gebhart/patrepeval huggingface dataset:
Vibronic dispersion in the copper oxide superconductors (1994)

Attempts to describe the normal-state electronic behavior of the copper oxide superconductors have been unable to reconcile the following observations: (i) a well-defined Fermi surface with a locus predicted by band theory, but having charge carriers of a sign predicted for a Mott-Hubbard splitting of the band; (ii) a change in sign of the carriers to that predicted by band theory, but without a significant change in the locus of the Fermi surface, on overdoping beyond the narrow superconductive compositional range; (iii) a remarkable stability of the narrow range of superconductive charge-carrier concentrations in the ${\mathrm{CuO}}_{2}$ sheets even in the presence of charge transfer from nonsuperconductive intergrowth layers; (iv) a dramatic sensitivity of the N\'eel temperature of the parent compound to oxidation of the ${\mathrm{CuO}}_{2}$ sheets, but the persistence of antiferromagnetic spin fluctuations into the superconductive compositions; and (v) unusual transport properties that cannot be treated within the Migdal approximation and are insensitive to high magnetic fields. To address this impasse, we propose a phenomenological polaron model based on the observation that the system must accommodate to the coexistence of ``ionic'' and ``covalent'' Cu-O bonding having different equilibrium Cu-O bond lengths.We designate this entity a correlation polaron. Covalent Cu-O bonding with molecular-orbital formation occurs within the polaron, which moves in a background of ionic Cu-O bonding. Vibronic coupling at the ``avoided crossover'' from ionic to covalent bonding allows diffusional motion of uncoupled polarons without any motional enthalpy in the mobility. At temperatures T&gt;${\mathit{T}}_{\mathit{l}}$\ensuremath{\gtrsim}300 K the polarons are uncoupled and move randomly; in the narrow superconductive compositional range they condense below ${\mathit{T}}_{\mathit{l}}$ to form a distinguishable thermodynamic phase consisting of extended vibronic states. In this ``polaron liquid,'' a distinction between bonding and antibonding states within the polarons opens a gap at the half-band position, not the Fermi energy, and some spectral weight associated with the ionic Cu-O bonding still remains at the energies of the upper and lower Hubbard bands of the parent compound.
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity (2022)

These results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.
ADMM approach for efficient iterative tomographic deconvolution reconstruction of 3D quantitative phase images (2021)

Tomographic deconvolution phase microscopy (TDPM) is a promising approach for 3D quantitative imaging of phase objects such as biological cells and optical fibers. In the present work, the alternating direction method of multipliers (ADMM) is applied to TDPM to shorten its image acquisition and processing times while simultaneously improving its accuracy. ADMM-TDPM is used to optimize the image fidelity by minimizing Gaussian noise and by using total variation regularization with the constraints of nonnegativity and known zeros. ADMM-TDPM can reconstruct phase objects that are shift variant in three spatial dimensions. ADMM-TDPM achieves speedups of 5x in image acquisition time and greater than 10x in image processing time with accompanying higher accuracy compared to TDPM.
Viruses and Human Breast Cancer (2006)

There are well-established risk factors for breast cancer, most of which relate to estrogens and growth hormones in females. These include early-age menarche, late-age menopause, postmenopausal obesity and use of hormone therapy. However, these factors do not account for the sixfold difference in breast cancer incidence and mortality between countries and the fact that these differences dramatically lessen after migration; nor do they account for male breast cancer. Accordingly, hormone-responsive viruses have become major suspects as etiological agents for human breast cancer. Human papillomaviruses, mouse mammary tumor virus and Epstein-Barr virus are the prime candidate viruses as causes of human breast cancer. Human papillomaviruses and the mouse mammary tumor virus have hormone responsive elements that appear to be associated with enhanced replication of these viruses in the presence of corticosteroid and other hormones. This biological phenomenon is particularly relevant because of the hormone dependence of breast cancer. Viral genetic material for each of these candidate viruses has been identified by polymerase chain reaction in breast tumors but rarely in normal breast tissue controls. Pooled data from controlled studies show substantial odds ratios for the presence of viral genetic material in breast tumors compared with normal controls. These and additional data provide substantial, but not conclusive, evidence that human papillomavirus, the mouse mammary tumor virus and Epstein-Barr virus may have a role in the etiology of human breast cancer. If conclusive evidence for a role of these viruses in breast carcinogenesis can be developed, there is a practical possibility of primary prevention.
Synthesis of a Copper 1,3,5-Triamino-2,4,6-benzenetriol Metal–Organic Framework (2020)

