gebhart/patrepeval huggingface dataset:
A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution (2012)

In vitro screening systems based on the coupled transcription and translation of genes using cell-free systems have a number of attractive features for protein engineering and directed evolution. We present a completely in vitro ultrahigh-throughput screening platform using droplet-based microfluidics. Single genes are compartmentalized in aqueous droplets, dispersed in inert carrier oil, and amplified using the polymerase chain reaction (PCR). After amplification, the droplets, now containing 30,000 copies of each gene, are fused one-to-one with droplets containing a cell-free coupled transcription-translation (IVTT) system and the reagents for a fluorogenic assay. Fluorescence-activated electrocoalescence with an aqueous stream is then used to selectively recover genes from droplets containing the desired activity. We demonstrate, by selecting mixtures of lacZ genes encoding the enzyme β-galactosidase and lacZmut genes encoding an inactive variant, that this system can sort at 2000 droplets s(-1): lacZ genes were enriched 502-fold from a 1 : 100 molar ratio of lacZ : lacZmut genes. Indeed, the false positive and false negative error rates were both <0.004 and the results indicate that enrichment is not limited by the sorting efficiency, but by the co-encapsulation of multiple genes in droplets, which is described by the Poisson distribution. Compared to screening using microtiter plate-based systems, the volume and cost of PCR and IVTT reagents are reduced by almost 10(5)-fold, allowing the screening of 10(6) genes using only 150 μL of reagents.
Comparison of total dose responses on high resolution analog-to-digital converter technologies (1998)

Two different 12-bit analog-to-digital converter technologies, CMOS and BiCMOS, from Burr-Brown were compared for total dose responses. The BiCMOS converter appears to be a better candidate for space applications. CMOS devices showed larger degradation with both high dose rate (HDR) and low dose rate (LDR). An external voltage reference can be used for a radiation hardened process 12-bit converter from Analog Devices to maintain accuracy up to 1 Mrad(Si). DATEL's 16-bit hybrid converter showed a low failure level with HDR.
Temperature Effects on the Susceptibility of the Colorado Potato Beetle (Coleoptera: Chrysomelidae) to Beauveria bassiana (Balsamo) Vuillemin in Poland, the Czech Republic and the United States2 (2000)

Beauveria bassiana (Balsamo) Vuillemin is a fungus with broad spectrum insecticidal activity. As a biological control agent used against Colorado potato beetles (Leptinotarsa decemlineata (Say)), this fungus has performed erratically in various field studies. This inconsistent performance has been attributed to formulation problems, UV sensitivity, and humidity. In a multi-site test, B. bassiana controlled Colorado potato beetle larvae in both Poland and the Czech Republic, but not in Maryland. Control was measured by reduction in populations of beetle larvae. One of the major differences among these sites was temperature. In Poland, the mean temperature ranged from 5°C to 23°C; in the Czech Republic the average temperature ranged from 6.7°C to 18.7°C; and in Maryland, temperatures at time of application exceeded 45°C at canopy level. This led us to examine B. bassiana growth in vitro.While B. bassiana grew in the laboratory from 16 to 30°C, the B. bassiana from a formulated product (Mycotrol™, Mycotech, Butte, MT) did not germinate at temperatures above 37°C. Germination and subsequent development of this entomopathogenic fungi are critical factors in the infection and control of the Colorado potato beetle. As a consequence of the inability to germinate at high temperatures, B. bassiana would not be expected to effectively control pest insects in climates with hot summers. This fungus, however, may be suitable for insect control in early spring or in cool temperature climates during the growing season.
Schistosomiasis Vaccine Development: The Missing Link (2016)

