bluuebunny/crossref_metadata_2025 huggingface dataset:
The Cell Cycle G2/M Block Is an Indicator of Cellular Radiosensitivity
Authors: Liu Chang , Nie Jing , Wang Rensheng , Mao Weidong
Published: December 2019

Background:

Determination of the radiosensitivity of a specific tumor is essential to its precision tumor radiotherapy, but the measurement of cellular radiosensitivity with a routine colony forming assay is both labor- and time-consuming. An alternative option allowing rapid and precise prediction of radiosensitivity is necessary.

Methods:

In this study, we exposed 4 in vitro cultured cell lines to various doses of X-rays or carbon ions and then measured their radiosensitivities with a routine colony-forming assay, and monitored the kinetics of cell cycle distribution with routine propidium iodine staining and flow cytometry.

Results:

Based on the results, we correlated cellular radiosensitivity with a dynamic assay of cell cycle distribution, specifically, the negative correlation of cellular radiosensitivity with the accumulated G2/M arrested cells at 48 hours after exposure. The higher the proportion of accumulated G2/M arrested cells at 48 hours after exposure, the lower the radiosensitivity of the cell line, that is, the higher radioresistance of the cell line.

Conclusion:

These findings provide an optional application of regular cell cycle analysis for the prediction of tumor radiosensitivity.
Radiation Responses of Human Mesenchymal Stem Cells Derived From Different Sources
Authors: He Ningning , Xiao Changyan , Sun Yuxiao , Wang Yan , Du Liqing , Feng Yu , Liu Yang , Wang Qin , Ji Kaihua , Wang Jinhan , Zhang Manman , Xu Chang , Liu Qiang
Published: December 2019

Mesenchymal stem cells (MSCs) derived from different tissues may aid in the regeneration of radiation-induced organ lesions; however, the radiation responses of human MSCs from different sources are unknown. In our study, a comparison of the results from cell proliferation, apoptosis, cell cycle, DNA damage, and DNA repair assays consistently showed that MSCs derived from adipose tissue possess a significantly stronger radiation resistance capacity than MSCs derived from umbilical cord and gingival, which is accompanied by a higher level of phosphorylated signal transducer and activator of transcription 3 (Stat3) expression. This reminds us Stat3 could be a potential biomarker of radiation resistance. These findings provide a better understanding of radiation-induced biologic responses in MSCs and may lead to the development of better strategies for stem cell treatment and cancer therapy.
Story Completion: Storying as a Method of Meaning-Making and Discursive Discovery
Authors: Gravett Karen
Published: December 2019

This article focuses on a method of data collection that exists in the margins of qualitative research: story completion. Story completion has a background of usage within disciplines such as psychology, feminist theory, and psychotherapy. However, this method is still uncommon and underutilized and has not been widely put to work as an approach for qualitative education research, despite its rich potential as a tool for accessing participants’ meaning-making. In this article, I argue that story completion can serve as an interesting and flexible method for researchers across the disciplines, particularly for those looking to adopt a post-structuralist lens, concerned with discursive discovery: the surfacing of discourses individuals draw upon to write. I introduce and explain a divergent approach to doing story completion from that described elsewhere in the literature, where a story completion exercise is enhanced by the addition of a traditional semi-structured interview. I also share an experimental approach to data analysis: using a rhizomatic perspective to analyze story completion data. Ultimately, I argue that story completion, the story-mediated interview, and a more experimental analytical approach offer exciting new directions for qualitative researchers to pursue.
Design of fixed-time synchronization algorithm with applications
Authors: Zhang Peng , Cong Yongzheng , Wu Di , Zhang Guorong , Tan Qi
Published: December 2019

Fixed-time synchronization problem for a class of leader–follower multi-agent systems with second-order nonlinearity is studied in this article. A new fixed-time synchronization control algorithm is developed by effectively combining homogeneous system theory, Lyapunov stability theory, and fixed-time/finite-time control technology. The leader–follower multi-agent system is considered to achieve fixed-time synchronization control. Finally, numerical simulations including coordination control multiple pendulum robot systems and electric power networks are carried out to verify the control performance of the control strategy.
Comparison of outcomes of three surgical approaches for proximal interphalangeal joint arthroplasty using a surface-replacing implant
Authors: Bodmer Elvira , Marks Miriam , Hensler Stefanie , Schindele Stephan , Herren Daniel B.
Published: December 2019

The objective was to compare outcomes of the volar, Chamay and tendon splitting approaches for proximal interphalangeal joint arthroplasty using a surface-replacing implant (CapFlex-PIP). One-hundred prospectively documented patients with a 2-year follow-up were included. Range of proximal interphalangeal joint motion, the brief Michigan Hand Outcomes Questionnaire and complications were analysed. Between baseline and follow-up, mean proximal interphalangeal joint motion increased for the volar (53° to 54°), Chamay (38° to 53°) and tendon splitting (40° to 61°) approaches. The volar approach yielded the greatest flexion and the highest extension deficit. The mean brief Michigan Hand Outcomes Questionnaire scores at baseline and 2 years were 45 and 74 (volar), 45 and 66 (Chamay) and 41 and 75 (tendon splitting). Seven patients in the Chamay group and two in the volar group required a reoperation consisting of teno-/arthrolysis. The tendon splitting approach tended to result in the best outcomes that were associated with fewer complications compared with the volar and Chamay approaches.

