gebhart/patrepeval huggingface dataset:
Abstract 64: Perlecan LG3 is Neuroprotective When Administered Intra-arterially After Experimental Ischemic Stroke (2016)

Despite recent advances in stroke therapy, stroke remains a leading cause of morbidity and mortality. We have previously demonstrated the therapeutic potential of exploiting the brain’s endogenous protection and repair processes following stroke. Specifically, we reported that the LG3 protein fragment of the heparan sulfate proteoglycan perlecan is neuroprotective and proangiogenic in vitro. We now hypothesize that LG3 could be therapeutic in experimental stroke. However, as previous in vivo LG3 studies suggest that it may not readily target stroke-affected brain upon systemic administration, we administered LG3 in a super selective intra-arterial (IA) model (into the ipsilateral common carotid artery) following transient (1 hour) middle cerebral artery occlusion in 3 month old male mice. Upon reperfusion the mice received LG3 or vehicle controls via IP (5 mg/kg) or IA (0.15 mg/kg) administration. No differences in vital signs were noted between the treatment groups. We observed that all LG3 treated mice, regardless of route of administration, had a smaller infarct compared to controls on post-stroke day 3. Importantly, those mice that received IA LG3 had much smaller strokes and performed significantly better in forced movement and in free movement settings than all other treatment conditions. Our results demonstrate that acute LG3 administration is beneficial after experimental ischemic stroke, IA LG3 is safe and much more effective than IP, and support further investigation of LG3 as a novel acute stroke therapy.
WE-D-330A-07: The Small-Animal Radiation Research Platform (SARRP): Focused Pencil Beam Dosimetry (2006)

Purpose: A small animal radiation platform equipped with on-board conebeam CT and conformal irradiation capabilities is being constructed for translational research. This work reports on the dosimetric characteristics of the x-ray lens subsystem used for high-resolution dose delivery. Method and Materials: A constant voltage 225 kVp x-ray beam from a 0.4 mm focal spot is shaped and directed to enter a 1.5 cm long, 2 cm diameter cylindrical multi-layer graphite x-ray lens placed 16 cm downstream from the source. The lens emits a converging circular beam of 40–80 keV x-rays which forms a narrow cylindrical beam centered at 33.5 cm downstream with a length of approximately 5 cm in air. The pencil beam disperses further downstream. We measured dosimetry of the beam in water equivalent plastic using Gaf-chromic EBT films (<0.1 mm pixel size) over a SSD range of 30 to 33.5 cm in steps of 5 mm. For each SSD, 36 films were orientated orthogonal to the beam and at every 2 mm between slabs in the depth direction. We established the optical density-to-dose calibration with a 6 MV beam. Results: The beam has a highly peaked cross-beam profile with a full width half maximum of about 1.5 mm in the focal zone. Irregular cylindrical symmetry is present due to imperfect lens construction. Dose deposition was defined as the average value over a circular area with a diameter of 1.5mm from the beam axis. Surface dose rates are 230 – 160 cGy/min over the 3.5 cm range of SSDs. The percent depth dose is approximately 34% at 2 cm depth for a beam at 33.5 cm SSD. Conclusion: Highly localized dose can be delivered with the focused pencil beam. Work is on-going to improve dose uniformity by lens rotation, and to develop a pencil beam algorithm for planning purposes.
Highly Enantioselective Simmons–Smith Fluorocyclopropanation of Allylic Alcohols via the Halogen Scrambling Strategy of Zinc Carbenoids (2013)

Highly enantio- and diastereoenriched monofluorocyclopropanes were accessed via the Simmons-Smith fluorocyclopropanation of allylic alcohols using difluoroiodomethane and ethylzinc iodide as the substituted carbenoid precursors. The scrambling of halogens at the zinc carbenoid led to the formation of the fluorocyclopropanating agent (fluoroiodomethyl)zinc(II) fluoride. This strategy circumvented the ongoing limitation in Simmons-Smith fluorocyclopropanations relying on the use of the relatively inaccessible and expensive carbenoid precursor fluorodiiodomethane.
Outgassing and Hydrogen Content of Untreated or Vacuum-Fired Stainless Steel after Bakeout or Airbake to 300-450oC (2001)

