Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliability of Droplet Digital PCR Alone and in Combination with Interleukin-6 and Procalcitonin for Prognosis of Bloodstream Infection

Purpose Bloodstream infection(BSI) is linked with high mortality, underscoring the significance of prompt etiological diagnosis for timely and precise treatment. This study aims to investigate the diagnostic value of droplet digital polymerase chain reaction(ddPCR) in combination with conventional inflammatory markers [interleukin-6(IL-6) and procalcitonin(PCT)] concerning disease progression and treatment prognosis in BSI patients. Furthermore, the study aims to explore a more efficient clinical application strategy. Patients and Methods This prospective case seried study centers on 176 patients suspected of or confirmed with BSI. Blood samples were collected to extract nucleic acids for identifying pathogens (bacteria, fungi, and viruses) and determining copy loads via ddPCR. Results The sensitivity of ddPCR was markedly higher compared to the culture method (74.71% vs 31.03%). A positive correlation existed between bacterial load and levels of inflammatory markers [IL-6 (P=0.0182), PCT (P=0.0029), and CRP (P=0.0005)]. In suspected BSI cases, the combination of ddPCR and inflammatory markers could predict sepsis risk [ROC: Area under the curve(AUC)=0.6071, P=0.0383]. Within confirmed BSI patients, the ddPCR bacterial load of those with SOFA<7 was lower than that of the SOFA≥7 (P=0.0334). ddPCR (OR: 1.789, P=0.035) monitoring combined with PCT (OR: 1.787, P=0.035) holded predictive value for SOFA progression (AUC=0.7913, P=0.0003). Similarly, BSI survivors displayed a lower burden than non-survivors (P=0.0170). Additionally, ddPCR combinated with IL-6 provided a more accurate and expedited insight into clinical outcomes prediction for BSI confirmed patients (AUC=0.7352, P=0.0030). Serial monitoring of bacterial load by ddPCR effectively mirrored the clinical course of BSI in patients. Notably, patients with positive ddPCR virus infection exhibited significantly reduced lymphocyte counts (P=0.0003). Conclusion In a clinical context, qualitative ddPCR results and quantitative continuous monitoring can more precisely assess sepsis progression and treatment prognosis in BSI patients. Furthermore, ddPCR results offer quicker and more accurate reference points for clinical antibacterial and antiviral interventions.
Interhemispheric Survey of Polar Cap Aurora

This study investigates the interhemispheric nature of polar cap auroras via ultraviolet imaging, combined with particle data, to determine whether they occur on open or closed field lines. Data from the SSUSI (Special Sensor Ultraviolet Spectrographic Imager) instrument on board the DMSP (Defence Meteorological Satellite Program) spacecraft are examined. The DMSP spacecraft are in 90‐min orbits; hence, images of each hemisphere are separated by 45 min providing a good opportunity for interhemispheric study. 21 polar cap arc (PCA) events are recorded in December 2015 which have particle data from the SSJ/4 particle spectrometer associated with an arc in at least one hemisphere. Nine events are found to contain "arcs" consistent with a closed field line mechanism, that is, arcs associated with an ion signature present in both hemispheres. Six events contained arcs that were consistent with an "open field line" mechanism, that is, they were associated with electron‐only precipitation. Events containing arcs that were not consistent with either of these expectations are also explored, including an example of a "non‐conjugate" theta aurora and an interesting example of auroral morphology similar to a PCA which is associated with a geomagnetic storm. Seasonal effects are also investigated through a statistical analysis of PCAs over 4 months in 2015. It is found that PCAs are visible in the SSUSI data at least 20% of the time and that it is likely some are missed due to the spacecraft field of view and poor sensitivity in the summer hemisphere due to increased solar illumination.
Comparison of low-dose gentamicin with minocycline as catheter lock solutions in the prevention of catheter-related bacteremia.

