gebhart/patrepeval huggingface dataset:
Femtosecond-comb distance meter: ultrahigh-resolution distance measurement using a mode-locked laser (2004)

An ultrahigh accuracy distance meter with a simple setup and high reliability for a practical measurement is developed using a broad and stable femtosecond frequency comb. This device is fabricated to overcome the problem of cyclic error that originates from the electric and optical crosstalks. Since the femtosecond-comb distance meter (FCDM) does not require an external modulator, the setup is simple and thus the cyclic error is significantly suppressed. In this study, a world-record 2-/spl mu/m uncertainty in the FCDM is achieved.
Is the Grass Always Greener? Comparing the Environmental Impact of Conventional, Natural and Grass-Fed Beef Production Systems (2012)

This study compared the environmental impact of conventional, natural and grass-fed beef production systems. A deterministic model based on the metabolism and nutrient requirements of the beef population was used to quantify resource inputs and waste outputs per 1.0 × 10⁸ kg of hot carcass weight beef in conventional (CON), natural (NAT) and grass-fed (GFD) production systems. Production systems were modeled using characteristic management practices, population dynamics and production data from U.S. beef production systems. Increased productivity (slaughter weight and growth rate) in the CON system reduced the cattle population size required to produce 1.0 × 10⁸ kg of beef compared to the NAT or GFD system. The CON system required 56.3% of the animals, 24.8% of the water, 55.3% of the land and 71.4% of the fossil fuel energy required to produce 1.0 × 10⁸ kg of beef compared to the GFD system. The carbon footprint per 1.0 × 10⁸ kg of beef was lowest in the CON system (15,989 × 10³ t), intermediate in the NAT system (18,772 × 10³ t) and highest in the GFD system (26,785 × 10³ t). The challenge to the U.S beef industry is to communicate differences in system environmental impacts to facilitate informed dietary choice.
Oxidative stability of purified canola oil triacylglycerols with altered fatty acid compositions as affected by triacylglycerol composition and structure (1994)

Abstract Canola oil triacylglycerols from genetically modified canola lines (InterMountain Canola Co., Cinnaminson, NJ) have been evaluated for their photooxidative and autoxidative stabilities, as influenced by their fatty acid compositions and their triacylglycerol compositions and structures. Purified canola oil triacylglycerols were oxidized in duplicate in fluorescent light at 25°C and in the dark at 60°C under oxygen, and their oxidative deterioration with time was monitored by determining colorimetric peroxide values. Also monitored with time, oxidation products were determined by reversed‐phase high‐performance liquid chromatography with ultraviolet absorbance detection. Total volatiles, generated by thermal decomposition of the oxidized triacylglycerols, were quantitated by static‐head‐space gas chromatography. These experimental parameters were statistically correlated with predicted oxidizability, fatty acid composition, position of fatty acids on glycerol carbons and triacylglycerol composition. Oxidative deterioration of canola triacylglycerols correlated negatively with oleic acid composition, with oleic acid content at carbon 2 and with trioleoylglycerol content of the oil. Deterioration was positively correlated with the amount of linolenic acid on nonspecific locations on glycerol carbons 1,2 and 3, the amount of linoleic acid on glycerol carbon 2 and with sn ‐oleoyllinoleoyllinolenoyl glycerol content. Differences in character or quantity of volatile product and triacylglycerol hydroperoxides were low, whether generated during autoxidation or photooxidation of the canola triacylglycerols.
Ultra wideband DS-CDMA via innovations in chip shaping (2002)

