bluuebunny/crossref_metadata_2025_split huggingface dataset:
How should systematic reviewers handle conference abstracts? A view from the trenches
Authors: Scherer Roberta W. , Saldanha Ian J. 
Published: November 2019

Abstract

Background
While identifying and cataloging unpublished studies from conference proceedings is generally recognized as a good practice during systematic reviews, controversy remains whether to include study results that are reported in conference abstracts. Existing guidelines provide conflicting recommendations.

Main body
The main argument for including conference abstracts in systematic reviews is that abstracts with positive results are preferentially published, and published sooner, as full-length articles compared with other abstracts. Arguments against including conference abstracts are that (1) searching for abstracts is resource-intensive, (2) abstracts may not contain adequate information, and (3) the information in abstracts may not be dependable. However, studies comparing conference abstracts and fully published articles of the same study find only minor differences, usually with conference abstracts presenting preliminary results. Other studies that have examined differences in treatment estimates of meta-analyses with and without conference abstracts report changes in precision, but usually not in the treatment effect estimate. However, in some cases, including conference abstracts has made a difference in the estimate of the treatment effect, not just its precision. Instead of arbitrarily deciding to include or exclude conference abstracts in systematic reviews, we suggest that systematic reviewers should consider the availability of evidence informing the review. If available evidence is sparse or conflicting, it may be worthwhile to search for conference abstracts. Further, attempts to contact authors of abstracts or search for protocols or trial registers to supplement the information presented in conference abstracts is prudent. If unique information from conference abstracts is included in a meta-analysis, a sensitivity analysis with and without the unique results should be conducted.

Conclusions
Under given circumstances, it is worthwhile to search for and include results from conference abstracts in systematic reviews.
Weak convergence of explicit extragradient algorithms for solving equilibirum problems
Authors: ur Rehman Habib , Kumam Poom , Cho Yeol Je , Yordsorn Pasakorn 
Published: November 2019

Abstract
This paper aims to propose two new algorithms that are developed by implementing inertial and subgradient techniques to solve the problem of pseudomonotone equilibrium problems. The weak convergence of these algorithms is well established based on standard assumptions of a cost bi-function. The advantage of these algorithms was that they did not need a line search procedure or any information on Lipschitz-type bifunction constants for step-size evaluation. A practical explanation for this is that they use a sequence of step-sizes that are updated at each iteration based on some previous iterations. For numerical examples, we discuss two well-known equilibrium models that assist our well-established convergence results, and we see that the suggested algorithm has a competitive advantage over time of execution and the number of iterations.
Antibiotic-modulated microbiome suppresses lethal inflammation and prolongs lifespan in Treg-deficient mice
Authors: He Baokun , Liu Yuying , Hoang Thomas K. , Tian Xiangjun , Taylor Christopher M. , Luo Meng , Tran Dat Q. , Tatevian Nina , Rhoads J. Marc 
Published: November 2019

AbstractBackgroundRegulatory T cell (Treg) deficiency leads to IPEX syndrome, a lethal autoimmune disease, in Human and mice. Dysbiosis of the gut microbiota in Treg-deficient scurfy (SF) mice has been described, but to date, the role of the gut microbiota remains to be determined.ResultsTo examine how antibiotic-modified microbiota can inhibit Treg deficiency-induced lethal inflammation in SF mice, Treg-deficient SF mice were treated with three different antibiotics. Different antibiotics resulted in distinct microbiota and metabolome changes and led to varied efficacy in prolonging lifespan and reducing inflammation in the liver and lung. Moreover, antibiotics altered plasma levels of several cytokines, especially IL-6. By analyzing gut microbiota and metabolome, we determined the microbial and metabolomic signatures which were associated with the antibiotics. Remarkably, antibiotic treatments restored the levels of several primary and secondary bile acids, which significantly reduced IL-6 expression in RAW macrophages in vitro. IL-6 blockade prolonged lifespan and inhibited inflammation in the liver and lung. By using IL-6 knockout mice, we further identified that IL-6 deletion provided a significant portion of the protection against inflammation induced by Treg dysfunction.ConclusionOur results show that three antibiotics differentially prolong survival and inhibit lethal inflammation in association with a microbiota—IL-6 axis. This pathway presents a potential avenue for treating Treg deficiency-mediated autoimmune disorders.
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling
Authors: Schmidt Jennifer E. , Kent Angela D. , Brisson Vanessa L. , Gaudin Amélie C. M. 
Published: November 2019

Abstract

Background
Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.

Results
Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.

