bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of cognitive schemas on the mixed anxiety-depressive symptoms of breast cancer patients
Authors: Bredicean Ana Cristina , Crăiniceanu Zorin , Oprean Cristina , Rivis Ioana Alexandra , Papavă Ion , Secosan Ica , Frandes Mirela , Giurgi-Oncu Catalina , Grujic Daciana
Published: December 2019

Background: The surgical treatment of breast cancer involves various psychological consequences, which differ according to individual characteristics. Our study aimed to identify the role that cognitive schemas had in triggering anxiety and depressive symptoms in patients diagnosed with breast cancer that underwent oncological and plastic surgery treatment. Methods: 64 female patients, diagnosed with breast cancer from an Oncology and Plastic Surgery Hospital, were selected to participate in this study between March-June 2018. They were divided into two groups: I. 28 patients who underwent mastectomy surgery; II. 36 patients, who required mastectomy and, subsequently, also chose to undergo breast reconstruction surgery. For the purposes of evaluating a possible change in mental health status, we employed two assessment scales: the Young Cognitive Schema Questionnaire - Short Form 3 (YSQ-S3) and the DASS-21R (Depression Anxiety Stress Scale - 21 Romanian version). Results: Participants who underwent mastectomy and subsequent breast reconstruction surgery employed cognitive schemas that did not generate symptoms of depression or anxiety. In contrast, the cognitive schemas found in women who refused reconstructive breast surgery were significantly correlated with the presence of anxiety-depressive symptoms.The cognitive schema domain of ‘disconnection and rejection' correlated uncertainly with the presence of anxiety-depressive symptoms for the group with breast reconstruction (Spearman's r= 0.091, p = 0.644), while for the other group the correlation was moderate-strong (Spearman’s r= 0.647, p < 0.01). Negative emotional schemas were significantly correlated with the presence of anxiety-depressive symptoms (Spearman's r= 0.598, p < 0.01) in the group of participants without reconstructive surgery. Conclusion:A correct identification of dysfunctional cognitive schemas and coping mechanisms at the commencement of the combined treatment in breast cancer patients could serve as an indicator for the evolution of their mental health, therefore assisting professionals in establishing the most suitable psychological, psychotherapeutic and psychiatric intervention plan. Keywords:breast cancer, cognitive schemas, anxiety, depression, mastectomy, breast reconstruction
Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues
Authors: Cheng Shifeng , Fu Yuan , Zhang Yaolei , Xian Wenfei , Wang Hongli , Grothe Benedikt , Lu Xin , Xu Xun , Klug Achim , McCullagh Elizabeth
Published: December 2019

BACKGROUND: The Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome sequencing and assembly from 27 different tissues samples. RESULTS: The genome was sequenced using Illumina HiSeq 2000 and after assembly resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 31 769 (>2000bp) predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome. CONCLUSIONS: We report the first de novo assembly of the Mongolian gerbil genome enhanced by assembly of transcriptome data from several tissues. Sequencing of this genome and transcriptome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools.
The PROMOTE study (High Protein diet and Resistance training Combination in Overweight and Obesity) - short-term weight loss and long-term weight maintenance for Chinese people: a protocol for a pilot randomised controlled trial.
Authors: Shaoyong Xu , Zhang Juan , Dong Yuxiang , Chen Ruikun , Xu Wenlei , Tan Zhijun , Gao Ling , Shang Lei
Published: December 2019

Background It is very important for clinicians and dieticians to explore reasonable weight management strategies for obese people that address both short-term weight loss and subsequent weight maintenance. We hypothesized that resistance training combined with a high-protein diet would result in similar short-term weight loss but better long-term weight maintenance than either conventional low-fat diet control or high-protein diet alone.Methods/design This is an 8-week randomized parallel controlled trial followed by a 24-week observational follow-up study. A 48-week supplementary follow-up study will be carried out if necessary. The study will be conducted between June 2019 and October 2020. The 90 overweight or obese participants will be randomly assigned to the conventional low-fat diet group, the high-protein diet group and the high-protein diet and resistance training combination group. Primary outcomes are body weight changes at week 8 and week 24 compared with the baseline level.Discussion High-quality research on the effect of a high-protein diet combined resistance training on weight loss and weight maintenance is limited in Chinese population. Our study will provide a basis for obesity management in China, and promote the development of exercise and diet-related studies.Trials registration ChiCTR1900023841, 14 June 2019
The Effects of If-Then Plans on Weight Loss: Results of the 24-Month Follow-up of the McGill CHIP Healthy Weight Program Randomized Controlled Trial
Authors: Knauper Barbel , shireen huma , Carriere Kimberly , Frayn Mallory , Ivanova Elena , Xu Zhen , Lowensteyn Ilka , Sadikaj Gentiana , Luszczynska Aleksandra , grover steven , Investigators McGill CHIP Healthy Weight Program
Published: December 2019

