bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of linear epitopes in SjSP-13 of Schistosoma japonicum using a GST-peptide fusion protein microplate array
Authors: Ma Li , Zhao Wenrong , Hou Xunya , Liu Mengmeng , Li Yanna , Shen Li , Xu Xindong
Published: October 2019

Background

The identification and characterization of epitopes facilitate the discovery and development of new therapeutics, vaccines and diagnostics for infectious diseases. In this study, we developed a glutathione S-transferase (GST)-peptide fusion protein microplate array for the identification of linear B-cell epitopes and applied this novel method to the identification of linear B-cell epitopes of SjSP-13, an immunodiagnostic biomarker of schistosomiasis japonica.

Methods

SjSP-13 was divided into 17 overlapped peptides (p1-17), and the coding sequence of each peptide was obtained by annealing two complementary oligonucleotides. SjSP-13 peptides were expressed by fusion with an N-terminal GST tag and a C-terminal 6xHis tag. The GST-peptide-His fusion protein was specifically bound to the Immobilizer Glutathione MicroWell 96-well plates without purification. SjSP-13 peptides and core epitopes that could be recognized by sera from schistosomiasis patients were identified by ELISA and confirmed by Western blot analysis. The receiver operating characteristic (ROC) analysis was performed to determine the diagnostic validity of the identified peptide.

Results

Full-length GST-peptide-His fusion proteins were successfully expressed and specifically bound to the Immobilizer Glutathione MicroWell 96-well plates. Two adjacent peptides (p7 and p8) were found to be highly immunogenic in humans. The core epitope of p7 and p8 is an 11-aa peptide (80KCLDVTDNLPE90) and an 8-aa peptide (90EKIIQFAE97), respectively. The area under the ROC curve (AUC) value of the peptide which contains the two identified epitopes is 0.947 ± 0.019. The diagnostic sensitivity and specificity of the peptide is 76.7% (95% CI: 68.8–84.5%) and 100%, respectively.

Conclusions

90EKIIQFAE97 and 80KCLDVTDNLPE90 are the two linear epitopes of SjSP-13 recognized by patient sera, and could be potential serological markers for schistosomiasis japonica.
In silico selection of functionally important proteins from the mialome of Ornithodoros erraticus ticks and assessment of their protective efficacy as vaccine targets
Authors: Pérez-Sánchez Ricardo , Manzano-Román Raúl , Obolo-Mvoulouga Prosper , Oleaga Ana
Published: October 2019

Background

New candidate protective antigens for tick vaccine development may be identified by selecting and testing antigen candidates that play key biological functions. After blood-feeding, tick midgut overexpresses proteins that play essential functions in tick survival and disease transmission. Herein,Ornithodoros erraticusmidgut transcriptomic and proteomic data were examined in order to select functionally significant antigens upregulated after feeding to be tested as vaccine candidate antigens.

Methods

Transcripts annotated as chitinases, tetraspanins, ribosomal protein P0 and secreted proteins/peptides were mined from the recently publishedO. erraticusmidgut transcriptome and filtered in a second selection step using criteria based on upregulation after feeding, predicted antigenicity and expression in the midgut proteome. Five theoretical candidate antigens were selected, obtained as recombinant proteins and used to immunise rabbits: one chitinase (CHI), two tetraspanins (TSPs), the ribosomal protein P0 (RPP0) and one secreted protein PK-4 (PK4).

Results

Rabbit vaccination with individual recombinant candidates induced strong humoral responses that mainly reduced nymph moulting and female reproduction, providing 30.2% (CHI), 56% (TSPs), 57.5% (RPP0) and 57.8% (PK4) protection toO. erraticusinfestations and 19.6% (CHI), 11.1% (TSPs), 0% (RPP0) and 8.1% (PK4) cross-protection to infestations by the African tickOrnithodoros moubata.The joint vaccine efficacy of the candidates was assessed in a second vaccine trial reaching 66.3% protection toO. erraticusand 25.6% cross-protection toO. moubata.

Conclusions

These results (i) indicate that argasid chitinases and RPP0 are promising protective antigens, as has already been demonstrated for ixodid chitinases and RPP0, and could be included in vaccines targeting multiple tick species; (ii) reveal novel protective antigens tetraspanins and secreted protein PK-4, never tested before as protective antigens in ticks; and (iii) demonstrate that multi-antigenic vaccines increased vaccine efficacy compared with individual antigens. Lastly, our data emphasize the value of the tick midgut as a source of protective candidate antigens in argasids for tick control.
DNA methylation in repeat negative prostate biopsies as a marker of missed prostate cancer
Authors: Fiano Valentina , Zugna Daniela , Grasso Chiara , Trevisan Morena , Delsedime Luisa , Molinaro Luca , Cassoni Paola , Papotti Mauro , Merletti Franco , Akre Olof , Pettersson Andreas , De Marco Laura , Richiardi Lorenzo
Published: October 2019

Background

Men often undergo repeat prostate biopsies because of suspicion of missed cancer. We assessed if (i) methylation of selected genes in prostate tissue vary with aging and (ii) methylation alterations in repeat biopsies predict missed prostate cancer.