Conclusions
Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.
Identification of key candidate genes and molecular pathways in white fat browning: an anti-obesity drug discovery based on computational biology
Authors: Pan Yuyan , Liu Jiaqi , Qi Fazhi 
Published: November 2019

AbstractBackgroundObesity—with its increased risk of obesity-associated metabolic diseases—has become one of the greatest public health epidemics of the twenty-first century in affluent countries. To date, there are no ideal drugs for treating obesity. Studies have shown that activation of brown adipose tissue (BAT) can promote energy consumption and inhibit obesity, which makes browning of white adipose tissue (WAT) a potential therapeutic target for obesity. Our objective was to identify genes and molecular pathways associated with WAT and the activation of BAT to WAT browning, by using publicly available data and computational tools; this knowledge might help in targeting relevant signaling pathways for treating obesity and other related metabolic diseases.ResultsIn this study, we used text mining to find out genes related to brown fat and white fat browning. Combined with biological process and pathway analysis in GeneCodis and protein-protein interaction analysis by using STRING and Cytoscape, a list of high priority target genes was developed. The Human Protein Atlas was used to analyze protein expression. Candidate drugs were derived on the basis of the drug-gene interaction analysis of the final genes. Our study identified 18 genes representing 6 different pathways, targetable by a total of 33 drugs as possible drug treatments. The final list included 18 peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists, 4 beta 3 adrenoceptor (β3-AR) agonists, 1 insulin sensitizer, 3 insulins, 6 lipase clearing factor stimulants and other drugs.ConclusionsDrug discovery using in silico text mining, pathway, and protein-protein interaction analysis tools may be a method of exploring drugs targeting the activation of brown fat or white fat browning, which provides a basis for the development of novel targeted therapies as potential treatments for obesity and related metabolic diseases.
Poisonous books: analyses of four sixteenth and seventeenth century book bindings covered with arsenic rich green paint
Authors: Delbey Thomas , Holck Jakob Povl , Jørgensen Bjarke , Alvis Alexandra , Smith Vanessa Haight , Kavich Gwénaëlle M. , Harmon Kimberly A. , Dorch Bertil Fabricius , Rasmussen Kaare Lund 
Published: November 2019

Abstract
Efforts to read medieval manuscript waste recycled as bookbinding material in the sixteenth and seventeenth centuries have resulted in the chemical analysis of four books housed at the University Library of Southern Denmark and the Smithsonian Libraries in Washington DC. Four green coloured book bindings have been investigated by optical microscopy, micro X-ray fluorescence, X-ray diffraction, Raman spectroscopy, mass spectroscopy, and laser ablation inductively coupled plasma mass spectrometry. The results show that the green pigments used to obscure the manuscript waste in all four cases contain orpiment (As2S3) and indigo (C16H11N2O2). Although the books were printed in diverse places in Europe—Basel, Bologna, and Lübeck—the styles of their bindings indicate that they were likely bound in the same region in the same period. It is further likely that they acquired their arsenic-rich paint as part of the bookbinding process. Issues concerning the toxicity, health issues for library staff, conservators and researchers handling the books are also addressed.
Temperature log simulations in high-enthalpy boreholes
Authors: Wang Jia , Nitschke Fabian , Gholami Korzani Maziar , Kohl Thomas 
Published: November 2019

Abstract
Temperature logs have important applications in the geothermal industry such as the estimation of the static formation temperature (SFT) and the characterization of fluid loss from a borehole. However, the temperature distribution of the wellbore relies on various factors such as wellbore flow conditions, fluid losses, well layout, heat transfer mechanics within the fluid as well as between the wellbore and the surrounding rock formation, etc. In this context, the numerical approach presented in this paper is applied to investigate the influencing parameters/uncertainties in the interpretation of borehole logging data. To this end, synthetic temperature logs representing different well operation conditions were numerically generated using our newly developed wellbore simulator. Our models account for several complex operation scenarios resulting from the requirements of high-enthalpy wells where different flow conditions, such as mud injection with- and without fluid loss and shut-in, occur in the drill string and the annulus. The simulation results reveal that free convective heat transfer plays an important role in the earlier evolution of the shut-in-time temperature; high accuracy SFT estimation is only possible when long-term shut-in measurements are used. Two other simulation scenarios for a well under injection conditions show that applying simple temperature correction methods on the non-shut-in temperature data could lead to large errors for SFT estimation even at very low injection flow rates. Furthermore, the magnitude of the temperature gradient increase depends on the flow rate, the percentage of fluid loss and the lateral heat transfer between the fluid and the rock formation. As indicated by this study, under low fluid losses (< 30%) or relatively higher flow rates (> 20 L/s), the impact of flow rate and the lateral heat transfer on the temperature gradient increase can be ignored. These results provide insights on the key factors influencing the well temperature distribution, which are important for the choice of the drilling data to estimate SFT and the design of the inverse modeling scheme in future studies to determine an accurate SFT profile for the high-enthalpy geothermal environment.
A study protocol for testing the feasibility of a randomised stepped wedge cluster design to investigate a Community Health Intervention through Musical Engagement (CHIME) for perinatal mental health in The Gambia
Authors: Sanfilippo Katie Rose M. , McConnell Bonnie , Cornelius Victoria , Darboe Buba , Huma Hajara B. , Gaye Malick , Ramchandani Paul , Ceesay Hassoum , Glover Vivette , Cross Ian , Stewart Lauren 
Published: November 2019

