gebhart/patrepeval huggingface dataset:
Origin of modern syphilis and emergence of a contemporary pandemic cluster (2016)

Abstract Syphilis swept across the world in the 16th century as one of most prominent documented pandemics and is re-emerging worldwide despite the availability of effective antibiotics. Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the non-cultivable and clonal nature of the causative bacterium Treponema pallidum subsp. pallidum . In this study, we used DNA capture and next generation sequencing to obtain whole genome data from syphilis patient specimens and from treponemes propagated in laboratory settings. Phylogenetic analyses indicate that the syphilis strains examined here share a common ancestor after the 15th century. Moreover, most contemporary strains are azithromycin resistant and members of a globally dominant cluster named here as SS14-Ω. This cluster diversified from a common ancestor in the mid-20 th century and has the population genetic and epidemiological features indicative of the emergence of a pandemic strain cluster.
Towards a simple on-line coupling of ion exchange chromatography and native mass spectrometry for the detailed characterization of monoclonal antibodies (2021)

This work describes the direct hyphenation of cation exchange chromatography (CEX) with a compact, easy-to-use benchtop Time of Flight mass spectrometer (ToF/MS) for the analytical characterization of monoclonal antibodies (mAbs). For this purpose, a wide range of commercial mAb products (including expired samples and mAb biosimilars) were selected to draw reliable conclusions. From a chromatographic point of view, various buffers and column dimensions were tested. When considering pH response, buffer stability over time and MS compatibility, the best compromise is represented by the following recipe: 50 mM ammonium acetate, titrated to pH 5.0 (mobile phase A) and 160 mM ammonium acetate, titrated to pH 8.5 (mobile phase B). Despite the broader peaks observed with the 2.1 mm i.d. CEX column, this was preferentially selected for CEX-MS operation, since the efficiency loss (caused by extra-column dispersion) was still acceptable while MS compatibility was strongly enhanced (thanks to low flow rate). In terms of MS, it was important to avoid the use of glass-bottled mobile phases, laboratory glassware and glass vials to minimize loss of MS resolution, sensitivity, and mass accuracy due to metal contaminants. With this new CEX-MS setup, straightforward and rapid analysis (in less than 10 min) of charge variants was possible, allowing the separation and identification of several charge variants.
Anthocyane und Heidelbeeren als therapeutische Chance für Patienten mit CED (2009)

Einleitung: Heidelbeeren (HB) sagt man eine positive Wirkung bei Darmentzündungen nach. Patienten mit M. Crohn berichten über eine Abnahme der Schubhäufigkeit oder einen gebesserten Verlauf eines Schubes bei Einnahme von HB. Diese bestehen zu ca. 10% aus Anthocyanen (AC), die den HB ihre dunkelblaue Färbung verleihen und aufgrund ihrer anti-oxidativen Eigenschaften verschiedene protektive Wirkungen haben. Ziel dieser Arbeit ist daher, die Wirkung von getrockneten HB und deren AC auf die experimentelle Colitis zu untersuchen.
Using Object-Awareness to Optimize Join Processing in the SAP HANA Aggregate Cache (2015)

The introduction of columnar in-memory databases, along with hardware evolution, has made the execution of transactional and analytical workloads on a single system both feasible and viable. Yet, doing analytics directly on the transactional data introduces an increasing amount of resourceintensive aggregate queries which can slow down the overall system performance in a multi-user environment. To increase the scalability of a system in the presence of multiple such queries, we propose an aggregate cache in the general delta-main architecture that provides an ecient means to handle costly aggregate queries by applying incremental materialized view maintenance and query compensation techniques. Handling aggregate queries based on joins of multiple tables however is still a challenge as query compensation can be very expensive in the delta-main architecture of columnar in-memory databases. Our analysis of enterprise applications has revealed several data schema and workload patterns that can be leveraged for addressing performance of query processing using the aggregate cache. We contribute by presenting an approach to transport the application object semantics into the database system, becoming object-aware, and optimize the query processing using the aggregate cache by applying partition pruning and predicate pushdown in such general delta-main architecture. Our experimental validation using customer data and workloads confirms that this type of optimizations enables ecient usage of the aggregate cache for an even higher share of aggregate queries as one mean to scale the system.
Cord blood-derived neuronal cells by ectopic expression of Sox2 and c-Myc (2012)

