Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing a Workflow Composite Score to Measure Clinical Information Logistics

Summary Background: Availability and usage of individual IT applications have been studied intensively in the past years. Recently, IT support of clinical processes is attaining in-creasing attention. The underlying construct that describes the IT support of clinical work-flows is clinical information logistics. This construct needs to be better understood, operationalised and measured. Objectives: It is therefore the aim of this study to propose and develop a workflow composite score (WCS) for measuring clinical information logistics and to examine its quality based on reliability and validity analyses. Methods: We largely followed the procedural model of MacKenzie and colleagues (2011) for defining and conceptualising the construct domain, for developing the measurement instrument, assessing the content validity, pre-testing the instrument, specifying the model, capturing the data and computing the WCS and testing the reliability and validity. Results: Clinical information logistics was decomposed into the descriptors data and information, function, integration and distribution, which embraced the framework validated by an analysis of the international literature. This framework was refined selecting representative clinical processes. We chose ward rounds, pre- and post-surgery processes and discharge as sample processes that served as concrete instances for the measurements. They are sufficiently complex, represent core clinical processes and involve different professions, departments and settings. The score was computed on the basis of data from 183 hospitals of different size, ownership, location and teaching status. Testing the reliability and validity yielded encouraging results: the reliability was high with rsplit-half = 0.89, the WCS discriminated between groups; the WCS correlated significantly and moderately with two EHR models and the WCS received good evaluation results by a sample of chief information officers (n = 67). These findings suggest the further utilisation of the WCS. Conclusion: As the WCS does not assume ideal workflows as a gold standard but measures IT support of clinical workflows according to validated descriptors a high portability of the WCS to other hospitals in other countries is very likely. The WCS will contribute to a better understanding of the construct clinical information logistics.
The Dissipation of Trapped Lee Waves. Part II: The Relative Importance of the Boundary Layer and the Stratosphere

AbstractDecaying trapped waves exert a drag on the large-scale flow. The two most studied mechanisms for such decay are boundary layer dissipation and leakage into the stratosphere. If the waves dissipate in the boundary layer, they exert a drag near the surface, whereas, if they leak into the stratosphere, the drag is exerted at the level where the waves dissipate aloft. Although each of these decay mechanisms has been studied in isolation, their relative importance has not been previously assessed.Here, numerical simulations are conducted showing that the relative strength of these two mechanisms depends on the details of the environment supporting the waves. During actual trapped-wave events, the environment often includes elevated inversions and strong winds aloft. Such conditions tend to favor leakage into the stratosphere, although boundary layer dissipation becomes nonnegligible in cases with shorter resonant wavelengths and higher tropopause heights. In contrast, idealized two-layer profiles with .
Determinants of Adherence to Diabetes Medications: Findings From a Large Pharmacy Claims Database

OBJECTIVE Adults with diabetes typically take multiple medications for hyperglycemia, diabetes-associated conditions, and other comorbidities. Medication adherence is associated with improved outcomes, including reduced health care costs, hospitalization, and mortality. We conducted a retrospective analysis of a large pharmacy claims database to examine patient, medication, and prescriber factors associated with adherence to antidiabetic medications. RESEARCH DESIGN AND METHODS We extracted data on a cohort of >200,000 patients who were treated for diabetes with noninsulin medications in the second half of 2010 and had continuous prescription benefits eligibility through 2011. Adherence was defined as a medication possession ratio ≥0.8. We used a modified adherence measure that accounted for switching therapies. Logistic regression analysis was performed to determine factors independently associated with adherence. RESULTS Sixty-nine percent of patients were adherent. Adherence was independently associated with older age, male sex, higher education, higher income, use of mail order versus retail pharmacies, primary care versus nonendocrinology specialist prescribers, higher daily total pill burden, and lower out-of-pocket costs. Patients who were new to diabetes therapy were significantly less likely to be adherent. CONCLUSIONS Several demographic, clinical, and potentially modifiable system-level factors were associated with adherence to antidiabetic medications. Patients typically perceived to be healthy (those who are younger, new to diabetes, and on few other medications) may be at risk for nonadherence. For all patients, efforts to reduce out-of-pocket costs and encourage use of mail order pharmacies may result in higher adherence.
Exploring the Goat Rumen Microbiome from Seven Days to Two Years

Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. We found that the bacterial communities were mainly composed of Bacteroidetes, Firmicutes, and Proteobacteria across all age groups. The relative abundance of Firmicutes was stable across all age groups. While changes in relative abundance were observed in Bacteroidetes and Proteobacteria, these two phyla reached a stable stage after weaning (day 90). Euryarchaeota (82%) and Thaumarchaeota (15%) were the dominant phyla of Archaea. Crenarchaeota was also observed, although at a very low relative abundance (0.68% at most). A clear age-related pattern was observed in the diversity of bacterial community with 59 OTUs associated with age. In contrast, no age-related OTU was observed in archaea. In conclusion, our results suggested that from 7 days to 2 years, the ruminal microbial community of our experimental goats underwent significant changes in response to the shift in age and diet.
Evolving concepts in the pathophysiology, diagnosis, and treatment of pheochromocytoma.

