bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of a Stable PSI–PSII Megacomplex in Rice That Conducts Energy Spillover
Authors: Kim Eunchul , Yokono Makio , Tsugane Kazuo , Ishii Asako , Noda Chiyo , Minagawa Jun 
Published: May 2023

Abstract
In green plants, photosystem I (PSI) and photosystem II (PSII) bind to their respective light-harvesting complexes (LHCI and LHCII) to form the PSI−LHCI supercomplex and the PSII−LHCII supercomplex, respectively. These supercomplexes further form megacomplexes, like PSI−PSII and PSII−PSII in Arabidopsis (Arabidopsis thaliana) and spinach to modulate their light-harvesting properties, but not in the green alga Chlamydomonas reinhardtii. Here, we fractionated and characterized the stable rice PSI−PSII megacomplex. The delayed fluorescence from PSI (lifetime ∼25 ns) indicated energy transfer capabilities between the two photosystems (energy spillover) in the rice PSI−PSII megacomplex. Fluorescence lifetime analysis revealed that the slow PSII to PSI energy transfer component was more dominant in the rice PSI−PSII supercomplexes than in Arabidopsis ones, suggesting that PSI and PSII in rice form a megacomplex not directly but through LHCII molecule(s), which was further confirmed by the negatively stained electron microscopy analysis. Our results suggest species diversity in the formation and stability of photosystem megacomplexes, and the stable PSI–PSII supercomplex in rice may reflect its structural adaptation.
In vivo noninvasive mitochondrial redox assessment of the optic nerve head to predict disease
Authors: Cakir Bertan , Tomita Yohei , Yagi Hitomi , Romfh Padraic , Allen William , Ko Minji , Chen Peili , Fu Zhongjie , Vakhshoori Daryoosh , Smith Lois E H 
Published: May 2023

Abstract
Eye diseases are diagnosed by visualizing often irreversible structural changes occurring late in disease progression, such as retinal ganglion cell loss in glaucoma. The retina and optic nerve head have high mitochondrial energy need. Early mitochondrial/energetics dysfunction may predict vulnerability to permanent structural changes. In the in vivo murine eye, we used light-based resonance Raman spectroscopy (RRS) to assess noninvasively the redox states of mitochondria and hemoglobin which reflect availability of electron donors (fuel) and acceptors (oxygen). As proof of principle, we demonstrated that the mitochondrial redox state at the optic nerve head correlates with later retinal ganglion loss after acute intraocular pressure (IOP) elevation. This technology can potentially map the metabolic health of eye tissue in vivo complementary to optical coherence tomography, defining structural changes. Early detection (and normalization) of mitochondrial dysfunction before irreversible damage could lead to prevention of permanent neural loss.
White-matter abnormalities and cognitive dysfunction are linked to astrocyte activation in sickle mice
Authors: Hazra Rimi , Pu Hongjian , Foley Lesley M , Little-Ihrig Lynda , Hitchens T Kevin , Ghosh Samit , Ofori-Acquah Solomon F , Hu Xiaoming , Novelli Enrico M 
Published: May 2023

Abstract
White-matter injury in sickle-cell disease (SCD) includes silent cerebral infarction diagnosed by diffusion tensor imaging (DTI), a complication associated with cognitive dysfunction in children with SCD. The link between white-matter injury and cognitive dysfunction has not been fully elucidated. The goal of this study was to define whether cerebrovascular lesions and cognitive function in SCD are linked to neuroaxonal damage and astrocyte activation in humanized Townes’ SCD mice homozygous for human sickle hemoglobin S (SS) and control mice homozygous for human normal hemoglobin A (AA). Mice underwent MRI with DTI and cognitive testing, and histology sections from their brains were stained to assess microstructural tissue damage, neuroaxonal damage, and astrocyte activation. Fractional anisotropy, showing microstructural cerebrovascular abnormalities identified by DTI in the white matter, was significantly associated with neuronal demyelination in the SS mouse brain. SS mice had reduced learning and memory function with a significantly lower discrimination index compared with AA control mice in the novel object recognition tests. Neuroaxonal damage in the SS mice was synchronously correlated with impaired neurocognitive function and activation of astrocytes. The interplay between astrocyte function and neurons may modulate cognitive performance in SCD.
The best practice for microbiome analysis using R
Authors: Wen Tao , Niu Guoqing , Chen Tong , Shen Qirong , Yuan Jun , Liu Yong-Xin 
Published: May 2023

