gebhart/patrepeval huggingface dataset:
Auto GC system for enhanced ozone monitoring network (1994)

A Perkin-Elmer Model ATD-400 Thermal Desorption System was specially adapted for the collection of whole-air samples. The C{sub 2} to n-C{sub 10} hydrocarbons were trapped using Peltier cooling on Carbotrap/Carbosieve adsorbents at {minus}30 C. A Deans switch allowed the C{sub 2} to C{sub 6} fraction to be separated using a porous layer open tubular column while a methyl silicone column separated the C{sub 6} to C{sub 10} fraction. No cryogen was used in the collection or analysis. Ozone precursor concentrations were detected at the 0.1 ppbV level. Area repeatability was less than 10%, with retention time precision over 100 hours of approximately 1% RSD for most compounds. Remote communications allowed chromatography to be monitored and files to be downloaded to a central office. Data in .CSV format was directly assimilated by spreadsheet software for diurnal inspection and customized reporting. Data were achieved using external Bernoulli disks.
Targeting Lentiviral Vectors to Antigen-Specific Immunoglobulins (2008)

Gene transfer into B cells by lentivectors can provide an alternative approach to managing B lymphocyte malignancies and autoreactive B cell-mediated autoimmune diseases.These pathogenic B cell populations can be distinguished by their surface expression of monospecific immunoglobulin.Development of a novel vector system to deliver genes to these specific B cells could improve the safety and efficacy of gene therapy.We have developed an efficient method to target lentivectors to monospecific immunoglobulin-expressing cells in vitro and in vivo.We were able to incorporate a model antigen CD20 and a fusogenic protein derived from the Sindbis virus as two distinct molecules into the lentiviral surface.This engineered vector could specifically bind to cells expressing surface immunoglobulin recognizing CD20 (␣CD20), resulting in efficient transduction of target cells in a cognate antigen-dependent manner in vitro, and in vivo in a xenografted tumor model.Tumor suppression was observed in vivo, using the engineered lentivector to deliver a suicide gene to a xenografted tumor expressing ␣CD20.These results show the feasibility of engineering lentivectors to target immunoglobulin-specific cells to deliver a therapeutic effect.Such targeting lentivectors also could potentially be used to genetically mark antigen-specific B cells in vivo to study their B cell biology.
Real-time Monitoring of Intermediates Reveals the Reaction Pathway in the Thiol-Disulfide Exchange between Disulfide Bond Formation Protein A (DsbA) and B (DsbB) on a Membrane-immobilized Quartz Crystal Microbalance (QCM) System (2013)

Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone.
[A case of non-small cell lung cancer accompanied with hemorrhage after chemotherapy including gemcitabine]. (2006)

A 51-year-old man underwent left upper lobectomy due to pulmonary adenocarcinoma (cT2N1M0, stage IIB) in August, 2003. Since he turned out pT2N3M0 stage IIIB, he received combination chemotherapy with carboplatin and gemcitabine. During a second course chemotherapy, he was admitted again because of dyspnea and the deterioration of diffuse interstitial shadows in both lungs. He was treated with various antibiotics and corticosteroids. Unfortunately, he could not recover. An autopsy was performed. Microscopic features of the lung revealed diffuse alveolar damage and pulmonary hemorrhage. In this case, pulmonary hemorrhage should be considered as a complication of gemcitabine-induced lung injury.
Lattice-Based ASR-MT Interface for Speech Translation (2010)

The usual approach to improve the interface between automatic speech recognition (ASR) and machine translation (MT) is to use ASR word lattices for translation. In comparison with the previous research along this line, this paper presents an efficient algorithm for lattice-based search in MT. This algorithm utilizes confusion network information to enable phrase-level reordering, and is also able to process general lattices. The proposed search is not constrained to be monotonic; thus, it is able to perform the same type of reordering given lattice input as any statistical phrase-based search algorithm with a single sentence input. Using the concept described in this paper, we are able to significantly improve speech translation results on several small and large vocabulary tasks. The improvements of the MT quality as measured by BLEU are as high as 5% relative. We also show that the proposed lattice-based translation can outperform state-of-the-art translation of confusion networks and has advantages in terms of translation speed. Furthermore, we propose and evaluate a novel approach that shares the benefits of lattice-based translation with those translation systems which are not designed to process word lattices.
Folding and aggregation of TEM β‐lactamase: Analogies with the formation of inclusion bodies in <i>Escherichia coli</i> (1994)

