gebhart/patrepeval huggingface dataset:
Designing industrial yeasts for the consolidated bioprocessing of starchy biomass to ethanol (2012)

Consolidated bioprocessing (CBP), which integrates enzyme production, saccharification and fermentation into a one step process, is a promising strategy for the effective ethanol production from cheap lignocellulosic and starchy materials. CBP requires a highly engineered microbial strain able to both hydrolyze biomass with enzymes produced on its own and convert the resulting simple sugars into high-titer ethanol. Recently, heterologous production of cellulose and starch-degrading enzymes has been achieved in yeast hosts, which has realized direct processing of biomass to ethanol. However, essentially all efforts aimed at the efficient heterologous expression of saccharolytic enzymes in yeast have involved laboratory strains and much of this work has to be transferred to industrial yeasts that provide the fermentation capacity and robustness desired for large scale bioethanol production. Specifically, the development of an industrial CBP amylolytic yeast would allow the one-step processing of low-cost starchy substrates into ethanol. This article gives insight in the current knowledge and achievements on bioethanol production from starchy materials with industrial engineered S. cerevisiae strains.
Ginkgolides:  Selective Acetylations, Translactonization, and Biological Evaluation (2002)

Protocols for selective acetylation of the hydroxyl groups of ginkgolide C have been developed. These acetylations have given rise to various ginkgolide C acetates and iso-ginkgolide C acetates, the latter having a rearranged skeleton resulting from translactonization. These acetyl derivatives, as well as ginkgolides A and B acetates have been investigated for their ability to bind to a cloned platelet-activating factor (PAF) receptor.
Epidermal growth factor intralesional infiltrations can prevent amputation in patients with advanced diabetic foot wounds (2006)

This study examined if a series of epidermal growth factor (EGF) local infiltrations can enhance the healing process of complicated diabetic wounds. Twenty-nine in-hospital patients with diabetic neuropathic or ischaemic lesions with high risk of amputation were treated in a non controlled pilot study conducted at the National Institute of Angiology, Havana. Lesions, classified as Wagner's grade 3 or 4, included ulcers > or = 20 cm2 for > or = 25 days or amputation residual bases > or = 30 cm2 for > or = 15 days, healing refractory despite comprehensive wound care. EGF (25 microg) intralesional infiltrations (approximately 250 microl of a 25 microg/ml solution/injection point) were performed thrice weekly up to the eighth week. Wound closure was monitored during the treatment and recurrence examined for a year following discharge from hospital. Eighty-six per cent of the patients treated showed a productive granulation at infiltration session 8. Histological examination at this point indicated a substantial wound matrix transformation, granulation tissue cell repopulation and angiogenesis. Of the 29 patients treated, amputation was prevented in 17 (58.6%) of them who completed 24 infiltration sessions. They averaged 71.1 +/- 18.3% of reepithelisation during a mean in-hospital period of 66.5 +/- 4.9 days. Wound recurrence after 1 year of follow-up appeared in only one patient. Preliminary evidences suggest that EGF intralesional infiltrations may be effective in reducing diabetic lower limb amputation.
Natural Feature Tracking for Extendible Robust Augmented Realities (1999)

Vision-based tracking systems for augmented reality often require that artificial fiducials be placed in the scene. In this paper we utilize our approach for robust detection and tracking of natural features such as textures or corners. The tracked natural features are automatically calibrated to the fiducials that are used to initialize and facilitate normal tracking. Once calibrated, the natural features are used to extend the system’s tracking range and to stabilize the tracked pose against occlusions and noise. The emphasis of this paper is the integration of natural feature tracking with fiducial tracking to increase the range and robustness of vision-based augmented reality tracking.
Improved catalysts for carbon and coal gasification (1984)

This invention relates to improved catalysts for carbon and coal gasification and improved processes for catalytic coal gasification for the production of methane. The catalyst is composed of at least two alkali metal salts and a particulate carbonaceous substrate or carrier is used. 10 figures, 2 tables.
Polishing of Sidewall Surfaces Using a Gas Cluster Ion Beam (2004)

