gebhart/patrepeval huggingface dataset:
Comparison between dual time point FDG PET imaging and partial volume correction of the standardized uptake value in the evaluation of pulmonary nodules (2006)

610 Objectives: The purpose of this study is to compare the diagnostic accuracy of two methods used for characterizing lung nodules in FDG PET: Dual time point imaging and partial volume correction for the first time point SUV. Methods: Two hundred sixty eight patients were included in this study (161men, 107 women, age range: 41–92 years). All patients had pulmonary nodules (0.5- 3 cm) discovered by computed tomography (CT), and the diagnosis was confirmed by biopsy or by follow up CT scanning. All patients underwent PET of the thorax at 2 time points: first scan at 60min post injection and second scan at 90 minutes post injection. The maximum standardized uptake value (SUV) was calculated for both time points. Partial volume correction for the first scan was applied as described in the literature using lung nodule size on CT to obtain volume corrected SUV (corSUV). Results: Biopsy and follow up revealed 72 patients with malignant lung nodules, and 196 patients with benign nodules. With dual time point scanning, when we considered any increase in SUV between initial and delayed images as the criterion for malignancy, the sensitivity, specificity and accuracy were 81%, 95% ,and 91% respectively. When we considered any increase or no change in SUV between initial and delayed images as the criterion for malignancy, the sensitivity, specificity, and accuracy were 92%, 92%, and 92% respectively. When considering corSUV of 3 as a threshold for malignancy using the partial volume correction of SUV (at time point 1), the sensitivity, specificity, and accuracy were 82%, 87%, and 86% respectively. For a threshold corSUV of 2.5 the sensitivity, specificity, and accuracy were 90%, 80% and 83% respectively, whereas, for a threshold corSUV of 2.0 sensitivity, specificity and accuracy were 96%, 74% and 80% respectively. Conclusions: Dual time point FDG PET imaging using any increase and/or no change in SUV between initial and delayed images as the criterion for malignancy, has significantly higher accuracy in the characterization of malignant lung nodules as compared to single time point corSUV.
Osteoarthritis: New Strategies for Transport and Drug Delivery Across Length Scales (2020)

Osteoarthritis (OA) is the fourth leading cause of disability in adults. Yet, few viable pharmaceutical options exist for pain abatement and joint restoration, aside from joint replacement at late and irreversible stages of the disease. From the first onset of OA, as joint pain increases, individuals with arthritis increasingly reach for drug delivery solutions, from taking oral glycosaminoglycans (GAGs) bought over the counter from retail stores (e.g., Costco) to getting injections of viscous, GAG-containing synovial fluid supplement in the doctor's office. Little is known regarding the efficacy of delivery mode and/or treatment by such disease-modulating agents. This Review addresses the interplay of mechanics and biology on drug delivery to affected joints, which has profound implications for molecular transport in joint health and (patho)physiology. Multiscale systems biology approaches lend themselves to understand the relationship between the cell and joint health in OA and other joint (patho)physiologies. This Review first describes OA-related structural and functional changes in the context of the multilength scale anatomy of articular joints. It then summarizes and categorizes, by size and charge, published molecular transport studies, considering changes in permeability induced through inflammatory pathways. Finally, pharmacological interventions for OA are outlined in the context of molecular weights and modes of drug delivery. Taken together, the current state-of-the-art points to a need for new drug delivery strategies that harness systems-based interactions underpinning molecular transport and maintenance of joint structure and function at multiple length scales from molecular agents to cells, tissues, and tissue compartments which together make up articular joints. Cutting edge and cross-length and -time scale imaging represents a key discovery enabling technology in this process.
Proline porter II is activated by a hyperosmotic shift in both whole cells and membrane vesicles of Escherichia coli K12. (1988)

