gebhart/patrepeval huggingface dataset:
Synthesis, characterization and ethylene reactivity of 2-diphenylphosphanylbenzamido nickel complexes (2004)

Addition of primary amines to N-[2-(diphenylphosphanyl)benzoyloxy]succinimide affords 2-diphenylphosphanylbenzamides, Ph2PC6H4C(O)NHR (R = C(CH3)3, 3; R = H, 4; R = CH2CH2CH3, 5; R = CH(CH3)2, 6). Addition of NiCl(eta3-CH2C6H5)(PMe3) to the deprotonated potassium salts of the amides and subsequent treatment of two equivalents of B(C6F5)3 to the resulting products furnishes eta3-benzyl zwitterionic nickel(II) complexes, [Ph2PC6H4C(O)NR-kappa2N,P]Ni(eta3-CH2C6H5) (R = C6H5, 9; R = C(CH3)3, 10; R = H, 11; R = CH2CH2CH3, 12; R = CH(CH3)2, 13). Solid structures of 9, 11, 13 and the intermediate eta1-benzyl nickel(II) complexes, [Ph2PC6H4C(O)NR-kappa2N,P]Ni(eta1-CH2C6H5)(PMe3) (R = C6H5, 7; R = C(CH3)3, 8) were determined by X-ray crystallography. When ethylene is added to the eta3-benzyl zwitterionic nickel(II) complexes, butene is obtained by the complexes 9-12 but complex 13 provides very high molecular-weight branched polyethylene (Mw, approximately 1300000) with excellent activity (up to 5200 kg mol-1 h-1 at 100 psi gauge).
Ferromagnetism and giant magnetoresistance in the rare-earth fulleridesEu6−xSrxC60 (2002)

We have studied crystal structure, magnetism, and electric transport properties of a europium fulleride ${\mathrm{Eu}}_{6}{\mathrm{C}}_{60}$ and its Sr-substituted compounds, ${\mathrm{Eu}}_{6\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{C}}_{60}.$ They have a bcc structure, which is an isostructure of other ${M}_{6}{\mathrm{C}}_{60}$ $(M$ represents an alkali atom or an alkaline-earth atom). Magnetic measurements revealed that magnetic moment is ascribed to the divalent europium atom with $S=7/2$ spin, and a ferromagnetic transition was observed at ${T}_{C}=10--14\mathrm{K}.$ In ${\mathrm{Eu}}_{6}{\mathrm{C}}_{60},$ we also confirm the ferromagnetic transition by heat-capacity measurement. The striking feature in ${\mathrm{Eu}}_{6\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{C}}_{60}$ is very large negative magnetoresistance at low temperature; the resistivity ratio $\ensuremath{\rho}(H=9\mathrm{T})/\ensuremath{\rho}(H=0\mathrm{T})$ reaches almost ${10}^{\ensuremath{-}3}$ at 1 K in ${\mathrm{Eu}}_{6}{\mathrm{C}}_{60}.$ Such large magnetoresistance is the manifestation of a strong $\ensuremath{\pi}\ensuremath{-}f$ interaction between conduction carriers on ${\mathrm{C}}_{60}$ and $4f$ electrons of Eu.
Toward a globally robust decentralized control for large-scale power systems (1997)

A robust control scheme is presented that stabilizes a nonlinear model of a power system to a very large class of disturbances that includes any disturbances causing the system to exhibit sustained oscillation. The disturbance can be anywhere in the power system. The fact that the improvement in stability is significant and system wide leads to the name globally robust control. The control is local or decentralized in the sense that the control of each generator depends only on information available at that generator, and is derived using Lyapunov's direct method. The derivation is quite general, permitting a second-order representation of the turbine/governor and any generator model. Simulation results are presented which show the effectiveness of the proposed control against instabilities of current importance including sustained oscillations following a major system disturbance such as a fault or major line outage. The control is also effective for steady-state operation.
Isolation of plasma from whole blood using planar microfilters for lab-on-a-chip applications (2005)

