bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of in utero transfusions on perinatal outcomes in patients with alpha thalassemia major: the UCSF registry
Authors: Schwab Marisa E. , Lianoglou Billie R. , Gano Dawn , Gonzalez Velez Juan , Allen Isabel E. , Arvon Regina , Baschat Ahmet , Bianchi Diana W. , Bitanga Melissa , Bourguignon Anne , Brown Richard N. , Chen Bruce , Chien May , Davis-Nelson Shareece , de Laat Monique W. M. , Ekwattanakit Supachai , Gollin Yvonne , Hirata Greigh , Jelin Angie , Jolley Jennifer , Meyer Paul , Miller Jena , Norton Mary E. , Ogasawara Keith K. , Panchalee Tachjaree , Schindewolf Erica , Shaw Steven W. , Stumbaugh Tammy , Thompson Alexis A. , Towner Dena , Tsai Pai-Jong Stacy , Viprakasit Vip , Volanakis Emmanuel , Zhang Li , Vichinsky Elliott , MacKenzie Tippi C. 
Published: October 2022

Abstract
Alpha thalassemia major (ATM) is a hemoglobinopathy that usually results in perinatal demise if in utero transfusions (IUTs) are not performed. We established an international registry (NCT04872179) to evaluate the impact of IUTs on survival to discharge (primary outcome) as well as perinatal and neurodevelopmental secondary outcomes. Forty-nine patients were diagnosed prenatally, 11 were diagnosed postnatally, and all 11 spontaneous survivor genotypes had preserved embryonic zeta-globin levels. We compared 3 groups of patients; group 1, prenatally diagnosed and alive at hospital discharge (n = 14), group 2, prenatally diagnosed and deceased perinatally (n = 5), and group 3, postnatally diagnosed and alive at hospital discharge (n = 11). Group 1 had better outcomes than groups 2 and 3 in terms of the resolution of hydrops, delivery closer to term, shorter hospitalizations, and more frequent average or greater neurodevelopmental outcomes. Earlier IUT initiation was correlated with higher neurodevelopmental (Vineland-3) scores (r = −0.72, P = .02). Preterm delivery after IUT was seen in 3/16 (19%) patients who continued their pregnancy. When we combined our data with those from 2 published series, patients who received ≥2 IUTs had better outcomes than those with 0 to 1 IUT, including resolution of hydrops, delivery at ≥34 weeks gestation, and 5-minute appearance, pulse, grimace, activity, and respiration scores ≥7. Neurodevelopmental assessments were normal in 17/18 of the ≥2 IUT vs 5/13 of the 0 to 1 IUT group (OR 2.74; P = .01). Thus, fetal transfusions enable the survival of patients with ATM and normal neurodevelopment, even in those patients presenting with hydrops. Nondirective prenatal counseling for expectant parents should include the option of IUTs.
Insertion/deletion hotspots in the Nsp2, Nsp3, S1, and ORF8 genes of SARS-related coronaviruses
Authors: Akaishi Tetsuya , Fujiwara Kei , Ishii Tadashi 
Published: October 2022

AbstractThe genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains many insertions/deletions (indels) from the genomes of other SARS-related coronaviruses. Some of the identified indels have recently reported to involve relatively long segments of 10–300 consecutive bases and with diverse RNA sequences around gaps between virus species, both of which are different characteristics from the classical shorter in-frame indels. These non-classical complex indels have been identified in non-structural protein 3 (Nsp3), the S1 domain of the spike (S), and open reading frame 8 (ORF8). To determine whether the occurrence of these non-classical indels in specific genomic regions is ubiquitous among broad species of SARS-related coronaviruses in different animal hosts, the present study compared SARS-related coronaviruses from humans (SARS-CoV and SARS-CoV-2), bats (RaTG13 and Rc-o319), and pangolins (GX-P4L), by performing multiple sequence alignment. As a result, indel hotspots with diverse RNA sequences of different lengths between the viruses were confirmed in the Nsp2 gene (approximately 2500–2600 base positions in the overall 29,900 bases), Nsp3 gene (approximately 3000–3300 and 3800–3900 base positions), N-terminal domain of the spike protein (21,500–22,500 base positions), and ORF8 gene (27,800–28,200 base positions). Abnormally high rate of point mutations and complex indels in these regions suggest that the occurrence of mutations in these hotspots may be selectively neutral or even benefit the survival of the viruses. The presence of such indel hotspots has not been reported in different human SARS-CoV-2 strains in the last 2 years, suggesting a lower rate of indels in human SARS-CoV-2. Future studies to elucidate the mechanisms enabling the frequent development of long and complex indels in specific genomic regions of SARS-related coronaviruses would offer deeper insights into the process of viral evolution.
Characteristics and potential functional effects of long insertions in Asian butternuts
Authors: Chen Yidan , Miao Yating , Bai Weining , Lin Kui , Pang Erli 
Published: October 2022

