Miracle-dz/UniFAR-FTUs huggingface dataset:
An appraisal of published usability evaluations of electronic health records via systematic review

Objective: In this systematic review, we aimed to evaluate methodological and reporting trends present in the current literature by investigating published usability studies of electronic health records (EHRs). Methods: A literature search was conducted for articles published through January 2015 using MEDLINE (Ovid), EMBASE, Scopus, and Web of Science, supplemented by citation and reference list reviews. Studies were included if they tested the usability of hospital and clinic EHR systems in the inpatient, outpatient, emergency department, or operating room setting. Results: A total of 4848 references were identified for title and abstract screening. Full text screening was performed for 197 articles, with 120 meeting the criteria for study inclusion. Conclusion: A review of the literature demonstrates a paucity of quality published studies describing scientifically valid and reproducible usability evaluations at various stages of EHR system development. A lack of formal and standardized reporting of EHR usability evaluation results is a major contributor to this knowledge gap, and efforts to improve this deficiency will be one step of moving the field of usability engineering forward.
A UK public health perspective: what is a healthy sustainable diet?

Summary The main constituents of a healthy diet are generally accepted but which dietary patterns are both healthy and sustainable? This is proving a complex question to answer given the many challenges that face the global food system, particularly the need to produce more food with fewer resources to feed the world's growing population. It is likely that change to the current UK diet could help ease the pressure on the global food system but it is important that this is balanced with the physiological requirement of nutrients for health. Therefore, the challenge ahead is to identify dietary patterns that provide us with the many nutrients we need for health, in appropriate amounts, that are also equitable, affordable and sustainable. This paper explores the challenges for the global food system and public health in providing a healthy diet for the expanding population, how UK diets may need to change to ensure they are both healthy and sustainable, and the challenges of changing people's diets. Although the issues are complex, it is essential that action is taken now to ensure a sustainable and healthy global food supply for future generations.
ISCN Standard Idiograms

Chromosome banding is used mainly to identify both normal and rearranged chromosomes, to define chromosome breakpoints, and to describe the specific location of DNA sequences on chromosomes. A nomenclature has been developed to standardize the identification of chromosomes and the naming of chromosome bands. The system currently in use is An International System for Human Cytogenetic Nomenclature, referred to as “ISCN 1995. ” It is the report of the standing committee on human cytogenetic nomenclature edited by Felix Mitelman. The report includes a chromosome band nomenclature, as well as standard idiograms, which are “diagrammatic representations of a karyotype, which may be based on measurements of the chromosomes” (ISCN 1995). The idiograms presented here, with the permission of S. Karger and Cytogenetics and Cell Genetics, are drawings of G‐banded chromosomes with band numbers indicated. Heterochromatic regions, which contain classes of repetitive DNA and can show individual differences in size, are indicated by patterned areas.
Developing an evidence base of best practices for integrating computerized systems into the exam room: a systematic review

Objective: The introduction of health information technology systems, electronic health records in particular, is changing the nature of how clinicians interact with patients. Lack of knowledge remains on how best to integrate such systems in the exam room. The purpose of this systematic review was to (1) distill “best” behavioral and communication practices recommended in the literature for clinicians when interacting with patients in the presence of computerized systems during a clinical encounter, (2) weigh the evidence of each recommendation, and (3) rank evidence-based recommendations for electronic health record communication training initiatives for clinicians. Methods: We conducted a literature search of 6 databases, resulting in 52 articles included in the analysis. We extracted information such as study setting, research design, sample, findings, and implications. Recommendations were distilled based on consistent support for behavioral and communication practices across studies. Results: Eight behavioral and communication practices received strong support of evidence in the literature and included specific aspects of using computerized systems to facilitate conversation and transparency in the exam room, such as spatial (re)organization of the exam room, maintaining nonverbal communication, and specific techniques that integrate the computerized system into the visit and engage the patient. Four practices, although patient-centered, have received insufficient evidence to date. Discussion and Conclusion: We developed an evidence base of best practices for clinicians to maintain patient-centered communications in the presence of computerized systems in the exam room. Further work includes development and empirical evaluation of evidence-based guidelines to better integrate computerized systems into clinical care.
Introduction to the Special Issue on Pathological Worrying

