gebhart/patrepeval huggingface dataset:
Effects of soluble aggregates of IgG on the binding, uptake and degradation of the Clq subcomponent of complement by adherent guinea pig peritoneal macrophages (1985)

Earlier studies have indicated that C1q, the first subcomponent of complement component C1, is bound to lymphocytes via specific C1q receptor sites. We have recently shown that adherent guinea pig peritoneal exudate macrophages express specific receptors for C1q (Veerhuis, R. et al., Immunology 1985. 54: 801). The present studies were performed to determine whether binding of 125I-labeled human C1q (125I-C1qhu) to adherent guinea pig peritoneal exudate macrophages would also result in ingestion and subsequent degradation of 125I-C1qhu. The binding of 125I-C1qhu to adherent peritoneal macrophages at 4 degrees C is inhibited fully not only by C1qhu and guinea pig C1q (C1qgp) but also by pepsin fragments of C1qhu. The amount of trichloroacetic acid nonprecipitable radioactivity that appeared in the supernatant was used as a measure for the degradation of 125I-C1qhu. 125I-C1qhu is degraded initially into fragments of 25 kDa, after which it is degraded further into small molecular weight peptides. Ingestion of 125I-C1q by the macrophages occurs before the 125I-C1q is degraded. In the presence of limited amounts of soluble aggregates of guinea pig IgG2 (AIgG), a known activator of C1, part of the C1q is bound to the AIgG and all of the AIgG in turn is bound to the cellular Fc receptors leading to an enhanced binding of 125I-C1q to the cells, a binding that was maximal at near equimolar concentrations of 125I-C1qhu and 131I-AIgG. In the presence of a 30-fold excess of AIgG, however, only a small percentage of the AIgG binds to cellular Fc receptors and the interaction of C1q with its receptor is decreased due to competitive inhibition. The results presented in this report thus suggest that free C1q may be eliminated by specific interaction with C1q receptors present on circulating and tissue phagocytoses and, in addition, that in the presence of immune complexes modulation of elimination of C1q may be encountered.
Ionic Silicon Protects Oxidative Damage and Promotes Skeletal Muscle Cell Regeneration (2021)

Volumetric muscle loss injuries overwhelm the endogenous regenerative capacity of skeletal muscle, and the associated oxidative damage can delay regeneration and prolong recovery. This study aimed to investigate the effect of silicon-ions on C2C12 skeletal muscle cells under normal and excessive oxidative stress conditions to gain insights into its role on myogenesis during the early stages of muscle regeneration. In vitro studies indicated that 0.1 mM Si-ions into cell culture media significantly increased cell viability, proliferation, migration, and myotube formation compared to control. Additionally, MyoG, MyoD, Neurturin, and GABA expression were significantly increased with addition of 0.1, 0.5, and 1.0 mM of Si-ion for 1 and 5 days of C2C12 myoblast differentiation. Furthermore, 0.1-2.0 mM Si-ions attenuated the toxic effects of H<sub>2</sub>O<sub>2</sub> within 24 h resulting in increased cell viability and differentiation. Addition of 1.0 mM of Si-ions significantly aid cell recovery and protected from the toxic effect of 0.4 mM H<sub>2</sub>O<sub>2</sub> on cell migration. These results suggest that ionic silicon may have a potential effect in unfavorable situations where reactive oxygen species is predominant affecting cell viability, proliferation, migration, and differentiation. Furthermore, this study provides a guide for designing Si-containing biomaterials with desirable Si-ion release for skeletal muscle regeneration.
Distance is not everything in imaging genomics of functional networks: reply to a commentary on <i>Correlated gene expression supports synchronous activity in brain networks</i> (2017)

