gebhart/patrepeval huggingface dataset:
Atomic Layer Deposition of Vanadium Dioxide and a Temperature-dependent Optical Model (2018)

Vanadium dioxide is a material that has a reversible metal-insulator phase change near 68 °C. To grow VO2 on a wide variety of substrates, with wafer-scale uniformity and angstrom level control of thickness, the method of atomic-layer deposition was chosen. This ALD process enables high-quality, low-temperature (≤150 °C) growth of ultrathin films (100-1000 Å) of VO2. For this demonstration, the VO2 films were grown on sapphire substrates. This low temperature growth technique produces mostly amorphous VO2 films. A subsequent anneal in an ultra-high vacuum chamber with a pressure of 7x10<sup>-4</sup> Pa of ultra-high purity (99.999%) oxygen produced oriented, polycrystalline VO2 films. The crystallinity, phase, and strain of the VO2 were determined by Raman spectroscopy and X-ray diffraction, while the stoichiometry and impurity levels were determined by X-ray photoelectron spectroscopy, and finally the morphology was determined by atomic force microscopy. These data demonstrate the high-quality of the films grown by this technique. A model was created to fit to the data for VO2 in its metallic and insulating phases in the near infrared spectral region. The permittivity and refractive index of the ALD VO2 agreed well with the other fabrication methods in its insulating phase, but showed a difference in its metallic state. Finally, the analysis of the films' optical properties enabled the creation of a wavelength- and temperature-dependent model of the complex optical refractive index for developing VO2 as a tunable refractive index material.
PD-1 Blockade and CD27 Stimulation Activate Distinct Transcriptional Programs That Synergize for CD8+ T-Cell–Driven Antitumor Immunity (2018)

<b>Purpose:</b> PD-1 checkpoint blockade has revolutionized the field of cancer immunotherapy, yet the frequency of responding patients is limited by inadequate T-cell priming secondary to a paucity of activatory dendritic cells (DC). DC signals can be bypassed by CD27 agonists, and we therefore investigated if the effectiveness of anti-PD-1/L1 could be improved by combining with agonist anti-CD27 monoclonal antibodies (mAb).<b>Experimental Design:</b> The efficacy of PD-1/L1 blockade or agonist anti-CD27 mAb was compared with a dual-therapy approach in multiple tumor models. Global transcriptional profiling and flow cytometry analysis were used to delineate mechanisms underpinning the observed synergy.<b>Results:</b> PD-1/PD-L1 blockade and agonist anti-CD27 mAb synergize for increased CD8<sup>+</sup> T-cell expansion and effector function, exemplified by enhanced IFNγ, TNFα, granzyme B, and T-bet. Transcriptome analysis of CD8<sup>+</sup> T cells revealed that combination therapy triggered a convergent program largely driven by IL2 and Myc. However, division of labor was also apparent such that anti-PD-1/L1 activates a cytotoxicity-gene expression program whereas anti-CD27 preferentially augments proliferation. In tumor models, either dependent on endogenous CD8<sup>+</sup> T cells or adoptive transfer of transgenic T cells, anti-CD27 mAb synergized with PD-1/L1 blockade for antitumor immunity. Finally, we show that a clinically relevant anti-human CD27 mAb, varlilumab, similarly synergizes with PD-L1 blockade for protection against lymphoma in human-CD27 transgenic mice.<b>Conclusions:</b> Our findings suggest that suboptimal T-cell invigoration in cancer patients undergoing treatment with PD-1 checkpoint blockers will be improved by dual PD-1 blockade and CD27 agonism and provide mechanistic insight into how these approaches cooperate for CD8<sup>+</sup> T-cell activation. <i>Clin Cancer Res; 24(10); 2383-94. ©2018 AACR</i>.
Functional Precision Medicine Provides Clinical Benefit in Advanced Aggressive Hematologic Cancers and Identifies Exceptional Responders (2021)

