gebhart/patrepeval huggingface dataset:
Myoelectric activity of the small intestine in enterotoxin-induced diarrhea of calves. (1992)

Electrodes were surgically implanted at 15-cm intervals in the jejunum and ileum of 4 healthy neonatal calves so that myoelectric activity could be recorded on 2 consecutive days. On the first day, each calf received a control treatment, and myoelectric activity was recorded for 340 minutes. Phase I was recorded for a mean of 175.8 +/- 22.8 minutes (51.5%), phase II for 124 +/- 27.4 minutes (36.5%), and phase III for 40.3 +/- 6 minutes (11.9%). On the second day, each calf was treated with approximately 200 micrograms of heat-stable enterotoxin (STa) of Escherichia coli orally. All calves developed diarrhea after the administration of STa. Phase I was recorded for a mean of 92.5 +/- 42.3 minutes (27.2%), phase II for 227.3 +/- 52.5 minutes (66.9%), and phase III for 20.3 +/- 11.4 minutes (6.0%). Increase in phase II and decrease in phases I and III after STa administration were significant (P less than 0.05). Duration of the migrating myoelectric complex was longer after STa administration (median, 64 minutes), compared with the control treatment (median, 54 minutes). Minute rhythms, recorded on the day of toxin administration, ranged from 49 to 153 minutes. There was no difference between the number of migrating action potential complexes on the control days (range, 1 to 10), compared with those on treatment days (range, 1 to 14). These findings are suggestive that enterotoxin-induced diarrhea of calves is accompanied by increased total spiking activity and minute rhythms in the distal portion of the jejunum and ileum.
Separations Consortium: Lignin Rich Stream Fractionation and Purification (2021)

In support of the Bioenergy Technologies Office in converting lignin to fuels and chemicals, this project develops scalable separations based on membranes and Electordeionization (EDI) to recover low molecular weight (LMW) compounds from lignin rich streams. The project addresses three technology barriers in developing the bioeconomy; (1) Cost of production (2) Selective separation of organic acid species, and (3) Advanced bioprocess development. Specifically, membrane cascades using Tangential Flow Filtration (TFF) are investigated for the recovery of LMW lignin compounds from lignin rich streams such as Alkaline Pretreatment Liquor (APL), Reductive Catalytic Fractionation (RCF) oil, and Catalytic Oxidation oil. Process concepts, including dynamic filtration, are investigated to meet specific performance targets indicated by the consortium's Industrial Advisory Board for the membrane filtration including maintaining permeance > 1 LMH/bar and an overall cost target of < $1/kg of LMW lignin. EDI is investigated as an integral part of the membrane cascade to recover LMW aromatic acids and as an alternative to nanofiltration. Economic analysis of the processes is presented with a focus on minimizing energy consumption and capital expenditure. Furthermore, a sensitivity analysis is presented to identify key cost drivers and optimize holistic process operating conditions.
Adopting Biophysics Methods in Pursuit of Biogeophysical Research: Advancing the Measurement and Modeling of Electrical Signatures of Microbe-Mineral Transformations Impacting Contaminant Transport (Final Report) (2014)

