gebhart/patrepeval huggingface dataset:
<title>Adaptive Bayesian networks</title> (1992)

The theory of adaptive Bayesian networks is summarized. A detailed discussion of the Adaptive Cluster Expansion (ACE) network is presented. ACE is a scalable Bayesian network designed specifically for high-dimensional applications, such as image processing.
Efficient Continuous Relaxations for Dense CRF (2016)

Dense conditional random fields (CRF) with Gaussian pairwise potentials have emerged as a popular framework for several computer vision applications such as stereo correspondence and semantic segmentation. By modeling long-range interactions, dense CRFs provide a more detailed labelling compared to their sparse counterparts. Variational inference in these dense models is performed using a filtering-based mean-field algorithm in order to obtain a fully-factorized distribution minimising the Kullback-Leibler divergence to the true distribution. In contrast to the continuous relaxation-based energy minimisation algorithms used for sparse CRFs, the mean-field algorithm fails to provide strong theoretical guarantees on the quality of its solutions. To address this deficiency, we show that it is possible to use the same filtering approach to speed-up the optimisation of several continuous relaxations. Specifically, we solve a convex quadratic programming (QP) relaxation using the efficient Frank-Wolfe algorithm. This also allows us to solve difference-of-convex relaxations via the iterative concave-convex procedure where each iteration requires solving a convex QP. Finally, we develop a novel divide-and-conquer method to compute the subgradients of a linear programming relaxation that provides the best theoretical bounds for energy minimisation. We demonstrate the advantage of continuous relaxations over the widely used mean-field algorithm on publicly available datasets.
Viscoelastic Modeling of Highly Hydrated Laminin Layers at Homogeneous and Nanostructured Surfaces:  Quantification of Protein Layer Properties Using QCM-D and SPR (2007)

The adsorption of proteins at material surfaces is important in applications such as biomaterials, drug delivery, and diagnostics. The interaction of cells with artificial surfaces is mediated through adsorbed proteins, where the type of protein, amount, orientation, and conformation are of consequence for the cell response. Laminin, an important cell adhesive protein that is central in developmental biology, is studied by a combination of quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance (SPR) to characterize the adsorption of laminin on surfaces of different surface chemistries. The combination of these two techniques allows for the determination of the thickness and effective density of the protein layer as well as the adsorbed mass and viscoelastic properties. We also evaluate the capacity of QCM-D to be used as a quantitative technique on a nanostructured surface, where protein is adsorbed specifically in a nanopattern exploiting PLL-g-PEG as a protein-resistant background. We show that laminin forms a highly hydrated protein layer with different characteristics depending on the underlying substrate. Using a combination of QCM-D and atomic force microscopy (AFM) data from nanostructured surfaces, we model laminin and antibody binding to nanometer-scale patches. A higher amount of laminin was found to adsorb in a thicker layer of a lower effective density in nanopatches compared to equivalent homogeneous surfaces. These results suggest that modeling of QCM-D data of soft viscoelastic layers arranged in nanopatterns may be applied where an independent measure of the "dry" mass is known.
Low HDL and high triglycerides predict COVID-19 severity (2021)

Lipids are indispensable in the SARS-CoV-2 infection process. The clinical significance of plasma lipid profile during COVID-19 has not been rigorously evaluated. We aim to ascertain the association of the plasma lipid profile with SARS-CoV-2 infection clinical evolution. Observational cross-sectional study including 1411 hospitalized patients with COVID-19 and an available standard lipid profile prior (n: 1305) or during hospitalization (n: 297). The usefulness of serum total, LDL, non-HDL and HDL cholesterol to predict the COVID-19 prognosis (severe vs mild) was analysed. Patients with severe COVID-19 evolution had lower HDL cholesterol and higher triglyceride levels before the infection. The lipid profile measured during hospitalization also showed that a severe outcome was associated with lower HDL cholesterol levels and higher triglycerides. HDL cholesterol and triglyceride concentrations were correlated with ferritin and D-dimer levels but not with CRP levels. The presence of atherogenic dyslipidaemia during the infection was strongly and independently associated with a worse COVID-19 infection prognosis. The low HDL cholesterol and high triglyceride concentrations measured before or during hospitalization are strong predictors of a severe course of the disease. The lipid profile should be considered as a sensitive marker of inflammation and should be measured in patients with COVID-19.
Induction of sarcomas in athymic mice. (1982)

