gebhart/patrepeval huggingface dataset:
Host Range and Population Survey of Spodoptera frugiperda Rhabdovirus (2019)

The Sf9 and Sf21 cell lines derived from ovarian tissues of the wide-host-range phytophagous lepidopteran <i>Spodoptera frugiperda</i> are widely used for research and commercial-scale production of recombinant proteins. These cell lines are chronically infected with a rhabdovirus (Sf-RV) that does not cause any overt cytopathic effects. We demonstrate that wild populations of <i>S. frugiperda</i> in the eastern United States and Caribbean are infected with genetically diverse strains of Sf-RV and that this virus is also capable of infecting cells of <i>Spodoptera exigua</i>, <i>Heliothis subflexa</i>, and <i>Bombyx mori</i> Feeding studies demonstrated the ability of <i>S. frugiperda</i> larvae to deposit Sf-RV onto human-consumed vegetables during feeding. Although no evidence for replication in two species of plant cells was detected, subcellular localization studies demonstrated that the Sf-RV nucleocapsid was targeted to plasmodesmata, while two forms of the accessory protein were differentiated on the basis of their ability to localize to nuclei. Collectively, the results from this study suggest that environmental exposure of humans to Sf-RV is likely to be commonplace and frequent, but its inability to replicate in plant or human cells suggests that there is no substantial risk to human health.<b>IMPORTANCE</b> Insect-derived cell lines are widely used commercially for the production of vaccines and protein-based pharmaceuticals. After decades of safe and beneficial use, it was a surprise to the biotechnology industry to discover an endemic rhabdovirus in Sf9 cells. This discovery was made possible only by the substantial advancements in DNA sequencing technologies. Given the public health concerns associated with many rhabdovirus species, several initiatives were undertaken to establish that <i>Spodoptera frugiperda</i> rhabdovirus (Sf-RV) does not pose a threat to humans. Such actions include the generation of cell lines that have been cleared of Sf-RV. Given that Sf9 is derived from a moth whose larvae feed on human-edible foods, we explored the prevalence of Sf-RV in its wild and lab-grown populations, as well as its ability to be deposited on food items during feeding. Collectively, our data suggest that there is no overt risk from exposure to Sf-RV.
Sequential Data Mining: A Comparative Case Study in Development of Atherosclerosis Risk Factors (2007)

Sequential data represent an important source of potentially new medical knowledge. However, this type of data is rarely provided in a format suitable for immediate application of conventional mining algorithms. This paper summarizes and compares three different sequential mining approaches based, respectively, on windowing, episode rules, and inductive logic programming. Windowing is one of the essential methods of data preprocessing. Episode rules represent general sequential mining, while inductive logic programming extracts first-order features whose structure is determined by background knowledge. The three approaches are demonstrated and evaluated in terms of a case study STULONG. It is a longitudinal preventive study of atherosclerosis where the data consist of a series of long-term observations recording the development of risk factors and associated conditions. The intention is to identify frequent sequential/temporal patterns. Possible relations between the patterns and an onset of any of the observed cardiovascular diseases are also studied.
Improved Synthesis of 7,5‐Fused Bicyclic Lactams for Use as Peptidomimetics (2005)

Abstract An improved synthesis of (3S, 7R, 10S)‐methyl‐2‐oxo‐3‐N‐phthaloylamino‐1‐azabicyclo[5.3.0]decane‐10‐carboxylate from L‐glutamic acid and L‐allylglycine is presented.
Treatment planning optimisation in proton therapy (2013)

