bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproductive cycle, fecundity and growth of the freshwater mussel Unio tumidus (Bivalvia: Unionidae) from Lake Viinijärvi, Finland
Authors: Abdelsaleheen Olfat , Taskinen Jouni , Kortet Raine 
Published: July 2024

ABSTRACT
Freshwater mussels have a substantial role in aquatic ecosystem function and provide valuable ecosystem services, including water filtration, nutrient cycling, habitat creation and sediment stabilization. While they face population declines globally that can negatively affect an ecosystem's health, such as reducing the water quality and increasing the turbidity, lack of information about the basic reproductive biology for most species makes their conservation much more difficult. Here, we monitored a population of Unio tumidus for a year to study its reproductive biology, gonad-dwelling parasites and growth rate in Lake Viinijärvi, Finland. Our data revealed that this species was dioecious with no evidence of hermaphroditism and was non-significantly female-biased (a male to female ratio of 1:1.3). Both sexes of U. tumidus had continuous gametogenesis during the study period with two peaks in the gonadosomatic index (GSI%) during November and May, followed by two clear declines in December and June. Gravidity period (brooding) of embryos or glochidia in the female's outer gills lasted from June to July. Therefore, this population of U. tumidus can be classified as a short-term breeder (tachytictic). The clear decline of GSI% in December might be a strategy that individuals of U. tumidus use to resorb resources back from the gonad for somatic maintenance during winter. Mean length of glochidia was 391 ± 0.049 µm, being among the largest known glochidia for Unionidae. No gonad-dwelling trematode parasites were detected and the population exhibited high fecundity (numbers of oocytes per female), with an average oocyte production of 242,000 ± 18,000. The studied population had a moderate growth rate with a maximum predicted age of 13 years and asymptotic length (the length at which growth slows down while the mussel continues to age, L∞) of 114 mm. Our study provides the first quantitative data and histological analysis of the reproductive biology of U. tumidus, serving as a basis for future research and conservation.
Clinicopathological phenotype and outcomes of NCAM-1+ membranous lupus nephritis
Authors: Xia Xi , Li Suchun , Jia Xiuzhi , Ye Siyang , Fan Yuting , Xiang Wang , Lu Xiaohui , Peng Wenxing , Chen Wenfang , Huang Fengxian , Tang Ruihan , Chen Wei 
Published: July 2024

ABSTRACT

Background
No studies have explored the long-term outcomes of neural cell adhesion molecule 1 (NCAM1)-associated membranous lupus nephritis (MLN) patients.

Method
We performed immunohistochemical studies on kidney biopsy specimens against NCAM1 in consecutive MLN patients. The clinical and histopathological characteristics and outcomes of cases of NCAM1-associated MLN patients are described and compared with NCAM1-negative patients. In addition, we detected serum circulating anti-NCAM1 antibodies through western blotting and indirect immunofluorescence assays.

Results
Among 361 MLN cases, 18 (5.0%) were glomerular NCAM1-positive. NCAM1-positive MLN patients were older [35 years (interquartile range, IQR 27–43) versus 28 (22–37); P = .050] and had lower systemic lupus erythematosus disease activity index [11 (IQR 8–12) versus 14 (10–18); P = .007], serum creatinine [60 μmol/L (IQR 50–70) versus 70 (54–114); P = .029] and activity index [3 (IQR 2–6) versus 6 (3–9); P = .045] at kidney biopsy compared with NCAM1-negative patients. The percentage of positive anti-Sjögren's syndrome–related antigen A antibodies in NCAM1-positive patients was significantly greater (83.3% versus 58.2%; P = .035) than in the NCAM1-negative patients. However, no evidence of neuropsychiatric disorders was found in these 18 patients. There were no significant differences in the treatment response and the risk of end-stage renal diseases between NCAM1-positive and -negative groups (P = .668 and P = .318, respectively). However, the risk of death was much higher in the NCAM1-positive group than the NCAM1-negative group (27.8% vs 8.1%; P = .007). Moreover, the risk of death was also much higher in the NCAM1-positive group than the matched NCAM1-negative group (Log-rank P = .013). Additionally, circulating anti-NCAM1 antibodies can be detected in 1/5 (20%) patients who had serum available.

