Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Inference for the Latent Space Network Model Using a Case-Control Approximate Likelihood

Network models are widely used in social sciences and genome sciences. The latent space model proposed by Hoff et al. (2002), and extended by Handcock et al. (2007) to incorporate clustering, provides a visually interpretable model-based spatial representation of relational data and takes account of several intrinsic network properties. Due to the structure of the likelihood function of the latent space model, the computational cost is of order O(N 2), where N is the number of nodes. This makes it infeasible for large networks. In this article, we propose an approximation of the log-likelihood function. We adapt the case-control idea from epidemiology and construct a case-control log-likelihood, which is an unbiased estimator of the log-full likelihood. Replacing the full likelihood by the case-control likelihood in the Markov chain Monte Carlo estimation of the latent space model reduces the computational time from O(N 2) to O(N), making it feasible for large networks. We evaluate its performance using simulated and real data. We fit the model to a large protein–protein interaction data using the case-control likelihood and use the model fitted link probabilities to identify false positive links. Supplemental materials are available online.
The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. Bacterial infection of the lower respiratory tract contributes to approximately 50% of COPD exacerbations. Even during periods of stable lung function, the lung harbors a community of bacteria, termed the microbiome. The role of the lung microbiome in the pathogenesis of COPD remains unknown. The COPD lung microbiome, like the healthy lung microbiome, appears to reflect microaspiration of oral microflora. Here we describe the COPD lung microbiome of 22 patients with Moderate or Severe COPD compared to 10 healthy control patients. The composition of the lung microbiomes was determined using 454 pyrosequencing of 16S rDNA found in bronchoalveolar lavage fluid. Sequences were analyzed using mothur, Ribosomal Database Project, Fast UniFrac, and Metastats. Our results showed a significant increase in microbial diversity with the development of COPD. The main phyla in all samples were Actinobacteria, Firmicutes, and Proteobacteria. Principal coordinate analyses demonstrated separation of control and COPD samples, but samples did not cluster based on disease severity. However, samples did cluster based on the use of inhaled corticosteroids and inhaled bronchodilators. Metastats analyses demonstrated an increased abundance of several oral bacteria in COPD samples.
Registered nurses' experiences of rewarding in a Finnish University Hospital - an interview study.

AIMS The purpose was to describe Finnish registered nurses' experiences of rewarding. The aim was to gather detailed information on the rewarding of nurses to help nurse managers and leaders to update existing reward strategy and to develop an effective reward system. BACKGROUND Rewarding has been found positively to influence nurses' occupational well-being and commitment to their work, and the attractiveness of the health care field. METHODS A series of focused interviews with 10 registered nurses was conducted in 2011. Qualitative content analysis method was used. RESULT The nurses reported positive experiences with rewarding in the form of monetary compensation and other benefits, the positive aspects of nursing work and opportunities for professional development. The experiences of unsatisfactory rewarding generally stemmed from negative emotional experiences, lacking rewards and inequality in rewarding. CONCLUSION It is essential to listen to nurses and to provide appropriate acknowledgement and appreciation of their work in order to develop an effective reward system. IMPLICATIONS FOR NURSING MANAGEMENT It is important to listen to nurses' experiences of rewarding because it enables nurse managers to maintain and increase the attractiveness of nursing and health care work in general.
Exploring information technology adoption by family physicians: survey instrument valuation

As the information needs of family physicians become more complex, there will be a greater need to successfully implement the technologies needed to manage that information. The ability to stratify primary care physicians can enable the implementation process to be more efficient. This research tested a new instrument on 101 family physicians, and was able to stratify physicians into high, intermediate, and low information technology (IT) usage groups. It is expected that this stratification would allow managers of IT implementation to target specific adoption strategies for each group. The instrument is available from ddixon@julian.uwo. ca.
Long-acting insulin analogue detemir compared with NPH insulin in type 1 diabetes: a systematic review and meta-analysis.

