gebhart/patrepeval huggingface dataset:
Immunologic responses to gene transfer into mice via the polymeric immunoglobulin receptor. (1996)

The respiratory epithelium is the primary target tissue for gene therapy of cystic fibrosis, and several methods of gene transfer permit the introduction of the gene encoding the normal cystic fibrosis transmembrane conductance regulator into cells of the respiratory tract in animals. DNA complexes based on Fab antibodies to secretory component have been used to mediate the delivery and uptake of expression plasmids into the respiratory tract via the polymeric immunoglobulin receptor both in vitro and in vivo. We evaluated the efficacy of gene transfer after several administrations of the DNA complexes, and examined the immunogenicity and toxicity of repetitive administration of anti-secretory component Fab-based complexes. Mice received single or multiple injections of the DNA complexes containing the plasmid pGL2 every 21 days after the initial treatment, and lysates from the lung and liver were assayed for luciferase expression. Luciferase activity was detected in the lungs of mice that received a single injection of the DNA complexes, whereas transgene expression was significantly lower in the mice that received three injections of the DNA complexes (17338 +/- 5469 integrated light units/mg and 3771 +/- 1778 integrated light units/mg, respectively). Serum samples from animals that underwent single or multiple injections were analyzed for a serologic response against the conjugate-DNA complexes by ELISA. No anticomplex antibodies were detected in the mice after a single injection. An escalating antibody response was noted with increasing number of treatments with the conjugate-DNA complexes. This serologic response was directed exclusively against the rabbit-derived, anti-secretory component (anti-SC) Fab antibody, and not against either the plasmid DNA or poly-L-lysine. Single injection of the conjugate-DNA complexes did not result in the consumption of circulating complement. Using direct immunofluorescence, perivascular deposits of immunoglobulin G were found in the liver of animals that received three treatments; no such deposition was detected in the lungs or kidneys. No increase in inflammatory cell infiltrates was observed in tissues after single and repeated injections of the DNA complexes. Thus, we conclude that repeated injections of the anti-SC Fab-based complexes evoked a humoral immune response against the heterologous Fab portion of the complex that was associated with reduced efficiency of gene transfer.
Internet routing instability (1998)

This paper examines the network interdomain routing information exchanged between backbone service providers at the major US public Internet exchange points. Internet routing instability, or the rapid fluctuation of network reachability information, is an important problem currently facing the Internet engineering community. High levels of network instability can lead to packet loss, increased network latency and time to convergence. At the extreme, high levels of routing instability have led to the loss of internal connectivity in wide-area, national networks. We describe several unexpected trends in routing instability, and examine a number of anomalies and pathologies observed in the exchange of inter-domain routing information. The analysis in this paper is based on data collected from border gateway protocol (BGP) routing messages generated by border routers at five of the Internet core's public exchange points during a nine month period. We show that the volume of these routing updates is several orders of magnitude more than expected and that the majority of this routing information is redundant, or pathological. Furthermore, our analysis reveals several unexpected trends and ill-behaved systematic properties in Internet routing. We finally posit a number of explanations for these anomalies and evaluate their potential impact on the Internet infrastructure.
Stomatal Opening Mechanism of CAM Plants (2010)

Stomata usually open when leaves are transferred from darkness to light. However, reverse-phase stomatal opening in succulent plants has been known. CAM plants such as cacti and Opuntia ficus–indica achieve their high water use efficiency by opening their stomata during the cool, desert nights and closing them during the hot, dry days. Signal transduction pathway for stomatal opening by blue light photoreceptors including phototropins and the carotenoid pigment zeaxanthin has been suggested. Blue light regulated signal transduction pathway on stomatal opening could not be applied to CAM plants, but the most possible theory for a nocturnal response of stomata in CAM plants is photoperiodic circadian rhythm.
Direct Recording of Integrated Band Intensities from a Linear Wavelength Spectrometer (1963)