Level of evidence: IV
Outcomes of esophagectomy after noncurative endoscopic resection of early esophageal cancer
Authors: Dermine Solène , Leconte Mahaut , Leblanc Sarah , Dousset Bertrand , Terris Benoit , Berger Arthur , Berger Anne , Rahmi Gabriel , Lepilliez Vincent , Plomteux Olivier , Leclercq Philippe , Coriat Romain , Chaussade Stanislas , Prat Frédéric , Barret Maximilien
Published: December 2019

Background:

Current guidelines recommend performing esophagectomy after endoscopic resection for early esophageal cancer when the risk of lymph node metastasis or residual cancer is found to be significant and endoscopic treatment is therefore noncurative. Our aim was to assess the safety and oncological outcomes of esophagogastric resection in this specific clinical setting.

Patients and methods:

A retrospective review from 2012 to 2018 was performed at four tertiary referral centers. All patients had a noncurative endoscopic resection of a clinical T1 esophageal cancer, followed by esophagectomy. Outcome measures were the rates of T0N0 specimens, overall survival, disease-free and cancer-specific survival, postoperative morbidity and mortality.

Results:

A total of 30 patients (13 with squamous cell carcinoma and 17 with adenocarcinoma) were included. The reasons for noncurative endoscopic resection were: positive vertical margins ( n = 12), squamous cell carcinoma with muscularis mucosae or submucosal layer invasion ( n = 3 and 9), adenocarcinoma with deep submucosal invasion ( n = 11), poorly differentiated tumor ( n = 6) and lymphovascular invasion ( n = 6). Overall, 63% of the esophagi were T0N0: most residual lesions were T1a metachronous lesions, and four (13%) patients had advanced pT status ( n = 3) or lymph node metastases ( n = 2). Overall survival, disease-free survival and cancer-specific survival were 83%, 75%, and 90% respectively. A total of 43% of patients had severe postoperative complications, and postoperative mortality was 7%.

Conclusion:

In this cohort, esophagectomy allowed the resection of residual advanced cancer or lymph node metastases in 13% of cases, at the cost of 43% severe morbidity and 7% mortality. Therefore, the possibility of close follow up needs to be balanced with a highly morbid surgical management in these patients.
Variability in the Chemical Composition of Eugenia biflora Essential Oils from the Brazilian Amazon
Authors: Figueiredo Pablo Luis B. , Fernandes Henryck A. , da Silva Alberto Ray C. , Alves Nayara Sabrina F. , Setzer William N. , da Silva Joyce Kelly R. , Maia José Guilherme S.
Published: December 2019

Eugenia species are well known for their great economic potential as edible fruits. The leaves of 4 Eugenia biflora specimens (Ebi-1 to Ebi-4) were sampled in the Caratateua Island, Pará state, Brazilian Amazon. Then, the essential oils were hydrodistilled, analyzed by gas chromatography (GC) and GC mass spectroscopy, and their volatile compositions submitted to multivariate analysis (principal component analysis and hierarchical cluster analysis). Ebi-1 and Ebi-2 specimens were classified in the caryophyllene group, with significant content for the sesquiterpenes ( E)-caryophyllene (16.8% and 11.4%) and caryophyllene oxide (28.6% and 20.5%). Ebi-3 specimen was grouped into the cadinane group, characterized by the presence of α-cadinol (14.7%), an oxygenated sesquiterpene. EBI-4 specimen was inserted into the aromadendrane group, with the predominance of the sesquiterpenes globulol (9.8%), germacrene B (7.9%), and γ-elemene (3.1%). Based on the results, a remarkable chemical variability was observed in the oils of Eugenia biflora with occurrence in Pará state, North Brazil. This work is presenting for the first time its caryophyllene, cadinane, and aromadendrane profiles.
Canal of Nuck hernias
Authors: Chan Donald , Kwon Jeannie K , Lagomarsino Elizabeth M , Veltkamp Jennifer G , Yang Mary S , Pfeifer Cory M
Published: December 2019

The canal of Nuck, caused by the failed closure of the processus vaginalis in the female, is the continued outpouching of parietal peritoneum through the inguinal canal to the labia majora. Disorders of the canal of Nuck include hernia and hydrocele. Some canal of Nuck hernias, especially of the ovary, may result in emergent complications such as incarceration, strangulation, and ovarian torsion. Knowledge of canal of Nuck disorders and prompt diagnosis are important to avoid serious complications. Imaging, especially ultrasound, is essential for timely diagnosis, leading to appropriate management and better patient care.
Do Rotation and Measurement Methods Affect Reliability of Anterior Cruciate Ligament Tunnel Position on 3D Reconstructed Computed Tomography?
Authors: Moon Hyun-Soo , Choi Chong-Hyuk , Jung Min , Lee Dae-Young , Chang Hsienhao , Kim Sung-Hwan
Published: December 2019

Background:

The literature has seldom investigated the anterior cruciate ligament (ACL) tunnel position while considering the effect of rotation of 3-dimensional computed tomography (3D-CT) images during measurements.

