gebhart/patrepeval huggingface dataset:
Compositional Grading – Theory and Practice (2000)

Abstract This paper quantifies the potential variation in composition and PVT properties with depth due to gravity, chemical, and thermal forces. A wide range of reservoir fluid systems have been studied using all of the known published models for thermal diffusion in the non-isothermal mass transport problem. Previous studies dealing with the combined effect of gravity and vertical thermal gradients on compositional grading have either been (1) of a theoretical nature, without examples from reservoir fluid systems, or (2) proposing one particular thermal diffusion model, usually for a specific reservoir, without comparing the results with other thermal diffusion models. We give a short review of gravity/non-isothermal models published to date. In particular, we show quantitative differences in the various models for a wide range of reservoir fluids systems. Solution algorithms and numerical stability problems are discussed for the non-isothermal models which require numerical discretization, unlike the exact analytical solution of the isothermal gradient problem. A discussion is given of the problems related to fluid initialization in reservoir models of complex fluid systems. This involves the synthesis of measured sample data and theoretical models. Specific recommendations are given for interpolation and extrapolation of vertical compositional gradients. The importance of dewpoint on the estimation of a gas-oil contact is emphasized, particularly for newly-discovered reservoirs where only a gas sample is available and the reservoir is near saturated. Finally, we present two field case histories – one where the isothermal gravity/chemical equilibrium model describes measured compositional gradients in a reservoir grading continuously from a rich gas condensate to a volatile oil; and another example where the isothermal model is grossly inconsistent with measured data, and convection has apparently resulted in a more-or-less constant composition over a vertical column of nearly 5000 ft.
Selective Synthesis of Conjugated Enynes from α‐Arylalkynols Using LiCl‐Acidic Al2O3 under Solvent‐Free Conditions. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Automatic garage door openers: hazard for children. (1996)

Automatic garage door openers pose a serious risk of severe injury or death to children. It is probable that many doors would not reverse if they came down on a young child. Therefore, we have devised a way for homeowners to test their door openers that closely mimics our evaluations using the mannequin by using a large roll of paper towels. If the door fails to reverse using this test, we suggest that homeowners disconnect their openers and operate the doors manually until the openers are serviced or replace their automatic openers with one that meets the latest Underwriters Laboratory standards. We also have other recommendations regarding the safe operation of the doors, including improving the safety standards for openers in apartment complexes. Compliance with these recommendations should reduce the number of injuries to children caused by garage door openers.
Influence of the Solvent in the Synthesis of Osmium Complexes Containing Cyclopentadienyl Ligands with a Pendant Donor Group (2004)

The course of the reactions between complex OsH2Cl2(PiPr3)2 (1) and the functionalized cyclopentadienyllithium derivatives Li[C5H4(CH2)2E] (E = NMe2 (2), OMe (3)) strongly depends on the solvent used. Thus, in the presence of donor solvents such as THF, the salts [OsH2{η5-C5H4(CH2)2E}(PiPr3)2][OsHCl2(CO)(PiPr3)2] (E = NMe2 [4][5], OMe [6][5]) with a carbonylated osmium anion are produced, while in hydrocarbon solvents the chloride salts [OsH2{η5-C5H4(CH2)2E}(PiPr3)2]Cl (E = NMe2 [4]Cl, OMe [6]Cl) are formed.
Solvent-Dictated Sodium Sulfur Redox Reactions: Investigation of Carbonate and Ether Electrolytes (2020)

Sulfur-based cathode chemistries are essential for the development of high energy density alkali-ion batteries. Here, we elucidate the redox kinetics of sulfur confined on carbon nanotubes, comparing its performance in ether-based and carbonate-based electrolytes at room temperature. The solvent is found to play a key role for the electrochemical reactivity of the sulfur cathode in sodium–sulfur (Na–S) batteries. Ether-based electrolytes contribute to a more complete reduction of sulfur and enable a higher electrochemical reversibility. On the other hand, an irreversible solution-phase reaction is observed in carbonate solvents. This study clearly reveals the solvent-dependent Na–S reaction pathways in room temperature Na–S batteries and provides an insight into realizing their high energy potential, via electrolyte formulation design.
[Visual field disturbances in epileptic patients treated with vigabatrin (sevril)]. (2002)

