gebhart/patrepeval huggingface dataset:
Photoreflectance study of narrow-well strained-layerInxGa1−xAs/GaAs coupled multiple-quantum-well structures (1988)

We have measured the photoreflectance (PR) spectra at 300 and 77 K of two strained-layer [001] ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As/GaAs (x\ensuremath{\approxeq}0.12) multiple quantum wells (MQW's) with nominal well (${L}_{Z}$) and barrier (${L}_{B}$) widths of (50 A\r{})/(100 A\r{}) and (30 A\r{})/(100 A\r{}), respectively, as deduced from the growth conditions. In both samples we have observed a number of features in the PR spectra corresponding to miniband dispersion (coupling between wells) of both confined and unconfined (above the GaAs barrier) transitions. The coupling between wells leads to different transition energies at the mini-Brillouin-zone center (\ensuremath{\Gamma}) and the edge (\ensuremath{\pi}) along the growth direction. This is the first observation of unconfined features and miniband dispersion in this system. Even though our samples have fairly wide barriers (${L}_{B}$\ensuremath{\approxeq}100 A\r{}), the coupling between wells is an important effect because of the relatively small confinement energies for x\ensuremath{\approxeq}0.12. Using the envelope-function approach, we have calculated the various transition energies taking into account both strain and quantum-well effects, including miniband dispersion. Good agreement with experiment is found for a heavy-hole valence-band discontinuity of 0.3\ifmmode\pm\else\textpm\fi{}0.05 and ${\mathit{L}}_{\mathit{Z}}$/${\mathit{L}}_{\mathit{B}}$=(52\ifmmode\pm\else\textpm\fi{}3 \AA{})/(105\ifmmode\pm\else\textpm\fi{}5 \AA{}) (x=0.11\ifmmode\pm\else\textpm\fi{}0.01) and (32\ifmmode\pm\else\textpm\fi{}3 \AA{})/(95\ifmmode\pm\else\textpm\fi{}5 \AA{}) (x=0.12\ifmmode\pm\else\textpm\fi{}0.01) for the two samples, respectively. The In composition and well and barrier widths are thus in good agreement with the growth conditions. Although the symmetric component of the fundamental light-hole--to--conduction-subband transition is a strong feature, the small observed amplitude of the antisymmetric component for both samples is evidence for the type-II nature of the light-hole--to--conduction-subband transitions.
The engineering of binding affinity at metal ion binding sites for the stabilization of proteins: subtilisin as a test case (1988)

A weak Ca2+ binding site in the bacterial serine protease subtilisin BPN' (EC 3.4.21.14) was chosen as a model to explore the feasibility of stabilizing a protein by increasing the binding affinity at a metal ion binding site. The existence of this weak Ca2+ binding site was first discovered through a study of the rate of thermal inactivation of wild-type subtilisin BPN' at 65 degrees C as a function of the free [Ca2+]. Increasing the [Ca2+] in the range 0.10-100 mM caused a 100-fold decrease in the rate of thermal inactivation. The data were found to closely fit a theoretical titration curve for a single Ca2+ specific binding site with an apparent log Ka = 1.49. A series of refined X-ray crystal structures (R less than or equal to 0.15, 1.7 A) of subtilisin in the presence of 0.0, 25.0, and 40.0 mM CaCl2 has allowed a detailed structural characterization of this Ca2+ binding site. Negatively charged side chains were introduced in the vicinity of the bound Ca2+ by changing Pro 172 and Gly 131 to Asp residues through site-directed and random mutagenesis techniques, respectively. These changes were found to increase the affinity of the Ca2+ binding site by 3.4- and 2-fold, respectively, when compared with the wild-type protein (ionic strength = 0.10). X-ray studies of these new variants of subtilisin revealed the carboxylate side chains to be 6.8 and 13.2 A, respectively, from the bound Ca2+. These distances and the degree of enhanced binding are consistent with simple electrostatic theory.(ABSTRACT TRUNCATED AT 250 WORDS)
Scaling the Ion Trap Quantum Processor (2013)

