gebhart/patrepeval huggingface dataset:
Tertiary and Quaternary Structures of Photoreactive Fe-Type Nitrile Hydratase from Rhodococcus sp. N-771:  Roles of Hydration Water Molecules in Stabilizing the Structures and the Structural Origin of the Substrate Specificity of the Enzyme, (1999)

The crystal structure analysis of the Fe-type nitrile hydratase from Rhodococcus sp. N-771 revealed the unique structure of the enzyme composed of the alpha- and beta-subunits and the unprecedented structure of the non-heme iron active center [Nagashima, S., et al. (1998) Nat. Struct. Biol. 5, 347-351]. A number of hydration water molecules were identified both in the interior and at the exterior of the enzyme. The study presented here investigated the roles of the hydration water molecules in stabilizing the tertiary and the quaternary structures of the enzyme, based on the crystal structure and the results from a laser light scattering experiment for the enzyme in solution. Seventy-six hydration water molecules between the two subunits significantly contribute to the alphabeta heterodimer formation by making up the surface shape, forming extensive networks of hydrogen bonds, and moderating the surface charge of the beta-subunit. In particular, 20 hydration water molecules form the extensive networks of hydrogen bonds stabilizing the unique structure of the active center. The amino acid residues hydrogen-bonded to those hydration water molecules are highly conserved among all known nitrile hydratases and even in the homologous enzyme, thiocyanate hydrolase, suggesting the structural conservation of the water molecules in the NHase family. The crystallographic asymmetric unit contained two heterodimers connected by 50 hydration water molecules. The heterotetramer formation in crystallization was clearly explained by the concentration-dependent aggregation state of NHase found in the light scattering measurement. The measurement proved that the dimer-tetramer equilibrium shifted toward the heterotetramer dominant state in the concentration range of 10(-2)-1.0 mg/mL. In the tetramer dominant state, 50 water molecules likely glue the two heterodimers together as observed in the crystal structure. Because NHase exhibits a high abundance in bacterial cells, the result suggests that the heterotetramer is physiologically relevant. In addition, it was revealed that the substrate specificity of this enzyme, recognizing small aliphatic substrates rather than aromatic ones, came from the narrowness of the entrance channel from the bulk solvent to the active center. This finding may give a clue for changing the substrate specificity of the enzyme. Under the crystallization condition described here, one 1,4-dioxane molecule plugged the channel. Through spectroscopic and crystallographic experiments, we found that the molecule prevented the dissociation of the endogenous NO molecule from the active center even when the crystal was exposed to light.
Humán erőforrás struktúra vizsgálata Markov-lánc szimulációval (2018)

Within the frame of the fourth industrial revolution manufacturing and service companies can transform their conventional processes into cyber-physical systems, where the applied Internet of Things technologies can accelerate the automation processes. This automation makes it necessary to change human resource management strategies. Within the frame of this article the author focuses on the analysis of the structure of human resources using Markov-chain model.
Animal models for diisocyanate asthma: answers for lingering questions (2004)

Recent progress using animal models has been instrumental in furthering current understanding of the involvement of the immune system in disease pathogenesis. The demonstration of diisocyanate occupational asthma in a murine model after sub-chronic inhalation exposure at relevant exposure levels should provide opportunities for more accurate risk assessment data.
Q-BAND EPR BIODOSIMETRY IN TOOTH ENAMEL MICROSAMPLES: FEASIBILITY TEST AND COMPARISON WITH X-BAND (2007)

A comparative study of electron paramagnetic resonance dosimetry in Q- and X-bands has shown that Q-band is able to provide accurate measurements of radiation doses even below 0.5 Gy with tooth enamel samples as small as 2 mg. The optimal amount of tooth enamel for dose measurements in Q-band was found to be 4 mg. This is less than 1% of the total amount of tooth enamel in one molar tooth. Such a small amount of tooth enamel can be harmlessly obtained in an emergency requiring after-the-fact radiation dose measurement. The other important advantage of Q-band is full resolution of the radiation-induced EPR signal from the native, background signal. This separation makes dose response measurements much easier in comparison to conventional X-band measurements in which these overlapping signals necessitate special methods for doses below 0.5 Gy. The main disadvantages of Q-band measurements are a higher level of noise and lower spectral reproducibility than in X-band. The effect of these negative factors on the precision of dose measurements in Q-band could probably be reduced by improvement of sample fixation in the resonance cavity and better optimization of signal filtration to reduce high-frequency noise.
Comparative study of extracellular fibrils on the ectodermal layer in gastrulae of five amphibian species (1983)