Conclusion
The prevalence of NCAM1 positivity was 5.0% in our cohort of MLN and the high mortality in these subgroup patients are needed to validate in future studies.
Missed Opportunities for Preexposure Prophylaxis Initiation in Hospitalized Persons With Opioid Use Disorder and Infectious Diseases
Authors: Parchinski Kaley , Neirinckx Victor , Frank Cynthia , Di Paola Angela , Tarfa Adati , Shenoi Sheela , Vander Wyk Brent , Roth Prerana , Ghantous Tracy , Wegman Mary Kay , Strong Michelle , Levin Frances R , Brady Kathleen , Nunes Edward , Litwin Alain H , Springer Sandra A 
Published: July 2024

Abstract
Hospitalizations are increasing among persons who use opioids, secondary to overdose and infections. Our study identified acute hospitalization as a reachable moment for engaging people who use drugs in increased screening and education about human immunodeficiency virus risk and prevention (preexposure prophylaxis).
Neighborhood-Level Burden of Social Risk Factors on Respiratory Syncytial Virus Hospitalization in Ontario, Canada, 2016–2019
Authors: Chen Kitty Y A , van Ingen Trevor , Smith Brendan T , Fitzpatrick Tiffany , Whelan Michael , Parpia Alyssa S , Alessandrini Jenna , Buchan Sarah A 
Published: July 2024

Abstract

Background
Beyond clinical risk factors, little is known about the impact of social determinants on respiratory syncytial virus (RSV) burden. Our study aimed to estimate RSV-related hospitalization rates across sociodemographic and housing characteristics.

Methods
We conducted a population-based study of all RSV-related hospitalizations in Ontario, Canada, between September 1, 2016, and August 31, 2019, using validated hospital discharge codes and census data. Crude and age-standardized annualized RSV incidence rates and rate ratios (RRs) were estimated for a range of individual-level demographics and neighborhood-level measures of marginalization and housing characteristics.

Results
Overall, the annual RSV-related hospitalization rate was 27 per 100 000, with the highest rates observed in children age &lt;12 months (1049 per 100 000) and 12–23 months (294 per 100 000) and adults age ≥85 years (155 per 100 000). Higher RSV-related hospitalization rates were associated with increasing marginalization quintile (Q) of material resources (RR, 1.4; Q5: 33 per 100 000 vs Q1: 24 per 100 000) and household instability (RR, 1.5; Q5: 31 per 100 000 vs Q1: 22 per 100 000).

Conclusions
The burden of RSV-related hospitalization was greatest in young children and older adults, with variation by sociodemographic and housing factors. Understanding the role of these social factors is crucial for informing equitable preventive program delivery.
FGFR2 fusion/rearrangement is associated with favorable prognosis and immunoactivation in patients with intrahepatic cholangiocarcinoma
Authors: Liu Shaoqing , Weng Jialei , Cao Manqing , Zhou Qiang , Xu Min , Xu Wenxin , Hu Zhiqiu , Xu Minghao , Dong Qiongzhu , Sheng Xia , Zhou Chenhao , Ren Ning 
Published: July 2024

Abstract
Increasing evidence highlights that fibroblast growth factor receptor 2 (FGFR2) fusion/rearrangement shows important therapeutic value for patients with intrahepatic cholangiocarcinoma (ICC). This study aims to explore the association of FGFR2 status with the prognosis and immune cell infiltration profiles of patients with ICC. A total of 226 ICC tissue samples from patients who received surgery at the Department of Liver Surgery at Zhongshan Hospital, Fudan University, were collected retrospectively and assigned to a primary cohort (n = 152) and validation cohort (n = 74) group. Fluorescence in situ hybridization was performed to determine FGFR2 status. Multiplex immunofluorescence (mIF) staining and immunohistochemistry were performed to identify immune cells. Thirty-two (14.2%) ICC tissues presented with FGFR2 fusion/rearrangement. FGFR2 fusion/rearrangement was associated with low levels of carcinoembryonic antigen (CEA, P = .026) and gamma glutamyl transferase (γ-GGT, P = .003), low TNM (P = .012), CNLC (P = .008) staging as well as low tumor cell differentiation (P = .016). Multivariate COX regression analyses revealed that FGFR2 fusion/rearrangement was an independent protective factor for both overall survival (OS) and relapse-free survival in patients with ICC. Furthermore, correlation analysis revealed that an FGFR2 fusion/rearrangement was associated with low levels of Tregs and N2 neutrophils and high levels of N1 neutrophils infiltrating into tumors but not with CD8+ T-cell or macrophage tumor infiltration. FGFR2 fusion/rearrangement may exert a profound impact on the prognosis of ICC patients and reprogram the tumor microenvironment to be an immune-activated state. FGFR2 status may be used for ICC prognostic stratification and as an immunotherapeutic target in patients with ICC.
Phycocyanobilin Binding and Specific Amino Acid Residues Near The Chromophore Contribute To Orange Light Perception By The Dualchrome Phytochrome Region
Authors: Fukazawa Mana , Miyake Keita , Hoshino Hiroki , Fushimi Keiji , Narikawa Rei 
Published: July 2024