Researchers are actively developing devices for the microanalysis of complex fluids, such as blood. These devices have the potential to revolutionize biological analysis in a manner parallel to the computer chip by providing very high throughput screening of complex samples and massively parallel bioanalytical capabilities. A necessary step performed in clinical chemistry is the isolation of plasma from whole blood, and effective sample preparation techniques are needed for the development of miniaturized clinical diagnostic devices. This study demonstrates the use of passive, operating entirely on capillary action, transverse-flow microfilter devices for the microfluidic isolation of plasma from whole blood. Using these planar microfilters, blood can be controllably fractionated with minimal cell lysis. A characterization of the device performance reveals that plasma filter flux is dependent upon the wall shear rate of blood in the filtration channel, and this result is consistent with macroscale blood filtration using microporous membranes. Also, an innovative microfluidic layout is demonstrated that extends device operation time via capillary action from seconds to minutes. Efficiency of these microfilters is approximately three times higher than the separation efficiencies predicted for microporous membranes under similar conditions. As such, the application of the microscale blood filtration designs used in this study may have broad implications in the design of lab-on-a-chip devices, as well as the field of separation science.
Viscoelastic shear properties of articular cartilage and the effects of glycosidase treatments (1993)

The objectives of this study were to determine the viscoelastic shear properties of articular cartilage and to investigate the effects of the alteration of proteoglycan structure on these shear properties. Glycosidase treatments (chondroitinase ABC and Streptomyces hyaluronidase) were used to alter the proteoglycan structure and content of the tissue. The dynamic viscoelastic shear properties of control and treated tissues were measured and statistically compared. Specifically, cylindrical bovine cartilage specimens were subjected to oscillatory shear deformation of small amplitude (gamma degrees = 0.001 radian) over a physiological range of frequencies (0.01-20 Hz) and at various compressive strains (5, 9, 12, and 16%). The dynamic complex shear modulus was calculated from the measurements. The experimental results show that the solid matrix of normal articular cartilage exhibits intrinsic viscoelastic properties in shear over the range of frequencies tested. These viscoelastic shear properties were found to be dependent on compressive strains. Our data also provide significant insights into the structure-function relationships for articular cartilage. Significant correlations were found between the material properties (the magnitude of dynamic shear modulus, the phase shift angle, and the equilibrium compressive modulus), and the biochemical compositions of the cartilage (collagen, proteoglycan, and water contents). The shear modulus was greatly reduced when the proteoglycans were degraded by either chondroitinase ABC or Streptomyces hyaluronidase. The results suggest that the ability of collagen to resist tension elastically provides the stiffness of the cartilage matrix in shear and its elastic energy storage capability. Proteoglycans enmeshed in the collagen matrix inflate the collagen network and induce a tensile prestress in the collagen fibrils. This interaction of the collagen and proteoglycan within the cartilage matrix provides the complex mechanism that allows the tissue to resist shear deformation.
Animal models of sacral neuromodulation for detrusor overactivity (2008)

The recent increase in the use of sacral neuromodulation (SN) for the treatment of detrusor overactivity has coincided with improved knowledge of micturition physiology and technological advances in nerve stimulation. Efficacy of SN treatment and patient satisfaction should continue to progress. Nevertheless, the exact mechanism of the action of this technique remains uncertain. Numerous theories have been proposed to explain the mechanism of action, including stimulation of efferents, or direct effect on the muscle, stimulation of the afferents, induction of spinal plasticity, and modifications of cortical activation. In experimental conditions, to evaluate the effects of electrical stimulation, animal models are generally focused on bladder inflammation or spinalization which both induce detrusor overactivity. Recently, experimental autoimmune encephalomyelitis in rats has proven useful to study bladder dysfunction characterized as both detrursor overactivity or acontractile detrursor. The present article reviews experimental approaches for SN for treatment of detrusor overactivity and provides explanations for the potential acting mechanisms.
Review article: probiotics and prebiotics in irritable bowel syndrome (2008)

Summary Background The human gut harbours a complex community of bacteria whose relationship with their host is normally mutually beneficial. Recent studies suggest a disturbance of this relationship in irritable bowel syndrome (IBS) and the potential to correct this using prebiotics and probiotics. Aim To review the mechanisms of action of probiotics and prebiotics in IBS and to assess their performance in clinical trials. Methods Articles relating to modes of action and randomized control trials of treatment were reviewed by searching PubMed using terms ‘probiotic’, ‘prebiotic’ and ‘irritable bowel’. Small uncontrolled studies in IBS were excluded. Results Probiotics can enhance gut barrier function, inhibit pathogen binding and modulate gut inflammatory response. They can also reduce visceral hypersensitivity associated with both inflammation and psychological stress. Probiotics can alter colonic fermentation and stabilize the colonic microbiota. Several large randomized, placebo‐controlled trials of adequate design have shown an improvement in flatulence and abdominal distension with a reduction in composite IBS symptoms scores. Conclusions Each probiotic has unique features and IBS patients are heterogeneous. Future efforts should be directed to identifying biomarkers of responsiveness to facilitate better targeting of treatment and hence improved efficacy.
Hypereosinophilic syndromes (2007)

