ResearchPad - brief-communications https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[TREC-COVID: rationale and structure of an information retrieval shared task for COVID-19]]> https://www.researchpad.co/article/elastic_article_12285 TREC-COVID is an information retrieval (IR) shared task initiated to support clinicians and clinical research during the COVID-19 pandemic. IR for pandemics breaks many normal assumptions, which can be seen by examining 9 important basic IR research questions related to pandemic situations. TREC-COVID differs from traditional IR shared task evaluations with special considerations for the expected users, IR modality considerations, topic development, participant requirements, assessment process, relevance criteria, evaluation metrics, iteration process, projected timeline, and the implications of data use as a post-task test collection. This article describes how all these were addressed for the particular requirements of developing IR systems under a pandemic situation. Finally, initial participation numbers are also provided, which demonstrate the tremendous interest the IR community has in this effort.

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<![CDATA[Chronic kidney disease is a main confounding factor for 25-vitamin D measurement]]> https://www.researchpad.co/article/elastic_article_6305 Current guidelines recommend assessment of 25-vitamin D status in patients with chronic kidney disease (CKD). Although significant differences among assays have been described, the impact of CKD on this variability has never been tested.Methods:We tested the variability between two 25-vitamin D assays in patients with CKD (eGFR < 60 mL/min/1.73m2) who had consecutive 25-vitamin D measurements in 2015 (Assay 1 - Diasorin LIASON 25 TOTAL - D assay®) and 2016 (Assay 2 - Beckman Coulter Unicel Xl 800®). The cohort consisted of 791 adult patients (122 with normal renal function and 669 with CKD - 33, 30, and 37% in stages 3, 4, and 5 on dialysis, respectively).Results:Levels of 25-vitamin D were lower and the prevalence of hypovitaminosis D using assay 1 was higher than using assay 2 in patients with CKD, regardless of similar levels of calcium, phosphate, and parathyroid hormone. As kidney function decreased, the percentage of disagreement between the assays increased.Conclusion:There is a noteworthy variability between assays in patients with CKD such that the diagnosis of hypovitaminosis D is modified. The mechanism behind this result is still unclear and might be due to a possible interference in the analytical process. However, the clinical significance is unquestionable, as the supplementation of vitamin D can be erroneously prescribed to these patients. ]]> <![CDATA[Engineered Cas9 variant tools expand targeting scope of genome and base editing in rice]]> https://www.researchpad.co/article/N0c6db65d-c353-487f-b805-563a69e82177 <![CDATA[CRISPR‐Cas12a enables efficient biallelic gene targeting in rice]]> https://www.researchpad.co/article/Nef115251-36eb-42c6-a904-16a4b364d7d3 <![CDATA[Maize <i>ZmRPH1</i> encodes a microtubule‐associated protein that controls plant and ear height]]> https://www.researchpad.co/article/Nab94eb54-624d-4c2c-ba24-68f84de95e01 <![CDATA[Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center]]> https://www.researchpad.co/article/Ndad5731a-cbce-43ef-8afd-54733d10145a The study sought to describe the development, implementation, and requirements of laboratory information system (LIS) functionality to manage test ordering, registration, sample flow, and result reporting during the coronavirus disease 2019 (COVID-19) pandemic.Materials and MethodsOur large (>12 000 000 tests/y) academic hospital laboratory is the Belgian National Reference Center for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We have performed a moving total of >25 000 SARS-CoV-2 polymerase chain reaction tests in parallel to standard routine testing since the start of the outbreak. A LIS implementation team dedicated to develop tools to remove the bottlenecks, primarily situated in the pre- and postanalytical phases, was established early in the crisis.ResultsWe outline the design, implementation, and requirements of LIS functionality related to managing increased test demand during the COVID-19 crisis, including tools for test ordering, standardized order sets integrated into a computerized provider order entry module, notifications on shipping requirements, automated triaging based on digital metadata forms, and the establishment of databases with contact details of other laboratories and primary care physicians to enable automated reporting. We also describe our approach to data mining and reporting of actionable daily summary statistics to governing bodies and other policymakers.ConclusionsRapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turnaround time of SARS-CoV-2 testing. It will be important to maintain an environment that is conducive for the rapid adoption of meaningful LIS tools after the COVID-19 crisis. ]]> <![CDATA[Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long-lasting immunity]]> https://www.researchpad.co/article/Nbec21d64-33ba-4ef7-8528-7914946e8ff2