Instrumentation that allows direct recording of integrated band intensities from a double-beam spectrometer is described. A potentiometer is geared directly to the linear wavelength drive of the spectrometer and used to servo the chart drive of a strip-chart recorder so that a linear wavenumber scale is produced. A maximum scan of 2 μ is possible, the 2 μ being located at the operator’s discretion in the 4–18 μ range of the spectrometer. A logarithmic potentiometer has been incorporated into the recorder to convert the transmittance data into optical density units while the integration is carried out with a, continuous ball-and-disk integrator.
Triphosphorus macrocycle complexes of divalent Group 6 transition metals; crystal structure of bromotricarbonyl-[1,5,9-tris(isopropyl)-1,5,9-triphosphacyclododecane]-molybdenum(II) tetraphenylborate (1995)

New triphosphamacrocycle complexes of molybdenum(II) and tungsten(II) have been prepared by oxidative addition of halogens to molybdenum and tungsten tricarbonyl complexes of 1,5,9-triphosphacyclododecane and tritertiary phosphine analogues. The behaviour of these macrocycle complexes is similar to that of previously reported examples with monodentate tertiary phosphines and the metal(0) precursors give rise initially to seven-co-ordinate salts containing a [M(CO)3X(L)]+ cation (L = tridentate triphosphamacrocycle) with a halide anion which may be exchanged for other counter ions. The seven-co-ordinate complexes are all fluxional in solution and give rise to temperature-variant NMR spectra. At the low-temperature limit an AB2 pattern was observed in the 31P NMR spectra of all the new complexes. The salts all convert slowly into the neutral seven-co-ordinate dicarbonyldihalogeno complexes [M(CO)2X2(L)] in solution. These are the first examples of metal complexes of the 1,5,9-triphosphacyclododecane family other than the metal(0) tricarbonyltemplate complexes upon which the macrocyclic ligands were originally made.
Broadly neutralizing human monoclonal antibodies: a novel resource against influenza viruses (2013)

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[NO TITLE AVAILABLE] (2011)

We demonstrate the feasibility of using effective medium theory to reduce the computational complexity of full-wave models of inductors that are placed over interconnects. Placing inductors over interconnects is one way that designers can tackle the problem of reducing overall chip size, however this has heretofore been a difficult option to evaluate because of the prohibitive memory requirements and run times for detailed simulations of the inductor. Here we replace the interconnects with a homogeneous equivalent layer that mimics their impact on the inductor to within 2% error, but reducing runtime and memory use by 90% or more.
TT-pocket/HIRAN: binding to 3′-terminus of DNA for recognition and processing of stalled replication forks (2022)

Stalled replication forks need to be swiftly detected and protected from collapse and the cause for fork stall be removed to restore the active replication fork. In bacteria, stalled forks are recognized and stabilized by PriA, a DEXH-type helicase, which also facilitates reassembly of an active replication fork. A TT-pocket (three-prime terminus binding pocket) present in the N-terminal segment of PriA plays a crucial role in stabilization of the stalled forks by specifically binding to the 3$^\prime$-terminus of the nascent leading strand. Eukaryotic proteins, Rad5/HLTF, contain a TT-pocket related domain, HIRAN, that specifically binds to 3'-terminus of DNA and play a role in stalled fork processing. While the TT-pocket of PriA facilitates the formation of an apparently stable and immobile complex on a fork with a 3'-terminus at the fork junction, HIRAN of Rad5/HLTF facilitates fork regression by itself. A recent report shows that HIRAN can displace 3 nucleotides at the end of the duplex DNA, providing mechanistic insight into how stalled forks are reversed in eukaryotes. In this article, I will compare the roles of 3'-terminus binding domains in stalled fork processing in prokaryotes and in eukaryotes.
Synthesis of polychlorinated unsaturated cyclic dicarboxylic acid imides (2008)

A procedure has been developed for the synthesis of 3,4,5,6-tetrachlorocyclohexa-3,5-diene-1,2- and 7,8,9,10-tetrachlorobicyclo[4.4.0]deca-7,9-diene-3,4-dicarboximides from the corresponding 3,4,5,6,7,7-hexachlorobicyclo[2.2.1]hept-5-ene-2,3- and 1,8,9,10,11,11-hexachlorotricyclo[6.2.1.02,7]undec-9-ene-4,5-dicarboxylic anhydrides and pyridine in dimethylformamide. Steric structure of the products has been studied.
The ShiA protein encoded by theShigella flexneriSHI-2 pathogenicity island attenuates inflammation (2003)