AbstractWith the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.
The impact of the COVID-19 pandemic on referrals to musculoskeletal services from primary care and subsequent incidence of inflammatory rheumatic musculoskeletal disease: an observational study
Authors: Burton Claire , Bajpai Ram , Mason Kayleigh J , Bailey James , Jordan Kelvin P , Mallen Christian D , Welsh Victoria K 
Published: May 2023

Abstract

Objective
The aim was to describe the impact of the COVID-19 pandemic upon referral patterns and incident diagnosis of inflammatory rheumatic and musculoskeletal diseases (iRMDs).

Methods
UK primary care data were used to describe referral patterns for patients with musculoskeletal conditions. Trends in referrals to musculoskeletal services and incident diagnoses of iRMDs (specifically, RA and JIA) were described using Joinpoint Regression and comparisons made between key pandemic time periods.

Results
The incidence of RA and JIA reduced by −13.3 and −17.4% per month, respectively, between January 2020 and April 2020, then increased by 1.9 and 3.7% per month, respectively, between April 2020 and October 2021. The incidence of all diagnosed iRMDs was stable until October 2021. Referrals decreased between February 2020 and May 2020 by −16.8% per month from 4.8 to 2.4% in patients presenting with a musculoskeletal condition. After May 2020, referrals increased significantly (16.8% per month) to 4.5% in July 2020. The time from first musculoskeletal consultation to RA diagnosis and from referral to RA diagnosis increased in the early pandemic period [rate ratio (RR) 1.11, 95% CI 1.07, 1.15 and RR 1.23, 95% CI 1.17, 1.30, respectively] and remained consistently higher in the late pandemic period (RR 1.13, 95% CI 1.11, 1.16 and RR 1.27, 95% CI 1.23, 1.32, respectively), compared with the pre-COVID-19 pandemic period.

Conclusion
Patients with underlying RA and JIA that developed during the pandemic might be yet to present or might be in the referral and/or diagnostic process. Clinicians should remain alert to this possibility, and commissioners should be aware of these findings, enabling the appropriate planning and commissioning of services.
Safety of the JAK and TNF inhibitors in rheumatoid arthritis: real world data from the Hong Kong Biologics Registry
Authors: Mok Chi Chiu , So Ho , Yim Cheuk Wan , To Chi Hung , Lao Weng Nga , Wong Stella Pui Yan , Ng Hoi Yan , Lee Jolly Man Yee , Lee Patrick Man Leung , Ying Shirley King Yee , Leung Moon Ho , Ho Carmen Tze Kwan 
Published: May 2023

Abstract

Objectives
To compare the incidence of major adverse cardiovascular events (MACEs), cancer and infective complications in RA patients using Janus kinase (JAKis) and TNF (TNFis) inhibitors.

Method
A retrospective analysis of data from the Hong Kong Biologics Registry 2008–2021 was performed. RA patients who had ever used JAKis or TNFis were included. The incidence of MACEs, cancer and infections were compared between the two groups, with adjustment for confounding factors.

Results
A total of 2471 courses of JAKis (n = 551) and TNFis (n = 1920) were used in 1732 RA patients (83.7% women, age 53.8 [12.5] years; follow-up 6431 patient-years). JAKi users had significantly older age, more atherosclerotic risk factors and higher frequency of past malignancies. A total of 15 and 40 MACEs developed in the JAKi and TNFi users, respectively (incidence 1.34 vs 0.75 per 100 patient-years; P = 0.22). There was no significant difference in the incidence of cancers between the two groups (0.81 [JAKi] vs 0.85 [TNFi] per 100 patient-years; P = 0.25). The adjusted hazard ratios of MACE and cancer in the JAKi users were 1.36 (95% CI: 0.62, 2.96) (P = 0.44) and 0.87 (95% CI: 0.39, 1.95) (P = 0.74), respectively. Rates of infections were significantly higher in the JAKi than TNFi users (16.3 vs 9.9 per 100 patient-years; P = 0.02), particularly herpes zoster (3.49 vs 0.94 per 100 patient-years; P &lt; 0.001).

