gebhart/patrepeval huggingface dataset:
Posttranslational Modification in Megakaryocytes Regulates β1 Integrin Expression, Migration and Platelet Production in Vivo (2014)

Abstract Platelet recovery following bone marrow transplant and radiochemotherapy is crucial to prevent bleeding complications. Defects in glycosylation have been associated with decrease in blood platelet counts. However, the role of posttranslational modification in platelet production remains elusive. We here investigated the role of β1,4 galactosyltransferase 1 (β4GalT1), the key glycosyltransferase regulating lactosaminoglycan (LacNAc or βGal1,4 GlcNAc) expression by adding galactose (Gal) to terminal N-acetylglucosamine (GlcNAc), in platelet production. Stromal cell-derived factor 1 (SDF-1), but not thrombopoietin promotes megakaryocyte (MK) migration towards the bone marrow sinusoids, thereby increasing platelet production. SDF-1 (CXCL12) upregulated LacNAc expression in fetal liver wild type (WT), but not β4galt1-null megakaryocytes (MKs) lacking β4GalT1, suggesting that SDF-1 promotes LacNAc expression in vivo to regulate MK migration and platelet production. In support of this hypothesis, β4galt1-null mice had severe macrothrombocytopenia with increased bone marrow MK numbers, but normal platelet clearance. Ploidy, expression of the major glycoproteins (GPIbα/V/IX and αIIbβ3) and the surface expression of the SDF-1 receptor CXCR4 were normal in β4galt1-null bone marrow MKs. However, β4galt1-null bone marrow MKs had increased surface and total β1 integrin expression, as determined by flow cytometry, immunoblot and immunofluorescence. Mature CD42b/CD41 positive β4galt1-null MKs co-localized poorly with endoglin positive bone marrow sinusoids (49.9 ± 2.1 %), compared to WT MKs (72.4 ± 0.6 %). Expression of laminin, the major β1 integrin ligand, was upregulated in β4galt1-null MKs, suggesting that loss of LacNAc expression on β1 integrin increased its function. To exclude an extrinsic contribution to the failure of β4galt1-null MKs to migrate, β4galt1-null fetal liver (E14.5) hematopoietic cells (FLHCs) were transplanted in lethally irradiated WT mice. Transplanted β4galt1-null FLHCs restored bone marrow MKs, but failed to migrate to sinusoids and produce circulating platelets. In marked contrast, production of β4galt1-null white blood cells was normal. Together, our results suggest that SDF-1 upregulates β4GalT1-dependent LacNAc expression to promote MK migration and interaction with BM sinusoids, likely regulating MK β1 integrin expression and interaction with components of the extracellular matrix, specifically laminin. Understanding of the mechanisms regulating posttranslational modifications induced by various hematopoietic stimulating chemokines and cytokines will contribute to better platelet recovery following bone marrow transplant and radiochemotherapy. Disclosures No relevant conflicts of interest to declare.
Research on MATLAB Simulation of Three Level Power Amplifier for Magnetic Bearing (2010)

For FPGA-based three level switching power amplifier, this paper completed full-bridge circuit model and the current sampling circuit model was created by using Power System Blockset (PSB) library in the MATALB/Simulink. Through embedded MATLAB function file, we simulated the internal FPGA data processing. Simulation and experimental results verified the correctness of this method of modeling. And this provided a new accurate method of simulation for digital power amplifier.
Direct Western Blot Detection of HA Epitope-Tagged Proteins Using Anti-HA-Peroxidase (1996)

conjugate of Anti-HA monoclonal antibody and the reporter enzyme horseradish per- oxidase, for direct detection of HA-tagged fusion proteins in western blot analyses. Use of Anti-HA-peroxidase eliminates the need for a secondary detection step, as well as the need for the multiple washes nor- mally required after incubation with the secondary polyclonal anti-mouse IgG- enzyme conjugate. In addition to saving time (approximately 2 hours), the Anti-HA- peroxidase conjugate can detect HA-tagged proteins on immunoblots after their immunoprecipitation with unconjugated Anti-HA, without the interferences observed in indirect detection using anti- mouse IgG-peroxidase. The method described here provides rapid immuno- detection of HA-tagged proteins in crude cell extracts with sensitivity equivalent to traditional two-step western blot analysis.
Accounting for adjuvant-induced artifacts in the characterization of vaccine formulations by polyacrylamide gel electrophoresis (2017)

