gebhart/patrepeval huggingface dataset:
Acidic pH Mediates Changes in Antigenic and Oligomeric Conformation of Herpes Simplex Virus gB and Is a Determinant of Cell-Specific Entry (2018)

Herpes simplex virus (HSV) is an important human pathogen with a high worldwide seroprevalence. HSV enters epithelial cells, the primary site of infection, by a low-pH pathway. HSV glycoprotein B (gB) undergoes low pH-induced conformational changes, which are thought to drive membrane fusion. When neutralized back to physiological pH, these changes become reversible. Here, HSV-infected cells were subjected to short pulses of radiolabeling, followed by immunoprecipitation with a panel of gB monoclonal antibodies (MAbs), demonstrating that gB folds and oligomerizes rapidly and cotranslationally in the endoplasmic reticulum. Full-length gB from transfected cells underwent low-pH-triggered changes in oligomeric conformation in the absence of other viral proteins. MAbs to gB neutralized HSV entry into cells regardless of the pH dependence of the entry pathway, suggesting a conservation of gB function in distinct fusion mechanisms. The combination of heat and acidic pH triggered irreversible changes in the antigenic conformation of the gB fusion domain, while changes in the gB oligomer remained reversible. An elevated temperature alone was not sufficient to induce gB conformational change. Together, these results shed light on the conformation and function of the HSV-1 gB oligomer, which serves as part of the core fusion machinery during viral entry.<b>IMPORTANCE</b> Herpes simplex virus (HSV) causes infection of the mouth, skin, eyes, and genitals and establishes lifelong latency in humans. gB is conserved among all herpesviruses. HSV gB undergoes reversible conformational changes following exposure to acidic pH which are thought to mediate fusion and entry into epithelial cells. Here, we identified cotranslational folding and oligomerization of newly synthesized gB. A panel of antibodies to gB blocked both low-pH and pH-neutral entry of HSV, suggesting conserved conformational changes in gB regardless of cell entry route. Changes in HSV gB conformation were not triggered by increased temperature alone, in contrast to results with EBV gB. Acid pH-induced changes in the oligomeric conformation of gB are related but distinct from pH-triggered changes in gB antigenic conformation. These results highlight critical aspects of the class III fusion protein, gB, and inform strategies to block HSV infection at the level of fusion and entry.
ChemInform Abstract: THE KINETICS OF A ZINC ELECTRODE IN ALKALINE ZINCATE ELECTROLYTES (1982)

Abstract An Zn‐Elektroden in 0.5 M ZnO‐Elektrolyten mit KOH‐Konzentrationen von 3 bis 14 Mwurden Impedanzund Polarisationsmessungen für die Auflösung und Abscheidung von Zn durchgeführt.
CFD MODELLING OF A FUNGICIDE THERMONEBULISATION SYSTEM FOR FRUIT STORAGE ROOMS (2010)

Inefficiency in fungicide treatment is one of the reasons for postharvest decay of fruits during the storage period. Postharvest treatment of fungicides using thermonebulisation fogging systems offers a promising means to minimize such postharvest decay. Moreover, this treatment method reduces the use of fungicides in the orchards, minimizes residues on the fruits and improves ecological and environmental sustainability. A three-dimensional computational fluid dynamics (CFD) model was developed to help optimize the application of the fungicide particles inside the fruit storage room. An Eulerian-Lagrangian multiphase flow model was used. The model takes into account two-way coupling with turbulent dispersion of the particles. The particle diameter distribution at the exit of the thermonebuliser was measured and used as an input to the model. The product loaded in vented bins was considered as a porous medium, where the loss coefficients to the three orthogonal directions were approximated using simulation of the flow through the vented boxes and stacks. The dynamic behaviour of the fan was also taken into account. The distribution of the fungicide particles was highly affected by the air flow distribution inside the room. Good agreement was found between measured and predicted results of deposition of fungicide particles.
RAS/BRAF Circulating Tumor DNA Mutations as a Predictor of Response to First-Line Chemotherapy in Metastatic Colorectal Cancer Patients (2018)

ctDNA was comparable with tumor tissue for mutation detection. RAS/BRAF mutations detected in ctDNA predict a worse PFS in mCRC patients with first-line chemotherapy. Our results provide support for the prognostic value of RAS/BRAF ctDNA mutation detection in mCRC patients.
A Robust Targeted Sequencing Approach for Low Input and Variable Quality DNA from Clinical Samples (2017)

