bluuebunny/crossref_metadata_2025_split huggingface dataset:
A clinical trial of therapeutic vaccination in lymphoma with serial tumor sampling and single-cell analysis
Authors: Shree Tanaya , Haebe Sarah , Czerwinski Debra K. , Eckhert Erik , Day Grady , Sathe Anuja , Grimes Susan , Frank Matthew J. , Maeda Lauren S. , Alizadeh Ash A. , Advani Ranjana , Hoppe Richard T. , Long Steven R. , Martin Brock , Ozawa Michael G. , Khodadoust Michael S. , Ji Hanlee P. , Levy Ronald 
Published: November 2023

Abstract
In situ vaccination (ISV) triggers an immune response to tumor-associated antigens at 1 tumor site, which can then tackle the disease throughout the body. Here, we report clinical and biological results of a phase 1/2 ISV trial in patients with low-grade lymphoma, combining an intratumoral toll-like receptor 9 (TLR9) agonist with local low-dose radiation and ibrutinib (an inhibitor of B- and T-cell kinases). Adverse events were predominately low grade. The overall response rate was 50%, including 1 complete response. All patients experienced tumor reduction at distant sites. Single-cell analyses of serial fine needle aspirates from injected and uninjected tumors revealed correlates of clinical response, such as lower CD47 and higher major histocompatibility complex class II expression on tumor cells, enhanced T-cell and natural killer cell effector function, and reduced immune suppression from transforming growth factor β and inhibitory T regulatory 1 cells. Although changes at the local injected site were more pronounced, changes at distant uninjected sites were more often associated with clinical responses. Functional immune response assays and tracking of T-cell receptor sequences provided evidence of treatment-induced tumor-specific T-cell responses. Induction of immune effectors and reversal of negative regulators were both important in producing clinically meaningful tumor responses. The trial was registered at www.clinicaltrials.gov as #NCT02927964.
Pre- and post-headache phases of migraine: multi-country results from the CaMEO – International Study
Authors: Lipton Richard B. , Lanteri-Minet Michel , Leroux Elizabeth , Manack Adams Aubrey , Contreras-De Lama Janette , Reed Michael L. , Fanning Kristina M. , Buse Dawn C. 
Published: November 2023

Abstract
Background
Individuals with migraine frequently experience pre- and post-headache symptoms. This analysis aimed to characterize the relative frequency and burden of pre- and post-headache symptoms in people with migraine using data collected through the Chronic Migraine Epidemiology and Outcomes – International Study.

Methods
This cross-sectional, observational, web-based survey was conducted in 2021–2022 in Canada, France, Germany, Japan, the United Kingdom, and the United States. Respondents who met modified International Classification of Headache Disorders, 3rd edition, criteria were offered the opportunity to participate. Information collected included migraine-related disability, depression/anxiety symptoms, cutaneous allodynia, activity limitations, and acute treatment optimization. Respondents indicated how often they had pre- or post-headache symptoms using a 5-point scale, ranging from 0 to 4, with a rating of 2 or higher classified as a pre- or post-headache symptom case. Modeling was used to examine relationships with monthly headache days (MHDs) and activity limitations during pre-headache and post-headache phases.

Results
Among a total of 14,492 respondents, pre-headache symptoms were reported by 66.9%, while post-headache symptoms were reported by 60.2%. Both pre-headache and post-headache symptoms were reported by 49.5% of respondents, only pre-headache by 17.4%, only post-headache by 10.7%, and neither pre- nor post-headache symptoms by 22.4%. Compared with respondents who experienced only pre- or post-headache symptoms, respondents who experienced both pre- and post-headache symptoms had the highest rates of 4–7, 8–14, and ≥ 15 monthly headache days (23.1%, 14.1%, and 10.9%, respectively). Of respondents with both pre- and post-headache symptoms, 58.5% reported moderate-to-severe disability, 47.7% reported clinically significant symptoms of depression, 49.0% reported clinically significant symptoms of anxiety, and 63.8% reported cutaneous allodynia with headache (ASC-12). Moderate-to-severe activity limitations were reported during the pre-headache (29.5%) and post-headache phases (27.2%). For all outcomes modeled, after controlling for covariates, having pre-headache symptoms, post-headache symptoms, or both were associated with worse outcomes than having neither.

