bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved Dysphagia Outcomes in Anchored Spacers Versus Plate-Screw Systems in Anterior Cervical Discectomy and Fusion: A Systematic Review
Authors: Gabr Mostafa A. , Touko Elisabeth , Yadav Amol P. , Karikari Isaac , Goodwin C. Rory , Groff Michael W. , Ramirez Luis , Abd-El-Barr Muhammad M.
Published: December 2019

Study Design:

Systematic review and meta-analysis.

Objective:

To perform a systematic review of clinical outcomes between stand-alone anchored spacers and traditional cages with plate fixation for dysphagia and pseudoarthrosis using data from clinical trials.

Methods:

Our search protocol was added to PROSPERO register and systematic review using PRISMA method was performed. Then, we systematically searched for studies addressing stand-alone anchored spacers in patients who underwent ACDF. Mean Neck Disability Index (NDI), dysphagia incidence % (Dinc%), and Swallowing–Quality of Life (SQOL) scores during preoperative, immediate postoperative and last follow-up visits were extracted. Chi-square and analysis of variance (ANOVA) tests were used for statistical comparisons ( P ≤ .05).

Results:

The initial search generated 506 articles in CENTRAL and 40 articles in MEDLINE. Finally, 14 articles were included. Total number of patients was 1173 (583 anchored stand-alone and 590 plate). Dinc% scores were statistically significantly lower in the stand-alone anchored spacer compared to the plate-screw construct ( P ≤ .05). ANOVA showed no statistically significant difference in the comparisons of SQOL. On the other hand, NDI scores were statistically significantly lower in baseline of stand-alone anchored spacer and the plate-screw construct compared with both immediate postoperative and last follow-up visits ( P ≤ .05).

Conclusions:

Our study results revealed that the stand-alone anchored spacers were associated with less dysphagia in the immediate and last follow-up.
Comparing Bleeding and Thrombotic Rates in Spine Surgery: An Analysis of 119 888 Patients
Authors: Pirkle Sean , Cook David J. , Kaskovich Samuel , Bhattacharjee Sarah , Ho Alisha , Shi Lewis L. , Lee Michael J.
Published: December 2019

Study Design:

Retrospective, database review.

Objectives:

Examine the utilization rate of postoperative deep vein thrombosis (DVT) prophylaxis and compare the incidence and severity of bleeding and thrombotic complications in elective spine surgery patients.

Methods:

We utilized PearlDiver, a national orthopedics claims database. All patients who underwent elective spine surgery from 2007 to 2017 were included. Patients were stratified by the presence of DVT prophylaxis drug codes, then by comorbidities for postoperative bleeding/thrombosis. The severity of all bleeding and thrombotic complications in each cohort was studied, including the incidence of complications requiring operative washout, diagnosis of pulmonary embolism, intensive care unit admission, and mortality.

Results:

A total of 119 888 patients were included. The majority of patients (118 720, >99%) were not administered postoperative DVT chemoprophylaxis while a minority of patients (1168) were. The overall rates of bleeding and thrombotic complications within the population not receiving DVT prophylaxis were 1.96% and 2.45%, respectively ( P < .001). The incidence of surgical intervention for a wound washout was 0.62% compared with 1.05% for pulmonary embolism ( P < .001). Intensive care unit admission rates related to a wound washout procedure or pulmonary embolism also significantly differed (0.07% vs 0.34%, P < .001). There were no observed differences in mortality. When controlling for patient comorbidity, patients with atrial fibrillation, cancer, or a prior history of thrombotic complications experienced the greatest increased risks of postoperative thrombosis.

Conclusions:

DVT prophylaxis is not routinely utilized following elective spine procedures. We report that there exist specific populations which may receive benefit from these practices, although further study is necessary to determine optimal prevention strategies for both thrombotic and bleeding complications in spine surgery.
Minimally invasive fasciotomy using a lighted retractor in the treatment of chronic exertional compartment syndrome
Authors: Broderick James M , Synnott Keith A , Mulhall Kevin J
Published: December 2019

