bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning models predicting multidrug resistant urinary tract infections using “DsaaS”
Authors: Mancini Alessio , Vito Leonardo , Marcelli Elisa , Piangerelli Marco , De Leone Renato , Pucciarelli Sandra , Merelli Emanuela 
Published: August 2020

Abstract
Background
The scope of this work is to build a Machine Learning model able to predict patients risk to contract a multidrug resistant urinary tract infection (MDR UTI) after hospitalization. To achieve this goal, we used different popular Machine Learning tools. Moreover, we integrated an easy-to-use cloud platform, called DSaaS (Data Science as a Service), well suited for hospital structures, where healthcare operators might not have specific competences in using programming languages but still, they do need to analyze data as a continuous process. Moreover, DSaaS allows the validation of data analysis models based on supervised Machine Learning regression and classification algorithms.

Results
We used DSaaS on a real antibiotic stewardship dataset to make predictions about antibiotic resistance in the Clinical Pathology Operative Unit of the Principe di Piemonte Hospital in Senigallia, Marche, Italy. Data related to a total of 1486 hospitalized patients with nosocomial urinary tract infection (UTI). Sex, age, age class, ward and time period, were used to predict the onset of a MDR UTI. Machine Learning methods such as Catboost, Support Vector Machine and Neural Networks were utilized to build predictive models. Among the performance evaluators, already implemented in DSaaS, we used accuracy (ACC), area under receiver operating characteristic curve (AUC-ROC), area under Precision-Recall curve (AUC-PRC), F1 score, sensitivity (SEN), specificity and Matthews correlation coefficient (MCC). Catboost exhibited the best predictive results (MCC 0.909; SEN 0.904; F1 score 0.809; AUC-PRC 0.853, AUC-ROC 0.739; ACC 0.717) with the highest value in every metric.

Conclusions
the predictive model built with DSaaS may serve as a useful support tool for physicians treating hospitalized patients with a high risk to acquire MDR UTIs. We obtained these results using only five easy and fast predictors accessible for each patient hospitalization. In future, DSaaS will be enriched with more features like unsupervised Machine Learning techniques, streaming data analysis, distributed calculation and big data storage and management to allow researchers to perform a complete data analysis pipeline. The DSaaS prototype is available as a demo at the following address: https://dsaas-demo.shinyapps.io/Server/
Data integration by fuzzy similarity-based hierarchical clustering
Authors: Ciaramella Angelo , Nardone Davide , Staiano Antonino 
Published: August 2020

Abstract
Background
High throughput methods, in biological and biomedical fields, acquire a large number of molecular parameters or omics data by a single experiment. Combining these omics data can significantly increase the capability for recovering fine-tuned structures or reducing the effects of experimental and biological noise in data.

Results
In this work we propose a multi-view integration methodology (named FH-Clust) for identifying patient subgroups from different omics information (e.g., Gene Expression, Mirna Expression, Methylation). In particular, hierarchical structures of patient data are obtained in each omic (or view) and finally their topologies are merged by consensus matrix. One of the main aspects of this methodology, is the use of a measure of dissimilarity between sets of observations, by using an appropriate metric. For each view, a dendrogram is obtained by using a hierarchical clustering based on a fuzzy equivalence relation with Łukasiewicz valued fuzzy similarity. Finally, a consensus matrix, that is a representative information of all dendrograms, is formed by combining multiple hierarchical agglomerations by an approach based on transitive consensus matrix construction. Several experiments and comparisons are made on real data (e.g., Glioblastoma, Prostate Cancer) to assess the proposed approach.

Conclusions
Fuzzy logic allows us to introduce more flexible data agglomeration techniques. From the analysis of scientific literature, it appears to be the first time that a model based on fuzzy logic is used for the agglomeration of multi-omic data. The results suggest that FH-Clust provides better prognostic value and clinical significance compared to the analysis of single-omic data alone and it is very competitive with respect to other techniques from literature.
Transcriptome analysis provides new insights into the transcriptional regulation of methyl jasmonate-induced flavonoid biosynthesis in pear calli
Authors: Premathilake Apekshika T. , Ni Junbei , Shen Jiaqi , Bai Songling , Teng Yuanwen 
Published: August 2020

Abstract
Background
Flavonoid biosynthesis is strongly influenced by phytohormones. For example, methyl jasmonate (MeJA) enhances the flavonoid accumulation in pear. However, the molecular mechanism underlying the MeJA-induced flavonoid biosynthesis in pear is largely uncharacterized. Therefore, the transcriptome of pear calli treated with MeJA was analyzed to elucidate the mechanism regulating MeJA-mediated flavonoid biosynthesis.

