gebhart/patrepeval huggingface dataset:
Transcription analysis of pyranose dehydrogenase from the basidiomycete Agaricus bisporus and characterization of the recombinantly expressed enzyme (2015)

Agaricus bisporus is a litter degrading basidiomycete commonly found in humic-rich environments. It is used as model organism and cultivated in large scale for food industry. Due to its ecological niche it produces a variety of enzymes for detoxification and degradation of humified plant litter. One of these, pyranose dehydrogenase, is thought to play a role in detoxification and lignocellulose degradation. It is a member of the glucose-methanol-choline family of flavin-dependent enzymes and oxidizes a wide range of sugars with concomitant reduction of electron acceptors like quinones. In this work, transcription of pdh in A. bisporus was investigated with real-time PCR revealing influence of the carbon source on pdh expression levels. The gene was isolated and heterologously expressed in Pichia pastoris. Characterization of the recombinant enzyme showed a higher affinity towards disaccharides compared to other tested pyranose dehydrogenases from related Agariceae. Homology modeling and sequence alignments indicated that two loops of high sequence variability at substrate access site could play an important role in modulating these substrate specificities.
<title>Project summary: applied research on remotely queried embedded microsensors</title> (2000)

This paper describes the final results of the Applied Research in Remotely-Queried Embedded Microsensors program. The program developed wireless and battery-less embedded strain/temperature gages suitable for embedding in aerospace and other composite structures. The program culminated in a working remotely queried strain rosette/temperature gage and testing of the device in several composite applications. The US Office of Naval Research funded this program to consolidate progress made in earlier programs towards self- contained microsensors.
The Art of Designing DNA Nanostructures with CAD Software (2021)

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.
The Association of Estimated Glomerular Filtration Rate With Diabetic Retinopathy and Macular Edema (2015)

Our results suggest that lower levels of eGFR were associated with the presence and severity of DR, but not with DME.
Enhancing unreinforced masonry wall resilience through nano-silica modified steel fiber reinforced mortar: A study on in-plane cyclic loading (2023)

Strengthening existing unreinforced masonry (URM) structures with plaster is a common technique used to improve the structural integrity and durability of buildings. However, using a thin layer of plaster alone may not provide sufficient reinforcement to adequately enhance the URM wall’s resistance to lateral or other types of loading. Therefore, incorporating additional materials, such as steel fibers and nano-silica, into the plaster mix has been explored in this study to further improve the URM wall’s resilience performance. The effect of nano-silica modified steel fibers reinforced (NS-SFR) mortar plastering on the axial and lateral load capacity of concrete masonry walls was experimentally investigated. The investigated URM walls were constructed with a dimension of 830×810×100 mm (length × width × thickness) using hollow concrete masonry blocks. These walls were categorized as a reference wall, plastered on one side only wall, and plastered on both sides wall. During the experimental testing, each sample was exposed to a combination of precompression and cyclic in-plane loading to assess its shear capacity. The tests also involved closely observing and identifying any cracks or types of failures that occurred. The results of the tests indicated that the walls that were strengthened with NS-SFR mortar exhibited a significant improvement in their compressive strength, shear strength capacity, and stiffness, in comparison to the walls that were not strengthened. Applying NS-SFR mortar as a plaster on the URM wall resulted in significant improvements in both compressive strength and shear capacity. Specifically, for the one-side plastered wall, the use of NS-SFR mortar increased compressive strength and shear capacity by 18.5% and 40%, respectively, while for the two sides plastered wall, the increase was even more significant, with improvements of 86.5% and 132% in compressive strength and shear capacity, respectively.
Biological activity of WIN 63759, an orally bioavailable inhibitor of human neutrophil elastase (1995)

