Miracle-dz/UniFAR-FTUs huggingface dataset:
More convenient 13C-urea breath test modifications still meet the criteria for valid diagnosis of Helicobacter pylori infection.

AIMS AND METHODS 13C-Urea breath tests (UBT) were performed in 217 patients with epigastric symptoms to assess (a) the validity of shorter intervals of breath sample collection and (b) of the non-fasting state on diagnosing H. pylori infection and to evaluate (c) a more simple sampling method. (a) In 186 patients, breath samples were taken before and at 10, 20, 30, 40, 50, 60, 90, and 120 minutes after ingestion of 75 mg 13C-urea. 13C-enrichment was measured by isotope ratio mass spectrometry [delta/1000] and the cumulative recovery rate (CRR) was calculated. (b) 31 patients performed 13C-UBTs on two occasions, i.e. fasted and in the postprandial state collecting breath before and 30 min after substrate ingestion. (c) 61 breath samples were obtained in duplicate, i.e. both with an aluminium foil breath bag using evacuated glass tubes, and by exhalation into open vials via straw. RESULTS (a) DOB-responses at 10, 20, 30, and 40 minutes after dose showed a linear correlation with the 120 min-CRR. Referring to a CRR > 3% at 120 min (criterion of H. pylori-infection), DOB-responses at 20 min with a cut off-value at 5/1000 (ROC-analysis) were shown to be valid for diagnosing H. pylori status in man (sensitivity 99.0%, specificity 100%). (b) Postprandially, mean DOB-responses of H.pylori positive patients were lower than in the fasting state (17.46/1000 vs. 27.63/1000; p < 0.01). With the cut-off at 5/1000, however, sensitivity still was 94.4% and specificity was 100%. (c) The straw and breath bag method gave equivalent results (r = 0.98, p < 0.0001). CONCLUSIONS (a) A two sample measurement using the DOB at 20 min and a cut-off value of 5/1000 can replace the CRR-calculation over 120 minutes. (b) Although quantitative DOB-responses are significantly affected, 13C-UBT can be performed in the postprandial state with no significant effect on the detection of the H. pylori infection. (c) The sample collection by a simple straw method meets precision requirements < 1.5 delta/1000. Thus, the 13C-UBT can be performed cheaper, faster and more conveniently.
Type 1 nitrergic (ND1) cells of the rabbit retina: Comparison with other axon‐bearing amacrine cells

NADPH diaphorase (NADPHd) histochemistry labels two types of nitrergic amacrine cells in the rabbit retina. Both the large ND1 cells and the small ND2 cells stratify in the middle of the inner plexiform layer, and their overlapping processes produce a dense plexus, which makes it difficult to trace the morphology of single cells. The complete morphology of the ND1 amacrine cells has been revealed by injecting Neurobiotin into large round somata in the inner nuclear layer, which resulted in the labelling of amacrine cells whose proximal morphology and stratification matched those of the ND1 cells stained by NADPHd histochemistry. The Neurobiotin‐injected ND1 cells showed strong homologous tracer coupling to surrounding ND1 cells, and double‐labelling experiments confirmed that these coupled cells showed NADPHd reactivity. The ND1 amacrine cells branch in stratum 3 of the inner plexiform layer, where they produce a sparsely branched dendritic tree of 400–600 μm diameter in ventral peripheral retina. In addition, each cell gives rise to several fine beaded processes, which arise either from a side branch of the dendritic tree or from the tapering of a distal dendrite. These axon‐like processes branch successively within the vicinity of the dendritic field before extending, with little or no further branching, for 3–5 mm from the soma in ventral peripheral retina. Consequently, these cells may span one‐third of the visual field of each eye, and their spatial extent appears to be greater than that of most other types of axon‐bearing amacrine cells injected with Neurobiotin in this study. The morphology and tracer‐coupling pattern of the ND1 cells are compared with those of confirmed type 1 catecholaminergic cells, a presumptive type 2 catecholaminergic cell, the type 1 polyaxonal cells, the long‐range amacrine cells, a novel type of axon‐bearing cell that also branches in stratum 3, and a type of displaced amacrine cell that may correspond to the type 2 polyaxonal cell. J. Comp. Neurol. 474:149–171, 2004. © 2004 Wiley‐Liss, Inc.
Uncoupling the Trade-Off between Somatic Proteostasis and Reproduction in Caenorhabditis elegans Models of Polyglutamine Diseases