Because of the many overt clinical manifestations of schistosomiasis, such as the swollen bellies with enlarged liver and spleen with S. mansoni, S. mekongi and S. japonicum as well as hematuria and urinary obstruction in S. haematobium, schistosomiasis has been known clinically for thousands of years (Ross et al. 2002; Olds et al. 1996, 2001; see also Berquist et al., Chapter 2). In addition, since adult worm pairs are visible with a naked eye and even the eggs of the parasite can be seen with low level microscopy, the basic pathophysiology of the disease was determined over a century ago (Bilharz 1853; Manson 1902; Symmers 1903; Migairi et al. 1914). The acute manifestations of swimmers itch and Katayama syndrome (Migairi and Suzuki 1914) as well as the chronic pathologic manifestations such as clay pipe-stem fibrosis (Symmers 1903), hepatosplenomegaly, bleeding esophageal varices and even frank corpulmonale were all described more than fifty years ago. Even the link between S. haematobium infection and squamous cell carcinoma of the bladder was made in the middle of the last century (Elsebai 1902).
Plasmonic Demultiplexer and Guiding (2010)

Two-dimensional plasmonic demultiplexers for surface plasmon polaritons (SPPs), which consist of concentric grooves on a gold film, are proposed and experimentally demonstrated to realize light-SPP coupling, effective dispersion, and multiple-channel SPP guiding. A resolution as high as 10 nm is obtained. The leakage radiation microscopy imaging shows that the SPPs of different wavelengths are focused and routed into different SPP strip waveguides. The plasmonic demultiplexer can thus serve as a wavelength division multiplexing element for an integrated plasmonic circuit and also as a plasmonic spectroscopy or filter.
In Situ Electrophysiological Examination of Pancreatic α Cells in the Streptozotocin-Induced Diabetes Model, Revealing the Cellular Basis of Glucagon Hypersecretion (2012)

Early-stage type 1 diabetes (T1D) exhibits hyperglucagonemia by undefined cellular mechanisms. Here we characterized α-cell voltage-gated ion channels in a streptozotocin (STZ)-induced diabetes model that lead to increased glucagon secretion mimicking T1D. GYY mice expressing enhanced yellow fluorescence protein in α cells were used to identify α cells within pancreas slices. Mice treated with low-dose STZ exhibited hyperglucagonemia, hyperglycemia, and glucose intolerance, with 71% reduction of β-cell mass. Although α-cell mass of STZ-treated mice remained unchanged, total pancreatic glucagon content was elevated, coinciding with increase in size of glucagon granules. Pancreas tissue slices enabled in situ examination of α-cell electrophysiology. α cells of STZ-treated mice exhibited the following: 1) increased exocytosis (serial depolarization-induced capacitance), 2) enhanced voltage-gated Na(+) current density, 3) reduced voltage-gated K(+) current density, and 4) increased action potential (AP) amplitude and firing frequency. Hyperglucagonemia in STZ-induced diabetes is thus likely due to increased glucagon content arising from enlarged glucagon granules and increased AP firing frequency and amplitude coinciding with enhanced Na(+) and reduced K(+) currents. These alterations may prime α cells in STZ-treated mice for more glucagon release per cell in response to low glucose stimulation. Thus, our study provides the first insight that STZ treatment sensitizes release mechanisms of α cells.
Yap1 Accumulates in the Nucleus in Response to Carbon Stress in Saccharomyces cerevisiae (2003)

Yap1 is a transcription factor of the AP-1 family that is required for the adaptive response to oxidative stress in Saccharomyces cerevisiae. We recovered Yap1 in a two-hybrid screen for proteins that interact with the Sip2 subunit of the Snf1 protein kinase, which is required for the adaptation of cells to glucose limitation. Yap1 becomes enriched in the nucleus when cells are subjected to oxidative stress. We show that the localization of Yap1 is similarly sensitive to carbon stress. When glucose-grown cells were shifted to medium containing glycerol or no added carbon source, green fluorescent protein (GFP)-Yap1 accumulated in the nucleus. After adaptation to growth in glycerol, GFP-Yap1 was again primarily cytoplasmic. Nuclear accumulation was independent of respiration and of the Snf1, PKA, TOR, and Yak1 pathways, and the mechanism is distinct from that involved in the response to hydrogen peroxide. Addition of glutathione to the medium inhibited nuclear accumulation of GFP-Yap1 in response to carbon stress but did not affect the relocalization of Gal83 or Mig1. Other stresses such as increased temperature, acidic pH, and ionic stress did not cause nuclear enrichment of GFP-Yap1. These findings suggest a role for Yap1 in the response to carbon stress.
Isolated intraocular histiocytosis—A rarely reported entity masquerading clinically as uveitis (2020)