One important requirement for next generation wireless communication systems is the ability to support a wide range of high rate data services. Despite advances in efficient modulation and multiple access technologies, very high data rate transfer will still require ultra-wide frequency bands. Traditional DS-CDMA systems operate over one single continuous bandwidth, and with the limited spectrum available from the FCC auctioned off in small blocks, it will not be possible for DS-CDMA to operate over a contiguous ultra-wide frequency band. This paper demonstrates how a novel chip shaping scheme, designed specifically for DS-CDMA systems, enables DS-CDMA to operate over non-adjacent frequency bands in a way that is identical to its operation if all these bands are made contiguous. The chip shape corresponds to an interferometry pattern created by the superposition of N carriers (adjacent or non-adjacent in the frequency domain). Besides the ability to operate over non-adjacent bands, this novel chip shaping enables DS-CDMA to achieve very high performance by exploiting frequency diversity (instead of path diversity) over the combined bands. With the exception of chip shape and receiver design for operation over non-contiguous bands, this new system retains all the features of a traditional DS-CDMA system.
Decade-long bacterial community dynamics in cystic fibrosis airways (2012)

The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8-9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3-V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from >633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function, was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short- and long-term resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway.
Genetic Modification of Smooth Muscle Cells to Control Phenotype and Function in Vascular Tissue Engineering (2004)

Rat smooth muscle cells (SMCs) stably transfected with the gene for the phenotype regulating protein cyclic guanosine monophosphate-dependent protein kinase (PKG) were used as a cell source in the preparation of three-dimensional (3D) collagen type I vascular constructs. PKG-transfected cells expressed severalfold higher levels of the contractile protein smooth muscle alpha-actin (SMA), relative to untransfected SMCs, both in monolayer culture and in 3D gels. The proliferation rate of PKG-transfected cells was lower than that of untransfected cells in both culture geometries. Three-dimensional collagen constructs made with PKG-transfected cells compacted to a similar degree as those made with untransfected cells, and this compaction could be augmented by biochemical stimulation with platelet-derived growth factor BB (PDGF) or transforming growth factor beta(1) (TGF). Application of cyclic mechanical strain to tubular collagen gels seeded with PKG-transfected cells resulted in a higher degree of gel compaction and circumferential matrix alignment, relative to statically grown controls, but cell proliferation and SMA expression were not affected. These results show that genetic modification of SMCs can be used as a tool to control cell function in vascular tissue engineering, and that the function of such cells can be further modulated by application of biochemical and mechanical stimulation.
Preclinical Characterization of AMG 330, a CD3/CD33-Bispecific T-Cell–Engaging Antibody with Potential for Treatment of Acute Myelogenous Leukemia (2014)

There is high demand for novel therapeutic options for patients with acute myelogenous leukemia (AML). One possible approach is the bispecific T-cell-engaging (BiTE, a registered trademark of Amgen) antibody AMG 330 with dual specificity for CD3 and the sialic acid-binding lectin CD33 (SIGLEC-3), which is frequently expressed on the surface of AML blasts and leukemic stem cells. AMG 330 binds with low nanomolar affinity to CD33 and CD3ε of both human and cynomolgus monkey origin. Eleven human AML cell lines expressing between 14,400 and 56,700 CD33 molecules per cell were all potently lysed with EC(50) values ranging between 0.4 pmol/L and 3 pmol/L (18-149 pg/mL) by previously resting, AMG 330-redirected T cells. Complete lysis was achieved after 40 hours of incubation. In the presence of AML cells, AMG 330 specifically induced expression of CD69 and CD25 as well as release of IFN-γ, TNF, interleukin (IL)-2, IL-10, and IL-6. Ex vivo, AMG 330 mediated autologous depletion of CD33-positive cells from cynomolgous monkey bone marrow aspirates. Soluble CD33 at concentrations found in bone marrow of patients with AML did not significantly affect activities of AMG 330. Neoexpression of CD33 on newly activated T cells was negligible as it was limited to 6% of T cells in only three out of ten human donors tested. Daily intravenous administration with as low as 0.002 mg/kg AMG 330 significantly prolonged survival of immunodeficient mice adoptively transferred with human MOLM-13 AML cells and human T cells. AMG 330 warrants further development as a potential therapy for AML.
Hydrophilic Quaternary Ammonium Type Ionic Liquids. Systematic Study of the Relationship among Molecular Structures, Osmotic Pressures, and Water-Solubility (2011)

