gebhart/patrepeval huggingface dataset:
Formation and removal of benzo(a)pyrene adducts of DNA in hamster tracheal epithelial cells. (1981)

A cloned cell line derived from normal hamster tracheal epithelium has been characterized with respect to its response to the environmental pollutant and carcinogen benzo(a)pyrene [B(a)P]. These cells metabolize B(a)P to ultimate reactive forms as assayed by alkylation of DNA. Alkylation with radiotracer amounts of B(a)P was maximum at 8 hr, at which time 70% of the applied hydrocarbon had been converted to water-soluble forms. At longer incubation times, the rate of removal of adducts exceeded the rate of formation. When B(a)P-containing medium was replaced with fresh medium at two or four hr, a subsequent biphasic removal of adducts occurred, a rapid removal for the first four hr postincubation and then a slower repair. About 50% of the DNA-bound hydrocarbon remained in DNA after 48 hr. Cells were able to divide in the presence of these lesions, undergoing five doublings (five days), while only 60% of the adducts were removed from the DNA. Integrity of DNA during this period was monitored by the alkaline elution technique. A toxic dose of B(a)P was required to cause any increase in the rate of elution. Minimal single-strand breakage was observed from two to eight hr of B(a)P treatment, but at 15 hr DNA appeared normal. Comparison was made with a nontoxic dose of methyl methanesulfonate which caused very rapid elution of DNA after only one hr treatment. At least 15 deoxyribonucleoside-bound B(a)P adducts were separated by high-pressure liquid chromatography. Four adducts, probably deoxyadenosine-B(a)P, were removed almost completely in 24 hr, while the others appeared to be poorly removed. The possible significance to neoplasia of persistent and repairable lesions is discussed.
Enterotoxigenic Escherichia coli (ETEC) vaccines: Priority activities to enable product development, licensure, and global access (2021)

Diarrhoeal disease attributable to enterotoxigenic Escherichia coli (ETEC) causes substantial morbidity and mortality predominantly in paediatric populations in low- and middle-income countries. In addition to acute illness, there is an increasing appreciation of the long-term consequences of enteric infections, including ETEC, on childhood growth and development. Provision of potable water and sanitation and appropriate clinical care for acute illness are critical to reduce the ETEC burden. However, these interventions are not always practical and may not achieve equitable and sustainable coverage. Vaccination may be the most cost-effective and equitable means of primary prevention; however, additional data are needed to accelerate the investment and guide the decision-making process for ETEC vaccines. First, to understand and quantify the ETEC disease burden, additional data are needed on the association between ETEC infection and physical and cognitive stunting as well as delayed educational attainment. Furthermore, the role of inappropriate or inadequate antibiotic treatment of ETEC-attributable diarrhoea may contribute to the development of antimicrobial resistance (AMR) and needs further elucidation. An ETEC vaccine that mitigates acute diarrhoeal illness and minimizes the longer-term disease manifestations could have significant public health impact and be a cost-effective countermeasure. Herein we review the ETEC vaccine pipeline, led by candidates compatible with the general parameters of the Preferred Product Characteristics (PPC) recently developed by the World Health Organization. Additionally, we have developed an ETEC Vaccine Development Strategy to provide a framework to underpin priority activities for researchers, funders and vaccine manufacturers, with the goal of addressing globally unmet data needs in the areas of research, product development, and policy, as well as commercialization and delivery. The strategy also aims to guide prioritization and co-ordination of the priority activities needed to minimize the timeline to licensure and use of ETEC vaccines, especially in in low- and middle-income countries, where they are most urgently needed.
Poly C binding protein, a single‐stranded DNA binding protein, regulates mouse µ‐opioid receptor gene expression (2005)

