bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of allele-level HLA matching on outcomes after double cord blood transplantation in adults with malignancies
Authors: Fatobene Giancarlo , Mariano Livia , Volt Fernanda , Moreira Frederico , Conelissen Jan , Furst Sabine , Daguindau Etienne , Sirvent Anne , Peffault de Latour Régis , Rafii Hanadi , Rivera-Franco Monica M. , Kenzey Chantal , Scigliuolo Graziana Maria , Cappelli Barbara , Ruggeri Annalisa , Gluckman Eliane , Rocha Vanderson 
Published: March 2023

Abstract
In single unrelated cord blood transplantation (UCBT), an increasing number of HLA allele mismatches (MM) has been associated with inferior overall survival (OS) and attributed to higher transplant-related mortality (TRM). Previous studies on the role of allele-level HLA matching after double UCBT (dUCBT) showed conflicting results. In this study, we report the impact of allele-level HLA matching on the outcomes of a large dUCBT cohort. We included 963 adults with hematologic malignancies, with available allele-level HLA matching at HLA-A, -B, -C, and -DRB1, receiving dUCBT between 2006 to 2019. Assignment of donor-recipient HLA match was performed considering the unit with the highest disparity with the recipient. Three hundred ninety-two patients received dUCBT with 0 to 3 MM and 571 with ≥4 allele MM. For recipients of dUCBT with 0 to 3 MM, day-100 and 4-year TRM were 10% and 23%, respectively, compared with 16% and 36% for those with ≥4 MM. A higher degree of allele MM was also associated with the worse neutrophil recovery and lower incidence of relapse; no significant effect on graft-versus-host disease was observed. Patients receiving units with 0 to 3 MM had a 4-year OS of 54% compared with 43% for those receiving units with ≥4 MM. The inferior OS associated with higher HLA disparity was only partially mitigated by increased total nucleated cell doses. Our results confirm that allele-level HLA typing is a significant factor for OS after dUCBT, and units with ≥4 MM (≤4/8 HLA-matched) should be avoided if possible.
What do patients think about palliative care? A national survey of hematopoietic stem cell transplant recipients
Authors: Barata Anna , Abrams Hannah R. , Meyer Christa , Mau Lih-Wen , Mattila Deborah , Burns Linda J. , Ullrich Christina , Murthy Hemant , Wood William A. , Petersdorf Effie , LeBlanc Thomas W. , El-Jawahri Areej 
Published: March 2023

Abstract
Palliative care (PC) benefits patients undergoing hematopoietic stem cell transplantation (HSCT), but it remains underutilized. Although transplant physicians report concerns regarding how patients perceive PC, HSCT recipients’ perceptions about PC remain unaddressed. We conducted a multisite, cross-sectional survey of autologous and allogeneic HSCT recipients 3 to 12 months after transplant to assess their familiarity, knowledge, and perception of PC, as well as their unmet PC needs. We computed a composite score of patients’ perceptions of PC and used a generalized linear regression model to examine factors associated with these perceptions. We enrolled 69.6% (250/359) of potential participants (median age = 58.1; 63.1% autologous HSCT). Overall, 44.3.8% (109/249) reported limited knowledge about PC and 52% (127/245) endorsed familiarity with PC. Most patients felt hopeful (54%) and reassured (50%) when they heard the term PC; 83% saw referral as a sign their doctor cared about what was happening to them. In multivariate analyses, patients who were more knowledgeable about PC were more likely to have positive perceptions of PC (B = 7.54, standard error = 1.61, P &lt; .001). Patients’ demographics, HSCT features, quality of life, and symptom burden were not significantly associated with perceptions of PC. HSCT recipients have positive perceptions of PC, though many have limited knowledge about its role. Patients who were more knowledgeable about PC were more likely to have positive perceptions of PC. These data do not support transplant physicians’ negative concerns about how patients perceive PC and underscore the need to further educate patients and transplant physicians about PC.
Use of statins and risk of myeloproliferative neoplasms: a Danish nationwide case-control study
Authors: Tuyet Kristensen Daniel , Kisbye Øvlisen Andreas , Hjort Kyneb Jakobsen Lasse , Tang Severinsen Marianne , Hannig Louise Hur , Starklint Jørn , Hagemann Hilsøe Morten , Pommer Vallentin Anders , Brabrand Mette , Hasselbalch Hans Carl , El-Galaly Tarec Christoffer , Stidsholt Roug Anne 
Published: March 2023

