gebhart/patrepeval huggingface dataset:
Genome structure and dynamics of the yeast pathogen Candida glabrata (2014)

The yeast pathogen Candida glabrata is the second most frequent cause of Candida infections. However, from the phylogenetic point of view, C. glabrata is much closer to Saccharomyces cerevisiae than to Candida albicans. Apparently, this yeast has relatively recently changed its life style and become a successful opportunistic pathogen. Recently, several C. glabrata sister species, among them clinical and environmental isolates, have had their genomes characterized. Also, hundreds of C. glabrata clinical isolates have been characterized for their genomes. These isolates display enormous genomic plasticity. The number and size of chromosomes vary drastically, as well as intra- and interchromosomal segmental duplications occur frequently. The observed genome alterations could affect phenotypic properties and thus help to adapt to the highly variable and harsh habitats this yeast finds in different human patients and their tissues. Further genome sequencing of pathogenic isolates will provide a valuable tool to understand the mechanisms behind genome dynamics and help to elucidate the genes contributing to the virulence potential.
Enhancing nonlinear effects with micron-scale graphene-coated plasmonic structures (2012)

We demonstrated efficient nonlinear coupling between local vibrating molecules and propagating polariton modes at the vibration frequency (namely, mid-IR frequencies) using suspended graphene waveguides. Each waveguide deposited a micron-scale periodic metal (plasmonic) structure. Nonlinear effect, at very modest pump laser intensities has been demonstrated; these intensity levels are often used in ordinary Raman experiments. The polariton mode propagated through fairly long distances, several IR wavelengths long, without a substantial loss. Thus, the suspended graphene has established itself as a unique waveguide for the THz/infrared region.
Organization and Differential Regulation of a Cluster of Lignin Peroxidase Genes of Phanerochaete chrysosporium (1999)

The lignin peroxidases of Phanerochaete chrysosporium are encoded by a minimum of 10 closely related genes. Physical and genetic mapping of a cluster of eight lip genes revealed six genes occurring in pairs and transcriptionally convergent, suggesting that portions of the lip family arose by gene duplication events. The completed sequence of lipG and lipJ, together with previously published sequences, allowed phylogenetic and intron/exon classifications, indicating two main branches within the lip family. Competitive reverse transcription-PCR was used to assess lip transcript levels in both carbon- and nitrogen-limited media. Transcript patterns showed differential regulation of lip genes in response to medium composition. No apparent correlation was observed between genomic organization and transcript levels. Both constitutive and upregulated transcripts, structurally unrelated to peroxidases, were identified within the lip cluster.
Organization of Knowledge and Problem-Solving (2016)

How is the problem space organized? What is the role of knowledge in organizing problem space and how is it structured?How is text analytics performed?How would a Cognitive Thing generate alternatives? Are there different approaches to the generation of alternatives?Can new features be created? How are the profiles enriched?Does problem solving take place in batch or real-time?
Consistent Device Simulation Model Describing Perovskite Solar Cells in Steady-State, Transient and Frequency Domain (2021)

A variety\nof experiments on vacuum-deposited methylammonium lead\niodide perovskite solar cells are presented, including &lt;i&gt;JV&lt;/i&gt; curves with different scan rates, light intensity-dependent open-circuit\nvoltage, impedance spectra, intensity-modulated photocurrent spectra,\ntransient photocurrents, and transient voltage step responses. All\nthese experimental data sets are successfully reproduced by a charge\ndrift-diffusion simulation model incorporating mobile ions and charge\ntraps using a single set of parameters. While previous modeling studies\nfocused on a single experimental technique, we combine steady-state,\ntransient, and frequency-domain simulations and measurements. Our\nstudy is an important step toward quantitative simulation of perovskite\nsolar cells, leading to a deeper understanding of the physical effects\nin these materials. The analysis of the transient current upon voltage\nturn-on in the dark reveals that the charge injection properties of\nthe interfaces are triggered by the accumulation of mobile ionic defects.\nWe show that the current rise of voltage step experiments allow for\nconclusions about the recombination at the interface. Whether one\nor two mobile ionic species are used in the model has only a minor\ninfluence on the observed effects. A delayed current rise observed\nupon reversing the bias from +3 to −3 V in the dark cannot\nbe reproduced yet by our drift-diffusion model. We speculate that\na reversible chemical reaction of mobile ions with the contact material\nmay be the cause of this effect, thus requiring a future model extension.\nA parameter variation is performed in order to understand the performance-limiting\nfactors of the device under investigation.
A completely monolithic sample/hold amplifier using compatible bipolar and silicon-gate FET devices (1974)

