scholarly journals The Immune Signatures Data Resource: A compendium of systems vaccinology datasets

2021 ◽  
Author(s):  
Joann Diray-Arce ◽  
Helen E.R. Miller ◽  
Evan Henrich ◽  
Bram Gerritsen ◽  
Matthew P Mulè ◽  
...  

Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern 'omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines, including those targeting seasonal influenza, yellow fever, and hepatitis B. These data are made available to the broader scientific community through the ImmuneSpace data portal and analysis engine leveraging the NIH/NIAID ImmPort repository. However, a barrier to progress in this area is that comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines and includes transcriptional profiles and antibody response measurements. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses.

2015 ◽  
Vol 20 (4) ◽  
pp. 242-251 ◽  
Author(s):  
Éva Kállay

Abstract. The last several decades have witnessed a substantial increase in the number of individuals suffering from both diagnosable and subsyndromal mental health problems. Consequently, the development of cost-effective treatment methods, accessible to large populations suffering from different forms of mental health problems, became imperative. A very promising intervention is the method of expressive writing (EW), which may be used in both clinically diagnosable cases and subthreshold symptomatology. This method, in which people express their feelings and thoughts related to stressful situations in writing, has been found to improve participants’ long-term psychological, physiological, behavioral, and social functioning. Based on a thorough analysis and synthesis of the published literature (also including most recent meta-analyses), the present paper presents the expressive writing method, its short- and long-term, intra-and interpersonal effects, different situations and conditions in which it has been proven to be effective, the most important mechanisms implied in the process of recovery, advantages, disadvantages, and possible pitfalls of the method, as well as variants of the original technique and future research directions.


NAR Cancer ◽  
2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Zachary V Thomas ◽  
Zhenjia Wang ◽  
Chongzhi Zang

Abstract Dysregulation of gene expression plays an important role in cancer development. Identifying transcriptional regulators, including transcription factors and chromatin regulators, that drive the oncogenic gene expression program is a critical task in cancer research. Genomic profiles of active transcriptional regulators from primary cancer samples are limited in the public domain. Here we present BART Cancer (bartcancer.org), an interactive web resource database to display the putative transcriptional regulators that are responsible for differentially regulated genes in 15 different cancer types in The Cancer Genome Atlas (TCGA). BART Cancer integrates over 10000 gene expression profiling RNA-seq datasets from TCGA with over 7000 ChIP-seq datasets from the Cistrome Data Browser database and the Gene Expression Omnibus (GEO). BART Cancer uses Binding Analysis for Regulation of Transcription (BART) for predicting the transcriptional regulators from the differentially expressed genes in cancer samples compared to normal samples. BART Cancer also displays the activities of over 900 transcriptional regulators across cancer types, by integrating computational prediction results from BART and the Cistrome Cancer database. Focusing on transcriptional regulator activities in human cancers, BART Cancer can provide unique insights into epigenetics and transcriptional regulation in cancer, and is a useful data resource for genomics and cancer research communities.


Author(s):  
Seyed MohammadReza Tabatabaei Nodoushan1 ◽  
Fatemeh Saadatjoo ◽  
Masoud Mirzaei

Introdution: Ischemic heart disease is one of the most common diseases, which has led to high mortality rates all over the world. This disease is caused by narrowing or blockage of coronary arteries, which are the provider of blood to the heart. Identifying the people susceptible to this disease and bringing changes in their lifestyles has been said to reduce the related mortality rates and increase the patient's longevity. Methods: Yazd people Health Study (YaHS) was conducted on a random sample of 10,000 people living in the city of Yazd, Iran in the years 2014-15 for a general health and disease survey. These data were first balanced by bootstrapping technique due to their unbalanced nature. Next, classification methods were used in the training phase. Various classifiers, such as artificial neural network, rule inducer, regression, and AdaBoost were used in order to evaluate the proposed method with two scenarios. Results: The results showed that the screening of the people susceptible to ischemic heart disease had the most significant effect on increasing the sensitivity of the discovery classifier of CN2 subgroup through using balanced data by bootstrapping method followed by their analysis for the purpose of producing a sample of the patients. This classifier proved to have the potential for detecting 83.6% of the people susceptible to this disease. Conclusion: Therefore, it can be concluded that data mining methods are effective in screening for susceptible people with ischemic heart disease. This method can be compared with other traditional screening methods in that it is more cost-effective and faster.