Hypothesis:

We hypothesized that (1) measurement of the ACL tunnel position in the femur and tibia through use of 3D-CT is considerably influenced by rotation of the 3D model and (2) there exists a reliable measurement method for ACL tunnel position least affected by rotation.

Study Design:

Controlled laboratory study.

Methods:

The 3D-CT images of 30 randomly selected patients who underwent single-bundle ACL reconstruction were retrospectively reviewed. For femoral tunnel assessments, rectangular reference frames were used that involved the highest point of the intercondylar notch and outer margins of the lateral femoral condyle (method 1), the highest point of the intercondylar notch and outer margins of the lateral wall of the intercondylar notch (method 2), and the lowest point of the intercondylar notch and outer margins of the lateral femoral condyle (method 3). For tibial tunnel assessments, rectangular reference frames with the cortical outline at the articular surface of the tibia (method A) and the cortical outline of the proximal tibia (method B) were used. For both femoral and tibial assessments, the tunnel positions at 5°, 10°, and 15° of rotation of the 3D model were compared with that at a neutral position.

Results:

The values measured by methods 1 and 3 showed significant differences at greater than 5° of rotation compared with the value at the neutral position, whereas method 2 showed relatively consistent results. However, the values measured with both methods A and B showed significant differences at greater than 5° of rotation compared with the value at the neutral position.

Conclusion:

The tunnel position on 3D-CT images was significantly influenced by rotation during measurements. For femoral tunnel position, measurement with a reference frame using the lateral wall of the intercondylar notch (method 2) was the least affected by rotation, with relatively consistent results.

Clinical Relevance:

This study demonstrates that measurement using the lateral wall of the intercondylar notch might be a consistent and reliable method for evaluating the ACL femoral tunnel position considering the effect of 3D-CT image rotation during measurements. However, both methods to measure tibial tunnel position described in this study were similarly affected by rotation.
What evidence is there that parenting interventions reduce child abuse and neglect among maltreating families? A systematic review
Authors: Whitcombe-Dobbs Sarah , Tarren-Sweeney Michael
Published: December 2019

In families where child abuse and neglect have already occurred, there is a strong imperative to provide interventions that reduce or eliminate harm done to children. Parenting programs lack tailoring for the needs of maltreating parents, and maltreating parents themselves are a heterogeneous group with varying needs. The literature on the effectiveness of parenting interventions for high-risk parents is limited, and this scarcity of knowledge can result in child protection cases being treated as a natural experiment. For children who experience ongoing maltreatment by their parents, the most stringent test for effectiveness goes beyond an improvement in positive parenting skills—child abuse and neglect must reduce or be eliminated. The present review addressed the research question What evidence is there that parenting interventions conducted with parents who maltreat their children, reduce the incidence of further child maltreatment? Databases were searched for trials of parenting interventions where participants were maltreating parents and outcome data included an objective measure of child abuse and neglect. Nine studies satisfied the selection criteria and are summarized. Four studies reported a statistically significant difference between groups in favor of the intervention group for two parenting interventions, Parent–Child Interaction Therapy and SafeCare. However, the review concludes that none of the reviewed parenting interventions have been demonstrated to be effective at reducing all types of child maltreatment through a high-quality RCT. Previous research is compromised by several critical methodological limitations, including low participant recruitment and retention, and narrow selection criteria. Recommendations are offered for future research on parenting interventions that aim to reduce child abuse and neglect.
‘Paintings for a Crime’: Composed Cognitive Maps for Measuring Crime and Situation
Authors: Castro Aniyar Daniel
Published: December 2019

The Ecuadorian State implemented policies to improve the quality and reliability of statistical material. Among these materials, composed cognitive maps were innovated and applied. These materials consist of drawings made by witnesses and victims of perceived hostile and dangerous territories that were analyzed through ethnographic and Grounded Theory Method.

