gebhart/patrepeval huggingface dataset:
Experimental observations of fracture dissolution: The role of Peclet number on evolving aperture variability (2003)

Dissolution of the surfaces of rock fractures can cause significant alteration of the fracture void space (aperture) and fracture permeability ( k ). Both surface reaction rates and transport of reactants within the fracture can limit local dissolution. We investigated the role of Peclet number ( Pe ), a measure of the relative importance of advective and diffusive transport of reactants, on fracture dissolution in two identical transparent analog fractures with different initial values of Pe ( Pe o ). High‐resolution light‐transmission techniques provided direct measurements of the evolving aperture field during each experiment. For Pe o = 54 distinct dissolution channels formed, while for Pe o = 216 we measured minimal channeling and a reduction in short wavelength aperture variability. The nature of the dissolution patterns strongly influenced the relative increase in k . A 110% increase in the mean aperture due to dissolution resulted in estimated permeability increases of 440% and 640% for the Pe o = 54 and Pe o = 216 experiments, respectively.
Synthesis and Evaluation of Folate-Based Chlorambucil Delivery Systems for Tumor-Targeted Chemotherapy (2011)

The development of tumor-targeting drug delivery systems, able to selectively transport cytotoxic agents into the tumor site by exploiting subtle morphological and physiological differences between healthy and malignant cells, currently stands as one of the most attractive anticancer strategies used to overcome the selectivity problems of conventional chemotherapy. Owing to frequent overexpression of folate receptors (FRs) on the surface of malignant cells, conjugation of cytotoxic agents to folic acid (FA) via suitable linkers have demonstrated to enhance selective drug delivery to the tumor site. Herein, the chemical synthesis and biological evaluation of two novel folate-conjugates bearing the anticancer agent chlorambucil (CLB) tethered to either an aminoether (4,7,10-trioxa-1,13-tridecanediamine) or a pseudo-β-dipeptide (β-Ala-ED-β-Ala) linker is reported. The two drug delivery systems have been prepared in high overall yields (54% and 34%) through straightforward and versatile synthetic routes. Evaluation of cell specificity was examined using three leukemic cell lines, undifferentiated U937 (not overexpressing FRs, FR(-)), TPA-differentiated U937 (overexpressing FRs, FR(+)), and TK6 (FR(+)) cells. Both conjugates exhibited high specificity only to FR(+) cells (particularly TK6), demonstrating comparable antitumor activity to CLB in its free form. These data confirm the reliability of folate-based drug delivery systems for targeted antitumor therapy; likewise, they lay the foundations for the development of other folate-conjugates with antitumor potential.
Automated Dyadic Data Recorder (ADDR) Framework and Analysis of Facial Cues in Deceptive Communication (2018)

We developed an online framework that can automatically pair two crowd-sourced participants, prompt them to follow a research protocol, and record their audio and video on a remote server. The framework comprises two web applications: an Automatic Quality Gatekeeper for ensuring only high quality crowd-sourced participants are recruited for the study, and a Session Controller which directs participants to play a research protocol, such as an interrogation game. This framework was used to run a research study for analyzing facial expressions during honest and deceptive communication using a novel interrogation protocol. The protocol gathers two sets of nonverbal facial cues in participants: features expressed during questions relating to the interrogation topic and features expressed during control questions. The framework and protocol were used to gather 151 dyadic conversations (1.3 million video frames). Interrogators who were lied to expressed the smile-related lip corner puller cue more often than interrogators who were being told the truth, suggesting that facial cues from interrogators may be useful in evaluating the honesty of witnesses in some contexts. Overall, these results demonstrate that this framework is capable of gathering high quality data which can identify statistically significant results in a communication study.
Genome-wide Analysis of the Response to Cell Wall Mutations in the Yeast Saccharomyces cerevisiae (2003)

