gebhart/patrepeval huggingface dataset:
A Flowthrough Assay for Rapid Bedside Stratification of Bloodstream Bacterial Infection in Critically Ill Patients: a Pilot Study (2018)

Bacterial infections affect more than 2 million people annually. Of these, systemic infections caused by bacteria in critically ill patients may lead to life-threatening conditions such as sepsis. We have developed a point-of-care (POC) device called Septiflo that can detect and stratify the Gram status of bloodstream bacterial infections in less than 10 min from a drop of human plasma. It works on the principle of identifying pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharides (LPS) and lipoteichoic acid (LTA) that are released into the bloodstream at the onset of Gram-negative and Gram-positive bacterial infections, respectively. The biomarkers are captured on a membrane without a receptor, and the Gram status specificity is conferred by the ligands attached to gold nanoparticles (AuNPs) used as signal amplification probes. The ultrasensitive colorimetric results are read by eye down to a 100-fg/ml detection limit without an instrument. No cross-interference between the PAMPs is seen during Gram stratification. Septiflo results also display better performance than commercial enzyme-linked immunosorbent assays (ELISAs). Tests performed on 60 clinical samples from patients showed a correlation accuracy of 70% against procalcitonin (PCT), an accepted surrogate biomarker for sepsis. A direct comparison with eubacterial PCR yielded up to 94% accuracy in 31 patients at a chosen cutoff level for LPS and LTA and area under the curve (AUC) values of 0.927 and 0.885, respectively, though blood culture was negative for most samples. The high sensitivity, low cost, and simple bedside utility of the assay may aid in better sepsis management apparently at the presymptomatic stage, lowering empirical therapy, medical costs, antimicrobial resistance, and mortality.
Comparison of Physicochemical Properties of New Ionic Liquids Based on Imidazolium, Quaternary Ammonium, and Guanidinium Cations (2007)

More than 50 ionic liquids were prepared by using imidazolium, quaternary ammonium, and guanidinium cations and various anions. In these series, different cationic structures such as 1-benzyl-3-methylimidazolium [Bzmim]+, 1,3-dibenzylimidazolium [BzmiBz]+, 1-octyl-3-methylimidazolium [C8mim]+, 1-decyl-3-methylimidazolium [C10mim]+, tricapryl-methylammonium [Aliquat]+, benzyltriethylammonium [BzTEA]+, phenyltrimethylammonium [PhTMA]+, and dimethyldihexylguanidinium [DMG]+ were combined with anions, p-toluenesulfonate [TSA](-), dicyanoamide [DCA]-, saccharine (2-sulfobenzoic acid imide sodium salt) [SAC]-, trifluoroacetate [TFA]-, bis(trifluoromethanesulfonyl)imide [Tf2N]-, trifluoromethanesulfonate [TfO]-, and thiocyanate [SCN]-. Important physical data for these ionic liquids are collated, namely solubility in common solvents, viscosity, density, melting point and water content. Apart from the viscosity, the Newtonian and non-Newtonian behavior of these ionic liquids is also disclosed. Stability of these ionic liquids under thermal, basic, acidic, nucleophilic, and oxidative conditions was also studied. The features of the solid-liquid phase transition were analyzed, namely the glass transition temperature and the heat capacity jump associated with the transition from the non-equilibrium glass to the metastable supercooled liquid. A degradation temperature of each ionic liquid was also determined. Comparisons of the properties of various ionic liquids were made.
GPUSGD: A GPU‐accelerated stochastic gradient descent algorithm for matrix factorization (2015)