Abstract:  In order to determine highly immunogenic severe acute respiratory syndrome coronavirus (SARS‐CoV) epitope peptides capable of inducing long‐lasting immunity, we first screened immunoglobulin‐G (IgG) antibodies reactive to 197 different overlapping 15‐mers from the SARS‐CoV proteins in the sera of three infected patients. Forty‐two peptides among them were reactive to the sera from all three patients. Consequently, we tested for the reactivity of these 42 peptides to patients' sera (n = 45) at 6‐month post‐infection. The significantly higher levels of IgG antibodies specific to three (S791, M207 and N161) of 42 peptides were detectable in the post‐infection sera from 23 (51%), 27 (60%) and 19 (42%) of 45 patients, respectively. These three peptides, recognized by their long‐lasting immunity, may provide a better understanding of the immunogenicity of SARS‐CoV.

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<![CDATA[Molecular Detection of a Novel Human Influenza (H1N1) of Pandemic Potential by Conventional and Real-Time Quantitative RT-PCR Assays]]> https://www.researchpad.co/article/Needb98be-7894-4efa-92ef-53b8c211a666

Abstract

Background: Influenza A viruses are medically important viral pathogens that cause significant mortality and morbidity throughout the world. The recent emergence of a novel human influenza A virus (H1N1) poses a serious health threat. Molecular tests for rapid detection of this virus are urgently needed.

Methods: We developed a conventional 1-step RT-PCR assay and a 1-step quantitative real-time RT-PCR assay to detect the novel H1N1 virus, but not the seasonal H1N1 viruses. We also developed an additional real-time RT-PCR that can discriminate the novel H1N1 from other swine and human H1 subtype viruses.

Results: All of the assays had detection limits for the positive control in the range of 1.0 × 10−4 to 2.0 × 10−3 of the median tissue culture infective dose. Assay specificities were high, and for the conventional and real-time assays, all negative control samples were negative, including 7 human seasonal H1N1 viruses, 1 human H2N2 virus, 2 human seasonal H3N2 viruses, 1 human H5N1 virus, 7 avian influenza viruses (HA subtypes 4, 5, 7, 8, 9, and 10), and 48 nasopharyngeal aspirates (NPAs) from patients with noninfluenza respiratory diseases; for the assay that discriminates the novel H1N1 from other swine and human H1 subtype viruses, all negative controls were also negative, including 20 control NPAs, 2 seasonal human H1N1 viruses, 2 seasonal human H3N2 viruses, and 2 human H5N1 viruses.

Conclusions: These assays appear useful for the rapid diagnosis of cases with the novel H1N1 virus, thereby allowing better pandemic preparedness.

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<![CDATA[Management of allergy transfer upon solid organ transplantation]]> https://www.researchpad.co/article/Nab71bb6f-6dfe-4fad-85a9-30f9b9cfe9de

Allergy transfer upon solid organ transplantation has been reported in the literature, although only few data are available as to the frequency, significance, and management of these cases. Based on a review of 577 consecutive deceased donors from the Swisstransplant Donor‐Registry, 3 cases (0.5%) of fatal anaphylaxis were identified, 2 because of peanut and 1 of wasp allergy. The sera of all 3 donors and their 10 paired recipients, prospectively collected before and after transplantation for the Swiss Transplant Cohort Study, were retrospectively processed using a commercial protein microarray fluorescent test. As early as 5 days posttransplantation, newly acquired peanut‐specific IgE were transiently detected from 1 donor to 3 recipients, of whom 1 liver and lung recipients developed grade III anaphylaxis. Yet, to define how allergy testing should be performed in transplant recipients and to better understand the impact of immunosuppressive therapy on IgE sensitization, we prospectively studied 5 atopic living‐donor kidney recipients. All pollen‐specific IgE and >90% of skin prick tests remained positive 7 days and 3 months after transplantation, indicating that early diagnosis of donor‐derived IgE sensitization is possible. Importantly, we propose recommendations with respect to safety for recipients undergoing solid‐organ transplantation from donors with a history of fatal anaphylaxis.