Personalized medicine aims to match the right drug with the right patient by using specific features of the individual patient's tumor. However, current strategies of personalized therapy matching provide treatment opportunities for less than 10% of patients with cancer. A promising method may be drug profiling of patient biopsy specimens with single-cell resolution to directly quantify drug effects. We prospectively tested an image-based single-cell functional precision medicine (scFPM) approach to guide treatments in 143 patients with advanced aggressive hematologic cancers. Fifty-six patients (39%) were treated according to scFPM results. At a median follow-up of 23.9 months, 30 patients (54%) demonstrated a clinical benefit of more than 1.3-fold enhanced progression-free survival compared with their previous therapy. Twelve patients (40% of responders) experienced exceptional responses lasting three times longer than expected for their respective disease. We conclude that therapy matching by scFPM is clinically feasible and effective in advanced aggressive hematologic cancers. SIGNIFICANCE: This is the first precision medicine trial using a functional assay to instruct n-of-one therapies in oncology. It illustrates that for patients lacking standard therapies, high-content assay-based scFPM can have a significant value in clinical therapy guidance based on functional dependencies of each patient's cancer.<i>See related commentary by Letai, p. 290</i>.<i>This article is highlighted in the In This Issue feature, p. 275</i>.
ChemInform Abstract: Serendipitous Synthesis of N‐Tetrachlorophthaloyldehydroalanine Methyl Ester, a Michael Acceptor which is a Potential Precursor of γ‐Carboxyglutamic Acid. (1999)

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.
Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data (2019)

Supplementary material is available at Bioinformatics online.
Electronic and optical applications of diamond-like carbon (1993)

In this contribution emphasis is placed on examining the electronic and optical properties of a-C and a-C:H in their own right as those belonging to an amorphous semiconductor. It is shown that the electronic density of states in semiconducting a-C and a-C:H is very different from that of other group IV amorphous semiconductors due to the presence of pi states associated with sp/sup 2/ hybridised bonds. Even in tetrahedral amorphous carbon (ta-C) with sp/sup 3/ bonding of up to 70-80%, the pi and pi * states tend to determine the electronic and optical properties. Such pi states are of course not present in diamond. This is in contrast to the mechanical properties of ta-C which can be very close to those of diamond. The presence of pi bonding (in addition to the sigma bonding) gives a-C and a-C:H some advantageous properties compared to a-Si and a-Ge. Passive use of a-C and a-C:H in applications such as IR windows and passivation layers and their potential for active use as electronic materials in optoelectronic devices are discussed. As examples of the latter, use of doped ta-C as a wide band-gap material with Si for heterojunctions and a-C:H in band-gap modulated amorphous superlattices are examined.
Cloning of the human homologue of the GABA transporter GAT-3 and identification of a novel inhibitor with selectivity for this site. (1994)

Molecular cloning has revealed the presence of four high-affinity GABA transporters in the brain. The existence of three of these sites, GAT-2, GAT-3, and BGT-1, was unknown prior to their cloning and almost nothing is known of the role they play in regulating GABAergic transmission. In large measure our paucity of knowledge is attributable to the lack of specific inhibitors for these sites. In the present communication we describe the cloning and expression of the human homologue of GAT-3, and the identification of an inhibitor, (S)-SNAP-5114, with selectivity for this site. (S)-SNAP-5114 displays an IC50 of 5 microM at GAT-3, 21 microM at GAT-2, and > or = 100 microM at GAT-1 and BGT-1. Due to its lipophilicity, (S)-SNAP-5114 is also expected to cross the blood-brain-barrier and therefore, should be an important tool for evaluating the role of GAT-3 in neural function.
Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum (2013)

This study is the first example of an engineered thermophile heterologously expressing a structural component of a cellulosome. To achieve this goal we developed and tested an inducible promoter for controlled expression in T. saccharolyticum as well as a synthetic cipA. In addition, we demonstrate a high degree of hydrolysis (up to 93%) on microcrystalline cellulose.
cis-2,2-Dimethyl-1,3-diphenyl-2,3-dihydro-1H-benzo[c]silole (2007)

