gebhart/patrepeval huggingface dataset:
Abstract 1727: Correlation between BRCA1 and LMO4 mRNA expression levels in Erlotinib-treated non small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations (2012)

Abstract Background Advanced NSCLC p harboring EGFR mutations show impressive progression-free survival (PFS) when treated with erlotinib. However, presence of EGFR mutations only imperfectly predicts outcome. We demonstrated that co-existence of the EGFR T790M pretreatment mutation was detected in one-third of p and, in conjunction with elevated BRCA1 mRNA levels, dramatically influenced PFS to erlotinib. Though this model is a breakthrough in outcome of EGFR-mutated NSCLC p treated with TKIs, we choose to analyze the impact of CTIP and LMO4 gene expression levels on p outcome and their correlation with BRCA1. CtIP binds to BRCA1 and LMO4 forming a complex. LMO4 is a negative regulator of BRCA1 function in sporadic breast cancers. Methods mRNA expression of LMO4 and CTIP was examined by RT-PCR in pretreatment tumor biopsies of 72 NSCLC p with EGFR mutations treated with erlotinib. Expression levels were correlated with outcome to erlotinib and BRCA1 expression levels. Results BRCA1 significantly correlated with CtIP (r=0.31;P=0.01) and LMO4 (r=0.32;P=0.02). There was no correlation between CtIP and LMO4 (r=0.09;P=0.49).PFS was not reached for p with high levels of LMO4 vs 13 months for p with low levels (P=0.006). Overall survival (OS) was not reached for p with high levels of LMO4 vs 29 months for p with low levels (P=0.10). Expression levels of CtIP did not correlate with PFS and OS. PFS was not reached for p with low levels of BRCA1 and high levels of LMO4 vs 19 months for p with low levels of both genes (P=0.04). PFS was 8 months for p with high levels of BRCA1 and low levels of LMO4 vs 18 months for p with high levels of both genes (P=0.03). Conclusions BRCA1 and LMO4 mRNA levels examined by RT-PCR could predict PFS to erlotinib in p with EGFR mutations and could be useful for development of new therapeutic strategies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1727. doi:1538-7445.AM2012-1727
Effect of Continuous Hypertonic Saline Infusion on Clinical Outcomes in Patients with Traumatic Brain Injury: A Retrospective Causal Analysis (2021)

Abstract Purpose: Intracranial pressure (ICP) control has long been recognized as an important requirement for traumatic brain injury (TBI) patients. Nevertheless, the long-term effect of hypertonic saline (HTS) remains unknown. The aim of this study was to elucidate the effect on clinical outcomes in TBI patients admitted to intensive care unit (ICU) settings. Methods: We retrospectively identified moderate to severe TBI patients from two public databases named Medical Information Mart for the Intensive Care (MIMIC)-IV and eICU Collaborative Research Database (eICU-CRD). A marginal structural Cox model (MSCM) was used, with time-dependent variates designed to reflect exposure over time during the ICU stay. A trajectory modeling, based on intracranial pressure evolution pattern, allowed identification of subgroups. Results: Overall, in our cohort of 1955 eligible patients, 130 (6.65%) received HTS. MSCM indicated that the HTS was significantly associated with better Glasgow coma score [(GCS): hazard ratio (HR) 1.19, 95% confidence interval (95% CI) 1.01-1.40, p = 0.041], higher infection complications [eg. urinary tract infection (HR 1.88, 95% CI 1.26-2.81, p = 0.002)], and increased ICU LOS (HR 2.02, 95% CI 1.71-2.40, p &lt; 0.001). A protective effect from GCS by the HTS was found in the subgroup with medium and low ICP. Conclusion: Our study revealed no significant difference in the all-cause mortality rates between patients receiving HTS or not. Increased occurrence rates of infection and electrolyte imbalance were inevitable outcomes caused by continuous HTS infusion. Although the study suggested the slight beneficial effects including better neurological outcome, the results warrant further validation.
Vita blue: A new 633‐nm excitable fluorescent dye for cell analysis (1989)

