Miracle-dz/UniFAR-FTUs huggingface dataset:
The M/GP5 Glycoprotein Complex of Porcine Reproductive and Respiratory Syndrome Virus Binds the Sialoadhesin Receptor in a Sialic Acid-Dependent Manner

The porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to swine health worldwide and is considered the most significant viral disease in the swine industry today. In past years, studies on the entry of the virus into its host cell have led to the identification of a number of essential virus receptors and entry mediators. However, viral counterparts for these molecules have remained elusive and this has made rational development of new generation vaccines impossible. The main objective of this study was to identify the viral counterparts for sialoadhesin, a crucial PRRSV receptor on macrophages. For this purpose, a soluble form of sialoadhesin was constructed and validated. The soluble sialoadhesin could bind PRRSV in a sialic acid-dependent manner and could neutralize PRRSV infection of macrophages, thereby confirming the role of sialoadhesin as an essential PRRSV receptor on macrophages. Although sialic acids are present on the GP3, GP4 and GP5 envelope glycoproteins, only the M/GP5 glycoprotein complex of PRRSV was identified as a ligand for sialoadhesin. The interaction was found to be dependent on the sialic acid binding capacity of sialoadhesin and on the presence of sialic acids on GP5. These findings not only contribute to a better understanding of PRRSV biology, but the knowledge and tools generated in this study also hold the key to the development of a new generation of PRRSV vaccines.
Variation in male effects on female fecundity in Drosophila melanogaster

In many species, males have the capacity to directly influence (either positively or negatively) the fitness of their mates and offspring, not only via parental care contributions and/or precopulatory resource provisioning, but also via the post‐copulatory activity of those substances passed on to their mates in their ejaculates. Here, we examine how an individual male's identity may be related to phenotypic variation in short‐term female fecundity in the model species, Drosophila melanogaster. The effect of male identity on short‐term fecundity stimulation of females was repeatable across time and accounted for over a fifth of the total observed phenotypic variation in fecundity in two independent populations. The functional explanations for these results and the implications for our understanding of the factors that contribute to the adaptive significance of mating preferences and/or sexual conflict are discussed.
Title Acoustic correlates of hypernasal fricatives Other

This study applied ERB analysis for measuring acoustic correlates of hypernasal fricatives produced by speakers with different aetiologies (cleft palate, maxillectomy and dysarthria). The speech materials were consonants /n/ and /s/ segmented from two Cantonese single words and four Cantonese oral sentences. Results showed that hypernasal speakers produced /s/ with significantly higher mean amplitudes at frequencies below 2500 Hz, and significantly lower mean amplitudes at frequencies above 3500 Hz. The findings were consistent with those obtained from a previous study with one-third-octave analysis using consonants (Chen, 2005). Slightly better correlations were found for ERB analysis in quantifying hypernasality than one-third-octave analysis.
Management of Acute Complicated and Uncomplicated Type B Dissection of the Aorta: Focus on Endovascular Stent Grafting

Endovascular repair of aortic dissection is the subject of multiple studies. This article aims to review the current literature on Type B complicated and uncomplicated dissection, including indications for medical therapy, open surgical therapy, and endovascular therapy. The review suggests a benefit for thoracic endovascular aortic repair in complicated dissection and medical therapy for uncomplicated dissection. Upcoming trials may shed more light on this issue.
Lysosomal, cytoskeletal, and metabolic alterations in cardiomyopathy of cathepsin L knockout mice

