gebhart/patrepeval huggingface dataset:
High affinity interactions promote T regulatory positive selection in the thymus (2008)

Many autoimmune disorders have been linked to a lack in T regulatory cells. As such, an understanding of how these cells develop and mature is critical. While thymic selection of effector T cells has been described, this process remains largely undefined for Tregs. Since only the DM20 form of proteolipid protein (PLP) is expressed in the thymus during fetal and neonatal life, thymic selection against PLP139‐151, which is missing in DM20 is not operative during those periods. PLP139‐151 (designated PLP 1 ) as well as PLP 1 derived altered peptides with degenerate affinity to PLP 1 ‐specific TCR were expressed on immunoglobulin (Ig) and the resulting chimeras were used to cross the maternal placenta, deliver the peptides from mother to fetus, and restore peptide selection during the fetal and neonatal period. This model was then used to determine whether Tregs are subject to thymic selection and to gauge the affinity required for such selection. The findings indicate that high affinity interactions promote the positive selection of Tregs. Indeed, Ig chimeras harboring high avidity peptides facilitated the positive selection of Tregs resulting in a higher number of Tregs progressing past the double positive stage in the thymus. However, chimeras incorporating low affinity peptide did not drive positive selection of Tregs in the thymus. Research supported by NIH grant NS37406.
UTILIZATION OF WHOLE EXOME SEQUENCING DATA TO IDENTIFY CLINICALLY RELEVANT PHARMACOGENOMIC VARIANTS IN INFLAMMATORY BOWEL DISEASE (2021)

Abstract Objectives We hypothesized that variants within clinically relevant pharmacogenes could be identified using a whole exome sequencing (WES) dataset derived from a cohort of over 1000 IBD patients. Methods Pediatric patients diagnosed with IBD underwent WES. We selected 18 genes with supporting literature where specific exonic variants would influence clinical care. Results We identified actionable pharmacogenes variants in 63% of patients. Importantly, 5% of IBD patients were at risk for serious adverse effects from anaesthesia and 3% were at increased risk for thrombosis. Conclusions We identified exonic variants in the majority of our IBD patients that directly impact clinical care. Flowchart of our pharmacogenomic analysis pipeline. After enrolment (n=2309), each patient underwent whole exome sequencing and sequence alignment. Available family members were also sequenced. Analyzed samples were limited to patients and family members with IBD (n=1097). Pharmacogenes relevant to patients with IBD were identified by literature review and evaluation of pharmGKB (total of 18 genes). Variant filtering was performed using Stargazer and GEMINI frameworks. In our cohort, there were 8 relevant pharmacogenes with variants that would alter clinical care based on current guidelines and standard of care. 63% of the patients had at least one variant that could impact care.
ChemInform Abstract: A Simple and Versatile Route to Novel Conjugated β‐Enaminonitriles and Their Application for the Highly Regioselective Synthesis of Nicotinonitriles Using a Vilsmeier‐Type Reagent. (2000)

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.
Autoschizis: A Novel Cell Death (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
An in-depth study of the azidobenzophenone–anthranil–acridone transformation (1983)

The title transformation, particularly the conversion of anthranils into acridones, is shown to be critically sensitive to temperature, solvent, substituent, and metal catalysts. Thus the conversion of 3-(p-tolyl)-anthranil into an acridone gives a ratio of 2- and 3-methyl derivatives varying from 0.6:1 to 4.7:1 with changing temperature and solvent. In other similar thermolyses, solvents (e.g. 1,2,4-trichlorobenzene) were incorporated into the product and traces of metals and their derivatives had a dramatic effect on the rate and course of the reaction. The most effective catalysts were iron powder and aluminium acetylacetonate. 3-(2,6-Disubstituted phenyl)anthranils gave acridones in which the substituents were either lost or rearranged onto N or C, the last cases involving sequential [1,5]-sigmatropic shifts.3-Thienylanthranils gave related thienoquinolones on thermolysis; again the reactions were very sensitive to catalysis. Blocked thienylanthranils also gave rearrangement products, but the non-aromatic intermediates could be isolated.
Fine mapping of the locus for nevoid basal cell carcinoma syndrome on chromosome 9q. (1997)

