gebhart/patrepeval huggingface dataset:
Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean (2015)

Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses.
Towards the Targeted Modulation of Gene Expression by Modified Triplex-Forming Oligonucleotides (2008)

DNA triple helices are formed when a third nucleic acid strand binds within the major groove of a DNA duplex. The formation of these structures can be used to achieve selective recognition of extended DNA sequences, which may be useful in several medical and biotechnological applications. Although triplex formation is relatively straightforward in vitro, there are several problems that limit its use in cellular contexts, including a low stability at physiological pH and a requirement for oligopurine.oligopyrimidine target sites. There are also concerns about the uptake, localisation and degradation of triplex-forming oligonucleotides (TFOs) in cells, as well as the accessibility of chromosomal DNA. Major advances in the chemistry of DNA triplex formation have been made in the last few years and this review highlights the current status of this approach, with an emphasis on the use of chemically modified TFOs for gene targeting.
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes (2017)

The significance of islet Ag-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects is unclear, partly because similar cells are also found in healthy control (HC) subjects. We hypothesized that key disease-associated cells would show evidence of prior Ag exposure, inferred from expanded TCR clonotypes, and essential phenotypic properties in their transcriptomes. To test this, we developed single-cell RNA sequencing procedures for identifying TCR clonotypes and transcript phenotypes in individual T cells. We applied these procedures to analysis of islet Ag-reactive CD4<sup>+</sup> memory T cells from the blood of T1D and HC individuals after activation with pooled immunodominant islet peptides. We found extensive TCR clonotype sharing in Ag-activated cells, especially from individual T1D subjects, consistent with in vivo T cell expansion during disease progression. The expanded clonotype from one T1D subject was detected at repeat visits spanning >15 mo, demonstrating clonotype stability. Notably, we found no clonotype sharing between subjects, indicating a predominance of "private" TCR specificities. Expanded clones from two T1D subjects recognized distinct IGRP peptides, implicating this molecule as a trigger for CD4<sup>+</sup> T cell expansion. Although overall transcript profiles of cells from HC and T1D subjects were similar, profiles from the most expanded clones were distinctive. Our findings demonstrate that islet Ag-reactive CD4<sup>+</sup> memory T cells with unique Ag specificities and phenotypes are expanded during disease progression and can be detected by single-cell analysis of peripheral blood.
Are we getting enough sulfur in our diet? (2007)

Sulfur, after calcium and phosphorus, is the most abundant mineral element found in our body. It is available to us in our diets, derived almost exclusively from proteins, and yet only 2 of the 20 amino acids normally present in proteins contains sulfur. One of these amino acids, methionine, cannot be synthesized by our bodies and therefore has to be supplied by the diet. Cysteine, another sulfur containing amino acid, and a large number of key metabolic intermediates essential for life, are synthesized by us, but the process requires a steady supply of sulfur.Proteins contain between 3 and 6% of sulfur amino acids. A very small percentage of sulfur comes in the form of inorganic sulfates and other forms of organic sulfur present in foods such as garlic, onion, broccoli, etc.The minimal requirements (RDA) for all the essential amino acids have always been estimated in terms of their ability to maintain a nitrogen balance. This method asses amino acid requirements for protein synthesis, only one of the pathways that methionine follows after ingestion. To adequately evaluate the RDA for methionine, one should perform, together with a nitrogen balance a sulfur balance, something never done, neither in humans nor animals.With this in mind we decided to evaluate the dietary intake of sulfur (as sulfur amino acids) in a random population and perform sulfur balance studies in a limited number of human volunteers. Initially this was done to try and gain some information on the possible mode of action of a variety of sulfur containing compounds (chondroitin sulfate, glucosamine sulfate, and others, ) used as dietary supplements to treat diseases of the joints. Out of this study came information that suggested that a significant proportion of the population that included disproportionally the aged, may not be receiving sufficient sulfur and that these dietary supplements, were very likely exhibiting their pharmacological actions by supplying inorganic sulfur.
Treatment with Monoclonal Antibodies against <i>Clostridium difficile</i> Toxins (2010)

