gebhart/patrepeval huggingface dataset:
Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction (2015)

RNA viruses have the highest known mutation rates. Consequently it is likely that a high proportion of individual RNA virus genomes, isolated from an infected host, will contain lethal mutations and be non-functional. This is problematic if the aim is to clone and investigate high-fitness, functional cDNAs and may also pose problems for sequence-based analysis of viral evolution. To address these challenges we have performed a study of the evolution of classical swine fever virus (CSFV) using deep sequencing and analysis of 84 full-length cDNA clones, each representing individual genomes from a moderately virulent isolate. In addition to here being used as a model for RNA viruses generally, CSFV has high socioeconomic importance and remains a threat to animal welfare and pig production. We find that the majority of the investigated genomes are non-functional and only 12% produced infectious RNA transcripts. Full length sequencing of cDNA clones and deep sequencing of the parental population identified substitutions important for the observed phenotypes. The investigated cDNA clones were furthermore used as the basis for inferring the sequence of functional viruses. Since each unique clone must necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones. Viruses rescued from the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral evolution. Importantly, ancestral reconstruction can be done even on the basis of a set of sequences that all correspond to non-functional variants.
Toxicity and Safety of Fats and Oils (2005)

Abstract The past two decades has produced an ever increasing awareness of the role of dietary fat in the etiology of different chronic diseases (e.g. diabetes, coronary heart disease and cancer). In addition, advances in food technology methods for preserving and processing food lipids for retained nutritional and sensory appeal has coincided with increased awareness concerning the safety of dietary fats and oil sources, as they relate to both the visible and non‐visible components of the total crude lipid fraction. Increased calorie consumed from fat sources not only provides consumer exposure to natural fat and oil components (e.g. fatty acids, sterols etc.), but also derived products of oxidation and hydrogenation and the presence of natural, environmental (pollutants) or intentional (e.g. additives) xenobiotics which co‐exist, or accumulate, in the crude lipid fraction. Thus, understanding the safety of dietary fats and oils requires not only an awareness of the elements of lipid chemistry of soluble constituents in the lipid phase, but also the associated reaction conditions that may convert them to toxic products. Moreover, by predicting a risk from the combined relative toxicity and the level of exposure to the organism will enable assessment of a hazard to exposure to these chemicals. In this chapter, a number of reactive and labile fat soluble constituents are assessed for safety and potential toxicity in regard to both initiating and propagating the cascade of events that may lead to a toxic end‐point measure. Endogenous (e.g. co‐oxidation reactions) as well as exposure to exogenous (e.g. photoxidation or presence of man made pollutants) xenobiotics are analyzed in respect to the potential for inducing adverse health effects.
ChemInform Abstract: Novel Cephalosporins. Part 1. Synthesis of 3‐Benzothiopyranylthiovinyl Cephalosporins and Antibacterial Activity Against Methicillin‐Resistant Staphylococcus aureus and Vacomycin‐Resistant Enterococcus faecalis. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparative corrosion performance of black oxide, sandblasted, and fine‐drawn nitinol wires in potentiodynamic and potentiostatic tests: Effects of chemical etching and electropolishing (2004)

