Data extraction methods for systematic review (semi)automation: Update of a living systematic review [version 2; peer review: 3 approved]

Background: The reliable and usable (semi)automation of data extraction can support the field of systematic review by reducing the workload required to gather information about the conduct and results of the included studies. This living systematic review examines published approaches for data extraction from reports of clinical studies. Methods: We systematically and continually search PubMed, ACL Anthology, arXiv, OpenAlex via EPPI-Reviewer, and the dblp computer science bibliography. Full text screening and data extraction are conducted within an open-source living systematic review application created for the purpose of this review. This living review update includes publications up to December 2022 and OpenAlex content up to March 2023. Results: 76 publications are included in this review. Of these, 64 (84%) of the publications addressed extraction of data from abstracts, while 19 (25%) used full texts. A total of 71 (93%) publications developed classifiers for randomised controlled trials. Over 30 entities were extracted, with PICOs (population, intervention, comparator, outcome) being the most frequently extracted. Data are available from 25 (33%), and code from 30 (39%) publications. Six (8%) implemented publicly available tools Conclusions: This living systematic review presents an overview of (semi)automated data-extraction literature of interest to different types of literature review. We identified a broad evidence base of publications describing data extraction for interventional reviews and a small number of publications extracting epidemiological or diagnostic accuracy data. Between review updates, trends for sharing data and code increased strongly: in the base-review, data and code were available for 13 and 19% respectively, these numbers increased to 78 and 87% within the 23 new publications. Compared with the base-review, we observed another research trend, away from straightforward data extraction and towards additionally extracting relations between entities or automatic text summarisation. With this living review we aim to review the literature continually

Treatment of Advanced Emphysema with Emphysematous Lung Sealant (AeriSeal (R))

Background: This report summarizes initial tests of an emphysematous lung synthetic polymer sealant (ELS) designed to reduce lung volume in patients with advanced emphysema. Objectives: The primary study objective was to define a therapeutic strategy to optimize treatment safety and effectiveness. Methods: ELS therapy was administered bronchoscopically to 25 patients with heterogeneous emphysema in an open-label, noncontrolled study at 6 centers in Germany. Treatment was performed initially at 2-4 subsegments. After 12 weeks, patients were eligible for repeat therapy to a total of 6 sites. Safety and efficacy were assessed after 6 months. Responses were evaluated in terms of changes from baseline in lung physiology, functional capacity, and health-related quality of life. Follow-up is available for 21 of 25 patients. Results: Treatment was well tolerated. There were no treatment-related deaths (i.e. within 90 days of treatment), and an acceptable short-and long-term safety profile. Physiological and clinical benefits were observed at 24 weeks. Efficacy responses were better among Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage III patients {[}n = 14; change in residual volume/total lung capacity (Delta RV/TLC) = -7.4 +/- 10.3%; Delta forced expiratory volume in 1 s (Delta FEV(1)) = +15.9 +/- 22.6%; change in forced vital capacity (Delta FVC) = +24.1 +/- 22.7%; change in carbon monoxide lung diffusion capacity (Delta DLCO) = +19.3 +/- 34.8%; change in 6-min walk test (Delta 6MWD) = +28.7 +/- 59.6 m; change in Medical Research Council Dyspnea (Delta MRCD) score = -1.0 +/- 1.04 units; change in St. George's Respiratory Questionnaire (Delta SGRQ) score = -9.9 +/- 15.3 units] than for GOLD stage IV patients (n = 7; Delta RV/TLC = -0.5 +/- 6.4%; Delta FEV 1 = +2.3 +/- 12.3%; Delta FVC = +2.6 +/- 21.1%; Delta DLCO = -2.8 +/- 17.2%; Delta 6MWD = +28.3 +/- 58.4 m; Delta MRCD = 0.3 +/- 0.81 units; Delta SGRQ = -6.7 +/- 7.0 units). Conclusions: ELS therapy shows promise for treating patients with advanced heterogeneous emphysema. Additional studies to assess responses in a larger cohort with a longer follow-up are warranted. Copyright (C) 2011 S. Karger AG, Base

The Effects of Kinesiotape on Scapular Kinematics in Symptomatic Baseball Players

