gebhart/patrepeval huggingface dataset:
Mclafferty Rearrangement (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.
Design of an Escherichia coli Expressed HIV-1 gp120 Fragment Immunogen That Binds to b12 and Induces Broad and Potent Neutralizing Antibodies (2013)

b12, one of the few broadly neutralizing antibodies against HIV-1, binds to the CD4 binding site (CD4bs) on the gp120 subunit of HIV-1 Env. Two small fragments of HIV-1 gp120, b121a and b122a, which display about 70% of the b12 epitope and include solubility-enhancing mutations, were designed. Bacterially expressed b121a/b122a were partially folded and could bind b12 but not the CD4bs-directed non-neutralizing antibody b6. Sera from rabbits primed with b121a or b122a protein fragments and boosted with full-length gp120 showed broad neutralizing activity in a TZM-bl assay against a 16-virus panel that included nine Tier 2 and 3 viruses as well as in a five-virus panel previously designed to screen for broad neutralization. Using a mean IC50 cut-off of 50, sera from control rabbits immunized with gp120 alone neutralized only one virus of the 14 non-Tier 1 viruses tested (7%), whereas sera from b121a- and b122a-immunized rabbits neutralized seven (50%) and twelve (86%) viruses, respectively. Serum depletion studies confirmed that neutralization was gp120-directed and that sera from animals immunized with gp120 contained lower amounts of CD4bs-directed antibodies than corresponding sera from animals immunized with b121a/b122a. Competition binding assays with b12 also showed that b121a/2a sera contained significantly higher amounts of antibodies directed toward the CD4 binding site than the gp120 sera. The data demonstrate that it is possible to elicit broadly neutralizing sera against HIV-1 in small animals.
Tritium confinement in a new tritium processing facility at the Savannah River Site (1991)

A new tritium processing facility, named the Replacement Tritium Facility (RTF), has been completed and is being prepared for startup at the Savannah River Site (SRS). The RTF has the capability to recover, purify and separate hydrogen isotopes from recycled gas containers. A multilayered confinement system is designed to reduce tritium losses to the environment. This confinement system is expected to confine and recover any tritium that might escape the process equipment, and to maintain the tritium concentration in the nitrogen glovebox atmosphere to less than 10{sup {minus}2} {mu}Ci/cc tritium.
The adult form of Niemann-Pick disease type C (2006)

Niemann-Pick disease type C (NPC) is a fatal neurovisceral lipid storage disease of autosomal inheritance resulting from mutations in either the NPC1 (95% of families) or NPC2 gene. The encoded proteins appear to be involved in lysosomal/late endosomal transport of cholesterol, glycolipids and other molecules but their exact function is still unknown. The clinical spectrum of the disease ranges from a neonatal rapidly fatal disorder to an adult-onset chronic neurodegenerative disease. Based upon a comprehensive study of 13 unrelated adult patients diagnosed in France over the past 20 years as well as the analysis of the 55 other cases published since 1969, we have attempted to delineate the major clinical, radiological, biochemical and genotypic characteristics of adult NPC. Overall, mean age at onset (+/-SD) of neuropsychiatric symptoms was 25 +/- 9.7 years. The diagnosis of NPC was established after a mean delay of 6.2 +/- 6.4 years and the mean age at death (calculated from 20 cases) was 38 +/- 10.2 years. Major clinical features included cerebellar ataxia (76%), vertical supranuclear ophthalmoplegia (VSO, 75%), dysarthria, (63%), cognitive troubles (61%), movement disorders (58%), splenomegaly (54%), psychiatric disorders (45%) and dysphagia (37%). Less frequent signs were epilepsy and cataplexy. During the course of the disease, clinical features could be subdivided into (i) visceral signs (hepatomegaly or splenomegaly), (ii) cortical signs (psychiatric cognitive disorders and epilepsy); and (iii) deep brain signs (VSO, ataxia, movement disorders, dysarthria, dysphagia, cataplexy) which exhibited different evolution patterns. Asymptomatic and non-evolutive visceral signs were often noticed since early childhood (38.5% of our patients), followed by mild cortical signs in childhood (learning difficulties) and early adulthood (62% of cases among which 38% were psychiatric disorders). Deep brain signs were observed in 96% of patients and were usually responsible for death. In general, there was a good correlation between clinical signs and the localization of brain atrophy on MRI. The 'variant' biochemical phenotype characterized by mild abnormalities of the cellular trafficking of endocytosed cholesterol was over-represented in the adult form of NPC and seemed associated with less frequent splenomegaly in childhood and lesser psychiatric signs. Involvement of the NPC1 gene was shown in 33 families and of the NPC2 gene in one. Improving the knowledge of the disease among psychiatrists and neurologists appears essential since emerging treatments should be more efficient at the visceral or cognitive/psychiatric stages of the disease, before the occurrence of widespread deep brain neurological lesions.
Banana-shaped biphotonic quadrupolar chromophores: from fluorophores to biphotonic photosensitizers (2011)

