gebhart/patrepeval huggingface dataset:
OP020 The clinical determinants affect gut microbial profile of inflammatory bowel disease patients (2018)

Alterations in gut microbial community of IBD patients still present inconsistency among the published studies and importantly did not completely allow for the unique identification of microbial signatures of CD and UC. We aimed molecularly to profile the intestinal microbiota of phenotypically and genotypically well-characterised Swiss IBD cohort (SIBDC) patients as well as newly recruited IBD patients in Bern as a local replica set including non-IBD subjects. We deeply characterised the microbiota of UC and CD from 941 biopsy samples of 346 patients from the SIBDCS Cohort and 1254 of biopsy samples of total 397 IBD patients and non-IBD subjects from the Bern cohort, thus building one of the largest cohorts covering sequence data generated. The microbiota composition at the site of biopsy was determined by 16S Amplicon sequencing on the Iontorrent platform. Data were analysed using the QIIME pipeline and correlated with the extensive long-term longitudinal clinical data (patients’ disease trajectory) of the Swiss IBD cohort study. In PCoA plots, CD and UC disease groups clustered into two distinct groups mostly characterised by altered bacterial composition and lower diversity in CD patients compared with UC patients and non-IBD subjects. Significant differences in taxa representation between the disease groups of each cohort were identified using multivariate association with linear models. This microbial “fingerprint” based on the Swiss IBD cohort and Bern cohort data could then be used in a machine learning algorithm process to correctly predict the CD and UC disease groups with more than 83% success rate. Disease status, disease location/behaviour, and stool consistency were the critically important variables that have effects on shaping the gut microbiota of IBD patients, as assessed in both cohort. Steroids and Anti-TNF agents’ responses, as well of surgery also induced several taxonomic changes, but not the response to thiopurines, methotrexate or 5-ASA. Our findings revealed that CD and UC are two distinct intestinal disorders at the microbiome level, which could be differentiate based on the microbial profile. A loss of beneficial microorganisms is more associated with CD. However, the observed bacterial dysbiosis in IBD patients is not only associated with disease status itself, it is also directly linked to several clinical parameters associated with the disease trajectory of patients.
Multi-Model Adaptive Control for CACC Applications (2020)

This paper proposes a multi-model adaptive control (MMAC) algorithm based on Youla-Kucera (YK) theory to deal with heterogeneity in cooperative adaptive cruise control (CACC) systems. The main idea of MMAC is to choose the plant in a predefined set that best approximates the system dynamics, applying the corresponding predesigned controller. A set of linear plants describing different vehicle dynamics is defined. Different CACC controllers are designed depending on these linear plants. Simulation and experimental results prove how MMAC determines the closest plant in the set, choosing the CACC system able to ensure string stability.
The Mixing Efficiency of an Eccentric‐Disc Kneading Zone in Intermeshing Co‐ and Counter‐Rotating Twin‐Screw Extruders (2004)

Abstract The distributive mixing efficiency of a twin‐screw extruder kneading zone consisting of eccentric disc elements was measured using an online video technique. Both co‐ and counter‐rotation were examined. Viscous Newtonian silicone oil was used as model liquid and black iron oxide pigment served as tracer substance. Under isoviscous, creeping flow and non‐diffusive conditions and for a fixed flow rate ratio of the colored and uncolored feed streams, the intensity of segregation S is only a function of the kinematic parameter Λ (the ratio of the imposed extruder throughput and the throughput at zero axial pressure gradient). The measured dependency of S on Λ is in qualitative agreement with the results of Pawlowski for a single screw extruder. The data was also plotted against the dimensionless speed of rotation, i.e. the product of the screw speed and the average residence time within the mixing section. This brings the abscissa ranges for mixers with different conveying capacity closer together, and differences in mixing efficiency between the tested configurations can be better interpreted. The energetic efficiency of the mixers investigated is compared by applying the concept of specific action. This helps to decide which mixer geometry and operating conditions produce a given homogeneity with the lowest amount of work done by viscous forces.
High-yield design of high-density SRAM for low-voltage and low-leakage operations (2017)