Introduction Baseball players are at an increased risk for shoulder dysfunction due to repetitive overhead throwing. Patients with symptomatic shoulders present with altered scapular kinematics, with the greatest variations found in upward rotation and posterior tilt which modify subacromial space. Previous investigations of the effects of kinesiotape (KT) on scapular kinematics have been inconclusive. Objective To determine the effects of KT on scapular kinematics in symptomatic collegiate baseball players. Participants Six Division II and III baseball players between 21 and 25 years old (mean 22.7) with a symptomatic throwing shoulder. Four were right hand dominant. Methods Symptomatic was defined as a report or pain or dysfunction in their throwing shoulder Participants were screened by student physical therapists (SPTs) to determine if they fit the inclusion criteria Kinesiotape was applied via a mechanical correction stabilization technique by a certified KT practitioner (Figure 1) Scapular posterior tilting (PT) and upward rotation (UR) were collected by a designated SPT during three planes of shoulder humerothoracic (HT) elevation with the G4 electromagnetic motion capture system (Innsport , Chicago, IL) Scapular kinematics with and without KT were analyzed between 30-90 degree elevation Differences in PT and UR during the three planes of elevation were explored descriptively Differences between conditions were compared proportionally to the maximum range of motion available Results PT was consistently greater in the KT condition. The largest difference was in abduction, where PT was 2.92 degrees greater. UR was consistently less in the KT condition. The largest difference was in abduction, where UR was 3.22 degrees less. The difference in PT was a larger proportion of available motion in abduction and was an equal proportion of available motion in elevation in the scapular plane as compared to UR. The PT proportion in abduction was 16 percent. The UR proportion in scapular plane elevation was 13 percent. Conclusions Increased posterior tilting widens the subacromial space, which is thought to decrease risk of subacromial impingement in overhead athletes. 3 Kinesiotape increased posterior tilting in symptomatic subjects during elevation in all 3 elevation planes. This advantage is somewhat countered by the decrease in upward rotation. Future work with an increased sample size may determine if there are statistical or clinically significant differences. Matched pair t tests with a Bonferonni correction would be an appropriate analysis. Clinical Implications These results indicate that KT may be an effective non invasive intervention to improve scapular kinematics and/or decrease injury risk in individuals with symptomatic shoulders

A new purple sulfur bacterium from saline littoral sediments, Thiorhodotvibrio winogradskyi gen. nov. and sp. nov.

Two strains of a new purple sulfur bacterium were isolated in pure culture from the littoral sediment of a saline lake (Mahoney Lake, Canada) and a marine microbial mat from the North Sea island of Mellum, respectively. Single cells were vibrioid-to spirilloid-shaped and motile by means of single polar flagella. Intracellular photosynthetic membranes were of the vesicular type. As photosynthetic pigments, bacteriochlorophyll a and the carotenoids lycopene, rhodopin, anhydrorhodovibrin, rhodovibrin and spirilloxanthin were present. Hydrogen sulfide and elemental sulfur were used under anoxic conditions for phototrophic growth. In addition one strain (06511) used thiosulfate. Carbon dioxide, acetate and pyruvate were utilized by both strains as carbon sources. Depending on the strain propionate, succinate, fumarate, malate, tartrate, malonate, glycerol or peptone may additionally serve as carbon sources in the light. Optimum growth rates were obtained at pH 7.2, 33 °C, 50 mol m-2 s-1 intensity of daylight fluorescent tubes and a salinity of 2.2–3.2% NaCl. During growth on sulfide, up to ten small sulfur globules were formed inside the cells. The strains grew microaerophilic in the dark and exhibited high specific respiration rates. No vitamins were required for growth. The DNA base composition was 61.0–62.4 mol% G+C. The newly isolated bacterium belongs to the family chromatiaceae and is described as a member of a new genus and species, Thiorhodovibrio winogradskyi gen. nov. and sp. nov. with the type strain SSP1, DSM No. 6702

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Dangerous drug interactions leading to hemolytic uremic syndrome following lung transplantation