Trapped atomic ions are standards for quantum information processing, serving as quantum memories, hosts of quantum gates in quantum computers and simulators, and nodes of quantum communication networks. Quantum bits based on trapped ions enjoy a rare combination of attributes: They have exquisite coherence properties, they can be prepared and measured with nearly 100% efficiency, and they are readily entangled with each other through the Coulomb interaction or remote photonic interconnects. The outstanding challenge is the scaling of trapped ions to hundreds or thousands of qubits and beyond, at which scale quantum processors can outperform their classical counterparts in certain applications. We review the latest progress and prospects in that effort, with the promise of advanced architectures and new technologies, such as microfabricated ion traps and integrated photonics.
A Model of Placebo Response in Antidepressant Clinical Trials (2013)

Placebo response in clinical trials of antidepressant medications is substantial and has been increasing. High placebo response rates hamper efforts to detect signals of efficacy for new antidepressant medications, contributing to trial failures and delaying the delivery of new treatments to market. Media reports seize upon increasing placebo response and modest advantages for active drugs as reasons to question the value of antidepressant medication, which may further stigmatize treatments for depression and dissuade patients from accessing mental health care. Conversely, enhancing the factors responsible for placebo response may represent a strategy for improving available treatments for major depressive disorder. A conceptual framework describing the causes of placebo response is needed in order to develop strategies for minimizing placebo response in clinical trials, maximizing placebo response in clinical practice, and talking with depressed patients about the risks and benefits of antidepressant medications. In this review, the authors examine contributors to placebo response in antidepressant clinical trials and propose an explanatory model. Research aimed at reducing placebo response should focus on limiting patient expectancy and the intensity of therapeutic contact in antidepressant clinical trials, while the optimal strategy in clinical practice may be to combine active medication with a presentation and level of therapeutic contact designed to enhance treatment response.
Dental caries: from infection to prevention. (2007)

Dental caries is one of the most prevalent diseases in humans, second only to the common cold. It causes irreversible damage to the grinding machinery involved in the intake of food and hence causes great distress. The changes in the homeostasis of the oral cavity with an overgrowth of Streptococcus mutans is recognized as the primary cause of the disease. Most treatments are now aimed at either elimination of this bacterium or suppression of its virulence. S. mutans strongly adheres and releases acids by the fermentation of carbohydrates, leading to the demineralization of the tooth. This attachment is mediated mostly by the interaction of surface proteins and bacterial polysaccharides. Ambiguities in the basic treatment of dental caries, such as the use of fluoride and antibiotics, vitalize the deployment of probiotic therapies for its cure. The growing research in herbal treatments has led to the discovery of various phytochemicals to limit the virulence of S. mutans. This review focuses on the properties of S. mutans in cariogenicity and outlines ways to combat dental caries.
Disturbance of cytokine networks in Sjögren's syndrome (2011)

The difficulty in predicting the consequences of interactions between different cytokine networks has increased with the expansion of the T helper (Th) cell universe and the discovery of numerous B lymphocyte-derived cytokines. Consequently, it is now difficult to conceptualize a straightforward view of the contribution of these disturbances to the pathogenesis of primary Sjögren's syndrome (SS). Th1 cells, which produce interferon-γ and IL-2, and Th17 cells, which make IL-17 and TNF-α, have been cast in the leading roles of the play. However, the complex role of T-cell subsets in SS is accentuated by the reciprocal effects of Th17 cells and regulatory T cells found in salivary glands of SS patients. Furthermore, B lymphocyte polarization into type-1 B effector (Be1) and Be2 cells and B-cell modulating factors of the TNF family, most notably the B-cell-activating factor (BAFF), and their prominent role in SS are additional complicating factors. Whereas Th17 cells orchestrate autoreactive germinal centers, local BAFF would repress the generation of Th17 cells. Such new insights into interconnected cytokines in primary SS may lead to new treatments for these patients.
Chemistry, physics, and engineering of electrically percolating arrays of nanoparticles: a mini review (2011)