During the course of serial passage of 50 human xenografts in the athymic mouse over a period of 5 years we have observed two cases of induction of sarcomas in the murine stromal tissue associated with the human xenografts. Both times the growth of the murine sarcomas overtook that of the human xenograft. This change was monitored by analysis of the lactate dehydrogenase isozyme profile and histology of each passage of the human xenografts in the athymic mice. The two murine sarcomas were subsequently established in tissue culture. The sarcoma cell lines were found to be malignant by morphological and growth characteristics and were tumorigenic. They contained large amounts of murine leukemia virus when assayed for reverse transcriptase activity by infection of mouse SC-1 cells and BALB/c and NIH Swiss fibroblasts with filtered supernates, and some type C virus particles were observed by electron microscopy in tumor tissues. However, we were unable to demonstrate the presence of murine sarcoma virus by in vitro transformation of fibroblasts or sarcoma formation in vivo will cell free filtrates. Preliminary biochemical data indicate that the sarcomas are extremely high in plasma membrane ATP phosphohydrolase.
Surface and electrochemical properties of polypropylene track membrane modified by plasma of non-polymerizing gases (2013)

The surface and electrochemical properties of polypropylene track membrane treated by plasma of nitrogen, air, and oxygen are studied. The effect of the plasma-forming gas composition on the surface morphology is considered. The membrane surface microrelief formed during the gas-discharge etching is found to change. Moreover, the non-polymerizing gas plasma treatment induces oxidation of the membrane surface layer and generates oxygen-containing functional groups, mostly carbonyl and carboxyl. The higher membrane roughness and its hydrophilization is shown to lead to its better wettability. In addition, the presence of polar groups in the membrane surface layer modifies its hydrodynamic and electrochemical properties so that water permeability and conductivity of modified membranes increase.
Rapid Multilabel Detection of Geranylgeranylated Proteins by Using Bioorthogonal Ligation Chemistry (2010)

One tag, two labels: Defects in protein prenylation lead to a number of serious diseases; here we show that an azide-tagged substrate enables multilabel detection of defective protein geranylgeranylation by two geranylgeranyl transferases. Rapid in-gel visualization and affinity purification have been demonstrated on recombinant proteins, cell lines, and mammalian disease models. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Compartment syndrome performance improvement project is associated with increased combat casualty survival (2012)

Therapeutic study, level IV.
Oxindoles from α‐acyloxyamides (1977)

Abstract Oxindoies have been obtained in good yields from the reaction of several a‐acyloxy‐α,α‐diphenylacetanilides and boron trifluoride etherate. The reaction probably occurs by hydrolysis of the ester followed by electrophilic substitution of the resultant carbonium ion on the anilide ring.
Conversion of a CO–CO2 co‐feed with a porous tubular copper catalyst at low potential (2022)

Abstract In the electrochemical reduction of CO 2 , copper electrodes are well known to be active and selective for a variety of products, depending on process conditions. However, the effect of feed composition on performance has not been extensively investigated, especially with respect to the conversion of CO 2 to CO. We now show for copper electrodes in a porous tubular configuration (Hollow Fibre Electrodes, HFEs) at a relatively low working potential (−1.1 V vs Ag/AgCl), that an increasing concentration of CO in the feed results in a decreasing CO 2 conversion rate to CO. Contrary, it is observed that the concomitant hydrogen production rate does not depend on the concentration of CO in the feed. These observations are in good agreement with thermodynamic predictions applying the equation for the Gibbs energy of reaction. On the basis of this conclusion, we anticipate that mass transfer limitations are minimized by the tubular morphology and flow‐through mode of operation. Most importantly, this study shows the necessity of a low CO concentration in the feed, to obtain a high CO 2 conversion rate.
P347 Vedolizumab for primary sclerosing cholangitis associated with inflammatory bowel disease: A multicentre cohort study from the GETAID (2018)

