bluuebunny/crossref_metadata_2025 huggingface dataset:
Nurse Telephone Counseling Services as a “Gatekeeper” in an Internet-Based Digital Doctor Reception: A Mixed Questionnaire Survey
Authors: Johansson Anders , Ivarsson Bodil
Published: November 2019

Objective: A large number of different types of digital innovations for health and medical care have been developed in Sweden under the concept of eHealth. Employees’ interest is of great importance in determining the success of different new digital interventions and technologies. Purpose: In this study, we aimed to elucidate the nurses’ experiences as a first “gatekeeper” in an Internet-based Digital Doctor Reception (DDR) concept. Methods: Our 16 informants were recruited among nurses who participated in a DDR pilot project that was completed in April 2019. A mixed questionnaire survey was used to elucidate the nurses’ experiences of collaboration & challenges, technical functionality, and DDR as an activity. The results were descriptively summarized with index values (IVs, 0-1.0), supplemented with a 10-point Likert-type scale that estimated satisfaction and views regarding personal experiences. Results: Collaboration and challenges were experienced as fairly good (IV, 0.58), and technical functionality was experienced as good (IV, 0.80). The experience of DDR as an activity was described positively with an IV of 0.75. The overall experience of the concept (IV, 0.68), corresponds well to the median satisfaction value of 6.5 (interquartile range, 6-9). Content analysis identified 2 main categories: “Facilitators in using DDR experienced by nurses” and “Barriers in using DDR experienced by nurses.” Nurses generally felt positive about participating in the development of an eHealth service. However, they suggested that DDR triaging should take place at the health care center level. The nurses also observed that certain patient groups were excluded from the DDR concept, and sometimes experienced this new way of triaging as less challenging. Conclusion: The informants in our study generally described satisfaction and an overall good experience with the DDR concept. However, some informants felt that the concept was sometimes more stressful and less challenging compared with normal working methods.
A case of acute compartment syndrome of the hand complicating subcutaneous emphysema due to accidental nitrogen gas insufflation
Authors: Looi Collin SK , Arumugam Manohar
Published: November 2019

Non-infectious subcutaneous emphysema of the hand has previously been mentioned in literature. In most cases, it presents in a benign and self-resolving form, which may be managed conservatively. However, in cases of subcutaneous emphysema involving insufflation with nitrogen gas, clinical vigilance is advised as acute compartment syndrome may be a potential complication due to the non-permeative nature of the gas. This would necessitate a complete change in the dynamics of management, warranting urgent surgical intervention. Current literature on acute compartment syndrome of the hand complicating subcutaneous emphysema is scarce. This report aims to highlight this unique case and add to the current literature on this rare condition.
Talking Children Into Literacy: Once More, With Feeling
Authors: Johnston Peter
Published: November 2019

Children’s literate development is mediated by classroom talk. That same talk also mediates children’s emotional, relational, self-regulatory, and moral development. Consequently, the discourse of some literacy teaching practices may be important for shaping the course of human development, and those dimensions of human development can play reciprocal roles in children’s literate development. For example, conversations about the inner life of book characters (and authors) expand children’s social imaginations, which improve their self-regulation, social relationships, and moral development. Coincidentally, literacy learning requires cognitive self-regulation (e.g., working memory, attention, focus), social self-regulation in interactions with peers and teachers, and emotional self-regulation (e.g., frustration and anxiety). Children who develop self-regulation earlier, and to higher levels, develop decoding and reading comprehension earlier. Similarly, when children’s conversations explore the pragmatics of their linguistic interactions, such as how to disagree productively, they become more able to comprehend texts and argue persuasively but also more able to learn from and with each other. Children need to acquire “the codes,” but the ecology of acquisition matters a great deal not only for the ease of acquisition but also for the nature of the literacy that is acquired and for the trajectory of human development. Children’s social and emotional development lies squarely in the bailiwick of the language arts and the literate talk within which they are immersed. But the accompanying human development, in turn, supports literate development.
Characteristics of Central Retinal Vein Occlusion in African Americans
Authors: Kiew Sieh Yean , Thomas George N. , Thomas Akshay S. , Fekrat Sharon
Published: November 2019

Purpose:

This article studies whether the characteristics and clinical course of African American patients with central retinal vein occlusion (CRVO) differ from other racial groups.

Methods:

This retrospective cohort study included consecutive patients diagnosed with CRVO at Duke Eye Center, Durham, North Carolina. Presenting characteristics, examination findings, treatment course, and functional and structural outcomes were compared based on patient-reported race.

