bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved two-stage model averaging for high-dimensional linear regression, with application to Riboflavin data analysis
Authors: Pan Juming 
Published: March 2021

AbstractBackgroundModel averaging has attracted increasing attention in recent years for the analysis of high-dimensional data. By weighting several competing statistical models suitably, model averaging attempts to achieve stable and improved prediction. In this paper, we develop a two-stage model averaging procedure to enhance accuracy and stability in prediction for high-dimensional linear regression. First we employ a high-dimensional variable selection method such as LASSO to screen redundant predictors and construct a class of candidate models, then we apply the jackknife cross-validation to optimize model weights for averaging.ResultsIn simulation studies, the proposed technique outperforms commonly used alternative methods under high-dimensional regression setting, in terms of minimizing the mean of the squared prediction error. We apply the proposed method to a riboflavin data, the result show that such method is quite efficient in forecasting the riboflavin production rate, when there are thousands of genes and only tens of subjects.ConclusionsCompared with a recent high-dimensional model averaging procedure (Ando and Li in J Am Stat Assoc 109:254–65, 2014), the proposed approach enjoys three appealing features thus has better predictive performance: (1) More suitable methods are applied for model constructing and weighting. (2) Computational flexibility is retained since each candidate model and its corresponding weight are determined in the low-dimensional setting and the quadratic programming is utilized in the cross-validation. (3) Model selection and averaging are combined in the procedure thus it makes full use of the strengths of both techniques. As a consequence, the proposed method can achieve stable and accurate predictions in high-dimensional linear models, and can greatly help practical researchers analyze genetic data in medical research.
Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line
Authors: Hadifar Shima , Mostafaei Shayan , Behrouzi Ava , Fateh Abolfazl , Riahi Parisa , Siadat Seyed Davar , Vaziri Farzam 
Published: March 2021

AbstractBackgroundA growing body of evidence has shown the association between tuberculosis (TB) infection and lung cancer. However, the possible effect of strain‐specific behavior ofMycobacterium tuberculosis(M.tb) population, the etiological agent of TB infection in this association has been neglected. In this context, this study was conducted to investigate this association with consideration of the genetic background of strains in theM.tbpopulation.ResultsWe employed the elastic net penalized logistic regression model, as a statistical-learning algorithm for gene selection, to evaluate this association in 129 genes involved in TLRs and NF-κB signaling pathways in response to two differentM.tbsub-lineage strains (L3-CAS1and L 4.5). Of the 129 genes, 21 were found to be associated with the two studiedM.tbsub-lineages. In addition,MAPK8IP3gene was identified as a novel gene, which has not been reported in previous lung cancer studies and may have the potential to be recognized as a novel biomarker in lung cancer investigation.ConclusionsThis preliminary study provides new insights into the mechanistic association between TB infection and lung cancer. Further mechanistic investigations of this association with a large number ofM.tbstrains, encompassing the other mainM.tblineages and using the whole transcriptome of the host cell are inevitable.
The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes
Authors: Rödelsperger Christian 
Published: March 2021

Abstract
Background
The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Over the past years, it developed into an independent animal model organism for elucidating the genetic basis of phenotypic plasticity. Community-based curations were employed recently to improve the quality of gene annotations of P. pacificus and to more easily facilitate reverse genetic studies using candidate genes from C. elegans.

Results
Here, I demonstrate that the reannotation of phylogenomic data from nine related nematode species using the community-curated P. pacificus gene set as homology data substantially improves the quality of gene annotations. Benchmarking of universal single copy orthologs (BUSCO) estimates a median completeness of 84% which corresponds to a 9% increase over previous annotations. Nevertheless, the ability to infer gene models based on homology already drops beyond the genus level reflecting the rapid evolution of nematode lineages. This also indicates that the highly curated C. elegans genome is not optimally suited for annotating non-Caenorhabditis genomes based on homology. Furthermore, comparative genomic analysis of apparently missing BUSCO genes indicates a failure of ortholog detection by the BUSCO pipeline due to the insufficient sample size and phylogenetic breadth of the underlying OrthoDB data set. As a consequence, the quality of multiple divergent nematode genomes might be underestimated.

