bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different applications of the KDIGO criteria for AKI lead to different incidences in critically ill patients: a post hoc analysis from the prospective observational SICS-II study
Authors: Wiersema Renske , Jukarainen Sakari , Eck Ruben J. , Kaufmann Thomas , Koeze Jacqueline , Keus Frederik , Pettilä Ville , van der Horst Iwan C. C. , Vaara Suvi T. 
Published: April 2020

Abstract
Background
Acute kidney injury (AKI) is a frequent and clinically relevant problem in critically ill patients. Various randomized controlled trials (RCT) have attempted to assess potentially beneficial treatments for AKI. Different approaches to applying the Kidney Disease Improving Global Outcomes (KDIGO) criteria for AKI make a comparison of studies difficult. The objective of this study was to assess how different approaches may impact estimates of AKI incidence and whether the association between AKI and 90-day mortality varied by the approach used.

Methods
Consecutive acutely admitted adult intensive care patients were included in a prospective observational study. AKI was determined following the KDIGO criteria during the first 7 days of ICU admission. In this post hoc analysis, we assessed whether AKI incidence differed when applying the KDIGO criteria in 30 different possible methods, varying in (A) serum creatinine (sCr), (B) urine output (UO), and (C) the method of combining these two into an outcome, e.g., severe AKI. We assessed point estimates and 95% confidence intervals for each incidence. Univariable regression was used to assess the associations between AKI and 90-day mortality.

Results
A total of 1010 patients were included. Baseline creatinine was available in 449 (44%) patients. The incidence of any AKI ranged from 28% (95%CI 25–31%) to 75% (95%CI 72–77%) depending on the approach used. Methods to estimate missing baseline sCr caused a variation in AKI incidence up to 15%. Different methods of handling UO caused a variation of up to 35%. At 90 days, 263 patients (26%) had died, and all 30 variations were associated with 90-day mortality.

Conclusions
In this cohort of critically ill patients, AKI incidence varied from 28 to 75%, depending on the method used of applying the KDIGO criteria. A tighter adherence to KDIGO definitions is warranted to decrease the heterogeneity of AKI and increase the comparability of future studies.
Improved lipid productivity in Nannochloropsis gaditana in nitrogen-replete conditions by selection of pale green mutants
Authors: Cecchin Michela , Berteotti Silvia , Paltrinieri Stefania , Vigliante Ivano , Iadarola Barbara , Giovannone Barbara , Maffei Massimo E. , Delledonne Massimo , Ballottari Matteo 
Published: April 2020

Abstract
Background
Nannochloropsis gaditana is a photosynthetic unicellular microalgae considered one of the most interesting marine algae to produce biofuels and food additive due to its rapid growth rate and high lipid accumulation. Although microalgae are attractive platforms for solar energy bioconversion, the overall efficiency of photosynthesis is reduced due to the steep light gradient in photobioreactors. Moreover, accumulation of lipids in microalgae for biofuels production is usually induced in a two-phase cultivation process by nutrient starvation, with additional time and costs associated. In this work, a biotechnological approach was directed for the isolation of strains with improved light penetration in photobioreactor combined with increased lipids productivity.

Results
Mutants of Nannochloropsis gaditana were obtained by chemical mutagenesis and screened for having both a reduced chlorophyll content per cell and increased affinity for Nile red, a fluorescent dye which binds to cellular lipid fraction. Accordingly, one mutant, called e8, was selected and characterized for having a 30% reduction of chlorophyll content per cell and an almost 80% increase of lipid productivity compared to WT in nutrient-replete conditions, with C16:0 and C18:0 fatty acids being more than doubled in the mutant. Whole-genome sequencing revealed mutations in 234 genes in e8 mutant among which there is a non-conservative mutation in the dgd1 synthase gene. This gene encodes for an enzyme involved in the biosynthesis of DGDG, one of the major lipids found in the thylakoid membrane and it is thus involved in chloroplast biogenesis. Lipid biosynthesis is strongly influenced by light availability in several microalgae species, including Nannochloropsis gaditana: reduced chlorophyll content per cell and more homogenous irradiance in photobioreactor is at the base for the increased lipid productivity observed in the e8 mutant.

