gebhart/patrepeval huggingface dataset:
Monte Carlo docking with ubiquitin (1995)

The development of general strategies for the performance of docking simulations is prerequisite to the exploitation of this powerful computational method. Comprehensive strategies can only be derived from docking experiences with a diverse array of biological systems, and we have chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple-start Monte Carlo docking method, we have reconstructed the known structure of diubiquitin from its two halves as well as from two copies of the uncomplexed monomer. For both of these cases, our relatively simple potential function ranked the correct solution among the lowest energy configurations. In the experiments involving the ubiquitin monomer, various structural modifications were made to compensate for the lack of flexibility and for the lack of a covalent bond in the modeled interaction. Potentially flexible regions could be identified using available biochemical and structural information. A systematic conformational search ruled out the possibility that the required covalent bond could be formed in one family of low-energy configurations, which was distant from the observed dimer configuration. A variety of analyses was performed on the low-energy dockings obtained in the experiment involving structurally modified ubiquitin. Characterization of the size and chemical nature of the interface surfaces was a powerful adjunct to our potential function, enabling us to distinguish more accurately between correct and incorrect dockings. Calculations with the structure of tetraubiquitin indicated that the dimer configuration in this molecule is much less favorable than that observed in the diubiquitin structure, for a simple monomer-monomer pair. Based on the analysis of our results, we draw conclusions regarding some of the approximations involved in our simulations, the use of diverse chemical and biochemical information in experimental design and the analysis of docking results, as well as possible modifications to our docking protocol.
Dense deformation field estimation for brain intraoperative images registration (2004)

A new fast non rigid registration algorithm is presented. The algorithm estimates a dense deformation field by optimizing a criterion that measures image similarity by mutual information and regularizes with a linear elastic energy term. The optimal deformation field is found using a Simultaneous Perturbation Stochastic Approximation to the gradient. The implementation is parallelized for symmetric multi-processor architectures. This algorithm was applied to capture non-rigid brain deformations that occur during neurosurgery. Segmentation of the intra-operative data is not required but preoperative segmentation of the brain allows the algorithm to be robust to artifacts due to the craniotomy.
Bronchial Responsiveness to Histamine in Infants and Older Children: Reply (1991)

"Bronchial Responsiveness to Histamine in Infants and Older Children: Reply." American Review of Respiratory Disease, 144(1), p. 237
cDNA-derived primary structure of the 25-kDa subunit of canine microsomal signal peptidase complex. (1994)

We purified the 25-kDa subunit of the pentameric signal peptidase complex (SPC 25) from canine pancreas microsomes and utilized amino acid sequence data from tryptic fragments for its molecular cloning and sequencing. Its primary structure (calculated molecular mass of 25,831 Da) shows the presence of two hydrophobic domains of which one is likely to serve as a transmembrane segment. Consistent with being the only SPC subunit with at least one intrachain disulfide bond, SPC 25 contains 4 Cys residues. SPC 25 does not contain a cleavable signal peptide, and it is proposed that the transmembrane segment doubles as signal sequence. The primary structure of SPC 25 is unrelated to any of the other three SPC subunits (SPC 22/23, SPC 21, and SPC 18) that have so far been molecularly cloned and sequenced. Neither is it similar to any protein in the data bases, except that it is 95% identical to an open reading frame of an incomplete and randomly isolated human cDNA clone.
Glycophorin a as a cell surface marker of early erythroid differentiation in acute leukemia (1979)

We show here that the leukemic blast cells from three patients of a total of 15 subsequently diagnosed as having acute leukemia express on their surface the major red cell sialoglycoprotein, glycophorin A (GP-A). This was demonstrated (1) by indirect immunofluorescence using rabbit anti GP-A anti-serum and (2) by immune precipitation of GP-A from surface radiolabelled leukemic cells. Since GP-A is exclusively present on erythroid cells and their precursors, these findings indicate that a higher proportion of the blast leukemias than previously recognized show features of early erythroid differentiation.
Hepatocyte Growth Factor Predicts Failure of Fontan Circulation (2020)

