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Toward a service-based workflow for automated information extraction from herbarium specimens
(2018)
Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses. The evolving system presently covers the generation of optical character recognition (OCR) from specimen images, the identification of regions of interest in images and the extraction of meaningful information items from OCR. These implementations were developed as part of the Deutsche Forschungsgemeinschaft funded a standardised and optimised process for data acquisition from digital images of herbarium specimens (StanDAP-Herb) Project.
The objective of this study was to investigate the association between teat skin colonization and intramammary infection (IMI) with Staphylococcus aureus or Streptococcus agalactiae at the quarter level in herds with automatic milking systems. Milk and teat skin samples from 1,142 quarters were collected from 300 cows with somatic cell count >200,000 cells/mL from 8 herds positive for Strep. agalactiae. All milk and teat skin samples were cultured on calf blood agar and selective media. A subset of samples from 287 quarters was further analyzed using a PCR assay (Mastit4 PCR; DNA Diagnostic A/S, Risskov, Denmark). Bacterial culture detected Staph. aureus in 93 (8.1%) of the milk samples and 75 (6.6%) of the teat skin samples. Of these, 15 (1.3%) quarters were positive in both the teat skin and milk samples. Streptococcus agalactiae was cultured in 84 (7.4%) of the milk samples and 4 (0.35%) of the teat skin samples. Of these, 3 (0.26%) quarters were positive in both the teat skin and milk samples. The PCR detected Staph. aureus in 29 (10%) of the milk samples and 45 (16%) of the teat skin samples. Of these, 2 (0.7%) quarters were positive in both the teat skin and milk samples. Streptococcus agalactiae was detected in 40 (14%) of the milk samples and 51 (18%) of the teat skin samples. Of these, 16 (5.6%) quarters were positive in both the teat skin and milk samples. Logistic regression was used to investigate the association between teat skin colonization and IMI at the quarter level. Based on bacterial culture results, teat skin colonization with Staph. aureus resulted in 7.8 (95% confidence interval: 2.9; 20.6) times higher odds of Staph. aureus IMI, whereas herd was observed as a major confounder. However, results from the PCR analyses did not support this association. Streptococcus agalactiae was isolated from the teat skin with both PCR and bacterial culture, but the number of positive teat skin samples detected by culture was too low to proceed with further analysis. Based on the PCR results, Strep. agalactiae on teat skin resulted in 3.8 (1.4; 10.1) times higher odds of Strep. agalactiae IMI. Our results suggest that Staph. aureus and Strep. agalactiae on teat skin may be a risk factor for IMI with the same pathogens. Focus on proper teat skin hygiene is therefore recommended also in AMS.
Background: Depletion of ovarian hormone in postmenopausal women has been associated with changes in the locomotor apparatus that may compromise walking function including muscle atrophy/weakness, weight gain, and bone demineralization. Therefore, handgrip strength (HGS), bone mineral density (BMD) and body composition [percentage body fat mass (%BFM), fat mass (FM), Fat-free mass (FFM) and body mass index (BMI)], may significantly vary and predict WB in postmenopausal women. Consequently, the study sought to 1. Explore body composition, BMD and muscle strength differences between premenopausal and postmenopausal women and 2. Explore how these variables [I.e., body composition, BMD and muscle strength] relate to WB in postmenopausal women.
Method: Fifty-one pre-menopausal (35.74 + 1.52) and 50 postmenopausal (53.32 + 2.28) women were selected by convenience sampling and studied. Six explanatory variables (HGS, BMD, %BFM, FFM, BMI and FM) were explored to predict WB in postmenopausal women: Data collected were analyzed using multiple linear regression, ANCOVA, independent t-test and Pearson correlation coefficient at p < 0.05.
Result: Postmenopausal women had higher BMI(t = + 1.72; p = 0.04), %BFM(t = + 2.77; p = .003), FM(t = + 1.77; p = 0.04) and lower HGS(t = − 3.05; p = 0.001),compared to the premenopausal women. The predicted main effect of age on HGS was not significant, F(1, 197) = 0.03, p = 0.06, likewise the interaction between age and %BFM, F(1, 197) = 0.02, p = 0.89; unlike the predicted main effect of %BFM, F(1, 197) = 10.34, p = .002, on HGS. HGS was the highest predictor of WB (t = 2.203; β=0.3046) in postmenopausal women and combined with T-score right big toe (Tscorert) to produce R2 = 0.11;F (2, 47)=4.11;p = 0.02 as the best fit for the predictive model. The variance (R2) change was significant from HGS model (R2 = 0.09;p = 0.03) to HGS + Tscorert model (R2 = 0.11;p = 0.02). The regression model equation was therefore given as: WB =5.4805 + 0.1578(HGS) + (− 1.3532) Tscorert.
