bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pediatric leukemia and maternal occupational exposure to anticancer drugs: the Japan Environment and Children’s Study
Authors: Yamamoto Shunsuke , Sanefuji Masafumi , Suzuki Maya , Sonoda Yuri , Hamada Norio , Kato Wakako , Ono Hiroaki , Oba Utako , Nakashima Kentaro , Ochiai Masayuki , Kusuhara Koichi , Koga Yuhki , Ohga Shouichi 
Published: October 2023

Abstract
Occupational exposure to medical agents and ionizing radiation has been suggested as a possible risk factor for childhood cancer. However, the relationship between such exposure and pediatric malignant neoplasms has not yet been comprehensively studied. This cohort study aimed to investigate the association between parental occupational exposure to hazardous medical agents or ionizing radiation and the risk of childhood cancer in offspring. Data from a large birth cohort in Japan, which included 104 062 fetuses, were analyzed. The primary outcome was the development of leukemia or brain tumors diagnosed by community physicians during the first 3 years after birth. Exposure factors were medical agents, including anticancer agents, ionizing radiation, and anesthetics, handled by mothers during pregnancy or by fathers for 3 months before conception. The incidence of leukemia, but not of brain tumors, was higher in mothers exposed to anticancer drugs. Multivariable regression analysis showed that maternal exposure to anticancer drugs was associated with an increased risk of leukemia in offspring older than 1 year (adjusted relative risk, 7.99 [95% confidence interval, 1.98-32.3]). Detailed information obtained from medical certificates of patients with identified leukemia revealed no infant leukemia but acute lymphoblastic leukemias in the exposed group. Our findings suggest that maternal occupational exposure to anticancer drugs may be a potential risk factor for acute lymphoblastic leukemia in offspring older than 1 year. Effective prevention methods may be necessary to prevent maternal exposure to anticancer drugs and to reduce the risk of childhood malignant neoplasms.
Predicting tumour content of liquid biopsies from cell-free DNA
Authors: Cardner Mathias , Marass Francesco , Gedvilaite Erika , Yang Julie L. , Tsui Dana W. Y. , Beerenwinkel Niko 
Published: September 2023

Abstract
Background
Liquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-free DNA (cfDNA) fragment lengths has been shown to differ between healthy subjects and cancer patients, whereby the distributional shift correlates with the sample’s tumour content. These fragmentomic data have not yet been utilised to directly quantify the proportion of tumour-derived cfDNA in a liquid biopsy.

Results
We used statistical learning to predict tumour content from Fourier and wavelet transforms of cfDNA length distributions in samples from 118 cancer patients. The model was validated on an independent dilution series of patient plasma.

Conclusions
This proof of concept suggests that our fragmentomic methodology could be useful for predicting tumour content in liquid biopsies.
DGDTA: dynamic graph attention network for predicting drug–target binding affinity
Authors: Zhai Haixia , Hou Hongli , Luo Junwei , Liu Xiaoyan , Wu Zhengjiang , Wang Junfeng 
Published: September 2023

AbstractBackgroundObtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins and drugs still need to be further analyzed. Recently, deep learning has been successfully used in many fields. Hence, designing a more effective deep learning method for predicting DTA remains attractive.ResultsDynamic graph DTA (DGDTA), which uses a dynamic graph attention network combined with a bidirectional long short-term memory (Bi-LSTM) network to predict DTA is proposed in this paper. DGDTA adopts drug compound as input according to its corresponding simplified molecular input line entry system (SMILES) and protein amino acid sequence. First, each drug is considered a graph of interactions between atoms and edges, and dynamic attention scores are used to consider which atoms and edges in the drug are most important for predicting DTA. Then, Bi-LSTM is used to better extract the contextual information features of protein amino acid sequences. Finally, after combining the obtained drug and protein feature vectors, the DTA is predicted by a fully connected layer. The source code is available from GitHub athttps://github.com/luojunwei/DGDTA.ConclusionsThe experimental results show that DGDTA can predict DTA more accurately than some other methods.
Reference-based genome compression using the longest matched substrings with parallelization consideration
Authors: Lu Zhiwen , Guo Lu , Chen Jianhua , Wang Rongshu 
Published: September 2023

Abstract
Background
A large number of researchers have devoted to accelerating the speed of genome sequencing and reducing the cost of genome sequencing for decades, and they have made great strides in both areas, making it easier for researchers to study and analyze genome data. However, how to efficiently store and transmit the vast amount of genome data generated by high-throughput sequencing technologies has become a challenge for data compression researchers. Therefore, the research of genome data compression algorithms to facilitate the efficient representation of genome data has gradually attracted the attention of these researchers. Meanwhile, considering that the current computing devices have multiple cores, how to make full use of the advantages of the computing devices and improve the efficiency of parallel processing is also an important direction for designing genome compression algorithms.

