gebhart/patrepeval huggingface dataset:
Synthesis of new adjuvants and carriers for foot and mouth disease virus (fmdv) (2002)

Foot and mouth disease virus (FMDV) is the etiological agent of an important disease in livestock. Despite the considerable amount of information accumulated in recent years, FMD still affects extensive areas of the world and is the most transmissible viral disease in animals: FMDV has been diagnosed in 34 countries during the past 18 months and 1,000 cases in the recent outbreak are accounted for in Great Britain alone. One of the difficulties in controlling FMDV is its occurrence in seven distinct serotypes and immunity conferred by vaccination against one serotype leaves the animals susceptible to infection by the other six. Vaccination is the first treatment against FMDV. The current vaccines consist of virus inactivated with imines and formulated with A1(OH)3/saponin (for ruminants) or incomplete oil-based formulations (for pigs and cattle). Based on previous results, a synthetic vaccine against FMDV was developed following the concept of adjuvant-carrier-epitope. Here we describe the synthesis and the development of novel synthetic adjuvants and carriers and their use in synthetic vaccines against foot and mouth disease virus. Different sets of lipophilic compounds were prepared in order to act as build-in adjuvants/carriers. They include cyclic and linear polyalcohols containing different numbers of alkylic chains. In-solution synthetic chemistry was used and separation and characterization of closely related lipid products, although successful, proved difficult. A synthetic dendrimeric polylysine carrier was also prepared but, following promising results of compounds lacking the MAP carrier, it was not linked to the constructs. The lipophilic constructs were then coupled to different copies of synthetic peptides corresponding to the VP1 (140-160) FMDV serotype C. Different kinds of synthetic liganding approaches were used for the conjugation, following the attachment of a residue of cysteine to the carboxy terminus of the peptides. The different approaches led to investigations of the role and the importance of different spacers between the adjuvant/carrier and the epitope.
Protein and Peptide Sequence Analysis by Tandem Mass Spectrometry in Combination with Either Capillary Electrophoresis or Micro-Capillary HPLC (1991)

Sequence analysis of peptides in mixtures by the combination of capillary electrophoresis, electrospray mass spectrometry is described. On-column digestion of proteins at the 1–10 pmol level followed by on-line separation and sequence analysis of the resulting peptides by micro-capillary HPLC/electrospray mass spectrometry is also presented.
Author response: Immunosuppression via adenosine receptor activation by adenosine monophosphate released from apoptotic cells (2014)

Infections, toxins, and trauma can all injure tissue and cause the cells inside the tissue to die. When a cell dies, the membrane that surrounds it ruptures and its contents spill out, triggering inflammation of the surrounding tissues. This inflammation is part of the body’s efforts to begin the healing process but, if left uncontrolled, inflammation itself can cause further tissue damage. Diseased or damaged cells can also ‘choose’ to kill themselves to protect other healthy cells. This process, which is called apoptosis, also eliminates about 100,000 cells that are too old, or just no longer needed, from the human body every second. A cell undergoing apoptosis essentially dismantles itself, and the remains of the cell are packaged up, and cleared away by the white blood cells. Interestingly, this programed cell death releases many of the same molecules as other dying cells, but does so without triggering inflammation. The reason behind this lack of inflammation has not been clear. Now, Yamaguchi et al. have addressed this issue, and shown that cells undergoing apoptosis also release a chemical called adenosine monophosphate (AMP) that acts as a ‘calm down’ signal. The AMP is processed by white blood cells to a simpler chemical, which ‘switches on’ various genes in the white blood cells. This leads to the production of proteins that suppress the inflammation that would otherwise be triggered by other molecules released from the cells undergoing apoptosis. The findings of Yamaguchi et al. show how the community of cells in our body is kept in a healthy balance, and in the future, could improve our understanding and the treatment of inflammatory diseases.
Retraction: Iterative Transmit/Receive Antenna Selection in MIMO Systems Based on Channel Capacity Analysis (2013)

Retraction notice.
Data from Epidermal Growth Factor Receptor Tyrosine Phosphorylation and Signaling Controlled by a Nuclear Receptor Coactivator, Amplified in Breast Cancer 1 (2023)

