gebhart/patrepeval huggingface dataset:
Surgical Outcomes of Ahmed or Baerveldt Tube Shunt Implantation for medically Uncontrolled Traumatic Glaucoma (2017)

Yadgarov A, Liu D, Crane ES, Khouri AS. Surgical Outcomes of Ahmed or Baerveldt Tube Shunt Implantation for medically Uncontrolled Traumatic Glaucoma. J Curr Glaucoma Pract 2017;11(1):16-21.
Depth-Guided Disocclusion Inpainting of Synthesized RGB-D Images (2016)

We propose to tackle the problem of RGB-D image disocclusion inpainting when synthesizing new views of a scene by changing its viewpoint. Indeed, such a process creates holes both in depth and color images. First, we propose a novel algorithm to perform depth-map disocclusion inpainting. Our intuitive approach works particularly well for recovering the lost structures of the objects and to inpaint the depth-map in a geometrically plausible manner. Then, we propose a depth-guided patch-based inpainting method to fill-in the color image. Depth information coming from the reconstructed depth-map is added to each key step of the classical patch-based algorithm from Criminisi et al. in an intuitive manner. Relevant comparisons to the state-of-the-art inpainting methods for the disocclusion inpainting of both depth and color images are provided and illustrate the effectiveness of our proposed algorithms.
Integrated approaches to academic anaesthesia – the Cambridge experience (2004)

There is mounting concern about the pressures experienced by University Departments of Anaesthesia, which, if lost, could threaten undergraduate peri-operative medicine teaching, development of critical appraisal skills among anaesthetists, and the future of coherent research programs. We have addressed these problems by establishing a foundation course in scientific methods and research techniques (the Cambridge SMART Course), complemented by competitive, fully funded, 12-month academic trainee attachments. Research conducted during academic attachments has been published and used to underpin substantive grant applications allowing work towards higher degrees. Following the attachment, a flexible scheme ensures safe reintroduction to clinical training. Research at consultant level is facilitated by encouraging applications for Clinician Scientist Fellowships, and by ensuring that the University Department champions, legitimises and validates the allocation of research time within the new consultant contract. We believe that these are important steps in safeguarding research and teaching in anaesthesia, critical care and peri-operative medicine.
Barriers to HIV Care: An Exploration of the Complexities That Influence Engagement in and Utilization of Treatment (2010)

This study is an exploration of engagement in outpatient medical care, medication utilization, and barriers to treatment utilization among 24 predominantly low-income, ethnic minority adults who were admitted to an urban hospital for HIV-related illnesses. A semi-structured interview was administered during the sample's hospital stay to explore patterns of service use and identify barriers to care. The majority of the sample was connected to an outpatient provider and satisfied with the care they received; however, most missed treatment appointments and skipped medication dosages. Health and treatment-related barriers, competing demands, and co-occurring mental health symptoms and illicit substance use were identified as barriers to care. Multiple obstacles indigenous to the individual, their treatment, and the environment prevented consistent treatment use among an economically disadvantaged ethnic minority sample: Implications and future directions in engaging vulnerable populations into health care for HIV are discussed.
Mechanisms of Gene Activation (1995)

S. Buratowski discusses two papers in this issue of Science (Sauer et al ., pp. 1783 and 1825 ) that show that the basal transcription factor complex TFIID is a target of transcriptional activators.
Indigenous kaolinite ore as cost effective adsorbent for re-refining of used lubricating oil (2018)