AbstractBackgroundPerinatal mental health problems affect up to one in five women worldwide. Mental health problems in the perinatal period are a particular challenge in low- and middle-income countries (LMICs) where they can be at least twice as frequent as in higher-income countries. It is thus of high priority to develop new low-cost, low-resource, non-stigmatising and culturally appropriate approaches to reduce symptoms of anxiety and depression perinatally, for the benefit of both mother and child. Music-centred approaches may be particularly useful in The Gambia since a range of musical practices that specifically engage pregnant women and new mothers already exist.MethodsThis protocol is for a study to examine the feasibility of undertaking a stepped wedge trial to test how a Community Health Intervention through Musical Engagement (CHIME) could be beneficial in alleviating perinatal mental distress in The Gambia. In this study, we plan to recruit 120 pregnant women (n = 60 intervention,n = 60 control) at four antenatal clinics over two 6-week stepped sequences. Women in the intervention will participate in weekly group-singing sessions, led by local Kanyeleng singing groups, for 6 weeks. The control group will receive standard care. We will assess symptoms of anxiety and depression using the Edinburgh Postnatal Depression Scale (EPDS) and the Self-Reporting Questionnaire (SRQ-20). The feasibility of the design will be assessed through recruitment, retention and attrition rates of participants, clinics' adherence to the schedule and completeness of data by site. Qualitative interviews and video and audio recordings will be used to evaluate the acceptability of the intervention.DiscussionThis feasibility trial will allow us to determine whether a larger trial with the same intervention and target group is feasible and acceptable in The Gambia.Trial registrationRetrospectively registered (24/01/2019) with Pan African Clinical Trials Registry (PACTR):PACTR201901917619299.
The role of host miRNAs on Mycobacterium tuberculosis
Authors: Behrouzi Ava , Alimohammadi Marjan , Nafari Amir Hossein , Yousefi Mohammad Hadi , Riazi Rad Farhad , Vaziri Farzam , Siadat Seyed Davar 
Published: November 2019

Abstract
MicroRNAs are non-coding RNAs, playing an important role in regulating many biological pathways, such as innate immune response against various infections. Different studies confirm that many miRNAs act as important regulators in developing a strategy for the survival of Mycobacterium tuberculosis in the host cell. On the other hand, an innate immune response is one of the important aspects of host defense against Mycobacterium. Considering the importance of miRNAs during tuberculosis infection, we focused on studies that performed on the role of various miRNAs related to pathogenic bacteria, M. tuberculosis in the host. Also, we have introduced important miRNAs that can be used as a biomarker for the detection of Mycobacterium.
Traditional methods of food habits and dietary preparations in Ayurveda—the Indian system of medicine
Authors: S. Dhanya , N V Ramesh , Mishra Abhayakumar 
Published: November 2019

AbstractAyurveda (the science of life) is one of the branches of Vedas. It is regarded as upaveda of Atharva Veda. It is a steam of knowledge coming down from generation to generation since eternity parallel to Vedic literature which is why its emergence has been said to be from the creator (Brahman) himself prior to the creation. It is taken as eternal because nobody knows when it was not there. In Ayurveda, food is considered to affect the mind as well as the body. By understanding how to prepare foods best suited to our minds and bodies, we can utilize nutrition as a source of healing. Food is the most essential to sustain a good life and the same food if consumed inappropriately becomes the root cause of many diseases. So, proper knowledge about food and its importance should be known by all human beings to have better benefits from it.
Evaluation of the electronic health record system in maternal and child health centers of Marie Stopes International Ethiopia
Authors: Gizaw Tizita , Bogale Mengistu , Alemayehu Tilahun 
Published: November 2019