This exploratory project involved laboratory experiments to investigate three hypotheses: (H1) Physics-based modeling of low-frequency dispersions (henceforth referred to as alpha) measured in broadband dielectric spectroscopy (DS) data can quantify pore-scale geometric changes impacting contaminant transport resulting from biomineralization; (H2) Physics-based modeling of high-frequency dispersions (henceforth referred to as beta) measured in broadband dielectric spectroscopy data can quantify rates of mineral growth in/on the cell wall; (H3) Application of this measurement and modeling approach can enhance geophysical interpretation of bioremediation experiments conducted at the RIFLE IFC by providing constraints on bioremediation efficiency (biomass concentration, mineral uptake within the cell wall, biomineralization rate). We tested H1 by performing DS measurements (alpha and beta range) on iron (Fe) particles of dimensions similar to microbial cells, dispersed within agar gels over a range of Fe concentrations. We have tested the ability of the physics-based modeling to predict volume concentrations of the Fe particles by assuming that the Fe particles are polarizable inclusions within an otherwise nonpolarizable medium. We evaluated the smallest volume concentration that can be detected with the DS method. Similar experiments and modeling have been performed on the sulfate-reducing bacteria D. vulgaris. Synchrotron x-ray absorption measurements were conducted to determine the local structure of biominerals coatings on D. vulgaris which were grown in the presence of different Fe concentrations. We imaged the mineral growth on cell wall using SEM. We used dielectric spectroscopy to differentiate between iron sulfide precipitates of biotic and abiotic nature. Biotic measurements were made on D. vulgaris bacteria grown in the presence of different concentrations of iron to form different thicknesses of iron sulfide precipitates around themselves and abiotic measurements were made on different concentrations of pyrrhotite particles suspended in agar. Results show a decrease in dielectric permittivity as a function of frequency for biotic minerals and an opposite trend is observed for abiotic minerals. Our results suggest that dielectric spectroscopy offers a noninvasive and fast approach for distinguishing between abiotic and biotic mineral precipitates.
Including probabilistic uncertainty in fuzzy logic controller modeling using Dempster-Shafer theory (1995)

Discusses some basic ideas from the Dempster-Shafer theory of evidence. The authors describe the concept of fuzzy systems modeling used in fuzzy logic control. The authors use the Dempster-Shafer framework to provide a machinery for including randomness in the fuzzy systems modeling process. The authors show how to represent additive noise in this combined framework.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evolutionarily Conserved Epitopes on Human Immunodeficiency Virus Type 1 (HIV-1) and Feline Immunodeficiency Virus Reverse Transcriptases Detected by HIV-1-Infected Subjects (2013)

Anti-human immunodeficiency virus (HIV) cytotoxic T lymphocyte (CTL)-associated epitopes, evolutionarily conserved on both HIV type 1 (HIV-1) and feline immunodeficiency virus (FIV) reverse transcriptases (RT), were identified using gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) and carboxyfluorescein diacetate succinimide ester (CFSE) proliferation assays followed by CTL-associated cytotoxin analysis. The peripheral blood mononuclear cells (PBMC) or T cells from HIV-1-seropositive (HIV(+)) subjects were stimulated with overlapping RT peptide pools. The PBMC from the HIV(+) subjects had more robust IFN-γ responses to the HIV-1 peptide pools than to the FIV peptide pools, except for peptide-pool F3. In contrast, much higher and more frequent CD8(+) T-cell proliferation responses were observed with the FIV peptide pools than with the HIV peptide pools. HIV-1-seronegative subjects had no proliferation or IFN-γ responses to the HIV and FIV peptide pools. A total of 24% (40 of 166) of the IFN-γ responses to HIV pools and 43% (23 of 53) of the CD8(+) T-cell proliferation responses also correlated to responses to their counterpart FIV pools. Thus, more evolutionarily conserved functional epitopes were identified by T-cell proliferation than by IFN-γ responses. In the HIV(+) subjects, peptide-pool F3, but not the HIV H3 counterpart, induced the most IFN-γ and proliferation responses. These reactions to peptide-pool F3 were highly reproducible and persisted over the 1 to 2 years of testing. All five individual peptides and epitopes of peptide-pool F3 induced IFN-γ and/or proliferation responses in addition to inducing CTL-associated cytotoxin responses (perforin, granzyme A, granzyme B). The epitopes inducing polyfunctional T-cell activities were highly conserved among human, simian, feline, and ungulate lentiviruses, which indicated that these epitopes are evolutionarily conserved. These results suggest that FIV peptides could be used in an HIV-1 vaccine.
Abstract 773: Identification and characterization of natural product-based inhibitors of hypoxia inducible factor-2 alpha (2010)