THE very first known successful operation for removal of a pheochromocytoma was performed by Cesar Roux in February 1926 in Lausanne, Switzerland (1). C. H. Mayo performed the first successful removal of a pheochromocytoma in North America in October of the same year (2). Since these first successful operations, considerable progress has been made in the diagnosis and treatment of pheochromocytoma. The availability of sensitive and specific immunoassay procedures, the development of simplified diagnostic testing, and the introduction of sensitive imaging techniques have enhanced the clinician's ability to make the diagnosis with greater certainty. In addition, a better understanding of catecholamine action and the pathophysiology of pheochromocytoma and an appreciation of the wide range of clinical manifestations associated with it have led not only to earlier recognition of the disease but also to a more rational approach to its diagnosis and management. Nevertheless, there are still uncertainties regard.
Early Production of Type I Interferon during West Nile Virus Infection: Role for Lymphoid Tissues in IRF3-Independent Interferon Production

ABSTRACT Infection of cells with flaviviruses in vitro is reduced by pretreatment with small amounts of type I interferon (IFN-α/β). Similarly, pretreatment of animals with IFN and experiments using mice defective in IFN signaling have indicated a role for IFN in controlling flavivirus disease in vivo. These data, along with findings that flavivirus-infected cells block IFN signaling, suggest that flavivirus infection can trigger an IFN response. To investigate IFN gene induction by the very first cells infected during in vivo infection with the flavivirus West Nile virus (WNV), we infected mice with high-titer preparations of WNV virus-like particles (VLPs), which initiate viral genome replication in cells but fail to spread. These studies demonstrated a brisk production of IFN in vivo, with peak levels of over 1,000 units/ml detected in sera between 8 and 24 h after inoculation by either the intraperitoneal or footpad route. The IFN response was dependent on genome replication, and WNV genomes and WNV antigen-positive cells were readily detected in the popliteal lymph nodes (pLN) of VLP-inoculated mice. High levels of IFN mRNA transcripts and functional IFN were also produced in VLP-inoculated IFN regulatory factor 3 null (IRF3−/−) mice, indicating that IFN production was independent of the IRF3 pathways to IFN gene transcription, consistent with the IFN type produced (predominantly α).
Correction: Distinct roles of neuroepithelial-like and radial glia-like progenitor cells in cerebellar regeneration

Zebrafish can regenerate after brain injury, and the regenerative process is driven by resident stem cells. Stem cells are heterogeneous in the vertebrate brain, but the significance of having heterogeneous stem cells in regeneration is not understood. Limited availability of specific stem cells might impair the regeneration of particular cell lineages. We studied regeneration of the adult zebrafish cerebellum, which contains two major stem and progenitor cell types: ventricular zone and neuroepithelial cells. Using conditional lineage tracing we demonstrate that cerebellar regeneration depends on the availability of specific stem cells. Radial glia-like cells are thought to be the predominant stem cell type in homeostasis and after injury. However, we find that radial glia-like cells play a minor role in adult cerebellar neurogenesis and in recovery after injury. Instead, we find that neuroepithelial cells are the predominant stem cell type supporting cerebellar regeneration after injury. Zebrafish are able to regenerate many, but not all, cell types in the cerebellum, which emphasizes the need to understand the contribution of different adult neural stem and progenitor cell subtypes in the vertebrate central nervous system.
Bayesian Subtree Alignment Model based on Dependency Trees

Word sequential alignment models work well for similar language pairs, but they are quite inadequate for distant language pairs. It is difficult to align words or phrases of distant languages with high accuracy without structural information of the sentences. In this paper, we pro- pose a Bayesian subtree alignment model that incorporates dependency relations be- tween subtrees in dependency tree struc- tures on both sides. The dependency re- lation model is a kind of tree-based re- ordering model, and can handle non-local reorderings, which sequential word-based models often cannot handle properly. The model is also capable of handling multilevel structures, making it possible to find many-to-many correspondences automatically without any heuristic rules. The size of the structures is controlled by nonparametric Bayesian priors. Experimental alignment results show that our model achieves 3.5 points better alignment error rate for English-Japanese than the word sequential alignment model, thereby verifying that the use of dependency information is effective for structurally different language pairs.
Effectiveness of tocilizumab with and without synthetic disease-modifying antirheumatic drugs in rheumatoid arthritis: results from a European collaborative study