Present study evaluates efficiency of indigenous kaolinite ore as environment friendly and low cost adsorbent for re-refining of used lubricating oil. Thermo gravimetric analysis was used to find the mass variation with rise in temperature. Different characterizing techniques such as XRD, SEM and EDS were used to see the physical and chemical changes, composition and available volume of pores before and after activation. Indigenous kaolinite ore was activated at 600 °C for one hour to increase pore size to surface area ratio. Adsorption was carried out by passing exhausted lube oil with commercial grade n-hexane in a fixed 1:2 v/v ratio over the surface of activated kaolinite in a glass column with length to diameter ratio of 16:1. The improvement in the quality of lube oil was determined by comparing quality parameters of used and refined lube oil. The process gave 95 % yield of good quality transparent pale-yellow oil having colour index of 2 with 99 % of metal reduction. Maximum capability of kaolinite ore to adsorbed oil was found to be 160 g of refined oil/200 g of kaolinite. Used adsorbent was regenerated and utilized again for the adsorption of more oil. Regenerated ore provided 150 g refined oil/200 g Kaolinite. The solvent was recovered through rotary evaporator under vacuum. Recovery of solvent and adsorbent regeneration suggest that proposed method for purification of lube oil is environment friendly and cost effective.
IP-10 differentiates between active and latent tuberculosis irrespective of HIV status and declines during therapy (2015)

IP-10 distinguished with high accuracy active TB from LTBI irrespective of HIV infection and declined during anti-TB chemotherapy. Plasma IP-10 may serve as a diagnostic biomarker to differentiate between the stages of TB infection and for monitoring therapy efficacy.
Developing Promiscuous Glycosidases for Glycoside Synthesis: Residues W433 and E432 in Sulfolobus solfataricus β‐Glycosidase are Important Glucoside‐ and Galactoside‐Specificity Determinants (2005)

Two residues that have been implicated in determining the substrate specificity of the thermophilic beta-glycosidase from the archaeon Sulfolobus solfataricus (SsbetaG), a member of the glycosyl hydrolase family 1, have been mutated by site-directed mutagenesis so as to create more versatile catalysts for carbohydrate chemistry. The wild-type and mutated sequences were expressed in E. coli with a His(7)-tag to allow one-step chromatographic purification. The E432C and W433C mutations removed key interactions with the OH-4 and OH-3 of the sugar substrates, thus reducing the discrimination of glucose, galactose and fucose with respect to other glycosides. This resulted in two glycosidases with greatly broadened substrate specificities. Observed changes include a 24-fold increase in Man:Gal activity and an 18-fold increase in GalA:Gal activity. This promiscuous substrate tolerance was further illustrated by the parallel synthesis of a beta-glycoside library of glucose, galactose, xylose and mannose in one pot at 50 degrees C, in organic solvent. The synthetic potential of the catalysts was further evaluated through alkyl glycoside transglycosylation yields, including the first examples of synthesis of beta-mannosides and beta-xylosides with SsbetaG.
Site‐directed mutagenesis of a single residue changes the binding properties of the serotonin 5‐HT2 receptor from a human to a rat pharmacology (1992)

Mesulergine displays approximately 50-fold higher affinity for the rat 5-HT2 receptor than for the human receptor. Comparison of the deduced amino acid sequences of cDNA clones encoding the human and rat 5-HT2 receptors reveals only 3 amino acid differences in their transmembrane domains. Only one of these differences (Ser----Ala at position 242 of TM5) is near to regions implicated in ligand binding by G protein-coupled receptors. We investigated the effect of mutating Ser242 of the human 5-HT2 receptor to an Ala residue as is found in the rat clone. Both [3H]mesulergine binding and mesulergine competition of [3H]ketanserin binding showed high affinity for rat membranes and the mutant human clone but low affinity for the native human clone, in agreement with previous studies of human postmortem tissue. These studies suggest that a single naturally occurring amino acid change between the human and the rat 5-HT2 receptors makes a major contribution to their pharmacological differences.
Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes (2011)

This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.
Solvent-Free Oxidation of Primary Carbon-Hydrogen Bonds in Toluene Using Au-Pd Alloy Nanoparticles (2011)

Selective oxidation of primary carbon-hydrogen bonds with oxygen is of crucial importance for the sustainable exploitation of available feedstocks. To date, heterogeneous catalysts have either shown low activity and/or selectivity or have required activated oxygen donors. We report here that supported gold-palladium (Au-Pd) nanoparticles on carbon or TiO(2) are active for the oxidation of the primary carbon-hydrogen bonds in toluene and related molecules, giving high selectivities to benzyl benzoate under mild solvent-free conditions. Differences between the catalytic activity of the Au-Pd nanoparticles on carbon and TiO(2) supports are rationalized in terms of the particle/support wetting behavior and the availability of exposed corner/edge sites.
Herpes simplex virus type 1 infection prevents detachment of nerve growth factor-differentiated PC12 cells in culture (2002)