Caenorhabditis elegans somatic protein homeostasis (proteostasis) is actively remodeled at the onset of reproduction. This proteostatic collapse is regulated cell-nonautonomously by signals from the reproductive system that transmit the commitment to reproduction to somatic cells. Here, we asked whether the link between the reproductive system and somatic proteostasis could be uncoupled by activating downstream effectors in the gonadal longevity cascade. Specifically, we examined whether over-expression of lipl-4 (lipl-4(oe)), a target gene of the gonadal longevity pathway, or increase in arachidonic acid (AA) levels, associated with lipl-4(oe), modulated proteostasis and reproduction. We found that lipl-4(oe) rescued somatic proteostasis and postponed the onset of aggregation and toxicity in C. elegans models of polyglutamine (polyQ) diseases. However, lipl-4(oe) also disrupted fatty acid transport into developing oocytes and reduced reproductive success. In contrast, diet supplementation of AA recapitulated lipl-4(oe)-mediated proteostasis enhancement in wild type animals but did not affect the reproductive system. Thus, the gonadal longevity pathway mediates a trade-off between somatic maintenance and reproduction, in part by regulating the expression of genes, such as lipl-4, with inverse effects on somatic maintenance and reproduction. We propose that AA could uncouple such germline to soma crosstalk, with beneficial implications protein misfolding diseases.
Cytokines regulating hematopoietic stem cell function

Purpose of reviewRegulation of the multiple fates of hematopoietic stem cells – including quiescence, self-renewal, differentiation, apoptosis, and mobilization from the niche – requires the cooperative actions of several cytokines and other hormones that bind to receptors on these cells. In this review we discuss recent advances in the identification of novel hematopoietic stem cell supportive cytokines and the mechanisms by which they control hematopoietic stem cell fate decisions. Recent findingsSeveral extrinsic factors that stimulate ex-vivo expansion of hematopoietic stem cells were recently identified by a number of experimental approaches, including forward genetic screening and transcriptional profiling of supportive stromal cells. Recent experiments in which multiple cytokine signaling pathways are activated or suppressed in hematopoietic stem cells reveal the complexity of signal transduction and cell-fate choice in hematopoietic stem cells in vivo and in vitro. SummaryThe study of genetically modified mice and improvements in the in-vitro hematopoietic stem cell culture system will be powerful tools to elucidate the functions of cytokines that regulate hematopoietic stem cell function. These will further reveal the complex nature of the mechanisms by which extrinsic factors regulate signal transduction and cell-fate decisions of hematopoietic stem cells.
Prefrontal cortical efferents in the rat synapse on unlabeled neuronal targets of catecholamine terminals in the nucleus accumbens septi and on dopamine neurons in the ventral tegmental area

Physiological and pharmacological studies indicate that descending projections from the prefrontal cortex modulate dopaminergic transmission in the nucleus accumbens septi and ventral tegmental area. We investigated the ultrastructural bases for these interactions in rat by examining the synaptic associations between prefrontal cortical terminals labeled with anterograde markers (lesion‐induced degeneration or transport of Phaseolus vulgaris leucoagglutinin; PHA‐L) and neuronal processes containing immunoreactivity for the catecholamine synthesizing enzyme, tryosine hydroxylase.
Family satisfaction in the ICU: differences between families of survivors and nonsurvivors.

BACKGROUND We previously noted that the families of patients dying in the ICU reported higher satisfaction with their ICU experience than the families of survivors. However, the reasons for this finding were unclear. In the current study, we sought to confirm these findings and identify specific aspects of care that were rated more highly by the family members of patients dying in the ICU compared to family members of ICU survivors. METHODS A total of 539 family members with a patient in the ICU were surveyed. Family satisfaction was measured using the 24-item family satisfaction in the ICU questionnaire. Ordinal logistic regression identified which components of family satisfaction were associated with the patient's outcome (ie, whether the patient lived or died). RESULTS A total of 51% of respondents had a loved one die in the ICU. Overall, the families of patients dying in the ICU were more satisfied with their ICU experience than were families of ICU survivors, and the largest differences were noted for care aspects directly affecting family members. Significant differences were found for inclusion in decision making, communication, emotional support, respect and compassion shown to family, and consideration of family needs (p<0.01). CONCLUSIONS The families of patients dying in the ICU were more satisfied with their ICU experience than were the families of ICU survivors. The reasons for this difference were higher ratings on family-centered aspects of care. These findings suggest that efforts to improve the support of ICU family members should focus not only on the families of dying patients but also on the families of patients who survive their ICU stay.
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

