gebhart/patrepeval huggingface dataset:
Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach (2021)

Abstract Salmonella infections (salmonellosis) pose serious health risks to humans, usually via contamination in our food chain. This foodborne pathogen causes major food losses and human illnesses that result in significant economic impacts. Pathogens such as Salmonella have traditionally been kept at bay through the use of antibiotics, but antibiotic overuse within the food industry has led to the development of numerous multidrug-resistant bacterial strains. Thus, governments are now restricting antibiotic use, forcing the industry to search for alternatives to secure safe food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics as they are natural components of the ecosystem. One example is BAFASEL, a commercial bacteriophage mixture that specifically targets Salmonella and is currently approved for use in poultry farming. However, when specifically used in the industry they can also make their way into humans through our food chain or exposure as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented in animal feeds. To the best of our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in vitro assay called RapidAIM to investigate BAFASAL’s potential impact on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex vivo human gut microbiota composition and function were unaffected by BAFASAL treatment providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment. Graphical Abstract
Benzodiazepine receptor distribution and cerebral blood flow in early blindness--a PET study. (2000)

We studied benzodiazepine receptor (BZR) distribution, which is thought to be affected by neuronal density in the cerebral cortex, and CBF using [11C]flumazenil and [15O]water PET in early blind (EB) and in blindfold sighted control (SC) subjects. PET images were co-registered to the subject's MRI. Using SPM96, MRI images were normalized in the Talairach and Tournoux coordinate system, and accordingly MRI-registered PET images were spatially normalized. Statistical parametric maps were computed on a voxel-by-voxel basis, using the general linear model. CBF for EB was significantly larger in the Brodmann area 17 and 18, especially anterior area, than that for SC, while there was no significant difference in BZR distribution. Our BZR data suggest that the amount of neurons do not change due to early visual deprivation in the visual cortex, in spite of high CBF in visual cortex of EB subjects.
V<sub>F</sub> Degradation of 4H-SiC PiN Diodes Using Low-BPD Wafers (2014)

In this paper, we found origin of V F degradation of SiC bipolar devices other than a basal plane dislocation (BPD) in the SiC substrate. A V F degradation of the 4H-SiC PiN diodes with low-BPD wafers was evaluated and its origins were discussed. Some diodes suffered V F degradation, even though they were fabricated on BPD-free area. PL mapping, TEM image, and optical observation after KOH etching showed that there were Shockley stacking faults and combined etch-pits arrays, which were presumed to be caused by the device process.
Dispersed fluorescence of doubly charged molecular ions using synchrotron excitation (1986)

First Page
Dependency Grammars in Freeling (2008)

Automatic deep parsing is necessary for any NLP applications requiring a certain level of semantic representation. One of the goals of the KNOW project is the development of wide-coverage deep parsing grammars whose outcome will be open to the scientific community. In this article we present a implementation of Spanish, Catalan and English grammars in the FreeLing environment. These three languages, together with Basque, are those we work on in KNOW.
NO signaling and S-nitrosylation regulate PTEN inhibition in neurodegeneration (2010)

This study demonstrates for the first time that NO-mediated redox regulation is the mechanism of PTEN protein degradation, which is distinguished from the H2O2-mediated PTEN oxidation, known to only inactivate the enzyme. This novel regulatory mechanism likely accounts for the PTEN loss observed in neurodegeneration such as in AD, in which NO plays a critical pathophysiological role.
Thin-Wafer Silicon IGBT With Advanced Laser Annealing and Sintering Process (2012)

A novel insulated gate bipolar transistor (IGBT) featuring thin-wafer processing and a combined dopant activation laser annealing and contact metal laser sintering is presented. The device concept includes a new back-side boron anode (collector) activation process by laser annealing through a titanium layer to enhance the absorption of the deposited energy from the laser beam. This technology enables improved activation control of the anode injection efficiency for thin-wafer-based IGBTs rated normally below 1700 V. The IGBT concept will therefore be provided with a wider range of performance options on the loss technology curve when compared to state-of-the-art devices processed with conventional activation techniques.
Accurate Elemental Analysis of Metal‐Containing Polymer Latexes Using ICP‐Optical Emission Spectrometry (2010)