Abstract The proteolytic activity of human neutrophil elastase (HNE) has been implicated in a number of pulmonary diseases. We report on the activity of an orally bioavailable, selective HNE inhibitor, WIN 63759 [6‐methoxy‐4‐(1‐methylethy)‐3‐oxo‐1,2‐benzisothiazol‐2(3H)‐yl]methyl 2,6‐dichloro‐3‐[2‐(4‐morpholinyl)ethoxy] benzoate S, S dioxide. WIN 63759 is a potent inhibitor of HNE (K i = 14 pM) and is at least 70,000‐fold selective for HNE relative to other serine proteases or receptors. In vivo, WIN 63759 produces dose‐related inhibition of HNE‐induced pulmonary hemorrhage following either intravenous (ED 50 = 3 mg/kg; 4.5 μmol/kg) or subcutaneous (ED 50 = 19 mg/kg; 28.5 μmol/kg) administration in hamsters. WIN 63759 selectivity inhibits HNE in vivo (relative to chymotrypsin or trypsin), and is equally efficacious following acute or chronic administration in the hamster. WIN 63759 is not orally bioavailable in hamsters, rats, or monkeys, and this lack of bioavailability is related to rapid in vitro metabolism in liver, jejunum, or blood. In contrast, WIN 63759 is stable in canine tissues in vitro and is orally bioavailable in dogs. Bioavailability is enhanced in fed relative to fasted dogs. Bronchoalveolar lavage studies indicate that WIN 63759 is present in the target organ (lung) at concentrations 3–5 X higher than those found in plasma following oral administration of 3–100 mg/kg (4.5–150 μmol) in dogs. These data show that WIN 63759 is a potent, selective, and orally bioavailable inhibitor of HNE. Since oral bioavailability was predictable based on in vitro metabolism, and since in vitro metabolism in humans is similar to that observed with dogs, WIN 63759 and other members of this chemical series may be orally bioavailable inhibitors of neutrophil elastase in man. © 1995 Wiley‐Liss, Inc.
Characterization of Newly Emerging Newcastle Disease Virus Isolates from the People's Republic of China and Taiwan (2001)

Seven Newcastle disease (ND) virus (NDV) isolates which were recovered from ND outbreaks in chicken and pigeon flocks in China and Taiwan between 1996 and 2000 were genotypically and pathotypically characterized. By phylogenetic analysis of the fusion protein genes, isolates Ch-A7/96, Ch/98-3, Ch/99, Ch/2000, and TW/2000 were placed into two novel subgenotypes, VIIc and VIId. Isolate Ch/98-1 was grouped into subgenotype VIb, while Ch-W6/96 was proven to be a mixture of isolates Ch-A7/96 and Ch/98-1. These isolates were pathotyped as viscerotropic velogenic for Ch/98-3, Ch/99, Ch/2000, and TW/2000; neurotropic velogenic for Ch-A7/96; and mesogenic for Ch/98-1. Three separate, comparative, genetic analyses of the F genes, including genetic distance measurement, phylogenetic tree analysis, and residue substitution analysis, were performed with our isolates and selected NDV strains from GenBank. Results showed that the close genetic similarity provided evidence for the epidemiological linkage between the outbreaks in China and Taiwan and that the 1990s outbreaks in Asia, the Middle East, Africa, and Europe constituted the fourth panzootic of ND. In combination with epidemiological analysis, an evolutionary model of the NDV strains, representative of the direction of transmission within the NDV strains, was proposed, and epidemiology of NDV transmission was evaluated with emphasis on molecular aspects. Finally, a cross-protective experiment indicated that at least one strain (Ch-A7/96) among our NDV isolates was an antigenic variant, responsible for recent outbreaks of ND in vaccinated chicken flocks.
Helicobacter pylori Possesses Two CheY Response Regulators and a Histidine Kinase Sensor, CheA, Which Are Essential for Chemotaxis and Colonization of the Gastric Mucosa (2000)