ABSTRACT Next-generation deep sequencing of gene panels is being adopted as a diagnostic test to identify actionable mutations in cancer patient samples. However, clinical samples, such as formalin-fixed, paraffin-embedded specimens, frequently provide low quantities of degraded, poor quality DNA. To overcome these issues, many sequencing assays rely on extensive PCR amplification leading to an accumulation of bias and artifacts. Thus, there is a need for a targeted sequencing assay that performs well with DNA of low quality and quantity without relying on extensive PCR amplification. We evaluate the performance of a targeted sequencing assay based on Oligonucleotide Selective Sequencing, which permits the enrichment of genes and regions of interest and the identification of sequence variants from low amounts of damaged DNA. This assay utilizes a repair process adapted to clinical FFPE samples, followed by adaptor ligation to single stranded DNA and a primer-based capture technique. Our approach generates sequence libraries of high fidelity with reduced reliance on extensive PCR amplification - this facilitates the accurate assessment of copy number alterations in addition to delivering accurate SNV and indel detection. We apply this method to capture and sequence the exons of a panel of 130 cancer-related genes, from which we obtain high read coverage uniformity across the targeted regions at starting input DNA amounts as low as 10 ng per sample. We further demonstrate the performance of this assay using a series of reference DNA samples, and by identifying sequence variants in DNA from matched clinical samples originating from different tissue types.
A Cortical Area Selective for Visual Processing of the Human Body (2001)

Despite extensive evidence for regions of human visual cortex that respond selectively to faces, few studies have considered the cortical representation of the appearance of the rest of the human body. We present a series of functional magnetic resonance imaging (fMRI) studies revealing substantial evidence for a distinct cortical region in humans that responds selectively to images of the human body, as compared with a wide range of control stimuli. This region was found in the lateral occipitotemporal cortex in all subjects tested and apparently reflects a specialized neural system for the visual perception of the human body.
Dimeric and tetrameric IgA are transcytosed equally by the polymeric Ig receptor (1995)

Polymeric IgA (pIgA) is transcytosed across epithelial cells and into external secretions by the polymeric Ig receptor (pIgR). Binding of dimeric IgA (dIgA) to the pIgR stimulates transcytosis of the pIgR. The pIgA in secretions is found as dimers (dIgA) and higher polymers, such as tetramers (tIgA), but little is known of the functional significance of the different sizes. Here we compared the ability of dIgA and tIgA to perform three functions that are essential to their transport into mucosal secretions. 1) Equilibrium binding studies showed that there were twice as many binding sites for tIgA as dIgA at the basolateral cell surface, but that the affinity of these sites for tIgA was one-half of that for dIgA. 2) Both dIgA and tIgA were rapidly transcytosed by the pIgR, although transcytosis of tIgA was slower. 3) Both dIgA and tIgA could stimulate transcytosis of the pIgR, although tIgA was less effective. The possible implications of these findings for the relative biologic roles of dIgA and tIgA are discussed.
FPGA's middleware for software defined radio applications (2005)

The division in several layers of the implementation of systems is a solution adopted to avoid complexity, provide flexibility and improve portability and code reusability through different hardware. Middleware (intermediate layer between two other layers) implementations are based on the use of increasingly high-level languages and application programming interfaces (API). The field programmable gate arrays (FPGA) world can also apply this approach to produce building blocks independent from hardware platforms and devices. This paper presents details of the implementation of a middleware, called platform and hardware abstraction layer (P-HAL) when applied to FPGA devices. It was specially designed for radio applications and allows designing specific functions independently of the hardware context where they are applied, thus providing flexibility to the so-called software radios employing FPGA devices.
Atrial natriuretic peptide and water and electrolyte transport in the human jejunum. (1991)