Abstract Clear cell renal cell carcinoma (RCC) is the most prevalent form of kidney cancer and is frequently associated with loss of von Hippel Lindau (VHL) gene function, resulting in the aberrant transcriptional activation of hypoxia response genes that contribute to tumor growth, angiogenesis and metastasis. Prior studies have shown that normoxic stabilization of hypoxia inducible factor (HIF)-1-alpha alone, while capable of mimicking some aspects of VHL loss, are not sufficient to reproduce tumorigenesis, indicating that it is not the most critical oncogenic substrate of VHL protein. To isolate compounds that selectively modulate HIF2-alpha for use as research tools and drug development leads, a cell-based high throughput screen of the NCI Natural Products Repository was performed. Stably transformed clones of the human renal clear cell carcinoma cell line 786-0 expressing a luciferase reporter construct under the control of the human vascular endothelial growth factor (VEGF) promoter-enhancer were used to identify natural product samples with inhibitory activity and minimal cellular toxicity. Leads from initial high throughput screen were chromatographically separated into component structures yielding several pure compounds with micromolar or submicromolar IC50 values, &amp;gt;80% inhibition and &amp;lt;5% cell toxicity. These compounds were then characterized biologically for their ability to inhibit VEGF protein secretion by intact 786-0 cells; several compounds showed &amp;gt;90% inhibition of VEGF secretion at micromolar doses under normoxic conditions. Studies to establish HIF selectivity and effects on RCC cell proliferation, survival, motility and anchorage independent growth are underway. 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 773.
Secreted Proteomes of Different Developmental Stages of the Gastrointestinal Nematode Nippostrongylus brasiliensis (2014)

Hookworms infect more than 700 million people worldwide and cause more morbidity than most other human parasitic infections. Nippostrongylus brasiliensis (the rat hookworm) has been used as an experimental model for human hookworm because of its similar life cycle and ease of maintenance in laboratory rodents. Adult N. brasiliensis, like the human hookworm, lives in the intestine of the host and releases excretory/secretory products (ESP), which represent the major host-parasite interface. We performed a comparative proteomic analysis of infective larval (L3) and adult worm stages of N. brasiliensis to gain insights into the molecular bases of host-parasite relationships and determine whether N. brasiliensis could indeed serve as an appropriate model for studying human hookworm infections. Proteomic data were matched to a transcriptomic database assembled from 245,874,892 Illumina reads from different developmental stages (eggs, L3, L4, and adult) of N. brasiliensis yielding∼18,426 unigenes with 39,063 possible isoform transcripts. From this analysis, 313 proteins were identified from ESPs by LC-MS/MS-52 in the L3 and 261 in the adult worm. Most of the proteins identified in the study were stage-specific (only 13 proteins were shared by both stages); in particular, two families of proteins-astacin metalloproteases and CAP-domain containing SCP/TAPS-were highly represented in both L3 and adult ESP. These protein families are present in most nematode groups, and where studied, appear to play roles in larval migration and evasion of the host's immune response. Phylogenetic analyses of defined protein families and global gene similarity analyses showed that N. brasiliensis has a greater degree of conservation with human hookworm than other model nematodes examined. These findings validate the use of N. brasiliensis as a suitable parasite for the study of human hookworm infections in a tractable animal model.
Perkin 1 Abstracts: Natural Product Synthesis (1999)

Perkin 1 Abstracts: Natural Product Synthesis aims to highlight syntheses that have been recently published. It includes brief descriptions of biological activity and key steps. A more comprehensive list of Natural Product syntheses and isolation can be found in Natural Product Updates.
Two-photon imaging of field enhancement by groups of gold nanostrip antennas (2009)

Resonant field enhancement by groups of 16 nm thin gold nanostrip antennas consisting of four strips (widths of 70, 100, and 130 nm) and fixed gap (50, 100, 150, or 200 nm) between them and positioned on a quartz substrate is investigated by reflection spectroscopy and two-photon photoluminescence scanning optical microscopy. We obtain good agreement with theoretical calculated reflection spectra and the investigated two-photon intensity dependence on the nanoantenna configurations and parameters of the illumination showed field enhancements increasing with increasing gaps in each group for the p-polarized (resonant) excitation, whereas these enhancement effects were not observed for the s-polarization (nonresonant) excitation.
Development of artificial life based optimization system (2002)

