gebhart/patrepeval huggingface dataset:
Suppressing qubit dephasing using real-time Hamiltonian estimation (2014)

Unwanted interaction between a quantum system and its fluctuating environment leads to decoherence and is the primary obstacle to establishing a scalable quantum information processing architecture. Strategies such as environmental and materials engineering, quantum error correction and dynamical decoupling can mitigate decoherence, but generally increase experimental complexity. Here we improve coherence in a qubit using real-time Hamiltonian parameter estimation. Using a rapidly converging Bayesian approach, we precisely measure the splitting in a singlet-triplet spin qubit faster than the surrounding nuclear bath fluctuates. We continuously adjust qubit control parameters based on this information, thereby improving the inhomogenously broadened coherence time (T2*) from tens of nanoseconds to >2 μs. Because the technique demonstrated here is compatible with arbitrary qubit operations, it is a natural complement to quantum error correction and can be used to improve the performance of a wide variety of qubits in both meteorological and quantum information processing applications.
X chromosome inactivation of the human TIMP gene (1990)

X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids under positive selection for the active or inactive human X chromosome has been created. Northern blot analysis of RNA from these hybrids showed that the human MIC2 gene, which is known to escape X inactivation, was transcribed in hybrids with either the active or inactive X chromosome. In contrast, the human TIMP gene was only transcribed in hybrids with an active human X chromosome. Further analysis using the polymerase chain reaction showed that there was at least one-hundred fold less transcription of the TIMP gene from the inactive X than from the active X chromosome. These findings demonstrate that the human TIMP gene is subject to X inactivation at the level of transcription, and illustrate the usefulness of the polymerase chain reaction to study the extent of X-linked gene repression by the process of X inactivation.
The ZiN/POZ domain of ZF5 is required for both transcriptional activation and repression (1997)

ZF5 is a ubiquitously expressed protein originally identified by its ability to bind and repress the murine c-myc promoter. It contains five C-terminal zinc fingers and a conserved N-terminal ZiN/POZ domain. This motif, found in a growing number of zinc finger proteins, can inhibit DNA binding and mediate dimerization [Bardwell, V.J. and Treisman,R. (1994) Genes Dev., 8,1664-1677]. In the current study, a cyclic amplification and selection of targets (CAST) protocol detected preferred ZF5 binding sites which are highly GC-rich. Binding to these sites by ZF5 depended upon the zinc fingers and was enhanced when the ZiN/POZ domain was removed. Using transient cotransfection assays, ZF5 was shown to activate the HIV-1 LTR and repress the beta-actin promoter. The ZiN/POZ domain was shown to mediate ZF5-dependent transcriptional activation and repression. From these data, we conclude that ZF5 can both activate and repress in the context of different natural promoters and that its ZiN/POZ domain can affect two functions; DNA binding and transcriptional modulation.
The Influence of Linkage and Inbreeding on Patterns of Nucleotide Sequence Diversity at Duplicate Alcohol Dehydrogenase Loci in Wild Barley (Hordeum vulgare ssp. spontaneum) (2002)

Patterns of nucleotide sequence diversity are analyzed for three duplicate alcohol dehydrogenase loci (adh1-adh3) within a species-wide sample of 25 accessions of wild barley (Hordeum vulgare ssp. spontaneum). The adh1 and adh2 loci are tightly linked (recombination fraction <0.01) while the adh3 locus is inherited independently. Wild barley is predominantly self-fertilizing (approximately 98%), and as a consequence, effective recombination is restricted by the extreme reduction in heterozygosity. Large reductions in effective recombination, in turn, widen the conditions for linkage to influence nucleotide sequence diversity through the action of selective sweeps or background selection. These considerations would appear to predict (1) homogeneity in patterns of nucleotide sequence diversity, especially between closely linked loci, and (2) extensive linkage disequilibrium relative to random-mating species. In contrast to these expectations, the wild barley data reveal heterogeneity in patterns of nucleotide sequence diversity and levels of linkage disequilibrium that are indistinguishable from those observed at adh1 in maize, an outbreeding grass species.
Head and neck cancer (2010)