This study aims at designing dual-role biphotonic chromophores that could be used for photodynamic therapy (PDT) while maintaining some fluorescence in order to locate them, thus allowing selective irradiation of cancer cells when combined with targeting. Quadrupolar two-photon absorbing fluorophores were synthesized from the symmetrical functionalization of a fluorene core bearing elongated conjugated rods made from arylene–vinylene or arylene–ethynylene building blocks in order to test modifications which could increase singlet oxygen production ability while retaining some fluorescence and high two-photon absorption (TPA) cross-sections in the biological spectral range of interest. All chromophores show a polar emissive excited state whose dipole moment is highly dependent on the nature of the conjugated linker. Interestingly, the largest TPA responses in the NIR region as well as singlet oxygen quantum yield are correlated with the smallest dipole moment of the emissive excited-state. The molecular optimization study led to a multifunctional biphotonic chromophore combining high TPA cross-sections in the whole spectral range of interest (700–900 nm), reasonable singlet oxygen production efficiency, significant remaining fluorescence, and alcohol end-groups for further covalent grafting. This compound offers thus interesting potentialities for highly selective spatially-resolved two-photon PDT by incorporation in nanostructures.
Human urate transporter 1 (hURAT1) mediates the transport of orotate (2011)

Orotate is a precursor of pyrimidine synthesis. The kidney uses exogenous orotate for the synthesis of uridine diphosphosugars, which are used in the glycosylation of collagen in glomerular and tubular basement membranes. Orotate uptake occurs in the liver and kidney, but its molecular mechanism is largely unknown. Since orotate has been shown to be a substrate of the renal urate/anion exchanger in brush border membrane vesicle studies, we investigated whether human URAT1 (hURAT1) mediates the transport of orotate using HEK293 cells expressing hURAT1 (HEK-hURAT1). hURAT1 mediated a time- and dose-dependent uptake of orotate (K (m) 5.2 μM). hURAT1-mediated [(3)H]orotate transport was inhibited strongly by non-labeled (cold) orotate and the uricouric agent benzbromarone, and moderately inhibited by urate, nicotinate, and another uricouric agent, probenecid. This is the first report demonstrating that hURAT1 mediates the transport of orotate. hURAT1 may function as one of the entrance pathways in renal proximal tubular cells.
Process highlights to enhance directed self-assembly contact patterning performances (2016)

We focus on the directed self-assembly (DSA) for contact hole (CH) patterning application using polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) block copolymers (BCPs). By employing the DSA planarization process, we highlight the DSA advantages for CH shrink, repair, and multiplication, which are extremely needed to push forward the limits of currently used lithography. Meanwhile, we overcome the issue of pattern density-related defects that are encountered with the commonly used graphoepitaxy process flow. Our study also aims to evaluate the DSA performances as functions of material properties and process conditions by monitoring main key manufacturing process parameters: CD uniformity (CDU), placement error (PE), and defectivity [hole open yield (HOY)]. Concerning process, it is shown that the control of surface affinity and the optimization of self-assembly annealing conditions enable significant enhancement of CDU and PE. Regarding material properties, we show that the best BCP composition for CH patterning should be set at 70/30 of PS/PMMA total weight ratio. Moreover, it is found that increasing the PS homopolymer content from 0.2% to 1% has no impact on DSA performances. Using a C35 BCP (cylinder-forming BCP of natural period L0=35 nm), good DSA performances are achieved: CDU-3σ=1.2 nm, PE-3σ=1.2 nm, and HOY=100%. Finally, the stability of DSA process is also demonstrated through the process follow-up on both patterned and unpatterned surfaces over several weeks.
Extraordinary properties of chalcogenide metamaterials (2018)