Perturbations of the yeast cell wall trigger a repair mechanism that reconfigures its molecular structure to preserve cell integrity. To investigate this mechanism, we compared the global gene expression in five mutant strains, each bearing a mutation (i.e. fks1, kre6, mnn9, gas1, and knr4 mutants) that affects in a different manner the cell wall construction. Altogether, 300 responsive genes were kept based on high stringency criteria during data processing. Functional classification of these differentially expressed genes showed a substantial subset of induced genes involved in cell wall construction and an enrichment of metabolic, energy generation, and cell defense categories, whereas families of genes belonging to transcription, protein synthesis, and cellular growth were underrepresented. Clustering methods isolated a single group of approximately 80 up-regulated genes that could be considered as the stereotypical transcriptional response of the cell wall compensatory mechanism. The in silico analysis of the DNA upstream region of these co-regulated genes revealed pairwise combinations of DNA-binding sites for transcriptional factors implicated in stress and heat shock responses (Msn2/4p and Hsf1p) with Rlm1p and Swi4p, two PKC1-regulated transcription factors involved in the activation genes related to cell wall biogenesis and G1/S transition. Moreover, this computational analysis also uncovered the 6-bp 5'-AGCCTC-3' CDRE (calcineurin-dependent response element) motif in 40% of the co-regulated genes. This motif was recently shown to be the DNA binding site for Crz1p, the major effector of calcineurin-regulated gene expression in yeast. Taken altogether, the data presented here lead to the conclusion that the cell wall compensatory mechanism, as triggered by cell wall mutations, integrates three major regulatory systems: namely the PKC1-SLT2 mitogen-activated protein kinase-signaling module, the "global stress" response mediated by Msn2/4p, and the Ca2+/calcineurin-dependent pathway. The relative importance of these regulatory systems in the cell wall compensatory mechanism is discussed.
Oriented ZnO Films for Microwave Shear Mode Transducers (1982)

Shear mode generation has been observed in the 2 to 4 GHz frequency r ange u sing ZnO thin film t ransducers with the c-axis tilted with respect to the substrate normal. These films were produced by RF diode sputtering from a pure ZnO target. Various parameters which influence the orientation of the film have b een investigated e xperimentally and will be reported. These effects include: substrate (contact) material, s ubstrate bias, s ubstrate position with respect to target, s ubstrate angle with respect to target and deposition rate. Extensive X-ray examination of the films was required to determine the effect of changing o ne or another of the above parameters. The best set of parameters obtained so far was used to fabricate the s hear mode transducers.
Combining Categorical And Primitives-Based Emotion Recognition (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
The “IT Productivity Paradox” Revisited: International Comparisons of Information Technology, Work Organisation and Productivity in Service Industries (2000)

Although many authors now regard the ‘IT productivity paradox’ as an issue which has been resolved at firm level (at least in the US), some puzzles still remain at industry and national economy level. In this article we have explored the relationship between IT investments and relative labour productivity performance through comparisons of matched samples of banking and hotel establishments in the US, Germany and Britain. In both industries a lack of correspondence between country productivity ranking and the incidence of different kinds of IT usage was attributable to inter-country differences in (1) the timing of IT investments and of adaptation of work organisation to take full advantage of the productivity-enhancing potential of IT; (2) the mix of product strategies deployed by service establishments; and (3) the supply of complementary assets required to secure high levels of pay-off to IT investments. Obwohl gegenwärtig viele Autoren das "Produktivitätsparadox der Informationstechnik" als ein Thema ansehen, das, zumindest in den USA, auf der Firmenebene gelöst wurde, bleiben noch einige Unklarheiten auf den Ebenen von Branchen- und Volkswirtschaft bestehen. Der vorliegende Beitrag untersucht die Beziehung zwischen Investitionen in Informationstechnik und relativer Arbeitsproduktivität durch Vergleiche von entsprechenden Stichproben im Banken- und Hotelgewerbe in den USA, Deutschland und England. In beiden Industrien kann die mangelnde Übereinstimmung zwischen Länderproduktivitätsranking und unterschiedlichem Einsatzgrad von Informationstechnik auf Unterschiede zwischen den Ländern in den folgenden drei Bereichen zurückgeführt werden: (1) In der zeitlichen Koordinierung von Investitionen im informationstechnischen Bereich und der Anpassung der Arbeitsorganisation, um das Potential der Informationstechnik zur Erhöhung der Produktivität voll auszuschöpfen; (2) der von den Dienstleistungseinrichtungen gewählte Einsatz der Produktmixstrategien; und (3) das erforderliche Angebot von komplementären Anlagen, um eine hohe Rendite von IT Investitionen zu gewährleisten.
An Attention Enhanced Multi-Task Model for Objective Speech Assessment in Real-World Environments (2020)

