gebhart/patrepeval huggingface dataset:
The Role of Heparanase and Sulfatases in the Modification of Heparan Sulfate Proteoglycans within the Tumor Microenvironment and Opportunities for Novel Cancer Therapeutics (2014)

Heparan sulfate proteoglycans (HSPGs) are an integral and dynamic part of normal tissue architecture at the cell surface and within the extracellular matrix. The modification of HSPGs in the tumor microenvironment is known to result not just in structural but also functional consequences, which significantly impact cancer progression. As substrates for the key enzymes sulfatases and heparanase, the modification of HSPGs is typically characterized by the degradation of heparan sulfate (HS) chains/sulfation patterns via the endo-6-O-sulfatases (Sulf1 and Sulf2) or by heparanase, an endo-glycosidase that cleaves the HS polymers releasing smaller fragments from HSPG complexes. Numerous studies have demonstrated how these enzymes actively influence cancer cell proliferation, signaling, invasion, and metastasis. The activity or expression of these enzymes has been reported to be modified in a variety of cancers. Such observations are consistent with the degradation of normal architecture and basement membranes, which are typically compromised in metastatic disease. Moreover, recent studies elucidating the requirements for these proteins in tumor initiation and progression exemplify their importance in the development and progression of cancer. Thus, as the influence of the tumor microenvironment in cancer progression becomes more apparent, the focus on targeting enzymes that degrade HSPGs highlights one approach to maintain normal tissue architecture, inhibit tumor progression, and block metastasis. This review discusses the role of these enzymes in the context of the tumor microenvironment and their promise as therapeutic targets for the treatment of cancer.
862. Adipose Tissue Transduction Using AAV8-Based Vectors: Inadvertent Gene Transfer into Liver (2005)

We have shown that intra-adipose tissue injection using AAV1 vectors resulted in tissue-specific transgene expression in db/db mice. To attain a more efficient expression, we tried the same method using AAV8-based vector (AAV8-CMV-Epo). Remarkably higher plasma Epo concentration was observed. When a vector encoding human Factor IX (AAV8-CMV-hFIX) was used at a dose of 2 |[times]| 1011 vg/body, more than 10% equivalent of normal human concentration was observed and considered as therapeutic level. In order to confirm tissue specific expression, transduced adipose tissues were surgically removed and plasma Factor IX concentration was pursued one week later. Surprisingly, approximately two-third of plasma concentration remained after total elimination of target tissue. Copy number of hFIX mRNA within the tissue correlated well with the plasma Factor IX concentration, supporting the contribution of both tissues. In vivo imaging analysis by IVIS system suggested transgene expression within liver when AAV8 vector encoding luciferase was used for adipose tissue transduction. Organ specific expression analyzed by ex vivo imaging confirmed robust expression in liver rather than adipose tissue. These data suggest extreme tropism of AAV8-based vectors to liver, and we should be careful about overestimating results when tissues other than liver were targeted.
High‐dose glucocorticoids for the treatment of ipilimumab‐induced hypophysitis is associated with reduced survival in patients with melanoma (2018)

Among patients with melanoma who had ipilimumab-induced hypophysitis, those who received higher doses of glucocorticoids had reduced survival. This is the first study to demonstrate a potential negative effect of high glucocorticoid doses on the efficacy of checkpoint inhibitors after an irAE. These findings have potential implications for the management of other irAEs.
Manipulation and dynamic mechanical testing of microscopic objects using a tele-micro-robot system (1990)

A microrobot having two high-performance parallel drive limbs which has been developed for manipulation, surgery, and dynamic mechanical testing of very small objects such as single living cells is described. The end points of each limb move in overlapping spherical workspaces of 1-mm diameter with minimum open- and closed-loop movements of 1 nm and 10 nm, respectively. The displacement bandwidth of all six microrobot axes exceeds 1 kHz for small displacements. A three-dimensional laser vision system with a resolution of 50 to 100 nm has been developed to provide the microrobot with volume images containing magnitude, phase, polarization, and spectral information. A macro version of the microrobot has been built to permit force-reflecting teleoperation of the microrobot. The telemicrorobot system permits both microscopic objects and continuum models to be felt. A high-performance parallel computer has been designed, and partially constructed, to meet the substantial computational and control requirements of the telemicrorobot system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Histomorphometric analysis of the repair of a segmental diaphyseal defect with ceramic and titanium fibermetal implants: Effects of bone marrow (1994)

