bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffuse large B-cell lymphoma: the significance of CD8+ tumor-infiltrating lymphocytes exhaustion mediated by TIM3/Galectin-9 pathway
Authors: Zhu Qiqi , Yang Yiming , Chen Kexin , Zhang Qiaoyu , Huang Yifan , Jian Shunhai 
Published: February 2024

Abstract
Background
Overexpression of T-cell immunoglobulin and mucin domain-containing protein 3 (TIM3) is related to the exhaustion of CD8+ tumor-infiltrating lymphocytes (TILs) in diffuse large B-cell lymphoma (DLBCL). However, the mechanism of TIM3-mediated CD8+TILs exhaustion in DLBCL remains poorly understood. Therefore, we aimed to clarify the potential pathway involved in TIM3-mediated CD8+TILs exhaustion and its significance in DLBCL.

Methods
The expression of TIM3 and its correlation with CD8+TILs exhaustion, the key ligand of TIM3, and the potential pathway of TIM3-mediated CD8+TILs exhaustion in DLBCL were analyzed using single-cell RNA sequencing and validated by RNA sequencing. The biological significance of TIM3-related pathway in DLBCL was investigated based on RNA sequencing, immunohistochemistry, and reverse transcription-quantitative polymerase chain reaction data. Finally, the possible regulatory mechanism of TIM3-related pathway in DLBCL was explored using single-cell RNA sequencing and RNA sequencing.

Results
Our results demonstrated that CD8+TILs, especially the terminally exhausted state, were the major clusters that expressed TIM3 in DLBCL. Galectin-9, mainly expressed in M2 macrophages, is the key ligand of TIM3 and can induce the exhaustion of CD8+TILs through TIM3/Galectin-9 pathway. Meanwhile, high TIM3/Galectin-9 enrichment is related to immunosuppressive tumor microenvironment, severe clinical manifestations, inferior prognosis, and poor response to CHOP-based chemotherapy, and can predict the clinical efficacy of immune checkpoint blockade therapy in DLBCL. Furthermore, the TIM3/Galectin-9 enrichment in DLBCL may be regulated by the IFN-γ signaling pathway.

Conclusions
Our study highlights that TIM3/Galectin-9 pathway plays a crucial role in CD8+TILs exhaustion and the immune escape of DLBCL, which facilitates further functional studies and could provide a theoretical basis for the development of novel immunotherapy in DLBCL.
Towards portable MRI in the plant sciences
Authors: Blystone Shannan , Nuixe Magali , Traoré Amidou Sissou , Cochard Hervé , Picon-Cochard Catherine , Pagés Guilhem 
Published: February 2024

AbstractPlant physiology and structure are constantly changing according to internal and external factors. The study of plant water dynamics can give information on these changes, as they are linked to numerous plant functions. Currently, most of the methods used to study plant water dynamics are either invasive, destructive, or not easily accessible. Portable magnetic resonance imaging (MRI) is a field undergoing rapid expansion and which presents substantial advantages in the plant sciences. MRI permits the non-invasive study of plant water content, flow, structure, stress response, and other physiological processes, as a multitude of information can be obtained using the method, and portable devices make it possible to take these measurements in situ, in a plant’s natural environment. In this work, we review the use of such devices applied to plants in climate chambers, greenhouses or in their natural environments. We also compare the use of portable MRI to other methods to obtain the same information and outline its advantages and disadvantages.
Exploring the impact of light intensity under speed breeding conditions on the development and growth of lentil and chickpea
Authors: Mitache Mohammed , Baidani Aziz , Bencharki Bouchaib , Idrissi Omar 
Published: February 2024

