gebhart/patrepeval huggingface dataset:
Dielectrophoretic Manipulation of DNA:  Separation and Polarizability (2007)

Although separation of polymers based on the combination of dielectrophoretic trapping and electrophoretic forces was proposed 15 years ago, experimental proof has not yet been reported. Here, we address this problem for long DNA fragments in a simple and easy-to-fabricate microfluidic device, in which the DNA is manipulated by electrophoresis and by electrodeless dielectrophoresis. By slowly increasing the strength of the dielectrophoretic traps in the course of the separation experiments, we are able to perform efficient and fast DNA separation according to length for two different DNA conformations: linear DNA (lambda (48.5-kbp) and T2 (164-kbp) DNA) and supercoiled covalently closed circular plasmid DNA (7 and 14 kbp). The underlying migration mechanism-thermally induced escape processes out of the dielectrophoretic traps in the direction of the electrophoretic force-is sensitive to different DNA fragments because of length-dependent DNA polarizabilities. This is analyzed in a second series of experiments, where the migration mechanism is exploited for the quantitative measurement of the DNA polarizabilities. This new and simple technique allows for the systematic characterization of the polarizability not only for DNA but also for other biomolecules like proteins. Furthermore, our results have direct implications to future biotechnological applications such as gene therapy and DNA vaccination.
Automatic gain control in mass spectrometry using a jet disrupter electrode in an electrodynamic ion funnel (2004)

We report on the use of a jet disrupter electrode in an electrodynamic ion funnel as an electronic valve to regulate the intensity of the ion beam transmitted through the interface of a mass spectrometer in order to perform automatic gain control (AGC). The ion flux is determined by either directly detecting the ion current on the conductance limiting orifice of the ion funnel or using a short mass spectrometry acquisition. Based upon the ion flux intensity, the voltage of the jet disrupter is adjusted to alter the transmission efficiency of the ion funnel to provide a desired ion population to the mass analyzer. Ion beam regulation by an ion funnel is shown to provide control to within a few percent of a targeted ion intensity or abundance. The utility of ion funnel AGC was evaluated using a protein tryptic digest analyzed with liquid chromatography Fourier transform ion cyclotron resonance (LC-FTICR) mass spectrometry. The ion population in the ICR cell was accurately controlled to selected levels, which improved data quality and provided better mass measurement accuracy.
Growth hormone (GH)-releasing hormone-(1-29) twice daily reverses the decreased GH and insulin-like growth factor-I levels in old men. (1992)

Aging is associated with decreased GH and insulin-like growth factor-I (IGF-I) levels and lean body mass, and increased body fat. Recombinant human GH treatment of old men partially reverses body composition changes. Administration of GH-releasing hormone (GHRH) to GH-deficient children and young adults increases GH and IGF-I levels while preserving physiological GH release. We investigated whether GHRH injections restore GH and IGF-I levels in old men to the levels in young men. Healthy young (n = 9; 26.2 +/- 4.1 yr; mean +/- SD) and old (n = 10; 68.0 +/- 6.2 yr) nonobese men underwent baseline blood sampling for measurements of IGF-I and 24-h profiles of GH release, followed by iv bolus GHRH stimulation tests. Old men then took, randomly, both low (0.5 mg) and high (1 mg) dose GHRH-(1-29) sc injections twice daily for 14 days, with an intervening 14-day nontreatment period. The study protocol was repeated on day 14 of each treatment. At baseline, the mean peak duration of spontaneous GH release (P less than 0.005) and IGF-I levels (P less than 0.0001) were lower in the old men. GHRH treatment evoked dose-related increases in all parameters, with significant differences (vs. old basal values) in mean 24-h GH (P less than 0.001), area under peaks (P less than 0.001), peak amplitude (P less than 0.05), and IGF-I (P less than 0.005) only at the high dose. After high dose treatment, there were no significant differences in these parameters between age groups. Peak and integrated responses to iv GHRH stimulation tests did not differ between young and old men either before or during GHRH treatment. Baseline serum levels of both testosterone (P less than 0.01) and phosphate (P less than 0.05) were lower in the older men. Phosphate levels increased (P less than 0.05) during GHRH treatment. GHRH treatment did not affect fasting glucose, urinary C-peptide, blood pressure, or chemistry and hematology profiles. Thus, short term sc administration of GHRH to healthy old men reverses age-related decreases in GH and IGF-I, suggesting that prolonged treatment could improve age-related alterations in body composition.
Regulatory Mechanisms of Chondrogenesis and Implications for Understanding Articular Cartilage Homeostasis (2008)

