gebhart/patrepeval huggingface dataset:
A mass spectral study of the acid‐catalysed oxygen exchange in laevulinic acid (1988)

Abstract The sequence, i.e. site selectivity of the acid‐catalysed 16 O/ 18 O exchange in laevulinic acid (1) is studied by mass spectrometry, ion kinetic energy spectroscopy and accurate mass measurements on 1 and its 13 C(1)‐labelled congener. In the fragmentation pathways all ions of interest in the spectrum of 1 originate from the molecular ion, which may exist in six tautomeric or isomeric forms (1a–1d). The mechanism of gas‐phase cyclization of 1a is rationalized in terms of three different pathways. Formation of the most prominent fragment ions and the sequence of 16 O/ 18 O exchange at the carbonyl and carboxy group are discussed. The results indicate the ions of m / z 56, m / z 61 and m / z 98 to be the only three which have incorporated oxygen atoms originating from the carboxy group in 1 and could thus be used in further elucidadon of the rearrangement mechanism of 5‐hydroxymethylfuran (2) or 5‐hydroxymethylfuran‐2‐carbaldehyde (3) into laevulinic acid (1).
Audiocentric Interface Design: A Building Blocks Approach (2003)

Proceedings of the 9th International Conference on Auditory Display (ICAD), Boston, MA, July 7-9, 2003.
Core Scale FEM Modeling of Thermochemical Fracturing on Cement Cube Samples (2021)

Abstract Brownfields and depleting conventional resources of fossil fuel energy are not enough to fulfill the tremendously increasing energy demands around the globe. Unconventional oil and gas resources are creating a huge impact on the enhancement of the global economy. Tight rocks are usually located in deep and high-strength formations. In this study, numerical simulation results on a new thermochemical fracturing approach is presented. The new fracturing approach was implemented to reduce the breakdown pressure of the unconventional tight formations. The hydraulic fracturing experiments presented in this study were carried out on ultra-tight cement block samples. The permeability of the block samples was less than 0.005mD. Thermochemical fracturing was carried out by a thermochemical fluids that caused a rapid exothermic reaction which resulted in the instantaneous generation of heat and pressure. Different salts of nitrogen such as sodium nitrite and ammonium chloride were used as a thermochemical fluid. The instantaneous generation of the heat and pressure caused the creation of micro-cracks. The fracturing results revealed that the novel thermochemical fracturing was able to reduce the breakdown pressure in ultra-tight cement from 1095 psi to 705 psi. The reference breakdown pressure was recorded from the conventional fracturing technique. A finite element (FEM) analysis was conducted using commercial software ABAQUS. In FEM, two approaches were used to model the thermochemical fractures namely, cohesive zone modeling (CZM) and concrete damage plasticity models (CDP). The sensitivity analysis of peak pressure and time to reach the peak pressure is also presented in this study. The sensitivity analysis can help in better designing thermochemical fluids that could lead to the maximum generation of micro-cracks and multiple fractures.
Analogue Signalling by Phase Shifting (2011)

This paper presents a novel method for overlaying an analogue value on top of a digital signal. By adding a phase rotation and a signature sequence to a block of digitally modulated data symbols, this analogue value can be conveyed to a receiver without significant degradation to the underlying digital data. A near-ML estimator is derived which is non-data driven and hence independent of the digital data sequence. It is shown that this method of signalling a value is superior to quantising it and adding it to the digital data stream. We analyse the performance of the analogue and digital methods and also compare them using simulations.
Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes (2014)

Genetic humanization, which involves replacing mouse genes with their human counterparts, can create powerful animal models for the study of human genes and diseases. One important example of genetic humanization involves mice humanized for their Ig genes, allowing for human antibody responses within a mouse background (HumAb mice) and also providing a valuable platform for the generation of fully human antibodies as therapeutics. However, existing HumAb mice do not have fully functional immune systems, perhaps because of the manner in which they were genetically humanized. Heretofore, most genetic humanizations have involved disruption of the endogenous mouse gene with simultaneous introduction of a human transgene at a new and random location (so-called KO-plus-transgenic humanization). More recent efforts have attempted to replace mouse genes with their human counterparts at the same genetic location (in situ humanization), but such efforts involved laborious procedures and were limited in size and precision. We describe a general and efficient method for very large, in situ, and precise genetic humanization using large compound bacterial artificial chromosome-based targeting vectors introduced into mouse ES cells. We applied this method to genetically humanize 3-Mb segments of both the mouse heavy and κ light chain Ig loci, by far the largest genetic humanizations ever described. This paper provides a detailed description of our genetic humanization approach, and the companion paper reports that the humoral immune systems of mice bearing these genetically humanized loci function as efficiently as those of WT mice.
Studies on Photosensitivity of Mono-substituted Phenylazides (1969)

