gebhart/patrepeval huggingface dataset:
Reducing biomass recalcitrance by heterologous expression of a bacterial peroxidase in tobacco (Nicotiana benthamiana) (2017)

Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and extracts from transgenic leaves showed higher activity on classic peroxidase substrates than the control. Intriguingly, in situ DypB activation and subsequent saccharification released nearly 200% more fermentable sugars from transgenic lines than controls, which were not explained by variation in initial structural and non-structural carbohydrates and lignin content. Pyrolysis-GC-MS analysis showed more reduction in the level of lignin associated pyrolysates in the transgenic lines than the control primarily when the enzyme is activated prior to pyrolysis, consistent with increased lignin degradation and improved saccharification. The findings reveal for the first time that accumulation and in situ activation of a peroxidase improves biomass digestibility.
Driving force for Sn whisker growth in the system Cu–Sn (2008)

The evolution of residual stress gradients in Sn thin films on Cu substrates upon aging at ambient temperature has been investigated, for specimens which do exhibit and which do not exhibit Sn whisker growth, by performing x-ray diffraction stress measurements at constant penetration depths. Comparison of the measured near-surface stress-depth profiles for both types of specimens, as function of aging time at ambient temperature, showed that a significant negative stress gradient from the surface toward the Sn∕Cu interface is decisive for Sn whisker growth in the system Cu–Sn.
Multipurpose Robot for Automated Cycle Sequencing (2003)

Paramagnetic beads have the superior advantages of easy separation and resuspension by controlling the magnetic filed. Previously, we have developed Magtration technology to automate paramagnetic bead handling and have built several automated instruments that handle 1-12 samples simultaneously. To achieve more high-throughput sample processing, two types of a 96-arrayed Integrated Magtration Unit (IMU) were developed, one installed with electromagnets and the other with thin rod-shaped magnets made of neodymium. A multipurpose robot (SX-96GC) equipped with the IMU was also developed for fully automatic processing of 96 samples in parallel. The cleanup of dye-terminator sequencing products was performed using the robot installed with the permanent magnet version of IMU. The results had quality comparable to those by the same protocol in manual handling or to those by the conventional protocols. The robot processed 96 samples in a microplate within 30 min. The protocol that can purify 384 samples within 1 h by processing two microplates concurrently was successfully designed.
Blizzard: a Distributed Consensus Protocol for Mobile Devices (2022)

We present Blizzard, a Byzantine Fault Tolerant (BFT) distributed ledger protocol that is aimed at making mobile devices first-class citizens in the consensus process. Blizzard introduces a novel two-tier architecture by having the mobile nodes communicate through online brokers, and includes a decentralized matching scheme to ensure each node connects to a certain number of random brokers. Through mathematical analysis, we derive a guaranteed safety region (i.e. the set of ratios of malicious nodes and malicious brokers for which the safety is assured) for the Blizzard protocol. Liveness is shown as well. We analyze the performance of Blizzard in terms of its throughput, latency and message complexity. Through experiments based on a software implementation, we show that Blizzard is capable of throughput on the order of several thousand transactions per second per shard, and sub-second confirmation latency.
A rationale for the development of a groundwater quality monitoring network for Scotland (2003)

Abstract An objective and representative groundwater quality monitoring network for Scotland that would be operated by the Scottish Environment Protection Agency (SEPA) was required to comply with EU Directives. The restricted spatial distribution of analytical data from existing abstractions and their potential bias limited their usefulness to give an objective assessment of the quality of all Scottish groundwaters. Therefore, an approach based on the risk of groundwater contamination was devised. A 39 class biophysical framework based on aquifer permeability, soil leaching potential and land use was developed. These classes encompass highly permeable, moderately permeable aquifers as well as largely superficial aquifers in weakly permeable bedrock. The classes were devised in such a manner that the groundwater resources within each have an equal risk of contamination no matter where they occurred. A number of existing abstractions were classified according to this framework and used as the basis for an objective sampling scheme which took account of land use pressures, groundwater usage and those groundwaters that contribute to summer base flows in rivers.
El papel de la Unión Europea en la gestión del conflicto armado en Colombia (2000-2010) (2016)

Con el estudio particular de la figura de los Laboratorios de Paz, creados como formula para acompanar los esfuerzos de la sociedad colombiana por resolver el conflicto armado que viene padeciendo desde hace mas de cincuenta anos, el presente articulo analiza el papel de la Union Europea en el ambito de la gestion de conflictos armados mas alla de sus fronteras. Asi, desde el examen de este caso concreto, a continuacion se ofrecera una aproximacion al enfoque, capacidad y nivel de involucramiento de este actor internacional como potencial acompanante en este tipo de procesos.
Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target (2016)