Nanoparticles and their arrays do not obey Ohm's law, even when the particles are made of metal, because of their small size. The non-Ohmic behavior is due to their low capacitance that allows (local) storage of charge at the single electron level to pose a substantial barrier to the passage of current at bias, V, below a threshold voltage, VT. The VT is inversely proportional to the size of the particle. For a typical <10 nm particle, the electrostatic barrier energy of the particle due to charging by a single electron is significantly larger compared to the thermal energy, affecting a substantial Coulomb blockade. The signature of the single electron effect is a highly non-linear current-bias behavior characterized by a critical point at VT with a subsequent rise in current that scales as (V/VT − 1)ζ, where ζ ≥ 1 is the critical exponent. We review the fabrication chemistry, device physics, and engineering applications of nanoparticle-based Single Electron Devices with architectures ranging from a single nanoparticle to arrays in one and two dimensions. The arrays are particularly interesting due to their natural integrability with microelectronic circuitry and robust single electron behavior at room temperature. These features open doors to a broad range of potential applications, such as chemical sensors, biomedical devices, data storage devices, and energy devices.
Towards a description for video indexation (2002)

This paper presents the overall scheme of an indexation system for broadcast video designed for very large databases. We discuss features which can possibly be extracted from a video sequence so as to be used for "queries by example". We present examples of semantic features (query by content) like text reading, face localisation and classification. As this study is still at its infancy, we point out the key features and temporary achievements and present some temporary results.
A chemokine receptor CCR-1 antagonist reduces renal fibrosis after unilateral ureter ligation (2002)

The expression of chemokines and their receptors is thought to contribute to leukocyte infiltration and progressive renal fibrosis after unilateral ureter obstruction (UUO).We hypothesized that blocking the chemokine receptor CCR1 using the nonpeptide antagonist BX471 could reduce leukocyte infiltration and renal fibrosis after UUO.UUO kidneys from BX471-treated mice (day 0-10 and day 6-10) revealed a 40-60% reduction of interstitial macrophage and lymphocyte infiltrate compared with controls.Treated mice also showed a marked reduction of CCR1 and CCR5 mRNA levels, and FACS analysis showed a comparable reduction of CD8 + /CCR5 + T cells.Markers of renal fibrosis, such as interstitial fibroblasts, interstitial volume, mRNA and protein expression for collagen I, were all significantly reduced by BX471-treatment compared with vehicle controls.By contrast treatment was ineffective when the drug was supplied only from days 0 to 5. In summary, blockade of CCR1 substantially reduces cell accumulation and renal fibrosis after UUO.Most interestingly, late onset of treatment is also effective.We therefore conclude that CCR1 blockade may represent a new therapeutic strategy for reducing cellular infiltration and renal fibrosis as major factors in the progression to end-stage renal failure.
Increased proteolysis. An effect of increases in plasma cortisol within the physiologic range. (1984)

Prolonged exposure to glucocorticoids in pharmacologic amounts results in muscle wasting, but whether changes in plasma cortisol within the physiologic range affect amino acid and protein metabolism in man has not been determined. To determine whether a physiologic increase in plasma cortisol increases proteolysis and the de novo synthesis of alanine, seven normal subjects were studied on two occasions during an 8-h infusion of either hydrocortisone sodium succinate (2 micrograms/kg X min) or saline. The rate of appearance (Ra) of leucine and alanine were estimated using [2H3]leucine and [2H3]alanine. In addition, the Ra of leucine nitrogen and the rate of transfer of leucine nitrogen to alanine were estimated using [15N]leucine. Plasma cortisol increased (10 +/- 1 to 42 +/- 4 micrograms/dl) during cortisol infusion and decreased (14 +/- 2 to 10 +/- 2 micrograms/dl) during saline infusion. No change was observed in plasma insulin, C-peptide, or glucagon during either saline or cortisol infusion. Plasma leucine concentration increased more (P less than 0.05) during cortisol infusion (120 +/- 1 to 203 +/- 21 microM) than saline (118 +/- 8 to 154 +/- 4 microM) as a result of a greater (P less than 0.01) increase in its Ra during cortisol infusion (1.47 +/- 0.08 to 1.81 +/- 0.08 mumol/kg X min for cortisol vs. 1.50 +/- 0.08 to 1.57 +/- 0.09 mumol/kg X min). Leucine nitrogen Ra increased (P less than 0.01) from 2.35 +/- 0.12 to 3.46 +/- 0.24 mumol/kg X min, but less so (P less than 0.05) during saline infusion (2.43 +/- 0.17 to 2.84 +/- 0.15 mumol/kg X min, P less than 0.01). Alanine Ra increased (P less than 0.05) during cortisol infusion but remained constant during saline infusion. During cortisol, but not during saline infusion, the rate and percentage of leucine nitrogen going to alanine increased (P less than 0.05). Thus, an increase in plasma cortisol within the physiologic range increases proteolysis and the de novo synthesis of alanine, a potential gluconeogenic substrate. Therefore, physiologic changes in plasma cortisol play a role in the regulation of whole body protein and amino acid metabolism in man.
Identification of the CD8 DE Loop as a Surface Functional Epitope (1998)

