gebhart/patrepeval huggingface dataset:
Overview of Micro- and Nano-Technology Tools for Stem Cell Applications: Micropatterned and Microelectronic Devices (2012)

In the past few decades the scientific community has been recognizing the paramount role of the cell microenvironment in determining cell behavior. In parallel, the study of human stem cells for their potential therapeutic applications has been progressing constantly. The use of advanced technologies, enabling one to mimic the in vivo stem cell microenviroment and to study stem cell physiology and physio-pathology, in settings that better predict human cell biology, is becoming the object of much research effort. In this review we will detail the most relevant and recent advances in the field of biosensors and micro- and nano-technologies in general, highlighting advantages and disadvantages. Particular attention will be devoted to those applications employing stem cells as a sensing element.
Compiling Fortran D for MIMD distributed-memory machines (1992)

:llel computing resents the only :usible way to continue to increase the computational power available to scientists and engineers. Parallel computers, however, are not likely to be widely successful until they are easy to program. A major component in the success of vector supercomputers is the ability of scientists to write Fortran programs in a "'vectorizable'" style and expect vectorizing compilers to automatically produce efficient code The resulting programs are easily maintained, debugged, and ported across different vector machines.
Portfolio Selection via Shrinkage by Cross Validation (2014)

Given the importance of the loss function choice [Christoffersen, P. and K. Jacobs (2004) The importance of the loss function in option valuation. J. Financial Economics 72: 291-318], this paper proposes the nonparametric technique of cross validation, to tuning the shrinkage intensity estimation of Ledoit and Wolf [Ledoit, O. and W. Michael (2003) Improved estimation of the covariance matrix of stock returns with an application to portfolio selection. J. Empirical Finance 10: 603-621; Ledoit, O. and W. Michael (2004) Honey, I Shrunk the Sample Covariance Matrix. J. Portfolio Management 30: 110-119; Ledoit, O. and W. Michael (2004) A well-conditioned estimator for large-dimensional covariance matrices. J. Multivariate Analysis 88: 365-411]. By aligning the loss function of out-of-sample forecast identical to the one used for the shrinkage intensity estimation, the proposed cross validation approach shows the significant gains in terms of both the variance reduction and information ratio improvement to various portfolios of the U.S. firms.
Essential role of YopD in inhibition of the respiratory burst of macrophages by Yersinia enterocolitica (1994)

The respiratory burst is a key element of the bactericidal armamentarium of phagocytes. In this study we have shown that a virulent strain of Yersinia enterocolitica serogroup O:9 completely inhibited the ability of murine bone marrow-derived macrophages to mount a respiratory burst in response to stimulation by zymosan. This property of the bacterium was abrogated by curing the strain of its 71.5-kb virulence plasmid and by transposon mutagenesis of the plasmid-borne yopD gene. Derivatives of the bacterium which were unable to inhibit the respiratory burst were also less able to disrupt cytoskeletal actin and to resist phagocytosis. yopD mutants also showed an impaired ability to dephosphorylate phosphotyrosine residues in macrophage proteins and were completely avirulent for mice. All of these defects were fully or partly restored by trans-complementation of a yopD mutant with a cloned yopD gene. The results of this study and those of previous work with YopD (R. Rosqvist, A. Forsberg, and H. Wolf-Watz, Infect. Immun. 59:4562-4569, 1991) suggest that YopD functions chiefly by facilitating the transport of virulence plasmid-encoded proteins, such as YopE, a cytotoxin, and YopH, a protein tyrosine phosphatase, across the cytoplasmic membrane to their targets within host cells. The combined action of these Yops on cytoplasmic proteins, especially actin, could explain the effects of virulent Y. enterocolitica on macrophage morphology, phagocytic capacity, and respiratory burst activity, all of which rely on cytoskeletal integrity to function normally.
Evaluation of plasma Epstein-Barr virus DNA load as a prognostic marker for nasopharyngeal carcinoma. (2006)

The blood plasma EBV DNA load was shown to be proportionately related to the presence of malignant disease. This preliminary study underscores the prognostic value of cell-free EBV DNA quantification.
Development and validation of an affinity chromatography step using a peptide ligand for cGMP production of factor VIII (2004)