INTRODUCTION Although numerous studies showed an improvement in glycemic control in type 1 diabetic patients treated with long-acting insulin analogue detemir compared with Neutral Protamine Hagedorn (NPH) insulin, the beneficial effects of insulin detemir has not been confirmed by all investigators. OBJECTIVES The aim of the study was to compare the effect of treatment with detemir insulin vs. NPH insulin on metabolic control, hypoglycemic episodes, and body weight gain in patients with type 1 diabetes by means of a systematic review and a meta-analysis. METHODS The following electronic databases were searched up to November 2010: MEDLINE, EMBASE, and the Cochrane Library. Additional references were obtained from the reviewed articles. Only randomized controlled trials of at least 12-week duration with basal-bolus regimen therapies using detemir insulin vs. NPH insulin were included. RESULTS The analysis included 10 studies involving 3825 patients with type 1 diabetes. Combined data from all trials showed a statistically significant reduction in hemoglobin A1c (HbA1c) (weighted mean difference: [WMD] -0.073, 95% CI -0.135 to -0.011, P = 0.021) in the detemir group compared with the NPH group. There was also a significant reduction of fasting plasma glucose (FPG) (WMD - 0.977 mmol/l, 95% CI -1.395 to -0.558, P <0.001), all-day hypoglycemic episodes (relative risk [RR] 0.978, 95% CI 0.961-0.996), severe hypoglycemic episodes (RR 0.665, 95% CI 0.547-0.810), nocturnal hypoglycemic episodes (RR 0.877, 95% CI 0.816-0.942), as well as smaller body weight gain (WMD -0.779 kg, 95% CI -0.992 to -0.567) in patients using detemir insulin compared with those using NPH insulin. CONCLUSIONS Basal-bolus treatment with insulin detemir, as compared with NPH insulin, provided a minor benefit in terms of the HbA1c value and significantly reduced FPG in type 1 diabetic patients. Treatment with detemir insulin was also superior to NPH insulin in reducing the risk of all-day, nocturnal, and severe hypoglycemic episodes, with the added benefit of reduced weight gain.
Elementary operations for the reorganization of minimally persistent formations

In this paper we study the construction and transformation of two-dimensional minimally persistent graphs. Persistence is a generalization to directed graphs of the undirected notion of rigidity. In the context of moving autonomous agent formations, persistence charac- terizes the efficacy of a directed structure of unilateral distances constraints seeking to preserve a formation shape. Analogously to the powerful results about Henneberg sequences in minimal rigidity theory, we propose different types of directed graph operations allowing one to sequen- tially build any minimally persistent graph (i.e. persistent graph with a minimal number of edges for a given number of vertices), each intermediate graph being also minimally persistent. We also consider the more generic problem of obtaining one minimally persistent graph from another, which corresponds to the on-line reorganization of an autonomous agent formation. We show that we can obtain any minimally persistent formation from any other one by a se- quence of elementary local operations such that minimal persistence is preserved throughout the reorganization process.
Factor VIII concentrates: matching what you see with what you get.

The article by Rock et al 1 in this issue ofThe Journalcalls attention to the problems of verifying the labeled potency of factor VIII concentrates. Rock et al report finding (in 1982) a considerable discrepancy between their measurements and the manufacturers-labeled factor VIII content, with the authors' assays showing overall levels of approximately 60% of the labeled values with each of four lots of one manufacturer's product. They point out the potential serious implications of such less-than labeled factor VIII content, including inadequate treatment of bleeding episodes with poor clinical response and increased factor VIII usage (at additional cost) if clinicians doubt that the bottle contains as much as stated on the label. This issue is not a new one and no doubt reflects several problems that have been of great concern to the manufacturers of clotting factor concentrates, the US Office of Biologics (OOB) and its British
Determination of Triterpenic Acids and Screening for Valuable Secondary Metabolites in Salvia sp. Suspension Cultures

