods
We assessed the impact of vaccination programme timing using an epidemiological and economic model. We fitted an age-specific dynamic transmission model to reported COVID-19 deaths in 27 African countries to approximate existing immunity resulting from infection before substantial vaccine roll-out. We then projected health outcomes (from symptomatic cases to overall disability-adjusted life years (DALYs) averted) for different programme start dates (01 January to 01 December 2021, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/million population-day, respectively) for viral vector and mRNA vaccines by the end of 2022. Roll-out rates used were derived from observed uptake trajectories in this region. Vaccination programmes were assumed to prioritise those above 60 years before other adults.
We collected data on vaccine delivery costs, calculated incremental cost-effectiveness ratios (ICERs) compared to no vaccine use, and compared these ICERs to GDP per capita. We additionally calculated a relative affordability measure of vaccination programmes to assess potential nonmarginal budget impacts.

Results
Vaccination programmes with early start dates yielded the most health benefits and lowest ICERs compared to those with late starts. While producing the most health benefits, fast vaccine roll-out did not always result in the lowest ICERs. The highest marginal effectiveness within vaccination programmes was found among older adults. High country income groups, high proportions of populations over 60 years or non-susceptible at the start of vaccination programmes are associated with low ICERs relative to GDP per capita. Most vaccination programmes with small ICERs relative to GDP per capita were also relatively affordable.

Conclusion
Although ICERs increased significantly as vaccination programmes were delayed, programmes starting late in 2021 may still generate low ICERs and manageable affordability measures. Looking forward, lower vaccine purchasing costs and vaccines with improved efficacies can help increase the economic value of COVID-19 vaccination programmes.
Diagnostic accuracy of circular RNA for diabetes Mellitus: a systematic review and diagnostic Meta-analysis
Authors: Dehghanbanadaki Hojat , Asili Pooria , Haji Ghadery Abdolkarim , Mirahmad Maryam , Dehnavi Ali Zare , Parsaei Amirhossein , Baradaran Hamid Reza , Azami Mobin , Jose Justo da Silva Gustavo , Parvan Reza , Moradi Yousef 
Published: March 2023

Abstract
Background
This study aimed to investigate the pooled diagnostic ability of circular RNA (circRNA) molecules for diabetes mellitus.

Methods
We searched PubMed, Scopus, and Web of Science for relevant studies. A total of 2070 participants, including 775 diabetic patients and 1295 healthy individuals, from five studies were included in this meta-analysis. True positive, true negative, false positive, and false negative data were extracted to calculate pooled sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio, and area under the receiver operating characteristics curve. The Deeks’ funnel plot was applied for publication bias assessment, Cochran’s Q test and I2 index were applied for inter-study heterogeneity assessment. Besides, a subgroup analysis was performed for determining the source of heterogeneity between studies. P value < 0.05 was considered significance. All analysis were done by STATA version 14.

Results
CircRNA presented a sensitivity of 76% (95% confidence interval [95%CI]: 66-84%), specificity of 77% (95%CI: 58-89%), positive LR of 3.25 (95%CI: 1.69–6.23), negative LR of 0.31 (95%CI: 0.21–0.46), DOR of 10.41 (95%CI: 4.26–25.41), and AUC of 0.82 (95%CI: 0.79–0.85) for diabetes mellitus detection. More specifically, hsa_circ_0054633 showed a sensitivity of 67% (95%CI: 53-81%) and a specificity of 82% (95%CI: 63-100%).

Conclusion
CircRNAs show highly accurate diagnostic capability for type 2 diabetes mellitus and gestational diabetes mellitus. High sensitivity of circRNAs introduces them as potential noninvasive biomarkers for early diagnosis of diabetes mellitus and their high specificity introduces them as potential therapeutic targets by regulation of their expression.
Efficient biosynthesis of resveratrol via combining phenylalanine and tyrosine pathways in Saccharomyces cerevisiae
Authors: Meng Lijun , Diao Mengxue , Wang Qingyan , Peng Longyun , Li Jianxiu , Xie Nengzhong 
Published: March 2023

Abstract
Background
Resveratrol is a commercially available stilbenoid widely used as dietary supplements, functional food ingredients, and cosmetic ingredients due to its diverse physiological activities. The production of resveratrol in microorganisms provides an ideal source that reduces the cost of resveratrol, but the titer in Saccharomyces cerevisiae was still much lower than that in other hosts.