Proline porter II is rapidly activated when nongrowing bacteria are subjected to a hyperosmotic shift (Grothe, S., Krogsrud, R. L., McClellan, D. J., Milner, J. L., and Wood, J. M. (1986) J. Bacteriol. 166, 253-259). Proline porter II was active in membrane vesicles prepared from bacteria grown under optimal conditions, nutritional stress, or osmotic stress. That activity was: (i) dependent on the presence of the energy sources phenazine methosulphate plus ascorbate or D-lactate; (ii) observed only when a hyperosmotic shift accompanied the transport measurement; (iii) inhibited by glycine betaine in a manner analogous to that observed in whole cells; and (iv) eliminated by lesions in proP. Membrane vesicles were able to transport serine but not glutamine and serine transport was reduced by the hyperosmotic shift. In whole cells, proline porter II activity was supported by glucose and by D-lactate in a strain defective for proline porters I and III and the F1F0-ATPase. Glucose energized proline uptake was eliminated by carbonyl cyanide m-chlorophenylhydrazone and KCN as was serine uptake. These results suggested that proline porter II was respiration-dependent and probably ion-linked. Activation of proline porter II in whole cells by sucrose or NaCl was sustained over 30 min, whereas activation by glycerol was transient. Proline porter II was activated by NaCl and sucrose with a half-time of approximately 1 min in both whole cells and membrane vesicles. Thus, activation of proline porter II was reversible. It occurred at a rate comparable to that of K+ influx and much more rapid than the genetic regulatory responses that follow a hyperosmotic shift.
The Association of Tuberculosis and HIV Infection in Burundi (1989)

AIDS and tuberculosis (TB) are both endemic in Bujumbura, Burundi. An 11% failure rate to standard antituberculosis treatment (n = 173) was observed at the Tuberculosis Treatment Center of Bujumbura (CATB) in 1985-1986. All resistant cases (n = 19) were HIV seropositive. Among 328 consecutive cases with tuberculosis at the CATB during a 3 month period in 1986, 54.5% were HIV seropositive, which is five times higher than the prevalence in the general population in Bujumbura. More female patients than male cases were HIV antibody positive (62 versus 49%, respectively; p less than 0.02). Persistent weight loss, cough, and an anergic tuberculin test were more common in the HIV-seropositive group. Among 48 household members of HIV-seropositive patients with tuberculosis, 6 (12.5%) new cases of tuberculosis were identified, compared with none among 28 household members of HIV-seronegative patients with tuberculosis (odds ratio, 3.8; 95% confidence interval, 0.43-33.2). HIV infection is a new risk factor for tuberculosis in Africa, and HIV-infected cases of tuberculosis may be more infectious than HIV-negative patients. The AIDS epidemic may drastically complicate the diagnosis, management, and control of tuberculosis in populations in which both infections are endemic.
Longitudinal changes in regional fat content in HIV-infected children and adolescents (2009)

Although no single pattern of change in regional fat distribution was uniquely associated with HIV, perinatally HIV-infected youth manifest significantly decreased leg fat and increased arm and trunk fat. These differences increase over time and may contribute to cardiovascular disease risk.
Enhanced green laser activation by antireflective gate structures in panel transistors (2008)

Antireflective gate structures of polycrystalline silicon (poly-Si) and silicon dioxide films enable postimplantation green continuous-wave laser annealing of all Si regions of green laser-crystallized panel Si transistors. About 40% of the incident laser-energy penetrates to the channels, owing to antireflective gate structures with the absorptive gate poly-Si, while 65% of the incident laser-energy enters the source/drain regions because of Fresnel reflections at the air/source (drain) interfaces. Such inverted laser-energy profiles and ascendant defect distributions along the channels/junctions/contact regions, yielded continuous, improved epilike Si microstructures over the entire active layer. The electron mobility of the transistors, 620cm2∕Vs, approaches that of integrated-circuits transistors.
A Uremic Pig Model for Peritoneal Dialysis (2022)