The polishing of silicon sidewalls at an average surface roughness of 0.3 nm is demonstrated for the first time by SF6 gas cluster irradiation at an incident angle of 82 degrees from the sidewalls. A new phenomenon for surface smoothing occurs on material surfaces irradiated by reactive gas clusters at incident angles above 60 degrees from the surface normal. A characteristic of this smoothing phenomenon is that the surface roughness decreases as the chemical reactivity between the material and gas clusters increases, whereas the surface roughness shows an opposite tendency for conventional gas cluster ion beam smoothing at angles below 60 degrees.
Energy resolution and high count rate performance of superconducting tunnel junction x-ray spectrometers (1998)

We present experimental results obtained with a cryogenically cooled, high-resolution x-ray spectrometer based on a 141 μm×141 μm Nb-Al-Al2O3-Al-Nb superconducting tunnel junction (STJ) detector in a demonstration experiment. Using monochromatized synchrotron radiation we studied the energy resolution of this energy-dispersive spectrometer for soft x rays with energies between 70 and 700 eV and investigated its performance at count rates up to nearly 60 000 cps. At count rates of several 100 cps we achieved an energy resolution of 5.9 eV (FWHM) and an electronic noise of 4.5 eV for 277 eV x rays (the energy corresponding to C K). Increasing the count rate, the resolution 277 eV remained below 10 eV for count rates up to ∼10 000 cps and then degraded to 13 eV at 23 000 cps and 20 eV at 50 000 cps. These results were achieved using a commercially available spectroscopy amplifier with a baseline restorer. No pile-up rejection was applied in these measurements. Our results show that STJ detectors can operate at count rates approaching those of semiconductor detectors while still providing a significantly better energy resolution for soft x rays. Thus STJ detectors may prove very useful in microanalysis, synchrotron x-ray fluorescence (XRF) applications, and XRF analysis of light elements (K lines) and transition elements (L lines).
Lignin Valorization through Catalytic Lignocellulose Fractionation: A Fundamental Platform for the Future Biorefinery (2016)

Current processes for the fractionation of lignocellulosic biomass focus on the production of high-quality cellulosic fibers for paper, board, and viscose production. The other fractions that constitute a major part of lignocellulose are treated as waste or used for energy production. The transformation of lignocellulose beyond paper pulp to a commodity (e.g., fine chemicals, polymer precursors, and fuels) is the only feasible alternative to current refining of fossil fuels as a carbon feedstock. Inspired by this challenge, scientists and engineers have developed a plethora of methods for the valorization of biomass. However, most studies have focused on using one single purified component from lignocellulose that is not currently generated by the existing biomass fractionation processes. A lot of effort has been made to develop efficient methods for lignin depolymerization. The step to take this fundamental research to industrial applications is still a major challenge. This review covers an alternative approach, in which the lignin valorization is performed in concert with the pulping process. This enables the fractionation of all components of the lignocellulosic biomass into valorizable streams. Lignocellulose fractions obtained this way (e.g., lignin oil and glucose) can be utilized in a number of existing procedures. The review covers historic, current, and future perspectives, with respect to catalytic lignocellulose fractionation processes.
Integrative (epi) Genomic Analysis to Predict Response to Androgen-Deprivation Therapy in Prostate Cancer (2018)

Therapeutic resistance is a central problem in clinical oncology. We have developed a systematic genome-wide computational methodology to allow prioritization of patients with favorable and poor therapeutic response. Our method, which integrates DNA methylation and mRNA expression data, uncovered a panel of 5 differentially methylated sites, which explain expression changes in their site-harboring genes, and demonstrated their ability to predict primary resistance to androgen-deprivation therapy (ADT) in the TCGA prostate cancer patient cohort (hazard ratio = 4.37). Furthermore, this panel was able to accurately predict response to ADT across independent prostate cancer cohorts and demonstrated that it was not affected by Gleason, age, or therapy subtypes. We propose that this panel could be utilized to prioritize patients who would benefit from ADT and patients at risk of resistance that should be offered an alternative regimen. Such approach holds a long-term objective to build an adaptable accurate platform for precision therapeutics.
Cooling of an Integrated Brillouin Laser below the Thermal Limit (2021)