Summary Matrix factorization is one of the leading techniques for many applications such as social network‐based recommendation systems. As of today, many parallel stochastic gradient descent (SGD) methods have been proposed to address the matrix factorization issue on shared‐memory (multi‐core) systems and distributed systems. However, these methods cannot be improved significantly on graphics processing unit (GPU) because the serious over‐writing problem and thread divergence may occur. The fundamental reason for such undesired results is that GPU is a parallel single instruction multiple data device, which only can greatly improve the applications with fine‐grained parallelism. In this paper, we propose an efficient GPU algorithm, named GPUSGD, to solve the matrix factorization problem based on SGD method. The major advantage of the proposed GPUSGD is that such method not only can handle the over‐writing problem but also can avoid the performance loss caused by the thread divergence. The experimental results show that GPUSGD performs much better in accelerating the matrix factorization compared with the existing state‐of‐the‐art parallel methods. To the best of our knowledge, this is the first work that develops a parallel SGD method to improve the matrix factorization on GPU. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Panniculitis in association with apomorphine infusion (1998)

This study was undertaken to ascertain the histopathology and aetiology of cutaneous nodules observed in Parkinson's patients treated with continuous subcutaneous apomorphine. Ten patients were recruited, answered questionnaires, and underwent skin biopsies and full blood count, and nine were patch tested to apomorphine and its preservative. Six had serum IgE levels measured. A florid panniculitis was seen in all biopsies; five were predominantly eosinophilic, three lymphocytic and two neutrophilic; in seven cases the panniculitis was mixed and in three it was septal. Patch testing was universally negative and the IgE levels were normal.
GENDER RECONFIGURED: Emily Roebling and the Construction of the Brooklyn Bridge (1998)

On May 24, 1883, the Brooklyn Bridge assumed a prominent site in New York Harbor. Although most canonical accounts attribute the Bridge to John A. Roebling (1806-1869) and his son Colonel Washington Roebling (1837-1926), its final builder was the Colonel's wife, Emily Warren Roebling (1843-1907). Using journalistic accounts from the time of the bridge's construction and research produced over the past century, this essay investigates the exclusion, silence, and subterfuge that have characterized descriptions of Emily Roebling. Her inclusion in the history of die bridge's development serves to locate the Bridge within a broader discussion of gender and public space.
Elevated IL‐10 mRNA expression and downregulation of Th1‐type cytokines in microfilaraemic individuals with Wuchereria bancrofti infection (1997)

To understand the molecular basis of parasite-specific anergy in human lymphatic filariasis caused by the nematode Wuchereria bancrofti, parasite antigen-dependent cellular proliferation and cytokine gene expression were investigated. By reverse transcriptase polymerase chain reaction (RT-PCR), the levels of cytokine mRNA were determined in the peripheral blood mononuclear cells (PBMCs) of different clinical groups of filariasis patients. This includes individuals with circulating microfilariae (MF), patients with chronic lymphatic obstruction (CP), and exposed but uninfected individuals (EN). Those with CP exhibited both a Th2 and a Th1 parasite antigen-driven response. In PBMCs from those with MF, there was a marked downregulation of cellular response to parasite antigens, with lowered expression of Th1-specific cytokines (IFN-gamma and IL-2) and this was paralleled by increased IL-10 expression. The EN individuals had a purely Th1-type pattern with absence of IL-4 and IL-5 expression. Further, the mRNA expression of the costimulatory surface marker, CD80 (B7-1), was not associated with either disease status or IL-10 expression. There was a significant negative correlation between IL-10 mRNA expression and PBMC proliferation in the MF individuals, thus indicating the possible role of IL-10 in antigen-specific hyporesponsiveness.
The Role of Thyroid Hormones in Prenatal and Neonatal Neurological Development—Current Perspectives (1993)

FOR YEARS thyroid hormones have been known to be important for normal neonatal brain development, and numerous reviews have covered this topic in depth. It now also appears that fetal thyroid hormones play an essential role in fetal brain development. In addition, as some placental transport of thyroid hormones has been shown to occur, it is possible that maternal thyroid hormones might influence fetal brain development. Animal models have been used to study the influence of thyroid hormones on neurological] evelopment. Rats and mice have been the primary animals studied; however, a significant amount of data have come from studies on sheep and nonhuman primates. While the merit of application of animal data to human problems is frequently questioned, valuable information can be obtained when the animal data are properly interpreted. Furthermore, most of the information obtained from animal experiments would be unavailable from humans.
Influenza virus hemagglutinin trimers and monomers maintain distinct biochemical modifications and intracellular distribution in brefeldin A-treated cells. (1991)

