gebhart/patrepeval huggingface dataset:
The role of the cytoskeleton in the polarized growth of the germ tube in Candida albicans (1994)

Cells of the dimorphic yeast Candida albicans are easily induced to germinate in synchrony. Using germinating cells of strain FC18, we examined the effects of several drugs that are known to affect the cytoskeleton on growth and cytoskeletal organization. Cytochalasin A (CA), an inhibitor of actin function, inhibited the germination of the yeast cells and changed the cylindrical expansion of the apex of the germ tube to swelling growth. Effects of CA on the organization of actin were examined with rhodamine-phalloidin (Rh-Ph), which specifically stains F-actin. In CA-untreated cells, Rh-Ph staining resulted in condensed dot-like fluorescence at the growing tip, as well as filamentous fluorescence (actin cables) that ran from the apex to the basal region. In CA-treated cells, condensed dot-like fluorescence was still observed at the swelling tip, but actin cables had disappeared completely. This result indicates that CA does not affect the asymmetrical distribution of actin, and suggests that the actin cables are not required for maintenance of the polarized localization of actin. Benomyl, an anti-microtubule drug, inhibited the germination of yeast cells and the apical growth of germinated cells. Benomyl not only disrupted microtubules (MTs), but also affected the distribution of actin. In benomyl-treated cells, actin dots were randomly dispersed all over the cell. This result indicates that benomyl destroyed the mechanism that maintains the asymmetrical distribution of actin, and suggests that MTs are involved in such a mechanism. The polarized localization of organelles is one of the most important factors associated with dimorphism.(ABSTRACT TRUNCATED AT 250 WORDS)
Efficient security for large and dynamic multicast groups (2002)

Proposals for multicast security that have been published so far are complex, often require trust in network components or are inefficient. We propose a series of novel approaches for achieving scalable security in IP multicast, providing privacy and authentication on a group-wide basis. They can be employed to efficiently secure multi party applications where members of highly dynamic groups of arbitrary size may participate. Supporting dynamic groups implies that newly joining members must not be able to understand past group communications, and that leaving members may not follow future communications. Key changes are required for all group members when a leave or join occurs, which poses a problem if groups are large. The algorithms presented here require no trust in third parties, support either centralized or fully distributed management of keying material, and have low complexity (O(log N) or less). This grants scalability even for large groups.
HBT low-noise performance in a 0.18 μm SiGe BiCMOS technology (2002)

Noise figure and gain are critical parameters in the design of any product featuring a high-frequency receiver. We present here for the first time a noise and gain characterization of HBTs fabricated in a development version of IBM's new 90 GHz, 0.18 /spl mu/m-generation SiGe BiCMOS process with copper interconnects. At 2 GHz, we report a noise figure of less than 0.4 dB and an associated gain of 14 dB, a significant (0.3-0.5 dB) improvement over prior SiGe and GaAs state of the art in a commercial process. At 10 GHz, we observe a noise figure of 1.45 dB, an approximately 0.7 dB improvement over previous offerings. This performance makes the 0.18 /spl mu/m SiGe BiCMOS technology attractive for RF, analog, and mixed-signal circuit design.
New mammalian transforming retrovirus: demonstration of a polyprotein gene product (1983)

A new acute transforming type C retrovirus was isolated from mice inoculated with a virus stock obtained by iododeoxyuridine induction of methylcholanthrene-transformed C3H/10T1/2 mouse cells. This virus, designated 3611-MSV, transforms embryo fibroblasts and epithelial cells in culture and induces fibrosarcomas in vivo. 3611-MSV is replication defective, requiring a type C helper virus for propagation both in vitro and in vivo. By using endpoint transmission of 3611-MSV to MMCE C17 mouse and FRE 3A rat cells, several nonproductively transformed clonal cell lines have been derived. Pseudotype virus stocks obtained from such clones transform cells in vitro, are highly oncogenic in vivo, and exhibit host range and serological properties that are characteristic of their helper virus component. Analysis of viral antigen expression in 3611-MSV-transformed cells has led to the demonstration of a 90,000-molecular-weight (Mr) polyprotein and a 75,000-Mr probable cleavage product, both containing the amino-terminal murine leukemia virus gag gene proteins p15 and p12. In contrast to gene products of many previously described mammalian transforming viruses, 3611-MSV-encoded polyproteins lack detectable protein kinase activity, and 3611-MSV-transformed cells resemble chemically transformed cell line C3H/MCA-5, from which 3611-MuLV was originally derived, in that they do not exhibit elevated levels of phosphotyrosine. By using molecular hybridization the 3611-MSV transforming gene was found to be distinct from previously described mammalian cellular oncogenic sequences, including c-ras, c-abl, c-fes, c-fms, c-sis, and c-mos.
RelB Enhances Prostate Cancer Growth: Implications for the Role of the Nuclear Factor-κB Alternative Pathway in Tumorigenicity (2009)