Abstract The use of ICP‐OES to determine the metal content of metal‐complex‐containing colloidal dispersions is explored. Colloidal dispersions containing a defined amount of metal complex were produced by miniemulsion polymerization. It was found that simple ICP‐OES measurements yielded apparent metal concentrations significantly below the expected value. To examine the behavior of the colloidal dispersions in the ICP spectrometer, a systematic study on measurement conditions was performed. It was found that the addition of a surfactant to both colloidal dispersions and standards led to measured metal contents close to the theoretical value. Most reliable results were obtained using SDS in concentrations above the cmc. magnified image
Propulsion and Energetic Materials Research in the Netherlands (2005)

Fundamental research on new and existing propellant formulations and energetic materials in the Netherlands is essentially carried out by the Delft University of Technology, Utrecht University, the Dutch Defense Laboratory ‘TNO Defense Security and Safety’ and the SME Aerospace Propulsion Products. Some of the results of the fruitful cooperation between the three entities are presented. A recurrent theme is the development of hydrazinium nitroformate (HNF) based propellant formulations. This includes the characterization of the effects of burning rate modifiers and the synthesis of additives and/or burning rate modifiers. Numerous energetic compounds were synthesized and characterized, including High Nitrogen (HiN) compounds and other High Energy Density Materials (HEDM). Several so-called Conceptual Process Designs were developed to investigate the possibilities of producing such a compound on an industrial scale. Issues like economic viability of the process design, the safety and the environmental impact of the process are an integral part of the design. Other topics to be discussed in this paper include the development of monopropellant formulations and the production of nitroform, an ingredient of hydrazinium nitroformate.
Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage (2020)

Abstract Most glioblastomas (GBMs) achieve cellular immortality by acquiring a mutation in the telomerase reverse transcriptase ( TERT ) promoter. TERT promoter mutations create a binding site for a GA binding protein (GABP) transcription factor complex, whose assembly at the promoter is associated with TERT reactivation and telomere maintenance. Here, we demonstrate increased binding of a specific GABPB1L isoform-containing complex to the mutant TERT promoter. Furthermore, we find that TERT promoter mutant GBM cells, unlike wild-type cells, exhibit a critical near-term dependence on GABPB1L for proliferation, both in cell culture and post-tumor establishment in vivo . Upregulation of the protein paralogue GABPB2, which is normally expressed at very low levels, can rescue this dependence. More importantly, when combined with frontline temozolomide (TMZ) chemotherapy, inducible GABPB1L knockdown and the associated TERT reduction led to an impaired DNA damage response that resulted in profoundly reduced growth of intracranial GBM tumors. Together, these findings provide new insights into the mechanism of cancer-specific TERT regulation, uncover rapid effects of GABPB1L-mediated TERT suppression in GBM maintenance, and establish GABPB1L inhibition in combination with chemotherapy as a novel therapeutic strategy for TERT promoter mutant GBM.
The Terahertz Intensity Mapper (TIM): a Next-Generation Experiment for Galaxy Evolution Studies (2020)

Understanding the formation and evolution of galaxies over cosmic time is one of the foremost goals of astrophysics and cosmology today. The cosmic star formation rate has undergone a dramatic evolution over the course of the last 14 billion years, and dust obscured star forming galaxies (DSFGs) are a crucial component of this evolution. A variety of important, bright, and unextincted diagnostic lines are present in the far-infrared (FIR) which can provide crucial insight into the physical conditions of galaxy evolution, including the instantaneous star formation rate, the effect of AGN feedback on star formation, the mass function of the stars, metallicities, and the spectrum of their ionizing radiation. FIR spectroscopy is technically difficult but scientifically crucial. Stratospheric balloons offer a platform which can outperform current instrument sensitivities and are the only way to provide large-area, wide bandwidth spatial/spectral mapping at FIR wavelengths. NASA recently selected TIM, the Terahertz Intensity Mapper, with the goal of demonstrating the key technical milestones necessary for FIR spectroscopy. The TIM instrument consists of an integral-field spectrometer from 240-420 microns with 3600 kinetic-inductance detectors (KIDs) coupled to a 2-meter low-emissivity carbon fiber telescope. In this paper, we will summarize plans for the TIM experiment's development, test and deployment for a planned flight from Antarctica.
Shift-invariant spaces (2014)

