bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between lithium in tap water and suicide mortality rates in Miyazaki Prefecture
Authors: Kozaka Naomi , Takeuchi Shouhei , Ishii Nobuyoshi , Terao Takeshi , Kuroda Yoshiki 
Published: June 2020

Abstract
Background
Most studies have reported that suicide mortality rates are negatively associated with lithium levels in tap water; however, a few studies showed either no association or a positive association. Thus, the association between suicide mortality and lithium levels in tap water remains controversial. To clarify the association, our study evaluated the association between lithium levels in tap water and suicide mortality rates in Miyazaki Prefecture of Japan, after adjusting for confounding factors.

Methods
We measured lithium levels in tap water across the 26 municipalities of Miyazaki Prefecture in Japan. We examined the standardized mortality ratio (SMR) for suicide in each municipality and used the data as the average suicide SMRs over 5 years (2009–2013). Weighted least-squares regression analysis, adjusted for the size of each municipality’s population, was used to investigate the association between lithium levels in tap water and suicide SMRs. In addition to a crude model, in an adjusted model, potential confounding factors (proportion of elderly people, proportion of one-person households, annual marriage rate, annual mean income, unemployment rate, the density of medical doctors per 100,000 people, annual total rainfall, and proportion of people with a college education or higher) were added as covariates.

Results
We showed that male and female suicide SMRs were not associated with lithium levels in tap water in Miyazaki Prefecture. After adjusting for confounders, male suicide SMRs were significantly and positively associated with the proportion of elderly people in the population and annual total rainfall, and female suicide SMRs were associated with the proportion of elderly people in the population.

Conclusions
No association between lithium levels in tap water and suicide mortality rates was found in Miyazaki Prefecture.
Intergenerational transmission of economic success in Austria with a focus on migration and gender
Authors: Reiter Daniel , Palz Mario Thomas , Kreimer Margareta 
Published: June 2020

AbstractIn this paper, we analyse the intergenerational transmission of economic success in Austria using the European Union Statistics on Income and Living Conditions 2011 dataset (EU-SILC 2011). Starting point of the investigation is a two-step estimation procedure, where we detect a significant positve intergenerational association between the economic situation of the parental household and educational attainments as well as gross hourly wages of their male and female descendants independently. Furthermore, we shed some light on the intergenerational social mobility black box by explaining the direct effect of the income situation of the parental generation on attainable wages of the child generation within the transmission system. It turns out that this effect is significantly underestimated when applying ordinary least squares regressions only, where the perceived socioeconomic status is taken exogenous. Finally, we apply instrumental variable quantile regressions to demonstrate that the direct intergenerational economic association between parents and their descendants is strongest for top earners. Alongside this proceeding, we introduce an alternative way to think about the impact of a bundle of additional intergenerational transmission channels like cognitive ability, noncognitive personal traits, and aspects of physical appearance on an empirical level. Overall, the findings of the paper, where special attention is paid to migrants, offer a better understanding on the intergenerational transmission of economic success mechanism and to what extent this process influences income persistence between generations.
Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies
Authors: Zindler Tristan , Frieling Helge , Neyazi Alexandra , Bleich Stefan , Friedel Eva 
Published: June 2020

Abstract
Background
Systematic technical effects—also called batch effects—are a considerable challenge when analyzing DNA methylation (DNAm) microarray data, because they can lead to false results when confounded with the variable of interest. Methods to correct these batch effects are error-prone, as previous findings have shown.

Results
Here, we demonstrate how using the R function ComBat to correct simulated Infinium HumanMethylation450 BeadChip (450 K) and Infinium MethylationEPIC BeadChip Kit (EPIC) DNAm data can lead to a large number of false positive results under certain conditions. We further provide a detailed assessment of the consequences for the highly relevant problem of p-value inflation with subsequent false positive findings after application of the frequently used ComBat method. Using ComBat to correct for batch effects in randomly generated samples produced alarming numbers of false discovery rate (FDR) and Bonferroni-corrected (BF) false positive results in unbalanced as well as in balanced sample distributions in terms of the relation between the outcome of interest variable and the technical position of the sample during the probe measurement. Both sample size and number of batch factors (e.g. number of chips) were systematically simulated to assess the probability of false positive findings. The effect of sample size was simulated using n = 48 up to n = 768 randomly generated samples. Increasing the number of corrected factors led to an exponential increase in the number of false positive signals. Increasing the number of samples reduced, but did not completely prevent, this effect.

