gebhart/patrepeval huggingface dataset:
Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding (2010)

The ring-shaped helicase of bacteriophage T7 (gp4), the product of gene 4, has basic beta-hairpin loops lining its central core where they are postulated to be the major sites of DNA interaction. We have altered multiple residues within the beta-hairpin loop to determine their role during dTTPase-driven DNA unwinding. Residues His-465, Leu-466, and Asn-468 are essential for both DNA unwinding and DNA synthesis mediated by T7 DNA polymerase during leading-strand DNA synthesis. Gp4-K467A, gp4-K471A, and gp4-K473A form fewer hexamers than heptamers compared to wild-type helicase and alone are deficient in DNA unwinding. However, they complement for the growth of T7 bacteriophage lacking gene 4. Single-molecule studies show that these three altered helicases support rates of leading-strand DNA synthesis comparable to that observed with wild-type gp4. Gp4-K467A, devoid of unwinding activity alone, supports leading-strand synthesis in the presence of T7 DNA polymerase. We propose that DNA polymerase limits the backward movement of the helicase during unwinding as well as assisting the forward movement necessary for strand separation.
Pyrrolinone-Based Peptidomimetics.“Let the Enzyme or Receptor be the Judge” (2010)

Peptides and proteins, evolved by nature to perform vital biological functions, would constitute ideal candidates for therapeutic intervention were it not for their generally poor pharmacokinetic profiles. Nonpeptide peptidomimetics have thus been pursued because they might overcome these limitations while maintaining both the potency and selectivity of the parent peptide or protein. Since the late 1980s, we have sought to design, synthesize, and evaluate a novel, proteolytically stable nonpeptide peptidomimetic scaffold consisting of a repeating structural unit amenable to iterative construction; a primary concern is maintaining both the appropriate peptide-like side-chains and requisite hydrogen bonding. In this Account, we detail how efforts in the Smith-Hirschmann laboratories culminated in the identification of the 3,5-linked polypyrrolinone scaffold. We developed effective synthetic protocols, both in solution and on solid supports, for iterative construction of diverse polypyrrolinones that present functionalized peptide-like side-chains. As a result of the rigid nature of the pyrrolinone scaffold, control over the backbone conformation could be exerted by modulation of the stereogenicity of the constituent monomers and the network of intramolecular hydrogen bonding. The extended conformation of the homochiral 3,5-linked polypyrrolinone scaffold proved to be an excellent mimic for β-strands and β-sheets. Application to enzyme inhibitor design and synthesis led not only to modest inhibitors of the aspartic acid protease renin and the matrix metalloprotease class of enzymes, but importantly to bioavailable HIV-1 protease inhibitors with subnanomolar binding constants. The design and synthesis of a competent peptide-pyrrolinone hybrid ligand for the class II major histocompatibility complex (MHC) antigen protein HLA-DR1 further demonstrated the utility of the 3,5-polypyrrolinone motif as a mimic for the extended polyproline type II peptide backbone. Equally important, we sought to define, by synthesis, the additional conformational space accessible to the polypyrrolinone structural motif, with the ultimate goal of accessing pyrrolinone-based turn and helix mimetics. Toward this end, a mono-N-methylated bispyrrolinone was found to adopt an extended helical array in the solid state. Subsequent synthesis of d,l-alternating (heterochiral) tetrapyrrolinones both validated the expected turn conformations in solution and led to a functionally active mimetic of a peptidal β-turn (similar to somatostatin). Finally, the design, synthesis, and structural evaluation of both acyclic and cyclic heterochiral (that is, d,l-alternating) hexapyrrolinones yielded nanotube-like assemblies in the solid state. Taken together, these results illustrate the remarkable potential of the 3,5-linked polypyrrolinone scaffold as β-strand, β-sheet, β-turn, and potentially helical peptidomimetics.
Design considerations for normally-off operation in Schottky gate p-GaN/AlGaN/GaN HEMTs (2020)

