gebhart/patrepeval huggingface dataset:
Detection of Myoglobin-Derived Radicals On Reaction of Metmyoglobin With Hydrogen Peroxide and Other Peroxidic Compounds (1990)

The reaction of metmyoglobin with equimolar concentrations of hydrogen peroxide has been studied using both electron spin resonance (e.s.r.) and optical spectroscopy. Using the former technique a strong anisotropic e.s.r. signal is observed, in the presence of the spin trap DMPO, which decays relatively rapidly. This previously unobserved signal, which is also observed on reaction of metmyoglobin with a number of other powerful oxidants (peracetic acid, 3-chloroperoxybenzoic acid, monoperoxyphthalic acid, iodosyl benzene, tBuOOH and cumene hydroperoxide) is assigned to a slowly-tumbling, metmyoglobin-derived, spin adduct. The parameters of this signal (aN 1.45, aH 0.83 mT) are consistent with the trapped radical having a heteroatom centre: this is believed to be oxygen. The concentration of this species is not affected by compounds such as 2-deoxyribose, mannitol and phenylalanine which are all efficient hydroxyl radical scavengers, demonstrating that the formation of this radical is not due to reaction of "free" HO. generated by breakdown of H2O2 by released iron ions. The concentration of this species is however decreased by desferal, ascorbate. Trolox C, salicylate and, to a lesser extent, linoleic acid; with the first three of these compounds further substrate-derived radicals are also observed. Examination of similar reaction systems (though in the absence of DMPO) by optical spectroscopy shows that the myoglobin (IV) species is formed and that this species behaves in a somewhat different manner with these added compounds. These results suggest that the radical trapped in the e.s.r. experiments is a myoglobin-derived species, probably a tyrosine peroxyl radical, arising from oxidative damage to the globin moiety. The diminution of both the e.s.r. signal of the spin adduct and the optical absorption of the myoglobin (IV) species in the presence of linoleic acid suggests that these myoglobin-derived species can initiate oxidative damage but that this process can be ameliorated by the presence of a number of water-soluble compounds such as ascorbate, Trolox C, desferal and salicylate.
Antigen-independent, integrin-mediated T cell activation. (1995)

The "outside-in" signals produced by the interaction of integrin molecules with the extracellular matrix (ECM) trigger a multitude of cellular events. The vitronectin receptor (VNR), an alpha v beta 3 heterodimer, functions as a costimulatory molecule for the activation of a subset of V gamma 1.1/C gamma 4-bearing gamma/delta T cells, which have been postulated to recognize a ubiquitous self-antigen. We addressed the question of whether stimulation of these T cells requires both engagement of the VNR by ECM proteins and engagement of the TCR by its Ag. We introduced into a TCR- but VNR+ mutant T cell hybridoma, TG40 (derived from 2B4), a chimeric molecule that contains the cytoplasmic tail of the TCR zeta-chain fused to the cytoplasmic and transmembrane region of either human CD8 or human CD25. The transfectants expressing the chimeric molecules secreted IL-2 constitutively when the VNR was engaged with a ligand, e.g., provided by ECM proteins present in FCS. This constitutive cytokine secretion could be blocked with mAb directed against the VNR, with or the peptide RGD, or by growth in serum-free medium. VNR-mediated cell activation also induced the phosphorylation of the zeta-chain. Signaling through the zeta-chain was required, as cells transfected with a chimera containing only a 22 amino-acid long, truncated zeta-chain did not secrete IL-2 constitutively. Thus, we demonstrated that the binding of the VNR to ECM protein in the presence of the zeta-chain is sufficient to induce cytokine secretion by T cells and does not require the recognition of an Ag by the TCR. Such integrin-mediated, Ag-independent activation of T cells may play a critical role in the potentiation of inflammatory responses.
Effect of Filtration on Subsequently Stored Platelet Concentrates (1994)