Results:

A total of 479 patients with CRVO were included (64.7% white, 22.2% African American, 1.7% mixed race, and 11.4% other races). African American patients were older (68.1 vs 64.3 years, P = .049), more likely to be hypertensive ( P = .001) and diabetic ( P = .000), and had higher rates of open-angle glaucoma ( P < .000). Presenting visual acuity (VA) was worse in African Americans (logarithm of the minimum angle of resolution 1.25 vs 0.96, P = .010). There were no significant differences in the proportion of patients requiring panretinal photocoagulation, intravitreal antivascular endothelial growth factor (anti-VEGF), or intravitreal corticosteroid; however, analysis of treatment-naive individuals showed a higher number of anti-VEGF injections in the first year in African Americans. Final VA was not significantly different between groups, but African Americans had higher rates of neovascular sequelae (25.0% vs 11.8%, P = .019; odds ratio, 2.295, P = .088).

Conclusions:

African Americans with CRVO presented with more severe visual impairment and more systemic and ocular risk factors for CRVO. Treatment-naive African Americans had a greater treatment burden during the first year of follow-up.
Numerical analysis of the forward roll coating of a Rabinowitsch fluid
Authors: M Zahid , Zafar M , Rana MA , Rana MTA , Lodhi MS
Published: November 2019

This paper analyses an isothermal roll coating for a Rabinowitsch fluid. Equations of motion are simplified using lubrication approximation theory. Analytical solutions of velocity, flow rate and pressure-gradient are calculated. Outcomes of coating thickness, pressure distribution, split position, stresses, forces, the power input to the roller and the temperature rise between the coating rollers and substrate are obtained. The effects of some involved parameters are displayed through graphs and tables. It is noted that the Rabinowitsch parameter is a controlling quantity for coating thickness, flow rate, separation point, separation force, pressure distribution, and power input. Moreover, an exponential and monotonic change in the above-mentioned engineering parameters is a function of the Rabinowitsch fluid parameter.
EBV microRNA-BHRF1-2-5p targets the 3′UTR of immune checkpoint ligands PD-L1 and PD-L2
Authors: Cristino Alexandre S. , Nourse Jamie , West Rachael A. , Sabdia Muhammed Bilal , Law Soi C. , Gunawardana Jay , Vari Frank , Mujaj Sally , Thillaiyampalam Gayathri , Snell Cameron , Gough Madeline , Keane Colm , Gandhi Maher K.
Published: November 2019

This article reports a novel mechanism by which Epstein-Barr virus (EBV) microRNA (miRNA) plays a role to fine-tune the expression of LMP1-driven amplification of inhibitory checkpoint programmed death ligand 1 (PD-L1) and PD-L2 in EBV+ diffuse large B-cell lymphoma. Identification and understanding of the immune checkpoint regulation via miRNA may enable potential novel RNA-based therapies to emerge.
Activation and suppression of hematopoietic integrins in hemostasis and immunity
Authors: Nolte Martijn A. , Margadant Coert
Published: November 2019

Nolte and Margadant review the current understanding of the activation and inactivation of integrin receptors expressed by hematopoietic cells and the role of these conformational changes in modulating platelet and leukocyte function.
Prevalence and burden of headache in children and adolescents in Austria – a nationwide study in a representative sample of pupils aged 10–18 years
Authors: Philipp Julia , Zeiler Michael , Wöber Christian , Wagner Gudrun , Karwautz Andreas F. K. , Steiner Timothy J. , Wöber-Bingöl Çiçek
Published: November 2019

Background

Headache disorders are highly prevalent worldwide, but not so well investigated in children and adolescents as in adults: few studies have included representative nationwide samples. No data exist for Austria until now. In a representative sample of children and adolescents in Austria, we estimated the prevalence and attributable burden of headache disorders, including the new diagnostic category of “undifferentiated headache” (UdH) defined as mild headache lasting less than 1 hour.

Methods

Within the context of a broader national mental health survey, children and adolescents aged 10–18 years were recruited from purposively selected schools. Mediated self-completed questionnaires included sociodemographic enquiry (gender, age, socioeconomic status, family constellation, residence [urban or rural] and migration background). Prevalence and attributable burden of all headache, UdH, migraine (definite plus probable), tension-type headache (TTH: definite plus probable) and headache on ≥15 days/month (H15+) were assessed using the Headache-Attributed Restriction, Disability, Social Handicap and Impaired Participation (HARDSHIP) questionnaire for children and adolescents. Health-related quality of life (HrQoL) was assessed using the KIDSCREEN questionnaire.

