gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Asymmetric Construction of the Azaspiro[5.5]undec‐8‐ene System Towards Gymnodimine Synthesis. (2002)

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.
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis (2022)

The kidney plays a critical role in excreting ammonia during metabolic acidosis and liver failure. The mechanisms behind this process have been poorly explored. The present study combines results of in vivo experiments of increased total ammoniagenesis with systems biology modeling, in which eight rats were fed an amino acid-rich diet (HD group) and eight a normal chow diet (AL group). We developed a method based on elementary mode analysis to study changes in amino acid flux occurring across the kidney in increased ammoniagenesis. Elementary modes represent minimal feasible metabolic paths in steady state. The model was used to predict amino acid fluxes in healthy and pre-hyperammonemic conditions, which were compared to experimental fluxes in rats. First, we found that total renal ammoniagenesis increased from 264 ± 68 to 612 ± 87 nmol (100 g body weight)<sup>-1</sup> min<sup>-1</sup> in the HD group (P = 0.021) and a concomitated upregulation of NKCC2 ammonia and other transporters in the kidney. In the kidney metabolic model, the best predictions were obtained with ammonia transport as an objective. Other objectives resulting in a fair correlation with the measured fluxes (correlation coefficient >0.5) were growth, protein uptake, urea excretion, and lysine and phenylalanine transport. These predictions were improved when specific gene expression data were considered in HD conditions, suggesting a role for the mitochondrial glycine pathway. Further studies are needed to determine if regulation through the mitochondrial glycine pathway and ammonia transporters can be modulated and how to use the kidney as a therapeutic target in hyperammonemia.
Photodegradation of Surfactants XVII Photo-oxidation Processes in Amphoteric Surfactants Catalyzed by Irradiated TiO2 Suspensions (1996)

Abstract Differences in photocatalytic degradations arising from oxidative cleavage of a peptide bond and a quaternary nitrogen moiety in a TiO
Phenoxyphenyl Alkoxyiminoacetamides (1995)

A number of substituted phenoxyphenyl alkoxyiminoacetamides were synthesized and their fungicidal activities against economically important plant diseases were examined. Our studies on the structure-activity relationships revealed that fungicidal activity was the strongest when the substituent of the oxyimino moiety was methyl and the acetamide moiety was mono-methylamide. The phenoxy group on the phenylacetamide moiety attached to the 2-position of benzene ring gave the highest activity. Introduction of various substituents on the benzene ring of the phenylacetamide moiety besides the 2-phenoxy group resulted in reduction of the fungicidal activity. However, introduction of some substituents on the phenoxy moiety increased the activity to the same extent as the unsubstituted lead compound. Among the compounds of the series, SSF-126, (E)-2-methoxyimino-N-methyl-2-(2-phenoxyphenyl)acetamide was selected as a new candidate fungicide for rice diseases because of its high activity and safety to mammals, fishes and plants.
Construction of a Highly Sensitive Thiol‐Reactive AIEgen‐Peptide Conjugate for Monitoring Protein Unfolding and Aggregation in Cells (2021)

Impairment of the protein quality control network leads to the accumulation of unfolded and aggregated proteins. Direct detection of unfolded protein accumulation in the cells may provide the possibility for early diagnosis of neurodegenerative diseases. Here a new platform based on a peptide-conjugated thiol-reactive aggregation-induced emission fluorogen (AIEgen), named MI-BTD-P (or D1), for labeling and tracking unfolded proteins in cells is reported. In vitro experiments with model proteins show that the non-fluorescent D1 only becomes highly fluorescent when reacted with the thiol group of free cysteine (Cys) residues on unfolded proteins but not glutathione or folded proteins with buried or surface exposed Cys. When the labeled unfolded proteins form aggregates, D1 fluorescence intensity is further increased, and fluorescence lifetime is prolonged. D1 is then used to measure unfolded protein loads in cells by flow cytometry and track the aggregate formation of the D1 labeled unfolded proteins using confocal microscopy. In combination with fluorescence lifetime imaging technique, the proteome at different folding statuses can be better differentiated, demonstrating the versatility of this new platform. The rational design of D1 demonstrates the outlook of incorporation of diverse functional groups to achieve maximal sensitivity and selectivity in biological samples.
Lipidomics Reveals a Tissue-Specific Fingerprint (2018)