We used a rat femoral diaphyseal defect/implant model to quantify the ingrowth of bone, cartilage, and fibrous connective tissue in a comparative study of woven sintered titanium fibermetal and porous hydroxyapatite/tricalcium phosphate ceramic implanted with and without the addition of syngeneic bone marrow cells. The patterns of tissue growth into the implants were analyzed with respect to time, type of implant, and the presence or absence of syngeneic marrow. Significantly more bone was found in ceramic implants than in fibermetal implants, with the addition of syngeneic marrow than without it, and at 4 months than at 2 months. Significantly more bone was found at both time periods in ceramic implants with bone marrow than in any other combination studied. We hypothesize that these findings resulted from interactions between the implanted material and its surroundings, specifically its ability to serve as a substratum for cell attachment, and cells in and around the defect, whether surgically implanted or arising from the soft-tissue bed.
Deethylsimazine: bacterial dechlorination, deamination, and complete degradation (1984)

Enrichment cultures utilizing deethylsimazine (6-chloro-N-ethyl-l,3,5-triazine-2,4-diamine)as a sole nitrogen source were obtained from soils that had had long exposure to s-triazine herbicides. A bacterium was isolated that utilized deethylsimazine quantitatively as a nitrogen source for growth, but only 1 mol of nitrogen was obtained/mol of deethylsimazine, whereas all six atoms in melamine were utilized. The bacterium, which was identified as a strain of Rhodococcus corallinus, converted deethylsimazine to 1 mol of 6-(ethylamino)-l,3,5-triazine-2,4(1H,3H)-dione, 1 mol of chloride ion, and 1 mol of ammonium ion. 4-Amino6-(ethylamino)-l,3,5-triazin-2(1H)-one was tentatively identified as a transient intermediate in the degradation, which was presumed to be due to a dechlorination followed by a deamination. Growth of R. corallinus together with Pseudomonas sp. strain NRRL B-12228, which utilized 6-(ethylamino)-1,3,5-triazine-2,4(1H,3H)-dione, resulted in complete conversion of deethylsimazine nitrogen to cell material.
Characterization of the RNA content of chromatin (2010)

Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.
Two-dimensional, real-time, sub-millimeter-wave imaging using a spatially selective mask (2011)

In the absence of detector arrays, a single pixel coupled with a spatially selective mask has been shown to be a practical solution to imaging problems in the terahertz and sub-millimeter wave domains. In this paper we demonstrate real-time two-dimensional imager for sub-millimeter waves that is based on a spatially selective image plane mask. The imager consists of a heterodyne source and receiver pair, image forming optics, a spatially selective mask, data acquisition hardware, and image reconstruction software. The optics form an image onto the spatially selective mask and linear measurements of the image are made. The mask must be designed to ensure maximum transmission, measurement linearity, and measurement to measurement independence and our design parameters are presented. Once enough linearly independent measurements are made, the image is reconstructed by solving a system of linear equations that is generated from the mask patterns and the corresponding measurements. We show that for image sizes envisioned for many current applications, this image reconstruction technique is computationally efficient and can be implemented in real time. We present images collected using this system, discuss the results, and discuss other applications for some components of the imager.
Mastitis treatment—Reduction in antibiotic usage in dairy cows (2017)

