bluuebunny/crossref_metadata_2025_split huggingface dataset:
TP53 mutations predict for poor outcomes in patients with newly diagnosed aggressive B-cell lymphomas in the current era
Authors: Landsburg Daniel J. , Morrissette Jennifer JD , Nasta Sunita D. , Barta Stefan K. , Schuster Stephen J. , Svoboda Jakub , Chong Elise A. , Bagg Adam 
Published: October 2023

Abstract
Genetic subgroups of diffuse large B-cell lymphoma (DLBCL) have been identified through comprehensive genomic analysis; however, it is unclear whether this can be applied in clinical practice. We assessed whether mutations detected by clinical laboratory mutation analysis (CLMA) were predictive of outcomes in patients with newly diagnosed DLBCL/high-grade B-cell lymphoma (HGBL). Patients diagnosed from 2018 to 2022 whose biopsy samples were subjected to CLMA and who received rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone or rituximab plus etoposide, prednisolone, vincristine, cyclophosphamide, and doxorubicin were analyzed for overall/complete response rate (ORR/CRR) and estimated progression-free/overall survival (PFS/OS). CLMA was successfully performed in 117 of 122 patient samples (96%), with a median turnaround time of 17 days. Median duration of follow-up was 31.3 months. Of the mutations detected in ≥10% of the samples, only TP53 was associated with both progression and death at 2 years. TP53 mutations were detected in 36% of tumors, and patients with TP53 mutations experienced significantly lower ORR (71% vs 90%; P = .009), CRR (55% vs 77%; P = .01), 2-year PFS (57% vs 77%; P = .006), 2-year OS (70% vs 91%; P = .001), and median OS after relapse (6.1 months vs not yet reached; P = .001) as than those without TP53 mutations. Furthermore, patients with TP53 loss-of-function (LOF) mutations experienced lower rates of 2-year PFS/OS than those with non-LOF mutations and inferior or near-inferior 2-year PFS if harboring high-risk clinicopathologic features. TP53 mutations identified through CLMA can predict for inferior outcomes in patients with newly diagnosed DLBCL/HGBL. Results of CLMA can be used in real time to inform prognosis and/or identify candidates for clinical trials.
Montelukast in paediatric asthma and allergic rhinitis: a systematic review and meta-analysis
Authors: Mayoral Karina , Lizano-Barrantes Catalina , Zamora Víctor , Pont Angels , Miret Carme , Barrufet Cristina , Caballero-Rabasco M. Araceli , Praena-Crespo Manuel , Bercedo Alberto , Valdesoiro-Navarrete Laura , Guerra Maria Teresa , Pardo Yolanda , Martínez Zapata Mª José , Garin Olatz , Ferrer Montse 
Published: October 2023

Background:We aim to assess the impact of montelukast on paediatric patients with asthma/allergic rhinitis, measured using patient-reported outcome measures, compared with other treatments or placebo.Methods:Protocol registration CRD42020216098 (www.crd.york.ac.uk/PROSPERO). MEDLINE and Embase databases were used to conduct the search. Two authors independently selected studies and extracted data, and a third reviewer resolved discrepancies. Meta-analyses were constructed to estimate the standardised mean difference (SMD) using a random-effects model.Results:Out of 3937 articles identified, 49 studies met the inclusion criteria, mostly randomised clinical trials (sample sizes: 21–689 patients). The SMD of change pooled estimators for the global, mental and physical domains of health-related quality of life were not statistically significant. For daytime and night-time symptoms scores, the SMD (95% CI) was in favour of inhaled corticosteroids (−0.12, −0.20– −0.05 and −0.23, −0.41– −0.06, respectively). The pooled estimator for global asthma symptoms was better for montelukast when compared with placebo (0.90, 0.44–1.36).Conclusions:The synthesis of the available evidence suggests that, in children and adolescents, montelukast was effective in controlling asthma symptoms when compared with placebo, but inhaled corticosteroids were superior in controlling symptoms, especially at night-time. These findings of our systematic review concur with current guidelines for asthma treatment.
Integrative proteomic and phosphoproteomic analysis in the female goat hypothalamus to study the onset of puberty
Authors: Ye Jing , Yan Xu , Zhang Wei , Lu Juntai , Xu Shuangshuang , Li Xiaoqian , Qin Ping , Gong Xinbao , Liu Ya , Ling Yinghui , Li Yunsheng , Zhang Yunhai , Fang Fugui 
Published: October 2023

