gebhart/patrepeval huggingface dataset:
Amino Acid Composition and Physicochemical Characterization of Chondroitinase from Arthrobacter aurescens (1975)

The amino acid and carbohydrate compositions of chondroitinase AC [EC 4.2.2.5] from Arthrobacter aurescens were determined, and its physicochemical properties were examined. 1. The enzyme has been shown to be a glycoprotein containing mannose, glucose, glucosamine, and glucuronic acid (3:5:4:2). 2. Its molecular wieght was estimated to be 76,000 by gel filtration on Sephadex G-200, 75,000-80,000 by SDS disc electrophoresis, and 75,800 by sedimentation veolcity. No subunits were detected in the molecule. 3. The physicochemical properties determined include: sedimentation coefficient (s(o)20, w=5.14 S), diffusion constant (D(o)=6.09 X 10(-7) cm2/sec), frictional ratio (f:f(o)=1.19) and apparent partial specific volume (v=0.73 ml/g). 4. The optical rotatory dispersion and circular dichroism of the enzyme were investigated. The contents of alpha-helix and beta-structure of the enzyme were estimated to be 16 and 25%, respectively.
The role of metals in neurodegenerative diseases. (2000)

There is increasing evidence in a number of neurodegenerative diseases that transition metal-mediated abnormalities play a crucial role in disease pathogenesis. In this treatise, we review the role of metal homeostasis as it pertains to alterations in brain function in neurodegenerative diseases. In fact, while there is documented evidence for alterations in transition metal homeostasis, redox-activity and localization, it is also important to realize that alterations in specific copper- and iron-containing metalloenzymes also appear to play a crucial role in the neurodegenerative process.
Gd-doped iron-oxide nanoparticles for tumour therapy via magnetic field hyperthermia (2007)

Gd-doped iron oxide nanoparticles were developed for use in tumour therapy via magnetic fluid hyperthermia (MFH). The nanoparticle composition was Gd0.02Fe2.98O4 as determined by ICP-AES. TEM image analysis showed the primary particles to be about 13 nm in diameter. The specific power adsorption rate (SAR) determined with a field strength of 246 Oe and 52 kHz was 36 W per gram of Fe. This value is about 4 times higher than the reported SAR values for Fe3O4. The heating rate for the nanoparticles in vivo and the potential for tumour therapy were determined in a mouse model. The mouse models treated with doped iron oxide displayed much slower tumour growth, the tumour doubled its mass after 7 days post-treatment compared to 4 days for those models treated with standard iron oxide or saline solution.
A functional tethered ligand thrombin receptor is present on human hematopoietic progenitor cells. (1996)

The processing of inflammatory signals occurs through a variety of mechanisms; the recent descriptions of the tethered ligand receptor for thrombin (JA Hoxie et al., J Biol Chem 268:13756, and TK Vu et al., Cell 64:1057) provide a novel route and mechanism for cellular activation after inflammation and thrombosis. Using standard flow-cytometric techniques, it has been shown that the tethered ligand receptor is found on a number of terminally differentiated hematopoietic cells including platelets, lymphocytes, and monocytes. In this paper, we show that the CD34+ subset of hematopoietic stem cells bears the tethered ligand receptor on its surface; in addition, stimulation of this receptor with the agonist peptide SFLLRN results in a dose-dependent increase in intracellular calcium levels. We also show that culturing bone marrow mononuclear cells in the presence of thrombin or the tethered ligand receptor agonist peptide results in a statistically significant increase in colony-forming units-erythroid and -granulocyte/macrophage (CFU-E and CFU-GM). Although more work is needed to establish the exact mechanism of this effect, our results suggest that activation of the tethered ligand thrombin receptor may modulate the proliferative responses of CD34+ hematopoietic progenitor cells.
The challenge of mapping the human connectome based on diffusion tractography (2017)

Tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain data set with ground truth tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. Here, we report the encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent). However, the same tractograms contain many more invalid than valid bundles, and half of these invalid bundles occur systematically across research groups. Taken together, our results demonstrate and confirm fundamental ambiguities inherent in tract reconstruction based on orientation information alone, which need to be considered when interpreting tractography and connectivity results. Our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations.
Polylactide-co-glycolide nanoparticles for controlled delivery of anticancer agents (2011)

