gebhart/patrepeval huggingface dataset:
Risk of Cancer as a Result of Community Exposure to Gasoline Vapors (2004)

The Tranguch Gasoline Spill leaked 50,000-900,000 gallons of gasoline from underground storage tanks, potentially exposing an area of Hazle Township and Hazleton, Pennsylvania, to chronic low levels of benzene since at least 1990. A retrospective cohort study of 663 individuals representing 275 households assessed whether affected residents were at increased risk for cancer from 1990-2000 compared with the Pennsylvania populace. Age-adjusted standard incidence ratios (SIRs) were calculated using Pennsylvania rates to determine expected numbers. The age-adjusted SIR for the gasoline-affected area was 4.40 (95% confidence interval: 1.09-10.24) for leukemia. These results suggest an association between living within the area affected by the Tranguch Gasoline Spill and increased risk for leukemia.
SECLAF: A Webserver and Deep Neural Network Design Tool for Biological Sequence Classification (2017)

Artificial intelligence (AI) tools are gaining more and more ground each year in bioinformatics. Learning algorithms can be taught easily by using the existing enormous biological databases, and the resulting models can be used for the high-quality classification of novel, un-categorized data in numerous areas, including biological sequence analysis. Here we introduce SECLAF, an artificial neural-net based biological sequence classifier framework, which uses the Tensorflow library of Google, Inc. By applying SECLAF for residue-sequences, we have reported (Methods (2017), https://doi.org/10.1016/j.ymeth.2017.06.034) the most accurate multi-label protein classifier to date (UniProt --into 698 classes-- AUC 99.99\%; Gene Ontology --into 983 classes-- AUC 99.45\%). Our framework SECLAF can be applied for other sequence classification tasks, as we describe in the present contribution. Availability and implementation: The program SECLAF is implemented in Python, and is available for download, with example datasets at the website https://pitgroup.org/seclaf/. For Gene Ontology and UniProt based classifications a webserver is also available at the address above.
A Research Plan Designed to Reduce Uncertainty in the Emission Inventory for Heavy-Duty Diesel-Powered Trucks (1992)

Author(s): Guensler, Randall; Sperling, Daniel; Jovanis, Paul | Abstract: Regulatory agencies are beginning to focus on the implementation of transportation control measures (TCMs) and economic incentives as means for reducing emissions from heavy-duty trucks. Rational implementation of heavy-duty vehicle emission control measures hinges upon our ability to assess complex transportation and air quality relationships in specific corridors. To determine the effects of these proposed measures, changes in vehicle activity and emission rates that result must be modelable/estimable. However, existing emission inventory methodologies were designed to produce bulk estimates of the emission inventory (i.e. crude estimates, based upon aggregate parameters). The existing models were never designed to provide estimates of emission rates in specific transportation corridors, making current methodologies extremely imprecise for local impact analysis.As described in our recent report, the methodologies used to estimate the emission contribution of heavy-duty trucks need significant improvement. The emission factors are based upon insufficient testing, vehicle activity estimates are sketchy at best, and a number of potentially critical activity/emission relationships are omitted from the existing models. If, through additional laboratory testing, the emission relationships prove to be significant (which appears likely), we believe that a complete overhaul of the methodologies will be required. Even though it is clear that all mobile source emission inventory methodologies require significant improvement, the deficiencies are so significant for heavy-duty trucks that a concerted extra effort will be required even to catch up to the current state of the practice.When a large amount of uncertainty exists in the relationships between variables of a physical system, determining what research projects should be undertaken to better understand these relationships is a difficult task.Interested parties must determine which research projects are likely to result in the most useful information, but they often face this task without certain knowledge of which existing methodologies and assumptions result in the greatest uncertainty. Determining which projects should be implemented and in what order proves to be as much an art as a science.In a resource constrained environment, the task becomes even more daunting, as any errors in research hierarchy can limit the pursuit of subsequent projects.This paper describes a proposed research framework to reduce uncertainty in heavy-duty truck emission inventory methodologies. Sixteen research projects that are consistent with the proposed framework are identified and discussed, and a relative timetable for project implementation is presented.
Intrinsic damping in silicon slab waveguides in the mid-infrared (2017)