フェニルアジドの置換基と感光性との関係を見る目的で一置換フェニルアジドを系統的に20種類合成した。電子スペクトルを測定した結果,フェニルアジドではメタノール溶液中で285.7,277.5,249.5,208.Omμ に吸収ピークを持ち,他のアジド化合物ではニトロ基とP位にジメチル基とジエチル基を導入したものを除いてほとんどフェニルアジドと同様のスペクトルを示す。これら化合物のメタノール希薄溶液中での光分解量子収率を真空熱電対と各吸収ピークに対応する単色光を用いて測定した。量子収率の値は0.2～1.0の範囲にあり,フェニルアジドでは286,278,250mμ でそれぞれ0.76,0.73,1.0であり,長波長側二つのピークでの値の方が短波長側での値より小さいことがわかった。同様の結果が他のアジド化合物についても得られる。これらの結果から置換基が感光性に与える影響は小さいことが考えられる。また溶媒が電子スペクトルに与える影響とHucke1近似の分子軌道法から各吸収ピークに対応する電子遷移の性質についても検討した。
Grid Synchronization of Wind Turbine Converters under Transient Grid Faults using a Double Synchronous Reference Frame PLL (2008)

This work employs the Double Synchronous Reference Frame PLL (DSRF-PLL) as an effective method for grid synchronization of WT's power converters in the presence of transient faults in the grid. The DSRF-PLL exploits a dual synchronous reference frame voltage characterization, adding a decoupling network to a standard SRF-PLL in order to effectively separate the positive- and negative-sequence voltage components in a fast and accurate way. Experimental evaluation of the proposed grid synchronization method and simulations regarding its application to ride through transient faults verify and validate the excellent behavior of the DSRF-PLL in the grid synchronization of WT's power converters under unfavorable grid conditions.
Alteration of pulmonary structure by Pseudomonas aeruginosa exoenzyme S (1988)

Intratracheal administration of purified Pseudomonas aeruginosa exoenzyme S elicited extensive, grossly observable damage in the rat lung within 2 h. Light and electronmicroscopy revealed injury and necrosis of bronchial epithelium, type I pneumocytes and capillary endothelial cells after 1 h; associated haemorrhage, fibrinous exudation and released type II cell lamellar bodies in alveolar lumina after 1-12 h; progressively increasing accumulations of polymorphonuclear leucocytes in the bronchi and alveoli and in alveolar septae (interstitial pneumonia) after 1-12 h; collapse of alveolar septal connective tissue and damage to pulmonary arterioles and venules. Treatment of monolayer cultures of bronchial fibroblasts with purified exoenzyme S elicited vacuolation of the cells with apparent membrane damage as revealed by light and electronmicroscopy. In-vivo production and activity of P. aeruginosa exoenzyme S may be an important pathogenicity determinant in the necrotising lung injury characteristic of P. aeruginosa pneumonia.
Nanocosm. Nanotechnology and the Big Changes Coming from the Inconceivably Small. By William Illsey Atkinson. (2004)

<em>Angewandte Chemie International Edition</em> is one of the prime chemistry journals in the world, publishing research articles, highlights, communications and reviews across all areas of chemistry.
Positron emission tomography–computed tomography predictors of progression after DA-R-EPOCH for PMBCL (2018)