BACKGROUND Catheter-restricted antibiotic lock solutions were found to be effective in the prevention of catheter-related bacteremia (CRB), but insufficient data are available about the ideal agent and dose. We hypothesized that a low concentration of gentamicin would be as effective as the high doses studied in the past. METHODS In this prospective, open-labeled, randomized, clinical trial of patients on long-term hemodialysis therapy, patients were randomly assigned to administration of an antibiotic lock solution of gentamicin/citrate (4 mg/mL), minocycline/EDTA, or the control solution of heparin. Patients were followed up until the study end point of CRB was reached or a censoring event occurred. Interim data analysis was performed after 6 months to assess data safety; efficacy was noted and the study was terminated early. RESULTS Sixty-two patients were enrolled into the study, evenly distributed in 3 arms, with data from 1 patient excluded from analysis. Seven of 20 patients in the heparin group (4.0 events/1,000 catheter days), 1 of 21 patients in the minocycline group (0.4 events/1,000 catheter days), and none of 20 patients in the gentamicin group developed bacteremia. Results were statistically significant by using 2-tailed Fisher exact test; heparin versus gentamicin, P = 0.008, and heparin versus minocycline, P = 0.020. CONCLUSION Antibiotic lock solutions are superior to the standard heparin lock alone in the prevention of CRBs, and low-dose gentamicin solution has efficacy similar to that of greater concentrations used in previous studies.
The Use of Routine Special Stains for Upper Gastrointestinal Biopsies

Helicobacter pylori and intestinal metaplasia (IM) are readily seen in hematoxylin and eosin-stained slides of gastric and/or esophageal biopsies, yet many pathology laboratories perform routine special stains on all of these biopsies. We wished to determine if special stains are necessary for every single gastric and/or esophageal biopsy. We prospectively studied 613 gastric and/or esophageal biopsies from 494 consecutive patients. The slides were stained with hematoxylin and eosin, toluidine blue (TB) for H. pylori, and Alcian blue (AB) for IM. The hematoxylin and eosin slide was classed as positive or negative for H. pylori and IM. Then it was determined if the case needed a TB or AB stain. A total of 436 cases (71.1%) were identified as H. pylori-negative and not needing a TB stain, and none was TB+. A total of 126 (20.6%) of hematoxylin and eosin slides were inconclusive for H. pylori and were regarded as needing a TB stain. Twenty of these (15.9%) were TB+. Fifty-one biopsies (8.3%) were regarded as H. pylori+ on hematoxylin and eosin; the TB stain was also positive in 49. IM was present in 113 (18.4%) hematoxylin and eosin biopsies. Hematoxylin and eosin slides were IM-negative in 498 cases (81.2%). The AB stain revealed rare goblet cells in 3 of 498 cases (0.6%). Only one of those biopsies was esophageal, and that had one goblet cell that was missed on hematoxylin and eosin. Only 2 (0.3%) were regarded as needing an AB stain. We conclude that routine special stains for all gastric and/or esophageal biopsies are not required, and hematoxylin and eosin assessment combined with selective ordering of these stains will identify virtually all cases of H. pylori gastritis and intestinal metaplasia.
Emerging executive skills in very preterm children at 2 years corrected age: A composite assessment

Executive Function (EF) deficits have previously been identified in preterm children. However, only recently have emerging executive functions been studied in preschool children who were born preterm without major brain damage. Our study provides a broad assessment of EFs in 72 extremely preterm births (gestational age < 34 weeks and birth weight < 2500 g) and 73 full-term children, born between 2006 and 2008, at 24 months of corrected age. Three factors were extracted from the EF administered measures: working memory, cognitive flexibility, and impulsivity control. Only cognitive flexibility was found to discriminate preterm children from controls.
Evaluation of Different PCR-Based Assays and LAMP Method for Rapid Detection of Phytophthora infestans by Targeting the Ypt1 Gene

Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating diseases affecting potato and tomato worldwide. Early diagnosis of the P. infestans pathogen causing late blight should be the top priority for addressing disease epidemics and management. In this study, we performed a loop-mediated isothermal amplification (LAMP) assay, conventional polymerase chain reaction (PCR), nested PCR, and real-time PCR to verify and compare the sensitivity and specificity of the reaction based on the Ypt1 (Ras-related protein) gene of P. infestans. In comparison with the PCR-based assays, the LAMP technique led to higher specificity and sensitivity, using uncomplicated equipment with an equivalent time frame. All 43 P. infestans isolates, yielded positive detection results using LAMP assay showing no cross reaction with other Phytophthora spp. , oomycetes or fungal pathogens. The LAMP assay yielded the lowest detectable DNA concentration (1.28 × 10-4 ng μL-1), being 10 times more sensitive than nested PCR (1.28 × 10-3 ng μL-1), 100 times more sensitive than real-time PCR (1.28 × 10-2 ng μL-1) and 103 times more sensitive than the conventional PCR assay (1.28 × 10-1 ng μL-1). In the field experiment, the LAMP assay outperformed the other tests by amplifying only diseased tissues (leaf and stem), and showing no positive reaction in healthy tissues. Overall, the LAMP assay developed in this study provides a specific, sensitive, simple, and effective visual method for detection of the P. infestans pathogen, and is therefore suitable for application in early prediction of the disease to reduce the risk of epidemics.
Real earnings disparities in Britain

This report estimates housing-cost-earnings differentials across labour market areas in Britain. We show that quality-adjusted housing costs rise on average, one for one with the skill-adjusted earnings of the average working household. However, the relationship is Ushaped, with relatively high housing costs in places at the bottom and top ends of the wage distribution. This variation in housing costs means nominal wages are uninformative about real income disparities. If we assume spatial equilibrium and treat the cost-earnings differentials as estimates of the value of amenities, we can rank cities in terms of quality of life and estimate the value of different amenities. Our work improves on previous research by using longitudinal data on workers to estimate skill-adjusted labour market earnings differentials (net of taxes), using micro data on housing transactions, and by considering the implications of capital gains for housing user cost calculations.
Losing Money on Arbitrages: Optimal Dynamic Portfolio Choice in Markets with Arbitrage Opportunities

In theory, an investor can make infinite profits by taking unlimited positions in an arbitrage. In reality, however, investors must satisfy margin requirements which completely change the economics of arbitrage. We derive the optimal investment policy for a risk-averse investor in a market where there are arbitrage opportunities. We show that it is often optimal to underinvest in the arbitrage by taking a smaller position than margin constraints allow. In some cases, it is actually optimal for an investor to walk away from a pure arbitrage opportunity. Even when the optimal policy is followed, the arbitrage strategy may underperform the riskless asset or have an unimpressive Sharpe ratio. Furthermore, the arbitrage portfolio typically experiences losses at some point before the final convergence date. These results have important implications for the role of arbitrageurs in financial markets.
Macrophage Migration Inhibitory Factor Deficiency Ameliorates High-Fat Diet Induced Insulin Resistance in Mice with Reduced Adipose Inflammation and Hepatic Steatosis

Macrophage infiltration is a critical determinant of high-fat diet induced adipose tissue inflammation and insulin resistance. The precise mechanisms underpinning the initiation of macrophage recruitment and activation are unclear. Macrophage migration inhibitory factor (MIF), a pro-inflammatory cytokine, displays chemokine-like properties. Circulating MIF levels are elevated during obesity however its role in high-fat diet induced adipose inflammation and insulin resistance remains elusive. Wildtype and MIF−/− C57Bl\6J mice were fed chow or high-fat diet. Body weight and food intake was assessed. Glucose homeostasis was monitored by glucose and insulin tolerance tests. Adipose tissue macrophage recruitment and adipose tissue insulin sensitivity was evaluated. Cytokine secretion from stromal vascular fraction, adipose explants and bone marrow macrophages was measured. Inflammatory signature and insulin sensitivity of 3T3-L1-adipocytes co-cultured with wildtype and MIF−/− macrophage was quantified. Hepatic triacylglyceride levels were assessed. MIF−/− exhibited reduced weight gain. Age and weight-matched obese MIF−/− mice exhibited improved glucose homeostasis coincident with reduced adipose tissue M1 macrophage infiltration. Obese MIF−/− stromal vascular fraction secreted less TNFα and greater IL-10 compared to wildtype. Activation of JNK was impaired in obese MIF−/−adipose, concomitant with pAKT expression. 3T3-L1-adipocytes cultured with MIF−/− macrophages had reduced pro-inflammatory cytokine secretion and improved insulin sensitivity, effects which were also attained with MIF inhibitor ISO-1. MIF−/− liver exhibited reduced hepatic triacyglyceride accumulation, enhanced pAKT expression and reduced NFκB activation. MIF deficiency partially protects from high-fat diet induced insulin resistance by attenuating macrophage infiltration, ameliorating adipose inflammation, which improved adipocyte insulin resistance ex vivo. MIF represents a potential therapeutic target for treatment of high-fat diet induced insulin resistance.
Effect of Periconceptional Undernutrition in Sheep on Late Gestation Expression of mRNA and Protein From Genes Involved in Fetal Adrenal Steroidogenesis and Placental Prostaglandin Production