Previous studies have shown the presence of a network of extracellular fibrils on the inner surface of the ectodermal layer of the Ambystoma maculatum gastrulae. The alignment of the network along the blastopore-animal pole axis has suggested that the network of fibrils guides the migrating mesodermal cells in gastrulae by contact guidance. We have also shown that these fibrils can be deposited on substrata by explanted embryonic fragments and that substrata conditioned in this manner support directed cell migration. In this study, we found that the appearance of the fibrils in the embryos coincides with the start of cell migration towards the animal pole. Gastrulae of three urodele species examined (A. maculatum, A. mexicanum and Cynops pyrrhogaster) have similar dense networks of fibrils. Xenopus laevis gastrulae also have similar fibrils but fewer fibrils compared to urodele embryos. Rana pipiens gastrulae have very few extracellular fibrils. The scarcity of the fibrils in anuran species may be related to the differences in arrangement of mesodermal cells during migration.
Three dimensional model based on image theory for low frequency correction factors evaluation in semi-anechoic chambers (2002)

The need to study the radiated emissions from electric and electronic devices whose main energy content is below 50 MHz calls for the prediction of correction factors that allows one to correlate the direct electromagnetic field radiated by the device to the total measured field inside a test chamber due to the reflections on all the chamber's walls. A three-dimensional prediction model of these factors, based on the image theory, is developed and validated by comparison with known theoretical results and with measurements. The model simulates both electric and magnetic source dipoles for both polarizations. This model allows a parametric analysis of such factors for different chamber dimensions, relative positions and variation of frequency.
Optimizing Software Cache-coherent Cluster Architectures (1998)

Software cache-coherent systems using programmable protocol processors provide a flexible infrastructure to expand the systems in size and function. However this flexibility comes at a cost in performance. First, the software implementation of protocols is inherently slower than a hardware implementation. Second, when multiple processors share a protocol processor, contention may result in a substantial increase in memory latency. In this paper, we study how the overhead of a software scheme can be reduced in the context of a shared- memory system consisting of SMP clusters. We study various design choices including hardware assists such as forwarding logic in the protocol processor and software hints through explicit communication primitives. We conduct our experiments via trace-driven simulation and compare the execution of three programs from the SPLASH-2 suite. We found that small cluster sizes (up to 4 processors/node) work well for both hardware and software implementations. When the forwarding logic is incorporated with the software scheme, the performance is competitive to that of the hardware scheme. When enhanced further by explicit communication primitives, the software scheme can perform even better than a pure hardware implementation. This is particularly noticeable when the network latency is high.
GDNF-inducible zinc finger protein 1 is a sequence-specific transcriptional repressor that binds to the HOXA10 gene regulatory region (2005)

The RET tyrosine kinase receptor and its ligand, glial cell line-derived neurotrophic factor (GDNF) are critical regulators of renal and neural development. It has been demonstrated that RET activates a variety of downstream signaling cascades, including the RAS/mitogen-activated protein kinase and phosphatidylinositol-3-kinase(PI3-K)/AKT pathways. However, nuclear targets specific to RET-triggered signaling still remain elusive. We have previously identified a novel zinc finger protein, GZF1, whose expression is induced during GDNF/RET signaling and may play a role in renal branching morphogenesis. Here, we report the DNA binding property of GZF1 and its potential target gene. Using the cyclic amplification and selection of targets technique, the consensus DNA sequence to which GZF1 binds was determined. This sequence was found in the 5' regulatory region of the HOXA10 gene. Electrophoretic mobility shift assay revealed that GZF1 specifically binds to the determined consensus sequence and suppresses transcription of the luciferase gene from the HOXA10 gene regulatory element. These findings thus suggest that GZF1 may regulate the spatial and temporal expression of the HOXA10 gene which plays a role in morphogenesis.
Dynamische Inversion-Recovery-Snapshot-FLASH-MRT der fokal nodulären Hyperplasie der Leber (1993)

