bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motive and opportunity: MYC rearrangements in high-grade B-cell lymphoma with MYC and BCL2 rearrangements (an LLMPP study)
Authors: Hilton Laura K. , Collinge Brett , Ben-Neriah Susana , Alduaij Waleed , Shaalan Haya , Weng Andrew P. , Cruz Manuela , Slack Graham W. , Farinha Pedro , Miyata-Takata Tomoko , Boyle Merrill , Meissner Barbara , Cook James R. , Ondrejka Sarah L. , Ott German , Rosenwald Andreas , Campo Elias , Amador Catalina , Greiner Timothy C. , Raess Philipp W. , Song Joo Y. , Inghirami Giorgio , Jaffe Elaine S. , Weisenburger Dennis D. , Chan Wing C. , Beiske Klaus , Fu Kai , Delabie Jan , Pittaluga Stefania , Iqbal Javeed , Wright George , Sehn Laurie H. , Savage Kerry J. , Mungall Andrew J. , Feldman Andrew L. , Staudt Louis M. , Steidl Christian , Rimsza Lisa M. , Morin Ryan D. , Scott David W. 
Published: May 2024

Abstract
Rearrangements that place the oncogenes MYC, BCL2, or BCL6 adjacent to superenhancers are common in mature B-cell lymphomas. Lymphomas with diffuse large B-cell lymphoma (DLBCL) or high-grade morphology with both MYC and BCL2 rearrangements are classified as high-grade B-cell lymphoma with MYC and BCL2 rearrangements (“double hit”; HGBCL-DH-BCL2) and are associated with aggressive disease and poor outcomes. Although it is established that MYC rearrangements involving immunoglobulin (IG) loci are associated with inferior outcomes relative to those involving other non-IG superenhancers, the frequency of and mechanisms driving IG vs non-IG MYC rearrangements have not been elucidated. Here, we used custom targeted capture and/or whole-genome sequencing to characterize oncogene rearrangements across 883 mature B-cell lymphomas including Burkitt lymphoma, follicular lymphoma, DLBCL, and HGBCL-DH-BCL2 tumors. We demonstrate that, although BCL2 rearrangement topology is consistent across entities, HGBCL-DH-BCL2 have distinct MYC rearrangement architecture relative to tumors with single MYC rearrangements or with both MYC and BCL6 rearrangements (HGBCL-DH-BCL6), including both a higher frequency of non-IG rearrangements and different architecture of MYC::IGH rearrangements. The distinct MYC rearrangement patterns in HGBCL-DH-BCL2 occur on the background of high levels of somatic hypermutation across MYC partner loci in HGBCL-DH-BCL2, creating more opportunity to form these rearrangements. Furthermore, because 1 IGH allele is already disrupted by the existing BCL2 rearrangement, the MYC rearrangement architecture in HGBCL-DH-BCL2 likely reflects selective pressure to preserve both BCL2 and B-cell receptor expression. These data provide new mechanistic explanations for the distinct patterns of MYC rearrangements observed across different lymphoma entities.
Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.)
Authors: Suppiyar Vithusan , Bonthala Venkata Suresh , Shrestha Asis , Krey Stephanie , Stich Benjamin 
Published: May 2024

AbstractGenes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
Atypical memory B cells increase in the peripheral blood of patients with breast cancer regardless of lymph node involvement
Authors: Azizi Atefeh , Mehdipour Fereshteh , Samadi Morteza , Rasolmali Reza , Talei Abdol-Rasoul , Ghaderi Abbas 
Published: May 2024

Abstract
Background
Breast cancer is the most common cancer in females. The immune system has a crucial role in the fight against cancer. B and T cells, the two main components of the adaptive immunity, are critical players that specifically target tumor cells. However, B cells, in contrast to T cells, and their role in cancer inhibition or progression is less investigated. Accordingly, in this study, we assessed and compared the frequency of naïve and different subsets of memory B cells in the peripheral blood of patients with breast cancer and healthy women.

