bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fuzzy Postprocessing to Advance the Quality of Continental Seasonal Hydrological Forecasts for River Basin Management
Authors: Macian-Sorribes Hector , Pechlivanidis Ilias , Crochemore Louise , Pulido-Velazquez Manuel 
Published: September 2020

AbstractStreamflow forecasting services driven by seasonal meteorological forecasts from dynamic prediction systems deliver valuable information for decision-making in the water sector. Moving beyond the traditional river basin boundaries, large-scale hydrological models enable a coordinated, efficient, and harmonized anticipation and management of water-related risks (droughts, floods). However, the use of forecasts from such models at the river basin scale remains a challenge, depending on how the model reproduces the hydrological features of each particular river basin. Consequently, postprocessing of forecasts is a crucial step to ensure usefulness at the river basin scale. In this paper we present a methodology to postprocess seasonal streamflow forecasts from large-scale hydrological models and advance their quality for local applications. It consists of fuzzy logic systems that bias-adjust seasonal forecasts from a large-scale hydrological model by comparing its modeled streamflows with local observations. The methodology is demonstrated using forecasts from the pan-European hydrological model E-HYPE at the Jucar River basin (Spain). Fuzzy postprocessed forecasts are compared to postprocessed forecasts derived from a quantile mapping approach as a benchmark. Fuzzy postprocessing was able to provide skillful streamflow forecasts for the Jucar River basin, keeping most of the skill of raw E-HYPE forecasts and also outperforming quantile-mapping-based forecasts. The proposed methodology offers an efficient one-to-one mapping between large-scale modeled streamflows and basin-scale observations preserving its temporal dependence structure and can adapt its input set to increase the skill of postprocessed forecasts.
Fractures are common within 18 months following first-line R-CHOP in older patients with diffuse large B-cell lymphoma
Authors: Booth Stephen , Plaschkes Hannah , Kirkwood Amy A. , Gibb Adam , Horgan Patrick , Higham Claire , Oladipo Joanna M. , Browning Joe , Khan Usman , Tseu Bing , Chen Lucia , Willan John , Wolf Julia , Gunawan Arief , Fields Paul , Ebsworth Tim , Lown Robert , Gordon-Walker Dominic , Shah Nimish , Linton Kim M. , Collins Graham P. , Kothari Jaimal , Hildyard Catherine , Eyre Toby A. 
Published: September 2020

AbstractDiffuse large B-cell lymphoma (DLBCL) and osteoporotic fracture are both more common in older patients. Exposure to R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone) is likely to increase the risk of fracture, but evidence is lacking to define fracture incidence in this group. Data on consecutive patients with DLBCL aged ≥70 years treated with 1 to 8 cycles of full or attenuated R-CHOP were retrospectively collected across 10 UK centers (2009-2019). Patients were followed up from starting R-CHOP for a minimum of 6 months and censored at 18 months; at last follow-up if &lt;18 months; or at progression or death. Of 877 patients identified, 148 were excluded: 121 had progression or died before 6 months; 23 had follow-up &lt;6 months. Across 729 remaining patients, the median age was 77 years, and 68% had an Eastern Cooperative Oncology Group performance status of 0 to 1. Eighty-one fractures occurred within 18 months of follow-up; 42 were symptomatic, including 30 requiring hospital attendance or admission. The cumulative fracture incidence was 6.2% (95% confidence interval [CI], 4.7-8.2) at 6 months; 9.7% (95% CI, 7.8-12.1) at 12 months; and 11.4% (95% CI, 9.3-14.0) at 18 months. Multivariate analysis identified a predisposing history (osteoporosis, osteopenia, prior fracture, and rheumatoid arthritis [RhA]), DLBCL bone involvement at baseline, and receipt of prephase steroids as independent risk factors for fracture. There is a clinically relevant fracture risk and significant associated morbidity in older patients receiving R-CHOP. Careful attention to bone health is warranted in older patients receiving R-CHOP. Randomized studies are required to better define the most effective strategies to reduce fracture risk.
Weekend and off-hour effects on the incidence of cerebral palsy: contribution of consolidated perinatal care
Authors: Toyokawa Satoshi , Hasegawa Junichi , Ikenoue Tsuyomu , Asano Yuri , Jojima Emi , Satoh Shoji , Ikeda Tomoaki , Ichizuka Kiyotake , Takeda Satoru , Tamiya Nanako , Nakai Akihito , Fujimori Keiya , Maeda Tsugio , Masuzaki Hideaki , Suzuki Hideaki , Ueda Shigeru 
Published: September 2020

Abstract
Objective
This study estimated the effects of weekend and off-hour childbirth and the size of perinatal medical care center on the incidence of cerebral palsy.