The mid-infrared region is prominent for gas sensing due to the unique footprint of various volatile organic compounds. We investigated the intrinsic damping in silicon slab waveguides in the mid-infrared region in order to provide a platform for evanescent-field sensing using silicon waveguides.
Selective Plasticization of Poly (ethylene oxide) (PEO) Block in Nanostructured Polystyrene− PEO− Polystyrene Triblock Copolymer Electrolytes (2022)

The plasticization of a polymer electrolyte usually promotes its ionic conductivity but decreases its storage modulus due to the increased polymer chain flexibility. Herein, we show that such a tradeoff between the ionic conductivity and the mechanical robustness of the polymer electrolyte can be alleviated by selective plasticization of the ion-conductive block, such as poly(ethylene oxide) (PEO) in a polystyrene (PS)− PEO−PS block copolymer (SEO) electrolyte using an ether type plasticizer, tetraethylene glycol dimethyl ether (TEGDME). At maximum plasticizer loading, the room temperature ionic conductivity increases by up to 3 orders, whereas the storage modulus, G′ reduces to half, is still on the order of 10 2 MPa. At above the melting temperature of the PEO block, the dynamic storage modulus, G′ of the plasticized membrane surpasses its dry PS-PEO-PS counterpart. Such a phenomenon results from that, a) TEGDME co-crystallizes with PEO to promote its crystallinity and hence the storage modulus, b) TEGDME swells the amorphous PEO phase to enhance the polymer chain segmental mobility and hence ionic conductivity, and c) the PS phase remains intact from TEGDME to keep the SEO elastic.
Oxalic acid production by Aspergillus niger: an oxalate-non-producing mutant produces citric acid at pH 5 and in the presence of manganese (1999)

The external pH appeared to be the main factor governing oxalic acid production by Aspergillus niger. A glucose-oxidase-negative mutant produced substantial amounts of oxalic acid as long as the pH of the culture was 3 or higher. When pH was decreased below 2, no oxalic acid was formed. The activity of oxaloacetate acetylhydrolase (OAH), the enzyme believed to be responsible for oxalate formation in A. niger, correlated with oxalate production. OAH was purified from A. niger and characterized. OAH cleaves oxaloacetate to oxalate and acetate, but A. niger never accumulated any acetate in the culture broth. Since an A. niger acuA mutant, which lacks acetyl-CoA synthase, did produce some acetate, wild-type A. niger is apparently able to catabolize acetate sufficiently fast to prevent its production. An A. niger mutant, prtF28, previously isolated in a screen for strains deficient in extracellular protease expression, was shown here to be oxalate non-producing. The prtF28 mutant lacked OAH, implying that OAH is the only enzyme involved in oxalate production in A. niger. In a traditional citric acid fermentation low pH and absence of Mn2+ are prerequisites. Remarkably, a strain lacking both glucose oxidase (goxC) and OAH (prtF) produced citric acid from sugar substrates in a regular synthetic medium at pH 5 and under these conditions production was completely insensitive to Mn2+.
GluR3 Flip and Flop:  Differences in Channel Opening Kinetics (2007)

Ample evidence from earlier studies of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, GluR3 included, suggests that alternative splicing not only enriches AMPA receptor diversity but also, more importantly, creates receptor variants that are functionally different. However, it is not known whether alternative splicing affects the receptor channel opening that occurs in the microsecond time domain. Using a laser-pulse photolysis technique combined with whole-cell recording, we characterized the channel opening rate process for two alternatively spliced variants of GluR3, i.e., GluR3flip and GluR3flop. We show that the alternative splicing that generates flip and flop variants of GluR3 receptors regulates the channel opening process by controlling the rate of channel closing but not the rate of channel opening or the glutamate binding affinity. Specifically, the flop variant closes its channel almost 4-fold faster than the flip variant. We therefore propose that the function of the flip-flop sequence module in the channel opening process of AMPA receptors is to stabilize the open channel conformation, presumably by its pivotal structural location. Furthermore, a comparison of the flip isoform among all AMPA receptor subunits, based on the magnitude of the channel opening rate constant, suggests that GluR3 is kinetically more similar to GluR2 and GluR4 than to GluR1.
Combination therapy using three novel prolactin receptor antagonist-based fusion proteins effectively inhibits tumor recurrence and metastasis in HER2/neu transgenic mice (2009)

