bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 neurovascular invasion supported by Mendelian randomization
Authors: Pan Yiji , Zhang Jun , He Tao 
Published: January 2024

Abstract
Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to affect vessels and nerves and can be easily visualized in the retina. However, the effect of SARS-CoV-2 on retinal morphology remains controversial. In the present research, we applied Mendelian randomization (MR) analysis to estimate the association between SARS-CoV-2 and changes in the thickness of the inner retina.

Methods
Two-sample MR analysis was conducted using summary-level data from 3 open genome-wide association study databases concerning COVID-19 infection (2,942,817 participants) and COVID-19 hospitalization (2,401,372 participants); moreover, the dataset of inner retina thickness, including the macular retinal nerve fiber layer (mRNFL) and macular ganglion cell-inner plexiform layer (mGCIPL), included 31,434 optical coherence tomography (OCT) images derived from healthy UK Biobank participants. All the participants were of European ancestry. The inverse variance weighted (IVW) meta-analysis was used as our primary method. Various complementary MR approaches were established to provide robust causal estimates under different assumptions.

Results
According to our MR analysis, genetically predicted COVID-19 infection was associated with an increased risk of mRNFL and mGCIPL thickness (OR = 1.74, 95% CI 1.20–2.52, P = 3.58 × 10–3; OR = 2.43, 95% CI 1.49–3.96, P = 3.6 × 10–4). The other MR methods produced consistent results. However, genetically predicted COVID-19 hospitalization did not affect the thickness of the inner retina (OR = 1.11, 95% CI 0.90–1.37, P = 0.32; OR = 1.28, 95% CI 0.88–1.85, P = 0.19).

Conclusion
This work provides the first genetically predictive causal evidence between COVID-19 infection and inner retinal thickness in a European population. These findings will contribute to further understanding of the pathogenesis of COVID-19 and stimulate improvements in treatment modalities.
Erythroid variant evolving from chronic myeloid leukemia resistant to multiple tyrosine kinase inhibitors: a rare case report
Authors: Lee Michelle Hyunju , Song Amy , Li Julie Y. 
Published: January 2024

Abstract
Background
Chronic myeloid leukemia (CML) is characterized by the presence of BCR::ABL1 fusion gene resulting from a reciprocal translocation, t(9;22)(q34;q11.2), leading to prominent granulocytic proliferation. The majority of patients initially present in chronic phase (CP), which may progress to advanced CML with predominantly granulocytic phenotypes in the absence of proper treatment or response to tyrosine kinase inhibitors (TKIs). We present an exceptionally rare case in which an erythroid variant emerged from a CML patient resistant to multiple TKIs. This variant is characterized by the detection of t(9;22) BCR::ABL1 fusion in erythroid precursors at various maturation stages and the absence of granulocytic progenitor hyperplasia typically seen in classical CML.

Case presentation
A 33-year-old female with CP-CML had received multiple TKI therapies since her initial diagnosis in 2015. Due to intolerable side effects and inconsistent adherence, she exhibited an inadequate response and developed new-onset pancytopenia. Bone marrow (BM) biopsy specimen revealed a hypercellular marrow with significant erythroid hyperplasia (90% of marrow cellularity) and a reversed myeloid-to-erythroid (M: E) ratio of 1:10. Both erythroid and myeloid cells displayed progressive maturation without dysplasia or excess blasts. Chromosomal analysis identified t(9;22) (q34;q11.2) in 19 out of 20 metaphase cells. BCR::ABL1 fusion transcript (p210 isoform) was confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) and next-generation sequencing (NGS). Notably, no additional pathogenic cytogenetic abnormalities or ABL1 kinase domain mutations were detected. Here, we report the first published case of an erythroid variant emerging in a CML patient resistant to multiple TKIs—a distinct entity from the erythroid blast crisis evolving from CML.

Conclusion
The erythroid variant of CML is distinguished by the presence of t(9;22) (q34;q11.2) BCR::ABL1 in predominant erythroid precursors at different stages of maturation. In a myeloid neoplasm showing predominant erythroid hyperplasia without typical CML features, it is vital to correlate morphology and t(9;22) BCR::ABL1 cytogenetic testing for accurate diagnosis, and to prevent confusion with PEL transformation in CML.
Improvement of germination rate and hybridization to facilitate breeding of an industrial oil crop, Euphorbia lagascae Spreng
Authors: Istaitieh Maram , Todd Jim F. , Van Acker Rene C. , Yoosefzadeh-Najafabadi Mohsen , Rajcan Istvan 
Published: January 2024

Abstract
Background
The potential of plant-based sources of vernolic acid to provide agricultural producers with a market diversification opportunity and industrial manufacturers with a renewable, environmentally friendly chemical feedstock is immense. The herbaceous wild spurge or caper spurge (Euphorbia lagascae Spreng) is the most promising source of vernolic acid, containing an average oil content of 50%, of which around 60% is vernolic acid. Its seed yield ranges between 500 and 2000 kg ha−1, and a theoretical yield of 180 kg ha−1 of pure vernolic acid is possible. The objective of this research was to characterize the flower and whole plant morphology so to allow for the development of a method to efficiently hybridize E. lagasce plants for breeding purposes.

