gebhart/patrepeval huggingface dataset:
Neutral glycolipids of the filamentous fungus Neurospora crassa:altered expression in plant defensin-resistant mutants (2005)

To defend themselves against fungal pathogens, plants produce numerous antifungal proteins and peptides, including defensins, some of which have been proposed to interact with fungal cell surface glycosphingolipid components. Although not known as a phytopathogen, the filamentous fungus Neurospora crassa possesses numerous genes similar to those required for plant pathogenesis identified in fungal pathogens (Galagan, J. E., et al. 2003. Nature 422: 859-868), and it has been used as a model for studying plant-phytopathogen interactions targeting fungal membrane components (Thevissen, K., et al. 2003. Peptides. 24: 1705-1712). For this study, neutral glycolipid components were extracted from wild-type and plant defensin-resistant mutant strains of N. crassa. The structures of purified components were elucidated by NMR spectroscopy and mass spectrometry. Neutral glycosphingolipids of both wild-type and mutant strains were characterized as beta-glucopyranosylceramides, but those of the mutants were found with structurally altered ceramides. Although the wild type expressed a preponderance of N-2'-hydroxy-(E)-Delta3-octadecenoate as the fatty-N-acyl component attached to the long-chain base (4E,8E)-9-methyl-4,8-sphingadienine, the mutant ceramides were found with mainly N-2'-hydroxyhexadecanoate instead. In addition, the mutant strains expressed highly increased levels of a sterol glucoside identified as ergosterol-beta-glucoside. The potential implications of these findings with respect to defensin resistance in the N. crassa mutants are discussed.
Adaptive packet marking for providing differentiated services in the Internet (2002)

This paper examines the use of adaptable priority marking for providing soft bandwidth guarantees to individual connections or connection groups over the Internet. In contrast to other proposals for service differentiation which focus on providing firm performance guarantees, the proposed scheme does not require resource reservation for individual connections and can be supported with minimal changes to the network infrastructure. It uses modest support from the network in the form of priority handling for appropriately marked packets and relies on intelligent transmission control mechanisms at the edges of the network to achieve the desired throughput levels. The paper describes the control mechanisms and evaluates their behaviour in various network environments. These mechanisms are shown to have several salient features which make them suitable for deployment in an evolving Internet.
Trapping lithium polysulfides of a Li–S battery by forming lithium bonds in a polymer matrix (2015)

Trapping lithium polysulfides of a Li–S battery has been successfully demonstrated by forming lithium bonds in a polymer matrix.
Synthesis and antibacterial activity of novel hydrazides containing thienopyrimidine (2015)

A series of novel thieno pyrimidine-4yl-pyrrolidine-2-carboxylic acid hydrazide derivatives were prepared by a facile six step procedure that afford mild reaction conditions, simple protocol and good yields. Synthesized compounds were test for the antibacterial activities. The structure of the prepared compounds was confirmed by ESMS, 1H NMR and elemental analysis.
Adsorption of PAA on Surface of CaCO3 Particles and its Effect on Dispersion and Fluid of CACO3 Suspensions (2010)

Article Adsorption of PAA on Surface of CaCO3 Particles and its Effect on Dispersion and Fluid of CACO3 Suspensions was published on October 1, 2010 in the journal Journal of Polymer Engineering (volume 30, issue 8).
CD38 Structure-Based Inhibitor Design Using the N1-Cyclic Inosine 5′-Diphosphate Ribose Template (2013)