Previously, prolactin receptor antagonist (G129R)- based fusion proteins were developed including G129R fusions with an angiogenesis inhibitor (endostatin), an immune system modulator (interleukin 2), and a modified truncated cytotoxin (PE38KDEL). Each fusion protein was designed to target the PRLR-positive cells via the G129R moiety and at the same time attack a hallmark common to cancer cells via the second moiety. In this study, we tested the efficacy of the three fusion proteins as a combination therapy in an aggressive but clinically relevant mouse tumor model. To test the feasibility and to optimize a treatment regimen, allografts of a mammary carcinoma cell line (McNeuA) derived from an MMTV-neu transgenic mouse were first used. Growth of the allografts was significantly retarded by regimens which combined all three fusion proteins. In addition, a significant increase in cytotoxic CD8+ T cells was observed within the tumors of the combination treated groups. After establishing the dosing regimen, two doses of cocktail treatment (low and high doses administered twice weekly) along with individual component controls were administered to female MMTV-neu transgenic mice after surgical removal of a naturally occurring tumor. The average tumor recurrence time was significantly delayed in both low and high combination treatment groups in comparison to the no treatment control group (34, 50 and 18 days, respectively). The total number of lung metastases was also significantly decreased in both combination treatment groups. In conclusion, using G129R-based fusion proteins to target mammary carcinomas and to tackle multiple hallmarks of cancer at the same time was an effective strategy for treating HER2-postive mammary cancer in this mouse tumor model.
Optimization of UAV-Femtocell Systems Positioning via Game Theory to Geolocate Mobile Terminals in a Post-Earthquake Scenario (2021)

The use of UAV-Femtocell systems for the geolocation of mobile terminals has recently been introduced in the literature as an alternative and effective method in civil protection scenarios and applications. In this context, one of the important aspects concerns the optimization of geolocation times, bearing in mind the limited duration of the flight time of drones. This paper proposes a game theory-based approach to geolocation using UAV-Femtocell systems. A game structure is proposed in which the rules of drone movement are defined according to criteria and utility functions that are linked to the power measurements of the mobile terminals and obtained by the UAV-Femtocell systems in order to optimize the geolocation process through a series of successive rounds in which the Nash equilibria are reached.
The Efficiency of Gears in Consideration of Gear Size and Skewness of Gear Axes (1978)

From the investigation about the dimensions of skew-axes gears now in common use, the ratio of the pitch radius of pinion to that of gear is found to depend almost only upon the gear ratio. On the other hand, the offset of the gear axes is desired to be as large as possible in usual cases of gear transmission mechanisms. Under these situations, the position of the mean contact point where a pair of gear teeth is expected to transmit power in high efficiency is investigated. The results are as follows: 1) The mean contact point which corresponds to high efficiency is in the neighborhood of the ruled surface swept by the instantaneous axis as the gear ratio continuously varies. 2) The majority of the mean contact points of gears now in use nearly coincide with the point mentioned in 1.
Cell Behavior on Gallium Nitride Surfaces: Peptide Affinity Attachment versus Covalent Functionalization (2013)

Gallium nitride is a wide band gap semiconductor that demonstrates a unique set of optical and electrical properties as well as aqueous stability and biocompatibility. This combination of properties makes gallium nitride a strong candidate for use in chemical and biological applications such as sensors and neural interfaces. Molecular modification can be used to enhance the functionality and properties of the gallium nitride surface. Here, gallium nitride surfaces were functionalized with a PC12 cell adhesion promoting peptide using covalent and affinity driven attachment methods. The covalent scheme proceeded by Grignard reaction and olefin metathesis while the affinity driven scheme utilized the recognition peptide isolated through phage display. This study shows that the method of attaching the adhesion peptide influences PC12 cell adhesion and differentiation as measured by cell density and morphological analysis. Covalent attachment promoted monolayer and dispersed cell adhesion while affinity driven attachment promoted multilayer cell agglomeration. Higher cell density was observed on surfaces modified using the recognition peptide. The results suggest that the covalent and affinity driven attachment methods are both suitable for promoting PC12 cell adhesion to the gallium nitride surface, though each method may be preferentially suited for distinct applications.
CD117 expression in diffuse large B‐cell lymphomas: Fact or fiction? (2005)