AbstractBackgroundStructural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species.ResultsWe used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS (https://github.com/CMB-BNU/PLAINS.git), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing.ConclusionsOur study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments.
Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau
Authors: Fu Pengcheng , Favre Adrien , Wang Rui , Huang Yizhuo , Sun Shanshan 
Published: October 2022

Abstract
Background
Mountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth. Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region.

Results
Combining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species.

Conclusion
Our study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.
Spectral-domain optical coherence tomography characteristics of cystic retinal tuft
Authors: Li Haidong , Chen Lifeng , Wu Meng’ai , Zheng Bin 
Published: October 2022

Abstract
Objective
To investigate the characteristics of cystic retinal tufts (CRTs) with 55° widefield spectral-domain optical coherence tomography.

Methods
This was a retrospective study. All subjects underwent a complete ocular examination, ultra-widefield (UWF) pseudocolor fundus photography and Spectral domain optical coherence tomography (SD-OCT) with a 55° widefield lens. The SD-OCT characteristics were analyzed in subjects with CRT.

Results
Twenty-six eyes of 25 subjects were scanned and 29 CRTs were analyzed for SD-OCT characteristics. On SD-OCT images, the CRTs exhibited hyperreflective irregular elevated lesions with internal hyporeflective cystoid cavities. Normal layers of the neuroepithelium could not be distinguished. The mean diameter of CRTs was 1022 microns (range, 117–3711 microns; standard deviation, 815 microns). There was vitreoretinal traction at the apex of CRTs. Among them, retinal tears in 24.14% (7/29), suspected retinal tears in 27.59% (8/29), and shallow neuroepithelium detachment in 31.03% (9/29).

Conclusions
The widefield SD-OCT imaging can provide detailed cross-sectional anatomic information of CRT and may guide clinical treatment.
Are perinatal measures associated with adolescent mental health? A retrospective exploration with original data from psychiatric cohorts
Authors: Basedow Lukas A. , Kuitunen-Paul Sören , Roessner Veit , Moll Gunther H. , Golub Yulia , Eichler Anna 
Published: October 2022

Abstract
Background
Perinatal markers of prenatal development are associated with offspring psychiatric symptoms. However, there is little research investigating the specificity of perinatal markers for the development of specific disorders. This study aimed to explore if perinatal markers are specifically associated with adolescent substance use disorder (SUDs).

Methods
Adolescent participants from two study centers, one for SUD patients (n = 196) and one for general psychopathology (n = 307), were recruited for participation. Since the SUD participants presented with a number of comorbid disorders, we performed a 1-on-1 matching procedure, based on age, gender, and specific pattern of comorbid disorders. This procedure resulted in n = 51 participants from each group. From all participants and their mothers we recorded perinatal markers (mode of birth, weeks of completed pregnancy, birth weight, Apgar score after 5 min) as well as intelligence quotient (IQ). The SUD sample additionally filled out the Youth Safe Report (YSR) as well as the PQ-16 and the DUDIT. We aimed to distinguish the two groups (SUD sample vs. general psychiatric sample) based on the perinatal variables via a logistic regression analysis. Additionally, linear regressions were performed for the total group and the subgroups to assess the relationship between perinatal variables and IQ, YSR, DUDIT and PQ-16.