The title compound, C22H22Si, is a benzosilacyclo­pentene in which the silacyclo­pentene ring assumes an envelope conformation. The Si atom is displaced by 0.722 (4) Å from the mean plane of the four C atoms, and is bonded to two methyl groups and to two Csp3 atoms in the silacyclo­pentene ring. One phenyl ring is attached to each of these two C atoms in a cis configuration. The Si atom and the two methyl groups lie on a crystallographic mirror plane which relates the two halves of the molecule. The average Si—Cmeth­yl bond distance is 1.852 (3) Å. The Si—Csp3 bond distance is 1.886 (2) Å, and the corresponding Csp3—Si—Csp3 angle is 93.0 (1)°. The displacement ellipsoids for the atoms in the fused benzene ring suggest a probable disorder, but no satisfactory disorder model could be found.
Analysis of Direct Air Capture Integrated with Wind Energy and Enhanced Oil Recovery (2023)

Direct air capture (DAC) is a decarbonization solution to remove carbon dioxide (CO<sub>2</sub>) from the atmosphere. The key challenges for accelerating DAC deployment are its energy requirements, high capital costs, and finding low-risk and low-cost sequestration or utilization pathways. Deploying DAC facilities proximal to sequestration or use sites and where the supply of low-cost renewable electricity is plentiful can minimize the energy, transportation, operational, and overall costs. Moreover, the increased 45Q tax credits in the Inflation Reduction Act of 2022 can further incentivize DAC deployment. This work provides a techno-economic assessment of two configurations: temperature swing adsorption-based DAC and membrane-based DAC integrated for operation with wind energy in West Texas to provide proximal access to enhanced oil recovery (EOR) operations. We evaluate the levelized cost of DAC and the cumulative cost of sequestering a ton of CO<sub>2</sub> through EOR to identify opportunities for economic viability. Finally, we determine the profitability of CO<sub>2</sub> sequestration under different EOR recovery factors and oil prices. We find that opportunities to reduce costs through proximal sequestration, integration with renewable energy, and the current level of policy support in the US can significantly incentivize and rapidly accelerate the deployment of DAC, especially for membrane-based technologies.
Structural basis of hepatitis C virus neutralization by broadly neutralizing antibody HCV1 (2012)

Hepatitis C virus (HCV) infects more than 2% of the global population and is a leading cause of liver cirrhosis, hepatocellular carcinoma, and end-stage liver diseases. Circulating HCV is genetically diverse, and therefore a broadly effective vaccine must target conserved T- and B-cell epitopes of the virus. Human mAb HCV1 has broad neutralizing activity against HCV isolates from at least four major genotypes and protects in the chimpanzee model from primary HCV challenge. The antibody targets a conserved antigenic site (residues 412-423) on the virus E2 envelope glycoprotein. Two crystal structures of HCV1 Fab in complex with an epitope peptide at 1.8-Å resolution reveal that the epitope is a β-hairpin displaying a hydrophilic face and a hydrophobic face on opposing sides of the hairpin. The antibody predominantly interacts with E2 residues Leu(413) and Trp(420) on the hydrophobic face of the epitope, thus providing an explanation for how HCV isolates bearing mutations at Asn(415) on the same binding face escape neutralization by this antibody. The results provide structural information for a neutralizing epitope on the HCV E2 glycoprotein and should help guide rational design of HCV immunogens to elicit similar broadly neutralizing antibodies through vaccination.
Follicular lymphoma prognostic factors in the modern era: what is clinically significant? (2011)