Previously, a single-stranded (ss) DNA element, polypyrimidine (PPy) element, was found to be important for the proximal promoter activity of mouse micro-opioid receptor (MOR) gene in a neuronal cell model. In this study, we identified the presence of unknown ssDNA binding proteins specifically bound to MOR ssPPy element in the mouse brain, implicating the physiological significance of these proteins. To identify the ssDNA binding proteins, yeast one-hybrid system with PPy element as the bait was used to screen a mouse brain cDNA library. The clone encoding poly C binding protein (PCBP) was obtained. Its full-length cDNA sequence and protein with molecular weight approximately 38 kDa were confirmed. Electrophoretic mobility shift analysis (EMSA) revealed that PCBP bound to ssPPy element, but not doubled-stranded, in a sequence-specific manner. EMSA with anti-PCBP antibody demonstrated the involvement of PCBP in MOR ssPPy/proteins complexes of mouse brain and MOR expressing neuroblastoma NMB cells. Functional analysis showed that PCBP trans-activated MOR promoter as well as a heterologous promoter containing MOR PPy element. Importantly, ectopic expression of PCBP in NMB cells up-regulated the expression level of endogenous MOR gene in vivo in a dose-dependent manner. Collectively, above results suggest that PCBP participates in neuronal MOR gene expression.
Understanding TCP's behavior over wireless links (2002)

During the last few years, both Internet and mobile systems have grown extremely fast. It is natural that nowadays these two worlds are converging. Adaptation of protocols designed for the wired Internet, such as TCP, to wireless specificity and conversely, design of wireless systems adapted to the Internet protocol stack is an area of wide interest. Many materials can be found in the research community but are often unreachable for the ordinary reader. This paper tries to explain basic TCP functionality and its behaviour over mobile cellular systems. Simulations highlight the spurious effects of the congestion avoidance algorithm of TCP, unwisely triggered by the bad quality of the wireless link. Then a survey and an analysis of the main propositions to improve TCP behaviour over wireless is given, to finally conclude that unfortunately there is no miraculous solution.
Digital trail libraries (2004)

We propose the idea of an online, user submitted digital library of recreation trails. Digital libraries of trails offer advantages over paper guidebooks in that they are more accurate, dynamic and not limited to the experience of the author(s). The basic representation of a trail is a GPS track log, recorded as recreators travel on trails. As users complete trips, the GPS track logs of their trips are submitted to the central library voluntarily. A major problem is that track logs will overlap and intersect each other. We present a method for the combination of overlapping and intersecting GPS track logs to create a network of GPS trails. Each trail segment in the network can then be characterized by automatic and manual means, producing a digital library of trails. We also describe the TopoFusion system which creates, manages and visualizes GPS data, including GPS networks.
Vein Harvesting by Long Blunt and Blind Dissection. A Standardized Technique in the Dog (1984)

A standardized method for harvesting veins from dogs is described. It involves skeletization of the vein and its collaterals by longitudinal blind and blunt dissection, thus separating the vein from its surroundings. This is followed by elevation and cutting of the subdermal tissue with an electrosurgical pencil. The method was found to be faster and less traumatic than the prevailing method which involves cutting the skin with a longitudinal incision and dissection of the vein in small increments.
Data from <i>BRCA1</i> Loss Preexisting in Small Subpopulations of Prostate Cancer Is Associated with Advanced Disease and Metastatic Spread to Lymph Nodes and Peripheral Blood (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; A preliminary study performed on a small cohort of multifocal prostate cancer (PCa) detected &lt;i&gt;BRCA1&lt;/i&gt; allelic imbalances among circulating tumor cells (CTC). The present analysis was aimed to elucidate the biological and clinical roles of &lt;i&gt;BRCA1&lt;/i&gt; losses in metastatic spread and tumor progression in PCa patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; To map molecular progression in PCa outgrowth, we used fluorescence &lt;i&gt;in situ&lt;/i&gt; hybridization analysis of primary tumors and lymph node sections, and CTCs from peripheral blood.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We found that 14% of 133 tested patients carried monoallelic &lt;i&gt;BRCA1&lt;/i&gt; loss in at least one tumor focus. Extended molecular analysis of chr17q revealed that this aberration was often a part of larger cytogenetic rearrangement involving chr17q21 accompanied by allelic imbalance of the tumor suppressor gene &lt;i&gt;PTEN&lt;/i&gt; and lack of &lt;i&gt;BRCA1&lt;/i&gt; promoter methylation. The &lt;i&gt;BRCA1&lt;/i&gt; losses correlated with advanced T stage (&lt;i&gt;P&lt;/i&gt; &lt; 0.05), invasion to pelvic lymph nodes (&lt;i&gt;P&lt;/i&gt; &lt; 0.05), as well as biochemical recurrence (&lt;i&gt;P&lt;/i&gt; &lt; 0.01). Their prevalence was twice as high within 62 lymph node metastases (LNM) as in primary tumors (27%, &lt;i&gt;P&lt;/i&gt; &lt; 0.01). The analysis of 11 matched primary PCa-LNM pairs confirmed the suspected transmission of genetic abnormalities between these two sites. In four of seven patients with metastatic disease, &lt;i&gt;BRCA1&lt;/i&gt; losses appeared in a minute fraction of cytokeratin- and vimentin-positive CTCs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Small subpopulations of PCa cells bearing &lt;i&gt;BRCA1&lt;/i&gt; losses might be one confounding factor initiating tumor dissemination and might provide an early indicator of shortened disease-free survival. Clin Cancer Res; 16(13); 3340–8. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
James Webb Space Telescope Optical Simulation Testbed I: overview and first results (2014)