Abstract
Background
Puberty marks the end of childhood and achieve sexual maturation and fertility. The role of hypothalamic proteins in regulating puberty onset is unclear. We performed a comprehensive differential proteomics and phosphoproteomics analysis in prepubertal and pubertal goats to determine the roles of hypothalamic proteins and phosphoproteins during the onset of puberty.

Results
We used peptide and posttranslational modifications peptide quantification and statistical analyses, and identified 69 differentially expressed proteins from 5,057 proteins and 576 differentially expressed phosphopeptides from 1574 phosphorylated proteins. Combined proteomic and phosphoproteomics, 759 correlated proteins were identified, of which 5 were differentially expressed only at the protein level, and 201 were only differentially expressed at the phosphoprotein level. Pathway enrichment analyses revealed that the majority of correlated proteins were associated with glycolysis/gluconeogenesis, Fc gamma R-mediated phagocytosis, focal adhesion, GABAergic synapse, and Rap1 signaling pathway. These pathways are related to cell proliferation, neurocyte migration, and promoting the release of gonadotropin-releasing hormone in the hypothalamus. CTNNB1 occupied important locations in the protein-protein interaction network and is involved in focal adhesion.

Conclusion
The results demonstrate that the proteins differentially expression only at the protein level or only differentially expressed at the phosphoprotein level and their related signalling pathways are crucial in regulating puberty in goats. These differentially expressed proteins and phosphorylated proteins may constitute the proteomic backgrounds between the two different stages.
Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks
Authors: Li Ying , Han Liqin , Li Peiluan , Ge Jing , Xue Yun , Chen Luonan 
Published: October 2023

AbstractTo explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and ‘dark’ genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the ‘dark’ genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the ‘dark’ gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by ‘dark’ genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.
Genes expression profiles in vascular cambium of Eucalyptus urophylla × Eucalyptus grandis at different ages
Authors: Liu Guo , Wu Zhihua , Luo Jianzhong , Wang Chubiao , Shang Xiuhua , Zhang Guowu 
Published: October 2023

Abstract
Background
Wood is a secondary xylem generated by vascular cambium. Vascular cambium activities mainly include cambium proliferation and vascular tissue formation through secondary growth, thereby producing new secondary phloem inward and secondary xylem outward and leading to continuous tree thickening and wood formation. Wood formation is a complex biological process, which is strictly regulated by multiple genes. Therefore, molecular level research on the vascular cambium of different tree ages can lead to the identification of both key and related genes involved in wood formation and further explain the molecular regulation mechanism of wood formation.

Results
In the present study, RNA-Seq and Pac-Bio Iso-Seq were used for profiling gene expression changes in Eucalyptus urophylla × Eucalyptus grandis (E. urograndis) vascular cambium at four different ages. A total of 59,770 non-redundant transcripts and 1892 differentially expressed genes (DEGs) were identified. The expression trends of the DEGs related to cell division and differentiation, cell wall biosynthesis, phytohormone, and transcription factors were analyzed. The DEGs encoding expansin, kinesin, cycline, PAL, GRP9, KNOX, C2C2-dof, REV, etc., were highly expressed in E. urograndis at three years old, leading to positive effects on growth and development. Moreover, some gene family members, such as NAC, MYB, HD-ZIP III, RPK, and RAP, play different regulatory roles in wood formation because of their sophisticated transcriptional network and function redundantly.