11 lesions of focal nodular hyperplasia (FNH) in 6 patients were studied by means of dynamic snapshot-FLASH MRI before and after bolus injection of Gd-DTPA. In addition, plain snapshot-FLASH images were compared with T1- and T2-weighted spin-echo (SE) images and with T1-weighted breathhold-FLASH images. Highest FNH-liver signal-difference-to-noise ratios were obtained with snapshot-FLASH followed by T2-SE. In all patients contrast-enhanced serial snapshot-FLASH demonstrated reliably the typical haemodynamic appearance of FNH known from dynamic computed tomography. Because of its high intrinsic lesion-liver contrast and high time-resolution dynamic snapshot-FLASH MRI may facilitate differential diagnosis of hepatic tumours.
Increased susceptibility to colitis in the Vasoactive Intestinal Peptide receptor type 2 (VPAC2) mouse : A negative role for VPAC1 receptor in the induction of intestinal inflammation (50.44) (2009)

Abstract Vasoactive intestinal peptide (VIP) is a prominent neuropeptide with effects on many immune functions which are transduced by VIP G-protein-coupled receptors type 1 (VPAC1) and type 2 (VPAC2) on immune cells. Previous studies have shown that VIP reduces clinical symptoms and inflammation in mouse models of human immune-based diseases such as rheumatoid arthritis, Crohn’s Disease, septic shock and multiple sclerosis. We recently demonstrated that VPAC2 knockout (KO) CD4 T cells in the presence of VIP and TGF-b develop into Th17 cells in a cAMP-Protein Kinase A dependent manner. Here we show that increased IL-17 induction in VPAC2-KO CD4 cells is accompanied by a reduced conversion of CD4 T cells into FoxP3+ regulatory T cells. To determine if VPACs play a role in the inflammatory bowel disease (IBD), VPAC2-KO mice were subjected to dextran sulfate sodium (DSS) in drinking water. Compared to wild type (WT), VPAC2-KO mice exhibited rapid and more severe clinical symptoms of colitis and had significantly higher colonic inflammation and increased inflammatory cytokines in colon. Severe colitis in VPAC2-KO mice was ameliorated in the presence of PKA inhibitors. Moreover, VPAC1-KO mice were resistant to the development of DSS-induced colitis. The results demonstrate a new role for VPAC1 which is responsible for increased inflammation in IBD and may provide a new therapeutic target.
Mouse Movement through Finger by Image Grabbing (2020)

Touch less Interactive screen or system is an upcoming technology in the real life world, which will be another biggest realization followed by the technologies based on the monitors cove as PC monitor, TV Screens without a stroke or touch. The aim of this project is to develop a touch less interactive screen which helps to ease the controlling of any kind of monitors. Project is based on MATLAB platform. In this work, the finger gestures which are captured by a webcam and that will be converted into mouse movements to control the screen. Various Analysis result has included in the report to show the feasibility of the application of this development. A Graphical Interface User (GUI) is developed to let the user to choose perform calibration and number of times it’s required to perform calibration and to trigger the program upon user’s request.
DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage? (2020)

6-methyladenine (6mA) is fairly abundant in nuclear DNA of basal fungi, ciliates and green algae. In these organisms, 6mA is maintained near transcription start sites in ApT context by a parental-strand instruction dependent maintenance methyltransferase and is positively associated with transcription. In animals and plants, 6mA levels are high only in organellar DNA. The 6mA levels in nuclear DNA are very low. They are attributable to nucleotide salvage and the activity of otherwise mitochondrial METTL4, and may be considered as a price that cells pay for adenine methylation in RNA and/or organellar DNA. Cells minimize this price by sanitizing dNTP pools to limit 6mA incorporation, and by converting 6mA that has been incorporated into DNA back to adenine. Hence, 6mA in nuclear DNA should be described as an epigenetic mark only in basal fungi, ciliates and green algae, but not in animals and plants.
The Use of Banding Recovery Data to Estimate Dispersal Rates and Gene Flow in Avian Species: Case Studies in the Red-Winged Blackbird and Common Grackle (1989)