Abstract Our 2015 paper (Richiardi et al., 2015), showed that transcriptional similarity of gene expression level is higher than expected by chance within functional brain networks (defined by functional magnetic resonance imaging), a relationship that is driven by around 140 genes. These results were replicated in vivo in adolescents, where we showed that SNPs of these genes where associated above chance with in-vivo fMRI connectivity, and in the mouse, where mouse orthologs of our genes showed above-chance association with meso-scale axonal connectivity. This paper has received a commentary on biorXiv (Pantazatos and Li, 2016), making several claims about our results and methods, mainly pointing out that Euclidean distance explains our results (“…high within-network SF is entirely attributable to proximity and is unrelated to functional brain networks…”). Here we address these claims and their weaknesses, and show that our original results stand, contrary to the claims made in the commentary.
Ocular Pathology in the Minimally Depigmented Subline of the Vitiliginous Smyth Chicken (1988)

Choroidal melanocytes and the retinal pigmented epithelium (RPE) were studied morphologically and histochemically in the Smyth chicken, an avian model for human vitiligo. The sequence of cytological events occurring in the ocular tissue of minimally depigmented Smyth birds was determined. Abnormalities of melanocytes and the associated inflammation was least severe in peripheral areas of the choroid and most pronounced in the back of the eye at the base of the optic nerve head. In the peripheral choroid, morphologically normal melanocytes and an occasional mononuclear leukocyte were observed. However, some of these morphologically normal melanocytes histochemically demonstrated atypical tyrosinase activity at the trans area of the Golgi apparatus. Toward the back of the eye, the melanocytes first appeared swollen and had retracting dendrites. Ultrastructurally these melanocytes demonstrated an increase in extramelanosomal cytoplasm. Later, melanocytes became spherical and had membrane bound, autophagosome-like compartments of pigment granules. As the melanocyte injury progressed, macrophages invaded the tissue and phagocytized melanocytic dendrites. These were followed by numerous plasma cells. Eventually, the back of the eye contained no pigment and was infiltrated with numerous mononuclear inflammatory cells. The retinal pigment epithelium also demonstrated a gradient in the degree of destruction, related to its topography. These cytological features consisted of the retraction of apical RPE processes, the disappearance of the basal plasma membrane infoldings, and the replacement of Bruch's membrane by collagen-like fibrils. These results demonstrate that the uveitis which develops in vitiligo appears to be a consequence of an inherent choroidal melanocyte defect.
Load Rather Than Length Sensitive Feedback Contributes to Soleus Muscle Activity During Human Treadmill Walking (2010)

Walking requires a constant adaptation of locomotor output from sensory afferent feedback mechanisms to ensure efficient and stable gait. We investigated the nature of the sensory afferent feedback contribution to the soleus motoneuronal drive and to the corrective stretch reflex by manipulating body load and ankle joint angle. The volunteers walked on a treadmill ( approximately 3.6 km/h) connected to a body weight support (BWS) system. To manipulate the load sensitive afferents the level of BWS was switched between 5 and 30% of body weight. The effect of transient changes in BWS on the soleus stretch reflex was measured by presenting dorsiflexion perturbations ( approximately 5 degrees, 360-400 degrees/s) in mid and late stances. Short (SLRs) and medium latency reflexes (MLRs) were quantified in a 15 ms analysis window. The MLR decreased with decreased loading (P = 0.045), but no significant difference was observed for the SLR (P = 0.13). Similarly, the effect of the BWS was measured on the unload response, i.e., the depression in soleus activity following a plantar-flexion perturbation ( approximately 5.6 degrees, 203-247 degrees/s), quantified over a 50 ms analysis window. The unload response decreased with decreased load (P > 0.001), but was not significantly affected (P = 0.45) by tizanidine induced depression of the MLR (P = 0.039, n = 6). Since tizanidine is believed to depress the group II afferent pathway, these results are consistent with the idea that force-related afferent feedback contributes both to the background locomotor activity and to the medium latency stretch reflex. In contrast, length-related afferent feedback may contribute to only the medium latency stretch reflex.
Binary de Bruijn interconnection network for a flexible LDPC/turbo decoder (2008)