Dose-adjusted rituximab plus etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin (DA-R-EPOCH) has produced good outcomes in primary mediastinal B-cell lymphoma (PMBCL), but predictors of resistance to this treatment are unclear. We investigated whether [<sup>18</sup>F]fluorodeoxyglucose positron emission tomography-computed tomography (PET-CT) findings could identify patients with PMBCL who would not respond completely to DA-R-EPOCH. We performed a retrospective analysis of 65 patients with newly diagnosed stage I to IV PMBCL treated at 2 tertiary cancer centers who had PET-CT scans available before and after frontline therapy with DA-R-EPOCH. Pretreatment variables assessed included metabolic tumor volume (MTV) and total lesion glycolysis (TLG). Optimal cutoff points for progression-free survival (PFS) were determined by a machine learning approach. Univariate and multivariable models were constructed to assess associations between radiographic variables and PFS. At a median follow-up of 36.6 months (95% confidence interval, 28.1-45.1), 2-year PFS and overall survival rates for the 65 patients were 81.4% and 98.4%, respectively. Machine learning-derived thresholds for baseline MTV and TLG were associated with inferior PFS (elevated MTV: hazard ratio [HR], 11.5; <i>P</i> = .019; elevated TLG: HR, 8.99; <i>P</i> = .005); other pretreatment clinical factors, including International Prognostic Index and bulky (>10 cm) disease, were not. On multivariable analysis, only TLG retained statistical significance (<i>P</i> = .049). Univariate analysis of posttreatment variables revealed that residual CT tumor volume, maximum standardized uptake value, and Deauville score were associated with PFS; a Deauville score of 5 remained significant on multivariable analysis (<i>P</i> = .006). A model combining baseline TLG and end-of-therapy Deauville score identified patients at increased risk of progression.
ALD TiN Schottky Gates for Improved Electrical and Thermal Stability in III-N Devices (2017)

TiN films were deposited by plasma-assisted atomic layer deposition on AlGaN/GaN structures to investigate the influence of impurities on the performance and stability of Schottky barrier diodes. Oxygen and carbon impurities were reduced, but not completely removed, with increasing TiN growth temperature up to 350 °C. However, the best films still had 4 at% O and 1 at% C impurities as-deposited. TiN films with lower impurity concentrations exhibited lower Schottky barrier heights, providing a way to tailor the properties for different device applications. Films were then exposed to sequential anneals from 400-800 °C in 200 °C increments. X-ray diffraction showed that increasing anneal temperature reduced compressive stress and resulted in higher crystalline quality films. All films maintained similar morphology up to 600 °C, but at 800 °C underwent complete relaxation through fracturing and grain growth that caused significantly rougher films. Despite the change in morphology, TiN gates showed stable operation and low leakage throughout the entire temperature range, while Ni/Au gates failed above 600 °C, suggesting ALD TiN gates could be used in applications where increased thermal stability is required.
Protective role of IgE in immunocompromised rat toxoplasmosis. (1988)

In contrast to euthymic adult Fischer rats, immunocompromised Nu/Nu animals develop a lethal infection when inoculated with the RH strain of the protozoan Toxoplasma gondii. However, a significant period of survival is obtained when Nu/Nu rats are passively transferred with sera from 28-day infected Fischer +/+ (euthymic) animals. Specific IgE are involved since IgE-depleted sera are unable to afford such a protection. Only excreted/secreted Ag or living tachyzoites are able to induce a significant protective IgE response in intact animals. In addition, platelets or, to a lesser extent, eosinophil-rich populations from Toxoplasma infected or excreted-secreted Ag-immunized euthymic animals bear surface IgE and are cytotoxic for the parasite in vitro. Also, adoptive transfer of immune platelets confers a significant degree of protection to Toxoplasma-infected Nu/Nu animals. Our results clearly show the key role of Ag present in both living parasites and excreted-secreted Ag to induce, in this model, a protective IgE response. In addition, as in other parasitic infections, platelets and probably eosinophils are the effector cells involved in controlling parasitic dissemination during Toxoplasma infection in immunocompromised rats.
Hypertonic Saline and the Cerebral Microcirculation in Obese Septic Mice (2007)

HTS exerts significant anti-inflammatory and anti-thrombogenic actions in obese septic mice. These responses may be related to the inhibitory effect of HTS on sepsis-induced P-selectin expression.
IcsB, secreted via the type III secretion system, is chaperoned by IpgA and required at the post‐invasion stage of Shigella pathogenicity (2003)