With increasing interest in home dialysis, there is a need for a translational uremic large animal model to evaluate technical innovations in peritoneal dialysis (PD). To this end, we developed a porcine model with kidney failure. Stable chronic kidney injury was induced by bilateral subtotal renal artery embolization. Before applying PD, temporary aggravation of uremia was induced by administration of gentamicin (10 mg/kg i.v. twice daily for 7 days), to obtain uremic solute levels within the range of those of dialysis patients. Peritoneal transport was assessed using a standard peritoneal permeability assessment (SPA). After embolization, urea and creatinine concentrations transiently increased from 1.6 ± 0.3 to 7.5 ± 1.2 mM and from 103 ± 14 to 338 ± 67 µM, respectively, followed by stabilization within 1-2 weeks to 2.5 ± 1.1 mM and 174 ± 28 µM, respectively. Gentamicin induced temporary acute-on-chronic kidney injury with peak urea and creatinine concentrations of 16.7 ± 5.3 mM and 932 ± 470 µM respectively. PD was successfully applied, although frequently complicated by peritonitis. SPA showed a low transport status (D/P creatinine at 4 h of 0.41 (0.36-0.53)) with a mass transfer area coefficient of 9.6 ± 3.1, 4.6 ± 2.6, 3.4 ± 2.3 mL/min for urea, creatinine, and phosphate respectively. In conclusion, this porcine model with on-demand aggravation of uremia is suitable for PD albeit with peritoneal transport characterized by a low transport status.
Capillarity‐Driven Fluidic Alignment of Single‐Walled Carbon Nanotubes in Reversibly Bonded Nanochannels (2007)

A simple, scalable method for one-dimensional alignment of single-walled carbon nanotubes (SWCNTs) inside reversibly bonded nanochannels is reported. Nanochannels are used as a guide for introducing a solution containing SWCNTs. Two nanochannels 50 and 200 nm in width are used. Highly oriented, one-dimensional arrays are generated along the channel direction. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2008/z700300_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Sweet-talk: role of host glycosylation in bacterial pathogenesis of the gastrointestinal tract (2011)

Glycosylation is a key modification of proteins and lipids and is involved in most intermolecular and intercellular interactions. The gastrointestinal mucus gel is continuous and can be divided into two layers: a secreted loosely associated layer and a layer firmly attached to the mucosa. In addition, the membrane-bound glycosylated proteins and lipids create a glycocalyx, which remains adherent on each cell and is dynamic and responsive to the physiological state and environment of the cell. The secreted glycans form a mucus gel layer that serves as a physicochemical sensor and barrier network and is primarily composed of mucins and associated peptides. These glycans protect gut epithelial cells from chemical, biological and physical insults and are continuously renewed. Pathogens colonise and invade the host epithelial cells using protein-protein and glycan-lectin interactions. During the process of colonisation and infection, the glycosylation state of both host and pathogen change in response to the presence of the other. This complex modulation of glycan expression critically determines pathogenesis and the host response in terms of structural changes and immune response. In addition, by influencing host immunity and gut glycosylation, the microbiota can further effect protection against pathogens. In this review, the roles of host glycosylation in interactions with two prevalent bacterial pathogens, Campylobater jejuni and Helicobacter pylori, are discussed to illustrate important concepts in pathogenesis.
Therapeutic homology-independent targeted integration in retina and liver (2022)

Challenges to the widespread application of gene therapy with adeno-associated viral (AAV) vectors include dominant conditions due to gain-of-function mutations which require allele-specific knockout, as well as long-term transgene expression from proliferating tissues, which is hampered by AAV DNA episomal status. To overcome these challenges, we used CRISPR/Cas9-mediated homology-independent targeted integration (HITI) in retina and liver as paradigmatic target tissues. We show that AAV-HITI targets photoreceptors of both mouse and pig retina, and this results in significant improvements to retinal morphology and function in mice with autosomal dominant retinitis pigmentosa. In addition, we show that neonatal systemic AAV-HITI delivery achieves stable liver transgene expression and phenotypic improvement in a mouse model of a severe lysosomal storage disease. We also show that HITI applications predominantly result in on-target editing. These results lay the groundwork for the application of AAV-HITI for the treatment of diseases affecting various organs.
<title>All solid state electrochromic device: WO<formula><inf><roman>3</roman></inf></formula>/LiA<formula><inf><roman>l</roman></inf></formula>F<formula><inf><roman>4</roman></inf></formula>:Li/VO<formula><inf><roman>2</roman></inf></formula></title> (1995)