Fascinating opportunities are offered by metamaterial nanostructures fabricated from materials with highly-dispersive optical properties, between those of ideally plasmonic (e.g. noble metal) and transparent dielectric media. Chalcogenide semiconductors are excellent examples – their optical properties can be engineered by controlling alloy composition and phase state to provide high and low refractive indices, plasmonic, dielectric and epsilon-near-zero characteristics at near-ultraviolet to near-infrared wavelengths. We report here on the application of chalcogenide materials to photonic metasurfaces.
<title>Six-million-pixel full-frame true 2-f CCD image sensor incorporating transparent gate technology and optional antiblooming protection</title> (1999)

This paper describes the performance of an advanced high- resolution full-frame architecture CCD imaging device for use in scientific, medical, and other high performance monochromatic digital still imaging applications. Of particular interest is the replacement of the polysilicon second gate electrode with that of a more spectrally transparent material, thereby dramatically improving device sensitivity. This has been achieved without compromising performance in other areas such as dark current, noise, transfer efficiency and, most importantly, yield. Devices have also been produced with and without antiblooming protection depending on an application's primary need for sensitivity or control of over-exposure conditions.
Saline-Dependent Regulation of Manganese Peroxidase Genes in the Hypersaline-Tolerant White Rot Fungus Phlebia sp. Strain MG-60 (2008)

The expression pattern of manganese peroxidases (MnPs) in nitrogen-limited cultures of the saline-tolerant fungus Phlebia sp. strain MG-60 is differentially regulated under hypersaline conditions at the mRNA level. When MG-60 was cultured in nitrogen-limited medium (LNM) containing 3% (wt/vol) sea salts (LN-SSM), higher activity of MnPs was observed than that observed in normal medium (LNM). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis demonstrated that two MnP isoenzymes were de novo synthesized in the culture of LN-SSM. Three MnP-encoding genes (MGmnp1, MGmnp2, and MGmnp3) were isolated by reverse transcription (RT)-PCR and rapid amplification of cDNA ends PCR techniques. The corresponding isozymes were identified by peptide mass fingerprinting analysis. MnP isozymes encoded by MGmnp2 and MGmnp3 were observed mainly in LN-SSM. Real-time RT-PCR analysis revealed high levels of MGmnp2 and MGmnp3 transcripts in LN-SSM 48 h after the addition of 2% NaCl. The induction of MnP production and the accumulation of gene transcripts by saline were well correlated in the presence of Mn(2+). However, in the absence of Mn(2+), there was no clear correlation between mnp transcripts levels and MnP activity, suggesting posttranscriptional regulation by Mn(2+).
Challenges and approaches to on-chip millimeter wave antenna pattern measurements (2011)

Summary form only given, as follows. We present two methods to remove wafer probe interference radiation from measured on-chip antenna patterns performed in a probe station environment. In this work, we use superposition and S-parameter techniques to de-embed the effects of probe tip radiation. On-chip Dipole, Yagi, and Rhombic antennas were fabricated using standard 180nm CMOS and radiation patterns were measured at 60 GHz. This work shows methods that improve the ability to reliably measure on-chip antenna patterns.
Role of a brush border membrane fatty acid binding protein in oleic acid uptake into rat and rabbit jejunal brush border membrane. (1995)

Oleic acid uptake was studied using adult rat and rabbit jejunal brush border membrane vesicles. The intestinal uptake of oleic acid is influenced by the activity of an amiloride-inhibitable brush border membrane Na+/H+ exchanger, NHE3: opposing Na+/H+ gradients (inward Na+ and outward H+ gradients) increased oleic acid uptake by about 40%, as compared with only an inward Na+ gradient, only an outward H+ gradient, or the absence of either Na+ or H+ gradients. This study was undertaken to test the hypothesis that a portion of oleic acid uptake is facilitated by a fatty acid binding protein in the brush border membrane (FABPPM) of adult rat jejunum. There was a reduction in the uptake of oleic acid when brush border membrane vesicles were incubated with a rat liver plasma membrane fatty acid binding protein antibody (anti-FABPPM-Ab) in the absence, but not in the presence, of opposing Na+/H+ gradients. Thus, oleic acid uptake occurs largely by partitioning of the lipid into the brush border membrane, as well as by a process which involves the activation of the brush border membrane Na+/H+ exchanger, and a membrane fatty acid binding protein.
Synthesis of Methyl Methacrylate From Coal-Derived Syngas (1998)