In sheep, maternal periconceptional undernutrition precociously activates fetal hypothalamic-pituitary-adrenal function in a high proportion of animals, resulting in preterm birth. We investigated whether the effects of periconceptional undernutrition were mediated through genes encoding enzymes involved in adrenal steroidogenesis and in placental production and metabolism of steroids and prostaglandins. Singleton-bearing ewes were fed ad libitum (control, N) throughout gestation or undernourished from 60 days before until 30 days after mating. Fetal adrenal and placentome tissues were collected on gestational day 131. Fetal adrenal P450C17 protein expression was significantly increased with undernutrition. Placental prostaglandin endoperoxide synthase-2 expression was not different between groups. In undernourished pregnancies, there were significant positive correlations between fetal plasma adrenocorticotrophic hormone and cortisol concentrations and between fetal plasma adrenocorticotrophic hormone concentrations and placental prostaglandin endoperoxide synthase-2 messenger RNA (mRNA) and protein. These studies suggest that periconceptional undernutrition affects fetal adrenal P450C17, consistent with an elevation in plasma cortisol, and this occurs prior to activation of placental prostaglandin endoperoxide synthase-2 expression at gestational day 131.
Individuals with the Dominant Hand Affected following Stroke Demonstrate Less Impairment Than Those with the Nondominant Hand Affected

Objective. The purpose was to determine if upper extremity impairment and function in individuals with chronic stroke is dependent upon whether the dominant or non-dominant hand is affected. Methods. Ninety-three community-dwelling individuals with stroke. The Modified Ashworth Scale (tone), handheld dynamometry (isometric strength), monofilaments (sensation), Brief Pain Inventory (pain), Chedoke Arm and Hand Activity Inventory Motor Activity Log (paretic arm use), and Reintegration to Normal Living Index (participation) were used to form impairment and function models. Results. Multivariate analysis models (Dominance × Severity) were created for impairment and function variables. There was a significant interaction and main effect of Dominance for the impairment model (P = 0.01) but not the function model (P = 0.75). The dependent variables of tone, grip strength, and pain were all significantly affected by Dominance, indicating less impairment if the dominant hand was affected. All dependent variables except pain were affected by Severity. Conclusion. This study looked at the effect of the dominant hand being affected versus the nondominant in individuals with chronic stroke. Individuals with the dominant hand affected demonstrated less impairment than those with the nondominant hand affected. However, there was no effect of dominance on paretic arm use or performance in activities of daily living. Prospective studies to further explore the issue of hand dominance and poststroke function are suggested.
In Vivo Imaging of Membrane-Associated Glycans in Developing Zebrafish

Glycans are attractive targets for molecular imaging but have been inaccessible because of their incompatibility with genetically encoded reporters. We demonstrated the noninvasive imaging of glycans in live developing zebrafish, using a chemical reporter strategy. Zebrafish embryos were treated with an unnatural sugar to metabolically label their cell-surface glycans with azides. Subsequently, the embryos were reacted with fluorophore conjugates by means of copper-free click chemistry, enabling the visualization of glycans in vivo at subcellular resolution during development. At 60 hours after fertilization, we observed an increase in de novo glycan biosynthesis in the jaw region, pectoral fins, and olfactory organs. Using a multicolor detection strategy, we performed a spatiotemporal analysis of glycan expression and trafficking and identified patterns that would be undetectable with conventional molecular imaging approaches.
Explorer Interpreting English Pitch Contours in Context