Several new derivatives of fluorescein were synthesized. The dyes were characterized by NMR; and the absorbance, excitation, and emission spectra were measured. The fluorescence quantum yields of the dyes were determined. The pKa3 values of the dyes were measured by fluorescence titration. The characteristics of the fluorescein and sulfonefluorescein derivatives were compared. The most promising dye for use in cell analysis appeared to be compound 9, which was given the name Vita Blue. The dibutyrate ester of Vita Blue was made and the compound was given the name Vita Blue dibutyrate (VBDB, 14). The Km of VBDB with pig liver esterase was measured and found to be 4 x 10(-5) M. The pKa3 of Vita Blue was 7.56 +/- 0.03; both acidic and basic forms were fluorescent (dual fluorescence). The use of VBDB as an intramolecular esterase substrate and its utility for the discrimination between live and dead cells by flow cytometry is described.
Virantmycin, a potent antiviral antibiotic produced by a strain of Streptomyces. (1980)

Virantmycin, a novel chlorine-containing antiviral antibiotic, has been isolated from Streptomyces nitrosporeus No. AM-2722. The active substance in culture broth is isolated as colorless needles by solvent extraction followed by high performance liquid chromatography on silicic acid. The molecular formula is C19H26NO3Cl (molecular weight 351) from the elemental analysis and mass spectrum. The antibiotic possesses antifungal activity and potent inhibitory activity against various RNA and DNA viruses.
Semantically Rich, Context Aware Access Control for Openstack (2018)

In an open source cloud computing platform such as OpenStack, operators use Role-Based Access Control (RBAC) model to grant access to cloud resources. However, these user-level role-based access control techniques fail to include comprehensive user context. We believe a situational aware framework will improve security by bringing in user's context to such cloud systems. In this paper, we create a semantically rich context-sensitive access control system for OpenStack by incorporating the user's current context attributes like location, time, etc. In a proof-of-concept implementation, we integrate a knowledge graph with our own access control system to express and enforce the contextual-situation policies in OpenStack. The proposed system provides enhanced, flexible access control while minimizing the overhead of altering the existing access control framework. We also discuss various use cases, to highlight the benefits of our system and show enforcement results.
ALD‐Coated Mesoporous Iridium‐Titanium Mixed Oxides: Maximizing Iridium Utilization for an Outstanding OER Performance (2022)

Abstract With the increasing production of renewable energy and concomitant depletion of fossil resources, the demand for efficient water splitting electrocatalysts continues to grow. Iridium (Ir) and iridium oxides (IrO x ) are currently the most promising candidates for an efficient oxygen evolution reaction (OER) in acidic medium, which remains the bottleneck in water electrolysis. Yet, the extremely high costs for Ir hamper a widespread production of hydrogen (H 2 ) on an industrial scale. Herein, the authors report a concept for the synthesis of electrode coatings with template‐controlled mesoporosity surface‐modified with highly active Ir species. The improved utilization of noble metal species relies on the synthesis of soft‐templated metal oxide supports and a subsequent shape‐conformal deposition of Ir species via atomic layer deposition (ALD) at two different reaction temperatures. The study reveals that a minimum Ir content in the mesoporous titania‐based support is mandatory to provide a sufficient electrical bulk conductivity. After ALD, a significantly enhanced OER activity results in dependency of the ALD cycle number and temperature. The most active developed electrocatalyst film achieves an outstanding mass‐specific activity of 2622 mA mg Ir –1 at 1.60 V RHE in a rotating‐disc electrode (RDE) setup at 25 °C using 0.5 m H 2 SO 4 as a supporting electrolyte.
Strategies for the synthesis of spiropiperidines – a review of the last 10 years (2018)

Spiropiperidines have gained in popularity in drug discovery programmes as medicinal chemists explore new areas of three-dimensional chemical space. This review focuses on the methodology used for the construction of 2-, 3- and 4-spiropiperidines, covering the literature from the last 10 years. It classifies the synthesis of each of the types of spiropiperidine by synthetic strategy: the formation of the spiro-ring on a preformed piperidine ring, and the formation of the piperidine ring on a preformed carbo- or heterocyclic ring. While 3- and 4-spiropiperidines are predominantly synthesised for drug discovery projects, 2-spiropiperidines are synthesised en route to natural products. The lack of 2-spiropiperidines in drug discovery is presumably due to limited general procedures for their synthesis.
Persistent Breakage (1992)