The effectiveness of anticancer agents may be hindered by low solubility in water, poor permeability, and high efflux from cells. Nanomaterials have been used to enable drug delivery with lower toxicity to healthy cells and enhanced drug delivery to tumor cells. Different nanoparticles have been developed using different polymers with or without surface modification to target tumor cells both passively and/or actively. Polylactide-co-glycolide (PLGA), a biodegradable polyester approved for human use, has been used extensively. Here we report on recent developments concerning PLGA nanoparticles prepared for cancer treatment. We review the methods used for the preparation and characterization of PLGA nanoparticles and their applications in the delivery of a number of active agents. Increasing experience in the field of preparation, characterization, and in vivo application of PLGA nanoparticles has provided the necessary momentum for promising future use of these agents in cancer treatment, with higher efficacy and fewer side effects.
Biodegradable polymers based on renewable resources. V. Synthesis and biodegradation behavior of poly(ester amide)s composed of 1,4:3,6‐dianhydro‐<scp>D</scp>‐glucitol, α‐amino acid, and aliphatic dicarboxylic acid units (2001)

Abstract A series of poly(ester amide)s were synthesized by solution polycondensations of various combinations of p ‐toluenesulfonic acid salts of O,O′ ‐bis(α‐aminoacyl)‐1,4:3,6‐dianhydro‐ D ‐glucitol and bis (p ‐nitrophenyl) esters of aliphatic dicarboxylic acids with the methylene chain lengths of 4–10. The p ‐toluenesulfonic acid salts were obtained by the reactions of 1,4:3,6‐dianhydro‐ D ‐glucitol with alanine, glycine, and glycylglycine, respectively, in the presence of p ‐toluenesulfonic acid. The polycondensations were carried out in N ‐methylpyrrolidone at 40°C in the presence of triethylamine, giving poly(ester amide)s having number‐average molecular weights up to 3.8 × 10 4 . Their structures were confirmed by FTIR, 1 H‐NMR, and 13 C‐NMR spectroscopy. Most of these poly(ester amide)s are amorphous, except those containing sebacic acid and glycine or glycylglycine units, which are semicrystalline. All these poly(ester amide)s are soluble in a variety of polar solvents such as dimethyl sulfoxide, N,N ‐dimethylformamide, 2,2,2‐trifluoroethanol, m ‐cresol, pyridine, and trifluoroacetic acid. Soil burial degradation tests, BOD measurements in an activated sludge, and enzymatic degradation tests using Porcine pancreas lipase and papain indicated that these poly(ester amide)s are biodegradable, and that their biodegradability markedly depends on the molecular structure. The poly(ester amide)s were, in general, degraded more slowly than the corresponding polyesters having the same aliphatic dicarboxylic acid units, both in composted soil and in an activated sludge. In the enzymatic degradation, some poly(ester amide)s containing dicarboxylic acid components with shorter methylene chain lengths were degraded more readily than the corresponding polyesters with Porcine pancreas lipase, whereas most of the poly(ester amide)s were degraded more rapidly than the corresponding polyesters with papain. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 81: 2721–2734, 2001
Autoreactivity of Human VH Domains from cDNA Libraries: Analysis with a Bacterial Expression System (1998)

Previous studies showed that VH domains of several anti-DNA Abs can bind DNA in the absence of VL. In the current work, we tested the VH autoreactive potential more generally, examining VH domains that did not come from known autoantibodies. Using a bacterial expression system, we produced 11 fusion proteins, each containing a VH domain and a B domain of staphylococcal protein A. The VH domains were coded in cDNA libraries from circulating B cells of healthy young adult humans. Thus, binding properties of the Ig molecules from which they came were unknown. The B cells had not been stimulated in vitro. Seven cDNA clones combined the frequently expressed VH3-23 gene segment with varied DH and JH segments. The other clones contained unmutated VH3-7, VH3-9, VH3-53, and VH4-39 segments. We compared these bacterial expression products with single-chain Fv, VH and VL domains of IgM mAb 18/2, a VH3-23-encoded, DNA-binding autoantibody. Submicromolar concentrations of 5 of the 11 VH domains bound to ssDNA. Those and one more also bound to immobilized poly(dT), and two bound to circular plasmid dsDNA. Soluble poly(dT) was the most potent inhibitor in competitive ELISA. Seven of the VH domains also bound to immobilized nuclear ribonucleoprotein, four to histone and none to thyroglobulin. Two interacted with the matrix of a Sephacryl S-100 column. The polyreactive autoantigen-binding properties of these VH domains raise the question of whether these properties may play a role in the formation of the VH repertoire of circulating B cells.
Spatially Selective Nucleation of Metal Clusters on the Tobacco Mosaic Virus (2004)