Results
In this study, we have characterized the flower and whole plant morphology in detail, thereby, developing an efficient method for hybridization of E. lagasce to allow for its breeding and improvement as a novel oil crop. Such method was not described previously in the literature making it difficult to breed this crop. We believe that the method will be of great value to plant breeders working on optimizing the crop, particularly in terms of the development of non-shattering cultivars with enhanced germination potential.

Conclusions
The successful development of this crop through plant breeding could provide substantial economic benefits to farmers by offering them a new industrial oilseed crop. This research could prove invaluable in unlocking the potential of E. lagasce, and in turn, the potential of vernolic acid as a renewable, environmentally friendly source of chemical feedstock.
KAS-seq profiling captures transcription dynamics during oocyte maturation
Authors: An Huiqing , Wang Xiuwan , Li Jiashuo , Sun Hongzheng , Zhu Shuai , Ge Juan , Han Longsen , Shen Bin , Wang Qiang 
Published: January 2024

AbstractIn fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation.
Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling
Authors: Zhang Naixin , Chen Qiaochu , Zhang Peipei , Zhou Kejun , Liu Yaqing , Wang Haiyan , Duan Shumeng , Xie Yongming , Yu Wenxiang , Kong Ziqing , Ren Luyao , Hou Wanwan , Yang Jingcheng , Gong Xiaoyun , Dong Lianhua , Fang Xiang , Shi Leming , Yu Ying , Zheng Yuanting 
Published: January 2024

Abstract
Background
Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets.

Results
As part of the Quartet Project, we establish a publicly available suite of four metabolite reference materials derived from B lymphoblastoid cell lines from a family of parents and monozygotic twin daughters. We generate comprehensive LC–MS-based metabolomic data from the Quartet reference materials using targeted and untargeted strategies in different laboratories. The Quartet multi-sample-based signal-to-noise ratio enables objective assessment of the reliability of intra-batch and cross-batch metabolomics profiling in detecting intrinsic biological differences among the four groups of samples. Significant variations in the reliability of the metabolomics profiling are identified across laboratories. Importantly, ratio-based metabolomics profiling, by scaling the absolute values of a study sample relative to those of a common reference sample, enables cross-laboratory quantitative data integration. Thus, we construct the ratio-based high-confidence reference datasets between two reference samples, providing “ground truth” for inter-laboratory accuracy assessment, which enables objective evaluation of quantitative metabolomics profiling using various instruments and protocols.

Conclusions
Our study provides the community with rich resources and best practices for inter-laboratory proficiency tests and data integration, ensuring reliability of large-scale and longitudinal metabolomic studies.
Growth instability index, and decomposition effect on production of large cardamom in Nepal
Authors: Dhungana S. M. , Regmi P. P. , Dhakal S. C. , Devkota N. R. 
Published: January 2024

Abstract
Background
Large cardamom is the third most costly and oldest spice in the world, then saffron and vanilla, which is referred to as "black gold." Nepal's exportable, high-value subsector produces large cardamom (Amomum subulatum Roxb.) for sale in particular global markets. This study was to assess large cardamom's compound annual growth rate (CAGR), instability index, and influence of decomposition in Nepal. Data were imported from Ministry of Agriculture and Livestock Development, Nepal (MOALD) & Trade Export Promotion Centre, Nepal (TEPC), and the custom office in Birtamod, Nepal, from 2009 to 2020. The compound growth rate was calculated by an exponential function. The area, production, productivity, unit price of large cardamom before export at birtamod custom office, export quantity, and value of large cardamom were evaluated by variation (CV) and the Cuddy–Della Valle index (CDVI). Stability and growth performance were analyzed to assess the proportional impact of area and yield on the overall production of larger cardamom.

Results
Area, production, and yield had compound annual growth rate of 1.25, 2.0, and 0.85, respectively, revealing a major expansion of Nepalese large cardamom. The Mechi corridor has proven favorable and rapid development rates, indicating its potential but there was a reduction in large cardamom farming indicating negative CAGR of − 0.68 in the Koshi corridor. The area, production, and yield CV and CDVI were comparatively low, indicated stability in large cardamom farming. With a negative CAGR of − 1.01, the average price showed a downward trend over time. While the export quantity had a positive CAGR of 0.67, the export value had a positive CAGR of 3.84, suggesting a considerable increase.