The finding that certain somatic cells can be directly converted into cells of other lineages by the delivery of specific sets of transcription factors paves the way to novel therapeutic applications. Here we show that human cord blood (CB) CD133(+) cells lose their hematopoietic signature and are converted into CB-induced neuronal-like cells (CB-iNCs) by the ectopic expression of the transcription factor Sox2, a process that is further augmented by the combination of Sox2 and c-Myc. Gene-expression analysis, immunophenotyping, and electrophysiological analysis show that CB-iNCs acquire a distinct neuronal phenotype characterized by the expression of multiple neuronal markers. CB-iNCs show the ability to fire action potentials after in vitro maturation as well as after in vivo transplantation into the mouse hippocampus. This system highlights the potential of CB cells and offers an alternative means to the study of cellular plasticity, possibly in the context of drug screening research and of future cell-replacement therapies.
Atomic Layer Deposition of Wet-Etch Resistant Silicon Nitride Using Di(sec-butylamino)silane and N2Plasma on Planar and 3D Substrate Topographies (2016)

The advent of three-dimensional (3D) finFET transistors and emergence of novel memory technologies place stringent requirements on the processing of silicon nitride (SiN<sub>x</sub>) films used for a variety of applications in device manufacturing. In many cases, a low temperature (<400 °C) deposition process is desired that yields high quality SiN<sub>x</sub> films that are etch resistant and also conformal when grown on 3D substrate topographies. In this work, we developed a novel plasma-enhanced atomic layer deposition (PEALD) process for SiN<sub>x</sub> using a mono-aminosilane precursor, di(sec-butylamino)silane (DSBAS, SiH<sub>3</sub>N(<sup>s</sup>Bu)<sub>2</sub>), and N<sub>2</sub> plasma. Material properties have been analyzed over a wide stage temperature range (100-500 °C) and compared with those obtained in our previous work for SiN<sub>x</sub> deposited using a bis-aminosilane precursor, bis(tert-butylamino)silane (BTBAS, SiH<sub>2</sub>(NH<sup>t</sup>Bu)<sub>2</sub>), and N<sub>2</sub> plasma. Dense films (∼3.1 g/cm<sup>3</sup>) with low C, O, and H contents at low substrate temperatures (<400 °C) were obtained on planar substrates for this process when compared to other processes reported in the literature. The developed process was also used for depositing SiN<sub>x</sub> films on high aspect ratio (4.5:1) 3D trench nanostructures to investigate film conformality and wet-etch resistance (in dilute hydrofluoric acid, HF/H<sub>2</sub>O = 1:100) relevant for state-of-the-art device architectures. Film conformality was below the desired levels of >95% and attributed to the combined role played by nitrogen plasma soft saturation, radical species recombination, and ion directionality during SiN<sub>x</sub> deposition on 3D substrates. Yet, very low wet-etch rates (WER ≤ 2 nm/min) were observed at the top, sidewall, and bottom trench regions of the most conformal film deposited at low substrate temperature (<400 °C), which confirmed that the process is applicable for depositing high quality SiN<sub>x</sub> films on both planar and 3D substrate topographies.
Anisotropic etching of silicon in (CH/sub 3/)/sub 4/NOH solutions (2002)

Detailed characteristics of tetramethyl ammoniumhydroxide, (CH/sub 3/)/sub 4/NOH, as silicon anisotropic etching solutions with various concentrations from 5 to 40 wt.% have been studied. The etch rates of
Optically multiplexed imaging with superposition space tracking (2009)

We describe a novel method to track targets in a large field of view. This method simultaneously images multiple, encoded sub-fields of view onto a common focal plane. Sub-field encoding enables target tracking by creating a unique connection between target characteristics in superposition space and the target's true position in real space. This is accomplished without reconstructing a conventional image of the large field of view. Potential encoding schemes include spatial shift, rotation, and magnification. We discuss each of these encoding schemes, but the main emphasis of the paper and all examples are based on one-dimensional spatial shift encoding. System performance is evaluated in terms of two criteria: average decoding time and probability of decoding error. We study these performance criteria as a function of resolution in the encoding scheme and signal-to-noise ratio. Finally, we include simulation and experimental results demonstrating our novel tracking method.
The relevance of host genes in malaria (2018)

Malaria is a devastating disease that affects extensive areas of Africa, Asia and South and Central America, causing up to 2.7 million deaths per year, mainly children under the age of five. The disease is caused by a protozoan parasite from the genus Plasmodium and transmitted through the bite of the female Anopheles mosquito. The hepatic stage of a Plasmodium infection constitutes an appealing target for the development of an intervention strategy since this would act before the onset of pathology, which only occurs during the blood stage of the parasite’s life cycle. The erythrocytic stage of Plasmodium’s life cycle corresponds to the symptomatic phase of a malaria infection. During this phase, Plasmodium merozoites invade red blood cells (RBCs), and degrade haemoglobin, releasing heme that is converted into haemozoin. The invading merozoites multiply in the RBCs and, upon rupturing the erythrocytic membrane, are eventually released into the blood where they target new RBCs.
Functional Characterization of the Pneumocystis jirovecii Potential Drug Targets dhfs and abz2 Involved in Folate Biosynthesis (2015)