Chronic exertional compartment syndrome can be a debilitating cause of lower leg pain that typically affects young, healthy people during a variety of aerobic activities. Conservative management has produced a poor success rate and numerous techniques for surgical decompression have been described. Many of these, however, involve blind fascial dissection which increases the risk of direct nerve injury or insufficient fascial release. We describe a novel technique of mini-open fasciotomy using a lighted retractor which enables direct visualization of the fascia and the superficial peroneal nerve using a single, small incision. By the use of a 3- to 4-cm laterally based incision, a lighted retractor with fiber-optic illumination is introduced into the subcutaneous plane and advanced distally and proximally. The retractor gently elevates the subcutaneous tissues while focusing light directly into the surgical area and a long Metzenbaum scissors is then used to release the fascia under direct vision. Fasciotomy using this technique avoids the risks of blind fascial release and is a straightforward, safe, and effective method for compartment decompression.
Ring-shaped lateral meniscus combined with an accessory meniscus: A rare anatomical variant
Authors: Lee Su-Keon , Yang Bong-Seok , Kim Tae-Woo , Choi Nam-Hong
Published: December 2019

A ring-shaped meniscus is a very rare anatomical variant among all meniscal abnormalities. Additionally, an accessory meniscus is extremely rare, and only a few cases have been reported. We herein report a case involving the combination of these two features in a single lateral meniscus. These abnormalities were found during arthroscopic surgery for removal of an osteochondral fragment that had detached from the patellar bone and plication of the medial patellofemoral ligament in a patient with acute patellar dislocation. To our knowledge, each variant is extremely rare and the combination of the two variants has not been reported.
Student Expectations of an RN-to-BSN Program: A Qualitative Analysis of Student and Faculty Perspectives
Authors: Linton Mary , Dabney Beverly W. , Knecht Linda , Koonmen Jamie
Published: December 2019

The expansion of RN-to-BSN (registered nurse to Bachelor of Science in Nursing) education is addressing the need for nursing workforce development. However, little is known about what RNs expect from their RN-to-BSN education experience. Lack of understanding of student expectations could lead to student-perceived gaps in service quality. The aim of this study was to explore students’ expectations of the RN-to-BSN program compared with the faculty’s perceptions of what students expect. A descriptive qualitative research study using structured interviews was conducted at a school of nursing in the Midwest region of the United States. Student and faculty reports revealed the common themes of workload, flexibility, coursework, and support. Congruencies were noted in the areas of workload and coursework, and differences were identified in the areas of flexibility and support. Conducting a gap analysis can be a worthwhile endeavor for educators seeking to understand the needs of their student population. Acknowledging RN-to-BSN student expectations and addressing gaps between their expectations and reality early in the program could improve student perceptions of program quality.
Prospective assessment of NGS-detectable mutations in CML patients with nonoptimal response: the NEXT-in-CML study
Authors: Soverini Simona , Bavaro Luana , De Benedittis Caterina , Martelli Margherita , Iurlo Alessandra , Orofino Nicola , Sica Simona , Sorà Federica , Lunghi Francesca , Ciceri Fabio , Galimberti Sara , Baratè Claudia , Bonifacio Massimiliano , Scaffidi Luigi , Castagnetti Fausto , Gugliotta Gabriele , Albano Francesco , Russo Rossi Antonella Vita , Stagno Fabio , di Raimondo Francesco , D’Adda Mariella , di Bona Eros , Abruzzese Elisabetta , Binotto Gianni , Sancetta Rosaria , Salvucci Marzia , Capodanno Isabella , Girasoli Mariella , Coluzzi Sabrina , Attolico Immacolata , Musolino Caterina , Calistri Elisabetta , Annunziata Mario , Bocchia Monica , Stella Stefania , Serra Anna , Errichiello Santa , Saglio Giuseppe , Pane Fabrizio , Vigneri Paolo , Mignone Flavio , Laginestra Maria Antonella , Pileri Stefano Aldo , Percesepe Antonio , Tenti Elena , Rosti Gianantonio , Baccarani Michele , Cavo Michele , Martinelli Giovanni
Published: December 2019

In chronic myeloid leukemia (CML) patients, tyrosine kinase inhibitors (TKIs) may select for drug-resistant BCR-ABL1 kinase domain (KD) mutants. Although Sanger sequencing (SS) is considered the gold standard for BCR-ABL1 KD mutation screening, next-generation sequencing (NGS) has recently been assessed in retrospective studies. We conducted a prospective, multicenter study (NEXT-in-CML) to assess the frequency and clinical relevance of low-level mutations and the feasibility, cost, and turnaround times of NGS-based BCR-ABL1 mutation screening in a routine setting. A series of 236 consecutive CML patients with failure (n = 124) or warning (n = 112) response to TKI therapy were analyzed in parallel by SS and NGS in 1 of 4 reference laboratories. Fifty-one patients (22 failure, 29 warning) who were negative for mutations by SS had low-level mutations detectable by NGS. Moreover, 29 (27 failure, 2 warning) of 60 patients who were positive for mutations by SS showed additional low-level mutations. Thus, mutations undetectable by SS were identified in 80 out of 236 patients (34%), of whom 42 (18% of the total) had low-level mutations somehow relevant for clinical decision making. Prospective monitoring of mutation kinetics demonstrated that TKI-resistant low-level mutations are invariably selected if the patients are not switched to another TKI or if they are switched to a inappropriate TKI or TKI dose. The NEXT-in-CML study provides for the first time robust demonstration of the clinical relevance of low-level mutations, supporting the incorporation of NGS-based BCR-ABL1 KD mutation screening results in the clinical decision algorithms.
Comparison of hepatitis B vaccine efficacy in Japanese students: a retrospective study
Authors: Ogawa Masanori , Akine Dai , Sasahara Teppei
Published: December 2019

