gebhart/patrepeval huggingface dataset:
The spacing of S-domains on HS glycosaminoglycans determines whether the chain is a substrate for intracellular heparanases (2000)

Heparanases are mammalian endoglucuronidases that degrade heparan sulfate (HS) glycosaminoglycans to short 5-6 kDa pieces. In the Golgi, HS glycosaminoglycans are modified by a series of interdependent reactions which result in chains that have regions rich in N- and O-sulfate groups and iduronate residues (S-domains), separated by regions that are nearly devoid of sulfate. Structural analysis of the short HS chains produced by Chinese hamster ovary (CHO) cell heparanases indicate that the enzymes recognize differences in sulfate content between S-domains and unmodified sequences, and cleave the chain at junctions between these regions. To look more closely at whether the spacing of S-domains on the gly- cosaminoglycan influences its ability to be cleaved by heparanases, we examined the susceptibility of the HS chains synthesized by the proteoglycan synthesis mutant, pgsE-606. PGS:E-606 cells are deficient in the modification enzyme N-deacetylase/N-sulfotransferase I, and synthesize HS chains that have fewer N- and O-sulfate groups and iduronate residues compared to wild-type (Bame et al., (1991), J. Biol. Chem., 266, 10287). HS glycosaminoglycans were isolated from wild-type and pgsE-606 cells and separated into populations based on sulfate content. Compared to wild-type HS, which has 14 S-domains, pgsE-606 cells synthesize three HS species, 606-1, 606-2, and 606-3, with 1, 4, and 8 S-domains, respectively. The spacing of the S-domains on the pgsE-606 HS chains is similar to the spacing the modified sequences on wild-type HS, indicating that each mutant glycosaminoglycan is composed of wild-type-like sequences and sequences devoid of S-domains. When incubated with partially purified CHO heparanases, only the portion of the mutant HS chains that had S-domains were degraded. Structural analysis of the heparanase-products confirmed that both the number and the arrangement of S-domains on the HS glycosaminoglycan are important for heparanase susceptibility. The structure of the different pgsE-606 HS chains also suggests mechanisms for the placement of S-domains when the gly- cosaminoglycan is synthesized.
Inhibition by Poly(acrylic acid) and Morphological Changes in Calcium Carbonate and Calcium Carbonate/Calcium Sulfate Crystallization on Silica Fibers (2014)

An intrinsic exposed core optical fiber sensor (IECOFS) made from fused silica was used to monitor the crystallization of calcium carbonate (CaCO3) and CaCO3/calcium sulfate (CaSO4) composite at 100 and 120 °C in the absence and presence of low-molar-mass (Mn ≤ 2000) poly(acrylic acid) (PAA) with different end groups. The IECOFS responded only to deposition and growth processes on the fiber surface rather than changes occurring in the bulk of the solution. Hexyl isobutyrate-terminated PAA (Mn = 1400) and hexadecyl isobutyrate-terminated PAA (Mn = 1700) were the most effective species in preventing CaCO3 deposition. Phase transformation from vaterite to aragonite/calcite decreased with increasing hydrophobicity of the PAA end group. Low-molar-mass PAA at 10 ppm showed very significant inhibition of CaCO3/CaSO4 composite formation for all end groups investigated.
Computational High-Resolution Dual-Comb Spectroscopy with a Free-Running All-Fiber Laser (2019)

Dual-comb spectroscopy (DCS) has experienced a remarkable growth propelled by recent advances in fiber and semiconductor technology. A key enabler for DCS is mutual stability between two repetition-rate-mismatched frequency combs, which conventionally relies on feedback loops employing additional optics and electronics to synchronize a pair of sources. This limitation can be overcome in several ways, of which one of the most promising is the generation of two frequency combs in a single free-running fiber laser cavity [1-3]. To date, however, the only configuration proven to be compatible with Doppler-limited spectroscopy was the dual-color laser presented in Ref. [2] requiring external spectral broadening, thus adding an extra layer of complexity.
Surgical Management of Facial Paralysis Following Temporal Bone Fractures (2005)

