gebhart/patrepeval huggingface dataset:
Effect of Amino Acid Substitutions on Biological Activity of Antimicrobial Peptide: Design, Recombinant Production, and Biological Activity. (2019)

Recently, antimicrobial peptides have been introduced as potent antibiotics with a wide range of antimicrobial activities. They have also exhibited other biological activities, including anti-inflammatory, growth stimulating, and anti-cancer activities. In this study, an analog of Magainin II was designed and produced as a recombinant fusion protein. The designed sequence contained 24 amino acid residues (P24), in which Lys, His, Ser residues were substituted with Arg and also, hydrophobic Phe was replaced with Trp. Recombinant production of P24 in <i>Escherichia coli (E. coli)</i> BL21 using pTYB21, containing chitin binding domain and intein sequence at the N-terminus of the peptide gene, resulted in 1 μg mL<sup>-1</sup> product from culture. Chitin column chromatography, followed by online peptide cleavage with thiol reducing agent was applied to purify the peptide. Antimicrobial activity was evaluated using five bacteria strains including <i>Staphylococcus aureus, Enterococcus faecalis, Klebsiella pneumonia, E. coli,</i> and <i>Pseudomonas aeruginosa</i>. Designed AMP exhibited promising antimicrobial activities with low minimum inhibitory concentration, in the range of 64-256 µg/mL. P24 showed potent antimicrobial activity preferably against Gram-positive bacteria, and more potent than pexiganan as a successful Magainin II analog for topical infections. In general, further modification can be applied to improve its therapeutic index.
Surface-Anchored Poly( N -isopropylacrylamide) Orthogonal Gradient Networks (2020)

We present a versatile synthetic route leading toward generating surface-attached polyacrylamide gels, in which the cross-link density varies continuously and gradually across the substrate in two orthogonal directions. We employ free radical polymerization to synthesize random copolymers comprising ~5% of photoactive methacrylyloxybenzophenone (MABP), ~5% of thermally active styrene sulfonyl azide (SSAz), and ~90% of N-isopropylacrylamide (NIPAAm) units. The presence of MABP and SSAz in the copolymer facilitates control over the cross-link density of the gel in an orthogonal manner using photoactivated and thermally activated cross-linking chemistries, respectively. Spectroscopic ellipsometry is employed to determine the degree of swelling of the gel in water and methanol as a function of position on the substrate. Network swelling varies continuously and gradually across the substrate and is high in regions of low gel fractions and low in regions of high gel fractions.
Effects of Relative Humidity and Kinds of Chlorides on Atmospheric Stress Corrosion Cracking of Stainless Steels at Room Temperature (1989)

In order to evaluate the effects of relative humidity (RH) at room temperature and kinds of chlorides on atmospheric stress corrosion cracking (SCC) of SUS 304 and 316 L stainless steels in contact with chlorides, SCC tests were carried out in RH controlled environments by using U-bend specimens deposit of 0.5 N chloride solutions (NaCl, MgCl2, CaCl2, ZnCl2, LiCl) or synthetic sea water. The maximum SCC susceptibility of steels was observed at the inherent relative humidity (RHmax) for each chloride. The SCC susceptibility in contact with synthetic sea water was governed by MgCl2 which is a minor solute component of sea water. Even with a long time test period of 24 months, atmospheric SCC was observed in a very limited RH range around RHmax. From measurements of the maximum crack length (Lmean) at RHmax of the different chloride solutions, it was concluded that a higher saturated concentration of chloride gave a higher SCC susceptibility. However, the acidic chloride, ZnCl2, gave a smaller Lmean than that overall tendency obtained without ZnCl2.
Coherent Multidimensional Vibrational Spectroscopy of Biomolecules: Concepts, Simulations, and Challenges (2009)