This paper presents a model of how pitch contours influence the illocutionary and perlocutionary effects of utterances in conversation. Our account is grounded in several insights from the prior literature. Our distinctive contribution is to replace earlier informal claims about the implicatures arising from intonation with logical derivations: we validate inferences in the SDRT framework that resolve the partial meaning we associate with a pitch contour to different specific interpretations in different contexts.
No . 041 December 29 , 2015 I-theory on depth vs width : hierarchical function composition by Tomaso Poggio with

Deep learning networks with convolution, pooling and subsampling are a special case of hierarchical architectures, which can be represented by trees (such as binary trees). Hierarchical as well as shallow networks can approximate functions of several variables, in particular those that are compositions of low dimensional functions. We show that the power of a deep network architecture with respect to a shallow network is rather independent of the specific nonlinear operations in the network and depends instead on the the behavior of the VC-dimension. A shallow network can approximate compositional functions with the same error of a deep network but at the cost of a VC-dimension that is exponential instead than quadratic in the dimensionality of the function. To complete the argument we argue that there exist visual computations that are intrinsically compositional. In particular, we prove that recognition invariant to translation cannot be computed by shallow networks in the presence of clutter. Finally, a general framework that includes the compositional case is sketched. The key condition that allows tall, thin networks to be nicer that short, fat networks is that the target input-output function must be sparse in a certain technical sense. This work was supported by the Center for Brains, Minds and Machines (CBMM), funded by NSF STC award CCF 1231216. I-theory on depth vs width: hierarchical function composition Tomaso Poggio with Fabio Anselmi and Lorenzo Rosasco
Multidimensional support vector machines for visualization of gene expression data

DNA microarray technology has helped us to understand the biological system because of its ability to monitor the expression levels of thousands of genes simultaneously. Since DNA microarray experiments provide us with huge amount of gene expression data, they should be analyzed with statistical methods to extract the meanings of experimental results.For visualization and class prediction of gene expression data, we have developed a new SVM-based method called multidimensional SVMs, that generate multiple orthogonal axes. This method projects high dimensional data into lower dimensional space to exhibit properties of the data clearly and to visualize the distribution of the data roughly. Furthermore, the multiple axes can be used for class prediction. The basic properties of conventional SVMs are retained in our method: solutions of mathematical programming are sparse, the optimal solutions can always be found due to its convexity, and nonlinear classification is implemented implicitly through the use of kernel functions. The application of our method to the experimentally obtained gene expression datasets for patients' samples indicates that our algorithm is efficient and useful for visualization and class prediction.
Coagulation and complement protein differences between septic and uninfected systemic inflammatory response syndrome patients.

BACKGROUND Systemic inflammatory response syndrome (SIRS) represents a host response to various insults. Recent advances have demonstrated an interconnection between inflammation, complement, and coagulation. This experiment was designed to evaluate differences in plasma protein profiles between clinically identical patients: septic versus uninfected SIRS patients, prior to clinical diagnosis of infection. METHODS Patients admitted to an intensive care unit of a major university, meeting two of four SIRS criteria were followed prospectively for development of sepsis. Plasma samples were collected daily and divided into two groups: a preseptic group that subsequently developed sepsis and a SIRS group that remained uninfected. Protein profiling was accomplished by three-dimensional liquid chromatography fractionation with electrospray ion trap mass spectrometry after immunodepletion of abundant proteins and a trypsin digest. Spectra peaks were identified using Agilent Technologies Spectrum Mill Workbench software. Relevance to biologic pathways was analyzed and statistical significance determined with DAVID 2.1 available at the National Institutes of Health. RESULTS A total of 134 unique proteins were significantly different between groups. Thirty-two of these (23.5%) mapped to the complement and coagulation cascade (KEGG), 10 (7.5%) mapped to classic complement pathway; 11 (8.2%) mapped to complement pathway, and 8 (6.0%) mapped to lectin binding complement pathway (Biocarta). These pathways were all significantly (p<0.0001) over-represented in sepsis patients compared to SIRS-only patients. CONCLUSION Using novel mass spectrometry methodology, we were able to demonstrate differential protein profiles in septic versus uninfected SIRS patients prior to clinical diagnosis of sepsis.