Shigella spp. are the aetiologic agents of dysentery, a severe diarrhoeal syndrome characterized by acute inflammation in the colon. The inflammatory response, which includes recruitment of polymorphonuclear leukocytes (PMN), damages the colonic mucosa and exacerbates the infection. Shigella encodes a pathogenicity island (PAI), SHI-2, which is localized in a region of the chromosome linked to the induction of inflammation. Surprisingly, SHI-2 deletion mutants induce a stronger inflammatory response than wild-type Shigella as measured by increased villus blunting, increased PMN infiltration and induction of apoptosis in a rabbit ileal loop model of shigellosis. Mutational analysis mapped the hyper-inflammatory phenotype to a single gene, shiA. Similar to SHI-2 deletion mutants, infection with a shiA mutant strain induces dramatically elevated levels of inflammation when compared to the wild-type strain. Furthermore, infection with a wild-type strain containing multiple copies of shiA results in fewer infiltrating PMN and apoptotic cells, as well as preservation of a normal villus architecture at the site of infection, thus acting in a dominant fashion over the pro-inflammatory mechanisms of Shigella. The molecular mechanism of action of ShiA is independent of any in vitro phenotype associated with Shigella virulence. Our data suggest that ShiA allows Shigella to attenuate the host inflammatory response in a novel manner.
Cover Image, Volume 10, Issue 4 (2016)

The cover image, by Farah Binti Ahmad et al., is based on the Modeling and Analysis Evaluation of oil production from oil palm empty fruit bunch by oleaginous microorganisms , DOI: 10.1002/bbb.1645 . Photo Credit: Farah Binti Ahmad. image
Perfusion Measurement in Brain Gliomas with Intravoxel (2013)

BACKGROUND AND PURPOSE: Intravoxel incoherent motion MRI has been proposed as an alternative method to measure brain perfusion. Our aim was to evaluate the utility of intravoxel incoherent motion perfusion parameters (the perfusion fraction, the pseudodiffusion coefficient, and the flow-related parameter) to differentiate high- and low-grade brain gliomas. MATERIALS AND METHODS: The intravoxel incoherent motion perfusion parameters were assessed in 21 brain gliomas (16 high-grade, 5 low-grade). Images were acquired by using a Stejskal-Tanner diffusion pulse sequence, with 16 values of b (0 –900 s/mm 2 ) in 3 orthogonal directions on 3T systems equipped with 32 multichannel receiver head coils. The intravoxel incoherent motion perfusion parameters were derived by fitting the intravoxel incoherent motion biexponential model. Regions of interest were drawn in regions of maximum intravoxel incoherent motion perfusion fraction and contralateral control regions. Statistical significance was assessed by using the Student t test. In addition, regions of interest were drawn around all whole tumors and were evaluated with the help of histograms. RESULTS: In the regions of maximum perfusion fraction, perfusion fraction was significantly higher in the high-grade group (0.127 0.031) than in the low-grade group (0.084 0.016, P .001) and in the contralateral control region (0.061 0.011, P .001). No statistically significant difference was observed for the pseudodiffusion coefficient. The perfusion fraction correlated moderately with dynamic susceptibility contrast relative CBV (r 0.59). The histograms of the perfusion fraction showed a “heavy-tailed” distribution for high-grade but not low-grade gliomas. CONCLUSIONS: The intravoxel incoherent motion perfusion fraction is helpful for differentiating high- from low-grade brain gliomas. ABBREVIATIONS: D diffusion coefficient; D* pseudodiffusion coefficient; f perfusion fraction; fD* flow-related parameter; IVIM intravoxel incoherent motion
Bioaccessibility of potentially toxic elements in mine residue particles (2021)