Describes the computer middleware called the Hyper Artificial Life (HAL) optimization system, which is based on artificial life theories and which is effective for almost all kinds of combinatorial optimization problems in our actual world. This middleware aids the efficient development of parallel processing of an application program for combinatorial optimization problems by adopting a conventional evolution procedure. The application based on this middleware has high autonomy and high robustness, and improves its performance on a parallel computer. In this case, a supply-chain management (SCM) scheduling program, which is actually used by many users, has been applied to this middleware in parallel in order to verify and evaluate HAL. In its evaluation, we found we could obtain a remarkable improvement in the performance. This model has the characteristics of reproduction, mutation and genetics, and we found a rare phenomenon, considered as emergence in the actual result. This obviously transcends the concept of many conventional algorithms and their ability for optimization. Moreover, the model has a hyper-structure, which is why we named it the Hyper Artificial Life system.
Abstract 2451: A novel single domain antibody targeting TIGIT for cancer use in combination therapies (2021)

Abstract T-cell immunoglobulin and ITIM domains (TIGIT) has emerged as another popular checkpoint receptor that negatively regulates T-cell functions. TIGIT is upregulated by immune cells, such as activated T cells, natural killer cells, and regulatory T cells. TIGIT binds to two ligands, CD155 (PVR) and CD112 (PVRL2, nectin-2), that are expressed by tumor cells and antigen-presenting cells in the tumor microenvironment. Beyond CTLA4 and PD1, TIGIT therapies recently demonstrated great combo potential in the clinic along with well-tolerated toxicity profile. Here we present HLX53, a novel single domain antibody (sdAb) targeting TIGIT with differentiated format, binding epitope, and functional activity. HLX53 binds to TIGIT and blocks CD155 and CD112 with sub-nanomolar affinity. In mixed lymphocyte reaction assay (MLR), HLX53 significantly increased IL2 secretion compared to Tiragolumab and Vibostolimab analogues. HLX53's IL2 induction seems to require an adequate bridging effect between T-cell and antigen-presenting cell via Fc-FcγR engagement, further promoting the maturation of antigen-specific T-cell. In vivo, HLX53 exhibits a better tumor inhibition than Tiragolumab analogue and shows synergy in combination with anti-PD-L1 antibody in MC38 model. In addition to its unique epitope/MOA, HLX53 being a sdAb has a shorter half-life and thus potentially a better tumor penetration and a differentiated PK/PD profile. Understanding pharmacokinetic and pharmacodynamic relationships enables a dosing regimen providing adequate target coverage and superior tumor eradication. Citation Format: Botong Hua, Ming Yang, Jie Xue, Chen Dong, Yi-Ting Mao, Ou Li, Eric Cheung, Hassan Issafras, Wenfeng Xu, Weidong Jiang. A novel single domain antibody targeting TIGIT for cancer use in combination therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2451.
Tuning Nano-Amorphous Calcium Phosphate Content in Novel Rechargeable Antibacterial Dental Sealant (2018)

Dental sealants with antibacterial and remineralizing properties are promising for caries prevention among children and adolescents. The application of nanotechnology and polymer development have enabled nanoparticles of amorphous calcium phosphate (NACP) and dimethylaminohexadecyl methacrylate (DMAHDM) to emerge as anti-caries strategies via resin-based dental materials. Our objectives in this study were to (1) incorporate different mass fractions of NACP into a parental rechargeable and antibacterial sealant; (2) investigate the effects on mechanical performance, and (3) assess how the variations in NACP concentration would affect the calcium (Ca) and phosphate (PO₄) ion release and re-chargeability over time. NACP were synthesized using a spray-drying technique and incorporated at mass fractions of 0, 10, 20 and 30%. Flexural strength, flexural modulus, and flowability were assessed for mechanical and physical performance. Ca and PO₄ ion release were measured over 70 days, and three ion recharging cycles were performed for re-chargeability. The impact of the loading percentage of NACP upon the sealant's performance was evaluated, and the optimized formulation was eventually selected. The experimental sealant at 20% NACP had flexural strength and flexural modulus of 79.5 ± 8.4 MPa and 4.2 ± 0.4 GPa, respectively, while the flexural strength and flexural modulus of a commercial sealant control were 70.7 ± 5.5 MPa (<i>p</i> > 0.05) and 3.3 ± 0.5 GPa (<i>p</i> < 0.05), respectively. A significant reduction in flow was observed in the experimental sealant at 30% NACP (<i>p</i> < 0.05). Increasing the NACP mass fraction increased the ion release. The sealant formulation with NACP at 20% displayed desirable mechanical performance and ideal flow and handling properties, and also showed high levels of long-term Ca and PO₄ ion release and excellent recharge capabilities. The findings provide fundamental data for the development of a new generation of antibacterial and rechargeable Ca and PO₄ dental sealants to promote remineralization and inhibit caries.
q-Space Deep Learning: Twelve-Fold Shorter and Model-Free Diffusion MRI Scans (2016)