Conclusions
Pre- and post-headache phases of migraine are common, carry unrecognized burden, and may be a target for treatment.

Graphical Abstract
Carbon monoxide intoxication with a CO-Hb of 30% while smoking waterpipe: a case report
Authors: Mohsen Ghaith , Kemmerer Michael , Eichhorn Lars 
Published: November 2023

AbstractCarbon monoxide (CO) poisoning is a significant public health issue and a considerable economic burden in developed countries. While the majority of non-fire-related CO poisonings are attributed to gas heating, there are several other less recognized sources that should be considered in the initial differential diagnosis.The patient in this case was a 21-year-old who experienced a brief episode of loss of consciousness and was subsequently admitted to the Emergency department. Upon evaluation, the patient was diagnosed with CO poisoning, which necessitated hyperbaric oxygen therapy to mitigate the effects of this toxic exposure.Despite exhibiting harmful symptoms initially, the patient stated in a phone interview two and a half years post-incident that they have not experienced any enduring effects such as cardiac arrhythmia or concentration deficits. While their understanding of the risks associated with waterpipe smoking has increased, it has not influenced any major changes in their waterpipe smoking habits.
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides
Authors: Prunier Grégoire , Cherkaoui Mehdi , Lysiak Albane , Langella Olivier , Blein-Nicolas Mélisande , Lollier Virginie , Benoist Emile , Jean Géraldine , Fertin Guillaume , Rogniaux Hélène , Tessier Dominique 
Published: November 2023

Abstract
Background
In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a limited number of false positives, and a huge search space allowing any number of modifications without a priori. The scientific community needs new developments in this area to aid in the discovery of novel post-translational modifications that may play important roles in disease.

Results
To make progress on this issue, we implemented SpecGlobX (SpecGlob eXTended to eXperimental spectra), a standalone Java application that quickly determines the best spectral alignments of a (possibly very large) list of Peptide-to-Spectrum Matches (PSMs) provided by any open modification search method, or generated by the user. As input, SpecGlobX reads a file containing spectra in MGF or mzML format and a semicolon-delimited spreadsheet describing the PSMs. SpecGlobX returns the best alignment for each PSM as output, splitting the mass difference between the spectrum and the peptide into one or more shifts while considering the possibility of non-aligned masses (a phenomenon resulting from many situations including neutral losses). SpecGlobX is fast, able to align one million PSMs in about 1.5 min on a standard desktop. Firstly, we remind the foundations of the algorithm and detail how we adapted SpecGlob (the method we previously developed following the same aim, but limited to the interpretation of perfect simulated spectra) to the interpretation of imperfect experimental spectra. Then, we highlight the interest of SpecGlobX as a complementary tool downstream to three open modification search methods on a large simulated spectra dataset. Finally, we ran SpecGlobX on a proteome-wide dataset downloaded from PRIDE to demonstrate that SpecGlobX functions just as well on simulated and experimental spectra. We then carefully analyzed a limited set of interpretations.