Conclusions
These candidate genes are a potential resource to further study wood formation, especially in fast-growing and adaptable eucalyptus. The results may also serve as a basis for further research to unravel the molecular mechanism underlying wood formation.
Mapping Hungarian procedure codes to SNOMED CT
Authors: Mészáros Ágota , Kovács Sándor , Héja Tibor , Bagyura Zsolt , Zemplényi Antal 
Published: October 2023

Abstract
Background
Data harmonisation is essential in real-world data (RWD) research projects based on hospital information systems databases, as coding systems differ between countries. The Hungarian hospital information systems and the national claims database use internationally known diagnosis codes, but data on medical procedures are recorded using national codes. There is no simple or standard solution for mapping the national codes to a standard coding system. Our aim was to map the Hungarian procedure codes (OENO) to SNOMED CT as part of the European Health Data Evidence Network (EHDEN) project.

Methods
We recruited 25 professionals from different specialties to manually map the procedure codes used between 2011 and 2021. A mapping protocol and training material were developed, results were regularly revised, and the challenges of mapping were recorded. Approximately 7% of the codes were mapped by more people in different specialties for validation purposes.

Results
We mapped 4661 OENO codes to standard vocabularies, mostly SNOMED CT. We categorized the challenges into three main areas: semantic, matching, and methodological. Semantic refers to the occasionally unclear meaning of the OENO codes, matching to the different granularity and purpose of the OENO and SNOMED CT vocabularies. Lastly, methodological challenges were used to describe issues related to the design of the above-mentioned two vocabularies.

Conclusions
The challenges and solutions presented here may help other researchers to design their process to map their national codes to standard vocabularies in order to achieve greater consistency in mapping results. Moreover, we believe that our work will allow for better use of RWD collected in Hungary in international research collaborations.
Adverse events of pancreatic extracorporeal shock wave lithotripsy: a literature review
Authors: Yi Jin-Hui , Li Zhao-Shen , Hu Liang-Hao 
Published: October 2023

AbstractPancreatic stones are the result of pathophysiologic changes in chronic pancreatitis with an incidence of more than 90%. At present, pancreatic extracorporeal shock wave lithotripsy (P-ESWL) can be used as the first-line treatment for large or complex stones. Although a large number of studies have proven the safety and effectiveness of P-ESWL, we should also pay attention to postoperative adverse events, mainly due to the scattering of shock waves in the conduction pathway. Adverse events can be classified as either complications or transient adverse events according to the severity. Because the anatomic location of organs along the shock wave conducting pathway differs greatly, adverse events after P-ESWL are varied and difficult to predict. This paper outlines the mechanism, definition, classification, management and risk factors for adverse events related to P-ESWL. It also discusses the technique of P-ESWL, indications and contraindications of P-ESWL, and adverse events in special populations.
Folate, vitamin B12 and vitamin D status in healthy and active home-dwelling people over 70 years
Authors: Kerlikowsky Felix , Schuchardt Jan Philipp , Hahn Andreas 
Published: October 2023

Abstract
Background
Ageing is characterised by physiological changes that can affect the nutrient availability and requirements. In particular, the status of vitamin D, cobalamin and folate has often been found to be critical in older people living in residential care. However, there is a lack of studies investigating the status of these nutrients in healthy and active home-dwelling elderly people.

Methods
The aim of this cross-sectional study was to assess the status of vitamin D based on serum concentrations of 25-hydroxycholecalciferol [25-(OH)D], cobalamin based on serum concentrations of holotranscobalamin (holoTC) and folate based on red blood cell (RBC) folate in unsupplemented, healthy and active German home-dwelling subjects ≥ 70 years of age (n = 134, mean ± SD: 75.8 ± 4.5 years). Dietary intake was assessed by 3-day food recalls. The study was conducted between March and November of 2021 (during the COVID-19 pandemic).

Results
The mean 25-(OH)D concentration was high at 85.1 ± 26.0 nmol/L, while the majority of women (92%) and men (94%) had 25-(OH)D concentrations ≥ 50 nmol/L. Less than 10% of men and women had 25-(OH)D concentrations < 50 nmol/L. The mean holoTC concentration was 88.9 ± 33.7 pmol/L (94.8 ± 34.6 pmol/L in women and 73.6 ± 25.6 in men). Only 8% of the women were cobalamin deficient (< 50 pmol/L holoTC) compared to 22% of the men. The mean RBC folate concentration was 831 ± 244 nmol/L, while the prevalence of folate deficiency was 10%. Linear regression analysis showed that only folate equivalent intake was associated with the relevant nutrient status marker.