An affinity chromatography step was developed for purification of recombinant B-Domain Deleted Factor VIII (BDDrFVIII) using a peptide ligand selected from a phage display library. The peptide library had variegated residues, contained both within a disulfide bond-constrained ring and flanking the ring. The peptide ligand binds to BDDrFVIII with a dissociation constant of approximately 1 microM both in free solution and when immobilized on a chromatographic resin. The peptide is chemically synthesized and the affinity resin is produced by coupling the peptide to an agarose matrix preactivated with N-hydroxysuccinimide. Coupling conditions were optimized to give consistent and complete ligand incorporation and validated with a robustness study that tested various combinations of processing limits. The peptide affinity chromatographic operation employs conditions very similar to an immunoaffinity chromatography step currently in use for BDDrFVIII manufacture. The process step provides excellent recovery of BDDrFVIII from a complex feed stream and reduces host cell protein and DNA by 3-4 logs. Process validation studies established resin reuse over 26 cycles without changes in product recovery or purity. A robustness study using a factorial design was performed and showed that the step was insensitive to small changes in process conditions that represent normal variation in commercial manufacturing. A scaled-down model of the process step was qualified and used for virus removal studies. A validation package addressing the safety of the leached peptide included leaching rate measurements under process conditions, testing of peptide levels in product pools, demonstration of robust removal downstream by spiking studies, end product testing, and toxicological profiling of the ligand. The peptide ligand affinity step was scaled up for cGMP production of BDDrFVIII for clinical trials.
Correction of count losses due to deadtime on a DST-XLi (SMVi-GE) camera during dosimetric studies in patients injected with iodine-131 (2002)

In dosimetric studies performed after therapeutic injection, it is essential to correct count losses due to deadtime on the gamma camera. This note describes four deadtime correction methods, one based on the use of a standard source without preliminary calibration, and three requiring specific calibration and based on the count rate observed in different spectrometric windows (20%, 20% plus a lower energy window and the full spectrum of 50-750 keV). Experiments were conducted on a phantom at increasingly higher count rates to check correction accuracy with the different methods. The error was less than +7% with a standard source, whereas count-rate-based methods gave more accurate results. On the assumption that the model was paralysable, preliminary calibration allowed an observed count rate curve to be plotted as a function of the real count rate. The use of the full spectrum led to a 3.0% underestimation for the highest activity imaged. As count losses depend on photon flux independent of energy, the use of the full spectrum during measurement allowed scatter conditions to be taken into account. A protocol was developed to apply this correction method to whole-body acquisitions.
Separating Sources of Manufacturing Distortion in Laminated Composites (2000)

Manufacturing distortion in composites has been a problem for many years and continues to impede the development of composite materials. Previous efforts have shown these manufacturing distortions to be related to differences in the in-plane and through-thickness properties. Often tooling is modified in an attempt to compensate for these fabrication induced distortions; however, the various sources of the problem have not been clearly identified, measured, nor accepted. Earlier efforts have suggested that both the cooldown from process temperature and shrinkage during cure play a role, yet no single work has measured the relative contributions of these effects. Further, researchers have suggested numerous other factors as being responsible for all, or some portion, of the measured distortion. In this work, distortion in autoclave-cured laminated composites has been experimentally measured, at temperatures ranging from 24 0 C to 178 0 C, to determine the reversible and irreversible contributions to manufacturing warpage and to attempt to separate the distortion into components related to different mechanisms. Three mechanisms, anisotropy, material property gradients, and stress gradients are described, and are further separated into thermoelastic and non-thermoelastic components. The measured reversible response closely matches computed distortion, based solely on the in-plane and through-thickness coefficients of thermal expansion. Further, it seems that the irreversible contributions can be separated into material dependent effects, such as cure shrinkage, and process related effects, such as part/tool interactions. Calculations, based on anisotropy, indicate that both temperature change and cure shrinkage contribute significantly to manufacturing distortion; but, their contribution does not account for the total distortion. The irreversible contribution is much greater than predicted, indicating the action of a mechanism which only involves a non-thermoelastic contribution, such as a part/tool interaction. Trends in the experimentally observed distortion indicate the presence of other non-thermoelastic process related contributions and show that these other contributions seem to diminish as the thickness, corner radius and included angle increase.
Reactivation of partially‐sulphated limestone particles from a cfb combustor by hydration (1994)