Multiple myeloma (MM) is a malignancy of the antibody-producing plasma cells. MM is a highly heterogeneous disease, which has hampered the identification of a common underlying mechanism for disease establishment as well as the development of targeted therapy. Here we present the first genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in MM patient samples, defining a common set of active H3K4me3-enriched genes and silent genes marked by H3K27me3 (H3K27me3 alone or bivalent) unique to primary MM cells, when compared to normal bone marrow plasma cells. Using this epigenome profile, we found increased silencing of H3K27me3 targets in MM patients at advanced stages of the disease, and the expression pattern of H3K27me3-marked genes correlated with poor patient survival. We also demonstrated that pharmacological inhibition of EZH2 had anti-myeloma effects in both MM cell lines and CD138+ MM patient cells. In addition, EZH2 inhibition decreased the global H3K27 methylation and induced apoptosis. Taken together, these data suggest an important role for the Polycomb repressive complex 2 (PRC2) in MM, and highlights the PRC2 component EZH2 as a potential therapeutic target in MM.
Renovación de la práctica arquitectónica desde los fundamentos de la teoría (2013)

Reseña del libro del Dr. Carlos Caballero Lizzeri. Arquitectura básica 2. Universidad Veracruzana.
Results with autonomous vehicles operating in specialty crops (2012)

Specialty crops constitute a $45 billion/year industry. As opposed to crops such as wheat, cotton, corn and soybean, they are characterized by the need for intensive cultivation. Specialty crops growers currently face serious labor cost and availability problems, and few technological solutions exist to increase their efficiency given the past history of abundant supply of low-cost labor. This leads to an opportunity to use recent technological advances to not only increase efficiency and reduce labor costs in specialty crops production but also to support a domestic engineering solutions industry for specialty crops. We envision a family of reconfigurable vehicles that can be rapidly tasked to automate or augment pruning, thinning, harvesting, mowing, spraying, etc. They would share a common sensing and computing infrastructure, allowing applications created for one to be easily transferable to others - much like software applications today are transferable from one computer to another. In this paper we describe our work over the last three years designing and deploying a family of such vehicles, the Autonomous Prime Movers (APMs). The five vehicles completed so far have traveled autonomously over 300 km in research and commercial tree fruit orchards; preliminary results in time trials conducted by extension educators indicate efficiency gains of up to 58%.
Estimation of Cell Membrane Permeability and Intracellular Diffusion Coefficient of Human Gray Matter (2009)

The signal intensity of diffusion-weighted imaging (DWI) is sensitive to the intra- and extracellular diffusion coefficient of water and cell membrane permeability. We applied a method we proposed in previous papers to estimate noninvasively the membrane permeability and intracellular diffusion coefficient of normal human brain (gray matter) in 3 normal volunteers. We theoretically compared predicted signals and experiment results using a 1.5-tesla magnetic resonance (MR) imaging system. We acquired images using an echo planar imaging (EPI) sequence, applying motion-probing gradient (MPG) pulses in 3 directions. We periodically performed numerical simulations for various combinations of membrane permeability and intracellular diffusion coefficients using the finite-difference method. By minimizing the difference between signals obtained experimentally and those from numerical simulation, we could estimate membrane permeability (76+/-9 mm2/s mum) and intracellular diffusion coefficient (1.0+/-0.0 mm2/s) for the human brain. The estimated membrane permeability was the criterion value for diagnosing disease in gray matter.
Informed home energy behavior : developing a tool for homeowners to monitor, plan and learn about energy conservation (2001)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Architecture, 2001.
Neural User Response Generator: Fake News Detection with Collective User Intelligence (2018)

Fake news on social media is a major challenge and studies have shown that fake news can propagate exponentially quickly in early stages. Therefore, we focus on early detection of fake news, and consider that only news article text is available at the time of detection, since additional information such as user responses and propagation patterns can be obtained only after the news spreads. However, we find historical user responses to previous articles are available and can be treated as soft semantic labels, that enrich the binary label of an article, by providing insights into why the article must be labeled as fake. We propose a novel Two-Level Convolutional Neural Network with User Response Generator (TCNN-URG) where TCNN captures semantic information from article text by representing it at the sentence and word level, and URG learns a generative model of user response to article text from historical user responses which it can use to generate responses to new articles in order to assist fake news detection. We conduct experiments on one available dataset and a larger dataset collected by ourselves. Experimental results show that TCNN-URG outperforms the baselines based on prior approaches that detect fake news from article text alone.
Enterprise model as a basis of administration on role-based access control (2002)