Background: The NIH-developed Diabetes Prevention Program (DPP) is successful in achieving clinically significant weight loss in individuals with overweight/obesity when delivered one-on-one. However, due to high cost of implementation, the long-term effectiveness remains limited. In response, a group-based version of the program, called the National DPP, was developed. The average weight loss following participation in this program was only about 3.5% with low long-term weight loss maintenance. Purpose: We aimed to optimize weight loss outcomes of the National DPP by integrating the habit formation tool of if-then plans into the program. Results at 3 and 12 months of participation showed no between-group differences between standard and enhanced DPP but higher weight loss in both groups compared to the National DPP. This paper reports the long-term weight loss maintenance data following participation in the program. Methods: Of the 172 participants enrolled at the beginning of the study, data from 110 participants was available and analyzed at 24 months, i.e. 12 months following the end of the 12-month intervention. Results: No between-group difference in weight loss maintenance was seen. Pooled results showed a significant weight regain from 12 to 24 months, i.e. an average of 7.85lbs of the 20.36lbs lost. However, participants from both groups were still 12.51lbs or 6.13% lighter at 24 months than at baseline. Conclusion: If-then plans did not result in a higher percentage of weight loss at 24-month follow-up. However, at 24 months, both groups maintained a significant portion of the weight lost at the end of intervention.
Paracetamol (acetaminophen) route in palliative care (PC) patients: Intravenous versus subcutaneous route pharmacokinetics study protocol for a randomized trial = ParaSCIVPallia
Authors: Vernant Marine , Lepoupet Marie , Creveuil Christian , Alix Antoine , Gourio Charlotte , Peyro-Saint-Paul Laure , Lelong-Boulouard Veronique , Guillaumé Cyril
Published: December 2019

Background: Among palliative care (PC) patients who are administered paracetamol, the subcutaneous (SC) route is often an alternative to the intravenous (IV) route. Yet pharmacological and clinical data are lacking. Many French palliative teams are now empirically using paracetamol by the SC route, but there are no data to support this practice.Aim: Compare pharmacokinetic (PK) parameters between the IV and SC routes for PC patients.Design: A randomized, open, crossover study in two PC centers. The primary endpoints are AUC0-t, AUC0-, Cmax, and Vd et t1/2. All adverse events will be reported for a safety analysis.Setting/participants: 20 adult PC patients with an IV device, having spontaneous pain, not related to care, with a numeric pain rate scale > 3/10, or having a systematic prescription of paracetamol in the usual treatment. They also have to meet all eligibility criteria.Conclusion: First study comparing PK parameters for IV paracetamol versus SC paracetamol.Trial registration:Clinical trial register number NCT03944044, 2019-06-04https://clinicaltrials.gov/ct2/show/NCT03944044Committee for the protection of persons (CPP) 18.09.05.58206 approval 2018/10/4National Drug Safety Agency (ANSM: Agence Nationale de Sécurité Médicament) MEDAECNAT-2018-09-00009 approval 2018/11/29
Enhanced genome assembly and a new official gene set for Tribolium castaneum
Authors: Herndon Nicolae , Shelton Jennifer , Gerischer Lizzy , Ioannidis Panos , Ninova Maria , Dönitz Jürgen , Waterhouse Robert M. , Liang Chun , Damm Carsten , Siemanowski Janna , Kitzmann Peter , Ulrich Julia , Dippel Stefan , Oberhofer Georg , Hu Yonggang , Schwirz Jonas , Schacht Magdalena , Lehmann Sabrina , Montino Alice , Posnien Nico , Gurska Daniela , Horn Thorsten , Seibert Jan , Jentzsch Iris M. Vargas , Panfilio Kristen A. , Li Jianwei , Wimmer Ernst A. , Stappert Dominik , Roth Siegfried , Schröder Reinhard , Park Yoonseong , Schoppmeier Michael , Chung Ho-Ryun , Klingler Martin , Kittelmann Sebastian , Friedrich Markus , Chen Rui , Altincicek Boran , Vilcinskas Andreas , Zdobnov Evgeny , Griffiths-Jones Sam , Ronshaugen Matthew , Stanke Mario , Brown Sue J. , Bucher Gregor
Published: December 2019

Background: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality.
Results: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4,753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1,452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI.
Conclusions: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.
iTRAQ-Based Proteomic Analysis Reveals the Mechanisms of Botrytis cinerea controlled with Wuyiencin
Authors: Shi Liming , Ge Beibei , Wang Jinzi , Liu Binghua , Ma Jinjin , Wei Qiuhe , Zhang Kecheng
Published: December 2019