Conclusions
SpecGlobX is helpful as a decision support tool, providing keys to interpret peptides carrying complex modifications still poorly considered by current open modification search software. Better alignment of PSMs enhances confidence in the identification of spectra provided by open modification search methods and should improve the interpretation rate of spectra.
Hybrid deep learning approach to improve classification of low-volume high-dimensional data
Authors: Mavaie Pegah , Holder Lawrence , Skinner Michael K. 
Published: November 2023

AbstractBackgroundThe performance of machine learning classification methods relies heavily on the choice of features. In many domains, feature generation can be labor-intensive and require domain knowledge, and feature selection methods do not scale well in high-dimensional datasets. Deep learning has shown success in feature generation but requires large datasets to achieve high classification accuracy. Biology domains typically exhibit these challenges with numerous handcrafted features (high-dimensional) and small amounts of training data (low volume).MethodA hybrid learning approach is proposed that first trains a deep network on the training data, extracts features from the deep network, and then uses these features to re-express the data for input to a non-deep learning method, which is trained to perform the final classification.ResultsThe approach is systematically evaluated to determine the best layer of the deep learning network from which to extract features and the threshold on training data volume that prefers this approach. Results from several domains show that this hybrid approach outperforms standalone deep and non-deep learning methods, especially on low-volume, high-dimensional datasets. The diverse collection of datasets further supports the robustness of the approach across different domains.ConclusionsThe hybrid approach combines the strengths of deep and non-deep learning paradigms to achieve high performance on high-dimensional, low volume learning tasks that are typical in biology domains.
Genome-wide identification and molecular expression profile analysis of FHY3/FAR1 gene family in walnut (Juglans sigillata L.) development
Authors: Chen Shengqun , Chen Yingfu , Liang Mei , Qu Shuang , Shen Lianwen , Zeng Yajun , Hou Na 
Published: November 2023

Abstract
Background
Juglans sigillata L. (walnut) has a high economic value for nuts and wood and has been widely grown and eaten around the world. Light plays an important role in regulating the development of the walnut embryo and promoting nucleolus enlargement, which is one of the factors affecting the yield and quality of walnut. However, little is known about the effect of light on the growth and quality of walnuts. Studies have shown that far red prolonged hypocotyl 3 (FHY3) and far red damaged response (FAR1) play important roles in plant growth, light response, and resistance. Therefore, FHY3/FAR1 genes were identified in walnuts on a genome-wide basis during their growth and development to reveal the potential regulation mechanisms involved in walnut kernel growth and development.

Results
In the present study, a total of 61 FHY3/FAR1 gene family members in walnuts have been identified, ranging in length from 117 aa to 895 aa. These gene family members have FHY3 or FAR1 conserved domains, which are unevenly distributed on the 15 chromosomes (Chr) of the walnut (except for the Chr16). All 61 FHY3/FAR1 genes were divided into five subclasses (I, II, III, IV, and V) by phylogenetic tree analysis. The results indicated that FHY3/FAR1 genes in the same subclasses with similar structures might be involved in regulating the growth and development of walnut. The gene expression profiles were analyzed in different walnut kernel varieties (Q, T, and F). The result showed that some FHY3/FAR1 genes might be involved in the regulation of walnut kernel ripening and seed coat color formation. Seven genes (OF07056-RA, OF09665-RA, OF24282-RA, OF26012-RA, OF28029-RA, OF28030-RA, and OF08124-RA) were predicted to be associated with flavonoid biosynthetic gene regulation cis-acting elements in promoter sequences. RT-PCR was used to verify the expression levels of candidate genes during the development and color change of walnut kernels. In addition, light responsiveness and MeJA responsiveness are important promoter regulatory elements in the FHY3/FAR1 gene family, which are potentially involved in the light response, growth, and development of walnut plants.

Conclusion
The results of this study provide a valuable reference for supplementing the genomic sequencing results of walnut, and pave the way for further research on the FHY3/FAR1 gene function of walnut.
Development and validation of a predictive models for predicting the cardiac events within one year for patients underwent percutaneous coronary intervention procedure at IJN
Authors: Ngew Kok Yew , Tay Hao Zhe , Yusof Ahmad K. M. 
Published: November 2023

Abstract
Purpose
Percutaneous coronary intervention (PCI) is a common treatment modality for coronary artery disease. Accurate prediction of patients at risk for complications and hospital readmission after PCI could improve the overall clinical management. We aimed to develop and validate predictive models to predict any cardiac event within a year post PCI procedure.