Background

Two types of recombinant hepatitis B virus (HBV) vaccines are available in Japan. One type uses the antigen from genotype A (Heptavax-II®) and the other uses the antigen from genotype C (Bimmugen®). Potential differences in productivity of the hepatitis B virus surface (HBs) antibody between vaccines have not been studied in detail. We investigated the acquired level of immunity against HBV in association with two vaccines, their administration routes, and patient sex. We present the appropriate inoculation method based on the characteristics of each vaccine.

Methods

Data of 1135 medical and nursing students (481 men and 651 women) were used, each of whom was unvaccinated prior to recruitment and subsequently vaccinated three times prior to the study. The vaccine type and administration route differed according to the university department and enrolling year. The students were categorized into the following three groups: Bimmugen®-subcutaneous group, Heptavax-II®-subcutaneous group, and Heptavax-II®-intramuscular group. The total and sex-segregated positive rates of the HBs antibody among the three groups were compared using Pearson’s chi-square test. The effect of time between the HBs antibody test and vaccine administration on the HBs antibody level was also analyzed similarly.

Results

The Bimmugen®-subcutaneous group showed the highest positive HBs antibody rate (92.0%) among the three groups. In the Heptavax-II® group, the positive rate was 66.3% in the subcutaneous injection group and 89.1% in the intramuscular injection group. There was a significant difference among these three groups. In terms of sex, women showed a significantly higher average positive rate than men in each group. In terms of effect of time between the HBs antibody test and vaccine administration, no significant differences were observed.

Conclusions

Bimmugen® is associated with more effective HBs antibody production than Heptavax-II® in Japanese students. However, the Heptavax-II® vaccine is an appropriate choice for HBV vaccination in areas where HB is caused predominantly by HBV genotype C. With both vaccines, women tended to acquire more immunogenicity than men. Intramuscular injection may be the preferred administration route due to the possibility of local reactions.
Assessing the ecological impact of chemical pollution on aquatic ecosystems requires the systematic exploration and evaluation of four lines of evidence
Authors: Backhaus Thomas , Brack Werner , Van den Brink Paul J. , Deutschmann Björn , Hollert Henner , Posthuma Leo , Segner Helmut , Seiler Thomas-Benjamin , Teodorovic Ivana , Focks Andreas
Published: December 2019

The aim of the European Water Framework Directive is to ensure good ecological status for all European surface waters. However, although current monitoring strategies aim to identify the presence and magnitude of ecological impacts, they provide little information on the causes of an ecosystem impairment. In fact, approaches to establish causal links between chemical pollution and impacts on the ecological status of exposed aquatic systems are largely lacking or poorly described and established. This is, however, crucial for developing and implementing appropriately targeted water management strategies. In order to identify the role of chemical pollution on the ecological status of an aquatic ecosystem, we suggest to systematically combine four lines of evidence (LOEs) that provide complementary evidence on the presence and potential ecological impact of complex chemical pollution: (1) component-based methods that allow a predictive mixture risk modeling; (2) effect-based methods; (3) in situ tests; (4) field-derived species inventories. These LOEs differ systematically in their specificity for chemical pollution, data demands, resources required and ecological relevance. They complement each other and, in their combination, allow to assess the contribution of chemical pollution pressure to impacts on ecological structure and function. Data from all LOEs are not always available and the information they provide is not necessarily consistent. We therefore propose a systematic, robust and transparent approach to combine the information available for a given study, in order to ensure that consensual conclusions are drawn from a given dataset. This allows to identify critical data gaps and needs for future testing and/or options for targeted and efficient water management.
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets
Authors: Netanely Dvir , Stern Neta , Laufer Itay , Shamir Ron
Published: December 2019

Background

Analysis of large genomic datasets along with their accompanying clinical information has shown great promise in cancer research over the last decade. Such datasets typically include thousands of samples, each measured by one or several high-throughput technologies (‘omics’) and annotated with extensive clinical information. While instrumental for fulfilling the promise of personalized medicine, the analysis and visualization of such large datasets is challenging and necessitates programming skills and familiarity with a large array of software tools to be used for the various steps of the analysis.