The nuclear factor-kappaB (NF-kappaB) classic pathway is thought to be critical for tumorigenesis, but little is known about the role of the NF-kappaB alternative pathway in cancer development. Recently, high constitutive nuclear levels of RelB have been observed in human prostate cancer specimens with high Gleason scores. Here, we used four complementary approaches to test whether RelB contributes to tumorigenicity of prostate cancer. Inhibiting RelB in aggressive androgen-independent PC-3 cells by stable or conditional expression of a dominant-negative p100 mutant significantly reduced the incidence and growth rate of tumors. The decrease in tumorigenicity coincided with a reduction in the NF-kappaB target interleukin-8 (IL-8). Consistently, down-regulation of RelB by small interfering RNA targeting also reduced tumor growth and decreased levels of IL-8. Conversely, stable expression of RelB in androgen-responsive LNCaP tumors increased the circulating IL-8 levels. Taken together, these results reveal a tumor-supportive role of RelB, implicate the NF-kappaB alternative pathway as a potential target for preventing prostate cancer, and suggest the use of IL-8 as a marker for prostate cancer prognosis.
Sequential priming and boosting with heterologous HIV immunogens predominantly stimulated T cell immunity against conserved epitopes (2006)

This is the first demonstration of a practical strategy to raise immune responses against conserved epitopes. This strategy has important implications for vaccine development against HIV and other pathogens that have high genetic diversity, such as influenza.
Selective up-regulation of chemokine receptors CCR4 and CCR8 upon activation of polarized human type 2 Th cells. (1998)

Polarized Th1 and Th2 cells differentially express adhesion molecules and chemokine receptors, endowing these cells with distinct tissue homing capabilities. Here we report that, in contrast to other chemokine receptors, the expression of CCR4 and CCR8 on Th2 cells is transiently increased following TCR and CD28 engagement. IL-4 is not required for this activation-induced up-regulation of CCR4 and CCR8. In accordance with receptor expression, the response of Th2 cells to I-309 (CCR8 ligand) and thymus- and activation-regulated chemokine (CCR4 and CCR8 ligand) is enhanced upon activation. Moreover, activated Th1 cells up-regulate CCR4 expression and functional responsiveness to thymus- and activation-regulated chemokine. Analysis of polarized subsets of CD8+ T cells reveals a similar pattern of chemokine receptor expression and modulation of responsiveness. Taken together, these findings suggest that an up-regulation of CCR4 and CCR8 following Ag encounter may contribute to the proper positioning of activated T cells within sites of antigenic challenge and/or specialized areas of lymphoid tissues.
HCl Selective Etching of Si1-xGex versus Si for Silicon On Nothing and Multi Gate Devices (2008)

We have studied the low temperature (~ 650oC), high HCl partial pressure (180 Torr) selective etch of SiGe versus Si inside a RP-CVD reactor. The surface roughness strongly increases while vertically etching fullsheet Si1-xGex layers. We have also laterally etched (Si / SiGe) multilayers patterned along the &lt;110&gt; directions. The best selectivities and the highest SiGe etch rates have been obtained for the highest Ge content studied, i.e. 40%. &lt;111&gt; facets have been revealed at the end of tunnels. A strong increase (x 18) of the &lt;110&gt; lateral HCl etch rates has been evidenced when increasing the Si0.6Ge0.4 layer thickness from 5 up to 20 nm. Very good SiGe versus Si selectivities have been obtained with slightly higher etch rates than on bulk Si when HCl etching (Si / SiGe) multilayers grown on Si0.8Ge0.2 virtual substrates. Finally, a strong HCl etch in-plane anisotropy has always been evidenced. &lt;100&gt; oriented pattern corners are indeed far more etched than &lt;110&gt; oriented edges.
Domain structure of as-cast and annealed FeSiB amorphous wires (1991)

