gebhart/patrepeval huggingface dataset:
Antimicrobial activity of short arginine‐ and tryptophan‐rich peptides (2002)

Highly antimicrobial active arginine- and tryptophan-rich peptides were synthesized ranging in size from 11 to five amino acid residues in order to elucidate the main structural requirement for such short antimicrobial peptides. The amino acid sequences of the peptides were based on previous studies of longer bovine and murine lactoferricin derivatives. Most of the peptides showed strong inhibitory action against the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, and the Gram-positive bacterium Staphylococcus aureus. For the most active derivatives, the minimal inhibitory concentration values observed for the Gram-negative bacteria were 5 microg/ml (3.5 microM), whereas it was 2.5 microg/ml (1.5 microM) for the Gram-positive bacterium. It was essential for the antimicrobial activity that the peptides contained a minimum of three tryptophan and three arginine residues, and carried a free N-terminal amino group and an amidated C-terminal end. Furthermore, a minimum sequence size of seven amino acid residues was required for a high antimicrobial activity against Pseudomonas aeruginosa. The insertion of additional arginine and tryptophan residues into the peptides resulted only in small variations in the antimicrobial activity, whereas replacement of a tryptophan residue with tyrosine in the hepta- and hexapeptides resulted in reduced antimicrobial activity, especially against the Gram-negative bacteria. The peptides were non-haemolytic, making them highly potent as prospective antibiotic agents.
A Logit Model of Brand Choice Calibrated on Scanner Data (1983)

A multinomial logit model of brand choice, calibrated on 32 weeks of purchases of regular ground coffee by 100 households, shows high statistical signficance for the explanatory variables of brand loyalty, size loyalty, presence/absence of store promotion, regular shelf price and promotional price cut. The model is parsimonious in that the coefficients of these variables are modeled to be the same for all coffee brand-sizes. The calibrated model predicts remarkably well the share of purchases by brand-size in a hold-out sample of 100 households over the 32-week calibration period and a subsequent 20-week forecast period. The success of the model is attributed in part to the level of detail and completeness of the household panel data employed, which has been collected through optical scanning of the Universal Product Code in supermarkets. Three short-term market response measures are calculated from the model: regular (depromoted) price elasticity of share, percent increase in share for a promotion with a median price cut, and promotional price cut elasticity of share. Response varies across brand-sizes in a systematic way with large share brand-sizes showing less response in percentage terms but greater in absolute terms. On the basis of the model a quantitative picture emerges of groups of loyal customers who are relatively insensitive to marketing actions and a pool of switchers who are quite sensitive.
Theta burst stimulation of human cortex. (2005)

It has proved possible in experimental animals to manipulate synaptic efficiency using direct electrical stimulation of central nervous pathways. The introduction of transcranial methods of non-invasively stimulating the human brain raised hopes that similar effects could be produced in humans, with the potential for eventual therapeutic application in disease states. However, largely due to safety limitations, human subjects often require lengthy conditioning with repetitive transcranial magnetic stimulation (rTMS), and even then effects are often weak, variable and not beneficial in the therapeutic setting. In view of the difficulties, I have explored novel methods of conditioning the brain in conscious humans using rTMS which can swiftly produce powerful and controllable long-term changes in the excitability of cortical circuits.
Auto-associative multi-layered neural networks for the classification of seismic signals (2003)

Autoassociative multilayered neural networks were used to validate the seismic shock classification performed by expert seismologists on the basis of somewhat heuristic criteria. It was possible to evaluate the degree to which each event in the training data set belonged to each class, independently of the seismologist's suggestions, avoiding errors when heuristic criteria were not adequate. The networks allow recognition of events incorrectly classified, so that they can be reanalyzed by the human expert.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phase I study of mesothelin-targeted immunotoxin LMB-100 in combination with tofacitinib in patients with advanced pancreatobiliary cancer. (2021)

