gebhart/patrepeval huggingface dataset:
Different cagA and vacA Polymorphisms are Found in the Chinese versus the Malay and Indian Populations: An Analysis of Helicobacter Pylori Virulence Genes in Singapore (2010)

Aim: Helicobacter pylori causes peptic ulcer disease and gastric cancer. Western studies suggest that polymorphisms in the virulence factors cagA and vacA may determine the ability of bacteria to cause gastroduodenal diseases. Differences in the cagA EPIYA motifs and polymorphisms of the signal (s), middle (m) and intermediate (i) regions of vacA are thought to be important. The aim of this study was to compare the polymorphisms of cagA and vacA of H. pylori isolated from the Chinese, Malay and Indian populations living in Singapore. Method: A total of 104 H. pylori isolates obtained from patients with dyspeptic symptoms were analysed. Of the 104 patients, 80 were Chinese, 9 Malays and 15 Indians. DNA was extracted from the isolates and the vacA allelic types and cagA EPIYA motifs were determined by polymerase chain reaction (PCR) and sequencing, respectively. Results: Differences in the vacA and cagA polymorphisms were found between the Chinese, Malays and Indians. Significantly more non-Chinese patients carried vacA s1/m1 strains versus Chinese patients ( p &lt; 0.05). All 9 Malay patients, 11/15 (73.3%) Indians and 31/80 (38.8%) Chinese patients carried H. pylori strains with the vacA s1/m1/i1. Significantly more Chinese patients carried isolates with East Asian cagA EPIYA motifs versus non-Chinese patients ( p &lt; 0.05). 79/80 (98.8%) of the Chinese isolates, 2/15 (13%) of Indian isolates, and 5/9(55.6%) of Malay isolates possessed CagA with the East Asian ABD type motif. Conclusion: Results from the current study demonstrated marked differences in the polymorphisms of vacA and CagA EPIYA motifs in strains isolated from Chinese versus non-Chinese patients. Epidemiologically, the Chinese are at the highest risk of developing gastric cancer. Work is ongoing to determine if differences found in the CagA EPIYA motifs of isolates from the Chinese patients can contribute to a subject's risk of developing gastric cancer.
Analysis of Stochastic Effect in Line-and-Space Resist Patterns Fabricated by Extreme Ultraviolet Lithography (2013)

Extreme ultraviolet (EUV) lithography is promising for the high-volume production of semiconductor devices for the 16 nm node and below. However, the stochastic effect is a significant concern in lithography using high-energy (92.5 eV) photons and highly sensitive resists. In this study, we report a technique for evaluating the stochastic effect on line edge roughness (LER). Resist patterns were analyzed using a Monte Carlo simulation on the basis of the sensitization and reaction mechanisms of chemically amplified EUV resists. The contribution of protected unit fluctuation to LER was estimated to be ±0.31 to ±0.37σ.
Abstract 2572: HSD3B1 genotype and abiraterone metabolism in patients with prostate cancer (2018)

Abstract Background The common HSD3B1 (1245C) germline variant encodes for a 3βHSD1 missense that increases enzyme activity that allows tumors to utilize extragonadal androgens and is a predictive biomarker of resistance to ADT and sensitivity to CYP17A1 inhibition by the nonsteroidal drug ketoconazole. However, 3βHSD is also the first enzyme necessary in the conversion from abiraterone, a steroidal CYP17A1 inhibitor, to 5α-abiraterone, which stimulates the androgen receptor (AR) and prostate cancer progression. The HSD3B1 (1245C) variant might therefore increase 5α-abiraterone synthesis in patients on abiraterone therapy, possibly limiting clinical benefit. Significance This work aims to characterize the pharmacokinetics of steroidal metabolites of abiraterone and to determine the association between HSD3B1 genotype and the generation of 5α-abiraterone metabolites. Patients and Methods Part 1: 15 healthy male volunteers received a single oral dose of 1000 mg abiraterone acetate plus 240 mg of the AR antagonist apalutamide, steroidal metabolites of abiraterone were quantitated at 12 time points from 0.5-96 hours post-dose. Part 2: 5α-abiraterone metabolites and HSD3B1 genotype was determine in 30 patients with castration-resistant prostate cancer (CRPC) on abiraterone therapy. Metabolite concentrations were normalized to the 8 hour time point of the pharmacokinetic study and the association between HSD3B1 genotype and 5α-abiraterone metabolites was determined. Results There were 8, 19, and 3 pts with homozygous wild-type, heterozygous, and homozygous variant HSD3B1 genotypes. Patients who inherit 0, 1 and 2 copies of the HSD3B1 (1245C) variant have a stepwise increase in serum concentrations of 5α-abiraterone metabolites (p=0.002). Conclusion The generation of 5α-abiraterone preferentially in patients with the HSD3B1 (1245C) variant might negate the benefits of abiraterone specifically in a patient subset that is otherwise more likely to benefit from CYP17A1 inhibition by the nonsteroidal drug ketoconazole. Citation Format: Mohammad Alyamani, Hamid Emamekhoo, Sunho Park, Jennifer Taylor, Nima Almassi, Sunil Upadhyay, Allison Tyler, Michael P. Berk, Tae Hyun Hwang, Petros Grivas, Brian Rini, Jorge Garcia, Richard J. Auchus, Nima Sharifi. HSD3B1 genotype and abiraterone metabolism in patients with prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2572.
ChemInform Abstract: Synthesis and Antitumor Activity of 2‐β‐D‐Ribofuranosyloxazole‐4‐carboxamide (Oxazofurin). (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.
Nitrogen-doped graphene interpenetrated 3D Ni-nanocages: efficient and stable water-to-dioxygen electrocatalysts (2014)