Vigabatrin, one of the newer anti-epileptic drugs (AED), whose effect is mediated via elevated levels of brain GABA, has proved to be effective in drug resistant partial seizures and infantile spasms. Recently, visual field constriction was found in up to 30% of adults, whereas information for the pediatric age group is sparse. We examined 24 visually-asymptomatic children, ages 3.5-18 years, treated for 3.01.6 years at doses of 25-90 mg/kg. These children underwent an ophthalmologic examination, visual evoked potentials, electroretinogram and when possible, perimetry. Over half of the children had at least one abnormal test and 11/17, who were able to undergo perimetric studies, had symmetrical, nasal visual field constriction. In view of the gravity and prevalence of visual field constriction, use of the AED vigabatrin should be weighed against its clinical benefits.
Trends and Exceptions of Physical Properties on Antibacterial Activity for Gram-Positive and Gram-Negative Pathogens (2014)

To better understand the difficulties surrounding the identification of novel antibacterial compounds from corporate screening collections, physical properties of ∼3200 antibacterial project compounds with whole cell activity against Gram-negative or Gram-positive pathogens were profiled and compared to actives found from high throughput (HTS) screens conducted on both biochemical and phenotypic bacterial targets. The output from 23 antibacterial HTS screens illustrated that when compared to the properties of the antibacterial project compounds, the HTS actives were significantly more hydrophobic than antibacterial project compounds (typically 2-4 log units higher), and furthermore, for 14/23 HTS screens, the average clogD was higher than the screening collection average (screening collection clogD = 2.45). It was found that the consequences of this were the following: (a) lead identification programs often further gained hydrophobic character with increased biochemical potency, making the separation even larger between the physicochemical properties of known antibacterial agents and the HTS active starting point, (b) the probability of plasma protein binding and cytotoxicity are often increased, and (c) cell-based activity in Gram-negative bacteria was severely limited or, if present, demonstrated significant efflux. Our analysis illustrated that compounds least susceptible to efflux were those which were highly polar and small in MW or very large and typically zwitterionic. Hydrophobicity was often the dominant driver for HTS actives but, more often than not, precluded whole cell antibacterial activity. However, simply designing polar compounds was not sufficient for antibacterial activity and pointed to a lack of understanding of complex and specific bacterial penetration mechanisms.
The application of Raman spectroscopy for the detection and identification of microorganisms (2015)

A fast and reliable detection and identification of microorganisms is crucial in environmental science, for food quality as well as medical diagnosis. In these fields, all types of Raman spectroscopy are gaining more and more importance during the last years. The review provides an extensive overview of recent research, technical expertise, and scientific findings based on Raman spectroscopic detection and identification of microorganisms within the years 2010 and 2015, demonstrating the diverse capability of Raman spectroscopy as a modern analytical tool. Raman spectroscopy distinguishes itself from other currently applied techniques by its easy application at low cost, its high speed of analysis, and its broad information content on both the chemical composition and the structure of biomolecules within the microorganisms. Slight chances in the chemical composition of microorganisms can be monitored by means of Raman spectroscopy and used to differentiate genera, species, or even strains. Detection of pathogens is possible from complex matrices, such as soil, food, and body fluids. Further, spectroscopic studies of host–pathogen interactions are addressed as well as the effect of antibiotics on bacteria. Copyright © 2015 John Wiley &amp; Sons, Ltd.
The level of HER2 expression is a predictor of antibody-HER2 trafficking behavior in cancer cells (2014)

The receptor tyrosine kinase HER2 is known to play a central role in mitogenic signaling, motivating the development of targeted, HER2-specific therapies. However, despite the longstanding use of antibodies to target HER2, controversies remain concerning antibody/HER2 trafficking behavior in cancer cells. Understanding this behavior has direct relevance to the mechanism of action and effective design of such antibodies. In the current study, we analyzed the intracellular dynamics of trastuzumab, a marketed HER2-targeting antibody, in a panel of breast and prostate cancer cell lines that have a wide range of HER2 expression levels. Our results reveal distinct post-endocytic trafficking behavior of antibody-HER2 complexes in cells with different HER2 expression levels. In particular, HER2-overexpressing cells exhibit efficient HER2 recycling and limited reductions in HER2 levels upon antibody treatment, and consequently display a high level of antibody persistence on their plasma membrane. By contrast, in cells with low HER2 expression, trastuzumab treatment results in rapid antibody clearance from the plasma membrane combined with substantial decreases in HER2 levels and undetectable levels of recycling. A cell line with intermediate levels of HER2 expression exhibits both antibody recycling and clearance from the cell surface. Significantly, these analyses demonstrate that HER2 expression levels, rather than cell origin (breast or prostate), is a determinant of subcellular trafficking properties. Such studies have relevance to optimizing the design of antibodies to target HER2.
Mesenchymal stem cells that produce neurotrophic factors reduce ischemic damage in the rat middle cerebral artery occlusion model (2004)