A monolithic sample/hold subsystem, including an integrated holding capacitor, which utilizes simultaneously fabricated bipolar transistors and silicon-gate FETs to achieve performance levels previously unattainable in a single chip design, will be discussed.
Targeting anti-apoptotic Bcl2 proteins with scyllatoxin-based BH3 domain mimetics (2015)

BH3 domain mimetics based on the small protein scyllatoxin (ScTx) were designed to target the anti-apoptotic protein Bcl2 in vitro. Intrinsically disordered ScTx variants were found to bind Bcl2 with nanomolar affinity, indicating that an induced fit binding mechanism is required for favorable BH3 : Bcl2 interaction.
Transition to instability in a periodically kicked Bose-Einstein condensate on a ring (2006)

A periodically kicked ring of a Bose-Einstein condensate is considered as a nonlinear generalization of the quantum kicked rotor, where the nonlinearity stems from the mean-field interactions between the condensed atoms. For weak interactions, periodic motion (antiresonance) becomes quasiperiodic (quantum beating) but remains stable. There exists a critical strength of interactions beyond which quasiperiodic motion becomes chaotic, resulting in an instability of the condensate manifested by exponential growth in the number of noncondensed atoms. In the stable regime, the system remains predominantly in the two lowest energy states and may be mapped onto a spin model, from which we obtain an analytic expression for the beat frequency and discuss the route to instability. We numerically explore a parameter regime for the occurrence of instability and reveal the characteristic density profile for both condensed and noncondensed atoms. The Arnold diffusion to higher energy levels is found to be responsible for the transition to instability. Similar behavior is observed for dynamically localized states (essentially quasiperiodic motions), where stability remains for weak interactions but is destroyed by strong interactions.
Social Determinants of Pediatric Residents' Injury Prevention Counseling (1998)

Perceived professional norms regarding injury prevention are related to pediatric residents' counseling, Preceptors should be aware that they transmit professional norms to residents. Also, the American Board of Pediatrics can increase residents' attention to injury prevention by informing them that it will be a topic included in the board examination.
Synthesis of polysiloxane/polyamine block copolymer using uniform size poly(dimethylsiloxane) with reactive end‐groups (1988)

Abstract Poly(dimethylsiloxane) (poly(DMS))/poly( N ‐ tert ‐butylaziridine) (poly(TBA)) block copolymer was synthesized by two different techniques; (1) the coupling reaction of poly(DMS) having a dimethylaminopropyl end‐group ( 1 ) with living poly(TBA) ( 2 ) which was prepared with methyl trifluoromethanesulfonate as an initiator, and ( 2 ) the polymerization of N ‐ tert ‐butylaziridine ( 5 ) using poly(DMS) having a p ‐toluenesulfonyl ester end‐group ( 4 ) as macromolecular initiator, respectively.
Tailoring the magnetism of Tb5Si2Ge2compounds by La substitution (2012)

In order to study the crystal structure, phase relationships, and magnetic properties of the system Tb${}_{5\ensuremath{-}\mathit{x}}$La${}_{\mathit{x}}$Si${}_{2}$Ge${}_{2}$, a series of polycrystalline samples with compositions ranging from $x=0$ to $x=5$ have been synthesized and characterized in detail. At room temperature, two structures have been detected: Compounds in the concentration range $0\ensuremath{\leqslant}x&lt;1$ present a monoclinic Gd${}_{5}$Si${}_{2}$Ge${}_{2}$-type structure, while for $x&gt;1$ a tetragonal Zr${}_{5}$Si${}_{4}$-type structure is observed. The unit cell volume increases linearly with La concentration but with two different slopes: $\ensuremath{\sim}$18 \AA{}${}^{3}/x$ and $\ensuremath{\sim}$33 \AA{}${}^{3}/x$ for $0\ensuremath{\leqslant}x&lt;1$ (monoclinic) and $x&gt;1$ (tetragonal), respectively. In the monoclinic region, an increase of ${T}_{C}$ was observed, reaching a maximum value of ${T}_{C}$ $\ensuremath{\sim}154$ K, at the $x=0.75$ composition. This feature is explained based on specific La occupancy at the $R2$ site which was supported by density functional calculations for low La concentration. The samples that crystallized in the tetragonal structure exhibit a linear decrease of ${T}_{C}(x)$ with a slope of $\ensuremath{\partial}{T}_{C}$/$\ensuremath{\partial}x$ $\ensuremath{\sim}\ensuremath{-}38$ K/$x$, reaching 0 K for the $x=5$ composition. A magnetic and structural $x$-$T$ phase diagram of the Tb${}_{5\ensuremath{-}\mathit{x}}$La${}_{\mathit{x}}$Si${}_{2}$Ge${}_{2}$ system in the temperature range 4--300 K is proposed.
Utilizing Linear Algebra Subspaces to Improve Cloud Security. (2012)