Computational objective metrics that use reference signals have been shown to be effective forms of speech assessment in simulated environments, since they are correlated with subjective listening studies. Recent efforts have been dedicated towards effective forms of reference-less assessment to make real-world assessment more practical, but these approaches predict a limited number of assessment measures and they have not been evaluated in real-world conditions. In this work, we present a novel reference-less based framework called the attention enhanced multi-task speech assessment (AMSA) model, which provides reliable estimates of multiple objective quality and intelligibility measures in simulated and real-world environments. The multi-task learning (MTL) architecture effectively generates discriminative features that assist in improving our model's robustness. An attention mechanism is employed to identify key features within the feature space, and it noticeably reduces the estimation errors. A classification-aided module is also included to further suppress prediction outliers. Our model achieves the state-of-the-art performance in simulated and real-world data environments, where the results are strongly correlated with the corresponding reference-based objective scores.
Techniques for the measurement of white adipose tissue metabolism: a practical guide. (1995)

A number of old and new techniques to study various aspects of white adipose tissue metabolism in vivo and in vitro are discussed. It is possible to determine lipolysis rates in vivo with tracer techniques using glycerol or fatty acids labelled with stable or radioactive isotopes. These methods allow the determination of whole body lipolysis rates but are not valuable for the investigations of regional variations in lipolysis. When combined they permit a calculation of the rate of re-esterification of free fatty acids. The vein draining abdominal subcutaneous adipose tissue can be cannulated in humans. By this method substrate turnover can be determined in vivo over the cannulated adipose region. With microdialysis it is possible to study local metabolism in vivo in different adipose tissue regions. At the same time it is possible to locally manipulate the tissue with metabolically active pharmacological substances. A number of in vitro methods to determine glucose transport in isolated fat cells are developed. The most accurate one uses 3-O-methyl glucose as tracer. These methods can be combined with studies of the further metabolism of glucose to lipids, lactate and carbon dioxide using simple (usually radioactive) methods. Lipolysis as well as release and re-esterification of free fatty acids can be investigated in detailed in vitro with sensitive techniques based on luminescence. Finally, triglyceride turnover and partial metabolism of acylglycerols can be investigated in vitro with a double isotope technique.
An 8–12GHz 0.92° Phase Error Quadrature Clock Generator Based on Two-Stage Poly Phase Filter with Intermediate Point Compensation (2019)

An ultra-low phase error, low power Quadrature Clock Generator (QCG) based on two-stage Poly Phase Filter (PPF) with intermediate point compensation is proposed. With the incorporation of a RC sensing network to detect the process variation, the PPF compensates its quadrature phase error by feeding the network's output to the intermediate point. Meanwhile, output amplitude of the PPF is enhanced as a benefit of intermediate point utilization. In comparison with conventional Type-I and Type-II PPF-based QCGs, the proposed one excels in broadband phase error as a result of lowest phase/amplitude error combination in a typical process variation scenario (ΔR=±20%, ΔC=±10%). Furthermore, it stands out in power consumption performance due to its amplitude enhancement, which effectively reduces the amplification power passive PPF implementations always need. The phase error of proposed QCG is less than 0.32° at 10GHz, and no more than 0.92 ° over 8GHz-12GHz with process variations in Global Foundry 55nm CMOS process. The QCG consumes 9.6mW from a 1.2V supply voltage.
Toll-like receptor 2 activation depends on lipopeptide shedding by bacterial surfactants (2016)