Conclusions
This study highlights the need for optimizing gene annotation protocols and it demonstrates the benefit of a high quality genome for phylogenomic data of related species.
Population aging and trends of pulmonary tuberculosis incidence in the elderly
Authors: Li Shi-jin , Li Yi-fan , Song Wan-mei , Zhang Qian-yun , Liu Si-qi , Xu Ting-ting , An Qi-qi , Liu Jin-yue , Li Huai-chen 
Published: March 2021

AbstractBackgroundTo explore population aging and the epidemic trend of pulmonary tuberculosis (PTB) in the elderly, and provide a basis for the prevention and control of pulmonary tuberculosis among the elderly.MethodsWe collected clinical information of 239,707 newly active PTB patients in Shandong Province from 2005 to 2017. We analyzed and compared the clinical characteristics, reported incidence and temporal trend of PTB among the elderly group (≥60 years) and the non-elderly group (< 60 years) through logistic model and Join-point regression model.ResultsAmong the total PTB cases, 77,192(32.2%) were elderly. Compared with non-elderly patients, newly active elderly PTB patients account for a greater proportion of male cases (OR 1.688, 95% CI 1.656–1.722), rural population cases (OR 3.411, 95% CI 3.320–3.505) and bacteriologically confirmed PTB cases (OR 1.213, 95%CI 1.193–1.234). The annual reported incidence of total, elderly, pulmonary bacteriologically confirmed cases were 35.21, 68.84, 35.63 (per 100,000), respectively. The annual reported incidence of PTB in the whole population, the elderly group and the non-elderly group has shown a slow downward trend since 2008. The joinpoint regression model showed that the overall reported incidence of PTB in the elderly significantly decreased from 2007 to 2017 (APC = -5.3,P < 0.05). The reported incidence of bacteriologically confirmed PTB among elderly patients declined rapidly from 2005 to 2014(2005–2010 APC = -7.2%,P < 0.05; 2010–2014 APC = -22.6%,P < 0.05; 2014–2017 APC = -9.0%,P = 0.1). The reported incidence of clinically diagnosed PTB among elderly patients from 2005 to 2017 (11.48–38.42/100,000) increased by about 235%. It rose significantly from 2007 to 2014 (APC = 9.4,P<0.05).ConclusionsCompared with the non-elderly population, the reported incidence of PTB in the elderly population is higher. The main burden of PTB will shift to the elderly, men, rural population, and clinically diagnosed patients. With the intensification of aging, more researches on elderly PTB prevention and treatment will facilitate the realization of the global tuberculosis (TB) control targets.
Improved detection of microbiological pathogens: role of partner and non-governmental organizations
Authors: Owusu Michael , Nkrumah Bernard , Acheampong Godfred , Mensah Ebenezer Kofi , Komei Abass Abdul-Karim , Sroda Festus Kofi , David Sambian , Emery Shannon , Robinson Lucy Maryogo , Asante Kwame , Opare David 
Published: March 2021

Abstract
Background
Proper detection of disease-causing organisms is very critical in controlling the course of outbreaks and avoiding large-scale epidemics. Nonetheless, availability of resources to address these gaps have been difficult due to limited funding. This report sought to highlight the importance of in-country partners and non-governmental organizations in improving detection of microbiological organisms in Ghanaian Public Health Laboratories (PHLs).

Methods/context
This study was conducted between June, 2018 to August, 2019. U. S CDC engaged the Centre for Health Systems Strengthening (CfHSS) through the Association of Public Health Laboratories to design and implement strategies for strengthening three PHLs in Ghana. An assessment of the three PHLs was done using the WHO/CDS/CSR/ISR/2001.2 assessment tool. Based on findings from the assessments, partner organizations (CfHSS/APHL/CDC) serviced and procured microbiological equipment, laboratory reagents and logistics. CfHSS provided in-house mentoring and consultants to assist with capacity building in detection of epidemic-prone infectious pathogens by performing microbiological cultures and antimicrobial susceptibility tests.