An immunocompetent, 25-year-old gentleman with bilateral chronic uveitis presented to various uveitis clinics at different points of time with documented typical clinical features of Toxoplasma Chorioretinitis (Headlight in fog appearance), Behcet's Disease (Hypopyon with peripheral retinal vasculitis), and Presumed Ocular Tuberculosis (Granulomatous Intermediate Uveitis with positive Interferon-gamma release assay) and had been treated with anti-toxoplasma drugs, oral prednisolone, and immunomodulation with oral Mycophenolate/oral Azathioprine to no avail. After cytological examination of vitreous aspirate, he was found to have non-Langerhans cell Histiocytosis which responded to chemotherapy with Vinblastine and Cyclophosphamide.
On-cue detachment of hydrogels and cells from optically transparent electrodes (2009)

The goal of the present communication was to develop a strategy for detachment of cells and biomaterial constructs from indium tin oxide (ITO) electrodes.
A Novel Method of Counting Eosinophils in Nasal Secretion of Allergic Rhinitis by Hemocytometric Method (1994)

The test for eosinophilia in nasal secretion is a useful tool for the diagnosis of allergic rhinitis. However, the nasal smear test which is commonly used is a subjective and nonquantitative evaluation. In this paper we describe a novel simple, objective and quantitative method in which mucin cluster in collected nasal secretion or lavage is solubilized with dithioerythritol, following which the number of eosinophils per unit volume of nasal secretion or the ratio of eosinophil to total leukocyte can be successfully counted in a blood cell counting chamber by using a hemocytometric method.
Análisis de la Interacción de la Prolina con Moléculas del Solvente mediante Cálculos Cuánticos Ab-Initio (2005)

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.
Prediction of Diabetes Based on Baseline Metabolic Characteristics in Individuals at High Risk (2013)

In a stepwise multiple-variable analysis, only HbA1c and β-cell function (ln insulin secretion/insulin resistance index) predicted the development of diabetes (r = 0.49; P < 0.0001).
Reactions colored according to the most distant species from in which the reaction could be inferred (2011)

<b>Copyright information:</b>Taken from "Reactome: a knowledge base of biologic pathways and processes"http://genomebiology.com/2007/8/3/R39Genome Biology 2007;8(3):R39-R39.Published online 16 Mar 2007PMCID:PMC1868929. Warmer colors indicate reactions found in distantly related species; cooler colors indicate reactions inferred only in closely related species.
How many people are living with undiagnosed HIV infection? An estimate for Italy, based on surveillance data (2016)

The estimate of people in Italy with undiagnosed HIV in 2012 was in a plausible range of 12,000-18,000 cases, corresponding to 11-13% of the overall prevalence. The method is straightforward to implement only requiring annual information from the HIV surveillance system about CD4⁺ cell count and clinical stage at HIV diagnosis. Thus, it could be used to monitor if a certain prevention initiative lead to the reduction of the undiagnosed HIV population over time. It can also be easily implemented in other countries collecting the same basic information from the HIV surveillance system.
[Immunological effect of immunoglobulin on experimental colitis induced by dextran sulfate]. (1995)

To clarify the mechanism of action of immunoglobulin (IgG) in intravenous immunoglobulin therapy for ulcerative colitis (UC) patients, we studied the effect of IgG on the dynamics of immunocompetent cells in the colonic mucosa of experimental colitis induced by dextran sulfate sodium (DSS) in rats. The administration of the same species' IgG suppressed the mucosal infiltration of immunocompetent cells (activated T cells, macrophages and neutrophils), although the different species' IgG didn't. We have already shown that the same species' IgG, suppressed the production of inflammatory cytokines (TNF alpha, IL-1 alpha and IL-8) in the colonic mucosa of experimental colitis induced by DSS. In the present report, we demonstrated the different species' IgG, as well as same species' IgG, suppressed the production of inflammatory cytokines (TNF alpha and IL-1 alpha) from lamina propria mononuclear cells of rat large intestine in vitro. Therefore, it was considered that the suppression of cytokine production was a consequence of the decreased immunocompetent cells in colitis mucosa. Furthermore, we demonstrated that the DSS-treated antigen presenting cells (APCs) activated antigen-specific T cells as a possible mechanism underlying the colitis induced by DSS and the same species' IgG inhibited this activation of T cells.
Personalized signal-independent beamforming for binaural hearing aids (2019)