Animal-friendly, economical, resource-saving milk production provides the basis for sustained consumer acceptance. Bovine mastitis plays a decisive role in the dairy industry-disturbing animal health and welfare and causing considerable economic losses on the other hand. Currently, antimicrobial treatment is indispensable to keep bovine udder health, animal welfare and economic aspects in balance. On the contrary, emergence and spread of antimicrobial resistance (AMR) is an urgent matter of particular public interest, and as a consequence, antimicrobial usage (AMU) in production livestock is a critically discussed subject. In urgent need of future reduction in AMU in the dairy industry, this review article describes and discusses possible approaches promising prompt implementation, including therapeutical alternatives as well as pro- and metaphylactic concepts such as the implementation of evidence-based mastitis therapy concepts and selective dry cow treatment (sDCT), in search of the most effective and contemporary methods for decreasing AMU and AMR in dairy production.
Human cortical regions activated by wide-field visual motion: an H2(15)O PET study (1995)

1. Several areas in the monkey dorsal visual pathway, including the dorsal part of the medial superior temporal area, have been found to contain cells responding to movements of a wide visual field and are suggested to be involved in analyzing self-induced motion information. In the present study, positron emission tomography was used to localize human cortical regions responding to wide-field visual motion. Changes in regional cerebral blood flow (rCBF) were measured when subjects maintained fixation and viewed low-contrast (0.15 log units brighter than the background) dots subtending 80 x 80 degrees and moving either coherently or incoherently. Brain foci were localized after activity in a fixation-only paradigm was subtracted from that in the two moving dot paradigms. 2. Both the coherent and incoherent movements significantly activated the primary/secondary visual cortex and surrounding visual areas in the cuneus and superior occipital gyrus. Subtraction of images between the coherent and incoherent movements showed that the activity caused by the two types of movement was comparable in these early visual cortical regions. 3. In the lateral occipitotemporoparietal cortex, the coherent movement specifically activated two separate areas; a posterior focus was located at the border of the right occipitotemporal gyri, and a dorsoanterior focus was located bilaterally in the temporoparietal cortex. The incoherent movement did not activate these regions. 4. A fine anatomic localization using individual magnetic resonance images was performed for the bilateral activation in the temporoparietal cortex, which was found to be located mainly in the depth of the inferior parietal lobule and a small portion of the superior and middle temporal gyri. 5. Both the coherent and incoherent movements activated a part of the superior parietal lobule located within the intraparietal sulcus (Brodmann area 7). The bilateral foci activated by the coherent movement were located more anteriorly than the focus activated by the incoherent movement. Subtraction images between the coherent and incoherent movements, however, did not reveal any significant rCBF increases in the superior parietal lobule. 6. Several other cortical regions known to be involved in visuospatial and visuomotor functions were also activated by the coherent movement, including the frontal eye field (Brodmann area 8) and premotor cortex (Brodmann area 6) in the frontal lobe. 7. The posteriorly located activation at the border of occipito-temporal gyri corresponds to the homologue of the middle temporal area reported in previous activation studies using small to medium-sized motion stimuli. The bilateral activation in the inferior parietal lobule appeared to rely on wide-field motion stimulation.
SQUID-Detected Magnetic Resonance Imaging in Microtesla Fields (2007)

The use of very low noise magnetometers based on Superconducting QUantum Interference Devices (SQUIDs) enables nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) in microtesla magnetic fields. An untuned superconducting flux transformer coupled to a SQUID achieves a magnetic field noise of 10(-15) T Hz(-1/2). The frequency-independent response of this magnetometer combined with prepolarization of the nuclear spins yields an NMR signal that is independent of the Larmor frequency omega0. An MRI system operating in a field of 132 microT, corresponding to a proton frequency of 5.6 kHz, achieves an in-plane resolution of 0.7 x 0.7 mm2 in phantoms. Measurements of the longitudinal relaxation time T1 in different concentrations of agarose gel over five decades of frequency reveal much greater T1-differentiation at fields below a few millitesla. Microtesla MRI has the potential to image tumors with substantially greater T1-weighted contrast than is achievable in high fields in the absence of a contrast agent.
Type III interferon-induced CBFβ inhibits HBV replication by hijacking HBx (2018)