Background and Objectives:Controversy persists in regard to the management of traumatic facial paralysis. We reviewed the cases of decompression of traumatic facial nerve according to the type of fracture, injury site of nerve, injured state of nerve, surgical timing, surgical approach and opening of epineurium to determine good prognostic factors and propose in this article a rationale of management. Subjects and Method:The authors reviewed retrospectively 35 cases of the decompression of traumatic facial paralysis at the Department of Otorhinolaryngology, Yonsei University College of Medicine from January 1991 to December 2002. Results:The most common site of the injury was perigeniculate area. The most common fracture type was longitudinal fracture. The results of immediate facial nerve decompression were excellent in functional recovery. The surgical findings of injured facial nerve were, in order, edematous swelling, bony impingement, fibrosis and partial transection, traumatic neuroma. Decompression with nerve sheath slitting appeared to provide better outcomes. The approach for decompression according to the injured sites was sufficiently adequate. Conclusion:According to our surgical experiences of traumatic facial paralysis, the important prognostic factors are timing of surgical intervention, injured state of the nerve and the slitting of the
Path Generation with LSTM Recurrent Neural Networks in the Context of the Multi-Agent Patrolling (2018)

We propose a conceptually simple new decentralised and non-communicating strategy for the multi-agent patrolling based on the LSTM architecture. The recurrent neural networks and more specifically the LSTM architecture, as machines to learn temporal series, are well adapted to the multi-agent patrol problem to the extent that they can be viewed as a decision problem over the time. For a given scenario, a LSTM neural network is first trained from data generated in simulation for that configuration, then embedded in agents that shall use it to navigate through the area to patrol choosing the next place to visit by feeding it with their current node. Finally, this new LSTM-based strategy is evaluated in simulation and compared with two representative strategies, a cognitive and centralised one, and a reactive and decentralised one. Preliminary results indicate that the proposed strategy is globally not better than the representative strategies for the aggregating criterion of average idleness, but better than the decentralised representative for the evaluation criteria of mean interval and quadratic mean interval.
Is It More Expensive, or Does It Just Cost More Money? (2002)

Most of us, from the general public to professional economists, use the term inflation pretty loosely. It?s increasingly applied to any rise in prices, and even economists use it interchangeably with a rise in the cost of living. This Commentary explains what inflation is, why it should be kept distinct from a rise in the cost of living, and how some statistical measures attempt to distinguish between the two.
Supplementary Figure from Prognostic Significance of DNA Methylation Profiles at MRI Enhancing Tumor Recurrence: a Report from the EORTC 26091 TAVAREC Trial (2023)

Supplementary Figure from Prognostic Significance of DNA Methylation Profiles at MRI Enhancing Tumor Recurrence: a Report from the EORTC 26091 TAVAREC Trial
Passive ventricular constraint amends the course of heart failure: a study in an ovine model of dilated cardiomyopathy (1999)

In this model of heart failure, ventricular constraint with a polyester jacket diminished the deterioration in cardiac function associated with progressive dilated cardiomyopathy. These results suggest that maintainance of a more normal cardiac size and shape may be beneficial in patients with dilated cardiomyopathy.
Efficient and flexible incremental parsing (1998)

Previously published algorithms for LR ( k ) incremental parsing are inefficient, unnecessarily restrictive, and in some cases incorrect. We present a simple algorithm based on parsing LR( k ) sentential forms that can incrementally parse an arbitrary number of textual and/or structural modifications in optimal time and with no storage overhead. The central role of balanced sequences in achieving truly incremental behavior from analysis algorithms is described, along with automated methods to support balancing during parse table generation and parsing. Our approach extends the theory of sentential-form parsing to allow for ambiguity in the grammar, exploiting it for notational convenience, to denote sequences, and to construct compact (“abstract”) syntax trees directly. Combined, these techniques make the use of automatically generated incremental parsers in interactive software development environments both practical and effective. In addition, we address information preservation in these environments: Optimal node reuse is defined; previous definitions are shown to be insufficient; and a method for detecting node reuse is provided that is both simpler and faster than existing techniques. A program representation based on self-versioning documents is used to detect changes in the program, generate efficient change reports for subsequent analyses, and allow the parsing transformation itself to be treated as a reversible modification in the edit log.
Nano Magnetite Particles Prepared under the Combined Addition of Urea and Ammonia (2006)