 This process allowed for a deeper understanding of hotspots, associated criminal situations and large victimization patterns throughout the national territory, than traditional ones. The composed cognitive maps and resulting spatial dynamics of crime helped to overcome the gap between the micro and macro level problem in criminology and gave important insights to design crime policies. We briefly describe the experience, compare the method to the traditional ones and give an example of its diagnostic potential compared to regular information managed to day by the police.
Patients with FLT3-mutant AML needed to enroll on FLT3-targeted therapeutic clinical trials
Authors: Bucy Taylor , Zoscak John M. , Mori Motomi , Borate Uma
Published: December 2019

We sought to identify the total number of therapeutic trials targeting FLT3-mutant acute myeloid leukemia (AML) to estimate the number of patients needed to satisfy recruitment when compared with the incidence of this mutation in the US AML population. A systematic review of all therapeutic clinical trials focusing on adult FLT3-mutated AML was conducted from 2000 to 2017. An updated search was performed using ClinicalTrials.gov for trials added between October 2017 and December 2018. Analysis was performed for ClinicalTrials.gov search results from 2000 to 2017 to provide descriptive estimates of discrepancies between anticipated clinical trial enrollment using consistently cited rates of adult participation of 1%, 3%, and 5%, as well as 10% participation identified by the American Society of Clinical Oncology in 2008. Twenty-five pharmaceutical or biological agents aimed at treating FLT3-mutant AML were identified. Pharmaceutical vs cooperative group/nonprofit support was 2.3:1, with 30 different pharmaceutical collaborators and 13 cooperative group/nonprofit collaborators. The number of patients needed to satisfy study enrollment begins to surpass the upper bound of estimated participation in 2010, noticeably surpassing projected participation rates between 2015 and 2016. The number of patients needed to satisfy study enrollment surpasses 3% and 5% rates of historical participation for US-only trials in 2017. We estimate that 15% of all US patients with FLT3-mutant AML would have to enroll in US and internationally accruing trials to satisfy requirements in 2017, or approximately 3 times the upper level of historical participation rates in the United States. The current clinical trial agenda in this space requires high percentage enrollment for sustainability.
Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion
Authors: Wienand Kirsty , Chapuy Bjoern , Stewart Chip , Dunford Andrew J. , Wu David , Kim Jaegil , Kamburov Atanas , Wood Timothy R. , Cader Fathima Zumla , Ducar Matthew D. , Thorner Aaron R. , Nag Anwesha , Heubeck Alexander T. , Buonopane Michael J. , Redd Robert A. , Bojarczuk Kamil , Lawton Lee N. , Armand Philippe , Rodig Scott J. , Fromm Jonathan R. , Getz Gad , Shipp Margaret A.
Published: December 2019

Key Points

Analyses of recurrent mutations, copy number alterations, and structural variants reveal complementary immune evasion mechanisms in cHL. The mutational burden in EBV– cHLs is among the highest reported, potentially contributing to the efficacy of PD-1 blockade.
Editorial focus: understanding off-target effects as the key to successful RNAi therapy
Authors: Bartoszewski Rafal , Sikorski Aleksander F.
Published: December 2019

With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
Near-Infrared Photoelectric Properties of Multilayer Bi2O2Se Nanofilms
Authors: Yang Hang , Chen Wei , Zheng Xiaoming , Yang Dongsheng , Hu Yuze , Zhang Xiangzhe , Ye Xin , Zhang Yi , Jiang Tian , Peng Gang , Zhang Xueao , Zhang Renyan , Deng Chuyun , Qin Shiqiao
Published: December 2019

The near-infrared (NIR) photoelectric properties of multilayer Bi2O2Se nanofilms were systematically studied in this paper. Multilayer Bi2O2Se nanofilms demonstrate a sensitive photo response to NIR, including a high photoresponsivity (~ 101 A/W), a quick response time (~ 30 ms), a high external quantum efficiency (~ 20,300%), and a high detection rate (1.9 × 1010 Jones). These results show that the device based on multilayer Bi2O2Se nanofilms might have great potentials for future applications in ultrafast, highly sensitive NIR optoelectronic devices.
flowEMMi: an automated model-based clustering tool for microbial cytometric data
Authors: Ludwig Joachim , zu Siederdissen Christian Höner , Liu Zishu , Stadler Peter F. , Müller Susann
Published: December 2019

Background

Flow cytometry (FCM) is a powerful single-cell based measurement method to ascertain multidimensional optical properties of millions of cells. FCM is widely used in medical diagnostics and health research. There is also a broad range of applications in the analysis of complex microbial communities. The main concern in microbial community analyses is to track the dynamics of microbial subcommunities. So far, this can be achieved with the help of time-consuming manual clustering procedures that require extensive user-dependent input. In addition, several tools have recently been developed by using different approaches which, however, focus mainly on the clustering of medical FCM data or of microbial samples with a well-known background, while much less work has been done on high-throughput, online algorithms for two-channel FCM.

Results

We bridge this gap with , a model-based clustering tool based on multivariate Gaussian mixture models with subsampling and foreground/background separation. These extensions provide a fast and accurate identification of cell clusters in FCM data, in particular for microbial community FCM data that are often affected by irrelevant information like technical noise, beads or cell debris. outperforms other available tools with regard to running time and information content of the clustering results and provides near-online results and optional heuristics to reduce the running-time further.

