Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring the Availability of Electronic Patient Data Across the Hospital and Throughout Selected Clinical Workflows

The workflow-oriented dissemination of electronic patient data is a central goal of IT deployment in hospitals. Against this background, the present study examines two research questions: (1.) Are there differences in the availability of electronic patient data (AEPD) between different clinical workflows and data types and (2.) which structural and organizational factors determine AEPD? Based on a Germany wide hospital survey, AEPD was assessed along six clinical workflows. While AEPD was lowest for ward rounds, discharge showed the highest AEPD with pre- and post-surgery processes ranging in between. With regard to the data types analyzed, patient demographics and observation findings obtained the highest AEPD scores. Electrophysiological results, checklists and warnings were less common electronically and received lower AEPD scores. Multiple linear regression analysis resulted in a significant model that explained 34.4% of the variance of AEPD. Large hospitals and those with a professional information management, a high health IT related innovation culture and a nursing informatics officer possess higher AEPD scores and thus have better clinical information logistics mechanisms at their command.
Determinants of Clinical Information Logistics: Tracing Socio-Organisational Factors and Country Differences from the Perspective of Clinical Directors

The establishment of successful clinical information logistics (CIL) within the care processes is one of the main objectives of strategic health IT management in hospitals. While technical realisations in terms of useful, usable and interoperable IT solutions are essential precursors of CIL, there is limited empirical research on what socio-organisational factors underlie an innovation-friendly culture and how they can affect successful information provision. We applied factor analysis on survey data from 403 clinical directors from Germany, Austria and Switzerland and used the dimensions identified to explain the level of CIL with ordered logistic regression analysis. The intensity of collaboration and exchange with the IT department as well as the degree of executive IT leadership showed to be strongly associated with better CIL while personal views and attitudes of clinical directors were not. Analysing country differences revealed the degree of the exchange with the IT department to be significantly lower in German hospitals. This points at a potential strategic lever for German hospital executives to focus on.
Mass Azithromycin Distribution and Community Microbiome: A Cluster-Randomized Trial

Abstract Background Mass distributions of oral azithromycin have long been used to eliminate trachoma, and they are now being proposed to reduce childhood mortality. The observed benefit appears to be augmented with each additional treatment, suggesting a possible community-level effect. Here, we assess whether 2 biannual mass treatments of preschool children affect the community’s gut microbiome at 6 months after the last distribution. Methods In this cluster-randomized controlled trial, children aged 1–60 months in the Dossa region of Niger were randomized at the village level to receive a single dose of azithromycin or placebo every 6 months. Fecal samples were collected 6 months after the second treatment for metagenomic deep sequencing. The prespecified primary outcome was the Euclidean PERMANOVA of the gut microbiome, or effectively the distance between the genus-level centroid at the community level, with the secondary outcome being the Simpson’s α diversity. Results In the azithromycin arm, the gut microbial structures were significantly different than in the placebo arm (Euclidean PERMANOVA, P < .001). Further, the diversity of the gut microbiome in the azithromycin arm was significantly lower than in the placebo arm (inverse Simpson’s index, P = .005). Conclusions Two mass azithromycin administrations, 6 months apart, in preschool children led to long-term alterations of the gut microbiome structure and community diversity. Here, long-term microbial alterations in the community did not imply disease but were associated with an improvement in childhood mortality. Clinical Trials Registration NCT02048007.
The modulation of eye movement control by word length in reading Chinese

Given there are no interword spaces marking word boundaries in Chinese text, it remains unclear how information about word length influences eye movement control during the reading of Chinese text. In this research, we set up strict controls for word frequency and other word properties, to study this knowledge gap. In Experiment 1A and Experiment 1B, a between-subjects design was used. Forty-eight pairs of one- and two-character words were selected as target words in Experiment 1A, while the same amount of two- and three-character words were selected in Experiment 1B. Conversely, a within-subjects design was used in Experiment 2. Sixty sets of one-, two- and three-character words were selected as target words. The results showed that long words were skipped less often and fixated on more often than short words. Total time was shorter for shorter than for longer words but first fixation durations were longer for one- than for two-character words. Most importantly, we did not find reliable evidence to support the view that word length could modulate initial landing position and incoming saccade length in the length-matched region analyses. These findings suggest that word length influences eye movement control during reading Chinese in a way that is slightly different from that in the process of reading English.
A Hierarchical Model of Visual Processing Simulates Neural Mechanisms Underlying Reflexive Attention