Magnetite (Fe3O4) particles were prepared for biomedical application through three different routes. Each route had the difference in the selection of pH controlling agents. Ammonia, Urea and combined use of ammonia and urea were tested in the synthesis through co-precipitation. With the combined use of urea and ammonia, the size of particles could be reduced as small as 10 nm while effectively suppressing the agglomeration among particles. The surface charge measured at physiological condition explained the good dispersion behavior of nano-magnetite particles. The superparamagnetism observed in nano magnetite particles was expected to be useful for biomedical application in the respect of magnetic localization and dispersion.
Surgical Management of Metastatic Disease of Bone at the Hip (1982)

Concordant advances in cancer chemotherapy, radiotherapy, and surgical technique have been of apparent benefit to many cancer patients suffering from skeletal involvement at the hip. Consideration of the effects of underlying disease and prior treatment must be evaluated prior to developing a surgical plan. Acetabular involvement can be treated by either conventional or augmented total hip arthroplasty using protrusio rings and acetabular meshes, depending upon minor or major degrees of tumor destruction. Girdlestone resection arthroplasty for massive degrees of acetabular involvement yields only modest results. Femoral neck fractures can be treated by endoprosthetic replacement. However, the association of acetabular disease should be considered, and if present, total hip arthroplasty should be performed. Intertrochanteric fractures can be stabilized with the use of a stout tubeplate nail device plus cement. Subtrochanteric fractures can be stabilized with a Zickel nail device plus cement. The goals of treatment are to relieve pain and restore function by using a device with an anticipated fatigue life which should exceed the patient's life expectancy.
Highly Selective Inhibition of Tyrosine Kinase 2 (TYK2) for the Treatment of Autoimmune Diseases: Discovery of the Allosteric Inhibitor BMS-986165 (2019)

Small molecule JAK inhibitors have emerged as a major therapeutic advancement in treating autoimmune diseases. The discovery of isoform selective JAK inhibitors that traditionally target the catalytically active site of this kinase family has been a formidable challenge. Our strategy to achieve high selectivity for TYK2 relies on targeting the TYK2 pseudokinase (JH2) domain. Herein we report the late stage optimization efforts including a structure-guided design and water displacement strategy that led to the discovery of BMS-986165 (<b>11</b>) as a high affinity JH2 ligand and potent allosteric inhibitor of TYK2. In addition to unprecedented JAK isoform and kinome selectivity, <b>11</b> shows excellent pharmacokinetic properties with minimal profiling liabilities and is efficacious in several murine models of autoimmune disease. On the basis of these findings, <b>11</b> appears differentiated from all other reported JAK inhibitors and has been advanced as the first pseudokinase-directed therapeutic in clinical development as an oral treatment for autoimmune diseases.
Bacterial Cell Surface Display of Organophosphorus Hydrolase for Selective Screening of Improved Hydrolysis of Organophosphate Nerve Agents (2002)

Organophosphorus hydrolase (OPH) is a bacterial enzyme that has been shown to degrade a wide range of neurotoxic organophosphate nerve agents. However, the effectiveness of degradation varies dramatically, ranging from highly efficient with paraoxon to relatively slow with methyl parathion. Sequential cycles of DNA shuffling and screening were used to fine-tune and enhance the activity of OPH towards poorly degraded substrates. Because of the inaccessibility of these pesticides across the cell membrane, OPH variants were displayed on the surface of Escherichia coli using the truncated ice nucleation protein in order to isolate novel enzymes with truly improved substrate specificities. A solid-phase top agar method based on the detection of the yellow product p-nitrophenol was developed for the rapid prescreening of potential variants with improved hydrolysis of methyl parathion. Two rounds of DNA shuffling and screening were carried out, and several improved variants were isolated. One variant in particular, 22A11, hydrolyzes methyl parathion 25-fold faster than does the wild type. Because of the success that we achieved with directed evolution of OPH for improved hydrolysis of methyl parathion, we believe that we can easily extend this method in creating other OPH variants with improved activity against poorly degraded pesticides such as diazinon and chlorpyrifos and nerve agents such as sarin and soman.
Compare the effect of Sarbanes-Oxley on audit pricing: application of partial adjustment model (2013)