&lt;div&gt;Abstract&lt;p&gt;The steroid receptor coactivator amplified in breast cancer 1 (AIB1) as well as epidermal growth factor receptor (EGFR) family members are frequently overexpressed in epithelial tumors, and their expression is associated with poor prognosis. However, a direct role of AIB1 in EGF signaling has not been determined. To address this, we reduced endogenous AIB1 levels using RNA interference in lung, breast, and pancreatic cancer cell lines. We found that a knockdown of AIB1 levels resulted in a loss of the growth response of these cell lines to EGF. Further analysis revealed that the depletion of AIB1 reduced tyrosine phosphorylation of EGFR at multiple residues both at autophosphorylation and Src kinase phosphorylation sites. AIB1 knockdown did not affect tyrosine phosphorylation of the receptor tyrosine kinases, platelet-derived growth factor receptor and HER3, or overall tyrosine phosphorylation of cellular proteins. However, EGF-dependent phosphorylation of HER2 was decreased. EGFR levels and membrane trafficking were not changed by AIB1 depletion, but there was less recruitment of Src homology 2 domain-containing proteins to the EGFR. This led to a substantial reduction in EGF-induced phosphorylation of signal transducers and activators of transcription 5 and c-Jun NH&lt;sub&gt;2&lt;/sub&gt;-terminal kinase but no significant change in the activation of AKT. Vanadate treatment of cells revealed that the reduction in EGFR tyrosine phosphorylation is dependent in part on changes in cellular phosphatase activity. We propose that a portion of the oncogenic effect of AIB1 could be through control of EGFR and HER2 activity and subsequent modulation of cellular signaling pathways. [Cancer Res 2007;67(15):7256–65]&lt;/p&gt;&lt;/div&gt;
Surface Properties of Colloidal Particles Affect Colloidal Self-Assembly in Evaporating Self-Lubricating Ternary Droplets (2021)

In this work, we unravel the role of surface properties of colloidal particles on the formation of supraparticles (clusters of colloidal particles) in a colloidal Ouzo droplet. Self-lubricating colloidal Ouzo droplets are an efficient and simple approach to form supraparticles, overcoming the challenge of the coffee stain effect <i>in situ</i>. Supraparticles are an efficient route to high-performance materials in various fields, from catalysis to carriers for therapeutics. Yet, the role of the surface of colloidal particles in the formation of supraparticles using Ouzo droplets remains unknown. Therefore, we used silica particles as a model system and compared sterically stabilized versus electrostatically stabilized silica particles─positively and negatively charged. Additionally, we studied the effect of hydration. Hydrated negatively charged silica particles and sterically stabilized silica particles form supraparticles. Conversely, dehydrated negatively charged silica particles and positively charged amine-coated particles form flat film-like deposits. Notably, the assembly process is different for all the four types of particles. The surface modifications alter (a) the contact line motion of the Ouzo droplet and (b) the particle-oil and particle-substrate interactions. These alterations modify the particle accumulation at the various interfaces, which ultimately determines the shape of the final deposit. Thus, by modulating the surface properties of the colloidal particles, we can tune the shape of the final deposit, from a spheroidal supraparticle to a flat deposit. In the future, this approach can be used to tailor the supraparticles for applications such as optics and catalysis, where the shape affects the functionality.
Woody Feedstocks 2020 State of Technology Report (2020)

The U.S. Department of Energy promotes production of advanced liquid transportation fuels from lignocellulosic biomass by funding fundamental and applied research that advances the state of technology (SOT). As part of its involvement with this overall mission, Idaho National Laboratory completes annual SOT reports for nth-plant biomass feedstock logistics. The purpose of the SOTs is to provide the status of feedstock supply system technology development for biomass to biofuels, based on actual data and experimental results relative to technical targets and cost goals from specific design cases. The 2020 Woody Feedstock SOT is separated into three separate pathways that utilize woody feedstocks: indirect liquefaction (IDL), catalytic fast pyrolysis (CFP), and algal-blend hydrothermal liquefaction (AHTL). The 2020 delivered cost for the feedstocks were found to be $63.23/dry ton, $67.03/dry ton and $70.31/dry ton, respectively (2016$).
Free-form V-groove reflector design with the SMS method in three dimensions (2011)