Conclusions
The results herein obtained presents a promising strategy to produce algal biomass enriched in lipid fraction to be used for biofuel and biodiesel production in a single cultivation process, without the additional complexity of the nutrient starvation phase. Genome sequencing and identification of the mutations introduced in e8 mutant suggest possible genes responsible for the observed phenotypes, identifying putative target for future complementation and biotechnological application.
Latest trends in L. infantum infection in dogs in Spain, Part II: current clinical management and control according to a national survey of veterinary practitioners
Authors: Montoya Ana , Gálvez Rosa , Checa Rocío , Sarquis Juliana , Plaza Alexandra , Barrera Juan Pedro , Marino Valentina , Miró Guadalupe 
Published: April 2020

Abstract
Background
Canine leishmaniosis (CanL) is a parasitic zoonotic disease, endemic in the Mediterranean basin including Spain. While knowledge about CanL, its management, treatment, prevention and control mounts, it remains unclear whether all clinical veterinarians follow the same international recommendations, such as those of the LeishVet group. This study was thus designed to assess recent trends in the clinical management of CanL in veterinary clinics across Spain through a questionnaire-based survey. Results were compared with those of a prior national multicenter questionnaire administered by our research team in 2005.

Methods
A questionnaire consisting of 28 questions about CanL was developed using Google Forms and distributed by email to 1428 veterinary clinics in Spain. Questions were designed to obtain data on common clinical signs, techniques and complementary exams used to diagnose the disease, and on its monitoring, treatment and control measures. Data were collected in a database for statistical analysis.

Results
Completed questionnaires were returned by 295 clinics. Compared to the situation in 2005, responses indicate that clinical signs of CanL have not changed significantly, cutaneous lesions being still the most prevalent sign observed by practitioners. Quantitative serological techniques are considered an adequate approach to diagnosis, provided their results are supported by the findings of a thorough physical exam, as well as complementary tests (complete blood count, biochemical profile, plasma protein electrophoretogram and complete urinalysis). Treatment protocols and check-ups follow international recommendations. Finally, a multimodal approach is being endorsed to adequately control CanL including preventive measures such as annual serological check-ups and the combination of repellents and vaccines. Additionally, owners are being better informed about CanL by veterinarians, which translates to the improved control of this zoonosis.

Conclusions
The clinical management of CanL has recently undergone significant changes owing to improvements in clinical knowledge of the disease, more unified international criteria, improved diagnostic techniques and their adequate interpretation, as well as a greater awareness of the disease transmitted to owners.
Shallow whole-genome sequencing of plasma cell-free DNA accurately differentiates small from non-small cell lung carcinoma
Authors: Raman Lennart , Van der Linden Malaïka , Van der Eecken Kim , Vermaelen Karim , Demedts Ingel , Surmont Veerle , Himpe Ulrike , Dedeurwaerdere Franceska , Ferdinande Liesbeth , Lievens Yolande , Claes Kathleen , Menten Björn , Van Dorpe Jo 
Published: April 2020

Abstract
Background
Accurate lung cancer classification is crucial to guide therapeutic decisions. However, histological subtyping by pathologists requires tumor tissue—a necessity that is often intrinsically associated with procedural difficulties. The analysis of circulating tumor DNA present in minimal-invasive blood samples, referred to as liquid biopsies, could therefore emerge as an attractive alternative.

Methods
Concerning adenocarcinoma, squamous cell carcinoma, and small cell carcinoma, our proof of concept study investigates the potential of liquid biopsy-derived copy number alterations, derived from single-end shallow whole-genome sequencing (coverage 0.1–0.5×), across 51 advanced stage lung cancer patients.

Results
Genomic abnormality testing reveals anomalies in 86.3% of the liquid biopsies (16/20 for adenocarcinoma, 13/16 for squamous cell, and 15/15 for small cell carcinoma). We demonstrate that copy number profiles from formalin-fixed paraffin-embedded tumor biopsies are well represented by their liquid equivalent. This is especially valid within the small cell carcinoma group, where paired profiles have an average Pearson correlation of 0.86 (95% CI 0.79–0.93). A predictive model trained with public data, derived from 843 tissue biopsies, shows that liquid biopsies exhibit multiple deviations that reflect histological classification. Most notably, distinguishing small from non-small cell lung cancer is characterized by an area under the curve of 0.98 during receiver operating characteristic analysis. Additionally, we investigated how deeper paired-end sequencing, which will eventually become feasible for routine diagnosis, empowers tumor read enrichment by insert size filtering: for all of the 29 resequenced liquid biopsies, the tumor fraction could be increased in silico, thereby “rescuing” three out of five cases with previously undetectable alterations.