Results

We developed PROMO (Profiler of Multi-Omic data), a friendly, fully interactive stand-alone software for analyzing large genomic cancer datasets together with their associated clinical information. The tool provides an array of built-in methods and algorithms for importing, preprocessing, visualizing, clustering, clinical label enrichment testing, and survival analysis that can be performed on a single or multi-omic dataset. The tool can be used for quick exploration and stratification of tumor samples taken from patients into clinically significant molecular subtypes. Identification of prognostic biomarkers and generation of simple subtype classifiers are additional important features. We review PROMO’s main features and demonstrate its analysis capabilities on a breast cancer cohort from TCGA.

Conclusions

PROMO provides a single integrated solution for swiftly performing a complete analysis of cancer genomic data for subtype discovery and biomarker identification without writing a single line of code, and can, therefore, make the analysis of these data much easier for cancer biologists and biomedical researchers. PROMO is freely available for download athttp://acgt.cs.tau.ac.il/promo/.
ICGRM: integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset
Authors: Jiang Dan , Xin Cong , Ye Jinhua , Yuan Yingbo , Fang Ming
Published: December 2019

Background

Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with genome-wide distributed SNPs instead of pedigree. The key step of it is to construct genomic relationship matrix (GRM) via genome-wide SNPs; however, usually the calculation of GRM needs huge computer memory especially when the SNP number and sample size are big, so that sometimes it will become computationally prohibitive even for super computer clusters. We herein developed an integrative algorithm to compute GRM. To avoid calculating GRM for the whole genome, ICGRM freely divides the genome-wide SNPs into several segments and computes the summary statistics related to GRM for each segment that requires quite few computer RAM; then it integrates these summary statistics to produce GRM for whole genome.

Results

It showed that the computer memory of ICGRM was reduced by 15 times (from 218Gb to 14Gb) after the genome SNPs were split into 5 to 200 parts in terms of the number of SNPs in our simulation dataset, making it computationally feasible for almost all kinds of computer servers. ICGRM is implemented in C/C++ and freely available viahttps://github.com/mingfang618/CLGRM.

Conclusions

ICGRM is computationally efficient software to build GRM and can be used for big dataset.
Exploring the changing landscape of cell-to-cell variation after CTCF knockdown via single cell RNA-seq
Authors: Wang Wei , Ren Gang , Hong Ni , Jin Wenfei
Published: December 2019

Background

CCCTC-Binding Factor (CTCF), also known as 11-zinc finger protein, participates in many cellular processes, including insulator activity, transcriptional regulation and organization of chromatin architecture. Based on single cell flow cytometry and single cell RNA-FISH analyses, our previous study showed that deletion of CTCF binding site led to a significantly increase of cellular variation of its target gene. However, the effect of CTCF on genome-wide landscape of cell-to-cell variation remains unclear.

Results

We knocked down CTCF in EL4 cells using shRNA, and conducted single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells using Fluidigm C1 system. Principal component analysis of single cell RNA-seq data showed that WT and CTCF-KD cells concentrated in two different clusters on PC1, indicating that gene expression profiles of WT and CTCF-KD cells were systematically different. Interestingly, GO terms including regulation of transcription, DNA binding, zinc finger and transcription factor binding were significantly enriched in CTCF-KD-specific highly variable genes, implying tissue-specific genes such as transcription factors were highly sensitive to CTCF level. The dysregulation of transcription factors potentially explains why knockdown of CTCF leads to systematic change of gene expression. In contrast, housekeeping genes such as rRNA processing, DNA repair and tRNA processing were significantly enriched in WT-specific highly variable genes, potentially due to a higher cellular variation of cell activity in WT cells compared to CTCF-KD cells. We further found that cellular variation-increased genes were significantly enriched in down-regulated genes, indicating CTCF knockdown simultaneously reduced the expression levels and increased the expression noise of its regulated genes.