Tumors of the head and neck comprise an important neoplasia group, the incidence of which is increasing in many parts of the world. Recent advances in diagnostic and therapeutic techniques for these lesions have yielded novel molecular targets, uncovered signal pathway dominance, and advanced early cancer detection. Proteomics is a powerful tool for investigating the distribution of proteins and small molecules within biological systems through the analysis of different types of samples. The proteomic profiles of different types of cancer have been studied, and this has provided remarkable advances in cancer understanding. This review covers recent advances for head and neck cancer; it encompasses the risk factors, pathogenesis, proteomic tools that can help in understanding cancer, and new proteomic findings in this type of cancer.
Patriarchy (2017)

Patriarchy is a concept originally deployed by Western, radical, second‐wave feminists to describe social structures governed by hierarchical power relations that privilege masculinity over femininity, and permit the domination, oppression, and exploitation of women by men. Such scholarship was critiqued, particularly by women of color, for producing ahistorical and acultural generalizations that overlook nuances and variations in power relations; however, anti‐essentialist poststructuralist and postmodern approaches to feminism have complicated understandings of gender and foregrounded the agency of women to bargain with patriarchy. Feminist geographical scholarship on patriarchy reveals how it is entangled in bodily and spatial ways with the historical, transterritorial, and transnational processes and particularities of capitalism and colonialism.
A gate-side air-gap structure (GAS) to reduce the parasitic capacitance in MOSFETs (2002)

A new parasitic capacitance reduction technologies, utilizing a Gate-side Air-gap Structure (GAS), has been developed for MOSFETs. The GAS in which a 5-nm-wide air-gap was formed next to the gate reduced the fringe capacitance by half. Hence, the gate delay time was reduced by 4.8 psec at FO=1 and by 16 psec at FO=3 in a 0.25 /spl mu/m CMOS, and power consumption was lowered compared to a conventional structure. We also propose pocket implantation through the GAS to suppress short channel effects with only a slight increase in the junction capacitance.
Primary sequence of ionic self‐assembling peptide gels affects endothelial cell adhesion and capillary morphogenesis (2008)

Appropriate choice of biomaterial supports is critical for the study of capillary morphogenesis in vitro as well as to support vascularization of engineered tissues in vivo. Self-assembling peptides are a class of synthetic, ionic, oligopeptides that spontaneously assemble into gels with an ECM-like microarchitecture when exposed to salt. In this paper, the ability of four different self-assembling peptide gels to promote endothelial cell adhesion and capillary morphogenesis is explored. Human umbilical vein endothelial cells (HUVECs) were cultured within ionic self-assembling peptide family members, RAD16-I ((RADA)(4)), RAD16-II ((RARADADA)(2)), KFE-8 ((FKFE)(2)), or KLD-12 ((KLDL)(3)). HUVECs suspended in RAD16-I or RAD16-II gels elongated and formed interconnected capillary-like networks resembling in vivo capillaries, while they remained round and formed clusters within KFE-8 or KLD-12 gels. As HUVECs attach to RAD16-I and RAD16-II significantly better than the other peptides, these differences appear to be explained by differences in cell adhesion. Although adhesion likely occurs via bound adhesion proteins, there appears to be no difference in protein binding to the peptides investigated. Results indicate that, although these oligopeptides have similar mechanisms of self- assembly, their primary sequence can greatly affect cell adhesion. Additionally, a subset of these biomimetic ECM-like materials support capillary morphogenesis and thus may be useful for supporting vascularization.
Targeting Three Distinct HER2 Domains with a Recombinant Antibody Mixture Overcomes Trastuzumab Resistance (2015)