3051 Background: LMB-100 recombinant immunotoxin consists of a mesothelin-binding Fab for targeting a modified Pseudomonas exotoxin A payload to tumors. Previous clinical trials demonstrated that almost all patients formed anti-drug-antibodies (ADAs) to LMB-100 that made administration beyond cycle 2 ineffective. Tofacitinib is an oral JAK inhibitor that prevented formation of ADAs against a closely related immunotoxin in pre-clinical studies. The primary objective of the dose escalation cohort was assessment of safety and tolerability of LMB-100 given with tofacitinib to patients with mesothelin-expressing solid tumors. The primary objective of the expansion cohort was to determine whether co-administration of tofacitinib delays formation of neutralizing LMB-100 ADAs. Methods: Patients (n = 13) with pancreatic adenocarcinoma and other mesothelin-expressing solid tumors (n = 3; cholangiocarcinoma, appendix, cystadenocarcinoma) were treated for up to 3 cycles with LMB-100 as a 30-minute infusion on days 4, 6, and 8 at two dose levels (100 and 140 mcg/kg) and co-treated with oral tofacitinib for the first 10 days of the cycle (10 mg BID). Results: Dose level 1 of LMB-100 was started at 100 mcg/kg one dose level below the single agent MTD. Dose escalation to 140 mcg/kg (dose level 2) resulted in DLTs in 2 of the 3 patients treated: grade 3 cardiac toxicity and grade 4 hyponatremia, both attributed to capillary leak syndrome. Ultimately, 7 patients were treated at dose level 1 without DLTs and 100 mcg/kg was chosen as the LMB-100 dose for the expansion cohort. The last of 6 patients treated in the expansion cohort developed grade 4 pericardial effusion leading to early closure of the study for toxicity. No objective responses were seen. Of the 8 patients who received two cycles of treatment at MTD, 4 met prespecified criteria for ADA prevention, and 2 patients who went on to receive cycle 3 had detectable LMB-100 plasma drug levels after administration. Conclusions: LMB-100 was unable to be co-administered safely with tofacitinib. ADA formation was prevented in 2 patients through 3 cycles, a rare occurrence. Clinical trial information: NCT04034238.
Regulation of Gene Expression in the Tryptophan Operon of Escherichia coli (1980)

INTRODUCTION The classic model of Jacob and Monod (1961) for induction and repression of operon expression provided a conceptual framework for integrating observations on cellular metabolism with a mechanism of regulation at the molecular level. In recent years, direct physical evidence has confirmed the essential predictions of their hypothesis for the lactose operon, as summarized elsewhere in this volume. In general, their ideas have been exceptionally valuable when applied to other systems as well. However, regulation of the lac gene cluster has proved more intricate than originally envisioned, and regulatory features have been discovered which cannot be accommodated in the simple repressor-operator model of regulation. The tryptophan ( trp ) operon of Escherichia coli also possesses regulatory features of several types in addition to repressor-operator interaction, and the purpose of this review is to summarize current knowledge of the molecular aspects of structure and regulation within the trp operon. The tryptophan operon consists of five contiguous structural genes (which code for enzymes participating in the biosynthetic pathway from chorismic acid to tryptophan) and the associated control elements (see Fig. 1). The five genes are transcribed as a single polycistronic messenger RNA approximately 7000 nucleotides long. Initiation of transcription is controlled by the interaction of the tryptophan represser (the protein product of trpR ) with its target site on the DNA, the operator ( trpO ). Represser binding at trpO competes with RNA polymerase binding at the adjacent promoter site, trpP (Squires et al. 1975). Transcription of the messenger RNA is initiated within the promoter-operator region...
Critical dimension (CD) control in 157-nm lithography (2003)

This paper describes the investigation on the feasibility of current coater/developer processes to the 157-nm lithography from the viewpoint of critical dimension (CD) control. The effect of coating, bake, and development process on the CD of a 157-nm resist, where fluorine is introduced in the side chain, is studied. A KrF and ArF resist is also used for comparison. Firstly, as for the coating process, the coverage performance and the film thickness uniformity of the 157-nm resist shows that the current coating methods are feasible to 157-nm resist, even though the 157-nm resist is highly hydrophobic. Secondly, as for the bake process, the post exposure bake (PEB) temperature dependence of CD for the 157-nm resist is found to be lower than that for 248 and 193-nm resist. This means that our current PEB temperature control system, which is suitable for 248 or 193-nm resist, is also effective for the 157-nm resist. Thirdly, as for the development process, it is found that a static puddle formation process shows a smaller line edge roughness (LER) than a dynamic puddle formation process. Therefore, the static puddle formation process, with the use of linear drive (LD) developer nozzle for instance, is attractive for the 157-nm resist process. Lastly, from the viewpoint of contamination control, it is found that the amine level should be controlled to be less than 0.1ppb in order to prevent the CD change during post exposure delay (PED) for the 157-nm resist.
Impact of 1h oral glucose tolerance test on the clinical status of adult cystic fibrosis patients over a 4-year period (2021)