This study investigates whether audit pricing has changed following the passage of the Sarbanes-Oxley Act of 2002 (SOX). A partial adjustment model has been developed and employed to examine and characterised the rigidity of audit fees and the effect of SOX on audit pricing. The data is collected from Compustat and Audit Analytics databases. The panel data sample consists of 8,120 US publicly-listed firms for the period of 2000–2007. The empirical results document that audit fees increase significantly in the post-SOX period. Auditors could adjust audit fees to remain consistent with auditors’ expectations more closely in the post-SOX period than in the pre-SOX period. The findings suggest that auditors have more bargaining power in post-SOX period that could be attributable to audit environment change. Finally, several robustness tests are performed to explore the differences of the determinants of audit fees before and after the advent of SOX.
Variation of glucoraphanin metabolismin vivoandex vivoby human gut bacteria (2011)

Glucosinolates, phytochemicals found in cruciferous vegetables, are metabolised to bioactive isothiocyanates (ITC) by certain bacteria in the human gut. Substantial individual variation in urinary ITC excretion has been observed in previous cruciferous vegetable-feeding studies. We hypothesised that individual differences in gut microbial community contribute to the observed variation in glucosinolate metabolism, i.e. gut microbiota composition between high- and low-ITC excreters differs. We recruited twenty-three healthy individuals and fed them a standardised meal containing 200 g of cooked broccoli. After the meal, 24 h urinary ITC excretion was measured. Study participants with the highest (n 5) and lowest (n 5) ITC excretion provided faecal samples for ex vivo bacterial cultivation with 50 μm-glucoraphanin, the major glucosinolate found in broccoli. When grown ex vivo, faecal bacteria from the selected high-ITC excreters were able to degrade more glucoraphanin than those from the low-ITC excreters (P = 0·05). However, bacterial fingerprints of faecal and ex vivo culture microbiota revealed no statistically significant differences between the high- and low-ITC excreters in terminal restriction fragment length polymorphism analysis of the bacterial 16S ribosomal RNA gene. In conclusion, glucosinolate degradation by faecal bacteria ex vivo may be associated with in vivo bacterial glucosinolate metabolism capacity, but no direct link to specific bacterial species could be established, possibly due to the complexity and functional redundancy of the gut microbiota.
Homogeneous and Heterogeneous Catalysis in the All-Vanadium Redox Flow Battery (2018)