Results
We found no significant differences in the frequencies of peripheral CD19+ B cells between the patients and controls. However, there was a significant decrease in the frequency of CD19+IgM+ B cells in patients compared to the control group (P=0.030). Moreover, the patients exhibited higher percentages of atypical memory B cells (CD19+CD27‒IgM‒, P=0.006) and a non-significant increasing trend in switched memory B cells (CD19+CD27+IgM‒, P=0.074). Further analysis revealed a higher frequency of atypical memory B cells (aMBCs) in the peripheral blood of patients without lymph node involvement as well as those with a tumor size greater than 2cm or with estrogen receptor (ER) negative/progesterone receptor (PR) negative tumors, compared with controls (P=0.030, P=0.040, P=0.031 and P=0.054, respectively).

Conclusion
Atypical memory B cells (CD19+CD27‒IgM‒) showed a significant increase in the peripheral blood of patients with breast cancer compared to the control group. This increase seems to be associated with tumor characteristics. Nevertheless, additional research is necessary to determine the precise role of these cells during breast cancer progression
Prevalence and molecular characterization of colistin resistance in Pseudomonas aeruginosa isolates: insights from a study in Ardabil hospitals
Authors: Jafari-Ramedani Saghar , Nazari Maryam , Arzanlou Mohsen , Peeri-Dogaheh Hadi , Sahebkar Amirhossein , Khademi Farzad 
Published: May 2024

Abstract
Background
Pseudomonas aeruginosa is a common cause of nosocomial infections. However, the emergence of multidrug-resistant strains has complicated the treatment of P. aeruginosa infections. While polymyxins have been the mainstay for treatment, there is a global increase in resistance to these antibiotics. Therefore, our study aimed to determine the prevalence and molecular details of colistin resistance in P. aeruginosa clinical isolates collected between June 2019 and May 2023, as well as the genetic linkage of colistin-resistant P. aeruginosa isolates.

Results
The resistance rate to colistin was 9% (n = 18) among P. aeruginosa isolates. All 18 colistin-resistant isolates were biofilm producers and carried genes associated with biofilm formation. Furthermore, the presence of genes encoding efflux pumps, TCSs, and outer membrane porin was observed in all colistin-resistant P. aeruginosa strains, while the mcr-1 gene was not detected. Amino acid substitutions were identified only in the PmrB protein of multidrug- and colistin-resistant strains. The expression levels of mexA, mexC, mexE, mexY, phoP, and pmrA genes in the 18 colistin-resistant P. aeruginosa strains were as follows: 88.8%, 94.4%, 11.1%, 83.3%, 83.3%, and 38.8%, respectively. Additionally, down-regulation of the oprD gene was observed in 44.4% of colistin-resistant P. aeruginosa strains.

Conclusion
This study reports the emergence of colistin resistance with various mechanisms among P. aeruginosa strains in Ardabil hospitals. We recommend avoiding unnecessary use of colistin to prevent potential future increases in colistin resistance.
Utilizing transcriptomics and proteomics to unravel key genes and proteins of Oryza sativa seedlings mediated by selenium in response to cadmium stress
Authors: Zhu Sixi , Sun Suxia , Zhao Wei , Yang Xiuqin , Mao Huan , Sheng Luying , Chen Zhongbing 
Published: May 2024

Abstract
Background
Cadmium (Cd) pollution has declined crop yields and quality. Selenium (Se) is a beneficial mineral element that protects plants from oxidative damage, thereby improving crop tolerance to heavy metals. The molecular mechanism of Se-induced Cd tolerance in rice (Oryza sativa) is not yet understood. This study aimed to elucidate the beneficial mechanism of Se (1 mg/kg) in alleviating Cd toxicity in rice seedlings.