We report the synthesis and characterization of a two-dimensional (2D) MX<sub>2</sub>Y<sub>2</sub>-type (M = metal, X, Y = N, S, O, and X ≠ Y) copper 1,3,5-triamino-2,4,6-benzenetriol metal-organic framework (Cu<sub>3</sub>(TABTO)<sub>2</sub>-MOF). The role of oxygen in the synthesis of this MOF was investigated. Copper metal is formed along with the MOF when the synthesis is done in argon as suggested by XRD. When the reaction was exposed to air with vigorous stirring, copper metal was not observed by XRD. However, if there is no stirring, then copper metal is formed, and we learned that this is because oxygen was not allowed to enter the solvent due to the formation of a MOF film at the air/water interface. For the sample synthesized in argon (Cu<sub>3</sub>(TABTO)<sub>2</sub>-Ar), an insulating Cu<sub>3</sub>(TABTO)<sub>2</sub>-Ar pellet (σ < 10<sup>-10</sup> S cm<sup>-1</sup>) became a metallic conductor with an electrical conductivity of 0.78 S cm<sup>-1</sup> at 300 K after exposure to iodine vapor. This work provides further insights into the role of oxygen in the synthesis of redox-active ligand-based MOFs, expands the family of 2D redox-active ligand-based electrically conductive MOFs, and offers more opportunities in sensing, photocatalytic, electronic, and energy-related applications.
Throughput Enhancement for Uploading TCP Flows in IEEE 802.11 Wireless LANs (2006)

This paper re-analyzes the relationship between MAC contention and TCP congestion control misled in previous efforts. By introducing a prioritized access of an access point, we seek to allow the optimal number of competing stations to contend for media access.
Combined liquid chromatograph/mass spectrometer for involatile biological samples. (1980)

A new liquid chromatograph/mass spectrometer has been developed in our laboratory for application to analysis of biological molecules of extremely low volatility. Oxyhydrogen flames rapidly vaporize the total liquid-chromatographic effluent, and molecular and particle beam techniques are used to efficiently transfer the sample to the ionization source of the mass spectrometer. This new instrument is comparable in cost and complexity to a combined gas chromatograph/mass spectrometer, but extends the capabilities of combined chromatography/mass spectrometry to a broad range of compounds not previously accessible. We are currently testing biologically significant samples with this instrument, using reversed-phase liquid-chromatographic separation and both positive and negative ion chemical-ionization mass spectrometry. Results have been obtained from mixtures of nucleic acid components--bases, nucleosides, and nucleotides--and from amino acids, peptides, saccharides, fatty acids, vitamins, and antibiotics. In all cases investigated to date, ions indicative of molecular mass are obtained in at least one of the operating modes available. Detection limits are typically in the 1-10 ng range for full mass scans (about 80-600 amu); sub-nanogram quantities are usually detectable with single-ion monitoring.
Measurements for Reynolds Stresses under Different Inlet Prewhirl in Centrifugal Compressor (2012)

The effects of inlet guide vanes(IGV) prewhirl angles on Reynolds stresses in radial gap between impeller and vane diffuser in a centrifugal compressor are experimentally investigated under design condition by X-type hot-film anemometry.The results show that the levels of the turbulence intensity and the Reynolds stresses in the radial gap get the highest under-20°of prewhirl angle,while they are moderate at 0°and the lowest at 20°of prewhirl angles.High levels of Reynolds shear stresses look to be related with high levels of turbulence kinetic energy,or vice versa.In the lengths of 10% and 50% spanwise,at three prewhirl angles,the time-average Reynolds stresses in the radial direction are obviously larger than that in the tangential direction to indicate the significant anisotropy of turbulence.At the impeller outlet,the time-average Reynolds stresses in the radial direction are above 1.5 times larger than those in the tangential direction,and this ratio decreases to 1.25 at the diffuser inlet.However,in the length of 90% spanwise,the turbulence is close to isotropy since the difference of the Reynolds stresses in two directions is less than 10%.The degree of turbulence anisotropy at 0°of prewhirl angle is higher than those under other two prewhirl angles.
Methods, compounds and systems for detecting a microorganism in a sample (2023)