Brefeldin A (BFA) induces the retrograde transport of proteins from the Golgi complex (GC) to the endoplasmic reticulum (ER). It is uncertain, however, whether the drug completely merges the ER with post-ER compartments, or whether some of their elements remain physically and functionally distinct. We investigated this question by the use of monoclonal antibodies specific for monomers and trimers of the influenza virus hemagglutinin (HA). In untreated influenza virus-infected cells, monomers and trimers almost exclusively partition into the ER and GC, respectively. In BFA-treated cells, both monomers and trimers are detected in the ER by immunofluorescence. Cell fractionation experiments indicate, however, that whereas HA monomers synthesized in the presence of BFA reside predominantly in vesicles with a characteristic density of the ER, HA trimers are primarily located in lighter vesicles characteristic of post-ER compartments. Biochemical experiments confirm that in BFA-treated cells, trimers are more extensively modified than monomers by GC-associated enzymes. Additional immunofluorescence experiments reveal that in BFA-treated cells, HA monomers can exist in an ER subcompartment less accessible to trimers and, conversely, that trimers are present in a vesicular compartment less accessible to monomers. These findings favor the existence of a post-ER compartment for which communication with the ER is maintained in the presence of BFA and suggest that trimers cycle between this compartment and the ER, but have access to only a portion of the ER.
The Pimlico Connection: Undergraduates as tutors in schools (1979)

Click to increase image sizeClick to decrease image size Additional informationNotes on contributorsJohn HarrisAsad Abidi, Peter Anslow and John Harris did the statistical analysis of the questionnaire results in 1976, 1977 and 1978 respectively. Each graduated with first-class honours in Electrical Engineering.
Improving water use in crop production (2007)

Globally, agriculture accounts for 80-90% of all freshwater used by humans, and most of that is in crop production. In many areas, this water use is unsustainable; water supplies are also under pressure from other users and are being affected by climate change. Much effort is being made to reduce water use by crops and produce 'more crop per drop'. This paper examines water use by crops, taking particularly a physiological viewpoint, examining the underlying relationships between carbon uptake, growth and water loss. Key examples of recent progress in both assessing and improving crop water productivity are described. It is clear that improvements in both agronomic and physiological understanding have led to recent increases in water productivity in some crops. We believe that there is substantial potential for further improvements owing to the progress in understanding the physiological responses of plants to water supply, and there is considerable promise within the latest molecular genetic approaches, if linked to the appropriate environmental physiology. We conclude that the interactions between plant and environment require a team approach looking across the disciplines from genes to plants to crops in their particular environments to deliver improved water productivity and contribute to sustainability.
Mice Producing Less Reactive Oxygen Species Are Relatively Resistant to Collagen Glycopeptide Vaccination against Arthritis (2010)

The bottleneck for the induction of collagen-induced arthritis in mice is the recognition of immunodominant type II collagen (CII) peptide (CII259-273) bound to the MHC class II molecule A(q). We have shown previously that the posttranslationally glycosylated lysine at position 264 in this epitope is of great importance for T cell recognition and tolerance induction to CII as well as for arthritis development. The Ncf1 gene, controlling oxidative burst, has been shown to play an important role for immune tolerance to CII. To investigate the effect of oxidation on the efficiency of immune-specific vaccination with MHC class II/glycosylated-CII peptide complexes, we used Ncf1 mutated mice. We demonstrate that normal reactive oxygen species (ROS) levels contribute to the establishment of tolerance and arthritis protection, because only mice with a functional oxidative burst were completely protected from arthritis after administration of the glycosylated CII259-273 peptide in complex with MHC class II. Transfer of T cells from vaccinated mice with functional Ncf1 protein resulted in strong suppression of clinical signs of arthritis in B10.Q mice, whereas the Ncf1 mutated mice as recipients had a weaker suppressive effect, suggesting that ROS modified the secondary rather than the primary immune response. A milder but still significant effect was also observed in ROS deficient mice. During the primary vaccination response, regulatory T cells, upregulation of negative costimulatory molecules, and increased production of anti-inflammatory versus proinflammatory cytokines in both Ncf1 mutated and wild type B10.Q mice was observed, which could explain the vaccination effect independent of ROS.
Lipid metabolism, contractility, and ultrastructure of hearts of rats fed a mustard seed oil diet. (1980)