AbstractThe use of high-performant varieties could help to improve the production of food legumes and thus meet the demand of the growing world population. However, long periods needed to develop new varieties through traditional breeding are a major obstacle. Thus, new techniques allowing faster genetic advance are needed. Speed breeding using longer periods of light exposure on plants, appears to be a good solution for accelerating plant life cycles and generation turnover. However, applying extended photoperiod causes plant stress and mortality due to lack of information on the adequate intensity to be used in speed breeding protocol. This study examines the impact of light intensity under speed breeding conditions on the development and growth of lentils and chickpeas, with a keen interest in enhancing genetic gain in these key food legumes. Four distinct levels of light intensity (T1: Green-house: 2000 µmol/m2/s; T2: 148–167 µmol/m2/s; T3: 111–129 µmol/m2/s; T4: 74–93 µmol/m2/s) under a photoperiod of 18 h of light and 6 h of darkness were tested in a growth chamber. Significant variation depending on light intensity was observed for plant height, total biomass, number of secondary stems, pods number, number of seeds per plant, growth rate, green canopy cover, time to flowering, time of pod set, time to maturity, vegetative stage length, reproduction stage length and seed filling stage length. Light intensity significantly influenced flowering/maturity and plant’s stress compared to normal conditions in green-house where flowering/maturity were around 67/97 days for lentil and 79/111 days for chickpea. Therefore, lentils in treatment 2 flowered and reached maturity in 30/45 days respectively, with high stress, while chickpeas in the same treatment did not flower. In contrast, treatment 4 showed interesting results, promoting optimal growth with low stress, and flowering/maturity in 27/46 days and 28/54 days, respectively for lentils and chickpeas. These results underline the crucial importance of light management in speed breeding to accelerate vegetative growth and phenology while allowing healthy growth conditions for plants to produce enough seeds for generation turnover.
Identification of chromosomal abnormalities in miscarriages by CNV-Seq
Authors: Shao Yuqi , Yang Saisai , Cheng Lin , Duan Jie , Li Jin , Kang Jiawei , Wang Fang , Liu Juan , Zheng Fang , Ma Jianhong , Zhang Yuanzhen 
Published: February 2024

Abstract
Objective
The primary object of this study is to analyze chromosomal abnormalities in miscarriages detected by copy number variants sequencing (CNV-Seq), establish potential pathways or genes related to miscarriages, and provide guidance for birth health in the following pregnancies.

Methods
This study enrolled 580 miscarriage cases with paired clinical information and chromosomal detection results analyzed by CNV-Seq. Further bioinformatic analyses were performed on validated pathogenic CNVs (pCNVs).

Results
Of 580 miscarriage cases, three were excluded as maternal cell contamination, 357 cases showed abnormal chromosomal results, and the remaining 220 were normal, with a positive detection rate of 61.87% (357/577). In the 357 miscarriage cases, 470 variants were discovered, of which 65.32% (307/470) were pathogenic. Among all variants detected, 251 were numerical chromosomal abnormalities, and 219 were structural abnormalities. With advanced maternal age, the proportion of numerical abnormalities increased, but the proportion of structural abnormalities decreased. Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology analysis revealed that eleven pathways and 636 biological processes were enriched in pCNVs region genes. Protein–protein interaction analysis of 226 dosage-sensitive genes showed that TP53, CTNNB1, UBE3A, EP300, SOX2, ATM, and MECP2 might be significant in the development of miscarriages.

Conclusion
Our study provides evidence that chromosomal abnormalities contribute to miscarriages, and emphasizes the significance of microdeletions or duplications in causing miscarriages apart from numerical abnormalities. Essential genes found in pCNVs regions may account for miscarriages which need further validation.
Biosynthesis of melatonin from l-tryptophan by an engineered microbial cell factory
Authors: Wang Lijuan , Deng Yongdong , Gao Jianjie , Wang Bo , Han Hongjuan , Li Zhenjun , Zhang Wenhui , Wang Yu , Fu Xiaoyan , Peng Rihe , Yao Quanhong , Tian Yongsheng , Xu Jing 
Published: February 2024

Abstract
Background
The demand for melatonin is increasing due to its health-promoting bioactivities such as antioxidant and sleep benefits. Although melatonin is present in various organisms, its low content and high extraction cost make it unsustainable. Biosynthesis is a promising alternative method for melatonin production. However, the ectopic production of melatonin in microorganisms is very difficult due to the low or insoluble expression of melatonin synthesis genes. Hence, we aim to explore the biosynthesis of melatonin using Escherichia coli as a cell factory and ways to simultaneously coordinated express genes from different melatonin synthesis pathways.

Results
In this study, the mXcP4H gene from Xanthomonas campestris, as well as the HsAADC, HsAANAT and HIOMT genes from human melatonin synthesis pathway were optimized and introduced into E. coli via a multi-monocistronic vector. The obtained strain BL7992 successfully synthesized 1.13 mg/L melatonin by utilizing L-tryptophan (l-Trp) as a substrate in a shake flask. It was determined that the rate-limiting enzyme for melatonin synthesis is the arylalkylamine N-acetyltransferase, which is encoded by the HsAANAT gene. Targeted metabolomics analysis of l-Trp revealed that the majority of l-Trp flowed to the indole pathway in BL7992, and knockout of the tnaA gene may be beneficial for increasing melatonin production.