These methods may be useful for improving characterization approaches of antigen-adjuvant mixtures by SDS-PAGE.
INDEPENDENT EXPRESSION OF HUMAN T CELL DIFFERENTIATION ANTIGENS AND E ROSETTE RECEPTOR ON PHYTOHEMAGGLUTININ-STIMULATED T LYMPHOCYTES (1978)

SUMMARY Phytohemagglutinin (PHA)-stimulated lymphocytes from peripheral blood (PBL) were used to examine whether T cell xenoantigens are the same or distinct from the receptor for sheep red blood cells (SRBC). An anti-T cell serum (AMT) was directly conjugated with fluorescein, adsorbed to specificity, and used in antibody excess. With resting PBL, AMT stained T cells with a continuous fluorescent ring and completely inhibited spontaneous E rosette formation. When aliquots of the same cells were stimulated with PHA, AMT did not inhibit E rosette formation at concentrations up to 7.5 mg/ml. All T cells incubated with PHA for 24 to 72 hr were double-labeled with SRBC and AMT. Independent modulation of the surface markers was observed on the same cells as evidenced by cap formation with AMT and ringed morulas of SRBC. As controls, B cells purified from PBL or B lymphoblastoid cell lines did not form E rosettes when incubated with PHA. The abrogation of AMT inhibition of E rosette formation upon PHA-stimulated T cells was a time-dependent process requiring 24 hr of PHA incubation. The results indicate that these surface markers unique to human T cells are distinct structural entities, and that the E rosette blocking phenomenon by this xenoantiserum was attributable to steric hindrance.
BIOAVAILABILITY AND BIODEGRADATION OF WEATHERED DIESEL FUEL IN AQUIFER MATERIAL UNDER DENITRIFYING CONDITIONS (1998)

During the in situ bioremediation of a diesel fuel-contaminated aquifer in Menziken, Switzerland, aquifer material containing weathered diesel fuel (WDF) and indigenous microorganisms was excavated. This material was used to identify factors limiting WDF biodegradation under denitrifying conditions. Incubations of this material for 360 to 390 d under denitrifying conditions resulted in degradation of 23% of the WDF with concomitant consumption of NO and production of inorganic carbon. The biodegradation of WDF and the rate of NO consumption was stimulated by agitation of the microcosms. Biodegradation was not stimulated by the addition of a biosurfactant (rhamnolipids) or a synthetic surfactant (Triton X-100) at concentrations above their critical micelle concentrations. The rhamnolipids were biodegraded preferentially to WDF, whereas Triton X-100 was not degraded. Both surfactants reduced the surface tension of the growth medium from 72 to <35 dynes/cm and enhanced the apparent aqueous solubility of the model hydrocarbon n-hexadecane by four orders of magnitude. Solvent-extracted WDF, added at a concentration equal to that already present in the aquifer material, was also biodegraded by the microcosms, but not at a higher rate than the WDF already present in the material. The results show that the denitrifying biodegradation of WDF is not necessarily limited by bioavailability but rather by the inherent recalcitrance of WDF.
Nonlinear Faraday rotation and detection of superposition states in cold atoms (2010)

We report on the observation of nonlinear Faraday rotation with cold atoms at a temperature of $~100$ $\ensuremath{\mu}$K. The observed nonlinear rotation of the light polarization plane is up to $0.1$ rad over the $1$-mm-size atomic cloud in approximately $10$-mG magnetic field. The nonlinearity of rotation results from long-lived coherence of ground-state Zeeman sublevels created by a near-resonant light. The method allows for creation, detection, and control of atomic superposition states. It also allows applications for precision magnetometry with high spatial and temporal resolution.
Thermal bleaching of photodarkening-induced loss in ytterbium-doped fibers (2009)

We study the thermal bleaching process of photodarkening-induced loss in ytterbium-doped fibers. The observed power-law time dependence of the normalized absorption coefficient is well represented by the thermal decay model of Erdogan et al. [J. Appl. Phys. 76, 73 (1994)]. Using this model, we derive the activation energy associated with thermal recovery of the induced loss to prephotodarkened state. For the studied commercial 20 microm core diameter large-mode-area fiber, the energy distribution consists of a single peak, located at 1.32 eV with a FWHM of approximately 0.31 eV. The results presented are of particular importance to understanding photodarkening and bleaching processes in high-power fiber lasers.
Soybean Aphid Development on, and BCMV Transmission to, Otebo Dry Bean (2008)