Research Triangle Institute (RTI), Eastman Chemical Company, and Bechtel collectively are developing a novel three-step process for the synthesis of methyl methacrylate (MMA) from coal-derived syngas that consists of the steps of synthesis of a propionate, its condensation with formaldehyde to form methacrylic acid (MAA), and esterification of MAA with methanol to produce MMA. RTI has completed the research on the three-step methanol-based route to MMA. Under an extension to the original contract, RTI is currently evaluating a new DME-based process for MMA. The key research need for DME route is to develop catalysts for DME partial oxidation reactions and DME condensation reactions. Over the last quarter(April-June, 1998), RTI has modified the reactor system including a new preheater and new temperature settings for the preheater. Continuous condensation of formaldehyde with propionic acid were carried out over 10% Nb O /SiO at 300°C without 2 5 2 interruption. Five activity and four regeneration cycles have been completed without plugging or material balance problems. The results show that 10% Nb O /SiO deactivates slowly with time 2 5 2 but can be regenerated, at least four times, to 100% of its original activity with 2% O in nitrogen 2 at 400°C. The cycles continue with consistent 90-95% of carbon balance. The reaction is scheduled to complete with 6 activity cycles and 5 regenerations. Used catalysts will be analyzed with TGA and XPS to determine bulk and surface coke content and coke properties. RTI will start the investigation of effects of propionic acid/formaldehyde ratio on reaction activity and product selectivity over 20% Nb O /SiO catalysts.
Supplementary Table 1 from Clinical Response to a Lapatinib-Based Therapy for a Li-Fraumeni Syndrome Patient with a Novel <i>HER2</i><sup>V659E</sup> Mutation (2023)

&lt;p&gt;Supplementary Table 1 - XLSX 39K, Exome sequencing results. The table contains the raw data for Figure 2B as well as the mutation allele frequency, the prediction of protein functionality, the inclusion in the Cancer Gene Census and the protein function. Sample legend: B, DCIS right; C, DCIS left; D, NSCLC left; E, NSCLC right; F, N2(4R)&lt;/p&gt;
A W-band stacked FET power amplifier with 17 dBm P<inf>sat</inf> in 45-nm SOI CMOS (2013)

A 90GHz power amplifier implemented with three series-connected (stacked) FETs in 45-nm SOI CMOS is reported. Stacking FETs allows increasing voltage handling capability of circuits with highly scaled CMOS transistors. This work shows for the first time that the stacking strategy is effective up to W band. The amplifier achieves power gain of 8 dB at 91 GHz with 3 dB bandwidth of 18 GHz using a supply voltage of 4.2 V. It delivers saturated output power of 17.3 dBm in 88-90 GHz range with peak PAE of 9 %. The PA chip occupies 0.256 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> including the pads. This chip demonstrates the highest output power from a CMOS PA in this frequency regime.
Fatigue Flexural Behavior of Pre-cracked Specimens of Special UHPFRC (2005)

The American Concrete Institute (ACI) is a leading authority and resource worldwide for the development and distribution of consensus-based standards, technical resources, educational programs, certification programs, and proven expertise for individuals and organizations involved in concrete design, construction, and materials, who share a commitment to pursuing the best use of concrete.
Thermospheric Propagation of Sonic Booms from the Concorde Supersonic Transport. (1979)