The effects of atrial natriuretic peptide were investigated on water and electrolyte transport in the human jejunum. Six healthy male volunteers (aged 21-33 years) were studied using a triple lumen perfusion technique. A plasma like electrolyte solution containing polyethylene glycol (5 milligrams) as a non-absorbable marker was perfused into the jejunum at 10 ml/min, and net water and electrolyte transport and transepithelial potential difference were measured. Subjects were studied single blind on two occasions with either intravenous atrial natriuretic peptide (6 pmol/min/kg for 90 minutes) or placebo (saline), both after controlled sodium intake over three days. Plasma atrial natriuretic peptide concentrations rose from (mean (SD)) 10.3 (3.6) pmol/l to a peak of 96.0 (61.8) pmol/l. Jejunal net water and electrolyte fluxes and potential difference were identical in both the atrial natriuretic peptide and the control studies. Compared with placebo atrial natriuretic peptide induced a significantly greater diuresis (peak 10.2 (6.0) v 1.8 (1.0) ml/min, p less than 0.05) and natriuresis (peak 1069 (351) v 376 (208) mumol/min, p less than 0.01) and haemoconcentration (haematocrit 0.405 (0.040) v 0.368 (0.018), p less than 0.01). There was no difference in blood pressure, pulse rate, plasma electrolytes, and plasma osmolality between the two studies. There was no evidence to suggest an effect of atrial natriuretic peptide on jejunal water and electrolyte transport in healthy human subjects.
Standards for the Industrial IoT: a Hands-on Tutorial with OpenWSN and OpenMote (2016)

Tutorial at the IEEE International Symposium on Personal, Indoor and Mobile Radio Communications (PIMRC), Valencia, Spain
Ultrafast Dynamics of Epicocconone, a Second Generation Fluorescent Protein Stain (2011)

Femtosecond upconversion experiment has been carried out for epicocconone and its butylamine adduct in acetonitrile and tert-butanol. An ultrafast component is found to dominate the decay of fluorescence of epicocconone in acetonitrile solution. Upon reacting with butylamine, a model for the epicocconone-protein adduct, this ultrafast component remains almost unaffected but an additional rise time occurs, indicating the formation of a highly emissive species from the locally excited state. This phenomenon is central to the extraordinary applications of epicocconone in biotechnology. The magnitude of the rise time of the butylamine adduct is similar to that of the longer component of the decay of epicocconone in acetonitrile, suggesting that the dynamics of epicocconone and its butylamine adduct are similar. The ultrafast component is slowed upon increasing the viscosity of the solvent. This results in a marked increase in quantum yield and suggests that it corresponds to rapid bond isomerization, leading to a nonradiative decay. Surprisingly, in water/sucrose mixtures, the ultrafast component remains unaffected but there is still an increase in quantum yield, suggesting that there are at least two nonradiative pathways, one involving bond isomerization and another involving proton transfer. The correct interpretation of these data will allow the design of second generation protein stains based on the epicocconone scaffold with increased quantum yields and photostability.
Soil Mechanics on the Moon, Mars, and Mulberry (1988)

From a soil mechanics point of view, the Moon is a relatively simple place. Without any water, organics, or clay minerals, the geotechnical properties of the lunar soil are confined to a fairly limited range. Furthermore, the major soil-forming agent is meteorite impact, which breaks the big particles into little particles; and simultaneously, cements the little particles back together again with molten glass. After about a hundred million years of exposure to meteorite impact, the distribution of particle sizes in the soil achieves a sort of steady state. The majority of the returned lunar soil samples have been found to be well-graded silty-sand to sandy-silt (SM in the Unified Soil Classification System). Each of the particle size distributions plots within a relatively narrow band, which appears to be uniform over the entire lunar surface. This further restricts the range of physical properties of the lunar surface. In contrast, Martian soils should exhibit an extremely wide range of properties. We already know that there is a small amount of water in the soil, greater than in the Martian atmosphere. Furthermore, the soil is suspected to be smectitic clay. That makes two out of the three factors that greatly affect the properties of terrestrial soils.
Building Data Literacy, Visualization, and Inquiry in Geoscience Education (2007)