The fabrication of such an all-solid-state EC device using the combination of amorphous WO<SUB>3</SUB> film as the electrochromic layer and VO<SUB>2</SUB> as the counter electrode is studied. Lithiation studies of two transition metal oxides (WO<SUB>3</SUB> and VO<SUB>2</SUB>) were done for their use as base electrochromic layer and counter electrode layer in the solid device. A dry method of lithiation of the device is proposed and characterized completely for it use in the fabrication of EC device. The properties of thermally evaporated LiAlF<SUB>4</SUB> were also studied for its use as the ion conducting layer. Using these three materials an all-solid-state electrochromic device has been fabricated and studied for its use as a `smart window.'
Wear Tolerance, Growth, and Quality of Seashore Paspalum in Response to Nitrogen and Potassium (2001)

Damage from traffic can seriously injure athletic field turfgrass, although fertility regimes can influence wear tolerance. While excess nitrogen (N) can reduce wear tolerance, moderate N has improved tolerance and hastened recovery from injury. Potassium (K) may enhance wear tolerance through regulation of turgor potential. This research was undertaken to determine shoot growth and wear tolerance of seashore paspalum ( Paspalum vaginatum Swartz) to N and K application. Field studies were conducted in 1998 at the Univ. of Georgia Experiment Station, Griffin. Grasses were established on U.S. Golf Association specification greens in 1996. Fertility treatments were applied at annual N rates of 196 and 392 kg·ha -1 and K rates of 92 and 392 kg·ha -1 . The higher N rate increased wear tolerance, shoot growth, shoot density, visual quality, and color of the two ecotypes, AP 10 and AP 14, but reduced their visible range spectral reflectance, indicating greater absorption of photosynthetically active radiation ( PAR ). Measured responses to K were minimal and no enhancement of wear tolerance in response to K treatment was noted.
Multiresolution stereo by simulated annealing (1990)

Maximum a posteriori (MAP) estimation of depth based on the Bayesian approach is described. The authors investigate simulated annealing in a hierarchical pyramid to accelerate the convergence. They also utilize an unobservable line process to recover the piecewise continuous depth map over the image plane. Simulation results are provided using random dot diagrams as well as synthesized images
Role of enzyme-peptide substrate backbone hydrogen bonding in determining protein kinase substrate specificities (1987)

As part of a search for peptides that have specificity for selected protein kinases, the possibility that adenosine cyclic 3',5'-phosphate dependent protein kinase (A-kinase) recognizes the hydrogen-bonding potential of its peptide substrates was investigated. A-Kinase catalyzes the phosphorylation of five N alpha-methylated and four depsipeptide derivatives of Leu-Arg-Arg-Ala-Ser-Leu-Gly (peptide 1) at rates that differ by at least 7 orders of magnitude. These peptide 1 analogues each lack the ability to donate a hydrogen bond at selected positions in the peptide chain. If a particular amide hydrogen of a peptide amide is involved in hydrogen bonding, which is important for enzyme recognition, the prediction is that peptides which contain an ester or a N-methylated bond at that position in peptide 1 will be comparatively poor substrates. In contrast, if a depsipeptide has a reactivity comparable to that of peptide 1 but the analogous N-methylated peptide has a poor reactivity with A-kinase, the result might indicate that the N-methyl group causes unfavorable steric effects. The depsipeptide that lacks a Leu6 amide proton is a good substrate for A-kinase, but the corresponding N-methylated peptide is phosphorylated far less efficiently. This result and others presented in this paper suggest that although enzyme-substrate hydrogen bonding may play some role in A-kinase catalysis of phosphoryl group transfer, other explanations are necessary to account for the relative reactivities of N alpha-methylated and depsi-containing peptide 1 analogues.(ABSTRACT TRUNCATED AT 250 WORDS)
Economic recycling of CdTe photovoltaic modules (2002)

While CdTe photovoltaics offer the promise of renewable, nonpolluting, and low cost electricity generation, cadmium and cadmium compounds have well known toxicological properties that demand consideration of nondispersive end-of-life module and manufacturing scrap disposal. With the support of a United States Department of Energy Small Business Innovation Research grant, Solar Cells Inc. has designed and installed a CdTe PV recycling pilot plant capable of processing 2 MW per shift per year of 60/spl times/120 cm modules, rated nominally at 50 W/sub p/. The primary process outputs are clean, salable glass cullet, cadmium carbonate, electrolytically refined tellurium and clean ethylene-vinyl acetate. Cost modeling shows these recovered materials are achieved at a processing cost of US $0.04 per watt or less.
Inactivation of the Lactobacillus leichmannii ribonucleoside triphosphate reductase by 2'-chloro-2'-deoxyuridine 5'-triphosphate: stoichiometry of inactivation, site of inactivation, and mechanism of the protein chromophore formation (1988)

