bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and molecular characterization of methicillin-resistant Staphylococcus aureus with mupirocin, fusidic acid and/or retapamulin resistance
Authors: Chen Wenjing , He Chunyan , Yang Han , Shu Wen , Cui Zelin , Tang Rong , Zhang Chuanling , Liu Qingzhong 
Published: June 2020

Abstract
Background
The data on the prevalence of resistance to mupirocin (MUP), fusidic acid (FA) and retapamulin (RET) in methicillin-resistant Staphylococcus aureus (MRSA) from China are still limited. This study aimed to examine these three antibiotics resistance in 1206 MRSA clinical isolates from Eastern China. Phenotypic MUP, FA and RET resistance was determined by minimum inhibitory concentrations (MICs), and genotypic by PCR and DNA sequencing of the mupA/B, fusB-D, cfr, vgaA/Av/ALC/B/C/E, lsaA-C/E and salA and mutations in ileS, fusA/E, rplC, and 23S RNA V domain. The genetic characteristics of resistance isolates were conducted by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

Results
Overall MRSA MUP, FA and RET resistance was low (5.1, 1.0 and 0.3%, respectively). MupA was the mechanism of high-level MUP resistance. All low-level MUP resistance isolates possessed an equivocal mutation N213D in IleS; of these, 2 reported an additional V588F mutation with an impact on the Rossman fold. FusA mutations, such as L461K, H457Q, H457Y and V90I were the primary FA mechanisms among high-level resistance isolates, most of which also contained fusC; however, all low-level resistance strains carried fusB. Except lsaE gene detected in one isolate, no other resistance mechanisms tested were found among RET-resistant isolates. Additionally, sixteen PFGE types (A-P) were observed, among which type B was the most common (49/76, 64.5%), followed by types E and G (4/76, 5.3% each) and types C and M (3/76, 3.9% each). All resistant strains were divided into 15 ST types by MLST. ST764 (24/76, 31.6%), ST630 (11/76, 14.5%), ST239 (9/76, 11.8%) and ST5 (7/76, 9.2%) were the major types. PFGE type B isolates with the aforementioned STs were mainly found in mupirocin resistant isolates.

Conclusions
MUP, FA and RET exhibited highly activity against the MRSA isolates. Acquired genes and chromosome-borne genes mutations were responsible for MUP and FA resistance; however, the mechanism for some RET-resistant isolates remains to be further elucidated. Also, the surveillance to MUP in MRSA should be strengthened to prevent elevated resistance due to the expansion of clones.
Don’t dismiss logistic regression: the case for sensible extraction of interactions in the era of machine learning
Authors: Levy Joshua J. , O’Malley A. James 
Published: June 2020

AbstractBackgroundMachine learning approaches have become increasingly popular modeling techniques, relying on data-driven heuristics to arrive at its solutions. Recent comparisons between these algorithms and traditional statistical modeling techniques have largely ignored the superiority gained by the former approaches due to involvement of model-building search algorithms. This has led to alignment of statistical and machine learning approaches with different types of problems and the under-development of procedures that combine their attributes. In this context, we hoped to understand the domains of applicability for each approach and to identify areas where a marriage between the two approaches is warranted. We then sought to develop a hybrid statistical-machine learning procedure with the best attributes of each.MethodsWe present three simple examples to illustrate when to use each modeling approach and posit a general framework for combining them into an enhanced logistic regression model building procedure that aids interpretation. We study 556 benchmark machine learning datasets to uncover when machine learning techniques outperformed rudimentary logistic regression models and so are potentially well-equipped to enhance them. We illustrate a software package,InteractionTransformer, which embeds logistic regression with advanced model building capacity by using machine learning algorithms to extract candidate interaction features from a random forest model for inclusion in the model. Finally, we apply our enhanced logistic regression analysis to two real-word biomedical examples, one where predictors vary linearly with the outcome and another with extensive second-order interactions.ResultsPreliminary statistical analysis demonstrated that across 556 benchmark datasets, the random forest approach significantly outperformed the logistic regression approach. We found a statistically significant increase in predictive performance when using hybrid procedures and greater clarity in the association with the outcome of terms acquired compared to directly interpreting the random forest output.ConclusionsWhen a random forest model is closer to the true model, hybrid statistical-machine learning procedures can substantially enhance the performance of statistical procedures in an automated manner while preserving easy interpretation of the results. Such hybrid methods may help facilitate widespread adoption of machine learning techniques in the biomedical setting.
Evaluation of breath, plasma, and urinary markers of lactose malabsorption to diagnose lactase non-persistence following lactose or milk ingestion
Authors: Shrestha Aahana , Barnett Matthew P. G. , Perry Jo K. , Cameron-Smith David , Milan Amber M. 
Published: June 2020