Abstract
Previous studies have indicated a possible cancer-protective effect of statins in solid cancers; however, this has never been investigated in myeloproliferative neoplasms (MPNs). We aimed to investigate the association between statin use and the risk of MPNs in a nested nationwide case-control study, using Danish national population registries. Information on statin use was obtained from the Danish National Prescription Registry, and patients diagnosed with MPNs between 2010 and 2018 were identified from the Danish National Chronic Myeloid Neoplasia Registry. The association between statin use and MPNs was estimated using age- and sex-adjusted odds ratios (ORs) and fully adjusted ORs (aORs), adjusting for prespecified confounders. The study population included 3816 cases with MPNs and 19 080 population controls (5:1) matched for age and sex using incidence density sampling. Overall, 34.9% of the cases and 33.5% of the controls ever used statins, resulting in an OR for MPN of 1.07 (95% confidence interval [CI], 0.99-1.16) and an aOR of 0.87 (95% CI, 0.80-0.96), respectively. 17.2% were categorized as long-term users (≥5 years) among the cases compared with 19.0% among controls, yielding an OR for MPN of 0.90 (95% CI, 0.81-1.00) and an aOR of 0.72 (95% CI, 0.64-0.81). Analysis of the effect of the cumulative duration of statin use revealed a dose-dependent response, and the association was consistent for sex, age, and MPN subgroups and across different statin types. Statin users were associated with significantly lower odds of being diagnosed with an MPN, indicating a possible cancer-preventive effect of statins. The retrospective design of this study precludes causal inferences.
Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM
Authors: Shachaf Lior I. , Roberts Elijah , Cahan Patrick , Xiao Jie 
Published: March 2023

Abstract
Background
A cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an elaborate gene regulatory network (GRN) in every single cell. In the past 20 years, many groups worked on reconstructing the topological structure of GRNs from large-scale gene expression data using a variety of inference algorithms. Insights gained about participating players in GRNs may ultimately lead to therapeutic benefits. Mutual information (MI) is a widely used metric within this inference/reconstruction pipeline as it can detect any correlation (linear and non-linear) between any number of variables (n-dimensions). However, the use of MI with continuous data (for example, normalized fluorescence intensity measurement of gene expression levels) is sensitive to data size, correlation strength and underlying distributions, and often requires laborious and, at times, ad hoc optimization.

Results
In this work, we first show that estimating MI of a bi- and tri-variate Gaussian distribution using k-nearest neighbor (kNN) MI estimation results in significant error reduction as compared to commonly used methods based on fixed binning. Second, we demonstrate that implementing the MI-based kNN Kraskov–Stoögbauer–Grassberger (KSG) algorithm leads to a significant improvement in GRN reconstruction for popular inference algorithms, such as Context Likelihood of Relatedness (CLR). Finally, through extensive in-silico benchmarking we show that a new inference algorithm CMIA (Conditional Mutual Information Augmentation), inspired by CLR, in combination with the KSG-MI estimator, outperforms commonly used methods.

Conclusions
Using three canonical datasets containing 15 synthetic networks, the newly developed method for GRN reconstruction—which combines CMIA, and the KSG-MI estimator—achieves an improvement of 20–35% in precision-recall measures over the current gold standard in the field. This new method will enable researchers to discover new gene interactions or better choose gene candidates for experimental validations.
Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs
Authors: Yalimaimaiti Saiyidan , Liang Xiaoqiao , Zhao Haili , Dou Hong , Liu Wei , Yang Ying , Ning Li 
Published: March 2023

Abstract
Objective
To establish a prognostic signature for lung adenocarcinoma (LUAD) based on cuproptosis-related long non-coding RNAs (lncRNAs), and to study the immune-related functions of LUAD.