Results
The application of exogenous MeJA significantly enhanced flavonoid accumulation, especially anthocyanin, in pear calli. A weighted gene co-expression network analysis identified the differentially expressed genes associated with MeJA-induced flavonoid biosynthesis. The MeJA treatment upregulated the expression of the flavonoid biosynthesis pathway structural genes (PcCHS, PcCHI, PcF3H, PcDFR, PcANS, PcANR2a, and PcLAR1). The MYB family members were the main transcription factors regulating the MeJA-induced flavonoid biosynthesis, but the bHLH, AP2-EREBP, NAC, WRKY, and TIFY families were also involved. In addition to PcMYB10, which is a known positive regulator of anthocyanin biosynthesis in pear, several novel MYB candidates that may regulate flavonol and proanthocyanidin biosynthesis were revealed. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that PcMYB10 and PcMYC2 can directly interact with each other and bind to JAZ repressors (PcJAZ1 and PcJAZ2).

Conclusions
The PcMYB10–PcMYC2 molecular complex is likely involved in the regulation of jasmonate-mediated flavonoid biosynthesis at the transcript level. The data generated in this study may clarify the transcriptional regulatory network associated with the MeJA-induced flavonoid accumulation in pear calli and provide a solid foundation for future studies.
A systematic review and meta-analysis comparing the effect of aquatic and land exercise on dynamic balance in older adults
Authors: Kim Youngwook , Vakula Michael N. , Waller Benjamin , Bressel Eadric 
Published: August 2020

Abstract
Background
Balance impairments are the leading causes of falls in older adults. Aquatic-based exercises have been broadly practiced as an alternative to land-based exercises; however, the effects on dynamic balance have not been comprehensively reviewed and compared to land exercises. Thus, the purpose of this systematic review and meta-analysis was to compare the effectiveness of aquatic exercises (AE) to land exercises (LE) on dynamic balance in older adults.

Methods
Electronic databases (PubMed, MEDLINE, CINAHL, SPORTDiscus, psycINFO), from inception to November 2019, were searched. Studies met the following eligibility criteria: Randomized controlled trials, English language, older adults aged 65 years or older, a minimum of one AE and LE group, at least one assessment for dynamic balance. For the meta-analysis, the effect sizes of dynamic balance outcomes were calculated using a standardized mean difference (SMD) and a 95% confidence interval (CI).

Results
A total of 11 trials met the inclusion criteria, and 10 studies were eligible for the meta-analysis. The meta-analysis presented that older adults in AE groups demonstrated comparable enhancements in dynamic steady-state balance (SMD = − 0.24; 95% CI, −.81 to .34), proactive balance (SMD = − 0.21; 95% CI, −.59 to .17), and balance test batteries (SMD = − 0.24; 95% CI, −.50 to .03) compared with those in LE groups.

Conclusions
AE and LE have comparable impacts on dynamic balance in older adults aged 65 years or older. Thus, this review provides evidence that AE can be utilized as a reasonable alternative to LE to improve dynamic balance and possibly reduce the risk of falls.
Can broad-spectrum multinutrients treat symptoms of antenatal depression and anxiety and improve infant development? Study protocol of a double blind, randomized, controlled trial (the ‘NUTRIMUM’ trial)
Authors: Bradley Hayley A. , Campbell Siobhan A. , Mulder Roger T. , Henderson Jaqueline M. T. , Dixon Lesley , Boden Joseph M. , Rucklidge Julia J. 
Published: August 2020

Abstract
Background
Untreated antenatal depression and anxiety can be associated with short and long term health impacts on the pregnant woman, her infant and the rest of the family. Alternative interventions to those currently available are needed. This clinical trial aims to investigate the efficacy and safety of a broad-spectrum multinutrient formula as a treatment for symptoms of depression and anxiety in pregnant women and to determine the impact supplementation has on the general health and development of the infant.