The addition of monoclonal antibodies against C. difficile toxins to antibiotic agents significantly reduced the recurrence of C. difficile infection. (ClinicalTrials.gov number, NCT00350298.)
Microfluidic chip for plasma separation from undiluted human whole blood samples using low voltage contactless dielectrophoresis and capillary force (2014)

A plasma separating biochip is demonstrated using a capillary-driven contactless dielectrophoresis method with low voltage (~1 V) and high frequency induced electrostatics between red blood cells. The polarized red blood cells were aggregated and separated from plasma with a 69.8% volume separation and an 89.4% removal rate of red blood cells.
Interpreting a 3D object from a rough 2D line drawing (2002)

Visualizing the third dimension while designing three-dimensional (3-D) objects is an awkward process in mechanical computer-aided-design (CAD) systems, given the current state of the art. The authors describe a computer system that automatically constructs the shape of a 3-D object from a single 2-D sketch. The method makes it convenient to create and manipulate 3-D objects, and is thus seen as an intelligent user interface for CAD and 3-D graphics applications. The proposed technique is built on well-known results in image analysis. These results are applied in conjunction with some perceptual rules to determine 3-D structure from a rough line drawing. The principles are illustrated by a computer implementation that works in a nontrivial object domain.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Geometry of power flows in tree networks (2012)

We investigate the problem of power flow and its relationship to optimization in tree networks. We show that due to the tree topology of the network, the general optimal power flow problem simplifies greatly. Our approach is to look at the injection region of the power network. The injection region is simply the set of all vectors of bus power injections that satisfy the network and operation constraints. The geometrical object of interest is the set of Pareto-optimal points of the injection region, since they are the solutions to the minimization of increasing functions. We view the injection region as a linear transformation of the higher dimensional power flow region, which is the set of all feasible power flows, one for each direction of each line. We show that if the voltage magnitudes are fixed, then the injection region becomes a product of two-bus power flow regions, one for each line in the network. Using this decomposition, we show that under the practical condition that the angle difference across each line is not too large, the set of Pareto-optimal points of the injection region remains unchanged by taking the convex hull. Therefore, the optimal power flow problem can be convexified and efficiently solved. This result improves upon earlier works since it does not make any assumptions about the active bus power constraints. We also obtain some partial results for the variable voltage magnitude case.
Structure-Activity Relationships of Saponins from<i>Gleditsia sinensis</i>in Cytotoxicity and Induction of Apoptosis<i /> (2004)

Thirteen compounds were isolated from the anomalous fruits of Gleditsia sinensis on the basis of bioassay-guided fractionation. These saponins together with six analogues or related compounds were tested for their cytotoxicities against six tumor cell lines by the MTT method. The induction of apoptosis in HL-60 cells by these compounds was determined through flow cytometric analysis. Some structure-activity relationships in cytotoxicity and induction of apoptosis were identified. The evaluation of the cytotoxicity and the ability to induce apoptosis revealed that some important structural features are required for activity. A valuable model which enables prediction of their activities was established and may be employed for the drug design of new Gleditsia saponin analogues.
Increased Oxidative Damage Is Correlated to Altered Mitochondrial Function in Heterozygous Manganese Superoxide Dismutase Knockout Mice (1998)

This study characterizes mitochondria isolated from livers of Sod2(-/+) and Sod2(+/+) mice. A 50% decrease in manganese superoxide dismutase (MnSOD) activity was observed in mitochondria isolated from Sod2(-/+) mice compared with Sod2(+/+) mice, with no change in the activities of either glutathione peroxidase or copper/zinc superoxide dismutase. However, the level of total glutathione was 30% less in liver mitochondria of the Sod2(-/+) mice. The reduction in MnSOD activity in Sod2(-/+) mice was correlated to an increase in oxidative damage to mitochondria: decreased activities of the Fe-S proteins (aconitase and NADH oxidoreductase), increased carbonyl groups in proteins, and increased levels of 8-hydroxydeoxyguanosine in mitochondrial DNA. In contrast, there were no significant changes in oxidative damage in the cytosolic proteins or nuclear DNA. The increase in oxidative damage in mitochondria was correlated to altered mitochondrial function. A significant decrease in the respiratory control ratio was observed in mitochondria isolated from Sod2(-/+) mice compared with Sod2(+/+) mice for substrates metabolized by complexes I, II, and III. In addition, mitochondria isolated from Sod2(-/+) mice showed an increased rate of induction of the permeability transition. Therefore, this study provides direct evidence correlating reduced MnSOD activity in vivo to increased oxidative damage in mitochondria and alterations in mitochondrial function.
Characterization of the Bovine Tenascin-X (1997)