<p>Abstract</p> <p>Background</p> <p>To report our experience of a rather uncommon drug interaction, resulting in hemolytic uremic syndrome (HUS).</p> <p>Methods</p> <p>Two consecutive cases of hemolytic uremic syndrome were diagnosed in our service. In both patients the use of macrolides in patients taking Tacrolimus, resulted in high levels of Tacrolimus.</p> <p>Results</p> <p>The first patient was a 48 years old female with Bilateral emphysema. She underwent Single Sequential Lung Transplantation. She developed reperfusion injury requiring prolonged stay. Tacrolimus introduced (Day 51). The patient remained well up till 5 months later; Erythromycin commenced for chest infection. High Tacrolimus levels and a clinical diagnosis of HUS were made. She was treated with plasmapheresis successfully.</p> <p>The second case was a 57 years old female with Emphysema & A1 Antithrypsin deficiency. She underwent Right Single Lung Transplantation. A2 rejection with mild Obliterative Bronchiolitis diagnosed 1 year later and she switched to Tacrolimus. She was admitted to her local Hospital two and a half years later with right middle lobe consolidation. The patient commenced on amoxicillin and clarithromycin. Worsening renal indices, high Tacrolimus levels, hemolytic anemia & low Platelets were detected. HUS diagnosed & treated with plasmapheresis.</p> <p>Conclusions</p> <p>There are 21 cases of HUS following lung transplantation in the literature that may have been induced by high tacrolimus levels. Macrolides in patients taking Cyclosporin or Tacrolimus lead to high levels. Mechanism of action could be glomeruloconstrictor effect with reduced GFR increased production of Endothelin-1 and increased Platelet aggregation.</p

Timescales of Massive Human Entrainment

The past two decades have seen an upsurge of interest in the collective behaviors of complex systems composed of many agents entrained to each other and to external events. In this paper, we extend concepts of entrainment to the dynamics of human collective attention. We conducted a detailed investigation of the unfolding of human entrainment - as expressed by the content and patterns of hundreds of thousands of messages on Twitter - during the 2012 US presidential debates. By time locking these data sources, we quantify the impact of the unfolding debate on human attention. We show that collective social behavior covaries second-by-second to the interactional dynamics of the debates: A candidate speaking induces rapid increases in mentions of his name on social media and decreases in mentions of the other candidate. Moreover, interruptions by an interlocutor increase the attention received. We also highlight a distinct time scale for the impact of salient moments in the debate: Mentions in social media start within 5-10 seconds after the moment; peak at approximately one minute; and slowly decay in a consistent fashion across well-known events during the debates. Finally, we show that public attention after an initial burst slowly decays through the course of the debates. Thus we demonstrate that large-scale human entrainment may hold across a number of distinct scales, in an exquisitely time-locked fashion. The methods and results pave the way for careful study of the dynamics and mechanisms of large-scale human entrainment.Comment: 20 pages, 7 figures, 6 tables, 4 supplementary figures. 2nd version revised according to peer reviewers' comments: more detailed explanation of the methods, and grounding of the hypothese

EpCAM expression varies significantly and is differentially associated with prognosis in the luminal B HER2+, basal-like, and HER2 intrinsic subtypes of breast cancer

BACKGROUND: Epithelial cell adhesion molecule (EpCAM) is frequently expressed in breast cancer, and its expression has been associated with poor prognosis. Breast cancer can be subdivided into intrinsic subtypes, differing in prognosis and response to therapy. METHODS: To investigate the association between EpCAM expression and prognosis in the intrinsic subtypes of breast cancer, we performed immunohistochemical studies on a tissue microarray encompassing a total of 1365 breast cancers with detailed clinicopathological annotation and outcomes data. RESULTS: We observed EpCAM expression in 660 out of 1365 (48%) cases. EpCAM expression varied significantly in the different intrinsic subtypes. In univariate analyses of all cases, EpCAM expression was associated with a significantly worse overall survival. In the intrinsic subtypes, EpCAM expression was associated with an unfavourable prognosis in the basal-like and luminal B HER2(+) subtypes but associated with a favourable prognosis in the HER2 subtype. Consistently, specific ablation of EpCAM resulted in increased cell viability in the breast cancer cell line SKBR3 (ER(−), PR(−), and HER2(+)) but decreased viability in the breast cancer cell line MDA-MB-231 (ER(−), PR(−), and HER2(−) ). CONCLUSION: The differential association of EpCAM expression with prognosis in intrinsic subtypes has important implications for the development of EpCAM-targeted therapies in breast cancer