The HGF is an independent predictor of a failure of a Fontan circulation. The HGF is an indicator for an additional catheter intervention after a Fontan operation.
A linear algorithm for labeling planar projections of polyhedra (2002)

A linear algorithm is given for the labelability problem of pictures with trihedral vertices and hidden lines. The main characteristic of the method is that it considers the faces of a given picture as Boolean variables and it constructs from the picture a Boolean formula. Based on the truth assignment of the picture's formula, a linear algorithm is developed for the labeling of the edges by the Clowes-Huffman scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design and characterization of DOE micro lens array for spatial light modulator (2011)

In the Multi-point Diffraction Strain Sensor (MDSS), a micro lens array is installed in front of the camera as the key component for wavefront sampling. Alternatively, a liquid crystal spatial light modulator (LC-SLM) can be used to replace the physical lens array, on which we have designed various Diffractive Optical Element (DOE)- based micro lens arrays to display. However it is difficult to investigate the quality of these lenses by traditional metrology since the wavefront profile is modulated by the inner LC cells instead of the solid surface of optical components. In this paper, we introduced the Digital Hologram (DH) method to characterize the quality of these DOE-based micro lenses or lens arrays by measuring the whole phase profile of outcome beam through the SLM. First the design formula of the DOE micro-lens array is given. Then the characterization procedure for such lens array is demonstrated. The reconstructed results of the lens profiles are shown, which can be used for further qualification.
Mössbauer Spectroscopy (2006)

57Fe-Mössbauer spectroscopy (MS) has played an important role in the elucidation of the iron centers in the photosynthetic apparatus. In 1975, G. Feher and collaborators demonstrated that the single iron of bacterial reaction centers (RC) was high-spin ferrous irrespective of the state of QA. Moreover, they showed that reduction of QA broadened the Mössbauer lines at 4.2K, indicative of spin coupling between the semiquinone and the iron, related to the broadening observed in the EPR signal of the semiquinone (Debrunner et al., 1975). Photosystem I (PSI) of green plants and algae contains three iron-sulfur centers labeled FA, FB and FX that have originally been identified by EPR. Evans et al. (1977, 1979, 1981) showed that the Mössbauer spectra of PSI were practically identical with those of the well understood bacterial 4Fe-4S centers. The low-potential center FX remained controversial, however, as others suggested a 2Fe-2S center instead. The controversy was resolved by Petrouleas et al. (1989), who studied a mutant lacking centers FA and FB and found that FX had indeed all the properties of a 4Fe-4S center. The more difficult task of analyzing Photosystem II(PSII) of green plants was undertaken by Petrouleas and Diner (1982, 1986, 1990), who identified the redox center known as Q400 with the iron-quinone complex and showed the iron to be redox active in contrast to the Fe(II) of the bacterial RC. The same group demonstrated, by MS, that formate affected the iron-quinone complex (Diner and Petrouleas, 1987), and finally that the Fe(II) formed an NO derivative. After a review of the methodology, the various iron sites of bacterial RC, of PSI and PSII will be discussed in detail to illustrate the application of the method.
The ‘swing-door’ technique for uncinectomy in endoscopic sinus surgery (1998)