Results

Of 7643 selected pupils, 3386 (44.3%) completed the questionnaires. The 1-year prevalence of headache was 75.7%, increasing with age and higher in girls (82.1%) than in boys (67.7%; p < 0.001). UdH, migraine, TTH and H15+ were reported by 26.1%, 24.2%, 21.6% and 3.0% of participants. Attributable burden was high, with 42% of those with headache experiencing restrictions in daily activities. Medication use (50% overall) was highest in H15+ (67%) and still considerable in UdH (29%). HrQoL was reduced for all headache types except UdH. Participants in single parent or patchwork families had a higher probability of migraine (respectively, OR 1.5, p < 0.001; OR 1.5, p < 0.01). Participants with a migration background had a lower probability of TTH (OR 0.7, p < 0.01).

Conclusions

Headache disorders are both very common and highly burdensome in children and adolescents in Austria. This study contributes to the global atlas of headache disorders in these age groups, and corroborates and adds knowledge of the new yet common and important diagnostic category of UdH. The findings call for action in national and international health policies, and for further epidemiological research.
De novo Nanopore read quality improvement using deep learning
Authors: LaPierre Nathan , Egan Rob , Wang Wei , Wang Zhong
Published: November 2019

Background

Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area.

Results

Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors.

Conclusions

MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub.
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species
Authors: Li Fang-Dong , Tong Wei , Xia En-Hua , Wei Chao-Ling
Published: November 2019

Background

Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes.

Results

We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS.

Conclusions

The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.
Quality control of imbalanced mass spectra from isotopic labeling experiments
Authors: Li Tianjun , Chen Long , Gan Min
Published: November 2019

Background

Mass spectra are usually acquired from the Liquid Chromatography-Mass Spectrometry (LC-MS) analysis for isotope labeled proteomics experiments. In such experiments, the mass profiles of labeled (heavy) and unlabeled (light) peptide pairs are represented by isotope clusters (2D or 3D) that provide valuable information about the studied biological samples in different conditions. The core task of quality control in quantitative LC-MS experiment is to filter out low-quality peptides with questionable profiles. The commonly used methods for this problem are the classification approaches. However, the data imbalance problems in previous control methods are often ignored or mishandled. In this study, we introduced a quality control framework based on the extreme gradient boosting machine (XGBoost), and carefully addressed the imbalanced data problem in this framework.

Results

In the XGBoost based framework, we suggest the application of the Synthetic minority over-sampling technique (SMOTE) to re-balance data and use the balanced data to train the boosted trees as the classifier. Then the classifier is applied to other data for the peptide quality assessment. Experimental results show that our proposed framework increases the reliability of peptide heavy-light ratio estimation significantly.

Conclusions

Our results indicate that this framework is a powerful method for the peptide quality assessment. For the feature extraction part, the extracted ion chromatogram (XIC) based features contribute to the peptide quality assessment. To solve the imbalanced data problem, SMOTE brings a much better classification performance. Finally, the XGBoost is capable for the peptide quality control. Overall, our proposed framework provides reliable results for the further proteomics studies.
Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp
Authors: Pinto Renan Terassi , Freitas Natália Chagas , Máximo Wesley Pires Flausino , Cardoso Thiago Bergamo , Prudente Débora de Oliveira , Paiva Luciano Vilela
Published: November 2019

Background

Coffee production relies on plantations with varieties fromCoffea arabicaandCoffea canephoraspecies. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, theGH3family members were identified onC. canephoragenome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point aGH3gene as a potential regulator of auxin homeostasis during early somatic embryogenesis inC. arabicaplants.

Results

We have searched within the publishedC. canephoragenome and found 17GH3family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential inC. arabica. TheCaGH3.15expression pattern is the most correlated with embryogenic potential and withCaBBM, aC. arabicaortholog of a major somatic embryogenesis regulator.

Conclusion

Therefore, one out of theGH3members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.
Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale
Authors: Vila Nova Meryl , Durimel Kévin , La Kévin , Felten Arnaud , Bessières Philippe , Mistou Michel-Yves , Mariadassou Mahendra , Radomski Nicolas
Published: November 2019

Background

Salmonella entericasubsp.enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440Salmonellagenomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).

Results

Based on a genome dataset includingSalmonellaserovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.