Abstract Design criteria for normally-off operation in Schottky gate p-GaN/AlGaN/GaN HEMTs have been investigated. The threshold voltage ( V th ) of this structure is determined by the following five parameters: (i) acceptor concentration of p-GaN layer ( N a ), (ii) thickness of p-GaN layer ( d p-GaN ), (iii) Al composition of AlGaN layer (Alx), (iv) thickness of AlGaN layer ( d AlGaN ), and (v) Schottky barrier height at gate metal/p-GaN interface (Φ B ). Analytical equations are derived to obtain the quantitative relations of these parameters and dependences of normally-off condition on these parameters are discussed. To derive the analytical equation, two cases are considered in this study, i.e., case 1; thick d p-GaN case, and case 2; thin d p-GaN case. For case 1, the normally-off condition is determined by Alx and d AlGaN , and independent of N a , d p-GaN , and Φ B . While for case 2, it is strongly affected by N a , d p-GaN , and Φ B . It is found that a thicker d p-GaN is needed for a lower N a , and with the increase of d AlGaN at a certain Alx to achieve a normally-off operation. Also, it is found that Alx has to be kept less than 0.26 because higher Alx will cause the electric field across AlGaN layer to exceed 3 MV cm −1 , which may lead to breakdown in the AlGaN layer.
Molecular relapse in chronic myelogenous leukemia patients after bone marrow transplantation detected by polymerase chain reaction. (1990)

Relapse of chronic myelogenous leukemia after bone marrow transplantation can be detected by using clinical, cytogenetic, or molecular tools. A modification of the polymerase chain reaction can be used in patients to detect low levels of the BCR-ABL-encoded mRNA transcript, a specific marker for chronic myelogenous leukemia. Early detection of relapse after bone marrow transplantation could potentially alter treatment decisions. We prospectively evaluated 19 patients for evidence of molecular relapse, cytogenetic relapse, and clinical relapse after bone marrow transplantation. We used the polymerase chain reaction to detect residual BCR-ABL mRNA in patients followed up to 45 months after treatment (median, 15 months; range, 6-45 months) and found 4 patients with BCR-ABL mRNA expression following bone marrow transplantation. In 2 patients BCR-ABL mRNA was detected in all samples, and both have developed cytogenetic relapse. In 1 patient BCR-ABL mRNA was detected transiently during the first month after transplant but was undetectable thereafter. The fourth patient had BCR-ABL mRNA 6 months after bone marrow transplantation but not in prior samples. Fifteen patients did not express detectable BCR-ABL mRNA. All 19 patients remain in clinical remission. In this prospective study of chronic myelogenous leukemia patients treated with bone marrow transplantation, molecular relapse preceded cytogenetic relapse in those patients who persistently express BCR-ABL mRNA. We recommend using standard clinical and cytogenetic testing to make patient care decisions until further follow-up determines the clinical outcome of those patients with residual BCR-ABL mRNA transcripts detected by polymerase chain reaction.
STATIC ELECTRIC FIELD INTERACTION WITH TISSUES (1999)

Suite 200 1450 San Pablo Street Los Angeles, Calif. 90033 Raphael C. Lee, M.D., Sc.D. 5841 S. Maryland Ave. MC 6035 Chicago, Ill. 60637
Fusion 360 gallery (2021)

Parametric computer-aided design (CAD) is a standard paradigm used to design manufactured objects, where a 3D shape is represented as a program supported by the CAD software. Despite the pervasiveness of parametric CAD and a growing interest from the research community, currently there does not exist a dataset of realistic CAD models in a concise programmatic form. In this paper we present the Fusion 360 Gallery , consisting of a simple language with just the sketch and extrude modeling operations, and a dataset of 8,625 human design sequences expressed in this language. We also present an interactive environment called the Fusion 360 Gym , which exposes the sequential construction of a CAD program as a Markov decision process, making it amendable to machine learning approaches. As a use case for our dataset and environment, we define the CAD reconstruction task of recovering a CAD program from a target geometry. We report results of applying state-of-the-art methods of program synthesis with neurally guided search on this task.
ChemInform Abstract: SYNTHESIS AND β‐ADRENOCEPTOR ACTIVITY OF THE ERYTHRO AND THREO ISOMERS OF SUBSTITUTED α‐HYDROXYTRIMETOQUINOL (1979)