The domain structures of amorphous FeSiB wires have been studied as a function of applied field. The main features of as-cast wires are: the proliferation of surface closure domains; a distinction between core and sheath domain behavior; and a reproducible switching behavior. Transverse magnetically annealed wires have larger domains, show little sign of a sheath and a greater variety of domain displacement mechanisms.
Glucagon-Like Peptide-1 Infusion Must Be Maintained for 24 h/day to Obtain Acceptable Glycemia in Type 2 Diabetic Patients Who Are Poorly Controlled on Sulphonylurea Treatment (2001)

This study demonstrated that GLP-1 should be given continuously to obtain the most optimal glycemic control. Because of the short plasma half-life of native GLP-1, long-acting derivatives should be developed to make GLP-1 treatment clinically relevant.
A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment (1994)

The divergence of 16S rDNA sequences in marine sediment was investigated. Twenty unique partial sequences were found among 33 cloned following PCR. Thirteen shared 82 to 91% similarity with sequences of delta subclass sulfate-reducing bacteria. Three contained the target sequence for a sulfate-reducing bacterium-specific oligonucleotide probe designed from pure-culture studies.
pH sensor based on upconverting luminescent lanthanide nanorods (2009)

The pH sensor exploits the phenomenon of upconversion luminescence and is based on a hydrogel matrix containing (a) nanorods of the NaYF(4):Er,Yb type that can be excited with 980-nm laser light to give a green and red (dual) emission, and (b) a longwave absorbing pH probe that causes a pH-dependent inner filter effect.
Factor Analytic Models: Viewing the Structure of an Assessment Instrument From Three Perspectives (2005)

The overarching purpose of this article is to present a nonmathematical introduction to the application of confirmatory factor analysis (CFA) within the framework of structural equation modeling as it applies to psychological assessment instruments. In the interest of clarity and ease of understanding, I model exploratory factor analysis (EFA) structure in addition to first- and second-order CFA structures. All factor analytic structures are based on the same measuring instrument, the Beck Depression Inventory-II (BDI-II; Beck, Steer, & Brown, 1996). Following a "walk" through the general process of CFA modeling, I identify several common misconceptions and improper application practices with respect to both EFA and CFA and tender caveats with a view to preventing further proliferation of these pervasive practices.
Modulation of Anxiety and Neuropeptide Y-Y1 Receptors by Antisense Oligodeoxynucleotides (1993)

The function of neuropeptide Y, one of the most abundant peptide transmitters of the mammalian brain, remains unclear because of a lack of specific receptor antagonists. An antisense oligodeoxynucleotide corresponding to the NH2-terminus of the rat Y1 receptor was constructed and added to cultures of rat cortical neurons. This treatment resulted in a reduced density of Y1 (but not Y2) receptors and diminished the decrease in adenosine 3',5'-monophosphate (cAMP) usually seen after Y1 receptor activation. Repeated injection of the same oligodeoxynucleotide into the lateral cerebral ventricle of rats was followed by a similar reduction of cortical Y1 (but not Y2) receptors. Such antisense-treated animals displayed behavioral signs of anxiety. Thus, specific inhibition of neurotransmitter receptor expression can be accomplished in the living brain and demonstrates that altered central neuropeptide Y transmission produces an anxiety-like state.
Nonlinear properties of hollow-core photonic band-gap fibers (2005)

Our measurements and modeling of two hollow-core photonic band-gap fibers show that glass contribution to the effective non-linearity strongly depends on the fiber structure. We investigate wavelength dependence of total fiber nonlinearity.
Concurrent Analysis of Nose and Groin Swab Specimens by the IDI-MRSA PCR Assay Is Comparable to Analysis by Individual-Specimen PCR and Routine Culture Assays for Detection of Colonization by Methicillin-Resistant Staphylococcus aureus (2006)