The effect of personalized microphone array calibration on the performance of hearing aid beamformers under noisy reverberant conditions is studied. The study makes use of a new, publicly available, database containing acoustic transfer function measurements from 29 loudspeakers arranged on a sphere to a pair of behind-the-ear hearing aids in a listening room when worn by 27 males, 14 females, and 4 mannequins. Bilateral and binaural beamformers are designed using each participant's hearing aid head-related impulse responses (HAHRIRs). The performance of these personalized beamformers is compared to that of mismatched beamformers, where the HAHRIR used for the design does not belong to the individual for whom performance is measured. The case where the mismatched HAHRIR is that of a mannequin is of particular interest since it represents current practice in commercially available hearing aids. The benefit of personalized beamforming is assessed using an intrusive binaural speech intelligibility metric and in a matrix speech intelligibility test. For binaural beamforming, both measures demonstrate a statistically signficant (p < 0.05) benefit of personalization. The benefit varies substantially between individuals with some predicted to benefit by as much as 1.5 dB.
Maltose-binding protein does not modulate the activity of maltoporin as a general porin in Escherichia coli (1985)

Maltoporin (lambda receptor) is part of the maltose transport system in Escherichia coli and is necessary for the facilitated diffusion of maltose and maltodextrins across the outer membrane. Maltoporin also allows the diffusion of nonmaltodextrin substrates, albeit with less efficiency. The preference of maltoporin for maltodextrins in vivo is thought to be the result of an interaction of maltoporin with the maltose-binding protein, the malE gene product. In a recent report Heuzenroeder and Reeves (J. Bacteriol. 144:431-435, 1980) suggested that this interaction establishes a gating mechanism which inhibits the diffusion of nonmaltodextrin substrates, such as lactose. To reinvestigate this important conclusion, we constructed ompR malTc strains carrying either the malE+ gene, the nonpolar malE444 deletion, or the malE254 allele, which specifies an interaction-deficient maltose-binding protein. Lactose uptake was measured at different concentrations below the Km of this transport system and under conditions where transport was limited by the diffusion through maltoporin. We found no difference in the kinetics of lactose uptake irrespective of the malE allele. We conclude that the maltose-binding protein does not modulate the activity of maltoporin as a general outer membrane porin.
CD4+ follicular helper T cell infiltration predicts breast cancer survival (2013)

CD4⁺ T cells are critical regulators of immune responses, but their functional role in human breast cancer is relatively unknown. The goal of this study was to produce an image of CD4⁺ T cells infiltrating breast tumors using limited ex vivo manipulation to better understand the in vivo differences associated with patient prognosis. We performed comprehensive molecular profiling of infiltrating CD4⁺ T cells isolated from untreated invasive primary tumors and found that the infiltrating T cell subpopulations included follicular helper T (Tfh) cells, which have not previously been found in solid tumors, as well as Th1, Th2, and Th17 effector memory cells and Tregs. T cell signaling pathway alterations included a mixture of activation and suppression characterized by restricted cytokine/chemokine production, which inversely paralleled lymphoid infiltration levels and could be reproduced in activated donor CD4⁺ T cells treated with primary tumor supernatant. A comparison of extensively versus minimally infiltrated tumors showed that CXCL13-producing CD4⁺ Tfh cells distinguish extensive immune infiltrates, principally located in tertiary lymphoid structure germinal centers. An 8-gene Tfh signature, signifying organized antitumor immunity, robustly predicted survival or preoperative response to chemotherapy. Our identification of CD4⁺ Tfh cells in breast cancer suggests that they are an important immune element whose presence in the tumor is a prognostic factor.
p53-mediated apoptosis of CLL cells: evidence for a transcription-independent mechanism (2008)