Conclusions

Our results suggest that the genetic and metabolic determinants ofSalmonellaadaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.
Transcriptome analysis reveals a positive effect of brassinosteroids on the photosynthetic capacity of wucai under low temperature
Authors: Zhao Mengru , Yuan Lingyun , Wang Jie , Xie Shilei , Zheng Yushan , Nie Libing , Zhu Shidong , Hou Jinfeng , Chen Guohu , Wang Chenggang
Published: November 2019

Background

Brassinosteroids (BRs) have a positive effect on many processes during plant growth and development, and in response to various abiotic stressors. Low-temperature (LT) stress constricts the geographic distribution, growth, and development of wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen). However, there is little information on the global gene expression of BRs under LT stress in wucai. In this study, the molecular roles of 24-epibrassinolide (EBR) after exogenously application, were explored by RNA sequencing under LT conditions.

Results

According to the Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, photosynthesis was significantly enriched after spraying EBR under LT. The transcripts encoding the photosystem II (PSII) oxygen-evolving enhancer protein, photosystem I (PSI) subunit, light-harvesting chlorophyll protein complexes I and II, and ferredoxin were up-regulated after the application of EBR. Transcripts encoding several key enzymes involved in chlorophyll biosynthesis were also up-regulated, accompanied by significant differences in the contents of 5-aminolevulinic acid (ALA), porphobilinogen (PBG), protoporphyrin IX (Proto IX), Mg-protoporphyrin IX (Mg-proto IX), protochlorophyllide (Pchl), and photosynthetic pigments. Notably, transcriptional and physiological analyses revealed that under LT stress, plant responses to EBR involved a major reorientation of photosynthesis, as well as porphyrin and chlorophyll metabolism.

Conclusion

This study explored the role of EBR as an LT stress tolerance mechanism in wucai. At the transcription level, LT tolerance manifests as an enhancement of photosynthesis, and the amelioration of porphyrin and chlorophyll metabolism.
Sex- and tissue-specific transcriptome analyses and expression profiling of olfactory-related genes in Ceracris nigricornis Walker (Orthoptera: Acrididae)
Authors: Yuan Hao , Chang Huihui , Zhao Lina , Yang Chao , Huang Yuan
Published: November 2019

Background

The sophisticated insect olfactory system plays an important role in recognizing external odors and enabling insects to adapt to environment. Foraging, host seeking, mating, ovipositing and other forms of chemical communication are based on olfaction, which requires the participation of multiple olfactory genes. The exclusive evolutionary trend of the olfactory system in Orthoptera insects is an excellent model for studying olfactory evolution, but limited olfaction research is available for these species. The olfactory-related genes of Ceracris nigricornis Walker (Orthoptera: Acrididae), a severe pest of bamboos, have not yet been reported.

Results

We sequenced and analyzed the transcriptomes from different tissues of C. nigricornis and obtained 223.76 Gb clean data that were assembled into 43,603 unigenes with an N50 length of 2235 bp. Among the transcripts, 66.79% of unigenes were annotated. Based on annotation and tBLASTn results, 112 candidate olfactory-related genes were identified for the first time, including 20 odorant-binding proteins (OBPs), 10 chemosensory-binding proteins (CSPs), 71 odorant receptors (ORs), eight ionotropic receptors (IRs) and three sensory neuron membrane proteins (SNMPs). The fragments per kilobase per million mapped fragments (FPKM) values showed that most olfactory-related differentially expressed genes (DEGs) were enriched in the antennae, and these results were confirmed by detecting the expression of olfactory-related genes with quantitative real-time PCR (qRT-PCR). Among these antennae-enriched genes, some were sex-biased, indicating their different roles in the olfactory system of C. nigricornis.

Conclusions

This study provides the first comprehensive list and expression profiles of olfactory-related genes in C. nigricornis and a foundation for functional studies of these olfactory-related genes at the molecular level.
Saccharomyces boulardii alleviates ulcerative colitis carcinogenesis in mice by reducing TNF-α and IL-6 levels and functions and by rebalancing intestinal microbiota
Authors: Wang Chunsaier , Li Wenbin , Wang Hongying , Ma Yiming , Zhao Xinhua , Zhang Xudong , Yang Hong , Qian Jiaming , Li Jingnan
Published: November 2019

Background and Aims

To explore the inhibition mechanism of Saccharomyces boulardii (S. boulardii) on ulcerative colitis (UC) carcinogenesis.

Methods

C57BL/6 mice were treated with azoxymethane and dextran sulfate sodium (AOM/DSS) to develop a UC carcinogenesis model. The treatment group was lavaged with S. boulardii (5 × 107 CFU/d) for 12 weeks. The mice were sacrificed and the tumor load in the treatment group was compared with that of a control group. The levels of TNF-α and IL-6 in colon tissue were measured by enzyme-linked immunosorbent assays. The influence of S. boulardii on TNF-α and IL-6 regulation was also investigated using different colon cell lines. Differences in intestinal microbiota in both stool and intestinal mucosa samples were assessed using 16S rDNA sequencing.