Methods
This is a retrospective cohort study utilizing data from the National Cardiovascular Disease (NCVD)-PCI registry. The data collected (N = 28,007) were split into training set (n = 24,409) and testing set (n = 3598). Four predictive models (logistic regression [LR], random forest method, support vector machine [SVM], and artificial neural network) were developed and validated. The outcome on risk prediction were compared.

Results
The demographic and clinical features of patients in the training and testing cohorts were similar. Patients had mean age ± standard deviation of 58.15 ± 10.13 years at admission with a male majority (82.66%). In over half of the procedures (50.61%), patients had chronic stable angina. Within 1 year of follow up mortality, target vessel revascularization (TVR), and composite event of mortality and TVR were 3.92%, 9.48%, and 12.98% respectively. LR was the best model in predicting mortality event within 1-year post-PCI (AUC: 0.820). SVM had the highest discrimination power for both TVR event (AUC: 0.720) and composite event of mortality and TVR (AUC: 0.720).

Conclusions
This study successfully identified optimal prediction models with the good discriminatory ability for mortality outcome and good discrimination ability for TVR and composite event of mortality and TVR with a simple machine learning framework.
Uric acid and evaluate the coronary vascular stenosis gensini score correlation research and in gender differences
Authors: Yang Bao , Ma Kanghua , Xiang Rui , Yang Guoli , Luo Yue , Wu Fan , Mao Min 
Published: November 2023

Abstract
Background and aims
Recent studies have shown that the negative effect of uric acid (UA) on coronary arteries determines the severity of atherosclerotic disease. This study aims to explore the relationship between serum UA level and Gensini score, which reflects the severity of coronary artery disease.

Methods
A total of 860 patients with suspected coronary heart disease who were admitted to hospital due to angina pectoris or myocardial ischemia related symptoms and received coronary angiography were selected. Based on the findings of the angiography, they were categorized into two groups: the coronary heart disease (CHD) group (n = 625) and the control group (n = 235). The uric acid levels and other clinical data were compared between these groups. Additionally, the prevalence of coronary heart disease and Gensini score were compared between the groups, considering gender-specific quartiles of uric acid levels. The clinical baseline data were analyzed using appropriate statistical methods, and multivariate logistic regression analysis was conducted to identify independent risk factors for coronary heart disease.

Results
Of 860 patients (mean age, 63.97 ± 11.87 years), 528 were men (mean age, 62.06 ± 11.5 years) and 332 were women (mean age, 66.99 ± 10.11 years). The proportion of smoking, diabetes, hypertension, and hyperlipidemia in the coronary heart disease group was higher than that in the control group (P < 0.05). HbA1C, Gensini score, BMI, TG and hsCRP in the coronary heart disease group were higher than those in the control group (P < 0.05), and HDL-C was lower than that in the control group (P < 0.05). There were no significant differences in age, heart rate, Cr, TC and LDL-C between the two groups (P > 0.05).Multivariate logistic regression analysis showed that age, hypertension, hsCRP and SUA levels increased the risk of coronary heart disease, and the difference was statistically significant(OR = 1.034,95%CI 1.016–1.052, P = 0.001; OR = 1.469,95%CI 1.007–2.142, P = 0.046;OR = 1.064,95%CI 1.026–1.105, P = 0.001; OR = 1.011,95%CI 1.008–1.014, P < 0.001).