Mesenchymal stem cells (MSC) were reported to ameliorate functional deficits after stroke in rats, with some of this improvement possibly resulting from the action of cytokines secreted by these cells. To enhance such cytokine effects, we previously transfected the telomerized human MSC with the BDNF gene using a fiber-mutant adenovirus vector and reported that such treatment contributed to improved ischemic recovery in a rat transient middle cerebral artery occlusion (MCAO) model. In the present study, we investigated whether other cytokines in addition to BDNF, i.e., GDNF, CNTF, or NT3, might have a similar or greater effect in this model. Rats that received MSC-BDNF (P < 0.05) or MSC-GDNF (P < 0.05) showed significantly more functional recovery as demonstrated by improved behavioral test results and reduced ischemic damage on MRI than did control rats 7 and 14 days following MCAO. On the other hand, rats that received MSC-CNTF or MSC-NT3 showed neither functional recovery nor ischemic damage reduction compared to control rats. Thus, MSC transfected with the BDNF or GDNF gene resulted in improved function and reduced ischemic damage in a rat model of MCAO. These data suggest that gene-modified cell therapy may be a useful approach for the treatment of stroke.
Anomaly detection in radiation signals using kernel machine intelligence (2015)

Acquisition of consecutive ultra-short interval measurements with a radiation detector serves in detecting anomalies in the ambient environment, potentially caused by hidden radioactive material. An anomaly is defined as the contribution of a man-made radiation source to the measured signal. In this paper a new methodology is presented and tested on detecting anomalies in various radiation signals. The methodology employs machine intelligence tools to perform automated detection of malignant source contribution. In particular, a Gaussian process (GP) modeled as a function of a learning kernel is used for post-processing of measured signals. For detection purposes, a window that slides over the measured signal is divided into three parts, where the two parts are used for training the GP that is subsequently used for predicting the values of the third part. Next, a comparison between predicted and measured values in the third part is conducted by computing the mean average percentage error (MAPE). If MAPE is relatively high, then the likelihood of an anomaly in the part under examination is respectively high. Adoption of a sliding window ensures that no part of signal will remain unchecked. Testing results obtained on a set of gamma-ray signals exhibit the potency of the presented methodology in effectively detecting anomalies.
A Novel, Highly Efficient Catalyst for Propane Dehydrogenation (2001)

Platinum and tin deposited on a calcined hydrotalcite constitute a new and highly efficient catalyst for the dehydrogenation of propane. The catalyst is superior to conventional alumina-supported systems in terms of lifetime stability, activity, and propene selectivity. The catalysts were characterized by BET, XRD, SEM, TEM, CO chemisorption, and chemical analysis. The preparation procedure used in the metal deposition step proved to be important for the performance of the catalyst. Impregnation of the calcined hydrotalcite in HCl-acidified aqueous solution with subsequent chlorine removal enhances regenerability and long-term stability of the catalyst compared to impregnation in ethanol. This is most likely due to a water-induced phase transition in the hydrated hydrotalcite. CO adsorption results indicate that activation is correlated with platinum dispersion.
RNA-Seq analyses of immune cell-type enrichments in 158 Asian colorectal cancers (CRCs). (2018)

e15597 Background: Responses to anti-PD1 is ~35% in microsatellite unstable (MSI-h) and near 0% in microsatellite stable (MSS) Colorectal cancer (CRC). Understanding the composition of immune cell populations in the tumor microenvironment of CRC is crucial to developing effective immunotherapeutic strategies in CRC. Methods: We performed whole genome sequencing (WGS) (60x tumor, 30x normal) and deep whole transcriptomic sequencing (RNA-Seq) (∼200x106 reads per tumor) on 158 fresh frozen (FF) colorectal cancers tumors, of which 32 are microsatellite instability high (MSI-H) tumours and 126 are microsatellite stable (MSS). We evaluated immune cell composition with 2 computational algorithms, MCP-counter (Becht et al., 2016) relying on counts of cell-type specific transcriptomic markers and an RNA deconvolution method based on immune-signature enrichment, tumor purity and a comparison with a pan-tumor transcriptomic database. We also performed RNA-Seq on FFPE tissue from amongst 20 patients (9 MSI-H, 11 MSS). Results: Immune cell enrichment scores by both methods correlated well with each other (R2 values for T cells: 0.81 NK: 0.43 B cells: 0.83monocytes: 0.59, neutrophils: 0.45). MSI-H & POLE mutant tumors had increased CD8, macrophage, NK, Th1,Th2, Tmem & aDC immune cell enrichment compared with MSS tumors. Amongst MSS tumors, immune cell enrichment patterns were not found to be clearly associated with mutational burden nor tumor sidedness. A subset of tumors were found to exhibit T-helper & in particular T-h2 immune cell enrichment. With RNASeq from FFPE, tumor enrichment scores were found to correlate with scores derived from matched FF-RNASeq. Conclusions: We evaluated immune cell compositions with computational cell type enrichment/deconvolution methodologies in RNASeq of a large cohort of Asian CRCs. Subset of tumors with distinct immune cell composition patterns were identified. These analyses could be reproduced using FFPE RNA-Seq potentially being extendible to large retrospective clinical trial cohorts.
ChemInform Abstract: Synthesis and Halogenolysis of Stable Pentacoordinate Bismuth Compounds (10‐Bi‐5): Formation of 1‐Chloro‐1,1‐diaryl‐3,3‐bis(trifluoromethyl)‐3H‐2,1‐benzoxabismoles. (1989)