Herein, we report the synthesis of a nitrogen-doped graphene (NGr) interpenetrated 3D Ni-nanocage (Ni-NGr) electrocatalyst by a simple water-in-oil (w/o) emulsion technique for oxidation of water to dioxygen. Correlation of adsorption of NGr and subsequent interpenetration through the specific surface plane of nickel particles as well as the concomitant interaction of N and C with Ni in the nano-regime has been investigated. Apart from the benefits of the synergistic interactions between Ni, N, and C, the overall integrity of the structure and its intra-molecular connectivity within the framework help in achieving better oxygen evolution characteristics at a significantly reduced overpotential. The engineered Ni-NGr nanocage displays a substantially low overpotential of ∼290 mV at a practical current density of 20 mA cm(-2) in 0.1 M KOH. In comparison, NGr and Ni-particles as separate entities give overpotentials of ∼570 and ∼370 mV under similar conditions. Moreover, the long term stability of Ni-NGr was investigated by anodic potential cycling for 500 cycles and an 8.5% increment in the overpotential at 20 mA cm(-2) was observed. Additionally, a chronoamperometric test was performed for 15 h at 20 mA cm(-2), which highlights the better sustainability of Ni-NGr under the actual operating conditions. Finally, the quantitative estimation of evolved oxygen was monitored by gas chromatography and was found to be 70 mmol h(-1) g(-1) of oxygen, which is constant in the second cycle as well.
Stent design properties and deployment ratio influence indexes of wall shear stress: a three-dimensional computational fluid dynamics investigation within a normal artery (2004)

Restenosis limits the effectiveness of stents, but the mechanisms responsible for this phenomenon remain incompletely described. Stent geometry and expansion during deployment produce alterations in vascular anatomy that may adversely affect wall shear stress (WSS) and correlate with neointimal hyperplasia. These considerations have been neglected in previous computational fluid dynamics models of stent hemodynamics. Thus we tested the hypothesis that deployment diameter and stent strut properties (e.g., number, width, and thickness) influence indexes of WSS predicted with three-dimensional computational fluid dynamics. Simulations were based on canine coronary artery diameter measurements. Stent-to-artery ratios of 1.1 or 1.2:1 were modeled, and computational vessels containing four or eight struts of two widths (0.197 or 0.329 mm) and two thicknesses (0.096 or 0.056 mm) subjected to an inlet velocity of 0.105 m/s were examined. WSS and spatial WSS gradients were calculated and expressed as a percentage of the stent and vessel area. Reducing strut thickness caused regions subjected to low WSS (<5 dyn/cm(2)) to decrease by approximately 87%. Increasing the number of struts produced a 2.75-fold increase in exposure to low WSS. Reducing strut width also caused a modest increase in the area of the vessel experiencing low WSS. Use of a 1.2:1 deployment ratio increased exposure to low WSS by 12-fold compared with stents implanted in a 1.1:1 stent-to-vessel ratio. Thinner struts caused a modest reduction in the area of the vessel subjected to elevated WSS gradients, but values were similar for the other simulations. The results suggest that stent designs that reduce strut number and thickness are less likely to subject the vessel to distributions of WSS associated with neointimal hyperplasia.
ChemInform Abstract: The Addition Reaction of β‐Keto Carboxylic Acids to Olefinic Compounds by Use of Mn(III) Tris(2‐pyridinecarboxylate) as an Oxidant. (1990)