Methods

We conducted a case-control study among men who underwent at least two negative prostate biopsies followed by a sampling either positive (cases n = 111) or negative (controls n = 129) for prostate cancer between 1995 and 2014 at the University Hospital (Turin, Italy). Two pathology wards were included for replication purposes. We analyzed methylation of GSTP1, APC, PITX2, C1orf114, GABRE, and LINE-1 in the first two negative biopsies. Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) of the association between genes methylation and prostate cancer.

Results

Age at biopsy and time interval between the two negative biopsies were not associated with methylation levels of the selected genes in neither cases nor controls. GSTP1 methylation in the first and in the second negative biopsy was associated with prostate cancer detection [OR per 1% increase: 1.14 (95% CI 1.01–1.29) for the second biopsy and 1.21 (95% CI 1.07–1.37) for the highest methylation level (first or second biopsy)]. A threshold > 10% for GSTP1 methylation corresponded to a specificity of 0.98 (positive likelihood ratio 7.87). No clear association was found for the other genes. Results were consistent between wards.

Conclusions

Our results suggest that GSTP1 methylation in negative prostate biopsies is stable over time and can predict missed cancer with high specificity.
Using weaker consistency models with monitoring and recovery for improving performance of key-value stores
Authors: Nguyen Duong , Charapko Aleksey , Kulkarni Sandeep S. , Demirbas Murat
Published: October 2019

Consistency properties provided by most key-value stores can be classified into sequential consistency and eventual consistency. The former is easier to program with but suffers from lower performance whereas the latter suffers from potential anomalies while providing higher performance. We focus on the problem of what a designer should do if he/she has an algorithm that works correctly with sequential consistency but is faced with an underlying key-value store that provides a weaker (e.g., eventual or causal) consistency. We propose a detect-rollback based approach: The designer identifies a correctness predicate, say P, and continues to run the protocol, as our system monitors P. If P is violated (because the underlying key-value store provides a weaker consistency), the system rolls back and resumes the computation at a state where P holds.We evaluate this approach with graph-based applications running on the Voldemort key-value store. Our experiments with deployment on Amazon AWS EC2 instances show that using eventual consistency with monitoring can provide a 50–80% increase in throughput when compared with sequential consistency. We also observe that the overhead of the monitoring itself was low (typically less than 4%) and the latency of detecting violations was small. In particular, in a scenario designed to intentionally cause a large number of violations, more than 99.9% of violations were detected in less than 50 ms in regional networks (all clients and servers in the same Amazon AWS region) and in less than 3 s in global networks.We find that for some applications, frequent rollback can cause the program using eventual consistency to effectively stall. We propose alternate mechanisms for dealing with re-occurring rollbacks. Overall, for applications considered in this paper, we find that even with rollback, eventual consistency provides better performance than using sequential consistency.
Updating PET/CT performance standards and PET/CT interpretation criteria should go hand in hand
Authors: Boellaard Ronald , Sera Terez , Kaalep Andres , Hoekstra Otto S. , Barrington Sally F. , Zijlstra Josée M.
Published: October 2019

This letter aims at explaining that adjusting the performance of PET/CT systems to a new standard also requires updating of interpretation criteria. Simply changing one aspect of the imaging procedure, i.e., PET/CT performance and image quality, and not adapting interpretation criteria will result in an increase of false positive (or negative) reads.
Camel milk production and marketing: Pastoral areas of Afar, Ethiopia
Authors: Gebremichael Belets , Girmay Shishay , Gebru Mu’uz
Published: October 2019

Dromedary camels produce more milk for a longer period of time than any other milk animal held under the same harsh conditions. Produced milk is a primary source of some pastoralists’ food, nutrition and income security all year round. However, there are limited research efforts on exploiting camel milk potential and its promotion for consumption and marketing. Thus, a cross-sectional survey was conducted on 100 camel herders; nine traders and three cooperatives during March to April 2017 in Afar region of Ethiopia. Besides, discussions were held with district leaders, end consumers and local elders. Collected data were analysed using descriptive statistical tools, figures and diagrams. The survey result revealed that 56.6% camel herds were lactating. Milking was done by men twice (67%) and three times (33%) per day with an average of 4.2 L per camel. A total of 82% of the camel herders were marketers, and women were dominant. Camel herders sold an average of 14.3 L milk per day at an average price of USD 0.95 per litre, whereas middlemen sold an average of 35.8 L at USD 1.22 per litre. The milk trade was done at herders’ farm gate (18.3%), main road-sides (58.5%) and nearest towns (23.2%) using small plastic pots (68.3%) and plastic jerrycans (31.7%). Amongst the three marketing channels, 69.9% of the milk was directly sold to end consumers and fetched a higher price than other marketing channels, but the routes are limited to local markets. The camel herders perceived that they satisfied with milk for its nutritional, medicinal, social and economic values. Therefore, interventions need to focus on exploiting opportunities, addressing challenges/constraints in camel milk production and its marketing chain efficiency and effectiveness.
Modeling the relationship between network operators and venue owners in public Wi-Fi deployment using non-cooperative game theory
Authors: Spruytte Jonathan , Benhamiche Amal , Chardy Matthieu , Verbrugge Sofie , Colle Didier
Published: October 2019