Results
To achieve enhanced production of resveratrol in S. cerevisiae, we constructed a biosynthetic pathway via combining phenylalanine and tyrosine pathways by introducing a bi-functional phenylalanine/tyrosine ammonia lyase from Rhodotorula toruloides. The combination of phenylalanine pathway with tyrosine pathway led to a 462% improvement of resveratrol production in yeast extract peptone dextrose (YPD) medium with 4% glucose, suggesting an alternative strategy for producing p-coumaric acid-derived compounds. Then the strains were further modified by integrating multi-copy biosynthetic pathway genes, improving metabolic flux to aromatic amino acids and malonyl-CoA, and deleting by-pathway genes, which resulted in 1155.0 mg/L resveratrol in shake flasks when cultured in YPD medium. Finally, a non-auxotrophic strain was tailored for resveratrol production in minimal medium without exogenous amino acid addition, and the highest resveratrol titer (4.1 g/L) ever reported was achieved in S. cerevisiae to our knowledge.

Conclusions
This study demonstrates the advantage of employing a bi-functional phenylalanine/tyrosine ammonia lyase in the biosynthetic pathway of resveratrol, suggesting an effective alternative in the production of p-coumaric acid-derived compounds. Moreover, the enhanced production of resveratrol in S. cerevisiae lays a foundation for constructing cell factories for various stilbenoids.

Graphical Abstract
Measurement properties of the EQ-5D-5L in sub-health: evidence based on primary health care workers in China
Authors: Liu Yueyue , Wan Chuchuan , Xi Xiaoyu 
Published: March 2023

Abstract
Background
Sub-health which is the state between health and disease is a major global public health challenge. As a reversible stage, sub-health can work as a effective tool for the early detection or prevention of chronic disease. The EQ-5D-5L (5L) is a widely used, generic preference-based instrument while its validity in measuring sub-health is not clear. The aim of the study was thus to assess its measurement properties in individuals with sub-health in China.

Methods
The data used were from a nationwide cross-sectional survey conducted among primary health care workers who were selected on the basis of convenience and voluntariness. The questionnaire was composited of 5L, Sub-Health Measurement Scale V1.0 (SHMS V1.0), social-demographic characteristics and a question assessing the presence of disease. Missing values and ceiling effects of 5L were calculated. The convergent validity of 5L utility and VAS scores was tested by assessing their correlations with SHMS V1.0 using Spearman’s correlation coefficient. The known-groups validity of 5L utility and VAS scores was assessed by comparing their values between subgroups defined by SHMS V1.0 scores using the Kruskal–Wallis test. We also did an analysis in subgroups according to different regions of China.

Results
A total of 2063 respondents were included in the analysis. No missing data were observed for the 5L dimensions and only one missing value was for the VAS score. 5L showed strong overall ceiling effects (71.1%). The ceiling effects were slightly weaker on the “pain/discomfort” (82.3%) and “anxiety/depression” (79.5%) dimensions compared with the other three dimensions (nearly 100%). The 5L weakly correlated with SHMS V1.0: the correlation coefficients were mainly between 0.2 and 0.3 for the two scores. 5L was yet not sensitive in distinguishing subgroups of respondents with different levels of sub-health, especially the subgroups with adjacent health status (p > 0.05). The results of subgroup analysis were generally consistent with those of the full sample.

Conclusions
It appears that the measurement properties of EQ-5D-5L in individuals with sub-health are not satisfactory in China. We thus should be cautious to use it in the population.
Previously reported and here added cases demonstrate euploid pregnancies followed by PGT-A as “mosaic” as well as “aneuploid” designated embryos
Authors: Gleicher Norbert , Patrizio Pasquale , Mochizuki Lyka , Barad David H. 
Published: March 2023

Abstract
Background
After the longest time opposing all transfers of embryos by preimplantation genetic testing for aneuploidy (PGT-A) diagnosed as “chromosomal-abnormal,” the field has over recent years slowly been moving toward selective transfers of by PGT-A as “mosaic” diagnosed embryos, but is still rejecting transfers of embryos by PGT-A defined as “aneuploid.”