Photonically integrated resonators are promising as a platform for enabling ultranarrow linewidth lasers in a compact form factor. Owing to their small size, these integrated resonators suffer from thermal noise that limits the frequency stability of the optical mode to ~100 kHz. Here, we demonstrate an integrated stimulated Brillouin scattering (SBS) laser based on a large mode-volume annulus resonator that realizes an ultranarrow thermal-noise-limited linewidth of 270 Hz. In practice, yet narrower linewidths are required before integrated lasers can be truly useful for applications such as optical atomic clocks, quantum computing, gravitational wave detection, and precision spectroscopy. To this end, we employ a thermorefractive noise suppression technique utilizing an auxiliary laser to reduce our SBS laser linewidth to 70 Hz. This demonstration showcases the possibility of stabilizing the thermal motion of even the narrowest linewidth chip lasers to below 100 Hz, thereby opening the door to making integrated microresonators practical for the most demanding future scientific endeavors.
In-situ thermography of automated fiber placement parts (2018)

Automated fiber placement (AFP) provides precision and repeatable manufacturing of both simple and complex geometry composite parts. However, AFP also introduces the possibility for unique flaws such as overlapping tows, gaps between tows, tow twists, lack of layer adhesion and foreign object debris. These types of flaws can all result in a significant loss of performance in the final part. The current inspection method for these flaws is a costly and time intensive visual inspection of each ply layer. This work describes some initial efforts to incorporate thermal inspection on the AFP head and analysis of the data to identify the previously mentioned flaws. Previous bench-top laboratory experiments demonstrated that laps, gaps, and twists were identified from a thermal image. The AFP head uses an on- board lamp to preheat the surface of the part during layup to increase ply consolidation. The preheated surface is used as a thermal source to observe the state of the new material after compaction. We will present data collected with the Integrated Structural Assembly of Advanced Composites (ISAAC) AFP machine at Langley Research Center showing that changes to the temperature profile is sufficient for identifying all types of flaws.
Atrial and ventricular anti-tachycardia pacing as a method of rhythm discrimination (2007)

Background: Inappropriate shock by implantable cardioverter defibrillators (ICD) remains a significant clinical problem. We evaluated a new algorithm for discriminating 1:1 SVT and VT, based on the response to atrial (A) and ventricular (V) anti-tachycardia pacing (ATP). Methods: 64 pts (age: 46 plusmn 16 yrs, 34 male, LVEF: 54 plusmn 11%) undergoing EP testing or SVT ablation underwent AATP and VATP through a customized external Marquis ICD once tachycardia was induced. The response to A or V ATP was classified as AT or non-AT according to predetermined criteria. Results: The V ATP algorithm correctly identified AT with a sensitivity of 70% (53%-82%) and specificity of 77% (61%-88%). The A ATP algorithm correctly identified AT with a sensitivity of 96% (84%-99%) and specificity of 91% (67%-98%). Conclusions: Analysis of cross chamber response patterns during and after ATP can successfully discriminate tachycardia mechanism and prevent inappropriate ICD shocks.
2a-[4-(Tetrahydropyridoindol-2-yl)butyl]tetrahydrobenzindole Derivatives:  New Selective Antagonists of the 5-Hydroxytryptamine<sub>7</sub>Receptor (2002)

A series of tetrahydrobenzindoles was prepared, and the affinity of these compounds for the 5-hydroxytryptamine7 (5-HT7) receptor and other receptors was evaluated. Most of the compounds showed high affinity for the 5-HT7 receptor, and 2a-[4-(tetrahydropyridoindol-2-yl)butyl]tetrahydrobenzindole derivatives (26a-j) exhibited high selectivity for this receptor. The nature of the substituent at the 9-position of the tetrahydropyridindole ring affected the affinity for the 5-HT7 receptor, and the 9-carbamoyl moiety afforded increased selectivity. Compound 26j exhibited high affinity for the 5-HT7 receptor, with at least 280-fold selectivity over the 5-HT2 receptor. In a functional model of 5-HT7 receptor activation, this compound was confirmed to have 5-HT7 receptor antagonist activity. It should be a useful tool for clarifying the biological role of the 5-HT7 receptor.
A Type III Protein Arginine Methyltransferase from the Protozoan Parasite Trypanosoma brucei (2009)