Conclusions
In a real-life setting, there is no increase in MACEs or cancers in users of JAKis compared with TNFis. However, the incidence of non-serious infections, including herpes zoster, was increased in users of JAKis.
Large muscle group movements during sleep in healthy people: normative values and correlation to sleep features
Authors: Ibrahim Abubaker , Ferri Raffaele , Cesari Matteo , Frauscher Birgit , Heidbreder Anna , Bergmann Melanie , Högl Birgit , Stefani Ambra 
Published: May 2023

Abstract

Study Objectives
To investigate the frequency and characteristics of large muscle group movements (LMMs) during sleep in healthy adults.

Methods
LMMs were scored following the International Restless Legs Syndrome Study Group criteria in 100 healthy participants aged 19–77 years. A LMM was defined as a temporally overlapping increase in EMG activity and/or the occurrence of movement artifacts in at least two channels. LMM indices and durations in total sleep time (TST), NREM and REM sleep, and association with arousals, awakenings, and/or respiratory events were calculated. Correlations of LMMs indices and durations with sleep architecture, respiratory and motor events, and subjective sleep quality were investigated.

Results
Median LMMs index in TST was 6.8/h (interquartile range (IQR), 4.5–10.8/h), median mean duration 12.4 s (IQR 10.7–14.4 s). Mean LMMs duration was longer in NREM (median 12.7 s, IQR 11.1–15.2 s) versus REM sleep (median 10.3 s, IQR 8.0–13.5s), p &lt; 0.001. LMMs associated with awakening increased with age (p = 0.029). LMMs indices in TST were higher in men than women (p = 0.018). LMMs indices correlated positively with N1 sleep percentage (ρ = 0.49, p &lt; 0.001), arousal index (ρ = 0.40, p = 0.002), sleep stages shift index (ρ = 0.43, p &lt; 0.001, apnea index (ρ = 0.36, p = 0.017), and video-visible movements indices (ρ = 0.45, p &lt; 0.001), and negatively with N3 sleep (ρ = −0.38, p= 0.004) percentage.

Conclusions
This is the first study providing normative data on LMMs frequency in healthy adults. LMMs are a ubiquitous phenomenon often associated with other events. Correlation with arousals and respiratory events suggests a potential clinical significance of LMMs in adults that awaits further investigation.
Predicting fecal composition, intake, and nutrient digestibility in beef cattle consuming high forage diets using near infrared spectroscopy
Authors: Peters Jenilee F , Swift Mary L , Penner Gregory B , Lardner Herbert A , McAllister Tim A , Ribeiro Gabriel O 
Published: May 2023