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Co-Development of Diagnostic Vectors to Support Targeted Therapies and Theranostics: Essential Tools in Personalized Cancer Therapy (2014)

Novel technologies are being developed to improve patient therapy through the identification of targets and surrogate molecular signatures that can help direct appropriate treatment regimens for efficacy and drug safety. This is particularly the case in oncology whereby patient tumor and biofluids are routinely isolated and analyzed for genetic, immunohistochemical, and/or soluble markers to determine if a predictive biomarker signature (i.e., mutated gene product, differentially expressed protein, altered cell surface antigen, etc.) exists as a means for selecting optimal treatment. These biomarkers may be drug-specific targets and/or differentially expressed nucleic acids, proteins, or cell lineage profiles that can directly affect the patient's disease tissue or immune response to a therapeutic regimen. Improvements in diagnostics that can prescreen predictive response biomarker profiles will continue to optimize the ability to enhance patient therapy via molecularly defined disease-specific treatment. Conversely, patients lacking predictive response biomarkers will no longer needlessly be exposed to drugs that are unlikely to provide clinical benefit, thereby enabling patients to pursue other therapeutic options and lowering overall healthcare costs by avoiding futile treatment. While patient molecular profiling offers a powerful tool to direct treatment options, the difficulty in identifying disease-specific targets or predictive biomarker signatures that stratify a significant fraction within a disease indication remains challenging. A goal for drug developers is to identify and implement new strategies that can rapidly enable the development of beneficial disease-specific therapies for broad patient-specific targeting without the need of tedious predictive biomarker discovery and validation efforts, currently a bottleneck for development timelines. Successful strategies may gain an advantage by employing repurposed, less-expensive existing agents while potentially improving the therapeutic activity of novel, target-specific therapies that may otherwise have off-target toxicities or less efficacy in cells exhibiting certain pathways. Here, we discuss the use of co-developing diagnostic-targeting vectors to identify patients whose malignant tissue can specifically uptake a targeted anti-cancer drug vector prior to treatment. Using this system, a patient can be predetermined in real-time as to whether or not their tumor(s) can specifically uptake a drug-linked diagnostic vector, thus inferring the uptake of a similar vector linked to an anti-cancer agent. If tumor-specific uptake is observed, then the patient may be suitable for drug-linked vector therapy and have a higher likelihood of clinical benefit while patients with no tumor uptake should consider other therapeutic options. This approach offers complementary opportunities to rapidly develop broad tumor-specific agents for use in personalized medicine.
Critical Design Features of Phenyl Carboxylate-Containing Polymer Microbicides (2006)