Mining companies used to abandon tailing heaps in countryside regions of Mexico and other countries. Mine residues (MRs) contain a high concentration of potentially toxic elements (PTE). The wind can disperse dust particles (<100 μm) and once suspended in the atmosphere, can be ingested or inhaled; this is a common situation in arid climates. Nowadays, there is little information on the risk of exposure to PTEs from particulate matter dispersed by wind. The pseudo-total PTE in bulk and fractionated MR after aqua regia digestion, the inhalable bioaccessibility with Gamble solution (pH = 7.4), and the gastric bioaccessibility with 0.4 M glycine solution at pH 1.5 were determined. As and Pb chemical species were identified by X-ray absorption near-edge structure (XANES) spectroscopy. The highest rate of dispersion was observed with 74-100 μm particles (104 mg m-2 s-1); in contrast, particles <44 μm had the lowest rate (26 mg m-2 s-1). The highest pseudo-total As (35 961 mg kg-1), Pb (3326 mg kg-1), Cd (44 mg kg-1) and Zn (up to 4678 mg kg-1) concentration was in the <20 μm particles and As in the 50-74 μm (40 236 mg kg-1) particles. The highest concentration of inhaled bioaccessible As (343 mg kg-1) was observed in the <20 μm fraction and the gastric bioaccessible As was 744 mg kg-1, Pb was 1396 mg kg-1, Cd was 19.2 mg kg-1, and Zn was 2048 mg kg-1. The predominant chemical As species was arsenopyrite (92%), while 54% of Pb was in the adsorbed form. Erodible particle matter is a potential risk for humans in case of inhalation or ingestion.
VentRa. Validation study of the ventricle feature estimation and classification tool to differentiate behavioral variant frontotemporal dementia from psychiatric disorders and other degenerative diseases (2022)

ABSTRACT Introduction Lateral ventricles are reliable and sensitive indicators of brain atrophy and disease progression in behavioral variant frontotemporal dementia (bvFTD). Here we validate our previously developed automated tool using ventricular features (known as VentRa) for the classification of bvFTD vs a mixed cohort of neurodegenerative, vascular, and psychiatric disorders from a clinically representative independent dataset. Methods Lateral ventricles were segmented for 1110 subjects - 14 bvFTD, 30 other Frontotemporal Dementia (FTD), 70 Lewy Body Disease (LBD), 898 Alzheimer Disease (AD), 62 Vascular Brain Injury (VBI) and 36 Primary Psychiatric Disorder (PPD) from the publicly accessible National Alzheimer’s Coordinating Center dataset to assess the performance of VentRa. Results Using ventricular features to discriminate bvFTD subjects from PPD, VentRa achieved an accuracy of 84%, 71% sensitivity and 89% specificity. VentRa was able to identify bvFTD from a mixed age-matched cohort (i.e., Other FTD, LBD, AD, VBI and PPD) and to correctly classify other disorders as ‘not compatible with bvFTD’ with a specificity of 83%. The specificity against each of the other individual cohorts were 80% for other FTD, 83% for LBD, 83% for AD and 84% for VBI. Discussion VentRa is a robust and generalizable tool with potential usefulness for improving the diagnostic certainty of bvFTD, particularly for the differential diagnosis with PPD.
A Memory Controller that Reduces Latency of Cached SDRAM (2005)

The proposed controller has two main control schemes, address-alignment control and dummy-cache control. These two schemes cooperatively control cached SDRAM to reduce its latency. Testing of the controller using benchmark programs demonstrated that latency was reduced 25% and execution time was reduced 13% compared to those of a sense-amplifier cache controller for standard SDRAM. The proposed controller requires 9.2 Kgates at a supply voltage of 1.8 V and an operating frequency of 133 MHz.
Leukocyte recruitment into human skin transplanted onto severe combined immunodeficient mice induced by TNF-alpha is dependent on E-selectin. (1994)

Abstract In order to study the in vivo role of E-selectin in human inflammation, we have developed a model in which human skin is transplanted onto severe combined immunodeficient (SCID) mice. The grafted skin closely resembles normal skin and retains its human vasculature. After intradermal injection of rTNF-alpha, human E-selectin was rapidly up-regulated on dermal microvessels, with significant expression (determined immunohistochemically) at 1 h postinjection and maximum expression at 2 h postinjection. To study the functional role of E-selectin, a murine Ab against human E-selectin (mAb HEL 3/2) was developed that inhibited the in vitro adhesion of both human U937 cells and murine 32D cells to TNF-alpha-stimulated human endothelial cells. After intradermal injection of TNF-alpha, large numbers of murine leukocytes migrated into the grafts within 2 h. Intravenous injection of the antihuman E-selectin mAb 3/2 completely inhibited murine white blood cell (WBC) transmigration into the skin grafts, but an isotype-matched control Ab that also bound to human endothelium had no effect. Antihuman E-selectin mAb 3/2 was also able to inhibit the migration of i.v. 51Cr-labeled human neutrophils. These findings demonstrate that E-selectin is important in early white blood cell adhesion events and is required for TNF-alpha-induced white blood cell transmigration in the human/SCID mouse chimeric model.
A Study of Unsharp Masking on HDR Visualization on low Dynamic Range Devices (2020)