The ribonucleoside triphosphate reductase (RTPR) of Lactobacillus leichmannii is inactivated by the substrate analogue 2'-chloro-2'-deoxyuridine 5'-triphosphate (ClUTP). Inactivation is due to alkylation by 2-methylene-3(2H)-furanone, a decomposition product of the enzymic product 3'-keto-2'-deoxyuridine triphosphate. The former has been unambiguously identified as 2-[(ethylthio)methyl]-3(2H)-furanone, an ethanethiol trapped adduct, which is identical by 1H NMR spectroscopy with material synthesized chemically. Subsequent to rapid inactivation, a slow process occurs that results in formation of a new protein-associated chromophore absorbing maximally near 320 nm. The terminal stages of the inactivation have now been investigated in detail. The alkylation and inactivation stoichiometries were studied as a function of the ratio of ClUTP to enzyme. At high enzyme concentrations (0.1 mM), 1 equiv of [5'-3H]ClUTP resulted in 0.9 equiv of 3H bound to protein and 83% inactivation. The amount of labeling of RTPR increased with increasing ClUTP concentration up to the maximum of approximately 4 labels/RTPR, yet the degree of inactivation did not increase proportionally. This suggests that (1) RTPR may be inactivated by alkylation of a single site and (2) decomposition of 3'-keto-dUTP is not necessarily enzyme catalyzed. The formation of the new protein chromophore was also monitored during inactivation and found to reach its full extent upon the first alkylation. Thus, out of four alkylation sites, only one appears capable of undergoing the subsequent reaction to form the new chromophore. While chromophore formation was prevented by NaBH4 treatment, the chromophore itself is resistant to reduction.(ABSTRACT TRUNCATED AT 250 WORDS)
A New Method for Long-Distance Data Reconstruction in Big Data Environment (2019)

In a big data environment, the data from long-term monitoring are of great importance in intelligent diagnoses, prognostic and health management of industrial components. However, in practice, it is difficult to ensure high reconstructive accuracy making the preservation performance of low-frequency information (e.g., periodic fault impulses) stable. To address this issue, this article proposes a new data reconstruction method that combines a smoothing sparse low-rank matrix (SSLRM) with online dictionary learning. This article first presents the design of SSLRM model for decomposing the raw data into a low resonance component (LRC) and a high resonance component (HRC), such that the periodic fault impulse can be isolated and preserved in advance. Then, both LRC and HRC are, respectively, reconstructed using an online dictionary learning algorithm, i.e., Hankel K-singular value decomposition; thus, the reconstructed data can be obtained accordingly. Both simulation case and engineering case are applied to show the effectiveness and practicality of the proposed approach.
Aryl hydrocarbon receptor negatively regulates LPS-induced IL-6 production through suppression of histamine production in macrophages (2011)

Macrophages play a pivotal role in innate immune responses to pathogens via toll-like receptors. We previously demonstrated that aryl hydrocarbon receptor (Ahr) in combination with signal transducer and activator of transcription 1 (Stat1) negatively regulates pro-inflammatory cytokine production by inhibiting nuclear factor-κB activation in macrophages after LPS stimulation. Here, we show that Ahr also negatively regulates production of the pro-inflammatory cytokine IL-6 by suppressing histamine production in macrophages stimulated by LPS. We found that Ahr-Sp1 complex, independent of Stat1, represses histidine decarboxylase expression by inhibiting LPS-induced Sp1 phosphorylation on Ser residues in macrophages; this leads to suppression of histamine production. Moreover, we found that loratadine and chlorpromazine, histamine 1 receptor (H1R) antagonists, more effectively impair the production of LPS-induced IL-6 than that of other inflammatory cytokines in Ahr(-/-) macrophages. Collectively, these results demonstrate that Ahr negatively regulates IL-6 production via H1R signaling through the suppression of histamine production in macrophages following LPS stimulation.