Access control is one of the important security issues for large enterprise organizations. The role-based access control (RBAC) model is well known and recognized as a good security model for the enterprise environment. Though RBAC is a good model, the administration of RBAC including building and maintaining access control information remains a difficult problem in large companies. The RBAC model itself does not tell the solution. Little research has been done on the practical ways of finding information that fills RBAC components such as role, role hierarchy, permission-role assignment, user-role assignment, and so on from the real world. We suggest model-based administration of RBAC in an enterprise environment. Model-based administration methods allow the security administrator to manage access control by a GUI that supports a graphical enterprise model. If the security administrator creates or changes some of the components of the graphical enterprise model, then it is translated to RBAC schema information by the administration tool. We focus on a practical way of deriving access control information from the real world. It is a core of model-based administration. We show the derivation method and implementation experiences.
Ykt6p, a Prenylated SNARE Essential for Endoplasmic Reticulum-Golgi Transport (1997)

Vesicular transport between secretory compartments requires specific recognition molecules called SNAREs. Here we report the identification of three putative SNAREs, p14 (Sft1p), p28 (Gos1p), and a detailed characterization of p26 (Ykt6p). All three were originally isolated as interacting partners of the cis Golgi target membrane-associated SNARE Sed5p, when Sec18p (yeast NSF) was inactivated. YKT6 is an essential gene that codes for a novel vesicle-associated SNARE functioning at the endoplasmic reticulum-Golgi transport step in the yeast secretory pathway. Depletion of Ykt6p results in the accumulation of the p1 precursor (endoplasmic reticulum form) of the vacuolar enzyme carboxypeptidase Y and morphological abnormalities consistent with a defect in secretion. Membrane localization of Ykt6p is essential for protein function and is normally mediated by isoprenylation. However, replacement of the isoprenylation motif with a bona fide transmembrane anchor results in a functional protein confirming that membrane localization, but not isoprenylation per se, is required for function. Ykt6p and its homologues are highly conserved from yeast to human as demonstrated by the functional complementation of the loss of Ykt6p by its human counterpart. This is the first example of a human SNARE protein functionally replacing a yeast SNARE. This observation implies that the specific details of the vesicle targeting code, like the genetic code, are conserved in evolution.
Sequence analysis of rat mitochondrial intermediate peptidase: similarity to zinc metallopeptidases and to a putative yeast homologue. (1992)

Proteolytic removal of amino-terminal octapeptides from mitochondrial intermediate proteins is a required step for a subgroup of nuclear-encoded mitochondrial precursors and is specifically catalyzed by mitochondrial intermediate peptidase (MIP). We recently reported the purification of MIP from rat liver and showed that the enzyme is a monomer of 75 kDa. We now report the sequence of a full-length rat MIP cDNA. This cDNA codes for a protein of 710 amino acids, including an amino-terminal mitochondrial leader peptide of 33 residues. The region surrounding the mature MIP amino terminus shows a cleavage site typically recognized by the general mitochondrial processing peptidase (MPP). In vitro synthesized MIP precursor is cleaved to mature MIP by purified MPP, and thus MIP is not required for its own proteolytic maturation. Comparison of the deduced MIP sequence with other sequences in the GenBank data base reveals two important similarities. The first is to a sequence encoding a putative MIP homologue in the recently reported sequence of yeast chromosome III. The putative yeast protein is predicted to be 712 amino acids long and includes a putative 23-residue mitochondrial leader peptide also with a MPP processing site. It shows 47% similarity and 24% identity to rat MIP. The second similarity is to members of a subfamily of metallopeptidases that includes rat metalloendopeptidase EC 3.4.24.15 and two bacterial proteases, oligopeptidase A and dipeptidyl carboxypeptidase. A region of greater than 50% similarity over 400 residues between MIP and these proteins is centered around the sequence motif HEXXH, typical of zinc metallopeptidases.
Structure of the Jab1/MPN Domain and Its Implications for Proteasome Function (2003)

The 26S proteasome is responsible for the degradation of polyubiquitinated proteins. During this process the polyubiquitin chain is removed. The identity of the proteasomal component that is responsible for this activity has not been clear, as it contains no subunits that resemble known deubiquitinating enzymes. The Jab1/MPN domain is a widespread 120 amino acid protein module found in archaea, bacteria, and eukaryotes. In eukaryotes the Jab1/MPN domain is found in subunits of several multiprotein complexes including the proteasome. Recently it has been proposed that the Jab1/MPN domain of the proteasomal subunit Rpn11 is responsible for the removal of the polyubiquitin chain from substrate proteins. Here we report the crystal structure and characterization of AF2198, a Jab1/MPN domain protein from Archaeoglobolus fulgidus. The structure reveals a fold that resembles that of cytidine deaminase and places the Jab1/MPN domain in a superfamily of metal dependent hydrolases.
Comparative Evaluation of Cultivars of Chrysanthemum morifolium Flowers by HPLC-DAD-ESI/MS Analysis and Antiallergic Assay (2012)