Conclusions

is a useful tool for the automated cluster analysis of microbial FCM data. It overcomes the user-dependent and time-consuming manual clustering procedure and provides consistent results with ancillary information and statistical proof.
Genomic insights into mite phylogeny, fitness, development, and reproduction
Authors: Zhang Yan-Xuan , Chen Xia , Wang Jie-Ping , Zhang Zhi-Qiang , Wei Hui , Yu Hai-Yan , Zheng Hong-Kun , Chen Yong , Zhang Li-Sheng , Lin Jian-Zhen , Sun Li , Liu Dong-Yuan , Tang Juan , Lei Yan , Li Xu-Ming , Liu Min
Published: December 2019

Background

Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida.

Results

We here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite,Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique toN. cucumerisbased on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages ofN. cucumerisprovide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified.

Conclusions

Our genomics and developmental transcriptomics analyses ofN. cucumerisprovide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general.
Bias in estimates of variance components in populations undergoing genomic selection: a simulation study
Authors: Gao Hongding , Madsen Per , Aamand Gert Pedersen , Thomasen Jørn Rind , Sørensen Anders Christian , Jensen Just
Published: December 2019

Background

After the extensive implementation of genomic selection (GS), the choice of the statistical model and data used to estimate variance components (VCs) remains unclear. A primary concern is that VCs estimated from a traditional pedigree-based animal model (P-AM) will be biased due to ignoring the impact of GS. The objectives of this study were to examine the effects of GS on estimates of VC in the analysis of different sets of phenotypes and to investigate VC estimation using different methods. Data were simulated to resemble the Danish Jersey population. The simulation included three phases: (1) a historical phase; (2) 20 years of conventional breeding; and (3) 15 years of GS. The three scenarios based on different sets of phenotypes for VC estimation were as follows: (1) Pheno1: phenotypes from only the conventional phase (1–20 years); (2) Pheno1 + 2: phenotypes from both the conventional phase and GS phase (1–35 years); (3) Pheno2: phenotypes from only the GS phase (21–35 years). Single-step genomic BLUP (ssGBLUP), a single-step Bayesian regression model (ssBR), and P-AM were applied. Two base populations were defined: the first was the founder population referred to by the pedigree-based relationship (P-base); the second was the base population referred to by the current genotyped population (G-base).

Results

In general, both the ssGBLUP and ssBR models with all the phenotypic and genotypic information (Pheno1 + 2) yielded biased estimates of additive genetic variance compared to the P-base model. When the phenotypes from the conventional breeding phase were excluded (Pheno2), P-AM led to underestimation of the genetic variance of P-base. Compared to the VCs of G-base, when phenotypes from the conventional breeding phase (Pheno2) were ignored, the ssBR model yielded unbiased estimates of the total genetic variance and marker-based genetic variance, whereas the residual variance was overestimated.

Conclusions

The results show that neither of the single-step models (ssGBLUP and ssBR) can precisely estimate the VCs for populations undergoing GS. Overall, the best solution for obtaining unbiased estimates of VCs is to use P-AM with phenotypes from the conventional phase or phenotypes from both the conventional and GS phases.
LRScaf: improving draft genomes using long noisy reads
Authors: Qin Mao , Wu Shigang , Li Alun , Zhao Fengli , Feng Hu , Ding Lulu , Ruan Jue
Published: December 2019

Background

The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-generation sequencing (NGS) technologies. To date, a few algorithms that are capable of improving draft assemblies have released. There are SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS. Hybrid assembly on large genomes remains challenging, however.

Results

We develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf, https://github.com/shingocat/lrscaf), that is capable of significantly boosting assembly contiguity using long reads. In this study, we summarise a comprehensive performance assessment for state-of-the-art scaffolders and LRScaf on seven organisms, i.e., E. coli, S. cerevisiae, A. thaliana, O. sativa, S. pennellii, Z. mays, and H. sapiens. LRScaf significantly improves the contiguity of draft assemblies, e.g., increasing the NGA50 value of CHM1 from 127.1 kbp to 9.4 Mbp using 20-fold coverage PacBio dataset and the NGA50 value of NA12878 from 115.3 kbp to 12.9 Mbp using 35-fold coverage Nanopore dataset. Besides, LRScaf generates the best contiguous NGA50 on A. thaliana, S. pennellii, Z. mays, and H. sapiens. Moreover, LRScaf has the shortest run time compared with other scaffolders, and the peak RAM of LRScaf remains practical for large genomes (e.g., 20.3 and 62.6 GB on CHM1 and NA12878, respectively).

