gebhart/patrepeval huggingface dataset:
Epithelial-Mesenchymal Transition in Breast Cancer Relates to the Basal-like Phenotype (2008)

Epithelial-mesenchymal transition (EMT) is defined by the loss of epithelial characteristics and the acquisition of a mesenchymal phenotype. In carcinoma cells, EMT can be associated with increased aggressiveness, and invasive and metastatic potential. To assess the occurrence of EMT in human breast tumors, we conducted a tissue microarray-based immunohistochemical study in 479 invasive breast carcinomas and 12 carcinosarcomas using 28 different markers. Unsupervised hierarchical clustering of the tumors and statistical analysis showed that up-regulation of EMT markers (vimentin, smooth-muscle-actin, N-cadherin, and cadherin-11) and overexpression of proteins involved in extracellular matrix remodeling and invasion (SPARC, laminin, and fascin), together with reduction of characteristic epithelial markers (E-cadherin and cytokeratins), preferentially occur in breast tumors with the "basal-like phenotype." Moreover, most breast carcinosarcomas also had a basal-like phenotype and showed expression of mesenchymal markers in their sarcomatous and epithelial components. To assess whether basal-like cells have intrinsic phenotypic plasticity for mesenchymal transition, we performed in vitro studies with the MCF10A cell line. In response to low cell density, MCF10A cells suffer spontaneous morphologic and phenotypic EMT-like changes, including cytoskeleton reorganization, vimentin and Slug up-regulation, cadherin switching, and diffuse cytosolic relocalization of the catenins. Moreover, these phenotypic changes are associated with modifications in the global genetic differentiation program characteristic of the EMT process. In summary, our data indicate that in breast tumors, EMT likely occurs within a specific genetic context, the basal phenotype, and suggests that this proclivity to mesenchymal transition may be related to the high aggressiveness and the characteristic metastatic spread of these tumors.
Pump interactions in a 100-nm bandwidth Raman amplifier (1999)

A design for a 100-nm bandwidth Raman amplifier is presented. The amplifier is pumped with eight, 130-mW lasers with wavelengths ranging from 1416 to 1502 nm. The peak-to-peak gain ripple is 1.1 dB. A new model was developed for this design that includes pump-to-pump and signal-to-signal interactions in addition to double Rayleigh scattering and amplified spontaneous emission. An understanding of the interactions among these various effects was essential to this design. These modeling results are based on measurements of the physical characteristics of the transmission fiber.
Intron-Exon Swapping of Transglutaminase mRNA and Neuronal Tau Aggregation in Alzheimer's Disease (2001)

In order to understand the mechanism for insoluble neurotoxic protein polymerization in Alzheimer's disease (AD) brain neurons, we examined protein and gene expression for transglutaminase (TGase 2; tissue transglutaminase (tTG)) in hippocampus and isocortex. We found co-localization of tTG protein and activity with tau-positive neurofibrillary tangles, whereas mRNA and sequence analysis indicated an absolute increase in tTG synthesized. Although apoptosis in AD hippocampus is now an established mode of neuronal cell death, no definite underlying mechanism(s) is known. Since TGase-mediated protein aggregation is implicated in polyglutamine ((CAG)(n)/Q(n) expansion) disorder apoptosis, and expanded Q(n) repeats are excellent TGase substrates, a role for TGase in AD is possible. However, despite such suggestions almost 20 years ago, the molecular mechanism remained elusive. We now present one possible molecular mechanism for tTG-mediated, neurotoxic protein polymerization leading to neuronal apoptosis in AD that involves not its substrates (like Q(n) repeats) but rather the unique presence of alternative transcripts of tTG mRNA. In addition to a full-length (L) isoform in aged non-demented brains, we found a short isoform (S) lacking a binding domain in all AD brains. Our current results identify intron-exon "switching" between L and S isoforms, implicating G-protein-coupled signaling pathways associated with tTG that may help to determine the dual roles of this enzyme in neuronal life and death processes.
Regulation of T cell function by the ubiquitin-specific protease USP9X via modulating the Carma1-Bcl10-Malt1 complex (2013)