Results
We proposed an algorithm (LMSRGC) based on reference genome sequences, which uses the suffix array (SA) and the longest common prefix (LCP) array to find the longest matched substrings (LMS) for the compression of genome data in FASTA format. The proposed algorithm utilizes the characteristics of SA and the LCP array to select all appropriate LMSs between the genome sequence to be compressed and the reference genome sequence and then utilizes LMSs to compress the target genome sequence. To speed up the operation of the algorithm, we use GPUs to parallelize the construction of SA, while using multiple threads to parallelize the creation of the LCP array and the filtering of LMSs.

Conclusions
Experiment results demonstrate that our algorithm is competitive with the current state-of-the-art algorithms in compression ratio and compression time.
Time course of changes in the transcriptome during russet induction in apple fruit
Authors: Straube Jannis , Suvarna Shreya , Chen Yun-Hao , Khanal Bishnu P. , Knoche Moritz , Debener Thomas 
Published: September 2023

Abstract
Background
Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear. Here, we present high-resolution transcriptomic data by controlled russet induction at very early stages of fruit development. During Phase I, a patch of the fruit surface is exposed to surface moisture. For Phase II, moisture exposure is terminated, and the formerly exposed surface remains dry. We targeted differentially expressed transcripts as soon as 24 h after russet induction.

Results
During moisture exposure (Phase I) of ‘Pinova’ apple, transcripts associated with the cell cycle, cell wall, and cuticle synthesis (SHN3) decrease, while those related to abiotic stress increase. NAC35 and MYB17 were the earliest induced genes during Phase I. They are therefore linked to the initial processes of cuticle microcracking. After moisture removal (Phase II), the expression of genes related to meristematic activity increased (WOX4 within 24 h, MYB84 within 48 h). Genes related to lignin synthesis (MYB52) and suberin synthesis (MYB93, WRKY56) were upregulated within 3 d after moisture removal. WOX4 and AP2B3 are the earliest differentially expressed genes induced in Phase II. They are therefore linked to early events in periderm formation. The expression profiles were consistent between two different seasons and mirrored differences in russet susceptibility in a comparison of cultivars. Furthermore, expression profiles during Phase II of moisture induction were largely identical to those following wounding.

Conclusions
The combination of a unique controlled russet induction technique with high-resolution transcriptomic data allowed for the very first time to analyse the formation of cuticular microcracks and periderm in apple fruit immediately after the onset of triggering factors. This data provides valuable insights into the spatial-temporal dynamics of russeting, including the synthesis of cuticles, dedifferentiation of cells, and impregnation of cell walls with suberin and lignin.
Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group
Authors: Rudrapatna Vivek A. , Ravindranath Vignesh G. , Arneson Douglas V. , Mosenia Arman , Butte Atul J. , Wang Shan 
Published: October 2023

Abstract
Background
The advent of clinical trial data sharing platforms has created opportunities for making new discoveries and answering important questions using already collected data. However, existing methods for meta-analyzing these data require the presence of shared control groups across studies, significantly limiting the number of questions that can be confidently addressed. We sought to develop a method for meta-analyzing potentially heterogeneous clinical trials even in the absence of a common control group.

Methods
This work was conducted within the context of a broader effort to study comparative efficacy in Crohn’s disease. Following a search of clnicaltrials.gov we obtained access to the individual participant data from nine trials of FDA-approved treatments in Crohn’s Disease (N = 3392). We developed a method involving sequences of regression and simulation to separately model the placebo- and drug-attributable effects, and to simulate head-to-head trials against an appropriately normalized background. We validated this method by comparing the outcome of a simulated trial comparing the efficacies of adalimumab and ustekinumab against the recently published results of SEAVUE, an actual head-to-head trial of these drugs. This study was pre-registered on PROSPERO (#157,827) prior to the completion of SEAVUE.

Results
Using our method of sequential regression and simulation, we compared the week eight outcomes of two virtual cohorts subject to the same patient selection criteria as SEAVUE and treated with adalimumab or ustekinumab. Our primary analysis replicated the corresponding published results from SEAVUE (p = 0.9). This finding proved stable under multiple sensitivity analyses.