The IDI-MRSA assay (Infectio Diagnostic, Inc., Sainte-Foy, Quebec, Canada) with the Smart Cycler II rapid DNA amplification system (Cepheid, Sunnyvale, CA) appears to be sensitive and specific for the rapid detection of nasal colonization by methicillin-resistant Staphylococcus aureus (MRSA). We assessed the sensitivity and specificity of this assay under conditions in which both the nose and cutaneous groin specimens were analyzed together and compared the accuracy of this PCR approach to that when these specimens were tested separately and by culture assays in an inpatient population with known high rates (12 to 15%) of MRSA colonization. Of 211 patients screened, 192 had results assessable by all three methods (agar-broth culture, separate nose and groin IDI-MRSA assay, and combined nose-groin IDI-MRSA assay), with MRSA carriage noted in 31/192 (16.1%), 41/192 (21.4%), and 36/192 (18.8%) patients by each method, respectively. Compared to agar culture results, the sensitivity and specificity of the combined nose-groin IDI-MRSA assay were 88.0% and 91.6%, respectively, whereas when each specimen was processed separately, the sensitivities were 90.0% (nose) and 83.3% (groin) and the specificities were 91.7% (nose) and 90.2% (groin). IDI-MRSA assay of a combined nose-groin specimen appears to have an accuracy similar to that of the current recommended PCR protocol, providing results in a clinically useful time frame, and may represent a more cost-effective approach to using this assay for screening for MRSA colonization.
Impedance spectroscopy of biological cells (2002)

Summary form only given as follows: A 6-electrode impedance chamber is used to perform wide bandwidth (1 Hz-3 MHz), high sensitivity, complex impedance measurements on living cells. Impedance measurements are performed under normal physiologic conditions to evaluate the electrical properties of living cells. The increase in sensitivity for the measurements, compared to cell suspension techniques, is accomplished by embedding the cells into the pores of a filter. This creates a "pseudo-epithelium" and markedly reduces the extracellular current pathways around the cells and consequently increases the sensitivity of the measurement. The advantages of this technique are discussed, as are the general insights and improvements in impedance measurements that are possible. In this technique, the cellular geometry and the portion of cell membrane under measurement are more precisely controlled than in suspension techniques. Essentially, the technique produces a multi-parallel, whole-cell, patch-clamp like structure. The resistance of the leak pathway is about 6-7/spl times/10/sup 7/ /spl Omega/ for each cell, compared to a gigaohm for the patch clamp resistance. The effects of: bandwidth mismatch between high-input impedance amplifiers, reference point drift due to solution resistivity changes, and the use of porous electrodes on the measured cellular impedance are discussed. The ability to alter extracellular solution temperature and composition, during an impedance experiment, provides a methodology to elucidate the underlying processes and structures responsible for the measured impedance. Lastly, the ability to electroporate the portion of the cell membrane under measurement, contributes another unique way to study the impedance of living cells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cyclic GMP-Dependent Protein Kinase Regulates Vascular Smooth Muscle Cell Phenotype (1997)

Nitric oxide (NO) and cyclic guanosine 3',5'-monophosphate (cGMP) have been reported to prevent vascular smooth muscle cell (VSMC) proliferation and have beneficial effects to reduce intimal thickening in response to arterial injury. The purpose of this study was to determine whether the downstream effector molecule of NO-cGMP signaling, cyclic GMP-dependent protein kinase (PKG), regulates phenotypic modulation and proliferation in cultured rat aortic VSMC. PKG-expressing VSMC lines were created by transfection of PKG-deficient cell lines and characterized. All forms of PKG, i.e. PKG-I alpha and PKG-I beta, as well as the constitutively active catalytic domain of PKG-I, transformed dedifferentiated 'synthetic' VSMC to a more contractile-like morphology. PKG expression resulted in an increased production of the contractile phenotype marker proteins, smooth muscle myosin heavy chain-2, calponin and alpha-actin and restored the capacity of cAMP and cGMP analogues to inhibit platelet-derived growth factor (PDGF)-induced cell migration. On the other hand, PKG expression had no significant effects on PDGF-induced cell proliferation. These results suggest that PKG expression contributes to the regulation of a contractile-like phenotypic expression in cultured VSMC, and the suppression of PKG expression during cultured growth in vitro may permit the modulation of cells to a more synthetic, dedifferentiated phenotype.
Activation of Natural Killer T Cells Promotes M2 Macrophage Polarization in Adipose Tissue and Improves Systemic Glucose Tolerance via Interleukin-4 (IL-4)/STAT6 Protein Signaling Axis in Obesity (2012)