The James Webb Space Telescope (JWST) Optical Simulation Testbed (JOST) is a tabletop workbench to study aspects of wavefront sensing and control for a segmented space telescope, including both commissioning and maintenance activities. JOST is complementary to existing optomechanical testbeds for JWST (e.g. the Ball Aerospace Testbed Telescope, TBT) given its compact scale and flexibility, ease of use, and colocation at the JWST Science &amp;amp; Operations Center. We have developed an optical design that reproduces the physics of JWST’s three-mirror anastigmat using three aspheric lenses; it provides similar image quality as JWST (80% Strehl ratio) over a field equivalent to a NIRCam module, but at HeNe wavelength. A segmented deformable mirror stands in for the segmented primary mirror and allows control of the 18 segments in piston, tip, and tilt, while the secondary can be controlled in tip, tilt and x, y, z position. This will be sufficient to model many commissioning activities, to investigate field dependence and multiple field point sensing &amp;amp; control, to evaluate alternate sensing algorithms, and develop contingency plans. Testbed data will also be usable for cross-checking of the WFS&amp;amp;C Software Subsystem, and for staff training and development during JWST’s five- to ten-year mission.
Macrophage response to bacteria: induction of marked secretory and cellular activities by lipoteichoic acids (1992)

Lipoteichoic acids (LTAs) from various bacterial species, including Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Enterococcus faecalis, and Listeria monocytogenes, were examined for the ability to induce secretory and cellular responses in a pure population of bone marrow-derived mononuclear phagocytes. Some of the highly purified LTAs, in particular LTAs from Bacillus subtilis, S. pyogenes, E. faecalis, and Enterococcus hirae, were able to affect each of the macrophage parameters measured, i.e., reductive capacity, secretion of tumor necrosis factor and nitrite, and tumoricidal activity. As after stimulation with whole organisms or other bacterial products, secretion of tumor necrosis factor induced by these LTAs reached its maximum within the first few hours of the interaction, while secretion of nitrite and tumoricidal activity required 24 to 36 h for full expression. Other purified LTAs, i.e., LTAs from Streptococcus sanguis, S. pneumoniae, and L. monocytogenes, as well as lipomannan from Micrococcus luteus affected only some of these parameters, while native LTA from S. aureus was inactive. There was no obvious correlation between biological activity and chain length, kind of glycosyl substituents, glycolipid structures, or fatty acid composition of LTAs. Deacylation of LTAs resulted in a complete loss of activity, and deacylated LTAs did not impair the activity of their acylated counterparts, suggesting that acyl chains may be essential for binding of LTA to the cell surface. The results demonstrate that some LTA species are potent inducers of macrophage secretory and cellular activities.
Service-Oriented Business Performance Management for Real-Time Enterprise (2006)