Abstract—Cloud computing is quickly becoming the infrastructure of choice for hosting data and software solutions for many individuals, businesses, and governmental organizations. While such systems may provide increased flexibility and utility, efficient and easily-managed cloud storage solutions that ensure data confidentiality are needed to maintain this trend. In this work, we propose an algebraic-based encoding solution to provide data confidentiality. Additionally, through the use of the various algebraic subspaces present in the coding process, we are able to verify basic Service Level Agreement (SLA) guarantees. We demonstrate the feasibility of our solution through implementations and deployments on test systems. I.
Electrolyte-Electrode Interactions and Interphases (2016)

As lithium-ion batteries evolve toward higher cell voltage and capacity, developing detailed knowledge of the electrolyte-electrode interface is critically important. While there is general agreement on solid electrolyte interphase (SEI) formation on graphitic anodes, clear evidence of passivation at the cathode interface remains elusive. This presentation discusses our efforts in investigating the interphases in Li ion batteries, on both cathodes and anodes. Primarily using in-situ electrochemical atomic force microscopy (EC-AFM) and confocal Raman spectroscopy, our studies focus on the live-formation of electrolyte-cathode interphases.
Supplementary methods from Stimulation of Oncogene-Specific Tumor-Infiltrating T Cells through Combined Vaccine and αPD-1 Enable Sustained Antitumor Responses against Established HER2 Breast Cancer (2023)

&lt;p&gt;Supplementary methods&lt;/p&gt;
The role of caveolin‐1 and endothelial nitric oxide synthase polymorphisms in susceptibility to prostate cancer (2021)

Caveolin-1(cav-1) is overexpressed in prostate cancer (PC) and is associated with progression of the disease. We investigated the effects of CAV1-T29107A and endothelial nitric oxide synthase (eNOS) G894T polymorphisms on the serum levels of testosterone, NO and prostate-specific antigen (PSA) in patients with PC. We genotyped cav-1 and eNOS genes in 112 PC patients and 150 healthy controls by PCR-RFLP. Serum levels of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mtext>NO</mml:mtext><mml:mn>2</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mtext>NO</mml:mtext><mml:mn>3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:math> were measured using spectrophotometry, and serum levels of testosterone and PSA were measured by ELISA. The frequencies of CAV1 genotypes A/T vs. A/A according to the dominant model AT + TT vs. AA genotype and T allele were significantly higher in PC patients in comparison with the control group and considerably increased the risk of disease by 2.19-, 1.44- and 1.6-fold, respectively. AT + TT genotypes were associated significantly with the increased risk of PC in those with smoking or diabetes by 3.08-fold (P = .004). Individuals carrying concurrently the T allele of CAV1 A29107T and the T allele of eNOS G894T genes had a significantly increased risk of PC by 2.52-fold (P = .009). We did not find any significant relationship between eNOS G894T genotypes and alleles with susceptibility to PC. Our results highlighted the significance of CAV1-T29107A SNP but not (eNOS) G894T in the susceptibility to PC in our the population that we have studied.
Detection of Corrosion Under Paint Using Magneto-Optic Imaging. (1998)

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Inhibitory and stimulatory G proteins of adenylate cyclase: cDNA and amino acid sequences of the alpha chains. (1986)