Abstract Auf den im Formelschema beschriebenen Wegen werden das erythro‐ (IV) und threo‐Isomere (VIII) dargestellt und zur Strukturaufklärung die Vorstufen (III) und (VII) in die Tetrahydroprotoberberine (V) bzw. (IX) umgewandelt.
Differential activation of the extracellular signal-regulated kinase, Jun Kinase and Janus Kinase-Stat pathways by oncostatin M and basic fibroblast growth factor in AIDS-derived Kaposiʼs sarcoma cells (1996)

We demonstrate that OSM and bFGF activate distinct as well as shared signalling cascades in KS cells, which integrate to provide a synergistic AP-1 response by which OSM and bFGF may sustain KS cell growth.
Robust Global Motion Estimation with Matrix Completion (2014)

Abstract. In this paper we address the problem of estimating the attitudes and positions of a set of cameras in an external coordinate system. Starting from a conventional global structure-from-motion pipeline, we present some substantial advances. In order to detect outlier relative rotations extracted from pairs of views, we improve a state-of-the-art algorithm based on cycle consistency, by introducing cycle bases. We estimate the angular attitudes of the cameras by proposing a novel gradient descent algorithm based on low-rank matrix completion, that naturally copes with the case of missing data. As for position recovery, we analyze an existing technique from a theoretical point of view, providing some insights on the conditions that guarantee solvability. We provide experimental results on both synthetic and real image sequences for which ground truth calibration is provided.
Structural acoustic modeling of aircraft fuselage structures (2002)

Recent studies at NASA Langley Research Center have examined the development and validation of finite element and boundary element modeling techniques for the prediction of structural acoustic response of aircraft fuselage structures. The goal of this work is to provide increased confidence in the modeling techniques so that interior noise criteria can be incorporated early in the design process. These efforts have focused on the development and validation of high-fidelity physics-based numerical models for structural acoustic predictions into the kilohertz region. Finite element models were developed based on the geometric and material properties of the aircraft fuselage structures. Experimental modal analysis and point force frequency response functions were used to validate and refine the finite element models. Once validated, the finite element predictions of the velocity response were used as boundary condition input for boundary element predictions of the radiated sound power. Experiments in the Structural Acoustic Loads and transmission (SALT) Facility at NASA Langley were used to validate the acoustic predictions. Numerical and experimental results will be presented for conventional aluminum rib and stringer-stiffened aircraft structures, a honey comb composite sidewall panel, and damped acrylic windows. Numerical predictions were in good agreement with the experimental data.
Stochastic Dynamics for Video Infilling (2018)

In this paper, we introduce a stochastic dynamics video infilling (SDVI) framework to generate frames between long intervals in a video. Our task differs from video interpolation which aims to produce transitional frames for a short interval between every two frames and increase the temporal resolution. Our task, namely video infilling, however, aims to infill long intervals with plausible frame sequences. Our framework models the infilling as a constrained stochastic generation process and sequentially samples dynamics from the inferred distribution. SDVI consists of two parts: (1) a bi-directional constraint propagation module to guarantee the spatial-temporal coherence among frames, (2) a stochastic sampling process to generate dynamics from the inferred distributions. Experimental results show that SDVI can generate clear frame sequences with varying contents. Moreover, motions in the generated sequence are realistic and able to transfer smoothly from the given start frame to the terminal frame. Our project site is https://xharlie.github.io/projects/project_sites/SDVI/video_results.html
Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone (2004)

The biosynthesis of pyrroloquinoline quinone (PQQ), a vitamin and redox cofactor of quinoprotein dehydrogenases, is facilitated by an unknown pathway that requires the expression of six genes, pqqA to -F. PqqC, the protein encoded by pqqC, catalyzes the final step in the pathway in a reaction that involves ring cyclization and eight-electron oxidation of 3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic-acid to PQQ. Herein, we describe the crystal structures of PqqC and its complex with PQQ and determine the stoichiometry of H2O2 formation and O2 uptake during the reaction. The PqqC structure(s) reveals a compact seven-helix bundle that provides the scaffold for a positively charged active site cavity. Product binding induces a large conformational change, which results in the active site recruitment of amino acid side chains proposed to play key roles in the catalytic mechanism. PqqC is unusual in that it transfers redox equivalents to molecular oxygen without the assistance of a redox active metal or cofactor. The structure of the enzyme-product complex shows additional electron density next to R179 and C5 of PQQ, which can be modeled as O2 or H2O2, indicating a site for oxygen binding. We propose a reaction sequence that involves base-catalyzed cyclization and a series of quinone-quinol tautomerizations that are followed by cycles of O2/H2O2-mediated oxidations.
Applications of Applying High Rate Coiled Tubing with Fiber Optic System to Meet the Growing Challenges of Coiled Tubing Interventions in Sour Gas Producer Wells (2019)