1996 ◽  
Vol 168 (4) ◽  
pp. 404-409 ◽  
Author(s):  
Matthew Hotopf ◽  
Glyn Lewis ◽  
Charles Normand

BackgroundSelective serotonin reuptake inhibitors (SSRIs) are more expensive than tricyclics. Reports have suggested that SSRIs are cost-effective because they are better tolerated and safer in overdose.MethodA systematic review of all randomised controlled trials (RCTs), meta-analyses, and cost-effectiveness studies comparing SSRIs and tricyclic antidepressants (TCAs).ResultsNone of the RCTs provided an economic analysis and there were methodological problems in the majority which would preclude this approach. Meta-analyses suggest that clinical efficacy is equivalent but slightly fewer patients prescribed SSRIs drop out of RCTs. Cost-effectiveness studies have been based on crude ‘modelling’ approaches and over-estimate the difference in attrition rates and the cost of treatment failure. It appears impossible to evaluate the economic aspects of suicide because of its rarity.ConclusionsThere is no evidence to suggest that SSRIs are more cost-effective than TCAs. The debate will only be concluded when a prospective cost-effectiveness study is done in the setting of a large primary care based RCT.


Animals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 37
Author(s):  
John McGlone ◽  
Arlene Garcia ◽  
Anoosh Rakhshandeh

The objective of this study was to examine the effectiveness of a novel 3-molecule boar pheromone (BOARBETTER®, BB,) to improve sow reproductive performance (breeding, conception, farrowing rates, pigs born alive, stillborn, mummies and total born). Data from 12 commercial farm sites were used to evaluate the effectiveness of BB. Each farm was used as the experimental unit in the meta-analyses. Individual sows records were collected, merged and analyzed in overall analyses. Relative to CON, BB increased the number of total born pigs per litter (13.81 ± 0.11 vs. 14.30 ± 0.11 pigs/litter, respectively; p < 0.01) and the number of pigs born alive (12.76 ± 0.14 vs. 13.13 ± 0.14 pigs/litter, respectively; p < 0.05). In the merged dataset analyses, the parity by treatment interaction was significant for total pigs and pigs born alive per litter (p < 0.01). In parities one through three, treatment with BB increased total pigs born by 0.88 per litter, and pigs born alive per litter by 0.73 pigs per litter (p < 0.05). However, BB had no effect on these parameters in sows from parities four through six. BOARBETTER® increased reproductive success, is cost effective, safe, and can meaningfully improve sow reproductive success and performance.


2020 ◽  
Vol 30 (11) ◽  
pp. 336-339
Author(s):  
Lucy Godfrey

The use of transfused blood, be it from an allogenic (donor) or autologous (same patient) source, is not a new treatment and in fact has been experimented with since the mid 1800s. The role of cell salvage and re-infusion of a patient’s own blood, however, has only begun to gain real popularity in the last 20 years, after the undertaking of several large scale meta-analyses which have shown that not only is autologous transfusion no less efficacious when compared to allogenic transfusion, but also potentially safer for a number of reasons. Autologous transfusion is also more cost effective overall and potentially quicker to initiate in an emergency situation. Despite the body of evidence to support the use of salvaged blood for transfusion, hesitation around its use still persists, with staff apprehension around set up of cell salvage equipment and general underestimation of intraoperative blood loss being key factors in its underuse.


2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1337-1337
Author(s):  
Linda Nebeling ◽  
Laura Dwyer ◽  
April Oh

Abstract Objectives The Family Life, Activity, Sun, Health and Eating (FLASHE) survey was conducted in 2014 to collect information on eating, physical activity, sedentary behaviors, and behavioral correlates from a national sample of parent-adolescent dyads in the United States. It is a publicly available data resource which can be used to research questions about psychosocial, generational, household and neighborhood correlates of health behaviors. Methods Data were collected from dyads of caregivers and their adolescent children (ages 12–17) (n = 1072 completed dyads) between April – October 2014. Two surveys for each respondent: one on diet-related behaviors and one on physical activity-related behaviors were collected. An additional 407 dyads wore an accelerometer for seven days and completed an activity log. A ‘geoFLASHE’ dataset used parent-provided address information for home and school to geocode these locations and compute a set of variables applied to several different neighborhood definitions, including both circular and street-network buggers with distances ranging from 400 – 1200 meters. Accelerometer variables were computed for a subset of adolescents who wore an Actigraph Gt3x+ for seven days and includes estimates from raw and activity counts data. Training webinars on dyadic analytical methods, models and applications were provided. Results The geoFLASHE dataset includes variables for neighborhood, socioeconomic status factor, factor scores for built environment characteristics (high density, older neighborhood, and short commutes), and other variables for each buffer configuration. The adolescent accelerometer dataset offers summary variables of accelerometer data and minute-level estimates of light, moderate, and vigorous activity using Crouter, Chandler, and GGIR processing methods. Additionally, training webinar, questionnaires, survey data files and codebooks are available. Conclusions The FLASHE study data resources can be used to understand cancer-related health behaviors in family dyads. Funding Sources FLASHE study was funded by the National Cancer Institute under contract number HHSN2612012000391 issued to Westat, Inc.