Sepsis caused by Gram-positive bacterial pathogens is a major fatal disease but its molecular basis remains elusive. Toll-like receptor 2 (TLR2) has been implicated in the orchestration of inflammation and sepsis but its role appears to vary for different pathogen species and clones. Accordingly, Staphylococcus aureus clinical isolates differ substantially in their capacity to activate TLR2. Here we show that strong TLR2 stimulation depends on high-level production of phenol-soluble modulin (PSM) peptides in response to the global virulence activator Agr. PSMs are required for mobilizing lipoproteins, the TLR2 agonists, from the staphylococcal cytoplasmic membrane. Notably, the course of sepsis caused by PSM-deficient S. aureus is similar in wild-type and TLR2-deficient mice, but TLR2 is required for protection of mice against PSM-producing S. aureus. Thus, a crucial role of TLR2 depends on agonist release by bacterial surfactants. Modulation of this process may lead to new therapeutic strategies against Gram-positive infections.
Developing a toolkit for comparing safety in spine surgery. (2014)

Safety information in spine surgery is important for informed patient choice and performance-based payment incentives, but measurement methods for surgical safety assessment are not standardized. Published reports of complication rates for common spinal procedures show wide variation. Factors influencing variation may include differences in safety ascertainment methods and procedure types. In a prospective cohort study, adverse events were observed in all patients undergoing spine surgery at two hospitals during a 2-year period. Multiple processes for adverse occurrence surveillance were implemented, and the associations between surveillance methods, surgery invasiveness, and observed frequencies of adverse events were examined. The study enrolled 1,723 patients. Adverse events were noted in 48.3% of the patients. Reviewers classified 25% as minor events and 23% as major events. Of the major events, the daily rounding team reported 38.4% of the events using a voluntary reporting system, surgeons reported 13.4%, and 9.1% were identified during clinical conferences. A review of medical records identified 86.7% of the major adverse events. The adverse events occurred during the inpatient hospitalization for 78.1% of the events, within 30 days for an additional 12.5%, and within the first year for the remaining 9.4%. A unit increase in the invasiveness index was associated with an 8.2% increased risk of a major adverse event. A Current Procedural Terminology-based algorithm for quantifying invasiveness correlated well with medical records-based assessment. Increased procedure invasiveness is associated with an increased risk of adverse events. The observed frequency of adverse events is influenced by the ascertainment modality. Voluntary reports by surgeons and other team members missed more than 50% of the events identified through a medical records review. Increased surgery invasiveness, measured from medical records or billing codes, is quantitatively associated with an increased risk of adverse events.
(WIP) CloudCAMP: Automating the Deployment and Management of Cloud Services (2018)

Users of cloud platforms often must expend significant manual efforts in the deployment and orchestration of their services on cloud platforms due primarily to having to deal with the high variabilities in the configuration options for virtualized environment setup and meeting the software dependencies for each service. Despite the emergence of many DevOps cloud automation and orchestration tools, users must still rely on specifying low-level scripting details for service deployment and management. Using these tools required domain expertise along with a steep learning curve. To address these challenges in a tool-and-technology agnostic manner, which helps promote interoperability and portability of services hosted across cloud platforms, we present initial ideas on a GUI based cloud automation and orchestration framework called CloudCAMP. CloudCAMP uses model-driven engineering techniques to provide users with intuitive and higher-level modeling abstractions that preclude the need to specify all the low-level details. CloudCAMP's generative capabilities leverage a built-in knowledge-base to automate the synthesis of Infrastructure-as-Code (IAC) solution that subsequently can be used to deploy and orchestrate services in the cloud. Preliminary results from a small user study are presented in the paper.
Synthesis and characterization of polyurethanes containing cholesterol and phosphatidylcholine analogous moieties (1995)

Abstract Several new polyurethanes containing cholesterol and phosphatidylcholine analogous moieties were synthesized by addition polymerization of 2‐[bis(2‐hydroxyethyl)methylammonio]ethyl 5‐cholesten‐3β‐yl phosphate ( 2 ) with diisocyanates such as hexamethylene diisocyanate (HDI), 2,4‐tolylene diisocyanate (TDI), 4,4′‐methylenediphenyl diisocyanate (MDI) and m ‐xylylene diisocyanate (XDI), respectively. They were characterized by their IR and 1 H NMR spectral data and elemental analyses. Preliminary studies suggest that these polyurethanes show the viscosity behavior of common polyelectrolytes.
Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq (2020)