The nevoid basal cell carcinoma syndrome is an autosomal dominant disorder, characterized by predisposition to multiple early basal cell carcinomas of the skin and several other tumours as well as frequent occurrence of developmental anomalies. The gene has previously been mapped to chromosome 9q22 and is believed to function as a tumour suppressor. We have applied linkage and haplotype analysis to four Swedish nevoid basal cell carcinoma syndrome families to refine the localization of the nevoid basal cell carcinoma syndrome gene. Information from critical recombinants localizes the gene proximal of marker D9S287, which in combination with analysis of loss of heterozygosity in a hereditary cardiac fibroma has allowed us to define a minimal candidate region of 1Mb or less for the nevoid basal cell carcinoma gene flanked by the markers D9S280 and D9S287 in the 9q22.3 area.
Double δ-Doped Enhancement-Mode InGaP/AlGaAs/InGaAs Pseudomorphic High Electron Mobility Transistor for Linearity Application (2006)

A high linearity and high efficiency enhancement-mode InGaP/AlGaAs/InGaAs pseudomorphic high electron mobility transistor (PHEMT) for single supply operation has been developed. The low voltage operation is achieved by the very low knee voltage of the device and the linearity is improved by the optimizing concentrations of the two δ-doped layers. Biased at drain-to-source voltage VDS = 2 V, the fabricated 0.5 ×200 µm2 device exhibited a maximum transconductance of 448 mS/mm. The measured minimum noise figure (NFmin) was 0.86 dB with 12.21 dB associated gain at 10 GHz. The device shows a high output third-order intercept point (OIP3)-P1 dB of 13.2 dB and a high power efficiency of 35% when under wideband code-division multiple-access (W-CDMA) modulation signal.
Microbiota profiling identifies gut microbes that shape metabolism in obese mice fed prebiotics (2011)

*Aims of the study*: To investigate deep and comprehensive analysis of gut microbial communities and biological parameters (glucose homeostasis, metabolic stresses, and gut permeability) following prebiotics administration in obese and diabetic mice. *Methods:* Obese and diabetic (ob/ob) mice were chronically fed with prebiotic-enriched diet (Ob-Pre) or with a normal chow diet (Ob-CT). Extensive gut microbiota analyses coupled with metabolic parameters were performed. We combined multiple molecular methods, including quantitative-PCR, bar-coded pyrosequencing of the 16S-ribosomal-RNA (rRNA), and phylogenetic-microarrays. Mice were subjected to glucose tolerance and gut permeability tests. Tight-junctions localization and distribution as well as intestinal enteroendocrine L-cells were quantified by immunohistological analyses. *Main findings:* We found that prebiotics reduced fat-mass development, improved glucose tolerance, alleviated oxidative-stress and low-grade inflammation and reduced gut permeability. We showed that the gut microbiota regulate stem-cell differentiation and increase the number of enteroendocrine L-cells. The dendrogram and principal-coordinate analysis of each method revealed two clusters corresponding to the dietary conditions. 102 distinct 16S-rRNA sequences were affected by the prebiotic treatment, 16 of which displayed a &gt;10-fold change in abundance after the treatment. Importantly, multivariate-analyses revealed strong correlations between specific bacteria and the observed biological footprints. *Principal conclusions:* We conclude that specific gut microbiota modulation target enteroendocrine cells, improve gut barrier integrity, and glucose intolerance. By profiling the gut microbiota, we demonstrated that specific bacteria can modulate the phenotype of obese mice, and identified novel bacterial targets that may affect host-metabolism and enteroendocrine cells numbers in obesity and diabetes.
Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus (2021)

Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
ResearchC, a resveratrol tetramer, activates PPARα and PPARβ/δ in vitro and in vivo (2010)