Recent studies of cellulose-based polymers substituted with carboxylic acids like cellulose acetate phthalate (CAP) have demonstrated the utility of using carboxylic acid groups instead of the more common sulfate or sulfonate moieties. However, the pK(a) of the free carboxylic acid group is very important and needs careful selection. In a polymer like CAP the pK(a) is approximately 5.28. This means that under the low pH conditions found in the vaginal lumen, CAP would be only minimally soluble and the carboxylic acid would not be fully dissociated. These issues can be overcome by substitution of the cellulose backbone with a moiety whose free carboxylic acid group(s) has a lower pK(a). Hydroxypropyl methylcellulose trimellitate (HPMCT) is structurally similar to CAP; however, its free carboxylic acids have pK(a)s of 3.84 and 5.2. HPMCT, therefore, remains soluble and molecularly dispersed at a much lower pH than CAP. In this study, we measured the difference in solubility and dissociation between CAP and HPMCT and the effect these parameters might have on antiviral efficacy. Further experiments revealed that the degree of acid substitution of the cellulose backbone can significantly impact the overall efficacy of the polymer, thereby demonstrating the need to optimize any prospective polymer microbicide with respect to pH considerations and the degree of acid substitution. In addition, we have found HPMCT to be a potent inhibitor of CXCR4, CCR5, and dual tropic strains of human immunodeficiency virus in peripheral blood mononuclear cells. Therefore, the data presented herein strongly support further evaluation of an optimized HPMCT variant as a candidate microbicide.
Increase in cochlear implant electrode impedances with the use of electrical stimulation (2020)

In this study, we report two cases of electrode impedances increasing as a function of device use. Numerous management strategies were employed to reduce this effect but none prevailed; a clear pathophysiologic mechanism remains elusive. Further study into the cause of this electrode impedance pattern is warranted to establish a management strategy for these cochlear implant users.
Self-aligned MSM low-temperature-grown GaAs traveling wave photodetector for 810 nm and 1230 nm (2004)

Traveling wave photodetectors (TWPD) are promising devices for high bandwidth and high efficiency. In this paper, electro-optic sampling measurements of this novel self-aligned metal-semiconductor-metal TWPD under different biases and pumping levels are performed at a wavelength of 810 nm and the electrical sampling measurements are performed at a wavelength of 1230 nm.
A fast method for generating neighborhood areas of moving objects in consideration of spatial structure (2012)

In this paper, we propose a method for representing “neighborhoods” of moving objects such as people. By using neighborhoods, it is possible to determine whether the spatial relations between objects and their surrounding spatial information are strong. It can be said that a neighborhood is the spatial area of an object's attention, interest or concern. It is preferable that neighborhoods move while remaining centered on each respective moving object, avoiding walls as they expand through passable areas. Therefore, neighborhoods cannot be represented by a simple shape such as a rectangle or circle, and they must be calculated quickly in order to synchronize them with their respective objects' movements. We denote a method for rapidly generating potential fields by making use of the charge simulation method (CSM) and determine neighborhoods in consideration of the spatial structure from CSM.
Over 2300 Phosphorylated Peptide Identifications with Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry in a 100 min Separation (2015)

Ultraperformance liquid chromatography (UPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) is typically employed for phosphoproteome analysis. Alternatively, capillary zone electrophoresis (CZE)-ESI-MS/MS has great potential for phosphoproteome analysis due to the significantly different migration times of phosphorylated and unphosphorylated forms of peptides. In this work, we systematically compared UPLC-MS/MS and CZE-MS/MS for phosphorylated peptide identifications (IDs) using an enriched phosphoproteome from the MCF-10A cell line. When the sample loading amount of UPLC was 10 times higher than that of CZE (2 μg vs 200 ng), UPLC generated more phosphorylated peptide IDs than CZE (3313 vs 1783). However, when the same sample loading amounts were used for CZE and UPLC (2-200 ng), CZE-MS/MS consistently and significantly outperformed UPLC-MS/MS in terms of phosphorylated peptide and total peptide IDs. This superior performance is most likely due to the higher peptide intensity generated by CZE-MS/MS. More importantly, compared with UPLC data from a 2 μg sample, CZE-MS/MS can identify over 500 unique phosphorylated peptides from a 200 ng sample, suggesting that CZE and UPLC are complementary for phosphorylated peptide IDs. With further improved loading capacity via a dynamic pH junction method, 2313 phosphorylated peptides were identified with single-shot CZE-MS/MS in a 100 min analysis. This number of phosphorylated peptide IDs is over 1 order of magnitude higher than the number of phosphorylated peptide IDs previously reported by single-shot CZE-MS/MS.
Influence of plasma power and sputtering agent on gap-fill and MOSFET performances in HDP-CVD STI oxide process (2014)