Methods
First, transcriptome data and clinical data related to LUAD were downloaded from the Cancer Genome Atlas (TCGA), and cuproptosis-related genes were analyzed to identify cuproptosis-related lncRNAs. Univariate COX analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate COX analysis were performed to analyze the cuproptosis-related lncRNAs, and a prognostic signature was established. Second, univariate COX analysis and multivariate COX analysis were performed for independent prognostic analyses. Receiver operating characteristic (ROC) curves, C index, survival curve, nomogram, and principal component analysis (PCA) were performed to evaluate the results of the independent prognostic analyses. Finally, gene enrichment analyses and immune-related function analyses were also carried out.

Results
(1) A total of 1,297 cuproptosis-related lncRNAs were screened. (2) A LUAD prognostic signature containing 13 cuproptosis-related lncRNAs was constructed (NIFK-AS1, AC026355.2, SEPSECS-AS1, AL360270.1, AC010999.2, ABCA9-AS1, AC032011.1, AL162632.3, LINC02518, LINC0059, AL031600.2, AP000346.1, AC012409.4). (3) The area under the multi-indicator ROC curves at 1, 3, and 5 years were AUC1 = 0.742, AUC2 = 0.708, and AUC3 = 0.762, respectively. The risk score of the prognostic signature could be used as an independent prognostic factor that was independent of other clinical indicators. (4) The results of gene enrichment analyses showed that 13 biomarkers were primarily related to amoebiasis, the wnt signaling pathway, hematopoietic cell lineage. The ssGSEA volcano map showed significant differences between high- and low-risk groups in immune-related functions, such as human leukocyte antigen (HLA), Type_II_IFN_Reponse, MHC_class_I, and Parainflammation (P < 0.001).

Conclusions
Thirteen cuproptosis-related lncRNAs may be clinical molecular biomarkers for the prognosis of LUAD.
INSnet: a method for detecting insertions based on deep learning network
Authors: Gao Runtian , Luo Junwei , Ding Hongyu , Zhai Haixia 
Published: March 2023

Abstract
Background
Many studies have shown that structural variations (SVs) strongly impact human disease. As a common type of SV, insertions are usually associated with genetic diseases. Therefore, accurately detecting insertions is of great significance. Although many methods for detecting insertions have been proposed, these methods often generate some errors and miss some variants. Hence, accurately detecting insertions remains a challenging task.

Results
In this paper, we propose a method named INSnet to detect insertions using a deep learning network. First, INSnet divides the reference genome into continuous sub-regions and takes five features for each locus through alignments between long reads and the reference genome. Next, INSnet uses a depthwise separable convolutional network. The convolution operation extracts informative features through spatial information and channel information. INSnet uses two attention mechanisms, the convolutional block attention module (CBAM) and efficient channel attention (ECA) to extract key alignment features in each sub-region. In order to capture the relationship between adjacent subregions, INSnet uses a gated recurrent unit (GRU) network to further extract more important SV signatures. After predicting whether a sub-region contains an insertion through the previous steps, INSnet determines the precise site and length of the insertion. The source code is available from GitHub at https://github.com/eioyuou/INSnet.

Conclusion
Experimental results show that INSnet can achieve better performance than other methods in terms of F1 score on real datasets.
A key gene for the climatic adaptation of Apis cerana populations in China according to selective sweep analysis
Authors: Zhang Yi , Xu Hao , Wang Zhi , Jie Haoliang , Gao Fuchao , Cai Minqi , Wang Kang , Chen Dafu , Guo Rui , Lin Zheguang , Niu Qingsheng , Ji Ting 
Published: March 2023

Abstract
Background
Apis cerana is widely distributed in China and, prior to the introduction of western honeybees, was the only bee species kept in China. During the long-term natural evolutionary process, many unique phenotypic variations have occurred among A. cerana populations in different geographical regions under varied climates. Understanding the molecular genetic basis and the effects of climate change on the adaptive evolution of A. cerana can promote A. cerana conservation in face of climate change and allow for the effective utilization of its genetic resources.

Result
To investigate the genetic basis of phenotypic variations and the impact of climate change on adaptive evolution, A. cerana workers from 100 colonies located at similar geographical latitudes or longitudes were analyzed. Our results revealed an important relationship between climate types and the genetic variation of A. cerana in China, and a greater influence of latitude compared with longitude was observed. Upon selection and morphometry analyses combination for populations under different climate types, we identified a key gene RAPTOR, which was deeply involved in developmental processes and influenced the body size.

