bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis and molecular dissection of the SPL gene family in Fraxinus mandshurica
Authors: He Biying , Gao Shangzhu , Lu Han , Yan Jialin , Li Caihua , Ma Minghao , Wang Xigang , Chen Xiaohui , Zhan Yaguang , Zeng Fansuo 
Published: September 2022

Abstract
Background
SQUAMOSA promoter binding protein-like (SPL) is a unique family of transcription factors in plants, which is engaged in regulating plant growth and development, physiological and biochemical processes. Fraxinus mandshurica is an excellent timber species with a wide range of uses in northeastern China and enjoys a high reputation in the international market. SPL family analysis has been reported in some plants while SPL family analysis of Fraxinus mandshurica has not been reported.

Results
We used phylogeny, conserved motifs, gene structure, secondary structure prediction, miR156 binding sites, promoter cis elements and GO annotation to systematically analyze the FmSPLs family. This was followed by expression analysis by subcellular localization, expression patterns at various tissue sites, abiotic stress and hormone induction. Because FmSPL2 is highly expressed in flowers it was selected to describe the SPL gene family of Fraxinus mandshurica by ectopic expression. Among them, 10 FmSPL genes that were highly expressed at different loci were selected for expression analysis under abiotic stress (NaCl and Cold) and hormone induction (IAA and ABA). These 10 FmSPL genes showed corresponding trends in response to both abiotic stress and hormone induction. We showed that overexpression of FmSPL2 in transgenic Nicotiana tabacum L. resulted in taller plants, shorter root length, increased root number, rounded leaves, and earlier flowering time.

Conclusions
We identified 36 SPL genes, which were classified into seven subfamilies based on sequence analysis. FmSPL2 was selected for subsequent heterologous expression by analysis of expression patterns in various tissues and under abiotic stress and hormone induction, and significant phenotypic changes were observed in the transgenic Nicotiana tabacum L. These results provide insight into the evolutionary origin and biological significance of plant SPL. The aim of this study was to lay the foundation for the genetic improvement of Fraxinus mandshurica and the subsequent functional analysis of FmSPL2.
BGFD: an integrated multi-omics database of barley gene families
Authors: Li Tingting , Bian Jianxin , Tang Minqiang , Shangguan Hongbin , Zeng Yan , Luo Ruihan , Sun Huifan , Ke Qinglin , Nie Xiaojun , Li Yihan , Cui Licao 
Published: September 2022

Abstract
Background
A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history.

Results
We constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable.

Conclusions
BGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.
Veterans’ ambulatory care experience during COVID-19: veterans’ access to and satisfaction with primary care early in the pandemic
Authors: Thomas Brice , Thadani Aanchal , Chen Patricia V. , Christie Israel C. , Kern Lisa M. , Rajan Mangala , Kadiyala Himabindu , Helmer Drew A. 
Published: September 2022

Abstract
Background
The COVID-19 pandemic caused widespread changes to healthcare, but few studies focus on ambulatory care during the early phase of the pandemic. We characterize veterans’ ambulatory care experience, specifically access and satisfaction, early in the pandemic.

Methods
We employed a semi-structured telephone interview to capture quantitative and qualitative data from patients scheduled with a primary care provider between March 1 – June 30, 2020. Forty veterans were randomly identified at a single large urban Veterans Health Administration (VHA) medical center. The interview guide utilized 56 closed and open-ended questions to characterize veterans’ perceptions of access to and satisfaction with their primary care experience at VHA and non-VHA primary care sources. We also explored the context of veterans' daily lives during the pandemic. We analyzed quantitative data using descriptive statistics and verbatim quotes using a matrix analysis.