Although lysosomal proteases are expressed in the heart at considerable levels, their specific functions in this organ remain elusive. Mice deficient for the lysosomal cysteine protease cathepsin L (CTSL) develop a late onset dilated cardiomyopathy (DCM) that is characterized by cardiac chamber dilation, fibrosis, and impaired cardiac contraction at 12 month of age. Investigation of the pathogenic sequence of DCM in ctsl−/− mice revealed numerous dysmor‐phic lysosome‐like structures in heart muscle as early as 3 days after birth, whereas skeletal muscle was not affected. Labeling of the acidic cell compartment of neonatal cardiomyocytes and detection of lysosomal markers after subcellular fractionation confirmed increased lysosome content in CTSL deficient myocar‐dium; however, specific storage materials were not detected. The myocardium of ctsl+/+ and ctsl−/− mice revealed no differences in incidence of cell death, proliferation, and capillary density during DCM progression. However, an observed increase in mRNA expression of natriuretic peptides in young adult mice indicates the activation of the adaptive “fetal” gene program, while proteome analysis revealed decreased levels of the sarcomere‐associated proteins α‐tropomy‐osin, desmin, and calsarcin 1, as well as considerable changes of metabolic enzymes. Bioinformatic pathway analysis suggested a switch to anaerobic catabolism and impairment of mitochondrial respiration. This interpretation was supported by a 50% reduction in resting state oxygen consumption and impaired respiration capacity in ctsl−/− myocardial homogenates. In summary, the data indicate an essential role of CTSL in maintaining the structure of the endosomal/lysosomal compartment in cardiomyocytes. Lysosomal impairment in ctsl−/− hearts results in metabolic and sarcomeric alterations that promote DCM development. —Petermann, I. , Mayer, C. , Stypmann, J., Biniossek, M. L. , Tobin, D. J., Engelen, M. A. , Dandekar, T. , Grune, T. , Schild, L. , Peters, C. , Reinheckel, T. Lysosomal, cytoskeletal, and metabolic alterations in cardiomyopa‐thy of cathepsin L knockout mice. FASEB J. 20, E587‐E598 (2006)
Neurocognitive Basis of Schizophrenia: Information Processing Abnormalities and Clues for Treatment

Schizophrenia is a chronic and severe psychiatric disorder that affects all aspects of patients’ lives. Over the past decades, research applying methods from psychology and neuroscience has increasingly been zooming in on specific information processing abnormalities in schizophrenia. Impaired activation of and connectivity between frontotemporal, frontoparietal, and frontostriatal brain networks subserving cognitive functioning and integration of cognition and emotion has been consistently reported. Major issues in schizophrenia research concern the cognitive and neural basis of hallucinations, abnormalities in cognitive-emotional processing, social cognition (including theory of mind), poor awareness of illness, and apathy. Recent findings from cognitive neuroscience studies in these areas are discussed. The findings may have implications for treatment, for example, noninvasive neurostimulation of specific brain areas. Ultimately, a better understanding of the cognitive neuroscience of schizophrenia will pave the way for the development of effective treatment strategies.
Analyses on Electromagnetic and Temperature Fields of Superhigh-Speed Permanent-Magnet Generator With Different Sleeve Materials

In this paper, a superhigh-speed permanent-magnet generator (SHSPMG) which has an alloy sleeve on the rotor outer surface is investigated. The purpose of the sleeve is to fix the permanent magnets and protect them from being destroyed by the large centrifugal force. However, the sleeve material characteristics have much influence on the superhigh-speed machine, and therewith, most of rotor eddy-current losses are generated in the alloy rotor sleeve, which could increase the device temperature. Taking a 117-kW 60 000-r/min SHSPMG as an example, the influence of the sleeve on the generator output performance is analyzed when the generator sleeve is made of stainless steel, carbon fiber, copper-iron alloy, and copper. In addition, the eddy-current loss distributions could be gotten, and therewith, the variations of the eddy-current losses in different kinds of sleeves are analyzed. Based on the 3-D coupling field between the fluid and temperature, the temperature distributions were obtained when the sleeve adopts different materials. Moreover, the temperature variations of the permanent magnets are further analyzed. The obtained conclusions may provide some references for the design and analyses of the SHSPMG.
In vitro mitomycin C absorption and delivery with different sponge materials used in filtering surgery