Wireless data demands keep rising at a fast rate. In 2016, Cisco measured a global mobile data traffic volume of 7.2 Exabytes per month and projected a growth to 49 Exabytes per month in 2021. Wi-Fi plays an important role in this as well. Up to 60% of the total mobile traffic was off-loaded via Wi-Fi (and femtocells) in 2016. This is further expected to increase to 63% in 2021. In this publication, we look into the roll-out ofpublicWi-Fi networks, public meaning in a public or semi-public place (pubs, restaurants, sport stadiums, etc.). More concretely we look into the collaboration between two parties, a technical party and a venue owner, for the roll-out of a new Wi-Fi network. The technical party is interested in reducing load on its mobile network and generating additional direct revenues, while the venue owner wants to improve the attractiveness of the venue and consequentially generate additional indirect revenues. Three Wi-Fi pricing models are considered: entirely free, slow access with ads or fast access via paid access (freemium), and paid access only (premium). The technical party prefers a premium model with high direct revenues, the venue owner a free/freemium model which is attractive to its customers, meaning both parties have conflicting interests. This conflict has been modeled using non-cooperative game theory incorporating detailed cost and revenue models for all three Wi-Fi pricing models. The initial outcome of the game is a premium Wi-Fi network, which is not the optimal solution from an outsider’s perspective as a freemium network yields highest total payoffs. By introducing an additional compensation scheme which corresponds with negotiation in real life, the outcome of the game is steered toward a freemium solution.
An efficient storage and service method for multi-source merging meteorological big data in cloud environment
Authors: Yang Ming , He Wenchun , Zhang Zhiqiang , Xu Yongjun , Yang Heping , Chen Yufeng , Xu Xiaolong
Published: October 2019

With the development of the meteorological IoT (Internet of Things) and meteorological sensing network, the collected multi-source meteorological data have the characteristics of large amount of information, multidimensional and high accuracy. Cloud computing technology has been applied to the storage and service of meteorological big data. Although the constant evolution of big data storage technology is improving the storage and access of meteorological data, storage and service efficiency is still far from meeting multi-source big data requirements. Traditional methods have been used for the storage and service of meteorological data, and a number of problems still persist, such as a lack of unified storage structure, poor scalability, and poor service performance. In this study, an efficient storage and service method for multidimensional meteorological data is designed based on NoSQL big data storage technology and the multidimensional characteristics of meteorological data. In the process of data storage, multidimensional block compression technology and data structures are applied to store and transmit meteorological data. In service, heterogeneous NoSQL common components are designed to improve the heterogeneity of the NoSQL database. The results show that the proposed method has good storage transmission efficiency and versatility, and can effectively improve the efficiency of meteorological data storage and service in meteorological applications.
Image steganography based on color palette transformation in color space
Authors: Margalikas Eugenijus , Ramanauskaitė Simona
Published: October 2019

In this paper, we present a novel image steganography method which is based on color palette transformation in color space. Most of the existing image steganography methods modify separate image pixels, and random noise appears in the image. By proposing a method, which changes the color palette of the image (all pixels of the same color will be changed to the same color), we achieve a higher user perception. Presented comparison of stegoimage quality metrics with other image steganography methods proved the new method is one of the best according to Structural Similarity Index (SSIM) and Peak Signal Noise Ratio (PSNR) values. The capability is average among other methods, but our method has a bigger capacity among methods with better SSIM and PSNR values. The color and pixel capability can be increased by using standard or adaptive color palette images with smoothing, but it will increase the embedding identification possibility.
Interpersonal psychotherapy for perinatal women: a systematic review and meta-analysis protocol
Authors: Bright Katherine S. , Charrois Elyse M. , Mughal Muhammad Kashif , Wajid Abdul , McNeil Deborah , Stuart Scott , Hayden K. Alix , Kingston Dawn
Published: October 2019

Background

Interpersonal psychotherapy (IPT) is an intervention that has established efficacy in the prevention and treatment of depressive disorders. Previous systematic reviews have not evaluated the effectiveness of IPT on symptoms of stress, anxiety, depression, quality of life, relationship satisfaction/quality, social supports, and an improved psychological sense of well-being. There is limited data regarding factors that moderate and mediate the effectiveness of IPT including the timing of the intervention or the mode of delivery of IPT intervention. The objective of this systematic review and meta-analysis is to evaluate the effectiveness, feasibility, and acceptability of IPT interventions to treat perinatal psychological distress and to summarize the evidence on predictors, mediators, and moderators of IPT.