Conclusions
Using the approach described, we demonstrate, that using ComBat for batch correction in DNAm data can lead to false positive results under certain conditions and sample distributions. Our results are thus contrary to previous publications, considering a balanced sample distribution as unproblematic when using ComBat. We do not claim completeness in terms of reporting all technical conditions and possible solutions of the occurring problems as we approach the problem from a clinician’s perspective and not from that of a computer scientist. With our approach of simulating data, we provide readers with a simple method to assess the probability of false positive findings in DNAm microarray data analysis pipelines.
A structural UGDH variant associated with standard Munchkin cats
Authors: Struck Ann-Kathrin , Braun Marina , Detering Kim Aline , Dziallas Peter , Neßler Jasmin , Fehr Michael , Metzger Julia , Distl Ottmar 
Published: June 2020

Abstract
Background
Munchkin cats were founded on a naturally occurring mutation segregating into long-legged and short-legged types. Short-legged cats showed disproportionate dwarfism (chondrodysplasia) in which all four legs are short and are referred as standard Munchkin cats. Long-legged animals are referred as non-standard Munchkin cats. A previous study using genome-wide single nucleotide polymorphisms (SNPs) for genome-wide association analysis identified a significantly associated region at 168–184 Mb on feline chromosome (FCA) B1.

Results
In this study, we validated the critical region on FCA B1 using a case-control study with 89 cats and 14 FCA B1-SNPs. A structural variant within UGDH (NC_018726.2:g.173294289_173297592delins108, Felis catus 8.0, equivalent to NC_018726.3:g.174882895_174886198delins108, Felis catus 9.0) on FCA B1 was perfectly associated with the phenotype of short-legged standard Munchkin cats.

Conclusion
This UGDH structural variant very likely causes the chondrodysplastic (standard) phenotype in Munchkin cats. The lack of homozygous mutant phenotypes and reduced litter sizes in standard Munchkin cats suggest an autosomal recessive lethal trait in the homozygote state. We propose an autosomal dominant mode of inheritance for the chondrodysplastic condition in Munchkin cats.
Comparative transcriptome analysis of the rice leaf folder (Cnaphalocrocis medinalis) to heat acclimation
Authors: Quan Peng-Qi , Li Ming-Zhu , Wang Gao-Rong , Gu Ling-Ling , Liu Xiang-Dong 
Published: June 2020

Abstract
Background
The rice leaf folder Cnaphalocrocis medinalis Güenée is a serious insect pest of rice in Asia. This pest occurs in summer, and it is sensitive to high temperature. However, the larvae exhibit heat acclimation/adaptation. To understand the underlying mechanisms, we established a heat-acclimated strain via multigenerational selection at 39 °C. After heat shock at 41 °C for 1 h, the transcriptomes of the heat-acclimated (S-39) and unacclimated (S-27) larvae were sequenced, using the unacclimated larvae without exposure to 41 °C as the control.