The goal of radiotherapy is to achieve uniform target coverage while sparing normal tissue. In proton therapy, the same sources of geometric uncertainty are present as in conventional radiotherapy. However, an important and fundamental difference in proton therapy is that protons have a finite range, highly dependent on the electron density of the material they are traversing, resulting in a steep dose gradient at the distal edge of the Bragg peak. Therefore, an accurate knowledge of the sources and magnitudes of the uncertainties affecting the proton range is essential for producing plans which are robust to these uncertainties. This review describes the current knowledge of the geometric uncertainties and discusses their impact on proton dose plans. The need for patient-specific validation is essential and in cases of complex intensity-modulated proton therapy plans the use of a planning target volume (PTV) may fail to ensure coverage of the target. In cases where a PTV cannot be used, other methods of quantifying plan quality have been investigated. A promising option is to incorporate uncertainties directly into the optimisation algorithm. A further development is the inclusion of robustness into a multicriteria optimisation framework, allowing a multi-objective Pareto optimisation function to balance robustness and conformity. The question remains as to whether adaptive therapy can become an integral part of a proton therapy, to allow re-optimisation during the course of a patient's treatment. The challenge of ensuring that plans are robust to range uncertainties in proton therapy remains, although these methods can provide practical solutions.
HPLC on Calixarene Bonded Silica Gels. I. Characterization and Applications of the p-tert-Butyl-Calix[4]arene Bonded Material (1995)

Molecules containing cavities of well-defined dimensions are able to include guest molecules stereoselectively. This work is concerned with the introduction and evaluation of a newly developed high-performance liquid chromatographic packing material based on calix[4]arene chemically bonded to silica gel. It is well documented that calixarenes representing cyclic condensates of para substituted phenols and formaldehyde have the ability to form intracavity inclusion complexes with ions and organic molecules in aqueous solutions. The silica bonded macrocyclic ligands form truncated cones similar to cyclodextrins. Data are presented illustrating the resolution characteristics for disubstituted aromatics, peptides, nucleosides, and nucleobases. The results indicate that the calix[4]arene silica gel behaves predominantly as a reversed-phase material. Some effects support the assumption that the cavity acting as an electron donator can influence the elution order.
Adaptive epsilon non-dominated sorting multi-objective evolutionary optimization and its application in shortest path problem (2009)

This paper presents an adaptive epsilon non-dominated sorting method for multi-objective evolutionary optimization which has the ability to preserve both the efficiency and diversity. In NSGA-II, a fast non-dominated sorting mechanism is applied to sort solutions in an efficient way. However, it may suffer from deterioration and diversity in population is not as great as expected. To solve this problem, the concept of epsilon-dominance is applied for updating solutions in non-dominate sorted layers according to adaptive epsilon value, and the novel update strategy could prevent deterioration and keep diversity well. A real-world city map with 410 nodes and 1334 arcs is used in experiment, and the result shows that the proposed algorithm (AENSGA) performs better than NSGA-II in multi-objective shortest path problem.
Wang Di, The Teahouse : Small business, everyday culture, and public politics in Chengdu, 1900-1950, 2008 (2009)

Paulès Xavier. Wang Di, The Teahouse : Small business, everyday culture, and public politics in Chengdu, 1900-1950, 2008. In: Études chinoises, n°28, 2009. Numéro spécial sur le droit chinois. pp. 305-309.
Contacts between 16S ribosomal RNA and mRNA, within the spacer region separating the AUG initiator codon and the Shine -Dalgarno sequence; a site-directed cross-linking study (1994)

mRNA analogues containing several 4-thiouridine (thio-U) residues at selected positions were prepared by T7-transcription. The spacer region between the Shine-Dalgarno sequence and the AUG codon consisted of four or eight bases with a single thio-U at a variable position; alternatively, cro-mRNA analogues were used carrying the thio-U substituted spacer sequence UUGU. The mRNAs were bound to E. coli ribosomes, and--after irradiation--the sites of cross-linking to 16S RNA were analysed. Three cross-links to the 16S RNA from the spacer region were observed, namely to positions 665, 1360, and a site close to nucleotide 1530. The cross-links were formed in different amounts in the presence or absence of tRNA(fMet), and were observed from thio-U residues located at various positions within the spacer sequence, although in the presence of tRNA they were in general stronger from positions close to the Shine-Dalgarno end of the spacer. The cross-linking behaviour in this upstream area of the mRNA is thus rather different in character from the previously published pattern in the downstream area. From considerations of structural conservation in small subunit RNA, we propose that both the upstream and downstream cross-links to 16S RNA reflect a universal mRNA path through the ribosome.
Approaching a reliable process simulation for the virtual product development (2005)