Results
Exogenous selenium addition significantly improved the toxic effect of cadmium stress on rice seedlings, increasing plant height and fresh weight by 20.53% and 34.48%, respectively, and increasing chlorophyll and carotenoid content by 16.68% and 15.26%, respectively. Moreover, the MDA, ·OH, and protein carbonyl levels induced by cadmium stress were reduced by 47.65%, 67.57%, and 56.43%, respectively. Cell wall metabolism, energy cycling, and enzymatic and non-enzymatic antioxidant systems in rice seedlings were significantly enhanced. Transcriptome analysis showed that the expressions of key functional genes psbQ, psbO, psaG, psaD, atpG, and PetH were significantly up-regulated under low-concentration Se treatment, which enhanced the energy metabolism process of photosystem I and photosystem II in rice seedlings. At the same time, the up-regulation of LHCA, LHCB family, and C4H1, PRX, and atp6 functional genes improved the ability of photon capture and heavy metal ion binding in plants. Combined with proteome analysis, the expression of functional proteins OsGSTF1, OsGSTU11, OsG6PDH4, OsDHAB1, CP29, and CabE was significantly up-regulated under Se, which enhanced photosynthesis and anti-oxidative stress mechanism in rice seedlings. At the same time, it regulates the plant hormone signal transduction pathway. It up-regulates the expression response process of IAA, ABA, and JAZ to activate the synergistic effect between each cell rapidly and jointly maintain the homeostasis balance.

Conclusion
Our results revealed the regulation process of Se-mediated critical metabolic pathways, functional genes, and proteins in rice under cadmium stress. They provided insights into the expression rules and dynamic response process of the Se-mediated plant resistance mechanism. This study provided the theoretical basis and technical support for crop safety in cropland ecosystems and cadmium-contaminated areas.
Remote ischemic conditioning may improve graft function following kidney transplantation: a systematic review and meta-analysis with trial sequential analysis
Authors: Zhang Yang , Long Yuqin , Li Yongjun , Liao Dawei , Hu Linkun , Peng Ke , Liu Hong , Ji Fuhai , Shan Xisheng 
Published: May 2024

Abstract
Background
Remote ischemic conditioning (RIC) has the potential to benefit graft function following kidney transplantation by reducing ischemia-reperfusion injury; however, the current clinical evidence is inconclusive. This meta-analysis with trial sequential analysis (TSA) aimed to determine whether RIC improves graft function after kidney transplantation.

Methods
A comprehensive search was conducted on PubMed, Cochrane Library, and EMBASE databases until June 20, 2023, to identify all randomized controlled trials that examined the impact of RIC on graft function after kidney transplantation. The primary outcome was the incidence of delayed graft function (DGF) post-kidney transplantation. The secondary outcomes included the incidence of acute rejection, graft loss, 3- and 12-month estimated glomerular filtration rates (eGFR), and the length of hospital stay. Subgroup analyses were conducted based on RIC procedures (preconditioning, perconditioning, or postconditioning), implementation sites (upper or lower extremity), and graft source (living or deceased donor).

Results
Our meta-analysis included eight trials involving 1038 patients. Compared with the control, RIC did not significantly reduce the incidence of DGF (8.8% vs. 15.3%; risk ratio = 0.76, 95% confidence interval [CI], 0.48–1.21, P = 0.25, I2 = 16%), and TSA results showed that the required information size was not reached. However, the RIC group had a significantly increased eGFR at 3 months after transplantation (mean difference = 2.74 ml/min/1.73 m2, 95% CI: 1.44–4.05 ml/min/1.73 m2, P < 0.0001, I2 = 0%), with a sufficient evidence suggested by TSA. The secondary outcomes were comparable between the other secondary outcomes. The treatment effect of RIC did not differ between the subgroup analyses.

Conclusion
In this meta-analysis with trial sequential analysis, RIC did not lead to a significant reduction in the incidence of DGF after kidney transplantation. Nonetheless, RIC demonstrated a positive correlation with 3-month eGFR. Given the limited number of patients included in this study, well-designed clinical trials with large sample sizes are required to validate the renoprotective benefits of RIC.