The non‐native soybean aphid (SBA), Aphis glycines , is now common on soybean across the Midwest. Dry beans are not listed as a host for SBA, but SBA outbreaks in Michigan correspond with increased incidence of Bean common mosaic potyvirus (BCMV) in susceptible dry bean varieties. This study examined SBA development on and BCMV transmission to Otebo beans. SBA females deposited nymphs on dry bean foliage after two days in the laboratory and field, but survival and reproduction were less on dry bean than on soybean. After six days in the laboratory and field, all adults and nymphs were dead on dry beans. However, studies using winged SBA confirmed their ability to transmit BCMV from and to Otebo dry bean.
Performance of hashing-based schemes for Internet load balancing (2002)

Load balancing is a key technique for improving Internet performance. Effective use of load balancing requires good traffic distribution schemes. We study the performance of several hashing schemes for distributing traffic over multiple links while preserving the order of packets within a flow. Although hashing-based load balancing schemes have been proposed in the past, this is the first comprehensive study of their performance using real traffic traces. We evaluate five direct hashing methods and one table-based hashing method. We find that hashing using a 16-bit CRC over the five-tuple gives excellent load balancing performance. Further, load-adaptive table-based hashing using the exclusive OR of the source and destination IP addresses achieves comparable performance to the 16-bit CRC. Table-based hashing can also distribute traffic load according to unequal weights. We also report on four other schemes with poor to moderate performance.
Loss of UHRF2 expression is associated with human neoplasia, promoter hypermethylation, decreased 5-hydroxymethylcytosine, and high proliferative activity (2016)

Ubiquitin-like with PHD and ring finger domains 2 (UHRF2) binds to 5-hydroxymethylcytosine (5hmC), a DNA base involved in tissue development, but it is unknown how their distribution compares with each other in normal and malignant human tissues. We used IHC on human tumor specimens (160 from 19 tumor types) or normal tissue to determine the expression and distribution of UHRF2, Ki-67, and 5hmC. We also examined UHRF2 expression in cord blood progenitors and compared its expression to methylation status in 6 leukemia cell lines and 15 primary human leukemias. UHRF2 is highly expressed, paralleling that of 5hmC, in most non-neoplastic, differentiated tissue with low Ki-67 defined proliferative activity. UHRF2 is expressed in common lymphoid progenitors and mature lymphocytes but not common myeloid progenitors or monocytes. In contrast, UHRF2 immunostaining in human cancer tissues revealed widespread reduction or abnormal cytoplasmic localization which correlated with a higher Ki-67 and reduced 5hmC. UHRF2 expression is reduced in some leukemia cell lines, this correlates with promoter hypermethylation, and similar UHRF2 methylation profiles are seen in primary human leukemia samples. Thus, UHRF2 and 5hmC are widely present in differentiated human tissues, and UHRF2 protein is poorly expressed or mislocalized in diverse human cancers.
A microsatellite perspective on the reproductive success of subordinate male honey badgers, <i>Mellivora capensis</i> (2004)

The dominance hierarchy system of male honey badg ers, Mellivora capensis, does not appear to determine reproductive success in the species as subordinate males are frequently seen to gain brief access to re ceptive females. To establish whether these interac tions lead to fertilization, five microsatellite loci were used to infer paternity in a honey badger population from the Kgalagadi Transfrontier National Park. In total, 26 individuals comprising 10 cubs, eight known mothers and eight potential fathers were analysed. Exclusion analysis and a likelihood based approach identified the dominant male in the study population as the most likely father of 50% of the cubs (≥80% likelihood confidence). The remaining five cubs were most likely fathered by four different subordi nate males (≥80% likelihood confidence). The results suggest that the brief mating opportunities afforded to subordinate males lead to fertilization, and hence that the dominance hierarchy system of the honey badger is not strong enough to exclude sneak fertil izations.
Reducing erythropoietin in cultures of human erythroid precursors elevates the proportion of fetal haemoglobin (1994)