Objectives To examine the effectiveness of tocilizumab (TCZ) with and without synthetic disease-modifying antirheumatic drugs (sDMARDs) in a large observational study. Methods Patients with rheumatoid arthritis treated with TCZ who had a baseline visit and information on concomitant sDMARDs were included. According to baseline data, patients were considered as taking TCZ as monotherapy or combination with sDMARDs. Main study outcomes were the change of Clinical Disease Activity Index (CDAI) and TCZ retention. The prescription of TCZ as monotherapy was analysed using logistic regression. CDAI change was analysed with a mixed-effects model for longitudinal data. TCZ retention was analysed with a stratified extended Cox model. Results Multiple-adjusted analysis suggests that prescription of TCZ as monotherapy varied according to age, corticosteroid use, country of the registry and year of treatment initiation. The change of disease activity assessed by CDAI as well as the likelihood to be in remission were not significantly different whether TCZ was used as monotherapy or in combination with sDMARDs in a covariate-adjusted analysis. Estimates for unadjusted median TCZ retention were 2.3 years (95% CI 1.8 to 2.7) for monotherapy and 3.7 years (lower 95% CI limit 3.1, upper limit not estimable) for combination therapies. In a covariate-adjusted analysis, TCZ retention was also reduced when used as monotherapy, with an increasing difference between mono and combination therapy over time after 1.5 years (p=0.002). Conclusions TCZ with or without concomitant sDMARDs resulted in comparable clinical response as assessed by CDAI change, but TCZ retention was shorter under monotherapy of TCZ.
Distribution and circadian expression of dbp in SCN and extra‐SCN areas in the mouse brain

The expression of dbp, a putative clock‐controlled transcription factor, was investigated in the mouse brain by in situ hybridization using antisense cRNA probe. Positive dbp mRNA signals were detected in various parts of the brain, with the highest expression in the suprachiasmatic nucleus (SCN). The circadian expression profile was investigated in SCN and extra‐SCN areas. In the SCN, dbp mRNA signals showed a peak at early daytime (ZT/CT4) and a trough at early nighttime (ZT/CT16) in both light–dark and constant dark conditions. In the cerebral cortex and the caudate‐putamen, dbp mRNA was also expressed in a circadian manner, but the phase of dbp mRNA expression in these structures showed a 4–8 hr delay compared to that in the SCN. These findings indicate that the circadian expression profile of dbp in the extra‐SCN brain areas is different from that in the SCN. J. Neurosci. Res. 59:291–295, 2000 © 2000 Wiley‐Liss, Inc.
Birth Defect Amelioration and Placental Cytokine Expression in Mnu-Exposed Dams Treated With Ifn-Gamma

BACKGROUND: Methylnitrosourea (MNU), an alkylating agent derived from creatinine metabolism, is cytotoxic, genotoxic, and mutagenic. Mid-gestational exposure to MNU leads to distal limb defects in mice. Previous studies have shown that nonspecific maternal immune stimulation protects against MNU-induced teratogenesis. A role for immune-mediated placental improvement in this effect remains uncertain. METHODS: The immune system of timed-pregnant C57BL/6N and CD-1 mice was stimulated by gestation day (GD) 7 intraperitoneal (IP) injection with the cytokine, interferon-gamma (IFN-γ). A teratogenic dose of MNU was then administered by IP injection on the morning of GD 9 to disrupt distal limb formation. Fetal limb length, body length, digital deformities and placental integrity were evaluated on GD 14. RESULTS: The incidence of syndactyly, polydactyly, and interdigital webbing in MNU-exposed mice was decreased by maternal IFN-γ treatment. In C57BL/6N mice, these defects were reduced by 47%, 100%, and 63%, respectively; as compared to previous reports in CD-1 mice, by 39%, 71%, and 20% respectively. Administration of IFN-γ significantly diminished MNU-induced endothelial and trophoblast placental damage in both strains of
Density Modeling of Images using a Generalized Normalization Transformation

We introduce a parametric nonlinear transformation that is well-suited for Gaussianizing data from natural images. The data are linearly transformed, and each component is then normalized by a pooled activity measure, computed by exponentiating a weighted sum of rectified and exponentiated components and a constant. We optimize the parameters of the full transformation (linear transform, exponents, weights, constant) over a database of natural images, directly minimizing the negentropy of the responses. The optimized transformation substantially Gaussianizes the data, achieving a significantly smaller mutual information between transformed components than alternative methods including ICA and radial Gaussianization. The transformation is differentiable and can be efficiently inverted, and thus induces a density model on images. We show that samples of this model are visually similar to samples of natural image patches. We demonstrate the use of the model as a prior probability density that can be used to remove additive noise. Finally, we show that the transformation can be cascaded, with each layer optimized using the same Gaussianization objective, thus offering an unsupervised method of optimizing a deep network architecture.
Improved Lighthill fish swimming model for bio-inspired robots: Modeling, computational aspects and experimental comparisons