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.
Modulation of Nonspecific Mechanisms of Defense by Lactic Acid Bacteria: Effective Dose (1999)

The purpose of this study was to determine the effect of a fermented milk product containing Lactobacillus johnsonii La1 (formerly known as Lactobacillus acidophilus La1) on the phagocytic activity of peripheral blood leukocytes in healthy adult volunteers. Furthermore, we sought to define the effective doses of the bacteria, examine the effect on respiratory burst activity, and, finally, examine the contribution made by the starter culture to the biological effects. Volunteers were randomly distributed among three groups; each subject received one pot (150 ml) of fermented milk each day for 3 wk. The first two groups received a freshly prepared product fermented by Streptococcus thermophilus (group A) alone or S. thermophilus and 10(7) cfu/ml L. johnsonii La1 (group B). Group C received a product stored for a period of 21 to 28 d and that contained S. thermophilus and 10(6) cfu/ml of L. johnsonii La1. Ingestion of L. johnsonii La1 did not significantly increase fecal lactobacilli counts. However, L. johnsonii La1 was able to survive intestinal transit and was only recovered from the feces of the volunteers of groups B and C. The fermented base alone showed a weak effect on respiratory burst but not on phagocytic activity. However, the product containing 10(7) cfu/ml L. johnsonii La1 significantly enhanced both functions. The product containing 10(6) cfu/ml of L. johnsonii La1 had no significant effect on either function. These results suggest that fecal persistence may not necessarily reflect in vivo colonization and may not be a prerequisite for all forms of immune reactivity.
Understanding Factors Affecting Corrosion Inhibitor Performance in Under-Deposit Testing with Sand (2013)

Abstract This paper seeks to increase the understanding of under-deposit corrosion with sand and the development of better inhibitors to mitigate this type of corrosion under sweet (carbon dioxide) conditions. In these tests an electrode exposed to the bulk solution and an electrode under the sand were galvanically coupled. This method represents the under-deposit corrosion condition within oil and gas pipelines, mimicking how the pipe surface can be covered by solids such as sand. The corrosion rates of both electrodes were monitored simultaneously using the linear polarization resistance technique. Zero resistance ammetry was used to measure the coupling current between the electrodes underneath the sand and in the bulk solution. After injection of inhibitors, the under-deposit electrode acted as the local anode and a dramatic acceleration of its corrosion was observed. The linear polarization resistance corrosion rate, the potential of the coupled electrodes, and the galvanic current density before and after the injection of inhibitors were used to characterize the corrosion inhibitor performance. Factors that affect the under-deposit corrosion measurement, such as the sand thickness, inhibitor concentration and temperature, were investigated and utilized in order to assist in the future development of higher performing corrosion inhibitors for this environment.
LIM homeobox 2 promotes interaction between human iPS-derived hepatic progenitors and iPS-derived hepatic stellate-like cells (2019)

Human induced pluripotent stem (iPS) cells can differentiate into hepatocyte lineages, although the phenotype of the differentiated cells is immature compared to adult hepatocytes. Improvement of cell-cell interactions between epithelium and mesenchyme is a potential approach to address this phenotype issue. In this study, we developed a model system for improving interactions between human iPS-derived hepatic progenitor cells (iPS-HPCs) and human iPS-derived hepatic stellate cell-like cells (iPS-HSCs). The phenotype of iPS-HSCs, including gene and protein expression profiles and vitamin A storage, resembled that of hepatic stellate cells. Direct co-culture of iPS-HSCs with iPS-HPCs significantly improved hepatocytic maturation in iPS-HPCs, such as their capacity for albumin production. Next, we generated iPS cell lines overexpressing LIM homeobox 2 (LHX2), which suppresses myofibroblastic changes in HSCs in mice. Hepatocytic maturation in iPS-HPCs was significantly increased in direct co-culture with iPS-HSCs overexpressing LHX2, but not in co-culture with a human hepatic stellate cell line (LX-2) overexpressing LHX2. LHX2 regulated the expression of extracellular matrices, such as laminin and collagen, in iPS-HSCs. In conclusion, this study provides an evidence that LHX2 upregulation in iPS-HSCs promotes hepatocytic maturation of iPS-HPCs, and indicates that genetically modified iPS-HSCs will be of value for research into cell-cell interactions.
Neurochemical alterations in spinocerebellar ataxia type 1 and their correlations with clinical status (2010)