Studies of chondrogenesis and embryonic limb development offer a wealth of knowledge regarding signals that regulate the behavior of chondrocytes. Many such chondrogenic regulators are upregulated in osteoarthritis-affected chondrocytes, suggesting a role in pathogenesis. Yet, some of the same factors also support adult articular cartilage homeostasis, and enhance neo-cartilage tissue formation in experimental models. In this review, we summarize many of the important regulatory mechanisms involved in chondrogenesis and examine how their disruption may contribute to functional changes in articular cartilage during osteoarthritis or aging.
Packet Forwarding With Multiprotocol Label Switching (2007)

MultiProtocol Label Switching (MPLS) is an emerging technology that aims to address many of the existing issues associated with packet forwarding in today-s Internetworking environment. It provides a method of forwarding packets at a high rate of speed by combining the speed and performance of Layer 2 with the scalability and IP intelligence of Layer 3. In a traditional IP (Internet Protocol) routing network, a router analyzes the destination IP address contained in the packet header. The router independently determines the next hop for the packet using the destination IP address and the interior gateway protocol. This process is repeated at each hop to deliver the packet to its final destination. In contrast, in the MPLS forwarding paradigm routers on the edge of the network (label edge routers) attach labels to packets based on the forwarding Equivalence class (FEC). Packets are then forwarded through the MPLS domain, based on their associated FECs , through swapping the labels by routers in the core of the network called label switch routers. The act of simply swapping the label instead of referencing the IP header of the packet in the routing table at each hop provides a more efficient manner of forwarding packets, which in turn allows the opportunity for traffic to be forwarded at tremendous speeds and to have granular control over the path taken by a packet. This paper deals with the process of MPLS forwarding mechanism, implementation of MPLS datapath , and test results showing the performance comparison of MPLS and IP routing. The discussion will focus primarily on MPLS IP packet networks – by far the most common application of MPLS today.
Ethyl caffeate suppresses NF‐κB activation and its downstream inflammatory mediators, iNOS, COX‐2, and PGE2in vitro or in mouse skin (2005)

Ethyl caffeate, a natural phenolic compound, was isolated from Bidens pilosa, a medicinal plant popularly used for treating certain inflammatory syndromes. The purpose of this study was to investigate the structural activity, and the anti-inflammatory functions and mechanism(s) of ethyl caffeate. Ethyl caffeate was found to markedly suppress the lipopolysaccharide (LPS)-induced nitric oxide (NO) production (IC(50) = 5.5 microg ml(-1)), mRNA and protein expressions of inducible nitric oxide synthase (iNOS), and prostaglandin E(2) (PGE(2)) production in RAW 264.7 macrophages. Transient gene expression assays using human cox-2 promoter construct revealed that ethyl caffeate exerted an inhibitory effect on cox-2 transcriptional activity in 12-O-tetradecanoylphorbol-13-acetate (TPA)-treated MCF-7 cells. Immunohistochemical studies of mouse skin demonstrated that TPA-induced COX-2 expression was significantly inhibited by ethyl caffeate with a superior effect to that of celecoxib, a nonsteroidal anti-inflammatory drug. The phosphorylation and degradation of inhibitor kappaB (IkappaB) and the translocation of nuclear transcription factor-kappaB (NF-kappaB) into the nucleus, as well as the activation of mitogen-activated protein kinases (MAPKs) induced by LPS in macrophages, were not affected by ethyl caffeate. Ethyl caffeate, however, could inhibit NF-kappaB activation by impairing the binding of NF-kappaB to its cis-acting element. These results suggest that ethyl caffeate suppresses iNOS and COX-2 expressions partly through the inhibition of the NF-kappaB.DNA complex formation. Structure-activity relationship analyses suggested that the catechol moiety and alpha,beta-unsaturated ester group in ethyl caffeate are important and essential structural features for preventing NF-kappaB.DNA complex formation. This study provides an insight into the probable mechanism(s) underlying the anti-inflammatory and therapeutic properties of ethyl caffeate.
Energy band offsets of dielectrics on InGaZnO4 (2017)