This paper presents a SOMA based methodology of defining SOA for business performance management. This method is coined as BPM SOMA. We will describe the essential capabilities that are supported by business performance management systems and how these capabilities can be materialized into BPM services that would constitute an SOA for business performance management (BPM). Business integration generates many technologies in last couple of decades, e.g., application integration, middleware, business process modeling and integration, business intelligence and business service management. To a larger extent, BPM contains part of all of the technologies for business integration. Customers are facing more severe business integration challenges than ever. For example, the gap between business and IT is becoming greater. Simple solution of exposing data to customers on the glass is not sufficient to help customers operate their businesses. BPM is aimed for resolving business integration issues by providing an integrated framework, enabling an organization to understand the status of business processes across business and IT, placing that understanding in context against goals and trends and taking timely action to improve business operations.
Computer aids for decision-making in diagnostic radiology—a literature review (1995)

This review looks at a variety of different ways in which computers can be used to assist in the interpretation of radiological images and in radiological decision-making. The issues involved in the design of computerized decision aids are introduced and four criteria proposed for evaluating such aids: need, practicality, veracity and relevance. These criteria are used to assess research into decision aids based on: image databases, numerical methods, expert systems, image processing and image understanding systems. Possible directions for research leading to aids of practical value are discussed in the conclusion.
Searches for Majorana neutrinos inB−decays (2012)

Searches for heavy Majorana neutrinos in ${B}^{\ensuremath{-}}$ decays in final states containing hadrons plus a ${\ensuremath{\mu}}^{\ensuremath{-}}{\ensuremath{\mu}}^{\ensuremath{-}}$ pair have been performed using $0.41\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of data collected with the LHCb detector in proton-proton collisions at a center-of-mass energy of 7 TeV. The ${D}^{+}{\ensuremath{\mu}}^{\ensuremath{-}}{\ensuremath{\mu}}^{\ensuremath{-}}$ and ${D}^{*+}{\ensuremath{\mu}}^{\ensuremath{-}}{\ensuremath{\mu}}^{\ensuremath{-}}$ final states can arise from the presence of virtual Majorana neutrinos of any mass. Other final states containing ${\ensuremath{\pi}}^{+}$, ${D}_{s}^{+}$, or ${D}^{0}{\ensuremath{\pi}}^{+}$ can be mediated by an on-shell Majorana neutrino. No signals are found and upper limits are set on Majorana neutrino production as a function of mass, and also on the ${B}^{\ensuremath{-}}$ decay branching fractions.
Lock-free linked lists and skip lists (2004)

Lock-free shared data structures implement distributed objects without the use of mutual exclusion, thus providing robustness and reliability. We present a new lock-free implementation of singly-linked lists. We prove that the worst-case amortized cost of the operations on our linked lists is linear in the length of the list plus the contention, which is better than in previous lock-free implementations of this data structure. Our implementation uses backlinks that are set when a node is deleted so that concurrent operations visiting the deleted node can recover. To avoid performance problems that would arise from traversing long chains of backlink pointers, we introduce flag bits, which indicate that a deletion of the next node is underway. We then give a lock-free implementation of a skip list dictionary data structure that uses the new linked list algorithms to implement individual levels. Our algorithms use the single-word C&S synchronization primitive.
An Outlook for Quantum Computing [Point of View] (2018)

We have ubiquitous presence of computers today, ranging from simple controllers in modern appliances to smartphones in our pockets that provide a wide range of everyday services, to powerful supercomputers and large data centers that carry out the most computationally intensive tasks. These computational machines have a few things in common: for example, the information they handle is stored in bits (0 or 1), and the procedure for processing the information is specified by a program. A great deal is known about the limits of what such computational machines can and cannot do efficiently. There are many important computational problems that are believed to be very difficult to solve using even the most powerful computers, where the resource requirement-whether it is the size of the machine or the time it takes to finish the task-increases exponentially as a function of the problem size.
Seasonal Fluctuation of Ergovaline and Total Ergot Alkaloid Concentrations in Tall Fescue Regrowth (2011)