Conclusion
Our findings suggest that healthy, independently living older people with high levels of education, physical activity, and health awareness are not necessarily at higher risk of vitamin D, folate and cobalamin deficiency. Further studies are needed to verify these findings and to identify lifestyle and dietary patterns that can predict adequate nutrient status for healthy ageing.

Trial registration
This study is officially recorded in the German Clinical Trials Register (DRKS00021302).
Documentation of cognitive impairment screening amongst older hospitalised Australians: a prospective clinical record audit
Authors: Rice Radhika , Bryant Jamie , Fisher Rob Sanson 
Published: October 2023

Abstract
Background
Failure to detect cognitive impairment (CI) in hospitalised older inpatients has serious medical and legal implications, including for the implementation of care planning. This mixed methods study aimed to determine amongst hospital in-patients aged ≥ 65 years: (1) Rates of documentation of screening for CI, including the factors associated with completion of screening; (2) Rates of undocumented CI amongst patients who had not received screening during their admission; (3) Healthcare provider practices and barriers related to CI screening.

Methods
A mixed methods study incorporating a clinical audit and interviews with healthcare providers was conducted at one Australian public hospital. Patients were eligible for inclusion if they were aged 65 years and older and were admitted to a participating ward for a minimum of 48 h. Patient characteristics, whether CI screening had been documented, were extracted using a template. Patients who had not been screened for CI completed the Montreal Cognitive Assessment (MoCA) to determine cognitive status. Interviews were conducted with healthcare providers to understand practices and barriers to screening for CI.

Results
Of the 165 patients included, 34.5% (n = 57) had screening for CI documented for their current admission. Patients aged > 85 years and those with two or more admissions had greater odds of having CI screening documented. Among patients without CI screening documented, 72% (n = 78) were identified as cognitively impaired. While healthcare providers agreed CI screening was beneficial, they identified lack of time and poor knowledge as barriers to undertaking screening.

Conclusions
CI is frequently unrecognised in the hospital setting which is a missed opportunity for the provision of appropriate care. Future research should identify feasible and effective strategies to increase implementation of CI screening in hospitals.
Feasibility and acceptability of an online mental health intervention for pregnant women and their partners: a mixed method study with a pilot randomized control trial
Authors: Canfield Shannon M. , Canada Kelli E. , Rolbiecki Abigail J. , Petroski Gregory F. 
Published: October 2023

Abstract
Background
Untreated perinatal mood and anxiety disorders (PMAD) have short- and long-term health and social consequences; online cognitive behavioral therapy (CBT) interventions can reduce symptoms. Despite partner support being protective online interventions rarely target couples. This study builds on research on an existing CBT-based intervention, the Mothers and Babies Online Course (eMB), by testing its feasibility with prenatal couples.

Methods
We conducted a pilot, randomized, controlled feasibility trial using a 1:1 parallel design. To be eligible, participant dyads were pregnant people (between 13–30 weeks gestation and with a score of 10 or greater on either the GAD-7 or PHQ-9 scale indicating elevated symptoms of anxiety or depression) and their cohabitating partners, living in Missouri, with access to the internet; both in the dyad consented to participate. Recruitment occurred via Facebook ads, flyers, and a snowball approach. The intervention group received eMB, and the control group received a list of community resources. We examined retention and adherence data extracted from eMB analytics and study databases. All participants were given depression and anxiety scales at baseline, 4 and 8 weeks to test preliminary efficacy; satisfaction and acceptability were measured at trial end (i.e., eight weeks) and via interview.

Results
There were 441 people who responded to recruitment materials, 74 pregnant people were screened; 19 partners did not complete enrolment, and 25 dyads were ineligible. There were 15 dyads per group (N = 30) who enrolled; all completed the study. The survey response rate was 90% but partners required nearly twice the number of reminders. No participant completed all lessons. Mean depression and anxiety scores dropped over time for dyads in control (M = -1.99, -1.53) and intervention (M = -4.80, -1.99). Intervention pregnant people’s anxiety significantly decreased (M = -4.05; 95% CI [0.82, 7.27]) at time two compared to control. Twelve pregnant people and four partners participated in post-intervention interviews and suggested improvements for eMB.