Abstract Tobacco mosaic virus (TMV) is a very stable nanotube complex of a helical RNA and 2130 coat proteins. The special shape makes it an interesting nano‐object, especially as a template for chemical reactions. Here we use TMV as a chemically functionalized template for binding metal ions. Different chemical groups of the coat protein can be used as ligands or to electrostatically bind metal ions. Following this activation step, chemical reduction and electroless plating produces metal clusters of several nanometers in diameter. The clusters are attached to the virion without destroying its structure. Gold clusters generated from an ascorbic acid bath bind to the exterior surface as well as to the central channel of the hollow tube. Very high selectivity is reached by tuning Pd II and Pt II activations with phosphate: When TMV is first activated with Pd II , and thereafter metallized with a nickel–phosphinate bath, 3 nm nickel clusters grow in the central channel; when TMV from phosphate‐buffered suspensions is employed, larger nickel clusters grow on the exterior surface. Phosphate buffers have to be avoided when 3 nm nickel and cobalt wires of several 100 nm in length are synthesized from borane‐based baths inside the TMV channel. The results are discussed with respect to the inorganic complex chemistry of precursor molecules and the distribution of binding sites in TMV.
MicroRNA‐137 promoter methylation is associated with poorer overall survival in patients with squamous cell carcinoma of the head and neck (2010)

The results of this study indicate that miR-137 is methylated in tumor tissue from pharyngeal and laryngeal squamous cancers, in addition to oral squamous cell carcinoma, and that miR-137 promoter methylation has potential utility as a prognostic marker for SCCHN.
New order preserving access methods for very large files derived from linear hashing (1992)

A class of order-preserving dynamic hashing structures is introduced and analyzed. The access method is referred to as the dynamic random-sequential access method (DRSAM) and is derived from linear hashing. A new logical to physical mapping that is based on sequential bucket allocations in hash order is proposed. With respect to previous methods, this allocation technique has the following characteristics: (1) the structure captures the hashed order in consecutive storage areas so that order preserving (OPH) schemes should result in performance improvements for range queries and sequential processing; and (2) it adapts elastic buckets for the control of file growth. Under specific conditions, this approach outperforms the partial expansion method previously proposed by P.-A. Larson (1982).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Iterative procedures for reduction of blocking effects in transform image coding (1992)

The authors propose an iterative block reduction technique based on the theory of a projection onto convex sets. The idea is to impose a number of constraints on the coded image in such a way as to restore it to its original artifact-free form. One such constraint can be derived by exploiting the fact that the transform-coded image suffering from blocking effects contains high-frequency vertical and horizontal artifacts corresponding to vertical and horizontal discontinuities across boundaries of neighboring blocks. Another constraint has to be with the quantization intervals of the transform coefficients. Specifically, the decision levels associated with transform coefficient quantizers can be used as lower and upper bounds on transform coefficients, which in turn define boundaries of the convex set for projection. A few examples of the proposed approach are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Linkage of Asthma and Total Serum IgE Concentration to Markers on Chromosome 12q: Evidence from Afro-Caribbean and Caucasian Populations (1996)

To identify genes potentially relevant in atopic asthma, we analyzed markers in chromosome 12q15-q24.1 for linkage to asthma and total serum IgE concentration. Sib-pair analyses of 10 markers in 345 full- and 219 half-sib pairs from 29 multiplex Afro-Caribbean families provided evidence for linkage to this region for both asthma and total serum IgE. Certain alleles at these loci showed significant evidence of transmission disequilibrium with both asthma and high IgE. Using 6 of these markers and 11 additional markers, evidence for linkage of total IgE to 12q was also found in 12 Caucasian Amish kindreds (24 nuclear families) by both sib-pair and transmission disequilibrium analyses. These findings suggest that the 12q15-q24.1 region may contain a gene(s) controlling asthma and the associated "high total IgE" trait.
Thermal Modeling of Porous Insertion Electrodes (2003)