The enzyme TEM beta-lactamase has been used as a model for understanding the pathway leading to formation of inclusion bodies in Escherichia coli. The equilibrium denaturation of TEM beta-lactamase revealed that an intermediate that has lost enzymatic activity, native protein fluorescence, and UV absorption, but retains 60% of the native circular dichroism signal, becomes populated at intermediate (1.0-1.4 M) concentrations of guanidium chloride (GdmCl). This species exhibits a large increase in bis-1-anilino-8-naphthalene sulfonic acid fluorescence, indicating the presence of exposed hydrophobic surfaces. When TEM beta-lactamase was unfolded in different initial concentrations of GdmCl and refolded to the same final conditions by dialysis a distinct minimum in the yield of active protein was observed for initial concentrations of GdmCl in the 1.0-1.5 M range. It was shown that the lower reactivation yield was solely due to the formation of noncovalently linked aggregates. We propose that the aggregation of TEM beta-lactamase involves the association of a compact state having partially exposed hydrophobic surfaces. This hypothesis is consistent with our recent findings that TEM beta-lactamase inclusion bodies contains extensive secondary structure (Przybycien TM, Dunn JP, Valax P, Georgiou G, 1994, Protein Eng 7:131-136). Finally, we have also shown that protein aggregation was enhanced at higher temperatures and in the presence of 5 mM dithiothreitol and was inhibited by the addition of sucrose. These conditions exert a similar effect on the formation of inclusion bodies in vivo.
Identification of Essential Residues for Catalysis of Rat Intestinal Phospholipase B/Lipase (2001)

Intestinal brush border membrane-associated phospholipase B/lipase (PLB/LIP) consists of four tandem homologous domains (repeats 1 through 4) and a COOH-terminal membrane binding domain, and repeat 2 is the catalytic domain that catalyzes phospholipase A2, lysophospholipase, and lipase activities. We examined the structural basis of the catalysis of PLB/LIP with this unique substrate specificity by site-directed mutagenesis of recombinant repeat 2 enzyme. Ser414 and Ser459 within the active serine-containing consensus sequence G-X-S-X-G in the best-established lipase family were dispensable for activity. In contrast, substitution of Ala for Ser404 almost completely inactivated the three lipolytic activities of PLB/LIP, even though the gross conformation was not altered as determined by CD spectroscopy. Notably, this Ser is located within the conserved G-D-S-L sequence on the NH2-terminal side in lipolytic enzymes of another group proposed recently. Furthermore, mutagenesis and CD spectroscopic analyses suggested that Asp518 and His659, lying within conserved short stretches in the latter group of lipolytic enzymes, were essential for activity. These three essential residues are conserved in the known PLB/LIP enzymes, suggesting that they form the catalytic triad in the active site. These results indicate that PLB/LIP represents a distinct class of the lipase family. PLB/LIP is the first mammalian member of that family. Repeat 2 is equipped with the triad, but not the other repeats, accounting for why only repeat 2 is the catalytic domain. Replacing Thr406 with Gly, matching the enzyme's sequence to the lipase consensus sequence exactly, led to a great decrease in secretion and accumulation of inactive enzyme in the cells, suggesting a role of Thr406 in the structural stability.
Vertical multi-layered implementation of a purely left-handed transmission line for super-compact and dual-band devices (2004)

A multi-layered left-handed transmission line (LH-TL) composed of veItically stacked unit cells is proposed and demonstrated by the FDTD and FEM analysis. In addition, the composite rightilefi-handed (CRLH) equivalent circuit is used and the corresponding parameters are extracted to characterize the smcture. The proposed LH-TL, including three unit cells, is extremely small (&/40x A, 140 x 4/57 @ 5GHz, conveniently shielded, and compatible with LTCC technology Both the backward wave propagation and anti-parallel phase and group velocities are observed in the LH passband (extending from 3.32 GHz to 6.89GHz) with global phase advance from509' to 87.5. The possibility of exploiting the left-handed (LH) phase advance of this transmission line (TL) for dual-band microwave components is suggested.
Design of resistive-input class E resonant rectifiers for variable-power operation (2013)