Recent studies have proposed that tumor-specific tumor-infiltrating CD8(+) T lymphocytes (CD8 TIL) can be classified into two main groups: “exhausted” TILs, characterized by high expression of the inhibitory receptors PD-1 and TIM-3 and lack of transcription factor 1 (Tcf1); and “memory-like” TILs, with self-renewal capacity and co-expressing Tcf1 and PD-1. However, a comprehensive definition of the heterogeneity existing within CD8 TILs has yet to be clearly established. To investigate this heterogeneity at the transcriptomic level, we performed paired single-cell RNA and TCR sequencing of CD8 T cells infiltrating B16 murine melanoma tumors, including cells of known tumor specificity. Unsupervised clustering and gene-signature analysis revealed four distinct CD8 TIL states – exhausted, memory-like, naïve and effector memory-like (EM-like) – and predicted novel markers, including Ly6C for the EM-like cells, that were validated by flow cytometry. Tumor-specific PMEL T cells were predominantly found within the exhausted and memory-like states but also within the EM-like state. Further, T cell receptor sequencing revealed a large clonal expansion of exhausted, memory-like and EM-like cells with partial clonal relatedness between them. Finally, meta-analyses of public bulk and single-cell RNA-seq data suggested that anti-PD-1 treatment induces the expansion of EM-like cells. Our reference map of the transcriptomic landscape of murine CD8 TILs will help interpreting future bulk and single-cell transcriptomic studies and may guide the analysis of CD8IL subpopulations in response to therapeutic interventions.
Plasma-assisted atomic layer deposition of Al<sub>2</sub>O<sub>3</sub> and parylene C bi-layer encapsulation for chronic implantable electronics (2012)

Encapsulation of biomedical implants with complex three dimensional geometries is one of the greatest challenges achieving long-term functionality and stability. This report presents an encapsulation scheme that combines Al(2)O(3) by atomic layer deposition with parylene C for implantable electronic systems. The Al(2)O(3)-parylene C bi-layer was used to encapsulate interdigitated electrodes, which were tested invitro by soak testing in phosphate buffered saline solution at body temperature (37 °C) and elevated temperatures (57 °C and 67 °C) for accelerated lifetime testing up to 5 months. Leakage current and electrochemical impedance spectroscopy were measured for evaluating the integrity and insulation performance of the coating. Leakage current was stably about 15 pA at 5 V dc, and impedance was constantly about 3.5 MΩ at 1 kHz by using electrochemical impedance spectroscopy for samples under 67 °C about 5 months (approximately equivalent to 40 months at 37 °C). Alumina and parylene coating lasted at least 3 times longer than parylene coated samples tested at 80 °C. The excellent insulation performance of the encapsulation shows its potential usefulness for chronic implants.
Simple Coupling Chemistry Linking Carboxyl-Containing Organic Molecules to Silicon Oxide Surfaces under Acidic Conditions (2010)

The coupling chemistry of carboxymethylated amylose with organo-silanized silicon oxide surfaces at pH 7.4 and 2.0 was investigated using atomic force microscopy (AFM) based single-molecule force spectroscopy. At close to neutral pH, carbodiimide activation of a carboxylic acid affords formation of an amide bond with an amino surface linker. At pH 2.0, no activation with carbodiimide was required to anchor carboxymethylated amylose between an AFM tip and a glass substrate. At the same time, the mean bond rupture force f(r) dropped from 1.65 ± 0.37 nN at pH 7.4 to 1.39 ± 0.30 nN at pH 2.0 without carbodiimide, indicating that a different link to the surface can be formed at low pH. The coupling mechanism at pH 2.0 was elucidated by a series of experiments, in which the surface was functionalized with four different organosilanes, each containing characteristic functional groups. The results are rationalized with an acid-catalyzed ester condensation between a carboxyl group and a free, unreacted silanol group in the surface anchor or on the surface.