Conclusions

To our knowledge, this is the first attempt to explore genome-wide landscape of cellular variation after CTCF knockdown. Our study not only advances our understanding of CTCF function in maintaining gene expression and reducing expression noise, but also provides a framework for examining gene function.
PaCBAM: fast and scalable processing of whole exome and targeted sequencing data
Authors: Valentini Samuel , Fedrizzi Tarcisio , Demichelis Francesca , Romanel Alessandro
Published: December 2019

Background

Interrogation of whole exome and targeted sequencing NGS data is rapidly becoming a preferred approach for the exploration of large cohorts in the research setting and importantly in the context of precision medicine. Single-base and genomic region level data retrieval and processing still constitute major bottlenecks in NGS data analysis. Fast and scalable tools are hence needed.

Results

PaCBAM is a command line tool written in C and designed for the characterization of genomic regions and single nucleotide positions from whole exome and targeted sequencing data. PaCBAM computes depth of coverage and allele-specific pileup statistics, implements a fast and scalable multi-core computational engine, introduces an innovative and efficient on-the-fly read duplicates filtering strategy and provides comprehensive text output files and visual reports. We demonstrate that PaCBAM exploits parallel computation resources better than existing tools, resulting in important reductions of processing time and memory usage, hence enabling an efficient and fast exploration of large datasets.

Conclusions

PaCBAM is a fast and scalable tool designed to process genomic regions from NGS data files and generate coverage and pileup comprehensive statistics for downstream analysis. The tool can be easily integrated in NGS processing pipelines and is available from Bitbucket and Docker/Singularity hubs.
Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis
Authors: Zumaquero A. , Kanematsu S. , Nakayashiki H. , Matas A. , Martínez-Ferri E. , Barceló-Muñóz A. , Pliego-Alfaro F. , López-Herrera C. , Cazorla F. M. , Pliego C.
Published: December 2019

Background

White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNA-Seq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado ‘Dusa’ roots with that obtained from the fungus cultured in rich medium.

Results

The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RGA) and R. necatrix growing on potato dextrose agar media (RGPDA) were analyzed using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1937 were differentially expressed genes (DEG), 137 exclusively expressed in RGA and 160 in RGPDA. During the root infection process, genes involved in the production of fungal toxins, detoxification and transport of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed. Interestingly, 24 out of the 137 contigs expressed only during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that three of the R. necatrix CEP showed homology with previously annotated effectors, already proven experimentally via pathogen-host interaction.

Conclusions

The analysis of the full-length transcriptome of R. necatrix during the infection process is suggesting that the success of this fungus to infect roots of diverse crops might be attributed to the production of different compounds which, singly or in combination, interfere with defense or signaling mechanisms shared among distinct plant families. The transcriptome analysis of R. necatrix during the infection process provides useful information and facilitates further research to a more in -depth understanding of the biology and virulence of this emergent pathogen. In turn, this will make possible to evolve novel strategies for white root rot management in avocado.
Archaic mitochondrial DNA inserts in modern day nuclear genomes
Authors: Bücking Robert , Cox Murray P , Hudjashov Georgi , Saag Lauri , Sudoyo Herawati , Stoneking Mark
Published: December 2019

Background

Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs).

Results

We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male.

Conclusions

Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.
Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens
Authors: Pandaranayaka Eswari PJ , Frenkel Omer , Elad Yigal , Prusky Dov , Harel Arye
Published: December 2019

Background

Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include secreted hydrolytic enzymes (e.g., cellulases and proteases) and secondary metabolites (e.g., toxins), central to the pathogenicity process. However, very few large-scale genomic comparisons have utilized complete proteomes from dozens of FEPs to reveal lifestyle-associated virulence mechanisms. Providing a powerful means for exploration, and the discovery of trends in large-scale datasets, network analysis has been used to identify core functions of the primordial cyanobacteria, and ancient evolutionary signatures in oxidoreductases.

Results

We used a sequence-similarity network to study components of virulence mechanisms of major pathogenic lifestyles (necrotroph (ic), N; biotroph (ic), B; hemibiotroph (ic), H) in complete pan-proteomes of 65 FEPs and 17 saprobes. Our comparative analysis highlights approximately 190 core functions found in 70% of the genomes of these pathogenic lifestyles. Core functions were found mainly in: transport (in H, N, B cores); carbohydrate metabolism, secondary metabolite synthesis, and protease (H and N cores); nucleic acid metabolism and signal transduction (B core); and amino acid metabolism (H core). Taken together, the necrotrophic core contains functions such as cell wall-associated degrading enzymes, toxin metabolism, and transport, which are likely to support their lifestyle of killing prior to feeding. The biotrophic stealth growth on living tissues is potentially controlled by a core of regulatory functions, such as: small G-protein family of GTPases, RNA modification, and cryptochrome-based light sensing. Regulatory mechanisms found in the hemibiotrophic core contain light- and CO2-sensing functions that could mediate important roles of this group, such as transition between lifestyles.