The response of complex molecules to sequences of femtosecond infrared pulses provides a unique window into their structure, dynamics, and fluctuating environments. Herein we survey the basic principles of modern two-dimensional infrared (2DIR) spectroscopy, which analogous to those of multidimensional NMR spectroscopy. The perturbative approach for computing the nonlinear optical response of coupled localized chromophores is introduced and applied to the amide backbone transitions of proteins, liquid water, membrane lipids, and amyloid fibrils. The signals are analyzed using classical molecular dynamics simulations combined with an effective fluctuating Hamiltonian for coupled localized anharmonic vibrations whose dependence on the local electrostatic environment is parameterized by an ab initio map. Several simulation methods, (cumulant expansion of Gaussian fluctuation, quasiparticle scattering, the stochastic Liouville equations, direct numerical propagation) are surveyed. Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen-bonding fluctuations, protein folding, and chemical-exchange processes are discussed.
The copper regulon of the human fungal pathogenCryptococcus neoformansH99 (2011)

Cryptococcus neoformans is a human fungal pathogen that is the causative agent of cryptococcosis and fatal meningitis in immuno-compromised hosts. Recent studies suggest that copper (Cu) acquisition plays an important role in C. neoformans virulence, as mutants that lack Cuf1, which activates the Ctr4 high affinity Cu importer, are hypo-virulent in mouse models. To understand the constellation of Cu-responsive genes in C. neoformans and how their expression might contribute to virulence, we determined the transcript profile of C. neoformans in response to elevated Cu or Cu deficiency. We identified two metallothionein genes (CMT1 and CMT2), encoding cysteine-rich Cu binding and detoxifying proteins, whose expression is dramatically elevated in response to excess Cu. We identified a new C. neoformans Cu transporter, CnCtr1, that is induced by Cu deficiency and is distinct from CnCtr4 and which shows significant phylogenetic relationship to Ctr1 from other fungi. Surprisingly, in contrast to other fungi, we found that induction of both CnCTR1 and CnCTR4 expression under Cu limitation, and CMT1 and CMT2 in response to Cu excess, are dependent on the CnCuf1 Cu metalloregulatory transcription factor. These studies set the stage for the evaluation of the specific Cuf1 target genes required for virulence in C. neoformans.
The killer cell immunoglobulin‐like receptor (KIR) genomic region: gene‐order, haplotypes and allelic polymorphism (2002)

Recent genetic studies have established that the killer cell immunoglobulin-like receptor (KIR) genomic region displays extensive diversity through variation in gene content and allelic polymorphism within individual KIR genes. It is demonstrated by family segregation analysis, genomic sequencing, and gene order determination that genomic diversity by gene content alone gives rise to more than 20 different KIR haplotypes and at least 40-50 KIR genotypes. In the most reductionist format, KIR haplotypes can be accommodated within one of 10 different prototypes, each with multiple permutations. Our haplotype model considers the KIR haplotype as two separate halves: the centromeric half bordered upstream by KIR3DL3 and downstream by 2DL4, and the telomeric half bordered upstream by 2DL4 and downstream by 3DL2. There are rare KIR haplotypes that do not fit into this model. Recombination, gene duplication, and inversion can however, readily explain these haplotypes. Additional allelic polymorphism imposes extensive individual variability. Accordingly, this segment of the human genome displays a level of diversity similar to the one observed for the human major histocompatibility complex. Recent application of immunogenetic analysis of KIR genes in patient populations implicates these genes as important genetic disease susceptibility factors.
Understanding Friction and Wear Behavior at the Nanoscale of Aluminum Matrix Composites Produced by Laser Powder Bed Fusion (2019)

Laser powder bed fusion (LPBF) is an additive manufacturing (AM) technique for the fabrication of components with a complex design, and it is particularly appropriate for structural applications in automotive and air‐space industries. Aluminum matrix composites (AMCs) are promising materials for these uses because they are ductile, light weight, and have an excellent strength‐to‐weight ratio. Herein, a study on microstructure, hardness, and the nanoscale tribological properties of the AlSi10Mg alloy with and without ceramic particles is presented. AMCs are realized with different compositions: 10 wt% of microsize TiB 2 , 1 wt% of nanosize TiB 2 , 0.5 wt% of nanosize SiO 2 , and 0.5 wt% of nanosize MgAl 2 O 4 . It is found that the nanocomposites show a lower coefficient of friction (COF), whereas in the case of microsize TiB 2 reinforcement, the COF is higher than with either nanosize reinforcements or AlSi10Mg alloy without reinforcement. Results indicate that the interfacial bond between the matrix and the particles of the ceramic reinforcement has a crucial role in wear processes.
Raman Spectroscopic and Visible Absorption Investigation of LiCrSi2O6 Pyroxene under Pressure (2008)