Methods
The cases were all children with severe cerebral palsy born in Japan from 2009 to 2012 whose data were stored at the Japan Obstetric Compensation System for Cerebral Palsy database, a nationally representative database. The inclusion criteria were the following: neonates born between January 2009 and December 2012 who had a birth weight of at least 2000 g and gestational age of at least 33 weeks and who had severe disability resulting from cerebral palsy independent of congenital causes or factors during the neonatal period or thereafter. Study participants were restricted to singletons and controls without report of death, scheduled cesarean section, or ambulance transportation. The controls were newborns, randomly selected by year and type of delivery (normal spontaneous delivery without cesarean section and emergency cesarean section) using a 1:10 case to control ratio sampled from the nationwide Japan Society of Obstetrics and Gynecology database.

Results
A total of 90 cerebral palsy cases and 900 controls having normal spontaneous delivery without cesarean section were selected, as were 92 cerebral palsy cases and 920 controls with emergent cesarean section. A significantly higher risk for cerebral palsy was found among cases that underwent emergent cesarean section on weekends (odds ratio [OR] 1.72, 95% confidence interval [CI] 1.06–2.81) and during the night shift (OR 2.29, 95% CI 1.30–4.02). No significant risk was found among normal spontaneous deliveries on weekends (OR 1.63, 95% CI 0.97–2.73) or during the quasi-night shift (OR 1.26, 95% CI 0.70–2.27). Regional perinatal care centers showed significantly higher risk for cerebral palsy in both emergent cesarean section (OR 2.35, 95% CI 1.47–3.77) and normal spontaneous delivery (OR 2.92, 95% CI 1.76–4.84).

Conclusion
Labor on weekends, during the night shift, and at regional perinatal medical care centers was associated with significantly elevated risk for cerebral palsy in emergency cesarean section.
NEMPD: a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information
Authors: Ji Bo-Ya , You Zhu-Hong , Chen Zhan-Heng , Wong Leon , Yi Hai-Cheng 
Published: September 2020

Abstract
Background
As an important non-coding RNA, microRNA (miRNA) plays a significant role in a series of life processes and is closely associated with a variety of Human diseases. Hence, identification of potential miRNA-disease associations can make great contributions to the research and treatment of Human diseases. However, to our knowledge, many existing computational methods only utilize the single type of known association information between miRNAs and diseases to predict their potential associations, without focusing on their interactions or associations with other types of molecules.

Results
In this paper, we propose a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information. Firstly, a heterogeneous network is constructed by integrating known associations among miRNA, protein and disease, and the network representation method Learning Graph Representations with Global Structural Information (GraRep) is implemented to learn the behavior information of miRNAs and diseases in the network. Then, the behavior information of miRNAs and diseases is combined with the attribute information of them to represent miRNA-disease association pairs. Finally, the prediction model is established based on the Random Forest algorithm. Under the five-fold cross validation, the proposed NEMPD model obtained average 85.41% prediction accuracy with 80.96% sensitivity at the AUC of 91.58%. Furthermore, the performance of NEMPD is also validated by the case studies. Among the top 50 predicted disease-related miRNAs, 48 (breast neoplasms), 47 (colon neoplasms), 47 (lung neoplasms) were confirmed by two other databases.