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<![CDATA[Using Persuasive Systems Design Model to Evaluate “Cuida tu Ánimo”: An Internet-Based Pilot Program for Prevention and Early Intervention of Adolescent Depression]]> https://www.researchpad.co/article/N356fb54f-6aeb-4516-9296-eb8943e914b5

Background: “Cuida tu Ánimo” (CTA [Take Care of Your Mood]) is an internet-based program for prevention and early intervention of adolescent depression implemented in Chile and Colombia. In the pilot application of the program, participants interacted with the program through a website that provided psychoeducational information, chat, and telephone appointments as well as monitoring and feedback messages. To date, most similar programs were not developed taking design features into consideration. The persuasive systems design (PSD) model is a comprehensive framework developed to aid in the design and evaluation of systems capable of influencing users' attitudes or behaviors. The purpose of this study was to evaluate the persuasiveness of CTA pilot program using the PSD model.

Methods: The methodology used was expert evaluation, where specialists evaluate the program against a list of design principles.

Results: Although the PSD model was not used to design the program, system features proposed by PSD were present, mainly “Dialogue support” features. Persuasion context analysis was not carried out by the developers. No aspects of the program could be related to “Primary task support” features because the developers did not define a primary task.

Discussion: Key aspects of the PSD model could be incorporated in the CTA program to enhance system persuasiveness and improve adherence.

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<![CDATA[Challenges to electronic clinical quality measurement using third-party platforms in primary care practices: the healthy hearts in the heartland experience]]> https://www.researchpad.co/article/Nd6ce9798-fc61-439a-9a8c-da913b34f1e2

Abstract

Third-party platforms have emerged to support small primary care practices for calculating and reporting electronic clinical quality measures (eCQM) for federal programs like The Medicare Access and CHIP Reauthorization Act of 2015 (MACRA) and Merit-based Incentive Payment System (MIPS). Yet little is known about the capabilities and limitations of electronic health record systems (EHRs) to enable data access for these programs. We connected 116 small- to medium-sized practices with seven different EHRs to popHealth, an open-source eCQM platform. We identified the prevalence of following problems with eCQM data for data extraction in seven different EHRs: (1) Lack of coded data in five of seven; (2) Incorrectly categorized data in four of seven; (3) Isosemantic data (data within the incorrect context) in four of seven; (4) Coding that could not be directly evaluated in six of seven; (5) Errors in date assignment and labeled as historical values in five of seven; and (6) Inadequate data to assign the correct code in two of seven. We recommend specific enhancements to EHR systems that can promote effective eCQM implementation and reporting to MACRA and MIPS.

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<![CDATA[Validity of social media for assessing treatment patterns in oncology patients: a case study in melanoma]]> https://www.researchpad.co/article/Ne171be4b-6a81-4c18-ae60-fdd0a32212ae

Abstract

There is a need to understand how patients are managed in the real world to better understand disease burden and unmet need. Traditional approaches to gather these data include the use of electronic medical record (EMR) or claims databases; however, in many cases data access policies prevent rapid insight gathering. Social media may provide a potential source of real-world data to assess treatment patterns, but the limitations and biases of doing so have not yet been evaluated. Here, we assessed whether patient treatment patterns extracted from publicly available patient forums compare to results from more traditional EMR and claims databases. We observed that the 95% confidence intervals of proportions of treatments received at first, second, and third line for advanced/metastatic melanoma generated from unstructured social media data overlapped with 95% confidence intervals from proportions obtained from 1 or more traditional EMR/Claims databases. Social media may offer a valid data option to understand treatment patterns in the real world.

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<![CDATA[The FDA authorization of direct-to-consumer genetic testing for three BRCA1/2 pathogenic variants: a twitter analysis of the public’s response]]> https://www.researchpad.co/article/N3479793a-5b42-430a-adbb-03dd6e1d9778

Abstract

Objectives

In March 2018, the Food and Drug Administration (FDA) announced its authorization of a direct-to-consumer (DTC) genetic test for three pathogenic BRCA1/2 variants. We sought to determine to whether social media discussion increased following the authorization, who was driving social media conversations, and what topics were discussed.

Methods

Using Crimson Hexagon, we described tweets before, during, and after the FDA announcement authorizing 23andMe to return BRCA1/2 results (3/4/18–3/10/18). We conducted qualitative coding of a subset of 605 tweets to better understand Twitter communication.