Results
Five generations of selection at 39 °C led larvae to acclimate to this heat stress. Exposure to 41 °C induced 1160 differentially expressed genes (DEGs) between the heat-acclimated and unacclimated larvae. Both the heat-acclimated and unacclimated larvae responded to heat stress via upregulating genes related to sensory organ development and structural constituent of eye lens, whereas the unacclimated larvae also upregulated genes related to structural constituent of cuticle. Compared to unacclimated larvae, heat-acclimated larvae downregulated oxidoreductase activity-related genes when encountering heat shock. Both the acclimated and unacclimated larvae adjusted the longevity regulating, protein processing in endoplasmic reticulum, antigen processing and presentation, MAPK and estrogen signaling pathway to responsed to heat stress. Additionally, the unacclimated larvae also adjusted the spliceosome pathway, whereas the heat-acclimated larvae adjusted the biosynthesis of unsaturated fatty acids pathway when encountering heat stress. Although the heat-acclimated and unacclimated larvae upregulated expression of heat shock protein genes under heat stress including HSP70, HSP27 and CRYAB, their biosynthesis, metabolism and detoxification-related genes expressed differentially.

Conclusions
The rice leaf folder larvae could acclimate to a high temperature via multigenerational heat selection. The heat-acclimated larvae induced more DEGs to response to heat shock than the unacclimated larvae. The changes in transcript level of genes were related to heat acclimation of larvae, especially these genes in sensory organ development, structural constituent of eye lens, and oxidoreductase activity. The DEGs between heat-acclimated and unacclimated larvae after heat shock were enriched in the biosynthesis and metabolism pathways. These results are helpful to understand the molecular mechanism underlying heat acclimation of insects.
How methodological frameworks are being developed: evidence from a scoping review
Authors: McMeekin Nicola , Wu Olivia , Germeni Evi , Briggs Andrew 
Published: June 2020

AbstractBackgroundAlthough the benefits of using methodological frameworks are increasingly recognised, to date, there is no formal definition of what constitutes a ‘methodological framework’, nor is there any published guidance on how to develop one. For the purposes of this study we have defined a methodological framework as a structured guide to completing a process or procedure. This study’s aims are to: (a) map the existing landscape on the use of methodological frameworks; (b) identify approaches used for the development of methodological frameworks and terminology used; and (c) provide suggestions for developing future methodological frameworks. We took a broad view and did not limit our study to methodological frameworks in research and academia.MethodsA scoping review was conducted, drawing on Arksey and O’Malley’s methods and more recent guidance. We systematically searched two major electronic databases (MEDLINE and Web of Science), as well as grey literature sources and the reference lists and citations of all relevant papers. Study characteristics and approaches used for development of methodological frameworks were extracted from included studies. Descriptive analysis was conducted.ResultsWe included a total of 30 studies, representing a wide range of subject areas. The most commonly reported approach for developing a methodological framework was ‘Based on existing methods and guidelines’ (66.7%), followed by ‘Refined and validated’ (33.3%), ‘Experience and expertise’ (30.0%), ‘Literature review’ (26.7%), ‘Data synthesis and amalgamation’ (23.3%), ‘Data extraction’ (10.0%), ‘Iteratively developed’ (6.7%) and ‘Lab work results’ (3.3%). There was no consistent use of terminology; diverse terms for methodological framework were used across and, interchangeably, within studies.ConclusionsAlthough no formal guidance exists on how to develop a methodological framework, this scoping review found an overall consensus in approaches used, which can be broadly divided into three phases: (a) identifying data to inform the methodological framework; (b) developing the methodological framework; and (c) validating, testing and refining the methodological framework. Based on these phases, we provide suggestions to facilitate the development of future methodological frameworks.
Effectiveness of SMS messaging for diarrhoea measurement: a factorial cross-over randomised controlled trial
Authors: Rego Ryan , Watson Samuel , Ishengoma Philbert , Langat Philemon , Otieno Hezekiah Pireh , Lilford Richard 
Published: June 2020

Abstract
Background
Text messaging systems are used to collect data on symptom prevalence. Using a text messaging system, we evaluated the effects of question load, question frequency, and financial incentive on response rates and reported infant diarrhoea rates in an infant diarrhoea survey.

Methods
We performed a factorial cross-over randomised controlled trial of an SMS surveying system for infant diarrhoea surveillance with treatments: financial incentive (yes/no), question load (1-question/3-question), and questioning frequency (daily/fortnightly). Participants progressed through all treatment combinations over eight two-week rounds. Data were analysed using multivariable logistic regressions to determine the impacts of the treatments on the response rates and reported diarrhoea rates. Attitudes were explored through qualitative interviews.