Arginine methylation is a widespread post-translational modification of proteins catalyzed by a family of protein arginine methyltransferases (PRMTs). The ancient protozoan parasite, Trypanosoma brucei, possesses five putative PRMTs, a relatively large number for a single-celled eukaryote. Trypanosomatids lack gene regulation at the level of transcription, instead relying on post-transcriptional control mechanisms that act at the levels of RNA turnover, translation, and editing, all processes that likely involve multiple RNA-binding proteins, which are common targets of arginine methylation. Here, we report the characterization of a trypanosome PRMT, TbPRMT7, which is homologous to human PRMT7. Interestingly, trypanosomatids are the only single-celled eukaryotes known to harbor a PRMT7 homologue. TbPRMT7 differs dramatically from all known metazoan PRMT7 homologues in lacking the second AdoMet binding-like domain that is required for activity of the human enzyme. Nevertheless, bacterially expressed TbPRMT7 exhibits robust methyltransferase activity toward multiple targets in vitro. High resolution ion exchange chromatography analysis of methylated substrates reveals that TbPRMT7 is a type III PRMT, catalyzing the formation of only monomethylarginine, thereby representing the only exclusively type III PRMT identified to date. TbPRMT7 is expressed in both mammalian and insect stage T. brucei and is apparently dispensable for growth in both life cycle stages. The enzyme is cytoplasmically localized and is a component of several higher order complexes in vivo. Together, our studies indicate that TbPRMT7 is a Type III PRMT, and its robust activity and presence in numerous complexes suggest it plays multiple roles during the complex T. brucei life cycle.
Ligand requirements of the human corticotropin-releasing factor-binding protein. (1995)

CRF-binding protein (CRF-BP), identified as a 37-kilodalton human serum protein, binds human (h) CRF (Kd = 0.17 +/- 0.01 nM) and blocks hCRF's ability to stimulate ACTH release by pituitary cells in vitro. The present study examines ligand requirements of CRF-BP by testing the affinity of recombinant CRF-BP for synthetic analogs of CRF and peptides in the CRF family. The relative affinities of various fragments of hCRF or related peptides for CRF-BP indicate that residues 9-28 are crucial for ligand binding. CRF-BP binds human/rat CRF and urotensin-I with high affinity, sauvagine with moderate affinity, and ovine (o) CRF with low affinity. The marked difference in the affinity of CRF-BP for oCRF (Ki = 1100 +/- 97 nM) compared to hCRF (Ki = 0.17 +/- 0.01 nM), when considered with the importance of the central domain, suggests that amino acids 22, 23, and/or 25 are critical for binding. Altering oCRF residues 22, 23, or 25 individually or collectively to match those of hCRF increases the affinity of CRF-BP for these ligands; [Ala22, Arg23, Glu25]oCRF, in which all three of these central amino acids are substituted by their hCRF counterparts, binds CRF-BP with an affinity equal to that of hCRF. CRF-BP has differential affinities for CRF receptor antagonists, binding alpha-helical CRF-(9-41) with high affinity and [D-Phe12, Nle21,38]hCRF-(12-41) with low affinity. Thus, the structural requirements for binding to CRF-BP can clearly be distinguished from those for CRF receptor recognition of both agonists and antagonists. Peptides such as hCRF-(9-33), with low biological activity but which retain high affinity for the binding protein, can competitively override the effects of CRF-BP to block CRF-induced ACTH secretion, raising the possibility that whereas endogenous CRF-BP serves to limit the distribution or duration of action of CRF, specific pharmacological inhibitors of the ligand-binding protein interaction might be used to therapeutically elevate free CRF levels.
Feasibility of noninvasive cavitation-guided blood-brain barrier opening using focused ultrasound and microbubbles in nonhuman primates (2011)