Abstract
Background
Adult lactase non-persistence (LNP) is due to low lactase expression, resulting in lactose malabsorption (LM). LNP is a genetic trait, but is typically determined by LM markers including breath H2, blood glucose, and urinary galactose after a lactose tolerance test. Known validity of these markers using milk is limited, despite being common practice. Compositional variation, such as β-casein variants, in milk may impact diagnostic efficacy. This study aimed to evaluate the diagnostic accuracy to detect LNP using these commonly measured LM markers after both lactose and milk challenges.

Methods
Fourty healthy young women were challenged with 50 g lactose then randomized for separate cross-over visits to ingest 750 mL milk (37.5 g lactose) as conventional (both A1 and A2 β-casein) and A1 β-casein-free (a2 Milk™) milk. Blood, breath and urine were collected prior to and up to 3 h following each challenge. The presence of C/T13910 and G/A22018 polymorphisms, determined by restriction fragment length polymorphism, was used as the diagnostic reference for LNP.

Results
Genetic testing identified 14 out of 40 subjects as having LNP (C/C13910 and G/G22018). All three LM markers (breath H2, plasma glucose and urinary galactose/creatinine) discriminated between lactase persistence (LP) and LNP following lactose challenge with an area under the receiver operating characteristic (ROC) curve (AUC) of 1.00, 0.75 and 0.73, respectively. Plasma glucose and urinary galactose/creatinine were unreliable (AUC < 0.70) after milk ingestion. The specificity of breath H2 remained high (100%) when milk was used, but sensitivity was reduced with conventional (92.9%) and a2 Milk™ (78.6%) compared to lactose (sensitivities adjusted for lactose content). The breath H2 optimal cut-off value was lower with a2 Milk™ (13 ppm) than conventional milk (21 ppm). Using existing literature cut-off values the sensitivity and specificity of breath H2 was greater than plasma glucose to detect LNP following lactose challenge whereas values obtained for urinary galactose/creatinine were lower than the existing literature cut-offs.

Conclusion
This study showed accurate diagnosis of LNP by breath H2 irrespective of the substrate used, although the diagnostic threshold may vary depending on the lactose substrate or the composition of the milk.

Trial registration
ACTRN12616001694404. Registered prospectively on December 9, 2016.
A novel stop-gain mutation in DPYS gene causing Dihidropyrimidinase deficiency, a case report
Authors: Mirzaei Malihe , Kavosi Arghavan , Sharifzadeh Mahboobeh , Mahjoub Ghazale , Faghihi Mohammad Ali , Habibzadeh Parham , Yavarian Majid 
Published: June 2020

Abstract
Background
Dihidropyrimidinase (DHP) deficiency is an inherited inborn error of pyrimidine metabolism with a variable clinical presentation and even asymptomatic subjects. Dihydropyrimidinase is encoded by the DPYS gene, thus pathogenic mutations in this gene can cause DHP deficiency. To date, several variations in the DPYS gene have been reported but only 23 of them have been confirmed to be pathogenic. Therefore, the biochemical, clinical and genetic aspects of this disease are still unclear.

Case presentation
Here, we report a 22-year-old woman with DHP deficiency. To identify the genetic cause of DHP deficiency in this patient, Whole Exome Sequencing (WES) was performed, which revealed a novel homozygote stop gain mutation (NM_001385: Exon 9, c.1501 A > T, p.K501X) in the DPYS gene. Sanger sequencing was carried out on proband and other family members in order to confirm the identified mutation. According to the homozygote genotype of the patient and heterozygote genotype of her parents, the autosomal recessive pattern of inheritance was confirmed. In addition, bioinformatics analysis of the identified variant using Mutation Taster and T-Coffee Multiple Sequence Alignment showed the pathogenicity of mutation. Moreover, mRNA expression level of DPYS gene in the proband’s liver biopsy showed about 6-fold reduction compared to control, which strongly suggested the pathogenicity of the identified mutation.