Methods
This randomised, controlled trial will be conducted in Canterbury, New Zealand between April 2017 and June 2022. One hundred and twenty women aged over 16 years, between 12 and 24 weeks gestation and who score ≥ 13 on the Edinburgh Postnatal Depression Scale (EPDS) will be randomly assigned to take the intervention (n = 60) or an active control formula containing iodine and riboflavin (n = 60) for 12 weeks. After 12 weeks, participants can enter an open-label phase until the birth of their infant and naturalistically followed for the first 12 months postpartum. Infants will be followed until 12 months of age. Randomisation will be computer-generated, with allocation concealment by opaque sequentially numbered envelopes. Participants and the research team including data analysts will be blinded to group assignment. The EPDS and the Clinical Global Impressions Scale of Improvement (CGI-I) will be the maternal primary outcome measures of this study and will assess the incidence of depression and anxiety and the improvement of symptomatology respectively. Generalized linear mixed effects regression models will analyse statistical differences between the multinutrient and active control group on an intent-to-treat basis. A minimum of a three-point difference in EPDS scores between the groups will identify clinical significance. Pregnancy outcomes, adverse events and side effects will also be monitored and reported.

Discussion
Should the multinutrient formula be shown to be beneficial for both the mother and the infant, then an alternative treatment option that may also improve the biopsychosocial development of their infants can be provided for pregnant women experiencing symptoms of depression and anxiety.

Trial registration
Trial ID: ACTRN12617000354381; prospectively registered at Australian New Zealand Clinical Trials Registry on 08/03/2017.
Risk of mini-mental state examination (MMSE) decline in the elderly with type 2 diabetes: a Chinese community-based cohort study
Authors: Zhao Lei , Han Chao , Zheng Zheng , Xiu Shuang Ling , Chan Piu 
Published: August 2020

Abstract
Background
We aimed to investigate the correlation of factors involved in the change of Mini-Mental State Examination (MMSE) and type 2 diabetes in the elderly.

Methods
This study was a secondary analysis of a prospective cohort study. Type 2 diabetes patients aged > 55 years were recruited and assigned into three groups based on their glycated hemoglobin (HbA1c) levels: HbA1c < 7, 7% ≤ HbA1c < 8% and HbA1c ≥8%. MMSE decline was considered the endpoint. Factors related to MMSE decline were identified by univariate and multivariate regression analyses.

Results
Altogether, 1519 subjects were included, 883 in the Low group, 333 in the Median group, and 303 in the High group. Age ≥ 75 years, education below elementary school level, not participating in seminars or consultation on healthcare, physical activity less than 30 min/day, cerebrovascular disease history, MMSE score at baseline, and HBA1c ≥8% were associated with cognitive decline by univariate and multivariate analysis. When the other factors were adjusted for, HBA1c ≥8% was independently associated with the severity of cognitive decline (β = 0.58, 95%CI:0.06–1.11, P = 0.029) and the occurrence of cognitive decline (odds ratio (OR) = 1.55, 95%CI:1.13–2.12, P = 0.007).

Conclusions
In elderly patients with type 2 diabetes, HbA1c ≥8% is an independent factor for cognitive decline and is also associated with the severity of the cognitive decline.
Using routine health information data for research in low- and middle-income countries: a systematic review
Authors: Hung Yuen W. , Hoxha Klesta , Irwin Bridget R. , Law Michael R. , Grépin Karen A. 
Published: August 2020

Abstract
Background
Routine health information systems (RHISs) support resource allocation and management decisions at all levels of the health system, as well as strategy development and policy-making in many low- and middle-income countries (LMICs). Although RHIS data represent a rich source of information, such data are currently underused for research purposes, largely due to concerns over data quality. Given that substantial investments have been made in strengthening RHISs in LMICs in recent years, and that there is a growing demand for more real-time data from researchers, this systematic review builds upon the existing literature to summarize the extent to which RHIS data have been used in peer-reviewed research publications.

Methods
Using terms ‘routine health information system’, ‘health information system’, or ‘health management information system’ and a list of LMICs, four electronic peer-review literature databases were searched from inception to February 202,019: PubMed, Scopus, EMBASE, and EconLit. Articles were assessed for inclusion based on pre-determined eligibility criteria and study characteristics were extracted from included articles using a piloted data extraction form.