In tissue culture, rat pheochromocytoma (PC12) cells differentiated with nerve growth factor (NGF) cease division, extend neuritic processes and acquire many properties characteristic of neuronal cells. In previous work, we have shown that NGF-differentiated PC12 cells can survive infection with herpes simplex virus type 1 (HSV-1) and maintain the viral genome in a quiescent but reactivatable state. In this study, we report that uninfected NGF-differentiated PC12 cells uniformly and predictably detach from the culture flask substratum after approximately 7 weeks. Although uninfected cells were uniformly lost from the culture by 7 weeks, surprisingly HSV-1-infected cells survived beyond 10 weeks, the time limit of the study. The detachment of uninfected cells was not the result of cell death or apoptosis, as determined by viability assays performed on cells after detachment. Expression of the HSV-1 latency associated transcript (LAT) gene and virus replication was not necessary for the virus to suppress the 'detachment' phenomenon, since NGF-differentiated PC12 cells infected with either wild-type, DNA polymerase mutant or LAT null mutant virus survived in culture for similar lengths of time. Viral gene expression does appear to be necessary for the suppression, however, since cells infected with UV-inactivated virus were lost from culture with kinetics similar to those of uninfected cells. These findings indicate that de novo viral gene synthesis mediates changes to the host NGF-differentiated PC12 cells, which results in prevention of detachment.
The First Tandem Acetalization/5-exo-dig Cyclizationof 6-Phenylethynyl-pyrimidine-5-carbaldehydes: EfficientSynthesis of 5-Alkoxy-(7Z)-7-benzylidene-5,7-dihydrofuro[3,4-d]pyrimidines (2008)

Correction to: The First Tandem Acetalization/5-exo-dig Cyclization of 6-Phenylethynylpyrimidine-5-carbaldehydes: Efficient Synthesis of 5-Alkoxy-(7Z)-7-benzylidene-5,7-dihydrofuro[3,4-d]pyrimidinesSynlett 2008; 2008(11): 1693-1697DOI: 10.1055/s-2008-1077824
A Small-Animal Pharmacokinetic/Pharmacodynamic PET Study of Central Serotonin 1A Receptor Occupancy by a Potential Therapeutic Agent for Overactive Bladder (2013)

Serotonin 1A (5-HT1A) receptors have been mechanistically implicated in micturition control, and there has been a need for an appropriate biomarker surrogating the potency of a provisional drug acting on this receptor system for developing a new therapeutic approach to overactive bladder (OAB). Here, we analyzed the occupancy of 5-HT1A receptors in living Sprague-Dawley rat brains by a novel candidate drug for OAB, E2110, using positron emission tomography (PET) imaging, and assessed the utility of a receptor occupancy (RO) assay to establish a pharmacodynamic index translatable between animals and humans. The plasma concentrations inducing 50% RO (EC50) estimated by both direct and effect compartment models were in good agreement. Dose-dependent therapeutic effects of E2110 on dysregulated micturition in different rat models of pollakiuria were also consistently explained by achievement of 5-HT1A RO by E2110 in a certain range (≥ 60%). Plasma drug concentrations inducing this RO range and EC50 would accordingly be objective indices in comparing pharmacokinetics-RO relationships between rats and humans. These findings support the utility of PET RO and plasma pharmacokinetic assays with the aid of adequate mathematical models in determining the in vivo characteristics of a drug acting on 5-HT1A receptors and thereby counteracting OAB.
The role of RIAM in platelets put to a test (2015)

In this issue of Blood, Stritt et al show that platelet functions dependent on integrin activation are unimpaired in mice lacking the Rap1-GTP-interacting adaptor molecule (RIAM).
Early assessment of treatment effect in advanced lung adenocarcinoma via longitudinal ctDNA analysis. (2018)