High G60 is not associated with a lower lung function at inclusion nor its decline over a 4-year follow-up. High I60 is slightly associated to a higher weight at inclusion, but not with BMI evolution over time in adult patients.
Residual-adaptive Key Provisioning in Quantum-Key-Distribution Enhanced Internet of Things (Q-IoT) (2020)

With the advent of smart homes, smart cities, and smart everything, the Internet of Things (IoT) has emerged as an area of incredible impact, potential, and growth. Internet of Things date security remain a major challenge, in the current Internet of Things systems, a relatively easy method of data encryption is used to ensure the security of data transmission, which is commonly called lightweight cryptography. However, such method is at the risk of being cracked by quantum computers, which will contribute to many challenges specially related to privacy and security in IoT. As a result, the architecture of IoT needs to be re-designed considering the security challenges brought by quantum computers. On the other hand, Quantum Key Distribution (QKD) allows two users to share unconditionally secure keys. Unlike classical cryptosystems, the security of QKD is based on the fundamentals of quantum mechanics. This security of QKD is independent of computational complexity and will not be affected, no matter how much computing power the adversary has. This paper introduces a quantum key distribution enhanced Internet of Things architecture and proposes a residual-adaptive key provisioning scheme, which is evaluated in terms of key distribution success rate in the simulation.
Coincidence and common fixed point theorems on TVS-valued cone metric spaces (2015)

In this paper, we obtained some coincidence and common fixed point theorems for a pair of weakly compatible maps on TVS-valued cone metric spaces, satisfying contractive mapping: d(fx; fy) ≤ad(fx;gx)+bd(fy;gy)+gd(gx;gy) and d(fx; fy) ≤ad(gx;gy)+b[d(fx;gx)+d(fy;gy)]+g[d(fx;gy)+d(fy;gx)]. Some corollaries on fixed point theorems on TVS-valued cone metric spaces are also provided.
Topology-Aware Surface Reconstruction for Point Clouds (2018)

We present an approach to inform the reconstruction of a surface from a point scan through topological priors. The reconstruction is based on basis functions which are optimized to provide a good fit to the point scan while satisfying predefined topological constraints. We optimize the parameters of a model to obtain likelihood function over the reconstruction domain. The topological constraints are captured by persistence diagrams which are incorporated in the optimization algorithm promote the correct topology. The result is a novel topology-aware technique which can: 1.) weed out topological noise from point scans, and 2.) capture certain nuanced properties of the underlying shape which could otherwise be lost while performing surface reconstruction. We showcase results reconstructing shapes with multiple potential topologies, compare to other classical surface construction techniques, and show the completion of real scan data.
The evaluation of two commercial electric sheep stunning systems: current applied and the effect on heart function (2016)

Abstract The maintenance of head-only minimum stunning currents for sheep to ≥ 1.0 Amp as per current legislation was examined in two trials in a commercial abattoir. In the first trial, a Jetco MS100 stunner failed to maintain the current to &gt; 1.0 Amp in 118 of the 228 sheep. In a second trial, a Jetco MS105 delivered sufficient current in all sheep (n = 275) to meet the legislative requirement, apart from a single animal. Recorded electrocardiograms showed a regular heartbeat, with no evidence of ventricular fibrillation, in all animals in both trials following stunning and neck-cut. Only one of the two stun units may therefore be considered to meet the statutory requirements but both may meet the requirements for halal slaughter where pre-stun is considered acceptable.
Thermally stable polyester polymers for second-order nonlinear optics (1994)