To visualize HDR contents on low dynamic range displays, a fast and efficient TMO is often preferred. One way to achieve this is to use a Global TMO. However, Global TMO often results in poor contrast tone-mapped images and often needs a postprocess that enhances the contrast, such as Unsharp Masking. This work illustrates that such Unsharp Masking can be directly integrated into several global TMOs, resulting in an alternative framework to apply the Unsharp Masking to the HDR visualization pipeline. The proposed framework is fast and delivers images with a proper contrast without the need for the additional image sharpening at the post process.
Biotransformation of terodiline. III. Opposed stereoselectivity in the benzylic and aromatic hydroxylations in rat liver microsomes (1987)

1. Terodiline (N-tert-butyl-4,4-diphenyl-2-butylamine) is a racemic drug with anticholinergic and/or calcium antagonistic activity, which is subject to renewed interest as a potential remedy for urinary incontinence. As part of the current investigations on terodiline, the metabolism of its enantiomers is being investigated. 2. The metabolism of the enantiomers of terodiline in rat liver microsomes is slow, as for the racemate, though the S-enantiomer is metabolized more rapidly than its optical antipode. Phenobarbitone pretreatment of the rats enhances the metabolism with a marked increase in the conversion of the S-enantiomer. 3. While aromatic p-hydroxylation greatly exceeds benzylic oxidation in the metabolism of R-terodiline, this situation is reversed in the metabolism of S-terodiline. Moreover, the rate of aromatic p-hydroxylation of racemic terodiline follows that of R-terodiline, while the rate of benzylic hydroxylation of racemic terodiline follows that of S-terodiline. Phenobarbital pretreatment of the rats had little or no effect on aromatic p-hydroxylation but markedly increased benzylic oxidation. 4. Separation of the mixture of p-hydroxylated metabolites into diastereomeric pairs showed that their composition is highly dependent on which form of terodiline is used as substrate. 5. The results from the study are compatible with the participation of multiple forms of cytochrome P-450 enzymes.
Location-Sharing Technologies: Privacy Risks and Controls (2018)

Due to the ability of cell phone providers to use cell phone towers to pinpoint users’ locations, federal E911 requirements, the increasing popularity of GPS-capabilities in cellular phones, and the rise of cellular phones for Internet use, a plethora of new applications have been developed that share users’ real-time location information online [27]. This paper evaluates users’ risk and benefit perceptions related to the use of these technologies and the privacy controls of existing location-sharing applications. We conducted an online survey of American Internet users (n = 587) to evaluate users’ perceptions of the likelihood of several location-sharing use scenarios along with the magnitude of the benefit or harm of each scenario (e.g. being stalked or finding people in an emergency).We find that although the majority of our respondents had heard of location-sharing technologies (72.4%), they do not yet understand the potential value of these applications, and they have concerns about sharing their location information online. Most importantly, participants are extremely concerned about controlling who has access to their location. Generally, respondents feel the risks of using location-sharing technologies outweigh the benefits. Respondents felt that the most likely harms would stem from revealing the location of their home to others or being stalked. People felt the strongest benefit were being able to find people in an emergency and being able to track their children. We then analyzed existing commercial location-sharing applications’ privacy controls (n = 89). We find that while location-sharing applications do not offer their users a diverse set of rules to control the disclosure of their location, they offer a modicum of privacy.
Plant-Microbe Interactions: Chemical Diversity in Plant Defense (2009)

The chemical diversity within the plant kingdom is likely to be a consequence of niche colonization and adaptive evolution. Plant-derived natural products have important functions in defense. They also have broader ecological roles and may in addition participate in plant growth and development. Recent data suggest that some antimicrobial phytochemicals may not serve simply as chemical barriers but could also have functions in defense-related signaling processes. It is important, therefore, that we should not to be too reductionist in our thinking when endeavoring to understand the forces and mechanisms that drive chemical diversification in plants.