The primary structure of flexilin, an extracellular matrix glycoprotein previously identified in bovine tissues (Lethias, C., Descollonges, Y., Boutillon, M.-M., and Garrone, R. (1996) Matrix Biol. 15, 11-19) was determined by cDNA cloning. The deduced amino acid sequence (4135 residues) reveals that this protein is composed of a succession of peptide motifs characteristic of the tenascin family: an amino-terminal domain containing cysteine residues and heptads of hydrophobic amino acids, 18.5 epidermal growth factor-like repeats, 30 fibronectin type III-like (FNIII) domains, and a carboxyl-terminal fibrinogen-like motif. Sequence analysis indicated that this protein is the bovine orthologue of human tenascin-X. By rotary shadowing, bovine tenascin-X was identified as monomers with a flexible aspect, which are ended by a globule. More FNIII motifs were characterized in the bovine protein than in human tenascin-X. The main difference between the human and bovine tenascin-X is found in the arrangement of the three classes of highly similar FNIII repeat types in the central region of tenascin-X. The bovine FNIII motif b10 exhibits an RGD putative cell attachment site. The functional role of this sequence is corroborated by cell adhesion on purified tenascin-X, which is inhibited by RGD peptides. Moreover, we demonstrate that this RGD site is conserved at the same location in the human molecule.
A non-linear gray-level appearance model improves active shape model segmentation (2002)

Active Shape Models (ASMs), a knowledge-based segmentation algorithm developed by Cootes and Taylor [1995, 1999], have become a standard and popular method for detecting structures in medical images. In ASMs-and various comparable approaches-the model of the object's shape and of its gray-level variations is based the assumption of linear distributions. In this work, we explore a new way to model the gray-level appearance of the objects, using a k-nearest-neighbors (kNN) classifier and a set of selected features for each location and resolution of the Active Shape Model. The construction of the kNN classifier and the selection of features from training images is fully automatic. We compare our approach with the standard ASMs on synthetic data and in four medical segmentation tasks. In all cases, the new method produces significantly better results (p<0.001).
A wireless packet multiple access method exploiting joint detection (2004)

A new packet-based, multiple access scheme for connectionless, uncoordinated random access is proposed using code-division multiple access (CDMA) as the typical access method. The new method uses a novel packet format with a common header with identical spreading codes for the data portion. The receiver operates in two stages: header detection using a conventional spread spectrum receiver and data detection using a multiuser detector to allow for decoding of overlapping active packets. The headers are spread with a large enough processing gain to allow detection even in severe interference. It is shown that this system is detector capability limited and that it can significantly outperform conventional ALOHA systems whose performance is limited by the collision mechanism. This system also experiences a much smaller packet retransmission rate and better spectral efficiency than conventional or spread ALOHA.
Qualitative Properties of Steady-State Poisson--Nernst--Planck Systems: Perturbation and Simulation Study (1997)

Poisson--Nernst--Planck (PNP) systems are considered in the case of vanishing permanent charge. A detailed case study, based on natural categories described by system boundary conditions and flux, is carried out via simulation and singular perturbation analysis. Our results confirm the rich structure inherent in these systems. A natural quantity, the quotient of the Debye and characteristic length scales, serves as the singular perturbation parameter. The regions of validity are carefully analyzed by critical comparisons and contrasts between the simulation and the perturbation solution, which can be represented in closed form.
The physics of electronic semiconductors (1947)