Conclusions

The selected set of enriched core functions identified in our work can facilitate future studies aimed at controlling FEPs. One interesting example would be to facilitate the identification of the pathogenic potential of samples analyzed by metagenomics. Finally, our analysis offers potential evolutionary scenarios, suggesting that an early-branching saprobe (identified in previous studies) has probably evolved a necrotrophic lifestyle as illustrated by the highest number of shared gene families between saprobes and necrotrophs.
Variation of growth characteristics of pneumococcus with environmental conditions
Authors: Tóthpál Adrienn , Desobry Katherine , Joshi Shreyas S. , Wyllie Anne L. , Weinberger Daniel M.
Published: December 2019

Background

Pneumococcus is exposed to a variety of temperature and oxygen levels in the upper respiratory tract and as it invades the lung, tissues, and blood. We sought to determine the effect of environmental variability on growth in vitro and to assess variability between strains. We evaluated the effect of temperature and oxygen on the growth of 256 isolates representing 53 serotypes, recovered from healthy carriers and disease patients. Strains were grown at a range of temperatures, anaerobically or in ambient air with catalase, and were monitored by reading the optical density. Regression models evaluated variation in the characteristics of the growth curves.

Results

Most isolates grew to the maximal density at low temperatures (~33C) and under aerobic conditions. There was considerable variability between strains, and some of this variability was linked to serotype. However, capsule-switch experiments suggest that the production of different capsules might not be sufficient to explain this variation, suggesting there could be interactions between the capsule and genetic background.

Conclusions

Pneumococcal strains vary in how they respond to environmental variations, some of this variation can be explained by the capsule type being produced, but capsule production itself is not sufficient to explain the variability. This variability could help to explain why different lineages of pneumococcus are more common in carriage or disease.
Comparative physiological, metabolomic, and transcriptomic analyses reveal developmental stage-dependent effects of cluster bagging on phenolic metabolism in Cabernet Sauvignon grape berries
Authors: Sun Run-Ze , Cheng Guo , Li Qiang , Zhu Yan-Rong , Zhang Xue , Wang Yu , He Yan-Nan , Li Si-Yu , He Lei , Chen Wu , Pan Qiu-Hong , Duan Chang-Qing , Wang Jun
Published: December 2019

Background

Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes.

Results

Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. Significantly elevated flavan-3-ol and flavonol contents were detected in re-exposed berries after bagging during early-developmental stages, while bagging after véraison markedly inhibited skin anthocyanin accumulation. Several anthocyanin derivatives and flavonol glycosides were identified as marker phenolic metabolites for distinguishing bagged and non-bagged grapes. Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes.

Conclusions

Altogether, our findings provide novel insights into the understanding of berry phenolic biosynthesis under light/darkness and practical guidance for improving grape features.
Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings
Authors: Zeng Houqing , Zhang Xin , Ding Ming , Zhu Yiyong
Published: December 2019

Background

Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina’s high-throughput small RNA sequencing and transcriptome sequencing.

Results

The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results.

Conclusion

These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.
Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol
Authors: Suntichaikamolkul Nithiwat , Tantisuwanichkul Kittitya , Prombutara Pinidphon , Kobtrakul Khwanlada , Zumsteg Julie , Wannachart Siriporn , Schaller Hubert , Yamazaki Mami , Saito Kazuki , De-eknamkul Wanchai , Vimolmangkang Sornkanok , Sirikantaramas Supaart
Published: December 2019

Background

Pueraria candollei var. mirifica, a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and deoxymiroestrol. Although these active constituents in P. candollei var. mirifica have been known for some time, actual knowledge regarding their biosynthetic genes remains unknown.

Results

Miroestrol biosynthesis was reconsidered and the most plausible mechanism starting from the isoflavonoid daidzein was proposed. A de novo transcriptome analysis was conducted using combined P. candollei var. mirifica tissues of young leaves, mature leaves, tuberous cortices, and cortex-excised tubers. A total of 166,923 contigs was assembled for functional annotation using protein databases and as a library for identification of genes that are potentially involved in the biosynthesis of isoflavonoids and miroestrol. Twenty-one differentially expressed genes from four separate libraries were identified as candidates involved in these biosynthetic pathways, and their respective expressions were validated by quantitative real-time reverse transcription polymerase chain reaction. Notably, isoflavonoid and miroestrol profiling generated by LC-MS/MS was positively correlated with expression levels of isoflavonoid biosynthetic genes across the four types of tissues. Moreover, we identified R2R3 MYB transcription factors that may be involved in the regulation of isoflavonoid biosynthesis in P. candollei var. mirifica. To confirm the function of a key-isoflavone biosynthetic gene, P. candollei var. mirifica isoflavone synthase identified in our library was transiently co-expressed with an Arabidopsis MYB12 transcription factor (AtMYB12) in Nicotiana benthamiana leaves. Remarkably, the combined expression of these proteins led to the production of the isoflavone genistein.