Results

We identified 11 055 twitter posts across the week of FDA’s announcement. Twitter discourse about 23andMe and the FDA authorization peaked the day following the FDA’s press release. Most tweets (48.6%) were informational and 26.3% were either expressing opinions (about 23andMe and/or FDA authorization, 14.9%) or testimonials (personal experiences with genetic testing, 11.4%). The types of tweets varied over the week-long period (P <  .001).

Discussion

Twitter discussion about the FDA’s authorization of DTC for three pathogenic BRCA1/2 variants increased immediately following the announcement. As more genetic technologies are brought to the DTC market, social media sites, like Twitter, will play a role in disseminating this information, providing a platform for information exchange, consumer testimonials, opinion pieces, and research.

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<![CDATA[Response to survey directed to patient portal members differs by age, race, and healthcare utilization]]> https://www.researchpad.co/article/Na3b67ee7-a2cd-4d17-bb70-d51e08393832

Abstract

Health care systems are increasingly utilizing electronic medical record—associated patient portals to facilitate communication with patients and between providers and their patients. These patient portals are growing in recognition as potentially valuable research tools. While there is much information about the response rates and demographics of internet-based surveys as well as the demographics of patients who are portal members, not much is known about the response rate of internet-based surveys directed to a group of patient portal members or the demographics of which portal members respond to internet-based surveys issued within that specific population. The objective of these analyses was to determine the demographics of patient portal users who respond to an internet-based survey request. We hypothesized that respondents would more likely be: (1) older (65+), (2) European American, (3) married, (4) female, (5) college educated, (6) have higher medical care utilization, (7) have more comorbidities, and (8) have a private practice primary care physician (as opposed to a salaried group practice primary care physician). We found that our respondents tended to be older, of European geographic ancestry, and more frequent users of healthcare. While patient portal members are an easily identifiable and contactable group that are potentially valuable participants for research, it is important to understand that respondents to surveys solicited from this sampling frame may not be entirely representative. It will be important to develop strategies to more fully engage populations that represent the target population in order to increase overall and subgroup response rates.

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<![CDATA[Usage of query-based health information exchange after event notifications]]> https://www.researchpad.co/article/Nb6c8bc6e-525c-411a-b4b5-053a4c684bfe

Abstract

Objectives

This study sought to quantify the association between event notifications and subsequent query-based health information exchange (HIE) use among end users of three different community health information organizations.

Materials and Methods

Using system-log data merged with user characteristics, regression-adjusted estimates were used to describe the association between event notifications and subsequent query-based HIE usage.

Results

Approximately 5% of event notifications were associated with query-based HIE usage within 30 days. In adjusted models, odds of query-based HIE usage following an event notification were higher for older patients and for alerts triggered by a discharge event. Query-based HIE usage was more common among specialty clinics and Federally Qualified Health Centers than primary care organizations.

Discussion and Conclusion

In this novel combination of data, 1 in 20 event notifications resulted in subsequent query-based HIE usage. Results from this study suggest that event notifications and query-based HIE can be applied together to address clinical and population health use cases.

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<![CDATA[A pilot study of the performance of captive‐reared delta smelt Hypomesus transpacificus in a semi‐natural environment]]> https://www.researchpad.co/article/N3c6ddc84-7163-4c83-9399-ad8d249e49a0

Abstract

A captive breeding programme was developed in 2008 for delta smelt Hypomesus transpacificus in reaction to dramatic population decline over several decades. We took 526 sub‐adult captive‐reared delta smelt and cultured them for 200 days without providing artificial food or water quality management to assess their performance once released in the wild. The results indicated captive‐reared sub‐adult delta smelt could survive in a semi‐natural environment with uncontrolled water quality and naturally produced wild prey through spawning and into their post spawning phase.