The effect of filtration on the quality of platelet concentrates (PC) during storage was investigated. Two leukocyte depletion filters (Pall PL50HF and Sepacell PL-10A) were applied to filter PC made from a pool of 4 huffy coats. For each experiment 3 PC were pooled and divided into 3 identical PC to eliminate differences between the PC. Two PC were filtered, and the third PC served as an unfil- tered control. A total of 12 experiments was performed. Before filtration, volumes of the PC were 263 ± 11.7 ml (mean±SD). Platelet and leukocyte counts per PC were 241±25.9 x 10^9 and7.2±1.8 x 10^6, respectively. After filtration leukocyte counts did not exceed 5 x 10^4 in any of the PC. In the PC filtered with the Pall PL50HF the mean platelet loss was approximately 14% and with the Sepacell PL-10A, 17%. During a 9-day storage period the pH, PO(2), PCO(2), bicarbonate, lactate and glucose concentration and LDH release as well as the morphology, examined by the swirling effect and microscopically, were not significantly different in filtered and unfiltered units. Filtration through the 2 investigated leukocyte depletion filters for PC did not adversely affect in vitro viability of the platelets during storage.
Prefetch injection based on hardware monitoring and object metadata (2004)

Cache miss stalls hurt performance because of the large gap between memory and processor speeds - for example, the popular server benchmark SPEC JBB2000 spends 45% of its cycles stalled waiting for memory requests on the Itanium® 2 processor. Traversing linked data structures causes a large portion of these stalls. Prefetching for linked data structures remains a major challenge because serial data dependencies between elements in a linked data structure preclude the timely materialization of prefetch addresses. This paper presents Mississippi Delta (MS Delta), a novel technique for prefetching linked data structures that closely integrates the hardware performance monitor (HPM), the garbage collector's global view of heap and object layout, the type-level metadata inherent in type-safe programs, and JIT compiler analysis. The garbage collector uses the HPM's data cache miss information to identify cache miss intensive traversal paths through linked data structures, and then discovers regular distances ( deltas ) between these linked objects. JIT compiler analysis injects prefetch instructions using deltas to materialize prefetch addresses.We have implemented MS Delta in a fully dynamic profile-guided optimization system: the StarJIT dynamic compiler [1] and the ORP Java virtual machine [9]. We demonstrate a 28-29% reduction in stall cycles attributable to the high-latency cache misses targeted by MS Delta and a speedup of 11-14% on the cache miss intensive SPEC JBB2000 benchmark.
Saccade-Related Activity in the Parietal Reach Region (2000)

In previous experiments, we showed that cells in the parietal reach region (PRR) in monkey posterior parietal cortex code intended reaching movements in an eye-centered frame of reference. These cells are more active when an arm compared with an eye movement is being planned. Despite this clear preference for arm movements, we now report that PRR neurons also fire around the time of a saccade. Of 206 cells tested, 29% had perisaccadic activity in a delayed-saccade task. Two findings indicate that saccade-related activity does not reflect saccade planning or execution. First, activity is often peri- or postsaccadic but seldom presaccadic. Second, cells with saccade-related activity were no more likely to show strong saccadic delay period activity than cells without saccade-related activity. These findings indicate that PRR cells do not take part in saccade planning. Instead, the saccade-related activity in PRR may reflect cross-coupling between reach and saccade pathways that may be used to facilitate eye-hand coordination. Alternatively, saccade-related activity may reflect eye position information that could be used to maintain an eye-centered representation of intended reach targets across eye movements.
Vagus nerve stimulation (VNS): utility in neuropsychiatric disorders (2003)

Early in the last century, neuroscientists initially speculated that it might be possible to influence brain activity and associated behaviours by stimulating the vagus nerve in the neck. Several animal studies pointed to this possibility. In the 1980s, Zabara discovered that vagus nerve stimulation (VNS) could reduce or eliminate seizures in dogs. His discovery led to enhanced methods of direct VNS and the development of an implantable device for human VNS. VNS is now an accepted long-term treatment for epilepsy, used by over 15000 patients worldwide. Many have wondered whether VNS could treat other neuropsychiatric disorders. This paper reviews the neurobiology involved in VNS, highlights the VNS clinical findings to date, and discusses potential VNS research opportunities for both clinical and basic investigators. Comments on the clinical utility of VNS in actual clinical practice are provided.
Tumour necrosis factor-α induces Langerhans cell migration in humans (1999)