Hepatitis B virus (HBV) and its associated chronic infection remain serious health threats worldwide. However, there is still no impactful approach for clinical treatment of hepatitis B patients. Therefore, developing a better understanding of the interactions between HBV and its host is particularly important. HBV infection has been reported to induce type-III but not type-I or type-II interferon (IFN). In this study, we identified CBFβ, an HIV enhancer, as an HBV restriction factor that is specifically induced by type-III IFN in the early stages of HBV infection. Type-III IFN-induced IL-10 played an important role in the production of CBFβ. Interestingly, the interaction between CBFβ- and HBV-encoded regulatory protein X (HBx) enhanced the stability of CBFβ, but notably blocked HBx-mediated promotion of HBV replication. CBFβ expression was lower in HBV patients than in healthy persons, and the addition of serum from HBV patients inhibited CBFβ expression in HepG2 cells. On the contrary, HBV via HBsAg inhibited type-III IFN-induced CBFβ expression and decreased the anti-HBV activity of type-III IFN, suggesting that HBV inhibits antiviral interferon-stimulated gene (ISG) expression and induces IFN resistance. Collectively, our results demonstrate that type-III IFN-triggered and IL-10-induced CBFβ are crucial factors for inhibiting HBV replication, and the HBx-CBFβ-HBsAg axis reveals a new molecular mechanism of interaction between HBV and its hosts.
DISC1 Modulates Neuronal Stress Responses by Gate-Keeping ER-Mitochondria Ca2+ Transfer through the MAM (2017)

A wide range of Ca<sup>2+</sup>-mediated functions are enabled by the dynamic properties of Ca<sup>2+</sup>, all of which are dependent on the endoplasmic reticulum (ER) and mitochondria. Disrupted-in-schizophrenia 1 (DISC1) is a scaffold protein that is involved in the function of intracellular organelles and is linked to cognitive and emotional deficits. Here, we demonstrate that DISC1 localizes to the mitochondria-associated ER membrane (MAM). At the MAM, DISC1 interacts with IP<sub>3</sub>R1 and downregulates its ligand binding, modulating ER-mitochondria Ca<sup>2+</sup> transfer through the MAM. The disrupted regulation of Ca<sup>2+</sup> transfer caused by DISC1 dysfunction leads to abnormal Ca<sup>2+</sup> accumulation in mitochondria following oxidative stress, which impairs mitochondrial functions. DISC1 dysfunction alters corticosterone-induced mitochondrial Ca<sup>2+</sup> accumulation in an oxidative stress-dependent manner. Together, these findings link stress-associated neural stimuli with intracellular ER-mitochondria Ca<sup>2+</sup> crosstalk via DISC1, providing mechanistic insight into how environmental risk factors can be interpreted by intracellular pathways under the control of genetic components in neurons.
Effect of protein kinase modulators on the induction of morphological differentiation of pheochromocytoma PC12 cells by nerve and fibroblast growth factors (1990)

The effect of protein kinase modulators on the ability of nerve and fibroblast growth factors to induce neurite outgrowth in pheochromocytoma PC12 cells was studied. The protein kinase inhibitor H7 increased the neurite-stimulating capacity of these factors. The effect of H7 was observed within 1 h and was dose-dependent. HA 1004, an inhibitor of cAMP- and cGMP-dependent protein kinases, did not affect the neurite-stimulating activity of NGF. Substances inhibiting protein kinase C, ganglioside GT1b and quercetin, acted in a similar way whereas sphingosine had an opposite effect.
A convenient field-installable antireflection coating for optical fiber connectors and other components (1988)

Abstract Disc-shaped pellicles 15 microns thick are antireflection coated and cemented to the polished ends of optical fiber connectors. Excess loss due to increased fiber separation is a maximum of 10% (.46 dB), typically 3.8% (.16 dB) in graded index fibers; Fresnel back-reflections are reduced by a factor of more than 10.
Torque ripple reduction of SRM by optimization of current reference (2010)