Results
The perinatal variables were not able to predict group membership (X2 [4] = 4.77, p = .312, Cox & Snell R² = 0.053). Odds ratios indicated a small increase in probability to belonging to the general psychiatric sample instead of the SUD sample if birth was completed via C-section. After Bonferroni-correction, the linear regression models showed no relation between perinatal markers and IQ (p = .60, R² = 0.068), YSR (p = .09, R² = 0.121), DUDIT (p = .65, R² = 0.020), and PQ-16 (p = .73, R² =0.021).

Conclusion
Perinatal markers were not able to distinguish SUD patients from patients with diverse psychopathologies. This pattern contradicts previous findings, perhaps because our chosen markers reflect general processes instead of specific mechanistic explanations. Future studies should take care to investigate specific prenatal markers and associate them with psychopathology on the symptom level.
The development and validation of a family functioning measure for Aboriginal and Torres Strait Islander adults
Authors: Brinckley Makayla-May , Jones Roxanne , Batterham Philip J. , Calear Alison L. , Lovett Raymond 
Published: October 2022

Abstract
Background
Family and kinship networks are a key aspect of culture for Aboriginal and Torres Strait Islander peoples from Australia. They are intrinsically connected to good health and wellbeing, and cultural knowledge exchange. However, despite the known importance of family and kinship networks in Aboriginal and Torres Strait Islander cultures, and the move towards family-centred approaches in healthcare service provision, there is no validated, national measure of family functioning for Aboriginal and Torres Strait Islander peoples. A valid tool to measure family functioning is necessary in order to better understand what fosters good family functioning, and to inform and develop programs and healthcare interventions.

Methods
Mayi Kuwayu: the National Study of Aboriginal and Torres Strait Islander Wellbeing is a longitudinal cohort study of Aboriginal and Torres Strait Islander adults aged 16 years and over. An existing family functioning scale was modified for use in the Mayi Kuwayu Study to measure family functioning at the national Aboriginal and Torres Strait Islander population level. This study used a national sample of Aboriginal and Torres Strait Islander adults (N = 8705, ≥16 years) for the psychometric assessment of the modified Mayi Kuwayu Study Family Functioning Measure. This involved face validity, acceptability, internal consistency/reliability, construct validity, and convergent and divergent validity testing.

Results
Participants in this study were 8705 Aboriginal and Torres Strait Islander peoples, with a mean age of 48 years, who primarily live in regional Australia (47.3%). The Mayi Kuwayu Family Functioning Measure demonstrated face validity for family functioning and had good internal consistency/reliability (Cronbach’s alpha > 0.90). Construct validity results were mixed, with an indication of uni-dimensionality (with one component explaining 59.5% of variance), but some item redundancy and inconsistency in responding patterns among groups of respondents. Balancing psychometric properties with Aboriginal and Torres Strait Islander expert and end-user feedback of the measure indicate that the full scale should be retained. Finally, the measure demonstrated strong convergent and divergent validity, with prevalence ratios exhibiting dose-response relationships between family functioning and conceptually related outcomes (convergent validity) and conceptually unrelated outcomes (divergent validity).

Conclusion
The Mayi Kuwayu Family Functioning Measure is a valid measure of family functioning in the Aboriginal and Torres Strait Islander adult population.
All-cause mortality risk in older patients with femoral neck fracture
Authors: Li Xin-ping , Zhang Ping , Zhu Shi-wen , Yang Ming-hui , Wu Xin-bao , Jiang Xie-yuan 
Published: October 2022

Abstract
Introduction
The mortality rate after hip fracture is high. However, the 1-year mortality rate after femoral intertrochanteric fracture and femoral neck fracture differs (Gibson-Smith D, Klop C, Elders PJ, Welsing PM, van Schoor N, Leufkens HG, et al., Osteoporos Int 25:2555-2563, 2014), although both are types of hip fracture. A previous real-world single-center prospective cohort study showed that older age and high Charlson comorbidity index score were risk factors for femoral intertrochanteric fracture. Additionally, therapy with zoledronic acid 5 mg (Aclasta) was a protective factor (Li XP, Zhang P, Zhu SW, Yang MH, Wu XB, Jiang XY, J Orthop Surg Res. 16:727, 2021). We wished to determine the risk factors for all-cause mortality in femoral neck fracture patients.