Conclusion
Serum uric acid is positively correlated with Gensini score in patients with coronary heart disease, which is an independent factor for evaluating the degree of coronary artery stenosis and has a predictive effect.
The notable relatedness between ESBL producing Enterobacteriaceae isolated from clinical samples and asymptomatic fecal carriers
Authors: Aghamohammad Shadi , Shahcheraghi Fereshteh 
Published: November 2023

Abstract
Background
The investigation of the presence of extended-spectrum beta-lactamase (ESBL) within Enterobacteriaceae in both fecal carriers and patients is an essential matter. Furthermore, the assessment of distinct characteristics exhibited by resistant bacteria obtained from fecal carriers and patients, as well as the comparison of these characteristics between the two groups, could provide a deeper understanding of how the resistant isolates can remain concealed within a dormant reservoir and intensify antimicrobial resistance. The aim of the present study was to concentrate on the comparison of the antimicrobial resistance pattern and molecular features between strains obtained from clinical and carrier sources.

Material and methods
A total of 142 clinical samples and 120 rectal swabs were collected from June to October 2016. ESBL screening was performed using the double-disk synergy test. PCR was done for the detection of ESBL genes. Assessment of biofilm formation, virulence factor genes, and MLVA was performed for K. pneumonae isolates. Phylogroup typing was performed for E. coli isolates.

Results
Of 146 samples, 67.6% were E. coli, and 32.4% were K. pneumoniae. The rate of blaCTXM-15 was 89.4%. In K. pneumoniae type D, ompk35 and fimH were the highest. All the K. pneumoniae isolates were classified into 12 mini clusters and the clinical isolates were characterized into 7 mini clusters. The phylogroup B2 in ESBL-EC was the highest (56.2%).

Discussion
Comparison of molecular characteristics and clonal relatedness between fecal carriers and patients showed noticeable relatedness and similarity which may indicate that ESBL-KP can be colonized with the same profiles in different settings and, therefore, may be widely distributed in both community and hospital settings. Therefore, implementation of control protocols, including surveillance of the fecal carriers, could impressively reduce silent reservoirs without clinical symptoms as well as patient rates.
Diabetes mellitus and latent tuberculosis infection: an updated meta-analysis and systematic review
Authors: Zhou Guozhong , Guo Xin , Cai Shunli , Zhang Yu , Zhou Yuanyuan , Long Rong , Zhou Yingchen , Li Hanse , Chen Nan , Song Chao 
Published: November 2023

Abstract
Background
Previous studies have demonstrated an association between diabetes mellitus (DM) and latent tuberculosis infection (LTBI). This study was conducted to update the current understanding of the association between DM and LTBI. By conducting a systematic review and meta-analysis using adjusted odds ratios (aOR) or risk ratios (aRR), we aimed to further explore the association between DM and LTBI and provide essential reference for future research.

Methods
We conducted comprehensive searches in Embase, Cochrane Library, and PubMed without imposing any start date or language restrictions, up to July 19, 2022. Our study selection encompassed observational research that compared from LTBI positive rates in both DM and non-DM groups and reported aRR or aOR results. The quality of the included studies was assessed utilizing the Newcastle–Ottawa Scale. Pooled effect estimates were calculated using random-effects models, along with their associated 95% confidence intervals (CI).

Results
We included 22 studies involving 68,256 subjects. Three cohort studies were eligible, with a pooled aRR of 1.26 (95% CI: 0.71–2.23). Nineteen cross-sectional studies were eligible, with a pooled aOR of 1.21 (95% CI: 1.14–1.29). The crude RR (cRR) pooled estimate for three cohort studies was 1.62 (95% CI: 1.03–2.57). Among the cross-sectional studies we included, sixteen studies provided crude ORs, and the crude OR (cOR) pooled estimate was 1.64 (95% CI: 1.36–1.97). In the diagnosis of diabetes, the pooled aOR of the HbA1c group was higher than that of self-reported group (pooled aOR: 1.56, 95% CI: 1.24–1.96 vs. 1.17, 95% CI: 1.06–1.28).

Conclusion
Our systematic review and meta-analysis suggest a positive association between DM and LTBI. Individuals with DM may have a higher risk of LTBI compared to those without DM. These findings provide important insights for future research and public health interventions in managing LTBI in diabetic populations.