Journal Article The Use of Banding Recovery Data to Estimate Dispersal Rates and Gene Flow in Avian Species: Case Studies in the Red-Winged Blackbird and Common Grackle Get access William S. Moore, William S. Moore Department of Biological Sciences, Wayne State University, Detroit, MI 48202 Search for other works by this author on: Oxford Academic Google Scholar Richard A. Dolbeer Richard A. Dolbeer Denver Wildlife Research Center, United States Department of Agriculture, 6100 Columbus Avenue, Sandusky, OH 44870 Search for other works by this author on: Oxford Academic Google Scholar The Condor, Volume 91, Issue 2, 1 May 1989, Pages 242–253, https://doi.org/10.2307/1368301 Published: 01 May 1989 Article history Received: 09 September 1988 Accepted: 03 January 1989 Published: 01 May 1989
Supplementary Figure S5 from Proinflammatory Macrophage Activation by the Polysialic Acid-Siglec-16 Axis Is Linked to Increased Survival of Patients with Glioblastoma (2023)

&lt;p&gt;OS analysis of the two GB cohorts individually stratified for CD163 to CD68 or CD74 to IBA1 ratios&lt;/p&gt;
Epidemiology, therapy, and prevention of infection with Salmonella organisms (1992)

With mass food production, particularly of poultry and dairy products, the problem of nontyphoid salmonella infections continues to increase. This is especially marked with Salmonella enteritidis that is associated with eating inadequately cooked (and often pooled) eggs or egg products that have been contaminated transovarially or in passage and collection. Increasing resistance to antimicrobial agents and growing numbers of immunocompromised patients pose special problems in managing salmonella infections. Although new antibiotics and vaccines show promise for both typhoid and nontyphoid salmonella infections, improved agricultural practices and sanitation continue to be of paramount importance.
The treatment of locally recurrent chondrosarcoma (2012)

The aim of this study was to define the treatment criteria for patients with recurrent chondrosarcoma. We reviewed the data of 77 patients to examine the influence of factors such as the intention of treatment (curative/palliative), extent of surgery, resection margins, status of disease at the time of local recurrence and the grade of the tumour. A total of 70 patients underwent surgery for recurrent chondrosarcoma. In seven patients surgery was not a viable option. Metastatic disease occurred in 41 patients, appearing synchronously with the local recurrence in 56% of cases. For patients without metastasis at the time of local recurrence, the overall survival at a mean follow-up after recurrence of 67 months (0 to 289) was 74% (5 of 27) compared with 19% (13 of 50) for patients with metastasis at or before the development of the recurrence. Neither the type/extent of surgery, site of tumour, nor the resection margins for the recurrent tumour significantly influenced the overall survival. With limited survival for patients with metastatic disease at the time of local recurrence (0% for patients with grade III and de-differentiated chondrosarcoma), palliative treatment, including local radiation therapy and debulking procedures, should be discussed with the patients to avoid long hospitalisation and functional deficits. For patients without metastasis at the time of local recurrence, the overall survival of 74% justifies an aggressive approach including wide resection margins and extensive reconstruction.
Two-Photon Laser Microprinting of Highly Ordered Nanoporous Materials Based on Hexagonal Columnar Liquid Crystals (2022)

Nanoporous materials relying on supramolecular liquid crystals (LCs) are excellent candidates for size- and charge-selective membranes. However, whether they can be manufactured using printing technologies remained unexplored so far. In this work, we develop a new approach for the fabrication of ordered nanoporous microstructures based on supramolecular LCs using two-photon laser printing. In particular, we employ photo-cross-linkable hydrogen-bonded complexes, that self-assemble into columnar hexagonal (Col<sub>h</sub>) mesophases, as the base of our printable photoresist. The presence of photopolymerizable groups in the periphery of the molecules enables the printability using a laser. We demonstrate the conservation of the Col<sub>h</sub> arrangement and of the adsorptive properties of the materials after laser microprinting, which highlights the potential of the approach for the fabrication of functional nanoporous structures with a defined geometry. This first example of printable Col<sub>h</sub> LC should open new opportunities for the fabrication of functional porous microdevices with potential application in catalysis, filtration, separation, or molecular recognition.
Amyloidosis in alkaptonuria (2015)