The role of tumour necrosis factor (TNF)-alpha in the mobilization and migration of human epidermal Langerhans cells (LC) has been investigated. Intradermal injection of normal human volunteers with homologous recombinant TNF-alpha was found to cause a dose-dependent reduction in the frequency of LC within epidermal sheets 2 h later. Equivalent results were obtained when epidermal LC were identified on the basis of either CD1a or HLA-DR expression. At the dose of TNF-alpha used routinely (500 U), treatment resulted in an average reduction in LC density of approximately 24%. Treatment with TNF-alpha was associated with a perivascular polymorphonuclear infiltration at 2 h, but the epidermis appeared normal with neither fibrinoid necrosis nor vasculitis, and LC morphology was not affected significantly. These results demonstrate that TNF-alpha provides an important signal for LC migration in humans and is likely therefore to play a crucial part in the induction of cutaneous immune responses.
Loss of ATM accelerates pancreatic cancer formation and epithelial–mesenchymal transition (2015)

Pancreatic ductal adenocarcinoma (PDAC) is associated with accumulation of particular oncogenic mutations and recent genetic sequencing studies have identified ataxia telangiectasia-mutated (ATM) mutations in PDAC cohorts. Here we report that conditional deletion of ATM in a mouse model of PDAC induces a greater number of proliferative precursor lesions coupled with a pronounced fibrotic reaction. ATM-targeted mice display altered TGFβ-superfamily signalling and enhanced epithelial-to-mesenchymal transition (EMT) coupled with shortened survival. Notably, our mouse model recapitulates many features of more aggressive human PDAC subtypes. Particularly, we report that low expression of ATM predicts EMT, a gene signature specific for Bmp4 signalling and poor prognosis in human PDAC. Our data suggest an intimate link between ATM expression and pancreatic cancer progression in mice and men.
mTOR inhibitors are synergistic with methotrexate: an effective combination to treat acute lymphoblastic leukemia (2008)

We have previously demonstrated that mTOR inhibitors (MTIs) are active in preclinical models of acute lymphoblastic leukemia (ALL). MTIs may increase degradation of cyclin D1, a protein involved in dihydrofolate reductase (DHFR) synthesis. Because resistance to methotrexate may correlate with high DHFR expression, we hypothesized MTIs may increase sensitivity of ALL to methotrexate through decreasing DHFR by increasing turn-over of cyclin D1. We tested this hypothesis using multiple ALL cell lines and nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice xenografted with human ALL. We found MTIs and methotrexate were synergistic in combination in vitro and in vivo. Mice treated with both drugs went into a complete and durable remission whereas single agent treatment caused an initial partial response that ultimately progressed. ALL cells treated with MTIs had markedly decreased expression of DHFR and cyclin D1, providing a novel mechanistic explanation for a combined effect. We found methotrexate and MTIs are an effective and potentially synergistic combination in ALL.
Kinetic competence of the cADP-ribose‒CD38 complex as an intermediate in the CD38/NAD+ glycohydrolase-catalysed reactions: implication for CD38 signalling (2001)