In order to clarify the mechanism of the effect of erythropoietin (Epo) on the fetal haemoglobin (HbF) phenotype of peripheral erythrocytes, we studied the dose-response effect of Epo on HbF production by erythroid precursors derived from the peripheral blood of normal adult individuals and grown in a two-phase liquid culture system. The proportion of HbF out of the total haemoglobin (Hb) content (%HbF) was dependent on the duration of exposure to Epo; on day 6 it comprised up to 15%, but dropped to < 2% on day 14. Both cell yield and cellular Hb content were markedly increased by high (1 U/ml) Epo, compared to normal physiological (20-50 mU/ml) levels, but neither the initial nor final %HbF were dependent on the increased Epo dose. However, when cells grown with high Epo were transferred on day 7 to low Epo, their progeny contained by day 14 a higher %HbF as compared to cells that were continuously exposed to high Epo. This was accompanied by acceleration and synchronization of their maturation process, as evidenced by their morphology, density and size, and restriction on cell multiplication, as indicated by the lower cell yield. These results are consistent with the following model. As early erythroid precursors, with relatively high HbF, mature under steady-state levels of Epo, HbA production predominates and HbF is diluted. However, when such precursors are switched from high to low levels of Epo they undergo a synchronized, accelerated maturation which shortens the period of HbA production, leading to a decreased Hb content and a relatively high proportion of HbF. This mechanism may contribute to the elevated HbF observed following Epo administration (due to short half-life of Epo in vivo), and might also explain the HbF-augmenting effect of Epo administered together with hydroxyurea observed in patients with sickle cell anaemia.
Prescribing patterns of neuroactive drugs in 98 schizophrenic patients. (1989)

Ninety-eight schizophrenic outpatients receiving pharmacotherapy were surveyed on two census days, 18 months apart. From this study sample it was found that, as recently as 1987, 18% of the patients were prescribed three classes of neuroactive drugs--16% two antipsychotic drugs simultaneously. Of antipsychotics receivers, 44% were prescribed anticholinergics, 3% antidepressants, and 4% benzodiazepines. Between census days, a significant shift from use of oral antipsychotics to the depot form of administration occurred, while polypharmacy frequency remained unchanged. An analysis of the data will provide guidelines for rendering a more rational pharmacological treatment.
Rapport d"avancemenet de la commutation sans capteur pour Pellenc SA (2000)

Keywords: commutation ; capteur ; Pellenc Reference EPFL-REPORT-166229 Record created on 2011-05-31, modified on 2017-05-10
Identification of two types of exchangeable sites for monovalent copper ions exchanged in MFI-type zeolite (2008)

Three different approaches have been used to characterize the state of exchanged copper ions in copper-ion-exchanged MFI (CuMFI) samples. (1) Two types of an ion-exchangeable site with different adsorption properties for N(2) or CO molecules were identified depending on the pre-treatment temperature (723 or 873 K) of a sample prepared by using an aqueous solution of CuCl(2). (2) The state of the active sites formed by the evacuation of a sample at 873 K that had been prepared using a mixture solution of aqueous NH(4)CH(3)COO and Cu(CH(3)COO)(2) was analysed utilizing both (13)C(18)O and (12)C(16)O to identify the two types of active adsorption sites for CO molecules. (3) CuMFI samples prepared by the ion-exchange method employing anhydrous CuCH(3)COO showed a surprising adsorption feature characterized by a single IR band occurring at 2159 cm(-1) due to the adsorbed CO molecules, but there was no corresponding IR band due to adsorbed N(2) molecules. A successful preparation of CuMFI, in which the monovalent copper ions exclusively occupied another one of the two types of ion-exchangeable sites, was also carried out utilizing the solid-ion exchange method using Cu(CH(3)COO)(2).H(2)O. This site exhibits an IR band occurring at 2151 cm(-1) for CO molecules and also acts as an active site for N(2) molecules. These experimental data correlate, and clearly indicate that there are at least two types of exchangeable sites for copper ions in MFI-type zeolites.
Design and implementation of a hypervisor-based platform for dynamic information flow tracking in a distributed environment (2011)