Conclusion
Online dyadic interventions can potentially reduce PMAD symptoms. However, to feasibly study eMB with couples, strategies to increase program adherence are necessary. Tailoring interventions to overtly include partners may be advantageous.

Trial registration
ClinicalTrials.gov NCT05867680, 19/05/2023.
Validation of hypermethylated DNA regions found in colorectal cancers as potential aging-independent biomarkers of precancerous colorectal lesions
Authors: Sajibu Sija , Sonder Emanuel , Tiwari Amit , Orjuela Stephany , Parker Hannah R. , Frans Olivier The , Gubler Christoph , Marra Giancarlo , Robinson Mark D. 
Published: October 2023

AbstractBackgroundWe previously identified 16,772 colorectal cancer-associated hypermethylated DNA regions that were also detectable in precancerous colorectal lesions (preCRCs) and unrelated to normal mucosal aging. We have now conducted a study to validate 990 of these differentially methylated DNA regions (DMRs) in a new series of preCRCs.MethodsWe used targeted bisulfite sequencing to validate these 990 potential biomarkers in 59 preCRC tissue samples (41 conventional adenomas, 18 sessile serrated lesions), each with a patient-matched normal mucosal sample. Based on differential DNA methylation tests, a panel of candidate DMRs was chosen on a subset of our cohort and then validated on the remaining part of our cohort and two publicly available datasets with respect to their stratifying potential between preCRCs and normal mucosa.ResultsStrong statistical significance for the difference in methylation levels was observed across the full set of 990 investigated DMRs. From these, a selected candidate panel of 30 DMRs correctly identified 58/59 tumors (area under the receiver operating curve: 0.998).ConclusionsThese validated DNA hypermethylation markers can be exploited to develop more accurate noninvasive colorectal tumor screening assays.
Denosumab administration for bone metastases from solid tumors: a retrospective cross-sectional study
Authors: Mizuta Kohei , Oshiro Hiromichi , Katsuki Ryo , Tsuha Yuichi , Aoki Yusuke , Tome Yasunori , Nishida Kotaro 
Published: October 2023

Abstract
Background
Little is known on how denosumab reduces skeletal-related events (SREs) by bone metastases from solid tumors. We sought to evaluate the effect of denosumab administration in patients with bone metastases from solid tumors.

Methods
Data of patients treated with denosumab were collected from electronic medical charts (n = 496). Eligible participants in this study were adult patients (age ≥ 18 years) with metastatic bone lesions from solid tumors treated with denosumab. SREs, surgical interventions, the spinal instability neoplastic score (SINS) for spinal region, and Mirels’ score for the appendicular region were evaluated. To assess whether denosumab could prevent SREs and associated surgery, the SINS and Mirels’ score were compared between patients with and without SREs.

Results
A total of 247 patients (median age, 65.5 years old; median follow-up period, 13 months) treated with denosumab for metastatic bone lesions from solid tumors were enrolled in this study. SREs occurred in 19 patients (7.7%). SREs occurred in 2 patients (0.8%) who took denosumab administration before SREs. Surgical interventions were undertaken in 14 patients (5.7%) (spinal and intradural lesions in five patients and appendicular lesions in nine patients). The mean SINS of patients without SREs compared to those with SREs were 7.5 points and 10.2 points, respectively. The mean Mirels’ scores of non-SREs patients and those with SREs were 8.07 points and 10.7 points, respectively. Patients with SREs had significantly higher Mirels’ score than non-SREs patients (p < 0.01). Patients with SREs had higher SINS than non-SREs patients (p = 0.09).

Conclusions
SREs occurred in patients with higher SINS or Mirels’ scores. Two patients suffered from SREs though they took denosumab administration before SREs. Appropriate management of denosumab for patients with bone metastasis is significant. Surgical interventions may be needed for patients who with higher SINS or Mirel’s scores.