Abstract The β‐keto acids (I), (IV), and (VII) undergo coupling with the vinyl silyl ethers (II) or (V) in the presence of the manganese salt mentioned in the title to yield the 1,4‐diketones (III) or (VI).
ChemInform Abstract: Structural Diversity of Multi‐Component Self‐Assembled Systems Incorporating p‐Sulfonatocalix[4]arene. (2010)

Abstract Review: 56 refs.
ChemInform Abstract: A Convenient Synthesis of L‐(S)‐Glyceraldehyde Acetonide from L‐Ascorbic Acid. (1987)

Abstract L‐Gulono‐1,4‐lactone (II), prepared by hydrogenation of ascorbic acid (I), is converted to 5,6‐O‐isopropylidene‐L‐gulono‐lactone (IV).
Supplementary Figure 3 from Aldehyde Dehydrogenase Activity Selects for Lung Adenocarcinoma Stem Cells Dependent on Notch Signaling (2023)

Supplementary Figure 3 from Aldehyde Dehydrogenase Activity Selects for Lung Adenocarcinoma Stem Cells Dependent on Notch Signaling
Effect of chiral 2-ethylhexyl side chains on chiroptical properties of the narrow bandgap conjugated polymers PCPDTBT and PCDTPT (2016)

Two narrow bandgap conjugated polymers containing chiral 2-ethylhexyl side chains were synthesized: poly[(4,4-bis(2-ethylhexyl)cyclopenta-[2,1-<i>b</i>:3,4-<i>b</i>']dithiophene)-2,6-diyl-<i>alt</i>-(2,1,3-benzothiadiazole)-4,7-diyl] (PCPDTBT*) and poly[(4,4-bis(2-ethylhexyl)cyclopenta[2,1-<i>b</i>:3,4-<i>b</i>0]dithiophene)-2,6-diyl-<i>alt</i>-[1,2,5]-thiadiazolo[3,4-<i>c</i>]pyridine] (PCDTPT*). The presence of a chiral substituent provides a handle to study the geometry of interchain aggregates and/or the secondary structure of these conjugated polymers in solution and in thin films <i>via</i> circular dichroism (CD) spectroscopy, provided that the asymmetry in the side-chain is translated to the optically active conjugated backbone. CD signals are observed for PCPDTBT* and PCDTPT* in poor solvent systems, which indicate the presence of chiral ordering in the aggregates. PCPDTBT* shows greater chiral order than PCDTPT* based on their relative anisotropy factors. Additionally, GIWAXS analysis reveals that PCPDTBT* films are more ordered than what is observed for the same polymer containing racemic 2-ethylhexyl chains. Upon solution deposition, the chiral ordering is found to translate to the solid-state microstructure for PCPDTBT* but not PCDTPT*. The presence of a pyridyl nitrogen on the thiadiazolo[3,4-<i>c</i>]pyridine ring of PCDTPT* favors a planar conformation for the backbone such that it has a higher rotational barrier compared to PCPDTBT*. This larger rotational barrier appears to limit the ability of PCDTPT* to adopt a helical structure or relevant chain distortions for achieving chiral aggregates.
PKA and Apicomplexan Parasite Diseases (2016)

The cAMP-dependent protein kinase PKA is a well-characterized member of the serine-threonine protein AGC kinase family and is the effector kinase of cAMP signaling. As such, PKA is involved in the control of a wide variety of cellular processes including metabolism, cell growth, gene expression and apoptosis. cAMP-dependent PKA signaling pathways play important roles during infection and virulence of various pathogens. Since fluxes in cAMP are involved in multiple intracellular functions, a variety of different pathological infectious processes can be affected by PKA signaling pathways. Here, we highlight some features of cAMP-PKA signaling that are relevant to <i>Plasmodium falciparum</i>-infection of erythrocytes and present an update on AKAP targeting of PKA in PGE2 signaling via EP4 in <i>Theileria annulata</i>-infection of leukocytes and discuss cAMP-PKA signling in Toxoplasma.
Adaptive task duplication using on-line bottleneck detection for streaming applications (2012)