Pathological or chronic worry is known to be a feature associated with most of the anxiety disorders and most specifically with Generalized Anxiety Disorder (GAD) (Brown, Antony & Barlow, 1992), and since the advent of DSM-III, worrying has been the central diagnostic feature of GAD. Pathological worrying in the anxiety disorders is characterized by a number of distinctive features, including perseveration at the worry activity, a sense of lack of control over the worry process, a tendency to catastrophize the worry topic, and concurrent feelings of discomfort and negative mood which in some cases leads to increasing levels of distress as worry progresses.
Identification of Human Antigen‐Specific T Cells Using MHC Class I and Class II Tetramers

Major histocompatibility complex (MHC) tetramers typically consist of a fluorophore‐streptavidin complex and biotinylated soluble MHC molecules carrying a peptide of interest. Tetramers bind to T cell receptors (TCR) that recognize the MHC molecule/peptide combination with high specificity. Native MHC molecules are expressed as cell‐surface glycoproteins capable of binding a variety of peptides generated from the degradation of self and non‐self proteins for display to T cells. The human MHC gene locus is highly polymorphic, with >800 class I and >500 class II alleles currently identified. This heterogeneity contributes to the uniqueness of each person's immune system. This unit describes procedures for labeling CD8+ T cells with MHC class I tetramers and CD4+ T cells with MHC class II tetramers. The protocols can be used for detecting and enumerating human antigen‐specific T cells. Both CD8+ and CD4+ antigen‐specific T cells are rare events and require that sufficient numbers of cells be evaluated. To minimize nonspecific tetramer binding contributed by irrelevant cell populations, a cumulative gating strategy using positive selection and/or exclusion gating is described.
Assessing Mitochondrial Redox Status by Flow Cytometric Methods: Vascular Response to Fluid Shear Stress

Mitochondria are an important source of superoxide production contributing to physiological and pathological responses, including vascular oxidative stress that is relevant to cardiovascular diseases. Vascular oxidative stress is intimately linked with pro‐inflammatory states and atherosclerosis. Oxidized low‐density lipoprotein (OxLDL) modulates intracellular redox status and induces apoptosis in endothelial cells. Hemodynamic, specifically, fluid shear stress imparts both biomechanical and metabolic effects on vasculature. Mitochondria are an important source of superoxide production contributing to vascular oxidative stress with relevance to cardiovascular diseases. We hereby present biophysical and biochemical approaches, including fluorescence‐activated cell sorting, to assess the dynamics of vascular redox status. Curr. Protoc. Cytom. 58:9.37. 1‐9.37. 14. © 2011 by John Wiley & Sons, Inc.
Microsphere‐Based Flow Cytometry Protease Assays for Use in Protease Activity Detection and High‐Throughput Screening

This protocol describes microsphere‐based protease assays for use in flow cytometry and high‐throughput screening. This platform measures a loss of fluorescence from the surface of a microsphere due to the cleavage of an attached fluorescent protease substrate by a suitable protease enzyme. The assay format can be adapted to any site or protein‐specific protease of interest and results can be measured in both real time and as endpoint fluorescence assays on a flow cytometer. Endpoint assays are easily adapted to microplate format for flow cytometry high‐throughput analysis and inhibitor screening. Curr. Protoc. Cytom. 54:13.12. 1‐13.12. 17. © 2010 by John Wiley & Sons, Inc.
Application of the PrimRglo Assay Chemistry to Multiplexed Bead Assays

In this unit, we describe a multiplex microsphere quantitative PCR. The system is based on the use of two additional oligonucleotides within a single tube PCR reaction. The first oligonucleotide is modified with a single base pair mismatch and is otherwise equivalent to a universal sequence added to the forward PCR primer. Further, this first extra oligonucleotide is coupled to Luminex microspheres. The second additional oligonucleotide is designed to be complementary to the universal sequence, and is modified with the fluorescent dye Cy3. As the PCR reaction proceeds, the second oligonucleotide is able to bind to the microspheres. Thus, quantitative monitoring of PCR progress takes place. The microsphere‐mediated Cy3‐detection is measured using flow cytometry directly after the PCR reaction. This allows a flow cytometer analysis from up to 150 different spheres and, therefore, multiple genes in one reaction. The multiplex microsphere qPCR is demonstrated using three target genes from Influenza A and Neisseria meningitidis. The multiplex microsphere system will enable a higher degree of multiplexing than is possible with currently available qPCR systems. Curr. Protoc. Cytom. 69:13.13. 1‐13.13. 10. © 2014 by John Wiley & Sons, Inc.
Biological Second and Third Harmonic Generation Microscopy