CD38/NAD(+) glycohydrolase is a type II transmembrane glycoprotein widely used to study T- and B-cell activation and differentiation. CD38 is endowed with two different activities: it is a signal transduction molecule and an ectoenzyme that converts NAD(+) into ADP-ribose (NAD(+) glycohydrolase activity) and small proportions of cADP-ribose (cADPR; ADP-ribosyl cyclase activity), a calcium-mobilizing metabolite, which, ultimately, can also be hydrolysed (cADPR hydrolase activity). The relationship between these two properties, and strikingly the requirement for signalling in the formation of free or enzyme-complexed cADPR, is still ill-defined. In the present study we wanted to test whether the CD38-cADPR complex is kinetically competent in the conversion of NAD(+) into the reaction product ADP-ribose. In principle, such a complex could be invoked for cross-talk, via conformational changes, with neighbouring partner(s) of CD38 thus triggering the signalling phenomena. Analysis of the kinetic parameters measured for the CD38/NAD(+) glycohydrolase-catalysed hydrolysis of 2'-deoxy-2'-aminoribo-NAD(+) and ADP-cyclo[N1,C1']-2'-deoxy-2'-aminoribose (slowly hydrolysable analogues of NAD(+) and cADPR respectively) ruled out that the CD38-cADPR complex can accumulate under steady-state conditions. This was borne out by simulation of the prevalent kinetic mechanism of CD38, which involve the partitioning of a common E.ADP-ribosyl intermediate in the formation of the enzyme-catalysed reaction products. Using this mechanism, microscopic rate conditions were found which transform a NAD(+) glycohydrolase into an ADP-ribosyl cyclase. Altogether, the present work shows that if the cross-talk with a partner depends on a conformational change of CD38, this is most probably not attributable to the formation of the CD38-cADPR complex. In line with recent results on the conformational change triggered by CD38 ligands [Berthelier, Laboureau, Boulla, Schuber and Deterre (2000) Eur. J. Biochem. 267, 3056-3064], we believe that the Michaelis CD38-NAD(+) complex could play such a role instead.
Long‐term assessment of reservoir integrity utilizing seismic source parameters as recorded with integrated microseismic‐pressure arrays (2011)

In this paper, we investigate how an integrated approach to long‐term reservoir monitoring utilizing pressure and micorsiemic data can be used to identify changes in reservoir behaviour leading to compromises in reservoir integrity. In particular, we examine the observations related to a cyclic steam operation and subsequent loss of steam containment. Based on these observations, we suggest that the integration of real‐time microseismic monitoring provides an opportunity to investigate reservoir integrity over long‐term field development.
Flexible transparent conductive coatings by combining self-assembly with sintering of silver nanoparticles performed at room temperature (2011)

Transparent conductive coatings are essential for fabrication of a variety of printed electronic devices such as flexible displays and solar cells. We report on a simple method to obtain such coatings by using aqueous dispersions of silver nanoparticles in an evaporative lithography process which is performed directly onto plastic substrates. In essence, a droplet containing silver nanoparticles is placed on top of a metallic mesh, instantaneously spreading over the mesh and the plastic substrate, and after the flow of the dispersion towards the wires of the mesh and drying, a transparent grid composed of the nanoparticles is formed. The silver nanoparticles are tailored to self-sinter upon short exposure to HCl vapors, due to the presence of polyacrylic acid salt on the surface of the particles. Therefore, immediate sintering of the silver nanoparticles in the thin lines of the grid occurs even at room temperature, enabling formation of transparent, flexible conductive grid on heat-sensitive substrates. The process yielded a conductive array having a very low sheet resistance, 9 ± 0.8 Ω/□, and a transparency above 75%. The application of the flexible conductive grid, which can replace conventional and expensive ITO, is demonstrated in an electroluminescent (EL) device.
Mitogenic properties of a bispecific single-chain Fv-Ig fusion generated from CD2-specific mAb to distinct epitopes. (1998)

The combination of anti-CD2 mAb 9.6 and 9-1, specific for distinct epitopes, induces proliferation of resting human T cells. The mitogenic activity of this mAb mixture depends upon accessory cells and the 9-1 mAb Fc domain. To further study the functional properties of these mAb, their variable regions were cloned and expressed as monospecific single-chain Fv (scFv) proteins fused to the human IgG1 Fc domain (scFvIg). A novel bispecific scFvIg was constructed by cloning the two monospecific scFv binding sites in tandem, with the 9.6 scFv placed N-terminal to the 9-1 scFvIg. Monospecific scFvIg binding to CD2 was comparable to that of the corresponding parental mAb, while the bispecific scFvIg exhibited binding activity similar to that of the 9-1 scFvIg. The combination of 9.6 scFvIg and 9-1 mAb was mitogenic, whereas mixtures including the 9-1 scFvIg were non-stimulatory, confirming the unique properties of the 9-1 IgG3 Fc. Without the IgG3 tail, the bispecific 9.6/9-1 scFvIg was directly mitogenic and was a more potent mitogen than the mAb mixture, but was accessory cell dependent. Unlike the combination of mAb, the bispecific reagent did not directly mobilize calcium in T cells. In comparison to the mAb mixture, bispecific 9.6/9-1 scFvIg-mediated stimulation of a mixed lymphocyte reaction was significantly more resistant to inhibition of the CD28 co-stimulatory pathway by the inhibitor CTLA-4-Ig. These results show that expression of the 9.6 and 9-1 binding sites together on a bispecific scFvIg increased the mitogenic properties of the mAb and altered the degree of accessory cell signals required for T cell activation.
The effect of pitch on deformation behavior and the stretching-induced failure of a polymer-encapsulated stretchable circuit (2010)

