gebhart/patrepeval huggingface dataset:
Bacterial biofilms in the human gastrointestinal tract. (2002)

Microbial biofilms were first described in 1936 and subsequent research has unveiled their ubiquity and physiological distinction from free-living (planktonic) microorganisms. In light of their emerging significance this review examines the bacterial biofilms within the human gastrointestinal tract. Attention is paid to the nature of these mucosally- associated populations, focusing on the protected environment afforded by the continual secretion of mucus by host epithelial cells. It also examines the attributes possessed by various bacterial species that facilitate habitation of this microenvironment. Additionally, contrasts are drawn between planktonic bacteria of the lumen and sessile (biofilm) bacteria growing in close association with host cells and food particles. In particular the different fermentation profiles exhibited by these two fractions are discussed. The potential role of these communities in host health and disease, as well as the stabilisation of the lumenal population, is also considered. Reference is made to the state of mutualism that exists between these little understood populations and the host epithelia, thus highlighting their ecological significance in terms of gastrointestinal health.
Effective operator formalism for open quantum systems (2012)

We present an effective operator formalism for open quantum systems. Employing perturbation theory and adiabatic elimination of excited states for a weakly driven system, we derive an effective master equation which reduces the evolution to the ground-state dynamics. The effective evolution involves a single effective Hamiltonian and one effective Lindblad operator for each naturally occurring decay process. Simple expressions are derived for the effective operators which can be directly applied to reach effective equations of motion for the ground states. We compare our method with the hitherto existing concepts for effective interactions and present physical examples for the application of our formalism, including dissipative state preparation by engineered decay processes.
Generating a Prion with Bacterially Expressed Recombinant Prion Protein (2010)

The prion hypothesis posits that a misfolded form of prion protein (PrP) is responsible for the infectivity of prion disease. Using recombinant murine PrP purified from Escherichia coli, we created a recombinant prion with the attributes of the pathogenic PrP isoform: aggregated, protease-resistant, and self-perpetuating. After intracerebral injection of the recombinant prion, wild-type mice developed neurological signs in approximately 130 days and reached the terminal stage of disease in approximately 150 days. Characterization of diseased mice revealed classic neuropathology of prion disease, the presence of protease-resistant PrP, and the capability of serially transmitting the disease; these findings confirmed that the mice succumbed to prion disease. Thus, as postulated by the prion hypothesis, the infectivity in mammalian prion disease results from an altered conformation of PrP.
Use of epitope libraries to identify exon-specific monoclonal antibodies for characterization of altered dystrophins in muscular dystrophy. (1993)

The majority of mutations in Xp21-linked muscular dystrophy (MD) can be identified by PCR or Southern blotting, as deletions or duplications of groups of exons in the dystrophin gene, but it is not always possible to predict how much altered dystrophin, if any, will be produced. Use of exon-specific monoclonal antibodies (mAbs) on muscle biopsies from MD patients can, in principle, provide information on both the amount of altered dystrophin produced and, when dystrophin is present, the nature of the genetic deletion or point mutation. For this purpose, mAbs which recognize regions of dystrophin encoded by known exons and whose binding is unaffected by the absence of adjacent exons are required. To map mAbs to specific exons, random "libraries" of expressed dystrophin fragments were created by cloning DNAseI digestion fragments of a 4.3-kb dystrophin cDNA into a pTEX expression vector. The libraries were then used to locate the epitopes recognized by 48 mAbs to fragments of 25-60 amino acids within the 1,434-amino-acid dystrophin fragment used to produce the antibodies. This is sufficiently detailed to allow further refinement by using synthetic peptides and, in many cases, to identify the exon in the DMD (Duchenne MD) gene which encodes the epitope. To illustrate their use in dystrophin analysis, a Duchenne patient with a frameshift deletion of exons 42 and 43 makes a truncated dystrophin encoded by exons 1-41, and we now show that this can be detected in the sarcolemma by mAbs up to and including those specific for exon 41 epitopes but not by mAbs specific for exon 43 or later epitopes.
Immunologic and Molecular Biologic Studies of Prion Proteins in Bovine Spongiform Encephalopathy (1993)