Introduction Data Sets for Inquiry in Geoscience (DIGS) is a two-year National Science Foundation-funded project (NSF GEO #0507828) that is developing modules to supplement existing geoscience curriculum. The modules consist of weeklong curriculum units and 1-2-day performance assessments on the commonly-taught secondary-level geoscience topics of plate boundaries and climate. The modules provide extended inquiry-based investigations employing real geoscience data sets and visualizations, as well as performance assessments that provide evidence of geoscience knowledge and inquiry strategies seldom captured in traditional test formats. These units and assessments yield evidence of students' abilities to demonstrate greater understanding of the conventions and constraints of inquiry about geoscience phenomena and provide models of how the interpretation and analysis of geoscientific data sets can be scaffolded through age-appropriate tasks that facilitate high-quality student inquiry. The goals of the project are to: • Study the impacts on student learning of Web-based supplementary curriculum modules that engage secondary-level students in projects in which students use real data sets, visualizations, and software tools to conduct investigations within two fundamental topics of study, climate change and plate boundaries. • Develop design principles, specification shells, and prototypes of technologybased performance assessments to provide evidence of o students’ geoscientific knowledge and inquiry skills (including data literacy skills); o students’ ability to access, use, analyze, and interpret technology-based geoscience data sets. • Develop scenarios based on the specification shells that describe curriculum modules and performance assessments that can be developed for other geoscience standards and curriculum programs.
Use of Mobile Information Technology during Planning, Implementation and Evaluation of a Polio Campaign in South Sudan (2015)

Pre-campaign community education and household awareness of polio is important to increase campaign participation and subsequent immunisation coverage in South Sudan. More emphasis should be placed on ensuring immunisation is equitable according to geographic area and household socio-economic index in future rounds. We demonstrate the utility of mobile information technology for household mapping, supervision and survey activities during a national round of polio immunisation and encourage future studies to compare the effectiveness of electronic data collection and its application in polio planning and programming.
Qa-1-Associated Antigens (1979)

Abstract In this report we present evidence for the generation of H-2-nonrestricted cytotoxic T lymphocytes (CTL) specific for determinants encoded in the Qa-1 region of the 17th chromosome. B10.BR (Qa-1a) CTL primed in vivo and restimulated in vitro with H-2-identical AKR, C3H, or CBA (Qa-1b) splenocytes lysend Qa-1b targets, irrespective of their H-2 haplotypes. Immunizations in the reverse direction produced H-2-nonrestricted CTL that lysed Qa-1a but not Qa-1b targets. Mapping experiments with target cells from B6 congenic mice confirmed that the locus controlling these reactions lies in the Qa-1 region. Although it has been difficult to raise antisera against Qa-1b gene products, our cytotoxic data argue that the recognition of the products of the Qa-1 region is bidirectional. Determinants encoded in the Qa-1 region, detected serologically or by CTL, were found on both T and B cell blasts. We also found that an antiserum against Qa-1a gene products specifically blocked the cell-mediated killing of Qa-1a targets, thus suggesting that CTL and antibodies bind products of the same genetic locus. Whether Qa-1 is a single locus or a complex of serologically and CTL-defined genes, the nonrestricted nature of anti-Qa-1 CTL suggests important functional and structural similarities between Qa-1 and the murine major histocompatibility complex.
Study on the Optimal Switching Frequency for Maximum Wireless Power Transfer in a Variable Airgap System (2014)

This paper presents the optimal switching frequency for maximum wireless power transfer (WPT) used in railway applications that have a variable airgap. Voltage gain is one of key elements judging the system performance, and can be presented as a function of the switching frequency and number of primary winding turns. The optimal switching frequency in the given parameters for WPT has been investigated in detail using a simulation. From the results, the optimal switching frequency obtained for maximum power transfer according to the design variables such as airgap, number of primary windings, mean length turns, and leakage flux, was different from the resonant frequency for maximum efficiency.
39.4: Polarization‐Independent Switching With High Contrast from a Liquid Crystal Polarization Grating (2006)

Abstract We report experimental results of a liquid crystal polarization grating (LCPG) modulating unpolarized light with high contrast for the first time. Striking results are observed: nearly ideal diffraction into the first orders at &gt; 99%, contrast ratios of up to 600:1 for monochromatic light, switching times of ∼ 2 ms for nematic LCs, and threshold voltage of 1.65 Vrms.
Solid‐State NMR of PEGylated Proteins (2016)