Results
A total of 3902 samples were tested: blood (1107), urine (1742), stool (249) and cerebrospinal fluid (CSF) (804). All-inclusive, 593 pathogenic bacteria were isolated from blood cultures (70; 11.8%); urine cultures (356; 60%); stool cultures (19; 3.2%) and from CSF samples (148; 25%). The most predominant pathogens isolated from blood, urine and stool were Staphylococcus aureus (22/70; 31%), Escherichia coli (153/356; 43%) and Vibrio parahaemolyticus (5/19; 26.3%), respectively. In CSF samples, Streptococcus pneumoniae was the most frequent pathogen detected (80/148; 54.1%). New bacterial species such as Pastuerella pneumotropica, Klebsiella oxytoca, Vibrio parahaemolyticus, and Halfnia alvei were also identified with the aid of Analytical Profile Index (API) kits that were introduced as part of this implementation. Streptococcus pneumoniae and Neisseria meningitidis detections in CSF were highest during the hot dry season. Antimicrobial susceptibility test revealed high rate of S. aureus, K. pneumoniae and E. coli resistance to gentamicin (35–55%). In urine, E. coli was highly resistant to ciprofloxacin (39.2%) and ampicillin (34%).

Conclusion
Detection of epidemic-prone pathogens can be greatly improved if laboratory capacity is strengthened. In-country partner organizations are encouraged to support this move to ensure accurate diagnosis of diseases and correct antimicrobial testing.
Glomerulonephritis with severe nephrotic syndrome induced by immune complexes composed of galactose-deficient IgA1 in primary Sjögren’s syndrome: a case report
Authors: Nishioka Ryo , Hara Satoshi , Kawahara Hiroyuki , Ito Kiyoaki , Mizushima Ichiro , Hirata Masayoshi , Nagata Michio , Kawano Mitsuhiro 
Published: March 2021

Abstract
Background
Primary Sjögren’s syndrome (pSS) is an auto-immune disease characterized by sialadenitis and dacryoadenitis with lymphoplasmacytic cell infiltration. In pSS, not only sicca symptoms, but also extra-glandular involvement induced by immune abnormalities based on pSS occurs. Renal involvement is one such important life-threatening extra-glandular involvement. Although the aberrant glycosylated IgA in pSS as a product of over-activated B cells is a risk factor of renal involvement, its association has not been clarified. Here we report a case of glomerulonephritis (GN) induced by immune complexes (IC) composed of galactose-deficient IgA1 (Gd-IgA1) in a patient with pSS.

Case presentation
A 48-year-old Japanese woman with pSS was admitted to our hospital because of a two-month history of nephrotic syndrome. Seven years before she had been diagnosed with pSS from keratoconjunctivitis sicca, elevation of serum anti-Ro/SSA antibody titer and lymphoplasmacytic cell infiltration around salivary ducts of the small salivary glands. Renal biopsy revealed diffuse bubbling appearance in glomerular basement membrane (GBM) with scarce mesangial proliferation. Immunofluorescence showed granular IgA, C3 and Gd-IgA1 staining of GBM. Light chain staining showed no monoclonality. Electron microscopy showed electron dense deposits mainly in the intra-membranous and paramesangial areas and slightly in the subepithelial area. Additional serum analysis confirmed elevation of Gd-IgA1 (13.5 μg/mL), which was comparable with that seen in IgA nephropathy, and qualitative enzyme-linked immunosorbent assay of IgA-containing circulating immune complex (IgA-CIC) was positive. Thus, we diagnosed GN induced by IC composed of Gd-IgA1. Furthermore, retrospectively performed immunofluorescence of the small salivary gland evaluated at the diagnosis of pSS showed positive Gd-IgA1 staining of infiltrating lymphoplasmacytic cells. Therefore, we concluded that Gd-IgA1 produced by over-activated B cells in pSS formed circulating IC and thereby induced GN. After induction therapy with high dose prednisolone and mycophenolate mofetil, the nephrotic syndrome remitted within 3 weeks, the serum Gd-IgA1 level decreased to the normal range (3.8 μg/mL), and serum IgA-CIC disappeared in the 6th month after induction therapy.