Background
Grey mould is an important plant disease worldwide, caused by Botrytis cinerea ，resulting in serious economic loss. Wuyiencin, a low toxicity, high efficiency, and broad-spectrum agricultural antibiotic, has been demonstrated effectiveness against B. cinerea.
Methods
In this study, we characterized the differential protein expression in wuyiencin-treated B. cinerea using high-resolution mass spectrometry and bioinformatic tools.
Results
Wuyiencin treatment inhibited growth and sporulation of B. cinerea, specifically altering hypha morphology and intracellular structures. These changes were accompanied by differential expression (fold change >2.0) of 316 proteins identified by iTRAQ-labelling LC-MS/MS analysis (P < 0.05). Up-regulation of 14 proteins, including carbohydrate metabolism proteins and cell wall stabilization proteins, was validated by parallel reaction monitoring (PRM). Down-regulation of 13 proteins was validated by PRM, including regulators of energy metabolism, nucleotide/protein synthesis, and the biosynthesis of mediators of plant stress and decay.
Conclusion
Our results confirm the inhibitory biological effects of wuyiencin on B . cinereal and elaborate on the differentially expressed proteins and associated pathways implicated in the capacity of wuyiencin to debilitate the growth and pathogenicity of grey mould. This study provides validated candidates for further targeted exploration with the goal of optimizing wuyiencin as a safe, low-toxicity agent for biological control.
Single Inhaler Triple Therapy (FF/UMEC/VI) Versus FF/VI and UMEC/VI in Patients with COPD: Subgroup Analysis of the China Cohort in the IMPACT Trial
Authors: Zheng Jinping , Zhong Nanshan , Wang Changzheng , Wei Li Ping , Zhou Xiang Dong , Zhao Li , Yuan Ya Dong , He Bei , Wu Bin , Du Xin , Lipson David A.
Published: December 2019

Background
In the Phase III InforMing the PAthway of COPD Treatment (IMPACT) trial, fluticasone furoate [FF]/umeclidinium [UMEC]/vilanterol [VI] single-inhaler triple therapy resulted in lower rates of moderate/severe exacerbations than dual therapy with FF/VI or UMEC/VI in patients with symptomatic chronic obstructive pulmonary disease (COPD) and a history of exacerbations. Here we present the result in the subpopulation of patients enrolled in China.
Methods
The IMPACT trial was a 52-week, randomized, double-blind, parallel-group, multicenter trial. Patients (≥40 years of age) with COPD and ≥1 moderate/severe exacerbations in the prior year were randomized 2:2:1 to once-daily FF/UMEC/VI 100/62.5/25 µg, FF/VI 100/25 µg, or UMEC/VI 62.5/25 µg administered via the Ellipta inhaler. Endpoints, assessed in the overall intent-to-treat (ITT) population and in patients from China, included annual rates of exacerbations, time-to-first on-treatment moderate/severe exacerbation, and change from baseline in trough forced expiratory volume in 1 second (FEV1) at Week 52.
Results
Of the 10,355 patients randomized, 535 (5.2%) were from China. In the China cohort, the rate of on-treatment moderate/severe exacerbations was 0.81 per year with FF/UMEC/VI versus 0.96 with FF/VI (rate ratio [RR]: 0.84; 95% confidence interval [CI]: 0.64, 1.11; p=0.227) and 0.80 with UMEC/VI (RR: 1.02; 95% CI: 0.72, 1.44; p=0.929). Hazard ratio for time-to-first moderate/severe exacerbation was 0.84 (95% CI: 0.63, 1.11; p=0.218) for FF/UMEC/VI versus FF/VI, and 0.89 (95% CI: 0.62, 1.27; p=0.516) for FF/UMEC/VI versus UMEC/VI. Improvements in mean change from baseline in trough FEV1 were observed for FF/UMEC/VI versus FF/VI (treatment difference 137 mL; 95% CI: 86, 188; p<0.001) and FF/UMEC/VI versus UMEC/VI (treatment difference 63 mL; 95% CI: 0, 125; p=0.0.050) in China. Health status was also improved with FF/UMEC/VI versus both dual therapies. Broadly, these results were in the same direction as those seen in the overall ITT population. No new safety signals were identified.
Conclusions
In the China cohort of the IMPACT trial, single-inhaler triple therapy with FF/UMEC/VI versus dual therapy with FF/VI or UMEC/VI reduced the rate and risk of exacerbations, and improved lung function and quality of life similar to the overall ITT population.
Trial registration: NCT02164513 (GSK study number CTT116855).
The Ambiguity of the Scope of Legal Liability of Japanese Nurse Practitioners with Regards to their Medical Practice: A Qualitative Research
Authors: Sugiyama Shoko , Asakura Kyoko , Takada Nozomu
Published: December 2019