Results

S. boulardii treatment reduced AOM/DSS-induced UC carcinogenesis in mice, as indicated by the reduced tumor load and reduced TNF-α and IL-6 levels in vivo, as well its effects on TNF-α and IL-6 activities in vitro. Significant changes in both fecal and mucosal microbiota were observed among the control, the AOM/DSS treated, and AOM/DSS plus S. boulardii treated groups. For fecal microbiota, the AOM/DSS treated group was lower in Lactobacillus, but higher in Oscillibacter and Lachnoclostridium than the control group. After intervention with S. boulardii, the percentage of Bacillus and Lactococcus increased, but Lachnoclostridium, Oscillibacter, Bacteroides, and Pseudomonas decreased. For the intestinal mucosal microbiota, the AOM/DSS treated group was lower in Bifidobacterium and Ruminococcaceae_UCG-014 and higher in Alloprevotella than the control group. After S. boulardii exposure, the percentage contributions of Lachnoclostridium and Lachnospiraceae_NK4A136 increased.

Conclusions

S. boulardii effectively reduced UC carcinogenesis in an AOM/DSS induced mice model. This positive result can likely be attributed to the reduction of TNF-α and IL-6 levels or the blockade of their function combined with alterations to the intestinal microbiota.
Elucidating the role of shikimate dehydrogenase in controlling the production of anthocyanins and hydrolysable tannins in the outer peels of pomegranate
Authors: Habashi Rida , Hacham Yael , Dhakarey Rohit , Matityahu Ifat , Holland Doron , Tian Li , Amir Rachel
Published: November 2019

Background

The outer peels of pomegranate (Punica granatum L.) possess two groups of polyphenols that have health beneficial properties: anthocyanins (ATs, which also affect peel color); and hydrolysable tannins (HTs). Their biosynthesis intersects at 3-dehydroshikimate (3-DHS) in the shikimate pathway by the activity of shikimate dehydrogenase (SDH), which converts 3-DHS to shikimate (providing the precursor for AT biosynthesis) or to gallic acid (the precursor for HTs biosynthesis) using NADPH or NADP+ as a cofactor. The aim of this study is to gain more knowledge about the factors that regulate the levels of HTs and ATs, and the role of SDH.

Results

The results have shown that the levels of ATs and HTs are negatively correlated in the outer fruit peels of 33 pomegranate accessions, in the outer peels of two fruits exposed to sunlight, and in those covered by paper bags. When calli obtained from the outer fruit peel were subjected to light/dark treatment and osmotic stresses (imposed by different sucrose concentrations), it was shown that light with high sucrose promotes the synthesis of ATs, while dark at the same sucrose concentration promotes the synthesis of HTs. To verify the role of SDH, six PgSDHs (PgSDH1, PgSDH3–1,2, PgSDH3a-1,2 and PgSDH4) were identified in pomegranate. The expression of PgSDH1, which presumably contributes to shikimate biosynthesis, was relatively constant at different sucrose concentrations. However, the transcript levels of PgSDH3s and PgSDH4 increased with the accumulation of gallic acid and HTs under osmotic stress, which apparently accumulates to protect the cells from the stress.

Conclusions

The results strongly suggest that the biosynthesis of HTs and ATs competes for the same substrate, 3-DHS, and that SDH activity is regulated not only by the NADPH/NADP+ ratio, but also by the expression of the PgSDHs. Since the outer peel affects the customer’s decision regarding fruit consumption, such knowledge could be utilized for the development of new genetic markers for breeding pomegranates having higher levels of both ATs and HTs.
Studies on genome size estimation, chromosome number, gametophyte development and plant morphology of salt-tolerant halophyte Suaeda salsa
Authors: Cheng Yan , Yang Pan , Zhao Lihua , Priyadarshani S. V. G. N. , Zhou Qiao , Li Zeyun , Li Weimin , Xiong Junjie , Lin Zhibin , Li Li , Huang Xinyu , Liu Jindian , Aslam Mohammad , Zhao Heming , Li Gang , Ma Jinbiao , Li Lei , Qin Yuan
Published: November 2019

Background

Soil salinization and alkalization are among the major agricultural threats that affect crop productivity worldwide, which are increasing day by day with an alarming rate. In recent years, several halophytes have been investigated for their utilization in soil remediation and to decipher the mechanism of salt-tolerance in these high salt tolerant genetic repositories. Suaeda salsa is an annual halophytic herb in the family Amaranthaceae, displaying high salt and alkali-resistance and having nutritive value. However, the fundamental biological characteristics of this valuable plant remain to be elucidated until today.