Conclusion
The selection of RAPTOR at the genomic level during adaptive evolution could allow A. cerana to actively regulate its metabolism, thereby fine-tuning body sizes in response to harsh conditions caused by climate change, such as food shortages and extreme temperatures, which may partially elucidate the size differences of A. cerana populations. This study provides crucial support for the molecular genetic basis of the expansion and evolution of naturally distributed honeybee populations.
Hypervirulent R20291 Clostridioides difficile spores show disinfection resilience to sodium hypochlorite despite structural changes
Authors: Malyshev Dmitry , Jones Imogen Anne , McKracken Matthew , Öberg Rasmus , Harper Glenn M. , Joshi Lovleen Tina , Andersson Magnus 
Published: March 2023

Abstract
Background
Clostridioides difficile is a spore forming bacterial species and the major causative agent of nosocomial gastrointestinal infections. C. difficile spores are highly resilient to disinfection methods and to prevent infection, common cleaning protocols use sodium hypochlorite solutions to decontaminate hospital surfaces and equipment. However, there is a balance between minimising the use of harmful chemicals to the environment and patients as well as the need to eliminate spores, which can have varying resistance properties between strains. In this work, we employ TEM imaging and Raman spectroscopy to analyse changes in spore physiology in response to sodium hypochlorite. We characterize different C. difficile clinical isolates and assess the chemical’s impact on spores’ biochemical composition. Changes in the biochemical composition can, in turn, change spores’ vibrational spectroscopic fingerprints, which can impact the possibility of detecting spores in a hospital using Raman based methods.

Results
We found that the isolates show significantly different susceptibility to hypochlorite, with the R20291 strain, in particular, showing less than 1 log reduction in viability for a 0.5% hypochlorite treatment, far below typically reported values for C. difficile. While TEM and Raman spectra analysis of hypochlorite-treated spores revealed that some hypochlorite-exposed spores remained intact and not distinguishable from controls, most spores showed structural changes. These changes were prominent in B. thuringiensis spores than C. difficile spores.

Conclusion
This study highlights the ability of certain C. difficile spores to survive practical disinfection exposure and the related changes in spore Raman spectra that can be seen after exposure. These findings are important to consider when designing practical disinfection protocols and vibrational-based detection methods to avoid a false-positive response when screening decontaminated areas.

Graphical Abstract
The predictive value of weight evolution in screening for malnutrition in community-dwelling older persons (70+) in Antwerp
Authors: Van Offenwert Evelien , Schoenmakers Birgitte 
Published: March 2023

Abstract
Background
Experience and research show that screening for malnutrition in primary care mainly takes place by monitoring the weight parameter and that validated screening instruments are hardly used. In this study we examined the effectiveness and predictive value of weight evolution in screening for (risk of) malnutrition in older people living at home, in comparison with a validated screening tool, namely the Mini Nutritional Assessment Short Form (MNA-SF).

Methods
This project was a prospective, longitudinal study with quantitative data that took place in the province of Antwerp (Belgium) from December 2020 until June 2021. The target group of this study consisted of people over 70 living at home who were visited by a home nurse on a regular basis (at least once a month). The outcome measure was the weight evolution over six months compared with the score on the MNA-SF at month six. Weight was measured and recorded once a month during 6 months. At the last weight measurement, the MNA-SF was administered. In order to assess their own nutritional state, three additional questions were asked after taking the MNA-SF.

Results
A total of 143 patients gave consent to participate, of which 89 were women and 54 men. The mean age was 83.7 years (SD6.62) with a range of 70 to 100 years. Based on the MNA-SF score measured after six months, 53.1% (76/143) of participants had a normal nutritional status, 37.8% (54/143) scored risk of malnutrition and 4.9% (7/ 143) was malnourished. In order to detect people with (risk of) malnutrition, a PPV of 78.6%, a NPV of 60.7%, a sensitivity of 19.3% and a specificity of 96.0% were established with a weight evolution of ≥ 5% weight loss at six months. To detect malnutrition, our results showed respectively 33.3%, 98.4%, 71.4% and 92.3%.