ABSTRACT Common cultivars of tall fescue [ Schedonorus arundinaceus (Schreb.) Dumort = Lolium arundinaceum (Schreb.) Darbysh.] host a fungal endophyte that produces ergot alkaloids. These alkaloids are linked to fescue toxicosis, a serious livestock disorder in the United States. This study was conducted to determine how ergot alkaloid concentrations fluctuate throughout the growing season in tall fescue regrowth. In 2005, plots were established in pastures of endophyte‐infected tall fescue growing in Missouri, Georgia, and South Carolina. Each month of the growing season, plots were clipped and forage allowed to regrow; regrowth was sampled from April through October 2006 and analyzed for ergovaline and total ergot alkaloid concentrations. At all three sites, ergovaline concentration was lowest during the spring, increasing slightly through the summer months and then sharply in the early autumn. This pattern of ergovaline fluctuation did not mimic data published from experiments in which tall fescue was grazed or was allowed to grow without defoliation. Total ergot alkaloid concentration followed a bimodal curve, with highest concentration in the spring and fall and lowest concentration in the summer. We conclude that common cultivars of endophyte‐infected tall fescue should be regarded as highly toxic in the autumn and less toxic in the summer, even if pastures are clipped. We also conclude that the toxicity potential of tall fescue regrowth in the spring depends on which ergot alkaloids prove most responsible for fescue toxicosis.
Convenient One-Pot Synthesis of Sulfonyl Chlorides from Thiols Using Sulfuryl Chloride and Metal Nitrate (1992)

Abstract Various sulfonyl chlorides were obtained in excellent yields by the reaction of alkyl and aryl thiols with sulfuryl chloride in the presence of metal nitrate under mild condition in aprotic solvents such as acetonitrile and N,N-dimethylformamide.
Modeling and Simulation Methods for MDOF Structures and Rotating Machinery With Impact Dampers (1997)

Previously published work on applied impact damping typically relates to SDOF models or simple MDOF models such as the classical cantilever beam. Structural models often require an extremely large number of DOF with mode shapes that are generally very complex. Dynamics simulation of these typically becomes both complicated and time consuming. The nonlinear behavior of impact dampers further complicates such simulation in that standard linear solutions are not possible. The primary objective in this research extends previous work by applying impact dampers to MDOF structures that are modeled with general three-dimensional “beam” finite elements. Modal-based models of the MDOF systems and efficient impact damper tracking algorithms were also developed that significantly reduced CPU time for simulation. Significant among the objectives was obtaining an impact damper design for the MDOF casing structure of the Space Shuttle Main Engine (SSME), High-Pressure Oxygen Turbo-Pump (HPOTP), subject to pump rotor shaft unbalance. Impact damper performance is based on suppression of vibration at casing critical frequencies for rotor speed ranges, at rotor full speed, and very high unbalance to simulate a defect such as losing an impeller blade fragment or a cracked bearing [6]. Simulations show significant reductions in vibration at the casing critical frequencies and very high unbalance levels while little or no improvement was observed off resonance. Additionally, the previous work with an experimental rotor bearing system (RBS) and impact damper was modeled using the developed modal-based methods. Simulation of the resulting model response shows remarkable agreement with the experimental. Finally, both the RBS and the HPOTP were modeled and simulated as unstable systems with attached impact dampers. The simulations predict that the impact damper is an excellent stabilizing mechanism for a range of instability driver values. Simulation of the models in this research with the developed modal based algorithms were accomplished with excellent efficiency, and accurate results.
Extended Halogen Bonding between Fully Fluorinated Aromatic Molecules (2015)

Halogen bonding is a noncovalent interaction where an electrophilic cap on a halogen atom, the so-called σ-hole, attracts a nucleophilic site on an adjacent molecule. The polarizability of halogens relates to the strength of the σ-hole, and accordingly the halogen-halogen distance becomes shorter in the order of Cl, Br, and I. Fully fluoro-substituted aromatic molecules, on the contrary, are generally believed not to form halogen bonds due to the absence of a σ-hole. Here, we study atomic-scale in-plane F-F contacts with high-resolution force microscopy. Our ab initio calculations show that the attractive dispersion forces can overcome the electrostatic repulsion between the fluorine atoms, while the anisotropic distribution of the negative electrostatic potential leads the directional bond and even changes the gap. The coexistence of these two competing forces results in the formation of a "windmill" structure, containing three C-F···F bonds among neighboring molecules. While the σ-hole is absent, the scheme of the C-F···F bonding has a high similarity to halogen bonding.