Background : The role of nurse practitioners (NPs) is always expanding. The Japanese Nurse Practitioner (JNP) system was initiated in 2015 with the goal of shifting some aspects of doctors' work to various other healthcare professionals including nurses. Depending on the way in which JNPs fulfill their roles, a certain degree of efficacy has been exemplified with regard to patients and facility users. NPs are considered legally liable for their medical practice, because they ultimately perform that practice on behalf of a doctor; however, there is a degree of ambiguity in real life. It is necessary to clarify NPs' legal liability, to ensure the safety of medical practice and protect them in medical procedures performed on behalf of physicians. This study aimed to clarify how JNPs fulfill their own legal liability in medical practice. Methods : A qualitative, inductive research design was adopted to record participants’ opinions. The survey was conducted from October 2017 to February 2018. The participants were nurses working as JNPs at general hospitals in eastern Japan. We recruited participants via snowball sampling. Results : With regard to JNPs’ legal liability in their medical practice, three scopes of understanding were observed: “identify whether the JNP has the ability to perform the assigned medical procedure,” “anxiety when performing medical procedures in place of a doctor,” and “follow up medical practice through to the end.” Conclusions : We demonstrated that JNPs fulfilled their own legal liability in medical practice. They were legally responsible for the implementation of medical procedures and had to protect themselves, as their legal position was ambiguous. Moreover, even if JNPs performed legally ambiguous medical procedures, they fulfilled their responsibility as JNP through their actions. Furthermore, JNPs accepted that diagnosis and prescribing could be performed on behalf of doctors if trusting relationships were established with doctors.
Metabolic engineering of Escherichia coli for efficient production of L-alanyl-L-glutamine
Authors: Zhu Jiangming , Yang Wei , Wang Bohua , Liu Qun , Zhong Xiaotong , Gao Quanxiu , Liu Jiezheng , Huang Jianzhong , Lin Baixue , Tao Yong
Published: December 2019

Background: L-alanyl-L-glutamine (AQ) is a functional dipeptide with high water solubility, good thermal stability and high bioavailability. It is widely used in clinical medicine, post-operative rehabilitation, sports health care and other fields. AQ is mainly produced by chemical synthesis which is complicated, time-consuming, labor-consuming, low yield and accompany with by-products. It is highly desirable to develop an efficient biotechnological process for AQ production.Results: A metabolic engineered E. coli strain for AQ production was developed by over-expressing L-amino acid-ligase (BacD) from Bacillus subtilis, peptidases including PepA, PepB, PepD, PepN and dipeptide transport system Dpp were inactivated. In order to use the more readily available substrate, glutamic acid, a glutamine synthetic module from glutamic acid to glutamine was constructed by introducing glutamine synthetase (GlnA), glsA-glsB catalyze the first step in glutamine metabolism and glnE-glnB involved in the ATP-dependent addition of AMP/UMP to a subunit of glutamine synthetase were blocked which resulted in increased glutamine supply. This glutamine synthetic module combined with AQ synthetic module to develope the engineered strain that using glutamic acid and alanine for AQ production. The expression of BacD and GlnA was further balanced to improve the AQ production. The engineered strain p15/AQ10 was used in the whole-cell biocatalysis and 65.6 mM AQ was produced with productivity of 7.29 mM/h and conversion rate of 65.6％.Conclusion: Metabolic engineered strains were developed for AQ production. Strategies including inactivation of peptidases, screening of BacD, introducing glutamine synthetic module, and balancing the glutamine and AQ synthetic modules were applied to improve the yield of AQ. This work provides the biosynthetically industrial potential for efficient production of AQ by microbial cell factory.
First evidence showing that Pepper vein yellows virus P4 protein is a movement protein
Authors: Li Sangsang , Su Xianyang , Luo Xiangwen , Zhang Yu , Zhang Deyong , Du Jiao , Zhang Zhanhong , OuYang Xian , Zhang Songbai , Liu Yong
Published: December 2019

Background Plant viruses move through plasmodesmata (PD) to infect new cells. To overcome the PD barrier, plant viruses have developed specific protein(s) to guide their genomic RNAs or DNAs to path through the PD.Results In the present study, we analyzed the function of Pepper vein yellows virus P4 protein. Our bioinformatic analysis showed that the P4 protein contains an transmembrane domain, encompassing the amino acid residue 117-138. The P4 protein was found to target PD and form small punctates near walls. The P4 deletion mutant or the substitution mutant lost their function to produce punctates near the walls inside the fluorescent loci. The P4-YFP fusion was found to move from cell to cell in infiltrated leaves, and P4 could complement Cucumber mosaic virus movement protein deficiency mutant to move between cells.Conclusion Taking together, we consider that the P4 protein is a movement protein of Pepper vein yellows virus.
Biofilm forming properties of quinolone resistant Escherichia coli from the broiler production chain and their dynamics in mixed biofilms
Authors: Nesse Live L. , Osland Ane Mohr , Mo Solveig Sølverød , Sekse Camilla , Slettemeås Jannice Schau , Bruvoll Anna Eline E. , Urdahl Anne Margrete , Vestby Lene K.
Published: December 2019

