gebhart/patrepeval huggingface dataset:
Enzyme inactivation by ethanol and development of a kinetic model for thermophilic simultaneous saccharification and fermentation at 50 °C with Thermoanaerobacterium saccharolyticum ALK2 (2010)

Studies were undertaken to understand phenomena operative during simultaneous saccharification and fermentation (SSF) of a model cellulosic substrate (Avicel) at 50°C with enzymatic hydrolysis mediated by a commercial cellulase preparation (Spezyme CP) and fermentation by a thermophilic bacterium engineered to produce ethanol at high yield, Thermoanaerobacterium saccharolyticum ALK2. Thermal inactivation at 50 °C, as shown by the loss of 50% of enzyme activity over 4 days in the absence of ethanol, was more severe than at 37 °C, where only 25% of enzyme activity was lost. In addition, at 50 °C ethanol more strongly influenced enzyme stability. Enzyme activity was moderately stabilized between ethanol concentrations of 0 and 40 g/L, but ethanol concentrations above 40 g/L accelerated enzyme inactivation, leading to 75% loss of enzymatic activity in 80 g/L ethanol after 4 days. At 37 °C, ethanol did not show a strong effect on the rate of enzyme inactivation. Inhibition of cellulase activity by ethanol, measured at both temperatures, was relatively similar, with the relative rate of hydrolysis inhibited 50% at ethanol concentrations of 56.4 and 58.7 g/L at 50 and 37 °C, respectively. A mathematical model was developed to test whether the measured phenomena were sufficient to quantitatively describe system behavior and was found to have good predictive capability at initial Avicel concentrations of 20 and 50 g/L.
Simulation of nonlinear shear rheology of dilute salt-free polyelectrolyte solutions (2007)

Brownian dynamics simulations are used to conduct a systematic analysis of the nonlinear shear rheology of dilute polyelectrolyte solutions, exploring its relationship to shear rate, Bjerrum length, and concentration. A simple coarse-grained bead-spring chain model that incorporates explicit counterions is used. It is found that the polyelectrolyte chains exhibit a shear thinning behavior at high shear rate (as characterized by bead Peclet number Pe) that is independent of the electrostatic strength due to the stripping of ions from close proximity to the chain caused by the flow. In contrast, at low values of Pe, the viscosity increases monotonically with increasing Bjerrum length over the range studied here, in contrast to the nonmonotonic trend displayed by the chain size. Furthermore, at fixed Bjerrum length, the reduced viscosity increases monotonically with concentration. The mechanism underlying these observations is essentially the primary electroviscous effect; the ion cloud surrounding a polyelectrolyte chain deforms in flow, causing a significant increase in viscosity as concentration increases. Finally, the authors have also considered the role of hydrodynamic interactions in these simulations, finding that for low concentration studies in shear flow, these do not qualitatively affect the results.
Investigating the use of synchronized clocks in tcp congestion control (2003)

In TCP Reno, the most common implementation of TCP, segment loss is the sole indicator of network congestion. TCP Reno only adjusts to congestion when segment loss has been detected in the network, thus TCP Reno’s congestion control is tied to its error recovery mechanism. My dissertation thesis is that precise knowledge of one-way transit times can be used to improve the performance of TCP congestion control. Performance is measured in terms of network-level metrics, including packet loss and average queue sizes at congested links, and in terms of application-level metrics, including HTTP response times and throughput per HTTP response. A connection’s forward path OTT is the amount of time it takes a packet to traverse all links from the sender to the receiver, including both propagation and queuing delays. Queues in routers build up before they overflow, resulting in increased OTTs. If all senders directly measure changes in OTTs and back off when the OTT indicates that congestion is occurring, congestion could be alleviated. I introduce a variant of TCP, called Sync-TCP, which uses synchronized clocks to gather a connection’s OTT data. I use Sync-TCP as a platform for investigating techniques for detecting and responding to changes in OTTs. This dissertation makes the following contributions: • a method for measuring a flow’s OTT and returning this exact timing information to the sender • comparison of several methods for using OTTs to detect congestion • Sync-TCP – a family of end-to-end congestion control mechanisms based on using OTTs for congestion detection • study of standards-track TCP congestion control and error recovery mechanisms in the context of HTTP traffic I will show that Sync-TCP provides lower packet loss, lower queue sizes, lower HTTP response times, and higher throughput per HTTP response than TCP Reno. Additionally, I will show that Sync-TCP offers performance comparable to that achieved by using router-based congestion control mechanisms. If all flows use Sync-TCP to react to increases in queuing delay, congestion could be alleviated quickly. This would result in overall shorter queues, faster response for interactive applications, and a more efficient use of network resources.
Can Radiosensitivity Associated with Defects in DNA Repair be Overcome by Mitochondrial-Targeted Antioxidant Radioprotectors (2014)