Conclusions

The new algorithm, LRScaf, yields the best or, at least, moderate scaffold contiguity and accuracy in the shortest run time compared with other scaffolding algorithms. Furthermore, LRScaf provides a cost-effective way to improve contiguity of draft assemblies on large genomes.
Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination
Authors: Dong Shanshan , Zhao Chaoxian , Zhang Shouzhou , Zhang Li , Wu Hong , Liu Huan , Zhu Ruiliang , Jia Yu , Goffinet Bernard , Liu Yang
Published: December 2019

Background

In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except forGymnomitrion concinnatumwhose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static.

Results

Liverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. Our phylogenetic analyses of the nuclear encoded double stand break repair protein families revealed liverwort-specific subfamilies expansions.

Conclusions

The low repeat recombination level, selection, along with the intensified nuclear surveillance, might together shape the structural evolution of liverwort mt genomes.
The Moraxella catarrhalis phase-variable DNA methyltransferase ModM3 is an epigenetic regulator that affects bacterial survival in an in vivo model of otitis media
Authors: Blakeway Luke V. , Tan Aimee , Jurcisek Joseph A. , Bakaletz Lauren O. , Atack John M. , Peak Ian R. , Seib Kate L.
Published: December 2019

Background

Moraxella catarrhalis is a leading cause of otitis media (OM) and chronic obstructive pulmonary disease (COPD). M. catarrhalis contains a Type III DNA adenine methyltransferase (ModM) that is phase-variably expressed (i.e., its expression is subject to random, reversible ON/OFF switching). ModM has six target recognition domain alleles (modM1–6), and we have previously shown that modM2 is the predominant allele, while modM3 is associated with OM. Phase-variable DNA methyltransferases mediate epigenetic regulation and modulate pathogenesis in several bacteria. ModM2 of M. catarrhalis regulates the expression of a phasevarion containing genes important for colonization and infection. Here we describe the phase-variable expression of modM3, the ModM3 methylation site and the suite of genes regulated within the ModM3 phasevarion.

Results

Phase-variable expression of modM3, mediated by variation in length of a 5′-(CAAC)n-3′ tetranucleotide repeat tract in the open reading frame was demonstrated in M. catarrhalis strain CCRI-195ME with GeneScan fragment length analysis and western immunoblot. We determined that ModM3 is an active N6-adenine methyltransferase that methylates the sequence 5′-ACm6ATC-3′. Methylation was detected at all 4446 5′-ACATC-3′ sites in the genome when ModM3 is expressed. RNASeq analysis identified 31 genes that are differentially expressed between modM3 ON and OFF variants, including five genes that are involved in the response to oxidative and nitrosative stress, with potential roles in biofilm formation and survival in anaerobic environments. An in vivo chinchilla (Chinchilla lanigera) model of otitis media demonstrated that transbullar challenge with the modM3 OFF variant resulted in an increased middle ear bacterial load compared to a modM3 ON variant. In addition, co-infection experiments with NTHi and M. catarrhalis modM3 ON or modM3 OFF variants revealed that phase variation of modM3 altered survival of NTHi in the middle ear during early and late stage infection.

Conclusions

Phase variation of ModM3 epigenetically regulates the expression of a phasevarion containing multiple genes that are potentially important in the progression of otitis media.
Prevalence of abdominal aortic aneurysm and associated lower extremity artery aneurysm in men hospitalized for suspected or known cardiopulmonary disease
Authors: Hohneck Anna , Keese Michael , Ruemenapf Gerhard , Amendt Klaus , Muertz Hannelore , Janda Katharina , Akin Ibrahim , Borggrefe Martin , Sigl Martin
Published: December 2019

Background

AAA is a disease affecting predominantly male patients ≥65 years and its dreaded complications such as rupture led to population-based screening programs as preventive measure. Nonetheless, the supposed prevalence may have been overestimated, so that targeted screening of high risk populations may be more effective.

This study was performed to evaluate the prevalence of abdominal aortic aneurysm (AAA) of an inpatient high-risk cohort and to estimate the co-prevalence of lower extremity arterial aneurysms.

Methods

Participants: 566 male inpatients, ≥ 65 years of age, hospitalized for suspected or known cardiopulmonary disease.

Primary and secondary outcome measures: Maximal infrarenal aortic diameters using abdominal ultrasound (leading edge to leading edge method). Upon detection of an AAA (diameter ≥ 30 mm), the lower extremity arteries were examined with regard to associated aneurysms.

Results

In 40 of 566 patients (7.1%) AAAs were detectable. Fourteen patients (2.5%) had a first diagnosis of AAA, none of which was large (> 55 mm), the remaining 26 patients were either already diagnosed (14 patients, 2.5%) or previously repaired (12 patients, 2.1%).

The three most common main diagnoses at discharge were acute coronary syndrome (43.3%), congestive heart failure (32.2%), and chronic obstructive pulmonary disease (12%). The cohort showed a distinct cardiovascular risk profile comprising arterial hypertension (82.9%), diabetes mellitus (44.4%), and a history of smoking (57.6%).