The minimum functional voltage of System-On-Chip manufactured in recent technology nodes is often that of its Static Random-Access Memories (SRAM). Operating SRAM at subnominal voltage requires the use of additional circuits named assist circuits. This paper details the write assist and the temperature- and process-compensated read assist circuits used against insufficient bitcell Write Margin (WM) and Static Noise Margin (SNM), respectively. A new graphic tool named yieldogram is introduced to monitor clearly over a supported temperature range the capacity-dependent safe design region at various yield targets, including the highest industrial standard (1ppm), and is used to evaluate graphically the effects of different combinations of assist. We show that our implementation of WordLine UnderDrive (WLUD) assist technique against SNM limitations has a minimum impact on the performance, since it is temperature- and process-compensated, while negative BitLine implementation against WM limitations improves performances. The combined use of both techniques allows to gain more than 20% Vddmin, improving the frequency by 15%, decreasing dynamic power by 10% with worst-case increases in area and static power of 10 %. Finally, with a small WLUD overhead, yield can be obtained on Mass-Scale Production even after ageing.
A Mechanistic Model for Amorphous Protein Aggregation of Immunoglobulin-like Domains (2013)

Protein aggregation is associated with many debilitating diseases including Alzheimer's, Parkinson's, and light-chain amyloidosis (AL). Additionally, such aggregation is a major problem in an industrial setting where antibody therapeutics often require high local concentrations of protein domains to be stable for substantial periods of time. However, despite a plethora of research in this field, dating back over 50 years, there is still no consensus on the mechanistic basis for protein aggregation. Here we use experimental data to derive a mechanistic model that well describes the aggregation of Titin I27, an immunoglobulin-like domain. Importantly, we find that models that are suitable for nucleated fibril formation do not fit our aggregation data. Instead, we show that aggregation proceeds via the addition of activated dimers, and that the rate of aggregation is dependent on the surface area of the aggregate. Moreover, we suggest that the "lag time" seen in these studies is not the time needed for a nucleation event to occur, but rather it is the time taken for the concentration of activated dimers to cross a particular solubility limit. These findings are reminiscent of the Finke-Watzky aggregation mechanism, originally based on nanocluster formation and suggest that amorphous aggregation processes may require mechanistic schemes that are substantially different from those of linear fibril formation.
Erosional and Mechanical Strengths of Deposited Cohesive Sediments (1998)

Erosion tests were run on soft cohesive sediment beds freshly deposited from a concentrated slurry, in a large rotating annular flume. A total of seven tests were carried out with the bed age varying between 1.8 and 18.9 days. A surface type erosion was observed for the applied shear stress range (0.1 to 1 Pa). Following the increase in the water flow, the erosion rate increases quickly to a peak value and then drops off to about zero. The eroded depth was less than 8 mm for all beds, but the resistance to erosion at a given depth and for a given bed structure increased with increasing bed age. This phenomenon was attributed to thixotropy. The erosional strength of a given sediment layer is found to be one order of magnitude lower than its undrained and drained mechanical shear strengths measured with innovative testing methods. Hypotheses are given to explain that difference. However, at constant density and soil-water chemistry, the erosional and mechanical strengths seem to be affected by the same factors, i.e., bed age, structure, and temperature.
Psychosocial outcome and psychiatric comorbidity in older adolescents with Tourette syndrome: controlled study (2010)

Clinically ascertained children with Tourette syndrome typically have impaired psychosocial functioning and high comorbidity rates in late adolescence.
Inhibition of neurotransmitter receptor binding by ergot derivatives (1981)