MOTIVATION Empirical models for the prediction of how changes in sequence alter protein-protein binding kinetics and thermodynamics can garner insights into many aspects of molecular biology. However, such models require empirical training data and proper validation before they can be widely applied. Previous databases contained few stabilizing mutations and no discussion of their inherent biases or how this impacts model construction or validation. RESULTS We present SKEMPI, a database of 3047 binding free energy changes upon mutation assembled from the scientific literature, for protein-protein heterodimeric complexes with experimentally determined structures. This represents over four times more data than previously collected. Changes in 713 association and dissociation rates and 127 enthalpies and entropies were also recorded. The existence of biases towards specific mutations, residues, interfaces, proteins and protein families is discussed in the context of how the data can be used to construct predictive models. Finally, a cross-validation scheme is presented which is capable of estimating the efficacy of derived models on future data in which these biases are not present. AVAILABILITY The database is available online at http://life.bsc. es/pid/mutation_database/.
Appendix to : Connecting Two Markets : An Equilibrium Framework for Shorts , Longs , and Stock Loans

This appendix discusses the effect of shocks to the supply of or demand for shares on prices taking into account the joint price setting in both the equity lending market and the stock market. Proofs are left until the end of the discussion. A. Appendix – The Effect of Supply or Demand Shocks on Prices This appendix concerns the effect of shocks to the supply of, or demand for, shares on prices. A sale of stock, short or otherwise, can be equivalently defined as a reduction in demand for, or increase in supply of, the stock. Similarly, a purchase, to own or to cover a short position, can be equivalently defined as an increase in demand for or decrease in supply of the stock. For the sake of clarity, we adopt the convention that all purchases and sales affect demand changes, and we define supply as the number of shares outstanding. If there is an exogenous reduction in demand for a stock, for example through a planned sale of founder’s shares, then somebody must absorb the new shares on the market. When the equity lending constraint is slack, the amount that the price must decline is determined by the demand shock and the elasticity of demand, but we show that when the constraint binds, the price response is typically greater: shocks to demand, in either direction, usually cause larger price changes when a stock is hard to borrow than when it is not. As demand increases, the price should increase. When a stock is not on special this is trivially so, since in this case implicitly differentiating the equity ownership equilibrium condition, Email addresses: jesse.blocher@owen.vanderbilt. edu (Jesse Blocher), adam_reed@unc.edu (Adam V. Reed), vanwesep@unc.edu (Edward D. Van Wesep) Preprint submitted to Journal of Financial Economics September 14, 2012 DL(p, ps) +DS(p, ps) + δ = N, and rearranging yields: dp∗ dδ = − 1 ∂ ∂pDL + ∂ ∂pDS . (A.1) Because ∂ ∂pDL and ∂ ∂pDS are negative, dp∗ dδ is positive. When a stock is on special, there are two relevant equilibrium conditions. Given an increase in demand from longs of δ, our equilibrium conditions are:1 [DL + δ] +DS = N (A.2) and r(ps) × [DL + δ] = −DS . (A.3)
Toward the adaptation of component‐based architectures by model transformation: behind smart user interfaces

Graphical user interfaces are not always developed for remaining static. There are GUIs with the need of implementing some variability mechanisms. Component‐based GUIs are an ideal target for incorporating this kind of operations, because they can adapt their functionality at run‐time when their structure is updated by adding or removing components or by modifying the relationships between them. Mashup user interfaces are a good example of this type of GUI, and they allow to combine services through the assembly of graphical components. We intend to adapt component‐based user interfaces for obtaining smart user interfaces. With this goal, our proposal attempts to adapt abstract component‐based architectures by using model transformation. Our aim is to generate at run‐time a dynamic model transformation, because the rules describing their behavior are not pre‐set but are selected from a repository depending on the context. The proposal describes an adaptation schema based on model transformation providing a solution to this dynamic transformation. Context information is processed to select at run‐time a rule subset from a repository. Selected rules are used to generate, through a higher‐order transformation, the dynamic model transformation. This approach has been tested through a case study which applies different repositories to the same architecture and context. Moreover, a web tool has been developed for validation and demonstration of its applicability. The novelty of our proposal arises from the adaptation schema that creates a non pre‐set transformation, which enables the dynamic adaptation of component‐based architectures. Copyright © 2014 Copyright © 2014 John Wiley & Sons, Ltd.
Taphonomic trade-offs in tropical marine death assemblages: Differential time averaging, shell loss, and probable bias in siliciclastic vs. carbonate facies