Abstract
The objective of this study was to develop near infrared spectroscopy (NIRS) calibrations to predict fecal nutrient composition, intake, and diet digestibility from beef cattle fed high forage diets. Heifers were fed 12 different forage-based diets (&gt;95% forage dry matter basis) in 3 total collection digestibility studies, resulting in individual fecal samples and related spectra (n = 135), corresponding nutrient intake, and apparent total tract digestibility (aTTD) data. Fecal samples were also collected from steers grazing two annual and two perennial forage mixtures over two growing seasons. Samples (n = 13/paddock) were composited by paddock resulting in 30 samples from year 1, and 24 from year 2. The grazing fecal spectra (n = 54) were added to the existing fecal composition spectral library. Dried and ground fecal samples were scanned using a FOSS DS2500 scanning monochromator (FOSS, Eden Prairie, MN). Spectra were mathematically treated for detrend and scatter correction and modified partial least squares (MPLS) regression was performed. The coefficient of determination for cross validation (R2cv) and standard error of cross validation (SECV) were used to evaluate the quality of calibrations. Prediction equations were developed for fecal composition [organic matter (OM), nitrogen (N), amylase-treated ash-corrected neutral detergent fiber (aNDFom), acid detergent fiber (ADF), acid detergent lignin (ADL), undigestible NDF after 240 h of in vitro incubation (uNDF), calcium (Ca), and phosphorus (P)], digestibility [DM, OM, aNDFom, N], and intake [DM, OM, aNDFom, N, uNDF]. The calibrations for fecal OM, N, aNDFom, ADF, ADL, uNDF, Ca, P resulted in R2cv between 0.86 and 0.97 and SECV of 1.88, 0.07, 1.70, 1.10, 0.61, 2.00, 0.18, and 0.06, respectively. Equations predicting intake of DM, OM, N, aNDFom, ADL, and uNDF resulted in R2cv values between 0.59 and 0.91, SECV values of 1.12, 1.10, 0.02, 0.69, 0.06, 0.24 kg·d−1, respectively, and SECV values between 0.00 and 0.16 when expressed as % body weight (BW). Digestibility calibrations for DM, OM, aNDFom, and N resulted in R2cv ranging from 0.65 to 0.74 and SECV values from 2.20 to 2.82. We confirm the potential of NIRS to predict fecal chemical composition, digestibility, and intake of cattle fed high forage diets. Future steps include validation of the intake calibration equations for grazing cattle using forage internal marker and modelling energetics of grazing growth performance.
STAR-Caregivers Virtual Training and Follow-up: a cultural adaptation for Latino caregivers of people with dementia
Authors: Ramirez Magaly , Duran Miriana C , Penfold Robert B , Pabiniak Chester J , Hansen Kelly E , Ornelas India J 
Published: May 2023

Abstract
STAR-Caregivers Virtual Training and Follow-up (STAR-VTF) is an evidence-based intervention that teaches family caregivers how to manage behavioral and psychological symptoms of dementia. The study objective was to identify what adaptations to STAR-VTF are needed to improve cultural relevance for Latino caregivers. A qualitative research study was conducted that interviewed Spanish- and English-speaking caregivers of people with dementia who self-identify as Hispanic/Latino (N = 30) and healthcare and social service providers of older Latino clients and/or Latino family caregivers (N = 14). Thematic analysis methods were applied to code and analyze interview transcripts. The codebook was theory-driven, relying mainly on codes that directly represented components of the Cultural Treatment Adaptation Framework. Based on the content of the excerpts, the codes were sorted into themes that represented opportunities to culturally adapt STAR-VTF. Three themes were identified: (i) there was a need to increase awareness about dementia and decrease stigma; (ii) semantics mattered as certain words and phrases could be stigmatizing, offensive, or culturally inappropriate; and (iii) there was a need to incorporate into program materials the traditional family structure and nature of caregiving in Latino families. Based on findings, adaptations were performed on STAR-VTF that included expanding content to improve understanding of dementia, revising language that was viewed as problematic, and adding cultural examples to reflect the range of family involvement in caring for people living with dementia and multigenerational living. Findings from this qualitative research study advance understanding of the Latino caregiver experience and how to modify programs to better serve their needs.
Childhood obesity is linked to putative neuroinflammation in brain white matter, hypothalamus, and striatum
Authors: Li Zhaolong Adrian , Samara Amjad , Ray Mary Katherine , Rutlin Jerrel , Raji Cyrus A , Shimony Joshua S , Sun Peng , Song Sheng-Kwei , Hershey Tamara , Eisenstein Sarah A 
Published: May 2023

AbstractNeuroinflammation is both a consequence and driver of overfeeding and weight gain in rodent obesity models. Advances in magnetic resonance imaging (MRI) enable investigations of brain microstructure that suggests neuroinflammation in human obesity. To assess the convergent validity across MRI techniques and extend previous findings, we used diffusion basis spectrum imaging (DBSI) to characterize obesity-associated alterations in brain microstructure in 601 children (age 9–11 years) from the Adolescent Brain Cognitive DevelopmentSM Study. Compared with children with normal-weight, greater DBSI restricted fraction (RF), reflecting neuroinflammation-related cellularity, was seen in widespread white matter in children with overweight and obesity. Greater DBSI-RF in hypothalamus, caudate nucleus, putamen, and, in particular, nucleus accumbens, correlated with higher baseline body mass index and related anthropometrics. Comparable findings were seen in the striatum with a previously reported restriction spectrum imaging (RSI) model. Gain in waist circumference over 1 and 2 years related, at nominal significance, to greater baseline RSI-assessed restricted diffusion in nucleus accumbens and caudate nucleus, and DBSI-RF in hypothalamus, respectively. Here we demonstrate that childhood obesity is associated with microstructural alterations in white matter, hypothalamus, and striatum. Our results also support the reproducibility, across MRI methods, of findings of obesity-related putative neuroinflammation in children.
A High-Quality Genome Assembly for Cercospora janseana, Causal Agent of Narrow Brown Leaf Spot of Rice
Authors: Searight Jacob , Famoso Adam N. , Zhou Xin-Gen , Doyle Vinson P. , Richards Jonathan K. 
Published: May 2023