We report electro-optic and thermal stability properties of a novel thermostable fluorene-based polyester polymer. The electro-optic coefficient, r33, at 810 nm is 2.6 pm/V for a poling field of 0.5 MV/cm. This value is comparable to that obtained from many reported side-chain polymers. Isothermal decay measurements of the charge transfer absorption band and electro-optic effect demonstrate that the chemical stability of the fluorene molecule appears to dominate over orientational relaxation in the decline of the electro-optic response at elevated temperatures.
Differentiable Multiple Shooting Layers (2021)

We detail a novel class of implicit neural models. Leveraging time-parallel methods for differential equations, Multiple Shooting Layers (MSLs) seek solutions of initial value problems via parallelizable root-finding algorithms. MSLs broadly serve as drop-in replacements for neural ordinary differential equations (Neural ODEs) with improved efficiency in number of function evaluations (NFEs) and wall-clock inference time. We develop the algorithmic framework of MSLs, analyzing the different choices of solution methods from a theoretical and computational perspective. MSLs are showcased in long horizon optimal control of ODEs and PDEs and as latent models for sequence generation. Finally, we investigate the speedups obtained through application of MSL inference in neural controlled differential equations (Neural CDEs) for time series classification of medical data.
Chiral separation of omeprazole and several related benzimidazoles using supercritical fluid chromatography (2004)

A study of the enantiomeric separation of omeprazole and several related benzimidazoles, using supercritical fluid chromatography (SFC), on the amylose based column Chiralpak AD is presented in this work. The effect of the organic modifier as well as temperature on the retention and enantioresolution was investigated. Alcohol-type modifiers provided the best results, allowing the enantiomeric separation of all the compounds studied with resolutions that were in most cases higher than 2, and analysis times lower than 10 minutes. An investigation of the temperature effect revealed that the isoelution temperature was below the working temperature range in only two cases, and hence it was better to work at the highest temperature permitted.
The Proteolytic Activation of (H3N2) Influenza A Virus Hemagglutinin Is Facilitated by Different Type II Transmembrane Serine Proteases (2016)

Influenza epidemics and recurring pandemics are responsible for significant global morbidity and mortality. Due to high variability of the virus genome, resistance to available antiviral drugs is frequently observed, and new targets for treatment of influenza are needed. Host cell factors essential for processing of the virus hemagglutinin represent very suitable drug targets because the virus is dependent on these host factors for replication. We reported previously that Tmprss2-deficient mice are protected against H1N1 virus infections, but only marginal protection against H3N2 virus infections was observed. Here we show that deletion of two host protease genes,Tmprss2 and Tmprss4, strongly reduced viral spread as well as lung pathology and resulted in increased survival after H3N2 virus infection. Thus, TMPRSS4 represents another host cell factor that is involved in cleavage activation of H3N2 influenza viruses in vivo.
Enhancing remotely sensed BT data for environmental analysis (2019)

With the growing use of the Vegetation Index in many remote sensing applications, it was imperative to examine the Brightness Temperature (BT) stability in the NOAA/NESDIS Global Vegetation Index (GVI) data, which was collected from five NOAA series satellites. An empirical distribution function (EDF) was developed to decrease the long-term inaccuracy of the BT data derived from the AVHRR sensor on NOAA polar orbiting satellite. The instability of data is a consequence of orbit degradation, and from the circuit drifts over the life of a satellite. Degradation of BT over time and shifts of BT between the satellites were estimated using the China data set, because it includes a wide variety of different ecosystems represented globally. It was found that the data for six particular years, four of which were consecutive, are not stable compared to other years because of satellite orbit drift, AVHRR sensor degradation, and satellite technical problems, including satellite electronic and mechanical satellite systems deterioration. The data for paired years for the NOAA-7, NOAA-9, NOAA-11, NOAA-14, and NOAA-16 were assumed to be standard because the crossing time of the satellite over the equator maximized the value of the coefficients. These years were considered the standard years, while in other years the quality of satellite observations significantly deviated from the standard. The deficiency of data for the affected years were normalized or corrected by using the EDF method and compared with the standard years. These normalized values were then utilized to estimate new BT time series that show significant improvement of BT data for the affected years so that the dataset is useful for environment monitoring.
ChemInform Abstract: Recent Progress in the Synthesis of Oxepanes and Medium Ring Ethers. (2012)