Purpose The purpose of this study is to evaluate and compare mitomycin C (MMC) absorption and delivery in different materials used in filtering surgery. Methods This is an in vitro study comparing polyvinyl alcohol triangular sponges (TS6, TS8), polyvinyl alcohol fluid wicks (EFW), and absorbable gelatin sponges (AGS3, AGS5), from which five different types of transport units were obtained. Seven pieces of sponge of each transport unit type were obtained as follows: two transverse strips were obtained at 6 and 8 mm from the apex of TS and divided into three equal pieces; 4×4 mm pieces of EFW; 3×3 and 5×5 mm pieces of absorbable gelatin sponges were cut. Filter paper was placed on a precision scale (0.01 mg). The seven sponge pieces of each type were weighed three times consecutively in dry and wet states, the latter after immersion for 15 seconds in 0.2 mg/mL MMC. The difference between the weights of the dry and wet filter paper at the end of each measurement sequence was also calculated and considered as an estimate of the amount of mitomycin delivered. Results The amounts of MMC absorbed by each transport unit were as follows: (mean ± standard deviation) 27.43±5.13 for TS6, 31.91±6.63 for TS8, 15.96±2.23 for EFW, 17.96±2.05 for AGS3, and 33.81±2.05 for AGS5. The amounts of MMC delivered to the filter paper were as follows: 21.70±2.84 for TS6, 23.83±4.03 for TS8, 12.93±1.75 for EFW, 14.69±1.79 for AGS3, and 27.30±1.58 for AGS5. Conclusion Percentage MMC delivered was similar for all materials, but there was a tendency for greater delivery using larger sponges and greater homogeneity in delivery with AGS5. No statistical differences were found in percentage delivered by the different transport materials.
Understanding Neural Networks Through Deep Visualization

Recent years have produced great advances in training large, deep neural networks (DNNs), including notable successes in training convolutional neural networks (convnets) to recognize natural images. However, our understanding of how these models work, especially what computations they perform at intermediate layers, has lagged behind. Progress in the field will be further accelerated by the development of better tools for visualizing and interpreting neural nets. We introduce two such tools here. The first is a tool that visualizes the activations produced on each layer of a trained convnet as it processes an image or video (e.g. a live webcam stream). We have found that looking at live activations that change in response to user input helps build valuable intuitions about how convnets work. The second tool enables visualizing features at each layer of a DNN via regularized optimization in image space. Because previous versions of this idea produced less recognizable images, here we introduce several new regularization methods that combine to produce qualitatively clearer, more interpretable visualizations. Both tools are open source and work on a pre-trained convnet with minimal setup.
Rapid and sensitive detection of ostreid herpesvirus 1 in oyster samples by real-time PCR

Herpes and herpes-like virus infections have been reported in various marine mollusc species associated with high mortality rates. Following the characterisation and genome sequencing of ostreid herpesvirus 1 (OsHV-1), specific diagnostic tools have been developed based on conventional PCR techniques or in situ hybridisation. We have now developed a real-time PCR assay for rapid, sensitive and quantitative detection of OsHV-1, and compared it with a conventional PCR technique described previously. The new assay utilised SYBR® Green chemistry with specific primers C9/C10 targeting the C region. The melt curve analysis of OsHV-1 DNA or DNA extracted from infected material showed only one melting temperature peak (75.75 ± 0.1 °C). The assay had a detection limit of 4 copies/μL of viral genomic DNA and a dynamic range of 5 logs. Using infected oyster samples as template, the assay was about 100-fold more sensitive than single PCR method using C2/C6 primers. The assay was applied successfully for rapid diagnosis (100 min) and quantitation of OsHV-1 in different developmental stages of Crassostrea gigas. Although it already exists a competitive PCR method to quantify OsHV-1 DNA, quantitative data that will emerge in future using the new sensitive and reliable assay will illuminate aspects of pathogenesis, in particular the viral loads in asymptomatic oysters and the kinetics of infection in specific target tissues.
Riluzole Enhances Ionizing Radiation–Induced Cytotoxicity in Human Melanoma Cells that Ectopically Express Metabotropic Glutamate Receptor 1 In Vitro and In Vivo