Bromocriptine, lergotrile, lisuride, metergoline, and the Sandoz ergot derivatives 25-397, 29-712, and 29-717 have been tested for their ability to inhibit the synaptic receptor binding of spiroperidol, 5-hydroxytryptamine (5-HT), d-lysergic acid diethylamide (LSD), quinuclidinyl benzilate (QNB), WB.4101, and gamma-aminobutyric acid (GABA). Only GABA binding was not affected, and QNB binding was decreased only by lergotrile and metergoline at high concentrations. The most potent inhibitors of the other ligands were bromocriptine and lisuride for spiroperidol (1-2 nMM), metergoline for 5-HT (29 nM), lisuride for LSD (15 nM), and lergotrile for WB.4101 (17 nM). The direct receptor effects of the ergot derivatives in vitro may contribute to understanding their in vivo effects on behavior and in predicting their therapeutic potential in neurological and neuroendocrine disorders.
NON-IMPLICATION OF HOP α- AND β- ACIDS AS SOURCES OF SULPHUR COMPOUNDS IN BEER (1985)

Whereas hop oil terpenoids can give rise to organoleptically undesirable sulphur compounds in beer brewed using hops dressed on the bine with sulphur, the hop resin α- and β-acids and their transformation products appear incapable of reactions with sulphur under analogous conditions. The evidence indicates that the hop resins are not potential sources of sulphur compounds in beer
Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5 (2022)

After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.
Overexpression of the Wild-Type SPT1 Subunit Lowers Desoxysphingolipid Levels and Rescues the Phenotype of HSAN1 (2009)

Mutations in the SPTLC1 subunit of serine palmitoyltransferase (SPT) cause an adult-onset, hereditary sensory, and autonomic neuropathy type I (HSAN1). We previously reported that mice bearing a transgene-expressing mutant SPTLC1 (tgSPTLC1(C133W)) show a reduction in SPT activity and hyperpathia at 10 months of age. Now analyzed at a later age, we find these mice develop sensory loss with a distal small fiber neuropathy and peripheral myelinopathy. This phenotype is largely reversed when these mice are crossed with transgenic mice overexpressing wild-type SPTLC1 showing that the mutant SPTLC1 protein is not inherently toxic. Simple loss of SPT activity also cannot account for the HSAN1 phenotype, since heterozygous SPTLC1 knock-out mice have reduced SPT activity but are otherwise normal. Rather, the presence of two newly identified, potentially deleterious deoxysphingoid bases in the tgSPTLC1(C133W), but not in the wild-type, double-transgenic tgSPTLC1(WT + C133W) or SPTLC1(+/-) mice, suggests that the HSAN1 mutations alter amino acid selectivity of the SPT enzyme such that palmitate is condensed with alanine and glycine, in addition to serine. This observation is consistent with the hypothesis that HSAN1 is the result of a gain-of-function mutation in SPTLC1 that leads to accumulation of a toxic metabolite.
5-Fluorouracil Derivatives. II. A Convenient Synthesis of 5-Fluoro-2′-deoxyuridine (1977)

Abstract The reaction of 5-fluorouridine with propionyl bromide in acetonitrile afforded 3′,5′-di-O-propionyl-2′-bromo-5-fluoro-2′-deoxyuridine (2). Compound 2 was then hydrogenated, using Pd–C as the catalyst, to afford 3′,5′-di-O-propionyl-5-fluoro-2′-deoxyuridine (3). Compound 3 was deacylated with methanolic ammonia to give 5-fluoro-2′-deoxyuridine (FUDR). In this way, FUDR, a good antitumor agent, can easily be prepared from 5-fluorouridine by three steps in a 48.9% total yield.
TGF-β1 Inhibits TLR-mediated Odontoblast Responses to Oral Bacteria (2009)