In biological systems lipids generate membranes and have a key role in cell signaling and energy storage. Therefore, there is a wide diversity of molecular lipid expressed at the compositional level in cell membranes and organelles, as well as in tissues, whose lipid distribution remains unclear. Here, we report a mass spectrometry study of lipid abundance across 7 rat tissues, detecting and quantifying 652 lipid molecular species from the glycerolipid, glycerophospholipid, fatty acyl, sphingolipid, sterol lipid and prenol lipid categories. Our results demonstrate that every tissue analyzed presents a specific lipid distribution and concentration. Thus, glycerophospholipids are the most abundant tissue lipid, they share a similar tissue distribution but differ in particular lipid species between tissues. Sphingolipids are more concentrated in the renal cortex and sterol lipids can be found mainly in both liver and kidney. Both types of white adipose tissue, visceral and subcutaneous, are rich in glycerolipids but differing the amount. Acylcarnitines are mainly in the skeletal muscle, gluteus and soleus, while heart presents higher levels of ubiquinone than other tissues. The present study demonstrates the existence of a rat tissue-specific fingerprint.
Uncovering new utility in infrared spectroscopic imaging by pushing the limits of accuracy, speed, and resolution (Conference Presentation) (2023)

Infrared spectroscopic imaging combines the ability to record molecular content with the ability to visualize chemistry in its spatial diversity. Given the need to record a significantly larger quantity of data than a typical microscopy image (MB vs. GB) and the extensive bandwidth of the spectra (~10 m), trade-offs often have to be made between the closely related considerations of signal to noise ratio, spatial-spectral coverage, resolution and optical arrangements. Here, we present a path from rigorous theory to modeling and design to realizing the advantages offered by new ideas on fundamentally changing these trade-offs. We first describe a new microscope design for increased speed and rapid coverage that is useful for biomedical and clinical tissue imaging. Next, we describe a configuration to measure chirality in samples that promises higher spectral information that present methods. Finally, we present a new approach to nanoscale IR imaging that provides greater fidelity and speed at unprecedented levels of signal to noise ratio. Finally, we show how emerging machine learning approaches can further augment these advances. For each instrumentation advance, examples of use cases will be presented.
Inhibition of Urea Transport across Renal Tubules by P&gamma;razinoylguanidine and Analogs (1992)

In addition to glomerular filtration and passive back diffusion of urea, there occurs across the renal tubule bidirectional transport of urea inhibitable in one or both directions by specific analogs of pyrazinoylguanidine (PZG). Effect of PZG on the profiles of sodium and urea concentrations along the tubule (stop flow) are consistent with their independent transport. Inhibition of urea and sodium reabsorption by PZG is dose dependent. PZG does not inhibit potassium excretion.
Exploring the Reactivity of B‐Connected Carboranylphosphines in Frustrated Lewis Pair Chemistry: A New Frame for a Classic System (2022)