Background: Appropriate long-term drinking of red wine is associated with a reduced risk of cardiovascular disease. Resveratrol, a well-known SIRT1 activator is considered to be one of the beneficial components contained in red wine, and also developed as a drug candidate. We previously demonstrated that resveratrol protects brain against ischemic stroke in mice through a PPARα-dependent mechanism. Here we report the different effects of the oligomers of resveratrol. Methods: We evaluated the activation of PPARs by e-viniferin, a resveratrol dimer, and vaticanol C, a resveratrol tetramer, in cell-based reporter assays using bovine arterial endothelial cells, as well as the activation of SIRT1. Moreover, we tested the metabolic action by administering vaticanol C with the high fat diet to wild-type and PPARαknockout male mice for eight weeks. Results: We show that vaticanol C activates PPARα and PPARβ/δ in cell-based reporter assays, but does not activate SIRT1. e-Viniferin shows a similar radical scavenging activity as resveratrol, but neither effects on PPARs and SIRT-1. Eight-week intake of vaticanol C with a high fat diet upregulates hepatic expression of PPARα-responsive genes such as cyp4a10, cyp4a14 and FABP1, and skeletal muscle expression of PPARβ/δ-responsive genes, such as UCP3 and PDK4 (pyruvate dehydrogenase kinase, isoform 4), in wild-type, but not PPARα-knockout mice. Conclusion: Vaticanol C, a resveratrol tetramer, activated PPARα and PPARβ/δ in vitro and in vivo. These findings indicate that activation of PPARα and PPARβ/δ by vaticanol C may be a novel mechanism, affording beneficial effects against lifestyle-related diseases.
The Impact of Application's Micro-Imbalance on the Communication-Computation Overlap (2011)

Although the community sees overlapping communication and computation as a perspective avenue for advancing parallel execution, it remains unclear what type of applications, under which conditions, and to which extent could benefit from this technique. To tackle this issue, we designed a simulation environment that allowed us to profoundly study overlap. We found out that overlapping potential in an application is determined by the application's parallel behavior and the pattern by which each process locally produces/consumes data involved in communication. We identified two behaviors that directly influence the application's overlapping potential - we name them microscopic imbalance of computation and microscopic imbalance of communication. In an application that expresses some of these two behaviors, a fine-grain overlapping technique can achieve a significant execution speedup, a speedup that can even be higher than 2. We believe that our findings can help a programmer estimate how much his application could benefit from overlap, and therefore decide whether implementing that technique is worth the effort.
Morphology Effects on Silver Vanadium Phosphorous Oxide SVPO (Ag<sub>2</sub>VO<sub>2</sub>PO<sub>4</sub>) Electrochemistry in a Lithium Cell (2010)

Abstract not Available.
Potential-game theoretical formulation of optimal power flow problems (2012)

This paper proposes a potential-game theoretical formulation of the optimal power flow (OPF) problem with practical operation constraints. Each generator operates as an independent player with marginal contribution utility function to minimize the generation cost. The proposed formulation alleviates the computational burden introduced by inequality constraints as they are converted to feasible action sets of players. Therefore, both the formulation and solution process of the constrained OPF problem are greatly simplified. A learning algorithm with guaranteed convergence to Nash equilibrium for potential games, called Carnot best response with inertia, is applied to solve the OPF. Analytical analysis on how players act as best responses to others is provided to investigate the economic reasoning of generator operations. As a numerical example, the solutions to a 15-unit system OPF by the proposed method are compared with solutions by particle swarm optimization (PSO) and genetic algorithms (GAs). The proposed formulation show faster convergence and better result in terms of less generation cost.
Hydrothermal Synthesis of Well-Defined Red-Emitting Eu-Doped GdPO4 Nanophosphors and Investigation of Their Morphology and Optical Properties (2023)

Rare-earth-doped GdPO4 nanoparticles have recently attracted much scientific interest due to the simultaneous optical and magnetic properties of these materials and their possible application in bio-imaging. Herein, we report the hydrothermal synthesis of GdPO4:Eu3+ nanoparticles by varying different synthesis parameters: pH, &lt;Gd&gt;:&lt;P&gt; molar ratio, and Eu3+ concentration. It turned out that the Eu3+ content in the synthesized nanoparticles had little effect on particle shape and morphology. The synthesis media pH, however, has showed a pronounced impact on particle size and distribution, i.e., the nanoparticle length can be adjusted from hundreds to tens of nanometers by changing the pH from 2 to 11, respectively. Increasing the &lt;Gd&gt;:&lt;P&gt; molar ratio resulted in a decrease in nanoparticle length and an increase in its width. The temperature-dependent measurements in the 77–500 K range revealed that the GdPO4:50%Eu3+ sample maintains half of its emission intensity, even at room temperature (TQ1/2 = 291 ± 19 K).
Vibration mode investigation of a resonant silicon tube structure for use as a fluid density sensor (2005)