Methods

We will include peer-reviewed studies that recruited perinatal women. The search strategy will involve the following databases: MEDLINE (Ovid), EMBASE (Ovid), PsycINFO (Ovid), Cochrane Central Register of Controlled Trials (Ovid), CINAHL with Full Text (EBSCO), Social Work Abstracts (EBSCO), SocINDEX with Full Text (EBSCO), Academic Search Complete (EBSCO), Family & Society Studies Worldwide (EBSCO), Family Studies Abstracts (EBSCO), and Scopus. Study inclusion criteria include (1) randomized controlled trials, quasi-experimental studies, and pre-post studies that evaluated the effectiveness of IPT; (2) qualitative studies that evaluated feasibility and acceptability of IPT; (3) study sample included and analyzed perinatal women; and (4) publication language was English. Using pilot-tested screening and data extraction forms, two reviewers will independently review studies in three steps: (1) abstract/title screening, (2) full-text screening of potentially accepted studies, and (3) data extraction of accepted studies. Disagreements will be resolved by a third reviewer. Studies will be aggregated for meta-synthesis and meta-analysis should the data allow for this. Two independent reviewers will grade methodological quality.

Discussion

Findings from this review will inform future development and implementation of IPT intervention research for perinatal women. Identifying key factors of successful IPT interventions will inform intervention design and adaptation of IPT interventions to increase the likelihood that perinatal women will engage in and benefit from IPT interventions. This review will also identify key considerations for increasing the effectiveness of IPT interventions during the perinatal period.

Systematic review registration

PROSPEROCRD42019114292
Impact of interventions on work-related outcomes for individuals with musculoskeletal injuries after road traffic crash: a systematic review protocol
Authors: Brakenridge Charlotte L. , Gane Elise M. , Smits Esther J. , Andrews Nicole E. , Johnston Venerina
Published: October 2019

Background

Musculoskeletal injuries are the most common non-fatal injury from road traffic crashes. Even when the injuries are mild, they can cause pain which can affect return to work rates and work ability post-crash. Workplace output losses are the biggest cost from traffic crash-related injuries. There is a need to identify effective interventions that can improve work-related outcomes (e.g. time to return to work, sick leave, and work ability) in this group and a need to understand the intervention components, external factors, and participant characteristics that may be associated with improvement.

Methods

A systematic review will be conducted using seven databases and search terms related to road traffic crash, musculoskeletal injury, work-related outcomes, and study design. Intervention studies will be eligible if they report on at least one work-related outcome, include adults with a traffic crash-related musculoskeletal injury (e.g. fracture or whiplash), include a comparison group, and are written in English. Interventions can be medical, therapeutic, work-based, multicomponent, or other. Two researchers will independently screen titles and abstracts, review full texts for inclusion in the review, and perform the data extraction. The main outcomes of the review will be time until return to work and duration of sick leave. The results will be narratively described, with meta-analyses conducted where possible.

Discussion

This review will explore the effectiveness of interventions in individuals with traffic crash-related musculoskeletal injury on work-related outcomes and will act as a useful source for researchers, policy makers, and stakeholders when developing and implementing interventions in this group.

Systematic review registration

PROSPEROCRD42018103746
Effectiveness and safety of inpatient versus extended venous thromboembolism (VTE) prophylaxis with heparin following major pelvic surgery for malignancy: protocol for a systematic review
Authors: Heijkoop Bridget , Parker Natalie , Kiroff George , Spernat Daniel
Published: October 2019

Background

Venous thromboembolism (VTE) is a common postoperative complication associated with significant morbidity and mortality. The use of prophylactic heparin postoperatively reduces this risk, and the use of extended duration prophylaxis is becoming increasingly common. Malignancy and pelvic surgery both independently further increase the risk of postoperative VTE and patients undergoing major pelvic surgery for malignancy are at particularly high risk of VTE. However, the optimum duration of prophylaxis specifically in this population currently remains unclear.

Methods

We will conduct a systematic review of literature in accordance with the Cochrane Handbook for Systematic Reviews of Interventions (Higgins JPT, Green S. Cochrane Handbook for Systematic Reviews of Interventions version 5.1.0.,2011) to evaluate current evidence of the effectiveness and safety of inpatient versus extended VTE prophylaxis with heparin (all forms) following major pelvic surgery for malignancy. We will search PubMed, EMBASE, and the Cochrane Library. Regarding safety, Food and Drug Administration (FDA), and Therapeutic Goods Administration (TGA) websites will be searched, including all levels of evidence. Results will be the postoperative timeframe in which a VTE event can be considered to have been provoked by the surgery, and the number of patients needed to treat with both inpatient and extended prophylaxis to prevent a VTE event in this timeframe, comparing these to determine if there is a significant benefit from extended prophylaxis.

Discussion

This systematic review will aim to identify the postoperative period in which patients undergoing major pelvic surgery for malignancy are at further increased risk of VTE as a result of their surgery and the optimum duration of heparin VTE prophylaxis with heparin to reduce this risk. Determining this will allow evidence-based recommendations to be made for the optimum duration of heparin VTE prophylaxis post major pelvic surgery for malignancy, leading to improved standards of care that are consistent between different providers and institutions.