The first observation of the vibrational spectrum of the synthetic pyroxene Li-kosmochlor (LiCrSi2O6) is reported herein. The Raman and visible spectra are reported as a function of pressure. Though the pyroxene retains its P21/c symmetry, changes in the Raman spectra are observed between 6.8 and 7.7 GPa, possibly due to the formation of an additional bond between Li and O3 or some other transition that retains the mineral's P21/c space group. Splitting of the peak appearing at approximately 700 cm(-1), used to characterize the P21/c phase in other studies, is not observed. Comparison is made with the Raman spectra of LiAlSi2O6 and LiFeSi2O6 in the P21/c phase and the visible spectra of NaCrSi2O6 at high pressures.
Estimating Phase Duration for SPaT Messages (2018)

A signal phase and timing (SPaT) message describes the current phase at a signalized intersection for each lane, together with an estimate of the residual time of that phase. Accurate SPaT messages can be used to construct a speed profile for a vehicle that reduces its fuel consumption as it approaches or leaves an intersection. This paper presents SPaT estimation algorithms at an intersection with a semi-actuated signal, using real-time signal phase measurements. The algorithms are evaluated using high-resolution data from an intersection in Montgomery County, MD, USA. The algorithms can be readily implemented at signal controllers. This paper supports three findings. First, real-time information dramatically improves the accuracy of the prediction of the residual time compared with the prediction based on historical data alone. Second, as time increases, the prediction of the residual time may increase or decrease. Third, as drivers differently weight errors in predicting “end of green” and “end of red,” drivers on two different approaches may prefer different estimates of the residual time of the same phase.
Coordination of Ortho-Chlorines in Copper (I) and Silver (I) 2,6-Di- and 2,4,6-Trichlorophenolates (1992)

Abstract The crystal structure of (Ph 3 P) 2 AgOC 6 H 2 Cl 3 (I) is reported along with the syntheses and 35 Cl and 63 Cu NQR spectra of I and several related silver (I) and copper (I) 2,6-di- and 2,4,6-trichlorophenolates containing phosphines, phosphites, and pyridine as co-ligands. I crystallizes in space group P2 1 /cc with a= 16.692(4) Å, b= 17.942 (4) A, c = 12.857 (3) Å, β = 97.60 (1)°, F = 3816.68 Å 3 , and Z = 4. The final R (F) = 0.0475 and R (W) = 0.0396. Ag is coordinated in a trigonal planar geometry by the P atoms of the two triphenylphosphine ligands and the O atom of the chlorophenolate; Ag is then capped by one ortho-chlorine of the trichlorophenolate ligand at a distance of 3.160 (2) Å. In the 35 Cl NQR spectrum of this compound the two ortho-chlorines of the trichlorophenolate ligand have a large frequency difference of 1.500 MHz, indicating that one ortho-chlorine is coordinated to the silver; 35 Cl NQR spectra of related complexes are also presented and discussed. The 35 Cl NQR frequency differences of coordinated and non-coordinated ortho-chlorines in metal chlorophenolates correlate well with the metal-chlorine distances but not with the metal-chlorine-carbon bond angles. A different correlation is found for the silver complexes of dichloroalkanes; possible reasons for this are discussed.
Delay predictors for customer service systems with time-varying parameters (2010)

Motivated by interest in making delay announcements in service systems, we develop new real-time delay predictors that effectively cope with customer abandonment and time-varying parameters. First, we focus on delay predictors exploiting recent customer delay history. We show that time-varying arrival rates can introduce significant prediction bias in delay-history-based predictors when the system experiences alternating periods of overload and underload. We then introduce a new delay-history-based predictor that effectively copes with time-varying arrival rates. Second, we consider a time-varying number of servers. We develop two new predictors which exploit an established deterministic fluid approximation for a many-server queueing model with time-varying demand and capacity. The new predictors effectively cope with those features, often observed in practice. Throughout, we use computer simulation to quantify the performance of the alternative delay predictors.
THERMAL PERFORMANCE OF MANAGED WINDOW SYSTEMS (2011)