The corrosion performance of sandblasted (SB) and smooth fine-drawn (FD) medical-use nitinol wires was compared with the performance of wires with black oxide (BO) formed in air during their manufacture. Potentiodynamic and ASTM F746 potentiostatic tests in a 0.9 % NaCl solution were conducted on wires in their as-received, chemically etched, aged in boiling water, and electropolished states. As-received wires with various surface finishes revealed breakdown potentials in the range from -100 mV to +500 mV; similar passive current density, 10(-6) A/cm(2); and a wide hysteresis on the reverse scan, demonstrating strong susceptibility to localized corrosion. Chemically etched wires with original black oxide displayed consistent corrosion performance and surpassed, in corrosion resistance, electropolished wires that showed significantly lower breakdown (400-700 mV) and localized corrosion potentials ( approximately -50 to +113 mV). Sandblasted and fine-drawn wires exhibited rather inconsistent corrosion behavior. In potentiodynamic tests these wires could perform with equal probability either on the level of pretreated BO wires or rather similar to as-received wires. Both SB and FD wires revealed low breakdown potentials in the PS regime. SEM analysis performed before tests indicated that sandblasting was not efficient for the complete removal of the original scaling, and fine drawing aggravated the situation, resulting in a persistent scaling that contributed to the inferior corrosion performance. Inclusions (oxides, carbides, and oxidized carbides) inherited from the bulk and retained on electropolished surfaces are the cause of their inferior performance compared to chemically etched surfaces. In electropolished wires corrosion was initiated around inclusions.
Tribocorrosion behaviour of cemented carbide coatings obtained by high velocity oxygen fuel spraying (2015)

Erosion-corrosion experiments on carbide coatings were conducted to quantify the contributions of erosion and corrosion components to the total wear weight loss. WC-17Co, WC-12Co and Cr3C2-25NiCr coatings were deposited by HP-HVOF spray onto steel substrate. Wear-corrosion tests were carried out in a rotatory tribometer. The main degradation mechanisms were evaluated by electrochemical methods and SEM. Erosion-corrosion tests showed that all of the sprayed coatings were strongly affected by the action of the erosive agent in the liquid media combining wear and corrosion. The main degradation forms were dissolution of the binder matrix at the hard phase/matrix interface followed with pulling out of the carbides. Cr3C2 coatings were found to possess the lowest wear resistance among all the tested coatings.
Effects of Paired and Unpaired Eye-Blink Conditioning on Purkinje Cell Morphology (1999)

This experiment addressed (1) the importance of conjunctive stimulus presentation for morphological plasticity of cerebellar Purkinje cells and inhibitory interneurons and (2) whether plasticity is restricted to the spiny branches of Purkinje cells, which receive parallel fiber input. These issues were investigated in naive rabbits and in rabbits that received paired or unpaired presentations of the conditioned stimulus (CS) and unconditioned stimulus (US). To direct CS input to the cerebellar cortex, pontine stimulation served as the CS. Air puffs to the cornea served as the US. Paired condition rabbits received pontine stimulation for 350 msec paired with a coterminating 100-msec air puff. Unpaired condition rabbits received the same stimuli in a pseudorandom order at 1- to 32-sec intervals. Rabbits were trained for a mean of 12 days. Naive rabbits received no treatment. In Golgi-stained Purkinje neurons in lobule HVI, total dendritic length, main branch length, total spiny branch length, and number of spiny branch arbors were all greater in the naive group than in the paired and unpaired groups, which did not differ. No differences were found between the hemispheres ipsilateral and contralateral to the trained eye. The dendritic length and number of branches for inhibitory interneurons did not differ across groups. The Purkinje cell morphological changes detected with these methods do not appear to be uniquely related to the conjunctive activation of the CS and US in the paired condition.
Event-Based, 6-DOF Camera Tracking from Photometric Depth Maps (2017)

Event cameras are bio-inspired vision sensors that output pixel-level brightness changes instead of standard intensity frames. These cameras do not suffer from motion blur and have a very high dynamic range, which enables them to provide reliable visual information during high-speed motions or in scenes characterized by high dynamic range. These features, along with a very low power consumption, make event cameras an ideal complement to standard cameras for VR/AR and video game applications. With these applications in mind, this paper tackles the problem of accurate, low-latency tracking of an event camera from an existing photometric depth map (i.e., intensity plus depth information) built via classic dense reconstruction pipelines. Our approach tracks the 6-DOF pose of the event camera upon the arrival of each event, thus virtually eliminating latency. We successfully evaluate the method in both indoor and outdoor scenes and show that-because of the technological advantages of the event camera-our pipeline works in scenes characterized by high-speed motion, which are still inaccessible to standard cameras.
The relation between catastrophizing and facial responsiveness to pain (2008)