Resonant rectifiers have important application in very-high-frequency power conversion systems, including dc-dc converters, wireless power transfer systems, and energy recovery circuits for radio-frequency systems. In many of these applications, it is desirable for the rectifier to appear as a resistor at its ac input port. However, for a given dc output voltage, the input impedance of a resonant rectifier varies in magnitude and phase as output power changes. A design method is introduced for realizing single-diode “shunt-loaded” resonant rectifiers, or class E rectifiers, that provide near-resistive input impedance over a wide range of output power levels. The proposed methodology is demonstrated in simulation for a 10:1 power range.
Alginate dialdehyde meets nylon membrane: a versatile platform for facile and green fabrication of membrane adsorbers (2018)

Alginate dialdehyde (ADA), a biocompatible polymer, was used as an intermediate layer on a nylon membrane to readily fabricate cation exchange (CEX), metal-affinity (Me-affinity), histidine-affinity (His-affinity) and peptide-affinity (Pep-affinity) membrane adsorbers without any organic solvent usage. All the membrane adsorbers exhibited a high selectivity in the fractionation of a IgG (immunoglobulin)/HSA (human serum albumin) mixture. Along with a high purity of 100%, a high IgG binding capacity of 30, 24, 21 and 28 mg mL⁻¹ (membrane volume) was achieved by the CEX, Me-affinity, His-affinity and Pep-affinity membrane adsorbers in flow-through mode respectively, which is superior to those of the reported membrane adsorbers. Furthermore, the CEX and Pep-affinity adsorbers were tested for the separation of IgG from human plasma solution. The carboxylic groups along with the peptides on the Pep-affinity adsorber captured IgG synergistically with a higher recovery and purity (99% and 98.6%). This synergetic adsorber showed a qₘₐₓ and dynamic binding capacity (DBC) of 138.4 and 38.7 mg mL⁻¹ respectively for IgG binding which was somewhat higher than that of the reported protein A agarose (having qₘₐₓ and DBC of 84 and 24.4 mg g⁻¹ respectively). The present work indicated that the ADA layer not only activated the membrane surface to attach various adsorptive ligands under mild conditions, but also reduced non-specific adsorption. Due to the versatile linking function and green reaction conditions, the ADA coating on the nylon membrane is promising for the preparation of diverse membrane adsorbers.
Recruitment of Patients Into an Internet-Based Clinical Trials Database: The Experience of OncoLink and the National Colorectal Cancer Research Alliance (2004)

The Internet has the potential to increase the likelihood that interested individuals find appropriate clinical trials. Some of the discrepancies that are known to exist for access to the Internet were also seen for those registering with the database through the Internet. Despite these differences, the potential to increase clinical trial enrollment with this type of Internet-based database is high.
Individual and Neighborhood Socioeconomic Status and Healthcare Resources in Relation to Black-White Breast Cancer Survival Disparities (2013)

Background. Breast cancer survival has improved significantly in the US in the past 10-15 years. However, disparities exist in breast cancer survival between black and white women. Purpose. To investigate the effect of county healthcare resources and SES as well as individual SES status on breast cancer survival disparities between black and white women. Methods. Data from 1,796 breast cancer cases were obtained from the Surveillance Epidemiology and End Results and the National Longitudinal Mortality Study dataset. Cox Proportional Hazards models were constructed accounting for clustering within counties. Three sequential Cox models were fit for each outcome including demographic variables; demographic and clinical variables; and finally demographic, clinical, and county-level variables. Results. In unadjusted analysis, black women had a 53% higher likelihood of dying of breast cancer and 32% higher likelihood of dying of any cause (P < 0.05) compared with white women. Adjusting for demographic variables explained away the effect of race on breast cancer survival (HR, 1.40; 95% CI, 0.99-1.97), but not on all-cause mortality. The racial difference in all-cause survival disappeared only after adjusting for county-level variables (HR, 1.27; CI, 0.95-1.71). Conclusions. Improving equitable access to healthcare for all women in the US may help eliminate survival disparities between racial and socioeconomic groups.
Two-dimensional metal-organic coordination networks of Mn-7,7,8,8-tetracyanoquinodimethane assembled on Cu(100): Structural, electronic, and magnetic properties (2009)