Conclusions
This new method may help reduce the bias of individual participant data meta-analyses, expand the scope of what can be learned from these already-collected data, and reduce the costs of obtaining high-quality evidence to guide patient care.
Implementation of interprofessional quality circles on deprescribing in Swiss nursing homes: an observational study
Authors: Mena Stephanie , Moullin Joanna C. , Schneider Marie , Niquille Anne 
Published: October 2023

Abstract
Background
Polypharmacy and potentially inappropriate medications (PIMs) are still frequent among older adults in nursing homes. Deprescribing is an intervention that has been shown to be effective in reducing their use. However, the implementation of deprescribing in clinical practice has not yet been widely evaluated. The Quality Circle Deprescribing Module (QC-DeMo) intervention has been trialled through an effectiveness-implementation hybrid type 2 design. The intervention consists of a quality circle workshop session between healthcare professionals HCPs (physicians, nurses, and pharmacists) within a nursing home, in which they define a consensus to deprescribe specific PIMs classes. The aim of this study was to evaluate the implementation of the QC-DeMo intervention in nursing homes.

Methods
This observational study focuses on the implementation part of the QC-DeMo trial. Implementation was based on the Framework for Implementation of Pharmacy Services (FISpH). Questionnaires at baseline and follow-up were used to evaluate reach, adoption, implementation effectiveness, fidelity, implementation, maintenance and the implementation strategies. Other data were collected from the QC-DeMo trial and routine data collected as part of the integrated pharmacy service where the QC-Demo trial was embedded. Implementation strategies included training of pharmacists, integration of the intervention into an existing quality circle dynamic and definition of tailored strategies to operationalise the consensus by each nursing home.

Results
The QC-DeMo intervention was successfully implemented in 26 nursing homes in terms of reach, fidelity, adoption, implementation and implementation effectiveness. However, the intervention was found to be implemented with low maintenance as none of the nursing homes repeated the intervention after the trial. Implementation strategies were well received by HCPs: training was adequate according to pharmacists. Pre-existing quality circle dynamic facilitated interprofessional collaboration as involvement and support of each HCP was rated as high. HCPs recognized a specific and important role for each HCP in the deprescribing process. The most relevant tailored strategies to implement the consensus defined by each nursing home were identification of the patients by the pharmacist and a systematic review of medication’s patients.

Conclusions
The implementation of a Quality Circle on Deprescribing is feasible but its maintenance in practice remains challenging. This study explores multiple implementation outcomes to better inform future implementation efforts of these types of interventions.

Trial registration
ClinicalTrials.gov (NCT03688542), registered on 26.09.2018.
Characterization of patients admitted to specialized geriatric acute care hospital units with the German version of the Standardized Evaluation and Intervention for Seniors at Risk (SEISAR) screening-instrument: a cross-sectional study
Authors: Wirth Rainer , Verdon J. , Frohnhofen H. , Djukic M. , Meisel M. , Musolf M. , Zinke A. , Heppner H. J. , Jamour M. , Denkinger M. , Trampisch U. S. 
Published: September 2023

Abstract
Background
The Standardized Evaluation and Intervention for Seniors at Risk (SEISAR) screening tool records major geriatric problems, originally applied in the emergency department. Particularly, the distinction of compensated and uncompensated problems is an interesting and new approach. Therefore, we translated the SEISAR in German language and used it to characterize patients in specialized geriatric hospital wards in Germany and to gather initial experience regarding its usability and practicability.

Methods
The tool was translated by three independent specialists in geriatric medicine and backtranslated for quality-assurance by a non-medical English native speaker. In a second step, 8 acute care geriatric hospital departments used the translated version to characterize all consecutive patients admitted over a period of one month between December 2019 and May 2020 at time of admission.

Results
Most of the 756 patients (78%) lived in an own apartment or house prior to hospital admission. Participants had on average 4 compensated and 6 uncompensated problems, a Barthel-Index of 40 pts. on admission with a median increase of 15 points during hospital stay, and a median length of stay of 16 days in the geriatric hospital department.

Conclusion
SEISAR is an interesting standardized brief comprehensive geriatric assessment tool for the identification of compensated and uncompensated health problems in older persons. The data of this study highlights the number, variability, and complexity of geriatric problems in patients treated in specialized acute care geriatric hospital wards in Germany.

Trial registration
German Clinical trial register (DRKS-ID: DRKS00031354 on 27.02.2023).
PB-LNet: a model for predicting pathological subtypes of pulmonary nodules on CT images
Authors: Zhang Yuchong , Qu Hui , Tian Yumeng , Na Fangjian , Yan Jinshan , Wu Ying , Cui Xiaoyu , Li Zhi , Zhao Mingfang 
Published: October 2023

Abstract
Objective
To investigate the correlation between CT imaging features and pathological subtypes of pulmonary nodules and construct a prediction model using deep learning.

Methods
We collected information of patients with pulmonary nodules treated by surgery and the reference standard for diagnosis was post-operative pathology. After using elastic distortion for data augmentation, the CT images were divided into a training set, a validation set and a test set in a ratio of 6:2:2. We used PB-LNet to analyze the nodules in pre-operative CT and predict their pathological subtypes. Accuracy was used as the model evaluation index and Class Activation Map was applied to interpreting the results. Comparative experiments with other models were carried out to achieve the best results. Finally, images from the test set without data augmentation were analyzed to judge the clinical utility.

