gebhart/patrepeval huggingface dataset:
Icosapent ethyl (eicosapentaenoic acid ethyl ester): Effects on remnant-like particle cholesterol from the MARINE and ANCHOR studies (2016)

Icosapent ethyl 4 g/day significantly reduced calculated and directly measured RLP-C levels versus placebo in patients with elevated TG levels from the MARINE and ANCHOR studies.
Alcohol oxidase: A complex peroxisomal, oligomeric flavoprotein (2005)

Alcohol oxidase (AO) is the key enzyme of methanol metabolism in methylotrophic yeast species. It catalyses the first step of methanol catabolism, namely its oxidation to formaldehyde with concomitant production of hydrogen peroxide. In its mature active form, AO is a molecule of high molecular mass (600 kDa) that consists of eight identical subunits, each of which carry one non-covalently bound flavin adenine nucleotide (FAD) molecule as the prosthetic group. In vivo, the protein is compartmentalized into special cell organelles, termed peroxisomes. AO is an abundant protein and its synthesis is strictly regulated by repression/derepression and induction mechanisms that occur at the transcriptional level. Various aspects of its sorting and assembly/activation render AO a unique protein. Recent developments of AO synthesis, sorting and assembly/activation are highlighted in this paper.
Ultralow‐Fouling, Functionalizable, and Hydrolyzable Zwitterionic Materials and Their Derivatives for Biological Applications (2009)

In recent years, zwitterionic materials such as poly(carboxybetaine) (pCB) and poly(sulfobetaine) (pSB) have been applied to a broad range of biomedical and engineering materials. Due to electrostatically induced hydration, surfaces coated with zwitterionic groups are highly resistant to nonspecific protein adsorption, bacterial adhesion, and biofilm formation. Among zwitterionic materials, pCB is unique due to its abundant functional groups for the convenient immobilization of biomolecules. pCB can also be prepared in a hydrolyzable form as cationic pCB esters, which can kill bacteria or condense DNA. The hydrolysis of cationic pCB esters into nonfouling zwitterionic groups will lead to the release of killed microbes or the irreversible unpackaging of DNA. Furthermore, mixed-charge materials have been shown to be equivalent to zwitterionic materials in resisting nonspecific protein adsorption when they are uniformly mixed at the molecular scale.
Multiple quantum well (MQW) waveguide modulators (1988)

Because the electroabsorption effect in semiconductor multiple quantum well material is approximately 50 times larger than in bulk semiconductors, significant interest has been generated in the use of MQW's in optical modulators. Small high-speed devices have been made which show promise for external modulators in optical transmission systems, as well as for encoding and processing components in optical interconnect and signal processing systems. The fact that these modulators are made from III-V semiconductors had led to interest in integration of these components with other active optoelectronic components. Although most devices have operated with light of a wavelength of 0.85 mu m, recently much progress has been made in applying this technology to devices operating near 1.55 mu m. The author reviews the work of the last few years in this field and indicates some future directions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Magic-state distillation with low overhead (2012)

We propose a family of error-detecting stabilizer codes with an encoding rate of $1/3$ that permit a transversal implementation of the gate $T=\mathrm{exp}(\ensuremath{-}i\ensuremath{\pi}Z/8)$ on all logical qubits. These codes are used to construct protocols for distilling high-quality ``magic'' states $T\left|+\right\ensuremath{\rangle}$ by Clifford group gates and Pauli measurements. The distillation overhead scales as $O({\mathrm{log}}^{\ensuremath{\gamma}}(1/\ensuremath{\epsilon}))$, where $\ensuremath{\epsilon}$ is the output accuracy and $\ensuremath{\gamma}={\mathrm{log}}_{2}(3)\ensuremath{\approx}1.6$. To construct the desired family of codes, we introduce the notion of a triorthogonal matrix, a binary matrix in which any pair and any triple of rows have even overlap. Any triorthogonal matrix gives rise to a stabilizer code with a transversal $T$ gate on all logical qubits, possibly augmented by Clifford gates. A powerful numerical method for generating triorthogonal matrices is proposed. Our techniques lead to a twofold overhead reduction for distilling magic states with accuracy $\ensuremath{\epsilon}\ensuremath{\sim}{10}^{\ensuremath{-}12}$ compared with previously known protocols.
The unfolded protein response represses nitrogen-starvation induced developmental differentiation in yeast (2000)