Radiation oncologists have observed variation in normal tissue responses between patients in many instances with no apparent explanation. The association of clinical tissue radiosensitivity with specific genetic repair defects (Wegner's syndrome, Ataxia telangiectasia, Bloom's syndrome, and Fanconi anemia) has been well established, but there are unexplained differences between patients in the general population with respect to the intensity and rapidity of appearance of normal tissue toxicity including radiation dermatitis, oral cavity mucositis, esophagitis, as well as differences in response of normal tissues to standard analgesic or other palliative measures. Strategies for the use of clinical radioprotectors have included modalities designed to either prevent and/or palliate the consequences of radiosensitivity. Most prominently, modification of total dose, fraction size, or total time of treatment delivery has been necessary in many patients, but such modifications may reduce the likelihood of local control and/or radiocurability. As a model system in which to study potential radioprotection by mitochondrial-targeted antioxidant small molecules, we have studied cell lines and tissues from Fanconi anemia (Fancd2(-/-)) mice of two background strains (C57BL/6NHsd and FVB/N). Both were shown to be radiosensitive with respect to clonogenic survival curves of bone marrow stromal cells in culture and severity of oral cavity mucositis during single fraction or fractionated radiotherapy. Oral administration of the antioxidant GS-nitroxide, JP4-039, provided significant radioprotection, and also ameliorated distant bone marrow suppression (abscopal effect of irradiation) in Fancd2 (-/-) mice. These data suggest that radiation protection by targeting the mitochondria may be of therapeutic benefit even in the setting of defects in the DNA repair process for irradiation-induced DNA double strand breaks.
Super-efficient rational proofs (2013)

Information asymmetry is a central problem in both computer science and economics. In many fundamental problems, an uninformed principal wants to obtain some knowledge from an untrusted expert. This models several real-world situations, such as a manager's relation with her employees, or the delegation of computational tasks in mechanical turk.
Major Volatile Components of the Juice of American Cranberry (1968)

SUMMARY– Volatiles from the juice of the American cranberry ( Vaccinium macrocarpon Ait.) were investigated using gas chromatography, mass spectrometry and infrared spectrophotometry. Forty‐two compounds comprising over 95% of the aroma complex were identified. These consist of 14 aromatic compounds, 7 terpenes, 9 aliphatic alcohols, 6 aliphatic aldehydes and 6 other compounds including the 2 acids, benzoic and 2‐methylbutyric. The aromatic compounds (benzaldehyde, benzyl and benzoate esters) and the terpenes appear to be the major contributors to the aroma of cranberry juice. The remaining 5% of the aroma complex contains over 200 components. Although these compounds occur in very small concentrations, they appear to be important in the overall aroma.
Telomere Length as an Indicator of the Robustness of B- and T-Cell Response to Influenza in Older Adults (2015)

Telomere length is positively associated with a robust lymphocyte response, and telomere attrition may contribute to the age-associated decline of adaptive immunity.
A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis (2019)

Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which particular gene(s) are relevant continues to be a challenge. Here, we conduct a cell-specific pathway analysis of the latest GWAS in multiple sclerosis (MS), which had analyzed a total of 47,351 cases and 68,284 healthy controls and found more than 200 non-MHC genome-wide associations. Our analysis identifies pan immune cell as well as cell-specific susceptibility genes in T cells, B cells and monocytes. Finally, genotype-level data from 2,370 patients and 412 controls is used to compute intra-individual and cell-specific susceptibility pathways that offer a biological interpretation of the individual genetic risk to MS. This approach could be adopted in any other complex trait for which genome-wide data is available.
Photometry based Blood Oxygen Estimation through Smartphone Cameras (2017)

We introduce a lightweight, cost-effective, and portable solution for real-time peripheral oxygen saturation SpO2 measurement using photometric sensing through a smartphone's camera. Specifically, we design a hardware plug-in module that snaps onto the smartphone's flashlight and estimates the blood oxygen content from the light intensity reflected off the user's finger and registered on camera images. The oxygen levels are mapped to equivalent photoplethysmography (PPG) signals used for the SpO2 estimation using a machine learning based one-time calibration. With the knowledge that blood oxygen largely responds to Infrared (IR) and Red wavelengths, state-of-the-art pulse oximetry techniques use IR and RED light emitting diodes and photodetectors to sense each channel. We further develop a novel solution that exploits the IR leakage of the LED white light of the smartphone. The system is incorporated with a hardware of IR and RED filters that are spatially separated such that the respective signals are registered on independent areas of the image sensor. We present the preliminary results and analyse possible challenges for further improvement.
Decision-directed coherent detection in multicarrier systems on Rayleigh fading channels (1999)