Audio files are EID restricted. Individuals without an EID should send an email request to apl-aaa@lib.utexas.edu.
A Validation Study for the Extraction and Analysis of DNA from Human Nail Material and Its Application to Forensic Casework (1999)

A validation study was conducted to demonstrate that deoxyribonucleic acid (DNA) could be successfully extracted from human nail material and analyzed using short tandem repeat (STR) profiling and/or mitochondrial DNA (mtDNA) sequencing. This study involved the development of a DNA extraction protocol that includes a cleaning procedure designed to remove external contaminants (e.g., biological, chemical). This protocol was used to test human nail material that had been soaked in whole blood from a second donor and coated with gold-palladium to simulate scanning electron microscopic analysis. The results showed no indication of a mixture and were consistent with that of the nail donor. Fresh human nail material usually yielded both STR profiles and mtDNA sequence information; however, aged human nail material (approximately eight years old) yielded only mtDNA sequence information. Upon completion of the validation study, the extraction protocol was used for the analysis of a torn fingernail fragment recovered from the scene of a violent homicide in 1983. A partial STR profile and mtDNA sequence information indicated that the fingernail fragment was excluded as originating from the suspect and was, in fact, consistent with originating from one of the victims.
Degradation of Blue AlGaN/InGaN/GaN LEDs Subjected to High Current Pulses (1995)

Short-wavelength, visible-light emitting optoelectronic devices are needed for a wide range of commercial applications, including high-density optical data storage, full-color displays, and underwater communications.In 1994, high-brightness blue LEDs based on gallium nitride and related compounds (InGaN/AlGaN) were introduced by Nichia Chemical Industries [l].The Nichia diodes are 100 times brighter than the previously available S i c blue LEDs.Group-111 nitrides combine a wide, direct bandgap with refractory properties and high physical strength.So far, no studies of degradation of GaN based LEDs have been reported.Our study, reported in this paper, focuses on the performance of GaN LEDs under high electrical stress conditions.Our observations indicate that, in spite of a high defect density, which normally would have be fatal to other III-V devices, defects in group-111 nitrides are not mobile even under high electrical stress.Defect tubes, however, can offer a preferential path for contact metals to electromigrate towards the p-n junction, eventually resulting in a short.The proposed mechanism of GaN diode degradation raises concern for prospects of reliable lasers in the group-III nitrides grown on sapphire.
The MTG-Jamendo dataset for automatic music tagging (2019)

Comunicació presentada a: ML4MD Machine Learning for Music Discovery Workshop del congrés ICML2019 celebrat el 15 de juny de 2019 a Long Beach, California.
Backbone chemical shift assignment and dynamics of the N-terminal domain of ClpB from Francisella tularensis type VI secretion system (2022)

The Hsp100 family member ClpB is a protein disaggregase which solubilizes and reactivates stress-induced protein aggregates in cooperation with the DnaK/Hsp70 chaperone system. In the pathogenic bacterium Francisella tularensis, ClpB is involved in type VI secretion system (T6SS) disassembly through depolymerization of the IglA-IglB sheath. This leads to recycling and reassembly of T6SS components and this process is essential for the virulence of the bacterium. Here we report the backbone chemical shift assignments and <sup>15</sup>N relaxation-based backbone dynamics of the N-terminal substrate-binding domain of ClpB (1-156).
Structural analysis of a dipole system in two-dimensional channels (2004)