Bovine spongiform encephalopathy (BSE) is a transmissible neurodegenerative disease. Six brain regions from 11 cattle were examined for the presence of the abnormal isoform of the prion protein (PrPBSE). The highest concentrations of PrPBSE were found in the brain stem, where the greatest degree of spongiform change was observed. Molecular cloning of the bovine PrP gene showed that it encodes a protein of 256 or 264 amino acids with five or six Gly:Pro-rich octarepeats, respectively, in contrast to all other mammalian PrP genes, which encode only five octarepeats. The bovine PrP gene is single copy, and the entire open-reading frame lies within a single exon. Since the transmission of prions across species seems to be restricted by differences in PrP sequence, the high degree of homology between sheep and bovine PrP (98%) correlates with the proposed cause of BSE.
Expression of an Arabidopsis cryptochrome gene in transgenic tobacco results in hypersensitivity to blue, UV-A, and green light. (1995)

The Arabidopsis HY4 gene, required for blue-light-induced inhibition of hypocotyl elongation, encodes a 75-kDa flavoprotein (CRY1) with characteristics of a blue-light photoreceptor. To investigate the mechanism by which this photoreceptor mediates blue-light responses in vivo, we have expressed the Arabidopsis HY4 gene in transgenic tobacco. The transgenic plants exhibited a short-hypocotyl phenotype under blue, UV-A, and green light, whereas they showed no difference from the wild-type plant under red/far-red light or in the dark. This phenotype was found to cosegregate with overexpression of the HY4 transgene and to be fluence dependent. We concluded that the short-hypocotyl phenotype of transgenic tobacco plants was due to hypersensitivity to blue, UV-A, and green light, resulting from over-expression of the photoreceptor. These observations are consistent with the broad action spectrum for responses mediated by this cryptochrome in Arabidopsis and indicate that the machinery for signal, transduction required by the CRY1 protein is conserved among different plant species. Furthermore, the level of these photoresponses is seen to be determined by the cellular concentration of this photoreceptor.
Electrochemical Properties of High-Power Supercapacitors Using Single-Walled Carbon Nanotube Electrodes (2001)

We have investigated the key factors determining the performance of supercapacitors constructed using single-walled carbon nanotube (SWNT) electrodes. Several parameters, such as composition of the binder, annealing temperature, type of current collector, charging time, and discharging current density have been optimized for the best performance of the supercapacitor with respect to energy density and power density. We find a maximum specific capacitance of 180 F/g and a measured power density of 20 kW/kg at energy densities in the range from 7 to 6.5 Wh/kg at 0.9 V in a solution of 7.5 N KOH (the currently available supercapacitors have energy densities in the range 6–7 Wh/kg and power density in the range 0.2–5 kW/kg at 2.3 V in non-aqueous solvents).
Towards Smart Tattoos: Implantable Biosensors for Continuous Glucose Monitoring (2012)

Diabetes can strike at any age, from childhood to adulthood, and lasts a lifetime. Thus, it is important to find ways to increase the quality of life for diabetic patients through intensive, continuous care of blood glucose concentrations. Glucose biosensors that are implanted under the skin are promising for continuous glucose monitoring because they can constantly read blood glucose concentrations and signal a warning in case of hypo- or hyperglycemia. The demand for subcutaneous glucose biosensors has led to the development of many glucose-sensing principles and sensor designs. This Review covers the effort to develop subcutaneous glucose biosensors, including the glucose-sensing principles, and discusses their current status for in vivo monitoring. In addition, the Review examines the future prospects for intensive diabetes care.
Some Mathematical Notes on Three-Mode Factor Analysis (1966)

The model for three-mode factor analysis is discussed in terms of newer applications of mathematical processes including a type of matrix process termed the Kronecker product and the definition of combination variables. Three methods of analysis to a type of extension of principal components analysis are discussed. Methods II and III are applicable to analysis of data collected for a large sample of individuals. An extension of the model is described in which allowance is made for unique variance for each combination variable when the data are collected for a large sample of individuals.
Pyrrolysine analogues as substrates for pyrrolysyl‐tRNA synthetase (2006)