Conclusions
A metabolic engineering approach was adopted and melatonin was successfully synthesized from low-cost l-Trp in E. coli. This study provides a rapid and economical strategy for the synthesis of melatonin.
Genotype data for 60 SNP genetic markers associated with eye, hair, skin color, ABO blood group, sex, core Y-chromosome haplogroups in Kazakh population
Authors: Bukayev Alizhan , Aidarov Baglan , Fesenko Denis , Saidamarova Viktoriya , Ivanovsky Ivan , Maltseva Elina , Naizabayeva Dinara , Bukayeva Ayagoz , Faizov Bekzhan , Pylev Vladimir , Darmenov Akynkali , Skiba Yuriy , Balanovska Elena , Zhabagin Maxat 
Published: February 2024

Abstract
Objectives
The collection of genotype data was conducted as an essential part of a pivotal research project with the goal of examining the genetic variability of skin, hair, and iris color among the Kazakh population. The data has practical application in the field of forensic DNA phenotyping (FDA). Due to the limited size of forensic databases from Central Asia (Kazakhstan), it is practically impossible to obtain an individual identification result based on forensic profiling of short tandem repeats (STRs). However, the pervasive use of the FDA necessitates validation of the currently employed set of genetic markers in a variety of global populations. No such data existed for the Kazakhs. The Phenotype Expert kit (DNA Research Center, LLC, Russia) was used for the first time in this study to collect data.

Data description
The present study provides genotype data for a total of 60 SNP genetic markers, which were analyzed in a sample of 515 ethnic Kazakhs. The dataset comprises a total of 41 single nucleotide polymorphisms (SNPs) obtained from the HIrisPlex-S panel. Additionally, there are 4 SNPs specifically related to the AB0 gene, 1 marker associated with the AMELX/Y genes, and 14 SNPs corresponding to the primary haplogroups of the Y chromosome. The aforementioned data could prove valuable to researchers with an interest in investigating genetic variability and making predictions about phenotype based on eye color, hair color, skin color, AB0 blood group, gender, and biogeographic origin within the male lineage.
MRI-based synthetic CT for assessment of the bony elements of the sacroiliac joints in children
Authors: Schiettecatte Eva , Vereecke Elke , Jaremko Jacob L. , Morbée Lieve , Vande Walle Caroline , Jans Lennart , Herregods Nele 
Published: February 2024

Abstract
Objectives
The purpose of this study is to assess the equivalency of MRI-based synthetic CT (sCT) to conventional CT for sacroiliac joint bony morphology assessment in children.

Methods
A prospective study was performed. Children who had (PET-)CT-scan underwent additional MRI. sCT-CT image quality was analyzed by two readers subjectively overall, semi-quantitatively in terms of cortical delineation, joint facet defects, growth plate fusion, ossified nuclei, lumbosacral transitional anomaly, and bony bridges, and quantitatively for disc space height, spinal canal width, and sacral vertebrae width and height. Cohen’s kappa and equivalence analyses with Bland–Altman plots were calculated for categorical and continuous measures respectively.

Results
Ten patients were included (6 boys; aged 9–16 years; mean age 14 years). Overall sCT image quality was rated good. Semi-quantitative assessment of cortical delineation of sacroiliac joints, bony bridges, and joint facet defects on the right iliac and sacral sides showed perfect agreement. Correlation was good to excellent (kappa 0.615–1) for the presence of lumbosacral transitional anomaly, fusion of sacral growth plates, joint facet defect, and presence of ossified nuclei. sCT-CT measurements were statistically equivalent and within the equivalence margins (–1–1 mm) for intervertebral disc space height and spinal canal width.
Intra- and inter-reader reliability was excellent for quantitative assessment (0.806 < ICC < 0.998). For categorical scoring, kappa ranged from substantial to excellent (0.615–1).

Conclusion
sCT appears to be visually equivalent to CT for the assessment of pediatric sacroiliac joints. sCT may aid in visualizing sacroiliac joints compared to conventional MRI, with the benefit that no ionizing radiation is used, especially important in children.

Critical relevance statement
MRI-based synthetic CT, a new technique that generates CT-like images without ionizing radiation, appears to be visually equivalent to CT for assessment of normal pediatric sacroiliac joints and can potentially assess structural damage as it clearly depicts bony cortex.