HER2 plays an important role in the development and maintenance of the malignant phenotype of several human cancers. As such, it is a frequently pursued therapeutic target and two antibodies targeting HER2 have been clinically approved, trastuzumab and pertuzumab. It has been suggested that optimal inhibition of HER2 is achieved when utilizing two or more antibodies targeting nonoverlapping epitopes. Superior clinical activity of the trastuzumab plus pertuzumab combination in metastatic breast cancer supports this hypothesis. Because trastuzumab and pertuzumab were not codeveloped, there may be potential for further optimizing HER2 targeting. The study herein evaluated functional activity of anti-HER2 antibody combinations identifying optimal epitope combinations that provide efficacious HER2 inhibition. High-affinity antibodies to all four extracellular domains on HER2 were identified and tested for ability to inhibit growth of different HER2-dependent tumor cell lines. An antibody mixture targeting three HER2 subdomains proved to be superior to trastuzumab, pertuzumab, or a combination in vitro and to trastuzumab in two in vivo models. Specifically, the tripartite antibody mixture induced efficient HER2 internalization and degradation demonstrating increased sensitivity in cell lines with HER2 amplification and high EGFR levels. When compared with individual and clinically approved mAbs, the synergistic tripartite antibody targeting HER2 subdomains I, II, and IV demonstrates superior anticancer activity.
On limiting characterizations of memoryless multiuser capacity regions (1993)

The restriction to Gaussian inputs in the limiting expression for the capacity regions of memoryless Gaussian interference and multiple-access channels is shown to fall short of achieving capacity even if the inputs are allowed to be dependent and nonstationary. In addition, the equality between the limiting and the single-letter characterizations of memoryless multiple-access channel capacity is established directly, without recourse to independent coding theorems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene Transfer of Inducible Nitric Oxide Synthase Complementary DNA Regresses the Fibrotic Plaque in an Animal Model of Peyronie’s Disease1 (2004)

The goal of the present study was to investigate the antifibrotic role of inducible nitric oxide synthase (iNOS) in Peyronie's disease (PD) by determining whether a plasmid expressing iNOS (piNOS) injected into a PD-like plaque can induce regression of the plaque. A PD-like plaque was induced with fibrin in the penile tunica albuginea of mice and then injected with a luciferase-expressing plasmid (pLuc), either alone or with piNOS, following luciferase expression in vivo by bioluminescence imaging. Rats were treated with either piNOS, an empty control plasmid (pC), or saline. Other groups were treated with pC or piNOS, in the absence of fibrin. Tissue sections were stained for collagen, transforming growth factor (TGF) beta1, and plasminogen-activator inhibitor (PAI-1) as profibrotic factors; copper-zinc superoxide dismutase (CuZn SOD) as scavenger of reactive oxygen species (ROS); and nitrotyrosine to detect nitric oxide reaction with ROS. Quantitative image analysis was applied. Both iNOS and xanthine oxido-reductase (XOR; oxidative stress) were estimated by Western blot analysis. Luciferase reporter expression was restricted to the penis, peaked at 3 days after injection, but continued for at least 3 wk. In rats receiving piNOS, iNOS expression also peaked at 3 days, but expression decreased at the end of treatment, when a considerable reduction of plaque size occurred. Protein nitrotyrosine, XOR, and CuZn SOD increased, and TGFbeta1 and PAI-1 decreased. The piNOS gene transfer regressed the PD plaque and expression of profibrotic factors, supporting the view that endogenous iNOS induction in PD is defense mechanism by the tissue against fibrosis.
Coding/Decoding and Reversibility of Droplet Trains in Microfluidic Networks (2007)

Droplets of one liquid suspended in a second, immiscible liquid move through a microfluidic device in which a channel splits into two branches that reconnect downstream. The droplets choose a path based on the number of droplets that occupy each branch. The interaction among droplets in the channels results in complex sequences of path selection. The linearity of the flow through the microchannels, however, ensures that the behavior of the system can be reversed. This reversibility makes it possible to encrypt and decrypt signals coded in the intervals between droplets. The encoding/decoding device is a functional microfluidic system that requires droplets to navigate a network in a precise manner without the use of valves, switches, or other means of external control.
Asymmetric induction in the additions of anions of allylic sulfoxides to benzaldehyde (1980)