In this paper an outline for a strategy to include manufacturing effects in subsequent simulations for the virtual product development from an industrial point of view is given. Especially the conditions for a successful mapping of geometry and results between different applications are discussed. An example shows the significance of the inclusion of previous simulations in the final assessment of a part.
Major Phenolics in Yerba Mate Extracts (&lt;i&gt;Ilex paraguariensis&lt;/i&gt;) and Their Contribution to the Total Antioxidant Capacity (2013)

Yerba mate (Ilex paraguariensis) is an indigenous crop which is highly consumed as an infusion in the South American subtropical forest. It has a high concentration of antioxidant substances, providing health benefits and helping to prevent diseases. The objectives of this work were to characterize an aqueous yerba mate extract by spectrophotometric and chromatographic (HPLC) methods and to study the effect of the freeze-drying process on the polyphenols profile and antioxidant activity, determined by a novel method. An aqueous extract was obtained and lyophilized to obtain a yerba mate powder with antioxidant properties. The extracts showed a high polyphenol content, determined by Folin-Ciocalteau and HPLC, and a high antioxidant activity towards the DPPH· radical and after the recently developed method of photochemiluminescence. A linear correlation was found between Folin-Ciocalteau and DPPH methods for lyophilized samples. HPLC analysis allowed determining antioxidant components like rutin, caffeine and chlorogenic acid. Lyophilization caused a decrease in total polyphenol content and antiradical activity of the extracts and this fact was mainly attributed to changes in the chlorogenic acid related compounds and rutin structures, after their photochemiluminescence data. The photoluminiscent method proves to be an advantageous approach for antioxidant capacity determination.
To Buffer, or Not to Buffer? A Case Study on FFT Accelerators for Ultra-Low-Power Multicore Clusters (2021)

Hardware-accelerated multicore clusters have recently emerged as a viable approach to deploy advanced digital signal processing (DSP) capabilities in ultra-low-power extreme edge nodes. As a critical basic block for DSP, Fast Fourier Transforms (FFTs) are one of the best candidates for implementation on a dedicated accelerator core; however, their peculiar memory access patterns make direct integration of an FFT accelerator with a core cluster challenging. In this paper, we compare two different approaches for cluster-coupled FFT accelerators: one with a large internal buffer to store and shuffle partial results; and a buffer-less accelerator sharing all memory with the cluster cores. Both versions can work on complex data with 8/16/32-bit real and imaginary parts. We show that, thanks to a newly proposed scheme to reorder data access and exploit full bandwidth also for sub-word FFTs, the buffer-less accelerator can be made as fast as the buffered one at only 0.26× the area cost. We report post-layout performance and power results showing that the buffer-less accelerator can provide up to 4/2/1 butterfly/cycle performance, with an average power consumption of 4.1/5.5/6.8 mW @ 350 MHz, 0.65 V operating point in 22 nm CMOS technology, respectively for complex data with 8/16/32-bit real and imaginary part. The buffer-less accelerator is 8 × faster than an optimized multicore software implementation working on 16-bit data and compares favorably with FFT accelerators presented in the recent literature.
Polyfunctional HCV‐specific T‐cell responses are associated with effective control of HCV replication (2008)

HCV infection has a severe course of disease in HIV/HCV co-infection and in liver transplant recipients. However, the mechanisms involved remain unclear. Here, we evaluated functional profiles of HCV-specific T-cell responses in 86 HCV mono-infected patients, 48 HIV/HCV co-infected patients and 42 liver transplant recipients. IFN-gamma and IL-2 production and ability of CD4 and CD8 T cells to proliferate were assessed after stimulation with HCV-derived peptides. We observed that HCV-specific T-cell responses were polyfunctional in HCV mono-infected patients, with presence of proliferating single IL-2-, dual IL-2/IFN-gamma and single IFN-gamma-producing CD4+ and dual IL-2/IFN-gamma and single IFN-gamma-producing CD8+ cells. In contrast, HCV-specific T-cell responses had an effector profile in HIV/HCV co-infected individuals and liver transplant recipients with absence of single IL-2-producing HCV-specific CD4+ and dual IL-2/IFN-gamma-producing CD8+ T cells. In addition, HCV-specific proliferation of CD4+ and CD8+ T cells was severely impaired in HIV/HCV co-infected patients and liver transplant recipients. Importantly, "only effector" T-cell responses were associated with significantly higher HCV viral load and more severe liver fibrosis scores. Therefore, the present results suggest that immune-based mechanisms may contribute to explain the accelerated course of HCV infection in conditions of HIV-1 co-infection and liver transplantation.
Epidermal Growth Factor Receptor–Targeted Immunoliposomes Significantly Enhance the Efficacy of Multiple Anticancer Drugs<i>In vivo</i> (2005)