The visual system deploys attention reflexively in response to important stimuli to facilitate rapid selection. To better understand how a system that is distributed across a hierarchy of brain areas coordinates this rapid response, we have developed a computational model that simulates reflexive attention as a recurrent lock-on state between topographically aligned cortical areas. This model provokes key questions about reflexive attention that we study through the N2pc, an EEG component that indexes the timing and lateralization of stimulus-driven attention. A key finding from such research is that for two sequential targets sharing a location, the second elicits no N2pc, despite being easily perceivable. This suggests that attention locks-on to a target’s location and carries forward in time to a second target without being redeployed. Here, we assess key properties of reflexive attention in four EEG experiments. First, the lock-on N2pc effect generalizes to feature target types. Second, the lock-on state is specific to a location, not just a visual hemifield. Third, reflexive attention decays as the interval between two targets increases, such that a second target will once-again elicit an N2pc at longer intervals. Finally, the lock-on state is not specific to a particular target type, which implies that reflexive attention is mediated using representations that are not stimulus-specific. These results provide important constraints on our understanding of visual attention. We incorporate those constraints in a formalized model of attention that elucidates the link between neural mechanisms and a key neural correlate of attention.
Effect of Crocus sativus L. stigma (saffron) against subacute effect of diazinon: histopathological, hematological, biochemical and genotoxicity evaluations in rats

Objective In this study, the effects of saffron stigma against subacute diazinon (DZN) toxicity on enzymes levels, biochemical, hematological, histopathological and genotoxicity indices were studied in rats. Methods Vitamin E (200 IU/kg) and the aqueous extract of saffron (50, 100 and 200 mg/kg) were injected intraperitoneally three times per week alone or with DZN (20 mg/kg/day, orally) for 4 weeks. The hematological and biochemical parameters were evaluated at the end of 4 weeks. Results Reticulocytes counts, alkaline phosphatase (ALP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), creatine phosphokinase, CPK-MB, gama glutamyl transferase (GGT), uric acid and micronucleus indices were increased significantly but total protein and RBC cholinesterase activity were decreased in the DZN-treated group. Saffron prevented the effect of DZN on GGT (50 mg/kg), LDH, CPK and CPK-MB (100 and 200 mg/kg) levels. An increased uric acid and reduced protein levels by DZN were prevented by vitamin E and some doses of saffron. A significant reduction was observed in platelets, RBC, hemoglobin and hematocrit indices in the DZN group. Saffron and vitamin E prevented this reduction. Vitamin E and saffron did not reduce the effect of DZN on RBC cholinesterase activity. The extract and vitamin E could not prevent DZN genotoxicity in the micronucleus assay. Other biochemical parameters and pathological evaluation did not show any abnormality in tissues of all groups. Conclusion This study shows that vitamin E and saffron reduce DZN induced hematological and biochemical toxicity. However, they do not prevent the genotoxicity induced by DZN.
Conducting ethical internet-based research with vulnerable populations: a qualitative study of bereaved participants’ experiences of online questionnaires

ABSTRACT Background: Bereavement can be considered a potentially traumatic experience, and concerns have been raised about conducting grief research responsibly online. Objective: Given that online research introduces new methodological opportunities and challenges, we aimed to develop a greater understanding of how bereaved individuals experience participation in online research. Method: One day after participation in an online grief study, 876 participants, bereaved on average for 40 months, received a ‘check-in’ email to support well-being and offer further contact if needed. Although not explicitly asked to respond if no help was needed, 300 participants sent email replies, with only six requesting support. These responses were analysed qualitatively using content analysis. Results: Results suggested that participants found it acceptable to be asked about their grief and while difficult emotions were frequently described in response to the questionnaires, these reactions were temporary. A range of positive reactions was also reported, including new realizations arising from completing the research and changes in thinking related to grief. Participants also wrote about their appreciation for the study and how it was carried out, as well as a desire to contribute more to the study and to help others in a similar position. Conclusions: We suggest that the use of the check-in email to support well-being following study completion, along with advice on preparing to take part, contributed to positive experiences of participation and we recommend these strategies for future studies. These findings could allay clinical concerns about conducting online research with vulnerable populations, as well as raising questions about the possible therapeutic impact of measurement.
Overexpression of a Brix Domain-Containing Ribosome Biogenesis Factor ARPF2 and its Interactor ARRS1 Causes Morphological Changes and Lifespan Extension in Arabidopsis thaliana