Results
We identified 132 studies that met our inclusion criteria, originating in 37 different countries. Overall, the majority of the studies identified were from Sub-Saharan Africa and were published within the last 5 years. Malaria and maternal health were the most commonly studied health conditions, although a number of other health conditions and health services were also explored.

Conclusions
Our study identified an increasing use of RHIS data for research purposes, with many studies applying rigorous study designs and analytic methods to advance program evaluation, monitoring and assessing services, and epidemiological studies in LMICs. RHIS data represent an underused source of data and should be made more available and further embraced by the research community in LMIC health systems.
Assessing and decomposing inequality of opportunity in access to child health and nutrition in sub-Saharan Africa: evidence from three countries with low human development index
Authors: Sanoussi Yacobou , Ahinkorah Bright Opoku , Banke-Thomas Aduragbemi , Yaya Sanni 
Published: August 2020

Abstract
Background
Inequality of opportunity in health and nutrition is a major public health issue in the developing regions. This study analyzed the patterns and extent of inequality of opportunity in health and nutrition among children under-five across three countries sub-Saharan Africa with low Human development index (HDI).

Methods
We used data from the Multiple Indicator Cluster Survey of the Democratic Republic of Congo (20,792 households, 21,756 women aged 15 to 49 and 21,456 children under five), Guinea Bissau (6601 households, 10,234 women aged 15–49 and 7573 children under five) and Mali (11,830 households, 18,409 women in 15–49 years and 16,468 children under five) to compute the human opportunity index (HOI) and the dissimilarity index (D-index). Secondly, the Shapley decomposition method was used to estimate the relative contribution of circumstances that are beyond the control of children under-five and affecting their development outcomes in later life stages.

Results
The study revealed that children belonging to the most favorable group had higher access rates for immunization (93.64%) and water and sanitation facilities (73.59%) in Guinea Bissau. In Congo DR, the access rate was high for immunization (93.9%) for children in the most favorable group. In Mali, access rates stood at 6.56% for children in the most favorable group. In Guinea Bissau, the inequality of opportunity was important in access to health services before and after delivery (43.85%). In Congo DR, the inequality of opportunity was only high for the immunization composite indicator (83.79%) while in Mali, inequality of opportunity was higher for access to health services before and after delivery (41.67%).

Conclusion
The results show that there are efforts in some places to promote access to health and nutrition services in order to make access equal without distinction linked to the socio-economic and demographic characteristics in which the children live. However, the inequalities of opportunity observed between the children of the most favorable group and those of the least favorable group, remain in general at significant levels and call on government of these countries to implement policies taking them into account.
Finding the optimal control level of intraoperative blood pressure in no tourniquet primary total knee arthroplasty combine with tranexamic acid: a retrospective cohort study which supports the enhanced recovery strategy
Authors: Wang Hao-Yang , Yuan Ming-cheng , Pei Fu-Xing , Zhou Zong-Ke , Liao Ren 
Published: August 2020

Abstract
Background
With the use of tranexamic acid and control of the blood pressure during the operation, total knee arthroplasty (TKA) without tourniquet can be achieved. There is no exact standard for the control level of blood pressure during no tourniquet TKA. We explored the optimal level of blood pressure control during no tourniquet TKA surgery with the use of tranexamic acid in this study.

Methods
Patients underwent TKA were divided into three groups: the mean intraoperative systolic blood pressure in group A was < 90 mmHg, 90–100 mmHg in group B, > 100 mmHg in group C. Total blood loss (TBL), intraoperative blood loss, hidden blood loss, transfusion rate, maximum hemoglobin drop, operation time, and postoperative hospitalization days were recorded.

Results
Two hundred seventy-eight patients were enrolled, 82 in group A, 105 in group B, and 91 in group C. Group A (663.3 ± 46.0 ml) and group B (679.9 ± 57.1 ml) had significantly lower TBL than group C (751.7 ± 56.2 ml). Group A (120.2 ± 18.7 ml) had the lowest intraoperative blood loss than groups B and C. Group C (26.0 ± 4.1 g/l) had the largest Hb change than groups A and B. Group A (62.3 ± 4.7 min) had the shortest operation time. The incidence rate of postoperative hypotension in group A (8, 9.8%) was significantly greater than groups B and C. No significant differences were found in other outcomes.