A compound two-dimensional (2D) monolayer mixing Mn atoms and 7,7,8,8-tetracyanoquinodimethane (TCNQ) molecules was synthesized by supramolecular assembly on a Cu(100) surface under ultrahigh vacuum conditions. Its structural, electronic, and magnetic properties were analyzed by scanning tunneling microscopy experiment and theory, low-energy electron diffraction, x-ray photoemission spectroscopy, and density-functional theory calculations. The 2D compound has a long-range ordered square planar network structure consisting of fourfold coordinated Mn centers with a Mn:TCNQ ratio of 1:2. The electronic-state analysis revealed a complex charge-transfer scenario indicating strong bonding of TCNQ with both the Mn adsorbates and the Cu surface atoms. The calculations reveal that the Mn centers carry a magnetic moment close to $5{\ensuremath{\mu}}_{\text{B}}$ with very weak coupling between adjacent Mn centers.
A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity (2021)

Abstract During the cancerous transformation of normal hepatocytes into hepatocellular carcinoma (HCC), the enzyme catalyzing the first rate-limiting step of glycolysis, namely the glucokinase (GCK), is replaced by the higher affinity isoenzyme, hexokinase 2 (HK2). Here, we show that in HCC tumors the highest expression level of HK2 is inversely correlated to GCK expression, and is associated to poor prognosis for patient survival. To further explore functional consequences of the GCK-to-HK2 isoenzyme switch occurring during carcinogenesis, HK2 was knocked-out in the HCC cell line Huh7 and replaced by GCK , to generate the Huh7- GCK + / HK2 − cell line. HK2 knockdown and GCK expression rewired central carbon metabolism, stimulated mitochondrial respiration and restored essential metabolic functions of normal hepatocytes such as lipogenesis, VLDL secretion, glycogen storage. It also reactivated innate immune responses and sensitivity to natural killer cells, showing that consequences of the HK switch extend beyond metabolic reprogramming.
PF-06804103, A Site-specific Anti-HER2 Antibody–Drug Conjugate for the Treatment of HER2-expressing Breast, Gastric, and Lung Cancers (2020)

The approval of ado-trastuzumab emtansine (T-DM1) in HER2<sup>+</sup> metastatic breast cancer validated HER2 as a target for HER2-specific antibody-drug conjugates (ADC). Despite its demonstrated clinical efficacy, certain inherent properties within T-DM1 hamper this compound from achieving the full potential of targeting HER2-expressing solid tumors with ADCs. Here, we detail the discovery of PF-06804103, an anti-HER2 ADC designed to have a widened therapeutic window compared with T-DM1. We utilized an empirical conjugation site screening campaign to identify the engineered ĸkK183C and K290C residues as those that maximized <i>in vivo</i> ADC stability, efficacy, and safety for a four drug-antibody ratio (DAR) ADC with this linker-payload combination. PF-06804103 incorporates the following novel design elements: (i) a new auristatin payload with optimized pharmacodynamic properties, (ii) a cleavable linker for optimized payload release and enhanced antitumor efficacy, and (iii) an engineered cysteine site-specific conjugation approach that overcomes the traditional safety liabilities of conventional conjugates and generates a homogenous drug product with a DAR of 4. PF-06804103 shows (i) an enhanced efficacy against low HER2-expressing breast, gastric, and lung tumor models, (ii) overcomes <i>in vitro</i>- and <i>in vivo</i>-acquired T-DM1 resistance, and (iii) an improved safety profile by enhancing ADC stability, pharmacokinetic parameters, and reducing off-target toxicities. Herein, we showcase our platform approach in optimizing ADC design, resulting in the generation of the anti-HER2 ADC, PF-06804103. The design elements of identifying novel sites of conjugation employed in this study serve as a platform for developing optimized ADCs against other tumor-specific targets.
RF03 | PMON300 Sex Hormones, Sex Hormone Binding Globulin, and Gonadotropins in Men with Inguinal Hernias (2022)