We previously reported the development of epidermal growth factor receptor (EGFR)-targeted immunoliposomes that bind and internalize in tumor cells which overexpress EGFR and/or mutant EGFR variant III (EGFRvIII), enabling intracellular delivery of potent anticancer agents in vitro. We now describe in vivo proof-of-concept for this approach for the delivery of multiple anticancer drugs in EGFR-overexpressing tumor models. Anti-EGFR immunoliposomes were constructed modularly with Fab' fragments of cetuximab (IMC-C225), covalently linked to liposomes containing probes and/or anticancer drugs. Pharmacokinetic and biodistribution studies confirmed long circulation times (t(1/2) = 21 hours) and efficient accumulation in tumors (up to 15% ID/g) irrespective of the presence of the targeting ligand. Although total accumulations of anti-EGFR immunoliposomes and nontargeted liposomes in EGFR-overexpressing tumors were comparable, only immunoliposomes internalized extensively within tumor cells (92% of analyzed cells versus <5% for nontargeted liposomes), indicating different mechanisms of delivery at the cellular level. In vivo therapy studies in a series of xenograft models featuring overexpression of EGFR and/or EGFRvIII showed the superiority of immunoliposomal delivery of encapsulated drugs, which included doxorubicin, epirubicin, and vinorelbine. For each of these drugs, anti-EGFR immunoliposome delivery showed significant antitumor effects and was significantly superior to all other treatments, including the corresponding free or liposomal drug (P < 0.001-0.003). We conclude that anti-EGFR immunoliposomes provide efficient and targeted drug delivery of anticancer compounds and may represent a useful new treatment approach for tumors that overexpress the EGFR.
Member spotlight (2021)

In this feature of the Bulletin, we highlight members of the SIGCSE community. In this issue, Bulletin co-editor Karen Davis interviewed Leo Porter, an Associate Teaching Professor of Computer Science at the University of California, San Diego, the current Secretary on the SIGCSE Board, and a former SIGCSE Bulletin Co-Editor.
Domain structure of the Moloney murine leukemia virus reverse transcriptase: mutational analysis and separate expression of the DNA polymerase and RNase H activities. (1988)

The reverse transcriptase of Moloney murine leukemia virus, like that of all retroviruses, exhibits a DNA polymerase activity capable of synthesis on RNA or DNA templates and an RNase H activity with specificity for RNA in the form of an RNA.DNA hybrid. We have generated a library of linker insertion mutants of the Moloney murine leukemia virus enzyme expressed in bacteria and assayed these mutants for both enzymatic activities. Those mutations affecting the DNA polymerase activity were clustered in the 5'-proximal two-thirds of the gene, and those affecting RNase H were in the remaining 3' one-third. Based on these maps, plasmids were made that expressed each one of the domains separately; assays of the proteins encoded by these plasmids showed that each domain exhibited only the expected activity.
A pinchable aerial virtual sphere by acoustic ultrasound stationary wave (2014)

In this paper, we propose a system to generate aerial virtual spheres which invokes tactile sensation and is omni-directionally pinchable. The acoustic radiation force of ultrasound stationary waves is known in the field of non-contact micro manipulation. This force applied to a small object in the stationary wave is in proportion to the gradient of the square of the acoustic pressure and directing from anti-node to node. We demonstrate a prototype system consisting of 996 transducers which generates a focal anti-node point at the center of the workspace. We performed the acoustic pressure distribution analysis and subjective experiments. As a result, it is discovered that the virtual sphere was sensed as the same size as theoretically expected.
Study on Metal-Induced Reactions of α-Diazocarbonyl Glucosides (2012)