This Letter examines the relationship between the structures of ionic liquids and their water-solubility or osmotic pressure with a number of synthesized quaternary ammonium type ionic liquids and organic salts containing a hydroxyl group as hydrophilic substituted groups on ammonium group cations, and bromide or methylsulfonate as anions. The study found a linear relation between the amount and osmotic pressure of the water-soluble ionic liquids synthesized here, strongly indicating that these water-soluble ionic liquids are perfectly ionized in water like inorganic salts with small diameter ions.
Polymeric Biomaterials with Degradation Sites for Proteases Involved in Cell Migration (1998)

A new class of biodegradable polymeric biomaterials is described which exhibits degradation by specific enzymes that are localized near cell surfaces during cell migration. These materials are telechelic BAB block copolymers of the water-soluble biocompatible polymer poly(ethylene glycol) (the A block, abbreviated PEG hereafter) and short oligopeptides that are cleavage sequences for targeted enzymes (the B block). These copolymers are further capped at each end with reactive acrylate groups to allow polymerization to form cross-linked hydrogel networks. Two materials were synthesized, one specifically degraded by collagenase and the other by plasmin. The incorporation of peptides that induce cell adhesion to similar materials has been previously reported. The combination of these two types of bioactive signals (one for cell-mediated degradation, one for cell adhesion) into one material should achieve a biomimetic polymeric hydrogel with properties of natural extracellular matrix (also a polymeric hydrogel, although of biological origin), while still affording the advantages of a synthetic polymer. These materials are expected to have numerous applications in wound healing and tissue engineering.
Structural Basis of Digoxin That Antagonizes RORγt Receptor Activity and Suppresses Th17 Cell Differentiation and Interleukin (IL)-17 Production (2011)

The retinoic acid-related orphan nuclear receptor γt (RORγt)/RORγ2 is well known as a master regulator of interleukin 17 (IL-17)-producing helper T (Th17) cell development. To develop a therapeutic agent against Th17-mediated autoimmune diseases, we screened chemical compounds and successfully found that digoxin inhibited IL-17 production. Further studies revealed that digoxin bound to the ligand binding domain of RORγt and suppressed Th17 differentiation without affecting Th1 differentiation. To better understand the structural basis for the inhibitory activity of digoxin, we determined the crystal structure of the RORγt ligand-binding domain in complex with digoxin at 2.2 Å resolution. The structure reveals that digoxin binds to the ligand-binding pocket protruding between helices H3 and H11 from the pocket. In addition, digoxin disrupts the key interaction important for the agonistic activity, resulting in preventing the positioning of helix H12 in the active conformation, thus antagonizing coactivator interaction. Functional studies demonstrated that digoxin inhibited RORγt activity and decreased IL-17 production but not RORα activity. Digoxin inhibited IL-17 production in CD4(+) T cells from experimental autoimmune encephalomyelitis mice. Our data indicates that RORγt is a promising therapeutic target for Th17-derived autoimmune diseases and our structural data will help to design novel RORγt antagonists.
The XAGE family of cancer/testis‐associated genes: Alignment and expression profile in normal tissues, melanoma lesions and Ewing's sarcoma (2002)