Multiphoton microscopy has become a standard method for noninvasive imaging of thick specimens with subcellular resolution. Higher harmonic generation microscopy (HHGM), based on nonlinear multiphoton excitation, is a contrast mechanism for the structural and molecular imaging of native samples in cell culture and in fixed and live tissues, for both, three‐dimensional and four‐dimensional reconstructions. HHGM comprises second and third harmonic generation (SHG, THG) of ordered molecules, can be obtained without exogenous labels, and provides detailed real‐time optical reconstruction of fibrillar collagen, myosin, microtubules, and membrane potential, as well as cell depolarization. This unit presents the principles of SHG and THG and the basic setup of a HHGM system, and summarizes current applications in cell biology. Multimodal multiphoton microscopy using HHGM together with two‐photon excited fluorescence will develop into a key approach to real‐time imaging of cell dynamics in the context of live tissues.
VETERİNER HEKİMLİKTE YENİ ANTİBİYOTERAPİ YAKLAŞIMLARI

OZET Antibiyotiklerle tedavide bakteriyel direnc gelisimi nedeniyle sagaltimi gun gectikce zorlasan enfeksiyonlar yayginlasmaktadir. Bakteriyel dirence neden olan olumsuzluk faktorleri arasinda yanlis dozaj rejimlerinin (doz, uygulama araliklari, uygulama yolu gibi) onemli katkisi vardir. Tam bir tedavinin garanti edilmesinin yaninda direncli patojenlerin yayilimi ve seleksiyonunu onleyen akilci antibiyotik tedavisi, dozaj rejimlerini dikkate almayi gerektirir. Uygulanan doz rejimi ile antibakteriyel etkinin zamana bagli iliskisini aciklamaya yonelik olarak antibiyotiklerin farmakokinetik (FK) ve farmakodinamik (FD) ozelliklerini birlestiren bir yaklasim (FK/FD) antibiyoterapi acisindan son yillarin ilgi cekici konularindan biri olmustur. Bu makalenin amaci antibiyoterapide FK/FD iliskisinin temellerini ve ozellikle veteriner hekimlik pratigi acisindan konunun onemini vurgulamaktir. Anahtar kelimeler: antibiyotik, farmakokinetik, farmakodinamik THE NEW APPROACH OF ANTIBIOTHERAPY IN VETERINARY MEDICINE ABSTRACT Because of the development resistance to antibiotics; enfections, which is treat hardly, become widespread. Unavailable dosage managements ( dose, dose interval, route ect.) cause to development of bacterial resistance. Dosage regimen must be considered for rationale antibiotic therapy, which is prevent selection and spread of resistant patogens so therapy can be guarantee. Nowadays; an approach called PK/PD which combines pharmacokinetic and pharmacodynamic properties of antibiotics and so that explain relationship of antibacterial effect with time by dosage, is the most interesting subject for antibiotherapy. Aim of this article to underline basis of PK/PD relation in antibiotherapy and this subject's importance for veterinary medicine. Keywords: antibiotic, pharmacokinetics, pharmacodynamics
Chemotaxis Assays for Eukaryotic Cells

Chemotaxis is a complex response of a cell to an external stimulus. It involves detecting and measuring the concentration of the chemoattractant, biochemical transmission of the information, and the motility and adhesive changes associated with the response. This unit describes a number of chemotaxis assays that can be used to identify chemoattractants individually and in large‐scale screenings, to distinguish chemotaxis from chemokinesis, and to analyze cellular behavioral and biochemical responses. Some of these assays such as the filter, under agarose, and small population assays, can be used to monitor the behavior of large groups of cells; the bridge, pipet, and upshift assays can be used to analyze the responses of single cells.
Determination of Akt/PKB Signaling