Natural killer T (NKT) cells are important therapeutic targets in various disease models and are under clinical trials for cancer patients. However, their function in obesity and type 2 diabetes remains unclear. Our data show that adipose tissues of both mice and humans contain a population of type 1 NKT cells, whose abundance decreases with increased adiposity and insulin resistance. Although loss-of-function of NKT cells had no effect on glucose tolerance in animals with prolonged high fat diet feeding, activation of NKT cells by lipid agonist α-galactosylceramide enhances alternative macrophage polarization in adipose tissue and improves glucose homeostasis in animals at different stages of obesity. Furthermore, the effect of NKT cells is largely mediated by the IL-4/STAT6 signaling axis in obese adipose tissue. Thus, our data identify a novel therapeutic target for the treatment of obesity-associated inflammation and type 2 diabetes.
Production, characterization and reactivity of monoclonal antibodies to porcine reproductive and respiratory syndrome virus (1995)

This report describes the preparation of six monoclonal antibodies (MAbs) raised against a British isolate of porcine reproductive and respiratory syndrome virus (PRRSV), their characterization in terms of protein specificity and their reactivity with different PRRS viruses from Europe and the USA. Radioimmunoprecipitation and Western blotting studies of MAb reactivity with proteins from cell lysates of infected cells and purified virus revealed that four of the six MAbs (WBE1 and WBE4-6) precipitated a 15 kDa viral protein. Further studies using in vitro translated products of the Lelystad virus genome showed that this protein was the product of ORF7, the putative nucleocapsid protein. The specificity of another MAb, WBE2, was found to be for a 45 kDa protein, determined to be the product of ORF3 and demonstrated to be present in purified virion preparations. The protein specificity of the sixth MAb, WBE3 could not be determined. Thirty-three PRRSV isolates from Europe and the USA were grown in alveolar macrophages and examined by immunoperoxidase staining, using the panel of six MAbs. All European isolates were recognized by the four MAbs specific for the putative nucleocapsid, but the viruses showed different patterns of reactivity with WBE2 and WBE3. Furthermore, these two MAbs stained only a small proportion of the cells infected with certain isolates, suggesting that a single isolate may be antigenically heterogeneous. No MAbs bound to US isolates, indicating a consistent antigenic difference between the putative nucleocapsid of US and European isolates. Detergent extraction of cell lysate antigen abrogated the binding of WBE1-3, suggesting that the epitopes are conformation dependent.
Enthalpic Stabilization of Brush-Coated Particles in a Polymer Melt (2002)

The interaction between spherical particles covered with end-grafted polymers (brushes) immersed in a polymer melt is studied theoretically. It has been known for some time that two densely grafted brushes may attract each other in the presence of a chemically identical polymer melt. In this study we show that this attraction can be eliminated by choosing the melt material to be such that the Flory interaction parameter of the melt chains with the grafted ones is negative (χ < 0). This effect is accompanied by a change in the structure of the brush from a dry brush, where the melt chains do not penetrate deeply into the brush, to a wet brush, where the melt chains penetrate the brush and force the grafted chains to extend into the melt. Scaling arguments are used to describe how the structure of a single brush depends on the Flory interaction parameter, the grafting density, and the indices of polymerization of the grafted and free chains. The density profiles and the interactions between the particles are calculated by solving numerically the self-consistent field equations of the system within the Derjaguin approximation. The effect of van der Waals interactions between brushes is studied by taking into account the particle−brush contrast as well as that of the brush−melt interfaces.