Radiocarbon-calibrated amino-acid racemization ages of individually dated bivalve mollusk shells from Caribbean reef, nonreefal carbonate, and siliciclastic sediments in Panama indicate that siliciclastic sands and muds contain significantly older shells (median 375 yr, range up to ;5400 yr) than nearby carbonate seafloors (median 72 yr, range up to ;2900 yr; maximum shell ages differ significantly at p , 0.02 using extreme-value statistics). The implied difference in shell loss rates is contrary to physicochemical expectations but is consistent with observed differences in shell condition (greater bioerosion and dissolution in carbonates). Higher rates of shell loss in carbonate sediments should lead to greater compositional bias in surviving skeletal material, resulting in taphonomic trade-offs: less time averaging but probably higher taxonomic bias in pure carbonate sediments, and lower bias but greater time averaging in siliciclastic sediments from humid-weathered accretionary arc terrains, which are a widespread setting of tropical sedimentation.
DESIGNATED SERVICE PROVIDERS : ENHANCING COMPETITION OR RAISING BARRIERS

With the drive to reduce spiraling costs of medical care, funders are increasingly engaging in selective contracting agreements with designated service provider networks. International experience suggests that this has several disparate effects on competition. In some instances it is argued that selective contracting increases competition between provider networks and drives down prices for funders and ultimately consumers. Others argue that such arrangements have negative impacts on the market by leading to foreclosure of non-contracted businesses and potentially raising prices to the uninsured. This paper seeks firstly to outline relevant theory related to selective contracting and its impact on competition. Secondly, to look at the implications on healthcare markets, and finally to draw lessons for South Africa.
6 Neuroimaging in Manganese-Induced Parkinsonism

Over the last 20 years, the impact of imaging on the clinical sciences has been immense. Tremendous progress has been made in medical imaging of the human body since the invention of computed tomography (CT) and magnetic resonance imaging (MRI). Neuroimaging of patients with metal neurotoxicity can be divided into two types: morphological neuroimaging (anatomy-based imaging) including CT and MRI; and functional neuroimaging (physiology-based imaging) such as magnetic resonance spectroscopy (MRS), single-photon emission computed tomography (SPECT), positron emission tomography (PET), diffusion tensor imaging (DTI), and functional MRI (fMRI). Neuroimaging is undergoing a shift from morphological to functional imaging as new technologies are introduced and technical problems associated with the local production of radioisotopes are solved (Lang, 2000; Walker et al., 2004). MRI, PET, and SPECT have been used for 10 years or more to evaluate workers exposed to manganese (Mn), and to examine the neurological consequences of such exposure. Very recently, functional neuroimaging modalities such as fMRI, MRS, and DTI have been applied to this end. The objectives of this chapter are (1) to review the use of neuroimaging in Mn-induced parkinsonism, and (2) to discuss recent developments in the functional neuroimaging in Mn-induced parkinsonism.
VanB Phenotype-vanA Genotype Enterococcus faecium with Heterogeneous Expression of Teicoplanin Resistance

ABSTRACT Six VanB phenotype-vanA genotype isolates of Enterococcus faecium with heterogeneous expression of teicoplanin resistance which gave rise to an outbreak at a Korean tertiary care teaching hospital have IS1216V in the coding region of vanS. This could be the underlying cause of the VanB phenotype-vanA genotype with heterogeneous expression of teicoplanin resistance.
The influence of wrist posture, grip type, and grip force on median nerve shape and cross‐sectional area