The primary factors that determine the net thermal performance of a window system are its overall heat transfer rate (U-value), its air leakage characteristics and its sun control capability.With managed window systems these basic properties may be drastically altered on an hourly basis as movable insulating and shading devices are deployed over the prime windows.A large building energy analysis computer program, DOE-2, has been modified to model the thermal performance of a variety of window management devices.The deployment of these devices is simulated based upon fixed hourly schedules or the value of critical climatic factors such as solar intensity.Automatic operation may be modeled or manual operation with varying degrees of human fallibility may be simulated.The model couples reductions in infiltration rate to the deployment of an insulating or shading device.Results of heating load calculations are presented for the cases of single-and double-glazed windows in a typical house with glass-tofloor area ratios of 15 to 40%, and for window management devices with varying thermal resistance, air leakage rates and different modes of operation.window syster.lswith building thermal characteristics, orientation, and climate as controlled variables.(1.)
Self-assembly at solid surfaces (2011)

The spontaneous formation of highly ordered amphiphilic monolayers on solid surfaces by adsorption from organic solutions at the liquid–solid interface was first reported in the seminal work of W. A. Zisman and co-workers in the mid-20th century [1]. In that work, attention was focused on the remarkable wetting properties of such monolayers, which were not only hydrophobic, but also oleophobic, i.e., they are not wetted by many organic oils, including the solutions from which they were obtained. Several directions of basic study and applications were then pursued employing these oleophobic monolayers: Confinement of molecules of interest for surface examination, prevention of spreading of liquids, friction and wear reduction, and surface passivation and protection.

Whereas the early study of such monolayers indeed attracted considerable attention over the years, perhaps their greatest impact was yet to come, in new directions of research that could not have been foreseen at the time. These avenues exploit the ability to finely tune a wide variety of surface properties, for many diverse potential applications, through the combination of molecular self-assembly, chemical design, and postassembly surface manipulation by various chemical and physical techniques. The term self-assembling monolayer was thus coined with reference to the planned layer-by-layer assembly of organized films thicker than a single monolayer [2]. These directions, which gained momentum in the 1980s and continue strongly today, are forging new avenues of development. With the advent of relatively recent technologies for small-scale patterning, interest in self-assembled films has seen a surge of activity throughout a wide range of areas ranging from biointerfaces to data storage and devices.

This Thematic Series presents a small, but significant sampling of these exciting areas of research. Thus, the functionality of self-assembled films or of structures derived from them is demonstrated, including mechanical, electrical, and catalytic properties. Unique nanoscale structures are prepared employing lithographic processes and the templating capabilities of the films. Finally, the different characterization techniques employed in these studies point to the unique challenges involved in surface analysis at the nanoscale, and reveal the fascinating properties of the various films and structures.

We hope that this Thematic Series will serve as an inspiration for those wanting to learn about and become involved in the field, and will help expand the horizons of those already engaged in its active research. We would like to thank the Beilstein-Institut for the opportunity to present this Thematic Series, and of course the contributors for their efforts and ingenuity in furthering the research and development of self-assembly at solid surfaces into ever-expanding new areas of scientific activity.

Sidney R. Cohen and Jacob Sagiv

Rehovot, December 2011
Anytime Exploitation of Stragglers in Synchronous Stochastic Gradient Descent (2017)

In this paper we propose an approach to parallelizing synchronous stochastic gradient descent (SGD) that we term “Anytime-Gradients”. The Anytime-Gradients is designed to exploit the work completed by slow compute nodes or “stragglers”. In many approaches work completed by these nodes, while only partial, is discarded completely. To maintain synchronization in our approach, each computational epoch is of fixed duration, and at the end of each epoch, workers send updated parameter vectors to a master mode for combination. The master weights each update by the amount of work done. The Anytime-Gradients scheme is robust to both persistent and non-persistent stragglers and requires no prior knowledge about processor abilities. We show that the scheme effectively exploits stragglers and outperforms existing methods.
Supplementary Figure S3 from Mitogenic Insulin Receptor-A Is Overexpressed in Human Hepatocellular Carcinoma due to EGFR-Mediated Dysregulation of RNA Splicing Factors (2023)