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<![CDATA[Diffusion basis spectrum imaging for identifying pathologies in MS subtypes]]> https://www.researchpad.co/article/Nda9d7f42-177e-45fe-93ce-36730276ceb0

Abstract

Diffusion basis spectrum imaging (DBSI) combines discrete anisotropic diffusion tensors and the spectrum of isotropic diffusion tensors to model the underlying multiple sclerosis (MS) pathologies. We used clinical MS subtypes as a surrogate of underlying pathologies to assess DBSI as a biomarker of pathology in 55 individuals with MS. Restricted isotropic fraction (reflecting cellularity) and fiber fraction (representing apparent axonal density) were the most important DBSI metrics to classify MS using brain white matter lesions. These DBSI metrics outperformed lesion volume. When analyzing the normal‐appearing corpus callosum, the most significant DBSI metrics were fiber fraction, radial diffusivity (reflecting myelination), and nonrestricted isotropic fraction (representing edema). This study provides preliminary evidence supporting the ability of DBSI as a potential noninvasive biomarker of MS neuropathology.

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<![CDATA[Cabozantinib Versus Sunitinib for Untreated Patients with Advanced Renal Cell Carcinoma of Intermediate or Poor Risk: Subgroup Analysis of the Alliance A031203 CABOSUN trial]]> https://www.researchpad.co/article/N47db00a9-5ee8-4e93-b123-580eb26586bc

The phase II CABOSUN trial compared cabozantinib with sunitinib as initial treatment in patients with advanced renal cell carcinoma of intermediate or poor risk. This article presents subgroup analyses by baseline patient characteristics.

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<![CDATA[Hermaphroditism promotes mate diversity in flowering plants]]> https://www.researchpad.co/article/N5106d0d4-26f7-4009-89fa-3374c83c4bd2

Premise

Genetically diverse sibships are thought to increase parental fitness through a reduction in the intensity of sib competition, and through increased opportunities for seedling establishment in spatially or temporally heterogeneous environments. Nearly all research on mate diversity in flowering plants has focused on the number of fathers siring seeds within a fruit or on a maternal plant. Yet as hermaphrodites, plants can also accrue mate diversity by siring offspring on several pollen recipients in a population. Here we explore whether mate composition overlaps between the dual sex functions, and discuss the implications for plant reproductive success.

Methods

We established an experimental population of 49 Mimulus ringens (monkeyflower) plants, each trimmed to a single flower. Following pollination by wild bees, we quantified mate composition for each flower through both paternal and maternal function. Parentage was successfully assigned to 240 progeny, 98% of the sampled seeds.

Results

Comparison of mate composition between male and female function revealed high mate diversity, with almost no outcross mates shared between the two sexual functions of the same flower.

Conclusions

Dual sex roles contribute to a near doubling of mate diversity in our experimental population of Mimulus ringens. This finding may help explain the maintenance of hermaphroditism under conditions that would otherwise favor the evolution of separate sexes.

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<![CDATA[Subcutaneous administration of a neutralizing IL-1β antibody prolongs limb allograft survival]]> https://www.researchpad.co/article/5c0cb61ad5eed0c4849e43ab

Cytokine‐expression profiles revealed IL‐1ß highly upregulated in rejecting skin of limb allografts. We investigate the effect of intragraft treatment with a neutralizing IL‐1β antibody in limb transplantation. Following allogenic hind‐limb transplantation, Lewis rats were either left untreated1 or treated with anti‐lymphocyte serum + tacrolimus (baseline)2; baseline immunosuppression + anti‐IL‐1β (1 mg/kg once/week, 6‐8 subcutaneous injections) into the transplanted3 or contralateral4 limb. Endpoint was rejection grade III or day 100. Graft rejection was assessed by histology, immunohistochemistry, flow cytometry phenotyping of immune cells, and monitoring cytokine expression. Anti‐IL‐1β injections into the allograft or contralateral limb resulted in a significant delay of rejection onset (controls: 58.60 ± 0.60; group 3: 75.80 ± 10.87, P = .044; group 4: 73.00 ± 6.49, P = .008) and prolongation of graft survival (controls: 64.60 ± 0.87; group 3: 86.60 ± 5.33, P = .002; group 4: 93.20 ± 3.82, P = .002), compared to controls. Although the phenotype of the graft infiltrating immune cells did not differ between groups, significantly decreased skin protein levels of IL‐1β, IL‐4, IL‐13, IP‐10, MCP‐1, and MCP‐3 in long‐term‐survivors indicate an overall decrease of chemoattraction and infiltration of immune cells as the immunosuppressive mechanism of anti‐IL‐1β. Inhibition of IL‐1β with short‐term systemic immunosuppression prolongs limb allograft survival and represents a promising target for immunosuppression in extremity transplantation.

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