Background Quinolone resistant Escherichia coli (QREC) have been found in samples from Norwegian broiler chicken, despite quinolones not being administered to poultry in Norway. Biofilm production may be one factor contributing to the observed persistence in the broiler production chain. In the present study, 158 QREC strains from chicken caecal and retail meat samples were screened for biofilm production in microtiter plates, biofilm morphotype on Congo Red (CR) agar plates and phylotype by multiplex PCR. Furthermore, the dynamics in mixed biofilms with strains of different morphotypes were studied on glass slides and on CR agar plates.Results All strains but one produced biofilm in microtiter plates and/or on CR agar plates at room temperature. There were no differences between strains from chicken caecum and chicken retail meat in the mean amount of biofilm produced in microtiter plates. Furthermore, no differences in biofilm production were observed between phylotypes. However, significant differences in biofilm production were found between biofilm morphotypes. The morphotype RDAR (red dry and rough, which has both curli and cellulose in the matrix, was displayed by 70% of the strains. Mean biofilm production by these strains were significantly higher than by strains with the morphotypes PDAR (pink dry and rough) with only cellulose or BDAR (brown dry and rough) with only curli. Interestingly, the two latter morphotypes produced biofilms with the morphotype RDAR when grown together. None of the strains achieved significantly higher numbers of colony forming units (cfu) in mixed biofilms than in single strain biofilms on glass slides.Conclusions The results indicate that QREC can form biofilm reservoirs on both inert and organic surfaces in production environments, as well as on meat. This may contribute to persistence and dissemination of the strains. Strains with both curli and cellulose in the biofilm matrix were significantly better biofilm formers than strains lacking one of these components. However, strains with only one of the components could compensate for this by producing mixed biofilms with strains having the other component, and thereby most likely enhance their probabilities of persistence in the production environment.
Changes in soil microbial communities at Jinsha earthen site are associated with earthen site degradation
Authors: Li Jing , Zhang Xiaoyue , Xiao Lin , Liu Ke , Li Yue , Zhang Ziwei , Chen Qiang , Ao Xiaolin , Liao Decong , Ma Menggen , Gu Yunfu , Yu Xiumei , Xiang Quanju , Chen Ji , Zhang Xiaoping , Yang Tao , Penttinen Petri , Zhao Ke
Published: December 2019

Background: Jinsha earthen site in Chengdu, China, plays an important role in understanding the ancient culture and history of Shu civilization. The site is undergoing soil degradation due to physical, chemical and biological factors, while very little is known about the influence of biological factors on earthen sites. To investigate the biological factor, we analyzed microbial communities and physicochemical properties from samples with no obvious, mild, moderate and severe degradation, referred to as S1, S2, S3 and S4 sample groups, respectively.Results: Amplicon sequencing targeting the 16S rRNA gene and ITS for bacteria and fungi, respectively, revealed high bacterial and relatively low fungal diversity; the bacterial OTUs were assigned into 36 phyla and 617 genera and the fungal OTUs into 5 phyla and 205 genera. The relative abundances of Bacteroidetes, Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of degradation. In the genus level, the relative abundances of Bacteroides and Ralstonia were higher and that of Rubrobacter lower with higher degree of degradation. The distribution of the fungal genera in the four sample groups seemed more random than that of bacteria; however, the relative abundance of the yeast genus Candida was highest in the severely degraded sample group. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH 4 + , K + , Mg 2+ , Ca 2+ and SO 4 2- .Conclusion: Taken together, the microbial communities in soil with different degree of degradation were distinctly different at Jinsha earthen site, and degradation was accompanied with bigger changes in the bacterial than in the fungal community.
Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production
Authors: Sukumaran Arjun , Geddes-McAlister Jennifer
Published: December 2019

Background: Microbial organisms encounter a variety of environmental conditions, including changes to metal ion availability. Metals ions play an important role in many biological processes for growth and survival. As such, microbes alter their cellular protein regulation and secretion patterns in adaptation to changing environmental conditions. This study focuses on Klebsiella pneumoniae, an opportunistic bacterium responsible for nosocomial infections and by using K. pneumoniae, we aim to determine how a nutrient-limited environment (e.g., zinc) modulates the cellular proteome and secretome of the bacteria. This information will inform on protein-level regulation of bacterial responses to nutritional immunity within the host and improve our understanding of the dynamic and complex relationship between host and pathogen during infection. Results: Analysis of intra- and extracellular changes identified 2,380 proteins from the total cellular proteome (cell pellet) and 246 secreted proteins (supernatant). Specifically, hutC, a repressor of the histidine utilization operon, showed significantl increases abundance under replete conditions, which coincided with an expected reduction in expression of genes within the hut operon from our validation qRT-PCR analysis. Additionally, we characterized a putative cation transport regulator, chaB that was significantly abundant under zinc-replete conditions. Phenotypic analysis of a chaBdeletion strain observe a reduction in capsule production, greater tolerance to high extracellular zinc concentrations, and unimpaired virulence when compared to the WT strain. Conclusions: This is first study to comprehensively profile the impact of zinc availability on the proteome and secretome of K. pneumoniae and uncover a novel connection between zinc transport and capsule production in the bacterial system.
Korean physicians’ perceptions regarding disclosure of patient safety incidents: A cross-sectional study
Authors: Pyo Jeehee , Choi Eun Young , Lee Won , Jang Seung Gyeong , Park Young-Kwon , Ock Minsu , Lee Sang-Il
Published: December 2019