In certain methanogenic archaea a new amino acid, pyrrolysine (Pyl), is inserted at in-frame UAG codons in the mRNAs of some methyltransferases. Pyl is directly acylated onto a suppressor tRNA(Pyl) by pyrrolysyl-tRNA synthetase (PylRS). Due to the lack of a readily available Pyl source, we looked for structural analogues that could be aminoacylated by PylRS onto tRNA(Pyl). We report here the in vitro aminoacylation of tRNA(Pyl) by PylRS with two Pyl analogues: N-epsilon-d-prolyl-l-lysine (d-prolyl-lysine) and N-epsilon-cyclopentyloxycarbonyl-l-lysine (Cyc). Escherichia coli, transformed with the tRNA(Pyl) and PylRS genes, suppressed a lacZ amber mutant dependent on the presence of d-prolyl-lysine or Cyc in the medium, implying that the E. coli translation machinery is able to use Cyc-tRNA(Pyl) and d-prolyl-lysine-tRNA(Pyl) as substrates during protein synthesis. Furthermore, the formation of active beta-galactosidase shows that a specialized mRNA motif is not essential for stop-codon recoding, unlike for selenocysteine incorporation.
Excitonic singlet-triplet ratio in a semiconducting organic thin film (1999)

A technique is presented to determine the spin statistics of excitons formed by electrical injection in a semiconducting organic thin film. With the aid of selective addition of luminescent dyes, we generate either fluorescence or phosphorescence from the archetype organic host material aluminum tris (8-hydroxyquinoline) $({\mathrm{Alq}}_{3}).$ Spin statistics are calculated from the ratio of fluorescence to phosphorescence in the films under electrical excitation. After accounting for varying photoluminescent efficiencies, we find a singlet fraction of excitons in ${\mathrm{Alq}}_{3}$ of $(22\ifmmode\pm\else\textpm\fi{}3)%.$
The Effects of Blue Light on Ocular Health (2000)

Why should we care about blue light? For years now, professionals in the fields of light energy and vision have known about the hazards ultraviolet (UV) light presents to ocular health. We are gradually having longer and more intense exposures to blue light; much of the world of commercial display and industry is lit with cool white fluorescent tubes which emit a strong spike of light in the blue range. Indeed many homes and offices are lit with cool white fluorescent tubes. No one doubts more people are spending time in front of video display terminals (VDTs) which produce blue light. While some people find blue light irritates their eyes or causes headache, most are able to ignore it. Scientists only now are beginning to investigate its long-term effects and offer some solutions for maintaining ocular health in the presence of blue light.
Endogenous ligands of carbohydrate recognition domains of the mannose receptor in murine macrophages, endothelial cells and secretory cells; potential relevance to inflammation and immunity (2001)

The macrophage mannose receptor (MR) has an established role in the phagocytosis of a wide range of microbes, and also functions in viral endocytosis, and clearance of a number of endogenous glycoproteins from the circulation. Its broad ligand specificity is mediated by tandemly linked carbohydrate recognition domains (CRDs). Recent studies suggest that binding or internalization of both natural and synthetic ligands of MR CRDs may modulate macrophage (MPhi ) function, for example to increase cidal capacity or cytokine synthesis. To identify endogenous ligands in the normal mouse we used an Fc-fusion protein (CRD4-7Fc) bearing four of the CRDs of MR. CRD4-7Fc recognized endocytic compartments of cultured MPhi, consistent with lysosomal enzymes being major ligands of MR. CRD4-7Fc also recognized MPhi and some endothelial cells in tissues, and intensely labeled secretory cells of the exocrine pancreas, salivary gland and thyroid. Strongly MR-positive interstitial cells were found in close proximity to the ligand-rich secretory cells, suggesting a role for MR in uptake of secretory glycoproteins, including thyroglobulin which was identified as a novel ligand in vitro. Endocytosis of these ligands by MR may have implications for tissue homeostasis and immunity, including antigen presentation, in secretory organs.
Physics-based switching model for Cu/SiO<inf>2</inf>/W quantum memristor (2016)

Memristive devices are leading candidates for realizing next generation non-volatile memory [1] and brain-inspired neuromorphic computing systems [2]. However, most of these devices operate at high voltages (1-3 V) and require 100s of μA for programming. We recently demonstrated a Cu/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /W memristor device, exhibiting half-integer quantum conductance states at room temperature and sub-300 mV switching [3]. In this paper we develop a physics based model for this device, capturing the observed experimental programming characteristics including its switching response, conductance quantization, and pulse response.
Gesture Recognition: A Survey (2007)