Trial registration
This systematic review and meta-analysis was registered at the International Prospective Register of Systematic Reviews (Number CRD42023464447).
Airway management and pulmonary aspiration during surgical interventions in pregnant women in the 2nd/3rd trimester and immediate postpartum – a retrospective study in a tertiary care university hospital
Authors: Becker Charlotte E. , Lorenz Wolfram , de Abreu Marcelo Gama , Koch Thea , Kiss Thomas 
Published: May 2024

Abstract
Background
Pregnancy is associated with an increased risk of pulmonary aspiration during general anaesthesia, but the incidence of this complication is not well defined.

Methods
We performed a retrospective database review in a tertiary care university hospital to determine the incidence of pulmonary aspiration in pregnant patients undergoing endotracheal intubation, with and without Rapid Sequence Induction (RSI), as well as face-mask ventilation and supraglottic airway devices. We included Patients in the 2nd or 3rd trimester of pregnancy and immediate postpartum undergoing surgical procedures. The primary endpoint was the occurrence of pulmonary aspiration.

Results
Data from 2,390 patients undergoing general anaesthesia for cerclage of cervix uteri, manual removal of retained placenta, repair of obstetric laceration, or postpartum bleeding were retrospectively evaluated. A supraglottic airway device or face-mask ventilation was used in 1,425/2,390 (60%) of patients, while 638/2,390 (27%) were intubated. RSI was used in 522/638 (82%) of patients undergoing tracheal intubation, or 522/2,390 (22%) of the entire cohort. In-depth review of the charts, including 54 patients who had been initially classified as “possible pulmonary aspiration" by anaesthetists, revealed that this adverse event did not occur in the cohort.

Conclusions
In conclusion, in this obstetric surgery patient population at risk for pulmonary aspiration, supraglottic airway devices were used in approximately 60% of cases. Yet, no aspiration event was detected with either a supraglottic airway or endotracheal intubation.
Missingness mechanisms and generalizability of patient reported outcome measures in colorectal cancer survivors – assessing the reasonableness of the “missing completely at random” assumption
Authors: Lyhne Johanne Dam , Smith Allan ‘Ben’ , Jensen Lars Henrik , Hansen Torben Frøstrup , Frostholm Lisbeth , Timm Signe 
Published: May 2024

Abstract
Background
Patient-Reported Outcome Measures (PROM) provide important information, however, missing PROM data threaten the interpretability and generalizability of findings by introducing potential bias. This study aims to provide insight into missingness mechanisms and inform future researchers on generalizability and possible methodological solutions to overcome missing PROM data problems during data collection and statistical analyses.

Methods
We identified 10,236 colorectal cancer survivors (CRCs) above 18y, diagnosed between 2014 and 2018 through the Danish Clinical Registries. We invited a random 20% (2,097) to participate in a national survey in May 2023. We distributed reminder e-mails at day 10 and day 20, and compared Initial Responders (response day 0–9), Subsequent Responders (response day 10–28) and Non-responders (no response after 28 days) in demographic and cancer-related characteristics and PROM-scores using linear regression.

Results
Of the 2,097 CRCs, 1,188 responded (57%). Of these, 142 (7%) were excluded leaving 1,955 eligible CRCs. 628 (32%) were categorized as initial responders, 418 (21%) as subsequent responders, and 909 (47%) as non-responders. Differences in demographic and cancer-related characteristics between the three groups were minor and PROM-scores only marginally differed between initial and subsequent responders.

Conclusion
In this study of long-term colorectal cancer survivors, we showed that initial responders, subsequent responders, and non-responders exhibit comparable demographic and cancer-related characteristics. Among respondents, Patient-Reported Outcome Measures were also similar, indicating generalizability. Assuming Patient-Reported Outcome Measures of subsequent responders represent answers by the non-responders (would they be available), it may be reasonable to judge the missingness mechanism as Missing Completely At Random.
The burden and predictors of 30-day unplanned readmission in patients with acute liver failure: a national representative database study
Authors: Xu Xianbin , Gong Kai , Hong Liang , Yu Xia , Tu Huilan , Lan Yan , Yao Junjie , Ye Shaoheng , Weng Haoda , Li Zhiwei , Shi Yu , Sheng Jifang 
Published: May 2024

Abstract
Background
Liver diseases were significant source of early readmission burden. This study aimed to evaluate the 30-day unplanned readmission rates, causes of readmissions, readmission costs, and predictors of readmission in patients with acute liver failure (ALF).