Results
Veterans reported completing more appointments (mean 2.6 (SD 2.2)) than scheduled (mean 2.3 (SD 2.2)) mostly due to same-day or urgent visits, with a shift to telephone (mean 2.1 (SD 2.2)) and video (mean 1.5 (SD 0.6)). Among those who reported decreased access to care early in the pandemic (n = 27 (67%)), 15 (56%) cited administrative barriers (“The phone would hang up on me”) and 9 (33%) reported a lack of provider availability (“They are not reaching out like they used to”). While most veterans (n = 31 (78%)) were highly satisfied with their VHA care (mean score 8.6 (SD 2.0 on a 0–10 scale), 9 (23%) reported a decrease in satisfaction since the pandemic. The six (15%) veterans who utilized non-VHA providers during the period of interest reported, on average, higher satisfaction ratings (mean 9.5 (SD 1.2)).
Many veterans reported psychosocial effects such as the worsening of mental health (n = 6 (15%)), anxiety concerning the virus (n = 12 (30%)), and social isolation (n = 8 (20%), “I stay inside and away from people”).

Conclusions
While the number of encounters reported suggest adequate access and satisfaction, the comments regarding barriers to care suggest that enhanced approaches may be warranted to improve and sustain veteran perceptions of adequate access to and satisfaction with primary care during times of crisis.
Prediction of physical functioning and general health status trajectories on mortality among persons with cognitive impairment
Authors: Zang Emma , Wang Xueqing , Shi Yu , Wu Bei , Fried Terri R. 
Published: September 2022

Abstract
Background
The concern posed by the confluence of aging and cognitive impairment is growing in importance as the U.S. population rapidly ages. As such, we sought to examine the predictive power of physical functioning (PF) and general health status (GHS) trajectories on mortality outcomes among persons with cognitive impairment (PCIs).

Methods
We used group-based trajectory models to identify latent group memberships for PF trajectories in 1,641 PCIs and GHS trajectories in 2,021 PCIs from the National Health and Aging Trends Survey (2011–2018) and applied logistic regressions to predict mortality using these memberships controlling for individual characteristics.

Results
We identified six trajectory groups for PF and four groups for GHS. Trajectory group memberships for both outcomes significantly predicted mortality. For PF, group memberships largely captured the average levels over time, and worse trajectories (i.e., lower baselines and faster declines) were associated with higher odds of death. The highest mortality risk was associated with the group experiencing a sharp decline early in its PF trajectory, although its average level across time was not the lowest. For GHS, we observed two groups with comparable average levels across time, but the one with a convex-shape trajectory had much higher mortality risks compared to the one with a concave-shape trajectory.

Conclusions
Our findings highlighted that health trajectories predicted mortality among PCIs, not only because of general levels but also because of the shapes of declines. Close monitoring health deterioration of PCIs is crucial to understand the health burden of this population and to make subsequent actions.
Long-term quantitative assessment of anti-SARS-CoV-2 spike protein immunogenicity (QUASI) after COVID-19 vaccination in older people living with HIV (PWH)
Authors: Tuan Jessica J. , Zapata Heidi , Barakat Lydia , Andrews Laurie , Behnegar Anousheh , Kim Yee Won , Kayani Jehanzeb , Mutic Suzana , Ryall Linda , Turcotte Barbara , Critch-Gilfillan Terese , Zhao Min , Salahuddin Syim , Gupta Shaili , Sutton Richard , Friedland Gerald , Emu Brinda , Ogbuagu Onyema 
Published: September 2022

Abstract
Background
The durability of immune responses to COVID-19 vaccines among older people living with HIV (PWH) is clinically important.

