gebhart/patrepeval huggingface dataset:
The Role of Bacteria in the Pathogenesis and Progression of Idiopathic Pulmonary Fibrosis (2014)

IPF is characterized by an increased bacterial burden in BAL that predicts decline in lung function and death. Trials of antimicrobial therapy are needed to determine if microbial burden is pathogenic in the disease.
Deformation resistance in soft tissue cutting: a parametric study (2004)

Characterizing and modeling of soft tissue deformation during cutting is important for developing a reality based haptic interaction model for surgical training and simulation. In this study, soft tissue cutting experiments were performed (ex-vivo) while monitoring the cutting forces and blade displacement for various cutting speeds (ranging from 0.1cm/sec-2.54cm/sec) and cutting angles (for 0/spl deg/ and 45/spl deg/ cutting angle). The measured force-displacement curves in all cases exhibit a characteristic pattern: repeating units formed by a segment of linear loading (deformation of tissue) and immediately followed by a segment of sudden unloading (localized crack extension in the tissue). This paper addresses the characterization of the deformation resistance during the deformation segment. The variation of this deformation resistance with cutting parameters is also determined. The deformation resistance to the cutting blade was quantified via a quantity designed as the local effective modulus (LEM) of the tissue. For a given cutting speed, the deformation resistance decreases as the cutting angle is varied from 0/spl deg/ to 45/spl deg/. For each cutting angle, the deformation resistance decreases with cutting speed. The variation of deformation resistance versus cutting speed is linear at 0/spl deg/ cutting angle and is nonlinear at 45/spl deg/ cutting angle.
Experimental and Numerical Studies of Stress Migration in Cu Interconnects Embedded in Different Dielectrics (2006)

In this work, package level stress migration (SM) test of Cu dual‐damascene interconnects in via‐line structures were performed. Two factors that were considered are stressing temperature and dielectric materials. The via‐line structures were studied at temperatures ranging from 150°C to 250°C, with highest failure rate being detected at 200°C. In comparing stress migration data on carbon doped oxide (CDO) with undoped silica glass (USG), a difference of two orders of magnitude was detected in the rate of change of resistance. More than 40% of the CDO samples showed open circuit failures after a 1344‐hour test, whereas the maximum resistance change in the USG samples was only 10%. Failure analysis based on FIB indicated that failures in both CDO & USG were very similar in nature with voids forming symmetrically at the bottom of the via, showing that the integrity of the Ta barrier in the via bottom area was of significant influence to SM. The line width of the two‐level interconnects is almost the same as the via size. The observed SM phenomenon is different from the voiding under and/or inside vias connected to wide Cu line, previously referred as SIV (stress‐induced voiding). Finite element analysis (FEA) indicated that the driving force for void growth, the gradient of hydrostatic stress, at via bottom in CDO structure is 30% higher than the one in USG.
Hyperelectronic polarization in macromolecular solids (1968)

Abstract Hyperelectronic polarization may be viewed as the electrical polarization in external fields due to the pliant interaction with the charge pairs of excitons, in which the charges are molecularly separated and range over molecularly limited domains. It is particularly pronounced in molecular solids composed of long polymeric molecules having extensive regions of electronic orbital delocalization. Hyperelectronic polarization is regarded as the principal contributor to the high polarizabilities of the following five macromolecular solids: four polyacene quinone radical polymers formed by condensation of aromatic hydrocarbon derivatives with aromatic acids and poly(Cu(II)‐ N , N ′‐ dimethyl rebeanate). The first four polymers at 100 hz had dielectric constants of 1800–2400, decreasing to about 58–100 at 100,000 hz, with relaxation times of 10 −3 to 10 −4 sec. A sixth polymer, a Schiff‐base condensate of 1,4‐napthaquinone and p ‐toluene diisocyanate, however, showed little hyperelectronic polarization, displaying a dielectric constant of 10, constant over 100–100,000 hz. By simple arguments it is shown that the relaxation times and the frequency response of conduction are consonant with the proposed model of charges roaming over long molecular domains (up to 4000 A.) but restricted by molecular boundaries.
Origin of Hydroxylated Brominated Diphenyl Ethers: Natural Compounds or Man-Made Flame Retardants? (2009)

Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants. The structurally related hydroxylated PBDEs (OH-PBDEs) and methoxylated PBDEs (MeO-PBDEs) occur in precipitation, surface water, wildlife, and humans. The formation of OH-PBDEs in wildlife and humans is of considerable concern due to their greater toxicities relative to PBDEs and MeO-PBDEs. Research to date suggests that OH-PBDEs are formed by hydroxylation of PBDEs, and MeO-PBDEs are then formed by methylation of the OH-PBDEs. Here we show significant metabolic production of OH-PBDEs from MeO-PBDEs while hydroxylation of synthetic PBDEs to OH-PBDEs was negligible. Concentrations of PBDEs, OH-PBDEs, and MeO-PBDEs were analyzed in tuna, albatross, and polar bears collected from marine environments worldwide, and we found a closer relationship between OH-PBDEs and MeO-PBDEs than had been previously reported. Furthermore, for the first time the metabolic relationships between PBDEs, OH-PBDEs, and MeO-PBDEs were elucidated in vitro using rainbow trout, chicken, and rat microsomes. We propose the production of OH-PBDEs from naturally occurring MeO-PBDEs as a previously unidentified mechanism that could be an important contributor for the occurrence of OH-PBDEs found in wildlife from remote areas. Our results suggest that risk assessment paradigms for PBDEs and their metabolites need reevaluation and that human exposure to MeO-PBDEs that occur naturally in marine organisms should be considered.
Magnetron reactive ion etching of GaAs in a BCl3 discharge (1993)

Magnetron reactive ion etching (MIE) of GaAs has been investigated using BCl3 as the etch gas. Etch rates are determined as a function of applied power density (0.16–0.80 W/cm2) and chamber pressure (2–6 mTorr). Patterned GaAs samples were etched anisotropically and exhibited smooth surfaces, with no indication of residues on surfaces or sidewalls. Transmission electron microscope measurements were performed to determine etch induced wafer damage. Schottky diode measurements on etched surfaces revealed minimal degradation of surface region electrical properties. Our results show that (MIE) in BCl3 is an attractive processing technique for GaAs device fabrication.
Properties of corn samples varying in percentage of dent and flint kernels (1995)

Commercial corn samples from three production areas, mid-western U.S.A., eastern Canada (Ontario) and western Canada (Alberta), were evaluated for their physical and chemical properties in relation to the percentage of dent and flint kernels. The percentage of dent-type kernels (97, 93, 42 and 22% for the U.S.A., Ontario and two Alberta samples) was positively correlated with starch content, and negatively correlated with ether extractable material of the kernels. Kernel density correlated negatively with protein content. Kernel weight correlated negatively with ether extractable material and total ash content. The Alberta corn contained more nonpolar lipids than the high dent corns from U.S.A. and Ontario. Total amounts of lipid and palmitic acid correlated negatively with dent percentage. The differences in physical and chemical properties were attributed to the flint character of Alberta corn.
Mechanism Underlying IκB Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex (2014)

The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex.
The Antiangiogenic Activity of Naturally-occurring and synthetic Homoisoflavonoids from the Hyacinthaceae (sensu APGII) (2019)

Excessive blood vessel formation in the eye is implicated in wet age-related macular degeneration, proliferative diabetic retinopathy, neovascular glaucoma, and retinopathy of prematurity, which are major causes of blindness. Small molecule antiangiogenic drugs are strongly needed to supplement existing biologics. Homoisoflavonoids have been previously shown to have potent antiproliferative activities in endothelial cells over other cell types. Moreover, they demonstrated a strong antiangiogenic potential in vitro and in vivo in animal models of ocular neovascularization. Here, we tested the antiangiogenic activity of a group of naturally occurring homoisoflavonoids isolated from the family Hyacinthaceae and related synthetic compounds, chosen for synthesis based on structure–activity relationship observations. Several compounds showed interesting antiproliferative and antiangiogenic activities in vitro on retinal microvascular endothelial cells, a disease-relevant cell type, with the synthetic chromane, ...
Relation of coronary heart disease and apolipoprotein E phenotype in patients with non-insulin dependent diabetes. (1991)