This paper proposes a novel on-chip interconnection network adapted to a flexible multiprocessor LDPC/turbo decoder and based on the de Bruijn network. The main characteristics of this network -including its logarithmic diameter, scalable aggregate bandwidth, and optimized routing technique- allow it to efficiently support the communication- intensive nature of the two decoding techniques. We present a detailed hardware implementation of the routers and the network interfaces as well as the packet format and the routing algorithm. In order to evaluate the performance of the proposed network, a generic RTL VHDL description has been developed and synthesized with ST CMOS 0.18 mum technology. The flexibility and the scalability of this on-chip communication network enable it to be used in the emerging multi-code applications and standards. In addition, the results obtained for a 16-processor network demonstrate a major aggregate bandwidth of 296 Gbps with a relative small area of 3.56 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
A Family of Fault-Tolerant Efficient Indirect Topologies (2015)

On the one hand, performance and fault-tolerance of interconnection networks are key design issues for high performance computing (HPC) systems. On the other hand, cost should be also considered. Indirect topologies are often chosen in the design of HPC systems. Among them, the most commonly used topology is the fat-tree. In this work, we focus on getting the maximum benefits from the network resources by designing a simple indirect topology with very good performance and fault-tolerance properties, while keeping the hardware cost as low as possible. To do that, we propose some extensions to the fat-tree topology to take full advantage of the hardware resources consumed by the topology. In particular, we propose three new topologies with different properties in terms of cost, performance and fault-tolerance. All of them are able to achieve a similar or better performance results than the fat-tree, providing also a good level of fault-tolerance and, contrary to most of the available topologies, these proposals are able to tolerate also faults in the links that connect to end nodes.
Perspective on This Article from Epigallocatechin-gallate Suppresses Tumorigenesis by Directly Targeting Pin1 (2023)

Perspective on This Article from Epigallocatechin-gallate Suppresses Tumorigenesis by Directly Targeting Pin1
Addition of a series spring to a lumped element model of a novel thermoacoustic refrigerator (2012)

A lumped element model is introduced for an “in-line” traveling-wave thermoacoustic refrigerator, based on a recent patent by Backhaus and Keolian [US Pat. No. 7,908,856 (22 Mar 2011)]. This model couples three electro-mechanical motors to the acoustical domain using a flexure sealed piston. Results of this lumped-element model were found to be in good agreement with a DELTAEC model. Since large displacements result in flexure fatigue, the addition of a series spring between the motor and piston was evaluated to reduce flexure seal displacement while matching the optimum load impedance. The assignment of the correct dynamic mass of the series spring when both the motor and flexure ends of the spring are moving has not been addressed previously in the literature. To determine the two effective masses required at each end of the spring, the spring is discretized into a large number of elements and is converted into a simplified circuit model to assign values to lumped-element components. These values depend upon an initial knowledge of both end velocity magnitudes and phases. This enables an iterative solution for the effective spring masses since velocities need to be known for effective masses to be determined and vice versa. [Work supported by the Applied Research Laboratory and the U.S. Department of Energy.]
Secretory Expression and Characterization of Two Hemicellulases, Xylanase, and β-Xylosidase, Isolated from Bacillus Subtilis M015 (2014)

Microbial hydrolysis of lignocellulosic biomass is becoming increasingly important for the production of renewable biofuels to address global energy concerns. Hemicellulose is the second most abundant lignocellulosic biopolymer consisting of mostly xylan and other polysaccharides. A variety of enzymes is involved in complete hydrolysis of xylan into its constituent sugars for subsequent biofuel fermentation. Two enzymes, endo-β-xylanase and β-xylosidase, are particularly important in hydrolyzing the xylan backbone into xylooligosaccharides and individual xylose units. In this study, we describe the cloning, expression, and characterization of xylanase and β-xylosidase isolated from Bacillus subtilis M015 in Escherichia coli. The genes were identified to encode a 213 amino acid protein for xylanase (glycoside hydrolase (GH) family 11) and a 533 amino acid protein for β-xylosidase (GH family 43). Recombinant enzymes were produced by periplasmic-leaky E. coli JE5505 and therefore secreted into the supernatant during growth. Temperature and pH optima were determined to be 50 °C and 5.5-6 for xylanase and 35 °C and 7.0-7.5 for β-xylosidase using beech wood xylan and p-nitrophenyl-β-D-xylopyranoside as the substrates, respectively. We have also investigated the synergy of two enzymes on xylan hydrolysis and observed 90 % increase in total sugar release (composed of xylose, xylobiose, xylotriose, and xylotetraose) for xylanase/β-xylosidase combination as opposed to xylanase alone.
Recurrent Deep Network Models for Clinical NLP Tasks: Use Case with Sentence Boundary Disambiguation (2019)