The best known analytical model of swimming was originally developed by Lighthill and is known as the large amplitude elongated body theory (LAEBT). Recently, this theory has been improved and adapted to robotics through a series of studies ranging from hydrodynamic modeling to mobile multibody system dynamics. This article marks a further step towards the Lighthill theory. The LAEBT is applied to one of the best bio-inspired swimming robots yet built: the AmphiBot III, a modular anguilliform swimming robot. To that end, we apply a Newton–Euler modeling approach and focus our attention on the model of hydrodynamic forces. This model is numerically integrated in real time by using an extension of the Newton–Euler recursive forward dynamics algorithm for manipulators to a robot without a fixed base. Simulations and experiments are compared on undulatory gaits and turning maneuvers for a wide range of parameters. The discrepancies between modeling and reality do not exceed 16% for the swimming speed, while requiring only the one-time calibration of a few hydrodynamic parameters. Since the model can be numerically integrated in real time, it has significantly superior accuracy compared with computational speed ratio, and is, to the best of our knowledge, one of the most accurate models that can be used in real-time. It should provide an interesting tool for the design and control of swimming robots. The approach is presented in a self contained manner, with the concern to help the reader not familiar with fluid dynamics to get insight both into the physics of swimming and the mathematical tools that can help its modeling.
PHR1 and PHR2 ofCandida albicans Encode Putative Glycosidases Required for Proper Cross-Linking of β-1,3- and β-1,6-Glucans

ABSTRACT PHR1 and PHR2 encode putative glycosylphosphatidylinositol-anchored cell surface proteins of the opportunistic fungal pathogen Candida albicans. These proteins are functionally related, and their expression is modulated in relation to the pH of the ambient environment in vitro and in vivo. Deletion of either gene results in a pH-conditional defect in cell morphology and virulence. Multiple sequence alignments demonstrated a distant relationship between the Phr proteins and β-galactosidases. Based on this alignment, site-directed mutagenesis of the putative active-site residues of Phr1p and Phr2p was conducted and two conserved glutamate residues were shown to be essential for activity. By taking advantage of the pH-conditional expression of the genes, a temporal analysis of cell wall changes was performed following a shift of the mutants from permissive to nonpermissive pH. The mutations did not grossly affect the amount of polysaccharides in the wall but did alter their distribution. The most immediate alteration to occur was a fivefold increase in the rate of cross-linking between β-1,6-glycosylated mannoproteins and chitin. This increase was followed shortly thereafter by a decline in β-1,3-glucan-associated β-1,6-glucans and, within several generations, a fivefold increase in the chitin content of the walls. The increased accumulation of chitin-linked glucans was not due to a block in subsequent processing as determined by pulse-chase analysis. Rather, the results suggest that the glucans are diverted to chitin linkage due to the inability of the mutants to establish cross-links between β-1,6- and β-1,3-glucans. Based on these and previously published results, it is suggested that the Phr proteins process β-1,3-glucans and make available acceptor sites for the attachment of β-1,6-glucans.
Electrocutaneous Pulse Rate and Pulse Width Psychometric Functions for Sensory Communications

Psychometric functions of pulse rate (PR) and pulse width (PW) from electrocutaneous stimuli were determined using the method of comparative judgments. The study revealed that changes in PR were more easily detected than changes in PW, as measured by the percent of just noticeable difference (jnd). The PR jnd data from test subjects indicated that maximum frequency discrimination occurred near 20 pulses per second. Using the PR and PW psychometric curves, compensatory transfer functions can be determined which will improve the efficacy of sensory communication systems based on electrocutaneous stimulation.
Crosstalk between Two bZIP Signaling Pathways Orchestrates Salt-Induced Metabolic Reprogramming in Arabidopsis Roots

A signaling module in Arabidopsis roots, consisting of SnRK1 kinases and bZIP1 transcription factors, reprograms metabolism to enable plants to adapt to salt stress conditions. Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.
A survey of logical models for OLAP databases

In this paper, we present different proposals for multidimensional data cubes, which are the basic logical model for OLAP applications. We have grouped the work in the field in two categories: commercial tools (presented along with terminology and standards) and academic efforts. We further divide the academic efforts in two subcategories: the relational model extensions and the cube-oriented approaches. Finally, we attempt a comparative analysis of the various efforts.