Aim
To identify the risk factors for postoperative all-cause mortality in aged patients with femoral neck fracture.

Materials and methods
We enrolled 307 aged patients with femoral neck fracture; 38 were lost to follow-up after 2–3 years. The patients’ general characteristics, bone mineral density, and anti-osteoporosis treatment after operation were recorded as potential risk factors. Kaplan–Meier curves and multivariate Cox proportional hazards models were constructed to analyze the influence of each factor on all-cause mortality.

Results
This was a real-world single-center prospective cohort study showing that (1) most of the patients who died were male, older (mean age of the patients who died: 84.8 years vs. 77.9 years for survivors), and had more comorbidities compared with surviving patients. Previous fracture history, body mass index, femoral neck T score, hemoglobin and 25-hydroxy vitamin D levels did not differ significantly between patients who died vs. survived. (2) Differing from patients with intertrochanteric fractures, older patients with femoral neck fracture experienced no reduction in all-cause mortality with treatment with zoledronic acid.

Conclusion
In Chinese patients with femoral neck fracture, physicians should pay careful attention to male patients, older patients, and those with high numbers of comorbidities.
Short-term efficacy and adverse effects of collagenase clostridium histolyticum injections, percutaneous needle fasciotomy and limited fasciectomy in the treatment of Dupuytren’s contracture: a network meta-analysis of randomized controlled trials
Authors: Obed Doha , Salim Mustafa , Schlottmann Frederik , Bingoel Alperen S. , Panayi Adriana C. , Dastagir Khaled , Vogt Peter M. , Koenneker Soeren 
Published: October 2022

Abstract
Aims
Dupuytren’s contracture (DC) is a chronic debilitating fibroproliferative disorder.
Common treatment options include collagenase clostridium histolyticum injections (CI), percutaneous needle fasciotomy (NF) and limited fasciectomy (LF). Superiority of one specific treatment remains controversial. This study aims to assess the short-term efficacy and safety of CI, NF, and LF for the treatment of DC.

Methods
We included randomized controlled trials of CI compared with placebo, NF and LF for patients with DC. PubMed, Embase and the Cochrane Library were searched from inception to August 2021. Contracture reduction rates in treated joints (within 0–5° of full extension within 30 days), relative reduction in total passive extension deficit (TPED), occurrence of one or more adverse events and number of treatment-related adverse events per patient were the outcomes of interest. The Cochrane risk-of-bias tool was employed for quality assessment of the studies. A network meta-analysis was performed using MetaXL.

Results
Nine studies met our inclusion criteria (n = 903). Overall, risk bias was mixed and mostly low. Short term TPED reduction achieved with LF was superior compared to CI and NF. Although CI achieved greater TPED reduction compared to NF, it was associated with the highest risk of overall adverse effects. The analyzed data was limited to a maximum three-year follow-up period and therefore insufficient for long-term outcome evaluation.

Conclusions
In DC, LF may be able to provide patients with severe disease, superior flexion contracture release postoperatively. CI is a valid treatment alternative to NF, however the higher risk of overall adverse effects must be considered. The quality-of-evidence is limited due to short-term follow-up periods and a lack of standardized definitions of complications and adverse events.
Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism
Authors: Liu Xuanzeng , Majid Muhammad , Yuan Hao , Chang Huihui , Zhao Lina , Nie Yimeng , He Lang , Liu Xiaojing , He Xiaoting , Huang Yuan 
Published: October 2022

Abstract
Background
Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis♀1C = 6.60 pg, Angaracris rhodopa♀1C = 16.36 pg) to ascertain the influence of piRNAs.

Results
We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria, and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level.

Conclusions
Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.