Addition reactions of anions of aryl allyl sulfoxides to benzaldehyde proceed readily in moderate yields and afford mixtures of products resulting from a- and ?-attack on the allyl anion. The ?-products all possess the (E)-configuration around the double bond, and asymmetric induction occurs in the addition to the extent that the major/minor diastereomer ratio exceeds 2 : 1, generally. Electronic factors are believed to be responsible for this 'remote' asymmetric induction. Mixtures of all four possible diastereomers are observed in the products from a-attack and evidence is presented which suggests that the ratios of these products are as a result of epimerization of two of the chiral centres by [2,3] sigmatropic rearrangement.
Open Wire Lines (1956)

The properties of two-wire lines and single wire lines (surface wave transmission lines) are discussed on a comparative basis. The two-wire line is actually a system of two coupled single wire lines and thus requires a high degree of symmetry to maintain the desired wave mode. While the single wire line is more affected by bends it has the advantages that it is simpler in construction and is less susceptible to weather conditions. The main domain of the two-wire lines lies in the frequency range below 100 mc and that of the single wire line in the range above 100 mc.
Anton, a special-purpose machine for molecular dynamics simulation (2008)

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond---several orders of magnitude beyond the duration of the longest current MD simulations. We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized highspeed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.
CD133 expression is not restricted to stem cells, and both CD133+ and CD133– metastatic colon cancer cells initiate tumors (2008)

Colon cancer stem cells are believed to originate from a rare population of putative CD133+ intestinal stem cells. Recent publications suggest that a small subset of colon cancer cells expresses CD133, and that only these CD133+ cancer cells are capable of tumor initiation. However, the precise contribution of CD133+ tumor-initiating cells in mediating colon cancer metastasis remains unknown. Therefore, to temporally and spatially track the expression of CD133 in adult mice and during tumorigenesis, we generated a knockin lacZ reporter mouse (CD133lacZ/+), in which the expression of lacZ is driven by the endogenous CD133 promoters. Using this model and immunostaining, we discovered that CD133 expression in colon is not restricted to stem cells; on the contrary, CD133 is ubiquitously expressed on differentiated colonic epithelium in both adult mice and humans. Using Il10-/-CD133lacZ mice, in which chronic inflammation in colon leads to adenocarcinomas, we demonstrated that CD133 is expressed on a full gamut of colonic tumor cells, which express epithelial cell adhesion molecule (EpCAM). Similarly, CD133 is widely expressed by human primary colon cancer epithelial cells, whereas the CD133- population is composed mostly of stromal and inflammatory cells. Conversely, CD133 expression does not identify the entire population of epithelial and tumor-initiating cells in human metastatic colon cancer. Indeed, both CD133+ and CD133- metastatic tumor subpopulations formed colonospheres in in vitro cultures and were capable of long-term tumorigenesis in a NOD/SCID serial xenotransplantation model. Moreover, metastatic CD133- cells form more aggressive tumors and express typical phenotypic markers of cancer-initiating cells, including CD44 (CD44+CD24-), whereas the CD133+ fraction is composed of CD44lowCD24+ cells. Collectively, our data suggest that CD133 expression is not restricted to intestinal stem or cancer-initiating cells, and during the metastatic transition, CD133+ tumor cells might give rise to the more aggressive CD133(- )subset, which is also capable of tumor initiation in NOD/SCID mice.
Biosynthesis and Secretion of Adrenomedullin and Proadrenomedullin N-Terminal 20 Peptide in a Rat Model of Endotoxin Shock. (2001)