A multicomponent quantification fingerprint based on HPLC coupled with diode array detection and electrospray ionization tandem mass spectrometry (HPLC-DAD-ESI/MS) technique has been established for the analysis of phenolic compounds in 12 samples originated from 5 different cultivars of Chrysanthemum morifolium flowers in China. Four caffeoylquinic acids and 15 flavonoids in the capitulum were identified by comparing the retention times and ultraviolet spectra as well as the mass spectrum and/or matching the empirical molecular formula with that of reference compounds, and the contents of these compounds have been determined simultaneously. The samples from three medicinal cultivars significantly differed in the quality and quantity of flavonoid aglycones and glycosides compared with those from two edible cultivars, which allows the possibility of showing the chemical distinctness of these cultivars and may be useful in their standardization. Moreover, the antiallergic effects of these cultivars were comparatively assayed for the first time. A representative medicinal cultivar, 'huaiju', showed potential activity on the inhibition of antigen-induced degranulation from RBL-2H3 cells and compound 48/80-induced scratching in mice, whereas the in vitro and in vivo antiallergic activities of two edible cultivars were weak. The results suggested that the quality and quantity of some active flavonoid aglycones should be responsible for the pharmacological profiles of these cultivars.
Prevalence study of signs and symptoms of temporomandibular disorders in university students (2003)

The aim of this study was to evaluate the prevalence of signs and symptoms of temporomandibular disorders (TMD) in university students from 19 to 25 years old, male and female, through the distribution of frequency of the data obtained from a questionnaire and physical examination. The results showed that 68% of the subjects exhibited some degree of TMD, and the women were the most affected. Signs and symptoms such as articular sounds, pain to palpation of the masticatory, cervical and scapular girdle musculature, subjective sensation of emotional stress, and postural and occlusal changes were more evident in the group with TMD, although they were also present in subjects classified as TMD-free. Limitations in the mandibular movements were not found. The association of the obtained data allowed identifying a high prevalence of signs and symptoms of TMD in the Brazilian university population.
Enhancement of transdermal delivery by superfluous thermodynamic potential. I. Thermodynamic analysis of nifedipine transport across the lipoidal barrier. (1987)

In vitro techniques were used to test certain concepts regarding the enhancement of the transdermal delivery of nifedipine from topical vehicles. Tested vehicles include the volatile solvent acetone, nonvolatile solvents such as propylene glycol and isopropyl myristate, volatile/nonvolatile mixtures, and those mixtures with a polymer additive. An ethylene-vinyl acetate (EVA) copolymer membrane was used as the lipoidal barrier for the diffusing drug. Not merely the rate of transport per unit area, but the activity coefficient and the diffusion coefficient of the penetrating agent in the barrier were obtained. Despite the 10,000-fold difference in the vehicle concentration, water and several hydrophilic vehicles containing finely ground suspensions of the drug produced nearly the same rate of penetration. Some lipophilic solvents affected the barrier function of the EVA membrane to promote penetration of the drug. It has been found that the activity coefficient in the EVA membrane is very susceptible to wide variations by imbibition of such solvents. From volatile/nonvolatile mixtures, a transient enhancement in the transport of nifedipine across the membrane was observed. The increase in the flux was accounted for by the increase in the thermodynamic activity of the drug in the nonvolatile vehicle caused by the evaporation of the volatile component. The eventual decrease in penetration was the result of the drug precipitation from the supersaturated solution. The precipitation was inhibited and/or retarded during the entire time course of the experiments when a polymer additive was present. The steady-state fluxes from mixtures with a polymer additive were higher by about 3 to 5 times than that of the control experiment.
A robust adaptive control scheme for under-actuated non-linear systems (2018)

An adaptive control architecture for uncertain, under-actuated, non-linear systems is proposed. The proposed methodology is tested in simulation in order to control a planar double inverted pendulum apparatus. The approach can be extended and applied to similar systems such mobile robots and exoskeletal assisted devices. Closed loop results show good performance of the adaptive control methodology.
Performance of the Vesta parallel file system (2002)

Vesta is an experimental parallel file system implemented on the IBM SPI. Its main features are support for parallel access from multiple application processes to file, and the ability to partition and re-partition the file data among these processes. This paper reports on a set of experiments designed to evaluate Vesta's performance. This includes basic single-node performance, and performance using parallel access with different file partitioning schemes. Results are that bandwidth scales with the number of I/O nodes accessed, and that orthogonal partitioning schemes achieve essentially the same performance. In many cases performance equals the disk hardware limit. This is often attributed to prefetching and write-behind in the I/O nodes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>