Robust biomarkers of neurodegeneration are critical for testing of neuroprotective therapies. The clinical applicability of such biomarkers requires sufficient sensitivity to detect disease in individuals. Here we tested the sensitivity of high field (4 tesla) proton magnetic resonance spectroscopy ((1)H MRS) to neurochemical alterations in the cerebellum and brainstem in spinocerebellar ataxia type 1 (SCA1). We measured neurochemical profiles that consisted of 10 to 15 metabolite concentrations in the vermis, cerebellar hemispheres and pons of patients with SCA1 (N = 9) and healthy controls (N = 15). Total NAA (N-acetylaspartate + N-acetylaspartylglutamate, tNAA) and glutamate were lower and glutamine, myo-inositol and total creatine (creatine + phosphocreatine, tCr) were higher in patients relative to controls, consistent with neuronal dysfunction/loss, gliotic activity, and alterations in glutamate-glutamine cycling and energy metabolism. Changes in tNAA, tCr, myo-inositol, and glutamate levels were discernible in individual spectra and the tNAA/myo-inositol ratio in the cerebellar hemispheres and pons differentiated the patients from controls with 100% specificity and sensitivity. In addition, tNAA, myo-inositol, and glutamate levels in the cerebellar hemispheres and the tNAA and myo-inositol levels in the pons correlated with ataxia scores (Scale for the Assessment and Rating of Ataxia, SARA). Two other biomarkers measured in the cerebrospinal fluid (CSF) of a subset of the volunteers (F(2)-isoprostanes asa marker of oxidative stress and glial fibrillary acidic protein (GFAP) as a marker of gliosis) were not different between patients and controls. These data demonstrate that (1)H MRS biomarkers can be utilized to noninvasively assess neuronal and glial status in individual ataxia patients.
High‐Resolution Transmission Electron Microscopy of Ti 4 AlN 3 , or Ti 3 Al 2 N 2 Revisited (1999)

The structure and chemistry of what initially was proposed to be Ti 3 Al 2 N 2 are incorrect. Using high‐resolution transmission electron microscopy, together with chemical analysis, the stoichiometry of this compound is concluded to be Ti 4 AlN 3‐delta (where delta = 0.1). The structure is layered, wherein every four layers of almost‐close‐packed Ti atoms are separated by a layer of Al atoms. The N atoms occupy ∼97.5% of the octahedral sites between the Ti atoms. The unit cell is comprised of eight layers of Ti atoms and two layers of Al atoms; the unit cell is hexagonal with P 6 3 / mmc symmetry (lattice parameters of a = 0.3 nm and c = 2.33 nm). This compound is machinable and closely related to other layered, ternary, machinable, hexagonal nitrides and carbides, namely M 2 AX and M 3 AX 2 (where M is an early transition metal, A is an A‐group element, and X is carbon and/or nitrogen).
Homochiral Perfluoroalkyl-Group-Substituted Secondary Alcohols Through Stereoselective Reduction of Perfluoroalkyl 1-(p-Tolylsulfinyl)alkyl Ketones (1988)

The reduction of some enantiomerically pure perfluoroalkyl α-(p-tolylsulfinyl) ketones was performed. Alcohols containing perfluoroalkyl and p-tolylsulfinyl groups were obtained with high diastereoselection when a phenyl residue was present on the sulfinylated carbon and with lower diastereoselection in the other cases. Removal of the chiral sulfinyl group from single diastereoisomers gave secondary alcohols containing a perfluoroalkyl group in enantiomerically pure form.
Study of White Noise Corner Frequency Location in Residual Phase Noise Measurement with Short and Long Cavity Lengths (2015)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text K. Bagnell, A. Klee, and P. Delfyett, "Study of White Noise Corner Frequency Location in Residual Phase Noise Measurement with Short and Long Cavity Lengths," in Frontiers in Optics 2015, OSA Technical Digest (online) (Optica Publishing Group, 2015), paper LTh4H.5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Outer membrane protein and biotype analysis of pathogenic nontypable Haemophilus influenzae (1982)