Diploid budding yeast exhibits two developmental programs in response to nitrogen starvation, pseudohyphal growth, and sporulation. Here we show that both programs are repressed by activation of the unfolded protein response (UPR), a stress-signal transduction pathway responsible for induction of endoplasmic reticulum (ER)-resident chaperones when protein folding in the ER is impaired. Pseudohyphal growth was derepressed in ire1Delta/ire1Delta and hac1Delta/hac1Delta strains. Activation of the UPR or overexpression of the transcription factor Hac1(i)p, the product of an unconventional splicing reaction regulated by the UPR, was sufficient for repression of pseudohyphal growth and meiosis. HAC1 splicing occurred in a nitrogen-rich environment but ceased rapidly on nitrogen starvation. Further, addition of ammonium salts to nitrogen-starved cells was sufficient to rapidly reactivate HAC1 splicing. We propose that high translation rates in a nitrogen-rich environment are coupled to limited protein unfolding in the ER, thereby activating the UPR. An activated UPR then represses pseudohyphal growth and meiosis. Nitrogen starvation slows translation rates, allowing for more efficient folding of nascent polypeptide chains, down-regulation of the UPR, and subsequent derepression of pseudohyphal growth and meiosis. These findings significantly broaden the range of physiological functions of the UPR and define a role for the UPR in nitrogen sensing.
Effect of phonon confinement on the thermoelectric figure of merit of quantum wells (1998)

Recently, it has been shown that the thermoelectric figure of merit is strongly enhanced in quantum wells and superlattices due to two-dimensional carrier confinement. We predict that the figure of merit can increase even further in quantum well structures with free-surface or rigid boundaries. This additional increase is due to spatial confinement of acoustic phonons and corresponding modification of their group velocities. The latter leads to an increase of the phonon relaxation rates and thus, a significant drop in the lattice thermal conductivity.
Characterization of clutter in IR images using maximum likelihood adaptive neural system (2003)

The use of neural networks to quantify IR image clutter is described. The characterization of image clutter is needed to improve target detection and to enhance the ability to compare performance of different algorithms using diverse images. The neural network presented is the maximum likelihood adaptive neural system (MLANS). MLANS is a parametric neural network that combines optimal statistical techniques with a model-based approach. It is shown that MLANS is better at image clutter characterization than the traditional quadratic classifier because MLANS is not limited to the usual Gaussian distribution assumption of statistical pattern recognition approaches and can adapt to the image clutter distribution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synergistic antibody induction by antigen–CD40 ligand fusion protein as improved immunogen (2005)

Full scale B-cell activation requires not only B-cell receptor (BCR) engagement with antigen, but also costimulatory signals provided by T helper cells through the CD40-CD40 ligand (CD40L) interaction. It is hypothesized that a fusion protein of an antigen and soluble CD40L (CD40LT) would selectively target the costimulation to antigen-specific B cells, leading to synergy in the antibody response. This hypothesis was investigated by fusing green fluorescence protein (GFP), a generic antigen, with mouse CD40LT. Studies revealed that immunization in mice with the plasmid encoding GFP-CD40LT fusion protein led to synergistic induction of GFP-specific antibodies, while control plasmid(s) for GFP, CD40LT, or GFP plus CD40LT did not. Immunization with a single dose of the fusion protein also provoked a vigorous GFP-specific immunoglobulin G1 antibody response, but not other antibody isotypes. These results suggest that GFP-CD40LT fusion protein induces a GFP-specific B-cell activation and antibody response in an antigen-guided fashion. The potential application of this novel strategy in vaccine development is discussed.
Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs (2007)