In this paper we describe an approach to dynamically improve the progress of streaming applications on SMP multi-core systems. We show that run-time task duplication is an effective method for maximizing application throughput in face of changes in available computing resources. Such changes can not be fully handled by static optimizations. We derive a theoretical performance model to identify tasks in need of more computing resources. We propose two on-line algorithms that use indications from the performance model to detect computation bottlenecks. In these algorithms, a task can identify itself as a bottleneck using only its local data. The proposed technique is transparent to end programmers and portable to systems with fair scheduling. Our on-line detection algorithms can be applied to other dynamic scenarios, for example, involving run-time variation of workload.
Weighted Fair Multicast Multigroup Beamforming Under Per-antenna Power Constraints (2014)

A multiantenna transmitter that conveys independent sets of common data to distinct groups of users is considered. This model is known as physical layer multicasting to multiple cochannel groups. In this context, the practical constraint of a maximum permitted power level radiated by each antenna is addressed. The per-antenna power constrained system is optimized in a maximum fairness sense with respect to predetermined quality of service weights. In other words, the worst scaled user is boosted by maximizing its weighted signal-to-interference plus noise ratio. A detailed solution to tackle the weighted max-min fair multigroup multicast problem under per-antenna power constraints is therefore derived. The implications of the novel constraints are investigated via prominent applications and paradigms. What is more, robust per-antenna constrained multigroup multicast beamforming solutions are proposed. Finally, an extensive performance evaluation quantifies the gains of the proposed algorithm over existing solutions and exhibits its accuracy over per-antenna power constrained systems.
Abstract 1782: Detection of T790M gefitinib resistance mutation in EGFR using the BEAMing method (2010)

Abstract Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), such as gefitinib or erlotinib, are effective therapies for non-small cell lung cancer (NSCLC) patients with primary EGFR mutations. However, most patients who initially respond to treatment with these drugs will develop resistance to EGFR TKIs. The secondary EGFR T790M mutation is reported to correlate with acquired resistance. We examined the T790M mutation in primary tumors with BEAMing (beads, emulsion, amplification, magnetic), which is the most sensitive technique to detect minor mutated alleles. Currently, we can detect point mutation at the level of 1/10,000 using an improved version of the BEAMing. We detected T790M mutant alleles in NSCLCs in 19 out of 270 NSCLCs with primary EGFR mutations. The detection of small fraction of T790M mutant alleles may be useful for predicting resistance of NSCLCs to TKIs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1782.
Racial differences in inflammation and outcomes of aging among kidney transplant candidates (2019)

Non-AAs with elevated inflammatory markers may need closer follow-up and may benefit from prehabilitation to improve physical function, reduce frailty burden, and improve quality of life prior to transplant.
Reproductive physiology of a humanized GnRH receptor mouse model: application in evaluation of human-specific analogs (2013)

The human GnRH receptor (GNRHR1) has a specific set of properties with physiological and pharmacological influences not appropriately modeled in laboratory animals or cell-based systems. To address this deficiency, we have generated human GNRHR1 knock-in mice and described their reproductive phenotype. Measurement of pituitary GNRHR1 transcripts from homozygous human GNRHR1 knock-in (ki/ki) mice revealed a severe reduction (7- to 8-fold) compared with the mouse Gnrhr1 in wild-type mice. ¹²⁵I-GnRH binding assays on pituitary membrane fractions corroborated reduced human GNRHR1 protein expression in ki/ki mice, as occurs with transfection of human GNRHR1 in cell lines. Female homozygous knock-in mice displayed normal pubertal onset, indicating that a large reduction in GNRHR1 expression is sufficient for this process. However, ki/ki females exhibited periods of prolonged estrous and/or metestrous and reduced fertility. No impairment was found in reproductive maturity or adult fertility in male ki/ki mice. Interestingly, the serum LH response to GnRH challenge was reduced in both knock-in males and females, indicating a reduced GNRHR1 signaling capacity. Small molecules targeting human GPCRs usually have poor activities at homologous rodent receptors, thus limiting their use in preclinical development. Therefore, we tested a human-specific GnRH1 antagonist, NBI-42902, in our mouse model and demonstrated abrogation of a GnRH1-induced serum LH rise in ki/ki mice and an absence of effect in littermates expressing the wild-type murine receptor. This novel model provides the opportunity to study the human receptor in vivo and for screening the activity of human-specific GnRH analogs.
New Therapeutic Approaches for Acute Myeloid Leukaemia (2021)