Conclusion: There are differences in body composition suggesting re-compartmentalization of the body, which may adversely impact the (HGS) muscle strength in postmenopausal women. Muscle strength and BMD areassociated with WB, although, only contribute to a marginal amount of the variance for WB. Therefore, other factors in addition to musculoskeletal health are necessary to mitigate fall risk in postmenopausal women.
Staphylococcus aureus is recognized worldwide as one of the major agents of dairy cow intra-mammary infections. This microorganism can express a wide spectrum of pathogenic factors used to attach, colonize, invade and infect the host. The present study evaluated 120 isolates from eight different countries that were genotyped by RS-PCR and investigated for 26 different virulence factors to increase the knowledge on the circulating genetic lineages among the cow population with mastitis. New genotypes were observed for South African strains while for all the other countries new variants of existing genotypes were detected. For each country, a specific genotypic pattern was found. Among the virulence factors, fmtB, cna, clfA and leucocidins genes were the most frequent. The sea and sei genes were present in seven out of eight countries; seh showed high frequency in South American countries (Brazil, Colombia, Argentina), while sel was harboured especially in one Mediterranean country (Tunisia). The etb, seb and see genes were not detected in any of the isolates, while only two isolates were MRSA (Germany and Italy) confirming the low diffusion of methicillin resistance microorganism among bovine mastitis isolates. This work demonstrated the wide variety of S. aureus genotypes found in dairy cattle worldwide. This condition suggests that considering the region of interest might help to formulate strategies for reducing the infection spreading.
A nonblinded, positively controlled, noninferiority trial was conducted to evaluate the efficacy of an alternative, nonantibiotic therapy with Masti Veyxym® to reduce ineffective antibiotic usage in the treatment of nonsevere clinical mastitis (CM) in cows with longer lasting udder diseases. The solely intramammary treatment with Masti Veyxym® (three applications, 12 hr apart) and the combined treatment with Masti Veyxym® and antibiotics as usual on the farm according to label of the respective product were compared with the reference treatment of solely antibiotic therapy. The matched field study was conducted on eight free-stall dairy farms located in Eastern Germany. Cases of mild-to-moderate CM in cows with longer lasting high somatic cell counts in preceding dairy herd improvement test days and with previous CM cases in current lactation were randomly allocated to one of the three treatment groups. A foremilk sample of the affected quarter was taken before treatment and again approximately 14 days and 21 days after the end of therapy for cyto-bacteriological examination. Primary outcomes were clinical cure (CC) and no CM recurrence within 60 days after the end of treatment (no R60). Bacteriological cure (BC) and quarter somatic cell count (QSCC) cure were chosen as secondary outcomes although low probabilities of BC and QSCC cure for selected cows were expected. The study resulted in the following findings: the pathogens mostly cultured from pretreatment samples were Streptococcus uberis, followed by Staphylococcus aureus and coagulase-negative staphylococci. There were no significant differences between the two test treatments in comparison with the reference treatment regarding all outcome variables. The sole therapy with Masti Veyxym® resulted in a numerically lower likelihood of BC without significant differences to the reference treatment. The combined therapy group showed a numerically higher nonrecurrence rate than the two other treatment groups and noninferiority compared to the reference treatment was proven. Having regard to the selection criteria of cows in this study, the findings indicated that sole treatment with Masti Veyxym® in nonsevere CM cases may constitute an alternative therapy to reduce antibiotics. However, noninferiority evaluations were mostly inconclusive. Further investigations with a larger sample size are required to confirm the results and to make a clear statement on noninferiority.
Für die Studiengang-Auswahl existiert eine Reihe i. d. R. Fragebogen-gestützter Online-Studiengangfinder. Eine Analyse zeigte Optimierungspotenziale: Studienangebote sind meist auf ein Bundesland oder eine Hochschule beschränkt oder, allgemein beschrieben, die individuelle Studiengang-Auswahl ist nur mit Unschärfen möglich. Letzteres wirkt sich z. B. bei Bindestrich-Studiengängen (z. B. Wirtschaftsingenieurwesen) aus, die je nach Hochschule inhaltlich variieren können. Hier setzt das Portal an. Ziele sind: Bereitstellung der in der Sprachwelt Studieninteressierter gehaltenen Fragebögen, Möglichkeit für Hochschulen/Einrichtungen, Studiengänge bereitzustellen.
Background: Given both the increase of nursing home residents forecast and challenges of current interprofessional interactions, we developed and tested measures to improve collaboration and communication between nurses and general practitioners (GPs) in this setting. Our multicentre study has been funded by the German Federal Ministry of Education and Research (FK 01GY1124).