Finding good drug leads de novo from large chemical libraries, real or virtual, is not an easy task. High-throughput screening is often plagued by low hit rates and many leads that are toxic or exhibit poor bioavailability. Exploiting the secondary activity of marketed drugs, on the other hand, may help in generating drug leads that can be optimized for the observed side-effect target, while maintaining acceptable bioavailability and toxicity profiles. Here, we describe an efficient computational methodology to discover leads to a protein target from safe marketed drugs. We applied an in silico "drug repurposing" procedure for identification of nonsteroidal antagonists against the human androgen receptor (AR), using multiple predicted models of an antagonist-bound receptor. The library of marketed oral drugs was then docked into the best-performing models, and the 11 selected compounds with the highest docking score were tested in vitro for AR binding and antagonism of dihydrotestosterone-induced AR transactivation. The phenothiazine derivatives acetophenazine, fluphenazine, and periciazine, used clinically as antipsychotic drugs, were identified as weak AR antagonists. This in vitro biological activity correlated well with endocrine side effects observed in individuals taking these medications. Further computational optimization of phenothiazines, combined with in vitro screening, led to the identification of a nonsteroidal antiandrogen with improved AR antagonism and marked reduction in affinity for dopaminergic and serotonergic receptors that are the primary target of phenothiazine antipsychotics.
Wiring Nanoscale Biosensors with Piezoelectric Nanomechanical Resonators (2010)

Nanoscale integrated circuits and sensors will require methods for unobtrusive interconnection with the macroscopic world to fully realize their potential. We report on a nanoelectromechanical system that may present a solution to the wiring problem by enabling information from multisite sensors to be multiplexed onto a single output line. The basis for this method is a mechanical Fourier transform mediated by piezoelectrically coupled nanoscale resonators. Our technique allows sensitive, linear, and real-time measurement of electrical potentials from conceivably any voltage-sensitive device. With this method, we demonstrate the direct transduction of neuronal action potentials from an extracellular microelectrode. This approach to wiring nanoscale devices could lead to minimally invasive implantable sensors with thousands of channels for in vivo neuronal recording, medical diagnostics, and electrochemical sensing.
Regulation of apoptosis induced by transforming growth factor-beta1 in nontumorigenic rat prostatic epithelial cell lines. (1996)

Transforming growth factor-beta1 (TGF-beta1), which is induced in the prostate following castration, has been speculated to mediate apoptosis of epithelial cells during prostatic involution. Here, we report the first evidence of a direct effect of TGF-beta on induction of apoptosis in prostatic epithelial cells in vitro, using NRP-152 nontumorigenic and NRP-154 tumorigenic rat prostatic epithelial cell lines. TGF-beta1 induces apoptosis of both cell lines within 24 h, as shown by a decrease in cell viability, in situ DNA nick-end labeling, and internucleosomal DNA fragmentation. Moreover, the ability of TGF-beta to induce apoptosis of NRP-152 is strictly dependent on culture conditions, because dexamethasone enhances while insulin and insulin-like growth factor-I specifically block apoptosis induced by TGF-beta. We suggest that TGF-betas are direct physiological regulators of apoptosis of prostatic epithelial cells.
6‐Hydroxycyclohex‐1‐ene‐1‐carbonyl‐CoA dehydrogenase and 6‐oxocyclohex‐1‐ene‐1‐carbonyl‐CoA hydrolase, enzymes of the benzoyl‐CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica (1999)

Benzoyl-CoA is a common intermediate in the anaerobic bacterial metabolism of many aromatic substrates. Two enzymes and ferredoxin of the central benzoyl-CoA pathway in Thauera aromatica have been purified so far. Benzoyl-CoA reductase reduces the aromatic ring with reduced ferredoxin yielding cyclohexa-1,5-diene-1-carbonyl-CoA [Boll, M. & Fuchs, G. (1995) Eur. J. Biochem. 234, 921-933]. Dienoyl-CoA hydratase subsequently adds one molecule of water and thereby produces 6-hydroxycyclohex-1-ene-1-carbonyl-CoA [Laempe, D., Eisenreich, W., Bacher, A., & Fuchs, G. (1998) Eur. J. Biochem. 255, 618-627]. Here two new enzymes, which convert this intermediate to the noncyclic product 3-hydroxypimelyl-CoA, were purified from T. aromatica and studied. 6-Hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase is an NAD(+)-specific beta-hydroxyacyl-CoA dehydrogenase that catalyzes 6-hydroxycyclohex-1-ene-1-carbonyl-CoA + NAD(+) --> 6-oxocyclohex-1-ene-1-carbonyl-CoA + NADH + H(+). 6-Oxocyclohex-1-ene-1-carbonyl-CoA hydrolase acts on the beta-oxoacyl-CoA compound and catalyzes the addition of one molecule of water to the double bound and the hydrolytic C-C cleavage of the alicyclic ring, 6-oxocyclohex-1-ene-1-carbonyl-CoA + 2 H(2)O --> 3-hydroxypimelyl-CoA. The genes for both enzymes, had and oah, were cloned, had was overexpressed in Escherichia coli and the recombinant protein was purified. Hence, presumably all enzymes of the central benzoyl-CoA pathway of anaerobic aromatic metabolism from this organism have now been purified and studied and the corresponding genes have been cloned and sequenced.
Quantitation of bcl-2 protein in bladder cancer tissue by enzyme immunoassay: comparison with Western blot and immunohistochemistry (1998)