Conclusions
Copy number profiling of cell-free DNA enables histological classification. Since shallow whole-genome sequencing is inexpensive and often fully operational at routine molecular laboratories, this finding has current diagnostic potential, especially for patients with lesions that are difficult to reach.
Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective
Authors: Maxwell Patrick H. 
Published: April 2020

AbstractGenomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identifying potential roles to clearly demonstrating the level of impact TEs have on genome evolution and possible functions that they contribute to their host organisms. I summarize TE content and distribution in four well-characterized yeast model systems in this review: the pathogensCandida albicansandCryptococcus neoformans, and the nonpathogenic speciesSaccharomyces cerevisiaeandSchizosaccharomyces pombe. I compare and contrast their TE landscapes to their lifecycles, genomic features, as well as the presence and nature of RNA interference pathways in each species to highlight the valuable diversity represented by these models for functional studies of TEs. I then review the regulation and impacts of the Ty1 and Ty3 retrotransposons fromSaccharomyces cerevisiaeand Tf1 and Tf2 retrotransposons fromSchizosaccharomyces pombeto emphasize parallels and distinctions between these well-studied elements. I propose that further characterization of TEs in the pathogenic yeasts would enable this set of four yeast species to become an excellent set of models for comparative functional studies to address outstanding questions about TE-host relationships.
Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma
Authors: Fan Jian , Li Jun , Guo Shicheng , Tao Chengcheng , Zhang Haikun , Wang Wenjing , Zhang Ying , Zhang Dake , Ding Shigang , Zeng Changqing 
Published: April 2020

Abstract
Background
Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer.

Methods
In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450 K) of normal (N = 20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA), integrated with GEO and ArrayExpress datasets (N = 833).

Results
We identified 209 and 8692 CpG sites that were significantly hyper-methylated in LGA and HGA, respectively. Pathway analysis identified nervous system-related methylation changes that are significantly associated with early adenoma development. Integration analysis revealed that DNA methylation in the promoter region of ADHFE1 has the most potential for being an early diagnostic biomarker for colorectal adenoma and cancer (sensitivity = 0.96, specificity = 0.95, area under the curve = 0.97).

Conclusions
Overall, we demonstrated that DNA methylation have been shown significant changes in the stage of LGA and HGA in the development of colon cancer. Genome-wide DNA methylation to LGA and HGA provided an important proxy to identify promising early diagnosis biomarkers for colorectal cancer.
Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders
Authors: Murtaza Nadeem , Uy Jarryll , Singh Karun K. 
Published: April 2020

AbstractProteomics is the large-scale study of the total protein content and their overall function within a cell through multiple facets of research. Advancements in proteomic methods have moved past the simple quantification of proteins to the identification of post-translational modifications (PTMs) and the ability to probe interactions between these proteins, spatially and temporally. Increased sensitivity and resolution of mass spectrometers and sample preparation protocols have drastically reduced the large amount of cells required and the experimental variability that had previously hindered its use in studying human neurological disorders. Proteomics offers a new perspective to study the altered molecular pathways and networks that are associated with autism spectrum disorders (ASD). The differences between the transcriptome and proteome, combined with the various types of post-translation modifications that regulate protein function and localization, highlight a novel level of research that has not been appropriately investigated. In this review, we will discuss strategies using proteomics to study ASD and other neurological disorders, with a focus on how these approaches can be combined with induced pluripotent stem cell (iPSC) studies. Proteomic analysis of iPSC-derived neurons have already been used to measure changes in the proteome caused by patient mutations, analyze changes in PTMs that resulted in altered biological pathways, and identify potential biomarkers. Further advancements in both proteomic techniques and human iPSC differentiation protocols will continue to push the field towards better understanding ASD disease pathophysiology. Proteomics using iPSC-derived neurons from individuals with ASD offers a window for observing the altered proteome, which is necessary in the future development of therapeutics against specific targets.
The scope of tobacco cessation randomized controlled trials in low- to middle-income countries: protocol for a scoping review
Authors: Kumar Navin , Ainooson Jessica , Billings Ameera , Chen Grace , Cueto Lauren , Janmohamed Kamila , Jiang Jeannette , Niaura Raymond , Zhang Amy 
Published: April 2020

Abstract
Background
Tobacco consumption is the leading cause of preventable death globally. The global mortality burden of tobacco use lies predominantly in low- to middle-income countries (LMICs). There is much evidence on the effectiveness of tobacco cessation RCTs in high-income nations. However, the evidence base in LMICs is far more limited. To effectively design randomized controlled trials (RCTs) that mitigate tobacco-related harms in LMICs, further understanding of RCTs in this environment will be helpful. We will provide quality evidence regarding the scope of tobacco cessation RCTs in LMICs.

Methods
A scoping review of tobacco cessation RCTs will be conducted. MEDLINE, Embase, PsycINFO, Global Health, Web of Science and Sociological Abstracts will be searched to capture current literature. We will review RCTs that have already been done on tobacco cessation in the LMICs. The key outcome will be tobacco cessation in adults. Examples of the key outcome include smoking abstinence and reduction of tobacco use. Study selection will conform to Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines and study quality assessed with a modified version of the Cochrane Collaboration’s instrument.