Infection of the mucous layer of the human stomach by Helicobacter pylori requires the bacterium to be motile and presumably chemotactic. Previous studies have shown that fully functional flagella are essential for motility and colonization, but the role of chemotaxis remains unclear. The two-component regulatory system CheA/CheY has been shown to play a major role in chemotaxis in other enteric bacteria. Scrutiny of the 26695 genome sequence suggests that H. pylori has two CheY response regulators: one a separate protein (CheY1) and the other (CheY2) fused to the histidine kinase sensor CheA. Defined deletion mutations were introduced into cheY1, cheY2, and cheA in H. pylori strains N6 and SS1. Video tracking revealed that the wild-type H. pylori strain moves in short runs with frequent direction changes, in contrast to movement of cheY2, cheAY2, and cheAY2 cheY1 mutants, whose motion was more linear. The cheY1 mutant demonstrated a different motility phenotype of rapid tumbling. All mutants had impaired swarming and greatly reduced chemotactic responses to hog gastric mucin. Neither cheY1 nor cheAY2 mutants were able to colonize mice, but they generated a significant antibody response, suggesting that despite impaired chemotaxis, these mutants were able to survive in the stomach long enough to induce an immune response before being removed by gastric flow. Additionally, we demonstrated that cheY1 failed to colonize gnotobiotic piglets. This study demonstrates the importance of the roles of cheY1, cheY2, and cheA in motility and virulence of H. pylori.
Broad-band optical parametric gain on a silicon photonic chip (2006)

Towards silicon photonics The development of silicon-compatible optical components that simultaneously amplify and process a broad range of wavelength channels is critical for future data communication technology based on photonic chips. Until now, such devices have only been able to amplify a single wavelength channel. Now, using nanoscale silicon waveguides designed for the purpose, Foster et al. have achieved broadband amplification. The key is the exploitation of a nonlinear optical effect known as four-wave mixing. This process can also be used for other all-optical functions previously only possible in extended lengths of optical fibre.
Vectorial Phase Conjugation for High-Fidelity Mode Transmission Through Multimode Fiber (2020)

Polarization and spatial mode cross-talk limit the usability of multimode fibers for data transfer. We implement vectorial phase conjugation to transmit modes through standard multimode fiber with an average fidelity of 84.1% for 210 modes.
Severity of radiation pneumonitis, from clinical, dosimetric and biological features: a pilot study. (2020)

Abstract Background and objective: Radiation pneumonitis (RP) could be a lethal complication of lung cancer treatment. No reliable predictors of RP severity have been recognized. This prospective pilot study was performed to identify early predictors of high grade lung toxicity and to evaluate clinical, biological or dosimetric features associated with different grades of toxicity. Method: Sixteen patients with non-small cell lung cancer with indication of concurrent chemoradiotherapy using 60Gy/2Gy/fraction starting at cycle one of platinum based chemotherapy were included. Bronchoalveolar lavage (BAL), pulmonary function testing (PFT), and 18 F-2-fluoro-2-deoxy-D-glucose positron-emission tomography was performed before radiotherapy (RT), after three weeks of treatment, and two months post-RT. For analysis, patients were grouped by grade (low [G1-G2] vs. high [G3-G5]). The two groups were compared to identify predictors of RP. Protein expression BAL and lung tissue metabolism was evaluated in two patients (RP-G1 vs. RP-G3). Categorical variables such as comorbidities, stages and locations were summarized as percentages. Radiation doses, pulmonary function values and time to RP were summarized by medians with ranges or as means with standard deviation. Longitudinal analysis PFT was performed by a T-test. Results: All 16 patients developed RP, as follows: G1 (5 pts; 31.3%); G2 (5 pts; 31.3%); G3 (5 pts; 31.3%); and G5 (1 pts; 6.1%). Patients with high grade RP presented significant decrease (p=0.02) in diffusing lung capacity for carbon monoxide (DLCO) after three weeks of RT. No correlation between dosimetric values and RP grades was observed. BAL analysis of the selected patients showed that CXCL-1, CD154, IL-1ra, IL-23, MIF, PAI-1 and IFN-g were overexpressed in the lungs of the RP-G3 patient, even before treatment. The pre-RT SUVmax value in the RP-G3 patient was non-significantly higher than in the patient with RP-G1. Conclusions: RT induces some degree of RP. Our data suggest that decrease in DLCO% is the most sensitive parameter for the early detection of RP. Moreover, we detect biological differences between the two grades of pneumonitis, highlighting the potential value of some cytokines as a prognostic marker for developing high grade lung toxicity. Further multicenter studies with larger sample size are essential to validate these findings.
A Swift Sandbox in the Cloud (2017)