The Simultaneous Multiple Surface design method in three dimensions (SMS3D) is applied to the design of free-form V-groove reflectors. The general design problem is how to achieve the coupling of two wavefronts after two reflections at the V-groove, no matter which side of the groove the rays hit first. This paper also explains a design procedure for thin dielectric grooved-reflector substitutes for conventional mirrored surfaces. Some canonical V-groove designs are ray-traced in detail.
SARS-CoV-2–neutralizing antibody treatment in patients with COVID-19 and immunodeficiency due to B-cell non-Hodgkin lymphoma (2021)

The adaptive humoral immune response to SARS-CoV-2 plays a critical role in establishing protective immunity after infection or vaccination. 1-3 Viral clearance and immunological control seems to be affected in patients with humoral deficiency, which can present with persistent viral shedding and prolonged COVID-19. 4-8 Impaired adaptive immunity related to dysfunctional or depleted B cells and hypogammaglobulinemia is a common feature in B-cell-related malignancies, such as B-cell non-Hodgkin lymphomas (B-NHLs). 9-12 Because of the inability to produce a sufficient amount of SARS-CoV-2-neutralizing antibodies, those patients are at risk of prolonged COVID-19 7,8 and vaccination failure. 13,14 Passive immunization with SARS-CoV-2-neutralizing monoclonal antibodies (nmAbs) demonstrated beneficial effects on mortality, clinical course, and viral load in immunocompetent unvaccinated patients with mild disease who were treated early, 15-17 before endogenous IgG production (IgG seronegative). 18 These trials did not focus on patients with immunosuppression or cancer. However, the results suggest that induction of humoral immune response several days after symptom onset marks a critical barrier for treatment efficacy. Thus, passive immunization with mAbs may be a rational treatment approach for patients who do not produce sufficient amounts of endogenous neutralizing antibodies after vaccination or infection, irrespective of symptom duration. Herein, we give a detailed description of hospitalized patients with COVID-19 who had impaired humoral immunity to underlying B-NHL and were successfully treated with nmAbs in the context of an individual healing attempt. Patients gave written informed consent for scientific evaluation. The study was approved by the local ethics committee of the University Hospital of Cologne.
Utility of mismatch repair protein expression screening via an endoscopic ultrasound assessment of treatment-naive pancreas ductal adenocarcinoma (2021)

We read with great interest the recent articles by Luchini et al 1 2 and Grant et al 3 highlighting the low prevalence (1%–2%) of mismatch repair deficient pancreatic ductal adenocarcinoma (dMMR PDAC) and offering further knowledge pertaining to the molecular spectrum of this disease subtype. A plea was raised to augment translational and clinical research efforts to improve our understanding of dMMR PDAC.

However, from a practical perspective, only 20% of patients with PDAC reach surgical oncologic resection.4 These resection specimens have served as the source of prior dMMR PDAC analysis. Following the United States Food and Drug Administration approval of pembrolizumab as the first cancer therapy targeting a specific molecular signature, we identified a dMMR prevalence of 3% in a small retrospective cohort of archived pancreas endoscopic ultrasound fine-needle biopsy (EUS FNB) specimens.5 We recently completed an 18-month prospective evaluation of 218 consecutive treatment-naive PDAC patients diagnosed by EUS (fine-needle aspiration: 112 (51.4%), FNB: 91 (41.7%) or both: 15 (6.9%)) for MMR screening as a companion diagnostic test (table 1). A specimen adequate for ancillary studies was acquired in 193 (88.5%) patients …
Electrochemical Deposition of a New n-Doping Polymer Based on Bis(thienyl)isopyrazole (2007)

A novel donor-acceptor polymer based on thiophene and isopyrazole has been prepared for use in n-doping applications. Nonpolymerizable monomer radical cations appear to be the predominant oxidation product, resulting in a need for extended cycling to produce adequate quantities of polymer for characterization. The electrochemical behavior of the polymer films produced is strongly dependent upon the conditions applied during electrodeposition and on the solvent used during cycling of the films. Cycling to reductive potentials during oxidative polymerization in acetonitrile was necessary to produce a polymer film capable of n-doping, likely resulting from a need to establish pathways for cation migration. The neutral polymer undergoes oxidation to the p-doped form at ca. vs in propylene carbonate and reduces back to neutral at ca. . Conversion of the neutral polymer to its n-doped form involves reductions at and , with reoxidation at and to return to the neutral form of the polymer.
Solid state NMR characterization of Sn-Beta catalysts (2014)