Conclusions

Our results provide compelling evidence regarding the integration of transcriptome and metabolome as a powerful tool for identifying biosynthetic genes and transcription factors possibly involved in the isoflavonoid and miroestrol biosyntheses in P. candollei var. mirifica.
A case presentation of patient from northern China with endomyocardial fibrosis
Authors: Yuan Yonggang , Li Yingkai , Xu Zesheng
Published: December 2019

Background

Endomyocardial fibrosis (EMF) is a rare condition and a major cause of death in tropical countries. The etiology of EMF remains elusive, and no specific treatment has been developed yet, therefore it carries poor prognosis.

Case presentation

An 81-year-old male Chinese patient with a history of long-standing exertional breathlessness, presented with worsening symptoms rapidly evolving to orthopnea. A proper specific treatment was prescribed to the patient in the following days, including diuretics, angiotensin-converting-enzyme inhibitor and beta blockers. The patient died of progressive multiple organ failure.

Conclusion

Echocardiography is technically limited due to the acoustic shadowing as a result of the calcification. Chest computed tomography is a more accurate diagnostic tool to examine the anatomic distribution and extent of endomyocardial calcification in this rare case.
Post-stroke patients with moderate function have the greatest risk of falls: a National Cohort Study
Authors: Wei Wycliffe E. , De Silva Deirdre A. , Chang Hui Meng , Yao Jiali , Matchar David B. , Young Sherry H. Y. , See Siew Ju , Lim Gek Hsiang , Wong Ting Hway , Venketasubramanian Narayanaswamy
Published: December 2019

Background

Stroke patients have increased risks of falls. We examined national registry data to evaluate the association between post-stroke functional level and the risk of low falls among post-stroke patients.

Methods

This retrospective cohort study analyzed data from national registries to examine the risk factors for post-stroke falls. Data for patients who suffered ischemic strokes and survived the index hospital admission was obtained from the Singapore National Stroke Registry and matched to the National Trauma Registry, from 2011 to 2015. The primary outcome measure was a low fall (fall height ≤ 0.5 m). Competing risk analysis was performed to examine the association between functional level (by modified Rankin score [mRS] at discharge) and the risk of subsequent low falls.

Results

In all, 2255 patients who suffered ischemic strokes had recorded mRS. The mean age was 66.6 years and 58.5% were men. By the end of 2015, 54 (2.39%) had a low fall while 93 (4.12%) died.

After adjusting for potential confounders, mRS was associated with fall risk with an inverted U-shaped relationship. Compared to patients with a score of zero, the sub-distribution hazard ratio (SHR) increased to a maximum of 3.42 (95%CI:1.21–9.65, p = 0.020) for patients with a score of 2. The SHR then declined to 2.45 (95%CI:0.85–7.12, p = 0.098), 2.86 (95%CI:0.95–8.61, p = 0.062) and 1.93 (95%CI:0.44–8.52, p = 0.38) for patients with scores of 3, 4 and 5 respectively.

Conclusions

An inverted U-shaped relationship between functional status and fall risk was observed. This is consistent with the complex interplay between decreasing mobility (hence decreased opportunity to fall) and increasing susceptibility to falls. Fall prevention intervention could be targeted accordingly.

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Life expectancy with and without cognitive impairment among Chilean older adults: results of the National Survey of Health (2003, 2009 and 2016)
Authors: Moreno Ximena , Lera Lydia , Moreno Francisco , Albala Cecilia
Published: December 2019

Background

Chile has one of the highest life expectancies within Latin American. This is the first study to determine health expectancies in older populations in Chile, considering cognitive status as a health indicator.

Methods

We estimated prevalence of cognitive decline among people aged 60 years and over based on the Mini-mental State Examination and the Pfeffer Functional Activities Questionnaire, with data from the National Survey of Health (2003, 2009, 2016). Life expectancy free of cognitive impairment was calculated using the Sullivan method.