The ubiquitin conjugation system plays an important role in immune regulation; however, the ubiquitin-specific proteases (USPs) that carry out deubiquitination of cellular substrates are poorly understood. Here we show that in vivo knockdown of the deubiquitinating enzyme USP9X attenuates T-cell proliferation. In addition, naïve CD4(+) T cells from USP9X knockdown chimeric mice display decreased cytokine production and T helper cell differentiation in vitro, which we confirmed in vivo by performing adoptive transfer of transgenic T cells and subsequent immunization. USP9X silencing in both a human T-cell line and mouse primary T cells reduced T-cell receptor (TCR) signaling-induced NF-κB activation. Mechanistically, USP9X interacts with Bcl10 of the Carma1-Bcl10-Malt1 (CBM) complex and removes the TCR-induced ubiquitin chain from Bcl10, which facilitates the association of Carma1 with Bcl0-Malt1. These results demonstrate that USP9X is a crucial positive regulator of the TCR signaling pathway and is required for T-cell function through the modulation of CBM complex formation.
Fault-tolerant quantum computation (2002)

It has recently been realized that use of the properties of quantum mechanics might speed up certain computations dramatically. Interest in quantum computation has since been growing. One of the main difficulties in realizing quantum computation is that decoherence tends to destroy the information in a superposition of states in a quantum computer making long computations impossible. A further difficulty is that inaccuracies in quantum state transformations throughout the computation accumulate, rendering long computations unreliable. However, these obstacles may not be as formidable as originally believed. For any quantum computation with t gates, we show how to build a polynomial size quantum circuit that tolerates O(1/log/sup c/t) amounts of inaccuracy and decoherence per gate, for some constant c; the previous bound was O(1/t). We do this by showing that operations can be performed on quantum data encoded by quantum error-correcting codes without decoding this data.
Radioimmunoassay of Human Apolipoprotein CII (1977)

A B S T R A C T A specific, precise, and sensitive double-antibody radioimmunoassay for the measurement of human apolipoprotein CII (apoCII) was developed. ApoCII was labeled with 1251 (chloramine- T) and monospecific antibody was raised in rabbits. No appreciable cross-reactivity with apolipoproteins CI, CIII, AI, AII, low density lipoproteins, and lipoprotein-free plasma was observed. Lipoporteins con- taining apoCII displaced the standard curve in parallel. ApoCII measurement was not affected by pretreatment of plasma with tetramethylurea, ethanol-diethyl ether, or heating.
Age-dependent changes in rat lacrimal gland anti-oxidant and vesicular related protein expression profiles. (2012)

These findings indicate that exocytotic and anti-oxidant mechanisms become impaired with age in the rat LG. In parallel with these structural alterations, functional declines may contribute to the pathophysiology caused by tear film modification in dry eye disease.
ACTION SPECTRA FOR KILLING NON‐DIVIDING NORMAL HUMAN AND XERODERMA PIGMENTOSUM CELLS (1980)

Abstract— Non‐dividing human cells degenerate and eventually detach from a culture vessel surface when exposed to UV light. Action spectra for this kind of cell inactivation were determined using eight monochromatic wavelengths from 240 to 313 nm and both a normal DNA excision‐repair‐proficient strain and a repair‐deficient Xeroderma pigmentosum (XP12BE) strain. The action spectra for both strains have similar shapes with a broad peak between 254 and 280 nm followed by a steep decline at wavelengths greater than 280 nm. The relative action spectra are similar to those for inactivation of reproductive capacity and pyrimidine dimer formation in rodent cells suggesting that the critical target and critical damage for inactivation of non‐dividing human cells is DNA and damage to DNA, respectively. Normal repair‐proficient cells are 5–7 times more resistant at all wavelengths, based on a comparison of D o values, than repair‐deficient XP12BE cells, supporting the conclusion that the inactivating damage at all wavelengths is to DNA.
Antithrombin III (AT III) Prevents LPS-Induced Pulmonary Vascular Injury: Novel Biological Activity of AT III (1997)