High-resoln. multi-nuclear solid state NMR characterization has been performed to obtain insight into the&#13;\nmechanism of glucose reactions with Sn-beta zeolites. Glucose isomerization or epimerization reactions in&#13;\nwater and non-aq. environments were examd. thoroughly, and correlations between catalyst structural changes&#13;\nand reaction selectivity were the primary focus in this study. In particular, we investigated local structural&#13;\nchanges around the catalytically active Sn sites of ^(119)Sn-labeled beta zeolite in different states, including in&#13;\ntheir as synthesized form, after calcination in flowing air, after adsorption of sugar mols., and after performing&#13;\ncatalytic reaction cycles. Magic angle spinning (MAS) and cross polarization (CP) (either from ^1H or ^(19)F) MAS&#13;\n^(119)Sn NMR spectra provided insight into changes in local Sn coordination in the framework of zeolite beta&#13;\nunder various conditions. Other NMR results, including ^(13)C NMR of adsorbed glucose or methanol, and ^(19)For&#13;\n^(29)Si NMR of zeolite framework, will be used in interpretations of the catalytic reaction mechanisms.
The effect of dietary fatty acids on bone marrow fat in a murine model of senile osteoporosis (2013)

Sponsor(s):Amer Geriatr Soc ; Supplement: 1<br/>Sponsor(s):Amer Geriatr Soc ; Supplement: 1
ChemInform Abstract: A Crown Ether Tetrathiafulvalene Cage (1990)

Abstract (V) (which shows two reversible one‐electron oxidation waves at +0.41 and +0.73 V in cyclic voltammetry vs.
Patch Clamp Detection in Capillary Electrophoresis (1997)

We describe a capillary electrophoresis-patch clamp (CE-PC) analysis of biomolecules that activate ligand-gated ion channels. CE-PC offers a powerful means for identifying receptor ligands based on the combination of the characteristic receptor responses they evoke and their differential electrophoretic migration rates. Corner frequencies, membrane reversal potentials, and mean and unitary single-channel receptor responses were calculated from currents recorded with patch clamp detection. This information was then combined with the electrophoretic mobility of the receptor ligand, which is proportional to the charge-to-frictional-drag ratio of that species. We applied CE-PC to separate and detect the endogenous receptor agonists gamma-aminobutyrate and L-glutamate and the synthetic glutamate receptor agonists N-methyl-D-aspartate and kainic acid. We present dose-response data for electrophoretically separated kainic acid and discuss its implications for making the CE-PC detection system quantitative.
Synthesis of Patient-Specific Nanomaterials (2018)

Nanoparticles are engineered from materials such as metals, polymers, and different carbon allotropes that do not exist within the body. Exposure to these exogenous compounds raises concerns surrounding toxicity, inflammation, and immune activation. These responses could potentially be mitigated by synthesizing nanoparticles directly from molecules derived from the host. However, efforts to assemble patient-derived macromolecules into structures with the same degree of size and shape tunability as their exogenous counterparts remains a significant challenge. Here we solve this problem by creating a new class of size- and shape-tunable personalized protein nanoparticles (PNP) made entirely from patient-derived proteins. PNPs are built into different sizes and shapes with the same degree of tunability as gold nanoparticles. They are biodegradable and do not activate innate or adaptive immunity following single and repeated administrations in vivo. PNPs can be further modified with specific protein cargos that remain catalytically active even after intracellular delivery in vivo. Finally, we demonstrate that PNPs created from different human patients have unique molecular fingerprints encoded directly into the structure of the nanoparticle. This new class of personalized nanomaterial has the potential to revolutionize how we treat patients and can become an integral component in the diagnostic and therapeutic toolbox.
Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods (2008)