Shigella deliver a subset of effector proteins such as IpaA, IpaB and IpaC via the type III secretion system (TTSS) into host cells during the infection of colonic epithelial cells. Many bacterial effectors including some from Shigella require specific chaperones for protection from degradation and targeting to the TTSS. In this study, we have investigated the role of the icsB gene located upstream of the ipaBCDA operon in Shigella infection because the role of IcsB as a virulence factor remains unknown. Here, we found that the IcsB protein is secreted via the TTSS of Shigella in vitro and in vivo. We show that IpgA protein encoded by ipgA, the gene immediately downstream of icsB, serves as the chaperone required for the stabilization and secretion of IcsB. We have shown that IcsB binds to IpgA in bacterial cytosol and the binding site is in the middle of the IcsB protein. Intriguingly, although its significance in Shigella pathogenicity is as yet unclear, the icsB gene can be read-through into the ipgA gene to create a translational fusion protein. Furthermore, the contribution of IcsB to the pathogenicity of Shigella was demonstrated by plaque-forming assay and the Sereny test. The ability of the icsB mutant to form plaques was greatly reduced compared with that of the wild type in MDCK cell monolayers. Furthermore, when guinea pig eyes were infected with a non-polar icsB mutant, the bacteria failed to provoke keratoconjunctivitis. These results suggest that IcsB is secreted via the TTSS, chaperoned by IpgA, and required at the post-invasion stage of Shigella pathogenicity
Surface Expression of Bcl-2 in Chronic Lymphocytic Leukemia and Other B-Cell Leukemias and Lymphomas Without a Breakpoint t(14;18) (2008)

Since its discovery in follicular lymphoma cells at the breakpoint t(14;18), Bcl-2 has been studied extensively in many basic and clinical science settings. Bcl-2 can locate as an integral mitochondrial membrane component, where its primary role is to block apoptosis by maintaining membrane integrity. Here we show that Bcl-2 also can position on the outer cell surface membrane of B cells from patients with chronic lymphocytic leukemia (B-CLL) and certain other leukemias that do not classically possess the chromosomal breakpoint t(14;18). Although low levels of Bcl-2 can be detected on the surface membrane of apparently healthy leukemic and normal B cells, expression of Bcl-2 correlates best with spontaneous or induced apoptosis. Notably, upon induction of apoptosis, B-CLL cells were much more efficient in upregulating surface Bcl-2 than normal B cells. It is not clear if this surface membrane expression is a passive consequence of the apoptotic process or an active attempt by the B cell to abort cell death by stabilizing the plasma membrane.
Study on fault-tolerant processors for advanced launch system (1990)

Issues related to the reliability of a redundant system with large main memory are addressed. The Fault-Tolerant Processor (FTP) for the Advanced Launch System (ALS) is used as a basis for the presentation. When the system is free of latent faults, the probability of system crash due to multiple channel faults is shown to be insignificant even when voting on the outputs of computing channels is infrequent. Using channel error maskers (CEMs) is shown to improve reliability more effectively than increasing redundancy or the number of channels for applications with long mission times. Even without using a voter, most memory errors can be immediately corrected by those CEMs implemented with conventional coding techniques. In addition to their ability to enhance system reliability, CEMs (with a very low hardware overhead) can be used to dramatically reduce not only the need of memory realignment, but also the time required to realign channel memories in case, albeit rare, such a need arises. Using CEMs, two different schemes were developed to solve the memory realignment problem. In both schemes, most errors are corrected by CEMs, and the remaining errors are masked by a voter.
Targeting the Minor Groove of DNA:  Crystal Structures of Two Complexes between Furan Derivatives of Berenil and the DNA Dodecamer d(CGCGAATTCGCG)2 (1996)

Crystal structures are reported of complexes of two novel furan derivatives of berenil with alkyl benzamidine groups bound to the DNA sequence d(CGCGAATTCGCG)2. They have both been determined to 2.2 A resolution and refined to R factors of 16.9% and 18.6%. In both structures the alkyl substituents, cyclopropyl and isopropyl, are found to be orientated away from the floor of the minor groove. The drugs are located in the minor groove by two strong amidinium hydrogen bonds, to the O2 of the thymines situated at the 5' and 3' ends of the AT-rich region. The isopropyl-substituted derivative has a tight hydrogen-bonded water network in the minor groove at one amidine site, which alters the orientation of the isopropyl substituent. This compound has superior DNA-binding properties and activity against Pneumocystis carinii and Cryptosporidium parvum infections in vivo compared to the cyclopropyl derivative, which in turn is superior to the parent furan compound. We suggest that the nature and extent of the interactions of these compounds in the DNA minor groove play an important role in these activities, possibly in conjunction with a DNA-binding protein. The overall effect of these alkyl benzamidine substitutions is to increase the binding of the drugs to the minor groove.
All-optical electrophysiology with improved genetically encoded voltage indicators reveals interneuron network dynamics in vivo (2021)