Results
For the 141 participants, the mean response rate was 47%. In terms of percentage point differences (ppd), daily questioning was associated with a lower response rate than fortnightly (− 1·2[95%CI:-4·9,2·5]); high (3-question) question loads were associated with a lower response rate than low (1-question) question loads (− 7·0[95%CI:− 10·8,-3·1]); and financial incentivisation was associated with a higher response rate than no financial incentivisation (6·4[95%CI:2·6,10·2]).
The mean two-week diarrhoea rate was 36·4%. Daily questioning was associated with a higher reported diarrhoea rate than fortnightly (29·9[95%CI:22·8,36·9]); with little evidence for impact by incentivisation or question load.

Conclusions
Close to half of all participants responded to the SMS survey. Daily questioning evoked a statistically higher rate of reported diarrhoea, while financial incentivisation and low (1-question) question loads evoked higher response rates than no incentive and high (3-question) question loads respectively.

Trial Registration
The protocol was prospectively registered on ISRCTN on the 20th of March 2019 under number ISRCTN11410773.
Increased incidence of metachronous gastric neoplasm after endoscopic resection in patients with synchronous gastric neoplasm
Authors: Shin Ga-Yeong , Cho Hye Jin , Park Jae Myung , Lim Chul-Hyun , Cho Yu Kyung , Choi Myung-Gyu 
Published: June 2020

Abstract
Background
Recurrence risk is a major concern after endoscopic resection (ER) of gastric neoplasms. This study was to compare metachronous risk in patients with and without synchronous neoplasms after complete ER.

Methods
After ER for gastric neoplasms, patients were divided into those with and without synchronous neoplasm. The metachronous risk of gastric neoplasms was compared between the two groups.

Results
After ER of 678 cancers and 891 adenomas, synchronous neoplasm was found in 11.8% of cancers and 11.4% of adenomas. In the multiple (n = 182) and the single group (n = 1387), metachronous neoplasms occurred in 18.1 and 8.6%, respectively (HR 2.40; 95% CI, 1.62–3.34). When the pathology of the recurred lesion was limited to cancer, metachronous risk was also significantly higher in the multiple than in the single group (HR, 2.2; 95% CI, 1.17–3.85). In the recurred pathology of the multiple group, cancer development was frequently observed in patients with cancer compared to those with only adenomas in the synchronous lesion (67.0% vs. 13.0%, respectively; P = 0.023).

Conclusions
This study demonstrated that metachronous risk was significantly higher in patients with synchronous gastric neoplasms after ER. Therefore, meticulous examination is important in patients with synchronous neoplasm.
Serum albumin and activities of daily living in Chinese centenarians: a cross-sectional study
Authors: Han Ke , Wang Shengshu , Jia Wangping , Cao Wenzhe , Liu Miao , Yang Shanshan , Wang Jianhua , He Yao 
Published: June 2020

Abstract
Background
Objective deterioration in activities of daily living (ADLs) exists among older population, and particularly worsens with age. Considering the criterion standard of positive aging and longevity, little information focusing on centenarians is available. This study set out to explore the relationship between serum albumin and ADLs among centenarians in long-lived areas.

Methods
This population-based cross-sectional study investigated a full sample of Chinese centenarians in Hainan, the longest-lived area of China (n = 1002). We assessed serum albumin levels and basic and instrumental activities of daily living (BADLs and IADLs).

Results
Of 1002 participants included in the analysis, 287 (28.64%) had BADL disabilities and 648 (64.67%) had IADL disabilities. The median level of serum albumin was 38.5 g/L (interquartile range, 36.2–41.3). The multivariable analyses controlling for socio-demographic characteristics, lifestyle, morbidities, and other influential factors showed that albumin level was associated with the total score of BADL (standard β = 0.335, P < 0.001) and IADL (standard β = 0.206, P < 0.001). With the increasing of albumin level, the risk of ADLs disability decreased (BADL: odds ratios [OR] = 0.835, 95% Confidence interval [CI]: 0.797–0.876; IADL: OR = 0.863, 95%CI: 0.824–0.905). In the stratified analyses, similar results were found in both sex, but were more prominent in women.