The G protein family of signal transducers includes five heterotrimers, which are most clearly distinguished by their different alpha chains. The family includes Gs and Gi, the stimulatory and inhibitory GTP-binding regulators of adenylate cyclase; Go, a protein of unknown function abundant in brain; and transducin 1 and transducin 2, proteins involved in retinal phototransduction. Using a bovine alpha t1 cDNA as a hybridization probe, we have isolated mouse cDNAs that encode alpha chains of two G proteins. One encodes a polypeptide of 377 amino acids (Mr 43,856), identified as alpha s because it specifically fails to hybridize with any transcript in an alpha s-deficient S49 mouse lymphoma mutant, cyc-; the other encodes a polypeptide of 355 amino acids (Mr 40,482), presumed to be alpha i. These alpha chains and those of the retinal transducins exhibit impressive sequence homology. Of the four, alpha t1 and alpha t2 are most alike (81% identical amino acid residues), whereas the presumptive alpha i is more similar than alpha s to alpha t1 (63% vs. 38% identical residues). Sequence homologies with p21ras and elongation factor Tu identify regions of the alpha chains that form the site for GTP binding and hydrolysis. Further comparison of the alpha-chain sequences suggests additional regions that may contribute to interactions with beta gamma subunits and the receptor and effector components of different signal transduction systems.
A lyotropic inverse ribbon phase in a branched-chain polyoxyethylene surfactant: pressure effects (2011)

A centred-rectangular lyotropic ribbon phase, rarely observed in inverse (type II) systems, has been found in the branched-chain polyoxyethylene surfactant tetradecyloctadecyl-tetraoxyethylene ether (C14C16EO4) in excess water. This phase is stabilised by the application of hydrostatic pressure. The ratio of the 2-D cell parameters, b/a, is observed to be less than √3 (1.732) over the range of temperatures and pressures studied. The constructed pressure–temperature phase diagram shows that, at high temperatures or low pressures, the inverse ribbon phase converts into an inverse micellar cubic phase of spacegroup Fd3m, and at the opposite extreme, a lamellar gel phase was formed. The lattice parameters of the inverse ribbon phase were found to vary with pressure, with the structure becoming increasingly distorted away from 2-D hexagonal symmetry (b/a = √3) with increasing pressure.
Phase-contrast x-ray imaging with a liquid-metal-jet-anode microfocus source (2007)

Phase-contrast methods increase contrast, detail, and selectivity in x-ray imaging. Present compact x-ray sources do not provide the necessary spatial coherence with sufficient power to allow the laboratory-scale high-resolution phase-contrast imaging with adequate exposure times. In this letter, the authors demonstrate phase-contrast imaging with few-micron detail employing a compact ∼6.5μm spot liquid-metal-jet-anode high-brightness microfocus source. The 40W source is operated at more than ten times higher electron-beam power density than present microfocus sources and is shown to provide sufficient spatial coherence as well as scalability to high power, thereby enabling the application of phase-contrast x-ray imaging with short exposure times in clinics and laboratories.
Problems in group theory motivated by cryptography (2018)

This is a survey of algorithmic problems in group theory, old and new, motivated by applications to cryptography.
Stressreaktion och välfärdsdata - en populationsstudie (2016)

Stressreaktion i en normalbefolkning visar samband med välfärdsdata.• Förstärkt stressreaktion uppvisade personer som uppbar sin försörjning genom sjukpenning, sjukersättning, socialbidrag och arbetslöshetskassa• Stressreaktion av lindrig grad framkom bland personer som uppbar studiemedel, ålderspensionärer, föräldralediga och personer i förvärvsarbete• Stressreaktion var väsentligen normal bland egna företagare• Stressreaktion skattades förstärkt vid begränsade möjligheter att kontrollera, påverka och styra sitt liv och när den egna upplevda hälsan bedömdes vara sänkt.
Circulating Betatrophin Levels Are Increased in Anorexia and Decreased in Morbidly Obese Women (2015)

These results suggest that metabolic status is an important regulator of circulating betatrophin levels.
Reducing Backlight Power Consumption for Streaming Video Applications on Mobile Handheld Devices. (2003)

Mobile handheld devices have stringent constraints on power consumption because they run on batteries that have a limited lifetime. Conserving power to prolong battery life is of primary importance for these devices. Several factors such as backlight intensity, the hard disk, the CPU, the network interface and the nature of the application contribute significantly towards power consumption for a mobile device. While significant research effort has been made to optimize power consumption at the application, network and processor levels, comparatively little work has been done to reduce or adapt to the power consumed by the backlight. In this paper, we propose an adaptive middleware based approach to optimize backlight power consumption for mobile handheld devices when playing streaming MPEG-1 video, without significantly compromising on video quality. Our performance results indicate that up to 60% of the power consumed by the backlight can be saved by using the proposed approach.
New Advances in Understanding the Molecular Biology of Plant/Potyvirus Interactions (1999)