Plant in vitro cultures are a prospective alternative for biochemicals production, for example the triterpenes oleanolic and ursolic acid present in plants and cell cultures of Salvia sp. Our objective was to develop a suitable analysis protocol for evaluation of triterpenic acid yield in plant raw material and in vitro cultures supporting selection processes. Moreover, valuable bioactive compounds had to be revealed. Thus, different strategies enhancing the separation for a sensitive and effective HPLC-UV method were investigated and the developed method was validated for linearity, precision, accuracy, limits of detection and quantification. A baseline separation of these isomers enabled detection limits of below 0.4 μg/mL and quantification limits of about 1.2 μg/mL. Over the tested concentration range a good linearity was observed (R2 > 0.9999). The variations in the method were below 6% for intra- and inter-day assays of concentration. Recoveries were between 85–98% for both compounds using ethanol as extraction solvent. Additionally, metabolite profiling of cell suspension culture extracts by GC-MS has shown the production variability of different plant metabolites and especially the presence of plant phenols and sterols. These studies provide a method suitable for screening plant and cell culture productivity of triterpenic acids and highlighted interesting co-products of plant cell cultures.
CORONARY ATHEROSCLEROSIS IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AT AUTOPSY

Using a computed image analyzer, coronary arteries from 50 autopsied patients with systemic lupus erythematosus (SLE) were examined on the three vessels (RCA, LAD, LCX) and compared with those of age‐matched controls. The intima of coronary artery was significantly thickened much more in the case of SLE than in the case of age‐matched controls. This was statistically significant (p<0.01). Hypertension and glomerulonephritis did not but corticosteroid therapy had an influence on the development of intimal thickening ratio of the coronary arteries in SLE patients. The mean intimal thickening ratio of the coronary arteries in the patients with SLE and without corticosteroid therapy was larger than that of patients with corticosteroid therapy (p<0.1). It appears possible to conclude that inflammatory change of SLE itself is one of the promoting factors of coronary atherosclerosis.
Optimal Stragies and Minimax Lower Bounds for Online Convex Games

A number of learning problems can be cast as an Online Convex Game: on each round, a learner makes a prediction x from a convex set, the environment plays a loss function f, and the learner’s long-term goal is to minimize regret. Algorithms have been proposed by Zinkevich, when f is assumed to be convex, and Hazan et al., when f is assumed to be strongly convex, that have provably low regret. We consider these two settings and analyze such games from a minimax perspective, proving minimax strategies and lower bounds in each case. These results prove that the existing algorithms are essentially optimal.
Understanding the delayed onset of action of azathioprine in IBD: are we there yet?

In this issue of Gut , Ben-Horin et al propose an innovative explanation for the well known phenomenon of the delayed onset of action of thiopurines ( see page 396 ). They thereby contribute to an improved insight into the exact mode of action of the classic immunosuppressive drug azathioprine.1 Developing azathioprine as an innovative immunosuppressive drug in 1957, Gertrude Elion and George Hitchings laid the basis for the currently utilised concept of steroid-sparing treatment strategies in inflammatory bowel diseases (IBD). 2 With regard to the evidence-based immunosuppressive capacity and clinical efficacy of azathioprine in the context of IBD as well as considering the proven long-term safety of this drug, which has been confirmed in numerous trials, the primary obstacle to the successful use of azathioprine in the treatment of acute flares of IBD is its delayed onset of action.3 4 As it often takes several months after initiating treatment with azathioprine until the first clinical effects can be monitored, it is sometimes impossible to avoid completely the parallel use of fast-acting steroids in order to control acute flares of intestinal inflammation.3 5 However, do we really have to accept this shortcoming of our old ally azathioprine in the induction of remission in IBD, or might there today, five decades after the birth of azathioprine, exist modern tools of biochemical and medical science which possibly can enable us to overcome these limitations by a rational design of innovative azathioprine-based immunosuppressive formulas? Thinking about this point, subsequently the question arises of what exactly should such a possible biochemical modification of azathioprine look like, in order to speed up its immunosuppressive capacity, and this would then automatically lead to the fundamental issue in this context—that is, do we really understand the detailed molecular mechanism of azathioprine and its metabolites which are …
Comparison of the effects of xylazine bolus versus medetomidine constant rate infusion on the stress response, urine production, and anesthetic recovery characteristics in horses anesthetized with isoflurane.

