gebhart/patrepeval huggingface dataset:
Structure of Adeno-Associated Virus Type 4 (2005)

Adeno-associated virus (AAV) is a member of the Parvoviridae, belonging to the Dependovirus genus. Currently, several distinct isolates of AAV are in development for use in human gene therapy applications due to their ability to transduce different target cells. The need to manipulate AAV capsids for specific tissue delivery has generated interest in understanding their capsid structures. The structure of AAV type 4 (AAV4), one of the most antigenically distinct serotypes, was determined to 13-A resolution by cryo-electron microscopy and image reconstruction. A pseudoatomic model was built for the AAV4 capsid by use of a structure-based sequence alignment of its major capsid protein, VP3, with that of AAV2, to which AAV4 is 58% identical and constrained by its reconstructed density envelope. The model showed variations in the surface loops that may account for the differences in receptor binding and antigenicity between AAV2 and AAV4. The AAV4 capsid surface topology also shows an unpredicted structural similarity to that of Aleutian mink disease virus and human parvovirus B19, autonomous members of the genus, despite limited sequence homology.
An improved search algorithm using incremental knowledge for continuous speech recognition (1993)

A search algorithm that incrementally makes effective use of detailed sources of knowledge is proposed. The algorithm incrementally applies all available acoustic and linguistic information in three search phases. Phase one is a left-to-right Viterbi beam search that produces word end times and scores using right context between-word models with a bigram language model. Phase two, guided by results from phase one, is a right-to-left Viterbi beam search that produces word begin times and scores based on left context between-word models. Phase three is an A* search that combines the results of phases one and two with a long-distance language model. The objective is to maximize the recognition accuracy with a minimal increase in computational cost. With the decomposed, incremental, search algorithm, it is shown that early use of detailed acoustic models can significantly reduce the recognition error rate with a negligible increase in computational cost. It is demonstrated that the early use of detailed knowledge can improve the word error bound by at least 22% for large-vocabulary, speaker-independent, continuous speech recognition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Leaf Oil Body Functions as a Subcellular Factory for the Production of a Phytoalexin in Arabidopsis (2013)

Oil bodies are intracellular structures present in the seed and leaf cells of many land plants. Seed oil bodies are known to function as storage compartments for lipids. However, the physiological function of leaf oil bodies is unknown. Here, we show that leaf oil bodies function as subcellular factories for the production of a stable phytoalexin in response to fungal infection and senescence. Proteomic analysis of oil bodies prepared from Arabidopsis (Arabidopsis thaliana) leaves identified caleosin (CLO3) and α-dioxygenase (α-DOX1). Both CLO3 and α-DOX1 were localized on the surface of oil bodies. Infection with the pathogenic fungus Colletotrichum higginsianum promoted the formation of CLO3- and α-DOX1-positive oil bodies in perilesional areas surrounding the site of infection. α-DOX1 catalyzes the reaction from α-linolenic acid (a major fatty acid component of oil bodies) to an unstable compound, 2-hydroperoxy-octadecatrienoic acid (2-HPOT). Intriguingly, a combination of α-DOX1 and CLO3 produced a stable compound, 2-hydroxy-octadecatrienoic acid (2-HOT), from α-linolenic acid. This suggests that the colocalization of α-DOX1 and CLO3 on oil bodies might prevent the degradation of unstable 2-HPOT by efficiently converting 2-HPOT into the stable compound 2-HOT. We found that 2-HOT had antifungal activity against members of the genus Colletotrichum and that infection with C. higginsianum induced 2-HOT production. These results defined 2-HOT as an Arabidopsis phytoalexin. This study provides, to our knowledge, the first evidence that leaf oil bodies produce a phytoalexin under a pathological condition, which suggests a new mechanism of plant defense.
Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death (2008)

When exposed to tumor necrosis factor (TNF) or TNF-related apoptosis-inducing ligand (TRAIL), a closely related death ligand and investigational therapeutic, cells enter a protracted period of variable duration in which only upstream initiator caspases are active. A subsequent and sudden transition marks activation of the downstream effector caspases that rapidly dismantle the cell. Thus, extrinsic apoptosis is controlled by an unusual variable-delay, snap-action switch that enforces an unambiguous choice between life and death. To understand how the extrinsic apoptosis switch functions in quantitative terms, we constructed a mathematical model based on a mass-action representation of known reaction pathways. The model was trained against experimental data obtained by live-cell imaging, flow cytometry, and immunoblotting of cells perturbed by protein depletion and overexpression. The trained model accurately reproduces the behavior of normal and perturbed cells exposed to TRAIL, making it possible to study switching mechanisms in detail. Model analysis shows, and experiments confirm, that the duration of the delay prior to effector caspase activation is determined by initiator caspase-8 activity and the rates of other reactions lying immediately downstream of the TRAIL receptor. Sudden activation of effector caspases is achieved downstream by reactions involved in permeabilization of the mitochondrial membrane and relocalization of proteins such as Smac. We find that the pattern of interactions among Bcl-2 family members, the partitioning of Smac from its binding partner XIAP, and the mechanics of pore assembly are all critical for snap-action control.
Integrated Codesign of Printable Robots (2015)