Few inhibitors exist for CD38, a multifunctional enzyme catalyzing the formation and metabolism of the Ca(2+)-mobilizing second messenger cyclic adenosine 5'-diphosphoribose (cADPR). Synthetic, non-hydrolyzable ligands can facilitate structure-based inhibitor design. Molecular docking was used to reproduce the crystallographic binding mode of cyclic inosine 5'-diphosphoribose (N1-cIDPR) with CD38, revealing an exploitable pocket and predicting the potential to introduce an extra hydrogen bond interaction with Asp-155. The purine C-8 position of N1-cIDPR (IC50 276 µM) was extended with an amino or diaminobutane group and the 8-modified compounds were evaluated against CD38-catalyzed cADPR hydrolysis. Crystallography of an 8-amino N1-cIDPR:CD38 complex confirmed the predicted interaction with Asp-155, together with a second H-bond from a realigned Glu-146, rationalizing the improved inhibition (IC50 56 µM). Crystallography of a complex of cyclic ADP-carbocyclic ribose (cADPcR, IC50 129 µM) with CD38 illustrated that Glu-146 hydrogen bonds with the ligand N6-amino group. Both 8-amino N1-cIDPR and cADPcR bind deep in the active site reaching the catalytic residue Glu-226, and mimicking the likely location of cADPR during catalysis. Substantial overlap of the N1-cIDPR "northern" ribose monophosphate and the cADPcR carbocyclic ribose monophosphate regions suggests that this area is crucial for inhibitor design, leading to a new compound series of N1-inosine 5'-monophosphates (N1-IMPs). These small fragments inhibit hydrolysis of cADPR more efficiently than the parent cyclic compounds, with the best in the series demonstrating potent inhibition (IC50 = 7.6 µM). The lower molecular weight and relative simplicity of these compounds compared to cADPR make them attractive as a starting point for further inhibitor design.
Distributing entanglement and single photons through an intra-city, free-space quantum channel (2005)

We have distributed entangled photons directly through the atmosphere to a receiver station 7.8 km away over the city of Vienna, Austria at night. Detection of one photon from our entangled pairs constitutes a triggered single photon source from the sender. With no direct time-stable connection, the two stations found coincidence counts in the detection events by calculating the cross-correlation of locally-recorded time stamps shared over a public internet channel. For this experiment, our quantum channel was maintained for a total of 40 minutes during which time a coincidence lock found approximately 60000 coincident detection events. The polarization correlations in those events yielded a Bell parameter, S=2.27+/-0.019, which violates the CHSH-Bell inequality by 14 standard deviations. This result is promising for entanglement-based freespace quantum communication in high-density urban areas. It is also encouraging for optical quantum communication between ground stations and satellites since the length of our free-space link exceeds the atmospheric equivalent.
The KMT2A recombinome of acute leukemias in 2023 (2023)

Chromosomal rearrangements of the human KMT2A/MLL gene are associated with de novo as well as therapy-induced infant, pediatric, and adult acute leukemias. Here, we present the data obtained from 3401 acute leukemia patients that have been analyzed between 2003 and 2022. Genomic breakpoints within the KMT2A gene and the involved translocation partner genes (TPGs) and KMT2A-partial tandem duplications (PTDs) were determined. Including the published data from the literature, a total of 107 in-frame KMT2A gene fusions have been identified so far. Further 16 rearrangements were out-of-frame fusions, 18 patients had no partner gene fused to 5'-KMT2A, two patients had a 5'-KMT2A deletion, and one ETV6::RUNX1 patient had an KMT2A insertion at the breakpoint. The seven most frequent TPGs and PTDs account for more than 90% of all recombinations of the KMT2A, 37 occur recurrently and 63 were identified so far only once. This study provides a comprehensive analysis of the KMT2A recombinome in acute leukemia patients. Besides the scientific gain of information, genomic breakpoint sequences of these patients were used to monitor minimal residual disease (MRD). Thus, this work may be directly translated from the bench to the bedside of patients and meet the clinical needs to improve patient survival.
The Impact of Sources of Variability on Parametric Response Mapping of Lung CT Scans (2015)