Abstract All-optical electrophysiology can be a powerful tool for studying neural dynamics in vivo , as it offers the ability to image and perturb membrane voltage in multiple cells simultaneously. The “Optopatch” constructs combine a red-shifted archaerhodopsin (Arch)-derived genetically encoded voltage indicator (GEVI) with a blue-shifted channelrhodopsin actuator (ChR). We used a video-based pooled screen to evolve Arch-derived GEVIs with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). By combining optogenetic stimulation of individual cells with high-precision voltage imaging in neighboring cells, we mapped inhibitory and gap junction-mediated connections, in vivo . Optogenetic activation of a single NDNF-expressing neuron in visual cortex Layer 1 significantly suppressed the spike rate in some neighboring NDNF interneurons. Hippocampal PV cells showed near-synchronous spikes across multiple cells at a frequency significantly above what one would expect from independent spiking, suggesting that collective inhibitory spikes may play an important signaling role in vivo . By stimulating individual cells and recording from neighbors, we quantified gap junction coupling strengths. Together, these results demonstrate powerful new tools for all-optical microcircuit dissection in live mice.
Alkane Dehydrogenation Catalyzed by a Fluorinated Phebox Iridium Complex (2021)

We report an iridium acetate complex with a fluorinated Phebox ligand (2,6-bis(4,4-dimethyl-4,5-dihydrooxazol-2-yl)-3,5-bis(trifluoromethyl)phenyl) that is a highly effective catalyst for acceptorless dehydrogenation of alkanes. Under typical acceptorless dehydrogenation conditions, a high turnover frequency is obtained, which is limited by the rate of expulsion of H2 from the reaction solution. Rates and turnover numbers for acceptorless dehydrogenation are significantly greater than found for the nonfluorinated analogue. As in the case of the nonfluorinated analogue, Na+ acts as a cocatalyst with the fluorinated catalyst again yielding greater rates and total turnovers. Computational studies shed light on the possible mechanistic pathways. The initial alkane activation is a net Ir–H/C–H bond metathesis leading to the formation of an Ir–alkyl bond and loss of H2; this is the slowest chemical step in the cycle. The lowest-energy pathway is calculated to proceed via concerted metalated deprotonation (CMD) of the alkane. Pathways proceeding via transition states with oxidative addition (Ir(V)) character, however, are calculated to be only slightly higher in energy. These transition states can lead either to Ir(V) intermediates, which then lose H2, or connect directly to a dihydrogen complex. The role of Na+ is largely to promote dechelation by coordinating to an acetate oxygen, opening a vacant coordination site that allows reaction with the alkane. This coordination by Na+ prevents the CMD mechanism from operating, but it significantly lowers the energy of the Ir(V) TSs. NBO analysis shows a net transfer of charge from the alkane atoms to the metal complex in the Ir(V) TSs, with and without coordinated Na+. Thus, the oxidative addition is actually reductive in nature, driven in part by electrophilicity of the metal center. The Na+ cation further increases electrophilicity in addition to promoting dechelation. The greater activity of the fluorinated catalyst compared with the parent complex can also be explained in terms of the electrophilic nature of the reaction. The fluorinated catalyst is also more resistant to decomposition than the nonfluorinated analogue.
Oxidation-specific epitopes are dominant targets of innate natural antibodies in mice and humans (2009)

Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of oxidized lipoproteins and apoptotic cells. Adaptive immune responses to various oxidation-specific epitopes play an important role in atherogenesis. However, accumulating evidence suggests that these epitopes are also recognized by innate receptors, such as scavenger receptors on macrophages, and plasma proteins, such as C-reactive protein (CRP). Here, we provide multiple lines of evidence that oxidation-specific epitopes constitute a dominant, previously unrecognized target of natural Abs (NAbs) in both mice and humans. Using reconstituted mice expressing solely IgM NAbs, we have shown that approximately 30% of all NAbs bound to model oxidation-specific epitopes, as well as to atherosclerotic lesions and apoptotic cells. Because oxidative processes are ubiquitous, we hypothesized that these epitopes exert selective pressure to expand NAbs, which in turn play an important role in mediating homeostatic functions consequent to inflammation and cell death, as demonstrated by their ability to facilitate apoptotic cell clearance. These findings provide novel insights into the functions of NAbs in mediating host homeostasis and into their roles in health and diseases, such as chronic inflammatory diseases and atherosclerosis.