A nonlinear theory for the long-range propagation of sonic booms through the thermosphere has been developed. Arealistic atmosphere is employed, and consideration is given to such factors as nonlinear stretching and decay of the wave, the effects of the caustic, the linear acoustic attenuation, and the increase in Mach number due to the decreasing density at high altitudes, detailed results are presented for the case of the Concorde SST in straight, level and steady flight at 17.5 km and a velocity of Mach 2. We predict maximum ground level pressures of 0.3 Pa with an N-wave period of about 10 seconds. The sound level is a minimum along the flight track with the maximum signal strength occurring about 300 km off the flight track. The strongest received signal travels Initially downward and reflects off the surface of the ocean to thermosphere. The wave turns around at an altitude of 160 km and is returned back to the ground at a horizontal distance of 320 km from the launch point. The acoustic Mach number of the wave never exceeds 0.2. Ninety percent of the wave's energy is attenuated below 100 km with 99% attenuated by the time the wave reaches the turning the turning point. (Author)
Upregulation of CD14 and CD18 on Monocytes In Vitro by Antineutrophil Cytoplasmic Autoantibodies (2000)

The expression of CD14, CD18, and major histocompatibility complex II on unprimed monocytes from healthy donors after incubation with IgG from patients with antineutrophil cytoplasmic autoantibody (ANCA)-positive active Wegener's granulomatosis (n = 6) and microscopic polyangiitis (n = 6) in comparison with IgG from healthy controls (n = 6) was studied. Monocytes were incubated with IgG (100 microg/ml) at 37 degrees C, and expression of antigens was measured by fluorescence-activated cell sorter after 18 h. Cytoplasmic ANCA (C-ANCA) IgG and perinuclear ANCA (P-ANCA) IgG in comparison with control IgG increased the expression of CD14 (49.2% [SD: 37, P: < 0. 001], and 55.8% [SD: 41, P: < 0.05]) and CD18 (11.4% [SD: 18, P: < 0. 01] and 8% [SD: 26, P: < 0.05]) but did not change the major histocompatibility complex II expression. Upregulation of CD14 started after 6 h and reached a peak after 10 to 14 h of incubation and was not inhibited by polymyxin B. F(ab)(2) fragments of C- and P-ANCA IgG also increased expression of CD14 and CD18 as compared with control IgG F(ab)(2), but for CD14 less than with complete IgG. ANCA IgG depleted of antiproteinase 3 and antimyeloperoxidase antibodies by immunoadsorption failed to upregulate CD14. Monoclonal murine antibodies against proteinase 3 and myeloperoxidase yielded a strong upregulation of CD14 when compared with an isotype control or human control IgG. The data show that CD14 and CD18 are upregulated on monocytes by C- and P-ANCA IgG in vitro, as well as by monoclonal antibodies against proteinase 3 and myeloperoxidase and that this effect is not dependent on Fc gamma receptor crosslinking. Upregulation of CD14 and CD18 on monocytes by ANCA suggests a pathogenetic role of ANCA monocyte interactions in systemic vasculitis.
Waveform of Loss Voltage in Ag-Sheathed Bi2223 Superconducting Tape Carrying AC Transport Current (2006)

In AC loss measurements of superconductors using the four‐terminal method, the voltage measured consists of two components. The loss voltage component is in phase with transport current while the inductive voltage is out of phase with transport current. Here we report on the use of a compensation coil to nearly cancel the inductive voltage. The loss voltage was amplified by a transformer amplifier and observed on a digital oscilloscope. The waveform of the measured voltage was compared with that of a calculated signal. The loss voltage was analytically calculated for a round wire using the critical state model. The effects of frequency on the waveform of the loss voltage are also studied. Finally, a comparison between waveforms of loss voltages obtained with sine‐wave and triangle‐wave transport currents are presented.
ChemInform Abstract: The Discharge and Charge Characteristics of FeOCl Modified by Aniline in Water. (1991)

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.
Limiting Acute Kidney Injury Progression In Sepsis: Study Protocol and Trial Simulation* (2021)

Findings of our Limiting acute kidney injury Progression In Sepsis trial simulation confirmed that (tissue inhibitor of metalloproteinases-2)•(insulin-like growth factor-binding protein 7) could identify patients with different rates of progression to moderate/severe acute kidney injury, death, or dialysis in 72 hours. The Limiting acute kidney injury Progression In Sepsis protocol algorithm is therefore feasible in terms of identifying suitably high-risk individuals for kidney-sparing sepsis bundle.