TGF-beta1 exerts diverse functions in tooth development and tissue repair, but its role in microbial defenses of the tooth is not well-understood. Odontoblasts extending their cellular processes into the dentin are the first cells to recognize signals from TGF-beta1 and bacteria in carious dentin. This study aimed to determine the role of TGF-beta1 in modulating odontoblast responses to oral bacteria. We show that these responses depend upon the expression levels of microbial recognition receptors TLR2 and TLR4 on the cell surface. Porphyromonas gingivalis, Prevotella intermedia, and Fusobacterium nucleatum activated both TLRs, but TLR4 played a greater role. Lack of cell-surface TLR2 was associated with poor response to Streptococcus mutans, Enterococcus faecalis, and Lactobacillus casei. TGF-beta1 inhibited TLR2 and TLR4 expression and attenuated odontoblast responses. Our findings suggest that the balance between TLR-mediated inflammation and TGF-beta1 anti-inflammatory activity plays an important role in pulpal inflammation.
Quantitative Analysis of Qualitative Data (1981)

This paper presents an overview of an approach to the quantitative analysis of qualitative data with theoretical and methodological explanations of the two cornerstones of the approach, Alternating Least Squares and Optimal Scaling. Using these two principles, my colleagues and I have extended a variety of analysis procedures originally proposed for quantitative (interval or ratio) data to qualitative (nominal or ordinal) data, including additivity analysis and analysis of variance; multiple and canonical regression; principal components; common factor and three mode factor analysis; and multidimensional scaling. The approach has two advantages: (a) If a least squares procedure is known for analyzing quantitative data, it can be extended to qualitative data; and (b) the resulting algorithm will be convergent. Three completely worked through examples of the additivity analysis procedure and the steps involved in the regression procedures are presented.
Clinical validity of alerts generated by the CareEngine Claims-Driven Decision Support Engine. (2008)

Clinical decision support based on administrative data is an important "real-world" challenge. At an academic medical center, we reviewed medical charts to assess the accuracy of 182 clinical alerts generated from administrative claims, pharmacy data, and lab results by a computerized clinical decision support (CDS) system. Overall accuracy was 82%. The primary factor affecting alert accuracy was availability of complete data. Claims-driven CDS may be sufficiently accurate to be a valuable adjunct to quality improvement.
Using New High Resolution Satellite Based Aerosol Optical Depth Data for a Hybrid Model of Spatio-Temporal PM2.5 Exposures across North Eastern USA (2014)

Background: The use of satellite based aerosol optical depth (AOD) to estimate fine particulate matter (PM2.5) for epidemiology studies has increased substantially over the past few years. These recent studies still generally report moderate predictive power, which still present bias. In addition they all lack detailed high resolution predictions across large space-time domains (especially in rural areas) which is critical for acute exposure in epidemiological studies. Methods: We make use of recent advances in MODIS satellite images algorithms (MAIAC) which allows us to use high 1km resolution AOD data. We developed and cross validated models to predict daily PM2.5 at a 1x1 km resolution across North Eastern USA (New England, New York and New Jersey) for the years 2003- 2011, allowing us to better differentiate daily and long term exposure between urban, suburban, and rural areas. Additionally, we developed an approach that allows us to generate daily high resolution 200m localized predictions that are separate from the area 1x1km grid predictions. We used mixed models regressing PM2.5 measurements against day-specific random intercepts, and fixed and random AOD and temperature slopes. We then use generalized additive mixed model with spatial smoothing to generate grid cell predictions when AOD is missing. Finally to get high resolution predictions, we regressed the residuals from the final model for each monitor against the local spatial and temporal variables specific for each monitor. Results: our model performance was excellent (mean out-of-sample R2=0.88). The spatial and temporal out of sample results also presented very good fits to the held out data (R2=0.87, R2=0.87). In addition, our results revealed absolutely no bias in the predicted concentrations (Slope of observed vs. predicted = 0.99). Conclusion: Our model results show high predictive accuracy at high spatial resolutions and could benefit upcoming epidemiology studies.
Choroid plexus cyst, intracardiac echogenic focus, hyperechogenic bowel and hydronephrosis in screening for trisomy 21 at 11 + 0 to 13 + 6 weeks (2007)