Numerous scientific fields rely on elaborate but partly suboptimal data processing pipelines. An example is diffusion magnetic resonance imaging (diffusion MRI), a non-invasive microstructure assessment method with a prominent application in neuroimaging. Advanced diffusion models providing accurate microstructural characterization so far have required long acquisition times and thus have been inapplicable for children and adults who are uncooperative, uncomfortable, or unwell. We show that the long scan time requirements are mainly due to disadvantages of classical data processing. We demonstrate how deep learning, a group of algorithms based on recent advances in the field of artificial neural networks, can be applied to reduce diffusion MRI data processing to a single optimized step. This modification allows obtaining scalar measures from advanced models at twelve-fold reduced scan time and detecting abnormalities without using diffusion models. We set a new state of the art by estimating diffusion kurtosis measures from only 12 data points and neurite orientation dispersion and density measures from only 8 data points. This allows unprecedentedly fast and robust protocols facilitating clinical routine and demonstrates how classical data processing can be streamlined by means of deep learning.
The mRNA-Destabilizing Protein Tristetraprolin Is Suppressed in Many Cancers, Altering Tumorigenic Phenotypes and Patient Prognosis (2009)

AU-rich element-binding proteins (ARE-BP) regulate the stability and/or translational efficiency of mRNAs containing cognate binding sites. Many targeted transcripts encode factors that control processes such as cell division, apoptosis, and angiogenesis, suggesting that dysregulated ARE-BP expression could dramatically influence oncogenic phenotypes. Using several approaches, we evaluated the expression of four well-characterized ARE-BPs across a variety of human neoplastic syndromes. AUF1, TIA-1, and HuR mRNAs were not systematically dysregulated in cancers; however, tristetraprolin mRNA levels were significantly decreased across many tumor types, including advanced cancers of the breast and prostate. Restoring tristetraprolin expression in an aggressive tumor cell line suppressed three key tumorgenic phenotypes: cell proliferation, resistance to proapoptotic stimuli, and expression of vascular endothelial growth factor mRNA. However, the cellular consequences of tristetraprolin expression varied across different cell models. Analyses of gene array data sets revealed that suppression of tristetraprolin expression is a negative prognostic indicator in breast cancer, because patients with low tumor tristetraprolin mRNA levels were more likely to present increased pathologic tumor grade, vascular endothelial growth factor expression, and mortality from recurrent disease. Collectively, these data establish that tristetraprolin expression is frequently suppressed in human cancers, which in turn can alter tumorigenic phenotypes that influence patient outcomes.
ChemInform Abstract: Enantioselective Chemoenzymatic Synthesis of the S‐Enantiomer of the Systemic Fungicide Fenpropimorph. (1996)

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.
Relative gain array variation for norm bounded uncertain systems (2015)

This article proposes computationally tractable, easy to expand and tight relative gain variation bound for uncertain systems. The proposed bound is a further development of previous work, which is summarized and discussed. Using several examples, the new method is compared with previous results and the advantages are highlighted. The prediction of sign changes in relative gain array elements due to uncertainties is important for pairing decisions. Based on the proposed bound, a method for the prediction of the uncertainty levels which render sign changes is suggested. The prediction method is currently limited to certain classes of systems. In this prediction method neither prior knowledge of the uncertainty nor numerous calculations are needed.