gebhart/patrepeval huggingface dataset:
Hepatitis E virus (2011)

Hepatitis E virus (HEV) is a small, non-enveloped, single-strand, positive-sense RNA virus of approximately 7.2 kb in size. HEV is classified in the family Hepeviridae consisting of four recognized major genotypes that infect humans and other animals. Genotypes 1 and 2 HEV are restricted to humans and often associated with large outbreaks and epidemics in developing countries with poor sanitation conditions, whereas genotypes 3 and 4 HEV infect humans, pigs and other animal species and are responsible for sporadic cases of hepatitis E in both developing and industrialized countries. The avian HEV associated with Hepatitis-Splenomegaly syndrome in chickens is genetically and antigenically related to mammalian HEV, and likely represents a new genus in the family. There exist three open reading frames in HEV genome: ORF1 encodes non-structural proteins, ORF2 encodes the capsid protein, and the ORF3 encodes a small phosphoprotein. ORF2 and ORF3 are translated from a single bicistronic mRNA, and overlap each other but neither overlaps ORF1. Due to the lack of an efficient cell culture system and a practical animal model for HEV, the mechanisms of HEV replication and pathogenesis are poorly understood. The recent identification and characterization of animal strains of HEV from pigs and chickens and the demonstrated ability of cross-species infection by these animal strains raise potential public health concerns for zoonotic HEV transmission. It has been shown that the genotypes 3 and 4 HEV strains from pigs can infect humans, and vice versa. Accumulating evidence indicated that hepatitis E is a zoonotic disease, and swine and perhaps other animal species are reservoirs for HEV. A vaccine against HEV is not yet available.
Texture Classification with Single- and Multiresolution Co-Occurrence Maps (1998)

We have developed methods for the classification of textures with multidimensional co-occurrence histograms. Gray levels of several pixels with a given spatial arrangement are first compressed linearly and the resulting multidimensional vectors are quantized using the self-organizing map. Histograms of quantized vectors are classified by matching them with precomputed texture model histograms. In the present study, a multiple resolution technique in linear compression of pixel values is evaluated. The multiple resolution linear compression was made with a local wavelet transform. The vectors were quantized with the tree-structured variant of the self-organizing map. In the tree-structured self-organizing map, the quantization error is reduced, in comparison to the traditional tree-structured codebook, by limited lateral searches in topologically-ordered neighborhoods. The performance of multiresolution texture histograms was compared with single-resolution histograms. The histogram method was compared with three well-established methods: co-occurrence matrices, Gaussian Markov random fields, and multiresolution Gabor energies. The results for a set of natural textures showed that the performance of single- and multiresolution texture histograms was similar. Thus, the benefit of multiresolution analysis was overridden by the multidimensionality of our texture models. Our method gave significantly higher classification accuracies than the three other methods.
The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli (2017)

The myxobacterial secondary metabolite carolacton inhibits growth of <i>Streptococcus pneumoniae</i> and kills biofilm cells of the caries- and endocarditis-associated pathogen <i>Streptococcus mutans</i> at nanomolar concentrations. Here, we studied the response to carolacton of an <i>Escherichia coli</i> strain that lacked the outer membrane protein TolC. Whole-genome sequencing of the laboratory <i>E. coli</i> strain TolC revealed the integration of an insertion element, IS<i>5</i>, at the <i>tolC</i> locus and a close phylogenetic relationship to the ancient <i>E. coli</i> K-12. We demonstrated via transcriptome sequencing (RNA-seq) and determination of MIC values that carolacton penetrates the phospholipid bilayer of the Gram-negative cell envelope and inhibits growth of <i>E. coli</i> TolC at similar concentrations as for streptococci. This inhibition is completely lost for a C-9 (<i>R</i>) epimer of carolacton, a derivative with an inverted stereocenter at carbon atom 9 [(<i>S</i>) → (<i>R</i>)] as the sole difference from the native molecule, which is also inactive in <i>S. pneumoniae</i> and <i>S. mutans</i>, suggesting a specific interaction of native carolacton with a conserved cellular target present in bacterial phyla as distantly related as <i>Firmicutes</i> and <i>Proteobacteria</i>. The efflux pump inhibitor (EPI) phenylalanine arginine β-naphthylamide (PAβN), which specifically inhibits AcrAB-TolC, renders <i>E. coli</i> susceptible to carolacton. Our data indicate that carolacton has potential for use in antimicrobial chemotherapy against Gram-negative bacteria, as a single drug or in combination with EPIs. Strain <i>E. coli</i> TolC has been deposited at the DSMZ; together with the associated RNA-seq data and MIC values, it can be used as a reference during future screenings for novel bioactive compounds. <b>IMPORTANCE</b> The emergence of pathogens resistant against most or all of the antibiotics currently used in human therapy is a global threat, and therefore the search for antimicrobials with novel targets and modes of action is of utmost importance. The myxobacterial secondary metabolite carolacton had previously been shown to inhibit biofilm formation and growth of streptococci. Here, we investigated if carolacton could act against Gram-negative bacteria, which are difficult targets because of their double-layered cytoplasmic envelope. We found that the model organism <i>Escherichia coli</i> is susceptible to carolacton, similar to the Gram-positive <i>Streptococcus pneumoniae</i>, if its multidrug efflux system AcrAB-TolC is either inactivated genetically, by disruption of the <i>tolC</i> gene, or physiologically by coadministering an efflux pump inhibitor. A carolacton epimer that has a different steric configuration at carbon atom 9 is completely inactive, suggesting that carolacton may interact with the same molecular target in both Gram-positive and Gram-negative bacteria.
Detection and analysis of change in remotely sensed imagery with application to wide area surveillance (1997)