The deformation behavior and failure mechanisms of parallel-aligned, horseshoe-patterned, stretchable conductors encapsulated in a polymer substrate were investigated by numerical and experimental analyses. A design guideline for the optimal pitch between the conductors was proposed through numerical analysis, and two extreme cases-fine and coarse pitches-were investigated by in situ experimental observations. The experimental results demonstrate that the stretchable conductors enable elongation up to 123 and 135% without metal rupture for the fine and coarse pitches, respectively. The difference between these numbers is much smaller (12%) than expected from the simulations. It is found and confirmed by a modified simulation model that the reason for this is interfacial delamination, the onset of which depends on the pitch of the conductors and occurs before metal rupture of the conductors. The definition of 'stretchability of the electronic interconnects' is discussed based on the facts that two different failure mechanisms occur: interfacial delamination and metal rupture.
Danazol and its principal metabolites interfere with binding of testosterone, cortisol, and thyroxin by plasma proteins. (1982)

Danazol and its three principal metabolites (2-hydroxy-methylethisterone, 2-hydroxymethyl-1,2-dehydroethisterone, and ethisterone) competitively displace cortisol and testosterone from plasma proteins. This effect is in addition to the reported inhibition of the production of testosterone-binding globulin and thyroxin-binding globulin. We saw no competitive inhibition of thyroxin binding. Concentrations of total testosterone, total cortisol, and total thyroxin were low, whereas percentages of free testosterone, free cortisol, and free thyroxin were abnormally high in women being treated with danazol. Values for testosterone, cortisol, and thyroxin in danazol-treated patients should therefore be appropriately corrected before interpretation. Protein-binding assays for testosterone or cortisol that involve testosterone- or cortisol-binding globulin may be invalid in danazol-treated subjects because of the competitive binding of danazol and its metabolites to these proteins.
Latex allergen database (1997)

Two-dimensional (2-D) electrophoresis followed by immunoblotting and N-terminal protein microsequencing were used to characterize and identify the IgE-reactive proteins of Hevea latex that are the main cause of the latex type I allergy affecting especially health care workers and spina bifida children. This approach generated a comprehensive latex allergen database, which facilitated the integration of most of the latex allergen data presented in the literature. The major latex allergens Hev b 1, Hev b 3, Hev b 6 and Hev b 7 have been localized on our 2-D maps. Moreover, we were able to identify six previously undescribed IgE-binding latex proteins, namely enolase, superoxide dismutase, proteasome subunit C5, malate dehydrogenase, triosephosphate isomerase and endochitinase. The generated latex 2-D maps will provide valuable information to develop strategies for the isolation of the novel IgE binding proteins in order to study the frequency of sensitization among both risk groups. Detailed knowledge of all proteins involved in latex allergy will allow better diagnosis of latex allergy and to monitor the success of prevention strategies that are needed to reduce the high prevalence of latex allergy among both risk groups.
Discontinuous Changes in Ionic Conductivity of a Block Copolymer Electrolyte through an Order–Disorder Transition (2012)

The ionic conductivity of a block copolymer electrolyte was measured in an in situ small-angle X-ray scattering experiment as it transitioned from an ordered lamellar structure to a disordered phase. The ionic conductivity increases discontinuously as the electrolyte transitions from order to disorder. A simple framework for quantifying the magnitude of the discontinuity is presented. This study lays the groundwork for understanding the effect of more complex phase transitions such as order-order transitions on ion transport.