Conclusions
The results emphasized the need for deliberate actions to increase stability, yield levels, market diversification, and lessen reliance on a single market for significant cardamom exports. Finally, prioritizing farmer capacity building programs will increase their proficiency with sustainable farming methods and resource management.
Dietary Bacillus spp. supplementation to both sow and progenies improved post-weaning growth rate, gut function, and reduce the pro-inflammatory cytokine production in weaners challenged with Escherichia coli K88
Authors: Sampath Vetriselvi , Cho Sungbo , Jeong Jinuk , Mun Seyoung , Lee Choon Han , Hermes Rafael Gustavo , Taechavasonyoo Apichaya , Smeets Natasja , Kirwan Susanne , Han Kyudong , Kim In Ho 
Published: January 2024

Abstract
Background
The use of probiotics (PRO) in late gestation sow and their impact on progenies’ performance during the post-weaning stage has received more attention from the researchers recently. This study aimed to analyze the effect of probiotic mixture (Bacillus subtilis and Bacillus licheniformis) on both sow and offspring’s performance.

Methods
First experiment (Exp.1) was conducted from the 100th day of gestation through to post-weaning. A total of twenty sows and their litters were assigned to one of two dietary treatments, Control (CON) based diet and PRO− CON+ 0.05% probiotic mixture. Dietary treatments were arranged in a split-plot pattern with sow and weaner treatment (CON and PRO diet) as the main and sub plot. Exp.2. E. coli challenge study was carried out two weeks after weaning with 40 piglets. Dietary treatments remained same while all pigs were orally administered with a 1.5 ml suspension of 1010 CFU of K88 strain of E. coli per ml.

Result
PRO group sow showed significantly decreased backfat thickness difference and body weight difference after farrowing and at the end of weaning d21. The nutrient digestibility of PRO group sows was significantly higher at the end of weaning. Moreover, piglets born from PRO group sow showed higher weaning weight and tend to increase average daily gain at the end of d21. The addition of mixed probiotic in sow and weaner diet had suppressed the production of TNF-α and interleukin-6 in E. coli challenged pigs. The phyla Firmicutes and Bacteroidetes in E. coli -challenged pigs were highly abundant while, the relative abundance of clostridium_sensu_stricto_1 at genus level was significantly reduced by the inclusion of probiotic in both the sow and weaner diet. Also, taxonomic distribution analysis showed significantly lower prevalence of Clostridium and Brachyspira and higher prevalence of Lactobacilli in E. coli-challenged pigs that were born from PRO group sow and fed CON and PRO weaner diet.

Conclusion
This study reveals that the inclusion of 0.05% mixed probiotics (Bacillus spp.) to both sow and their progenies diet would be more beneficial to enhance the post-weaning growth rate, gut health, and immune status of E. coli challenged pigs.
Precision in bipolar disorders
Authors: Grande I. 
Published: January 2024

Abstract
In many fields of heath, precision medicine has been integrated in clinical practise, for instance in oncology. In the case of psychiatry, and in particular bipolar disorder, we are in a prior step for the moment. Different proposal of stratification will be described during the talk for instance the classification of staging. Moreover some proposal of precision psychiatry in bipolar disorder will be put forward.

Disclosure of Interest
None Declared
Developments in the management of psychosis: key evidence from 2022
Authors: Chakraborty N. 
Published: January 2024

Abstract
The field of treatment and understanding in psychosis is evolving at an unprecedented pace with advances in neuroscience. It takes time before research findings are translated to clinical practice. Daunting as it is, clinicians need to keep up with findings which change our practice straightaway (new medication), findings which suggest that changes are expected in future (new theories about how illness develops and can be predicted) and findings which remind us of continuing practice and the evidence behind them (long term follow-up studies which give no big surprises but consolidate existing knowledge).
In a snap shot, I bring to you a range of five papers published in 2022 which enrich our understanding of psychosis, its development and treatment.

Disclosure of Interest
None Declared
Fluctuation of lysosomal protein degradation in neural stem cells of the postnatal mouse brain
Authors: Zhang He , Ishii Karan , Shibata Tatsuya , Ishii Shunsuke , Hirao Marika , Lu Zhou , Takamura Risa , Kitano Satsuki , Miyachi Hitoshi , Kageyama Ryoichiro , Itakura Eisuke , Kobayashi Taeko 
Published: January 2024