Apoptosis (programmed cell death) and the genes regulating this process (e.g., bcl-2), have recently become a focus of interest in the study of cancer development and progression. We adapted and evaluated a new enzyme immunoassay method (EIA) for quanitifying bcl-2 in cell lysates. The range of detection of the assay was 5-400 kilounits/L with inter- and intraassay CVs of 5.5-9.2% and 5.0-8.8%, respectively. The recovery of added bcl-2 protein to cell lysates was 96-104%. The concordance rates with Western blotting and immunohistochemistry were 97.5% and 93.7%, respectively. Bcl-2 concentrations were measured in the cell lysate of bladder tumors. The amount of bcl-2 in 158 bladder cancer (mean rank, 71.3 kilounits/g protein; range, 8.4-324 kilounits/g protein), was significantly higher than in nondiseased bladder tissues distant to the tumors (mean rank, 31.5 kilounits/g protein; range, 5-54.9 kilounits/g protein), P = 0.00001. Bcl-2 expression was correlated to tumor proliferative capacity, which was measured by DNA flow cytometry as the percentage of cells in the synthetic phase of the cell cycle. The enzyme immunoassay provides a rapid, quantitative, and reliable technique for measurement of bcl-2 in tumor tissue. The detection of substantial amounts of bcl-2 in invasive tumors (compared with nondiseased tissues) suggests that the assay should be a useful tool for investigating the prognostic value of bcl-2 in bladder tumors and for selecting patients for future anti-bcl-2 therapy.
Clinical Patterns and Biological Correlates of Cognitive Dysfunction Associated with Cancer Therapy (2008)

Standard oncological therapies, such as chemotherapy and cranial radiotherapy, frequently result in a spectrum of neurocognitive deficits that includes impaired learning, memory, attention, and speed of information processing. In addition to classical mechanisms of neurotoxicity associated with chemo- and radiotherapy, such as radiation necrosis and leukoencephalopathy, damage to dynamic progenitor cell populations in the brain is emerging as an important etiologic factor. Radiation- and chemotherapy-induced damage to progenitor populations responsible for maintenance of white matter integrity and adult hippocampal neurogenesis is now believed to play a major role in the neurocognitive impairment many cancer survivors experience.
Epidermal Growth Factor Receptor (EGFR) Is Overexpressed in Anaplastic Thyroid Cancer, and the EGFR Inhibitor Gefitinib Inhibits the Growth of Anaplastic Thyroid Cancer (2004)

ATC cells consistently overexpress EGFR, rendering this receptor a potential target for molecular therapy. Gefitinib effectively blocks activation of EGFR by EGF, inhibits ATC cellular proliferation, and induces apoptosis in vitro. Our in vivo results show that gefitinib has significant antitumor activity against ATC in a subcutaneous nude mouse tumor model and therefore is a potential candidate for human clinical trials.
T cell determinant structure: cores and determinant envelopes in three mouse major histocompatibility complex haplotypes. (1991)