One of the central security concerns in managing an organization is protecting the flow of sensitive information, by which we mean either maintaining an audit trail or ensuring that sensitive documents are disseminated only to the authorized parties. 
A promising approach to securing sensitive data involves designing mechanisms that interpose at the software-hardware boundary and track the flow of information with high precision—at the level of bytes and machine instructions. Fine-grained information flow tracking (IFT) is conceptually simple: memory and registers containing sensitive data are tagged with taint labels and these labels are propagated in accordance with the computation. However, previous efforts have demonstrated that full-system IFT faces two major practical limitations—enormous performance overhead and taint explosion. These challenges render existing IFT implementations impractical for deployment outside of a laboratory setting. 
This dissertation describes our progress in addressing these challenges. We present the design and implementation of PIFT (for Practical Information Flow Tracking)—a hypervisor-based IFT platform that achieves substantial performance improvements over previous systems and largely eliminates the problem of kernel taint explosion. PIFT takes advantage of spare CPU cores to track the flow of information asynchronously and in parallel with the primary instruction stream. 
To the best of our knowledge, PIFT is the most efficient full-system IFT platform available at the time of writing and is the only implementation that supports real-time tracking of information flow in graphical desktop environments.
The in vivo and in vitro substrate specificity of quinoprotein glucose dehydrogenase of<i>Acinetobacter calcoaceticus</i>LMD79.41 (1987)

Quinoprotein glucose dehydrogenase (GDH; EC 1.1.99.17) was partially purified from cell-free extracts of <it>Acinetobacter calcoaceticus</it> LMD79.41. The enzyme oxidized monosaccharides (<scp>d</scp>-glucose, <scp>d</scp>-allose, 2-deoxy-<scp>d</scp>-glucose, <scp>d</scp>-galactose, <scp>d</scp>-mannose, <scp>d</scp>-xylose, <scp>d</scp>-ribose and <scp>l</scp>-arabinose) as well as disaccharides (<scp>d</scp>-lactose, <scp>d</scp>-maltose and <scp>d</scp>-cellobiose). Intact cells of <it>A. calcoaceticus</it> LMD79.41 also oxidized these monosaccharides, but not the disaccharides. The difference in substrate specificity can not be explained by impermeability of the outer membrane for disaccharides, since right-side-out membrane vesicles did not oxidize disaccharides either. Destruction of the cytoplasmic membrane strongly affected the catalytic properties of GDH. Not only did the affinity towards some monosaccharides change substantially, but disaccharides also became good substrates upon solubilization of the enzyme. Thus, at least in <it>A. calcoaceticus</it> LMD79.41, the oxidation of disaccharides by GDH can be considered as an in vitro ‘artefact’ caused by the removal of the enzyme from its natural environment.
3‐Lithiopyrroles by Halogen‐Metal Interchange of 3‐Bromo‐1‐(triissopropylsilyl)pyrroles. Synthesis of Verucarin E and Other 3‐Substituted Pyrroles. Preliminary Communication (1984)

Abstract 3‐Lithio‐1‐(trimethylsilyl)pyrrole ( 7 , Schem 2 ), obtained by halogen‐metal interchange from the 3‐bromo compound 2 , reacted with various electrophilic reagents to provide products, which on fluoride ion desilylation, gave 3‐substituted pyrroles in good overall yields. One such pyrrole 13 ( Schem 3 ), was converted into 2‐formyl‐3‐octadeclpyrrole ( 14 ), reputed to be a metabolite of the marine sponge Oscarella lobularis . 3,4‐Dibromo‐1‐(triisopropylsityl)pyrrole ( 5 ) was efficiently transformed, by a process involving two consecutive bromine‐lithium exchange reactions ( Scheme 4 ), into the antibiotic verrucarin E 17 .
An advanced scan format converter with flexible and high quality signal processing (2002)

We have developed a flexible scan format converter, a one-chip device that converts various types of input signals (standard TV signals and high-definition TV signals as well as VGA and SVGA signals) to a required formatted output signal with high picture quality for displaying on any of a wide range of display devices such as PDPs, LCDs and CRTs.
Bovine spongiform encephalopathy infection alters endogenous retrovirus expression in distinct brain regions of cynomolgus macaques (Macaca fascicularis) (2011)

We provide evidence that dysregulation of ERVs in response to BSE-infection can be detected on both, the RNA and the protein level. To our knowledge, this is the first report on the differential expression of ERV-derived structural proteins in prion disorders. Our findings suggest that endogenous retroviruses may induce or exacerbate the pathological consequences of prion-associated neurodegeneration.