&lt;p&gt;Supplementary Figure S3 - PDF file 53K, Basal and EGFR-activated ERK levels in HCC cell lines&lt;/p&gt;
Asymmetric Hydrogenation of α, β, and γ-Aminoketones Catalyzed by Cationic Rhodium(I){AMPP} Complexes (1997)

The chiral cationic rhodium aminophosphine-phosphinite complexes 4-6 were applied successfully in the asymmetric hydrogenation of α- (7-9), β- (10, 11) and γ- (12) aminoketone hydrochloride derivatives leading to the corresponding aminoalcohols in up to 97, 93, and 92 % enantiomeric excesses for the three types of substrates respectively.
Quality Analysis of Pear Fruit of Shah Miveh variety Using Nondestructive Ultrasonic Technique (2014)

Development of ultrasound technique has not been progressing for evaluating the internal quality of fruits as fast as that of processed foods. In this research for quality assessment of pear fruit (Shah Miveh variety) an ultrasonic measurement system was constructed to transmit and receive the ultrasonic waves. The apparatus included a pulser-receiver, a pair of 75 kHz ultrasonic transducers with exponential horn, and a computer system for data acquisition and analysis. Several mechanical and chemical properties, including firmness, TSS, acidity, elastic modulus, pH and total dry matter for destructive quality assessment were measured. Velocity and attenuation of ultrasonic waves for nondestructive tests were also measured. The fruit quality levels for the experiment were: unripe, ripe and overripe. The results of tests showed that firmness was the best parameter for measuring fruit quality, as it decreased significantly with ripeness. The effect of ripeness on the velocity and attenuation of ultrasonic waves was also significant. Investigation showed a positive linear relationship between fruit firmness and wave velocity (R2=0.81). Furthermore, the relationship between fruit firmness and attenuation was exponential and wave attenuation decreased with increasing fruit firmness (R2=0.895). The Relationship between ultrasonic properties and fruit modulus of elasticity showed that the wave velocity increased and attenuation decreased with ‌increasing elasticity. It can be concluded that the ultrasonic instrument equipped with exponential horns can effectively be utilized for pear quality assessment based on measurement of wave velocity and attenuation.
Effect of Dissolved Oxygen on Two Bacterial Pathogens Examined using ATR-FTIR Spectroscopy, Microelectrophoresis, and Potentiometric Titration (2010)

The effects of dissolved oxygen tension during bacterial growth and acclimation on the cell surface properties and biochemical composition of the bacterial pathogens Escherichia coli O157:H7 and Yersinia enterocolitica are characterized. Three experimental techniques are used in an effort to understand the influence of bacterial growth and acclimation conditions on cell surface charge and the composition of the bacterial cell: (i) electrophoretic mobility measurements; (ii) potentiometric titration; and (iii) ATR-FTIR spectroscopy. Potentiometric titration data analyzed using chemical speciation software are related to measured electrophoretic mobilities at the pH of interest. Titration of bacterial cells is used to identify the major proton-active functional groups and the overall concentration of these cell surface ligands at the cell membrane. Analysis of titration data shows notable differences between strains and conditions, confirming the appropriateness of this tool for an overall charge characterization. ATR-FTIR spectroscopy of whole cells is used to further characterize the bacterial biochemical composition and macromolecular structures that might be involved in the development of the net surficial charge of the organisms examined. The evaluation of the integrated intensities of HPO(2)(-) and carbohydrate absorption bands in the IR spectra reveals clear differences between growth protocols. Taken together, the three techniques seem to indicate that the dissolved oxygen tension during cell growth or acclimation can noticeably influence the expression of cell surface molecules and the measurable cell surface charge, though in a strain-dependent fashion.
Short Paper: Location Privacy with IP Mobility (2006)

Privacy when using IP communication has become an important problem. It is a challenging problem that spans multiple layers in the OSI reference model with various constant identifiers that can be profiled. This leads to user privacy concerns. Location Privacy, on the other hand, is primarily concerned with revealing a user’s identity as a function of mobility. When a user visits a new network and uses a fixed identifier, such as a Mobile IPv6 Home Address for communication, on-lookers can determine that the user has roamed. We address this problem of location privacy and provide a Privacy-Tag for use in place of a fixed identifier to protect user privacy. Our method is readily implementable using the Mobile IPv6 Return Routability [2] protocol and the Binding Update procedure.