Purpose: Brain metastases are a common preterminal event in patients with metastatic melanoma and require radiation therapy. Our group has previously shown that human GRM1 (hGRM1) expressing melanoma cells release excess extracellular glutamate and are growth inhibited by riluzole, an inhibitor of glutamate release. Riluzole-treated cells accumulate in G2/M phase of the cell cycle at 24 hours, and then undergo apoptotic cell death. We evaluated whether riluzole enhanced radiosensitivity in melanoma cells. Experimental Design: Clonogenic assays were performed to evaluate clonogenic survival after treatment in hGRM1 expressing and nonexpressing melanoma cells. Western immunoblots were performed to confirm apoptotic cell death. A xenograft mouse model was used to validate the in vitro experiments. Tumors harvested from the xenografts were fixed and stained for apoptosis and DNA damage markers. Results: In the hGRM1-positive cell lines C8161 and UACC903, riluzole enhanced the lethal effects of ionizing radiation; no difference was seen in the hGRM1-negative UACC930 cell line. C8161 cells treated with riluzole plus irradiation also showed the highest levels of the cleaved forms of PARP and caspase-3; excised C8161 xenografts showed the greatest number of apoptotic cells by immunohistochemistry (P < 0.001). On cell cycle analysis, a sequence-dependent enrichment in the G2/M phase was shown with the combination of riluzole and irradiation. Xenografts treated with riluzole and weekly radiation fractions showed significant growth inhibition and revealed markedly increased DNA damage. Conclusions: We have shown, in vitro and in vivo, that the combination of riluzole and ionizing radiation leads to greater cytotoxicity. These results have clinical implications for patients with brain metastases receiving whole brain radiation therapy. Clin Cancer Res; 17(7); 1807–14. ©2011 AACR.
Reducing Failure Analysis Time: An Industrial Evaluation

Testing and debugging automotive cyber physical systems are challenging. Developing and integrating cyber and physical components require extensive testing to ensure reliable and safe releases. One important cost factor in the debugging process is the time required to analyze failures. Since large number of failures usually happen due to a few underlying faults, clustering failures based on the responsible faults helps reduce analysis time. We focus on the software-in-the-loop and hardware-in-the-loop levels of testing where test execution times are high. We devise a methodology for adapting existing clustering techniques to a real context. We augment an existing clustering approach by a method for selecting representative tests. To analyze failures, rather than investigating all failing tests one by one, testers inspect only these representatives. We report on the results of a large scale industrial case study. We ran experiments on ca. 850 KLOC. Results show that utilizing our clustering tool, testers can reduce failure analysis time by more than 80%.
New Procedures for Purification of l-Asparaginase with High Yield from Escherichia coli

l-Asparaginase is now known to be a potent antineoplastic agent in animals and has given complete remission in some human leukemias. Extensive clinical trials of this enzyme, however, were not possible in the past because of inadequate production of this substance. We have developed practical procedures for producing l-asparaginase in yields of sufficient quantity and purity for more extensive clinical evaluation. The nutritional requirements for optimal production of biologically active l-asparaginase by a strain of Escherichia coli have been ascertained. The highest yields of enzyme were obtained when cells were grown aerobically in a corn steep medium. Good enzyme production was associated with media containing l-glutamic acid, l-methionine, and lactic acid. The addition of glucose to the medium, however, resulted in depressed production of l-asparaginase. Sodium ion appeared to suppress l-asparaginase production. With the procedure described for isolation of biologically active l-asparaginase from E. coli, stable l-asparaginase preparations with a specific activity of 620 IU per mg of protein (1,240-fold purification with 40% total recovery) were obtained.
Formal Reasoning Ability and Misconceptions concerning Genetics and Natural Selection.