Conclusions
This study identified a novel pathogenic stop gain mutation in DPYS gene in a DHP deficient patient. Our findings can improve the knowledge about the genetic basis of the disease and also provide information for accurate genetic counseling for the families at risk of these types of disorders.
Assessment of the necessity of uterine artery embolization during suction and curettage for caesarean scar pregnancy: a prospective cohort study
Authors: Ou Jie , Peng Ping , Li Chunying , Teng Lirong , Liu Xinyan 
Published: June 2020

Abstract
Background
Uterine artery embolization (UAE) followed by suction and curettage is a common conservative treatment for caesarean scar pregnancy (CSP), but the advantages of suction and curettage alone are underestimated due to the lack of standards for selecting appropriate cases for which this approach would be applicable. We sought to identify indicators with which to assess the need for UAE during suction and curettage.

Methods
The prospective cohort consisted of 105 women diagnosed with CSP in Peking Union Medical College Hospital between January 2016 and September 2018 who were followed up until 60 days after surgery. The main outcome was the therapy used, and secondary outcomes included recovery, bleeding, surgery time, length of hospital stay, and total cost.

Results
We found that β-human chorionic gonadotropin (β-hCG) levels were significantly lower (P < 0.05), foetal cardiac activity was significantly lower (P < 0.05), the myometrial layer was significantly thicker (P < 0.05), expenditures were lower and lengths of hospital stay were shorter in patients who received suction and curettage alone (the non-UAE group) than in those who received UAE followed by suction and curettage (the UAE+ group). In addition, for CSP patients, UAE might be less necessary when the myometrial thickness is ≥2 mm and the gestational sacmeasures ≤5 cm, and suction and curettage alone may be safer for these patients.

Conclusion
Suction and curettage alone is a more suitable option than UAE followed by suction and curettage because the former carries a lower cost, shorter length of hospital stay, and lower risk of adverse events. Regarding risk factors, patients with a lower uterine segment thickness ≥ 2 mm and a gestational mass diameter ≤ 5 cm have an increased probability of being successfully treated with suction and curettage alone.
Body mass index increases the lymph node metastasis risk of breast cancer: a dose-response meta-analysis with 52904 subjects from 20 cohort studies
Authors: Wang Junyi , Cai Yaning , Yu Fangfang , Ping Zhiguang , Liu Li 
Published: June 2020

Abstract
Background
Since body mass index (BMI) is a convincing risk factor for breast cancer, it is speculated to be associated with lymph node metastasis. However, epidemiological studies are inconclusive. Therefore, this study was conducted to investigate the effect of BMI on the lymph node metastasis risk of breast cancer.

Methods
Cohort studies that evaluating BMI and lymph node metastasis in breast cancer were selected through various databases including PubMed, PubMed Central (PMC), Web of science, the China National Knowledge Infrastructure (CNKI), Chinese Scientific Journals (VIP) and Wanfang Data Knowledge Service Platform (WanFang) until November 30, 2019. The two-stage, random effect meta-analysis was performed to assess the dose-response relationship between BMI and lymph node metastasis risk. Between-study heterogeneity was assessed using I2. Subgroup analysis was done to find possible sources of heterogeneity.

Results
We included a total of 20 studies enrolling 52,904 participants. The summary relative risk (RR) (1.10, 95%CI: 1.06–1.15) suggested a significant effect of BMI on the lymph node metastasis risk of breast cancer. The dose-response meta-analysis (RR = 1.01, 95%CI: 1.00–1.01) indicated a positive linear association between BMI and lymph node metastasis risk. For every 1 kg/m2 increment of BMI, the risk of lymph node metastasis increased by 0.89%. In subgroup analyses, positive linear dose-response relationships between BMI and lymph node metastasis risk were observed among Asian, European, American, premenopausal, postmenopausal, study period less than 5 years, and more than 5 years groups. For every 1 kg/m2 increment of BMI, the risk of lymph node metastasis increased by 0.99, 0.85, 0.61, 1.44, 1.45, 2.22, and 0.61%, respectively.