Acute respiratory distress syndrome (ARDS) adversely affects the outcome of patients with disseminated intravascular coagulation (DIC) associated with sepsis. To determine whether antithrombin III (AT III) is useful for the treatment of ARDS in sepsis, we evaluated the effect of AT III on lipopolysaccharide (LPS)-induced pulmonary vascular injury in rats. Although the intravenous administration of AT III (250 U/kg) prevented LPS-induced pulmonary accumulation of leukocytes, increases in pulmonary vascular permeability, and coagulation abnormalities, inactivated factor Xa, a selective inhibitor of thrombin generation, did not prevent such events other than the coagulation abnormalities. AT III promotes the endothelial release of prostacyclin by interacting with cell surface glycosaminoglycans in vivo. Trp49-modified AT III, which lacks affinity for heparin, did not prevent LPS-induced pulmonary vascular injury. Plasma levels of 6-keto-prostaglandin F1alpha were markedly increased in rats after the administration of LPS and significantly decreased in the LPS-treated rats administered Trp49-modified AT III, but not altered in those LPS-treated rats receiving AT III. Preventive effects of AT III were not observed in rats pretreated with indomethacin, which inhibits prostacyclin biosynthesis. Prostacyclin prevents LPS-induced pulmonary vascular injury by inhibiting leukocyte accumulation in the lungs. These observations strongly suggest that AT III prevents pulmonary vascular injury induced by LPS by promoting the endothelial release of prostacyclin, a potent inhibitor of leukocyte activation.
Noninvasive Cuffless Estimation of Blood Pressure from Pulse Arrival Time and Heart Rate with Adaptive Calibration (2009)

We study the problem of noninvasively estimating Blood Pressure (BP) without using a cuff, which is attractive for continuous monitoring of BP over Body Area Networks. It has been shown that the Pulse Arrival Time (PAT) measured as the delay between the ECG peak and a point in the finger PPG waveform can be used to estimate systolic and diastolic BP. Our aim is to evaluate the performance of such a method using the available MIMIC database, while at the same time improve the performance of existing techniques. We propose an algorithm to estimate BP from a combination of PAT and heart rate, showing improvement over PAT alone. We also show how the method achieves recalibration using an RLS adaptive algorithm. Finally, we address the use case of ECG and PPG sensors wirelessly communicating to an aggregator and study the effect of skew and jitter on BP estimation.
Fatty Acid Composition of Unicellular Strains of Blue-Green Algae (1972)

The fatty acids of 34 strains of unicellular blue-green algae provisionally assigned to the genera Synechococcus, Aphanocapsa, Gloeocapsa, Microcystis, and Chlorogloea by Stanier et al. have been chemically characterized. The strains analyzed can be divided into a series of compositional groups based upon the highest degree of unsaturation of the major cellular fatty acids. Twenty strains fall into the group characterized by one trienoic fatty acid isomer (alpha-linolenic acid), and seven strains fall into a group characterized by another trienoic acid isomer (gamma-linolenic acid). These groups in many cases correlate well with groupings based upon other phenotypic characters of the strains, e.g., deoxyribonucleic acid base composition. The assignment of a strain to a compositional group is not altered when the strain is grown under a variety of different culture conditions. All strains contain glycolipids with the properties of mono- and digalactosyldiglycerides.
Femtosecond energy relaxation of nonthermal electrons injected in p-doped GaAs base of a heterojunction bipolar transistor (2001)

We study femtosecond relaxation of minority carriers (electrons) injected into a heavily p-doped base of a heterojunction bipolar transistor (HBT). Here, we consider the case of p-doped GaAs, to be specific. The electrons are assumed to have a peaked energy distribution at t=0, with kinetic energies a few hundred meV above the conduction band threshold. We solve the time dependent Boltzmann equation governing the dynamics of these electrons. The main feature of this work is a detailed calculation of the time dependent nonthermal, nonequilibrium electron energy distribution, that relaxes due to single particle excitations via electron–hole scattering and interaction with coupled optical phonon-hole plasmon modes in the sub and picosecond time domains. We highlight the significant role that the electron-hole scattering plays in this relaxation. The majority carriers (holes) are assumed to remain in quasiequilibrium with the lattice, taken to be at room temperature (or at 77 K). We present calculations of electron energy relaxation with the hole density varied from 1×1018 to 1×1020 cm−3. In the initial, subpicosecond stages of the relaxation, the energy distribution evolves into two major components: a quasiballistic but broad component, at energies near the injection energy, and an energy relaxed component near E=0. The latter becomes dominant in a picosecond or so. The electrons with an initial mean velocity of ∼1.5×108 cm/s attain a cooler distribution with a mean velocity of ∼4×107 cm/s within about 1 ps for p doping in excess of 1×1019 cm−3. The temporal evolution of average velocity 〈v〉 of the electrons should be useful in obtaining values of the base width suitable for effective operation of HBTs.
R-Spondin Proteins: A Novel Link to &beta;-catenin Activation (2005)