Systematic review registration

In accordance with guidelines, our systematic review was submitted to PROSPERO for consideration of registration on 16/12/17 and was registered on 12/1/18 with the registration number CRD42018068961, and it was last updated on December 1, 2018.
Clinical, microbiological, and molecular epidemiological characteristics of Klebsiella pneumoniae-induced pyogenic liver abscess in southeastern China
Authors: Zhang Siqin , Zhang Xiucai , Wu Qing , Zheng Xiangkuo , Dong Guofeng , Fang Renchi , Zhang Yizhi , Cao Jianming , Zhou Tieli
Published: October 2019

Background

Klebsiella pneumoniae-induced pyogenic liver abscess (KP-PLA) has emerged as a life-threatening disease worldwide. However, to date, a limited number of scholars have attempted to systematically elucidate the characteristics of KP-PLA. The aim of the present study was to analyze clinical, microbiological, and molecular epidemiological characteristics of KP-PLA patients in Southeastern China.

Methods

The KP-PLA cases from a tertiary teaching hospital in China from January 2016 to December 2017 were systemically studied and elucidated comprehensively. The virulence factors, resistant spectrum, and clones of K. pneumoniae isolates were identified with string test, polymerase chain reaction (PCR), antimicrobial susceptibility test, and multilocus sequence typing. Moreover, the characteristics in KP-PLA patients with and without other hepatobiliary diseases (OHD) were also been compared.

Results

A total of 163 KP-PLA cases were enrolled, in which the majority of those cases were senior males, and often associated with multiple underlying diseases, including diabetes (49.7%). The remaining cases belonged to healthy individuals (50.3%). The clinical symptoms were common but nonspecific, characterized by increased inflammatory parameters and abnormal liver function parameters. The abscess was often right-sided solitary presentation (58.3%). Cephalosporin or carbapenem plus metronidazole combined with percutaneous puncture or catheter drainage were favorable therapeutics. Although low resistance rates of commonly used antimicrobial drugs (< 10%) were observed, twelve strains were identified as multidrug resistant (MDR) strains, and were mainly isolated from the OHD patients. The hypermucoviscosity, as well as K1 and K2 serotypes accounted for 30.7, 40.5, and 19.0%, respectively. Except for iroN (24.5%) and magA (45.4%), the high prevalence of virulence genes (e.g. aerobactin, rmpA, mrkD, fimH, uge, ureA, entB, ybtA, kfuBC, and wcaG) was identified (68.7–100.0%). Additionally, ST23 was found as a predominant sequence type (ST; 38.7%), and three novel STs (ST3507, ST3508 and ST3509) were noted as well.

Conclusions

The present study reported the abundant hvKp strains in KP-PLA, as well as convergence of hypervirulent and MDR K. pneumoniae isolates from the KP-PLA patients, particularly those cases with OHD. Given the various clinical manifestations and destructive pathogenicity, determination of the comprehensive characteristics of such isolates is highly essential to effectively carry out for optimal management and treatment of KP-PLA.
Genomic characterization of Citrobacter freundii strains coproducing OXA-48 and VIM-1 carbapenemase enzymes isolated in leukemic patient in Spain
Authors: Lalaoui Rym , Djukovic Ana , Bakour Sofiane , Hadjadj Linda , Sanz Jaime , Salavert Miguel , López-Hontangas Jose Luis , Sanz Miguel A. , Ubeda Carles , Rolain Jean-Marc
Published: October 2019

Background

The emergence of carbapenemase-producing (CP) Citrobacter freundii poses a significant threat to public health, especially in high-risk populations. In this study, whole genome sequencing was used to characterize the carbapenem resistance mechanism of three C. freundii clinical isolates recovered from fecal samples of patients with acute leukemia (AL) from Spain.

Materials and methods

Twelve fecal samples, collected between 2013 and 2015 from 9 patients with AL, were screened for the presence of CP strains by selecting them on MacConkey agar supplemented with ertapenem (0.5 mg/L). Bacteria were identified by MALDI-TOF mass spectrometry and were phenotypically characterized. Whole genome sequencing of C. freundii isolates was performed using the MinION and MiSeq Illumina sequencers. Bioinformatic analysis was performed in order to identify the molecular support of carbapenem resistance and to study the genetic environment of carbapenem resistance encoding genes.

Results

Three carbapenem-resistant C. freundii strains (imipenem MIC≥32 mg/L) corresponding to three different AL patients were isolated. Positive modified Carba NP test results suggested carbapenemase production. The genomes of each C. freundii tested were assembled into a single chromosomal contig and plasmids contig. In all the strains, the carbapenem resistance was due to the coproduction of OXA-48 and VIM-1 enzymes encoded by genes located on chromosome and on an IncHI2 plasmid, respectively. According to the MLST and the SNPs analysis, all strains belonged to the same clone ST169.