Key points
• MRI-based sCT is a new image technique that can generate CT-like images.
• We found that sCT performs similarly to CT in displaying bony structures of pediatric sacroiliac joints.
• sCT has already been clinically validated in the sacroiliac joints in adults.
• sCT can potentially assess structural damage from erosions or ankylosis as it clearly depicts bony cortex.

Graphical Abstract
Intraoperative vascular air embolism and intracardiac thrombosis complicating liver transplantation: a case report
Authors: Sinclair De Frías Jorge , Olivero Lorenzo , Fleissner Zachary , Burns Justin , Chadha Ryan , Moreno Franco Pablo 
Published: February 2024

Abstract
Background
Intracardiac thrombus and vascular air embolism represent rare complications in the context of orthotopic liver transplantation. While isolated reports exist for intracardiac thrombus and vascular air embolism during orthotopic liver transplantation, this report presents the first documentation of their simultaneous occurrence in this surgical setting.

Case presentation
This case report outlines the clinical course of a 60-year-old white female patient with end-stage liver disease complicated by portal hypertension, ascites, and hepatocellular carcinoma. The patient underwent orthotopic liver transplantation and encountered concurrent intraoperative complications involving intracardiac thrombus and vascular air embolism. Transesophageal echocardiography revealed the presence of air in the left ventricle and a thrombus in the right atrium and ventricle. Successful management ensued, incorporating hemodynamic support, anticoagulation, and thrombolytic therapy, culminating in the patient’s discharge after a week.

Conclusions
This report highlights the potential for simultaneous intraoperative complications during orthotopic liver transplantation, manifesting at any phase of the surgery. It underscores the critical importance of vigilant monitoring throughout orthotopic liver transplantation to promptly identify and effectively address these rare yet potentially catastrophic complications.
Prolonged versus intermittent β-lactam infusion in sepsis: a systematic review and meta-analysis of randomized controlled trials
Authors: Zhao Yang , Zang Bin , Wang Qian 
Published: February 2024

Abstract
Background
The two latest studies on prolonged versus intermittent use of β-lactam antibiotics in patients with sepsis did not reach consistent conclusions, further contributing to the controversy surrounding the effectiveness of the prolonged β-lactam antibiotics infusion strategy. We conducted a systemic review and meta-analysis to evaluate the efficacy and safety of prolonged and intermittent β-lactam infusion in adult patients with sepsis.

Methods
We systematically searched PubMed, EMBASE, and Cochrane Library databases for original randomized controlled trials comparing prolonged and intermittent β-lactam infusion in sepsis patients. A random-effects model was used to evaluate mortality, clinical success, microbiological success, and adverse events. We also conducted subgroup analyses to explore the impact of various factors on the mortality rates. Relative risk (RR) and corresponding 95% confidence intervals (CIs) were used to calculate the overall effect sizes for dichotomous outcomes. This meta-analysis was registered in PROSPERO (CRD42023463905).

Results
We assessed 15 studies involving 2130 patients. In our comprehensive assessment, we found a significant reduction in all-cause mortality (RR, 0.83; 95% CI 0.72–0.97; P = 0.02) and a notable improvement in clinical success (RR, 1.16; 95% CI 1.03–1.31; P = 0.02) in the prolonged infusion group compared to the intermittent infusion group, whereas microbiological success did not yield statistically significant results (RR, 1.10; 95% CI 0.98–1.23; P = 0.11). No significant differences in adverse events were observed between the two groups (RR, 0.91; 95% CI 0.64–1.29; P = 0.60). Additionally, remarkable conclusions were drawn from subgroup analyses including studies with sample sizes exceeding 20 individuals per group (RR, 0.84; 95%CI 0.72–0.98; P = 0.03), research conducted post-2010 (RR, 0.84; 95%CI 0.72–0.98; P = 0.03), cases involving infections predominantly caused by Gram-negative bacteria (RR, 0.81; 95%CI 0.68–0.96; P = 0.02), as well as the administration of a loading dose (RR, 0.84; 95% CI 0.72–0.97; P = 0.02) and the use of penicillin (RR, 0.61; 95% CI 0.38–0.98; P = 0.04).