The R-spondin (Rspo) protein family is a recently described group of four distinct human secreted proteins. Reported activities for Rspo proteins include essential roles in vertebrate development and their ligand-type activities overlap substantially with those of the canonical Wnt ligands in that both Rspo and canonical Wnt signaling result in the activation of beta-catenin. In a general functional screen for human secreted proteins using transgenic mouse models, we identified human R-spondin1 (hRspo1) protein as a potent and specific mitogen for the gastrointestinal epithelium and demonstrated a potential therapeutic application for the protein in mouse models of cancer therapy-induced mucositis. In contrast to previous studies, our data indicated only partial overlap between Wnt and Rspo ligand activities, suggesting that there may be independent receptor/signaling pathways for Rspo proteins that intersect those of Wnt at the level of beta-catenin. Here we summarize the current reported data on the Rspo family and discuss these results in terms of alternate mechanisms of action. We have extended our observations on the potential therapeutic application of Rspo proteins by showing that all four human Rspo family members are capable of inducing epithelial proliferation and report the first non-vertebrate Rspo family member.
Speech-Model Based Accurate Blind Reverberation Time Estimation Using an LPC Filter (2012)

In this paper, we propose a speech-model based method using the linear predictive (LP) residual of the speech signal and the maximum-likelihood (ML) estimator proposed in “Blind estimation of reverberation time,” (R. Ratnam , J. Acoust. Soc. Amer., 2004) to blindly estimate the reverberation time (RT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> ). The input speech is passed through a low order linear predictive coding (LPC) filter to obtain the LP residual signal. It is proven that the unbiased autocorrelation function of this LP residual has the required properties to be used as an input to the ML estimator. It is shown that this method can successfully estimate the reverberation time with less data than existing blind methods. Experiments show that the proposed method can produce better estimates of RT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> , even in highly reverberant rooms. This is because the entire input speech data is used in the estimation process. The proposed method is not sensitive to the type of input data (voiced, unvoiced), number of gaps, or window length. In addition, evaluation using white Gaussian noise and recorded babble noise shows that it can estimate RT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> in the presence of (moderate) background noise.
Aging effects on DNA methylation modules in human brain and blood tissue (2012)

Overall, our analysis revealed a robustly defined age-related co-methylation module that is present in multiple human tissues, including blood and brain. We conclude that blood is a promising surrogate for brain tissue when studying the effects of age on DNA methylation profiles.
Efficacy of rhBMP-2 loaded PCL/PLGA/ β -TCP guided bone regeneration membrane fabricated by 3D printing technology for reconstruction of calvaria defects in rabbit (2014)

We successfully fabricated a three-dimensional (3D) printing-based PCL/PLGA/β-TCP guided bone regeneration (GBR) membrane that slowly released rhBMP-2. To impregnate the GBR membrane with intact rhBMP-2, collagen solution encapsulating rhBMP-2 (5 µg ml(-1)) was infused into pores of a PCL/PLGA/β-TCP membrane constructed using a 3D printing system with four dispensing heads. In a release profile test, sustained release of rhBMP-2 was observed for up to 28 d. To investigate the efficacy of the GBR membrane on bone regeneration, PCL/PLGA/β-TCP membranes with or without rhBMP-2 were implanted in an 8 mm calvaria defect of rabbits. Bone formation was evaluated at weeks 4 and 8 histologically and histomorphometrically. A space making ability of the GBR membrane was successfully maintained in both groups, and significantly more new bone was formed at post-implantation weeks 4 and 8 by rhBMP-2 loaded GBR membranes. Interestingly, implantation with rhBMP-2 loaded GBR membranes led to almost entire healing of calvaria defects within 8 weeks.
Lithiation of 2-Me3SiCHRC5H4N(R = H or SiMe3): influence of solvent on the nature of the product (from X-ray structure determinations) and asymmetric induction. A note on the lithiation of some analogous 3- and 4-methylpyridines (1990)