Parametric response mapping (PRM) of inspiration and expiration computed tomography (CT) images improves the radiological phenotyping of chronic obstructive pulmonary disease (COPD). PRM classifies individual voxels of lung parenchyma as normal, emphysematous, or nonemphysematous air trapping. In this study, bias and noise characteristics of the PRM methodology to CT and clinical procedures were evaluated to determine best practices for this quantitative technique. Twenty patients of varying COPD status with paired volumetric inspiration and expiration CT scans of the lungs were identified from the baseline COPD-Gene cohort. The impact of CT scanner manufacturer and reconstruction kernels were evaluated as potential sources of variability in PRM measurements along with simulations to quantify the impact of inspiration/expiration lung volume levels, misregistration, and image spacing on PRM measurements. Negligible variation in PRM metrics was observed when CT scanner type and reconstruction were consistent and inspiration/expiration lung volume levels were near target volumes. CT scanner Hounsfield unit drift occurred but remained difficult to ameliorate. Increasing levels of image misregistration and CT slice spacing were found to have a minor effect on PRM measurements. PRM-derived values were found to be most sensitive to lung volume levels and mismatched reconstruction kernels. As with other quantitative imaging techniques, reliable PRM measurements are attainable when consistent clinical and CT protocols are implemented.
Design of a Side-View Particle Imaging Velocimetry Flow System for Cell-Substrate Adhesion Studies (2005)

Experimental models that mimic the flow conditions in microcapillaries have suggested that the local shear stresses and shear rates can mediate tumor cell and leukocyte arrest on the endothelium and subsequent sustained adhesion. However, further investigation has been limited by the lack of experimental models that allow quantitative measurement of the hydrodynamic environment over adherent cells. The purpose of this study was to develop a system capable of acquiring quantitative flow profiles over adherent cells. By combining the techniques of side-view imaging and particle image velocimetry (PIV), an in vitro model was constructed that is capable of obtaining quantitative flow data over cells adhering to the endothelium. The velocity over an adherent leukocyte was measured and the shear rate was calculated under low and high upstream wall shear. The microcapillary channel was modeled using computational fluid dynamics (CFD) and the calculated velocity profiles over cells under the low and high shear rates were compared to experimental results. The drag force applied to each cell by the fluid was then computed. This system provides a means for future study of the forces underlying adhesion by permitting characterization of the local hydrodynamic conditions over adherent cells.
Simulering av ett framtida luftförsvar till sjöss : kryssningsrobotar vs långräckviddiga luftvärnsrobotar (2001)

Utvecklingen av sjöstridskrafternas luftförsvarssystem blir allt mer kostsam. Om luft-försvaret får en mer offensiv roll i framtiden, tvingas man kanske välja mellan ett kryssningsrobotsystem och ett långräckviddigt luftvärnsrobotsystem. En stokastisk modell har tagits fram. Med denna modell som grund har 23625 simuleringar genom-förts med 189 olika kombinationer av parametrar. Enligt dessa simuleringar bör en sjöstyrka bestyckas med både ett kryssningsrobotsystem och ett långräckviddigt luft-värnsrobotsystem. Bestyckningen bör bestå av minst lika många kryssningsrobotar som långräckviddiga luftvärnsrobotar.
Cellular apoptosis susceptibility (CAS) is linked to integrin β1 and required for tumor cell migration and invasion in hepatocellular carcinoma (HCC) (2016)

Importins and exportins represent an integral part of the nucleocytoplasmic transport machinery with fundamental importance for eukaryotic cell function. A variety of malignancies including hepatocellular carcinoma (HCC) show de-regulation of nuclear transport factors such as overexpression of the exportin Cellular Apoptosis Susceptibility (CAS). The functional implications of CAS in hepatocarcinogenesis remain, however, poorly understood. Here we integrated proteomics, transcriptomics and functional assays with patient data to further characterize the role of CAS in HCC. By analyzing ~ 1700 proteins using quantitative mass spectrometry in HCC cells we found that CAS depletion by RNAi leads to de-regulation of integrins, particularly down-regulation of integrin β1. Consistent with this finding, CAS knockdown resulted in substantially reduced migration and invasion of HCC cell lines as analyzed by 2D 'scratch' and invasion chamber assays, respectively. Supporting the potential in vivo relevance, high expression levels of CAS in HCC tissue samples were associated with macroangioinvasion and poorer patient outcome. Our data suggest a previously unanticipated link between CAS and integrin signaling which correlates with an aggressive HCC phenotype.
Reagent Gas (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Stark-induced adiabatic Raman ladder for preparing highly vibrationally excited quantum states of molecular hydrogen (2017)