Conclusion

We report in our study, the intestinal carrying of C. freundii clone ST169 coproducing OXA-48 and VIM-1 identified in leukemic patients.
A conceptual framework for the phylogenetically constrained assembly of microbial communities
Authors: Aguirre de Cárcer Daniel
Published: October 2019

Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs’ identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.
Network vulnerability‐based and knowledge‐guided identification of microRNA biomarkers indicating platinum resistance in high‐grade serous ovarian cancer
Authors: Qi Xin , Yu Chunjiang , Wang Yi , Lin Yuxin , Shen Bairong
Published: October 2019

Background

High‐grade serous ovarian cancer (HGSC), the most common ovarian carcinoma type, is associated with the highest mortality rate among all gynecological malignancies. As chemoresistance has been demonstrated as the major challenge in improving the prognosis of HGSC patients, we here aimed to identify microRNA (miRNA) biomarkers for predicting platinum resistance and further explore their functions in HGSC.

Results

We developed and applied our network vulnerability‐based and knowledge‐guided bioinformatics model first time for the study of drug‐resistance in cancer. Four miRNA biomarkers (miR‐454‐3p, miR‐98‐5p, miR‐183‐5p and miR‐22‐3p) were identified with potential in stratifying platinum‐sensitive and platinum‐resistant HGSC patients and predicting prognostic outcome. Among them, miR‐454‐3p and miR‐183‐5p were newly discovered to be closely implicated in platinum resistance in HGSC. Functional analyses highlighted crucial roles of the four miRNA biomarkers in platinum resistance through mediating transcriptional regulation, cell proliferation and apoptosis. Moreover, expression patterns of the miRNA biomarkers were validated in both platinum‐sensitive and platinum‐resistant ovarian cancer cells.

Conclusions

With bioinformatics modeling and analysis, we identified and confirmed four novel putative miRNA biomarkers, miR‐454‐3p, miR‐98‐5p, miR‐183‐5p and miR‐22‐3p that could serve as indicators of resistance to platinum‐based chemotherapy, thereby contributing to the improvement of chemotherapeutic efficiency and optimization of personalized treatments in HGSC.
Vigilante Innovation (VIX): case study on the development of student skills through a team-based design process and environment
Authors: Oliver Kendra H. , Ehrman Jonathan D. , Marasco Christina C.
Published: October 2019

Background

Many undergraduate students majoring in science, technology, engineering, and mathematics (STEM) fields lack experience in collaborative thinking, limiting their effectiveness as they enter careers in academic and industrial environments. The SyBBURE Searle Undergraduate Research Program has incorporated a team-based design component into its curriculum to fill this gap in training. This design framework, called Vigilante Innovation (VIX) to highlight its emphasis on self-initiation and action, has evolved into a multi-semester-long group undertaking that combines just-in-time training in entrepreneurship and project design with student-driven collaborations aimed at solving a real-world problem. We hypothesize that this framework provides a hands-on, realistic workplace simulation task through which students can develop an understanding of teamwork.

Results

Using a case-study approach, we discuss the development of the VIX design framework since its inception in 2014 and assess the impact of the VIX framework on student learning and growth using a student survey from 2016 to 2017 and student interviews from 2018.

Conclusions

A flexible approach, an annualized project timeline, a student-driven prototyping space, and self-selecting project areas emerged as key contributors to the successful implementation of the VIX design and to deepened student learning. The diversity of VIX teams, the self-reported success of student projects, and student interviews indicate that students who participate in VIX possess an in-depth understanding of team-based strategies. These findings support the VIX framework as an effective method of providing undergraduates in STEM fields with efficient and meaningful exposure to the team-based entrepreneurial skills that are vital in their future careers. Additional work is needed to determine if this approach has a long-term impact on student success in team-based environments. The website vigilanteinnovation.com houses a customizable, freely available version of the design guide for educators and innovators alike.
Increased mortality in elderly patients with acute respiratory distress syndrome is not explained by host response
Authors:   the MARS consortium, Schouten Laura R. A. , Bos Lieuwe D. J. , Serpa Neto A. , van Vught Lonneke A. , Wiewel Maryse A. , Hoogendijk Arie J. , Bonten Marc J. M. , Cremer Olaf L. , Horn Janneke , van der Poll Tom , Schultz Marcus J. , Wösten-van Asperen Roelie M.
Published: October 2019

Background

Advanced age is associated with increased mortality in acute respiratory distress syndrome (ARDS) patients. Preclinical studies suggest that the host response to an injurious challenge is age-dependent. In ARDS patients, we investigated whether the association between age and mortality is mediated through age-related differences in the host response.

Methods

This was a prospective longitudinal observational cohort study, performed in the ICUs of two university-affiliated hospitals. The systemic host response was characterized in three predefined age-groups, based on the age-tertiles of the studied population: young (18 to 54 years, N = 209), middle-aged (55 to 67 years, N = 213), and elderly (67 years and older, N = 196). Biomarkers of inflammation, endothelial activation, and coagulation were determined in plasma obtained at the onset of ARDS. The primary outcome was 90-day mortality. A mediation analysis was performed to examine whether age-related differences in biomarker levels serve as potential causal pathways mediating the association between age and mortality.