Methods
We aimed to assess vaccine-induced humoral immunity and durability in older PWH (≥ 55 years, n = 26) over 6 months (post-initial BNT162b2 series). A secondary and exploratory objective was to assess T-cell response and BNT162b2 booster reactogenicity, respectively. Our Visit 1 (3 weeks post-initial BNT162b2 dose) SARS-CoV-2 humoral immunity results are previously reported; these subjects were recruited for Visit 2 [2 weeks (+ 1 week window) post-second vaccination] and Visit 3 [6 months (± 2 week window) post-initial vaccination] in a single-center longitudinal observational study. Twelve participants had paired Visit 2/3 SARS-CoV-2 Anti-Spike IgG data. At Visit 3, SARS-CoV-2 Anti-Spike IgG testing occurred, and 5 subjects underwent T-cell immune response evaluation. Thereafter, subjects were offered BNT162b2 booster (concurrent day outside our study) per US FDA/CDC guidance; reactogenicity was assessed. The primary study outcome was presence of detectable Visit 3 SARS-CoV-2 Anti-Spike-1-RBD IgG levels. Secondary and exploratory outcomes were T-cell immune response and BNT162b2 booster reactogenicity, respectively. Wilcoxon signed-rank tests analyzed median SARS-CoV-2 Anti-Spike IgG 6-month trends.

Results
At Visit 3, 26 subjects underwent primary analysis with demographics noted: Median age 61 years; male n = 16 (62%), female n = 10 (38%); Black n = 13 (50%), White n = 13 (50%). Most subjects (n = 20, 77%) had suppressed HIV viremia on antiretroviral therapy, majority (n = 24, 92%) with CD4 > 200 cells/µL. At Visit 3, 26/26 (100%) had detectable Anti-Spike-1-RBD (≥ 0.8 U/mL). Among 12 subjects presenting to Visit 2/3, median SARS-CoV-2 Anti-Spike 1-RBD was 2087 U/mL at Visit 2, falling to 581.5 U/mL at Visit 3 (p = 0.0923), with a median 3.305-fold decrease over 6 months. Among subjects (n = 5) with 6-month T-cell responses measured, all had detectable cytokine-secreting anti-spike CD4 responses; 3 had detectable CD4 + Activation induced marker (AIM) + cells. Two had detectable cytokine-secreting CD8 responses, but all had positive CD8 + AIM + cells.

Conclusions
Among older PWH, SARS-CoV-2 Anti-Spike IgG and virus-specific T-cell responses are present 6 months post-primary BNT162b2 vaccination, and although waning, suggest retention of some degree of long-term protective immunity.
SARS-CoV-2 in dialysis patients and the impact of vaccination
Authors: Moore Louise Rachel , Al-Jaddou Noor , Wodeyar Harsha , Sharma Asheesh , Schulz Michael , Rao Anirudh , Abraham Kottarathil 
Published: September 2022

Abstract
Background
In centre haemodialysis (ICHD) patients have been identified as high risk of contracting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection due to frequent healthcare contact and poor innate and adaptive immunity. Our ICHD patients were offered immunisation from January 2021. We aimed to assess outcomes following SARS-CoV-2 infection and report on the effect of vaccination in our ICHD patients.

Methods
Demographics, SARS-CoV-2 status, hospitalisation, mortality and vaccination status were analysed. From 11th March 2020 to 31st March 2021, 662 ICHD patients were included in the study and these patients were then followed up until 31st August 2021.

Results
SARS-CoV-2 infection occurred in 28.4% with 51.1% of them requiring hospitalisation in contrast to community infection rates of 13.9% and hospitalisation of 9.0%. 28-day mortality was 19.2% in comparison to 1.9% of the community. Mortality increased to 34.0% over the study period. Mortality over the study period was 1.8 times in infected patients (HR 1.81 (1.32–2.49) P < 0.001) despite adjustment for age, gender and ethnicity. 91.3% of ICHD patients have now received both doses of SARS-CoV-2 vaccinations.

Conclusions
ICHD patients are at increased risk of acquiring SARS-CoV-2, with increased rates of hospitalisation and mortality. The increased mortality extends well beyond the 28 days post-infection and persists in those who have recovered. Peaks and troughs in infection rates mirrored community trends. Preliminary data indicates that the SARS-CoV-2 vaccination provides protection to ICHD patients, with ICHD case rates now comparable to that of the local population.
Group antenatal care (gANC) for Somali-speaking women in Sweden – a process evaluation
Authors: Ahrne Malin , Byrskog Ulrika , Essén Birgitta , Andersson Ewa , Small Rhonda , Schytt Erica 
Published: September 2022

Abstract
Background
Language supported group antenatal care (gANC) for Somali-born women was implemented in a Swedish public ANC clinic. The women were offered seven 60-min sessions, facilitated by midwives and starting with a presentation of a selected topic, with an additional 15-min individual appointment before or after. The aim of this study was to assess the feasibility for participants and midwives of implementing The Hooyo (“mother” in Somali) gANC intervention, including implementation, mechanisms of impact and contextual factors.