Whether vedolizumab is effective and safe as a treatment of primary sclerosing cholangitis (PSC) is unclear. We performed a retrospective observational study, collecting data from 22 tertiary centres in France and Belgium affiliated to the GETAID from January 2015 to June 2016, on all consecutive patients with IBD and associated PSC treated with vedolizumab for at least 30 weeks unless vedolizumab was discontinued for PSC-related complications. Patients were retrospectively evaluated until week 54. Routine laboratory test values including alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), γ-glutamyltransferase (GGT), total bilirubin, C-reactive protein (mg/l) and serum albumin (g/l) were analysed. Liver enzymes changes were given according to the upper limit of normal (ULN). The primary efficacy objective was a decrease of at least 50% in the serum ALP concentration from baseline to week 30. A total of 56 patients (39 males; 21 with Crohn’s disease (CD), 34 with ulcerative colitis (UC) and 1 with indeterminate IBD; median age at diagnosis of PSC 25.1 [18.0–35.3] years; median age at diagnosis of IBD 19.8 [16.4–32.5] years) were included in this study. At baseline, concomitant treatment included ursodeoxycholic acid in 47 (83.9%) patients, steroids in 28 (50.9%), and immunomodulators in 19 (33.9%). At baseline, ALP, ALT, AST, total bilirubin and GGT, CRP and serum albumin were 2.2 ± 2.9 ULN, 1.7 ± 2.0 ULN, 1.3 ± 1.1 ULN, 1.2 ± 2.0 ULN, 5.3 ± 9.0 ULN, 17.5 ± 23.8 mg/l and 36.6 ± 5.3 g/l, respectively. At week 30 and 54, the data of 54 and 33 patients could be analysed. A decrease of at least 50% in the serum ALP concentration from baseline to week 30 was achieved in only 4 (7.4%) patients at week 30 and 3 (9.1%) at week 54. No changes in other liver tests was observed at week 30 and 54 with the exception of a mild increase in ALP concentration at week 54 (+0.4 ± 1.0 ULN, p = 0.02) whereas the mean CRP level significantly decreased at week 54. Adverse events were reported in 12 (21.4%) patients, mostly consisting in incidental infections in 7 patients and incidental cases of digestive cancers in 5 patients (three cases of colorectal cancer between week 22 and week 30 and two cases of cholangiocarcinoma between week 2 and week 6). Although VDZ showed effectiveness in patients with active refractory IBD, it did not improve liver tests at weeks 30 and 54 in PSC patients. The safety profile was consistent with previous data reported in IBD patients without PSC. Five cases of digestive cancer occurred during the follow-up period confirming the need for a tight surveillance program of patients with concomitant IBD and PSC.
Compliance with CPAP therapy in patients with the sleep apnoea/hypopnoea syndrome. (1994)

Patients with sleep apnoea/hypopnoea syndrome used CPAP for less than five hours/night on average with no correlation between severity of sleep apnoea/hypopnoea syndrome and CPAP usage. Patients who complained of side effects used their CPAP therapy less. It is recommended that, as a minimum, CPAP run time should be regularly recorded in all patients receiving CPAP therapy.
A new approach to determining the rates of recruitment of circulating leukocytes into tissues: Application to the measurement of leukocyte recruitment into atherosclerotic lesions (1997)

Recruitment of circulating monocytes into the artery wall is an important feature of early atherogenesis. In vitro studies have identified a number of adhesion molecules and chemokines that may control this process but very little work has been done to evaluate their relative importance in vivo, in part because there have been no methods available of sufficient sensitivity and reliability. This paper proposes a new approach in which advantage is taken of naturally occurring or transgenically induced mutations to "mark" donor cells and to follow their fate in recipient animals using highly sensitive PCR methods. The feasibility of the approach is demonstrated by preliminary studies of monocyte recruitment into atherosclerotic lesions. However, the method should in principle be applicable to the study of any of the circulating leukocytes and their rate of entry into any tissue or tissues of interest.
Comparison of K&#x03B1; x-ray source from different metal targets using Sub-mJ kilohertz femto-second laser pulses (2009)

Summary form only given. We have developed an efficient Cu Kalpha X-ray source produced by a commercial kilohertz fs laser system. The source has a high X-ray conversion efficiency of 4x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> into Cu Kalpha line emission at 8.05 keV. The microplasma X-ray source is produced by focusing 260 muJ laser pulses of 130 fs (FWHM) on a moving Cu-wire target. The source has a size of < 10 mum as measured by a knife edge technique and is expected to have a short temporal duration on the order of a picosecond. Recently we have extended the operation of the source to new wavelengths by using steel wire and silver coated copper wire targets. The Fe and Ag Kalpha line emission is at 6.4 keV and 22.2 keV respectively. The emission energy and spectra at these new photon energies has been characterized using three different detector systems which include a filtered PIN diode detector, pulse height spectrometer using a CdTe detector along with multichannel analyzer and a single hit CCD camera used in pulse height analysis mode. The conversion efficiencies and spectra will be presented at these new wavelengths and compared to scaling laws for expected conversion efficiency from the energetic laser-produced electrons into X-rays. An average X-ray photon flux of > 109 ph/sr/s is achieved and the emission provides sufficient spatial coherence and intensity for applications such as phase contrast imaging of biological samples or testing of X-ray microscope components. It is expected that this compact source can be developed into a durable low cost operating system for time resolved pulse probe experiments, phase contrast imaging of biological specimens and testing of X-ray optics.
Effects of Human Menopausal Gonadotropin and Ovine Follicle Stimulating Hormone on Lactic Acid Production by Ovaries from Prepubertal Rats (1968)