This chapter discusses the announcement of the IBM Swift Sandbox from IBM in response to Apple Inc.'s Swift language open source on Swift.org, examining varied use cases like support on mobile devices. There are many cloud environments that serve niche needs and a few that serve large-scale enterprise requirements. Amazon Web Services is an example of an enterprise cloud platform, and so is Microsoft Azure as well as Google cloud platform. IBM also offers an enterprise cloud platform called IBM Bluemix. It is the cloud environment in which the Swift@IBM team builds and hosts a Swift Sandbox. The platform includes software development tools too, so one can set up an automated continuous integration, continuous delivery pipeline to process code changes for one's application as soon as they are committed. The Bluemix catalog of cloud services also includes a wide variety of cognitive computing application services. These services are especially useful for enabling users' application to interact with users in more natural ways.
Modulating metastasis by a lymphangiogenic switch in prostate cancer (2007)

Prostate cancer dissemination is difficult to detect in the clinic, and few treatment options exist for patients with advanced-stage disease. Our aim was to investigate the role of tumor lymphangiogenesis during metastasis. Further, we implemented a noninvasive molecular imaging technique to facilitate the assessment of the metastatic process. The metastatic potentials of several human prostate cancer xenograft models, LAPC-4, LAPC-9, PC3 and CWR22Rv-1 were compared. The cells were labeled with luciferase, a bioluminescence imaging reporter gene, to enable optical imaging. After tumor implantation the animals were examined weekly during several months for the appearance of metastases. Metastatic lesions were confirmed by immunohistochemistry. Additionally, the angiogenic and lymphangiogenic profiles of the tumors were characterized. To confirm the role of lymphangiogenesis in mediating metastasis, the low-metastatic LAPC-9 tumor cells were engineered to overexpress VEGF-C, and the development of metastases was evaluated. Our results show CWR22Rv-1 and PC3 tumor cell lines to be more metastatic than LAPC-4, which in turn disseminates more readily than LAPC-9. The difference in metastatic potential correlated with the endogenous production levels of lymphangiogenic growth factor VEGF-C and the presence of tumor lymphatics. In agreement, induced overexpression of VEGF-C in LAPC-9 enhanced tumor lymphangiogenesis leading to the development of metastatic lesions. Taken together, our studies, based on a molecular imaging approach for semiquantitative detection of micrometastases, point to an important role of tumor lymphatics in the metastatic process of human prostate cancer. In particular, VEGF-C seems to play a key role in prostate cancer metastasis.
Variational self-consistent estimates for viscoplastic polycrystals with highly anisotropic grains (2000)

A recently established variational procedure is used to compute self-consistent estimates for viscoplastic polycrystals with highly anisotropic ionic and HCP grains. For large values of the grain anisotropy M, the predictions for the macroscopic flow stress are found to scale as Mγ, where γ depends on the number (less than 5) of independent slip systems that are available for plastic flow, but not on the strain-rate sensitivity. The predictions of other nonlinear extensions of the self-consistent scheme are inconsistent with this scaling law, suggesting that they may be less accurate than the variational estimates proposed here. Une méthode variationnelle récente est appliquée à l'estimation autocohérente du comportement de polycristaux viscoplastiques constitués de cristaux ioniques ou de structure hexagonale. Lorsque l'anisotropie M du comportement des grains croît, la réponse macroscopique évolue en Mγ, oú γ dépend du nombre (inférieur à 5) de systèmes indépendants mais pas de la sensibilité à la vitesse de déformation. Les estimations des autres extensions non-linéaires du modèle auto-cohérent semblent ne pas satisfaire à cette loi, ce qui suggère qu 'elles sont moins précises que les estimations variationnelles développées ici.
The spectrum of sonographic findings in pancreatic carcinoma. (1986)