The gap-fill capability and plasma charging damage (PCD) of high-density plasma chemical vapor deposition (HDP-CVD) process have been investigated in this study. During HDP-CVD process, the physical sputtering behavior impacts PCD and gap-fill performances. Two sputtering agents, Ar and H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , are admitted to the HDP-CVD. In the process with high bias radio frequency power, the utility of H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> plasma successfully reduces PCD on gate oxide in Id-Vg curve. The gap-fill capability and PCD have been improved by the combination of H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas and increasing plasma power.
Ischemia-reperfusion induced microvascular responses in LDL-receptor −/− mice (1999)

The objective of this study was to determine whether the microvascular responses to ischemia and reperfusion (I/R) are altered in an animal model of atherosclerosis, the low-density lipoprotein-receptor knockout (LDLr -/-) mouse. Intravital video microscopy was used to monitor venular wall shear rate, leukocytes rolling velocity, the number of rolling, adherent and emigrated leukocytes, and albumin leakage in cremasteric postcapillary venules of wild-type (B6129) and LDLr -/- mice exposed to 60 min of ischemia and 60 min of reperfusion. The postcapillary venules of LDLr -/- mice exhibited two- to threefold larger increments in the number of adherent leukocytes and a more profound albumin leakage response to I/R than venules in wild-type mice. The exaggerated inflammatory responses noted in LDLr -/- mice placed on a normal diet were not exacerbated by a high-cholesterol diet. Treatment of LDLr -/- mice with either a platelet-activating factor (PAF) receptor antagonist (WEB-2086) or a monoclonal antibody (YN-1) against the endothelial cell adhesion molecule, intercellular adhesion molecule 1 (ICAM-1), markedly attenuated the I/R-induced leukocyte adherence and albumin leakage. These findings indicate that atherogenic mice are more vulnerable to the deleterious microvascular effects of I/R and that PAF-mediated, ICAM-1-dependent leukocyte adhesion contributes to this exaggerated response to I/R.
033 Don't Stop in the Name of Love (2018)

Assess patient refill patterns in the treatment of vulvar and vaginal atrophy (VVA). Analysis of compliance metrics of prescriptions for 858,311 women who filled at least one prescription for VVA treatment was longitudinally tracked utilizing LifeLinkTM Longitudal LRx Prescription Data from IMS Health. The study period spanned 34 months (2013-2016), divided into the following: 1) cohort selection period (4-month period to select women who had either a new-to-therapy or continued prescription); 2) look-back period (18-month period preceding the prescription; 3) look-forward (observation) period (12-month period following the prescription used to evaluate adherence). Approximately 33% of women were new to therapy; the majority used Premarin® and Estrace® creams. While vaginal creams are the leaders for new prescriptions, ∼ 60% of women filled only their initial prescription. Women using vaginal ring, tablet, or the oral SERM (Osphena®) were likely to fill more than one prescription (65% vs ∼40% creams). The trend for multiple fills (5+) followed a similar pattern: ∼7% of women using vaginal estrogen creams, ∼22% of women using a vaginal ring or tablet, and 31% using the oral SERM. Overall, the average number of refills for all products is low, ranging from 2.0 (creams) to 3.9 for the SERM. Average time on therapy was: 369 days for creams, 560 and 604 days for tablet and ring, respectively, and 417 days for the SERM.
Targeting GLI1 expression in human inflammatory breast cancer cells enhances apoptosis and attenuates migration (2011)

Our data reveal a role for GLI1 in IBC cell proliferation, survival and migration, which supports the feasibility of targeting GLI1 as a novel therapeutic strategy for IBC patients.
ChemInform Abstract: Organocatalytic Stereoselective Direct Aldol Reaction of Trifluoroethyl Thioesters. (2011)

Abstract The reaction proceeds via trichlorosilyl ketene thioacetals, generated in situ.