Alkaptonuria (AKU) is an ultra-rare inborn error of metabolism developed from the lack of homogentisic acid oxidase activity, causing homogentisic acid (HGA) accumulation that produces an HGA-melanin ochronotic pigment, of hitherto unknown composition. Besides the accumulation of HGA, the potential role and presence of unidentified proteins has been hypothesized as additional causal factors involved in ochronotic pigment deposition. Evidence has been provided on the presence of serum amyloid A (SAA) in several AKU tissues, which allowed classifying AKU as a novel secondary amyloidosis. In this paper, we will briefly review all direct and indirect lines of evidence related to the presence of amyloidosis in AKU. We also report the first data on abnormal SAA serum levels in a cohort of AKU patients.
A continuous test data method to determine a reference curve and shift rate for isothermal physical aging (1999)

Abstract The mechanical response of a material undergoing isothermal physical aging is governed by a reference curve (typically time‐dependent modulus or compliance) and a shift rate (which describes the rate of aging). In the standard analysis approach, these parameters are determined from a series of load/unload creep or relaxation tests, in which only the load portion data is used for property evaluation. In this paper, a new continuous test data (CTD) method is presented to determine these parameters using both the load and unload data from such a test series. This is accomplished by employing effective time theory to predict the full load/unload data set, with the reference curve and shift rate obtained as those which best fit the experimental data. It is demonstrated that the references curve obtained via the standard approach is not capable of predicting the full load/unload data set, while the CTD method using a Prony series fits this same data very well. Several concerns regarding the CTD method are addressed, including the differences in the CTD and standard method shift rate, the effect of vertical shifting or material nonlinearity on the results, and application of the method to other loading scenarios. Results are presented for long‐term and variable stress tests. The data used in the study was obtained from polyimide resin and polyimide/carbon fiber composite specimens at several temperatures below T g .
Inhibition of Platelet Integrin α IIb β 3 by Peptides That Interfere With Protein Kinases and the β 3 Tail (2000)

alpha-Thrombin stimulation of human platelets initiates inside-out signaling to integrin alpha(IIb)beta(3) (glycoprotein IIb/IIIa), resulting in the exposure of ligand binding sites. In the present study, the regulation of alpha(IIb)beta(3) via protein kinases was investigated in platelets permeabilized with streptolysin O by introducing peptides that interfere with these enzymes and with possible regulatory domains in the cytosolic tail of the beta(3) subunit. Compared with intact platelets, the permeabilized platelets preserved >80% of the aggregation, secretion, and alpha(IIb)beta(3) ligand binding capacity. The peptide YIYGSFK, a substrate for Src kinases, inhibited alpha-thrombin-induced ligand binding to alpha(IIb)beta(3), but a reversed peptide with Y-->F substitutions (KFSGFIF) had no effect. Ligand binding to alpha(IIb)beta(3) was also inhibited by the peptide RKRCLRRL, which binds irreversibly to the catalytic domain of protein kinase C. Peptides corresponding to parts of the protein C inhibitor and beta(2)-glycoprotein I were used as negative controls and failed to interfere with ligand binding. Possible target domains for protein kinases are present in the cytoplasmic tail of the beta(3) subunit. The LLITIHDR peptide, matching the membrane-proximal domain of beta(3) (residues 717 to 724), had no effect, but NNPLYKEA (residues 743 to 750), EATSTFTN (residues 749 to 756), and TNITYRGT (residues 755 to 762), which mimicked overlapping domains of the carboxy-terminal part of beta(3), reduced alpha-thrombin-induced ligand binding by 60+/-4%, 97+/-1%, and 97+/-2% (n=3) at 500 micromol/L peptide, respectively. These observations indicate that Src kinases and protein kinase C take part in inside-out signaling to integrin alpha(IIb)beta(3) and identify target domains in beta(3) that contribute to the regulation of this integrin.