ABSTRACT
Lysosomes are intracellular organelles responsible for degrading diverse macromolecules delivered from several pathways, including the endo-lysosomal and autophagic pathways. Recent reports have suggested that lysosomes are essential for regulating neural stem cells in developing, adult and aged brains. However, the activity of these lysosomes has yet to be monitored in these brain tissues. Here, we report the development of a new probe to measure lysosomal protein degradation in brain tissue by immunostaining. Our results indicate that lysosomal protein degradation fluctuates in neural stem cells of the hippocampal dentate gyrus, depending on age and brain disorders. Neural stem cells increase their lysosomal activity during hippocampal development in the dentate gyrus, but aging and aging-related disease reduce lysosomal activity. In addition, physical exercise increases lysosomal activity in neural stem cells and astrocytes in the dentate gyrus. We therefore propose that three different stages of lysosomal activity exist: the state of increase during development, the stable state during adulthood and the state of reduction due to damage caused by either age or disease.
Properties of biomolecular condensates defined by Activator of G-protein Signaling 3
Authors: Vural Ali , Lanier Stephen M. 
Published: January 2024

ABSTRACT
Activator of G-protein signaling 3 (AGS3; also known as GPSM1), a receptor-independent activator of G-protein signaling, oscillates among defined subcellular compartments and biomolecular condensates (BMCs) in a regulated manner that is likely related to the functional diversity of the protein. We determined the influence of cell stress on the cellular distribution of AGS3 and core material properties of AGS3 BMCs. Cellular stress (oxidative, pHi and thermal) induced the formation of AGS3 BMCs in HeLa and COS-7 cells, as determined by fluorescent microscopy. Oxidative stress-induced AGS3 BMCs were distinct from G3BP1 stress granules and from RNA processing BMCs defined by the P-body protein Dcp1a. Immunoblots indicated that cellular stress shifted AGS3, but not the stress granule protein G3BP1 to a membrane pellet fraction following cell lysis. The stress-induced generation of AGS3 BMCs was reduced by co-expression of the signaling protein Gαi3, but not the AGS3-binding partner DVL2. Fluorescent recovery following photobleaching of individual AGS3 BMCs indicated that there are distinct diffusion kinetics and restricted fluidity for AGS3 BMCs. These data suggest that AGS3 BMCs represent a distinct class of stress granules that serve as a previously unrecognized signal processing node.
Role of BicDR in bristle shaft construction and support of BicD functions
Authors: Jejina Aleksandra , Ayala Yeniffer , Beuchle Dirk , Höhener Thomas , Dörig Ruth E. , Vazquez-Pianzola Paula , Hernández Greco , Suter Beat 
Published: January 2024

ABSTRACT
Cell polarization requires asymmetric localization of numerous mRNAs, proteins and organelles. The movement of cargo towards the minus end of microtubules mostly depends on cytoplasmic dynein motors. In the dynein–dynactin–Bicaudal-D transport machinery, Bicaudal-D (BicD) links the cargo to the motor. Here, we focus on the role of Drosophila BicD-related (BicDR, CG32137) in the development of the long bristles. Together with BicD, it contributes to the organization and stability of the actin cytoskeleton in the not-yet-chitinized bristle shaft. BicD and BicDR also support the stable expression and distribution of Rab6 and Spn-F in the bristle shaft, including the distal tip localization of Spn-F, pointing to the role of microtubule-dependent vesicle trafficking for bristle construction. BicDR supports the function of BicD, and we discuss the hypothesis whereby BicDR might transport cargo more locally, with BicD transporting cargo over long distances, such as to the distal tip. We also identified embryonic proteins that interact with BicDR and appear to be BicDR cargo. For one of them, EF1γ (also known as eEF1γ), we show that the encoding gene EF1γ interacts with BicD and BicDR in the construction of the bristles.
The active space of sperm whale codas: inter-click information for intra-unit communication
Authors: Jacobs Ellen R. , Gero Shane , Malinka Chloe E. , Tønnesen Pernille H. , Beedholm Kristian , DeRuiter Stacy L. , Madsen Peter T. 
Published: January 2024

ABSTRACT
Sperm whales (Physeter macrocephalus) are social mega-predators who form stable matrilineal units that often associate within a larger vocal clan. Clan membership is defined by sharing a repertoire of coda types consisting of specific temporal spacings of multi-pulsed clicks. It has been hypothesized that codas communicate membership across socially segregated sympatric clans, but others propose that codas are primarily used for behavioral coordination and social cohesion within a closely spaced social unit. Here, we test these hypotheses by combining measures of ambient noise levels and coda click source levels with models of sound propagation to estimate the active space of coda communication. Coda clicks were localized off the island of Dominica with a four- or five-element 80 m vertical hydrophone array, allowing us to calculate the median RMS source levels of 1598 clicks from 444 codas to be 161 dB re. 1 μPa (IQR 153–167), placing codas among the most powerful communication sounds in toothed whales. However, together with measured ambient noise levels, these source levels lead to a median active space of coda communication of ∼4 km, reflecting the maximum footprint of a single foraging sperm whale unit. We conclude that while sperm whale codas may contain information about clan affiliation, their moderate active space shows that codas are not used for long range acoustic communication between units and clans, but likely serve to mediate social cohesion and behavioral transitions in intra-unit communication.