Gesture recognition pertains to recognizing meaningful expressions of motion by a human, involving the hands, arms, face, head, and/or body. It is of utmost importance in designing an intelligent and efficient human-computer interface. The applications of gesture recognition are manifold, ranging from sign language through medical rehabilitation to virtual reality. In this paper, we provide a survey on gesture recognition with particular emphasis on hand gestures and facial expressions. Applications involving hidden Markov models, particle filtering and condensation, finite-state machines, optical flow, skin color, and connectionist models are discussed in detail. Existing challenges and future research possibilities are also highlighted
Determinants of Sensitivity and Resistance to Rapamycin-Chemotherapy Drug Combinations In vivo (2006)

The phosphatidylinositol-3-OH kinase [PI(3)K] pathway is frequently activated in human cancers and represents a rational target for therapeutic intervention. We have previously shown that enforced expression of Akt, which is a downstream effector of PI(3)K, could promote tumorigenesis and drug resistance in the Emu-myc mouse lymphoma model, and that these tumors were particularly sensitive to inhibition of mammalian target of rapamycin (mTOR) with rapamycin when combined with conventional chemotherapy. We now show that reduced dosage of PTEN, a negative regulator of PI(3)K signaling, is sufficient to activate Akt, but has only a modest effect on lymphomagenesis in the same model. Nonetheless, loss of even one PTEN allele resulted in lymphomas that were resistant to conventional chemotherapy yet sensitive to rapamycin/chemotherapy combinations. These effects could be recapitulated by using RNA interference to suppress PTEN expression in lymphomas, which were previously established in the absence of PI(3)K lesions. Finally, the introduction of lesions that act downstream of mTOR (eIF4E) or disable apoptosis (Bcl-2 and loss of p53) into PTEN+/- lymphomas promoted resistance to rapamycin/chemotherapy combinations. Thus, whether activation of the PI(3)K pathway confers sensitivity or resistance to therapy depends on the therapy used as well as secondary genetic events. Understanding these genotype-response relationships in human tumors will be important for the effective use of rapamycin or other compounds targeting the PI(3)K pathway in the clinic.
Generating human hematopoietic stem cells in vitro –exploring endothelial to hematopoietic transition as a portal for stemness acquisition (2016)

Advances in cellular reprogramming technologies have created alternative platforms for the production of blood cells, either through inducing pluripotency in somatic cells or by way of direct conversion of nonhematopoietic cells into blood cells. However, de novo generation of hematopoietic stem cells (HSCs) with robust and sustained multilineage engraftment potential remains a significant challenge. Hemogenic endothelium (HE) has been recognized as a unique transitional stage of blood development from mesoderm at which HSCs arise in certain embryonic locations. The major aim of this review is to summarize historical perspectives and recent advances in the investigation of endothelial to hematopoietic transition (EHT) and HSC formation in the context of aiding in vitro approaches to instruct HSC fate from human pluripotent stem cells. In addition, direct conversion of somatic cells to blood and HSCs and progression of this conversion through HE stage are discussed. A thorough understanding of the intrinsic and microenvironmental regulators of EHT that lead to the acquisition of self-renewal potential by emerging blood cells is essential to advance the technologies for HSC production and expansion.
Inhibition of wild-type and mutant Bcr-Abl by pyrido-pyrimidine-type small molecule kinase inhibitors. (2003)