We present a new sensor for on-line measurements of fluid density. The sensor consists of a tube system in single crystalline silicon which oscillates in mechanical resonance. The fluid is conveyed into and through two identical, serially and planarly arranged tube loops. A change in the density of the fluid in the tube changes the resonance frequency due to the change in the mass of the vibrating tube system. The sensor is fabricated using double-sided silicon KOH-etching and silicon fusion bonding. The silicon tube system (without the frame) is 8.6 by 17.7 mm with a thickness of 1 mm. The tubes have an inner diameter of approximately 0.8 mm and an outer diameter of approximately 1 mm. The micromachining process results in a total tube length of 61 mm and a sample volume of 0.035 ml. Fluid density measurements are presented and the vibration modes investigated.
Conservation and Discovery: Peterborough Cathedral nave ceiling and related structures. Edited by Jackie Hall and Susan Wright. 310mm. Pp xvi + 193, 202 ills (chiefly col). Museum of London Archaeology, London, 2015. <scp>isbn</scp> 9781907586392. £25 (hbk). (2016)

Conservation and Discovery: Peterborough Cathedral nave ceiling and related structures. Edited by Jackie Hall and Susan Wright. 310mm. Pp xvi + 193, 202 ills (chiefly col). Museum of London Archaeology, London, 2015. isbn 9781907586392. £25 (hbk). - Volume 96
Submillimeter Polarimetric Observations of the Galactic Center (2000)

We report the first detection of polarized submillimeter emission from the Sagittarius A region at the Galactic center. We observed three separate 2' × 2' fields: one centered on the circumnuclear disk, one centered on the peak of the molecular cloud M-0.02-0.07 (also called the "50 km s-1 cloud"), and one centered on the peak of the molecular cloud M-0.13-0.08 (also called the "20 km s-1 cloud"). Linear polarization at λ = 350 μm was detected in each of the three regions, at a total of 106 distinct sky positions. In the circumnuclear disk, the projected magnetic field directions that we infer from our measurements are similar to those inferred from previous far-infrared (λ = 100 μm) polarimetry. In the "curved ridge" region of M-0.02-0.07 that has been compressed by the expansion of Sgr A East, our results show clearly the effects of this compression on the magnetic field. In M-0.13-0.08, we observe what appears to be a stretched magnetic field, as expected for this tidally sheared cloud. It has been suggested that a "finger-like extension" or "streamer" from M-0.13-0.08 is falling into the circumnuclear disk. We tentatively interpret a flaring of magnetic field lines that we see in M-0.13-0.08 as evidence that the entire cloud has a velocity component in the Galactic eastern direction, i.e., toward the circumnuclear disk. Further observations are needed to test this interpretation. We argue that polarimetry of dust emission provides a promising tool for obtaining new information on the complex dynamics of neutral gas in the Galactic center.
Asymptotics of Sums of Cosine Series with Fractional Monotonicity Coefficients (2021)

The paper examines the following question: Under what orders of monotonicity are the upper and lower bounds of the sum of a cosine series near zero valid if they are obtained using the function $$\sum_{n=0}^{[\pi/x]}(n+1)\Delta(\mathbf a)_n$$ ?
Supplementary Figure 2 from Altered Steroid Milieu in AI-Resistant Breast Cancer Facilitates AR Mediated Gene-Expression Associated with Poor Response to Therapy (2023)

&lt;p&gt;Characterisation of ZR75aro-LetR. Validation of ER AR siRNA&lt;/p&gt;
The C-Terminus of the PSMA3 Proteasome Subunit Preferentially Traps Intrinsically Disordered Proteins for Degradation (2022)