12088 Background: Despite routine use of chemotherapy in advanced non-small-cell lung cancer (NSCLC) patients, the knowledge of optimal prognostic methods is still limited to imaging-based methods. We hypothesized that an early response assessed by mutant molecules count in plasma could predict the treatment effect. Methods: We employed AVENIO ctDNA Surveillance Kit, a 197-gene NGS assay, which allowed us to perform longitudinal ctDNA analysis and measure the mutant molecules per milliliter-of-plasma (MMPM), which quantifies ctDNA at the variant level. The association between changes in ctDNA levels and survival was evaluated in advanced lung adenocarcinoma subjects. Post-treatment MMPM values were compared with the MMPM value at baseline and/or the previous treatment timepoint. Results: At baseline (b0), we identified variants in all (93/93) subjects to enable ctDNA monitoring. From the training cohort (50 subjects), we were able to set the cutoff of 40 for the mean MMPM at post-first treatment cycle (p1). Applying the MMPM cutoff of p1 to the validation cohort (43 subjects with stage IV lung adenocarcinoma, from a prospective, observational study) low levels of ctDNA toward the end of first treatment cycle was associated with better progression-free survival (PFS) (P = 0.0088 HR 0.4; 95% CI 0.20 - 0.83) and overall survival (OS) (P = 0.0026 HR 0.32; 95% CI 0.15 - 0.71). The prognostic value is increased by applying the Continuous Responder algorithm, defined by a continuous drop in ctDNA levels represented by mean MMPM reduction over time (p2 < p1 < b0), to a mean MMPM below 8 at p2. As a result, continuous responders 13/43 (30%) were associated with a better therapy response indicated by PFS (P = 0.028 HR 0.45; 95% CI 0.23 - 0.90) and OS (P = 0.0074 HR 0.3; 95% CI 0.12 - 0.77). The continuous responders demonstrated a median overall survival benefit of 11.25 months over the poor responders. Conclusions: A decrease in post-treatment ctDNA level measured by NGS was associated with better prognosis in advanced lung adenocarcinoma. An early assessment of treatment effect can be measured by mutant molecule counts in the plasma within 1 or 2 treatment cycles.
Adaptive Sliding Mode Spacecraft Attitude Control (2014)

An adaptive sliding mode spacecraft attitude controller is derived in this paper. It has the advantage of not requiring knowledge of the inertia of the spacecraft, and rejecting unexpected external disturbances, with global asymptotic position and velocity tracking. The sliding manifold is designed using optimal control analysis of the quaternion kinematics. The sliding mode control law and the parameter adaptation law are designed using Lyapunov stability. Numerical simulations are performed to demonstrate both the nominal and the robust performance.
Golden Reference-Free Hardware Trojan Localization using Graph Convolutional Network (2022)

The globalization of the Integrated Circuit (IC) supply chain has moved most of the design, fabrication, and testing process from a single trusted entity to various untrusted third-party entities worldwide. The risk of using untrusted third-Party Intellectual Property (3PIP) is the possibility for adversaries to insert malicious modifications known as Hardware Trojans (HTs). These HTs can compromise the integrity, deteriorate the performance, deny the service, and alter the functionality of the design. While numerous HT detection methods have been proposed in the literature, the crucial task of HT localization is overlooked. Moreover, a few existing HT localization methods have several weaknesses: reliance on a golden reference, inability to generalize for all types of HT, lack of scalability, low localization resolution, and manual feature engineering/property definition. To overcome their shortcomings, we propose a novel, golden reference-free HT localization method at the pre-silicon stage by leveraging Graph Convolutional Network (GCN). In this work, we convert the circuit design to its intrinsic data structure, graph and extract the node attributes. Afterward, the graph convolution performs automatic feature extraction for nodes to classify the nodes as Trojan or benign. Our automated approach does not burden the designer with manual code review. It locates the Trojan signals with 99.6% accuracy, 93.1% F1-score, and a false-positive rate below 0.009%.
Tramonto: Software for Nanostructured Fluids in Materials and Biology. (2020)