Imatinib mesylate (STI571, Glivec), a 2-phenylaminopyrimidine small-molecule ATP competitor-type kinase inhibitor, proved to be active in Philadelphia-positive leukemias. Resistance toward imatinib develops frequently in advanced-stage Philadelphia-positive leukemia, and is even observed in chronic-phase chronic myelogenous leukemia. Point mutations within the BCR-ABL kinase domain emerged as a major mechanism of resistance toward imatinib. Mutations occur at positions that determine specific contacts of imatinib to the ATP-binding site. We aimed to examine whether pyrido-pyrimidine-type kinase inhibitors were capable of inhibiting both wild-type and mutant forms of BCR-ABL. We screened 13 different pyrido-pyrimidine with cells expressing wild-type and mutant BCR-ABL. All of the substances specifically suppressed the Bcr-Abl dependent phenotype and inhibited Bcr-Abl kinase activity with higher potency than imatinib. Two of the most active compounds were PD166326 and SKI DV-M016. Interestingly, these compounds suppressed the activation loop mutant Bcr-Abl H396P as effectively as wild-type Bcr-Abl. In addition, nucleotide-binding loop mutations (Y253H, E255K, and E255V) were selectively and potently inhibited. In contrast, T315I, a mutant located at a position that makes a direct contact with imatinib, was not affected. This observation is consistent with the hypothesis that unlike imatinib, pyrido-pyrimidine inhibitors bind Bcr-Abl regardless of the conformation of the activation loop. We conclude that pyrido-pyrimidine-type kinase inhibitors are active against different frequently observed kinase domain mutations of BCR-ABL that cause resistance toward imatinib. Resistance as a consequence of selection of mutant BCR-ABL by imatinib may be overcome using second-generation kinase inhibitors because of their higher potency and their ability to bind Bcr-Abl irrespective of the conformation of the activation loop.
GLUT8, a Novel Member of the Sugar Transport Facilitator Family with Glucose Transport Activity (2000)

GLUT8 is a novel glucose transporter-like protein that exhibits significant sequence similarity with the members of the sugar transport facilitator family (29.4% of amino acids identical with GLUT1). Human and mouse sequence (86.2% identical amino acids) comprise 12 putative membrane-spanning helices and several conserved motifs (sugar transporter signatures), which have previously been shown to be essential for transport activity, e.g. GRK in loop 2, PETPR in loop 6, QQLSGVN in helix 7, DRAGRR in loop 8, GWGPIPW in helix 10, and PETKG in the C-terminal tail. An expressed sequence tag (STS A005N15) corresponding with the 3'-untranslated region of GLUT8 has previously been mapped to human chromosome 9. COS-7 cells transfected with GLUT8 cDNA expressed a 42-kDa protein exhibiting specific, glucose-inhibitable cytochalasin B binding (K(D) = 56.6 +/- 18 nm) and reconstitutable glucose transport activity (8.1 +/- 1. 4 nmol/(mg protein x 10 s) versus 1.1 +/- 0.1 in control transfections). In human tissues, a 2.4-kilobase pair transcript was predominantly found in testis, but not in testicular carcinoma. Lower amounts of the mRNA were detected in most other tissues including skeletal muscle, heart, small intestine, and brain. GLUT8 mRNA was found in testis from adult, but not from prepubertal rats; its expression in human testis was suppressed by estrogen treatment. It is concluded that GLUT8 is a sugar transport facilitator with glucose transport activity and a hormonally regulated testicular function.
A Survey of Shading and Reflectance Models (1994)

Abstract Since the beginning of computer graphics, three decades ago, a large number of models intended to describe the behaviour of light on a given point of a surface have been proposed. Almost every author uses his own terminology and/or notation. To understand clearly the similarities and the differences between existing models, reformulating them with a unified notation is essential. This has been done by Hall in 1986. This paper is a new survey of shading and reflectance models, including the most recent models. Moreover, after the lengthy enumeration, some original models are proposed, which attempt to include interesting features of previous disjointed work into new formulations.
Design and CAD Challenges in sub-90nm CMOS Technologies (2003)

This paper discusses design challenges of scaled CMOS circuits in sub-90nm technologies for high-performance digital applications. To continue scaling of the CMOS devices deep into sub-90nm technologies, fully depleted SOI, strained-Si on SiGe, FinFETs with double gate, and even further, three-dimensional circuits will be utilized to design high-performance circuits. We will discuss unique design aspects and issues resulting from this scaling such as gate-to-body tunneling, self-heating, reliability issues, and process variations. As the scaling approaches various physical limits, new SOI design issues such as Vt modulation due to leakage, low-voltage impact ionization, and higher V/sub t,lin/ to maintain adequate V/sub t,sat/, continue to surface. With an eye towards the future, design and CAD issues related to sub-65nm device structures such as double gate FinFET will be discussed.