Hypereosinophilic syndromes (HES) constitute a rare and heterogeneous group of disorders, defined as persistent and marked blood eosinophilia (> 1.5 x 10(9)/L for more than six consecutive months) associated with evidence of eosinophil-induced organ damage, where other causes of hypereosinophilia such as allergic, parasitic, and malignant disorders have been excluded. Prevalence is unknown. HES occur most frequently in young to middle-aged patients, but may concern any age group. Male predominance (4-9:1 ratio) has been reported in historic series but this is likely to reflect the quasi-exclusive male distribution of a sporadic hematopoietic stem cell mutation found in a recently characterized disease variant. Target-organ damage mediated by eosinophils is highly variable among patients, with involvement of skin, heart, lungs, and central and peripheral nervous systems in more than 50% of cases. Other frequently observed complications include hepato- and/or splenomegaly, eosinophilic gastroenteritis, and coagulation disorders. Recent advances in underlying pathogenesis have established that hypereosinophilia may be due either to primitive involvement of myeloid cells, essentially due to occurrence of an interstitial chromosomal deletion on 4q12 leading to creation of the FIP1L1-PDGFRA fusion gene (F/P+ variant), or to increased interleukin (IL)-5 production by a clonally expanded T cell population (lymphocytic variant), most frequently characterized by a CD3-CD4+ phenotype. Diagnosis of HES relies on observation of persistent and marked hypereosinophilia responsible for target-organ damage, and exclusion of underlying causes of hypereosinophilia, including allergic and parasitic disorders, solid and hematological malignancies, Churg-Strauss disease, and HTLV infection. Once these criteria are fulfilled, further testing for eventual pathogenic classification is warranted using appropriate cytogenetic and functional approaches. Therapeutic management should be adjusted to disease severity and eventual detection of pathogenic variants. For F/P+ patients, imatinib has undisputedly become first line therapy. For others, corticosteroids are generally administered initially, followed by agents such as hydroxycarbamide, interferon-alpha, and imatinib, for corticosteroid-resistant cases, as well as for corticosteroid-sparing purposes. Recent data suggest that mepolizumab, an anti-IL-5 antibody, is an effective corticosteroid-sparing agent for F/P-negative patients. Prognosis has improved significantly since definition of HES, and currently depends on development of irreversible heart failure, as well as eventual malignant transformation of myeloid or lymphoid cells.
Transcriptional regulation of human MAP2 gene in melanoma: role of neuronal bHLH factors and Notch1 signaling (2006)

Microtubule-associated protein 2 (MAP2), a neuron-specific protein, stabilizes microtubules and is critical for neurite outgrowth and dendrite development. Although MAP2 is widely used as a marker of neuronal differentiation, regulation of its transcription has not been investigated. We showed that MAP2 is frequently activated in human cutaneous melanoma. Here, we identified a 2.2 kb region that is sufficient for neuronal-specific expression in vitro and in vivo. Comparative analysis of the mouse, rat and human MAP2 promoter sequences showed the presence of a conserved bHLH factor binding sites. Electrophoretic mobility shift analysis, promoter mutagenesis and co-transfection experiments showed that NeuroD, a pro-neuronal differentiation factor, and Hairy and Enhancer of Split (HES1), a transcription repressor, are involved in the regulation of MAP2 promoter activity. Melanoma cells express both NeuroD and HES1. Chromatin immunoprecipitation showed that in metastatic melanoma cells N-box region of the MAP2 promoter is occupied by endogenous HES1. We show that the inhibition of Notch signaling, a regulator of HES1 gene expression, and/or shRNA knockdown of HES1 results in the upregulation of MAP2 promoter activity. Thus, our data suggest that Notch signaling, which is implicated in melanoma progression, and HES1 play a role in MAP2 gene regulation during melanoma progression.
14.2 DNPU: An 8.1TOPS/W reconfigurable CNN-RNN processor for general-purpose deep neural networks (2017)