Conclusions
The proposed NEMPD model has a good performance in predicting the potential associations between miRNAs and diseases, and has great potency in the field of miRNA-disease association prediction in the future.
Automated classification of protein subcellular localization in immunohistochemistry images to reveal biomarkers in colon cancer
Authors: Xue Zhen-Zhen , Wu Yanxia , Gao Qing-Zu , Zhao Liang , Xu Ying-Ying 
Published: September 2020

AbstractBackgroundProtein biomarkers play important roles in cancer diagnosis. Many efforts have been made on measuring abnormal expression intensity in biological samples to identity cancer types and stages. However, the change of subcellular location of proteins, which is also critical for understanding and detecting diseases, has been rarely studied.ResultsIn this work, we developed a machine learning model to classify protein subcellular locations based on immunohistochemistry images of human colon tissues, and validated the ability of the model to detect subcellular location changes of biomarker proteins related to colon cancer. The model uses representative image patches as inputs, and integrates feature engineering and deep learning methods. It achieves 92.69% accuracy in classification of new proteins. Two validation datasets of colon cancer biomarkers derived from published literatures and the human protein atlas database respectively are employed. It turns out that 81.82 and 65.66% of the biomarker proteins can be identified to change locations.ConclusionsOur results demonstrate that using image patches and combining predefined and deep features can improve the performance of protein subcellular localization, and our model can effectively detect biomarkers based on protein subcellular translocations. This study is anticipated to be useful in annotating unknown subcellular localization for proteins and discovering new potential location biomarkers.
Species delimitation in the cyanolichen genus Rostania
Authors: Košuthová Alica , Bergsten Johannes , Westberg Martin , Wedin Mats 
Published: September 2020

AbstractBackgroundIn this study, we investigate species limits in the cyanobacterial lichen genusRostania(Collemataceae, Peltigerales, Lecanoromycetes). Four molecular markers (mtSSU rDNA, β-tubulin, MCM7, RPB2) were sequenced and analysed with two coalescent-based species delimitation methods: the Generalized Mixed Yule Coalescent model (GMYC) and a Bayesian species delimitation method (BPP) using a multispecies coalescence model (MSC), the latter with or without an a priori defined guide tree.ResultsSpecies delimitation analyses indicate the presence of eight strongly supported candidate species. Conclusive correlation between morphological/ecological characters and genetic delimitation could be found for six of these. Of the two additional candidate species, one is represented by a single sterile specimen and the other currently lacks morphological or ecological supporting evidence.ConclusionsWe conclude thatRostaniaincludes a minimum of six species:R. ceranisca,R. multipunctata,R. occultata1,R. occultata2,R. occultata3, andR. occultata4,5,6. Three distinctNostocmorphotypes occur inRostania, and there is substantial correlation between these morphotypes andRostaniathallus morphology.
ComHapDet: a spatial community detection algorithm for haplotype assembly
Authors: Sankararaman Abishek , Vikalo Haris , Baccelli François 
Published: September 2020

AbstractBackgroundHaplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual’s susceptibility to hereditary and complex diseases and affect how our bodies respond to therapeutic drugs. Reconstructing haplotypes of an individual from short sequencing reads is an NP-hard problem that becomes even more challenging in the case of polyploids. While increasing lengths of sequencing reads and insert sizes helps improve accuracy of reconstruction, it also exacerbates computational complexity of the haplotype assembly task. This has motivated the pursuit of algorithmic frameworks capable of accurate yet efficient assembly of haplotypes from high-throughput sequencing data.ResultsWe propose a novel graphical representation of sequencing reads and pose the haplotype assembly problem as an instance of community detection on a spatial random graph. To this end, we construct a graph where each read is a node with an unknown community label associating the read with the haplotype it samples. Haplotype reconstruction can then be thought of as a two-step procedure: first, one recovers the community labels on the nodes (i.e., the reads), and then uses the estimated labels to assemble the haplotypes. Based on this observation, we propose – a novel assembly algorithm for diploid and ployploid haplotypes which allows both bialleleic and multi-allelic variants.ConclusionsPerformance of the proposed algorithm is benchmarked on simulated as well as experimental data obtained by sequencing Chromosome 5 of tetraploid biallelicSolanum-Tuberosum(Potato). The results demonstrate the efficacy of the proposed method and that it compares favorably with the existing techniques.
The relationship between the level of μ-opioid receptor (μORs) and postoperative analgesic use in patients undergoing septoplasty: a prospective randomized controlled trial
Authors: Gencer Muzaffer , Göçmen Ayşe Yeşim 
Published: September 2020

Abstract
Background
In this study, the μ-Opioid receptor activity was assessed pre-operatively for its association with postoperative pain level and second analgesic requirement in patients undergoing septoplasty.