Outgassing and Hydrogen Content of Untreated or Vacuum-Fired Stainless Steel after Bakeout or Airbake to 300-450oC
Photochemical and Photophysical Studies of 3‐Amino‐6‐lodoacridine and the Inactivation of λ Phage (1996)

The photochemistry and photophysics of 3-amino-6-iodoacridine (Acr-I) was studied. Photolysis (350 nm) of Acr-I (free base) generates products consistent with a free radical intermediate in methanol, benzene and carbon tetrachloride. The Acr-I hydrochloride is shown to bind to calf thymus DNA and to the self-complementary dinucleotide cytidylyl-(3'-5')-guanosine (CpG) miniduplex in a manner similar to that of proflavine (Acr-NH2), a known DNA intercalator. The Acr-I is shown to more efficiently nick supercoiled plasmid DNA pBR322 upon 350 nm or 420 nm photolysis than Acr-NH2. The efficiency of Acr-I-sensitized DNA nicking is not oxygen dependent. Photolysis of the Acr-I/(CpG)2 complex leads to cleavage of the dinucleotide and to cytidine base release by selective damage to a specific ribose moiety. Dinucleotide cleavage occurs equally well in the presence or absence of oxygen, thereby eliminating a singlet oxygen- or peroxyl radical-mediated process. Photolysis of Acr-I in the presence of a mononucleotide (GMP) or a non-self-complementary dinucleotide (uridylyl-[3'-5']-cytidine-UpC) does not lead to fragmentation and base release. Similarly, photolysis of the Acr-NH2/(CpG)2 complex does not lead to fragmentation and base release. The data indicate that photolysis of an iodinated intercalator bound to CpG or plasmid DNA generates an intercalated aryl radical and that the reactive intermediate initiates a sequence of reactions that efficiently nick nucleic acids. The inactivation of lambda phage sensitized by Acr-I with UV (350 nm) light is oxygen independent but with visible (420 nm) light is strongly oxygen dependent. The Acr-I fluoresces more intensely when excited at 446 than at 376 nm. Thus, UV photolysis may lead to C-I bond homolysis and free radical formation, a process that is not energetically feasible with visible light. The results demonstrate the difficulty of extrapolating model studies involving simple molecules and DNA to understanding the mechanism of viral inactivation with a particular sensitizer.
Direct discrimination of structured light by humans (2020)

We predict and experimentally verify an entoptic phenomenon through which humans are able to perceive and discriminate optical spin-orbit states. Direct perception and discrimination of these particular states of light with polarization-coupled spatial modes is possible through the observation of distinct profiles induced by the interaction between polarization topologies and the radially symmetric dichroic elements that are centered on the foveola in the macula of the human eye. A psychophysical study was conducted where optical states with a superposition of right and left circular polarization coupled to two different orbital angular momentum (OAM) values ([Formula: see text] and [Formula: see text]) were directed onto the retina of participants. The number of azimuthal fringes that a human sees when viewing the spin-orbit states is shown to be equal to the number (N) of radial lines in the corresponding polarization profile of the beam, where [Formula: see text] The participants were able to correctly discriminate between two states carrying OAM [Formula: see text] and differentiated by [Formula: see text] and [Formula: see text], with an average success probability of 77.6% (average sensitivity [Formula: see text], [Formula: see text], [Formula: see text]). These results enable methods of robustly characterizing the structure of the macula, probing retina signaling pathways, and conducting experiments with human detectors and optical states with nonseparable modes.
Increased semantic priming in patients with dementia of the Alzheimer's type (1994)

Semantic priming on a lexical decision task(LDT) was examined in 50 patients with mild to moderate dementia of the Alzheimer's Type(DAT), and 25 normal age-matched controls. DAT patients were slower in their responses, and showed significantly greater priming effects (mean 54 ms vs. 27 ms in controls). The size of the priming effect correlated with the speed of response on the LDT task for the individual DAT patients but not for controls. Twenty of the DAT patients (vs. one control) showed priming greater than 60 ms. This subgroup of DAT patients with "hyperpriming" was slower than the nonhyperpriming group on "yes" responses to targets preceded by unassociated prime words and more impaired on tests of clock drawing and verbal fluency. Slowing of responses alone, however, seems unable to account for the presence of increased priming in DAT patients. Its presence may reflect semantic memory deficits, as well as impaired attentional processing and supervisory control systems. The exact mechanism of this increased priming remains to be established.
Investigation of the presence of rod-shaped bacteria on food surface via elastic light scattering (2012)