This work presents a system by which users can easily create printable origami-inspired robots from high-level structural specifications. Starting from a library of basic mechanical, electrical, and software building blocks, users can hierarchically assemble integrated electromechanical components and programmed mechanisms. The system compiles those designs to cogenerate complete fabricable outputs: mechanical drawings suitable for direct manufacture, wiring instructions for electronic devices, and firmware and user interface (UI) software to control the final robot autonomously or from human input. This process allows everyday users to create on-demand custom printable robots for personal use, without the requisite engineering background, design tools, and cycle time typical of the process today. This paper describes the system and its use, demonstrating its abilities and versatility through the design of several disparate robots.
Atomic recovery units: failure atomicity for logical disks (2002)

Atomic recovery units (ARUs) are a mechanism that allows several logical disk operations to be executed as a single atomic unit with respect to failures. For example, ARUs can be used during file creation to update several pieces of file meta-data atomically. ARUs simplify systems, as they isolate issues of atomicity within the logical disk system, ARUs are designed as part of the Logical Disk (LD), which provides an interface to disk storage that separates file and disk management by using logical block numbers and block lists. This paper discusses the semantics of concurrent ARUs, as well as the concurrency control they require. A prototype implementation in a log-structured logical disk system is presented and evaluated. The performance evaluation shows that the run-time overhead to support concurrent ARUs is negligible for Read and Write operations, and small but pronounced for file creation (4.0%-7.2%) and deletion (17.9%-20.5%) which mainly manipulate meta-data. The low overhead (when averaged over file creation, writing, reading, and deletion) for concurrent ARUs shows that issues of atomicity can be successfully isolated within the disk system.
Deep learning with coherent nanophotonic circuits (2017)

Artificial Neural Networks have dramatically improved performance for many machine learning tasks. We demonstrate a new architecture for a fully optical neural network that enables a computational speed enhancement of at least two orders of magnitude and three orders of magnitude in power efficiency over state-of-the-art electronics.
Radioligand Therapy of Prostate Cancer with a Long-Lasting Prostate-Specific Membrane Antigen Targeting Agent 90Y-DOTA-EB-MCG (2018)

Several radioligands targeting prostate-specific membrane antigen (PSMA) have been clinically introduced as a new class of radiotheranostics for the treatment of prostate cancer. Among them, ((( R)-1-carboxy-2-mcercaptoethyl)carbamoyl)-l-glutamic acid (MCG) has been successfully labeled with radioisotopes for prostate cancer imaging. The aim of this study is to conjugate MCG with an albumin binding moiety to further improve the in vivo pharmacokinetics. MCG was conjugated with an Evans blue (EB) derivative for albumin binding and a DOTA chelator. PSMA positive (PC3-PIP) and PSMA negative (PC3) cells were used for both in vitro and in vivo studies. Longitudinal PET imaging was performed at 1, 4, 24, and 48 h post-injection to evaluate the biodistribution and tumor uptake of <sup>86</sup>Y-DOTA-EB-MCG. DOTA-EB-MCG was also labeled with <sup>90</sup>Y for radionuclide therapy. Besides tumor growth measurement, tumor response to escalating therapeutic doses were also evaluated by immunohistochemistry and fluorescence microscopy. Based on quantification from <sup>86</sup>Y-DOTA-EB-MCG PET images, the tracer uptake in PC3-PIP tumors increased from 22.33 ± 2.39%ID/g at 1 h post-injection (p.i.), to the peak of 40.40 ± 4.79%ID/g at 24 h p.i. Administration of 7.4 MBq of <sup>90</sup>Y-DOTA-EB-MCG resulted in significant regression of tumor growth in PSMA positive xenografts. No apparent toxicity or body weight loss was observed in all treated mice. Modification of MCG with an Evans blue derivative resulted in a highly efficient prostate cancer targeting agent (EB-MCG), which showed great potential in prostate cancer treatment after being labeled with therapeutic radioisotopes.
A Side Order of Stem Cells: The SP Phenotype (2006)