Novel coherent detectors for DQPSK and /spl pi//4-DQPSK on Rayleigh fading channels are presented. The detectors are based on decision feedback and minimum mean-square error (MMSE) channel estimation. The proposed detectors may be used in both single carrier and multicarrier systems. Analytical results in the form of expressions for channel estimation error variance and bit error probability, both with and without diversity, are derived. The MMSE-based detector has a significantly lower irreducible bit error probability floor compared to a conventional differential detector. For most practical applications, the error floor of the MMSE-based detector is negligible. Simulated results are presented to verify the analysis and justify the approximations made.
Stem Cells as an Emerging Paradigm in Stroke 3 (2013)

C ell-based therapy continues to grow as a new field to explore investigational treatments for stroke. Leaders from academia and industry convened an inaugural meeting in 2007 with members of the National Institutes of Health and Food and Drug Administration (FDA) to generate consensus-based guidelines on the development of cell therapies for stroke, entitled "Stem Cells as an Emerging Paradigm in Stroke" (STEPS). 1 These guidelines focused on preclinical studies that are considered important as part of a development program to support clinical testing of cell therapies. The STEPS meeting also provided recommendations on the conduct of early-stage clinical trials. Given the rapid advances in the field, a second meeting was held in 2009 to update and expand these guidelines, which were published as STEPS 2. Since the prior STEPS meeting, there are now several active cell therapy platforms for stroke and other neurological disorders, in stages that range from preclinical to clinical trials, and with sponsors that include industry, the National Institutes of Health, and the California Institute of Regenerative Medicine. As the field continues to progress and as pilot clinical studies are starting to show safety for some cell types, it has become necessary to formulate a new set of guidelines that address topics not covered in prior STEPS publications. Specifically, the current document reflects a compilation of recommendations that focus on more advanced stages of clinical testing, as well as the testing of cell therapies in a broader stroke population that includes chronic stroke.
P-selectin glycoprotein ligand-1 (PSGL-1)-abhängige Leukozytenrekrutierung vermittelt die Leberzellschädigung im Rahmen der obstruktiven Cholestase P-selectin glycoprotein ligand-1 leukocyte recruitment regulates hepatocellular damage in obstructive cholestasis (2010)

Introduction: Leukocytes mediate hepatocellular injury in obstructive cholestasis. The aim of the present study was to define the role of P-selectin glycoprotein ligand-1 (PSGL-1) in cholestasisinduced leukocyte recruitment and liver damage. Materials and Methods: C57BL/6 mice were pre-treated with an anti-PSGL-1 antibody or a control antibody prior to bile duct ligation (BDL) for 12 hours. Hepatic recruitment of leukocytes and sinusoidal perfusion were determined by means of intravital fluorescence microscopy. Liver damage was monitored by measuring serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Hepatic levels of CXC chemokines were determined by ELISA. Results: BDL caused significant hepatocellular damage indicated by increased serum activities of ALT and ADT as well as decreased sinusoidal perfusion and clear-cut hepatic infiltration of leukocytes. Administration of the anti-PSGL-1 antibody reduced BDL-induced levels of ALT by 78 % and AST by 77 %. Inhibition of PSGL-1 decreased BDL-provoked leukocyte rolling and adhesion in postsinusoidal venules by more than 81 %. Moreover, we found that immunoneutralization of PSGL-1 restored sinusoidal perfusion in cholestatic mice. Platelet-endothelial cell interactions were intact in BDL mice treated with the anti-PSGL-1 antibody. Conclusion: Our novel data show that PSGL-1 plays an important role in cholestatic liver damage by regulating leukocyte rolling in postsinusoidal venules. Interference with PSGL-1 attenuates cholestasis-provoked leukocyte adhesion and extravasation in the liver. Thus, inhibition of PSGL-1 may help to protect against hepatocellular damage in cholestatic diseases. Einleitung Obstruktive Cholestase bedingt eine inflammatorische Reaktion des Lebergewebes. Diese fuhrt zur Leukozytenakkumulation im Lebergewebe und zur konsekutiven Leberzellschadigung. Ziel der vorliegenden Studie war es zu klaren, welche Rolle die P-selectin glycoprotein ligand-1 (PSGL-1)-abhangige Leukozytenrekrutierung bei der Entstehung des hepatozellularen Gewebeschadens bei obstruktiver Cholestase spielt. Methodik Bei C57BL/6 Mausen wurde durch Ligatur des Ductus hepaticus communis (BDL) eine obstruktive Cholestase induziert. Vor Ligatur erfolgte entweder die intravenose Applikation eines anti-PSGL-1Antikorpers oder eines Kontroll-Antikorpers ohne PSGL-1-Spezifitat. Tiere ohne Gallengangsligatur dienten als Kontrolle. Nach 12 Stunden wurde mittels intravitaler Fluoreszenzmikroskopie die hepatische Leukozytenakkumulation sowie die sinusoidale Perfusion untersucht. Die extravaskulare
Use of Psychoacoustic Metrics for the Analysis of Next Generation Computer Graphic Card Noise (2005)