Background: The Health Information Management Systems Society (HIMSS) defines an Electronic Health Record (EHR) as a longitudinal electronic record of patient health information generated by one or more encounters in any care delivery setting”. EHR systems improve quality and adaptability of care, contributing to patient safety. The system is also efficient and provides real-time administration to patients. Driven by the need to facilitate clinical and administrative process, and to reduce medical errors, Marie Stopes international Ethiopia (MSIE) implemented EHR system in its maternal and child health (MCH) centers. This study sought to evaluate the EHR system in six departments (inpatient, outpatient, pharmacy, laboratory, reception cashiers and MCH managers) of these MCH centers in terms of ease of performing tasks and satisfaction with the system. Methods: A cross-sectional method with formative evaluation was used to address the objective. A sample size of 54 were used for the investigation. The participants were from six departments (inpatient, outpatient, pharmacy, laboratory, reception cashiers and MCH managers) within three MCH centers. Data was collected using structured, self-administered questionnaires and interviews and analyzed using SPSS 20. Results: In total, 83% of respondents found that performing tasks using EHR made tasks easier; the lowest score was from Pharmacy department (48%). The overall satisfaction with EHR was 87%. The lowest score is from the indicator “the system meets my needs” (80%). Conclusions: Staffs in all department reported the EHR system as “very good” for both ease of performing their daily tasks and satisfaction with the system. In addition, the study revealed that ease of performing tasks and satisfaction with the system were varied by department and specific task within the department. It is essential to know the needs and requirements of each department before implementation of the system and user feedback for long lasting uptake and impact.
Ovarian inguinal hernia
Authors: Prodromidou A , Machairas N , Garoufalia Z , Kostakis ID , Kyriakidis AV , Spartalis E , Sotiropoulos GC 
Published: November 2019

Introduction Gynaecological structures such as the ovaries, fallopian tubes, ligaments and uterus are rarely encountered inside a hernial sac. The prevalence of groin hernias containing parts of female genitalia remains unknown. The aim of this review was to summarise the existing evidence on inguinal hernias containing ovaries with or without the other female adnexa. Methods A systematic search was conducted for literature published up to February 2018 using the MEDLINE®, Scopus® and Google Scholar™ databases along with the references of the full-text articles retrieved. Papers on observational studies and case reports concerning women who were diagnosed with an ovarian inguinal hernia (pre or intraoperatively) were considered eligible for inclusion in the review. Results Fifteen papers (13 case reports, 2 case series) comprising seventeen patients (mean age 47.9 years) were evaluated. A left-sided hernia was noted in 13 cases (77%) whereas 4 patients had a right-sided hernia. Eight patients underwent preoperative imaging with computed tomography, ultrasonography or both. This was diagnostic in five cases. In 11 patients, hernia contents were repositioned, 2 had a salpingo-oophorectomy and 2 an oophorectomy. Eight patients underwent hernia repair with mesh placement while three had a herniorrhaphy. Conclusions Ovarian inguinal hernias should be considered among the differential diagnoses of a groin mass or swelling. In women of reproductive age, repair of the hernia with the intent to preserve fertility is of critical importance.
Effects of One Year of Vitamin D and Marine Omega-3 Fatty Acid Supplementation on Biomarkers of Systemic Inflammation in Older US Adults
Authors: Costenbader Karen H , MacFarlane Lindsey A , Lee I-Min , Buring Julie E , Mora Samia , Bubes Vadim , Kotler Gregory , Camargo Carlos A , Manson JoAnn E , Cook Nancy R 
Published: November 2019

AbstractBACKGROUNDObservational studies suggest vitamin D and marine ω-3 fatty acid (n-3 FA) supplements are associated with lower systemic inflammation. However, past trials have been inconsistent.METHODSThe randomized, double-blind, placebo-controlled VITamin D and OmegA-3 TriaL (VITAL) tested vitamin D (2000 IU/day) and/or n-3 FA (1 g/day) supplementation in a 2 × 2 factorial design among women ≥55 and men ≥50 years of age. We assessed changes in interleukin (IL)-6, tumor necrosis factor receptor 2 (TNFR2), and high-sensitivity C-reactive protein (hsCRP) concentrations from baseline to 1 year among participants randomized to vitamin D + n-3 FA (392), vitamin D (392), n-3 FA (392), or placebo only (385). Geometric means and percent changes were compared, adjusting for baseline factors.RESULTSBaseline characteristics were well balanced. In the active arms, 25-OH vitamin D rose 39% and n-3 FA rose 55% vs minimal change in placebo arms. Neither supplement reduced biomarkers at 1 year. Vitamin D resulted in 8.2% higher IL-6 (95% CI, 1.5%–15.3%; adjusted P = 0.02), but TNFR2 and hsCRP did not. Among 784 receiving vitamin D, hsCRP increased 35.7% (7.8%–70.9%) in those with low (&lt;20 ng/mL) but not with higher baseline serum 25(OH) vitamin D [0.45% (−8.9% to 10.8%); P interaction = 0.02]. Among 777 randomized to n-3 FA, hsCRP declined [−10.5% (−20.4% to 0.8%)] in those with baseline low (&lt;1.5 servings/week), but not with higher fish intake [6.4% (95% CI, −7.11% to 21.8%); P interaction = 0.06].CONCLUSIONSIn this large sample from a population-based randomized controlled trial, neither vitamin D nor n-3 FA supplementation over 1 year decreased these biomarkers of inflammation.ClinicalTrials.gov IdentifierNCT01169259; NCT01351805