Abstract Spent limestone samples from the bed and baghouse of a 22 MWe circulating fluidized bed (CFB) boiler were hydrated and then sulphated in a thermogravimetric analyzer under conditions similar to those found in CFB combustors (850°C, 0.3% SO 2 , 9% O 2 , 9% CO 2 and 81.7% N 2 ). Hydration using water gave faster rates and higher levels of conversion of the residual CaO to Ca (OH) 2 than immersion in pure steam at 150 and 200°C. The particles expanded during hydration and their internal volume increased from 0.1 cm 3 /g Ca before hydration to nearly 0.6 cm 3 /g Ca after dehydration. Hydration rejuvenated the reactivity of the bed material but not that of the baghouse particles. The conversion of Ca to CaSO 4 , in the treated bed particles increased from 32% to over 80% during re‐sulphation.
Synthesis of high specific activity (+)- and (-)-6-[18F]fluoronorepinephrine via the nucleophilic aromatic substitution reaction (1991)

The first example of a no-carrier-added 18F-labeled catecholamine, 6-[18F]fluoronorepinephrine (6-[18F]FNE), has been synthesized via nucleophilic aromatic substitution. The racemic mixture was resolved on a chiral HPLC column to obtain pure samples of (-)-6-[18F]FNE and (+)6-[18F]FNE. Radiochemical yields of 20% at the end of bombardment (EOB) for the racemic mixture (synthesis time 93 min), 6% for each enantiomer (synthesis time 128 min) with a specific activity of 2-5 Ci/mumol at EOB were obtained. Chiral HPLC peak assignment for the resolved enantiomers was achieved by using two independent methods: polarimetric determination and reaction with dopamine beta-hydroxylase. Positron emission tomography (PET) studies with racemic 6-[18F]FNE show high uptake and retention in the baboon heart. This work demonstrates that nucleophilic aromatic substitution by [18F]fluoride ion is applicable to systems having electron-rich aromatic rings, leading to high specific activity radiopharmaceuticals. Furthermore, the suitably protected dihydroxynitrobenzaldehyde 1 may serve as a useful synthetic precursor for the radiosynthesis of other complex 18F-labeled radiotracers.
Rapid Degradation of AU-Rich Element (ARE) mRNAs Is Activated by Ribosome Transit and Blocked by Secondary Structure at Any Position 5′ to the ARE (1995)

The 3' noncoding region (NCR) AU-rich element (ARE) selectively confers rapid degradation on many mRNAs via a process requiring translation of the message. The role of cotranslation in destabilization of ARE mRNAs was examined by insertion of translation-blocking stable secondary structure at different sites in test mRNAs containing either the granulocyte-macrophage colony-stimulating factor (GM-CSF) ARE or a control sequence. A strong (-80 kcal/mol [1 kcal = 4.184 kJ]) but not a moderate (-30 kcal/mol) secondary structure prevented destabilization of mRNAs when inserted at any position upstream of the ARE, including in the 3' NCR. Surprisingly, a strong secondary structure did not block rapid mRNA decay when placed immediately downstream of the ARE. Studies are also presented showing that the turnover of mRNAs containing control or ARE sequences is not altered by insertion of long (1,000-nucleotide) intervening segments between the stop codon and the ARE or between the ARE and poly(A) tail. Characterization of ARE-containing mRNAs in polyadenylated and whole cytoplasmic RNA fractions failed to find evidence for decay intermediates degraded to the site of strong secondary structure from either the 5' or 3' end. From these and other data presented, this study demonstrates that complete translation of the coding region is essential for activation of rapid mRNA decay controlled by the GM-CSF ARE and that the structure of the 3' NCR can strongly influence activation. The results are consistent with activation of ARE-mediated decay by possible entry of translation-linked decay factors into the 3' NCR or translation-coupled changes in 3' NCR ribonucleoprotein structure or composition.
Characterization of insulin-like growth factor-binding protein 5-degrading proteases produced throughout murine osteoblast differentiation. (1995)