The primary phosphines MesPH<sub>2</sub> and tBuPH<sub>2</sub> react with 9-iodo-m-carborane yielding B9-connected secondary carboranylphosphines 1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PHR (R=2,4,6-Me<sub>3</sub> C<sub>6</sub> H<sub>2</sub> (Mes; 1 a), tBu (1 b)). Addition of tris(pentafluorophenyl)borane (BCF) to 1 a, b resulted in the zwitterionic compounds 1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PHR(p-C<sub>6</sub> F<sub>4</sub> )BF(C<sub>6</sub> F<sub>5</sub> )<sub>2</sub> (2 a, b) through nucleophilic para substitution of a C<sub>6</sub> F<sub>5</sub> ring followed by fluoride transfer to boron. Further reaction with Me<sub>2</sub> SiHCl prompted a H-F exchange yielding the zwitterionic compounds 1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PHR(p-C<sub>6</sub> F<sub>4</sub> )BH(C<sub>6</sub> F<sub>5</sub> )<sub>2</sub> (3 a, b). The reaction of 2 a, b with one equivalent of R'MgBr (R'=Me, Ph) gave the extremely water-sensitive frustrated Lewis pairs 1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PR(p-C<sub>6</sub> F<sub>4</sub> )B(C<sub>6</sub> F<sub>5</sub> )<sub>2</sub> (4 a, b). Hydrolysis of the B-C<sub>6</sub> F<sub>4</sub> bond in 4 a, b gave the first tertiary B-carboranyl phosphines with three distinct substituents, 1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PR(p-C<sub>6</sub> F<sub>4</sub> H) (5 a, b). Deprotonation of the zwitterionic compounds 2 a, b and 3 a, b formed anionic phosphines [1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PR(p-C<sub>6</sub> F<sub>4</sub> )BX(C<sub>6</sub> F<sub>5</sub> )<sub>2</sub> ]<sup>-</sup> [DMSOH]<sup>+</sup> (R=Mes, X=F (6 a), R=tBu, X=F (6 b); R=Mes, X=H (7 a), R=tBu, X=H (7 b)). Reaction of 2 a, b with an excess of Grignard reagents resulted in the addition of R' at the boron atom yielding the anions [1,7-H<sub>2</sub> C<sub>2</sub> B<sub>10</sub> H<sub>9</sub> -9-PR(p-C<sub>6</sub> F<sub>4</sub> )BR'(C<sub>6</sub> F<sub>5</sub> )<sub>2</sub> ]<sup>-</sup> (R=Mes, R'=Me (8 a), R=tBu, R'=Me (8 b); R=Mes, R'=Ph (9 a), R=tBu, R'=Ph (9 b)) with [MgBr(Et<sub>2</sub> O)<sub>n</sub> ]<sup>+</sup> as counterion. The ability of the zwitterionic compounds 3 a, b to hydrogenate imines as well as the Brønsted acidity of 3 a were investigated.
Analytical and clinical performance of a homogeneous enzymatic LDL-cholesterol assay compared with the ultracentrifugation-dextran sulfate-Mg2+ method (1998)

LDL-cholesterol (LDL-C) concentration is currently determined in most clinical laboratories by the Friedewald calculation. This approach has several limitations and may not meet the current total error requirement in LDL-C measurement of < or = 12%. We evaluated the analytical and clinical performance of the direct N-geneous LDL-C assay (Equal Diagnostics). The N-geneous method correlated highly with the modified beta-quantification assay (r = 0.95; y = 0.91x + 70.6 mg/L; n = 199), showed no significant effect of increased triglyceride or other common interferants, and performed adequately in serum samples from nonfasting individuals. This assay demonstrated a mean total error of 6.75% over a wide range of LDL-C concentrations. In addition, at the medical decision cutoff points, this LDL-C assay showed positive predictive values of 78-95% and negative predictive values of 84-99%. We conclude that the N-geneous LDL-C meets the currently established analytical performance goals and appears to have a role in the diagnosis and management of hypercholesterolemic patients.
UNDERSTANDING COGNITION IN THE CONTEXT OF URBAN-RURAL ENVIRONMENT AND CHILDHOOD SOCIOECONOMIC STATUS (2018)

We examined the joint effects of childhood SES (cSES) and late-adolescent urbanicity on long-term consequences for eight cognitive outcomes at mean age 62 in a national sample of 1009 men from the Vietnam Era Twin Study of Aging. Urbanicity predicted abstract reasoning and verbal fluency (ps<.05) after adjusting for covariates including early-adult general cognitive ability (GCA). There was no main effect of cSES. Adjusting for the same covariates, the urbanicity-by-cSES interaction was significant for five cognitive abilities (adult GCA, verbal fluency, visual spatial ability, working memory, and executive functions; ps<.05). Thus, the effects of cSES and urbanicity on late-midlife cognitive outcomes are primarily due to their interaction, highlighting the importance of considering environmental context when examining the relation between SES and cognition. The results suggest that it is important to consider availability of resources (which may be low in very rural environments) in addition to accessibility to resources (e.g., SES/income).
Pre-filtering techniques for MC-CDMA downlink transmissions (2005)

We consider the downlink of a multi-carrier code-division multiple-access (MC-CDMA) system operating in a time division duplexing (TDD) mode and propose a non-linear pre-filtering scheme based on Tomlinson-Harashima pre-coding. In designing the pre-filtering matrices we adopt a minimum mean square error (MMSE) approach under a constraint on the overall transmit power since multiple access interference and multipath distortions are pre-compensated at the base station, low-complex receivers can be employed at the mobile units. Compared to other existing solutions, the proposed scheme provides better error rate performance
Performance estimation and architecture exploration of a video IP design in a smart phone SoC context (2014)