CD117 (KIT) is expressed in a variety of hematopoietic neoplasms but there are a paucity of data regarding its expression in diffuse large B-cell lymphomas (DLBCL). The purpose of the present paper was to describe the authors' experience of two CD117+ DLBCL (one of follicle center-cell origin and one nasal Epstein-Barr virus (EBV)- plasmablastic lymphoma associated with lytic bone lesions), as determined by tissue immunohistochemistry and flow cytometry. The CD117 expression in DLBCL was further evaluated using tissue microarrays and seven additional plasmablastic lymphomas, using two commercially available anti-CD117 antibodies (Ab-1, Oncogene and A4502, DakoCytomation). Membranous +/- cytoplasmic staining was seen with Ab-1 in 24/65 (37%) DLBCL, including 21/56 microarray DLBCL, two index cases, and 1/7 additional plasmablastic lymphomas, with persistent staining in 13% of microarray DLBCL despite preincubation with KIT peptide. However, A4502 had only membranous staining of the index cases and one additional EBV- plasmablastic lymphoma with medullary disease. The present study suggests that (i) CD117 expression can be detected sporadically in DLBCL of follicle center-cell origin and a subset of plasmablastic lymphomas; (ii) staining for CD117 might help in identifying EBV- plasmablastic lymphomas associated with bone marrow involvement; and (iii) CD117 antibodies should be carefully validated prior to use, because non-specific staining, as observed with Ab-1, could lead to false-positive results.
Gd-DTPA contrast enhancement and tissue differentiation in MR imaging of experimental breast carcinoma. (1986)

Gadolinium-DTPA (Gd-DTPA) enhancement of magnetic resonance (MR) imaging was tested for diagnostic utility in evaluating carcinoma. Human breast carcinoma implanted in ten nude mice was studied before and after injection of Gd-DTPA at two different doses (0.2 and 0.5 mmol/kg body weight). Before injection, all tumors appeared homogeneous in intensity on spin-echo images; after injection, it was possible to distinguish areas of strong enhancement from areas of weak enhancement. Histologic correlations showed that the strongly enhanced areas corresponded to richly vascularized connective tissue and apparently viable tumoral tissues, while the weakly enhanced areas corresponded to nonvascularized necrotic tissue. The results indicate that intravenously administered paramagnetic agents such as Gd-DTPA may improve the specificity and diagnostic accuracy of MR imaging by permitting better differentiation of tumor elements.
Characterisation of Cu(In1–xGax)5Se8 by spectroscopic ellipsometry (2009)

Abstract Optical measurements of Cu(In 1–x Ga x ) 5 Se 8 were performed at room temperature in the photon energy range from 0.8 to 4.7 eV. Spectral dependence of the complex dielectric functions was derived. The structures observed in the measured spectra have been analyzed by fitting the second derivative of the experimental spectrum to analytical line shapes and have been attributed to the interband transitions E 0 , and E 1A . The energies corresponding to the electronic transitions as well as the parameters as strength and broadening were determined. Besides, the values of E 0 and E 1A are found to increase linearly with increasing Ga content. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Warping and morphing of graphical objects (1998)

1 Introduction to Basic Concepts 2 Graphical Objects 3 Transformation of Graphical Objects 4 Warping and Morphing 5 Domain and Range Morphing 6 Image Mapping 7 Introduction to Graphical Objects 8 Description of Graphical Objects 9 Representation of Graphical Objects 10 Reconstruction of Graphical Objects 11 Introduction to Transformations of Graphical Objects 12 Specification of Transformations 13 Computation of Transformations 14 Warping and Morphing Techniques 15 Introduction to A Tour of Warping and Morphing 16 Image-Based Rendering 17 Warping and Morphing of Plane Curves 18 Warping and Morphing of Images 19 Warping and Morphing of Surfaces 20 Warping and Morphing of Volumetric Objects 21 The Morphos System
The new personalized medicine is inexpensive biosensors in a ubiquitous computing environment (2009)