Methods: The measures were developed iteratively in a continuous process, which is the focus of this article. In part 1 “exploration of the situation”, interviews were conducted with GPs, nurses, nursing home residents and their relatives focusing on interprofessional interactions and medical care. They were analysed qualitatively. Based on these results, in part 2 “development of measures to improve collaboration”, ideas for improvement were developed in nine focus groups with GPs and nurses. These ideas were revisited in a final expert workshop. We analysed the focus groups and expert workshop using mind mapping methods, and finally drew up the compilation of measures. In an exploratory pilot study "study part 3" four nursing homes chose the measures they wanted to adopt. These were tested for three months. Feasibility and acceptance of the measures were evaluated via guideline interviews with the stakeholders which were analysed by content analyses.
Results: Six measures were generated: meetings to establish common goals, main contact person, standardised pro re nata medication, introduction of name badges, improved availability of nurse/GP and standardised scheduling/ procedure for nursing home visits. In the pilot study, the measures were implemented in four nursing homes. GPs and nurses reviewed five measures as feasible and acceptable, only the designation of a “main contact person” was not considered as an improvement.
Conclusions: Six measures to improve collaboration and communication could be compiled in a multistep qualitative process respecting the perspectives of involved stakeholders. Five of the six measures were positively assessed in an exploratory pilot study. They could easily be transferred into the daily routine of other nursing homes, as no special models have to exist in advance. Impact of the measures on patient oriented outcomes should be examined in further research.
Trial registration: Not applicable.
Delphi is a frequently used research method in the information systems (IS) field. The last fifteen years have seen many variants of the Delphi Method proposed and used in IS research. However, these variants do not seem to be properly derived; while all variants share certain characteristics, their reasoning for differentiation inconsistently varies. It seems that researchers tend to create “new” Delphi Method variants, although the underlying modification of the Delphi Method is, in fact, minor. This leads to a heterogeneity of Delphi Method variants and undermines scientific rigor when using Delphi. The study addresses this deficit and (1) identifies different variants of Delphi and determines their characteristics, (2) critically reflects to what extent a clear distinction between these variants exists, (3) shows the clearly distinguishable Delphi Method variants and their characteristics, (4) develops a proposed taxonomy of Delphi Method variants, and (5) evaluates and applies this taxonomy. The proposed taxonomy helps clearly differentiate Delphi Method variants and enhances methodological rigor when using the Delphi Method.
Objectives:
The aim was to identify theoretically expected as well as actually reported benefits from drug development and the importance of individual patient benefits compared to the collective benefits to society in general.
Background:
Ethical guidelines require that clinical research involving humans offer the potential for benefit. A number of characteristics can be applied to define research benefit. Often benefit is categorized as being either direct or indirect. Indirect benefits can involve collective benefits for society rather than any benefits to the trial patient or subject. The purpose of this review was to examine which potential individual and societal benefits were mentioned as being expected in publications from government experts and which were mentioned in publications describing completed drug development trial results.
Methods:
Literature on research benefit was first identified by searching the PubMed database using several combinations of the key words benefit and clinical research. The search was limited to articles published in English. A Google search with the same combinations of key words but without any language limitation was then performed. Additionally, the reference lists of promising articles were screened for further thematically related articles. Finally, a narrative review was performed of relevant English- and German-language articles published between 1996 and 2016 to identify which of several potential benefits were either theoretically expected or which were mentioned in publications on clinical drug development trial results.
Results:
The principal benefits from drug development discussed included 2 main types of benefit, namely individual benefits for the patients and collective benefits for society. Twenty-one of an overall total of 26 articles discussing theoretically expected benefits focused on individual patient benefits, whereas 17 out of 26 articles mentioned collective benefits to society. In these publications, the most commonly mentioned theoretically expected individual patient benefit was the chance to receive up-to-date care (38.1%). A general increase in knowledge about health care, treatments, or drugs (70.6%) was the most commonly mentioned theoretically expected benefit for society. In contrast, all 13 publications reporting actual benefits of clinical drug development trials focused on personal benefits and only 1 of these publications also mentioned a societal benefit. The most commonly mentioned individual benefit was an increased quality of life (53.9%), whereas the only mentioned collective benefit to society was a general gain of knowledge (100.0%).
Conclusions:
Both theoretically expected and actually reported benefits in the majority of the included publications emphasized the importance of individual patient benefits from drug development rather than the collective benefits to society in general. The authors of these publications emphasized the right of each individual patient or subject to look for and expect some personal benefit from participating in a clinical trial rather than considering societal benefit as a top priority. From an ethical point of view, the benefits each individual patient receives from his or her participation in a clinical trial might also be seen as a societal benefit, especially when the drug or device tested, if approved for marketing, would eventually be made available for other similar patients from the country in which the clinical trial was conducted.