H.264 and HEVC are popular video standards for current and next generation systems. Texas Instruments has developed an IP architecture for real-time encode and decode of 4k×2k video streams at 30 frames per second (fps) or 1080p streams at 120 fps, on these standards. We present the architecture modeling methodology driving the design and performance validation of the IP. The IP model contains three key components. First, a pipeline modeling framework to capture the dynamic control flow across the algorithm blocks which are implemented as hardware modules. The framework enables quick representation of all pipeline configurations being considered. Second, micro-architecture models for the DMA engines. Third, trace players to generate the L2 and L3 traffic for various use-cases expressed as traces. The IP model is integrated into an SoC model to study the impact of system traffic on the L3 responses. We run simulations to evaluate the design w.r.t. the performance targets and for architecture exploration. Our H.264 results show that the IP meets targets for typical use-cases, but there is a risk for worst-case streams. Our HEVC architecture exploration study enables us to select recommended design configurations. We see this as a powerful methodology for performance validation and architecture definition.
Ruthenium-Catalyzed Cycloisomerizations of Diynols (2005)

A wide variety of diynols containing tertiary, secondary, and primary propargylic alcohols undergo a cycloisomerization reaction to form dienones and dienals in the presence of a catalytic amount of [CpRu(CH(3)CN)(3)]PF(6). The formation of five- and six-membered rings is possible using this methodology. Secondary diynols react to form single geometrical isomeric dienones and -als. Primary diynols undergo a cycloisomerization as well as a hydrative cyclization process. The utility of primary diynol cycloisomerization is demonstrated in a synthesis of (+)-alpha-kainic acid.
Characterisation of a novel group B oncolytic adenovirus, ColoAd1 (2011)

&lt;p&gt;Developing high potent oncolytic virus with multimodal antitumour capabilities is crucial for realizing the full potential of oncolytic virotherapy in cancer treatment. ColoAd1 is a novel replicating chimeric group B adenovirus recently bioselected from a large library of recombinant viruse. This thesis aims at evaluating the oncolysis ability of ColoAd1, characterization of its cellular activities and the corresponding responses from host tumour cells, elucidating the killing mechanism as well as exploring its potential applications in the advanced cancer therapy. &lt;/p&gt; &lt;p&gt;Among all oncolytic adenoviruses tested, ColoAd1 elicited the strongest cytotoxicity with a rapid killing kinetics in tumour cells. The virus displayed high infection efficiency, enhanced genome replication (compared to other adenoviruses) and strict selectively in tumour cells.The viral oncolysis also induced a bystander killing effect. &lt;/p&gt; &lt;p&gt;Investigation of the host cells responses during ColoAd1 oncolysis showed the virus mediated cell killing is not classic apoptosis but rather necrosis-like. The dying cells displayed the early cytoplasmic membrane leakage, falling intracellular ATP with a rise in calcium, disruption of the cell cycle and cellular DNA damage, with rapid release of progeny virions from the cell; on the other hand, ColoAd1-killing lacked the characteristic hallmarks of apoptosis. Autophagy may play a role in final execution of oncolysis but is not the main death mechanism. The cellular pathway involved in ColoAd1 oncolysis was further studied by using a panel of specific inhibitors. The results indicated the ColoAd1 mediated cell death is PARP- and RIP1- dependent and necroptosis could be the major death mechanism.&lt;/p&gt; &lt;p&gt;The highly oncolytic potency and special killing mechanism of ColoAd1 may have beneficial implication for advanced cancer therapies, including the possibility of circumventing drug resistance and invoking cancer immunotherapy. &lt;/p&gt; &lt;p&gt;The data in this thesis supported ColoAd1 as a novel potent oncolytic virus candidate. It promises to overcome the major drawbacks of Ad5 and therefore could have enhanced therapeutic efficacy in future clinical trial.&lt;/p&gt;
Distribution and protective function of pituitary adenylate cyclase-activating polypeptide in the retina (2012)

Pituitary adenylate cyclase-activating polypeptide (PACAP), which is found in 27- or 38-amino acid forms, belongs to the VIP/glucagon/secretin family. PACAP and its three receptor subtypes are expressed in neural tissues, with PACAP known to exert a protective effect against several types of neural damage. The retina is considered to be part of the central nervous system, and retinopathy is a common cause of profound and intractable loss of vision. This review will examine the expression and morphological distribution of PACAP and its receptors in the retina, and will summarize the current state of knowledge regarding the protective effect of PACAP against different kinds of retinal damage, such as that identified in association with diabetes, ultraviolet light, hypoxia, optic nerve transection, and toxins. This article will also address PACAP-mediated protective pathways involving retinal glial cells.
Research and application on full information hydrocarbon-detection method based on sparse inversion spectral decomposition (2017)