At 11 + 0 to 13 + 6 weeks the prevalence of intracardiac echogenic focus, hydronephrosis and hyperechogenic bowel is higher in trisomy 21 than in chromosomally normal fetuses. As there is no significant association between the presence of these markers and nuchal translucency thickness, they could be included in the assessment of risk to improve accuracy of screening.
An antigenic determinant of human gamma-globulin susceptible to papain digestion. (1967)

Summary An antigenic determinant in human γG-globulin (HGG) is described which is susceptible to papain digestion. Both γ 1 - and γ 2 -antibodies against this determinant are readily shown in guinea pigs which have been rendered tolerant to papain digested HGG and immunized with the intact HGG molecule. Normal guinea pigs immunized solely with HGG, however, also possess antibodies against this determinant, but to a less marked degree. The determinant is specific for the γ-type of heavy chain of human γG-globulin. γG-globulin preparations from a number of other species; human γA- and γM-immunoglobulins; Bence-Jones proteins types K and L and light chain preparations from normal human γG-globulin, all lack the antigenic determinant. It was present in all of the γG-myeloma proteins tested, however, including representatives of the γG 1 -, γG 2 -, γG 3 - and γG 4 -subclasses and was also found in isolated γ-chain preparations from normal γG-globulin. The determinant is destroyed by papain and pepsin digestion, and evidence is presented to indicate that the site is essentially composed of secondary and tertiary structural forces.
Sex-Specific Dissociations in Autonomic and HPA Responses to Stress and Cues in Alcohol-Dependent Patients with Cocaine Abuse (2009)

While SA males showed a generalized suppression of HPA, SAM system and cardiovascular markers following both stress and cue, SA women demonstrated a selective sympatho-adrenal suppression to stress only and an enhanced HPA response to both stress and cue. These gender variations are discussed in terms of their potential impact on relapse vulnerability and treatment outcome.
A short biodegradable helical spiral ureteric stent provides better antireflux and drainage properties than a double-J stent (2011)

A self-expandable, SR-PLGA partial ureteric stent presented with superior drainage and antireflux properties compared to a double-J stent. The reflux commonly related to double-J stent use can be minimized by using a partial ureteric stent design.
Enhanced Potency of Nucleotide−Dendrimer Conjugates as Agonists of the P2Y 14 Receptor: Multivalent Effect in G Protein-Coupled Receptor Recognition (2020)

The P2Y14 receptor is a G protein-coupled receptor activated by uridine-5′-diphosphoglucose and other nucleotide sugars that modulates immune function. Covalent conjugation of P2Y14 receptor agonists to PAMAM (polyamidoamine) dendrimers enhanced pharmacological activity. Uridine-5′-diphosphoglucuronic acid (UDPGA) and its ethylenediamine adduct were suitable functionalized congeners for coupling to several generations (G2.5–6) of dendrimers (both terminal carboxy and amino). Prosthetic groups, including biotin for avidin complexation, a chelating group for metal complexation (and eventual magnetic resonance imaging), and a fluorescent moiety, also were attached with the eventual goals of molecular detection and characterization of the P2Y14 receptor. The activities of conjugates were assayed in HEK293 cells stably expressing the human P2Y14 receptor. A G3 PAMAM conjugate containing 20 bound nucleotide moieties (UDPGA) was 100-fold more potent (EC50 2.4 nM) than the native agonist uridine-5′-diphosphoglucose. A molecular model of this conjugate docked in the human P2Y14 receptor showed that the nucleotide-substituted branches could extend far beyond the dimensions of the receptor and be available for multivalent docking to receptor aggregates. Larger dendrimer carriers and greater loading favored higher potency. A similar conjugate of G6 with 147 out of 256 amino groups substituted with UDPGA displayed an EC50 value of 0.8 nM. Thus, biological activity was either retained or dramatically enhanced in the multivalent dendrimer conjugates in comparison with monomeric P2Y14 receptor agonists, depending on size, degree of substitution, terminal functionality, and attached prosthetic groups.
Mapping Stratigraphic Traps with Seislogs: ABSTRACT (1977)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.