Uncinectomy is an important step in endoscopic sinus surgery. The traditional method of performing uncinectomy has the risk of penetration of the lamina papyracea with orbital fat exposure. If the orbital penetration is not recognized, major complications may follow. In this study the authors used historical consecutive controls to compare the incidence of orbital penetration, identification of the natural ostium and lacrimal apparatus injury by the traditional surgical technique and a new technique of uncinectomy. Six hundred and thirty-six uncinectomies have been performed using the 'swing-door' technique. The 636 uncinectomies performed prior to changing techniques were used as historical controls. The incidence of orbital penetration (six compared to 0; p < 0.05) and ostium non-identification (42 not identified as compared to 0; p < 0.001) was significantly less with the new technique. One lacrimal injury occurred with the 'swing-door' technique compared to zero with the standard technique (p > 0.05). The techniques are described and the complications discussed. The authors recommend this technique as it is easy to learn, allows removal of the uncinate flush with the lateral nasal wall and allows easy identification of the natural ostium of the maxillary sinus.
EPR19-069: Opioid Use Among Cancer Patients Undergoing Surgery and Their Associated Risk of Re-admissions and Emergency Department Visits in the 1-Year Postsurgical Period (2019)

Background: Prescription opioid use and overdose has steadily increased over the past years, resulting in a dramatic increase in opioid-related emergency department (ED) visits and hospitalizations. Methods: This study used a prospective cohort of cancer patients having undergone surgery in Montreal (Quebec) to describe their post-discharge opioid use and identify potential patterns of unplanned health service use (ED visits, hospitalizations). Provincial health administrative claims were used to measure opioid dispensation as well as hospital re-admissions and ED visits. The hospital warehouse, patient chart and patient interview will be used to further describe patient’s medical profile. Marginal structural models will be used to model the association between use of opioids and risk of ED visits and hospitalizations. Inverse probability of treatment and censoring weights will be constructed to properly adjust for confounders that may be unbalanced between the opioid and non–opioid users as well as to account for competing risk due to mortality. Reasons for the re-admissions will also be presented as part of the analyses. Covariates will include patient comorbidities, medication history, and healthcare system characteristics such as nurse-to-patient and attending physician-to-patient ratios. Results (interim): A total of 821 were included in the study; of these, 73% (n=597) were admitted for a cancer procedure. At postoperative discharge, 605 (74%) of patients had at least one opioid dispensation, of which the majority (67%) were oxycodone with hydromorphone being the second most prescribed (28%). Among those who filled a prescription, mean age was 66 (13.4), 68% had no previous history of opioid use, and 10% have had 3 or more dispensing pharmacies in the year prior to admission, compared to less than 1% for the non–opioid users. Overall, 343 people refilled their opioid prescription at least once and 128 at least twice during the 1-year postoperative period. Among cancer patients who were opioid users, 214 ED visits occurred in the 1 year after surgery compared to only 40 for the non-cancer opioid users. Conclusion: This study will help to identify the risk profile of cancer patients who are most likely to continue using opioids for prolonged periods following surgical procedures as well as quantify the impact of opioid use and its associated burden on the healthcare system in order to identify areas for possible interventions.
Real-time feedback from iterative electronic structure calculations (2015)

Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semiempirical methods as the data source and apply the surrogate-potential mediator to deliver reliable real-time feedback.
High-Dose Antipsychotic Medication; A Practical Pocket Checklist (2010)

There is evidence that a significant number of patients with schizophrenia and other chronic psychotic psychosis are prescribed high-dose antipsychotic drugs despite the fact that clinical guidelines recommend the routine use of a single antipsychotic drug in a standard dose. The prescriptions for high-dose and combined antipsychotic drugs are relatively common in clinical practice. This occurs despite the fact that results of published trials of high-dose antipsychotic drug treatment for schizophrenia provide little evidence to support effectiveness of using high-dose antipsychotic treatment and most importantly such strategy is not recommended. Moreover, there is mounting evidence of higher incidence of side effects and mortality associated with high dose antipsychotic treatment. Therefore we are presenting a practical pocket checklist which is aimed at minimizing predicted and unpredicted side effects during such treatments.
Updating of abdominal cytological punctures: preliminary results (1989)

info:eu-repo/semantics/nonPublished
Boundary Graph Neural Networks for 3D Simulations (2021)