Existing post-stack hydrocarbon detection methods usually use the amplitude and frequency information of the seismic data to detect oil and gas, such as the bright spot, sweetness, low-frequency shadow and fluid mobility. However, these hydrocarbon detection methods cannot effectively identify hydrocarbon-bearing reservoirs in different fluid-bearing reservoirs which have the same seismic response characteristics, so they have certain limitations. Therefore, we study and propose a full information hydrocarbon detection method (FIHDM), which introduces the phase information to supplement the amplitude and frequency information. So this method can make full use of the dynamic characteristics to detect oil and gas. Finally, the FIHDM is applied to process the synthetic data and real data. The processing results show that the FIHDM has high-resolution and well imaging capability to hydrocarbon-bearing reservoir, which reduces the multi-solution and uncertainty of hydrocarbon detection. Presentation Date: Tuesday, September 26, 2017 Start Time: 3:05 PM Location: Exhibit Hall C, E-P Station 1 Presentation Type: EPOSTER
Water-Free Fracturing: A Case History (2015)

Abstract While hydraulic fracturing is primarily used to recover oil and gas from reservoirs, water-free fracturing may soon become the center stage to extract hydrocarbons in certain formations or situations. DryFrac™ waterless fracturing technology, as the name implies, does not use water to create the fracture. Instead, this process uses liquid CO2 to crack open the formation providing a highly conductive path for hydrocarbons to flow into the well. This technology can provide superior technical advantages over water-based hydraulic fracturing by eliminating the need for water, resulting in formations free from water damage and maintaining the intended proppant pack conductivity with no polymer residue. This paper presents in-depth information on a case history where liquid CO2 is used to fracture a formation. The presented data includes background, modeling, liquid CO2 implementation as a fracturing fluid, results and analyses.
Genetic and small molecule inhibition of arylamine N‐acetyltransferase 1 reduces anchorage‐independent growth in human breast cancer cell line MDA‐MB‐231 (2018)

Arylamine N-acetyltransferase 1 (NAT1) expression is reported to affect proliferation, invasiveness, and growth of cancer cells. MDA-MB-231 breast cancer cells were engineered such that NAT1 expression was elevated or suppressed, or treated with a small molecule inhibitor of NAT1. The MDA-MB-231 human breast cancer cell lines were engineered with a scrambled shRNA, a NAT1 specific shRNA or a NAT1 overexpression cassette stably integrated into a single flippase recognition target (FRT) site facilitating incorporation of these different genetic elements into the same genomic location. NAT1-specific shRNA reduced NAT1 activity in vitro by 39%, increased endogenous acetyl coenzyme A levels by 35%, and reduced anchorage-independent growth (sevenfold) without significant effects on cell morphology, growth rates, anchorage-dependent colony formation, or invasiveness compared to the scrambled shRNA cell line. Despite 12-fold overexpression of NAT1 activity in the NAT1 overexpression cassette transfected MDA-MB-231 cell line, doubling time, anchorage-dependent cell growth, anchorage-independent cell growth, and relative invasiveness were not changed significantly when compared to the scrambled shRNA cell line. A small molecule (5E)-[5-(4-hydroxy-3,5-diiodobenzylidene)-2-thioxo-1,3-thiazolidin-4-one (5-HDST) was 25-fold more selective towards the inhibition of recombinant human NAT1 than N-acetyltransferase 2. Incubation of MDA-MB-231 cell line with 5-HDST resulted in 60% reduction in NAT1 activity and significant decreases in cell growth, anchorage-dependent growth, and anchorage-independent growth. In summary, inhibition of NAT1 activity by either shRNA or 5-HDST reduced anchorage-independent growth in the MDA-MB-231 human breast cancer cell line. These findings suggest that human NAT1 could serve as a target for the prevention and/or treatment of breast cancer.
Antimicrobial and Larvicidal Activities of Stingless Bee Pollen from Maues, Amazonas, Brazil (2019)

The Amazon region has huge potential for sustainable forms of production and business models due to its abundant renewable resources. In this region, there are countless animals and plant species s...