Insulin-like growth factor (IGF)-binding protein-5 (IGFBP-5) is uniquely regulated throughout MC3T3-E1 osteoblast differentiation: IGFBP-5 is first detectable in conditioned medium (CM) of replicating preosteoblasts (day 5); IGFBP-5 levels peak between culture days 8-12, then decline to almost undetectable levels in mature osteoblast cultures (> day 18) despite the persistence of IGFBP-5 messenger RNA. These observations suggest that IGFBP-5 concentrations may be regulated by posttranslational mechanisms. To determine whether proteolysis contributes to the disappearance of IGFBP-5 in CM of mature osteoblasts, serial samples of MC3T3-E1 cell CM obtained during a 30-day culture period were analyzed for IGFBP-5-degrading protease activity. Using [125I]recombinant human IGFBP-5 substrate zymography, we demonstrated that proteases with M(r) of 52-72 and 97 kilodaltons (kDa) were present in CM, and protease activity increased in concentration as cultures matured. The 52- to 72-kDa proteases were cation dependent and were inhibited by tissue inhibitor of metalloproteinase 1, a specific inhibitor of matrix metalloproteinases (MMPs), identifying them as MMPs. Furthermore, antisera to human MMP-1 and -2 immunoprecipitated IGFBP-5-degrading proteases with M(r) of 52 and 69/72 kDa, respectively, suggesting that homologous murine MMPs degrade IGFBP-5. Finally, MC3T3-E1 cell CM contained immunoreactive MMP-1 and -2, and MMP-2, in particular, increased significantly throughout differentiation. In contrast, the 97-kDa protease was neither inhibited by tissue inhibitor of metalloproteinase 1 nor immunoprecipitated by antisera to MMPs, suggesting that the 97-kDa protease is not a MMP. Together, these data suggest that MMPs along with an unidentified 97-kDa protease degrade IGFBP-5 in MC3T3-E1 cell cultures. Because truncated forms of IGFBP-5 have been shown to enhance the action of IGF in bone cells, IGFBP-5 proteases may be instrumental in IGF-mediated bone morphogenesis.
Evidence for expression of vasopressin V2 receptor mRNA in human lung (1996)

Studies using fetal sheep, goats, and guinea pigs indicate that vasopressin may play a role in preparing the fetal lung for the transition from a uterine to an air-breathing environment by slowing lung liquid secretion. The mechanism of vasopressin action is believed to occur through V2 receptors with subsequent activation of amiloride-sensitive sodium channels. However, the presence of the V2 receptor in human lung has not yet been documented. In the present study, expression of the vasopressin V2 receptor in fetal and adult human lung was examined using reverse transcription-polymerase chain reaction (RT-PCR), Northern blot analysis, and DNA sequencing. Using RT-PCR and primer pairs specific for the human V2 receptor, PCR products of the predicted sizes of 512 and 862 bp were obtained from adult human lung. DNA sequencing of the cloned PCR products revealed exact identity with the published sequence for the V2 receptor. Northern blot analysis revealed the expression of a approximately 1.9 kb mRNA in adult human lung as well as in kidney, but not in fetal human lung at 22-24 weeks of gestation. However, using the more sensitive RT-PCR assay the 862-bp product was successfully amplified from human fetal lung, although the data indicate the mRNA for this receptor is expressed in lower levels than in adult human lung or kidney. Using RT-PCR and primers specific for the rat V2 receptor, a PCR product of the predicted size of 461 bp was amplified from adult rat lung and kidney, despite an earlier report that this receptor mRNA is absent from the lung of this species. The role for the V2 receptor in adult human lung is unknown at this time, but, as in the human kidney and lungs of fetal sheep, goats, and guinea pigs, this receptor may play a role in fluid balance.
Selective growth of Ge on Si(100) through vias of SiO2 nanotemplate using solid source molecular beam epitaxy (2003)

We demonstrate that Ge can be selectively grown on Si(100) through openings in a SiO2 nanotemplate by solid source molecular beam epitaxy. The selectivity relies on the thermal instability of GeO and SiO near 650 °C. Ge islands grow in the template windows and coalesce on top of the template, forming an epitaxial lateral overgrowth (ELO) layer. Cross-sectional transmission electron microscopy images show that the Ge seeds and the ELO layer are free of threading dislocations. Only stacking faults are generated but terminate within 70 nm of the Ge–Si interface, while twins along {111} planes are observed in the ELO layer. The threading-dislocation-free Ge seeds and ELO layer are attributed to epitaxial necking as well as Ge–Si intermixing at the interface.
CHEMISTRY: Colloidal Molecules and Beyond (2003)

About a hundred years ago, Jean Perrin's experiments on colloids—particles a few nanometers to a few micrometers in diameter—convinced even the skeptics that matter consists of atoms and molecules. More recently, the analogy between atoms and colloids has led to insights into crystal nucleation and growth, the glass transition, and the influence of the range of particle-particle interactions on phase behavior. Moreover, the ability to manipulate colloid crystallization has led to advanced materials such as photonic crystals.
Abstract WP265: Anti-inflammatory Effects Of Ceria Nanoparticles In Experimental Intracerebral Hemorrhage Models (2016)