The existence of XAGE genes was first reported after database homology searches for PAGE-like sequences identified 3 XAGE EST clusters. One of these clusters, XAGE-1, has in later studies been identified as a cancer/testis-associated gene. Here, we report the expression profiles of all 3 reported XAGE genes, as well as several splice variants of XAGE-1, in normal human tissues, Ewing's sarcoma and melanocytic tumors. We also provide the genetic structure of the corresponding genes. Moreover, by searching the databases for XAGE homologues, we identified 3 additional GAGE-like genes. RT-PCR studies showed frequent expression in melanoma metastases and Ewing's sarcoma for 2 XAGE-1-derived transcripts. XAGE-2 was expressed at lower frequency in these tissues, while XAGE-3 was seen only in normal placenta. Due to a frameshift, the largest XAGE-1 putative protein is far less homologous to GAGE-like proteins than the other XAGEs. Interestingly, all GAGE-like genes contain a large secondary open reading frame, coding for putative proteins homologues to the XAGE-1 primary protein. The XAGE family of cancer/testis-associated genes is located on chromosome Xp11.21-Xp11.22. The data outline a superfamily of GAGE-like cancer/testis antigens, consisting of at least 19 genes.
Changes in Subphase Aggregates in Rabbits Injured by Free Fatty Acid (1994)

Rabbits treated with intravenous free fatty acid suffer an acute lung injury. Material obtained from these lungs by bronchoalveolar lavage (BAL) has dramatically impaired ability to lower surface tension in vitro despite normal levels of surfactant phospholipids. Although large quantities of surface-active inhibitors are present in BAL, their effects are not sufficient to explain the magnitude of surfactant inactivation. This study determines if alterations in the surfactant aggregates can explain the loss of surfactant function in fatty acid lung injury. In injured animals, the larger, most active surfactant particles recovered by centrifugal pelleting were found to be decreased in amount. The remaining large particles had reduced surface activity compared with control aggregates. In addition, large particles in injured animals had a higher density than control animals on sucrose gradients following equilibrium centrifugation. Interaction with serum components present in the injured BAL could explain these higher densities. The ability of the injured BAL to lower surface tension was improved by supplementation with normal levels of particles from injured lungs. Supplementation of injured BAL with control large aggregates improved activity further and restored the ability to lower surface tension to < 1 mN/m. Therefore both the decreased amount and activity of large surfactant aggregates in injured animals contributed significantly to the observed inactivation of surfactant. Diminished surfactant function from alteration in surfactant aggregates is a mechanism common to other forms of acute lung injury, and the design of therapies with exogenous surfactants in injured lungs will need to consider strategies that restore surfactant function towards normal.
Novel and Efficient Synthesis of Iminocoumarins via Copper-Catalyzed Multicomponent Reaction (2006)

A variety of substituted iminocoumarins are prepared in good to excellent yields via a copper-catalyzed multicomponenet reaction of sulfonyl azides, terminal alkynes, and salicylaldehydes or o-hydroxylacetophenones. The method is general, mild, versatile, and efficient. A plausible mechanism for the domino process is proposed.
Native LDL Upregulation of ATP-Binding Cassette Transporter-1 in Human Vascular Endothelial Cells (2002)

ATP-binding cassette transporter-1 (ABCA1) mediates the lipid efflux from cells to apolipoproteins. In studying the gene expression and regulation of ABCA1 in human vascular endothelial cells (ECs), we found that native low density lipoprotein (LDL) elevates ABCA1 in both protein and mRNA levels in a time- and dose-dependent fashion. Transfection of full-length human ABCA1 in ECs lowers cellular cholesterol content and increases apolipoprotein (apo) A-I-mediated cholesterol efflux. Transfection of the ABCA1 promoter-luciferase reporter results in a 2-fold induction after LDL exposure. The responsive element was mapped within -116 to -54 of the promoter region with use of promoter deletion constructs, as reported in other cells. A mutation of the DR4 site greatly diminished the LDL effect. Results showing that LDL increases the liver X receptor responsive element (LXRE)-driven luciferase activity demonstrate the effect of LDL on LXR activation. Furthermore, ligands of the retinoid X receptor and LXR activate ABCA1 in ECs at levels of both promoter activation and mRNA induction. Therefore, ABCA1 is expressed in vascular ECs and is transcriptionally upregulated by LDL. Overexpression of ABCA1 in these cells prevents overloading of cholesterol by increasing the efflux of cholesterol. Thus, ABCA1 plays an important role in the homeostasis of cholesterol in the vascular endothelium.
Real-time refinement and simplification of adaptive triangular meshes (2004)