Conclusion
The systolic blood pressure from 90 to 100 mmHg was the optimal strategy for no tourniquet primary TKA with tranexamic acid.
Two rare cases of acute myeloid leukemia with t(8;16)(p11.2;p13.3) and 1q duplication: case presentation and literature review
Authors: Liu Meng , Ren Yuan , Wang Xianfu , Lu Xianglan , Li Ming , Kim Young Mi , Li Shibo , Zhang Lijun 
Published: August 2020

Abstract
Background
Acute myeloid leukemia (AML) is a complex hematological disease characterized by genetic and clinical heterogeneity. The identification and understanding of chromosomal abnormalities are important for the diagnosis and management of AML patients. Compared with recurrent chromosomal translocations in AML, t(8;16)(p11.2;p13.3) can be found in any age group but is very rare and typically associated with poor prognosis.

Methods
Conventional cytogenetic studies were performed among 1,824 AML patients recorded in our oncology database over the last 20 years. Fluorescence in situ hybridization (FISH) was carried out to detect the translocation fusion. Array comparative genome hybridization (aCGH) was carried out to further characterize the duplication of chromosomes.

Results
We identified three AML patients with t(8;16)(p11.2;p13.3) by chromosome analysis. Two of the three patients, who harbored an additional 1q duplication, were detected by FISH and aCGH. aCGH characterized a 46.7 Mb and 49.9 Mb gain in chromosome 1 at band q32.1q44 separately in these two patients. One patient achieved complete remission (CR) but relapsed 3 months later. The other patient never experienced CR and died 2 years after diagnosis.

Conclusion
A 1q duplication was detected in two of three AML patients with t(8;16)(p11.2;p13.3), suggesting that 1q duplication can be a recurrent event in AML patients with t(8;16). In concert with the findings of previous studies on similar patients, our work suggests that 1q duplication may also be an unfavorable prognostic factor of the disease.
Paraneoplastic dermatomyositis associated with metastatic leiomyosarcoma of unknown primary
Authors: Merry Eve , Smrke Alannah , Halai Kapil , Patel Gulam , Thway Khin , Jones Robin L. , Benson Charlotte 
Published: August 2020

Abstract
Background
Sarcomas are rare and heterogeneous tumours of mesenchymal origin, with over 100 histological subtypes. Paraneoplastic dermatomyositis has rarely been described in sarcoma. This is the first documented case of paraneoplastic dermatomyositis in a patient with metastatic leiomyosarcoma.

Case presentation
A 43-year-old female diagnosed with metastatic leiomyosarcoma of unknown primary presented with a mild rash in sun-exposed areas of her face and upper chest, with no other neuromuscular symptoms. This rash resolved with systemic treatment with doxorubicin for metastatic leiomyosarcoma. Imaging assessment confirmed overall stable disease after chemotherapy completion. She presented acutely 2 months later with new onset rash in a shawl-like distribution, periorbital oedema and proximal muscle weakness. Based on the characteristic cutaneous signs and symmetrical proximal muscle weakness, abnormal electromyography and raised skeletal muscle enzymes with a positive anti-transcription intermediary factor-1 gamma antibody result, a diagnosis of paraneoplastic dermatomyositis was made. Re-evaluation of her metastatic leiomyosarcoma revealed disease progression. Second-line chemotherapy was commenced once the dermatomyositis was controlled on steroid therapy. Systemic anti-cancer therapy was again associated with mild improvement in dermatomyositis symptoms.

Discussion
Paraneoplastic dermatomyositis heralded disease progression after first-line chemotherapy; however, in hindsight, subtle cutaneous features were present at sarcoma diagnosis. The temporal relationship between paraneoplastic dermatomyositis and metastatic leiomyosarcoma is key in this case, as fluctuations in dermatomyositis severity correlated with growth of metastatic disease. Understanding this relationship may provide clues for tumour progression and prompt timely initiation of anti-cancer therapy. It is important to recognise that in addition to the more common cancers associated with paraneoplastic dermatomyositis, it can also occur in rarer tumours such as leiomyosarcoma.