We used an approach of protein surface epitope mapping by synthetic peptides to analyze the surface structure-function relationship of the CD8 protein. Small synthetic peptide mimics of the CD8 DE loop were shown to effectively block CD8 binding to major histocompatibility complex (MHC) class I molecules and possess significant inhibitory activity on in vitro CD8(+) T cell function. These results suggested that the DE loop region of the CD8 protein is an important functional epitope mediating CD8-MHC class I interaction and the activation of CD8(+) T cells, a finding that is consistent with the recently reported crystal structure of the CD8-MHC class I complex. The structural basis for the biological activity of the DE loop peptide was further analyzed in a series of analogs containing alanine substitutions. This study provides support for the concept of bioactive peptide design based on protein surface epitopes and suggests that such an approach may be applicable to other protein-protein complexes, particularly those of immunoglobulin superfamily molecules.
8 Non-programmed and Engineered Chromosome Breakage (1995)

The integrity of the chromosome as a genetic package is central to the essential processes of meiosis and mitosis. Our ability to construct genetic and physical maps of genomes is based on this stability, a key component of which is provided by the telomere’s role in replicating the end of the DNA molecule contained in the chromosome and also protecting it from recombination. DNA introduced into the nucleus of a mammalian cell does not exist as an independent molecule but becomes integrated into the existing chromosomes. In contrast, the chromosomes themselves cannot normally undergo nonhomologous recombination because dicentric and multicentric chromosomes would result. Where two active centromeres are present on a single chromosome, forces imposed on the two centromeres may attempt to segregate them to different cells at cell division and result in chromosome breakage. If breakage in chromosomes that naturally have only a single centromere results in loss of the acentric fragment produced and the end of the centromeric part is not healed, the chromosome enters successive rounds of breakage-fusion-bridge cycles. These cycles can be terminated by healing of the break or, presumably, by cell death as a result of loss of genetic material. In yeast a single break in the genome can be sensed by the cell and results in arrested cell division. Equivalent checkpoint mechanisms probably also exist in mammalian and other cell types, with the p53 gene as an example. Loss of DNA or cell cycle perturbations are deleterious, and in mammalian systems, chromosome breaks are...
A high throughput platform for systematic evolution of ligands by exponential enrichment (SELEX). (1999)

The systematic evolution of ligands by exponential enrichment (SELEX) process is a combinatorial chemistry method for the isolation of nucleic acid ligands (aptamers) that bind to a desired target molecule with high affinity. In order to increase throughput via automation, we have adapted the SELEX process for protein targets to a robotics-compatible microtiter plate format. A remarkable feature of the platform is that targets are immobilized by hydrophobic adsorption onto the plate surface. Hydrophobic immobilization procedures are simple and require no specialized modification of the protein target. This format was tested by manually performing four independent SELEX experiments. All were concluded within 8 rounds of selection and yielded aptamers that bind in solution to their respective protein target, calf intestinal alkaline phosphatase, human alpha-thrombin or human platelet derived growth factor, with equilibrium dissociation constants below 3 x 10-10 M.
Excretion of Methamphetamine and Amphetamine in Human Sweat Following Controlled Oral Methamphetamine Administration (2007)