Apolipoprotein E phenotypes E4/4 and E4/3 modulate the risk of coronary heart disease in men with non-insulin dependent diabetes.
Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. I. Taxonomy of the producing organism and fermentation. (1989)

The pacidamycins are a new complex of nucleosidyl-peptide antibiotics with highly specific activity against Pseudomonas aeruginosa. They are produced by Streptomyces coeruleorubidus AB 1183F-64 which was isolated from a soil sample collected at Offenburg in the FRG. The mature spore masses of the producing organism are greenish gray to blue, and the spore chains are arranged in spirals. After the structures of the pacidamycins were determined, the fermentation medium was supplemented with component amino acids. This resulted in the directed biosynthesis of several members of the complex. The overall antibiotic recovered was increased from 1 approximately 2 mg/liter to more than 100 mg/liter through a combination of strain selection, medium manipulation and amino acid feeding experiments.
All-fiber Q-switched and self-mode-locking Er3+/Yb3+-codoped ring laser (2005)

A high efficiency Q-switched and self-mode-locked Er<sup>3+</sup>/Yb<sup>3+</sup> co-doped fiber ring laser with a Mach-Zehnder interferometer (MZI) is proposed. The fiber laser with threshold of 126.84 mw and linewidth of 0.06nm has been demonstrated. The average power of 62.6mW, the peak power of 1231.8mW of the Q-switched giant pulses with the pulse duration of 2.6&#956;s can be achieved. It is found that in order to generate Q-switched giant pulses, different repetition frequency must be selected as pumping power is changed. This phenomenon is observed for the first time to our knowledge. In the experiment, it is also found that stable passive Q-switch pulses can be observed, which waveform is not the same with the different pump power, although the arms lengths of the interferometer is not changed. When the absorbed pumped power is increased to 591.8mW, a self-mode-locking pulse can be formed and it is given a detailed theoretically illustration in this paper.
Gravity currents with large salinity in a gravel bed valley: an experimental study (2022)

Abstract In the current study experiments in a valley (a composite cross-sectional tank consisting of a rectangular upper cross section and a lower trapezoidal) were performed. The purpose of this research is to study the gravel bed in gravity currents with large salinity. The tank is separated in two parts by a vertical gate, which separates the fresh water with the gravel bed from the salt water with the impermeable bed. When the gate opens, a flow is created due to density difference. The salinity densities are large (from 1,050 to 1,090 kg/m3). These specific densities have been chosen to simulate liquid wastes that affect the environment. Compared to experiments in the same tank without a gravel bed, it is observed that the gravel bed reduces the propagation of currents and mainly reduces the current with the smallest density difference at the lowest height. The main conclusion of this study is that the kind of channel bed plays a key role in the propagation of gravity currents. The gravel bed affects significantly the velocity and the distance traveled by the currents in comparison with impermeable bed.
SYNTHESIS Special Issue in Honor of Professor Sarah Reisman (2021)

Received: 21 October 2021 Accepted after revision: 25 October 2021 Article published online:28 October 2021
Is non-unique decoding necessary? (2012)

In mutiterminal communication systems, signals carrying messages meant for different destinations are often observed together at any given destination receiver. Han and Kobayashi (1981) proposed a receiving strategy which performs a joint unique decoding of messages of interest along with a subset of messages which are not of interest. It is now well-known that this provides an achievable region which is, in general, larger than if the receiver treats all messages not of interest as noise. Nair and El Gamal (2009) and Chong, Motani, Garg, and El Gamal (2008) independently proposed a generalization called indirect or non-unique decoding where the receiver uses the codebook structure of the messages to only uniquely decode its messages of interest. Indirect (non-unique) decoding has since been used in various scenarios. The main result in this paper is to provide an interpretation and a systematic proof technique for why indirect decoding, in all known cases where it has been employed, can be replaced by a particularly designed joint unique decoding strategy, without any penalty from a rate region viewpoint <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Yttrate-Mediated Ligand Transfer and Direct Synthesis as a Route to Amidopalladium Complexes (1998)