Thin-film transistors (TFTs) with channels made of hydrogenated amorphous silicon (a-Si:H) and polycrystalline silicon (poly-Si) are used extensively in the display industry. Amorphous silicon continues to dominate large-format display technology, but a-Si:H has a low electron mobility, μ ∼ 1 cm2/V s. Transparent, conducting metal-oxide materials such as Indium-Gallium-Zinc Oxide (IGZO) have demonstrated electron mobilities of 10–50 cm2/V s and are candidates to replace a-Si:H for TFT backplane technologies. The device performance depends strongly on the type of band alignment of the gate dielectric with the semiconductor channel material and on the band offsets. The factors that determine the conduction and valence band offsets for a given material system are not well understood. Predictions based on various models have historically been unreliable and band offset values must be determined experimentally. This paper provides experimental band offset values for a number of gate dielectrics on IGZO for next generation TFTs. The relationship between band offset and interface quality, as demonstrated experimentally and by previously reported results, is also explained. The literature shows significant variations in reported band offsets and the reasons for these differences are evaluated. The biggest contributor to conduction band offsets is the variation in the bandgap of the dielectrics due to differences in measurement protocols and stoichiometry resulting from different deposition methods, chemistry, and contamination. We have investigated the influence of valence band offset values of strain, defects/vacancies, stoichiometry, chemical bonding, and contamination on IGZO/dielectric heterojunctions. These measurements provide data needed to further develop a predictive theory of band offsets.
Genetics and molecular pathogenesis of pheochromocytoma and paraganglioma (2012)

Although most pheochromocytomas (PCCs) and paragangliomas (PGLs) are sporadic, molecular genetic medicine has revealed that a considerable number of patients with apparently sporadic PCC actually have a genetic predisposition to the development of these tumors. After decades of intensive research, several genes are now known to play an important role in the pathogenesis of PCC. At present, these are RET proto-oncogene, von Hippel-Lindau disease tumor suppressor gene (VHL), neurofibromatosis type 1 tumor suppressor gene (NF1), genes encoding the succinate dehydrogenase (SDH) complex subunits SDHB, SDHC, and SDHD, but also SDHA, the gene encoding the enzyme responsible for the flavination of SDHA (SDHAF2 or hSDH5), and the newly described TMEM127 and MAX tumor suppressor genes. In addition to these ten PCC susceptibility genes, two other genes, KIF1B and PHD2, have also been associated with PCC. Studying the pathogenesis and the molecular correlation of these mutations has revealed the existence of two main transcription signatures: a pseudohypoxic cluster (VHL and SDH mutations) and a cluster rich in kinase receptor signaling and their downstream pathways (RET, NF1, TMEM127, and MAX mutations). However, the general mechanism in the pathogenesis of a syndrome does not entirely apply in the particular pathogenesis of PCC as a manifestation of that syndrome. A better understanding of the complexity and high genetic diversity of PCC and PGL may lead to more efficient diagnosis and management of the disease.
Macrophages are an abundant component of myeloma microenvironment and protect myeloma cells from chemotherapy drug–induced apoptosis (2009)

Multiple myeloma remains an incurable disease. One of the major problems is that myeloma cells develop drug resistance on interaction with bone marrow stromal cells. In this study, we examined the effects of macrophages (Mvarphis), a type of stromal cells, on myeloma cell survival and response to chemotherapy. We showed that Mvarphi, in particular tumor-associated Mvarphi, is a protector of myeloma cells. The protective effect was dependent on direct contact between Mvarphis and myeloma cells. Mvarphis protected both myeloma cell lines and primary myeloma cells from spontaneous and chemotherapy drug-induced apoptosis by attenuating the activation and cleavage of caspase-dependent apoptotic signaling. These findings are clinically relevant because we found that CD68+ Mvarphis heavily infiltrate the bone marrow of patients with myeloma but not the bone marrow of control patients. Thus, our results indicate that Mvarphis may contribute to myeloma cell survival and resistance to chemotherapeutic treatment in vivo.
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing (2013)