Les lymphomes folliculaires representent 25 a 30 % des lymphomes non hodgkiniens. Ils ont une evolution souvent lente mais heterogene avec, d’une part, des risques de rechutes repetees et de moins en moins sensibles aux traitements et, d’autre part, une possible transformation en un lymphome agressif de mauvais pronostic. Evaluer des le diagnostic ces risques evolutifs permet de proposer au malade le traitement le plus adapte parmi les tres nombreuses approches envisageables. Dans ce but, il a ete propose depuis quelques annees des index pronostiques cliniques specifiques, d’abord l’index FLIPI 1 (Follicular Lymphoma International Prognostic Index) portant sur la survie globale et, plus recemment, l’index FLIPI2 portant sur la survie sans progression. Le pouvoir discriminant de l’index FLIPI1 a ete confirme dans de multiples etudes retrospectives et prospectives. Ces analyses de confirmation sont en cours pour l’index FLIPI2. Ces index cliniques ne peuvent rendre compte seuls de l’heterogeneite evolutive des lymphomes folliculaires. Ils ont donc ete completes par des analyses pronostiques biologiques. Les etudes de signatures geniques ont d’abord montre que le pronostic ne dependait pas de la signature des cellules tumorales mais de celle des multiples cellules du micro-environnement : cellules T, macrophages, cellules folliculaires dendritiques, etc. Les resultats des etudes immunohistochimiques de ce micro-environnement se sont averes contradictoires rendant actuellement impossible l’elaboration d’un modele biologique pronostique fiable utilisable en pratique clinique. Les interactions entre cellules tumorales et micro-environnement restent donc a preciser, tâche d’autant plus complexe que les traitements modifient profondement ces interactions.
Force Sensorless Fine Force Control Based on Notch-Type Friction-Free Disturbance Observers (2018)

In order to realize force sensorless fine force control, this paper proposes a new notch-type friction-free disturbance observer (DOB) and a new notch-type friction-free reaction force observer (FFRFO). Generally, a force sensorless force control system is always influenced by the static friction phenomenon. In order to suppress the estimation error due to static friction, a force sensorless force control system uses a dither signal, and a friction free reaction force observer (FFRFO) is used to consider this dither signal. Since the high frequency gain charactheristics of conventional FFRFO are significantly higher than 0dB, the entire force control system sometimes becomes unstable or produces oscillating responses. To overcome this problem, this paper proposes a new force sensorless control system using the notch-type friction free reaction force observer, whose inner system is the proposed acceleration control based on the notch-type friction free disturbance observer. The effectiveness of the proposed system is confirmed by experiments using an actual industrial robot.
Use of triolein-semipermeable membrane devices to assess the bioconcentration and sediment sorption of hydrophobic organic contaminants in the Huaihe River, China (2002)

Triolein-containing semipermeable membrane devices (triolein-SPMD) were deployed I m above the sediments at two sampling sites in the Huaihe River, China, for a period of 28 d. Sediment and fish samples were simultaneously collected from the same sampling sites. Concentrations of substituted benzenes, selected pesticides, polycyclic aromatic hydrocarbon (PAH), and polychlorinated biphenyls (PCBs) were measured in triolein-SPMDs, sediments, and fishes. The concentrations of these hydrophobic organic contaminants (HOCs) in fish and in sediment organic carbon were correlated with HOCs accumulation in triolein-SPMDs. Our results showed reasonably good correlations between the log concentrations of contaminants in fish lipid and in triolein-SPMDs. Good correlations were also found between the log concentrations of contaminants in sediment organic carbon and in triolein-SPMDs (except for PAHs). The results were discussed in terms of the partitioning of hydrophobic organic contaminants among different compartments in the aquatic environment and the suitability of using triolein-SPMDs to predict bioconcentration factor (BCF) and sediment-water partitioning coefficient (K(oc)).
Effects of tetracycline on water quality, soil and gases in aerated and unaerated leachfield mesocosms (2008)