Background: Physicians are in the most critical position vis-à-vis disclosure of patient safety incidents (DPSI), and improper perceptions of DPSI among them could be a major barrier to proper execution of DPSI in clinical practice. The present study investigated physicians’ perceptions regarding the need for, effects of, and barriers to DPSI. Methods: An anonymous online questionnaire survey was conducted to investigate physicians’ perception regarding DPSI, in particular of when DPSI was needed in various situations and of methods for facilitating DPSI. Physicians’ perceptions were then compared to the general public’s perceptions regarding DPSI identified in a previous study, and a chi-squared test was performed to check for statistically significant differences. Results: A total of 910 physicians participated. Most participants (94.9%) agreed that any serious medical error should be disclosed to patients and their caregivers, whereas only 39.8% agreed that even near-miss errors, which did not cause harm to patients, should be disclosed. Among the six known effects of DPSI presented, participating physicians showed the highest level of agreement (89.6%) that “DPSI will lead physicians to pay more attention to patient safety in the future.” Among six barriers to DPSI, participants showed the most agreement (75.9%) that “It is unreasonable to demand DPSI in only the medical field, and disclosure is not actively conducted in other fields.” With respect to methods for facilitating DPSI, participants agreed that “A guideline for DPSI is needed” (91.2%) and “Manpower to support DPSI in hospitals is required” (89.1%). Meanwhile, 79.3% agreed that “If an apology law is enacted, physicians will perform more DPSI” and 72.4% that “I support the introduction of an apology law.” Conclusions: Korean physicians generally have a positive perception of DPSI, but less than the general public. The items used here allow comprehensive examination of physicians’ perceptions regarding DPSI across countries.
Motives of contributing personal data for health research:(Non-)participation in a Dutch biobank
Authors: Broekstra Reinder , Maeckelberghe Els , Aris-Meijer Judith , Stolk Ronald , Otten Sabine
Published: December 2019

Background: Large-scale, centralized data repositories are playing a critical and unprecedented role in fostering innovative health research, leading to new opportunities as well as dilemmas for the medical sciences. Uncovering the reasons as to why citizens do or do not contribute to such repositories, for example, to population-based biobanks, is therefore crucial. We investigated and compared the views of existing participants and non-participants on contributing to large-scale, centralized health research data repositories with those of ex-participants regarding the decision to end their participation. This comparison could yield new insights into motives of participation and non-participation, in particular the behavioural change of withdrawal. Methods: We conducted 36 in-depth interviews with ex-participants, participants, and non-participants of a three-generation, population-based biobank in the Netherlands. The interviews focused on the respondents’ decision-making processes relating to their participation in a large-scale, centralized repository for health research data. Results: The decision of participants and non-participants to contribute to the biobank was motivated by a desire to help others. Whereas participants perceived only benefits relating to their participation and were unconcerned about potential risks, non­-participants and ex-participants raised concerns about the threat of large-scale, centralized public data repositories and public institutes, such as social exclusion or commercialization. Our analysis of ex-participants’ perceptions suggests that intrapersonal characteristics, such as levels of trust in society and public goods, participation conceived as a social norm, and basic societal values account for differences between participants and non-participants. Conclusions: Our findings indicate the fluidity of motives centring on helping others in decisions to participate in large-scale, centralized health research data repositories. Efforts to improve participation should focus on enhancing the trustworthiness of such data repositories and developing layered strategies for communication with participants and with the public. Accordingly, personalized approaches for recruiting participants and transmitting information along with appropriate regulatory frameworks are required, which have important implications for current data management and informed consent procedures.
Endowments or Returns to Endowments or Both? Deciphering Disparities in Childhood Stunting in Bihar, India
Authors: Ghosh Saswata , Sharma Santosh Kumar , Bhattacharya Debarshi
Published: December 2019

Background Unacceptably high rate of childhood stunting for decades remained a puzzle in the Indian state of Bihar, located in the eastern part of the country. Despite various programmatic interventions, nearly half of the under-five children (numerically about 10 million) are still stunted in this resource-constrained state. Data and Methods Using four successive rounds of National Family Health Survey (NFHS) data spread over more than two decades and employing quantile regressions and counterfactual decomposition (QR-CD), the present study aims to assess effects of various endowments as well as returns to those endowments in disparities in childhood stunting over the period. Results The results show that although child’s height-for-age Z-scores (HAZ) disparity was largely accounted for differing levels of endowments during earlier decade, in the later periods, inadequate access to the benefits from various development programmes was also found responsible for HAZ disparities. Moreover, effects of endowments and their returns vary across quantiles. We argue that apart from equalizing endowments, ensuring adequate access to different nutrition-centric programmes are essential to lessen the burden of childhood stunting. Conclusion The state must focus on intersectoral convergence of different schemes in the form of state nutrition mission, and, strengthen nutrition-centric policy processes and their political underpinnings to harness better dividend.
Comprehensive analysis of polygalacturonase family highlights candidate genes related to pollen development and male fertility in wheat (Triticum aestivum L.)
Authors: Ye Jiali , Yang Xuetong , Yang Zhiquan , Li Wei , Liu Qi , Niu Fuqiang , Chen Yanru , Zhang Lingli , Song Xiyue
Published: December 2019