Conclusion
BMI significantly increases the lymph node metastasis risk of breast cancer as linear dose-response reaction. Further studies are needed to identify this association.
Hyperacusis in children: a scoping review
Authors: Potgieter Iskra , Fackrell Kathryn , Kennedy Veronica , Crunkhorn Rosa , Hoare Derek J. 
Published: June 2020

Abstract
Background
Hyperacusis is a chronic condition commonly defined as a lowered tolerance or increased sensitivity to everyday environmental sounds. It has been viewed as a paediatric disorder which can cause significant impairment to a child’s normal functioning. Although clinical guidance highlights the importance of identifying whether the child has intolerance to loud sounds and managing this appropriately, there are currently no assessment or treatment methods that have been designed and tested for use with children with hyperacusis. A review is therefore indicated to consider the profile of children with hyperacusis as a basis for future research into their assessment and treatment.

Method
A scoping review methodology was followed with literature searches conducted in Embase, PsychINFO, PubMed CENTRAL, Scopus, Web of Science and Google Scholar. Research articles were included if they reported on research studies describing children diagnosed with hyperacusis, providing clinical profile information, and/or reporting on an assessment or management method for children with a primary complaint of hyperacusis. Data were charted on Excel and verified by a second researcher. Twenty-one research articles were included.

Results
Children with hyperacusis are typically described in terms of age at presentation, troublesome sounds, physical sensation, behavioural reactions, coping strategies, comorbid conditions and impact on daily life. Methods of assessing the children include semi-structured interviews, questionnaires, neurological assessment, observation and uncomfortable loudness levels. Management methods include psychological therapy, sound therapy, tinnitus retraining therapy, medication and neuro-rehabilitation.

Conclusion
The information we catalogued on various elements of clinical profile, assessment and management can serve as a stepping stone in future research developing questionnaires for clinical measurement of the impact of hyperacusis on children, and the measurement of treatment related change in clinic and in trials. Positive outcomes were noted by the authors following all of the above treatments; future research must compare these and specify the parameters for optimal results.
Severe constipation as the first clinical manifestation in multiple endocrine neoplasia type 2B: a case report and literature review
Authors: Zhang Lidan , Guo Yan , Ye Lei , Lu Wenli , Dong Zhiya , Wang Wei , Xiao Yuan 
Published: June 2020

Abstract
Background
The occurrence of multiple endocrine neoplasia type 2B (MEN2B) in Asians is very rare. In particular, patients with intractable constipation as the main clinical manifestation are even rarer. Atypical clinical manifestations are likely to lead to a diagnostic delay. In this report, we described a case of a delayed diagnosis of MEN2B, and the first clinical manifestation was intractable constipation.

Case presentation
A female teenager had suffered from intractable constipation since infancy. Because the colonoscopy and biopsy results from local hospitals did not confirm the presence of congenital megacolon, the girl had been followed up at a local clinic for a long time. The diagnosis was not confirmed until thyroid masses were found in the Pediatric Department of Shanghai Ruijin Hospital when she was 12 years old. According to our detailed evaluation, she suffered from Hirschsprung disease (HD), growth retardation, medullary thyroid carcinoma (MTC) and mucosal neuroma due to a mutation in the RET gene. Thus, the diagnosis of MEN2B was confirmed. Afterward, the girl underwent several surgeries and was still being followed up before the article was published.

Conclusion
MEN2B has atypical clinical symptoms in the early stage. Refractory constipation may be the only clinical manifestation that lasts for several years. Therefore, we recommend that early screening and gene sequencing should be performed for patients with severe constipation due to HD to determine the cause of the disease and to improve the survival outcome.
The prevalence and associated factors of alcohol use among pregnant women attending antenatal care at public hospitals Addis Ababa, Ethiopia, 2019
Authors: Tesfaye Getaneh , Demlew Demeke , G/tsadik Meseret , Habte Fikreselam , Molla Gebeyaw , Kifle Yohannes , Gebreegziabhier Gebreslassie 
Published: June 2020

Abstract
Background
Alcohol use during pregnancy is a significant public health problem, ultimately affecting the neonatal offspring. Recent studies explore that no safe amount and safe time to drink alcohol during pregnancy. Even though drinking in pregnancy has a wide range of problems, a small number of scientific publications document on the magnitude of drinking alcohol during pregnancy in Sub-Saharan African countries including Ethiopia. The aim of this study was to assess prevalence and associated factors of alcohol use among pregnant women attending prenatal care at public hospitals, Addis Ababa, Ethiopia.