The techniques of biotype determination and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of outer membrane protein preparations were applied to 35 epidemiologically unrelated isolates of pathogenic nontypable Haemophilus influenzae. Three of five isolates obtained from the blood of unrelated newborns with sepsis had concordant major outer membrane from the blood of unrelated older children or adults with bacteremia had concordant major outer membrane protein profiles, distinct from the common profile of neonatal strains, and were biotype II. The outer membrane protein profiles of the remaining 5 isolates from blood, 2 isolated from cerebrospinal fluid, and 23 isolated from middle ear aspirates of children with otitis media were unique, although each isolate had peptides with apparent molecular weights of 16,000 and 31,500. These results suggest that a subset of nontypable isolates associated with bacteremia has distinctive strain markers. Their pathogenicity may relate to a prediction for colonizing the female genital tract in the case of the common neonatal strain or an increased ability to evade host defenses.
Metabolite Profile, Ruminal Methane Reduction, and Microbiome Modulating Potential of Seeds of Pharbitis nil (2022)

We identified metabolites in the seeds of <i>Pharbitis nil</i> (PA) and evaluated their effects on rumen methanogenesis, fiber digestibility, and the rumen microbiome <i>in vitro</i> and <i>in sacco</i>. Four rumen-cannulated Holstein steers (mean body weight 507 ± 32 kg) were used as inoculum donor for <i>in vitro</i> trial and live continuous culture system for <i>in sacco</i> trial. PA was tested <i>in vitro</i> at doses ranging from 4.5 to 45.2% dry matter (DM) substrate. The <i>in sacco</i> trial was divided into three phases: a control phase of 10 days without nylon bags containing PA in the rumen, a treatment phase of 11 days in which nylon bags containing PA (180 g) were placed in the rumen, and a recovery phase of 10 days after removing the PA-containing bags from the rumen. Rumen headspace gas and rumen fluid samples were collected directly from the rumen. PA is enriched in polyunsaturated fatty acids dominated by linoleic acid (C18:2) and flavonoids such as chlorogenate, quercetin, quercetin-3-<i>O</i>-glucoside, and quinic acid derivatives. PA decreased (<i>p</i> < 0.001) methane (CH<sub>4</sub>) production linearly <i>in vitro</i> with a reduction of 24% at doses as low as 4.5% DM substrate. A quadratic increase (<i>p</i> = 0.078) in neutral detergent fiber digestibility was also noted, demonstrating that doses < 9% DM were optimal for simultaneously enhancing digestibility and CH<sub>4</sub> reduction. <i>In sacco</i>, a 50% decrease (<i>p</i> = 0.087) in CH<sub>4</sub> coupled with an increase in propionate suggested increased biohydrogenation in the treatment phase. A decrease (<i>p</i> < 0.005) in ruminal ammonia nitrogen (NH<sub>3</sub>-N) was also noted with PA in the rumen. Analysis of the rumen microbiome revealed a decrease (<i>p</i> < 0.001) in the Bacteroidetes-to-Firmicutes ratio, suggesting PA to have antiprotozoal potential. At the genus level, a 78% decrease in <i>Prevotella</i> spp. and a moderate increase in fibrolytic <i>Ruminococcus</i> spp. were noted in the treatment phase. <i>In silico</i> binding of PA metabolites to <i>cyclic GMP-dependent protein kinase</i> of <i>Entodinium caudatum</i> supported the antiprotozoal effect of PA. Overall, based on its high nutrient value and antiprotozoal activity, PA could probably replace the ionophores used for CH<sub>4</sub> abatement in the livestock industry.
An asymmetric random Rado theorem for single equations: the\n $0$-statement (2020)

A famous result of Rado characterises those integer matrices $A$ which are\npartition regular, i.e. for which any finite colouring of the positive integers\ngives rise to a monochromatic solution to the equation $Ax=0$. Aigner-Horev and\nPerson recently stated a conjecture on the probability threshold for the\nbinomial random set $[n]_p$ having the asymmetric random Rado property: given\npartition regular matrices $A_1, \\dots, A_r$ (for a fixed $r \\geq 2$), however\none $r$-colours $[n]_p$, there is always a colour $i \\in [r]$ such that there\nis an $i$-coloured solution to $A_i x=0$. This generalises the symmetric case,\nwhich was resolved by R\\"odl and Ruci\\'nski, and Friedgut, R\\"odl and Schacht.\nAigner-Horev and Person proved the $1$-statement of their asymmetric\nconjecture. In this paper, we resolve the $0$-statement in the case where the\n$A_i x=0$ correspond to single linear equations. Additionally we close a gap in\nthe original proof of the 0-statement of the (symmetric) random Rado theorem.\n