Metallation of 2-Me3SiCHRC5H4N (R = H or SiMe3) using LiBun in hexane, and in the presence of diethyl ether, and the ditertiary amines tmen (N,N,N′,N′-tetramethylethylenediamine) or sp [(–)sparteine] yields crystalline lithium complexes. These have been characterized using X-ray diffraction data for [Li{2-C(SiMe3)2C5H4N}{2-CH(SiMe3)2C5H4N}](1), [{Li[2-C(SiMe3)2C5H4N]}2](2), [Li(tmen){2-C(SiMe3)2C5H4N}](3), [{Li(OEt2)[2-CH(SiMe3)C5H4N]}2](4), [{Li(tmen)[2-CH(SiMe3)C5H4N]}2](5), and [Li(sp){2-CH(SiMe3)C5H4N}](6). In (1), (3), (4), and (6) the hydrocarbyl group acts as an η3-aza-allyl through the ring nitrogen [2.00(1), 1.96(2), 2.19(1), and 1.985(6)Å], ipso-carbon [2.22(1), 2.43(2), 2.356(9), and 2.323(6)Å], and adjacent ring carbon [2.32(1), 2.46(2), 2.34(1), and 2.353(6)Å]; in (4) the nitrogen centre also bridges to another metal centre [2.041(1)Å]. Complex (2) has two co-ordinated lithium centres, each lithium bound by the ipso-carbon [2.213(7)Å] and a nitrogen centre from a centrosymmetric ligand [1.936(6)Å] and is thus an alkylmetal species; it can be recrystallized from tetrahydrofuran even though the lithiums are co-ordinatively unsaturated. In complex (5), the anionic ligand acts as an amide bridging two metal centres through the ring N [Li–N 2.08(1), 2.25(1)Å, N–Li–N 103.6(7), 93.0(9)°]. Treating (6) with MeI in hexane at –78 °C yields 2-[(1-trimethylsilyl)ethyl]pyridine of 20% estimated optical purity. The isomeric complex [Li(sp){4-CH(SiMe3)C5H4N}] under the same conditions gave no asymmetric induction; other metallations of 4-Me3SiCH2C5H4N, and some of 3-Me3SiCH2C5H4N are also reported.
A GaAs high power RF single-pole dual throw switch IC for digital-mobile communication system (1995)

A high power GaAs monolithic RF switch IC that can handle powers over 5 W (P1 dB: 37 dBm) with a positive 5-V control voltage was developed. This high power handling capability was achieved by using a novel circuit configuration that makes possible the feeding forward of the input-signal to the control gates. The implemented Single Pole Dual Throw switch IC integrated with the coupling capacitors using a high dielectric material, Barium Strontium Titanate, shows an insertion loss less than 0.8 dB at 1 GHz and an isolation over 25 dB in a frequency range of 0.5-1.5 GHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solution structure of the Alzheimer amyloid β‐peptide (1–42) in an apolar microenvironment (2002)

The major components of neuritic plaques found in Alzheimer disease (AD) are peptides known as amyloid beta-peptides (Abeta), which derive from the proteolitic cleavage of the amyloid precursor proteins. In vitro Abeta may undergo a conformational transition from a soluble form to aggregated, fibrillary beta-sheet structures, which seem to be neurotoxic. Alternatively, it has been suggested that an alpha-helical form can be involved in a process of membrane poration, which would then trigger cellular death. Conformational studies on these peptides in aqueous solution are complicated by their tendency to aggregate, and only recently NMR structures of Abeta-(1-40) and Abeta-(1-42) have been determined in aqueous trifluoroethanol or in SDS micelles. All these studies hint to the presence of two helical regions, connected through a flexible kink, but it proved difficult to determine the length and position of the helical stretches with accuracy and, most of all, to ascertain whether the kink region has a preferred conformation. In the search for a medium which could allow a more accurate structure determination, we performed an exhaustive solvent scan that showed a high propensity of Abeta-(1-42) to adopt helical conformations in aqueous solutions of fluorinated alcohols. The 3D NMR structure of Abeta-(1-42) shows two helical regions encompassing residues 8-25 and 28-38, connected by a regular type I beta-turn. The surprising similarity of this structure, as well as the sequence of the C-terminal moiety, with those of the fusion domain of influenza hemagglutinin suggests a direct mechanism of neurotoxicity.