Conclusions
Higher levels of serum albumin was a protective factor for the decline of ADLs in centenarians. This association can be observed in both genders and is more pronounced in women.
Impact of lower body mass index on risk of all-cause mortality and infection-related death in Japanese chronic kidney disease patients
Authors: Yamamoto Tae , Nakayama Masaaki , Miyazaki Mariko , Sato Hiroshi , Matsushima Masato , Sato Toshinobu , Ito Sadayoshi 
Published: June 2020

Abstract
Background
Several studies have reported that lower body mass index (BMI) is associated with high mortality in patients with chronic kidney disease (CKD). Rate of infection-related death in CKD patients is increasing. However, the relationship between BMI and infection-related death is unclear.

Methods
Overall, 2648 CKD outpatients (estimated glomerular filtration rate < 60 mL/min and/or presenting with proteinuria) under the care of nephrologists were prospectively followed for 5 years. Patients were stratified by quartile of BMI levels. Data on all-cause mortality before progression to end-stage kidney disease (ESKD) and the cause of death were collected.

Results
The median follow-up time was 3.9 years (interquartile range, 1.7–5.0); 114 patients died and 308 started renal replacement therapy. The leading causes of death were as follows; cardiovascular (41%), infection-related (21%), and malignancy-related (18%). Advanced age and lower BMI were the significant risk factors for all-cause mortality before progression to ESKD. Advanced age was statistically associated with respective causes of death, while lower BMI was associated with infection-related death only. CKD stage had no significant impact on all-cause or individual mortality.

Conclusions
Low BMI was associated with significant risk of all-cause mortality and infection-related death, which may indicate the novel clinical target to improve CKD outcomes.
Failure of preventive treatments in migraine: an observational retrospective study in a tertiary headache center
Authors: Delussi Marianna , Vecchio Eleonora , Libro Giuseppe , Quitadamo Silvia , de Tommaso Marina 
Published: June 2020

Abstract
Background
Although the criteria for acute migraine treatment and prevention have been well described, there are still unmet needs, general underuse and low benefits of preventive drugs.
The aim of the present study was to retrospectively observe the short-term effect of preventive treatment in a cohort of migraine patients attending a tertiary headache center, using data from electronic medical records.

Methods
This was an observational retrospective cohort study based on data collected in a tertiary headache center. Data were extracted from an electronic dataset collected from January 2009 to December 2019. The main selection criteria were as follows: age of 18–75 years; diagnosis of migraine without aura (MO), migraine with aura (MA) or chronic migraine (CM); a control visit 3 months after the first access; and prescription of preventive treatment with level of evidence 1 as reported by Italian guidelines. As the primary outcome, we considered the change in the frequency of headache at the follow-up visit. Then, as secondary outcome measures, we used disability scores, intensity of headache, and allodynia. As predictive factors, we considered age, migraine duration, sex, headache frequency, allodynia, anxiety and depression at baseline, and comorbidity with fibromyalgia.

Results
Among the 6430 patients screened, 2800 met the selection criteria, 1800 returned to the follow-up visit, 550 withdrew because of adverse events, and 1100 were included the analysis. One hundred thirty-four patients had a frequency reduction of 50% or more. Flunarizine was used for less severe migraine, with a better effect compared to those of other drugs (odds ratio: 1.48; p: 0.022). Low headache frequency and absent or mild allodynia predicted a better outcome.

Conclusions
The mild effect of preventive drugs on migraine features and even the number of patients who were lost to follow-up or dropped out because of adverse events confirm that in severe and chronic patients, the first line of prevention can only delay a more focused therapeutic approach.