Abstract Background More than 1 in 4 men will undergo inguinal hernia repair during their lifetime. Age is a significant risk factor for inguinal hernias in men with increased incidence in older age. Sex steroid hormone changes are observed with a higher ratio of serum estradiol (E2) to testosterone (T) as men age. We previously demonstrated that a shift from androgen to estrogen action caused inguinal hernia formation in a transgenic male mouse model with increased estrogen action in lower abdominal muscle tissues. However, age-related changes in serum E2 levels in men are conflicting, as some studies have reported increases but others have noted unchanged or even decreased E2 levels with advancing age. Method: This study was performed on 212 men with inguinal hernias, aged 20 to 90 years, stratified at 10-year intervals of age (20-30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90 years). We assessed total T (TT), total E2 (TE2), dehydroepiandrosterone (DHEA), sex hormone-binding globulin (SHBG), and gonadotropins (FSH and LH). Body mass index (BMI) was calculated using height and weight. Results The BMI distribution was balanced for men with inguinal hernias among all age groups. TE2 was low in 23.7%, normal in 65.8%, and high in 10.5% of men 50 years or younger. In contrast, the percentage of patients with high TE2 was increased 2.6-fold in men over the age of 50 (20.1% in low, 52.3% in normal, and 27.6% in high). TT was normal in all men 50 years and younger but was low in 3.5% and normal in 96.5% of men over the age of 50. We found that serum TE2 levels and the ratio of TE2/TT positively correlated with age (p=0.001). In addition, serum TE2 levels were significantly higher in the advanced age groups (71-80 and 81-90 years) than in the young age group (20-40 years). Serum TT levels decreased but did not reach significance in the advanced age groups compared to the young age group. Remarkably the ratio of E2/T was higher in the advanced age groups than in the young age group (20-30 years). Serum DHEA levels in men over the age of 50 were significantly higher than in men 50 years or younger. SHBG levels were higher in men over 70 years than men 50 years or younger (p&amp;lt; 0.01). Serum levels of FSH and LH in men over 60 years were 3-fold greater than in men 50 or younger (p&amp;lt;0.01). Conclusions Our findings suggest a correlation of increased estrogen action in the formation of inguinal hernias at an advanced age. This points to a potential utilization of inhibitors of estrogen synthetase or estrogen antagonists in a subset of elderly inguinal hernia patients with increased circulating estrogen as a non-surgical intervention. Presentation: Saturday, June 11, 2022 1:42 p.m. - 1:47 p.m., Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.
Control of directional evanescent coupling in fs laser written waveguides (2007)

We investigate the evanescent coupling of femtosecond laser written waveguides with elliptical and circular shape. A directional tuning the coupling properties is realized in a cubic array by tilting the elliptical waveguides. This allows to specifically pronounce diagonal coupling. In contrast, directional insensitive coupling is demonstrated in a circular waveguide array based on circular waveguides.
New knowledge for old using the crystal learning lamp (2002)

RSCL (random seeded crystal learning) methods address the principal problem met in the design and programming of solutions to complex problems; namely, the automation of redundant tasks. Such automation entails the evolution of a rule base. The problem then pertains to cracking the knowledge acquisition bottleneck. RSCL methods are predicated upon the existence of symmetry in the domain universe. Symmetry facilitates the induction of new knowledge-not merely a statistical interpolation of existing data. Like neural networks, RSCL methods are best matched to parallel platforms. Eventually, so-called expert /sup n/ compilers will capture all knowledge applied in the design of software. These translators acquire knowledge from the programmer and assist him/her by assuming an ever increased scope of redundant translation tasks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of the Efficacy of ChAd63-MVA Vectored Vaccines Expressing Circumsporozoite Protein and ME-TRAP Against Controlled Human Malaria Infection in Malaria-Naive Individuals (2014)

NCT01623557.