When male weaning rats were fed a high fat-high erucic acid and diet (mustard seed oil) for 1 week, there were increases in the triglyceride and erucic acid contents in the myocardium, and an increase in the rate of incorporation of [1-14C]palmitic acid into triglyceride in the perfused heart, in comparison to rats that had consumed a high fat-high linoleic acid diet (corn oil) or a low fat diet (laboratory chow). However, continuation of the mustard seed oil diet (3-6 weeks) tended to normalize these biochemical parameters. The size of the papillary muscle isolated from the mustard seed oil-fed rats was greater than that of the muscle of the chow-fed rats, and its developed isometric tension was lower. Electron microscopic examination revealed that, in the hearts of rats having eaten the mustard seed oil diet, there were isolated foci where the number and size of mitochondria appeared to be increased.
DLTS of gold impurities in germanium (1987)

The band-gap levels introduced by gold in germanium have been investigated using DLTS. The samples were taken from well characterised n- and p-type germanium crystals and were doped with gold by diffusion at 700 degrees C followed by a quench to room temperature. Three acceptor levels at Ec-0.056 eV, Ec-0.215 eV and Ev+0.135 eV and one donor level at Ev+0.044 eV are observed, in agreement with published data obtained from Hall effect studies. All four levels are attributed to one amphoteric defect, i.e. the gold substitutional.
Faculty Opinions recommendation of Methylglyoxal modification of Nav1.8 facilitates nociceptive neuron firing and causes hyperalgesia in diabetic neuropathy. (2012)

This study establishes a mechanism for metabolic hyperalgesia based on the glycolytic metabolite methylglyoxal. We found that concentrations of plasma methylglyoxal above 600 nM discriminate between diabetes-affected individuals with pain and those without pain. Methylglyoxal depolarizes sensory neurons and induces post-translational modifications of the voltage-gated sodium channel Na(v)1.8, which are associated with increased electrical excitability and facilitated firing of nociceptive neurons, whereas it promotes the slow inactivation of Na(v)1.7. In mice, treatment with methylglyoxal reduces nerve conduction velocity, facilitates neurosecretion of calcitonin gene-related peptide, increases cyclooxygenase-2 (COX-2) expression and evokes thermal and mechanical hyperalgesia. This hyperalgesia is reflected by increased blood flow in brain regions that are involved in pain processing. We also found similar changes in streptozotocin-induced and genetic mouse models of diabetes but not in Na(v)1.8 knockout (Scn10(-/-)) mice. Several strategies that include a methylglyoxal scavenger are effective in reducing methylglyoxal- and diabetes-induced hyperalgesia. This previously undescribed concept of metabolically driven hyperalgesia provides a new basis for the design of therapeutic interventions for painful diabetic neuropathy. PMID: 22581285 Funding information This work was supported by: NIDDK NIH HHS, United States Grant ID: 2R56DK33861-21
Deep learning-based brain transcriptomic signatures associated with the neuropathological and clinical severity of Alzheimer’s disease (2021)