Abstract PEGylated proteins are widely used in biomedicine but, in spite of their importance, no atomic‐level information is available since they are generally resistant to structural characterization approaches. PEGylated proteins are shown here to yield highly resolved solid‐state NMR spectra, which allows assessment of the structural integrity of proteins when PEGylated for therapeutic or diagnostic use.
Newer vaccines against typhoid fever and gastrointestinal salmonelloses (2006)

Typhoid and paratyphoid fever result from infection with Salmonella enterica serovars Typhi and Paratyphi respectively. Humans are the only reservoir of these infections that are spread by the fecal-oral route. The control and near elimination of this disease in Western countries has been achieved largely because of improved sanitation, surveillance, contact tracing and successful therapy. In locations where this infrastructure does not exist, vaccines can be used as one measure to control the incidence of typhoid fever (Tarr et al., 1999) and possibly even to contribute to the eventual eradication of the disease.
Early and mid‐term results with the growth stent—A possible concept for transcatheter treatment of aortic coarctation from infancy to adulthood by stent implantation? (2007)

The Growth Stent is suitable for the acute treatment of aortic coarctation in infants and can be overstented later on--if necessary--with a larger stent without causing restriction.
SA4. Integrity of Thalamocortical Circuitry is Associated With Sleep Spindle Deficits in Schizophrenia (2017)

Background: Cognitive deficits, a highly disabling feature of schizophrenia (SZ), are the strongest predictor of functional outcome. Recent evidence points to thalamocortical circuitry as the culprit in SZ risk and cognitive deficits. Patients with SZ have reduced sleep spindles (bursts of 12–15 Hz electroencephalogram activity during non-rapid eye movement sleep), which are initiated by the thalamic reticular nucleus and propagated to and synchronized in the cortex via thalamocortical feedback loops. Sleep spindles mediate memory consolidation and are associated with impaired sleep-dependent memory consolidation and symptom severity in SZ. Here we used resting state functional magnetic resonance imaging (fMRI) to investigate whether spindle deficits in SZ are associated with changes in the connectivity of thalamocortical networks. Methods: Participants were chronic, medicated SZ patients (n = 26) and demographically matched healthy controls (HC, n = 29). The scanning protocol included resting-state fMRI (two 6-minute scans) and diffusion-weighted imaging on a 3T Siemens Trio scanner. We performed a seed-based functional connectivity analysis based on the FSL-Oxford thalamic connectivity atlas (7 thalamic seeds: prefrontal, premotor, primary motor, sensory, temporal, posterior parietal, and occipital). Following standard preprocessing, motion artifacts and physiological noise were regressed out, and functional connectivity was computed. All reported clusters survived a multiple comparison correction of pFDR <.05. Nocturnal sleep was monitored with polysomnography in a separate session. Sleep was scored according to standard criteria, and sleep spindles during N2 were identified using an automated wavelet spindle detector. Results: Connectivity between the thalamus and prefrontal cortices was reduced in SZ (MNI coordinates: x = 22, y = 46, z = −6; cluster size: 442 voxels; pFDR = .04). In contrast, connectivity between the thalamus and sensory motor cortices was increased in SZ (−38, −14, 48; cluster size: 4989 voxels; pFDR = .001). Patients showed consistent, widespread reductions in sleep spindle density that reached significance in a centroparietal cluster (pFDR = .042). Reduced spindle density predicted abnormal hyperconnectivity of the thalamus with sensory motor cortex in SZ (−32, −34, 52; cluster size: 257 voxels; pFDR = .007). Conclusion: This is the first demonstration that a prominent biomarker of SZ, sleep spindles, correlates with a regionally specific abnormality in sensory motor thalamocortical functional connectivity suggesting TRN-mediated thalamocortical circuit dysfunction. This relationship between spindle density and sensory motor thalamocortical connectivity is in line with recent animal work showing that the firing of sensory projecting TRN neurons correlate with sleep spindles (Halassa et al., 2014). Future plans include complementing functional connectivity analysis with measurements of thalamocortical white matter integrity.