The p53 protein plays a key role in securing the apoptotic response of chronic lymphocytic leukemia (CLL) cells to genotoxic agents. Transcriptional induction of proapoptotic proteins including Puma are thought to mediate p53-dependent apoptosis. In contrast, recent studies have identified a novel nontranscriptional mechanism, involving direct binding of p53 to antiapoptotic proteins including Bcl-2 at the mitochondrial surface. Here we show that the major fraction of p53 induced in CLL cells by chlorambucil, fludarabine, or nutlin 3a was stably associated with mitochondria, where it binds to Bcl-2. The Puma protein, which was constitutively expressed in a p53-independent manner, was modestly up-regulated following p53 induction. Pifithrin alpha, an inhibitor of p53-mediated transcription, blocked the up-regulation of Puma and also of p21(CIP1). Surprisingly, pifithrin alpha dramatically augmented apoptosis induction by p53-elevating agents and also accelerated the proapoptotic conformation change of the Bax protein. These data suggest that direct interaction of p53 with mitochondrial antiapoptotic proteins including Bcl-2 is the major route for apoptosis induction in CLL cells and that p53's transcriptional targets include proteins that impede this nontranscriptional pathway. Therefore, strategies that block up-regulation of p53-mediated transcription may be of value in enhancing apoptosis induction of CLL cells by p53-elevating drugs.
Quantifying changes in the IFR and IHR over 23 months of the SARS-CoV-2 pandemic in England (2022)

Abstract Background The relationship between prevalence of infection and severe outcomes such as hospitalisation and death changed over the course of the COVID-19 pandemic. The REal-time Assessment of Community Transmission-1 (REACT-1) study estimated swab positivity in England approximately monthly from May 2020 to 31 March 2022. This period covers widespread circulation of the original strain, the emergence of the Alpha, Delta and Omicron variants and the rollout of England’s mass vaccination campaign. Methods Here, we explore this changing relationship between prevalence of swab positivity and the infection fatality rate (IFR) and infection hospitalisation rate (IHR) over 23 months of the pandemic in England, using publicly available data for the daily number of deaths and hospitalisations, REACT-1 swab positivity data, time-delay models and Bayesian P-spline models. We analyse data for all age groups together, as well as in two sub-groups: those aged 65 and over and those aged 64 and under. Results During 2020, we estimated the IFR to be 0.67% and the IHR to be 2.6%. By late-2021/early-2022 the IFR and IHR had both decreased to 0.097% and 0.76% respectively. Continuous estimates of the IFR and IHR of the virus were observed to increase during the periods of Alpha and Delta’s emergence. During periods of vaccination rollout, and the emergence of the Omicron variant, the IFR and IHR of the virus decreased. During 2020, we estimated a time-lag of 19 days between hospitalisation and swab positivity, and 26 days between deaths and swab positivity. By late-2021/early-2022 these time-lags had decreased to 7 days for hospitalisations, and 18 days for deaths. Conclusion Even though many populations have high levels of immunity to SARS-CoV-2 from vaccination and natural infection, waning of immunity and variant emergence will continue to be an upwards pressure on IHR and IFR. As investments in community surveillance are scaled back, alternative methods should be developed to accurately track the ever changing relationship between infection, hospitalisation and death.
DMESH: FAST DEPTH-IMAGE MESHING AND WARPING (2004)

In this paper we present a novel and efficient depth-image representation and warping technique called DMesh which is based on a piece-wise linear approximation of the depth-image as a textured and simplified triangle mesh. We describe the application of a hierarchical multiresolution triangulation method to generate adaptively triangulated depth-meshes efficiently from reference depth-images, discuss depth-mesh segmentation methods to avoid occlusion artifacts and propose a new hardware accelerated depth-image rendering technique that supports per-pixel weighted blending of multiple depth-images in real-time. Applications of our technique include image-based object representations and the use of depth-images in large scale walk-through visualization systems.
Predicting football scores using machine learning techniques (2011)

Predicting the results of football matches poses an interesting challenge due to the fact that the sport is so popular and widespread. However, predicting the outcomes is also a difficult problem because of the number of factors which must be taken into account that cannot be quantitatively valued or modeled. As part of this work, a software solution has been developed in order to try and solve this problem. During the development of the system, a number of tests have been carried out in order to determine the optimal combination of features and classifiers. The results of the presented system show a satisfactory capability of prediction which is superior to the one of the reference method (most likely a priori outcome).