The Brix domain is a conserved domain in several proteins involved in ribosome biogenesis in yeast and animals. In the Arabidopsis genome, six Brix domain-containing proteins are encoded; however, their molecular functions have not been fully characterized, as yet. Here we report the functional analysis of a Brix domain-containing protein, ARPF2, which is homologous to yeast Rpf2 that plays an essential role in ribosome biogenesis as a component of the 5S ribonucleoprotein particle. By phenotypic characterization of arpf2 mutants, histochemical GUS staining, and analysis using green fluorescence protein, we show that ARPF2 is an essential and ubiquitously expressed gene encoding a nucleolar protein. Co-immunoprecipitation and split-GFP-based bimolecular fluorescence complementation assays revealed that ARPF2 interacts with a protein named ARRS1, which is homologous to yeast Rrs1 that forms a complex with Rpf2 in yeast. Furthermore, the result of RNA immunoprecipitation assay indicated that ARPF2 interacts with 5S ribosomal RNA (rRNA) or the precursor of 5S rRNA, as well as with the internal transcribed spacer 2 in the precursors of 25S rRNA. Most intriguingly, we found that the overexpression of ARPF2 and ARRS1 leads to characteristic phenotypes, including short stem, abnormal leaf morphology, and long lifespan, in Arabidopsis. These results suggest that the function of Brix domain-containing ARPF2 protein in ribosome biogenesis is intimately associated with the growth and development in plants.
A Novel Method for Extrinsic Calibration of Multiple RGB-D Cameras Using Descriptor-Based Patterns

This paper presents a novel method to estimate the relative poses between RGB-D cameras with minimal overlapping fields of view. This calibration problem is relevant to applications such as indoor 3D mapping and robot navigation that can benefit from a wider field of view using multiple RGB-D cameras. The proposed approach relies on descriptor-based patterns to provide well-matched 2D keypoints in the case of a minimal overlapping field of view between cameras. Integrating the matched 2D keypoints with corresponding depth values, a set of 3D matched keypoints are constructed to calibrate multiple RGB-D cameras. Experiments validated the accuracy and efficiency of the proposed calibration approach.
Beyond the snapshot: Landscape genetic analysis of time series data reveal responses of American black bears to landscape change

Landscape genetic studies typically focus on the evolutionary processes that give rise to spatial patterns that are quantified at a single point in time. Although landscape change is widely recognized as a strong driver of microevolutionary processes, few landscape genetic studies have directly evaluated the change in spatial genetic structure (SGS) over time with concurrent changes in landscape pattern. We introduce a novel approach to analyze landscape genetic data through time. We demonstrate this approach using genotyped samples (n = 569) from a large black bear (Ursus americanus) population in Michigan (USA) that were harvested during 3 years (2002, 2006, and 2010). We identified areas that were consistently occupied over this 9‐year period and quantified temporal variation in SGS. Then, we evaluated alternative hypotheses about effects of changes in landscape features (e.g., deforestation or crop conversion) on fine‐scale SGS among years using spatial autoregressive modeling and model selection. Relative measures of landscape change such as magnitude of landscape change (i.e., number of patches changing from suitable to unsuitable states or vice versa), and during later periods, measures of fragmentation (i.e., patch aggregation and cohesion) were associated with change in SGS. Our results stress the importance of conducting time series studies for the conservation and management of wildlife inhabiting rapidly changing landscapes.
Optimizing DNA transduction by selection of mutations that evade bacterial defense systems

ABSTRACT We recently developed a platform where phage-transducing particles optimize DNA delivery to a wide range of hosts. Here, we use this platform to optimize DNA transduction into hosts that naturally restrict specific DNA sequences. We first show that a specific plasmid is restricted for transduction into a particular Salmonella strain. Using the platform, we select for a mutated plasmid that overcomes the restriction barrier. Insertion of the non-mutated sequence into a permissive plasmid restricts transduction. We further show that epigenetic modification enables the DNA to evade restriction by the putative defense system. Our results validate this straightforward genetic approach for optimization of DNA transduction into new hosts.
Role of Ezrin Phosphorylation in HIV-1 Replication