Conclusions
Our findings clearly demonstrate an association between aberrant glycosylated IgA and the renal involvement seen in pSS, thereby helping to clarify the renal significance of aberrant glycosylated IgA in pSS.
Association between chronic kidney disease and the most common corneal ectasia disease (keratoconus): a nationwide cohort study
Authors: Jan Ren-Long , Weng Shih-Feng , Wang Jhi-Joung , Chang Yuh-Shin 
Published: March 2021

AbstractBackgroundBoth keratoconus (KCN) and chronic kidney disease (CKD) are multifactorial conditions with multiple aetiologies and share several common pathophysiologies. However, the few studies that have described the relationship between KCN and CKD are limited to case reports and small case series. This study aimed to evaluate the association between KCN and CKD.MethodsThe study cohort included 4,609 new-onset keratoconus patients ≥ 12 years identified by the International Classification of Diseases, Ninth Revision, Clinical Modification, code 371.6 and recruited between 2004 and 2011 from the Taiwan National Health Insurance Research Database. The age-, sex-, and comorbidity-matched control group included 27,654 non-KCN patients, selected from the Taiwan Longitudinal Health Insurance Database, 2000. Information for each patient was collected and tracked from the index date until December 2013. The incidence and risk of CKD were compared between the two groups. The adjusted hazard ratios (HRs) for CKD were calculated with Cox proportional hazard regression analysis. Kaplan–Meier analysis was used to calculate the cumulative CKD incidence rate.ResultsThe incidence rate of CKD was 1.36 times higher in KCN patients than in controls without statistically significant difference (95 % confidence interval [CI] = 0.99–1.86,p = 0.06). In total, 29 male KCN patients and 90 male controls developed CKD during the follow-up period. The incidence rate of CKD was 1.92 times (95 % [CI] = 1.26–2.91;p = 0.002) higher in male KCN patients than in controls. After adjusting for potential confounders, including age, hypertension, hyperlipidaemia, and diabetes mellitus, male KCN patients were 1.75 times (adjusted HR = 1.75, 95 % [CI] = 1.14–2.68,p < 0.05) more likely to develop CKD.ConclusionsWe found that male KCN patients have an increased risk of CKD. Therefore, it is recommended that male KCN patients should be aware of CKD.
Birthweight: EN-BIRTH multi-country validation study
Authors:   EN-BIRTH Study Group, Kong Stefanie , Day Louise T. , Zaman Sojib Bin , Peven Kimberly , Salim Nahya , Sunny Avinash K. , Shamba Donat , Rahman Qazi Sadeq-ur , K.C. Ashish , Ruysen Harriet , El Arifeen Shams , Mee Paul , Gladstone Miriam E. , Blencowe Hannah , Lawn Joy E. 
Published: March 2021

Abstract
Background
Accurate birthweight is critical to inform clinical care at the individual level and tracking progress towards national/global targets at the population level. Low birthweight (LBW) < 2500 g affects over 20.5 million newborns annually. However, data are lacking and may be affected by heaping. This paper evaluates birthweight measurement within the Every Newborn Birth Indicators Research Tracking in Hospitals (EN-BIRTH) study.

Methods
The EN-BIRTH study took place in five hospitals in Bangladesh, Nepal and Tanzania (2017–2018). Clinical observers collected time-stamped data (gold standard) for weighing at birth. We compared accuracy for two data sources: routine hospital registers and women’s report at exit interview survey. We calculated absolute differences and individual-level validation metrics. We analysed birthweight coverage and quality gaps including timing and heaping. Qualitative data explored barriers and enablers for routine register data recording.