We examined the effects of tetracycline (TET) addition on the function of mesocosms representing aerated and unaerated septic system leachfields. Replicate mesocosms (n = 3) were filled with soil and either vented to a leachfield (LEACH) or aerated intermittently to maintain an O(2) level of approximately 0.21 mol mol(-1) (AIR). All mesocosms were dosed every 6 h for 10 d with 3 cm of domestic wastewater amended with 5 mg TET L(-1). Water quality parameters, headspace gas composition, and soil properties were measured prior to and during the dosing period, and for 42 days after the last antibiotic dose. No significant effect of TET was observed on the pH, level of dissolved O(2) or dissolved organic carbon (DOC) in drainage water from either treatment. In contrast, levels of Fe(2+) and SO(4) in drainage water from LEACH mesocosms decreased in response to TET dosing, with lower levels persisting until Day 52. Persistent increases were observed in the level of NO(3) in drainage water from AIR lysimeters and in NH(4) in LEACH mesocosms in response to TET additions. Removal of total P and DOC were unaffected by TET dosing in either treatment. Nitrogen removal in AIR mesocosms decreased during the TET dosing period, returning to pre-dosing values by Day 52. In contrast, TN removal in LEACH mesocosms increased during TET dosing, returning to pre-dosing values by Day 52. The composition of headspace gases in AIR mesocosms was not affected by tetracycline dosing. TET dosing resulted in significant increases in soil NH(4) concentration in LEACH mesocosms, whereas significant decreases were apparent in AIR mesocosms. Elevated levels of H(2)S and CH(4) in the headspace of LEACH mesocosms coincided with TET dosing and returned to pre-dosing levels when antibiotic dosing ceased. The effects of tetracycline on leachfield mesocosms differed as a function of aeration. Although most effects were transient, with values returning to pre-dosing levels after a 6-week recovery period in both treatments, persistent effects were observed in LEACH mesocosms.
Electrophoresis in Nanochannels (2006)

Micro- and nanofabrication technology enables the application of electrokinetics as a method of performing chemical analyses and achieving liquid pumping in electronically-controlled microchip systems with no moving parts. We are studying and leveraging the unique separation modalities offered by nanoscale electrokinetic channels. We report analytical, numerical, and experimental investigations of nanochannel electrophoretic transport and separation dynamics of neutral and charged analytes. Our study includes continuum-theory-based analytical and numerical studies of nanofluidic electrophoretic separation dynamics, as well as experimental validation of these models. We have used 40, 100, and 1,560 nm deep channels etched in fused silica to independently measure mobility and valence of small ions. We also use these devices to separate 10 to 100 base pair DNA in the absence of a gel separation matrix. The effective free-solution mobilities of the ds-DNA oligonucleotides measured in 1560 nm deep channel are consistent with reported literature values, while smaller values of the mobility were measured for 4o nm deep channels for the same charge-species. The goal of our work is to explore and exploit electrokinetic flow regimes with extreme scales of length and charge density.
Selective Synthesis of Renewable Bio-Jet Fuel Precursors from Furfural and 2-Butanone via Heterogeneously Catalyzed Aldol Condensation (2023)

This study aims to synthesize α,β-unsaturated carbonyl compounds with branched structures via aldol condensation of furfural and 2-butanone using magnesium–aluminum (MgAl) mixed oxides as heterogeneous acid–base catalysts. Regarding the molecular structure of 2-butanone, there are two possible enolate ions generated by subtracting the α-hydrogen atoms at the methyl or methylene groups of 2-butanone. The branched-chain C9 products, derived from the methylene enolate ion, can be applied as bio-jet fuel precursors. The most suitable catalyst, contributing the highest furfural conversion (63%) and selectivity of the branched-chain C9 products (77%), is LDO3, the mixed oxides with 3:1 Mg:Al atomic ratio, with a high surface area and a large number of medium basic sites. The suitable reaction conditions to produce the branched-chain C9 ketones are 1:5 furfural:2-butanone molar ratio, 5 wt.% catalyst loading, 120 °C reaction temperature, and 8 h reaction time. Additionally, this study investigates the adsorption of 2-butanone onto a mixed oxide using in situ Fourier transform infrared spectroscopy; the results of which suggest that the methylene enolate of 2-butanone is the likely dominant surface intermediate at elevated temperatures. Accordingly, the calculation, based on density functional theory, indicates that the methylene enolate ion of 2-butanone is the kinetically favorable intermediate on an MgO(100) as a model oxide surface.