Pneumocystis species are fungal parasites colonizing mammal lungs with strict host specificity. Pneumocystis jirovecii is the human-specific species and can turn into an opportunistic pathogen causing severe pneumonia in immunocompromised individuals. This disease is currently the second most frequent life-threatening invasive fungal infection worldwide. The most efficient drug, cotrimoxazole, presents serious side effects, and resistance to this drug is emerging. The search for new targets for the development of new drugs is thus of utmost importance. The recent release of the P. jirovecii genome sequence opens a new era for this task. It can now be carried out on the actual targets to be inhibited instead of on those of the relatively distant model Pneumocystis carinii, the species infecting rats. We focused on the folic acid biosynthesis pathway because (i) it is widely used for efficient therapeutic intervention, and (ii) it involves several enzymes that are essential for the pathogen and have no human counterparts. In this study, we report the identification of two such potential targets within the genome of P. jirovecii, the dihydrofolate synthase (dhfs) and the aminodeoxychorismate lyase (abz2). The function of these enzymes was demonstrated by the rescue of the null allele of the orthologous gene of Saccharomyces cerevisiae.
Ion dispersion near parallel wire grids in orthogonal acceleration time‐of‐flight mass spectrometry: predicting the effect of the approach angle on resolution (2002)

Ions experience small deflections in the vicinity of grids in accelerators and ion mirrors in time-of-flight (TOF) mass spectrometers. Recent experiments with an orthogonal acceleration (oa) TOF instrument have verified that the effect can significantly degrade resolution when ions approach grids at an angle deviating from 90 degrees. The phenomenon becomes significant only when ions have components of velocity at right angles to the wires of the grids. A model is presented in this study to predict this phenomenon for parallel wire grids. The fractional energy spread of ions (calculated in the static TOF-spectrometer frame of reference) scales directly with the approach angle of ions to the grid (as measured from normal approach). The energy spread also scales with the range of angles that is a consequence of the focusing effect in each gap between the wires of the grid. The equations imply that closely spaced parallel wire grids are best for deployment in oa-TOF systems where non-zero approach angles are unavoidable. Such grids are relatively impractical to manufacture and support but rectangular repeat cell grids with relatively few wires at right angles to the source axis are shown experimentally to introduce minimal energy spread. When these grids are rotated by 90 degrees, the resolution measured in a Q-TOF spectrometer is degraded in approximate agreement with the parallel wire model. A practical implication of this work is that grid transmissions in oa-TOF systems may be significantly increased without loss of resolution. Improvements of approximately 200% (V-mode) and approximately 400% (W-mode) in ion transmission were obtained in this study without compromising resolution. This was achieved with approximately 73% transmission grids and greater potential improvements in transmission are being realised since this study with approximately 89% transmission grids having similar geometry.
ChemInform Abstract: Peroxo‐Zr/Hf‐Containing Undecatungstosilicates and ‐Germanates. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Top-Emission Organic Light-Emitting Diodes with Ink-Jet Printed Self-Aligned Emission Zones (2006)

We have investigated a method of fabricating ink-jet printed self-aligned emission zones for top-emission organic light-emitting diodes. To obtain a bright emission, the number of ink-jet printed shots was varied. From the viewpoint of surface roughness of the bottom electrode, AlNd was used. To reduce sputtering damage, a buffer layer with the hole transport ability of MoO3 was also employed. As a result, the maximum luminance obtained was 1,000 cd/m2. By application of this fabrication technique, we have achieved a printed display panel 30×30 mm2 resolution of 300 pixels per inch.
Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial (2017)

ClinicalTrials.gov NCT01435135.
Carrier Transport Properties of Monodisperse Glassy-Nematic Oligofluorenes in Organic Field-Effect Transistors (2004)

A heptafluorene, F(Pr)5F(MB)2, a dodecafluorene, F(MB)10F(EH)2, and poly(9,9‘-dioctylfluorene), PFO, were used to prepare field-effect transistors. Monodomain and polydomain glassy-nematic films as well as glassy-amorphous films were prepared for the measurement of hole mobility. In a monodomain film, the μ∥ value is determined by the chain length in oligofluorene and the persistence length in polyfluorene. Mobility in a polydomain film lies between μ∥ and μ⊥ of a monodomain film. Amorphous films possess the lowest mobility of all presumably because of the geometric and energetic disorder. The OFET containing a monodomain glassy-nematic film of F(MB)10F(EH)2 exhibits a field-effect mobility of 0.012 cm2/Vs with an on/off current ratio of 1.0 × 104, a substantial improvement over a monodomain glassy-nematic film of PFO.
A single-photon counter for long-haul telecom (1999)