This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin.
Recognition of Human Cytomegalovirus by Human Primary Immunoglobulins Identifies an Innate Foundation to an Adaptive Immune Response (2005)

Most primates, including humans, are chronically infected with cospecifically evolved, potentially pathogenic CMV. Abs that bind a 10-aa linear epitope (antigenic determinant 2 site 1) within the extracellular domain of human CMV glycoprotein B neutralize viral infectivity. In this study, we show that genes generated by recombinations involving two well-conserved human germline V elements (IGHV3-30 and IGKV3-11), and IGHJ4, encode primary Ig molecules that bind glycoprotein B at this key epitope. These particular V(H), J(H), and V(kappa) genes enable humans to generate through recombination and N nucleotide addition, a useful frequency of primary Igs that efficiently target this critical site on human CMV and thus confer an innate foundation for a specific adaptive response to this pathogen.
Screen Savers of the World Unite! (2000)

Unused CPU time on desktop computers could be put to good use, if distributed computing succeeds in capturing people's imagination. In their Perspective, Shirts and Pande describe existing distributed computing projects and recent efforts to overcome parallelization problems. This vast underused resource could raise biological and other scientific computation to fundamentally new predictive levels.
Robust extraction of multiple structures from non-uniformly sampled data (2004)

The extraction of multiple coherent structures from point clouds is crucial to the problem of scene modeling. While many statistical methods exist for robust estimation from noisy data, they are inadequate for addressing issues of scale, semi-structured clutter, and large point density variation together with the computational restriction of autonomous navigation. This paper extends an approach of nonparametric projection-pursuit based regression to compensate for the non-uniform and directional nature of data sampled in outdoor environments. The proposed algorithm is employed for extraction of planar structures and clutter grouping. Results are shown for scene abstraction of 3D range data in large urban scenes.
Switchable diffractive cholesteric gratings (1997)

Electrically switchable diffractive gratings based on cholesteric liquid crystals are suggested. An electric field switches the cholesteric cell between three states: two with a uniform in-plane director and one with a periodic in-plane director modulation. The modulated state produces a Raman–Nath diffractive effect. Characteristic time of switching is of the order of 10 ms. Diffractive properties depend on the polarization of the incident beam and the direction of surface orientation.
Large deuterium isotope effects and their use: a historical review (2011)

Isotope effects are differences in the properties of the isotopes of an element resulting in different reaction rates of a corresponding compound, in equilibrium constants and in the spectra. Shortly after the discovery of stable isotopes of hydrogen, oxygen, and carbon, Jacob Bigeleisen formulated a theory of isotope effects and calculated possible maximum values. Large isotope effects of 2H (deuterium) against 1H (protium) were seen to possibly influence interpretations of reaction mechanisms if corresponding labelling is used. Much work was invested to ensure the safety of deuterium use in men in spite of the large isotope effect. On the other hand, large deuterium isotope effects gave rise to several practical applications. Examples are the enhancement of the stability of some technical products against oxidative and against hydrolytic degradation (oils, pharmaceuticals) as well as alterations of the detoxification metabolism of pharmaceuticals in vivo.
Characterization of the Saccharomyces cerevisiae YMR318C (ADH6) gene product as a broad specificity NADPH-dependent alcohol dehydrogenase: relevance in aldehyde reduction (2001)