Results

Ninety-day mortality rates were 30% (63/209) in young, 37% (78/213) in middle-aged, and 43% (84/196) in elderly patients. Middle-aged and elderly patients had a higher risk of death compared to young patients (adjusted odds ratio, 1.5 [95% confidence interval 1.0 to 2.3] and 2.1 [1.4 to 3.4], respectively). Relative to young patients, the elderly had significantly lower systemic levels of biomarkers of inflammation and endothelial activation. Tissue plasminogen activator, a marker of coagulation, was the only biomarker that showed partial mediation (proportion of mediation, 10 [1 to 28] %).

Conclusion

Little evidence was found that the association between age and mortality in ARDS patients is mediated through age-dependent differences in host response pathways. Only tissue plasminogen activator was identified as a possible mediator of interest.

Trial registration

This trial was registered at ClinicalTrials.gov (identifier NCT01905033, date of registration July 23, 2013).
Differential cell stress responses to food availability by the nestlings of Asian Short-toed Lark (Calandrella cheleensis)
Authors: Zhang Liang , Zhao Lidan , Zhang Xinjie , Liang Wei , Zhang Shuping
Published: October 2019

Background

Timing of breeding season of temperate passerines has been considered to be adjusted to their food availability. There is little work to reveal the cell stress responses of the nestlings hatched asynchronized with the food abundance peak, which is important for understanding the physiological link between the timing of breeding and the fitness of offspring.

Methods

Using gene expression level of blood HSP70 and HSP90 as indicators, we compared the cell stress response of Asian Short-toed Lark (Calandrella cheleensis) nestlings hatched under conditions of low, mid or high food (grasshopper nymph) availability in 2017.

Results

Nymph biomass, sample time and interaction of these two factors significantly influenced the blood gene expression level of HSP70 and HSP90 of Asian Short-toed Lark nestlings. HSP70 and HSP90 gene expression levels of the nestlings at 14:00 were significantly higher than those at 5:00. At either 5:00 or 14:00, the gene expression levels of HSP70 and HSP90 increase with the decrease of nymph biomass.

Conclusions

These results indicate that food availability is an important environment factor inducing cellular stress of Asian Short-toed Lark nestlings. The interactive effect of the nymph abundance and sample time on the HSPs response may be related with the daily temperature variation of the grassland. Over cell stress response may be one of physiological factor mediating the effect of food availability and the nestling’s fitness.
Obstructive pneumonia owing to migration of a Teflon pledget at 8 years after surgery for a pulmonary carcinoid tumor: a case report
Authors: Watanabe Hikaru , Abe Kohei , Kanauchi Naoki
Published: October 2019

Background

It is uncommon for a bronchial stump-related complication to develop during the remote postoperative period in a case of obstructive pneumonia owing to migration of the suture material. Here, we describe a case of bronchial obstructive pneumonia that developed owing to migration of the suture material in the airway 8 years after pulmonary resection.

Case presentation

A 34-year-old woman underwent left lower lobectomy for a pulmonary carcinoid tumor (pT1bN0M0-stage IA) in 2010. She experienced obstructive pneumonia, and chest computed tomography revealed a mass protruding from the bronchial stump to the bronchial lumen in 2018. After treatment for pneumonia, flexible bronchoscopy showed the presence of a fibrous suture material (Teflon pledget) completely obstructing the left second carina. A week later, the Teflon pledget obstructing the bronchial lumen was removed using a flexible bronchoscope with the patient under general anesthesia. The procedure was completed without removing the small amount of granulation tissue because the bronchial lumen opened after removing the Teflon pledget. She has remained asymptomatic for 1 year after removal.

Conclusions

In this case, the complication of obstructive pneumonia developed owing to migration of the non-absorbable suture materials used to suture the bronchial stump. Bronchoscopic management of this rare complication comprised endobronchial removal with the patient under general anesthesia. Given our experience with this case, we believe that such conservative management should allow for excellent results in most instances and avoid the need for reoperation.
Effects of taurine supplementation in low fish meal diets for red seabream (Pagrus major) in low water temperature season
Authors: Gunathilaka G. L. B. E. , Kim Min-Gi , Lee Chorong , Shin Jaehyeong , Lee Bong-Joo , Lee Kyeong-Jun
Published: October 2019

Background

Taurine is a conditional essential amino acid for fish. A study was conducted to investigate the compensating effect of supplemental taurine in diets for red seabream (Pagrus major) on impaired growth performance by fish meal (FM) replacement with soybean meal (SM) at low water temperature (14.15 ± 1.95 °C).

Methods

A FM-based diet was considered as a high FM diet and three other experimental diets were formulated to replace FM with SM by 20, 35, or 50% (HFM, SM20, SM35, or SM50, respectively) without taurine and other four diets were formulated by adding 1% taurine to the diets (HFM-T, SM20-T, SM35-T, or SM50-T, respectively). Triplicate groups of fish (108.9 ± 1.58 g/fish) were distributed into 24 polyvinyl circular tanks (215 L) with 20 fish per tank and fed one of the diets to satiation for 20 weeks.