Recently, deep learning with convolutional neural networks (CNNs) and recurrent neural networks (RNNs) has become universal in all-around applications. CNNs are used to support vision recognition and processing, and RNNs are able to recognize time varying entities and to support generative models. Also, combining both CNNs and RNNs can recognize time varying visual entities, such as action and gesture, and to support image captioning [1]. However, the computational requirements in CNNs are quite different from those of RNNs. Fig. 14.2.1 shows a computation and weight-size analysis of convolution layers (CLs), fully-connected layers (FCLs) and RNN-LSTM layers (RLs). While CLs require a massive amount of computation with a relatively small number of filter weights, FCLs and RLs require a relatively small amount of computation with a huge number of filter weights. Therefore, when FCLs and RLs are accelerated with SoCs specialized for CLs, they suffer from high memory transaction costs, low PE utilization, and a mismatch of the computational patterns. Conversely, when CLs are accelerated with FCL- and RL-dedicated SoCs, they cannot exploit reusability and achieve required throughput. So far, works have considered acceleration of CLs, such as [2-4], or FCLs and RLs like [5]. However, there has been no work on a combined CNN-RNN processor. In addition, a highly reconfigurable CNN-RNN processor with high energy-efficiency is desirable to support general-purpose deep neural networks (DNNs).
Comparison of the Functional Differences for the Homologous Residues within the Carboxy Phosphate and Carbamate Domains of Carbamoyl Phosphate Synthetase (1996)

Carbamoyl phosphate synthetase (CPS) from Escherichia coli catalyzes the formation of carbamoyl phosphate from two molecules of MgATP, bicarbonate, and glutamine. It has been previously shown that the amino- and carboxy-terminal halves of the large subunit of this protein are homologous. A working model for the active site structure of the carboxy-terminal domain of the large subunit of CPS was constructed based upon amino acid sequence alignments and the previously determined three-dimensional structures of two mechanistically related proteins, biotin carboxylase and D-alanine:D-alanine ligase. The model was tested by mutation of ten amino acid residues predicted to be important for binding and/or catalysis. The mutated residues were as follows: R571, R675, R715, D753, E761, N827, Q829, E841, N843, and R845. The mutant proteins were expressed, purified to homogeneity and the catalytic properties determined for a variety of assay formats. The mutants E761A, E841Q, N843D, and R845Q were diminished in their ability to synthesize carbamoyl phosphate. The R715A, Q829A, and R675A mutants displayed elevated Michaelis constants for MgADP in the partial back reaction. The mutants E761A, N827A, E841Q, N843D, and R845Q showed significant increases in the Michaelis constants for either bicarbonate or carbamoyl phosphate. No significant alterations were noted upon mutation of either R571 or D753 to an alanine residue and thus these amino acids do not appear essential for structure or catalytic activity. These results have been utilized to further support the proposal that the C-terminal half of the large subunit of CPS is primarily responsible for the phosphorylation of the carbamate intermediate during the final formation of carbamoyl phosphate. The measured effects on the catalyic activities displayed by these mutations were found to be comparable to the previously determined effects after mutation of the homologous residues located on the N-terminal half of CPS and also for those residues mutated within D-alanine:D-alanine ligase [Shi, Y., & Walsh, C.T. (1995) Biochemistry 34, 2768-2776].
A Retroviral Oncogene, akt , Encoding a Serine-Threonine Kinase Containing an SH2-Like Region (1991)

The v-akt oncogene codes for a 105-kilodalton fusion phosphoprotein containing Gag sequences at its amino terminus. Sequence analysis of v-akt and biochemical characterization of its product revealed that it codes for a protein kinase C-related serine-threonine kinase whose cellular homolog is expressed in most tissues, with the highest amount found in thymus. Although Akt is a serine-threonine kinase, part of its regulatory region is similar to the Src homology-2 domain, a structural motif characteristic of cytoplasmic tyrosine kinases that functions in protein-protein interactions. This suggests that Akt may form a functional link between tyrosine and serine-threonine phosphorylation pathways.
Immunogenicity of fresh and preserved cortical and cancellous allogeneic bone grafts as tested by modified migration inhibition test in mice. (1978)