To study the biosyntheses and pathophysiological roles of adrenomedullin (AM) and proadrenomedullin N-terminal 20 peptide (PAMP) in septic shock, we compared the time course of plasma concentrations of these peptides and blood pressure in rats injected with either 0.9% saline (control group) or lipopolysaccharide (LPS group). The plasma AM concentration in the LPS group did not increase 30 and 60 min after LPS injection, at which time points the blood pressure remained low. Thereafter, AM rapidly increased, and it amounted to 35 times the basal value 4 h after injection, when the blood pressure returned to the basal level. The increment of plasma PAMP in the LPS group was lower than that of AM. We also examined the tissue concentration of AM and PAMP--as well as the tissue expression of proadrenomedullin (proAM) mRNA--in the LPS and control groups. LPS significantly increased the tissue concentrations of AM and PAMP in the lung, but decreased them in the adrenal gland and cardiac atrium. The LPS injection augmented proAM gene transcription in the lung, adrenal gland and aorta. In an immunohistochemical examination, AM staining was intense in alveolar endothelial cells of the lung in the LPS group. Thus, this septic shock model had high plasma levels of PAMP as well as AM, while the biosynthesis and secretion of the two peptides may have been differentially regulated in various tissues of rats injected with LPS. The present results suggest that these two bioactive peptides may play different roles in the pathophysiology of septic shock.
Demonstration of CPRI over Self-seeded WDM-PON in Commercial LTE Environment (2015)

CPRI between BBU and RRU equipment is carried by self-seeded WDM-PON prototype system within commercial LTE end-to-end environment. Delay and jitter meets CPRI requirements while services demonstrated show the same performance as bare fiber.
THREE-DIMENSIONAL MECHANICS, KINEMATICS, AND MORPHOLOGY OF THE KNEE VIEWED IN VIRTUAL REALITY (2005)

Eckhoff, Donald G. MD, MS; Bach, Joel M. PHD; Spitzer, Victor M. PHD; Reinig, Karl D. PHD; Bagur, Michelle M. BS; Baldini, Todd H. MS; Flannery, Nicolas M.P. BS Author Information
Tissue micro array analysis of ganglioside N-glycolyl GM3 expression and signal transducer and activator of transcription (STAT)-3 activation in relation to dendritic cell infiltration and microvessel density in non-small cell lung cancer (2009)

GM3 and pSTAT3 are widely expressed in NSCLC. Based on CD83 expression, GM3, but not pSTAT3, appeared to be involved in tumor-induced DC suppression. pSTAT3 expression was not associated with MVD, while GM3 might play an anti-angiogenic role.
Identification of a lipolysis-stimulated receptor that is distinct from the LDL receptor and the LDL receptor-related protein (1994)

This paper provides further characterization of a receptor that, in cells lacking the LDL receptor (FH fibroblasts), mediates lipoprotein binding, uptake, and degradation when incubated with oleate at concentrations not exceeding albumin binding capacity. This oleate-activated receptor is genetically distinct from the LDL receptor and is hereafter referred to as the lipolysis-stimulated receptor (LSR). Its apparent affinity was higher for triglyceride-rich lipoproteins (chylomicrons, VLDL) and for lipid emulsions supplemented with recombinant apoE, than for LDL which contains solely apoB. In contrast, VLDL isolated from a Type III hyperlipidemic patient (apoE2/2 phenotype) failed to bind to the LSR. Five lines of evidence indicated that the LSR is distinct from the LDL receptor-related protein (LRP): (1) the LRP ligand, alpha 2-macroglobulin-methylamine (alpha 2-MG*), did not bind to the oleate-induced LDL binding site; (2) oleate had no effect on the binding of alpha 2-MG* to LRP; (3) the LRP-associated protein, RAP, which inhibits LRP, had no effect on the LSR; (4) binding of lipoproteins to LSR was independent of Ca2+; and (5) LSR activity resolved as two proteins smaller than LRP (apparent molecular masses as determined by ligand blots: 115 and 85 kDa). That LSR provides a new candidate receptor contributing to the clearance of chylomicron remnants (CMR) is supported by the observation that LSR was inhibited by lactoferrin, a milk protein that delays CMR clearance when injected in vivo. Furthermore, in primary cultures of rat hepatocytes, oleate stimulated binding, uptake, and degradation of LDL with kinetic characteristics similar to that of LSR expressed in FH fibroblasts.(ABSTRACT TRUNCATED AT 250 WORDS)