Results

In this study, we observed the morphology and development of Suaeda salsa, including seed morphology, seed germination, plant morphology, and flower development. Using microscopy, we observed the male and female gametophyte developments of Suaeda salsa. Also, chromosome behaviour during the meiosis of male gametophyte was studied. Eventually, the genome size of Suaeda salsa was estimated through flow cytometry using Arabidopsis as reference.

Conclusions

Our findings suggest that the male and female gametophyte developments of Suaeda salsa are similar to those of the model plant Arabidopsis, and the diploid Suaeda salsa contains nine pairs of chromosomes. The findings also indicate that the haploid genome of Suaeda salsa is approximately 437.5 MB. The observations and results discussed in this study will provide an insight into future research on Suaeda salsa.
WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat
Authors: Cram Dustin , Kulkarni Manoj , Buchwaldt Miles , Rajagopalan Nandhakishore , Bhowmik Pankaj , Rozwadowski Kevin , Parkin Isobel A. P. , Sharpe Andrew G. , Kagale Sateesh
Published: November 2019

Background

CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement.

Description

We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184–191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR.

Conclusion

The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/.
Induction techniques that reduce redistribution hypothermia: a prospective, randomized, controlled, single blind effectiveness study
Authors: Roth Jonathan V. , Braitman Leonard E. , Hunt Lacy H.
Published: November 2019

Background

While much effort has been devoted to correcting intraoperative hypothermia, less attention has been directed to preventing redistribution hypothermia. In this study, we compared three different anesthetic induction techniques to standard IV propofol inductions (control) in their effect on reducing redistribution hypothermia.

Methods

Elective, afebrile patients, age 18 to 55 years, were randomly assigned to one of four groups (n = 50 each). Group “INH/100” was induced with 8% sevoflurane in 100% oxygen, Group “INH/50” with 8% sevoflurane in 50% oxygen and 50% nitrous oxide, Group “PROP” with 2.2 mg/kg propofol, and Group “Phnl/PROP” with 2.2 mg/kg propofol immediately preceded by 160 mcg phenylephrine. Patients were maintained with sevoflurane in 50% nitrous oxide and 50% oxygen in addition to opioid narcotic. Forced air warming was used. Core temperatures were recorded every 15 min after induction for 1 h.

Results

Compared to control group PROP, the mean temperatures in groups INH/100, INH/50, and Phnl/PROP were higher 15, 30, 45 and 60 min after induction (p < 0.001 for all comparisons), averaging between 0.39 °C and 0.54 °C higher. In group PROP, 60% of patients had at least one temperature below 36.0 °C in the first hour whereas only 16% did in each of groups INH/100, INH/50, and Phnl/PROP (p < 0.0001 in each group compared to PROP).

Conclusions

In this effectiveness trial, inhalation inductions with sevoflurane or with prophylactic phenylephrine bolus prior to propofol induction reduced the magnitude of redistribution hypothermia by an average of 0.4 to 0.5 °C in patients aged 18 to 55 years.

Trial registration

Retrospectively registered on clinical-trials.gov asNCT02331108, November 20, 2014.
Thrombelastometry guided blood-component therapy after cardiac surgery: a randomized study
Authors: Haensig Martin , Kempfert Joerg , Kempfert Pia-Maria , Girdauskas Evaldas , Borger Michael Andrew , Lehmann Sven
Published: November 2019

Background

Significant bleeding is a well known complication after cardiac surgical procedures and is associated with worse outcome. Thrombelastometry (ROTEM®) allows point-of-care testing of the coagulation status but only limited data is available yet. The aim was to evaluate the ROTEM®-guided blood component therapy in a randomized trial.

Methods

In case of significant postoperative bleeding (> 200 ml/h) following elective isolated or combined cardiac surgical procedures (including 14% re-do procedures and 4% requiring circulatory arrest) patients were randomized to either a 4-chamber ROTEM®-guided blood-component transfusion protocol or received treatment guided by an algorithm based on standard coagulation testing (control). One hundred four patients (mean age: 67.2 ± 10.4 years, mean log. EuroSCORE 7.0 ± 8.8%) met the inclusion criteria. Mean CPB-time was 112.1 ± 55.1 min., mean cross-clamp time 72.5 ± 39.9 min.