Results

Growth performance and feed utilization of red seabream were significantly improved by the dietary taurine supplementation. SM20-T and SM35-T diets increased fish growth that are comparable to HFM diet. Feed intake, feed conversion ratio, and protein efficiency ratio of fish fed SM20-T and SM35-T diets were not significantly different from those of HFM group. Dietary taurine supplementation in each FM replaced group numerically increased innate immunity of the fish. Lysozyme and superoxide dismutase activities were significantly decreased in fish fed SM35, SM50, and SM50-T diets compared to those of fish fed HFM diet while they were not significantly lower in SM20, SM20-T, SM35, and SM35-T groups. Glutathione peroxidase activity was significantly lower in fish group fed SM50 diet while SM50-T group did not significantly lower compared to that of HFM group. The relative expression level of hepatic IGF-1 mRNA was improved in fish fed taurine-supplemented diets compared to their respective SM diets.

Conclusions

Growth performance and feed utilization of red seabream can be accelerated or restored by 1% taurine supplementation when they are fed high level of SM up to 35% in diets during low water temperature season.
Optimized chronomodulated dual release bilayer tablets of fexofenadine and montelukast: quality by design, development, and in vitro evaluation
Authors: Singh Bhupendra , Saini Geetanjali , Vyas Manish , Verma Surajpal , Thakur Sourav
Published: October 2019

Background

The conventional oral dosage forms are not effective in dealing with chronopathological conditions, such as nocturnal asthma. Therefore, there is an unmet need to develop a delivery system that can deliver drug as per the chronopharmacology of the diseases. The purpose of the study is to use quality by design (QbD) technique and pulsatile principles for the development of Eudragit-coated dual release bilayer tablets. The dual layer consists of immediate release layer of fexofenadine HCl and sustained release layer of montelukast sodium.

Results

The quality target product profile of the formulation was developed, and the critical quality attributes were identified. Three-level, three-factor Box-Behnken design was used for the optimization of the bilayer tablets. Based on the design, a total of 13 formulation combinations (F1–F13 and M1–M13) were made having acceptable micromeritic properties. The developed immediate and sustained release layers were evaluated for physicochemical properties. Depending upon the value of the diffusion exponent, the Fickian diffusion mechanism is dominant among immediate and sustained release tablet layers. Response curve for immediate release layer showed that concentrations of sodium starch glycolate and sodium bicarbonate had a negative effect on disintegration time and a positive effect on drug release. For sustained release tablet layer, concentrations of HPMC E 5 LV and magnesium stearate had a significant effect on drug release. The ANOVA and diagnostic plots confirmed the significance and goodness of fit of the used model. Based on desirability plot values, optimized formulation was developed and coated with Eudragit coat. The coated bilayer tablet showed met the requirement of providing an immediate release during the first hour and a sustained release action for a period of more than 8 h after passing the gastric region.

Conclusions

The formulation can be fruitful in curbing the menace of nocturnal asthma and providing a high degree of patient compliance as the patient will not have to wake up at night to take the medication.
Ethnic disparities in psychotic experiences explained by area-level syndemic effects
Authors: Coid Jeremy , Gonzalez Rodriguez Rafael , Kallis Constantinos , Zhang Yamin , Bhui Kamaldeep , De Stavola Bianca , Bebbington Paul , Ullrich Simone
Published: October 2019

Background

Ethnic inequalities in health outcomes are often explained by socioeconomic status and concentrated poverty. However, ethnic disparities in psychotic experiences are not completely attenuated by these factors.

Aims

We investigated whether disparities are better explained by interactions between individual risk factors and place-based clustering of disadvantage, termed a syndemic.

Method

We performed a cross-sectional survey of 3750 UK men, aged 18–34 years, oversampling Black and minority ethnic (BME) men nationally, together with men residing in London Borough of Hackney. Participants completed questionnaires covering psychiatric symptoms, substance misuse, crime and violence, and risky sexual health behaviours. We included five psychotic experiences and a categorical measure of psychosis based on the Psychosis Screening Questionnaire.

Results

At national level, more Black men reported psychotic experiences but disparities disappeared following statistical adjustment for social position. However, large disparities for psychotic experiences in Hackney were not attenuated by adjustment for social factors in Black men (adjusted odds ratio, 3.24; 95% CI 2.14–4.91; P < 0.002), but were for South Asian men. A syndemic model of joint effects, adducing a four-component latent variable (psychotic experiences and anxiety, substance dependence, high-risk sexual behaviour and violence and criminality) showed synergy between components and explained persistent disparities in psychotic experiences. A further interaction confirmed area-level effects (Black ethnicity × Hackney residence, 0.834; P < 0.001).

Conclusions

Syndemic effects result in higher rates of non-affective psychosis among BME persons in certain inner-urban settings. Further research should investigate how syndemics raise levels of psychotic experiences and related health conditions in Black men in specific places with multiple deprivations.