Background: Polygalacturonase (PG) belongs to a large family of hydrolases with important functions in cell separation during plant growth and development via the degradation of pectin. The specific expression of PG genes in anthers may be significant for male sterility research and hybrid wheat breeding, but it has not been characterized in wheat (Triticum aestivum L.). Results: We systematically studied the PG gene family using the latest published wheat reference genomic information. In total, 113 wheat PG genes were identified and renamed as TaPG01–113 based on their chromosomal positions. The PG genes are unequally distributed on 21 chromosomes and classified according to six categories from A–F. Analysis of the gene structures and conserved motifs demonstrated that the Class C and D TaPGs have relatively short gene sequences and a small number of introns. Class E TaPGs are the least conserved and lack conserved domain III. Polyploidy and segmental duplications in wheat were mainly responsible for the expansion of the wheat PG gene family. Predictions of cis-elements indicate that TaPGs have a wide range of functions, including the responses to light, hypothermia, anaerobic conditions, and hormonal stimulation, as well as being involved in meristematic tissue expression. RNA-seq showed that TaPGs have specific temporal and spatial expression characteristics. Twelve spike-specific TaPGs were screened using RNA-seq data and verified by qRT-PCR in the sterile and fertile anthers of thermo-sensitive male-sterile wheat. Four important candidate genes were identified as involved in the male fertility determination process. In fertile anthers, TaPG09 may be involved in the separation of pollen. TaPG87 and TaPG95 could play important roles in anther dehiscence. TaPG93 may be related to pollen development and pollen tube elongation. Conclusions: We analyzed the wheat PG gene family and identified four important TaPGs with differential expression levels in the wheat fertility conversion process. Our findings may facilitate functional investigations of the wheat PG gene family and provide new insights into the fertility conversion mechanism in male-sterile wheat.
The association of dry eye syndrome and psychiatric disorders: a nationwide population-based cohort study
Authors: Liang Chiao-Ying , Cheang Wai-Man , Wang Chun-Yuan , Lin Keng-Hung , Wei Li-Chen , Chen Yu-Yen , Shen Ying-Cheng
Published: December 2019

Background
Several previous studies reported a greater prevalence of dry eye syndrome (DES) among patients with psychiatric diseases. The aim of this study is to investigate the prevalence and risk factors of DES in patients with psychiatric disorders (PD) using nationwide population-based data in Taiwan.
Methods
This population-based cohort study retrospectively identified patients with PD from 1997 to 2011. Patients with both PD and DES served as the DES cohort, and PD patients without DES comprised the non-DES cohort. PD was defined as a diagnosis of PD (ICD-9-CM 290-319) made by psychiatrists only, with at least three consecutive outpatient visits or at least one inpatient visit. DES was defined as a diagnosis of DES (ICD-9-CM 375.15) and a prescription for an eye lubricant (anatomical therapeutic chemical code, ATC code: S01XA). The main outcome measures were the prevalence of DES in these patients and associated risk factors.
Results
A total of 75,650 patients with PD (3,665 in the DES cohort and 71,985 in the non-DES cohort) were included in the final analysis. The majority of patients in the DES group were women (72.6%), compared the non-DES group (57.8%). The mean age of patients in the DES cohort was 62.2 ± 14.9, which was significantly older than those in the non-DES group (50.9 ± 17.5). The patients with DES had a significantly greater likelihood of having dementia, bipolar disorder, depression, and neurotic disorders. Conditional regression analyses revealed that patients with dry eye disease were more likely to have schizophrenia (OR = 1.34), bipolar disorder (OR = 1.9), depression (OR = 1.54), and neurotic disorders (OR = 1.62). In addition, patients with DES were more likely to use 1st generation anti-psychotics (OR=1.28) and had a lower risk of using 2nd generation anti-psychotics (OR=0.64)
Conclusion
The study demonstrated that among PD patients, DES is highly prevalence in certain subtypes of PD, such as depression, bipolar disorder, and neurotic disorders, after adjusting for the comorbidities.
The PICO Study: Impact of Phenylalanine on Cognitive, Cerebral and Neurometabolic Parameters in Adult Patients with Phenylketonuria: a Randomized, Placebo-Controlled, Crossover, Non-inferiority Trial
Authors: Trepp Roman , Muri Raphaela , Abgottspon Stephanie , Bosanska Lenka , Hochuli Michel , Slotboom Johannes , Kreis Roland , Rummel Christian , Everts Regula
Published: December 2019

Background
The population of adult patients with early-treated phenylketonuria (PKU) following newborn screening is growing substantially. The ideal target range of blood Phenylalanine (Phe) levels in adults outside pregnancy is a matter of debate. Therefore, prospective intervention studies are needed to evaluate the effects of an elevated Phe concentration on cognition and structural, functional and neurometabolic parameters of the brain.

Methods
The PICO (Phenylalanine and Its Impact on Cognition) Study evaluates the effect of a 4-week Phe load on cognition and cerebral parameters in adults with early-treated PKU in a double-blind, randomized, placebo-controlled, crossover, non-inferiority trial.