This unit provides a basic protocol for assaying the level of activity, as well as the activation capacity and dynamics of inhibition of Akt/PKB in cultured cells. All these data can be obtained in a single nonradioactive experiment by standard techniques including immunoblotting and immunodetection with phosphospecific antibodies.
High Hemoglobin A1c levels and glycemic variability increase risk of severe hypoglycemia in diabetic hemodialysis patients

While hyperglycemia is central to the pathogenesis and management of diabetes mellitus, hypoglycemia and glucose variability also contribute to outcomes. We previously reported on the relationship of glycemic control to outcomes in a large population of diabetic end‐stage renal disease (ESRD) patients. Recognizing that ESRD is a risk factor for severe hypoglycemia, we have now analyzed the association between glycosylated hemoglobin A1c (HgbA1c) levels and glycemic variability in those with hypoglycemia. This is a retrospective study of patients with diabetes enrolled in a large hemodialysis program. Hypoglycemia was identified from hospital discharge diagnostic codes. Glycemic variability was assessed by the standard deviation of HgbA1c and glucose levels over time. Hypoglycemia as a discharge diagnosis was documented in 4.1% of patients. Higher baseline HgbA1c was associated with greater risk for hypoglycemia hospitalization, a finding confirmed by time‐lagged HgbA1c levels drawn a quarter earlier. Higher baseline HgbA1c categories were also associated with greater variability in HgbA1c levels during the analysis period. Similarly, greater glucose variability was associated with higher mean glucose levels by trend analysis. High, not low, HgbA1c levels are associated with greater risk of severe hypoglycemia, which may derive from glucose variability in the setting of treatment for hyperglycemia. High HgbA1c and glycemic variability are associated with increased risk of hypoglycemia in individuals with diabetes and ESRD.
Analysis of Membrane Traffic in Polarized Epithelial Cells

Spatial asymmetry is fundamental to the structure and function of most eukaryotic cells. A basic aspect of this polarity is that the cell's plasma membrane is divided into discrete domains. The best studied and simplest example of this occurs in epithelial cells, which line exposed body surfaces. Epithelial cells use two pathways to send proteins to the cell surface. Newly made proteins can travel directly from the trans‐Golgi network (TGN) to either the apical or basolateral surface. Alternatively, proteins can be sent to the basolateral surface and then endocytosed and transcytosed to the apical surface. Epithelial cells grown on porous filters adopt a typical polarized morphology; transfected epithelial cells can be used to biosynthetically characterize the trafficking patterns of a given protein. These cells can also be used to study delivery to a particular surface and to localize the protein by immunofluorescence.
Gender, low Kt/V, and mortality in Japanese hemodialysis patients: Opportunities for improvement through modifiable practices

Guidelines have recommended single pool Kt/V > 1.2 as the minimum dose for chronic hemodialysis (HD) patients on thrice weekly HD. The Dialysis Outcomes and Practice Patterns Study (DOPPS) has shown that “low Kt/V” (<1.2) is more prevalent in Japan than many other countries, though survival is longer in Japan. We examined trends in low Kt/V, dialysis practices associated with low Kt/V, and associations between Kt/V and mortality overall and by gender in Japanese dialysis patients. We analyzed 5784 HD patients from Japan DOPPS (1999–2011), restricted to patients dialyzing for >1 year and receiving thrice weekly dialysis. Logistic regression models estimated the relationships of patient characteristics with Kt/V. Logistic models also were used to estimate the proportion of low Kt/V cases attributable to various treatment practices. Multivariable Cox regression was used to estimate the associations of low Kt/V, blood flow rate (BFR), and treatment time (TT), with all‐cause mortality. From 1999 to 2009, the prevalence of low Kt/V declined in men (37–27%) and women (15–10%). BFR <200 mL/min, TT <240 minutes, and dialyzate flow rate (DFR) < 500 mL/min were common (35, 13, and 19% of patients, respectively) and strongly associated with low Kt/V. Fifteen percent of low Kt/V cases were attributable to BFR <200 and 13% to TT <240, compared to only 3% for DFR <500. Lower Kt/V was associated with elevated mortality, more so among women (hazard ratio [HR] = 1.13 per 0.1 lower Kt/V, 95% CI: 1.07–1.20) than among men (HR = 1.06 per 0.1 lower Kt/V, 95% CI: 1.00–1.12). The relatively large proportion of low Kt/V cases in Japanese facilities may potentially be reduced 30% by increasing BFR to 200 mL/min and TT to 4 hours thrice weekly in HD patients. Associations of low Kt/V with elevated mortality suggest that modification of these practices may further improve survival for Japanese HD patients.
Induction of ES Cell–Derived Cartilage Formation