Cercospora janseana causes narrow brown leaf spot of rice. A nearly complete telomere-to-telomere reference genome was assembled with a combination of Oxford Nanopore and Illumina sequences. The genome assembly has a total length of 39,075,509 bp and consists of 15 chromosomes, 14 of which have telomeric repeats at both ends. The assembly N50 is 2.97 Mb and the L50 is five contigs. RNA-seq-mediated gene annotation identified 10,850 genes, including 955 predicted secreted proteins and 361 predicted effector proteins. This highly contiguous and almost complete C. janseana reference genome will be a vital resource for further investigation of host-pathogen interactions and genome evolution within this pathosystem. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
The triggering receptor expressed on myeloid cells 2–apolipoprotein E signaling pathway in diseases
Authors: Lyu Shukai , Lan Zhuoqing , Li Caixia 
Published: May 2023

Abstract
Triggering receptor expressed on myeloid cells 2 (TREM2) is a membrane receptor on myeloid cells and plays an important role in the body's immune defense. Recently, TREM2 has received extensive attention from researchers, and its activity has been found in Alzheimer's disease, neuroinflammation, and traumatic brain injury. The appearance of TREM2 is usually accompanied by changes in apolipoprotein E (ApoE), and there has been a lot of research into their structure, as well as the interaction mode and signal pathways involved in them. As two molecules with broad and important roles in the human body, understanding their correlation may provide therapeutic targets for certain diseases. In this article, we reviewed several diseases in which TREM2 and ApoE are synergistically involved in the development. We further discussed the positive or negative effects of the TREM2–ApoE pathway on nervous system immunity and inflammation.
Primary Cutaneous Marginal Zone Lymphoproliferative Disorder of Donor Origin after Allogeneic Hematopoietic Stem Cell Transplantation
Authors: Bejarano Lía , Sayagués Jose María , Alcoceba Miguel , Balanzategui Ana , Lopez-Corral Lucia , Cañueto Javier , Santos-Briz Angel 
Published: May 2023

Abstract
Primary cutaneous posttransplant lymphoproliferative disorders (PTLDs) after allogeneic hematopoietic stem cell transplant (allo-HSCT) are exceedingly rare, with only 6 published cases, all of them consisting in T-cell neoplasms. In this report, we present for the first time a donor-derived B-cell PTLD consisting in a primary, cutaneous, B-cell, marginal zone, lymphoproliferative disorder (PCMZLPD). The patient, a 37-year-old woman with a history of Hodgkin lymphoma received an allo-HSCT from her healthy, matched, related father, achieving complete host chimerism in the bone marrow and peripheral blood. However, 8 years after the allo-HSCT, she presented asymptomatic skin lesions consisting in oval, well-defined, slightly raised erythematous plaques, located on the arms, trunk, and legs. Skin biopsies of 2 lesions demonstrated a class-switched IgG+, EBV-, PCMZLPD, showing kappa light chain restriction and monoclonal rearrangement of the IgH gene. Microsatellite genotyping and 2-color fluorescence in situ hybridization (X and Y chromosomes) confirmed that the origin of the neoplastic cells was the donor graft. The lesions showed an indolent behavior, good response to topical corticosteroids, and no need for systemic treatment. Our case broadens the spectrum of PTLD, a diverse group of lymphoid and/or plasmacytic proliferations with variable clinical presentations and histopathological features.