Chronic disease is the new great health challenge. Management requires the patient to have real-time information about the state of his or her illness in order to make informed judgments. We designed and built a family of small, inexpensive biosensors to monitor cardiac output, blood pressure, airway flow and other parameters. They connect via mobile phone or WiFi allowing people with chronic disease to monitor and modify their illnesses thus avoiding unexpected exacerbations or decompensation events. The combination of ubiquitous computing and personalized interpretation algorithms can be expected to provide a substantially higher quality interaction between the health care establishment and the chronic disease patient. Although not the solution to the health care dilemma, empowerment is an important feature of improved outcomes.
Distinct Chromatin Modulators Regulate the Formation of Accessible and Repressive Chromatin at the Fission Yeast Recombination Hotspotade6-M26 (2008)

Histone acetyltransferases (HATs) and ATP-dependent chromatin remodeling factors (ADCRs) regulate transcription and recombination via alteration of local chromatin configuration. The ade6-M26 allele of Schizosaccharomyces pombe creates a meiotic recombination hotspot that requires a cAMP-responsive element (CRE)-like sequence M26, the Atf1/Pcr1 heterodimeric ATF/CREB transcription factor, the Gcn5 HAT, and the Snf22 SWI2/SNF2 family ADCR. Chromatin alteration occurs meiotically around M26, leading to the activation of meiotic recombination. We newly report the roles of other chromatin remodeling factors that function positively and negatively in chromatin alteration at M26: two CHD-1 family ADCRs (Hrp1 and Hrp3), a Spt-Ada-Gcn5 acetyltransferase component (Ada2), and a member of Moz-Ybf2/Sas3-Sas2-Tip60 family (Mst2). Ada2, Mst2, and Hrp3 are required for the full activation of chromatin changes around M26 and meiotic recombination. Acetylation of histone H3 around M26 is remarkably reduced in gcn5Delta, ada2Delta and snf22Delta, suggesting cooperative functions of these HAT complexes and Snf22. Conversely, Hrp1, another CHD-1 family ADCR, maintains repressive chromatin configuration at ade6-M26. Interestingly, transcriptional initiation site is shifted to a site around M26 from the original initiation sites, in couple with the histone acetylation and meiotic chromatin alteration induced around 3' region of M26, suggesting a collaboration between these chromatin modulators and the transcriptional machinery to form accessible chromatin. These HATs and ADCRs are also required for the regulation of transcription and chromatin structure around M26 in response to osmotic stress. Thus, we propose that multiple chromatin modulators regulate chromatin structure reversibly and participate in the regulation of both meiotic recombination and stress-induced transcription around CRE-like sequences.
On Fault Predictability in Stochastic Discrete Event Systems (2013)

Abstract Fault predictability in stochastic discrete event systems is considered. The notion of asymptotically almost sure predictability (or AAS ‐predictability) is introduced, and a necessary and sufficient condition for AAS ‐predictability is obtained.
The nonstructural glycoprotein of rotavirus affects intracellular calcium levels (1994)

Rotavirus infection of monkey kidney cells has been reported to result in a significant increase in the concentration of intracellular calcium. This increase in intracellular calcium was associated with viral protein synthesis and cytopathic effects in infected cells. We tested the effect of individual rotavirus proteins on intracellular calcium concentrations in insect Spodoptera frugiperda (Sf9) cells. Insect cells were infected with wild-type baculovirus or baculovirus recombinants that contained an individual rotavirus gene. The cells were harvested at different times postinfection, and the intracellular calcium concentration was measured by using fura-2 as a fluorescent calcium indicator. We found that the concentration of intracellular calcium was increased nearly fivefold in infected Sf9 cells that expressed the nonstructural glycoprotein (NSP4) of group A rotavirus, and this increase in intracellular calcium concentration coincided with NSP4 expression. A similar result was observed in insect cells expressing NSP4 from a group B rotavirus, suggesting the conservation of this function among rotavirus groups. Expression of the other 10 rotavirus proteins or of wild-type baculovirus proteins in Sf9 cells did not significantly increase intracellular calcium levels. These results suggest that the nonstructural glycoprotein NSP4 is responsible for the increase in cytosolic calcium observed in rotavirus-infected cells.