Abstract The triarylbismuth dihalides (II) react with the dilithio compound (I) to give the benzoxabismoles (III).
Importance of the Cyanobacterial Gun4 Protein for Chlorophyll Metabolism and Assembly of Photosynthetic Complexes (2008)

Gun4 is a porphyrin-binding protein that activates magnesium chelatase, a multimeric enzyme catalyzing the first committed step in chlorophyll biosynthesis. In plants, GUN4 has been implicated in plastid-to-nucleus retrograde signaling processes that coordinate both photosystem II and photosystem I nuclear gene expression with chloroplast function. In this work we present the functional analysis of Gun4 from the cyanobacterium Synechocystis sp. PCC 6803. Affinity co-purification of the FLAG-tagged Gun4 with the ChlH subunit of the magnesium chelatase confirmed the association of Gun4 with the enzyme in cyanobacteria. Inactivation of the gun4 gene abolished photoautotrophic growth of the resulting gun4 mutant strain that exhibited a decreased activity of magnesium chelatase. Consequently, the cellular content of chlorophyll-binding proteins was highly inadequate, especially that of proteins of photosystem II. Immunoblot analyses, blue native polyacrylamide gel electrophoresis, and radiolabeling of the membrane protein complexes suggested that the availability of the photosystem II antenna protein CP47 is a limiting factor for the photosystem II assembly in the gun4 mutant.
Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant (2021)

Interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the receptor ACE2 on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies, and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, N-terminal domain (NTD) and S2 subunits of Spike. To understand how these mutations affect Spike antigenicity, we isolated and characterized >100 monoclonal antibodies targeting epitopes on RBD, NTD, and S2 from SARS-CoV-2-infected individuals. Approximately 45% showed neutralizing activity, of which ∼20% were NTD specific. NTD-specific antibodies formed two distinct groups: the first was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Mutations present in B.1.1.7 Spike frequently conferred neutralization resistance to NTD-specific antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes should be considered when investigating antigenic drift in emerging variants.
Advanced coding techniques for asynchronous fiber-optical CDMA (2005)

We develop new coding methods for asynchronous optical CDMA systems with increased spectral efficiency and better BER performance. Furthermore, our approach allows random variations of the transmission rate, thus improving the physical level security.
Eyeriss: An Energy-Efficient Reconfigurable Accelerator for Deep Convolutional Neural Networks (2016)

Eyeriss is an accelerator for state-of-the-art deep convolutional neural networks (CNNs). It optimizes for the energy efficiency of the entire system, including the accelerator chip and off-chip DRAM, for various CNN shapes by reconfiguring the architecture. CNNs are widely used in modern AI systems but also bring challenges on throughput and energy efficiency to the underlying hardware. This is because its computation requires a large amount of data, creating significant data movement from on-chip and off-chip that is more energy-consuming than computation. Minimizing data movement energy cost for any CNN shape, therefore, is the key to high throughput and energy efficiency. Eyeriss achieves these goals by using a proposed processing dataflow, called row stationary (RS), on a spatial architecture with 168 processing elements. RS dataflow reconfigures the computation mapping of a given shape, which optimizes energy efficiency by maximally reusing data locally to reduce expensive data movement, such as DRAM accesses. Compression and data gating are also applied to further improve energy efficiency. Eyeriss processes the convolutional layers at 35 frames/s and 0.0029 DRAM access/multiply and accumulation (MAC) for AlexNet at 278 mW (batch size N = 4), and 0.7 frames/s and 0.0035 DRAM access/MAC for VGG-16 at 236 mW (N = 3).