OBJECTIVE To compare the effect of xylazine bolus versus medetomidine constant rate infusion (MCRI) on serum cortisol and glucose concentrations, urine production, and anesthetic recovery characteristics in dorsally recumbent, spontaneously breathing, isoflurane-anesthetized horses. DESIGN Prospective, randomized crossover study. ANIMALS 10 healthy Standardbreds. PROCEDURES Horses were premedicated with xylazine or medetomidine IV. Anesthesia was induced with diazepam and ketamine and maintained with isoflurane for 150 minutes. For the xylazine treatment, end-tidal isoflurane concentration was maintained at 1.7% and xylazine (0.2 mg/kg [0.09 mg/lb]), IV) was administered as a bolus at the end of anesthesia. For the MCRI treatment, end-tidal isoflurane concentration was maintained at 1.4% and medetomidine (0.005 mg/kg/h [0.0023 mg/lb/h], IV) was infused throughout anesthesia. Serum cortisol and glucose concentrations were measured before, during, and after anesthesia. Urine specific gravity and volume were measured during anesthesia. Unassisted anesthetic recoveries were recorded by a digital video camera for later evaluation by 2 observers who were blinded to treatment. RESULTS Serum cortisol concentration was lower and serum glucose concentration was higher with MCRI treatment, compared with xylazine treatment. Time to sternal recumbency was longer with MCRI treatment, but no difference was seen between treatments for times to extubation, first movement, or standing. Objective (mean attempt interval) and subjective (visual analog score) recovery scores were significantly better with MCRI treatment, compared with xylazine treatment. CONCLUSIONS AND CLINICAL RELEVANCE In isoflurane-anesthetized horses, premedication and administration of medetomidine as a constant rate infusion resulted in decreased serum cortisol concentration, increased serum glucose concentration, and superior anesthetic recovery characteristics, compared with conventional treatment with xylazine.
Developmental Analysis of the Achaete-Scute System of DROSOPHILA MELANOGASTER.

The interpretation of the wild-type function of a gene depends on our knowledge of the phenotype caused by its absence. We have first defined the genetic extent of the achaete-scute system by studying the phenotype of different terminal and intercalary deficiencies including these genes. When these deficiencies were lethal, we have defined the phenoeffective phase of lethality and studied their phenotype in genetic mosaics (gynandromorphs and mitotic recombination clones). The achaete-scute system affects two functions, one necessary for the differentiation of the embryonic (central? ) nervous system and the other necessary for the differentiation of peripheral nervous elements of the chaetes and sensillae of the adult cuticle. The possibility that these functions correspond to differential expression of a single mechanism is discussed.
Sequencing antiretroviral drugs.

Despite the availability of at least 14 Food and Drug Administration (FDA)-approved antiretroviral drugs, only a minority of HIV-infected individuals achieve a durable suppression of viral replication receiving antiretroviral therapies [1±3]. Toxicity issues, poor drug compliance, lack of potency, and pharmacokinetic interactions seem to account for this limited bene®t of therapy in clinical practice [4,5]. In the absence of the maximal suppression of viral replication while a patient is under antiretroviral therapy, the selection and accumulation of drug resistance mutations is inevitable. Because cross-resistance to agents within each of the three currently available classes of drugs occurs to a variable extent, the effectiveness of subsequent antiretroviral regimens is always limited [6±9].
SAGE-VAR: AN INFRARED SURVEY OF VARIABILITY IN THE MAGELLANIC CLOUDS

We present the first results from the Surveying the Agents of Galaxy Evolution (SAGE)-Var program, a follow up to the Spitzer legacy program SAGE (Meixner et al.). We obtained four epochs of photometry at 3.6 and 4.5 μm covering the bar of the LMC and the central region of the SMC in order to probe the variability of extremely red sources missed by variability surveys conducted at shorter wavelengths, and to provide additional epochs of observation for known variables. Our six total epochs of observations allow us to probe infrared (IR) variability on 15 different timescales ranging from ∼20 days to ∼5 yr. Out of a full catalog of 1 717 554 (LMC) and 457 760 (SMC) objects, we find 10 (LMC) and 6 (SMC) large amplitude Asymptotic Giant Branch (AGB) variables without optically measured variability owing to circumstellar dust obscuration. The catalog also contains multiple observations of known AGB variables, type I and II Cepheids, eclipsing variables, R CrB stars, and young stellar objects, which will be discussed in following papers. Here we present IR Period–Luminosity (PL) relations for classical Cepheids in the Magellanic Clouds, as well as improved PL relationships for AGB stars pulsating in the fundamental mode using mean magnitudes constructed from six epochs of observations.
Organizational decision making