Abstract Dealing with tight high pressure/high temperature (HPHT) sour gas reservoirs encounters many challenges. One challenge associated with these reservoirs is the development of hard and heavy scale mixture in the production tubing, causing flow and accessibility restrictions. To restore full accessibility, a mechanical de-scaling operations using special milling and cleanout assemblies is the best current solution to this problem, due to the fact that chemical dissolving methods do not deliver the desired results. Another challenge is conventional perforation in some tight wells gives limited penetration, which does not establish the required wellbore reservoir communication. In this case, utilizing the abrasive jetting tool will offer the best solution to overcome the casing string, cement, formation damage achieve optimum penetration which will optimize the stimulation design and enhance the well productivity. In recent years, using coiled tubing (CT) equipped with fiber optics with aforementioned coil tubing intervention operations, have become a common practice in gas wells. Using this system provides the ability to acquire on-job real time data such as pressure, temperature and gamma ray depth correlation. Furthermore, the incorporation of a new rugged fiber optics system into the intervention strategy has enabled increasing operational success rate and results in robust control on the operation parameters, minimizing the risk of gas influx, reducing coil tubing runs and improving decision making process during the operations. This paper describes the challenges in mechanical de-scaling and slot cuttings operations, overview of different applications using CT with fiber optics system, provides a comparison between the rugged and standard fiber optics systems and lessons learned of recent implementation of the rugged CT fiber optic system.
Rainfall thresholds and flood warning: an operative case study (2009)

Abstract. An operative methodology for rainfall thresholds definition is illustrated, in order to provide at critical river section optimal flood warnings. Threshold overcoming could produce a critical situation in river sites exposed to alluvial risk and trigger the prevention and emergency system alert. The procedure for the definition of critical rainfall threshold values is based both on the quantitative precipitation observed and the hydrological response of the basin. Thresholds values specify the precipitation amount for a given duration that generates a critical discharge in a given cross section and are estimated by hydrological modelling for several scenarios (e.g.: modifying the soil moisture conditions). Some preliminary results, in terms of reliability analysis (presence of false alarms and missed alarms, evaluated using indicators like hit rate and false alarm rate) for the case study of Mignone River are presented.
Properties of high-j/sub c/ SINIS junctions (2003)

Nb/Al/AlO/sub x//Al/AlO/sub x//Al/Nb junctions with high critical current densities, j/sub c/, above 20 kA/cm/sup 2/ were fabricated and characterized. A critical voltage of V/sub c/=1.25 mV and small hysteresis (about 6% of the critical current) at 4.2 K were obtained for j/sub c/=21 kA/cm/sup 2/. Also, devices with a modified geometry, Nb/Al/AlO/sub x//Al/Nb/Al/AlO/sub x//Al/Nb, were fabricated. In these devices, j/sub c//spl cong/50 kA/cm/sup 2/ at 4.5 K, and the temperature dependence of the critical current, I/sub c/(T), is improved (as compared with our earlier results) in that the steep raise of I/sub c/ is shifted toward higher temperatures. We suggest a theoretical model which satisfactory describes the enhanced critical current for these SINS'NIS junctions as compared with ordinary SINIS junctions.
Complications of Thoracolumbar Deformity Surgery (2004)