Acute myeloid leukaemia (AML) is a genetically heterogeneous haematopoietic neoplasm characterised by the accumulation of transformed immature blood progenitors in bone marrow. Since 1973, the backbone treatment has relied on the combination of cytarabine and an anthracycline, followed by allogeneic haematopoietic transplant if eligible. Therefore, the treatment decisions have largely revolved around chemotherapy drug intensity. Despite advances in our understanding of the underlying biology over the past decades, AML remains a therapeutic challenge as the overall survival is poor and treatment options are limited for relapsed/refractory AML or for unfit patients. After four decades without substantial changes, eight new noncytostatic drugs have been granted approval: vyxeos, enasidenib, gilteritinib, glasdegib, gemtuzumab ozogamicin, ivosidenib, midostaurin, and venetoclax. Despite promising preliminary results, some indications are based on early efficacy data, obtained in single-arm nonrandomised trials, highlighting the necessity for further validation in extended clinical trials. Interestingly, several druggable targets have been identified recently, associated with specific target-directed drugs. Based on the preclinical data available, great impact on clinical outcomes for patients with AML is expected, potentially increasing the therapeutic landscape for this disease.
Monitoring of Radiation Therapy Response of Head and Neck Tumors by Non-Invasive Optical Blood Flow Measurements (2005)

The aim is to evaluate the usefulness of optical blood flow measurements for predicting early tumor response to radiation therapy in patients with head and neck tumors. The results suggest a correlation between tumor blood flow changes with clinical outcome.
Magnesium-neurohypophyseal hormone interactions in contraction of vascular smooth muscle (1975)

The contractile responses of helically cut rat aortic strips to neurohypophyseal hormones and synthetic analogues in the presence and absence of 1.2 mM external magnesium ions [Mg++]o was studied. These experiments demonstrate that 1) [Mg++]o potentiates the contractile actions of a variety of neurohypophyseal peptides on vascular smooth muscle. 2) [Mg++]o can alter both the ED50s (i.e., hormone-receptor affinities) and intrinsic activities (or maximum contractile responses) of these molecules on vascular muscle. 3) The amino acid moieties in positions 1, 2, 3, and 8 of the vasopressin molecule interact, differentially, with [Mg++] to produce contraction of vascular muscle. 4) The length of the side chain, and basicity, in position 8 of the vasopressin molecule are probably important in Mg potentiation in mammalian vascular muscle. 5) Interaction of Mg with an aromatic group in position 3 might be critical for potency of vasopressin hormones of mammalian vascular muscle; the ED50 for oxytocin is not shifted to lower concentrations in the presence of [Mg++]o. Collectively, these data suggest that Mg probably acts at more than one site in vascular smooth muscle in the production of neurohypophyseal peptide-activated contractions. In addition, the present findings indicate that the Mg dependence of these peptides on at least one vascular muscle, rat aorta, is a direct function of the rat pressor potency of the molecules.
Heat Transfer and Flow on the First Stage Blade Tip of a Power Generation Gas Turbine: Part 2 — Simulation Results (1999)

A combined experimental and computational study has been performed to investigate the detailed distribution of convective heat transfer coefficients on the first stage blade tip surface for a geometry typical of large power generation turbines (&gt;100MW). This paper is concerned with the numerical prediction of the tip surface heat transfer. Good comparison with the experimental measured distribution was achieved through accurate modeling of the most important features of the blade passage and heating arrangement as well as the details of experimental rig likely to affect the tip heat transfer. A sharp edge and a radiused edge tip was considered. The results using the radiused edge tip agreed better with the experimental data. This improved agreement was attributed to the absence of edge separation on the tip of the radiused edge blade.
Silicon Carbide for Diesel Particulate Filter Applications:Material Development and Thermal Design (2002)

&lt;div class="htmlview paragraph"&gt;Recently, SiC has been investigated and pursued as an alternative material for diesel particulate filter (DPF) applications. SiC has acceptable physical properties such as good thermal conductivity, refractoriness, and chemical durability. Materials for DPF applications require a particular mean pore size, porosity, and permeability. In addition, these material attributes must be coupled to an appropriate thermal design so that the filter can survive the extreme temperature gradients generated during the regeneration process. In this report several approaches to making porous SiC will be discussed and performance data based on material properties and thermal design will be presented.&lt;/div&gt;