In multivariate analysis, three-vessel coronary artery disease (Odds ratio (OR): 4.5, 95% confidence interval (CI): 2.3–8.9, p <  0.0001) and history of smoking (OR: 3.7, CI: 1.6–8.6, p <  0.01) were positively associated with AAA, while diabetes mellitus (OR: 0.5, CI: 0.2–0.9, p = 0.0295) showed a negative association with AAA.

Among the subjects with AAA, we found two large iliac and two large popliteal aneurysms.

Conclusion

Ultrasound screening in male inpatients, hospitalized for suspected or known cardiopulmonary disease, revealed a high AAA prevalence in comparison to the present epidemiological screening programs. There was a moderate proportion of newly-screen detected AAA and additional screening of the lower extremity arteries yielded some associated aneurysms with indication for possible intervention.
Evaluating audio-visual falls prevention messages with community-dwelling older people using a World Café forum approach
Authors: de Jong Lex D. , Francis-Coad Jacqueline , Wortham Chris , Haines Terry P. , Skelton Dawn A. , Weselman Tammy , Hill Anne-Marie
Published: December 2019

Background

Falls risk increases sharply with older age but many older people are unaware or underestimate their risk of falling. Increased population-based efforts to influence older people’s falls prevention behavior are urgently needed. The aim of this study was to obtain a group of older people’s collective perspectives on newly developed prototypes of audio-visual (AV) falls prevention messages, and evaluate changes in their falls prevention behaviour after watching and discussing these.

Methods

A mixed-method study using a community World Café forum approach.

Results

Although the forum participants (n = 38) mostly responded positively to the three AV messages and showed a significant increase in their falls prevention capability and motivation after the forum, the participants collectively felt the AV messages needed a more inspirational call to action. The forum suggested this could be achieved by means of targeting the message and increasing the personal connection. Participants further suggested several alternatives to online falls prevention information, such as printed information in places in the community, as a means to increase opportunity to seek out falls prevention information.

Conclusions

Falls prevention promotion messages need to be carefully tailored if they are to be more motivating to older people to take action to do something about their falls risk. A wider variety of revised and tailored AV messages, as one component of a community-wide falls prevention campaign, could be considered in an effort to persuade older people to take decisive action to do something about their falls risk.

Trial registration

This study was registered prospectively: NCT03154788. Registered 11 May 2017.
Incidence, clinical implications and impact on public health of infections with Shigella spp. and entero-invasive Escherichia coli (EIEC): results of a multicenter cross-sectional study in the Netherlands during 2016–2017
Authors:   on behalf of the IBESS working group, van den Beld Maaike J. C. , Warmelink Esther , Friedrich Alexander W. , Reubsaet Frans A. G. , Schipper Maarten , de Boer Richard F. , Notermans Daan W. , Petrignani Mariska W. F. , van Zanten Evert , Rossen John W. A. , Friesema Ingrid H. M. , Kooistra-Smid A. M. D. ( Mirjam)
Published: December 2019

Background

Shigella spp. and entero-invasive E. coli (EIEC) use the same invasive mechanism to cause diarrheal diseases. Public health regulations apply only to Shigella spp. infections, but are hampered by the lack of simple methods to distinguish them from EIEC. In the last decades, molecular methods for detecting Shigella spp. and EIEC were implemented in medical microbiological laboratories (MMLs). However, shigellosis cases identified with molecular techniques alone are not notifiable in most countries. Our study investigates the impact of EIEC versus Shigella spp. infections and molecular diagnosed shigellosis versus culture confirmed shigellosis for re-examination of the rationale for the current public health regulations.

Methods

In this multicenter cross-sectional study, fecal samples of patients suspected for gastro-enteritis, referred to 15 MMLs in the Netherlands, were screened by PCR for Shigella spp. or EIEC. Samples were cultured to discriminate between the two pathogens. We compared risk factors, symptoms, severity of disease, secondary infections and socio-economic consequences for (i) culture-confirmed Shigella spp. versus culture-confirmed EIEC cases (ii) culture positive versus PCR positive only shigellosis cases.

Results

In 2016–2017, 777 PCR positive fecal samples with patient data were included, 254 of these were culture-confirmed shigellosis cases and 32 were culture-confirmed EIEC cases. EIEC cases were more likely to report ingestion of contaminated food and were less likely to be men who have sex with men (MSM). Both pathogens were shown to cause serious disease although differences in specific symptoms were observed. Culture-negative but PCR positive cases were more likely report travel or ingestion of contaminated food and were less likely to be MSM than culture-positive cases. Culture-negative cases were more likely to suffer from multiple symptoms. No differences in degree of secondary infections were observed between Shigella spp. and EIEC, and culture-negative and culture-positive cases.