Abstract : Traditionally top management decision making relies heavily on informal techniques--intuitive judgements by experienced managers, traditions and 'rules of thumb' peculiar to each organization, or informal consensus among a group of managers. This report surveys the potential role of and desirability of more formal approaches to some top management decision problems.
Reliability of muscle function and sensory perception measurements of the wrist extensors

This study determined the reliability of muscle function and sensory perception measures of the wrist extensors. The test-retest reliability of the measurements was determined by an intraclass correlation coefficient (ICC), coefficient of variation (CV), standard error of measurements (SEMs), and one-way repeated measures ANOVA using the values collected from 25 young (20.6 ± 1.3 years) healthy male volunteers on two occasions separated by 1 day. The measures consisted of grip strength, wrist extension strength (WES), range of motion in active and passive wrist flexion and extension, choice reaction time (CRT), vibration sense (VIB), joint position error sense (JPE), cold pain (CP) and heat pain threshold, and pressure pain threshold. An acceptable reliability was determined as the ICC values greater than 0.85, CV less than 15%, and SEMs less than 5%. ICC of all measures except for JPE were greater than 0.85, only CV of JPE, CP, and VIB exceeded 15%, SEMs were higher than 5% only for JPE and CP, and the ANOVA showed a significant time effect for CRT and WES. It is concluded that most of the measurements except JPE are reliable and can be used to investigate effects of a physiotherapy intervention on the wrist extensors.
Serum titres of anti‐glutamic acid decarboxylase‐65 and anti‐IA‐2 autoantibodies are associated with different immunoregulatory milieu in newly diagnosed type 1 diabetes patients

Several studies correlated genetic background and pancreatic islet‐cell autoantibody status (type and number) in type 1A diabetes mellitus (T1AD), but there are no data evaluating the relationship among these markers with serum cytokines, regulatory T cells and β cell function. This characterization has a potential importance with regard to T1AD patients' stratification and follow‐up in therapeutic prevention. In this study we showed that peripheral sera cytokines [interleukin (IL)‐12, IL‐6, II‐1β, tumour necrosis factor (TNF)‐α, IL‐10] and chemokines (CXCL10, CXCL8, CXCL9, CCL2) measured were significantly higher in newly diagnosed T1AD patients when compared to healthy controls (P < 0·001). Among T1AD, we found a positive correlation between CXCL10 and CCL‐2 (r = 0·80; P = 0·000), IL‐8 and TNF‐α (r = 0·60; P = 0·000); IL‐8 and IL‐12 (r = 0·57; P = 0·001) and TNF‐α and IL‐12 (r = 0·93; P = 0·000). Glutamic acid decarboxylase‐65 (GAD‐65) autoantibodies (GADA) were associated negatively with CXCL10 (r = −0·45; P = 0·011) and CCL2 (r = −0·65; P = 0·000), while IA‐2A showed a negative correlation with IL‐10 (r = −0·38; P = 0·027). Human leucocyte antigen (HLA) DR3, DR4 or DR3/DR4 and PTPN22 polymorphism did not show any association with pancreatic islet cell antibodies or cytokines studied. In summary, our results revealed that T1AD have a proinflammatory cytokine profile compared to healthy controls and that IA‐2A sera titres seem to be associated with a more inflammatory peripheral cytokine/chemokine profile than GADA. A confirmation of these data in the pre‐T1AD phase could help to explain the mechanistic of the well‐known role of IA‐2A as a more specific marker of beta‐cell damage than GADA during the natural history of T1AD.