Host-cell expression of the ezrin protein is required for CXCR4 (X4)-tropic HIV-1 infection. Ezrin function is regulated by phosphorylation at threonine-567. This study investigates the role of ezrin phosphorylation in HIV-1 infection and virion release. We analyzed the effects of ezrin mutations involving substitution of threonine-567 by alanine (EZ-TA), a constitutively inactive mutant, or by aspartic acid (EZ-TD), which mimics phosphorylated threonine. We also investigated the effects of ezrin silencing on HIV-1 virion release using a specific siRNA. We observed that X4-tropic HIV-1 vector infection was inhibited by expression of the EZ-TA mutant but increased by expression of the EZ-TD mutant, suggesting that ezrin phosphorylation in target cells is required for efficient HIV-1 entry. Expression of a dominant-negative mutant of ezrin (EZ-N) and ezrin silencing in HIV-1 vector-producing cells significantly reduced the infectivity of released virions without affecting virion production. This result indicates that endogenous ezrin expression is required for virion infectivity. The EZ-TD but not the EZ-TA inhibited virion release from HIV-1 vector-producing cells. Taken together, these findings suggest that ezrin phosphorylation in target cells is required for efficient HIV-1 entry but inhibits virion release from HIV-1 vector-producing cells.
Robust identification of target genes and outliers in triple-negative breast cancer data

Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal. Our analysis identifies statistical outliers that may correspond to misdiagnosed patients. Furthermore, it is illustrated that classical statistical methods may fail to identify outliers due to their heavy influence, prompting the need for robust statistics. Using robust sparse logistic regression we obtain 36 relevant genes, of which ca. 60% have been previously reported as biologically relevant to triple-negative breast cancer, reinforcing the validity of the method. The remaining 14 genes identified are new potential biomarkers for triple-negative breast cancer. Out of these, JAM3, SFT2D2, and PAPSS1 were previously associated to breast tumors or other types of cancer. The relevance of these genes is confirmed by the new DetectDeviatingCells outlier detection technique. A comparison of gene networks on the selected genes showed significant differences between triple-negative breast cancer and non-triple-negative breast cancer data. The individual role of FOXA1 in triple-negative breast cancer and non-triple-negative breast cancer, and the strong FOXA1-AGR2 connection in triple-negative breast cancer stand out. The goal of our paper is to contribute to the breast cancer/triple-negative breast cancer understanding and management. At the same time it demonstrates that robust regression and outlier detection constitute key strategies to cope with high-dimensional clinical data such as omics data.
Association of genetic risk score and chronic kidney disease in a Japanese population

Chronic kidney disease (CKD) is a public health problem worldwide including Japan. Recent genome‐wide association studies have discovered CKD susceptibility variants. We developed a genetic risk score (GRS) based on CKD‐associated variants and assessed a possibility that the GRS can improve the discrimination capability for the prevalence of CKD in a Japanese population. The present study consists of 11 283 participants randomly selected from 12 Japan Multi‐Institutional Collaborative Cohort Study sites. Individual GRS was constructed combining 18 single‐nucleotide polymorphisms identified in a Japanese population. Participants with eGFR <60 mL/min per 1.73 m2 was defined as case (stage 3 CKD or higher) in this study. Logistic regression analysis was used to examine the association between the GRS and CKD risk with adjustment for sex, age, hypertension and type 2 diabetes mellitus. The frequency of individuals with CKD was 8.3%, which was relatively low compared with those previously reported in a Japanese population. The odds ratio of having CKD was 1.120 (95% confidence interval: 1.042–1.203) per 10 GRS increment in the fully adjusted model (P = 0.002). The C‐statistic was significantly increased in the model with the GRS, comparing with the model without the GRS (0.720 vs 0.719, Pdifference = 0.008). Increment of the GRS was associated with increased risk of CKD. Additionally, the GRS significantly improved the discriminatory ability of CKD prevalence in a Japanese population; however, the improvement of discriminatory ability brought about by the GRS seemed to be small compared with that of non‐genetic CKD risk factors.
Phylogenetic relationships of North American Gomphidae and their close relatives

Intrafamilial relationships among clubtail dragonflies (Gomphidae) have been the subject of many morphological studies, but have not yet been systematically evaluated using molecular data. Here we present the first molecular phylogeny of Gomphidae. We include six of the eight subfamilies previously suggested to be valid, and evaluate generic relationships within them. We have included examples of all genera reported from the Nearctic except Phyllocycla. This sample includes all North American species of Ophiogomphus, which has allowed us to explore intrageneric relationships in that genus. Our particular focus is on the closest relatives of the genus Gomphus, especially those North American species groups that have been commonly treated as subgenera of Gomphus. The Gomphus complex is split into additional genera, supported by molecular and morphological evidence: Phanogomphus, Stenogomphurus, Gomphurus and Hylogomphus are here considered to be valid genera. The genus Gomphus, in our restricted sense, does not occur in the western hemisphere; in addition, G. flavipes is transferred to Stylurus.