We present a multi-color ladder excitation scheme that exploits Stark-induced adiabatic Raman passage to selectively populate a highly excited vibrational level of a molecule. We suggest that this multi-color coherent ladder excitation provides a practical way of accessing levels near the vibrational dissociation limit as well as the dissociative continuum, which would allow the generation of an entangled pair of fragments with near-zero relative kinetic energy. Specifically, we consider four- and six-photon coherent excitation of molecular hydrogen to high vibrational levels via intermediate vibrational levels, which are pairwise coupled by two-photon resonant interaction. Using a sequence of three partially overlapping, single-mode, nanosecond laser pulses we show that the sixth vibrational level of H2, which is too weakly coupled to be easily accessed by direct two-photon Raman excitation from the ground vibrational level, can be efficiently populated without leaving any population stranded in the intermediate level. Furthermore, we show that the fourteenth vibrational level of H2, which is the highest vibrational level in the ground electronic state with a binding energy of 22 meV, can be efficiently and selectively populated using a sequence of four pulses. The present technique offers the unique possibility of preparing entangled quantum states of H atoms without resorting to an ultracold system.
Dual cure luting composites – Part II: Clinically related properties (1994)

Thirteen dual cure luting composites were compared in function of film thickness, consistency, and working time by using the American National Standard/American Dental Association (ANS/ADA) specifications for zinc phosphate cement and direct filling resins. The effect of temperature and setting reaction on the film thickness was also evaluated for some representative products. All three clinically related properties varied widely among the products investigated. A strong linear correlation was found between film thickness and consistency. This relation is supported by the temperature dependence of film thickness of dual cure luting composites. Cooling of the material increased the consistency, resulting in a larger film thickness, while heating reduced the film thickness because of the lower consistency. However, one product with a rather short working time at room temperature occasionally exhibited a dramatically enlarged film thickness after heating, probably caused by accelerated chemical polymerization. No correlation emerged between film thickness and maximum filler size or between consistency and filler weight content. Maximum filler size and filler weight content had been measured previously in Part I of this study. Scanning electron microscope (SEM) analysis of the cured film thickness samples revealed that the largest filler particles had been crushed under the heavy load pressure during film thickness measurement. The lack of correlation between consistency and filler weight content can be explained by the multifactorial determination of the consistency. It is concluded that the great diversity in the currently available luting composites makes clear specifications with regard to the optimum composition of luting composites urgently needed. Furthermore, more adequate methods for testing the film thickness of luting composites are also required.
Advances in service platform technologies for next-generation mobile systems: part 2 (2006)

S.60-61
Waterjet Peening and Surface Preparation at 600MPa: A Preliminary Experimental Study (2006)

An experimental study was conducted to explore the surface preparation as well as the effects of high-pressure waterjet peening at 600MPa on the surface integrity and finish of metals. The concept of larger droplet size and multiple droplet impacts resulting from an ultra-high-pressure waterjet was used to explore and develop the peening process. A combination of microstructure analysis, microhardness measurements, and profilometry were used in determining the depth of plastic deformation and surface finish that result from the surface treatment process. It was found that waterjet peening at 600MPa induces plastic deformation to greater depths in the subsurface layer of metals than laser shock peening. The degree of plastic deformation and the state of the material surface were found to be strongly dependent on the peening conditions and desired surface roughness. Based on these first investigation results, water peening at 600MPa may serve as a new method for introducing compressive residual stresses in engineering components.
Chronic cigarette smoking is linked with structural alterations in brain regions showing acute nicotinic drug-induced functional modulations (2016)