Aim: Ceria nanoparticles (NPs) are potent anti-oxidants because of their small size and surface characteristics. In addition to this, they have anti-inflammatory effects. However, their effects on post-stroke inflammation have not been evaluated in experimental intracerebral hemorrhage (ICH). Methods: Ceria NPs were made by a modified double-decomposition method. RAW 264.7 macrophages (MΦs) were activated by 30% hemolysate from blood by checking morphology and inflammatory products. They were treated by 0.125 mM ceria NPs or not. Overall reactive oxygen species (ROS) after the activation of MΦs were measured by oxidized DCF-DA in FACS. Inflammatory cytokines, IL-1β and TNF-α, were evaluated by ELISA, and inflammatory end-products, COX2 and iNOS, were done by Western blots. Animal ICH was induced by the stereotactic injection of collagenase into the rat brain, and ceria NPs were injected intravenously. Water contents were measured by wet and dry weights of brain after induction of ICH. We calculated hematoma volumes by an image-analyzer and the recruitment of MΦs in perihematomal area by the immunofluorescent staining using CD68 antibody. Results: Ceria NPs were made as 3-nm small sized, uniform round-shaped, and well-dispersed agents, which were suitable for biomedical applications. Ceria NPs reduced oxidized DCF-DA (a marker of overall ROS) after hemolysate-induced activation of MΦs (ceria-treated group, 391 unit vs. control, 567 unit, P=0.03). In this in vitro hemorrhage model, MΦs secreted less cytokines, IL-1β and TNF-α, in ceria-treated group than control, and in Western blots, the expression of COX2 and iNOS decreased in ceria group compared to control. In rat ICH model, ceria NPs reduced water contents in hemorrhagic hemisphere, which is closely related to perihematomal inflammation (0.5 mg/kg ceria group, 79,9% vs. control, 81.1%, P=0.01). Although hematoma volumes were not different between two groups, the CD68-positive MΦs in immunofluorescent staining were less recruited into the perihematomal area in ceria-treated group than control. Conclusion: Ceria NPs decreased inflammation after ICH in both in vitro and in vivo models. From these anti-inflammatory effects, they could be potential therapeutic agents in acute period after ICH.
Matrix‐assisted laser desorption of peptides and proteins on a quadrupole ion trap mass spectrometer (1993)

The use of ultraviolet matrix-assisted laser desorption (MALD) to ionize peptides and proteins for analysis in a quadrupole ion trap is described. An ion source was modified to accommodate a fiber optic to transmit laser radiation from a nitrogen laser (337 nm) to the tip of the sample probe containing peptide or protein samples in a matrix of 2,5-dihydroxybenzoic acid (DHB) or 3,4-dimethoxy-4-hydroxy-cinnamic acid. Detection limits are demonstrated with 10 fmol of sperm-whale myoglobin. The dimer of sperm-whale myoglobin was also observed at m/z 34,430. A comparison is made of the tandem mass spectrum of (MS/MS) of human angiotensin I desorbed by MALD to that of the peptide desorbed by liquid secondary-ion mass spectrometry. Both spectra were found to contain abundant structural information.
Initial Characterization of a Bgo-Photodiode Detector for High Resolution Positron Emission Tomography (1984)

Spatial resolution in positron emission tomography is currently limited by the resolution of the detectors. This work presents the initial characterization of a detector design using small bismuth germanate (BGO) crystals individually coupled to silicon photodiodes (SPOs) for crystal identification, and coupled in groups to phototubes (PMTs) for coincidence timing. A 3 mm × 3 mm × 3 mm BGO crystal coupled only to a SPD can achieve a 511 keV photopeak resolution of 8.7% FWHM at -150°C, using a pulse peaking time of 10 μs. When two 3 mm × 3 mm × 15 mm BGO crystals are coupled individually to SPDs and also coupled to a common 14 mm diam PMT, the SPDs detect the 511 keV photopeak with a resolution of 30% FWHM at -76°C. In coincidence with an opposing 3 mm wide BGO crystal, the SPDs are able to identify the crystal of interaction with good signal-to-noise ratio, and the detector pair resolution is 2 mm FWHM.