Conversions of diazocarbonyl carbohydrate compounds catalyzed by a series of rhodium and copper catalysts in conventional heating or microwave conditions were investigated. C-H insertion product was obtained in the presence of Rh(2)(OAc)(4). Intermolecular reactions rather than intramolecular reactions occurred in the presence of copper catalysts.
Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts (1978)

A computer branching model is used to analyze cellular evolution. Attention is given to certain key amino acids and nucleotide residues (ferredoxin, 5s ribosomal RNA, and c-type cytochromes) because of their commonality over a wide variety of cell types. Each amino acid or nucleotide residue is a sequence in an inherited biological trait; and the branching method is employed to align sequences so that changes reflect substitution of one residue for another. Based on the computer analysis, the symbiotic theory of cellular evolution is considered the most probable. This theory holds that organelles, e.g., mitochondria and chloroplasts invaded larger bodies, e.g., bacteria, and combined functions to form eucaryotic cells.
Diagnosis, microbial epidemiology, and antibiotic treatment of acute otitis media in children: a systematic review. (2010)

Otoscopic findings are critical to accurate AOM diagnosis. AOM microbiology has changed with use of PCV7. Antibiotics are modestly more effective than no treatment but cause adverse effects in 4% to 10% of children. Most antibiotics have comparable clinical success.
The Marine Dynamics and Changing Trend off the Modern Yellow River Mouth (2015)

Topography around the Yellow River mouth has changed greatly in recent years, but studies on the current state of ma- rine dynamics off the Yellow River mouth are relatively scarce. This paper uses a two-dimension numerical model(MIKE 21) to reveal the tidal and wave dynamics in 2012, and conducts comparative analysis of the changes from 1996 to 2012. The results show that M2 amphidromic point moved southeastward by 11 km. It further reveals that the tides around the Yellow River mouth are relatively stable due to the small variations in the tidal constituents. Over the study period, there is no noticeable change in the distribution of tidal types and tidal range, and the mean tidal range off the river mouth during the period studied is 0.5–1.1 m. However, the tidal currents changed greatly due to large change in topography. It is observed that the area with strong tidal currents shifted from the old river mouth(1976–1996) to the modern river mouth(1996–present). While the tidal current speeds decreased continually off the old river mouth, they increased off the modern river mouth. The Maximum Tidal Current Speed(MTCS) reached 1.4 m s-1, and the maximum current speed of 50-year return period reached 2.8 m s-1. Waves also changed greatly due to change in topography. The significant wave height(H1/3) of 50-year return period changed proportionately with the water depth, and the ratio of H1/3 to depth being 0.4–0.6. H1/3 of the 50-year return period in erosion zone increased continually with increasing water depth, and the rate of change varied between 0.06 and 0.07 m yr-1. Based on the results of this study, we infer that in the future, the modern river mouth will protrude gradually northward, while the erosion zone, comprising the old river mouth and area between the modern river mouth and the old river mouth(Intermediate region) will continue to erode. As the modern river mouth protrudes towards the sea, there will be a gradual increase in the current speed and decrease in wave height. Conversely, the old
<i>Escherichia coli</i> chorismate synthase: a deuterium kinetic-isotope effect under single-turnover and steady-state conditions shows that a flavin intermediate forms before the C-(6<i>proR</i>)-H bond is cleaved (1995)

We report the observation of a deuterium kinetic isotope effect for the conversion of 5-enolpyruvylshikimate-3-phosphate into chorismate (6proR2HV = 1.13 +/- 0.03) using recombinant chorismate synthase from Escherichia coli. Similar isotope effects were observed for the decay of a spectroscopically characterized flavin intermediate (6proR2Hk = 1.17 +/- 0.04) during single-turnover experiments. The main rate-limiting steps and C-(6proR)-H bond breaking are therefore distinct and both must occur after the formation of the flavin intermediate and either before or concomitant with its decay.
Deferoxamine posttreatment reduces ischemic brain injury in neonatal rats. (1994)

Deferoxamine administered after induction of cerebral hypoxia-ischemia reduces injury in 7-day-old rats. Deferoxamine concentrates in the brain at levels between 100 and 200 mumol/L. At the concentrations achieved, deferoxamine might protect the brain through mechanisms unrelated to its ability to chelate iron.