Participants: 30 adult patients with early-treated PKU and 30 healthy controls comparable to patients with regard to age, sex and educational level will be recruited from the University Hospitals Bern and Zurich, Switzerland. Patients are eligible for the study if they are age ≥18 years and have PKU diagnosed after a positive newborn screening and treated with a Phe-restricted diet starting within the first 30 days of life.

Intervention: The cross-over intervention consists of a 4-week oral Phe or placebo administration in patients with PKU. The study design mimics a Phe-restricted and a Phe-unrestricted diet using a double-blinded, placebo-controlled approach.

Objectives: The primary objective of the PICO Study is to prospectively assess whether a temporarily elevated Phe-level influences cognitive performance (working memory assessed with a n-back task) in adults with early-treated PKU. As secondary objective, the PICO Study will elucidate cerebral (fMRI: neural activation during a n-back task; rsfMRI: functional connectivity at rest; DTI: white matter integrity; ASL: cerebral blood flow) and neurometabolic mechanisms (cerebral Phe-level), which accompany changes in Phe concentration. Cognition, structural and functional parameters of the brain of adult patients with early-treated PKU will be cross-sectionally compared to healthy controls. All assessments will take place at the University Hospital Bern, Switzerland.

Randomization: Central randomization will be used to assign participants to the different treatment arms with age, sex and center serving as stratification factors. Randomization lists will be generated by an independent statistician.

Blinding: All trial personnel but the statistician generating the randomization list and the personnel at the facility preparing the interventional product are blinded to the assigned treatment.
On‐Farm Research: Experimental Approaches, Analytical Frameworks, Case Studies, and Impact
Authors: Kyveryga Peter M.
Published: December 2019

On‐farm research is becoming widespread due to a growing interest among farmers, agronomists and the research community. While the concept of on‐farm research is not new, the scale and influence of on‐farm studies conducted by farmers in partnership with industry and university researchers are expanding. New technologies, tools, and analytical approaches are rapidly evolving to advance the reach and impact of on‐farm research. Papers in this special issue include the use of on‐farm testing to increase economic and environmental sustainability in Africa and South America, the development of a new analytical collaborative frameworks for better summarization, visualization and communication of research results, and a new analytical approaches based on Bayesian hierarchical and multivariate analyses that can be used to assess complex relationships between management, genetics, soils, and the environment. Simulation approaches were also tested to identify the most efficient experimental designs and estimation methods of statistical parameters. In all situations, on‐farm research leads to improved productivity, better economics, higher adoption of conservation practice and greater farmer satisfaction.

Core Ideas

Precision agriculture technology adoption benefits on‐farm research expansion.

New analytical and visual frameworks aid in farmer decision making.

On‐farm research reduces barriers to adoption of new management techniques.

On‐farm research increases farmer interest and motivation.
Enigmatic diamonds from the Tolbachik volcano, Kamchatka
Authors: Galimov Erik M. , Kaminsky Felix V. , Shilobreeva Svetlana N. , Sevastyanov Vyacheslav S. , Voropaev Sergei A. , Khachatryan Galina K. , Wirth Richard , Schreiber Anja , Saraykin Vladimir V. , Karpov Gennady A. , Anikin Leonid P.
Published: December 2019

Approximately 700 diamond crystals were identified in volcanic (mainly pyroclastic) rocks of the Tolbachik volcano, Kamchatka, Russia. They were studied with the use of SIMS, scanning and transmission electron microscopy, and utilization of electron energy loss spectroscopy and electron diffraction. Diamonds have cube-octahedral shape and extremely homogeneous internal structure. Two groups of impurity elements are distinguished by their distribution within the diamond. First group, N and H, the most common structural impurities in diamond, are distributed homogeneously. All other elements observed (Cl, F, O, S, Si, Al, Ca, and K) form local concentrations, implying the existence of inclusions, causing high concentrations of these elements. Most elements have concentrations 3–4 orders of magnitude less than chondritic values. Besides N and H, Si, F, Cl, and Na are relatively enriched because they are concentrated in micro- and nanoinclusions in diamond. Mineral inclusions in the studied diamonds are 70–450 nm in size, round- or oval-shaped. They are represented by two mineral groups: Mn-Ni alloys and silicides, with a wide range of concentrations for each group. Alloys vary in stoichiometry from MnNi to Mn2Ni, with a minor admixture of Si from 0 to 5.20–5.60 at%. Silicides, usually coexisting with alloys, vary in composition from (Mn,Ni)4Si to (Mn,Ni)5Si2 and Mn5Si2, and further to MnSi, forming pure Mn-silicides. Mineral inclusions have nanometer-sized bubbles that contain a fluid or a gas phase (F and O). Carbon isotopic compositions in diamonds vary from –21 to –29‰ δ13CVPDB (avg. = –25.4). Nitrogen isotopic compositions in diamond from Tolbachik volcano are from –2.32 to –2.58‰ δ15NAir. Geological, geochemical, and mineralogical data confirm the natural origin of studied Tolbachik diamonds from volcanic gases during the explosive stage of the eruption.