T lymphocytes recognize discrete regions on an antigen. The specificity of the T cell responses in three mouse strains of differing major histocompatibility complex (MHC) haplotype to a protein antigen, lysozyme, was analyzed using a series of peptides that walk the antigen in single amino acid steps. These peptide series were synthesized using the pin synthesis system, which was modified to allow the peptides to be cleaved from the pins into a physiological buffer free of toxic compounds. This methodology overcomes many of the problems associated with the production of peptides for screening proteins for antigenic determinants. The T cell determinants for the three strains were markedly different. This result points out the limitations of algorithms predicting determinants without reference to the MHC, and the importance of the empirical methodology. This analysis of the T cell response to lysozyme constitutes the most complete study of reactivity to a foreign protein to date and illustrates many important features of antigen recognition by T cells, e.g., presence of major and minor determinant regions. The outer boundaries of each immunogenic region, the determinant envelope, are difficult to define from recently immunized lymph nodes because of the heterogeneity in T cell recognition. However, core sequences common to all the immunogenic peptides in a continuous sequence can be easily defined.
What a Tangled Web We Weave: Emerging Resistance Mechanisms to Inhibition of the Phosphoinositide 3-Kinase Pathway (2013)

There are multiple ongoing clinical trials targeting the PI3K pathway members in several malignancies. This review summarizes the known mechanisms of resistance to targeting the PI3K pathway. Understanding of resistance mechanisms will help to inform more rational clinical trial design to optimize the clinical impact of targeting the PI3K pathway in cancer.
A Novel Decentralized Ethernet-Based PON Access Architecture for Provisioning Differentiated QoS (2004)

To date, the mainstream ethernet passive optical network (EPON) bandwidth allocation schemes as well as the new IEEE 802.3ah Ethernet in the first mile Task Force specifications have been centralized, relying on a component in the central office [optical line termination (OLT)] to provision upstream traffic. Hence, the OLT is the only device that can arbitrate time-division access to the shared channel. Since the OLT has global knowledge of the state of the entire network, this is a centralized control plane in which the OLT has centralized intelligence. This paper proposes novel distributed EPON architectures, and in the process proves that these distributed networking architectures and the associated bandwidth allocation algorithms and protocols have characteristics that make them far better suited for provisioning quality of service (QoS) schemes necessary for properly handling data, voice, video, and other real-time streaming advanced multimedia services over a single line. Specifically, this paper proposes a novel ethernet over star coupler-based PON architecture that uses a fully distributed time-division multiple-access (TDMA) arbitration scheme. Supported by the decentralized scheme, this paper proposes several QoS-based dynamic bandwidth allocation (DBA) algorithms in which the OLT is excluded from the implementation of the time slot assignment. In contrast with the mainstream centralized EPON architectures that combine priority queuing [intra-optical network unit (ONU) scheduling] with DBA schemes (inter-ONU scheduling), the proposed distributed EPON architecture supports differentiated services through the integration of both scheduling mechanisms at the ONU (intra-ONU scheduling). The introduction of this integration feature that can only be supported by a decentralized architecture provides better QoS guarantees. Furthermore, in addition to the added flexibility and reliability, the overall performance of the proposed decentralized EPON architecture and the associated bandwidth allocation algorithms are shown to be at least as efficient as their centralized counterparts.
Impact of curcumin on sirtuins: A review (2018)

Curcumin is a bioactive phytochemical that modulates several physiological and cellular processes leading to therapeutic effects against different diseases. Sirtuins are highly conserved nicotine adenine dinucleotide-dependent proteins that regulate the activity of target enzymes and transcription factors by deacetylation. Curcumin possesses both antioxidant and anti-inflammatory properties and has been shown to increase sirtuin-1 (SIRT1) by activating small molecules. Upregulation of SIRT1 by curcumin has been reported to confer protective effects against a range of neurological disorders including glutamate excitotoxicity, β-amyloid-induced cell death in cortical neurons, cerebral ischemic damage, and stroke. Activation of AMPK and SIRT1 by curcumin has also been noted to mediate the protective effects of curcumin against ischemia/reperfusion injury, cardiac fibrosis, diabetes, and lipid metabolism abnormalities. These protective effects of SIRT1 activation are partly mediated by the deacetylation of p53 and reduction of apoptosis. In this review, we summarize the role of SIRT1 in mediating the pharmacological effects of curcumin in several diseases.
Germline Stem Cell Transplantation and Transgenesis (2002)

The recently developed testis cell transplantation method provides a powerful approach to studying the biology of the male germline stem cell and its microenvironment, the stem cell niche. The technique also is being used to examine spermatogenic defects, correct male infertility, and generate transgenic animals.