The present paper introduces new current profiles for torque ripple reduction of the SRM. A reduction method using the ideal current profile for instantaneous flat torque has been proposed. The problem with this method is that, as the rotation speed increases, the real current cannot keep up with the reference for the requirement of a high di/dt. This results in increasing torque ripple in the high-speed region. In order to overcome this problem, we propose a novel method for improving the traceability of the real current by changing the reference shape. The validity of the newly obtained current reference was examined by MATLAB/Simulink-based simulations.
BZLF1 (ZEBRA, Zta) protein of Epstein-Barr virus selected in a yeast one-hybrid system by binding to a consensus site in the IgH intronic enhancer: a role in immunoglobulin expression? (1996)

We have used a yeast one hybrid screen to search for factors interacting with a subsegment of the immunoglobulin heavy chain (IgH) intronic enhancer. The 51 bp enhancer segment harbored a so-called E-box and an octamer site, known to bind helix-loop-helix transcription factors and Oct factors, respectively. Mammalian Oct-2A protein was also expressed in yeast, to select for transcription factors possibly cooperating with Oct-2. Six strongly interacting protein clones were selected from a peripheral blood lymphocyte library. These included a B cell-specific co-activator, termed Bob1, that directly binds to Oct-2 (Gstaiger et al., 1995, Nature 373, 360-362). Three further clones represent the helix-loop factors ITF-1 and ITF-2, another one the nucleolar protein nucleophosmin, or B23. Unexpectedly, the sixth clone with strong activity encoded the BZLF1 (= ZLF1, zta, ZEBRA, EB1) protein of Epstein-Barr virus (EBV). BZLF1 is a leucine zipper-related transcription factor and induces the switch from viral latency to lytic growth. We found that BZLF1 also activated transcription in transiently transfected mammalian cells via a consensus binding site located within the IgH intron enhancer. BZLF1 may thus influence immunoglobulin heavy chain expression in EBV-infected B lymphocytes.
Modelling and compensation of quadrature error for silicon MEMS microgyroscope (2005)

This paper presents the mathematical modelling on the quadrature error of a microgyroscope due to the imbalance of the asymmetric spring flexures and compensation circuit to draw the fin back to the balanced position (equal gap between the upper and lower capacitor banks). Quadrature error is a major concern in a microgyroscope for low-rate sensing, e.g. a few degrees per hour.
Indoor Tracking: Theory, Methods, and Technologies (2015)

In the last decade, the research on and the technology for outdoor tracking have seen an explosion of advances. It is expected that in the near future, we will witness similar trends for indoor scenarios where people spend more than 70% of their lives. The rationale for this is that there is a need for reliable and high-definition real-time tracking systems that have the ability to operate in indoor environments, thus complementing those based on satellite technologies, such as the Global Positioning System (GPS). The indoor environments are very challenging, and as a result, a large variety of technologies have been proposed for coping with them, but no legacy solution has emerged. This paper presents a survey on indoor wireless tracking of mobile nodes from a signal processing perspective. It can be argued that the indoor tracking problem is more challenging than the problem on indoor localization. The reason is simple: From a set of measurements, one has to estimate not one location but a series of correlated locations of a mobile node. The paper illustrates the theory, the main tools, and the most promising technologies for indoor tracking. New directions of research are also discussed.
Cellular retinoic acid binding protein is associated with mitochondria (2000)

We report that immunohistochemical staining for cellular retinoic acid-binding protein (CRABP) was restricted to the cytoplasm of cortical cells in bovine adrenal. In contrast, staining for the similar protein, cellular retinol-binding protein (CRBP), was found throughout these cells. After transfections of CRABP and CRBP into cultured cells, immunofluorescence analyses again revealed cytoplasmic restriction only for CRABP, with a pronounced punctate appearance. Use of organelle-specific fluorochromes indicated that CRABP immunofluorescence overlaid exactly with the pattern of the mitochondrial-specific fluorochrome. Confirmation of this association came with subcellular fractionation of the adrenal cortex. CRABP, but not CRBP, co-sedimented with the mitochondria, a novel finding for a member of this superfamily of cellular lipid-binding proteins.