Methods
A process evaluation was performed, using The Medical Research Council (MRC) guidelines for evaluating complex interventions as a framework. A range of qualitative and quantitative data sources were used including observations (n = 9), complementary, in-depth and key-informant interviews (women n = 6, midwives n = 4, interpreters and research assistants n = 3) and questionnaire data (women n = 44; midwives n = 8).

Results
Language-supported gANC offered more comprehensive ANC that seemed to correspond to existing needs of the participants and could address knowledge gaps related to pregnancy, birth and the Swedish health care system. The majority of women thought listening to other pregnant women was valuable (91%), felt comfortable in the group (98%) and supported by the other women (79%), and they said that gANC suited them (79%). The intervention seemed to enhance knowledge and cultural understanding among midwives, thus contributing to more women-centred care. The intervention was not successful at involving partners in ANC.

Conclusions
The Hooyo gANC intervention was acceptable to the Somali women and to midwives, but did not lead to greater participation by fathers-to-be. The main mechanisms of impact were more comprehensive ANC and enhanced mutual cultural understanding. The position of women was strengthened in the groups, and the way in which the midwives expanded their understanding of the participants and their narratives was promising. To be feasible at a large scale, gANC might require further adaptations and the “othering” of women in risk groups should be avoided.

Trial registration
The study was registered in ClinicalTrials.gov (Identifier: NCT03879200).
Collagen fiber features and COL1A1: are they associated with elastic parameters in breast lesions, and can COL1A1 predict axillary lymph node metastasis?
Authors: Jiang Ying , Wang Bo , Li Jun Kang , Li Shi Yu , Niu Rui Lan , Fu Nai Qin , Zheng Jiao Jiao , Liu Gang , Wang Zhi Li 
Published: September 2022

Abstract
Background
This study aimed to explore whether collagen fiber features and collagen type I alpha 1 (COL1A1) are related to the stiffness of breast lesions and whether COL1A1 can predict axillary lymph node metastasis (LNM).

Methods
Ninety-four patients with breast lesions were consecutively enrolled in the study. Amongst the 94 lesions, 30 were benign, and 64 were malignant (25 were accompanied by axillary lymph node metastasis). Ultrasound (US) and shear wave elastography (SWE) were performed for each breast lesion before surgery. Sirius red and immunohistochemical staining were used to examine the shape and arrangement of collagen fibers and COL1A1 expression in the included tissue samples. We analyzed the correlation between the staining results and SWE parameters and investigated the effectiveness of COL1A1 expression levels in predicting axillary LNM.

Results
The optimal cut-off values for Emax, Emean, and Eratio for diagnosing the benign and malignant groups, were 58.70 kPa, 52.50 kPa, and 3.05, respectively. The optimal cutoff for predicting axillary LNM were 107.5 kPa, 85.15 kPa, and 3.90, respectively. Herein, the collagen fiber shape and arrangement features in breast lesions were classified into three categories. One-way analysis of variance (ANOVA) showed that Emax, Emean, and Eratio differed between categories 0, 1, and 2 (P < 0.05). Meanwhile, elasticity parameters were positively correlated with collagen categories and COL1A1 expression. The COL1A1 expression level > 0.145 was considered the cut-off value, and its efficacy in benign and malignant breast lesions was 0.808, with a sensitivity of 66% and a specificity of 90%. Furthermore, when the COL1A1 expression level > 0.150 was considered the cut-off, its efficacy in predicting axillary LNM was 0.796, with sensitivity and specificity of 96% and 59%, respectively.