These data characterize the excretion of MAMP and AMP after controlled MAMP administration and provide a framework for interpretation of MAMP sweat test results in clinical and forensic settings.
PLCG1 mutations in cutaneous T-cell lymphomas (2014)

Cutaneous T-cell lymphoma (CTCL) is a heterogeneous group of primary cutaneous T-cell lymphoproliferative processes, mainly composed of mycosis fungoides and Sézary syndrome, the aggressive forms of which lack an effective treatment. The molecular pathogenesis of CTCL is largely unknown, although neoplastic cells show increased signaling from T-cell receptors (TCRs). DNAs from 11 patients with CTCL, both normal and tumoral, were target-enriched and sequenced by massive parallel sequencing for a selection of 524 TCR-signaling-related genes. Identified variants were validated by capillary sequencing. Multiple mutations were found that affected several signaling pathways, such as TCRs, nuclear factor κB, or Janus kinase/signal transducer and activator of transcription, but PLCG1 was found to be mutated in 3 samples, 2 of which featured a redundant mutation (c.1034T>C, S345F) in exon 11 that affects the PLCx protein catalytic domain. This mutation was further analyzed by quantitative polymerase chain reaction genotyping in a new cohort of 42 patients with CTCL, where it was found in 19% of samples. Immunohistochemical analysis for nuclear factor of activated T cells (NFAT) showed that PLCG1-mutated cases exhibited strong NFAT nuclear immunostaining. Functional studies demonstrated that PLCG1 mutants elicited increased downstream signaling toward NFAT activation, and inhibition of this pathway resulted in reduced CTCL cell proliferation and cell viability. Thus, increased proliferative and survival mechanisms in CTCL may partially depend on the acquisition of somatic mutations in PLCG1 and other genes that are essential for normal T-cell differentiation.
Nogo-A and Myelin-Associated Glycoprotein Mediate Neurite Growth Inhibition by Antagonistic Regulation of RhoA and Rac1 (2002)

The adult mammalian CNS has a limited capacity for nerve regeneration and structural plasticity. The presence of glia-derived inhibitory factors myelin-associated glycoprotein (MAG) and Nogo-A have been suggested to provide a nonpermissive environment for elongating nerve fibers. In particular, Nogo-A, an integral membrane protein predominantly expressed by oligodendrocytes, has been demonstrated to impair neurite growth in vitro and in vivo. Structure function analysis revealed that Nogo-A protein contains at least two active domains, NiG and Nogo-66, with diverse effects on neurite outgrowth and cell spreading. We now provide evidence that these inhibitory domains mediate their effects via an antagonistic regulation of the small GTPases RhoA and Rac1, resulting in activation of RhoA and suppression of Rac1. By inactivating RhoA with C3 transferase or the downstream effector Rho-kinase ROCK with, the inhibitory effects of both Nogo-A fragments and MAG on neurite outgrowth and oligodendrocyte-mediated growth cone collapse were abolished. Furthermore, we show that the recently cloned receptor for Nogo-66 and MAG, NgR, is not necessary for either NiG- or MAG-induced RhoA activation.
Smart Cities: Challenges and Beyond (2015)

A smart city is an interconnection of objects in which each object plays a role of a source node. The data and information is collected from the source node for further computation and communication. A city can only be called a smart city if certain attributes are available such as clean water, good transport, energy efficiency, well-structured infrastructure, Internet of Things (IoT), mobile health (m-health), and Information and Communication Technologies (ICT). In this paper, we provide a comprehensive overview of the things that form a smart city. We focus on applications and technologies and identify different challenges in a smart city. Furthermore, the critical evaluation of different standards, architectures and frameworks form part of the paper.
Surveillance and Deferred Treatment for Localized Prostate Cancer. Population Based Study in the National Prostate Cancer Register of Sweden (2008)

Surveillance was a common treatment for patients younger than 70 years with localized prostate cancer in Sweden in 1997 to 2002, 26% of men with localized prostate cancer started surveillance and after a median followup of 4 years, 66% of these men remained on surveillance.