A ligand transfer from yttrium to palladium and the regeneration of 1 are the crucial steps in the efficient synthesis of the very strained amidopallium complex 2 from [(cod)PdCl<sub>2</sub> ] and 1 (cod=cyclooctadiene). In the light of the numerous "ate" complexes of early transition metals, this synthetic route should have enormous potential.
X‐Ray Photoelectron Spectroscopic Studies of Tin Electrodes after Polarization in Sodium Hydroxide Solution (1977)

The surface of tin electrodes after potentiostatic polarization in 0.50 mole dm−3 sodium hydroxide solution has been examined by x‐ray photoelectron spectroscopy. Stannous oxide and hydroxide are shown to be present in the prepassive region. At higher potentials stannic oxide and hydroxide are formed. The thickness of the layer is evaluated over the potential range −0.95 to +0.40V using various models and is in the range 30–86Å.
Effects of irradiation on grafted skin--vascular changes after irradiation. (1985)

Early changes in the vascularity of grafted skin after X-ray irradiation were evaluated using the microangiographic technique. There was a correlation betweeen the vascular density at the time of irradiation and the vascular density two weeks after irradiation. The grafts irradiated in the early hypovascular stage showed mild-moderate vascular reactions to irradiation, whereas those irradiated in the hypervascular stage showed severe vascular reactions. The grafts irradiated in the late hypo­ vascular stage showed mild vascular reactions. There was also a relation between the skin reaction and vascular reaction to irradiation. It was concluded that primary consideration should be given to the vascular damage of grafted skin when determining the proper time for postoperative irradi­ ation.
Toward a Consistent Treatment of Polarization in Model QM/MM Calculations (2008)

The concept of model chemistries within hybrid QM/MM calculations has been addressed through analysis of the polarization energy determined by two distinct approaches based on (i) induced charges and (ii) induced dipoles. The quantum mechanical polarization energy for four configurations of the water dimer has been determined for a range of basis sets using Morokuma energy decomposition analysis. This benchmark value has been compared to the fully classical polarization energy determined using the induced dipole approach, and the molecular mechanics polarization energy calculated using induced charges within the MM region of hybrid QM/MM calculations. From the water dimer calculations, it is concluded that the induced charge approach is consistent with medium sized basis set calculations whereas the induced dipole approach is consistent with large basis set calculations. This result is highly relevant to the concept of QM/MM model chemistries.
Generalized Jones matrix method for homogeneous biaxial samples (2015)

The generalized Jones matrix (GJM) is a recently introduced tool to describe linear transformations of three-dimensional light fields. Based on this framework, a specific method for obtaining the GJM of uniaxial anisotropic media was recently presented. However, the GJM of biaxial media had not been tackled so far, as the previous method made use of a simplified rotation matrix that lacks a degree of freedom in the three-dimensional rotation, thus being not suitable for calculating the GJM of biaxial media. In this work we propose a general method to derive the GJM of arbitrarily-oriented homogeneous biaxial media. It is based on the differential generalized Jones matrix (dGJM), which is the three-dimensional counterpart of the conventional differential Jones matrix. We show that the dGJM provides a simple and elegant way to describe uniaxial and biaxial media, with the capacity to model multiple simultaneous optical effects. The practical usefulness of this method is illustrated by the GJM modeling of the polarimetric properties of a negative uniaxial KDP crystal and a biaxial KTP crystal for any three-dimensional sample orientation. The results show that this method constitutes an advantageous and straightforward way to model biaxial media, which show a growing relevance for many interesting applications.
The C. elegans NeuroD homolog cnd-1 functions in multiple aspects of motor neuron fate specification (2000)