Pain catastrophizing has recently been suggested to have a social function based on a positive association observed with facial responsiveness to noxious stimulation. However, this assumption is based on studies applying nociceptive stimuli of fixed intensity, such that high catastrophizers not only displayed increased pain behavior but also rated the stimulation as being more painful. The aim of this study was to investigate the relation between catastrophizing and facial responsiveness while controlling for individual differences in pain sensitivity. The facial expression of pain was investigated in 44 young and pain-free individuals in response to painful and non-painful phasic heat stimuli. Painful temperatures were tailored to the individual sensitivity to produce moderate pain. Facial responses were videotaped and objectively examined using the Facial Action Coding System. We also assessed skin conductance activity as an autonomic indicator of pain-related responses. Catastrophizing was assessed using the Pain Catastrophizing Scale (PCS). In accordance with previous findings, subjects scoring higher on pain catastrophizing required lower thermal intensities to induce a moderately painful sensation (r=-0.40, p=0.007). However, catastrophizing did not correlate with facial responsiveness to perceptually controlled painful stimulation (r=-0.02, p=0.88). Moreover, correlation analyses revealed no significant associations between catastrophizing and skin conductance responses. The present findings provide further support for the impact of pain catastophizing on pain sensitivity. However, our finding of no relation between catastrophizing and facial responsiveness when participants are experiencing comparable psychophysical pain intensities, challenges previous assumptions that high catastrophizers display amplified pain behavior; at least in young and pain-free individuals.
Retrospective and Multivariate Statistical Analysis of Three-Spatial-Dimension ToF-SIMS Data Sets. (2007)

Abstract not provided.
Building a time machine for efficient recording and retrieval of high-volume network traffic (2005)

There are times when it would be extraordinarily convenient to record the entire contents of a high-volume network traffic stream, in order to later "travel back in time" and inspect activity that has only become interesting in retrospect.Two examples are security forensics-determining just how an attacker compromised a given machine-and network trouble-shooting, such as inspecting the precursors to a fault after the fault.We describe the design and implementation of a Time Machine to efficiently support such recording and retrieval.The efficiency of our approach comes from leveraging the heavy-tailed nature of network traffic: because the bulk of the traffic in high-volume streams comes from just a few connections, by constructing a filter that records only the first N bytes of each connection we can greatly winnow down the recorded volume while still retaining both small connections in full, and the beginnings of large connections (which often suffices).The system is designed for operation in Gbps environments, running on commodity hardware.It can hold a few minutes of a high volume stream in RAM, and many hours to days on disk; the user can flexibly configure its operation to suit the site's nature.We present simulation and operational results from three distinct Gbps production environments exploring the feasibility and efficiency of a Time Machine implementation.The system has already proved useful in enabling analysis of a break-in at one of the sites.
Induction of Apoptosis through the PKC Pathway in Cultured Dermal Papilla Fibroblasts (1997)

The dermal papilla (DP) consists of a discrete population of specialized fibroblasts that are important in the morphogenesis of the hair follicle in the embryo and in the control of the hair growth cycle in the adult. This mitotically quiescent and long-lived cell population expresses gene products that promote cell survival such as Bcl-2, and thus normally might be protected from apoptosis. We investigated whether cultured DP fibroblasts are able to undergo apoptosis by treatment with the protein kinase inhibitor staurosporine. Involvement of the PKC signaling pathway in DP fibroblast survival/death was investigated by inhibition (staurosporine and Bisindolylmaleimide (Bis) treatment) or activation (TPA; 12-O-tetradecanoylphorbol-13-acetate treatment) of PKC and characterization of DP-expressed PKC isoforms by RT-PCR. We determined that cultured DP fibroblasts undergo apoptosis, in a dose-related manner, when treated with staurosporine but not when treated with Bis, an inhibitor with narrow PKC isoform specificity. TPA confers partial and transient resistance to staurosporine-induced DP apoptosis. Staurosporine and Bis each induced G1 arrest, whereas TPA treatment of cultured DP resulted in increased entry into S-phase. The differential responses to individual inhibitors and activators of PKC may be related to the multiple PKC isoforms that DP fibroblasts express. Flow cytometric analysis indicates that the mechanism of staurosporine-induced apoptosis may be through decrease of Bcl-2 in treated DP cells or through modulation of cell cycle regulators. Correlation between sensitivity to induction of apoptosis and proliferation suggests that dermal papilla cells may normally be protected from apoptosis in vivo by their mitotically quiescent state.
Capacity-Achieving Rate-Compatible Polar Codes for General Channels (2017)