Although a number of foundational natural language processing (NLP) tasks like text segmentation are considered a simple problem in the general English domain dominated by well-formed text, complexities of clinical documentation lead to poor performance of existing solutions designed for the general English domain. We present an alternative solution that relies on a convolutional neural network layer followed by a bidirectional long short-term memory layer (CNN-Bi-LSTM) for the task of sentence boundary disambiguation and describe an ensemble approach for domain adaptation using two training corpora. Implementations using the Keras neural-networks API are available at https://github.com/NLPIE/clinical-sentences.
A novel ABCR nonsense mutation responsible for late-onset fundus flavimaculatus. (1999)

A heterozygous nonsense ABCR gene mutation was found in a patient affected with FFM. No other mutation has been identified in the entire coding sequence and the promoter region, suggesting that a heterozygous severe ABCR mutant may be responsible for a mild and delayed FFM phenotype, different from that of age-related macular degeneration.
Detailed Analysis of the Microstructure of the Metal/Oxide Interface Region in Zircaloy-2 after Autoclave Corrosion Testing (2012)

Two varieties of Zircaloy-2, with different second phase particle (SPP) size distributions and different corrosion resistance, were oxidized in a steam autoclave. Transmission electron microscopy (TEM) of large thin-foil cross-sections of the oxide and the adjacent metal shows an undulating metal/oxide interface in both materials with a periodicity of slightly less than 1 μm and an amplitude of around 100 nm. The SPPs oxidize slower than the surrounding metal, and the absence of volume increase leads to void and crack formation as the SPPs become embedded in the oxide. On SPP oxidation, iron diffuses out of the particles into the surrounding oxide. A sub-oxide with an oxygen content of approximately 50 at. % and a layer thickness of about 200 nm was observed close to the metal/oxide interface. There is a 200 nm oxygen concentration gradient into the metal, from the level close to the sub-oxide of about 30 at. % down to a few atomic percent. All tin in the matrix is incorporated in the sub-oxide, and no segregation to the metal/oxide interface was found.
RESEARCH NOTE - Human Genetic Bi-allelic Sequences, HGBASE, a Database of Intra-genic Polymorphisms (1998)

The Human Genome Project is providing a wealth of information about the\nhuman gene repertoire, and promises to furnish a complete genome\nsequence (and thereby a complete gene catalog) by the year 2005. This\nenormous output of data is beginning to be complemented by large scale\nstudies designed to uncover normally occurring variations within human\ngene sequences. Much of this variability is very subtle, often\ncomprises single nucleotide polymorphisms (SNPs) which are ideally\ncompatible with a number of large scale detection procedures. SNPs will\nbe the basis of future highly dense polymorphic marker maps, and those\nrelated to known genes can be exploited in genetic association studies\naimed at defining the genetic basis of all manner of complex\nphenotypes, not least disorders such as mental illness, diabetes,\ncardiovascular disease and cancer. All indications are that\n100,000-200,000 human genome SNPs will be identified within the next\ntwo years.
Transient-capacitance studies of the pressure dependence of defect energy levels in Al/sub x/Ga/sub 1-x/As (1982)

The pressure dependence of the energy levels associated with defects in III-V compounds can reveal valuable additional information about such centers. Using the technique of DLTS, we have studied the pressure dependence of defect energy levels in gamma irradiated LPE Al/sub x/Ga/sub 1-x/As p/sup +/n junctions. The results indicate that 4 out of 5 traps observed in AlGaAs are sensitive to pressure, and that their response to pressure is strongly valence-band like. Further, this type of pressure response is accentuated by increases in Al content.
RDMA-Based Direct Transfer of File Data to Remote Page Cache (2015)