The abundance of data has given machine learning considerable momentum in natural sciences and engineering, though modeling of physical processes is often difficult. A particularly tough problem is the efficient representation of geometric boundaries. Triangularized geometric boundaries are well understood and ubiquitous in engineering applications. However, it is notoriously difficult to integrate them into machine learning approaches due to their heterogeneity with respect to size and orientation. In this work, we introduce an effective theory to model particle-boundary interactions, which leads to our new Boundary Graph Neural Networks (BGNNs) that dynamically modify graph structures to obey boundary conditions. The new BGNNs are tested on complex 3D granular flow processes of hoppers, rotating drums and mixers, which are all standard components of modern industrial machinery but still have complicated geometry. BGNNs are evaluated in terms of computational efficiency as well as prediction accuracy of particle flows and mixing entropies. BGNNs are able to accurately reproduce 3D granular flows within simulation uncertainties over hundreds of thousands of simulation timesteps. Most notably, in our experiments, particles stay within the geometric objects without using handcrafted conditions or restrictions.
Eco-friendly and highly efficient multigram synthesis of 3-chloro-1,2-propanediol using sonochemistry (2016)

A new short, simple, green and an inexpensive industrially practical process for the preparation of 3-chloro-1,2-propanediol was developed by using ultrasound irradiation avoiding the use of solvents, of acidic or basic conditions. The only reagent used is water and no waste is generated. Optimal conditions and yield (82%) were obtained by using 2.2 molar equivalents of water at 90 W for 1 hr.
Hong Kong: From Worker to Manager (1998)

Review article on: Made by Hong Kong . Edited by Suzanne Berger and Richard K. Lester The Hong Kong Advantage . By Michael T. enright, Edit E. Scott and David Dodwell
IMMUNOLOGICAL DETERMINATION OF HUMAN PITUITARY LUTEINIZING HORMONE (LH) (1961)

ABSTRACT Human pituitary LH inhibits an haemagglutination reaction between anti-HCG-sera and HCG-coated blood cells. This immunological technique can be used for quantitative and qualitative estimation of human pituitary LH and of LH in human urine, provided no chorionic gonadotrophin is present.
ChemInform Abstract: TOTAL SYNTHESIS OF OLEANDROSE AND THE AVERMECTIN DISACCHARIDE, BENZYL α‐L‐OLEANDROSYL‐α‐L‐4‐ACETOXYOLEANDROSIDE (1984)

Abstract Avermectine sind als Anthelmintica sowie wegen ihrer ecto‐ und epdo‐antigarasitären Wirksamkeit von Interesse.
Design and logical analysis on the access authentication scheme for satellite mobile communication networks (2012)

It is important for security of satellite mobile communication networks to design an efficient access authentication process. A two-way access authentication scheme among mobile users, gateways and the Network Control Centre (NCC) is designed in this study. The authentication scheme consists of four phases: mobile users registration, mobile users management, mobile authentication and mobile authentication update. Furthermore, the Syverson-van Oorschot (SVO) logic is introduced to reason the authentication scheme to verify the security. This scheme highlights the authentication role of gateways, and decreases the authentication computation load of the NCC. The access authentication scheme can resist attacks from any side, including the identity spoofing, tampering, replay etc. The integrity of the transmission data is also protected. Therefore the security for satellite mobile communication networks is enhanced. This access authentication scheme is implemented on the developed satellite mobile communication simulation platform. The obtained simulation results suggest that the authenticated overheads for audio service and video service are low, and the proposed scheme does not degrade the quality of service (QoS) of the satellite mobile communication.
Synthesis of Phosphatidylcholine Having a Very Long Chain Polyunsaturated Fatty Acid (1998)

Abstract A phosphatidylcholine 9 bearing icosadienoyl and docosahexaenoyl groups at the 1- and 2-positions respectively was synthesized. The synthetic route involves carbon chain elongation of linoleic acid via malonic ester synthesis, preparation of lyso-phosphatidylcholine via lipase-catalyzed mon-acylation of 2-O-methoxyethoxymethylglycerol and phosphodiester synthesis, and finally DCC-mediated esterification.
Proposal of a local DC distribution network with distributed energy resources (2005)