Results

At age 60, life expectancy free of cognitive impairment was more than 3 years longer for women, compared to men of the same age. Life expectancy free from cognitive impairment was higher for both men and women aged 60 in 2016 when compared to 2003 (2.1 and 2 years higher, respectively).

Conclusions

Longer life expectancy in women was accompanied by more years free of cognitive impairment. Men expected to live a similar proportion of years free of cognitive impairment, compared to women. Common and standardised assessments of health status of older people should be adopted in Latin American studies, to allow for time-trend analyses and international comparisons.
“Being in good hands”: next of kin’s perceptions of continuity of care in patients with heart failure
Authors: Östman Malin , Bäck-Pettersson Siv , Sandvik Ann-Helén , Sundler Annelie J.
Published: December 2019

Background

Heart failure (HF) is a chronic condition with a variety of diverse symptoms. Patients with HF are usually elderly with multimorbidity, which are both multifaceted and challenging. Being a next of kin to patients with HF is described as a complex task consisting of managing care and treatment, monitoring illness and being an emotional support, while also being able to navigate the healthcare system especially in long-term contact. However, few studies have investigated next of kin’s perceptions of continuity of care in connection with HF. The present study aimed to describe continuity of care as perceived by the next of kin who care for patients with HF.

Methods

This study used a qualitative descriptive design. Semi-structured interviews were conducted with the next of kin (n = 15) of patients with HF to obtain their perceptions of continuity of care. A phenomenographic analysis method was used to capture the participants’ perceptions of the phenomenon.

Results

The analysis reveals that the next of kin perceive that support from healthcare professionals was strongly associated with experiences of continuity of care. Four categories reveal the next of kin’s perceptions of continuity of care: Want to be involved without being in charge; A desire to be in control without acting as the driving force in the care situation; A need for sustainability without being overlooked; and Focusing on making life meaningful while being preoccupied with caregiving activities.

Conclusions

Next of kin perceive continuity of care, when they have access to care and treatment and when caregivers collaborate, regardless of healthcare is given by primary care, municipalities or specialist clinics. A sense of “being in good hands” sums up the need for continuous support, shared decision-making and seamless transitions between caregivers. It seems important that healthcare organisations safeguard effective and collaborative models. Moreover, professionals need to plan and perform healthcare in collaboration with patients and next of kin.
1g versus 2 g daily intravenous ceftriaxone in the treatment of community onset pneumonia – a propensity score analysis of data from a Japanese multicenter registry
Authors:   on behalf of the Adult Pneumonia Study Group-Japan, Hasegawa Shinya , Sada Ryuichi , Yaegashi Makito , Morimoto Konosuke , Mori Takahiro
Published: December 2019

Background

Community-onset pneumonia (COP) is a combined concept of community acquired pneumonia and the previous classification of healthcare-associated pneumonia. Although ceftriaxone (CRO) is one of the treatment choices for COP, it is unclear whether 1 or 2 g CRO daily has better efficacy. We compared the effectiveness of 1 g with 2 g of CRO for COP treatment. We hypothesized that 1 g CRO would show non-inferiority over 2 g CRO.

Methods

This study was an analysis of prospectively registered data of the patients with COP from four Japanese hospitals (the Adult Pneumonia Study Group-Japan: APSG-J). We included subjects who were initially treated solely with 1 or 2 g of CRO. The propensity score was estimated from the 33 pre-treatment variables, including age, sex, weight, pre-existing comorbidities, prescribed drugs, risk factors for aspiration pneumonia, vital signs, laboratory data, and a finding from chest xrays. The primary endpoint was the cure rate, for which a non-inferiority analysis was performed with a margin of 0.05. In addition, we performed three sensitivity analyses; using data limited to the group in which CRO solely was used until the completion of treatment, using data limited to inpatient cases, and performing a generalized linear mixed-effect logistic regression analysis to assess the primary outcome after adjusting for random hospital effects.

Results

Of the 3817 adult subjects with pneumonia who were registered in the APSG-J study, 290 and 216 were initially treated solely with 1 or 2 g of CRO, respectively. Propensity score matching was used to extract 175 subjects in each group. The cure rate was 94.6 and 93.1% in the 1 and 2 g CRO groups, respectively (risk difference 1.5%; 95% confidence interval − 3.1 to 6.0; p = 0.009 for non-inferiority). The results of the sensitivity analyses were consistent with the primary result.

Conclusions

The propensity score-matched analysis of multicenter cohort data from Japan revealed that the cure rate for COP patients treated with 1 g daily CRO was non-inferior to that of patients treated with 2 g daily CRO.