The surgical management of spinal deformity is challenging, and numerous adverse outcomes may result from the surgical approach and correction of spinal deformity in the adolescent and adult patient. The goals of surgery for deformity of the spine include the treatment of present pain and disability and the prevention of future consequences of progressive deformity. Surgical correction of spinal deformity introduces the risk of both perioperative and long-term complications (1,2). Knowledge of these complications is important and valuable for both the patient and the surgeon. The patient beneﬁts by gaining information on potential adverse outcomes and being empowered to make an informed choice regarding the beneﬁts and risks of surgery (3). The surgeon treating the spinal deformity beneﬁts from recognition of these potential complications and being informed as to the choice of surgical strategies and implant options that optimize the ability to eﬀectively realign the spinal column while minimizing the risks of complications. Recognition of potential complications may lead to prevention of adverse outcomes in practice (4). The purpose of this chapter is to identify the major complications of deformity correction in the thoracic and lumbar spine and to suggest strategies for avoiding these complications.
Damage-free plasma etching of porous organo-silicate low-k using micro-capillary condensation above −50 °C (2018)

The micro-capillary condensation of a new high boiling point organic reagent (HBPO), is studied in a periodic mesoporous oxide (PMO) with ∼34 % porosity and k-value ∼2.3. At a partial pressure of 3 mT, the onset of micro-capillary condensation occurs around +20 °C and the low-k matrix is filled at -20 °C. The condensed phase shows high stability from -50 < T ≤-35 °C, and persists in the pores when the low-k is exposed to a SF<sub>6</sub>-based plasma discharge. The etching properties of a SF<sub>6</sub>-based 150W-biased plasma discharge, using as additive this new HBPO gas, shows that negligible damage can be achieved at -50 °C, with acceptable etch rates. The evolution of the damage depth as a function of time was studied without bias and indicates that Si-CH<sub>3</sub> loss occurs principally through Si-C dissociation by VUV photons.
Room-Temperature Continuous-Wave Operation of InGaN Multi-Quantum-Well Laser Diodes Grown on an n-GaN Substrate with a Backside n-Contact (1999)

Continuous-wave operation at room-temperature has been demonstrated for InGaN multi-quantum-well (MQW) laser diodes (LDs) grown on low-dislocation-density n-GaN substrates with a backside n-contact. The current, current density and voltage at the lasing threshold were 144 mA, 10.9 kA/cm 2 and 10.5 V, respectively, for a 3 µm wide ridge-geometry diode with high-reflection dielectric coated mirrors. Single-transverse-mode emission was observed in the far-field pattern of the LDs and the beam full width at half power in the parallel and perpendicular directions was 6° and 25°, respectively.
Integrating Sensing Hydrogel Microstructures into Micropatterned Hepatocellular Cocultures (2009)

In this paper we describe a microfabrication-derived approach for defining interactions between distinct groups of cells and integrating biosensors with cellular micropatterns. In this approach, photoresist lithography was employed to micropattern cell-adhesive ligand (collagen I) on silane-modified glass substrates. Poly(ethylene glycol) (PEG) photolithography was then used to fabricate hydrogel microstructures in registration with existing collagen I domains. A glass substrate modified in this manner had three types of micropatterned regions: cell-adhesive collagen I domains, moderately adhesive silanized glass regions, and nonadhesive PEG hydrogel regions. Incubation of this substrate with primary rat hepatocytes or HepG2 cells resulted in attachment of hepatic cells on collagen I domains with no adhesion observed on silane-modified glass regions or hydrogel domains. 3T3 fibroblasts added onto the same surface attached on the glass regions around the hepatocytes, completing the coculture. Significantly, PEG hydrogel microstructures remained free of cells and were used to "fence" hepatocytes from fibroblasts, thus limiting communication between the cell types. We also demonstrated that entrapment of enzyme molecules inside hydrogel microstructures did not compromise nonfouling properties of PEG. Building on this result, horse radish peroxidase-containing hydrogel microstructures were integrated into micropatterned cocultures and were used to detect hydrogen peroxide in the culture medium. The surface micropatterning approach described here may be used in the future to simultaneously define and detect endocrine signaling between two distinct cell types.
ChemInform Abstract: Generation of Hydroxyl Radicals from 1‐Hydroxypyridine‐2(1H)‐thione and Their Application to Organic Synthesis. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: A Powder Neutron Diffraction Investigation of the Two Rhombohedral NASICON Analogues: γ‐Na3Fe2(PO4)3 and Li3Fe2(PO4)3. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.