YMR318C represents an open reading frame from Saccharomyces cerevisiae with unknown function. It possesses a conserved sequence motif, the zinc-containing alcohol dehydrogenase (ADH) signature, specific to the medium-chain zinc-containing ADHs. In the present study, the YMR318C gene product has been purified to homogeneity from overexpressing yeast cells, and found to be a homodimeric ADH, composed of 40kDa subunits and with a pI of 5.0–5.4. The enzyme was strictly specific for NADPH and was active with a wide variety of substrates, including aliphatic (linear and branched-chain) and aromatic primary alcohols and aldehydes. Aldehydes were processed with a 50-fold higher catalytic efficiency than that for the corresponding alcohols. The highest kcat/Km values were found with pentanal&amp;gt;veratraldehyde &amp;gt; hexanal &amp;gt; 3-methylbutanal &amp;gt;cinnamaldehyde. Taking into consideration the substrate specificity and sequence characteristics of the YMR318C gene product, we have proposed this gene to be called ADH6. The disruption of ADH6 was not lethal for the yeast under laboratory conditions. Although S. cerevisiae is considered a non lignin-degrading organism, the catalytic activity of ADHVI can direct veratraldehyde and anisaldehyde, arising from the oxidation of lignocellulose by fungal lignin peroxidases, to the lignin biodegradation pathway. ADHVI is the only S. cerevisiae enzyme able to significantly reduce veratraldehyde in vivo, and its overexpression allowed yeast to grow under toxic concentrations of this aldehyde. The enzyme may also be involved in the synthesis of fusel alcohols. To our knowledge this is the first NADPH-dependent medium-chain ADH to be characterized in S. cerevisiae.
Structural and Biophysical Characterization of the EphB4·EphrinB2 Protein-Protein Interaction and Receptor Specificity (2006)

Increasing evidence implicates the interaction of the EphB4 receptor with its preferred ligand, ephrinB2, in pathological forms of angiogenesis and in tumorigenesis. To identify the molecular determinants of the unique specificity of EphB4 for ephrinB2, we determined the crystal structure of the ligand binding domain of EphB4 in complex with the extracellular domain of ephrinB2. This structural analysis suggested that one amino acid, Leu-95, plays a particularly important role in defining the structural features that confer the ligand selectivity of EphB4. Indeed, all other Eph receptors, which promiscuously bind many ephrins, have a conserved arginine at the position corresponding to Leu-95 of EphB4. We have also found that amino acid changes in the EphB4 ligand binding cavity, designed based on comparison with the crystal structure of the more promiscuous EphB2 receptor, yield EphB4 variants with altered binding affinity for ephrinB2 and an antagonistic peptide. Isothermal titration calorimetry experiments with an EphB4 Leu-95 to arginine mutant confirmed the importance of this amino acid in conferring high affinity binding to both ephrinB2 and the antagonistic peptide ligand. Isothermal titration calorimetry measurements also revealed an interesting thermodynamic discrepancy between ephrinB2 binding, which is an entropically driven process, and peptide binding, which is an enthalpically driven process. These results provide critical information on the EphB4*ephrinB2 protein interfaces and their mode of interaction, which will facilitate development of small molecule compounds inhibiting the EphB4*ephrinB2 interaction as novel cancer therapeutics.
Genetic control of specific immune suppression. II. H-2-linked dominant genetic control of immune suppression by the random copolymer L-glutamic acid50-L-tyrosine50 (GT). (1975)

Several inbred as well as congenic resistant strains of mice, which fail to respond to the random copolymer of L-glutamic acid50-L-tyrosine50 (GT), were shown to develop specific PFC responses when stimulated by GT complexed to an immunogenic carrier such as methylated bovine serum albumin (MBSA). In these studies we have found that GT preimmunization has a tolerogenic effect on the response to GT-MBSA in some mouse strains; whereas in other strains of mice, GT fails to inhibit the GT-MBSA response. We may, therefore, conclude that immune suppression cannot account for nonresponsiveness in all cases. The development of specific immune suppression in response to GT was shown to be inherited as a dominant trait in F1 hybrids resulting from the mating of suppressor with nonsuppressor strains. This trait is, therefore, under the control of a gene or genes that we have designated as specific immune suppression gene(s) Is genes. The strain distribution of GT induced suppression demonstrates that Is genes are coded for in the H-2 complex. Furthermore, immune suppression by the two related copolymers, GT and GAT, are distinct in different strains of mice. The significance of these data for our understanding of the regulation of the immune response is discussed.