The phylogenetic diversity of Bacteria and Archaea within a biodegraded, mesothermic petroleum reservoir in the Schrader Bluff Formation of Alaska was examined by two culture-independent methods based on fosmid and small-subunit rRNA gene PCR clone libraries. Despite the exclusion of certain groups by each method, there was overall no significant qualitative difference in the diversity of phylotypes recovered by the two methods. The resident Bacteria belonged to at least 14 phylum-level lineages, including the polyphyletic Firmicutes, which accounted for 36.2% of all small-subunit rRNA gene-containing (SSU(+)) fosmid clones identified. Members of uncultured divisions were also numerous and made up 35.2% of the SSU(+) fosmid clones. Clones from domain Archaea accounted for about half of all SSU(+) fosmids, suggesting that their cell numbers were comparable to those of the Bacteria in this microbial community. In contrast to the Bacteria, however, nearly all archaeal clones recovered by both methods were related to methanogens, especially acetoclastic methanogens, while the plurality of bacterial fosmid clones was affiliated with Synergistes-like acetogenic Firmicutes that possibly degrade longer-chain carboxylic acid components in the crude oil to acetate. These data suggest that acetate may be a key intermediary metabolite in this subsurface anaerobic food chain, which leads to methane production as the primary terminal electron sink.
Cinnamic acid based thiazolidinediones inhibit human P450c17 and 3beta-hydroxysteroid dehydrogenase and improve insulin sensitivity independent of PPARgamma agonist activity (2004)

Thiazolidinediones improve insulin sensitivity in type 2 diabetes mellitus by acting as peroxisome proliferator-associated receptor gamma (PPARgamma) agonists, and decrease circulating androgen concentrations in polycystic ovary syndrome by unknown mechanisms. Some thiazolidinediones directly inhibit the steroidogenic enzymes P450c17 and 3beta-hydroxysteroid dehydrogenase type II (3betaHSDII) by distinct mechanisms. We synthesized five novel thiazolidinediones, CLX-M1 to -M5 by linking a 2,4-thiazolidinedione moiety to a substituted alpha-phenyl cinnamic acid previously shown to have glucose-lowering effects. Using yeast microsomes expressing human P450c17 and 3betaHSDII we found that cinnamic acid methyl esters with a double bond in the thiazolidinedione core structure (M3, M5) were stronger inhibitors of P450c17 than methyl esters with the conventional core (M1, M4). These four compounds inhibited 3betaHSDII equally well, while the free cinnamic acid analog (M2) did not inhibit either enzyme. Thus, the inhibition of P450c17 and 3betaHSDII by these novel thiazolidinediones reveals structure-activity relationships independent of PPARgamma transactivation. PPARgamma transactivation was moderate (M1), weak (M2, M3) or even absent (M4, M5). While the PPARgamma agonist activity of M1 was only 3% of that of rosiglitazone, both increased glucose uptake by 3T3-L1 adipocytes and reduced serum glucose levels in ob/ob and db/db mice to a similar extent. The similar glucose-lowering effects of M1 and rosiglitazone, despite their vast differences in PPARgamma agonist activity, suggests these two actions may occur by separate mechanisms.
Ultra Small Modulator and Demodulator for Differential Phase-Shift-Keying Data Format Based on Silicon Microring (2007)

Proposed microring-based modulator and demodulator of DPSK data format can be a thousand times smaller than conventional scheme (Mach-Zehnder modulator + delay interferometer). With optimized Q-factor of 22000, back-to-back power penalty is diminished to 0.8-dB.
Nonlinear optical interactions in silicon waveguides (2016)

Abstract The strong nonlinear response of silicon photonic nanowire waveguides allows for the integration of nonlinear optical functions on a chip. However, the detrimental nonlinear optical absorption in silicon at telecom wavelengths limits the efficiency of many such experiments. In this review, several approaches are proposed and demonstrated to overcome this fundamental issue. By using the proposed methods, we demonstrate amongst others supercontinuum generation, frequency comb generation, a parametric optical amplifier, and a parametric optical oscillator.
Total Synthesis of (±)-Bisabosqual A (2012)

The synthesis of the novel squalene synthase inhibitor, bisabosqual A, was completed in 14 steps (longest linear sequence) from commercially available starting materials. The doubly convergent route employs a tandem 5-exo, 6-exo radical cyclization as the key step. This reaction assembles the fully functionalized tetracyclic core and introduces three stereogenic centers. Other effective transformations are the regioselective deoxygenation of an advanced enone intermediate and the chemo- and diastereoselective addition of trimethylaluminum to a ketone in the presence of esters.
Health-related quality of life correlates with clinical and endoscopic activity indexes but not with demographic features in patients with ulcerative colitis (2006)

This study points out the strong relationship between CAI and EAI and all domains of HRQOL in patients with UC. Therefore, the IBDQ-D is a valid and reliable assessment tool that reflects changes in the health status of UC patients. It is a useful measure of therapeutic efficacy and should be used in clinical trials in IBD.