Methods
Patients admitted for ALF from 2019 National Readmission Database were enrolled. Weighted multivariable logistic regression models were applied and based on Directed Acyclic Graphs. Incidence, causes, cost, and predictors of 30-day unplanned readmissions were identified.

Results
A total of 3,281 patients with ALF were enrolled, of whom 600 (18.3%) were readmitted within 30 days. The mean time from discharge to early readmission was 12.6 days. The average hospital cost and charge of readmission were $19,629 and $86,228, respectively. The readmissions were mainly due to liver-related events (26.6%), followed by infection (20.9%). The predictive factors independently associated with readmissions were age, male sex (OR 1.227, 95% CI 1.023–1.472; P = 0.028), renal failure (OR 1.401, 95% CI 1.139–1.723; P = 0.001), diabetes with chronic complications (OR 1.327, 95% CI 1.053–1.672; P = 0.017), complicated hypertension (OR 1.436, 95% CI 1.111–1.857; P = 0.006), peritoneal drainage (OR 1.600, 95% CI 1.092–2.345; P = 0.016), etc.

Conclusions
Patients with ALF are at relatively high risk of early readmission, which imposes a heavy medical and economic burden on society. We need to increase the emphasis placed on early readmission of patients with ALF and establish clinical strategies for their management.
Structural- and DTI- MRI enable automated prediction of IDH Mutation Status in CNS WHO Grade 2–4 glioma patients: a deep Radiomics Approach
Authors: Yuan Jialin , Siakallis Loizos , Li Hongwei Bran , Brandner Sebastian , Zhang Jianguo , Li Chenming , Mancini Laura , Bisdas Sotirios 
Published: May 2024

Abstract
Background
The role of isocitrate dehydrogenase (IDH) mutation status for glioma stratification and prognosis is established. While structural magnetic resonance image (MRI) is a promising biomarker, it may not be sufficient for non-invasive characterisation of IDH mutation status. We investigated the diagnostic value of combined diffusion tensor imaging (DTI) and structural MRI enhanced by a deep radiomics approach based on convolutional neural networks (CNNs) and support vector machine (SVM), to determine the IDH mutation status in Central Nervous System World Health Organization (CNS WHO) grade 2–4 gliomas.

Methods
This retrospective study analyzed the DTI-derived fractional anisotropy (FA) and mean diffusivity (MD) images and structural images including fluid attenuated inversion recovery (FLAIR), non-enhanced T1-, and T2-weighted images of 206 treatment-naïve gliomas, including 146 IDH mutant and 60 IDH-wildtype ones. The lesions were manually segmented by experienced neuroradiologists and the masks were applied to the FA and MD maps. Deep radiomics features were extracted from each subject by applying a pre-trained CNN and statistical description. An SVM classifier was applied to predict IDH status using imaging features in combination with demographic data.

Results
We comparatively assessed the CNN-SVM classifier performance in predicting IDH mutation status using standalone and combined structural and DTI-based imaging features. Combined imaging features surpassed stand-alone modalities for the prediction of IDH mutation status [area under the curve (AUC) = 0.846; sensitivity = 0.925; and specificity = 0.567]. Importantly, optimal model performance was noted following the addition of demographic data (patients’ age) to structural and DTI imaging features [area under the curve (AUC) = 0.847; sensitivity = 0.911; and specificity = 0.617].

Conclusions
Imaging features derived from DTI-based FA and MD maps combined with structural MRI, have superior diagnostic value to that provided by standalone structural or DTI sequences. In combination with demographic information, this CNN-SVM model offers a further enhanced non-invasive prediction of IDH mutation status in gliomas.