Abstract
A novel photoreceptor dualchrome 1 (DUC1), containing a fused structure of cryptochrome and phytochrome, was discovered in the marine green alga Pycnococcus provasolli. The DUC1 phytochrome region (PpDUC1-N) binds to the bilin (linear tetrapyrrole) chromophores, phytochromobilin (PΦB) or phycocyanobilin (PCB), and reversibly photoconverts between the orange-absorbing dark-adapted state and the far-red-absorbing photoproduct state. This contrasts with typical phytochromes, which photoconvert between the red-absorbing dark-adapted and far-red-absorbing photoproduct states. In this study, we examined the molecular mechanism of PpDUC1-N to sense orange light by identifying the chromophore species synthesized by P. provasolli and the amino acid residues within the PpDUC1-N responsible for sensing orange light in the dark-adapted state. We focused on the PcyA homolog of P. provasolli (PpPcyA). Coexpression with the photoreceptors followed by an enzymatic assay revealed that PpPcyA synthesized PCB. Next, we focused on the PpDUC1-N GAF domain responsible for chromophore binding and light sensing. Ten amino acid residues were selected as the mutagenesis target near the chromophore. Replacement of these residues with those conserved in typical phytochromes revealed that three mutations (F290Y/M304S/L353M) resulted in a 23-nm red shift in the dark-adapted state. Finally, we combined these constructs to obtain the PΦB-binding F290Y/M304S/L353M mutant and a 38-nm red shift was observed compared with the PCB-binding wild-type PpDUC1. The binding chromophore species and the key residues near the chromophore contribute to blue-shifted orange light sensing in the dark-adapted state of the PpDUC1-N.
The HD-ZIP II Gene PaHAT14 Increases Cuticle Deposition by Downregulating ERF Gene PaERF105 in Phalaenopsis
Authors: Mao Wan-Ting , Hsu Wei-Han , Song Jia-Lin , Yang Chang-Hsien 
Published: July 2024

Abstract
To analyze the genes involved in orchid floral development, a homeodomain-leucine zipper II gene PaHAT14, which is specifically and highly expressed in perianth during early flower development, was identified from Phalaenopsis. Transgenic Arabidopsis plants expressing 35S::PaHAT14 and 35S::PaHAT14 + SRDX (fused with the repressor motif SRDX) exhibited similar altered phenotypes, including small leaves, early flowering and bending petals with increased cuticle production. This suggests that PaHAT14 acts as a repressor. In contrast, transgenic Arabidopsis plants expressing 35S::PaHAT14 + VP16 (fused with the activation domain VP16) exhibited curled leaves, late flowering and folded petals with decreased cuticle production within hardly opened flowers. Additionally, the expression of the ERF gene DEWAX2, which negatively regulates cuticular wax biosynthesis, was downregulated in 35S::PaHAT14 and 35S::PaHAT14 + SRDX transgenic Arabidopsis, while it was upregulated in 35S::PaHAT14 + VP16 transgenic Arabidopsis. Furthermore, transient overexpression of PaHAT14 in Phalaenopsis petal/sepal increased cuticle deposition due to the downregulation of PaERF105, a Phalaenopsis DEWAX2 ortholog. On the other hand, transient overexpression of PaERF105 decreased cuticle deposition, whereas cuticle deposition increased and the rate of epidermal water loss was reduced in PaERF105 virus-induced gene silencing Phalaenopsis flowers. Moreover, ectopic expression of PaERF105 not only produced phenotypes similar to those in 35S::PaHAT14 + VP16 Arabidopsis but also compensated for the altered phenotypes observed in 35S::PaHAT14 and 35S::PaHAT14 + SRDX Arabidopsis. These results suggest that PaHAT14 promotes cuticle deposition by negatively regulating downstream gene PaERF105 in orchid flowers.
A database of nutritional strategies of nanoplankton genera present in North American lake surface waters
Authors: Le Noac’h Philippe , Beisner Beatrix E 
Published: July 2024