Quite a few groups have turned their attention to using commercially available InGaAs/InP APDs, originally developed for optical communication applications, as SPADs for photon counting at 1300 nm and 1550 nm. This research has turned out to be quite fruitful, and there are many applications emerging in optical metrology (optical time-domain reflectometry) in eye-safe range finding and in future quantum technologies, where databits are encoded on individual photons. This article describes the status of these commercially available InGaAs/InP APDs used as single-photon counters in the telecom wavelength region of 1550 nm.
Practical decomposition for physically admissible differential Mueller matrices (2014)

The differential Mueller matrix expresses the local action of an optical medium on the evolution of a propagating electromagnetic field, including partially coherent and partially polarized waves. Here, we present a derivation of the differential Mueller matrix from the canonical form of Type I Mueller matrices without making use of the exponential generators of uniform media. We demonstrate how to practically obtain this parameterization numerically using an eigenvalue decomposition and find validity criteria to ensure that the matrix satisfies the constraints of a physical system. This provides a convenient tool-set to investigate depolarization effects and extends previous treatments of the differential Mueller matrix formalism.
P4‐497: FUNCTIONAL COOPERATION OF α‐SYNUCLEIN AND VAMP2 IN SYNAPTIC VESICLE RECYCLING (2019)

Alpha-synuclein (α-syn) is a small presynaptic protein, genetically and neuropathologically linked to a large group of neurodegenerative disorders called synucleinopathies. An understanding of normal α-syn function is likely critical to appreciate the pathologic triggers in disease. Over the years, two seemingly divergent views of α-syn function have emerged. In one, α-syn binds to VAMP2 (synaptobrevin-2) and chaperones SNARE-complexes, but with no effect on neurotransmission. Alternatively, we and others have advocated the concept that α-syn physiologically attenuates neurotransmitter release, by restricting synaptic-vesicle (SV) mobilization and recycling. Here we examined if α-syn/VAMP2 binding regulates α-syn-induced synaptic attenuation, and if the two seemingly divergent views can be reconciled. We identified the precise α-syn amino acid (AA) sequences required for VAMP2 binding by mutagenesis mapping and immunoprecipitation. SV recycling was evaluated in cultured hippocampal neurons using pHluorin assays that report exo/endocytic cycles. Optical single vesicle clustering assays were used to directly visualize effects of α-syn on the clustering of small synaptic-like vesicles in vitro. While full-length α-syn (AA 1-140) interacts with VAMP2 and attenuates SV recycling, an α-syn C-terminal deletion (AA 1-95) lacking the VAMP2-binding domain fails to attenuate SV recycling. Mutagenesis mapping identified ∼9 critical amino acid in α-syn (AA 96-104) required for VAMP2 binding. Perturbation of this α-syn/VAMP2 binding region blocks α-syn-induced synaptic attenuation. In vitro single vesicle clustering experiments show that wild type α-syn induces vesicle-clustering, while perturbation in the α-syn/VAMP2 binding region abrogates this effect. Our data indicate that α-syn/VAMP2 binding is essential for α-syn-induced synaptic attenuation and advocate an “interlocking model” where α-syn multimers on SV surface interact with VAMP2 on adjacent SVs. We propose that these α-syn/VAMP2 interactions help tether synaptic vesicles and maintain physiologic SV clustering.
Nanotechnology for Cancer Therapy (2006)

Cancer is caused by damage of genes which control the growth and division of cells.Detection/diagnose/treatment is possible by confirming the growth of the cells and treated by rectifying the damaging mechanism of the genes or by stopping the blood supply to the cells or by destroying it.The application of nanotechnology for cancer therapy has received considerable attention in recent years.Cancer nanotechnology (an interdisciplinary area of research in science, engineering and medicine) is an upcoming field with extensive applications.Recent developments in nanotechnology have provided researchers with new tools for cancer imaging and treatment.This technology has enabled the development of nanoscale devices that can be conjugated with several functional molecules simultaneously, including tumour-specific ligands, antibodies, anticancer drugs, and imaging probes.Since these nanodevices are 100 to 1,000-fold smaller than cancer cells, they can be easily transferred through leaky blood vessels and interact with targeted tumour-specific proteins both on the surface of and inside cancer cells.
Model to predict the probability of recognition of shapes viewed through a thermal imager (1996)

A computer model has been developed to predict the probability of recognition of particular shapes when viewed through a thermal imager employing either scanned or focal plane array detectors. This model is based on the results of a series of psychophysical trials during which human observers have considered over 120,000 images of shapes having a range of initial contrasts, and which have been degraded by various combinations of blurring and sampling. These computer generated images were presented to the observers in a random order and with a random degradation, using programs to select images and display them on a computer monitor. After each presentation the observer decided which was the most likely shape to represent the image displayed on the screen. The responses collected have been used to calculate the human recognition probability of each image. A correlation has been found between the probability of recognition of any specified degraded shape and the relative contrast between the image of that shape, and the image of a similarly degraded circle of the same area. The present work is related to earlier models of human detection and recognition probabilities, and has recently been extended to include the effect of contrast.