The degradation of intrinsically disordered proteins (IDPs) by a non-26S proteasome process does not require proteasomal targeting by polyubiquitin. However, whether and how IDPs are recognized by the non-26S proteasome, including the 20S complex, remains unknown. Analyses of protein interactome datasets revealed that the 20S proteasome subunit, PSMA3, preferentially interacts with many IDPs. In vivo and cell-free experiments revealed that the C-terminus of PSMA3, a 69-amino-acids-long fragment, is an IDP trapper. A recombinant trapper is sufficient to interact with many IDPs, and blocks IDP degradation in vitro by the 20S proteasome, possibly by competing with the native trapper. In addition, over a third of the PSMA3 trapper-binding proteins have previously been identified as 20S proteasome substrates and, based on published datasets, many of the trapper-binding proteins are associated with the intracellular proteasomes. The PSMA3-trapped IDPs that are proteasome substrates have the unique features previously recognized as characteristic 20S proteasome substrates in vitro. We propose a model whereby the PSMA3 C-terminal region traps a subset of IDPs to facilitate their proteasomal degradation.
0542 Inactivation of Listeria innocua on cheddar cheese by supercritical fluid CO2 (2016)

Hard cheeses contaminated with L. monocytogenes and potential illness in consumers are unacceptable risks in today's commercial environment. Novel methods, such as supercritical fluid extraction with CO2 (SFE), could potentially reduce the risk of microbial contamination and increase the safety of cheeses. The aim of this study was to evaluate the efficacy of SFE in reducing the population of Listeria innocua (a surrogate for L. monocytogenes) on the surface of cheddar cheese. The effects of SFE on the pH, water activity, and appearance of cheddar cheese were also evaluated. Cheddar cheeses were inoculated with L. innocua (106 log CFU/g) and incubated overnight at 4°C to emulate post pasteurization contamination. The treatment with SFE was measured at two pressure and temperature combinations (120 bar at 40°C and 150 bar at 50°C) for 30 min. Treated and untreated samples were analyzed for L. innocua, coliforms, pH, and water activity immediately after treatment. Counts results were analyzed and compared using ANOVA. Listeria innocua in cheddar cheese decreased approximately 2.0 and 4.0 log CFU/g after SFE treatment at 120 bar and 40°C and SFE treatment at 150 bar and 50°C for 30 min, respectively. The water activities and pH were 0.9640 and 5.35 for treated and untreated cheddar cheeses. Cheddar cheeses showed some signs of deformation, such as some openings and splits in the surface after SFE treatment, because treatment was done in unrestrained cubes. These data suggest that SFE could potentially be used to reduce L. monocytogenes in cheese products.
Femtosecond Spectroscopy of a 13-Demethylrhodopsin Visual Pigment Analogue:  The Role of Nonbonded Interactions in the Isomerization Process (1996)

The photoisomerization reaction of the visual pigment analogue 11-cis-13-demethylrhodopsin is investigated using femtosecond pump−probe techniques. Following excitation with a 40-fs pump pulse at 500 nm, differential transient absorption spectra are measured from 470 to 560 nm using a 10-fs probe pulse centered at 500 nm and from 560 to 650 nm using a 10-fs probe pulse centered at 620 nm. The persistence of the excited-state absorption, the recovery kinetics of the ground-state bleach, and the formation time of the photoproduct absorption all indicate that this photoisomerization reaction is complete on the 400-fs time scale. Comparison of the reaction dynamics of 11-cis-rhodopsin with 11-cis-13-demethylrhodopsin suggests that the removal of the nonbonded steric interaction between the C13-methyl group and the C10-hydrogen atom slows down the initial torsional dynamics and that this in turn results in a lower isomerization quantum yield and a slower overall reaction time. Our results support the hypothesis that the quantum yield and the speed of the isomerization reaction are coupled according to a dynamic potential-surface crossing mechanism.
Technical Note: Influence of Compton currents on profile measurements in small‐volume ion chambers (2015)

Microchambers can demonstrate significant (>5%) deviations from properties as measured with larger volume chambers (0.125 cm(3) and above). These deviations can be substantially reduced by averaging measurements conducted at opposite polarities.