Conclusions

No convincing evidence was found to support the current guidelines that employs different measures based on species or detection method. Therefore, culture and molecular detection methods for Shigella spp. and EIEC should be considered equivalent for case definition and public health regulations regarding shigellosis. Differences were found regarding risks factors, indicating that different prevention strategies may be required.
The efficacy of managing fluid overload in chronic peritoneal dialysis patients by a structured nurse-led intervention protocol
Authors:   Philip Kam-Tao Li, Law Man Ching , Kwan Bonnie Ching-Ha , Fung Janny Suk-Fun , Chow Kai Ming , Ng Jack K.C. , Pang Wing-Fai , Cheng Phyllis Mei-Shan , Leung Chi Bon , Szeto Cheuk Chun
Published: December 2019

Background

Extracellular volume overload is a common problem in peritoneal dialysis (PD) patients and is associated with excessive mortality. We determine the effectiveness of treating PD patients with extracellular volume overload by a structured nurse-led intervention program.

Methods

The hydration status of PD patients was screened by bioimpedance spectroscopy (BIS). Fluid overload was defined as overhydration volume ≥ 2 L. Patients were classified into Symptomatic and Asymptomatic Groups and were managed by a structured nurse-led intervention protocol that focused on education and motivation. Hypertonic cycles were given for short term symptom relief for the Symptomatic group. Patients were followed for 12 weeks for the change in volume status, blood pressure, knowledge and adherence as determined by standard questionnaires.

Results

We recruited 103 patients (53 Symptomatic, 50 Asymptomatic Group. There was a significant reduction in overhydration volume 4 weeks after intervention, which was sustained by week 12; the overall reduction in overhydration volume was 0.96 ± 1.43 L at 4 weeks, and 1.06 ± 1.70 L at 12 weeks (p < 0.001 for both). The improvement was significant for both Symptomatic and Asymptomatic Groups. There was a concomitant reduction in systolic blood pressure in the Asymptomatic (146.9 ± 20.7 to 136.9 ± 19.5 mmHg,p = 0.037) but not Symptomatic group. The scores of knowledge, adherence to dietary control and advices on daily habit at week 4 were all significantly increased, and the improvement was sustained at week 12.

Conclusions

The structured nurse-led intervention protocol has a lasting benefit on the volume status of PD patients with extracellular volume overload. BIS screening allows prompt identification of volume overload in asymptomatic patients, and facilitates a focused effort on this high risk group.
The prevalence and root causes of delay in seeking healthcare among mothers of under five children with pneumonia in hospitals of Bahir Dar city, North West Ethiopia
Authors: Bantie Getasew Mulat , Meseret Zemene , Bedimo Melkamu , Bitew Abebayehu
Published: December 2019

Background

Globally pneumonia is the leading cause of under-five child mortality. Several risk factors for pneumonia mortality have been identified, including delay in seeking health care. For successful reduction of delay in seeking healthcare, further evidence is crucial on its magnitude and factors associated with it in the country particularly in the study area. Therefore, this study aimed to determine the prevalence and root causes of delay in seeking health care among mothers of under-five children with pneumonia in hospitals of the Bahir Dar city, 2019.

Methods

A hospital-based cross-sectional study was conducted from March 15 to May 15, 2019 among 356 mothers of under-five children with pneumonia in hospitals of the Bahir Dar city. The study participants were selected by using a stratified sampling technique and data was collected through face to face interview. Binary logistic regression was used to identify the associated factors of delay in seeking healthcare. The P - value < 0.05 was considered statistically significant. Associations between outcome and exposure variables were expressed by the adjusted odds ratio with a 95% confidence interval (CI).

Results

A total of 356 mothers participated in the study yielded a response of 89.4%. The proportion of delay in seeking health care was 48.6%. Rural residence (AOR = 2. 3, 95% CI: 1.1, 4.9, seek healthcare in a governmental hospital (AOR = 3. 3, 95% CI: 1.8, 6.1), health care decision by mothers (AOR = 2. 9, 95% CI: 1.6, 5.4), poorest household (AOR = 2. 8, 95% CI: 1.1, 7.2), using self-medication (AOR = 7. 5, 95% CI: 3.8, 14.7), using traditional medicine before healthcare-seeking (AOR = 2. 7, 95% CI: 1.4, 5.1), and no information about early healthcare-seeking for childhood pneumonia treatment (AOR = 5. 1, 95% CI: 2.8, 9.1) were the identified determinants significantly associated with delay in seeking healthcare among mothers of under-five children with pneumonia.

Conclusion

This study showed that nearly half of the mothers delayed in seeking healthcare. Rural residence, healthcare seeking at government hospitals, healthcare decision by mothers, poorest household, using self-medication, using traditional medicine before health care seeking, and lack of information about early healthcare-seeking were factors associated with a delay in seeking healthcare for under-five children with pneumonia. Hence, the government and other concerned stakeholders should give due emphasis to tackle on the identified causes of delay in seeking health care for the under five children with pneumonia.