Abstract
A database of nutritional strategies of nanoplankton genera present in North American lake surface waters is presented. This work represents an integrated and updated database of nutritional strategies for nanoplankton genera commonly found in surface waters of North American lakes. We tabulate the nutritional strategies (autotroph, phago-mixotroph and phago-heterotroph) for nanoplankton genera identified during several pan-continental lake surveys: the EPA-NLA surveys conducted in 2012 and 2017 across the continental USA and the NSERC Canadian Lake Pulse survey campaign conducted from 2017 to 2019. We expect that this work will serve others in the plankton community interested in assessing nanoplankton feeding strategies.
Evaluating research waste and traits among randomized controlled trials of scars over the past 20 years: a cross-sectional study
Authors: Chen Hongrui , Huang Zening , Sun Bin , Hua Chen , Lin Xiaoxi 
Published: July 2024

Abstract

Purpose
To analyze the changes in the characteristics of randomized controlled trials (RCTs) in the field of scarring over the last two decades, unveil the components of research waste (RW) within these RCTs, and identify targets for improvement.

Methods
A search was conducted on ClinicalTrials.gov for RCTs registered from January 2000 to December 2023, using “scar” as the keyword. The search was carried out in January 2024.

Results
391 RCTs were included in this analysis. The global registration of RCTs in scarring has exhibited a consistent increase annually, with the proportion in Asia gradually rising, while the shares in North America and Europe have demonstrated a declining trend. In the analysis of RW, 232 RCTs were included, of which 96 (41.4%) have been published. Among the published RCTs, 56 (58.3%) were evaluated to have sufficient reporting, while 47 RCTs (48.9%) were identified as having avoidable design flaws. Ultimately, 183 RCTs (78.9%) exhibited at least one form of RW. Multicenter design (OR: 3.324, 95%CI: 1.385–7.975, P = 0.018), non-pharmacological interventions (OR: 2.61, 95%CI: 1.253–5.435, P = 0.010), the absence of external funding (OR: 0.325, 95%CI: 0.144–0.732, P = 0.031), and participant numbers exceeding 50 (OR: 3.269, 95%CI: 1.573–6.794, P = 0.002) were identified as independent protective factors against waste.

Conclusions
This study delineates the changes in the characteristics of scar RCTs globally over the past two decades, uncovering a substantial burden of RW in scarring research. It provides an evidential reference for more rational planning of future scar-related RCTs and for minimizing RW.
Correlation Functions Involving Dirac Fields from Homotopy Algebras II: The Interacting Theory
Authors: Konosu Keisuke 
Published: July 2024

Abstract
We extend the formula for correlation functions of free scalar field theories and Dirac field theories in terms of quantum $A_{\infty }$ algebras presented in arXiv:2305.11634 to general scalar-Dirac systems. We obtain the result that the same formula as in the previous paper holds in this case. We show that correlation functions from our formula satisfy the Schwinger–Dyson equations. We therefore confirm that correlation functions from our formula express correlation functions from the ordinary approach of quantum field theory.
Electromagnetic Response of Spinful Majorana Fermions
Authors: Kobayashi Shingo , Sato Masatoshi 
Published: July 2024

Abstract
A remarkable feature of topological superconductors is the emergence of Majorana fermions in electron systems. Whereas the emergent Majorana fermions share the self-antiparticle property with Majorana fermions in particle physics, they may have essentially different electromagnetic properties. In this paper, we discuss the electromagnetic response of spinful Majorana fermions in topological superconductors. We present a general theory of the electromagnetic response of spinful Majorana fermions in topological superconductors and clarify how the pairing symmetry is encoded in the electromagnetic response. As an application, we predict the sublattice-dependent dipole (Ising)-type magnetic response of corner Majorana fermions in iron-based superconductors.
Associations of Cognitive Expectancies With Auditory Hallucinations and Hallucinatory-Like Experiences in Patients With Schizophrenia
Authors: Kowalski Joachim , Dąbkowska Małgorzata , Aleksandrowicz Adrianna , Jarkiewicz Michał , Larøi Frank , Gawęda Łukasz 
Published: July 2024

Abstract

Background
Various neurocognitive models explore perceptual distortions and hallucinations in schizophrenia and the general population. A variant of predictive coding account suggests that strong priors, like cognitive expectancy, may influence perception. This study examines if stronger cognitive expectancies result in more auditory false percepts in clinical and healthy control groups, investigates group differences, and explores the association between false percepts and hallucinations.

Study Design
Patients diagnosed with schizophrenia with current auditory hallucinations (n = 51) and without hallucinations (n = 66) and healthy controls (n = 51) underwent the False Perception Task under various expectancy conditions. All groups were examined for the presence and severity of hallucinations or hallucinatory-like experiences.