Results

Baseline demographics were comparable in both groups. Overall there was no significant difference in transfusion requirements regarding red blood cells, platelets, plasma, fibrinogen or pooled factors and the re-thoracotomy rate was comparable (ROTEM®: 29% vs. control: 25%). However, there was a trend towards less 24-h drainage loss visible in the ROTEM®-group (ROTEM®: 1599.1 ± 834.3 ml vs. control: 1867.4 ± 827.4 ml;p = 0.066). In the subgroup of patients with long CPB-times (> 115 min.;n = 55) known to exhibit an increased risk for diffuse coagulopathy ROTEM®-guided treatment resulted in a significantly lower 24-h drainage loss (ROTEM®: 1538.2 ± 806.4 ml vs. control: 2056.8 ± 974.5 ml;p = 0.032) and reduced 5-year mortality (ROTEM®: 0% vs. control: 15%;p = 0.03).

Conclusion

In case of postoperative bleeding following cardiac surgical procedures a treatment algorithm based on “point-of-care” 4-chamber ROTEM® seems to be at least as effective as standard therapy. In patients with long CPB-times ROTEM®-guided treatment may result in less bleeding, a marked reduction in costs and long-term mortality.

Trial registration

German Clinical Trials Register, TRN:DRKS00017367, date of registration: 05.06.2019, ‘retrospectively registered’.
A case report: a giant cardiac atypical lipoma associated with pericardium and right atrium
Authors: Wang Xin , Yu Xiaona , Ren Weidong , Li Dongyu
Published: November 2019

Background

Among primary cardiac tumors, atypical lipoma is very rare. In particular, cases with lipomas in both the pericardium and the atria are even rare.

Case presentation

We report the case of a 49-year-old male patient presented to our department because of chest pain. Echocardiography revealed two large masses in both the pericardium and the right atrium. Then the tumors were completely resected and the histopathological examination revealed atypical lipoma. The patient recovered well without any complication and discharged from hospital.

Conclusions

We report a very rare case of a huge atypical lipomas located on the pericardium and right atrium. These tumors were easily detected by echocardiography and final diagnosed after surgical resection and pathological examination.
Association of Japan Coma Scale score on hospital arrival with in-hospital mortality among trauma patients
Authors: Yumoto Tetsuya , Naito Hiromichi , Yorifuji Takashi , Aokage Toshiyuki , Fujisaki Noritomo , Nakao Atsunori
Published: November 2019

Background

The Japan Coma Scale (JCS) score has been widely used to assess patients’ consciousness level in Japan. JCS scores are divided into four main categories: alert (0) and one-, two-, and three-digit codes based on an eye response test, each of which has three subcategories. The purpose of this study was to investigate the utility of the JCS score on hospital arrival in predicting outcomes among adult trauma patients.

Methods

Using the Japan Trauma Data Bank, we conducted a nationwide registry-based retrospective cohort study. Patients 16 years old or older directly transported from the trauma scene between January 2004 and December 2017 were included. Our primary outcome was in-hospital mortality. We examined outcome prediction accuracy based on area under the receiver operating characteristic curve (AUROC) and multiple logistic regression analysis with multiple imputation.

Results

A total of 222,540 subjects were included; their in-hospital mortality rate was 7.1% (n = 15,860). The 10-point scale JCS and the total sum of Glasgow Coma Scale (GCS) scores demonstrated similar performance, in which the AUROC (95% CIs) showed 0.874 (0.871–0.878) and 0.878 (0.874–0.881), respectively. Multiple logistic regression analysis revealed that the higher the JCS score, the higher the predictability of in-hospital death. When we focused on the simple four-point scale JCS score, the adjusted odds ratio (95% confidence intervals [CIs]) were 2.31 (2.12–2.45), 4.81 (4.42–5.24), and 27.88 (25.74–30.20) in the groups with one-digit, two-digit, and three-digit scores, respectively, with JCS of 0 as a reference category.

Conclusions

JCS score on hospital arrival after trauma would be useful for predicting in-hospital mortality, similar to the GCS score.
Pneumatosis cystoides intestinalis: a case report and literature review
Authors: Ling Fangmei , Guo Di , Zhu Liangru
Published: November 2019

Background

Pneumatosis cystoides intestinalis (PCI) is a low-incidence disease that confuses many doctors. A vast number of factors are suspected to contribute to its pathogenesis, such as Crohn’s disease, intestinal stenosis, ulcerative colitis, drug use, extra-gastrointestinal diseases, and chronic obstructive pulmonary disease. Most consider its pathogenesis interrelated to an increase in intra-intestinal pressure and the accumulation of gas produced by aerogenic bacteria, and patients with atypical symptoms and imaging manifestations tend to be misdiagnosed.