In recent years, researchers have adopted many new technologies to help understand potyvirus pathogenesis. Their findings have illuminated key aspects of the interactions between the host and the virus, and between the virus and its aphid vector. This review focuses on advances in our understanding of the molecular determinants of systemic infection, symptom expression, aphid and seed transmission, and natural and engineered resistance to potyviruses. Very recent developments in the area of post-transcriptional gene silencing indicate not only that the process is fundamental to engineered resistance, but may also underlie many aspects of the biology of plant viruses.
Formation Control for Underactuated Surface Vessel Networks (2020)

Abstract Developing distributed control algorithms for multi-agent systems is difficult when each agent is modeled as a nonlinear dynamical system. Moreover, the problem becomes far more complex if the agents do not have sufficient number of actuators to track any arbitrary trajectory. In this paper, we present the first fully decentralized approach to formation control for networks of underactuated surface vessels. The vessels are modeled as three degree of freedom planar rigid bodies with two actuators. Algebraic graph theory is used to model the network as a directed graph and employing a leader-follower model. We take advantage of the cascade structure of the combined nonlinear kinematic and dynamic model of surface vessels and develop a reduced-order error dynamic model using a state transformation definition. The error dynamics and consequently all system states are then stabilized using sliding mode control approach. It is shown that the stabilization of the reduced-order error dynamics guarantees uniform global asymptotic stability of the closed-loop system subject to bounded uncertainties. The proposed control method can be implemented in directed time-invariant communication networks without the availability of global position measurements for any of the vehicles participating in the network. An example of a a network of five surface vessels is simulated to verify the effective performance of the proposed control approach.
Ca2+ Homeostasis in the Endoplasmic Reticulum: Coexistence of High and Low [Ca2+] Subcompartments in Intact HeLa Cells (1997)

Two recombinant aequorin isoforms with different Ca2+ affinities, specifically targeted to the endoplasmic reticulum (ER), were used in parallel to investigate free Ca2+ homeostasis in the lumen of this organelle. Here we show that, although identically and homogeneously distributed in the ER system, as revealed by both immunocytochemical and functional evidence, the two aequorins measured apparently very different concentrations of divalent cations ([Ca2+]er or [Sr2+]er). Our data demonstrate that this contradiction is due to the heterogeneity of the [Ca2+] of the aequorin-enclosing endomembrane system. Because of the characteristics of the calibration procedure used to convert aequorin luminescence into Ca2+ concentration, the [Ca2+]er values obtained at steady state tend, in fact, to reflect not the average ER values, but those of one or more subcompartments with lower [Ca2+]. These subcompartments are not generated artefactually during the experiments, as revealed by the dynamic analysis of the ER structure in living cells carried out by means of an ER-targeted green fluorescent protein. When the problem of ER heterogeneity was taken into account (and when Sr2+ was used as a Ca2+ surrogate), the bulk of the organelle was shown to accumulate free [cation2+]er up to a steady state in the millimolar range. A theoretical model, based on the existence of multiple ER subcompartments of high and low [Ca2+], that closely mimics the experimental data obtained in HeLa cells during accumulation of either Ca2+ or Sr2+, is presented. Moreover, a few other key problems concerning the ER Ca2+ homeostasis have been addressed with the following conclusions: (a) the changes induced in the ER subcompartments by receptor generation of InsP3 vary depending on their initial [Ca2+]. In the bulk of the system there is a rapid release whereas in the small subcompartments with low [Ca2+] the cation is simultaneously accumulated; (b) stimulation of Ca2+ release by receptor-generated InsP3 is inhibited when the lumenal level is below a threshold, suggesting a regulation by [cation2+]er of the InsP3 receptor activity (such a phenomenon had already been reported, however, but only in subcellular fractions analyzed in vitro); and (c) the maintenance of a relatively constant level of cytosolic [Ca2+], observed when the cells are incubated in Ca2+-free medium, depends on the continuous release of the cation from the ER, with ensuing activation in the plasma membrane of the channels thereby regulated (capacitative influx).