Methods
Upon review of the literature, we report published cases of euploid pregnancies following transfers of PGT-A as “aneuploid” diagnosed embryos and add several additional, ongoing cases at our center.

Results
Among the published cases from our center, we identified seven euploid pregnancies from “aneuploid” embryos, four of which preceded the PGT-A industry’s 2016 switch from binary “euploid” – “aneuploid” reporting to “euploid,” “mosaic,” and “aneuploid” reporting. That those four cases post 2016 PGT-A definition involving “mosaic” embryos, therefore, cannot be ruled out. Since then, we recently established three additional ongoing pregnancies from transfers of “aneuploid” embryos which still await confirmation of euploidy after delivery. A recent fourth pregnancy from the transfer of a trisomy 9 embryo miscarried before a fetal heart. Outside our own center’s experience, the literature revealed only one additional such transfer, involving PGT-A as a “chaotic-aneuploid” diagnosed embryo with six abnormalities, leading to normal euploid delivery. In reviewing the literature, we furthermore demonstrate why current PGT-A reporting that differentiates between “mosaic” and “aneuploid” embryos based on relative percentages of euploid and aneuploid DNA in a single trophectoderm biopsy of on average 5-6 cells, is biologically non-sensical.

Conclusion
Basic biological evidence and a clinically still very limited experience with transfers of PGT-A as “aneuploid” labeled embryos demonstrate beyond reasonable doubt that at least some “aneuploid” embryos can lead to healthy euploid births. Therefore, this observation establishes beyond reasonable doubt that the rejection of all “aneuploid” embryos from transfer reduces pregnancy and live birth chances for IVF patients. Whether (and to what possible degree) pregnancy and live birth chances differ between “mosaic” and “aneuploid” embryos, remains to be determined. The answer will likely depend on the aneuploidy(ies) of an embryo and to what degree percentages of “mosaicism” in a single, on average 5/6-cell trophectoderm biopsy can reflect the ploidy-status of a complete embryo.
Effect of COVID-19 on antenatal care: experiences of medical professionals in the Netherlands
Authors: Gamberini Carlotta , Angeli Federica , Knight Lucia , Zaami Mariama , Al-Nasiry Salwan , Ambrosino Elena 
Published: March 2023

Abstract
Background
COVID-19 has greatly affected the delivery of all health care services globally. Antenatal care is one area of care that has been impacted, despite the fact that attending antenatal check-ups is essential for pregnant women and cannot be postponed. Little is known about how exactly ANC provision has changed in the Netherlands, or how the changes have impacted midwives and gynaecologists providing those services.

Methods
This study used a qualitative research design to investigate changes in individual and national practice following the onset of the COVID-19 pandemic. The study involved a document analysis of protocols and guidelines for ANC provision to evaluate how those changed following the onset of the COVID-19 pandemic and semi-structured interviews with ANC care providers (i.e., gynaecologists and midwives).

Results
Guidance was issued by multiple organizations, during the pandemic, on how to approach the risk of infection in pregnant women, recommending several changes to ANC to protect both pregnant women and ANC providers. Both midwives and gynaecologists reported changes in their practice. With less face-to-face consultations happening, digital technologies became critical in the care of pregnant women. Shorter and fewer visits were reported, with midwifery practices adjusting their guidelines further than hospitals. Challenges, with high workloads and lack of personal protective equipment were discussed.

Conclusions
The COVID-19 pandemic has had an immense impact on the health care system. This impact has had both negative and positive effects on the provision of ANC in the Netherlands. It is important to learn from the current COVID-19 pandemic and adapt ANC, as well as health care systems as a whole, to be better prepared for future health crises and ensure continuous provision of good quality care.