We investigated the presence and related signal-to-noise ratio (SNR) of rod-shaped bacteria on a produce surface using elastic scattering. The theoretical noise was defined as a scattering signal from a rough produce surface while the signal was defined as a scattering signal from the increasing numbers of rod-shaped bacteria on the produce surface. In this research, we measured the surface topography of a tomato using BioAFM to provide the quantitative nature of the surface roughness which was, in turn, modeled with the discrete dipole approximation (DDA) for an accurate estimation of the background scattering signature. Then we included the DDA model of rod-shaped bacteria and calculated the combined elastic scattering signature in the upper hemispherical space with different polarizations, wavelengths, and incident angles. The total scattering cross-section (TSC) and partial scattering cross-section (PSC) were both computed on six predefined aperture locations. The results indicate that, upon proper selection of the wavelength and incident angle, it was possible to provide the minimum number of bacteria (~32) to provide a differentiable elastic scattering signal from the produce surface.
1H, 13C, 15N and 195Pt NMR studies of Au(III) and Pt(II) chloride organometallics with 2‐phenylpyridine (2009)

(1)H, (13)C, (15)N and (195)Pt NMR studies of gold(III) and platinum(II) chloride organometallics with N(1),C(2')-chelated, deprotonated 2-phenylpyridine (2ppy*) of the formulae [Au(2ppy*)Cl(2)], trans(N,N)-[Pt(2ppy*)(2ppy)Cl] and trans(S,N)-[Pt(2ppy*)(DMSO-d(6))Cl] (formed in situ upon dissolving [Pt(2ppy*)(micro-Cl)](2) in DMSO-d(6)) were performed. All signals were unambiguously assigned by HMBC/HSQC methods and the respective (1)H, (13)C and (15)N coordination shifts (i.e. differences between chemical shifts of the same atom in the complex and ligand molecules: Delta(1H)(coord) = delta(1H)(complex) - delta(1H)(ligand), Delta(13C)(coord) = delta(13C)(complex) - delta(13C)(ligand), Delta(15N)(coord) = delta(15N)(complex) - delta(15N)(ligand)), as well as (195)Pt chemical shifts and (1)H-(195)Pt coupling constants discussed in relation to the known molecular structures. Characteristic deshielding of nitrogen-adjacent H(6) protons and metallated C(2') atoms as well as significant shielding of coordinated N(1) nitrogens is discussed in respect to a large set of literature NMR data available for related cyclometallated compounds.
Translocations among antibody genes in human cancer. (1985)

The characteristic chromosomal translocations that occur in certain human malignancies offer opportunities to understand how two gene systems can affect one another when they are accidentally juxtaposed. In the case of Burkitt's lymphoma, such a translocation joins the cellular oncogene, c-myc, to a region encoding one of the immunoglobulin genes. In at least one example, the coding sequence of the rearranged c-myc gene is identical to that of the normal gene, implying that the gene must be quantitatively, rather than qualitatively, altered in its expression if it is to play a role in transformation. One might expect to find the rearranged c-myc gene in a configuration that would allow it to take advantage of one of the known immunoglobulin promoters or enhancer elements. However, the rearranged c-myc gene is often placed so that it can utilize neither of these structures. Since the level of c-myc messenger RNA is often elevated in Burkitt cells, the translocation may lead to a deregulation of the c-myc gene. Further, since the normal allele in a Burkitt cell is often transcriptionally silent in the presence of a rearranged allele, a model for c-myc regulation is suggested that involves a trans-acting negative control element that might use as its target a highly conserved portion of the c-myc gene encoding two discrete transcriptional promoters.
Controlling light polarization by swirling surface plasmons (2018)