Results
Among 23,471 observed births, 98.8% were weighed. Exit interview survey-reported weighing coverage was 94.3% (90.2–97.3%), sensitivity 95.0% (91.3–97.8%). Register-reported coverage was 96.6% (93.2–98.9%), sensitivity 97.1% (94.3–99%). Routine registers were complete (> 98% for four hospitals) and legible > 99.9%. Weighing of stillbirths varied by hospital, ranging from 12.5–89.0%. Observed LBW rate was 15.6%; survey-reported rate 14.3% (8.9–20.9%), sensitivity 82.9% (75.1–89.4%), specificity 96.1% (93.5–98.5%); register-recorded rate 14.9%, sensitivity 90.8% (85.9–94.8%), specificity 98.5% (98–99.0%). In surveys, “don’t know” responses for birthweight measured were 4.7%, and 2.9% for knowing the actual weight. 95.9% of observed babies were weighed within 1 h of birth, only 14.7% with a digital scale. Weight heaping indices were around two-fold lower using digital scales compared to analogue. Observed heaping was almost 5% higher for births during the night than day. Survey-report further increased observed birthweight heaping, especially for LBW babies. Enablers to register birthweight measurement in qualitative interviews included digital scale availability and adequate staffing.

Conclusions
Hospital registers captured birthweight and LBW prevalence more accurately than women’s survey report. Even in large hospitals, digital scales were not always available and stillborn babies not always weighed. Birthweight data are being captured in hospitals and investment is required to further improve data quality, researching of data flow in routine systems and use of data at every level.
Barriers and enablers to routine register data collection for newborns and mothers: EN-BIRTH multi-country validation study
Authors:   EN-BIRTH Study Group, Shamba Donat , Day Louise T. , Zaman Sojib Bin , Sunny Avinash K. , Tarimo Menna Narcis , Peven Kimberly , Khan Jasmin , Thakur Nishant , Talha Md. Taqbir Us Samad , K.C. Ashish , Haider Rajib , Ruysen Harriet , Mazumder Tapas , Rahman Md. Hafizur , Shaikh Md. Ziaul Haque , Sæbø Johan Ivar , Hanson Claudia , Singh Neha S. , Schellenberg Joanna , Vaz Lara M. E. , Requejo Jennifer , Lawn Joy E. 
Published: March 2021

Abstract
Background
Policymakers need regular high-quality coverage data on care around the time of birth to accelerate progress for ending preventable maternal and newborn deaths and stillbirths. With increasing facility births, routine Health Management Information System (HMIS) data have potential to track coverage. Identifying barriers and enablers faced by frontline health workers recording HMIS source data in registers is important to improve data for use.

Methods
The EN-BIRTH study was a mixed-methods observational study in five hospitals in Bangladesh, Nepal and Tanzania to assess measurement validity for selected Every Newborn coverage indicators. We described data elements required in labour ward registers to track these indicators. To evaluate barriers and enablers for correct recording of data in registers, we designed three interview tools: a) semi-structured in-depth interview (IDI) guide b) semi-structured focus group discussion (FGD) guide, and c) checklist assessing care-to-documentation. We interviewed two groups of respondents (January 2018–March 2019): hospital nurse-midwives and doctors who fill ward registers after birth (n = 40 IDI and n = 5 FGD); and data collectors (n = 65). Qualitative data were analysed thematically by categorising pre-identified codes. Common emerging themes of barriers or enablers across all five hospitals were identified relating to three conceptual framework categories.

Results
Similar themes emerged as both barriers and enablers. First, register design was recognised as crucial, yet perceived as complex, and not always standardised for necessary data elements. Second, register filling was performed by over-stretched nurse-midwives with variable training, limited supervision, and availability of logistical resources. Documentation complexity across parallel documents was time-consuming and delayed because of low staff numbers. Complete data were valued more than correct data. Third, use of register data included clinical handover and monthly reporting, but little feedback was given from data users.

Conclusion
Health workers invest major time recording register data for maternal and newborn core health indicators. Improving data quality requires standardised register designs streamlined to capture only necessary data elements. Consistent implementation processes are also needed. Two-way feedback between HMIS levels is critical to improve performance and accurately track progress towards agreed health goals.