Methods
Hospital based cross sectional study was employed from May 7 to June 6, 2019 at public hospitals, Addis Ababa. A total of 585 pregnant women participated in the study selected through systematic random sampling technique. Frequency of consumption was measured by using AUDIT. Frequency tables and graphs were used to describe the study variable. The association between variables analyzed with bi-variable and multivariable binary logistic regression. A statistical significance was declared at p value < 0.05 with 95% confidence interval.

Result
A total of 585 participants were included in the study with the response rate of 98.6%. The study showed that the prevalence of alcohol use among pregnant women were 37.1% with (95% CI, 33.2–41). Factors like no formal education [AOR = 3.22, 95%CI, 1.72, 6.02], pre-pregnancy alcohol use [AOR = 3.16, 95%CI, 2.03, 4.91], partner alcohol use [AOR = 3.43, 95%CI, 2.21, 5.32], and poor social support [AOR = 3.16, 95%CI, 1.88, 5.31] were statistically associated with alcohol use during pregnancy.

Conclusion
In this study the prevalence of alcohol use during pregnancy was high as compared to majority of other studies. This study observed that no formal education, pre-pregnancy alcohol use, partner alcohol use, and poor social support, were highly associated with alcohol use during pregnancy. Based on the findings of this study early management of alcohol use and problematic alcohol use is needed for pregnant women.
Effectiveness of diet and physical activity interventions among Chinese-origin populations living in high income countries: a systematic review
Authors: Beasley Jeannette M. , Wagnild Janelle M. , Pollard Tessa M. , Roberts Timothy R. , Ahkter Nasima 
Published: June 2020

Abstract
Background
This review examines the effectiveness of diet and physical activity interventions to reduce cardiometabolic risk among Chinese immigrants and their descendants living in high income countries. The objective of this review is to provide information to help build future interventions aimed at improving diet and increasing physical activity levels among Chinese immigrants.

Methods
Outcomes included BMI, weight, waist circumference (WC), waist-hip ratio (WHR), cholesterol (LDL, HDL), systolic and diastolic blood pressure (SBP, DBP), hemoglobin A1c (HgbA1c), fasting blood glucose (FBG), and HOMA-IR. Six databases were systematically searched from database inception to date of search (February 2020). Meta-analyses used random effect models to estimate pooled effects of outcomes with 95% confidence intervals. The outcomes assessed were changes in mean outcomes (post-intervention versus baseline) among the intervention group versus control groups.

Results
Twenty-one articles were included for synthesis, and eight of these were included in the meta-analysis. Among children/adolescents, there were no significant effects of intervention for any of the outcomes having sufficient data for meta-analysis (BMI, WHR, SBP, and DBP). Among adults, the pooled effect including three studies showed significant changes in BMI (effect size = − 1.14 kg/m2; (95% CI: − 2.06, − 0.21), I2 = 31%). There were also significant effects of intervention among adults in terms of changes in SBP and DBP, as the pooled effect across three studies was − 6.08 mmHg (95% CI − 9.42, − 2.73), I2 = 0% and − 3.81 mmHg (95% CI: − 6.34, − 1.28), I2 = 0%, respectively. Among adults there were no other significant effects among the meta-analyses conducted (weight, WC, LDL, HgbA1c, and FBG).

Conclusions
This review is the first to summarize the effectiveness of diet and physical activity interventions specifically designed for Chinese immigrants living in high income countries. There were clinically meaningful changes in BMI and blood pressure among adults, but evidence was weak for other cardiometabolic outcomes (weight, WC, LDL, HgbA1c, and FBG), and among children, there was no evidence of effect for any cardiometabolic outcomes. Given our mixed findings, more work is needed to support the design of successful interventions, particularly those targeting children and their families.

Trial registration
The systematic review protocol was registered in PROSPERO on December 17, 2018, the international prospective register of systematic reviews (registration number: CRD42018117842).