Light polarization is a key aspect of modern optics. Current methods for polarization control utilize birefringence and dichroism of anisotropic materials or of arrays of anisotropically shaped nanostructures. Based on collective optical effects, the resulting components remain much larger than the wavelength of light, which limits design strategies. Here, we present a travelling-wave plasmonic antenna that overcomes this limit using a gold-coated helical nanowire non-radiatively fed with a dipolar aperture nanoantenna. Our non-resonant hybrid nanoantenna enables tightly confined circularly polarized light by swirling surface plasmons on the subwavelength scale and taking advantage of optical spin-orbit interaction. Four closely packed circularly polarized light sources of opposite handedness and tunable intensities are demonstrated. By reaching near-field interaction between neighboring nanoantennas, we obtain a highly miniaturized wave plate whose polarization properties have never previously been demonstrated.
Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model (2011)

A variable dielectric model based on residue types for better description of protein-ligand electrostatics in MM-GBSA scoring is reported. The variable dielectric approach provides better correlation with binding data and reduces the score dynamic range, typically observed in the standard MM-GB/SA method. The latter supports the view that exaggerated enthalpic separation between weak and potent compounds due to the lack of shielding effects in the model is greatly responsible for the wide scoring spread.
Thermo-optically tunable linear photonic crystal microcavities in advanced SOI CMOS technology (2014)

We demonstrate linear photonic crystal (PhC) microcavities with thermo-optic tuning capability realized in the IBM 45nm (12SOI) silicon-on-insulator CMOS microelectronics fabrication process. The PhC microcavities can be used as efficient integrated optical wavelength add-drop filters. The cavity is created in the monocrystalline silicon transistor body layer of the CMOS process, with a resonance wavelength of 1520 nm. The cavity device layer is doped to lower the electrical resistance so that current sent through it generates local heating with reasonable drive voltages. The dissipated heat increases the temperature of the cavity and, because of the high thermo-optic coefficient of silicon, increases the index of refraction, shifting the resonance wavelength. This method should be more effective than an adjacent metal or polysilicon heater because the hot spot is right in the middle of the optical mode of the cavity.
Diagnosis of osteomyelitis by MR imaging (1988)

Bone scans are highly sensitive for the diagnosis of acute osteomyelitis, but the difficulty of separating bone-marrow processes from soft-tissue disease limits the specificity and accuracy. A diagnostic technique capable of distinguishing bone-marrow processes from soft-tissue disease would improve the diagnostic accuracy of osteomyelitis. To evaluate the use of MR in the diagnosis of osteomyelitis, MR examinations were performed in 35 patients with suspected acute osteomyelitis. Twelve of these were proved to have osteomyelitis either by surgery (nine patients) or by clinical follow-up (three patients). In the other 23, osteomyelitis was excluded by surgery (12 patients) or by the clinical course (11 patients). Evidence of osteomyelitis on MR consisted of abnormalities of the bone marrow with decreased signal intensity on the T1-weighted images and increased signal intensity on the T2-weighted or short-T1 inversion recovery (STIR) images. MR and bone scintigraphy were interpreted by two radiologists who were given no clinical information other than to rule out osteomyelitis. The sensitivities of MR and static bone scan were 100% for bone-marrow abnormality. Because bone-marrow abnormality in osteomyelitis associated with healing fractures was incorrectly diagnosed by MR (one case) and bone scintigraphy (two cases), the sensitivities of MR and scintigraphy for the diagnosis of osteomyelitis were 92% and 82%, respectively. The specificities of MR and scintigraphy were 96% and 65%, respectively (p less than .05). The overall accuracy for the diagnosis of osteomyelitis was 94% for MR and 71% for bone scan (p less than .05). Because of its ability to separate soft-tissue disease from underlying bone marrow, MR may be used to evaluate patients with positive bone scintigraphy to improve the specificity and accuracy of diagnosis for osteomyelitis.
Detection and biochemical characteristics of the receptor for complexes of soluble CD14 and bacterial lipopolysaccharide (1997)