Methods
In our prospective study, 120 adult patients underwent septoplasty from June 2015 to January 2019 were randomly divided into 2 pre-operative groups. The first group (n = 60) was patients given tramadol (1–2 mg/kg) for post-operative analgesia, and the second group (control group) (n = 60) was initially prescribed only fentanyl (1 μg/ kg-i.v.) in the induction. Acetaminophen with codeine analgesic 325/30 mg (p.o.) was used as an rescue painkiller in the post-operative period. The μ-Opioid receptor activity was investigated in pre-operative blood samples and compared to post-operative pain level and time required for second round of analgesic administration. The visual analogue score (VAS) was used to evaluate the post-operative pain degree (0 no pain; 10 worst pain). The patients’ post-operative VAS scores were evaluated upon arrival to recovery room, and at the 1st, 3rd, 7th, 10th, and 24th hour post-operative period.

Results
Demographic data and peri-operative variables were similar in both study group (p < 0.05).There was no significant difference between the receptor levels in both groups and the mean receptor level was 200.94 ± 15.34 pg/mL (max:489.92 ± 22.36 pg/mL, min: 94.56 ± 11.23 pg/mL).In patients who used tramadol as the levels of μ-Opioid receptors increased, VAS scores of patients and second analgesic use decreased in post-operative period.The VAS scores in patients with higher receptor levels were lower in the recovery room (p < 0.05), 1st (p < 0.05) and 3rd hours (p < 0.05).The VAS scores were lower in the tramadol group compared to the control group (p < 0.05).Number of secondary analgesic requirement was significantly lower in patients of the tramadol group with higher receptor levels compared to the ones with lower receptor (p < 0.05) for arrival at the recovery room and 1st hour. Patients in the tramadol group needed a second pain killer much later than patients in the control group.

Conclusions
Our study demonstrates that patients with higher μOR levels have a higher efficacy of opioid analgesic agents and an lesser need for additional analgesic agents.

Trial registration
This trial was registered retrospectively (The ACTRN: ACTRN12619001652167, registration date: 26/11/2019).
Traffic police officers’ use of first aid skills at work: a qualitative content analysis of focus group discussions in Dar Es Salaam, Tanzania
Authors: Ndile Menti L. , Saveman Britt-Inger , Lukumay Gift G. , Mkoka Dickson A. , Outwater Anne H. , Backteman-Erlanson Susann 
Published: September 2020

Abstract
Background
The World Health Organisation (WHO) recommends involving lay people in prehospital care. Several training programmes have been implemented to build lay responder first aid skills. Findings show that most programmes significantly improved participants’ first aid skills. However, there is a gap in knowledge of what factors influence the use of these skills in real situations. The current study aimed to describe police officers’ views on and experiences of factors that facilitate or hinder their use of trained first aid skills at work.

Methods
Thirty-four police officers participated in five focus group discussions. A structured interview guide was used to collect data. Interviews were audio-recorded and transcribed verbatim. Data were analysed using qualitative content analysis.

Results
We identified five categories of facilitators or hindrances. Training exposure was considered a facilitator; work situation and hospital atmosphere were considered hindrances; and the physical and social environments and the resources available for providing first aid could be either facilitators or hindrances.

Conclusion
Practical exposure during training is perceived to improve police officers’ confidence in applying their first aid skills at work. However, contextual factors related to the working environment need to be addressed to promote this transfer of skills.
Successful treatment of pulmonary haemorrhage and acute respiratory distress syndrome caused by fulminant Stenotrophomonas maltophilia respiratory infection in a patient with acute lymphoblastic leukaemia – case report
Authors: Andrei Stefan , Ghiaur Alexandra , Brezeanu Lavinia , Martac Cristina , Nicolau Andreea , Coriu Daniel , Droc Gabriela 
Published: September 2020

Abstract
Background
Stenotrophomonas maltophilia-induced pulmonary haemorrhage is considered a fatal infection among haematological patients. The outcome can be explained by the patients’ immunity status and late diagnosis and treatment.