Conclusion
In this study, weight evolution has a low sensitivity in screening for (risk of) malnutrition in people over 70 living at home compared to the MNA-SF. However, in order to detect people with malnutrition, this study demonstrated a sensitivity of 71.4% and a specificity of 92.3% for a weight loss of ≥ 5% at six months.
Psychometric properties of the Alzheimer’s Disease Cooperative Study – Activities of Daily Living for Mild Cognitive Impairment (ADCS-MCI-ADL) scale: a post hoc analysis of the ADCS ADC-008 trial
Authors: Potashman Michele , Pang Menglan , Tahir Muna , Shahraz Saeid , Dichter Sascha , Perneczky Robert , Nolte Sandra 
Published: March 2023

Abstract
Background
The Alzheimer's Disease Cooperative Study – Activities of Daily Living Scale for use in Mild Cognitive Impairment (MCI), the ADCS-ADL-MCI, is an evaluation scale with information provided by an informant/caregiver to describe the functional impairment of patients with MCI. As the ADCS-ADL-MCI has yet to undergo a full psychometric evaluation, this study aimed to evaluate the measurement properties of the ADCS-ADL-MCI in subjects with amnestic MCI.

Methods
Measurement properties, including item-level analysis, internal consistency reliability, test–retest reliability, construct validity (convergent/discriminant, known-groups validity), and responsiveness were evaluated using data from the ADCS ADC-008 trial, a 36-month, multicenter, placebo-controlled study in 769 subjects with amnestic MCI (defined by clinical criteria and a global clinical dementia rating, CDR, score of 0.5). Due to most subjects' mild condition at baseline and resulting low variance in scores, psychometric properties were assessed using both baseline and 36-month data.

Results
Ceiling effects were not apparent at the total score level, with 3% of the cohort reaching the maximum score of 53, despite most subjects having a relatively high score at baseline (mean score = 46.0 [standard deviation = 4.8]). Item-total correlations were overall weak at baseline, most likely due to low variability in responses; however, at month 36, good item homogeneity was found. Cronbach's alpha values ranged from acceptable (0.64 at baseline) to good (0.87 at month 36), indicating overall very good internal consistency reliability. Further, moderate to good test–retest reliability was found (intraclass correlation coefficients ranging from 0.62–0.73). The analyses also largely supported convergent/discriminant validity, especially at month 36. Finally, the ADCS-ADL-MCI discriminated well between groups showing good known-groups validity, and was responsive in patients who indicated a longitudinal change in other instruments.

Conclusions
This study provides a comprehensive psychometric evaluation of the ADCS-ADL-MCI. Findings suggest that the ADCS-ADL-MCI is a reliable, valid and responsive measure capable of capturing functional abilities in patients with amnestic MCI.

Trial registration
ClinicalTrials.gov Identifier: NCT00000173.
The impact of stroke on the ability to live an independent life at old age: a community-based cohort study of Swedish men
Authors: Lindvall Elias , Franzon Kristin , Lundström Erik , Kilander Lena 
Published: March 2023

Abstract
Introduction
Few studies with controls from the same cohort have investigated the impact of stroke on the ability to live an independent life at old age. We aimed to analyze how great an impact being a stroke survivor would have on cognition and disability. We also analyzed the predictive value of baseline cardiovascular risk factors.

Methods
We included 1147 men, free from stroke, dementia, and disability, from the Uppsala Longitudinal Study of Adult Men, between 69–74 years of age. Follow-up data were collected between the ages of 85–89 years and were available for 481 of all 509 survivors. Data on stroke diagnosis were obtained through national registries. Dementia was diagnosed through a systematic review of medical charts and in accordance with the current diagnostic criteria. The primary outcome, preserved functions, was a composite outcome comprising four criteria: no dementia, independent in personal activities of daily living, ability to walk outside unassisted, and not living in an institution.

Results
Among 481 survivors with outcome data, 64 (13%) suffered a stroke during the follow-up. Only 31% of stroke cases, compared to 72% of non-stroke cases (adjusted OR 0.20 [95% CI 0.11–0.37]), had preserved functions. The chance of being free of dementia was 60% lower in the stroke group, OR 0.40 [95% CI 0.22–0.72]. No cardiovascular risk factors were independently able to predict preserved functions among stroke cases.

Conclusion
Stroke has long lasting consequences for many aspects of disability at very high age.