The ultrasound studies of 59 patients with cancer of the pancreas were reviewed and the findings grouped into two categories: intrapancreatic, which included the appearance of the primary tumor and the pancreatic duct; and extrapancreatic, which included biliary obstruction, hepatic metastases, regional lymph node involvement, ascites, spleen enlargement and invasion, and alteration of the upper abdominal veins. Pancreatic duct dilatation was more evident with smaller tumors of the pancreatic head, while inferior vena cava compression was found not to be a constant finding even with large tumors of the head of the pancreas. Tumor extension to regional lymph nodes was difficult to detect and consequently underestimated. Nonvisualization, occlusion with or without collaterals, and displacement or deformity of the major branches of the portal venous system were detectable sonographically. The liver metastases of pancreatic carcinoma tended to be small and hypoechoic. This is a different pattern from that typically described for other gastrointestinal adenocarcinomas and, in particular, markedly different and distinguishable from the metastatic pattern seen with malignant pancreatic islet cell tumors. The significance of the intra- and extrapancreatic changes seen sonographically in cancer of the pancreas by ultrasound is discussed in relationship to clinical staging and prognosis.
Diamond nanophotonics and quantum optics (2013)

Design, fabrication and characterization of nanophotonic and nanomechanic devices fabricated in single crystal diamond substrates will be discussed, as well as their applications in quantum information processing and optoelectronics.
Efficient T-Cell Surveillance of the CNS Requires Expression of the CXC Chemokine Receptor 3 (2004)

T-cells play an important role in controlling viral infections inside the CNS. To study the role of the chemokine receptor CXCR3 in the migration and positioning of virus-specific effector T-cells within the brain, CXCR3-deficient mice were infected intracerebrally with lymphocytic choriomeningitis virus (LCMV). Analysis of the induction phase of the antiviral CD8+ T-cell response did not reveal any immune defects in CXCR3-deficient mice. Yet, when mice were challenged with LCMV intracerebrally, most CXCR3-deficient mice survived the infection, whereas wild-type mice invariably died from CD8+ T-cell-mediated immunopathology. Quantitative analysis of the cellular infiltrate in CSF of infected mice revealed modest, if any, decrease in the number of mononuclear cells recruited to the meninges in the absence of CXCR3. However, immunohistological analysis disclosed a striking impairment of CD8+ T-cells from CXCR3-deficient mice to migrate from the meninges into the outer layers of the brain parenchyma despite similar localization of virus-infected target cells. Reconstitution of CXCR3-deficient mice with wild-type CD8+ T-cells completely restored susceptibility to LCMV-induced meningitis. Thus, taken together, our results strongly point to a critical role for CXCR3 in the positioning of effector T-cells at sites of viral inflammation in the brain.
Blue Gene system software---Designing a highly-scalable operating system (2006)

Blue Gene/L is currently the world's fastest and most scalable supercomputer. It has demonstrated essentially linear scaling all the way to 131,072 processors in several benchmarks and real applications. The operating systems for the compute and I/O nodes of Blue Gene/L, are among the components responsible for that scalability. Compute nodes are dedicated to running application processes, whereas I/O nodes are dedicated to performing system functions. The operating systems adopted for each of these nodes reflect this separation of function. Compute nodes run a lightweight operating system called the compute node kernel. I/O nodes run a port of the Linux operating system. This paper discusses the architecture and design of this solution for Blue Gene/L in the context of the hardware characteristics that led to the design decisions. It also explains and demonstrates how those decisions are instrumental in achieving the performance and scalability for which Blue Gene/L is famous.
Carrier leakage calibration in DCT (2009)

In this paper, an improved version of the digital calibration method for carrier leakage, which is caused by the DC offset on direct conversion transmitter, is proposed. We have used a power detector for estimating the DC offset. After, we have injected a compensation voltage for eliminating this DC offset. In order to validate our technique, a new direct conversion transmitter that operates at 2 GHz, is proposed. The simulation and the implementation of the calibration were performed using the Agilent-ADS software.