Abstract not provided.
Abstract 12087: Prevalence and Prognostic Implications of CMR Detected Myocardial Fibrosis in Patients With Mitral Valve Prolapse (2016)

Background: Mitral valve prolapse (MVP) is the most common cause of primary mitral regurgitation (MR). Arrhythmia and sudden cardiac death (SCD) have been associated with MVP; however, the mechanism is unclear. Prior studies suggested left ventricular (LV) fibrosis as an arrhythmic substrate. Hypothesis: MVP patients have an increased prevalence of LV fibrosis which associated with adverse outcome. Methods: Patients referred for CMR to assess mitral valve disease were enrolled. Confounding causes of LV fibrosis (CAD, LVEF &lt; 50% etc.) and secondary MR were excluded. Primary MR patients were classified into MVP (&gt;2 mm leaflet displacement) and a non-MVP group. Cine, phase contrast CMR were performed to assess cardiac morphology/function and MR severity. Late gadolinium enhancement (LGE) CMR was performed to identify LV fibrosis. Patients were followed for 1) arrhythmic events comprised of SCD/aborted SCD, or sustained/inducible ventricular arrhythmia requiring ICD and 2) composite outcome that included arrhythmic events or cardiovascular death. Results: 356 primary MR patients (177 MVP, and 179 non-MVP) were enrolled. Baseline characteristics were relatively similar except MVP patients had more severe MR (MR fraction 42.1±14.3% vs. 32.8±12.2%, p&lt;0.03). LGE representing LV fibrosis was more prevalent in MVP group (36.7% vs. 6.7%, p&lt;0.001) and for each MR severity (figure 1A). On multivariate analysis, although lower LVEF, and increasing MR severity were associated with increased LV fibrosis, presence of MVP had the strongest association (OR 6.82, p &lt; 0.001). During the follow up period (median 673 days), MVP patients with LV fibrosis had the highest annualized event rate for arrhythmic events and composite outcome (figure1B). Conclusion: LV fibrosis is more prevalent in MVP than non-MVP patients with primary MR suggesting a unique pathophysiology in MVP. Presence of LV fibrosis in MVP may represent a risk marker of arrhythmic events and adverse clinical outcome.
THE NEED FOR CHOLECYSTECTOMY AFTER ENDOSCOPIC SPHINCTEROTOMY (ES) FOR BILE DUCT STONE IN ELDERLY PATIENTS: A RANDOMIZED STUDY (2001)

Background: Long‐term biliary complications after ES for bile duct stones are infrequent. In the elderly, the role of routine cholecystectomy after ES is unclear. Patients and Methods: Between September 1997 and December 2000, patients (age &gt;60) with bile duct stones and gall stones presenting with obstructive jaundice, cholangitis or pancreatitis were randomized to receive early elective cholecystectomy (LC) or expectant management after clearance of bile duct stones with ERCP + ES. Exclusion criteria included severe co‐morbidity, concomitant intrahepatic duct stones, recurrence pyogenic cholangitis, cholecystitis and failure to clear bile duct stones endoscopically. They were then seen at regular intervals. Outcome variables included further biliary complications defined as: cholangitis, pancreatitis, obstructive jaundice, cholecystitis and severe biliary colic. Results: 165 patients, aged 60–89 years were randomized (85 in LC group &amp; 80 in expectant group). Both groups were similar in age (60–87 vs. 60–89), ASA grading and mode of presentation. Median follow‐up period was 24 months. 9 patients developed biliary complications in the expectant group (5 cholangitis, 3 cholecystitis and 1 severe biliary colic) while 1 patient in the LC group refused surgery and developed cholangitis. By intention‐to‐treat analysis, the expectant group shows higher incidence of biliary complications than the LC group: (9/80 vs. 1/85, p = 0.008; Difference in probability of complications = 13%, 95% C.I. = 4.8%, 21.2%) Conclusion: With higher incidence of biliary complications in the expectant group, cholecystectomy should be offered to patients whenever is possible after endoscopic clearance of bile duct stones.