Discussion
As researchers attempt to minimize the harms from tobacco in LMICs, they need to be aware of scientific evidence to develop RCTs to achieve their aim. The review will complement the evidence base on tobacco cessation in LMICs.
Refinements of the integral form of Jensen’s and the Lah–Ribarič inequalities and applications for Csiszár divergence
Authors: Pečarić J. , Perić J. 
Published: April 2020

AbstractIn this paper, we give refinements of the integral form of Jensen’s inequality and the Lah–Ribarič inequality. Using these results, we obtain a refinement of the Hölder inequality and a refinement of some inequalities for integral power means and quasiarithmetic means. We also give applications in information theory, namely, we give some interesting estimates for the integral Csiszár divergence and its important particular cases.
Correction to: Molecular characterization of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates identifies local transmission of infection in Kuwait, a country with a low incidence of TB and MDR-TB
Authors: Al-Mutairi Noura M. , Ahmad Suhail , Mokaddas Eiman M. 
Published: April 2020

The original publication of this article [1] contained few erroneous paragraphs and errors in Table 1 and Table 2. The first four paragraphs are in the ‘Results’ section while the last four paragraphs are in the ‘Discussion’ section. The errors in Table 1 involve the number of isolates tested for pyrazinamide and pyrazinamide susceptible isolates, ethambutol-susceptible isolates with a mutation and number of resistant isolates with a mutation for streptomycin. The error in Table 2 involves wrong codon number for a mutation in isolate KM17-01 in Cluster XII for gidB gene. The updated informations have been indicated in bold and also refer corrected Tables 1 and 2.
CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits
Authors: Zheng Xianrui , Zhao Pengju , Yang Kaijie , Ning Chao , Wang Haifei , Zhou Lei , Liu Jianfeng 
Published: April 2020

Abstract
Background
Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood.

Results
In this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by next-generation sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight.

Conclusions
The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.
Hippocampal granule cell dispersion: a non-specific finding in pediatric patients with no history of seizures
Authors: Roy Achira , Millen Kathleen J. , Kapur Raj P. 
Published: April 2020

AbstractChronic epilepsy has been associated with hippocampal abnormalities like neuronal loss, gliosis and granule cell dispersion. The granule cell layer of a normal human hippocampal dentate gyrus is traditionally regarded as a compact neuron-dense layer. Histopathological studies of surgically resected or autopsied hippocampal samples primarily from temporal lobe epilepsy patients, as well as animal models of epilepsy, describe variable patterns of granule cell dispersion including focal cell clusters, broader thick segments, and bilamination or “tram-tracking”. Although most studies have implicated granule cell dispersion as a specific feature of chronic epilepsy, very few “non-seizure” controls were included in these published investigations. Our retrospective survey of 147 cadaveric pediatric human hippocampi identified identical morphological spectra of granule cell dispersion in both normal and seizure-affected brains. Moreover, sections across the entire antero-posterior axis of a control cadaveric hippocampus revealed repetitive occurrence of different morphologies of the granule cell layer – compact, focally disaggregated and bilaminar. The results indicate that granule cell dispersion is within the spectrum of normal variation and not unique to patients with epilepsy. We speculate that sampling bias has been responsible for an erroneous dogma, which we hope to rectify with this investigation.
The synergistic effect of an imidazolium salt and benzotriazole on the protection of bronze surfaces with chitosan-based coatings
Authors: Silva da Conceição Debora Kelen , Nunes de Almeida Kauana , Nhuch Elsa , Raucci Maria Grazia , Santillo Chiara , Salzano de Luna Martina , Ambrosio Luigi , Lavorgna Marino , Giuliani Chiara , Di Carlo Gabriella , Staccioli Maria Paola , Falcade Tiago , Schrekker Henri Stephan 
Published: April 2020

Abstract
The class of imidazolium salts contains effective anticorrosion additives for metal substrates. This study evaluated the potential of 1-carboxymethyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide (HO

2

CC

1

MImNTf

2
) for application in cultural heritage, exploring it as anticorrosion additive in chitosan-based coatings for the protection of copper-based alloys. Under accelerated corrosion conditions with HCl vapor, the chitosan coating with HO

2

CC

1

MImNTf

2
was less effective than the one with benzotriazole. The coating with a combination of HO

2

CC

1

MImNTf

2
and benzotriazole resulted in the optimal protective efficacy of the bronze surface, and it also maintained high transparency without changing the bronze appearance.