A defining property of murine hematopoietic stem cells (HSCs) is low fluorescence after staining with Hoechst 33342 and Rhodamine 123. These dyes have proven to be remarkably powerful tools in the purification and characterization of HSCs when used alone or in combination with antibodies directed against stem cell epitopes. Hoechst low cells are described as side population (SP) cells by virtue of their typical profiles in Hoechst red versus Hoechst blue bivariate fluorescent-activated cell sorting dot plots. Recently, excitement has been generated by the findings that putative stem cells from solid tissues may also possess this SP phenotype. SP cells have now been isolated from a wide variety of mammalian tissues based on this same dye efflux phenomenon, and in many cases this cell population has been shown to contain apparently multipotent stem cells. What is yet to be clearly addressed is whether cell fusion accounts for this perceived SP multipotency. Indeed, if low fluorescence after Hoechst staining is a phenotype shared by hematopoietic and organ-specific stem cells, do all resident tissue SP cells have bone marrow origins or might the SP phenotype be a property common to all stem cells? Subject to further analysis, the SP phenotype may prove invaluable for the initial isolation of resident tissue stem cells in the absence of definitive cell-surface markers and may have broad-ranging applications in stem cell biology, from the purification of novel stem cell populations to the development of autologous stem cell therapies.
Some uses of the head shake (2002)

A context-of-use study is reported of the ‘head shake’. A large number of examples are described and compared, drawn from video recordings of naturally occasioned interactions in the circumstances of everyday life, made in Campania, Italy, central England and the Eastern United States. Eight different kinds of uses for the head shake are illustrated. It is concluded that the head shake is not to be understood simply as the kinesic equivalent of a unit of verbal expression. It appears as an expression in its own right which, furthermore, the speaker uses as a component in the construction of an utterance which, it seems, is so often a multimodal construction in which the different modalities of expression available are deployed by the speaker in the course of building a unit of expression according to the rhetorical needs of the interactive moment.
GC/MS and EMIT Analyses for Δ9-Tetrahydrocannabinol Metabolites in Plasma and Urine of Human Subjects* (1986)

Ten male subjects smoked placebo marijuana cigarettes spiked with delta 9-tetrahydrocannabinol (THC) at 150 micrograms/kg body weight. Plasma and urine samples were collected for 22 hr after smoking. Total cross-reacting cannabinoids were measured by immunoassay (EMIT) and THC and major metabolites were identified and quantitated by gas chromatographic/mass spectrometric (GC/MS) procedures. In plasma, THC concentration provided the best indication of recent (less than 6 hr) smoking. In enzyme-hydrolyzed urine, 8 beta, 11-dihydroxy-THC at high concentration was identified in the earliest voidings, falling rapidly to the limit of detection before 22 hr in most subjects. Levels above 15 to 20 ng/mL were indicative of use within the previous 4 to 6 hr.
Effects of cytochaslasin B and colcemide on myogenic cultures. (1975)

Muscle cultures treated with cytochalasin B yield mono- and oligonucleated cells of two kinds: (i) arborized, replicating precursor myogenic cells and fibroblasts; and (ii) round, post-mitotic, terminally differentiating myoblasts and myotubes. The arborized cells do not bind fluorescein-labeled antibody against myosin, do not contract rhythmically, and do not display hexagonally stacked thick and thin filaments. The round, mono-nucleated myoblasts and round, oligonucleated myotubes bind the fluorescein-labeled antibody against myosin, contract rhythmically, and display clusters of hexagonally-stacked thick and thin filaments. When cytochalasin B is removed and replaced by colcemide, the arborized cells, but not the post-mitotic muscle cells, acquire a radial symmetry and are induced to assemble massive, meandering cables that may occupy over 25% of the cell volume. These tortuous calbes are positively birefringent and consist exclusively of enormous numbers of 100-A, intermediate-sized filaments.
Structure and Function of Plant Photoreceptors (2010)

Signaling photoreceptors use the information contained in the absorption of a photon to modulate biological activity in plants and a wide range of organisms. The fundamental-and as yet imperfectly answered-question is, how is this achieved at the molecular level? We adopt the perspective of biophysicists interested in light-dependent signal transduction in nature and the three-dimensional structures that underpin signaling. Six classes of photoreceptors are known: light-oxygen-voltage (LOV) sensors, xanthopsins, phytochromes, blue-light sensors using flavin adenine dinucleotide (BLUF), cryptochromes, and rhodopsins. All are water-soluble proteins except rhodopsins, which are integral membrane proteins; all are based on a modular architecture except cryptochromes and rhodopsins; and each displays a distinct, light-dependent chemical process based on the photochemistry of their nonprotein chromophore, such as isomerization about a double bond (xanthopsins, phytochromes, and rhodopsins), formation or rupture of a covalent bond (LOV sensors), or electron transfer (BLUF sensors and cryptochromes).
Quantum theory of chiral interactions in cholesteric liquid crystals (1999)