During grasping, the median nerve undergoes mechanical stress in the carpal tunnel which may contribute to carpal tunnel syndrome. This study investigated the effects of wrist posture, grip type, and grip force on the shape and cross‐sectional area of the median nerve. Ultrasound examination was used to obtain cross‐sectional images of the dominant wrist of 16 healthy subjects (8 male) at the proximal carpal tunnel during grasping. The cross‐sectional area, circularity, and axis lengths of the median nerve were assessed in 27 different conditions (3 postures × 3 grip types × 3 force levels). There were no significant changes in median nerve cross‐sectional area (P > 0.05). There were significant interactions across posture, grip type, and grip force affecting nerve circularity and axis lengths. When the wrist was flexed, increasing grip force caused the median nerve to shorten in the mediolateral direction and lengthen in the anteroposterior direction (P < 0.04), becoming more circular. These effects were significant during four finger pinch grip and chuck grip (P < 0.05) but not key grip (P > 0.07). With the wrist extended, the nerve became more flattened (less circular) as grip force increased during four finger pinch grip and chuck grip (P < 0.04) but not key grip (P > 0.3). Circularity was lower during the four finger pinch compared to chuck or key grip (P < 0.03). The findings suggest that grip type and wrist posture significantly alter the shape of the median nerve. Clin. Anat. 30:470–478, 2017. © 2017 Wiley Periodicals, Inc.
Extra Credit

The following computational problems use the inner product space C[−π, π] of all continuous, real-valued functions on [−π, π], together with the inner product f, g = 1 π π −π f (x)g(x)dx. is an orthogonal set. Show also that all vectors have length 1. 2. Find the Fourier expansion of f (x) = x. In other words, find the coefficients in ˆ f := f (x), 1 √ 2 1 √ 2 + ∞ n=1 f (x), sin nx sin nx + ∞ n=1 f (x), cos nx cos nx. ∞ n=1 1 n 2 = π 2 6 .
School Closure and Mitigation of Pandemic (H1N1) 2009, Hong Kong

In Hong Kong, kindergartens and primary schools were closed when local transmission of pandemic (H1N1) 2009 was identified. Secondary schools closed for summer vacation shortly afterwards. By fitting a model of reporting and transmission to case data, we estimated that transmission was reduced ≈25% when secondary schools closed.
Mechanical testing of orthopaedic suture material and a crimp clamp system for the extracapsular stabilisation of canine cruciate-deficient stifles.

The cranial cruciate ligament (CCL) provides cranio-caudal stability, prevents hyperextension and constrains medial rotation of the tibia in the canine stifle joint and CCL rupture is the leading cause of hind leg lameness in dogs. Treatment of CCL rupture aims to resolve lameness caused by joint instability and provide good long-term function of the affected hind limb. The extracapsular technique is one of the most popular methods to restore joint stability. The technique involves a suture loop that is placed around the lateral fabella and through the tibial tuberosity. The ideal suture material should be strong, aseptic, easily handled, inexpensive, and provide excellent knot security and knot compactness. A critical property of the loop is the application of either a knot or crimp to maintain the tension on the loop. There is a variety of orthopaedic suture materials used for the extra- capsular technique. Our aim was to compare the mechanical properties of four commercially available materials in pure tension. The materials tested were monofilament nylon leader (MNL) 100 lb, MNL 80 lb, Supramid and Silon. Our second objective was to compare the interoperator variability of applying either a knot or a crimp to secure the suture loop. Ultimate tensile strength was greatest with MNL 100 lb (373 N) followed by MNL 80 lb (285 N), Supramid (160 N) and Silon (103 N). Based on our results, we conclude that MNL 100 lb and MNL 80 lb are mechanically superior to Silon and Supramid. Our study also shows significant effects for the operator and method of loop fixation (P < 0.0001). Intraoperator differences were also found to be significant, for operator 1 (P < 0.0001), for operator 2 (P < 0.001) and operator 3 (P < 0.01). Our findings indicate that MNL is most suit - able orthopaedic material and that loop fixation should remain the method of choice for surgeons treating CCL.
Antiferromagnetism in 3d transition metals.

Etude de la dependance des proprietes electroniques et magnetiques des metaux de transition 3d vis-a-vis du volume. Ces metaux sont contraints a des environnements cubiques dans des mailles unitaires a un ou deux atomes. Les volumes couvrent les transitions non magnetique-ferromagnetique et non magnetique-antiferromagnetique