In vivo transcranial and noninvasive cavitation detection with blood-brain barrier (BBB) opening in nonhuman primates is hereby reported. The BBB in monkeys was opened transcranically using focused ultrasound (FUS) in conjunction with microbubbles. A passive cavitation detector, confocal with the FUS transducer, was used to identify and monitor the bubble behavior. During sonication, the cavitation spectrum, which was found to be region-, pressure-, and bubble-dependent, provided real-time feedback regarding the opening occurrence and its properties. These findings demonstrate feasibility of transcranial, cavitation-guided BBB opening using FUS and microbubbles in noninvasive human applications.
Workload Balancing for Highly Available Services: The Case of the N+M Redundancy Model (2011)

In today's information based world the demand on highly available services is ever increasing. Fault tolerant systems are capable of providing the expected services even in the presence of a failure. This is achieved through the redundancy of the service providers, where service assignments i.e. workloads are shifted to redundant healthy service providers when a failure occurs. The assignment and the shift are performed according to a redundancy model. A well-known redundancy model is the N+M where we have N active service providers and M standbys. In case of a failure of an active provider, the services are reassigned to its standbys. Maintaining a balanced workload before and after a failure in the N+M redundancy is a challenging task. Especially when the solution is decided at configuration time, and no runtime information is available. This is exactly the issue we tackle in this paper. We present three different approaches aiming at solving this problem with different priorities of the relevant constraints. Our solutions do not require any runtime information and can maintain a balanced workload even after a failure by anticipating the workload redistribution.
Magnetically responsive colloidal photonic crystals (2008)

Magnetically responsive colloidal photonic crystals have been fabricated by using highly charged superparamagnetic Fe3O4 colloidal nanocrystal clusters (CNCs) as the building blocks. The colloids form chainlike structures with regular interparticle spacing of a few hundred nanometers along the external field so that the system strongly diffracts light. The diffraction wavelength can be tuned across the entire visible spectrum by simply changing the strength of the magnetic field. The fast and reversible response suggests great potential of these photonic materials in applications such as displays and sensors. Further modification of the Fe3O4 CNCs with silica coating allows the dispersion of the particles in nonaqueous solutions. The modified particles also self-assemble into ordered structures in alcohol solvents under an external magnetic field. Embedding droplets of such a colloidal solution in a polymer matrix produces solid composite materials with magnetically responsive optical properties.
Abstract 666: Synthesis and structure-activity relationships of compounds that induce methuosis, a novel type of non-apoptotic cell death (2011)

Abstract Methuosis is a caspase-independent form of necrotic cell death in which massive accumulation of vacuoles derived from macropinosomes ultimately causes cells to detach from the substratum and rupture. This form of death was initially described in glioblastoma cells overexpressing activated GTPases, such as Ras or Rac1, but methuosis-like forms of death have since been reported in other types of cells exposed to different stimuli. We have been interested in developing small molecules that can induce methuosis because of the possibility that stimulating this alternative death pathway may represent a useful therapeutic strategy for cancers that are refractory to apoptosis. We now describe the synthesis and biological testing of a class of small molecules that can effectively induce methuosis in glioblastoma cells at low micromolar concentrations. Details of the design and synthesis of a directed library of these novel compounds will be presented, including complete chemical structures and definition of structure-activity relationships. Each compound was evaluated for its ability to induce cytoplasmic vacuolization and reduce cell viability in U251 glioblastoma cells, using phase contrast microscopy, MTT and colony-forming assays as readouts. The results highlight a lead compound with an EC50 of approximately 1-3 micromolar, based on results from both MTT and colony-forming assays. Although the specific molecular target of these compounds is currently unknown, preliminary evidence indicates that they work at the level of endosome trafficking steps mediated by the Rab5 and Rab7 GTPases. The status of work toward target identification will be discussed. The potential significance of these studies is underscored by our recent observation that this class of compounds can induce methuosis in glioblastoma cells resistant to the front-line chemotherapeutic drug, temozolomide. This raises the possibility that the current lead compound may serve as a prototype for development of agents that could be used to trigger death by methuosis in drug-resistant cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 666. doi:10.1158/1538-7445.AM2011-666
Grade of Cataract and Its Influence on Measurement of Macular Pigment Optical Density Using Autofluorescence Imaging (2018)

Cataracts affected MPOD measurements with the Spectralis-MP, but corrected MPOD results could be obtained via regression equations.