2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Felice Lorusso ◽  
Francesco Inchingolo ◽  
Antonio Scarano

Background. The academic scientific research in the field of dentistry has rapidly increased in the last 20 years under the pressure of the multidisciplinary technological advancements and the growing demand for new predictable and cost-effective techniques and materials. The aim of the present investigation was to analyze the academic scientific production conducted by Italian Academies and Dental Schools. Methods. The list of MED/28 academic researchers, associate and full professors, and academic affiliations was collected from the national database of CINECA to evaluate the scientific output of the Italian Universities. The complete list of scientific contributions and the bibliometric parameters were recorded in the Scopus database. Results. The scientific production of 37 Italian Universities, 416 researchers, and 23689 papers was evaluated. The measurement of total academic papers, citations, h-index, and relative citation ratio (RCR) was calculated. The study data showed an increase of the academic scientific production over the last 5 years. Conclusions. The results presented show how scientific research is increasingly pursued by dental clinicians.


2020 ◽  
Vol 41 (Supplement_1) ◽  
pp. S88-S89
Author(s):  
Alice Liu ◽  
Raquel Minasian ◽  
Ellen Maniago ◽  
Justin Gillenwater ◽  
Warren L Garner ◽  
...  

Abstract Introduction Hospitalized burn patients meet the criteria for Virchow’s triad (endothelial damage, hypercoagulability, and stasis), predisposing them to venous thromboembolism (VTE). While the cost, morbidity, and mortality of VTE suggest a need for prevention in this population, unreliable reported VTE rates, variable and complicated prophylaxis regimens, and risks associated with chemoprophylaxis have prevented the establishment of a universal protocol. This paper reviews the thromboprophylaxis practices both in the literature and at our own institution. Methods A systematic review was conducted according to Preferred Reported Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines identifying studies pertaining to VTE chemoprophylaxis in burn patients. Additionally, medical records of patients admitted to an American Burn Association-verified burn center between June 2015 and June 2019 were retrospectively reviewed for patient demographics, chemoprophylaxis, and presence of VTE defined as either deep vein thrombosis (DVT) or pulmonary embolism (PE). Results 35 studies met inclusion criteria. In the 11 studies that reported VTE incidence, rates ranged widely from 0.27 to 23.3%. The two largest retrospective studies (n = 33,637 and 36,638) reported a VTE incidence of 0.61% and a DVT incidence of 0.8% in populations with unknown or inconsistently recorded chemoprophylaxis. Throughout the literature, prevention protocols were mixed, though a trend toward using dose-adjusted subcutaneous low molecular weight heparin based on serum anti-factor Xa level was noted. At our institution, 1440 patients were admitted over four years. At-risk patients received a simple chemoprophylaxis regimen of 5000U of subcutaneous unfractionated heparin every eight hours. No routine monitoring tests were performed to limit cost. Ten cases of DVT and two cases of PE were identified with an incidence of 0.69% and 0.14%, respectively, and a total VTE incidence of 0.83%. One patient developed heparin-induced thrombocytopenia (0.07%). There were no other heparin-associated complications. Conclusions VTE incidence rates reported in the literature are wide-ranging and poorly capture the effect of any one chemoprophylaxis regimen in the burn population. Our center uses a single, safe, and cost-effective protocol with a VTE rate comparable to that of large national retrospective studies. Applicability of Research to Practice VTE continues to represent a threat to the burn population. While simple and safe chemoprophylaxis regimens exist, the optimal prevention protocol remains elusive.


PLoS ONE ◽  
2017 ◽  
Vol 12 (4) ◽  
pp. e0176210 ◽  
Author(s):  
Christine M. Schmucker ◽  
Anette Blümle ◽  
Lisa K. Schell ◽  
Guido Schwarzer ◽  
Patrick Oeller ◽  
...  

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