Isothermal calorimetry was performed on in ethylene carbonate:dimethyl carbonate cells. The measured rate of heat generation varied substantially with time. To understand why, we investigated the entropy, irreversible resistance, and heats of mixing. Two methods for computing the heat of mixing, one computational and one analytic, are derived. We demonstrate how the energy balance of Rao and Newman accounts for heat of mixing across electrodes, but neglects heat of mixing within particles and in the electrolyte, which may be of equal magnitude. In general, the magnitude of the heat of mixing, which is the amount of heat released during relaxation after interruption of the current, will be small in materials with transport properties sufficiently high to provide acceptable battery performance, with the possible exception of heat of mixing within the insertion particles if the particle radius is large. Comparing simulations of heat generation to calorimetry measurements reveals that the entropic heat is significant and accounts for much of the variation of the rate of heat generation. The rate of irreversible heat generation is larger when the open-circuit potential varies steeply with lithium concentration, because of diffusion limitations within the solid. © 2002 The Electrochemical Society. All rights reserved.
Caspase-Dependent Apoptosis by 2′,5′-Oligoadenylate Activation of RNase L Is Enhanced by IFN-β (2000)

The 2',5'-oligoadenylate (2-5A) system is an interferon (IFN)-regulated RNA decay pathway that provides innate immunity against viral infections. The biologic action of the 2-5A system is mediated by RNase L, an endoribonuclease that becomes enzymatically active after binding to 2-5A. RNase L is also implicated in mediating apoptosis in response to both viral and nonviral inducers. To study the cellular effects of RNase L activation directly, 2-5A was transfected into the human ovarian cancer cell line, Hey1B. Activation of RNase L by 2-5A resulted in specific 18S rRNA cleavage and induction of apoptosis, as measured by TUNEL and annexin V binding assays. In contrast, the dimeric form of 2-5A, ppA2'p5'A, neither activated RNase L nor caused apoptosis. Treatment with IFN-beta prior to 2-5A transfection enhanced cellular RNase L levels (< or = 2.2-fold) and increased the proportion of cells undergoing apoptosis (by < or =40%). However, rRNA cleavages after 2-5A transfections were not enhanced by IFN-beta pretreatments, indicating that basal levels of RNase L were sufficient for this activity. Apoptosis in response to RNase L activation was accompanied by cytochrome c release from mitochondria. Induction of apoptosis by either 2-5A alone or by the combination of 2-5A and IFN-beta was effectively blocked with either the pancaspase inhibitor, Z-VAD-fmk, or with the caspase 3 inhibitor, DEVD-fmk. Therefore, activation of RNase L by 2-5A leads to cytochrome c release into the cytoplasm and then to caspase activation and apoptosis. These results suggest potential uses for 2-5A in augmenting the anticancer activities of IFN.
Selective lysis of the autologous tumor by δTCS1<sup>+</sup> γ/δ<sup>+</sup> tumor‐infiltrating lymphocytes from human lung carcinomas (1990)

Two distinct non-overlapping populations of TcR1+ (gamma/delta) T cells have been described: the first, bearing the disulfide-linked gamma/delta heterodimer, is predominant in the peripheral blood; the second, expressing the non-disulfide-linked form of TcR1, is mostly confined to epithelial tissues (lung, gut, skin). TcR1+ lymphocytes may be cytotoxic and could be involved in anti-tumor immunity, especially against tumors at epithelial sites. Freshly derived tumor-infiltrating lymphocytes (TIL) obtained from two patients with lung cancer were enriched in CD3+WT31- cells. The percentage of this subset substantially increased upon culture in the presence of interleukin 2. These cells were TcR1+ as demonstrated by immunofluorescence and immunoprecipitation. In one case only 40% of this population reacted with delta TCS1 mAb, that recognizes the non-disulfide-linked form of TcR1, and co-expressed the CD8 antigen. Cultured TcR1+ TIL were able to kill fresh autologous tumor cells, K-562 and, to a lesser extent, some natural killer-resistant cell lines and allogeneic lung tumor cells in 4-h 51Cr-release cytotoxicity assays. The fractionated delta TCS1+ TIL lysed only autologous tumor cells and K-562, whereas the lytic activity against all the other targets was confined to the delta TCS1- subset. Moreover, the autotumor cytotoxicity was inhibited by anti-HLA class I but not by anti-CD1c or anti-LFA-1 mAb, suggesting that killing of the autologous tumor cells and non-major histocompatibility complex-restricted cytotoxicity are mediated by different mechanisms.
Comparison of ultraviolet light-emitting diodes with peak emission at 340 nm grown on GaN substrate and sapphire (2002)