The performance of a distributed file system significantly affects data-intensive applications that frequently execute I/O operations on large amounts of data. Although many modern distributed file systems are geared to provide highly efficient I/O performance, their operations are nonetheless affected by runtime overhead in data transfer between client nodes and I/O servers. A large part of the overhead is caused by memory copies executed by the client interface using the FUSE framework or a special kernel module. In this paper, we propose a method based on InfiniBand RDMA that improves data transfer performance between client and server in a distributed file system. The major characteristic of the method is that it transfers file data directly from a server's memory to the page cache of a client node. The method minimizes memory copies that are otherwise executed in the client interface or the operating system kernel. We implemented the proposed method in the Gfarm distributed file system and tested it using I/O benchmark software and real applications. The experimental results showed that our method effected a performance improvement of up to 78.4% and 256.0% in sequential and random file reads, respectively, and an improvement of up to 6.3% in data-intensive applications.
Vision-based motion sensing for underwater navigation and mosaicing of ocean floor images (2002)

The authors propose a direct solution for real-time estimation of the 3D motion of a submersible vehicle from the video images of the seafloor, acquired by an on-board camera, in order to perform the following tasks: Maintaining a prescribed trajectory, or determining position relative to a reference point, during short-range navigation along the seafloor. Constructing a mosaic image of the bottom scene within the scanned area by registering consecutive frames. The authors present experimental results with images recorded in a water tank to evaluate performance based on accuracy in the estimation of 3D motion and the registration of consecutive frames in the mosaic image.
Calibrating Fiber Bragg Gratings for Temperature and Strain (2017)

This chapter discusses the systematic procedures to calibrate a FBG sensor under temperature and strain. The process starts with the inscription of a FBG in the fiber, followed by spectral characterization, transducer prototype development, laboratory optical setup, and the development of transducers for field application. The characterization must be initially performed without applied temperature or strain and then subsequently with their calibrated application. This section introduces the theory and isolates the necessary FBG parameters to be calculated during the calibration process for temperature and strain. Recalling the basic Bragg equation, the Bragg wavelength shift is a function of the temperature and strain: (7.1)
Three-Dimensional Electrostatics- and Atomistic Doping-Induced Variability of RTN Time Constants in Nanoscale MOS Devices—Part I: Physical Investigation (2012)

This paper presents a detailed simulation analysis of the impact of 3-D electrostatics and atomistic doping on the variability of the random telegraph noise (RTN) time constants in nanoscale MOS devices. Results on a template decananometer Flash cell show that both the effects contribute to a large statistical dispersion of the capture/emission time constants of oxide traps placed at the same distance from the silicon surface, mainly due to nonuniform channel inversion. The statistical dispersion has an orders-of-magnitude increase when moving from the on-state to the subthreshold cell regimes and has major implications on the spectroscopic investigation of RTN traps, as will be discussed in Part II of this work.
Analysis of Structural Variation Among Inbred Mouse Strains Identifies Genetic Factors for Autism-Related Traits (2021)

Abstract The genomes of six inbred strains were analyzed using long read (LR) sequencing. The results revealed that structural variants (SV) were very abundant within the genome of inbred mouse strains (4.8 per gene), which indicates that they could impact genetic traits. Analysis of the relationship between SNP and SV alleles across 53 inbred strains indicated that we have a very limited ability to infer whether SV are present using short read sequence data, even when nearby SNP alleles are known. The benefit of having a more complete map of the pattern of genetic variation was demonstrated by identifying at least three genetic factors that could underlie the unique neuroanatomic and behavioral features of BTBR mice that resemble human Autism Spectrum Disorder (ASD). Similar to the genetic findings in human ASD cohorts, the identified BTBR-unique alleles are very rare, and they cause high impact changes in genes that play a role in neurodevelopment and brain function.