The continuing challenge to deliver performance improvements in computer graphic cards has long since progressed to the point of requiring finned, passive, cooling devices to dissipate the heat generated by the graphics processing unit (GPU). The heat flux generated by further improvements now exceeds that dissipation capacity so that passive cooling can no longer provide adequate cooling the GPU. The dissipation rates required by the latest generation of designs can be delivered by forced air cooling of finned heat sinks. The concurrent challenge to the industry is to provide this cooling while minimizing the noise generated by these cooling fans. A significant aspect associate with this problem is missed if one only considers the problem to be a one-dimensional sound level issue. From a consumer’s perspective, the perceived quality of the noise emitted takes precedence over what traditional acoustical analysis techniques of this fan noise may imply. Here, psychoacoustic or sound quality metrics, may be a more applicable analysis tool as it provides the quantification of these qualitative human impressions. The present study investigates the validity of using several psychoacoustic metrics for the analysis of fan cooled computer graphics card noise. Using experimentally measured fan noise from three different cooling fan designs, a sound quality analysis was performed using loudness, sharpness, roughness, fluctuation strength, prominent tone and articulation index. A discussion and comparison of measured results using traditional analysis techniques is also included. It was found that some of the metrics proved more useful than others as an analysis tool for this specific noise source. A discussion of the applicability of the various sound quality metrics along with justifications is presented.
Electron-beam Induced Processes and their Applicability to Mask Repair (2002)

The applicability of electron-beam induced chemical reactions to mask repair is investigated. To achieve deposition and chemical etching with a focused electron-beam system, it is required to disperse chemicals in a molecular beam to the area of interest with a well-defined amount of molecules and monolayers per second. For repair of opaque defects the precursor gas reacts with the absorber material of the mask and forms a volatile reaction product, which leaves the surface. In this way the surface atoms are removed layer by layer. For clear defect repair, additional material, which is light absorbing in the UV, is deposited onto the defect area. This material is rendered as a nanocrystalline deposit from metal containing precursors. An experimental electron-beam mask repair system is developed and used to perform exploratory work applicable to photo mask, EUV mask, EPL and LEEPL stencil mask repair. The tool is described and specific repair actions are demonstrated. Platinum deposited features with lateral dimensions down to 20 nm demonstrate the high resolution obtainable with electron beam induced processes, while AFM and AIMS measurements indicate, that specifications for mask repair at the 70 nm device node can be met. In addition, examples of etching quartz and TaN are given.
Effect of Modifications of the Alkylpiperazine Moiety of Trazodone on 5HT2Aand α1Receptor Binding Affinity (1999)

A series of triazolopyridine derivatives (compounds 2a-l) were synthesized in order to explore the effect of modifications of the alkylpiperazine moiety of trazodone (fragment A) on binding affinity for 5HT2A and alpha1 receptors. All of the synthesized compounds show a decrease of affinity for both 5HT2A and alpha1 receptors, as compared to trazodone, with the exception of compounds 2b,c which bear a methyl group in an alpha position to the aliphatic nitrogen atom N1. These compounds showed a decrease of affinity only for the alpha1 receptor. The stereochemical influence of the piperazine moiety of compound 2c was also evaluated. Enantiomer (S)-2c showed the most significant differences between 5HT2A and alpha1 receptor affinity (IC50 values) and among the corresponding functional properties (pA2 values). Since (S)-2c cannot generate the metabolite 4-(3-chlorophenyl)piperazine this product was selected for further pharmacological studies.
Photochemically Cross-Linked Perfluoropolyether-Based Elastomers: Synthesis, Physical Characterization, and Biofouling Evaluation (2009)

A series of reactive liquid perfluoropolyether (PFPE) precursors were synthesized which call be photochemically cross-linked (UV-cured) into high-performance PFPE elastomers in one step. To investigate how fundamental changes in the PFPE molecular structure correlate to bulk and surface properties, the variable functional end group, molecular weight, and the copolymer content were systematically explored in relation to thermal stability, contact angle/surface tension, modulus, and biofouling behavior. The morphologies of these PFPE materials were studied using differential scanning calorimetry, dynamic mechanical thermal analysis, and small-angle X-ray scattering. From these studies, it was determined that clusters of polymerized functional end groups were found to be nanophase separated within the PFPE matrix. By varying the cross-link density. the Young's modulus of the fully cross-linked PFPE clastomeric film could be tuned from 1.5 to 90 MPa with a critical surface tension of 8.6-16 mN/m. The marine antifouling and fouling-release properties of the cross-linked PFPE elastomeric coatings were evaluated by settlement and release assays involving zoospores and sporelings (Young plants), respectively, of green fouling alga Ulva.