Energy storage for intermittent renewable energy has become increasingly more important. The all vanadium redox flow battery (VRFB) is one of the few options to store energy electrochemically. One of the remaining challenges is the low power density (&lt; 0.1 W cm -2 ) of the VRFB, caused by sluggish kinetics of the redox reactions. To alleviate this drawback, many studies tried to heterogeneously catalyse the redox reactions. However, up to now, there is no consensus in the literature which of the two half-cell reactions, the V 2+ /V 3+ - or the VO 2+ /VO 2 + -reaction, features the higher rate constant [1]. In the literature, rate constants of the two half-cell reactions spread over four orders of magnitude [2]. We will show that this uncertainty in the literature is due to two factors: An apparent catalytic effect appears when porous electrode materials are investigated with linear or cyclic voltammetry. The porosity reduces the separation between anodic and cathodic peak suggesting enhanced kinetics when indeed only an interplay of enlarged electrochemical surface area and impeded diffusion within the porous electrode is present; The Faradaic current I F is proportional to both wetted surface area A wet and the rate constant k 0 : I F ∝ A wet k 0 . As both parameters vary with electrode composition, it is often difficult to distinguish catalytic from surface-area effects. This complex situation is unravelled by using a newly developed procedure based on electrochemical impedance spectroscopy. Combining these results and x-ray photoelectron spectroscopy we showed that surface functional groups such as hydroxyl, carbonyl and carboxyl increase the wetted surface area A wet , increase the rate constant k 0 for the V 2+ /V 3+ -redox reaction but decrease the rate constant k 0 for the VO 2+ /VO 2 + -redox reaction. In addition, we investigated homogeneous catalysis of the VO 2+ /VO 2 + redox reaction. We show that transferring the system from 1 M sulfuric acid to 1 M phosphoric acid increases the electron transfer constant k 0 up to 67 times [3]. This observation was confirmed by chronoamperometry, electrochemical impedance spectroscopy as well as qualitatively by cyclic voltammetry and symmetric flow cell tests. We discuss the complex reaction mechanism which is a combination of electron transfer and chemical reaction. In a laboratory scale flow cell that employed dilute vanadium electrolyte, we were able to show that the over-voltages can be significantly lower in phosphoric acid as compared to sulfuric acid. [1] Fink, H.; Friedl, J.; Stimming, U. Composition of the Electrode Determines Which Half-Cell’s Rate Constant Is Higher in a Vanadium Flow Battery. J. Phys. Chem. C 2016 , 120 (29), 15893–15901. [2] Friedl, J.; Stimming, U. Determining Electron Transfer Kinetics at Porous Electrodes. Electrochim. Acta 2017 , 227, 235–245. [3] Holland-Cunz, M.; Friedl, J.; Stimming, U. Anion effects on the redox kinetics of positive electrolyte of the all-vanadium redox flow battery. Journal of Electroanalytical Chemistry 2017 , 10.1016/j.jelechem.2017.10.061.
IKK/NF-κB system protects from Hepatitis B surface antigen-induced hepatocarcinogenesis (2012)

Background and aims: The NF-κB transcription factors are constitutively activated in many tumors, where they are thought to provide a critical survival signal for cancer cells. Accordingly, an inhibition of NF-κB signaling is considered a potential approach in anti-tumor therapy. We studied the oncogenic role NF-κB signaling in hepatocytes and immune cells using animals overexpressing hepatitis B virus surface antigen (HBsAg), an established model of virus-induced hepatocarcinogenesis.
Detection of Small-Sized Radar Objects Using Multi-Scanning Observation Method (2020)

In this paper we consider a surveillance radar with an additional multi-scanning observation device. In each channel of the multi-scanning observation device the well- known procedure “track-before-detect” is implemented. Combined processing of the results of several scannings is based on Hough transform. In conditions of high probability of false alarms due to the low threshold of primary detection, an excessive number of potential candidate tracks is formed. We analyse the functioning of the device for these conditions, assume variants of signal processing of several space scannings and estimate their efficiency.
Free-paced high-performance brain–computer interfaces (2007)

Neural prostheses aim to improve the quality of life of severely disabled patients by translating neural activity into control signals for guiding prosthetic devices or computer cursors. We recently demonstrated that plan activity from premotor cortex, which specifies the endpoint of the upcoming arm movement, can be used to swiftly and accurately guide computer cursors to the desired target locations. However, these systems currently require additional, non-neural information to specify when plan activity is present. We report here the design and performance of state estimator algorithms for automatically detecting the presence of plan activity using neural activity alone. Prosthesis performance was nearly as good when state estimation was used as when perfect plan timing information was provided separately ( approximately 5 percentage points lower, when using 200 ms of plan activity). These results strongly suggest that a completely neurally-driven high-performance brain-computer interface is possible.
Analysis of a Plate Containing a Polygon-Shaped Inclusion With a Uniform Eigencurvature (2003)

An infinite isotropic plate containing a polygon-shaped inclusion with a uniform eigencurvature is analyzed. An algorithmic closed-form solution of the curvature is derived for both interior and exterior points of the polygon.