The basic helix-loop-helix transcription factor NeuroD (Neurod1) has been implicated in neuronal fate determination, differentiation and survival. Here we report the expression and functional analysis of cnd-1, a C. elegans NeuroD homolog. cnd-1 expression was first detected in neuroblasts of the AB lineage in 14 cell embryos and maintained in many neuronal descendants of the AB lineage during embryogenesis, diminishing in most terminally differentiated neurons prior to hatching. Specifically, cnd-1 reporter genes were expressed in the precursors of the embryonic ventral cord motor neurons and their progeny. A loss-of-function mutant, cnd-1(ju29), exhibited multiple defects in the ventral cord motor neurons. First, the number of motor neurons was reduced, possibly caused by the premature withdrawal of the precursors from mitotic cycles. Second, the strict correlation between the fate of a motor neuron with respect to its lineage and position in the ventral cord was disrupted, as manifested by the variable expression pattern of motor neuron fate specific markers. Third, motor neurons also exhibited defects in terminal differentiation characteristics including axonal morphology and synaptic connectivity. Finally, the expression patterns of three neuronal type-specific transcription factors, unc-3, unc-4 and unc-30, were altered. Our data suggest that cnd-1 may specify the identity of ventral cord motor neurons both by maintaining the mitotic competence of their precursors and by modulating the expression of neuronal type-specific determination factors. cnd-1 appears to have combined the functions of several vertebrate neurogenic bHLH proteins and may represent an ancestral form of this protein family.
Complex WKB method for a difference Schrödinger equation with the potential being a trigonometric polynomial (2018)

The difference SchrÃ¶dinger equation $\psi (z+h)+\psi (z-h)+ v(z)\psi (z)=E\psi (z)$, $z\in \mathbb {C}$, is considered; here $h$ is a positive number, $E$ is the spectral parameter, and $v$ is a trigonometric polynomial. The asymptotics of its entire solutions is studied as $h\to 0$.
Electric Field-Driven Coherent Spin Reorientation of Optically Generated Electron Spin Packets in InGaAs (2012)

Full electric-field control of spin orientations is one of the key tasks in semiconductor spintronics. We demonstrate that electric-field pulses can be utilized for phase-coherent ±π spin rotation of optically generated electron spin packets in InGaAs epilayers detected by time-resolved Faraday rotation. Through spin-orbit interaction, the electric-field pulses act as local magnetic field pulses. By the temporal control of the local magnetic field pulses, we can turn on and off electron spin precession and thereby rotate the spin direction into arbitrary orientations in a two-dimensional plane. Furthermore, we demonstrate a spin-echo-type spin drift experiment and find an unexpected partial spin rephasing, which is evident by a doubling of the spin dephasing time.
ChemInform Abstract: Synthesis of CF3‐Containing 1,2,3,4‐Tetrahydroisoquinoline‐3‐phosphonates via Regioselective Ruthenium‐Catalyzed Co‐Cyclotrimerization of 1,7‐Azadiynes. (2013)

Abstract The synthesis of the title compounds is achieved through N‐propargylation of substrates (I) and (VIII) followed by cyclotrimerization with alkynes.
Growth of Cu particles on a Cu2O truncated octahedron: tuning of the Cu content for efficient glucose sensing (2015)

A simple and versatile hydrothermal method is developed to synthesize Cu-Cu2O, in which Cu particles grow on the surface of a Cu2O truncated octahedron. Through the reduction of Cu(2+) by glucose in an alkaline solution, the Cu2O truncated octahedron is quickly formed via a kinetic control process, and then Cu particles selectively nucleate on the high-energy (110) facets of Cu2O, generating a heterostructure. The amount of Cu in the sample is successfully tuned by varying the reaction temperature. Compared to Cu2O, the hybrid Cu-Cu2O architecture shows superior electrocatalytic performance for glucose oxidation due to the synergistic effect between more electrocatalytic active but less conductive Cu2O and more conductive but less electrocatalytic active Cu. By tuning the content of Cu in the heterostructure, the highest electrocatalytic activity is achieved at the Cu/Cu2O molar ratio of 0.83.