Brain tissue gene expression from donors with and without Alzheimer's disease has been used to help inform the molecular changes associated with the development and potential treatment of this disorder. Here, we use a deep learning method to analyse RNA-seq data from 1114 brain donors from the Accelerating Medicines Project for Alzheimer's Disease consortium to characterize post-mortem brain transcriptome signatures associated with amyloid-β plaque, tau neurofibrillary tangles and clinical severity in multiple Alzheimer's disease dementia populations. Starting from the cross-sectional data in the Religious Orders Study and Memory and Aging Project cohort (<i>n</i> = 634), a deep learning framework was built to obtain a trajectory that mirrors Alzheimer's disease progression. A severity index was defined to quantitatively measure the progression based on the trajectory. Network analysis was then carried out to identify key gene (index gene) modules present in the model underlying the progression. Within this data set, severity indexes were found to be very closely correlated with all Alzheimer's disease neuropathology biomarkers (<i>R</i> ∼ 0.5, <i>P</i> < 1e-11) and global cognitive function (<i>R</i> = -0.68, <i>P</i> < 2.2e-16). We then applied the model to additional transcriptomic data sets from different brain regions (MAYO, <i>n</i> = 266; Mount Sinai Brain Bank, <i>n</i> = 214), and observed that the model remained significantly predictive (<i>P</i> < 1e-3) of neuropathology and clinical severity. The index genes that significantly contributed to the model were integrated with Alzheimer's disease co-expression regulatory networks, resolving four discrete gene modules that are implicated in vascular and metabolic dysfunction in different cell types, respectively. Our work demonstrates the generalizability of this signature to frontal and temporal cortex measurements and additional brain donors with Alzheimer's disease, other age-related neurological disorders and controls, and revealed that the transcriptomic network modules contribute to neuropathological and clinical disease severity. This study illustrates the promise of using deep learning methods to analyse heterogeneous omics data and discover potentially targetable molecular networks that can inform the development, treatment and prevention of neurodegenerative diseases like Alzheimer's disease.
Bacille Calmette-Guérin vaccination enhances human gamma delta T cell responsiveness to mycobacteria suggestive of a memory-like phenotype. (1998)

Bacille Calmette-Guérin (BCG) immunity can be studied as one experimental model for mycobacterial protective immunity. We have used flow cytometry to investigate human T cell subsets induced by BCG vaccination. PBMC harvested from BCG-vaccinated individuals and controls were stimulated with mycobacterial Ags, and the T cell subsets present after 7 days of in vitro expansion were characterized. The most dramatic expansions induced by mycobacterial Ags were detected in gamma delta T cells. The gamma delta T cell expansions measured after in vitro stimulation with mycobacterial Ags were significantly greater in BCG responders compared with nonsensitized controls, indicating that BCG vaccination induced gamma delta T cell activation associated with enhanced secondary responses. The majority of gamma delta T cells induced by BCG vaccination were gamma 9+ delta 2+ T cells reactive with isoprenyl pyrophosphates. Coculture with CD4+ T cells induced optimal gamma delta T cell expansion, although IL-2 alone could provide this helper function in the absence of CD4+ T cells. Gamma delta T cells were found to provide helper functions for mycobacterial specific CD4+ and CD8+ T cells as well, demonstrating reciprocal stimulatory interactions between gamma delta T cells and other T cell subsets. Finally, prominent mycobacterial specific gamma delta T cell expansions were detected in a subset of unvaccinated controls with evidence for prior sensitization to mycobacterial lysates (elevated mycobacterial specific lymphoproliferative responses). These latter findings are consistent with the hypothesis that exposure to atypical mycobacteria or related environmental Ags may induce gamma delta T cells cross-reactive with Ags present in the Mycobacterium tuberculosis complex. Our results suggest that gamma delta T cells may be capable of developing a memory immune-like phenotype, and therefore might be important targets for new vaccines.
On fast prototyping LoRaWAN: a cheap and open platform for daily experiments (2018)

Low‐power wide area networks (LPWANs) are gaining momentum within Internet of Things circles, thanks to their inherent capabilities to simplify network topologies and increase coverage in low‐rate and low‐power communications. This study focuses on a specific LPWAN technology, namely Long Range Wireless Area Network (LoRaWAN), which is being widely investigated by the research community worldwide. LoRaWAN offers many noticeable features, including wide coverage areas, security by design, power consumption and bandwidth optimisation, and a high degree of flexibility and reconfigurability. Unfortunately, in spite of these valuable characteristics, LoRaWAN appliances are often closed source and proprietary. To bridge the gap, this study proposes a prototype, which has been designed and set up using open low‐cost experimental boards and programming tools, only. Moreover, an experimental campaign has been carried out in order to demonstrate the effectiveness of the developed platform.