Conclusions
Compared to intermittent infusion, prolonged infusion of β-lactam antibiotics significantly decreases all-cause mortality among patients with sepsis and enhances clinical success without increasing adverse events.
Water quality and habitat drive phytoplankton taxonomic and functional group patterns in the Yangtze River
Authors: Gao Wenqi , Xiong Fangyuan , Lu Ying , Xin Wei , Wang Haihua , Feng Gangpeng , Kong Chiping , Fang Lei , Gao Xiaoping , Chen Yushun 
Published: February 2024

Abstract
Background
Although phytoplankton are important primary producers in food webs, they are relatively less studied in large rivers compared to other types of systems. To fill this research gap, we studied phytoplankton taxonomic and functional composition and their relationships with water quality, habitat, climate, and land use across 30 river sections in the middle and lower reaches of the Yangtze River during 2017–2018.

Results
Major observed phytoplankton groups were cyanobacteria, bacillariophyta, and chlorophyta. Phytoplankton total abundance, total biomass, and species richness significantly decreased in the dry season compared to the wet season, with the species and functional composition differing significantly between seasons. Phytoplankton species differences between seasons were mainly contributed by Oscillatoria sp., Pseudanabaena sp., and Melosira granulata. The dfferences in phytoplankton functional groups between seasons were mainly contributed by P (including Closterium sp., Melosira sp.), Lo (including Merismopedia sp., Peridinium sp., Ceratium sp., and Gymnodinium sp.), and J (including Pediastrum sp., Tetraedron sp., Crucigenia sp., Scenedesmus sp., and Coelastrum sp.). The variance partitioning showed that water quality (NO3-N, total suspended solids, turbidity) and habitat (water flow, river bank and river channel conditions) were critical factors in shaping phytoplankton patterns, followed by climate and land use.

Conclusions
Results indicated that there was significant seasonal variation of phytoplankton in the Yangtze River, with water quality and habitat primarily driving phytoplankton patterns. Our study contributes to the understanding of natural and anthropogenic factors that drive seasonal successional processes of phytoplankton in the Yangtze River. These findings have important implications for environmental management as well as towards the ecological restoration of large rivers.
Excess dietary Lys reduces feed intake, stimulates jejunal CCK secretion and alters essential and non-essential blood AA profile in pigs
Authors: Müller Maximiliano , Van Liefferinge Elout , Tilbrook Alan , van Barneveld Robert , Roura Eugeni 
Published: February 2024

Abstract
Background
Commercial diets are frequently formulated to meet or exceed nutrient levels including those of limiting essential amino acids (AA) covering potential individual variations within the herd. However, the provision of dietary excess of AA, such as Lys, may lead to reduced appetite and growth in pigs. The mechanisms modulating these responses have not been extensively investigated. This study evaluated the effect of Lys dietary excesses on performance and satiety biomarkers in post weaning pigs.

Methods
Twenty-four pigs aged 21 d and weighing 6.81 ± 0.12 kg (mean ± SEM) were individually housed and offered 1 of 4 dietary treatments for 3 weeks: a diet containing a standardized ileal digestible Lys reaching 100% (T0), 120% (T1), 150% (T2) or 200% (T3) of the NRC (2012) requirements. At the end of the experiment, blood samples from the cephalic vein of the T0 and T3 groups were obtained for AA analysis. In addition, primary intestinal cultures from T0 pigs were used, following their humane killing, to evaluate the effect of Lys on gut hormone secretion and AA sensors gene expression under ex vivo conditions.

Results
Feed intake was linearly reduced (P < 0.001) and the weight gain to feed ratio reduced (P < 0.10) with increased dietary levels of Lys during the third- and first-week post weaning, respectively. Cholecystokinin concentration (P < 0.05) and the metabotropic glutamate receptor 1 and the solute carrier family 7 member 2 (P < 0.10) gene expression was enhanced in proximal jejunum tissues incubated with Lys at 20 mmol/L when compared to the control (Lys 0 mmol/L). Plasma Lys and Glu (P < 0.05) concentration increased in the T3 compared to T0 pigs. In contrast, plasma levels of His, Val, Thr, Leu (P < 0.05) and Gln (P < 0.10) were lower in T3 than T0 pigs.

Conclusion
The present results confirm that excess dietary Lys inhibits hunger in pigs. Moreover, the results provide evidence of pre- and post-absorptive mechanisms modulating these responses. Lys dietary excesses should be narrowed, when possible, to avoid negative effects of the AA on appetite in pigs.