The effective chiral interaction between molecules arising from long-range quantum interactions between fluctuating charge moments is analyzed in terms of a simple model of chiral molecules. This model is based on the approximations that (a) the dominant excited states of a molecule form a band whose width is small compared to the average energy of excitation above the ground state and (b) biaxial orientational correlation between adjacent molecules can be neglected. Previous treatments of quantum chiral interactions have been based on a multipole expansion of the effective interaction energy within second-order perturbation theory. We consider a system consisting of elongated molecules and, although we invoke the expansion in terms of coordinates transverse to the long axis of constituent molecules, we treat the longitudinal coordinate exactly. Such an approximation is plausible for molecules in real liquid crystals. The macroscopic cholesteric wave vector Q (Q=2 pi/P, where P is the pitch) is obtained via Q=h/K(2), where K2 is the Frank elastic constant for twist and h is the torque field which we calculate from the effective chiral interaction kappa(IJ)a(I)xa(J) x R(IJ), where the unit vector a(I) specifies the orientation of molecule I and R(IJ) is the displacement of molecule I relative to molecule J. We identify two distinct physical limits depending on whether one or both of the interacting molecules are excited in the virtual state. When both molecules are excited, we regain the R(-8)(IJ) dependence of kappa(IJ) on intermolecular separation found previously by Van der Meer et al. [J. Chem. Phys. 65, 3935 (1976)]. The two-molecule, unlike the one-molecule term, can be interpreted in terms of a superposition of pairwise interactions between individual atoms (or local chiral centers) on the two molecules. Contributions to kappa(IJ) when one molecule is excited in the virtual state are of order R(-7)(IJ) for helical molecules which are assumed not to have a global dipole moment, but whose atoms possess a dipole moment. It is shown that for a helical molecule Q can have either the same or the opposite sign as the chiral pitch of an individual molecule, depending on the details of the anisotropy of the atomic polarizability. The one-molecule mechanism can become important when the local atomic dipoles become sizable, although biaxial correlations (ignored here) should then be taken into account. Our results suggest how the architecture of molecular dipole moments might be adjusted to significantly influence the macroscopic pitch.
Soluble Tie2 and Flt1 extracellular domains in serum of patients with renal cancer and response to antiangiogenic therapy. (2001)

Antiangiogenesis drugs can be difficult to evaluate because they produce disease stabilization rather than tumor regression. Markers of endothelial mass in tumors may be of value to monitor therapy and evaluate such drugs. Soluble domains of the endothelial receptor tyrosine kinases, sTie2 (angiopoietin receptor) and sFlt1 (vascular endothelial growth factor receptor-1) were analyzed by sandwich ELISA in serum samples from 43 patients with advanced renal cancer before and 1 month after antiangiogenic therapy with razoxane. Pretreatment sFlt1 levels were 0.77 ng/ml +/- 0.48 (SD) and sTie2 74.3 ng/ml +/- 15 (SD). Pretreatment sFlt1 levels above the median were associated with a lesser chance of stable disease (P = 0.04) and poorer survival (P = 0.01). Fall of sTie2 on treatment was associated with stable disease (P = 0.05) and improved survival (P = 0.04). The soluble receptors measured weeks before response were assessed and correlated with response and survival, showing they may be useful to monitor and develop antiangiogenic therapy.
In vitro evaluation of the role of the Duffy blood group in erythrocyte invasion by Plasmodium vivax. (1989)

A short-term in vitro culture system that allows for significant re-invasion of target erythrocytes by Plasmodium vivax was used to study the role of the Duffy blood group antigen as a ligand for merozoite invasion by this human malaria species. Using human Duffy-positive and -negative erythrocytes, various primate erythrocytes, enzymatic modification of erythrocytes, and mAb that defines a new Duffy determinant (Fy6) we conclude that the erythrocyte glycoprotein carrying Duffy determinants is required as a ligand for the invasion of human erythrocytes by P. vivax merozoites. Blockade of invasion by Fab fragments of the anti-Fy6 mAb equal to that of the intact molecule and the correlation of P. vivax susceptibility with the presence of the Fy6 determinant suggests this epitope or a nearby domain may be an active site on the Duffy glycoprotein. However, as for P. knowlesi, there is evidence that an alternate pathway for P. vivax invasion of simian erythrocytes may exist.
How Injector, Engine, and Fuel variables Impact Smoke and Hydrocarbon Emissions with Port Fuel Injection (1989)

&lt;div class="htmlview paragraph"&gt;Statistically designed experiments with a port fuel injected, single-cylinder engine were run to determine the effects of injector-, engine-, and fuel-related variables on exhaust smoke and hydrocarbon (HC) emissions. Among injector-related variables, targeting the fuel spray at the inlet valve centerline toward the valve head resulted in low smoke and HC emissions. These factors apparently help break up the fuel spray and they help subsequent vaporization of the fuel droplets.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Among engine-related variables, high coolant temperatures and lean mixtures resulted in less smoke and HC emissions, probably because of better fuel vaporization.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Gasolines with aromaticity and 90% point close to the maximum of the ranges of commercial gasolines significantly increased HC and smoke emissions compared with gasolines representing the average or minimum values, of these ranges.&lt;/div&gt;