We present a rate-compatible polar coding scheme that achieves the capacity of any family of channels. Our solution generalizes the previous results [1], [2] that provide capacity-achieving rate-compatible polar codes for a degraded family of channels. The motivation for our extension comes from the fact that in many practical scenarios, e.g., MIMO systems and non-Gaussian interference, the channels cannot be ordered by degradation. The main technical contribution of this paper consists in removing the degradation condition. To do so, we exploit the ideas coming from the construction of universal polar codes. Our scheme possesses the usual attractive features of polar codes: low complexity code construction, encoding, and decoding; super-polynomial scaling of the error probability with the block length; and absence of error floors. On the negative side, the scaling of the gap to capacity with the block length is slower than in standard polar codes, and we prove an upper bound on the scaling exponent.
Use of a mechanical dissociation device to improve standardization of flow cytometric cytokeratin DNA measurements of colon carcinomas (1999)

In order to standardize dual-fluorescence DNA flow cytometry using cytokeratin (CK) antibodies, normal colonic mucosa and tumor tissue were sampled from 308 colorectal surgical specimens. Fresh colon specimens were processed directly and stored frozen until dissociation. The samples were divided into aliquots for manual dissociation with tweezers and scalpel, and parallel dissociation with an automated disaggregation device (Medimachine, DAKO Diagnostika GmbH, Hamburg, Germany). An indirect immunofluorescence method with anti-cytokeratin antibodies and propidiumiodide was applied and measured on a single-laser flow cytometer (FACScan, Becton Dickinson [BDI], Heidelberg, Germany). Evaluation with CellFit (BDI) or MultiPlus (Phoenix Flow Systems, San Diego, CA) showed that dual-parameter fluorescence propidiumiodide (DNA staining) and fluorescein-isothiocyanate (cytokeratin labeling) provides a reasonable staining method for DNA analysis of epithelial cells. No significant differences in coefficient of variation in CK-gated versus ungated cells could be observed. Normal colon mucosa served as a reliable internal, diploid DNA control. Medimachine dissociation led to a significantly higher gain of cytokeratin-positive cells compared to percentage of cytokeratin-positive cells after manual tissue disaggregation. Cytokeratin gating led to a clear-cut separation of S-phase fractions within the respective ploidy groups, irrespective of manual or automated dissociation. The S-phase fraction increased significantly from normal tissue to diploid and nondiploid tumors. In general, automated tissue preparation with the Medimachine allows simple cell-isolation for dual DNA/CK-flow cytometric measurement, improving the gain of CK-positive cells, and facilitating a standardized DNA analysis.
Hot-exciton luminescence and energy transfer intod-electron states inZn1−xMnxSe (1993)