A system of magnetic dipoles in two-dimensional (2D) channels was studied using Brownian dynamics simulations. The dipoles interact with a purely repulsive r(-3) potential and are confined by two hard walls in one of the dimensions. Solid crystals were annealed in the 2D channels and the structural properties of the crystals were investigated. The long-ranged nature of the purely repulsive dipoles combined with the presence of hard walls led to structural deviations from the unbounded (infinite) 2D dipolar crystal. The structures in the channels were characterized by a high density of particles along the walls. The particles along the wall became increasingly localized as the channel width was increased. The spacing of the walls was important in determining the properties of the structures formed in the channel. Small changes in the width of the channel induced significant structural changes in the crystal. These structural changes were manifested in the density profiles, defect concentrations, and local bond-orientation order of the system. Oscillations in the structural properties were observed as the channel width was increased, indicating the existence of magic-number channel widths for this system. As the channel width was increased the properties of the confined system approached those of the unbounded system surprisingly slowly.
Fluorigenic Derivatization of Oxazepam. Application to Its Determination in Pharmaceuticals (1994)

Abstract Oxazepam, when heated in mixtures of acetic acid and methanol, undergoes a reaction giving an intense fluorescence at excitation and emission wavelengths of 364 and 469 nm, respectively. The best reaction conditions were a 7:25 methanol:acetic acid volume ratio, a temperature of 100 °C (examinated range 50–100 °C), and a reaction time of 5 minutes. A linear range from 0.025 to 50 μg/ml with a limit of detection of 0.014 μg/ml and a reproducibility within day of less than 5% were attained. A Flow Injection Analysis method was designed and a linear range from 0.1 to 100 μg/ml with a limit of detection of 0.035 μg/ml and a reproducibility within day of less than 5% were obtained. These methods were applied to the determination of oxazepam in five pharmaceutical formulations.
Coordination of Human-Robot Teaming with Human Task Preferences. (2015)

Advanced robotic technology is opening up the possibility of integrating robots into the human workspace to improve pro-ductivity and decrease the strain of repetitive, arduous phys-ical tasks currently performed by human workers. However, coordinating these teams is a challenging problem. We must understand how decision-making authority over scheduling decisions should be shared between team members and how the preferences of the team members should be included. We report the results of a human-subject experiment investigat-ing how a robotic teammate should best incorporate the pref-erences of human teammates into the team’s schedule. We find that humans would rather work with a robotic teammate that accounts for their preferences, but this desire might be mitigated if their preferences come at the expense of team efficiency.
Design parameter selection in the presence of noise (1992)

The method of imprecision is a design method whereby a multi-objective design problem is resolved by maximizing the overall degree of designer preference: values are iteratively selected based on combining the degree of preference placed on them. Consider, however, design problems that exhibit multiple uncertainty forms (noise). In addition to degrees of preference (imprecision) there are probabilistic uncertainties caused by, for example, measuring and fabrication limitations. There are also parameters that can take on any value possible within a specified range, such as a manufacturing or tuning adjustment. Finally, there may be parameters which must necessarily satisfy all values within the range over which they vary, such as a horsepower requirement over a motor’s different speeds. This paper defines a “best” set of design parameters for design problems with such multiple uncertainty forms and requirements.
Importance of 2-O-Sulfate Groups of Uronate Residues in Heparin for Activation of FGF-1 and FGF-2 (1997)

Complete drying of heparin with various concentrations of NaOH by lyophilization caused specific 2-O-desulfation to various degrees without detectable depolymerization or other chemical changes. In order to assess the importance of 2-O-sulfate groups in uronate residues to promote FGF-1 and FGF-2 activities, various 2-O-desulfated (2-O-DS-) heparins were quantitatively examined for their effects on FGF-1– and FGF-2-induced proliferation of BALB/c3T3 clone A31 (A31) cells and the chlorate-treated cells. Twenty-seven percent or less loss of the 2-O-sulfate groups had no effect on the ability to activate both FGF-1 and FGF-2, while 44% loss resulted in a significant loss of the ability. Complete loss of the ability was observed in 2-O-DS-heparins with 75% or more 2-O-desulfation. These results suggest that a high content of 2-O-sulfate groups in uronate residues of heparin is required for activation of both FGF-1 and FGF-2.
Molecular Mechanisms of Ion-Specific Effects on Proteins (2012)