Based on AlInGaN/AlInGaN multiquantum wells, we compare properties of ultraviolet light-emitting diodes (LED) with peak emission at 340 nm grown on free-standing hydride vapor phase epitaxially grown GaN substrate and on sapphire. For the LED grown on GaN substrate, a differential resistance as low as 13 Ω and an output power of more than one order of magnitude higher than that of the same structure grown on sapphire are achieved. Due to higher thermal conductivity of GaN, output power of the LEDs saturates at higher injection currents compared to the devices grown on sapphire.
Human JIK, a Novel Member of the STE20 Kinase Family That Inhibits JNK and Is Negatively Regulated by Epidermal Growth Factor (1999)

Mammalian members related to Saccharomyces cerevisiae serine/threonine kinase STE20 can be divided into two subfamilies based on their structure and function. The PAK subfamily is characterized by an N-terminal p21-binding domain (also known as CRIB domain), a C-terminal kinase domain, and is regulated by the small GTP-binding proteins Rac1 and Cdc42Hs. The second group is represented by the GCK-like members, which contain an N-terminal catalytic domain and lack the p21-binding domain. Some of them have been demonstrated to induce c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK) cascade, while others have been shown to be activated by a subset of stress conditions or apoptotic agents, although little is known about their specific function. Here, we have identified a novel human STE20-related serine/threonine kinase, belonging to the GCK-like subfamily. This kinase does not induce the JNK/SAPK pathway, but, instead, inhibits the basal activity of JNK/SAPK, and diminishes its activation in response to human epidermal growth factor (EGF). Therefore, we designated this molecule JIK for JNK/SAPK-inhibitory kinase. The inhibition of JNK/SAPK signaling pathway by JIK was found to occur between the EGF receptor and the small GTP-binding proteins Rac1 and Cdc42Hs. In contrast, JIK does not activate nor does it inhibit ERK2, ERK6, p38, or ERK5. Furthermore, JIK kinase activity is not modulated by any exogenous stimuli, but, interestingly, it is dramatically decreased upon EGF receptor activation. Thus, JIK might represent the first member of the STE20 kinase family whose activity can be negatively regulated by tyrosine kinase receptors, and whose downstream targets inhibit, rather than enhance, JNK/SAPK activation.
Decreased PERP Expression on Peripheral Blood Mononuclear Cells from Patient with Rheumatoid Arthritis Negatively Correlates with Disease Activity (2013)

These results demonstrated that PERP might be involved in the pathogenesis and a potential therapeutic target of RA by regulating the expression of IL-17.
Texture analysis of cervical cell nuclei by segmentation of chromatin patterns. (1979)

Texture parameters of the nuclear chromatin pattern can contribute to the automated classification of specimens on the basis of single cell analysis in cervical cytology. Current texture parameters are abstract and therefore hamper understanding. In this paper texture parameters are described that can be derived from the chromatin pattern after segmentation of the nuclear image. These texture parameters are more directly related to the visual properties of the chromatin pattern. The image segmentation procedure is based on a region grow algorithm which specifically isolates high chromatin density. The texture analysis method has been tested on a data set of images of 112 cervical nuclei on photographic negatives digitized with a step size of 0.125 micron. The preliminary results of a classification trial indicate that these visually interpretable parameters have promising discriminatory power for the distinction between negative and positive specimens.
An increase in cancer stem cell population after primary systemic therapy is a poor prognostic factor in breast cancer (2011)

The present study provides the clinical evidence that the putative CSCs in breast cancer are chemoresistant and are associated with tumour progression, emphasising the need for targeting of CSCs in the breast cancer therapeutics.