Rapid electronic energy transfer from photoexcited electron-hole pairs into d-electron states of the ${\mathrm{Mn}}^{2+}$ion in the diluted magnetic semiconductor ${\mathrm{Zn}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Mn}}_{\mathit{x}}$Se can serve as an efficient channel to reduce the role of thermalized excitons in the recombination spectrum. This circumstance allows clear observation and characterization of luminescence from nonthermal, or ``hot,'' excitons, which have rapidly relaxed via multiple longitudinal-optical (LO) phonon emission to the excitonic band-gap state (${\mathit{E}}_{\mathit{g}\mathit{x}}$). A resonant enhancement in the hot-exciton emission is observed whenever the photon energy of excitation is exactly an integer number of LO phonons above ${\mathit{E}}_{\mathit{g}\mathit{x}}$. Tuning of the gap states in a magnetic field serves as a means of sweeping through the resonant condition for the identification of the hot luminescence. Strikingly, the amplitude variations in the hot-exciton luminescence are reflected in the Mn-ion internal d-electron emission at yellow wavelengths.
How Can We Expand the Criteria of Liver Transplantation in Hepatocellular Carcinoma? (2012)

Background: Liver transplantation (LT) has been known as a suitable treatment for hepatocellular carcinoma (HCC). The aim of this study was to evaluate the risk factors of HCC recurrence and propose new criteria for LT based on pretransplantation findings. Methods: A hundred eighty patients who underwent LT for HCC between 2002 and 2008, were reviewed retrospectively. Outcome measures included maximal tumor size and number of tumors revealed by radiologic studies before transplantation, demographics and tumor recurrence. Results: From the data of transplanted patients, maximal tumor size >6, number of tumor>7, and alpha-fetoprotein >1000 were identified as independent prognostic factors of HCC recurrence in univariate and multivariate analysis. Recurrence free survival rates in patients within these criteria at 1-year and 3-year were 97.8% and 92.6%, but those beyond these criteria were 69.8% and 50.4% (P< 0.0001). ROC curve for HCC recurrence in Milan criteria and UCSF criteria showed lower area under curve (55.9% and 49%). However, area under curve of our criteria showed high predictive value (71.5%). Conclusion: LT can improve survival for patients with advanced HCC defined as maximal tumor size ≤6cm, tumor number ≤7, or/and alphafetoprotein ≤1000ng/mL.
Biological Active Fluorobenzoates of Piperidine Range (2020)

P-fluorine, m-fluorine, o-fluorinebenzoates of 1-propyl-4-hydroxypiperidine and 1-benzyl-4-hydroxypiperidine p-fluorobenzoate have been synthesized, which showed local anesthetic activity of varying degrees. Fluorobenzoic esters of secondary alcohols cause deep and prolonged anesthesia, the introduction of fluorine leads to local anesthetics with varying degrees of effectiveness.
Occurrence and distribution of halophilic vibrios in subtropical coastal waters of Hong Kong (1986)

The summer occurrence and distribution of halophilic vibrios in the subtropical coastal waters of Hong Kong were investigated. The density of vibrios in six sample sites ranged from 90 to 6,700 per ml, which made up 0.41 to 40% of the total bacterial populations of these sample sites. The sucrose-positive vibrios were found to be much more common (88% of total vibrios) than the sucrose-negative ones. A total of 48 strains belonging to six Vibrio species were fully characterized. Among these, Vibrio alginolyticus was the most frequently isolated, followed by V. parahaemolyticus, V. harveyi, V. vulnificus, V. campbellii, and V. fluvialis. The finding that eight of the nine strains of V. harveyi showed a positive Kanagawa reaction warrants further study.
A Case for Girl-child Education to Prevent and Curb the Impact of Emerging Infectious Diseases Epidemics. (2020)

Not only do epidemics such as HIV/AIDS, Ebola Virus Disease (EVD), and the current Coronavirus Disease (COVID-19) cause the loss of millions of lives, but they also cost the global economy billions of dollars. Consequently, there is an urgent need to formulate interventions that will help control their spread and impact when they emerge. The education of young girls and women is one such historical approach. They are usually the vulnerable targets of disease outbreaks - they are most likely to be vehicles for the spread of epidemics due to their assigned traditional roles in resource-limited countries. Based on our work and the work of others on educational interventions, we propose six critical components of a cost-effective and sustainable response to promote girl-child education in resource-limited settings.