The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG)(120), were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN(-) and I(-) interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl(-) binds far more weakly to the amide nitrogen/α-carbon binding site, while SO(4)(2-) is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na(+) counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.
The Many Faces of Turbine Surface Roughness (2001)

Results are presented for contact stylus measurements of surface roughness on in-service turbine blades and vanes. Nearly 100 turbine components were assembled from four land-based turbine manufacturers. Both coated and uncoated, cooled and uncooled components were measured, with part sizes varying from 2 to 20cm. Spanwise and chordwise 2D roughness profiles were taken on both pressure and suction surfaces. Statistical computations were performed on each trace to determine centerline averaged roughness, rms roughness, and peak to valley height. In addition, skewness and kurtosis were calculated as well as the autocorrelation length and dominant harmonics in each trace. Extensive 3D surface maps made of deposits, pitting, erosion, and coating spallation expose unique features for each roughness type. Significant spatial variations are evidenced and transitions from rough to smooth surface conditions are shown to be remarkably abrupt in some cases. Film cooling sites are shown to be particularly prone to surface degradation.
Variabilité enzymatique des riz traditionnels malgaches Oryza sativa L. (1988)

Plus de quatre cents plantes de riz traditionnel, collectees a Madagascar, ont ete analysees par electrophorese en vue d'etudier leur polymorphisme enzymatique
Microstructure of Ferroelectric Domains inBaTiO3Observed via X-Ray Microdiffraction (2005)

X-ray microdiffraction utilizing Fresnel zone plate focusing optics has been used to study microstructural properties of individual 90\ifmmode^\circ\else\textdegree\fi{} ferroelectric domains in ${\mathrm{BaTiO}}_{3}$. Diffraction measurements at a microfocused spot resolution of $0.3\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$ over domain widths of $\ensuremath{\sim}10\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$ unambiguously reveal features of lattice buckling, rotation, and strain near domain boundaries. Our results may be understood within the context of bound residual strain due to lattice mismatch and elastic interactions between neighboring domains.
Sequence determination and comparison of the exfoliative toxin A and toxin B genes from Staphylococcus aureus (1987)

The DNA encoding the exfoliative toxin A gene (eta) of Staphylococcus aureus was cloned into bacteriophage lambda gt11 and subsequently into plasmid pLI50 on a 1,391-base-pair DNA fragment of the chromosome. Exfoliative toxin A is expressed in the Escherichia coli genetic background, is similar in length to the toxin purified from culture medium, and is biologically active in an animal assay. The nucleotide sequence of the DNA fragment containing the gene was determined. The protein deduced from the nucleotide sequence is a polypeptide of 280 amino acids. The mature protein is 242 amino acids. The DNA sequence of the exfoliative toxin B gene was also determined. Corrections indicate that the amino acid sequence of exfoliative toxin B is in accord with chemical sequence data.
One-transistor nonvolatile SRAM (ONSRAM) on silicon nanowire SONOS (2009)

A one-transistor nonvolatile SRAM (ONSRAM) on a silicon nanowire (SiNW) SONOS is demonstrated. A nonvolatile memory (NVM) property is attained by employment of O/N/O gate dielectric stacks as an electron storage node, and SRAM functionality is achieved by exploiting latch phenomena of a floating body in SiNW. Abrupt inverter switching, superior sensing current (≥21µA), and robust interference immunity between SRAM and NVM verify the feasibility for the suggested ONSRAM.
The design and implementation of PowerMill (1995)

In this paper we discuss the design and implementation of the simulator PowerMill, a novel transistor level simulator for the simulation of current and power behavior in vlsi circuits. With a new transistor modeling technology and a versatile event driven simulation algorithm, PowerMill is capable of simulating detailed current behavior in modern deep-submicron cmos circuits, including sophisticated circuitries such as exclusive-or gates and sense-ampliers, with speed and capacity approaching conventional gate level simulators. The high accuracy and speed have made it possible for designers to study and verify detailed current behavior of large functional blocks or even an entire chip with a reasonable amount of CPU resources, making it a de facto industry standard for power simulation.