Students often hold misconceptions about natural phenomena. To overcome misconceptions students must become aware of the scientific conceptions, the evidence that bears on the validity of their misconceptions and the scientific conceptions, and they must be able to generate the logical relationships among the evidence and alternative conceptions. Because formal operational reasoning patterns are necessary to generate these logical relationships, it was predicted that, following instruction, formal operational students would hold significantly fewer misconceptions than their concrete operational classmates. To test this hypothesis 131 seventh-grade students were administered an essay test on principles of genetics and natural selection following instruction. Responses were categorized in terms of the number of misconceptions present. The number of misconceptions was compared to reasoning ability (concrete, transitional, formal), mental capacity (<6, 6, 7), verbal intelligence (low, medium, high), and cognitive style (field dependent, intermediate, field independent). The only student variable consistently and significantly related to the number of misconceptions was reasoning ability; thus, support for the major hypothesis of the study was obtained.
Generalization of Efficacy as a Function of Collective Action and Intergroup Relations: Involvement in an Anti‐Roads Struggle1

A questionnaire survey (n=90) and an interview study (n=63) of anti-roads activities suggest links between participation and generalization. First, level of activism predicted whether others were perceived as encouraged to act environmentally. Second, participants' failure to stop construction of the road did not prevent them from developing related feelings of efficacy. Participants' perceptions of out-groups were also examined. Participants were least hostile to those they defined as sharing their interests and capable of subjective change; they were most hostile to those seen as betraying the environmental cause. Practically, these findings suggest the importance of collective participation. Theoretically, the paper argues that efficacy theory be developed to acknowledge that identity can be collective as well as individual.
Revisiting the Racial Threat Thesis: The Role of Police Organizational Characteristics in Predicting Race‐Specific Drug Arrest Rates

Previous research examining the relationship between structural factors and drug arrest rates has neglected the role of the police organization. A central proposition of racial threat theory is that indicators of a threatening Black population will be associated with law enforcement actions as a form of social control. In order to fully test this proposition, however, organizational aspects of law enforcement beyond size of the police force must be considered. Hence, the present study examines police organizational factors as direct predictors of race‐specific drug arrest rates but also as potential moderators of the effects of structural factors on drug arrest rates. Using data from 260 cities, we find that police organizational factors matter, both directly and as moderators of the association between racial economic competition and Black drug arrest rates. Consistent with expectations derived from racial threat and organizational theory, we find that racial threat measures are associated with Black drug arrest rates under conditions of relatively low organizational control.
Assimilation of Surface Pressure Observations Using an Ensemble Filter in an Idealized Global Atmospheric Prediction System

An ensemble filter data assimilation system is tested in a perfect model setting using a low resolution Held–Suarez configuration of an atmospheric GCM. The assimilation system is able to reconstruct details of the model’s state at all levels when only observations of surface pressure (PS) are available. The impacts of varying the spatial density and temporal frequency of PS observations are examined. The error of the ensemble mean assimilation prior estimate appears to saturate at some point as the number of PS observations available once every 24 h is increased. However, increasing the frequency with which PS observations are available from a fixed network of 1800 randomly located stations results in an apparently unbounded decrease in the assimilation’s prior error for both PS and all other model state variables. The error reduces smoothly as a function of observation frequency except for a band with observation periods around 4 h. Assimilated states are found to display enhanced amplitude high-frequency gravity wave oscillations when observations are taken once every few hours, and this adversely impacts the assimilation quality. Assimilations of only surface temperature and only surface wind components are also examined. The results indicate that, in a perfect model context, ensemble filters are able to extract surprising amounts of information from observations of only a small portion of a model’s spatial domain. This suggests that most of the remaining challenges for ensemble filter assimilation are confined to problems such as model error, observation representativeness error, and unknown instrument error characteristics that are outside the scope of perfect model experiments. While it is dangerous to extrapolate from these simple experiments to operational atmospheric assimilation, the results also suggest that exploring the frequency with which observations are used for assimilation may lead to significant enhancements to assimilated state estimates.