Collectively, these findings emphasize brain regions (e.g., ventromedial PFC, insula, thalamus) critically linked with cigarette smoking, suggest neuroimaging paradigms warranting additional consideration among smokers (e.g., pain processing), and highlight regions in need of further elucidation in addiction (e.g., cerebellum).
An Approach for Improving Correlation of Solid Finite Element Models (2005)

&lt;div class="htmlview paragraph"&gt;The quest to simulate noise problems has led to the building of larger and more detailed finite element models in order to perform vibration solutions to higher frequencies. This leads to the building of solid finite element models of complex geometries, such as castings, which might previously have contained less detail or even been built with shell elements. Unfortunately, detailed geometric representations used to build models do not always agree with as built parts and lead to discrepancies between analysis results and test data. This paper presents an approach that reduces the time and cost necessary to identify these differences.&lt;/div&gt;
22-nm immersion interference lithography (2006)

Immersion interference lithography was used to pattern gratings with 22-nm half pitch. This ultrahigh resolution was made possible by using 157-nm light, a sapphire coupling prism with index 2.09, and a 30-nm-thick immersion fluid with index 1.82. The thickness was controlled precisely by spin-casting the fluid rather than through mechanical means. The photoresist was a diluted version of a 193-nm material, which had a 157-nm index of 1.74. An analysis of the trade-off between fluid index, absorption coefficient, gap size and throughput indicated that, among the currently available materials, employing a high-index but absorbing fluid is preferable to using a highly transparent but low-index immersion media.
<title>Waveguide optical scanner with increased deflection sensitivity for optical data storage</title> (1994)

Waveguide electrooptic (EO) beam scanners are of interest for applications requiring high speed, high throughput, low power consumption, and modest deflection. Such devices can be used in high performance optical recording and laser printer heads. We are pursuing a novel waveguide device structure in which prisms are formed by ferroelectric domain inversion in a substrate containing a planar waveguide. The device uses TM optical modes in z-cut substrates and is therefore compatible with waveguides used for high-efficiency optical second harmonic generation (SHG).
Supplementary Methods from Targeted Treatment of Metastatic Breast Cancer by PLK1 siRNA Delivered by an Antioxidant Nanoparticle Platform (2023)

&lt;p&gt;Detailed description of the methods used in the manuscript.&lt;/p&gt;
Maternally Derived Microduplications at 15q11-q13: Implication of Imprinted Genes in Psychotic Illness (2011)

These findings suggest that the presence of two maternal copies of a fragment of chromosome 15q11.2-q13.1 that overlaps with the Prader-Willi/Angelman syndrome critical region may be a rare risk factor for schizophrenia and other psychoses. Given that maternal duplications of this region are among the most consistent cytogenetic observations in autism, the findings provide further support for a shared genetic etiology between autism and psychosis.
High-speed router filter for blocking TCP flooding under DDoS attack (2003)

We present a hardware solution that can reliably block most of the malicious TCP traffic at the edge routers while passing the legitimate TCP traffic during a distributed denial-of-service (DDoS) attack on the Internet. By allocating bandwidths separately for TCP, the TCP portion of the bandwidth can be protected. In a simulation study, the filter successfully blocked 99.9% of the attack traffic while legitimate traffic showed nearly identical performance as in the non-attacked condition. This filtering is transparent to the hosts or routers and a filtering device can be easily attached to router ports.
Directed self-assembly process implementation in a 300mm pilot line environment (2013)

The patterning capability of the directed self-assembly (DSA) of a 42nm-pitch block copolymer on an 84nm-pitch guiding pattern was investigated in a 300mm pilot line environment. The chemoepitaxy guiding pattern was created by the IBM Almaden approach using brush materials in combination with an optional chemical slimming of the resist lines. Critical dimension (CD) uniformity, line-edge/line-width roughness (LER/LWR), and lithographic process window (PW) of the DSA process were characterized. CD rectification and LWR reduction were observed. The chemical slimming process was found to be effective in reducing pattern collapse, hence, slightly improving the DSA PW under over-dose conditions. However, the overall PW was found to be smaller than without using the slimming, due to a new failure mode at under-dose region.