Case presentation

A 64-year-old man complained of a 3-month history of bloody stool without mucopurulent discharge, abdominal pain, or diarrhea. Colonoscopy revealed multiple nodular projections into the segmental mucosa of the sigmoid colon. Crohn’s disease and malignant disease ware suspected first according to the patient’s history, but laboratory examinations did not confirm either. Endoscopic ultrasound (EUS) revealed multiple cystic lesions in the submucosa. Moreover, computer tomography scan showed multiple bubble-like cysts. Combined with ultrasonography, computed tomography, and pathology findings, we ultimately made a diagnosis of PCI. Instead of surgery, we recommended conservative treatment consisting of endoscopy and oral drug administration. His symptoms improved with drug therapy after discharge, and no recurrence was noted on follow-up.

Conclusions

The incidence of PCI is low. Due to a lack of specificity in clinical manifestations and endoscopic findings, it often misdiagnosed as intestinal polyps, tumors, inflammatory bowel disease, or other conditions. Colonoscopy, computed tomography, and ultrasonography have demonstrated benefit in patients with multiple nodular projections in colon. Compared to the treatment of the above diseases, PCI treatment is effective and convenient, and the prognosis is optimistic. Therefore, clinicians should increase their awareness of PCI to avoid unnecessary misdiagnosis.
Comparison of different endoscopic resection techniques for submucosal tumors originating from muscularis propria at the esophagogastric junction
Authors: Xu Hong-wei , Zhao Qi , Yu Shu-xia , Jiang Ying , Hao Jing-hua , Li Bin
Published: November 2019

Background

To compare the outcomes of submucosal tunneling endoscopic resection (STER) and submucosal excavation (ESE) for the treatment of submucosal tumors (SMTs) arising from the muscularis propria (MP) at the esophagogastric junction (EGJ).

Methods

A retrospective analysis of patients with SMTs at EGJ who underwent STER and ESE from October 2011 to October 2017 was performed. The outcomes evaluated were operation time, complete resection rate, adverse events, and tumor recurrence.

Results

Ninety patients were included in this study. Complete resection rates in the STER group were higher than those of the ESE group (100 vs. 92%, p < 0.05). For tumors ≤15 mm, both techniques achieved 100% complete resection rate; but for tumors > 15 mm, complete resection rate was higher in the STER group than the ESE group (100% vs. 77.8%, p < 0.05). Subgroup analyses revealed that the operation time of STER for in cardiac-gastric group was longer than that for ESE (145.14 ± 42.43 min vs. 70.32 ± 39.84 min, p <  0.05). The air leakage symptoms were more frequent in STER group (90.9% vs. 50.0%, p < 0.05). No tumor recurrence occurred in both the STER and ESE groups.

Conclusions

For SMTs ≤15 mm, both STER and ESE have similar satisfactory therapeutic outcomes. However, in the cardiac-gastric subgroup, STER had a longer operative time compared to the ESE procedure. For SMTs > 15 mm, STER is the preferred choice due to its higher complete resection rate.
Impact of metformin use among tuberculosis close contacts with diabetes mellitus in a nationwide cohort study
Authors: Lee Ming-Chia , Lee Chih-Hsin , Lee Meng-Rui , Wang Jann-Yuan , Chen Shih-Ming
Published: November 2019

Background

The protective effect of metformin against active tuberculosis (TB) among TB close contacts is unknown.

Methods

TB close contacts with diabetes mellitus (DM) and normal renal function were selected from the National Health Insurance Research Database of Taiwan. Metformin users were patients who received ≥90 cumulative defined daily doses within 1 year before the index date. For each metformin user, a propensity-score matched metformin nonuser and an age- and sex-matched healthy TB close contact were selected. The outcome was incident TB, identified using previously validated diagnostic criteria. Independent predictors were investigated using stratified Cox regression analysis. Interaction analysis was also performed.

Results

A total of 5846 TB close contacts who were metformin users, metformin non-users, and healthy contacts were analysed. The incidence of active TB was 755 (600–938), 1117 (927–1335), and 526 (393–689) cases per 100,000 person-years in each group, respectively. Multivariate analysis revealed that healthy contacts had the lowest risk of developing active TB (adjusted hazard ratio [aHR]: 0.42 [0.30–0.60]) and metformin use partially reversed the risk associated with DM (aHR: 0.73 [0.54–0.98]). Subpopulation analysis revealed a significant interaction between insulin use and metformin use.

Conclusions

Metformin use is associated with a lower risk of developing active TB among TB close contacts with DM, especially for insulin users. It may be an alternative choice for primary prevention against active TB if no contraindications exist. However, prospective studies are needed to confirm the findings.