Results
Four hundred seventy-seven patients were included and the nodules were divided into six groups: benign lesions, precursor glandular lesions, minimally invasive adenocarcinoma, invasive adenocarcinoma Grade 1, Grade 2 and Grade 3. The accuracy of the test set was 0.84. Class Activation Map confirmed that PB-LNet classified the nodules mainly based on the lungs in CT images, which is in line with the actual situation in clinical practice. In comparative experiments, PB-LNet obtained the highest accuracy. Finally, 96 images from the test set without data augmentation were analyzed and the accuracy was 0.89.

Conclusions
In classifying CT images of lung nodules into six categories based on pathological subtypes, PB-LNet demonstrates satisfactory accuracy without the need of delineating nodules, while the results are interpretable. A high level of accuracy was also obtained when validating on real data, therefore demonstrates its usefulness in clinical practice.
Risk of venous thromboembolism in patients undergoing gastric cancer surgery: a systematic review and meta-analysis
Authors: Xiang Lin , Jin Shuai , Yu Yang , Wang Dengfeng , Chen Hao 
Published: October 2023

Abstract
Background
Venous thromboembolism (VTE) is a common postoperative complication in patients undergoing surgery for gastric cancer (GC). Although VTE incidence may vary among cancers, guidelines rarely stratify preventive methods for postoperative VTE by cancer type. The risk of VTE in patients undergoing surgery for GC remains unclear.

Methods
A systematic review and meta-analysis was undertaken to determine the risk of VTE after GC surgery and discuss the clinical value of pharmacological thromboprophylaxis in these cases. Medline, Embase, Web of Science, and Cochrane Library databases were searched for articles published from their inception to September 2022.

Results
Overall, 13 studies (111,936 patients) were included. The overall 1-month incidence of VTE, deep vein thrombosis (DVT), and pulmonary embolism (PE) after GC surgery was 1.8% (95% CI, 0.8–3.1%; I²=98.5%), 1.2% (95% CI, 0.5–2.1%; I²=96.1%), and 0.4% (95% CI, 0.1–1.1%; I²=96.3%), respectively. The prevalence of postoperative VTE was comparable between Asian and Western populations (1.8% vs. 1.8%; P > 0.05). Compared with mechanical prophylaxis alone, mechanical plus pharmacological prophylaxis was associated with a significantly lower 1-month rate of postoperative VTE and DVT (0.6% vs. 2.9% and 0.6% vs. 2.8%, respectively; all P < 0.05), but not PE (P > 0.05). The 1-month postoperative incidence of VTE was not significantly different between laparoscopic and open surgery (1.8% vs. 4.3%, P > 0.05).

Conclusion
Patients undergoing GC surgery do not have a high risk of VTE. The incidence of VTE after GC surgery is not significantly different between Eastern and Western patients. Mechanical plus pharmacological prophylaxis is more effective than mechanical prophylaxis alone in postoperative VTE prevention. The VTE risk is comparable between open and laparoscopic surgery for GC.
Effects of immediate and distant health consequences: different types of health warning messages on sweets affect the purchase probability
Authors: Mehlhose Clara , Risius Antje 
Published: September 2023

Abstract
Background
Several health control policies have been discussed as a regulatory approach to tackle the increasing prevalence of obesity and other health risks related to sugar consumption. Health warnings, like the ones used in tobacco control worldwide, are one of the most promising approaches. However, in the case of health warning messages for food products, it is much more complicated and involves much more consumer involvement than tobacco guidance. Therefore, it is important to better understand the efficacy, evaluation, and reactance of health warning labels in the food sector regarding consumers’ behavior, persuasion, and perceptions. The aim of this study was to examine how different types (design and message) of health warning messages in combination with graphical applications affect consumer behavior.

Methods
In a 3 × 3 × 3 symmetrical design, 1,040 German participants completed an online discrete choice experiment including various text-only and image-and-text health warning labels on sweets. An accompanying questionnaire assessed socio-demographic variables as well as psychometric scales to understand the relationship between fear, control, reactance, and shocking/inhibiting/mediating health-related warnings.

Results
Our results suggest that especially emotional graphical images combined with text health warning labels might be more influential. The health effects of immediate (caries) and more distant health consequences (diabetes/obesity) differ in their impact. Further, results show that especially when consumers engage in a danger control process for overweight, warning messages have a negative impact on their choices.

Conclusion
Hence, warning labels on sweets can potentially be a decisive factor when communicating health threats related to excessive sugar consumption. In the context of a targeted health policy, we see the need for further research, especially concerning the perception and understanding of noncommunicable diseases (NCDs) in the population.