Abstract Review: 127 refs.
Augmentation of Ultraviolet B Radiation-induced Tumor Necrosis Factor Production by the Epidermal Platelet-activating Factor Receptor (1999)

Ultraviolet B radiation (UVB) has been shown to damage human keratinocytes in part by inducing oxidative stress and cytokine production. Indeed, UVB-induced production of the pro-inflammatory and cytotoxic cytokine tumor necrosis factor alpha (TNF-alpha) has been implicated in the epidermal damage seen in response to acute solar radiation. Though the lipid mediator platelet-activating factor (PAF) is synthesized in response to oxidative stress, and keratinocytes express PAF receptors linked to cytokine biosynthesis, it is not known whether PAF is involved in UVB-induced epidermal cell cytokine production. These studies examined the role of the PAF system in UVB-induced epidermal cell TNF-alpha biosynthesis using a novel model system created by retroviral-mediated transduction of the PAF receptor-negative human epidermal cell line KB with the human PAF receptor (PAF-R). Treatment of PAF-R-expressing KB cells with the metabolically stable PAF-R agonist carbamoyl-PAF resulted in increased TNF-alpha mRNA and protein, indicating that activation of the epidermal PAF-R was linked to TNF-alpha production. UVB irradiation of PAF-R-expressing KB cells resulted in significant increases in both TNF-alpha mRNA and protein in comparison to UVB-treated control KB cells. However, UVB treatment up-regulated cyclooxygenase-2 mRNA levels to the same extent in both PAF-R-expressing and control KB cells. Pretreatment with the antioxidant vitamin E or the PAF-R antagonists WEB 2086 and A-85783 inhibited UVB-induced TNF-alpha production in the PAF-R-positive but not control KB cells. These studies suggest that the epidermal PAF-R may be a pharmacological target for UVB in skin.
Epitaxial growth and properties of YBa2Cu3O7−y/LaSrGaO4/YBa2Cu3O7−y trilayer structures (1994)

We report the successful synthesis of insulating LaSrGaO4(LSGO) thin films and YBa2Cu3O7−y(YBCO)/LSGO heteroepitaxial multilayer structures using a pulsed laser deposition technique. SrTiO3(STO)(100) was used as a substrate. The formation of highly c-axis oriented YBCO/LSGO/YBCO trilayer structures is demonstrated. Epitaxial YBCO films on LSGO//STO and LSGO/YBCO//STO have a zero resistance temperature of 88.5 and 88.3 K, respectively. Sandwich-type YBCO/LSGO/YBCO junctions were produced by a suitable patterning technique. The observed (dI/dV)-V characteristics exhibit a clear single gap structure (width ∼26 meV) at temperatures below 30 K.
Interleukin-lfl (IL-lfl), IL-i receptor antagonist, and TNFa production in whole blood (2015)

Abstract: The ability of an individual to mount defense responses to infection depend in part on the capacity to produce cytokines such as interleukin 1 (IL-i) and tumor necrosis factor (TNF). The specialized equipment, labor intensity, and sterile practice required for the standard in vitro evaluation of cytokine production can make such evaluation impractical in some clinical situations. We report a method for stimulating whole blood to produce cytokines that can be implemented in laboratories without tissue culture facilities and requires minimal sample preparation. IL-1f3 and TNFa production in whole blood samples was stimulated with endotoxin and/or phyto-hemagglutinin in standard EDTA-containing vacuum col-lection tubes. After incubation, plasma was removed and frozen for later assay. Comparison of this whole blood method with isolated mononuclear cell cultures indicated a significant correlation for IL-113 production (r = 0.746, P = 0.005). This technique also produced the newly de-scribed cytokine, IL-i receptor antagonist. We conclude that the whole blood method is an acceptable alternative to isolated cell culture methods for measuring IL-13 in situations that preclude the standard in vitro approach. J.