gebhart/patrepeval huggingface dataset:
Transport near the metal-insulator transition: Polypyrrole doped withPF6 (1994)

Heavily doped polypyrrole-hexafluorophosphate, PPy(${\mathrm{PF}}_{6}$), undergoes a metal-insulator (M-I) transition at resistivity ratio ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$=\ensuremath{\rho}(1.4 K)/${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$(300 K)\ensuremath{\approxeq}10: for ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$10, the system is metallic with \ensuremath{\rho}(T) remaining finite as T\ensuremath{\rightarrow}0, whereas for ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$&gt;10, the system is an insulator with \ensuremath{\rho}\ensuremath{\rightarrow}\ensuremath{\infty} as T\ensuremath{\rightarrow}0. In the critical regime, \ensuremath{\rho}(T) shows a power-law temperature dependence, \ensuremath{\rho}(T)=${\mathit{T}}^{\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\beta}}}$, with 0.31. The effect of the partially screened Coulomb interaction is substantial at low temperatures for samples on both sides of the M-I transition. In the insulating regime, the crossover from Mott variable-range hopping (VRH) to Efros-Shklovskii hopping is observed. In the metallic regime, the sign of the temperature coefficient of the resistivity changes at ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$\ensuremath{\approxeq}2. At T=1.4 K, the interaction length ${\mathit{L}}_{\mathit{T}}$=(\ensuremath{\Elzxh}D/${\mathit{k}}_{\mathit{B}}$T${)}^{1/2}$\ensuremath{\approxeq}30 \AA{}.Since this is smaller than the inelastic-scattering length, ${\mathit{L}}_{\mathrm{in}\mathrm{\ensuremath{\approxeq}}}$300 \AA{}, the contribution to \ensuremath{\rho}(T) from the electron-electron interaction is dominant. Application of high pressure decreases ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$, induces the transition into the metallic regime, and enables fine tuning of the M-I transition. For samples close to the M-I transition, the thermoelectric power is proportional to the temperature in both the metallic and insulating regimes. The correlation length (${\mathit{L}}_{\mathit{c}}$) increases as the disorder, characterized by ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$, approaches the M-I transition from either side. The expected divergence in ${\mathit{L}}_{\mathit{c}}$ at the M-I transition is qualitatively consistent with the values for ${\mathit{L}}_{\mathit{c}}$ inferred from the extrapolated \ensuremath{\sigma}(0) in the metallic regime and from analysis of the VRH magnetoresistance in the insulating regime. Thus, by using ${\mathrm{\ensuremath{\rho}}}_{\mathit{r}}$ to characterize the magnitude of the disorder, a complete and fully consistent picture of the M-I transition in PPy(${\mathrm{PF}}_{6}$) is developed.
Integrated approach to 3-D seismic acquisition geometry analysis: Emphasizing the influence of the inhomogeneous subsurface (2006)

The seismic reflection method for imaging of the earth's interior is an essential part of the exploration and exploitation of hydrocarbon resources. A seismic survey should be designed such that the acquired data leads to a sufficiently accurate subsurface image. The survey geometry analysis method presented in this thesis is based on the previously developed focal beam analysis concept. It emphasizes the separate analysis of the source geometry and the detector geometry. In this thesis the concept is implemented for application to an inhomogeneous subsurface, by using recursive depth extrapolation of wavefields. In addition, a direct link is made to reservoir characterization. The analysis shows whether proper focusing of the wavefield can be achieved for the chosen source and detector geometries, how the image resolution is affected, and how the angle-dependent amplitudes are affected. This includes the influences of the acquisition geometry, the overburden structure, and the focusing operators. Both P-wave acquisition and converted wave acquisition can be handled. Analysis of well-sampled, stationary geometries shows the fundamental limitations of the acquisition system. Analysis results for - more realistic - parallel and orthogonal geometries show which information is lost in practice. For subsalt imaging, a strong dependence of image quality on the target point location is observed, in addition to fundamental limitations to the image quality due to critical reflection at the salt boundaries.
Role of Toll-Like Receptors in Pathogen Recognition (2003)

The innate immune system relies on a vast array of non-clonally expressed pattern recognition receptors for the detection of pathogens. Pattern recognition receptors bind conserved molecular structures shared by large groups of pathogens, termed pathogen-associated molecular patterns. The Toll-like receptors (TLRs) are a recently discovered family of pattern recognition receptors which show homology with the Drosophila Toll protein and the human interleukin-1 receptor family. Engagement of different TLRs can induce overlapping yet distinct patterns of gene expression that contribute to an inflammatory response. The TLR family is characterized by the presence of leucine-rich repeats and a Toll/interleukin-1 receptor-like domain, which mediate ligand binding and interaction with intracellular signaling proteins, respectively. Most TLR ligands identified so far are conserved microbial products which signal the presence of an infection, but evidence for some endogenous ligands that might signal other danger conditions has also been obtained. Molecular mechanisms for pathogen-associated molecular pattern recognition still remain elusive but seem to be more complicated than initially anticipated. In most cases, direct binding of microbial ligands to TLRs still has to be demonstrated. Moreover, Drosophila TLRs bind endogenous ligands, generated through a proteolytic cascade in response to an infection. In the case of endotoxin, recognition involves a complex of TLR4 and a number of other proteins. Moreover, TLR heterodimerization further extends the spectrum of ligands and modulates the response towards specific ligands. The fact that TLR expression is regulated in both a cell type- and stimulus-dependent fashion further contributes to the complexity.
III-nitride metal-insulator-semiconductor heterojunction field-effect transistors using sputtered AlON thin films (2005)

In this letter, a III-nitride metal-insulator-semiconductor heterostructure field-effect transistors (MISHFET) was demonstrated by incorporating a sputtered AlON layer in the AlGaN∕GaN heterostructure field-effect transistors (HFET). The AlON layer was deposited on the HFET structure by magnetron sputtering, followed by rapid thermal annealing at 850°C for 45s. A reverse gate leakage current that is four orders of magnitude lower was obtained in the MISHFET, compared to that in HFET. The MISHFET also shows 20% increase in the drain saturation current. For a MISHFET with 1-μm-long gate, the current gain cutoff frequency, ft and the power gain cutoff frequency, fmax are measured to be 13 and 37GHz, respectively.
The Mitotic Spindle: A Self-Made Machine (2001)

The mitotic spindle is a highly dynamic molecular machine composed of tubulin, motors, and other molecules. It assembles around the chromosomes and distributes the duplicated genome to the daughter cells during mitosis. The biochemical and physical principles that govern the assembly of this machine are still unclear. However, accumulated discoveries indicate that chromosomes play a key role. Apparently, they generate a local cytoplasmic state that supports the nucleation and growth of microtubules. Then soluble and chromosome-associated molecular motors sort them into a bipolar array. The emerging picture is that spindle assembly is governed by a combination of modular principles and that their relative contribution may vary in different cell types and in various organisms.
Probing viruses with mass spectrometry (1998)

Mass spectrometry offers a new perspective on the solution and gas-phase properties of viruses. Its broad application to local and global viral structure provides unique insights into many biological processes, including viral-antibody binding, protein-protein interactions and protein dynamics. Mass measuring viral proteins is now routine and since viruses are typically well characterized, in that the capsid proteins and DNA (or RNA) sequences are known, identifying a virus based on the mass of the protein and enzymatic digestion fragments is relatively straightforward. Using mass spectrometry, this paper describes the identification of viral protein post-translational modifications such as myristoylation, phosphorylation and disulfide bridging. Furthermore, complementary data obtained with mass spectrometry and x-ray crystallography demonstrate that viruses are highly dynamic particles whose viral capsid's mobility could, until recently, be inferred only from inherently static spectroscopic methods. Lastly, mass spectrometry has been applied on a global scale via the mass measurement of entire intact viruses. Given the general utility of mass spectrometry, its continuing development should further its application to viral dynamics, structure, function and identification.
The systemic inflammatory response is involved in the regulation of K+ channel expression in brain via TNF‐α‐dependent and ‐independent pathways (2004)

TNF-alpha, generated during the systemic inflammatory response, triggers a wide range of biological activities that mediate the neurologic manifestations associated with cancer and infection. Since this cytokine regulates ion channels in vitro (especially Kv1.3 and Kir2.1), we aimed to study Kv1.3 and Kir2.1 expression in brain in response to in vivo systemic inflammation. Cancer-induced cachexia and LPS administration increased plasma TNF-alpha. Kv1.3 and Kir2.1 expression was impaired in brain during cancer cachexia. However, LPS treatment induced Kv1.3 and downregulated Kir2.1 expression, and TNF-alpha administration mimicked these results. Experiments using TNF-alpha double receptor knockout mice demonstrated that the systemic inflammatory response mediates K(+) channel regulation in brain via TNF-alpha-dependent and -independent redundant pathways. In summary, distinct neurological alterations associated with systemic inflammation may result from the interaction of various cytokine pathways tuning ion channel expression in response to neurophysiological and neuroimmunological processes.
Conformationally Rigid Diamide Complexes of Zirconium:  Electron Deficient Analogues of Cp2Zr (1996)

Zirconium complexes bearing a pyridine−diamide ligand [2,6-(RNCH2)2NC5H3]2- (R = 2,6-diisopropylphenyl, 2,6-diethylphenyl (BDEP), 2,6-dimethylphenyl) have been synthesized. The mixed amide complexes [2,6-(RNCH2)2NC5H3]Zr(NMe2)2 are prepared in high yield from [2,6-(RHNCH2)2NC5H3] and Zr(NMe2)4. The mixed amides react with excess ClSiMe3 to afford the dichlorides [2,6-(RNCH2)2NC5H3]ZrCl2 in nearly quantitative yield. Dimethyl complexes are prepared from [2,6-(RNCH2)2NC5H3]ZrCl2 and 2 equiv of MeMgBr. A single-crystal X-ray diffraction study of (BDEP)ZrMe2 revealed a distorted trigonal bipyramid structure with the amides occupying the axial positions. The frontier orbitals of a model of the fragment (BDEP)Zr are very similar the those of Cp2Zr, suggesting that complexes bearing the pyridine−diamide ligand may behave as sources of Cp2Zr.
Bone Marrow-Derived Mesenchymal Stem Cells and Their Conditioned Medium Attenuate Fibrosis in an Irreversible Model of Unilateral Ureteral Obstruction (2015)

The therapeutic potential of mesenchymal stem cells (MSCs) and their conditioned medium (MSC-CM) has been extensively studied. MSCs can repair tissue, reduce local inflammation, and modulate the immune response. Persistent renal tubular interstitial inflammation results in fibrosis and leads to chronic kidney disease (CKD). Unilateral ureteral obstruction (UUO) is a very well-accepted renal fibrosis model. In this study, we evaluated factors influenced by the administration of MSCs or MSC-CM in the UUO model. MSCs extracted from rat bone marrow were cultivated in vitro and characterized by flow cytometry and cellular differentiation. Eight groups of female rats were used in experiments (n = 7, each), including Sham, UUO, UUO + MSC (obstruction + MSC), and UUO + CM (obstruction + MSC-CM) for 7 days of obstruction and Sham, UUO, UUO + MSC, and UUO + CM for 14 days of obstruction. The MSCs or MSC-CM was administered via the abdominal vena cava after total ligation of the left ureter. After 7 or 14 days, rats were euthanized, and serum and obstructed kidney samples were collected. MSCs or MSC-CM decreased the expression of molecules, such as Col1a1, α-SMA, and TNF-α. We also observed reductions in the levels of caspase 3, α-SMA, and PCNA in treated animals by immunohistochemistry. Our results suggest that the intravenous administration of MSCs or MSC-CM improves fibrosis progression and factors involved in apoptosis, inflammation, cell proliferation, and epithelial-mesenchymal transition in Wistar rats subjected to UUO, indicating a potential tool for preventing CKD.
Modulation of LPS stimulated NF-kappaB mediated Nitric Oxide production by PKCε and JAK2 in RAW macrophages (2007)

The results further define the role of NF-kappaB in LPS stimulated NO production in RAW macrophages. The data support a function for PKCepsilon, JAK2 and p38 MAPK in NF-kappaB activation following p65 nuclear import.
Technology for supporting supply chain management: introduction (2001)

article Share on Technology for supporting supply chain management: introduction Author: Kuldeep Kumar Florida International Univ., and Erasmus Univ., The Netherlands Florida International Univ., and Erasmus Univ., The NetherlandsView Profile Authors Info & Claims Communications of the ACMVolume 44Issue 6June 2001 pp 58–61https://doi.org/10.1145/376134.376165Published:01 June 2001Publication History 101citation9,303DownloadsMetricsTotal Citations101Total Downloads9,303Last 12 Months478Last 6 weeks24 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Preservation solutions used during abdominal transplantation: Current status and outcomes (2015)

Organ preservation remains an important contributing factor to graft and patient outcomes. During donor organ procurement and transportation, cellular injury is mitigated through the use of preservation solutions in conjunction with hypothermia. Various preservation solutions and protocols exist with widespread variability among transplant centers. In this review of abdominal organ preservation solutions, evolution of transplantation and graft preservation are discussed followed by classification of preservation solutions according to the composition of electrolytes, impermeants, buffers, antioxidants, and energy precursors. Lastly, pertinent clinical studies in the setting of hepatic, renal, pancreas, and intestinal transplantation are reviewed for patient and graft survival as well as financial considerations. In liver transplants there may be some benefit with the use of histidine-tryptophan-ketoglutarate (HTK) over University of Wisconsin solution in terms of biliary complications and potential cost savings. Renal grafts may experience increased initial graft dysfunction with the use of Euro-Collins thereby dissuading its use in support of HTK which can lead to substantial cost savings. University of Wisconsin solution and Celsior are favored in pancreas transplants given the concern for pancreatitis and graft thrombosis associated with HTK. No difference was observed with preservation solutions with respect to graft and patient survival in liver, renal, and pancreas transplants. Studies involving intestinal transplants are sparse but University of Wisconsin solution infused intraluminally in combination with an intra-vascular washout is a reasonable option until further evidence can be generated. Available literature can be used to ameliorate extensive variation across centers while potentially minimizing graft dysfunction and improving associated costs.
BIOCHEMICAL STUDY OF ENDONUCLEASE V AND ITS APPLICATION IN MUTATION SCANNING (2007)

The integrity of the genetic information encoded by DNA is essential to all living organisms, yet the reactive bases of DNA are constantly attacked by endogenous and exogenous agents resulting in as many as one million individual molecular lesions per cell per day. Excessive DNA damage or deficiency in DNA repair enzymes may cause cancer, premature aging, and neurodegenerative diseases. \t\t\t Endonuclease V (Endo V) is a DNA repair enzyme which can recognize all four types of DNA deamination products, specifically, uracil, hypoxanthine, xanthine and oxanine. It was also shown that endo V can recognize mismatches. We screened about 60 mutants of endo V from Thermotoga maritima and found some mutants had altered base preferences for mismatches. Tma endo V Y80A was shown to become a C-specific mismatch endonuclease. G13D mutation in K-ras oncogene which was not recognized by wild type Tma endo V was successfully cleaved by Tma endo V Y80A. This study provides valuable information on base recognition and active site organization of Tma endo V. Tma endo V mutants can be used for cancer mutation scanning and mutation recognition. \t\t\t In order to further understand the role of Y80 of endo V in base recognition, we substituted the Y80 with sixteen amino acids. Together with three Y80 mutants isolated before, we characterized all nineteen mutants of Tma endo V Y80 using deaminated base-containing DNA substrates and mismatch-containing DNA substrates. This comprehensive amino acid substitution at a single site (Y80) underlines the importance of aromatic ring and hydrogen bond donor capacity in base recognition by endo V, reveals additional Y80 mutants with altered base preferences in mismatch cleavage, and offers new insight on the role of Y80 in base recognition. \t\t\t Though endo V was shown to be important for repair of deaminated lesions in vivo, its DNA repair pathway remains unknown. In order to understand the DNA repair pathway mediated by endo V, we have developed a cell-free system from Escherichia coli. The preliminary results indicated that the repair patch of endo V mediated DNA repair pathways may consist of a long patch and a short patch repair pathway.
Preparation of Monodisperse Nanoparticle of Layered Double Hydroxides and Polyoxyethylene Sulfate (2005)

In order to obtain the bio-molecule/ LDHs nanocomposites having regular crystal structure,three nanocomposites of layered double hydroxides and polyoxyethylene sulfates were prepared by ion-exchange method. TEM analysis reveals that the monodisperse rigid .sphere of approximately 200 nm in diameter could be gotten when the intergallery anion was PEGS-400. Such monodisperse nanoparticle could be used as a promising precursor for preparing bio-molecule/LDHs nanocomposites.
Intracellular Sequestration of Hetero-oligomers Formed by Wild-Type and Glaucoma-Causing Myocilin Mutants (2004)

Formation of heteromeric WT/mutant complexes may provide a critical mechanism by which mutant myocilin polypeptides produce autosomal dominant open-angle glaucoma. The intracellular sequestration of abnormal WT/mutant complexes could lead to the malfunction of MYOC-expressing cells and to POAG potentially involving a dominant negative effect.
Interplay of Enzyme Therapy and Dietary Management of Murine Homocystinuria (2020)

Albeit effective, methionine/protein restriction in the management of classical homocystinuria (HCU) is suboptimal and hard to follow. To address unmet need, we developed an enzyme therapy (OT-58), which effectively corrected disease symptoms in various mouse models of HCU in the absence of methionine restriction. Here we evaluated short- and long-term efficacy of OT-58 on the background of current dietary management of HCU. Methionine restriction resulted in the lowering of total homocysteine (tHcy) by 38-63% directly proportional to a decreased methionine intake (50-12.5% of normal). Supplemental betaine resulted in additional lowering of tHcy. OT-58 successfully competed with betaine and normalized tHcy on the background of reduced methionine intake, while substantially lowering tHcy in mice on normal methionine intake. Betaine was less effective in lowering tHcy on the background of normal or increased methionine intake, while exacerbating hypermethioninemia. OT-58 markedly reduced both hyperhomocysteinemia and hypermethioninemia caused by the diets and betaine in HCU mice. Withdrawal of betaine did not affect improved metabolic balance, which was established and solely maintained by OT-58 during periods of fluctuating dietary methionine intake. Taken together, OT-58 may represent novel, highly effective enzyme therapy for HCU performing optimally in the presence or absence of dietary management of HCU.
Let's stay together: Towards traffic aware virtual machine placement in data centers (2014)

As tenants take networked virtual machines (VMs) as their requirements, effective placement of VMs is needed to reduce the network cost in cloud data centers. The cost is one of the major concerns for the cloud providers. In addition to the cost caused by network traffics (N-cost), the cost caused by the utilization of physical machines (PM-cost) is also non-negligible. In this paper, we focus on the optimized placement of VMs to minimize the cost, the combination of N-cost and PM-cost. We define N-cost by various functions, according to different communication models. We formulate the placement problem, and prove it to be NP-hard. We investigate the problem from two aspects. Firstly, we put a special emphasis on minimizing the N-cost with fixed PM-cost. For the case that tenants request the same amount of VMs, we present optimal algorithms under various definitions of N-cost. For the case that tenants require different numbers of VMs, we propose an approximation algorithm. Also, a greedy algorithm is implemented as the baseline to evaluate the performance. Secondly, we study the general case of the VM placement problem, in which both N-cost and PM-cost are taken into account. We present an effective binary-search-based algorithm to determine how many PMs should be used, which makes a tradeoff between PM-cost and N-cost. For all of the algorithms, we conduct theoretical analysis and extensive simulations to evaluate their performance and efficiency.
Single-molecule detection with total internal reflection excitation: Comparing signal-to-background and total signals in different geometries (1999)

Excitation of fluorescence with total internal reflection (TIR) excitation yields very low background scattered light and good signal-to-background contrast. The background and its associated noise can be made low enough to detect single fluorescent molecules under ambient conditions. In this paper, different TIR geometries were compared for excitation and detection of single rhodamine 6G (R6G) molecules at air-silica interfaces and single B-phycoerythrin proteins at water-silica interfaces. Through-objective, objective-coverslip, and prism-based TIR geometries were investigated. The signal-to-background ratio (SBR) and the number of photons detected before photobleaching (Nb) were optimum in different geometries. The greatest image contrast was obtained when using prism-TIR (SBR = 11.5), but the largest number of detected signal photoelectrons was obtained by using through-objective TIR for R6G-air-silica (<Nb> = 10(4)). The results were discussed in terms of the TIR field enhancements and the modified dipole emission pattern near a dielectric interface. The SBR and total detected photons are important parameters for designing photon-limited experiments.