Soluble CD14 (sCD14) has been found to bind LPS and mediate LPS activation of several cell types. It has been postulated that sCD14-LPS complexes induce cell responses by interacting with a cell surface structure, which, in turn, triggers cell activation. There has been no biochemical evidence, however, for a direct interaction of sCD14 with a cell surface structure, and the putative receptor has not been identified. To rigorously test this hypothesis, we studied the interaction of human rsCD14 with cells in the absence of serum and in the presence and the absence of LPS. We found 1) there was specific and saturable binding of 125I-sCD14, indicative of a typical receptor-ligand interaction, to several cell types, including endothelial cells, epithelial cells, astrocytes, and human monocytes; 2) specific binding to all the cell types and IL-6 induction in membrane-bound CD14 (mCD14)-negative cells occurred only when both sCD14 and LPS were present; 3) competitive displacement experiments of 125I-sCD14 binding to astrocytes and Scatchard plots revealed a binding of high affinity (Kd = 3.3 +/- 0.4 nM) and approximately 25,000 single class binding sites/cell; 4) the steady state for the association of 125I-sCD14 was obtained after 180-200 min; 5) chemical cross-linking experiments revealed the association of sCD14 with a binding structure of approximately 216 kDa; 6) binding of 125I-sCD14 to CD14-expressing cell transfectants was about 50% lower than that to nontransfected cells. Maximal binding, however, was recovered after removing mCD14, suggesting that the sCD14-LPS receptor may also interact with mCD14. These results provide direct biochemical evidence for the existence of a cell surface signal-mediating binding structure for LPS-bearing sCD14 and suggest that this structure may represent the signaling unit of the postulated multimeric LPS receptor in mCD14-bearing cells.
Diastereoselectivity is in the Details: Minor Changes Yield Major Improvements to the Synthesis of Bedaquiline (2022)

Bedaquiline is a crucial medicine in the global fight against tuberculosis, yet its high price places it out of reach for many patients. Herein, we describe improvements to the key industrial lithiation-addition sequence that enable a higher yielding and therefore more economical synthesis of bedaquiline. Prioritization of mechanistic understanding and multi-lab reproducibility led to optimized reaction conditions that feature an unusual base–salt pairing and afford a doubling of the yield of racemic bedaquiline. We anticipate that implementation of these improvements on manufacturing scale will be facile, thereby substantially increasing the accessibility of this essential medication.
PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation (2016)

The PAF complex (Paf1C) has been shown to regulate chromatin modifications, gene transcription, and RNA polymerase II (PolII) elongation. Here, we provide the first genome-wide profiles for the distribution of the entire complex in mammalian cells using chromatin immunoprecipitation and high throughput sequencing. We show that Paf1C is recruited not only to promoters and gene bodies, but also to regions downstream of cleavage/polyadenylation (pA) sites at 3' ends, a profile that sharply contrasted with the yeast complex. Remarkably, we identified novel, subunit-specific links between Paf1C and regulation of alternative cleavage and polyadenylation (APA) and upstream antisense transcription using RNAi coupled with deep sequencing of the 3' ends of transcripts. Moreover, we found that depletion of Paf1C subunits resulted in the accumulation of PolII over gene bodies, which coincided with APA. Depletion of specific Paf1C subunits led to global loss of histone H2B ubiquitylation, although there was little impact of Paf1C depletion on other histone modifications, including tri-methylation of histone H3 on lysines 4 and 36 (H3K4me3 and H3K36me3), previously associated with this complex. Our results provide surprising differences with yeast, while unifying observations that link Paf1C with PolII elongation and RNA processing, and indicate that Paf1C subunits could play roles in controlling transcript length through suppression of PolII accumulation at transcription start site (TSS)-proximal pA sites and regulating pA site choice in 3'UTRs.
Buller från godståg : detaljerad kartläggning av buller från godståg samt utvärdering av skärmar (2003)

Validerat; 20101217 (root)
Mitochondrial sequence variants in patients with schizophrenia. (1998)

To investigate whether mitochondrial mutations underly susceptibility to schizophrenia, we sequenced the mtDNAs of two unrelated Swedish patients with schizophrenia and low cytochrome oxidase activity and two maternally related Scottish patients from a family with suspected maternal inheritance of the disease. We found five substitutions in coding regions that have not previously been described as polymorphisms. These new substitutions were studied in 81 schizophrenic patients and five control groups from Sweden and Scotland and found to differ in frequency between populations, emphasizing the importance of using large and well-defined control materials for evaluating the association of mtDNA mutations with disease. The results do not lend strong support to the association of a particular mtDNA substitution with increased risk for schizophrenia. However, the trend towards a higher frequency of substitutions in the patients deserves further attention.