The spread of the electronics, both for control and power applications, in the realization of apparatuses in low voltage (LV) electrical systems, requires the conversion of the electric power from alternating current to direct current by means of a rectifier stage, generally constituted by a diode bridge. Moreover, modern technologies provide various types of distributed energy resources (DER), constituted by small size generators and storage systems, that generate in direct current, such as photovoltaic arrays, fuel cells, storage, or that need DC section before the interfacing with the AC network (microturbines, variable speed wind generators, flywheels). It can be thought to integrate the various generators, storage systems and DC loads in a local DC distribution network, that is interfaced with public grid by means of one or more inverters. This solution makes easy the islanding operation of the generators. The aim of this work is to analyze a local DC distribution system both with diode and IGBT bridge interface converter in the presence of small scale generation and storage systems. After suitable modeling of the entire system, some simulation results are given.
Numerisch robuste Implementierung von Abtastreglern für Flugsteuerungsaktuatoren (1999)

Die konventionelle Realisierung von Abtastreglern für elektrohydraulische Flugsteuerungsaktuatoren zeigt erhebliche Schwächen bezüglich der Wahl der Abtastzeit, der Zahlendarstellung endlicher Wortlänge und Signalquantisierung. Eine deutliche Verbesserung verspricht die Verwendung der modifizierten Beschreibungsform auf der Basis des d–Operators. Dieses wird anhand verschiedener Überlegungen plausibilisiert und durch Prüfstandsversuche belegt.
The Regulatory Activity of GIPC1 on RhoA‐Mediated bFGF Angiogenic Functions (2021)

Introduction Vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) are the best characterized pro‐angiogenic factors involved in tumor angiogenesis. Acquired resistance upon anti‐VEGF therapy remains a serious disadvantage of current approaches. Here we show that the small GTPase RhoA, which is known to regulate VEGF‐induced angiogenesis, also regulates bFGF‐induced angiogenesis and we further explore the role of the scaffolding protein GAIP Interacting Protein C‐terminus (GIPC1) as a regulator of RhoA activation and bFGF angiogenic outcomes. Methods We performed in vitro angiogenesis assays (cell migration, tube formation, spheroid sprouting) to assess the impact of pharmacological inhibition or knockdown of endothelial RhoA on bFGF‐induced angiogenesis using human umbilical vein endothelial cells (HUVECs). RhoA and GEF Pull‐down experiments, along with other biochemical assays were performed to identify the molecular mechanism(s) of bFGF‐induced RhoA activation and regulatory function of GIPC1. In vivo, endothelial‐specific inducible RhoA‐deficient mice with a fluorescent reporter were used in a modified matrigel plug angiogenesis assay and in the ex vivo aortic ring assay. Results In vitro, bFGF‐induced angiogenesis was abrogated by pharmacological RhoA inhibition or RhoA knockdown. In vivo, tamoxifen‐induced endothelial RhoA‐deficiency blocked bFGF‐induced angiogenesis. Mechanistically, bFGF activates RhoA, through the RhoA‐specific GEFs GEFH1, P115, LARG and PDZ‐RhoGEF. Among the bFGF receptors, FGFR1 is predominantly expressed in HUVECs and FGFR1 knockdown abrogated bFGF‐induced RhoA activation and angiogenesis. The scaffolding protein GIPC1 interacts with FGFR1 and has an inhibitory effect, since its downregulation induced RhoA activation as well as basal and bFGF‐induced angiogenesis. Ongoing experiments are aiming to further delineate the FGFR1‐GIPC1‐RhoA relationship. Conclusions Our data suggest that GIPC1 is an important element of bFGF‐induced angiogenesis through its regulatory effect on endothelial RhoA.