Case presentation
We present the rare case of successful outcome in a 61-year-old female who developed alveolar haemorrhage and acute respiratory distress syndrome 8 days after a chemotherapy session for her acute lymphoblastic leukaemia, in the context of secondary bone marrow aplasia. Stenotrophomonas maltophilia was isolated in sputum culture. The patient benefitted from early empirical treatment with colistin followed by trimethoprim/sulfamethoxazole, according to the antibiogram. Despite a severe initial clinical presentation in need of mechanical ventilation, neuromuscular blocking agents infusion, and ventilation in prone position, the patient had a favourable outcome and was discharged from intensive care after 26 days.

Conclusions
Stenotrophomonas maltophilia severe pneumonia complicated with pulmonary haemorrhage is not always fatal in haematological patients. Empirical treatment of multidrug-resistant Stenotrophomonas maltophilia in an immunocompromised haematological patient presenting with hemoptysis should be taken into consideration.
Risk of Parkinson’s disease following gout: a population-based retrospective cohort study in Taiwan
Authors: Hu Li-Yu , Yang Albert C. , Lee Shyh-Chyang , You Zi-Hong , Tsai Shih-Jen , Hu Chang-Kuo , Shen Cheng-Che 
Published: September 2020

Abstract
Background
The progressive neurodegenerative disorder Parkinson disease (PD) is well-established as the second most common neurodegenerative disease. Associations between the sequential risk of PD and gout have been addressed in other studies, but findings have been inconclusive. Accordingly, we executed the present study with the purpose of assessing PD risk in patients with gout.

Methods
From Taiwan’s National Health Insurance Research Database, we identified the data of patients newly diagnosed as having gout between January 1, 2000 and December 1, 2000. A cohort of patients without gout, matched for sex and age, was constructed for comparison. Hazard ratios (HRs) and the incidence rate of subsequent PD were calculated for both cohorts and separately for male and female groups. The gout and comparison cohorts consisted of 7900 patients each.

Results
The HR for PD was not significantly higher in the gout cohort compared with the control cohort (HR 1.01, 95% confidence interval [CI], 0.93–1.31, P = .268), even after adjustment for age, urbanization, monthly income, sex, and comorbidities. We did not observe gender differences in the gout–PD association (male: HR 1.01, 95% CI, 0.88–1.36, P = .400; female: HR 1.11, 95% CI, 0.84–1.46, P = .466).

Conclusions
Our study identified that there was no protective effect of gout for the risk of PD in the Taiwanese population.
Efficacy of combination-chemotherapy with pirarubicin, ifosfamide, and etoposide for soft tissue sarcoma: a single-institution retrospective analysis
Authors: Saito Shiro , Aiba Hisaki , Yamada Satoshi , Okamoto Hideki , Hayashi Katsuhiro , Kimura Hiroaki , Miwa Shinji , Otsuka Takanobu , Murakami Hideki 
Published: September 2020

Abstract
Background
The standard chemotherapy regimens for soft tissue sarcoma are doxorubicin-based. This retrospective study aimed to assess the efficacy and safety of pirarubicin, ifosfamide, and etoposide combination therapy for patients with this disease.

Methods
Between 2008 and 2017, 25 patients with soft tissue sarcoma were treated with pirarubicin (30 mg/m2, 2 days), ifosfamide (2 g/m2, 5 days), and etoposide (100 mg/m2, 3 days) every 3 weeks. The primary endpoint was overall response, and the secondary endpoint was adverse events of this regimen.

Results
Responses to this regimen according to RECIST criteria were partial response (n = 9, 36%), stable disease (n = 9, 36%) and progressive disease (n = 7, 28%). During the treatment phase, frequent grade 3 or worse adverse events were hematological toxicities including white blood cell decreases (96%), febrile neutropenia (68%), anemia (68%), and platelet count decreases (48%). No long-term adverse events were reported during the study period.

Conclusion
This regimen was comparable to previously published doxorubicin-based combination chemotherapy in terms of response rate. Although there were no long-lasting adverse events, based on our results, severe hematological toxicity should be considered.