Mice were grafted with allogeneic compact and cancellous bone. The bone used was fresh and preserved by either lyophilization or deep freezing. Preserved grafts were radiosterilized by a dose of 3.3 MRads. The immunization of recipients was assessed by a modified migration inhibition test based on migration of cells from three-dimensional clot culture. Both preservation methods seem to change bone immunogenicity and enhancement of migration instead of inhibition occurring in the case of fresh bone was noted.
Pharmacological evidence for a novel cysteinyl‐leukotriene receptor subtype in human pulmonary artery smooth muscle (2002)

1. To characterize the cysteinyl-leukotriene receptors (CysLT receptors) in isolated human pulmonary arteries, ring preparations were contracted with leukotriene C(4) (LTC(4)) and leukotriene D(4) (LTD(4)) in either the absence or presence of the selective CysLT(1) receptor antagonists, ICI 198615, MK 571 or the dual CysLT(1)/CysLT(2) receptor antagonist, BAY u9773. 2. Since the contractions induced by the cysteinyl-leukotrienes (cysLTs) in intact preparations failed to attain a plateau response over the concentration range studied, the endothelium was removed and the tissue treated continuously with indomethacin (Rubbed+INDO). In these latter preparations, the pEC(50) for LTC(4) and LTD(4) were not significantly different (7.61+/-0.07, n=20 and 7.96+/-0.09, n=22, respectively). However, the LTC(4) and LTD(4) contractions were markedly potentiated when compared with data from intact tissues. 3. Leukotriene E(4) (LTE(4)) did not contract human isolated pulmonary arterial preparations. In addition, treatment of preparations with LTE(4) (1 microM; 30 min) did not modify either the LTC(4) or LTD(4) contractions. 4. Treatment of preparations with the S-conjugated glutathione (S-hexyl-GSH; 100 microM, 30 min), an inhibitor of the metabolism of LTC(4) to LTD(4), did not modify LTC(4) contractions. 5. The pEC(50) values for LTC(4) were significantly reduced by treatment of the preparations with either ICI 198615, MK 571 or BAY u9773 and the pK(B) values were: 7.20, 7.02 and 6.26, respectively. In contrast, these antagonists did not modify the LTD(4) pEC(50) values. 6. These findings suggest the presence of two CysLT receptors on human pulmonary arterial vascular smooth muscle. A CysLT(1) receptor with a low affinity for CysLT(1) antagonists and a novel CysLT receptor subtype, both responsible for vasoconstriction. Activation of this latter receptor by LTC(4) and LTD(4) induced a contractile response which was resistant to the selective CysLT(1) antagonists (ICI 198615 and MK 571) as well as the non-selective (CysLT(1)/CysLT(2)) antagonist, BAY u9773.
Physiological Framework for the Regulation of Quorum Sensing-Dependent Public Goods in Pseudomonas aeruginosa (2013)

Many bacteria possess cell density-dependent quorum-sensing (QS) systems that often regulate cooperative secretions involved in host-microbe or microbe-microbe interactions. These secretions, or "public goods," are frequently coregulated by stress and starvation responses. Here we provide a physiological rationale for such regulatory complexity in the opportunistic pathogen Pseudomonas aeruginosa. Using minimal-medium batch and chemostat cultures, we comprehensively characterized specific growth rate-limiting macronutrients as key triggers for the expression of extracellular enzymes and metabolites directly controlled by the las and rhl QS systems. Expression was unrelated to cell density, depended on the secreted product's elemental composition, and was induced only when the limiting nutrient was not also a building block of the product; rhl-dependent products showed the strongest response, caused by the largely las-independent induction of the regulator RhlR and its cognate signal. In agreement with the prominent role of the rhl system, slow growth inverted the las-to-rhl signal ratio, previously considered a characteristic distinguishing between planktonic and biofilm lifestyles. Our results highlight a supply-driven, metabolically prudent regulation of public goods that minimizes production costs and thereby helps stabilize cooperative behavior. Such regulation would be beneficial for QS-dependent public goods that act broadly and nonspecifically, and whose need cannot always be accurately assessed by the producing cell. Clear differences in the capacities of the las and rhl systems to integrate starvation signals help explain the existence of multiple QS systems in one cell.