The band theory of solids is capable of explaining such fundamental properties of electronic semiconductors as the dependency of specific resistance on impurity content, the negative temperature coefficient of resistance, the sign of the Hall and thermoelectric effects, and the direction of rectification. Measurements of the specific resistance and the Hall constant enable the calculation of density, mobility, and mean free path of the electric carriers as a function of temperature and impurity.
Positioning System using Dynamic Location-convergence Adjustment Factor for Wireless LAN Infrastructures (2006)

Location positioning of an object is essential technology for Location-Based Services (LBS). Most location positioning systems use specially designed equipment. Because distribution of this specialized equipment is costly, many studies have been conducted on location positioning using only wireless equipment under a wireless LAN infrastructure. A cooperative location positioning system (CLPS) that uses the RSSI (Received Signal Strength Indicator) between mobile equipment, including mobile equipment and access points, requires great concentration in their applications to increase accuracy. This study investigates the relationship between nodes by analyzing a WiPS (Wireless LAN based indoor Positioning System), a similar type of CLPS, and proposes a improved cooperative positioning system to increase performance.
A Structure-Preserving Model and Sufficient Condition for Frequency Synchronization of Lossless Droop Inverter-Based AC Networks (2013)

This paper presents a new method for analysis of frequency synchronization of lossless power networks whose sources are frequency-droop controlled inverters. Unlike most existing approaches, our method focuses on the interaction between inverters and the network to provide new physical insight into how those interactions create frequency synchronization. We introduce two structure-preserving models of such a network (one bus-oriented and one line-oriented), and show that frequency synchronization corresponds to convergence to an equilibrium of these models. We derive a necessary condition for existence of such equilibria, and determine a simple test for their local stability. Finally, we introduce a sufficient condition for frequency synchronization of such networks, and show that it consists of a set of local criteria which can each be determined from local measurements.
Tentative anatomy of ZnS-type electroluminescence (1994)

The paper reviews the electrical and optical mechanisms at work in sulfide-based thin-film electroluminescence display devices within the framework of general semiconductor physics. The electrical problem is twofold: (i) charge carriers are sourced at high electric field in a nominally insulating material, the carrier density increasing by almost eight orders of magnitude; (ii) the carriers are transported at high field, with an average energy largely exceeding the thermal one. (i) Carrier sourcing is best understood from direct-current-driven ZnS films, and is ascribed to partly filled deep donors transferring electrons to the conduction band by Fowler–Nordheim tunneling. The deep donors also act as carrier sinkers, and evidence for space charge is afforded by small-signal impedance analysis disclosing a markedly inductive behavior. The conduction picture obtained from dc-driven films is then used to clarify the operation of alternating-current electroluminescence structures where the sulfide is sandwiched between two blocking oxide layers. The electrostatics of the ac structure is investigated in detail including space charge and field nonuniformity, and external observables are related to internal quantities. The simple model of interfacial carrier sourcing and sinking is examined. (ii) High-field electronic transport is controlled by the electron-phonon interaction, and the modeling resorts to numerical simulations or the lucky-drift concept. At low electron energies the interaction with phonons is predominantly polar, while at optical energies it proceeds via deformation potential scattering. In spite of the uncertainties in transport models in that range, it is likely that ∼50% of the electrons overtake 2 eV at the usual operating fields in ZnS. Light emission is associated with impurity luminescence centers embedded in the sulfide host. They are excited while current is flowing, and the ensuing relaxation is partly radiative. We describe the two ways in which an impurity may be excited electrically, namely, impact excitation (internal promotion of the center to a state of higher energy) or impact ionization (with an electron released to the host conduction band). The actual excitation mechanism depends on the position of the impurity excited level relative to the host energy bands. A calculation of the excitation yield (number of excited centers per transferred electron) is detailed in the case of impact excitation. Lastly, a phenomenological description of the various relaxation channels is given in terms of formal kinetics, and the relative importance of radiative relaxation is assessed by means of the deexcitation yield (fraction of centers decaying radiatively), which is defined in the case of the impulse response.