In this paper we present a generic method for incremental mesh adaptation based on hierarchy of semi-regular meshes. Our method supports any refinement rule mapping vertices onto vertices such as 1-to-4 split or /spl radic/3-subdivision. Resulting adaptive mesh has subdivision connectivity and hence good aspect ratio of triangles. Hierarchic representation of the mesh allows incremental local refinement and simplification operations exploiting frame-to-frame coherence. We also present an out-of-core storage layout scheme designed for semi-regular meshes of arbitrary subdivision connectivity. It provides high cache coherency in the data retrieval and relies on the interleaved storage of resolution levels and maintaining good geometrical proximity within each level. The efficiency of the proposed method is demonstrated with applications in physically-based cloth simulation, real-time terrain visualization and procedural modeling.
Chemoenzymatic Synthesis of Size-Defined Polysaccharides by Sialyltransferase-Catalyzed Block Transfer of Oligosaccharides (2007)

A novel chemoenzymatic method has been developed for the synthesis of size-defined polysaccharides with sialic acid-containing repeating units by sialyltransferase-catalyzed block transfer of oligosaccharides. The synthesized polysaccharides are mimics of surface polysaccharides produced by some pathogenic bacteria. Bacterial sialyltransferases, once again, have been confirmed to have flexible substrate specificity. They are extremely useful catalysts for efficient synthesis of diverse and complex sialic acid-containing carbohydrates and glycoconjugates.
Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase. (1996)

The 1.4-kb downstream region from a nitrilase gene (nitA) of an actinomycete Rhodococcus rhodochrous J1, which is industrially in use, was found to be required for the isovaleronitrile-dependent induction of nitrilase synthesis in experiments using a Rhodococcus-Escherichia coli shuttle vector pK4 in a Rhodococcus strain. Sequence analysis of the 1.4-kb region revealed the existence of an open reading frame (nitR) of 957 bp, which would encode a protein with a molecular mass of 35,100. Deletion of the central and 3'-terminal portion of nitR resulted in the complete loss of nitrilase activity, demonstrating that nitR codes for a transcriptional positive regulator in nitA expression. The deduced amino acid sequence of nitR showed similarity to a positive regulator family including XylS from Pseudomonas putida and AraC from E. coli. By Northern blot analysis, the 1.4-kb transcripts for nitA were detected in R. rhodochrous J1 cells cultured in the presence of isovaleronitrile, but not those cultured in the absence of isovaleronitrile. The transcriptional start site for nitA was mapped to a C residue located 26 bp upstream of its translational start site. Deletion analysis to define the nitA promoter region suggested the possible participation of an inverted repeat sequence, centered on base pair -52, in induction of nitA transcription.
A linear work, O(n1/6) time, parallel algorithm for solving planar Laplacians (2007)

We present a linear work parallel iterative algorithm for solving linear systems involving Laplacians of planar graphs. In particular, if Ax = b, where A is the Laplacian of any planar graph with n nodes, the algorithm produces a vector x such that ||x--x||A ≤ e, in O(n1/6+clog(1/e)) parallel time, doing O(nlog(1/e)) work, where c is any positive constant. One of the key ingredients of the solver, is an O(nklog2k) work, O(klogn) time, parallel algorithm for decomposing any embedded planar graph into components of size O(k) that are delimited by O(n/√k) boundary edges. The result also applies to symmetric diagonally dominant matrices of planar structure.
Palpable Breast Masses (2000)

Percutaneous imaging-guided core biopsy is useful in the evaluation of palpable breast masses that are small, deep, mobile, vaguely palpable, or multiple. In this study, percutaneous imaging-guided core biopsy spared additional diagnostic tissue sampling in 74% women with palpable breast masses.