Two preparations of follicle stimulating hormone extracted from human menopausal urine have been compared with an ovine preparation of FSH in relation to their effects on lactic acid production by ovaries from prepubertal rats. It was found that all 3 preparations stimulated lactic acid production when added in vitro and that the slopes of the dose-response curves did not differ. These results strongly support our previous suggestion (4) that FSH has effects on the carbohydrate metabolism of the prepubertal rat ovary. (Endocrinology82: 420, 1968)
MEASUREMENTS OF LOCAL SWEAT RATES AND EVAPORATION RATES AND THE DIRECT DETERMINATION OF LOCAL EVAPORATIVE HEAT TRANSFER COEFFICIENTS (1994)

Local calorimetry was studied using a device to measure local evaporation rates (disk) and a ventilated capsule to measure local sweat rates (msw). Changes in msw and msk at chest, forearm and front thigh were observed while two young male subjects were exposed to the heat (46-48℃) for 1 hour. During the first 30-40 minutes, m_<SK> increased progressively with m_<SW> and became appreciably less than m_<SW> when the skin was fully wetted. Thus, the critical m_<Sk> value can be clearly defined so as to determine local evaporative heat transfer coefficients.
Four Orders of Magnitude Acceleration of Electron Recombination at the Dye-TiO2/Electrolyte Interface Severely Limiting Photocurrent with High-Oxidation-Potential Cu2+/1+ Complexes (2023)

High-oxidation-potential Cu1+ complexes have been claimed to exhibit fast electron transfer toward oxidized dyes (dye)•+ on electrode surfaces (regeneration) at a low driving force. Herein, we show that the regeneration of the surface-bound (dye)•+ with heteroleptic Cu1+ complex electrolytes with a high oxidation potential, defined by the lowest oxidation potential redox peak, with a dye regeneration driving force of 170 meV is slow. On the other hand, the recombination reaction between the electrons in the semiconductor and the (dye)•+ is accelerated by 4 orders of magnitude in the presence of a Cu2+ complex. Thus, using the Cu2+/1+ complex mixture in an electrolyte solution, such previously unknown acceleration of recombination could easily be misinterpreted as dye regeneration. This significant finding helps to explain the previously unknown origin of the photocurrent drop of solar cells using high-redox-potential Cu2+/1+ complexes with high apparent regeneration yield. Although the origin of such unprecedented acceleration of kinetics is not yet fully identified, partial oxidation of the dye layer by the Cu2+ complexes is one of the key sources. The study is expected to influence the design of new redox mediators at a low driving force and specifically how their regeneration efficiency is evaluated. The huge acceleration of kinetics could provide a new avenue to control electron transfer rates at semiconductor/organic molecule interfaces relevant to a number of electrochemical applications involving electron transfer at semiconductor/electrolyte junctions, including photocatalysis, photosynthetic systems, and sensing.
RT‐PCR/MALDI‐TOF mass spectrometry‐based detection of SARS‐CoV‐2 in saliva specimens (2021)

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.
Static and Dynamic Analysis of Bistable Piezoelectric-Composite Plates for Energy Harvesting (2012)

Peer Reviewed
SNOBFIT -- Stable Noisy Optimization by Branch and Fit (2008)

The software package SNOBFIT for bound-constrained (and soft-constrained) noisy optimization of an expensive objective function is described. It combines global and local search by branching and local fits. The program is made robust and flexible for practical use by allowing for hidden constraints, batch function evaluations, change of search regions, etc.
A mutation in the interferon sensitivity‐determining region is associated with responsiveness to interferon‐ribavirin combination therapy in chronic hepatitis patients infected with a Japan‐specific subtype of hepatitis C virus genotype 1b (2006)

The interferon sensitivity-determining region (ISDR) is useful as a predictive marker of the response to interferon (IFN) therapy for chronic hepatitis patients with a Japan-specific subtype (J-type) of hepatitis C virus (HCV) genotype 1b. This marker is not useful for predicting responsiveness of a worldwide subtype (W-type) of HCV 1b, which could explain the restricted usefulness of this system only to Japan. In the present study, we examined the predictive value of the ISDR for ribavirin combination therapy. A total of 79 patients with HCV 1b comprising 35 patients with J-type and 44 patients with W-type were treated with IFN in combination with ribavirin for more than 48 weeks. Mutations in the ISDR were detected more frequently often seen in J-type HCV 1b than in W-type; however, the sustained virological response (SVR) rate for the combination therapy was similar between the two subtypes. Multivariate analysis revealed that factors associated with SVR were IFN dose and the number of amino acid substitutions in ISDR but not with subtypes J and W. The correlation between the number of substitutions in ISDR and responses to IFN-ribavirin combination therapy was restricted to patients with J-type HCV 1b. The ISDR is a useful predictive marker for response to IFN-ribavirin combination therapy in J-type HCV.