Study Results
We observed a main effect of condition across all groups, ie, the stronger the cognitive expectancy, the greater the ratio of auditory false percepts. However, there was no group effect for the ratio of auditory false percepts. Despite modest pairwise correlations in the hallucinating group, the ratio of auditory false percepts was not predicted by levels of hallucinations and hallucinatory-like experiences in a linear mixed model.

Conclusions
The current study demonstrates that strong priors in the form of cognitive expectancies affect perception and play a role in perceptual disturbances. There is also a tentative possibility that overreliance on strong priors may be associated with hallucinations in currently hallucinating subjects. Possible, avoidable confounding factors are discussed in detail.
Eurycoma longifolia (Tongkat Ali) supplementation enhances sleep and wake consolidation in wild-type, but not in narcoleptic mice
Authors: Sakai Noriaki , Komi Kazuhiro , Nishino Naoya , Kuroki Yutaka , Nishino Seiji 
Published: July 2024

Abstract
Tongkat Ali (TA), also known as Eurycoma longifolia, has been used as a traditional herbal medicine for anti-aging, evidenced by clinical trials presenting the beneficial effects on energy, fatigue, and mood disturbance. We have recently shown that TA supplementation dose-dependently enhances the rest–activity pattern in C57BL/6 mice. Since destabilization of wakefulness and sleep is one of the typical symptoms of not only the elderly but also narcolepsy, we performed sleep analysis with and without dietary TA extract supplementation in middle-aged (10–12 months old) wild-type (WT) and narcoleptic DTA mice. We found that TA supplementation enhanced diurnal rhythms of locomotion and temperature in a time-of-day-dependent manner in WT mice but attenuated in DTA mice. In WT mice, TA supplementation consolidated wakefulness with a long bout duration and led to less entries into the sleep state during the active period, while it consolidated NREM sleep with long bout duration during the resting period. Neither disturbed sleep and wake cycles nor cataplexy was sufficiently improved in DTA mice. EEG spectral analysis revealed that TA supplementation enhanced slow wave activity (SWA) at both delta and low delta frequencies (0.5–4.0 and 0.5–2.0 Hz) during the light period, suggesting TA extract may induce vigilance during the active period, which then elicits a rebound effect during the resting period. Interestingly, DTA mice also slightly, but significantly, increased SWA at low frequencies during the light period. Taken together, our results suggest that TA supplementation enhances the Yin-Yang balance of sleep, temperature, and locomotion in WT mice, while its efficacy is limited in narcoleptic mice.
Development of a CRISPR/Cas9-Mediated Gene Knockout Method for Functional Genomics of the Barley Spot Blotch Pathogen Bipolaris sorokiniana
Authors: Poursafar Alireza , Leng Yueqiang , Zhong Shaobin 
Published: July 2024

Bipolaris sorokiniana (= Cochliobolus sativus) is an important fungal pathogen that causes spot blotch, common root rot, and kernel blight in barley and wheat. In this study, we aimed to develop a CRISPR/Cas9-mediated approach for efficiently knocking out genes of B. sorokiniana. We first assessed the efficiency of a split-marker system combined with Cas9 and single guide RNA (sgRNA) for gene replacement. We designed sgRNAs to target a polyketide synthase gene ( PKS1) that is required for melanin biosynthesis of the fungus. When the preassembled Cas9/sgRNA ribonucleoproteins (RNPs) and the split hygromycin B resistance gene ( HygB) fragments that each harbored 449-bp-upstream and 595-bp-downstream flanking sequences of PKS1 were cotransformed into the protoplasts of B. sorokiniana, the number of transformants with PKS1 replaced by the selection marker were significantly increased compared to the control without RNPs. We then used the RNPs and PCR-amplified HygB gene cassette carrying 40- or 60-bp arms homologous to the flanking sequences of the PKS1 target site for fungal transformation and showed that the RNPs significantly enhanced gene disruption efficiency through the short-homology recombination and that more gene knockout mutants were generated with longer (60-bp) homologous arms than with the shorter (40-bp) ones. Finally, we disrupted an uncharacterized nonribosomal peptide synthetase (NRPS) gene ( NPSx) in B. sorokiniana strain ND90Pr using the RNP-mediated gene knockout approach and showed that the mutants lost virulence on barley cultivar Bowman. The Cas9/sgRNA-mediated gene knockout method developed will facilitate large-scale functional genomics studies of B. sorokiniana. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .