gebhart/patrepeval huggingface dataset:
Self-Assembling Multidomain Peptide Nanofibers for Delivery of Bioactive Molecules and Tissue Regeneration (2017)

Multidomain peptides (MDPs) are a class of self-assembling peptides that are organized in a β-sheet motif, resulting in a nanofibrous architecture. This structure is stabilized by hydrophobic packing in the fiber core and a hydrogen-bonding network down the fiber long axis. Under easily controllable conditions, regulated by electrostatic interactions between the peptides and the pH and salt composition of the solvent, the nanofiber length can be dramatically extended, resulting in fiber entanglement and hydrogel formation. One of the chief strengths of this supramolecular material is that the design criteria governing its structure and assembly are robust and permit a wide range of modifications without disruption. This allows the MDPs to be tailored to suit a wide range of applications, particularly in biomedical engineering. For example, delivery of small molecules, proteins, and cells is easily achievable. These materials can be trapped within the matrices of the hydrogel or trapped within the hydrophobic core of the nanofiber, depending on the cargo and the design of the MDP. Interactions between the nanofibers and their cargo can be tailored to alter the release profile, and in the most sophisticated cases, different cargos can be released in a cascading time-dependent fashion. The MDP hydrogel and its cargo can be targeted to specific locations, as the thixotropic nature of the hydrogel allows it to be easily aspirated into a syringe and then delivered from a narrow-bore needle. The sequence of amino acids making up the MDP can also be modified to permit cross-linking or enzymatic degradation. Selection of sequences with or without these modifications allows one to control the rate of degradation in vivo from as rapidly as 1 week to well over 6 weeks as the MDP nanofibers are degraded to their amino acid components. MDP sequences can also be modified to add biomimetic sequences derived from growth factors and other signaling proteins. These chemical signals are displayed at a very high density on the fibers' surface, where they contribute to the modification of cellular behavior. We have used this approach to drive blood vessel formation, which is critical for tissue regeneration generally and more specifically for the treatment of diseases related to poor blood flow. MDPs represent an ideal case of bottom-up design where control of chemical structure leads to control of self-assembly and nanostructure and thereby control of material properties that collectively can control biological function.
Chronic Dorsal Column Stimulation via Percutaneously Inserted Epidural Electrodes (1977)

31 patients suffering from intractable pain associated with chronic low back syndrome, terminal cancer, and other disorders have been studied after an average 6 months' treatment by electrical stimulation of the spinal cord applied via electrodes inserted through a Tuohy needle into the epidural space. As judged by three different subjective rating methods, epidural stimulation successfully relieved otherwise intractable chronic pain in from 23 to 26 of the 31 patients. Reported improvements in the ability to perform various everyday activities, and elimination of drug usage by many patients, corroborate this finding. The side effects of stimulation, both as reported subjectively and as measured objectively by sensory testing, were not clinically significant. Spontaneous electrode displacements, leading to loss of analgesia and requiring minor surgery for repositioning, were encountered frequently, as were lead wire failures necessitating replacement. The partially implanted, externally powered stimulation system presently in use also suffers from problems of reliability and convenience to the patient.
Molecular Beam Studies of the Kinetics of the Thermal Conversion of N2O on Rh(111) Single-Crystal Surfaces (2004)

The thermal conversion of N2O on Rh(111) single-crystal surfaces has been studied using a collimated effusive molecular beam technique coupled with mass spectroscopy detection. The decomposition of pure N2O was determined to occur at temperatures as low as 120 K, to follow first-order kinetics, and to lead to the stoichiometric production of N2(g) and atomic adsorbed oxygen. Lower rates and total yields are observed with increasing reaction temperatures, presumably because of the increased importance of N2O desorption and surface mobility in the overall kinetics. N2O conversion is poisoned by the adsorbed oxygen byproduct unless a reducing agent such as CO is used for their removal from the surface, in which case N2O reduction can be carried out catalytically. Steady-state reaction rates were determined for different temperatures and N2O:CO beam mixtures, and were deemed controlled by the rate of oxygen removal, not by the decomposition of the N2O. The role of adsorbed N2O as an intermediate during NO reduction is discussed.
Fairness enhanced dynamic routing and spectrum allocation in elastic optical networks (2016)

The finer spectrum granularity unit in elastic optical networks makes wider spectrum services more likely to be restricted by the constraints of spectrum continuity and spectrum contiguity (2SC), leading to higher blocking probability (BP). Obviously, it would deteriorate the fairness among multi‐granularity services. Therefore, a fair dynamic routing and spectrum allocation algorithm is proposed. By virtualising the network resources as a ‘resource pool’, a two‐dimensional rectangle packing model in combination with service holding‐time is introduced to satisfy the 2SC constraints and to optimise the allocation of the ‘resource pool’ for dynamic multi‐granularity services. Besides multi‐granularity service fairness is achieved by tackling heterogeneous‐size services together. Simulation results show that the benefit in terms of fairness can be reaped. Meanwhile, the authors also investigate the proposed algorithm's impact on performance metrics: namely, spectrum resource utilisation and BP. The results indicate that the proposed algorithm can achieve lower BP and higher spectrum efficiency.
Gas-dynamic trap: an overview of the concept and experimental results (2013)

A gas dynamic trap (GDT) is a version of a magnetic mirror whose characteristic features are a long mirror-to-mirror distance, which exceeds the effective mean free path of ion scattering into a loss cone, a large mirror ratio (R ∼ 100) and axial symmetry. Under these conditions, the plasma confined in a GDT is isotropic and Maxwellian. The rate at which it is lost out of the ends is governed by a set of simple gas-dynamic equations, hence the name of the device. Plasma magnetohydrodynamic stability is achieved through a plasma outflow through the end mirrors into regions, where the magnetic-field lines' curvature is favorable for this stability. A high flux volumetric neutron source based on a GDT is proposed, which benefits from the high β achievable in magnetic mirrors. Axial symmetry also makes the GDT neutron source more maintainable and reliable, and technically simpler. This review discusses the results of a conceptual design of the GDT-based neutron source for fusion materials development and fission–fusion hybrids. The main physics issues related to plasma confinement and heating in a GDT are addressed by the experiments performed with the GDT device in Novosibirsk. The review concludes by updating the experimental results obtained, a discussion about the limiting factors in the current experiments and a brief description of the design of a future experimental device for more comprehensive modeling of the GDT-based neutron source.
A methodology for hiding knowledge in databases (2002)

In this paper, we present a methodology to analyze the impact of data mining technology on database security. Our methodology consists of six steps that make up a new data analysis process that we call Knowledge Hiding in Databases (KHD). The specific contributions of this paper include a description of the KHD process, and the initial application of KHD to classification and association mining algorithms.
Calcium-mediated Interactions Regulate the Subcellular Localization of Extracellular Signal-regulated Kinases (2008)

The subcellular localization of ERKs in cells, which is important for proper signaling, may be regulated through protein-protein interactions. We found that inactive ERK2 interacts with a large number of proteins through its cytosolic retention sequence/common docking domain, whereas the phospho-ERK2 interacts with only few substrates. Varying calcium concentrations significantly modified the repertoire of ERK2-interacting proteins, of which many were identified. The effect of calcium on ERK interactions also influenced the localization of ERKs, as calcium chelators enhanced nuclear translocation, whereas elevated calcium levels prevented it. This effect of calcium was apparent upon lysophosphatidic acid stimulation, where ERKs translocation was delayed compared with that induced by EGF in a calcium-dependent manner. In vitro translocation assay revealed that high calcium concentrations affect ERK translocation by preventing the shuttling machinery through the nuclear envelope, probably due to higher binding to nuclear pore proteins. These results are consistent with a model in which ERKs in quiescent cells are bound to several cytoplasmic proteins. Upon stimulation, ERKs are phosphorylated and released from cytoplasmic anchors to allow shuttling toward the nucleus. This translocation is delayed when calcium levels are increased, and this modifies the localization of ERKs and, therefore, also their spatiotemporal regulation. Thus, calcium regulates ERK localization, which is important for the compartmentalization of ERKs with their proper substrates and thereby their signaling specificity.
Cytotoxicity of degrading and cross-linking agents (2011)

<b>Copyright information:</b>Taken from "Bonding of articular cartilage using a combination of biochemical degradation and surface cross-linking"http://arthritis-research.com/content/9/3/R47Arthritis Research &amp; Therapy 2007;9(3):R47-R47.Published online 15 May 2007PMCID:PMC2206351. The relative cytotoxicity of degrading and cross-linking agents was determined using the resazurin assay (expressed as relative fluorescence units). Cartilage blocks were treated with the respective reagents for either one or two hours. The controls were incubated in PBS. values are from Tukey test for pairwise comparisons. EDC, 1-ethyl-3-diaminopropyl-carbodiimide; NHS, N-hydroxysuccinimide.
Transient reduction of human left ventricular mass in carnitine depletion induced by antibiotics containing pivalic acid. (1995)

Extended treatment with pivalic acid containing antibiotics causes carnitine depletion which may lead to changes in cardiac structure.
Genetic Analysis of Adult-Specific Surface Antigenic Differences Between Varieties of the Nematode Caenorhabditis elegans (1987)

We have studied developmental stage-specificity and genetic specification of surface antigens in the nematode Caenorhabditis elegans. Rabbit antisera directed against the adult C. elegans cuticle were used in conjunction with antiserum adsorption experiments to obtain antibody reagents with specificity for the adult surface. Adult-specific antibodies were used to identify several varietal strains of C. elegans that display antigen-negative phenotypes as adults. Genetic mapping results using the surface antigen phenotype as a marker indicated that a single gene (designated srf-1) or cluster of genes on linkage group II determines the adult surface antigen phenotype.
Hydrophobic interactions drive ligand-receptor recognition for activation and inhibition of staphylococcal quorum sensing (2004)

Two-component systems represent the most widely used signaling paradigm in living organisms. Encoding the prototypical two-component system in Gram-positive bacteria, the staphylococcal agr (accessory gene regulator) operon uses a polytopic receptor, AgrC, activated by an autoinducing peptide (AIP), to coordinate quorum sensing with the global synthesis of virulence factors. The agr locus has undergone evolutionary divergence, resulting in the formation of several distinct inter- and intraspecies specificity groups, such that most cross-group AIP-receptor interactions are mutually inhibitory. We have exploited this natural diversity by constructing and analyzing AgrC chimeras generated by exchange of intradomain segments between receptors of different agr groups. Functional chimeras fell into three general classes: receptors with broadened specificity, receptors with tightened specificity, and receptors that lack activation specificity. Testing of these chimeric receptors against a battery of AIP analogs localized the primary ligand recognition site to the receptor distal subdomain and revealed that the AIPs bind primarily to a putative hydrophobic pocket in the receptor. This binding is mediated by a highly conserved hydrophobic patch on the AIPs and is an absolute requirement for interactions in self-activation and cross-inhibition of the receptors. It is suggested that this recognition scheme provides the fundamental basis for agr activation and interference.
A novel synthesis of 3β-hydroxy-5α-cholest-8(14)-en-15-one (1979)

Jones oxidation of 5α-cholesta-8,14-dien-3β-yl acetate furnishes 9α-hydroxy-15-oxo-5α-cholest-8(14)-en-3β-yl acetate (4a). Treatment of (4a) with zinc dust and sulphuric acid followed by saponification gives 3β-hydroxy-5α-cholest-8(14)-en-15-one. On the basis of chemical and spectroscopic evidence, the product obtained by oxidation of 5α-cholest-8,14-dien-3β olis formulated as 9α-hydroxy-5α-cholest-8(14)-ene-3,15-dione (4b) and not as 14α-hydroxy-5α-cholest-8-ene-3,7-dione (3) as reported by others.
Environment-Dependent Photophysics of Polymer-Bound J Aggregates Determined by Time-Resolved Fluorescence Spectroscopy and Time-Resolved Near-Field Scanning Optical Microscopy (1996)

Exciton migration and annihilation dynamics in J aggregates comprised of a pseudoisocyanine (PIC) dye and poly(vinyl sulfate) (PVS) are studied by time-correlated, single-photon-counting (TCSPC) methods coupled with near-field scanning optical microscopy (TCSPC-NSOM) and also by conventional, far-field TCSPC. Far-field TCSPC studies of the aggregates in aqueous solution demonstrate that the exciton lifetime in the absence of annihilation (at low excitation intensities) is 789 ± 36 ps with biexponential exciton decay occurring at high excitation intensities due to exciton annihilation. Analysis of the intensity-dependent decay with conventional exciton decay theories demonstrates that the observed decay dynamics are consistent with exciton migration limited to finite molecular domains. In contrast to the solution studies, deposition of a thin PIC/PVS aggregate film onto fused quartz results in a dramatic reduction in the exciton lifetime to ∼10 ps. This lifetime demonstrates only modest dependence on excitation intensity. Possible mechanisms for the reduction in exciton lifetime for the adsorbed aggregates are discussed. Finally, the dependence of the exciton lifetime on the nanostructure of the aggregates is explored with TCSPC-NSOM. A new TCSPC-NSOM instrument with an instrument response of 30 ps and spatial resolution of ∼100 nm is presented and used to perform the first direct measurement of exciton lifetimes for a single aggregate. TCSPC-NSOM studies demonstrate that the exciton lifetime is not sensitive to the structural details of the aggregates on the ∼100 nm length scale. The combination of measurements presented here demonstrate that the exciton diffusion length is limited to short distances (∼100 nm) relative to the aggregate size. The homogeneous spectral properties observed for these aggregates are therefore not due to site-averaging resulting from long-range exciton migration but instead are due to the structural homogeneity of the aggregates on the length scales investigated here.
.BETA. Cell Neogenesis from Ducts and Phenotypic Conversion of Residual Islet Cells in the Adult Pancreas of Glucose Intolerant Mice Induced by Selective Alloxan Perfusion. (2002)

The aim of this study was to clarify the pattern of beta cell neogenesis in the alloxan-perfused, beta cells-depleted segment of glucose intolerant mice induced by selective alloxan perfusion. First, duct cells proliferated in the perfused segment, then cells co-expressing multiple islet hormones and transcription factors such as PDX-1, Nkx2.2, Isl1, and Pax6 were observed in duct cells, and newly formed islet-like cell clusters (ICCs) containing beta cells were recognized. In residual beta cell-depleted islets, glucagon or somatostatin and PDX-1 double-positive immature endocrine cells were recognized. Glucagon or somatostatin, insulin and PDX-1 triple-positive cells then appeared and these cells appeared to undergo terminal differentiation into beta cells. In conclusion, we demonstrated at least two different processes of beta cell neogenesis, i.e., formation of new ICCs from ductal epithelium and redifferentiation of residual non-beta islet cells in this model. In addition, transcription factors that appear in the processes of endocrine cell development may also play essential roles during beta cell neogenesis from duct cells.
A Study of the Development of CVD Precursors III-Synthesis and Properties of New Lead $\beta$-diketonate Derivatives (1999)

To improve the volatility and stability of lead complexes, the principle of stabilization by saturating the metal coordination sphere by intramolecular coordination through a β-diketonates with an ethereal group has was tested. Several new lead complexes with alkoxyalkyl-substituted β-diketonates, Pb(R1C(O)CHC(O)(CH2)3OR2)2(Rl=t-Bu, Me, OMe, i-Pr, R2=Me, Et), or carboxylate, Pb(OC(O)(CH2)3OEt)2, were prepared by the reaction between Pb(OAc)2 and corresponding alkoxyalkyl-substituted β-diketonates, and they were found to have a viscous liquid phase. The nature of the head (β-diketonate or carboxylate) or tails and substituents of β-diketonates appeared not to be important for the formation of the liquid phase. It is worth mentioning that Pb(OAc)2, which has limited use due to its low solubility, was successfully adopted as a starting material for the preparation of new lead complexes. Easy hydrolysis, reaction with HCl, and 13C NMR spectra indicated that tail portions were not coordinated to the metal as a copper derivative, Cu(t-BuC(O)CHC(O)(CH2)3OMe)2. All these complexes were not volatile enough for the MOCVD experiments, but a methyl derivative, Pb(MeC(O)CHC(O)(CH2)3OEt)2, showed some sublimation. The methoxy derivative, Pb(MeOC(O)CHC(O)(CH2)3OEt)2, was thermally unstable due to possible equilibrium between species coordinating with a keto oxygen atom and an ethereal atom of a methoxy group, which was confirmed by IR and 13C NMR spectra.
Control-Oriented, Data-Driven Models of Thermal Dynamics (2021)

We investigate data-driven, simple-to-implement residential environmental models that can serve as the basis for energy saving algorithms in both retrofits and new designs of residential buildings. Despite the nonlinearity of the underlying dynamics, using Koopman operator theory framework in this study we show that a linear second order model embedding, that captures the physics that occur inside a single or multi zone space does well when compared with data simulated using EnergyPlus. This class of models has low complexity. We show that their parameters have physical significance for the large-scale dynamics of a building and are correlated to concepts such as the thermal mass. We investigate consequences of changing the thermal mass on the energy behavior of a building system and provide best practice design suggestions.
CAN THE LONG HEAD OF THE BICEPS BE HEALTHY IN ROTATOR CUFF TEARS? EPIDEMIOLOGY AND DYNAMIC BEHAVIOUR (2010)

Purpose of the study: Injury of the long head of the biceps (LHB) can cause pain in rotator cuff tears (RCT). Our objectives were to: establish an epidemiological database on LHB injuries in RCT; study the dynamic behaviour of LHB in RCT; search for a correlation between injected imaging findings and arthroscopic findings. Materials and Methods: Prospective, consecutive, multi-centric study (April 2005-June 2006). Inclusion criteria: partial or full-thickness RCT demonstrated arthroscopically, arthorscopic description of LHB, imaging with injection (arthroscan or arthro-MR), data collected on the internet site of the Socite Francaise d’Arthroscopie (SFA). Other reasons for arthroscopy, past surgery and MRI were excluded. The dynamic examination consisted in a search for the incapacity to glide the LHB in its gutter during passive abduction of the arm leading to intra-articular fold (hourglass test) and instability of the LHB in its groove during external rotation (medial instability) or internal rotation (lateral instability) with the arm at 90° abduction (RE2 and RI2 tests). Extension of the RCT in the frontal and sagittal plane were determined using the classification of the French Arthroscopic Society. Results: 378 patients (378 shoulders, 211 women, 167 men, mean age 57.9 years, age range 28–93 years). Arthroscan for 312 shoulders and arthroMR for 66 shoulders revealed 61 partial deep RCT and 317 full-thickness RCT. Among the full-thickness tears, 15 involved the subscapularis (SSc) alone, one the infraspinatus (ISp) alone and 301 the supraspinatus (SSp) alone (with 52 posterior extensions to the ISp, 90 anterior to the SSc and 31 mixted). Epidemiological data (static test): LHB intact 21%, tenosynovitis 51%, hypertrophy 21%, delamination 12%, pre-tears 7%, subluxation 18%, dislocation 9%, tear 2%. No influence of age, gender or side operated. Conversely, the rate of lesions increased significantly with extention of the RCT in the frontal and sagittal plane. Dynmaic study: positive hourglass test 29%, instability in RE2 26%, instability in RI2 8%. Hourglass test correlated with intra-articular hypertrophy of the LHB (76% versus 2%). Subscapularis tears lead to medial instability in 82% of cases. Among the 81 shoulders with an intact LBH statically, 17% presented a dynamic anomaly. In all the static and dynamic tests only left 18% of the LHB intact. Imaging-dynamic arthroscopy correlation: 25% of LHB lesions were not diagnosed by injected imaging. Inversely, there was a good correlation to determine the position of the LHB in its groove.
Human Renal Cancers Resistant to IFN's Antiproliferative Action Exhibit Sensitivity to IFN's Gene-Inducing and Antiviral Actions (1996)

The resistance of RC lines to IFN's antiproliferative action is not due to defects in ligand binding or in IFN-receptor structure. Our results indicate that the defective antiproliferative response in most RC cells is not due to their failure to induce the gene-inducing and antiviral effects of IFN alpha.
Distributed Feedback Optimisation for Robotic Coordination (2021)

Feedback optimisation is an emerging technique aiming at steering a system to an optimal steady state for a given objective function. We show that it is possible to employ this control strategy in a distributed manner. Moreover, we prove asymptotic convergence to the set of optimal configurations. To this scope, we show that exponential stability is needed only for the portion of the state that affects the objective function. This is showcased by driving a swarm of agents towards a target location while maintaining a target formation. Finally, we provide a sufficient condition on the topological structure of the specified formation to guarantee convergence of the swarm in formation around the target location.