Conclusions
The collagen fiber features and expression levels of COL1A1 positively correlated with the elastic parameters of breast lesions. The expression of COL1A1 may help diagnose benign and malignant breast lesions and predict axillary LNM.
Different visual evoked potentials in neuromyelitis optica spectrum disorder-related optic neuritis and idiopathic demyelinating optic neuritis: a prospective longitudinal analysis
Authors: Zheng Cong , Wang Ling , Xu Xiaoyu , Zhou Manli , Liu Kaiqun , Zhang Yuxin , Zhao Xiujuan , Lu Lin , Qiu Wei , Zhang Xinyu , Yang Hui 
Published: September 2022

Abstract
Background
To investigate different visual evoked potential (VEP) patterns in neuromyelitis optica spectrum disorder-related optic neuritis (NMOSD-ON) and idiopathic demyelinating optic neuritis (IDON).

Methods
This was a longitudinal, prospective, case-control study. Eighty-four Chinese patients with acute optic neuritis were enrolled, including 26 NMOSD-ON patients and 58 IDON patients. All the patients underwent best-corrected visual acuity (BCVA) and full-field pattern reversal VEP recordings at the onset, 1 month, 3 months, and 6 months.

Results
Within 15′ checks, the NMOSD-ON patients had more severe VEP amplitude reduction at 6 months (2.39 ± 4.63 μV vs. 6.96 ± 8.88 μV, P = 0.034). However, the IDON patients showed more frequently normal VEP response at 3 months (24.0% vs. 4.5%, P = 0.017), and only prolonged P100 peak latency with normal amplitude (L) at 6 months (30.0% vs. 57.8%, P = 0.048). Within 60′ checks, no significant difference in VEP parameters between the two groups was found at each follow-up (P > 0.05).

Conclusions
The NMOSD-ON patients showed more severe axonal damage and worse axonal recovery than the IDON patients. VEP elicited by smaller check size was more sensitive to visual pathway abnormality in NMOSD-ON.
Clinical outcomes of new multifocal intraocular lenses with hydroxyethyl methacrylate and comparative results of contrast sensitivity, objective scatter, and subjective photic phenomena
Authors: Lee Yong Woo , Choi Chul Young , Moon Kun , Jeong Yong Jin , An Sang Il , Lee Je Myung , Lee Jong Ho , Seong Min Cheol 
Published: September 2022

Abstract
Background
We investigate the performance of new hydrophobic diffractive multifocal intraocular lenses (IOL) with hydroxyethyl methacrylate (HEMA) and compare their optical quality, contrast sensitivity, and subjective photic phenomena.

Methods
Medical records of patients who underwent routine simple cataract surgery and insertion of an existing multifocal IOL (TFNT, TF group) or a new multifocal IOL (CNWT, CN group) were retrospectively reviewed. Clinical data was collected 2 months postoperatively and included optical quality analysis system (OQAS) indices, contrast sensitivity, and subjective degrees of photic phenomena.

Results
One hundred thirty-five eyes of 135 patients were included (CN group, 71; TF group, 64). There was no significant difference between the two groups in the visual acuity and defocus curve. The indices of OQAS did not show a significant difference between groups. Contrast sensitivity was significantly better in the CN group at all degrees, including the area under the log contrast sensitivity function (p = 0.01). The subjective photic phenomena survey showed better results for the CN group, with the proportion of patients reporting no photic phenomena as 9.9% and 3.1% in the CN and TF groups, respectively. The proportion of patients who reported severe photic phenomena was 11.3% in the CN group and 25.0% in the TF group. Although the follow-up period was only 2 months, glistening, surface scattering, and posterior capsule opacity were not observed in any patient.

Conclusions
The new multifocal IOL with HEMA is safe, and provides stable visual acuity as well as superior contrast sensitivity and lower subjective photic phenomena, over the prior IOL.