This unit describes the protocols used for cultivation of murine embryonic stem (ES) cells and their differentiation into chondrogenic cell types in vitro. ES cells cultivated as cellular aggregates, so‐called embryoid bodies (EBs), differentiate spontaneously into chondrogenic cell types recapitulating cellular events of chondro‐ and osteogenesis. The undifferentiated ES cells differentiate into mesenchymal prechondrogenic cells in the EB outgrowths. These progenitor cells aggregate and form mesenchymal condensations. During further cultivation, these cells form cartilage nodules, show a phenotype typical for chondroblasts, and start to express marker molecules of cartilage tissue. Later, the chondrocytes become hypertrophic, and finally, marker molecules indicating bone formation can be detected in the nodules. This unit also contains protocols for characterization of the differentiated cells by immunostaining, mRNA‐in situ hybridization, electron microscopy, and RT‐PCR analysis.
Can primary failure of arteriovenous fistulas be anticipated?

Primary failure, early thrombosis, and inadequate maturation are the main complications encountered in arteriovenous fistulas. Doppler ultrasonographic assessment of flow‐mediated dilatation (FMD) is currently used for the early diagnosis of atherosclerosis. Clinical experience in the use of FMD for preoperative assessment of vasculature is rather limited; therefore, we sought to elucidate the relationship between preoperative FMD and primary failure of the fistula. Thirty‐three patients with end‐stage renal disease who were admitted to our hospital between January and July 2005 were included in our study. Medical histories were established and the internal diameter, wall thickness, peak systolic flow rate, and resistive index (RI) were measured in the cephalic vein and radial and brachial arteries. Flow‐mediated dilatation and nitrate‐mediated dilatation (NMD) of the brachial artery were assessed. Fistulas were evaluated 48 hours and 30 days postoperatively. Brachial arterial internal diameter was lower in all fistulas that developed primary failure in 48 hours (0.4 ± 0.07 cm vs. 0.35 ± 0.07 cm, P = 0.016). The radial artery RI was found to be significantly elevated in fistulas with both early (48‐hour) and late‐term (30‐day) failure (0.9 ± 0.08 vs. 0.68 ± 0.3, P = 0.01, and 0.86 ± 0.8 vs. 0.67 ± 0.3, P = 0.038, respectively). The brachial artery peak systolic flow rate was significantly reduced in patients in the radiocephalic fistula group that developed early and late‐term failure (42.9 ± 12 cm/sec vs. 68.4 ± 10 cm/sec, P = 0.01, and 44.1 ± 13 cm/sec vs. 57.7 ± 16 cm/sec, P = 0.038, respectively). Our study, constrained by a smaller, older patient group, was unable to show a statistically significant correlation between FMD, NMD, and fistula success. Any single parameter may not be sufficient to assess vascular health preoperatively. A multifactorial approach incorporating parameters evaluating arterial and venous function might be more effective in predicting fistula success. Further studies on larger patient groups may indeed demonstrate the value of these assessments.
FAMS and FAMSBASE for Protein Structure

The computer program FAMS (Full Automatic Modeling System) performs homology modeling of protein structures by means of an algorithm consisting of database searches and simulated annealing. FAMS produces a model in which the torsion angles of the backbone and sidechains are highly accurate. The operations of the FAMS algorithm are fully automated, and, therefore, special knowledge, techniques or experience are not required in order to obtain a biologically worthwhile protein structure.
The impact of education and cooking methods on serum phosphate levels in patients on hemodialysis: 1‐year study

Introduction: Control of serum phosphate is important for patients on hemodialysis. The aim of the study was to determine if education based on phosphorus‐reducing techniques in food preparation and thermal processing, and accordingly prepared and applied diets, will lead to better outcomes than a standard education program to improve phosphate control in patients on hemodialysis.