A new approach to wide area surveillance is described that is based on the detection and analysis of changes across two or more images over time. Methods for modeling and detecting general patterns of change associated with construction and other kinds of activities that can be observed in remotely sensed imagery are presented. They include a new nonlinear prediction technique for measuring changes between images and temporal segmentation and filtering techniques for analyzing patterns of change over time. These methods are applied to the problem of detecting facility construction using Landsat Thematic Mapper imagery. Full scene results show the methods to be capable of detecting specific patterns of change with very few false alarms. Under all conditions explored, as the number of images used increases, the number of false alarms decreases dramatically without affecting the detection performance. It is argued that the processing gain that results in using more than two images justifies the increased computational complexity and storage requirements of our approach over single image object detection and conventional change detection techniques.
Innovative approach for in-vivo ablation validation on multimodal images (2014)

Radiofrequency ablation (RFA) is an important therapeutic procedure for small hepatic tumors. To make sure that the target tumor is effectively treated, RFA monitoring is essential. While several imaging modalities can observe the ablation procedure, it is not clear how ablated lesions on the images correspond to actual necroses. This uncertainty contributes to the high local recurrence rates (up to 55%) after radiofrequency ablative therapy. This study investigates a novel approach to correlate images of ablated lesions with actual necroses. We mapped both intraoperative images of the lesion and a slice through the actual necrosis in a common reference frame. An electromagnetic tracking system was used to accurately match lesion slices from different imaging modalities. To minimize the liver deformation effect, the tracking reference frame was defined inside the tissue by anchoring an electromagnetic sensor adjacent to the lesion. A validation test was performed using a phantom and proved that the end-to-end accuracy of the approach was within 2mm. In an in-vivo experiment, intraoperative magnetic resonance imaging (MRI) and ultrasound (US) ablation images were correlated to gross and histopathology. The results indicate that the proposed method can accurately correlate invivo ablations on different modalities. Ultimately, this will improve the interpretation of the ablation monitoring and reduce the recurrence rates associated with RFA.
A multianalyte algorithm PCR-based gene blood test compared to single analyte ELISA-based blood tests for neuroendocrine tumor detection. (2014)

e15168 Background: A critical requirement in NET management is a blood biomarker test that is sensitive, specific and reproducible. We evaluated a PCR-based 51 transcript signature, the NETest, to detect tumors, compared it to Chromogranin A (CgA), pancreastatin and neurokinin A. Methods: The multigene signature was evaluated in prospectively collected NETs (n=41, 61% small intestinal, 50% had metastastic disease, 44% under treatment). These were age (NETs: mean 56.9, range: 31-76; controls: mean 56.4, range: 33-75) and sex-matched (M:F = 10:31) with controls (1:1). All samples were analyzed by a 2-step PCR (51 marker genes) protocol and ELISAs: (DAKO-CgA), pancreastatin (MyBiosource-PST) and neurokinin A (RayBiotech-NKA). Sensitivity comparisons included chi-square, non-parametric measurements, ROC curves and predictive feature importance analyses. Results: PCR analysis was robust (inter/intra-assay variation <2%; inter/intra-assay reproducibility: <1.2). NETest performance metrics were: sensitivity 92.8%, specificity 92.8%, PPV 92.8% and NPV 92.8%. For the single analyte ELISA assays, metrics ranged from sensitivities: 75.6-80.5%, specificities: 31.7-87.8%, PPVs: 54.1-86.1% and NPVs: 61.9-78.3%. The AUCs from ROC analysis were: NETest: 0.96±0.025, CgA: 0.67±0.06, pancreastatin: 0.51±0.07 and neurokinin A: 0.73±0.05. The multigene transcript NETest was significantly better than any single analyte test (difference between areas: 0.13-0.45, Z-statistic = 2.6-6.58, p<0.01). Predictive Feature Importance analysis determined that NETest contributed the most value (61%) in arriving at the correct diagnosis compared to NKA (21%), CgA (9%), and PST (8%). Conclusions: A 51 panel multigene blood transcript analysis is significantly more sensitive than any single analyte assay (CgA, PST or NKA) for NET detection. The test is robust (<2% variation) and efficient (>93%). Our data indicate that a blood-based multigene analytic measurement will provide data that enables early detection of disease recurrence and predicts the efficacy of therapy.
Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization (2012)

Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
Characterization and properties of polyethylene blends II. Linear low‐density with conventional low‐density polyethylene (1987)

Abstract Melting and crystallization phenomena in blends of a linear low‐density polyethylene (LLDPE) (ethylene butene‐1 copolymer) with a conventional low‐density (branched) polyethylene (LDPE) are explored with emphasis on composition by differential scanning calorimetry (DSC) and light scattering (LS). Two endotherms are evident in the DSC studies of the blends, which suggests the formation of separate crystals. Light‐scattering studies indicate that the blend system is predominantly volume filled by the LLDPE component whereby the LDPE component crystallizes as a secondary process within the domain of the LLDPE spherulites. In contrast to those of the LLDPE/HDPE blends, the mechanical and optical relaxation behavior of the LLDPE/LDPE blends are dominated by the LLDPE component in the vicinities of γ and β regions, whereas the trend reverses at high temperature α regions. This observation is accounted for on the basis of the relative restrictions imposed by the deformation of spherulites (which are primarily made up of the LLDPE component) at different time scales.
Pi sampling: a methodical and flexible approach to initial macromolecular crystallization screening (2011)

The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting `Pi screens' have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample.
Linking equations between photon statistics and photocurrent statistics for time-varying stochastic photon rates (1998)

Detected photons originating from classical light beams can be described either by means of photon statistics or by means of photocurrent statistics on a semiclassical basis. The statistical parameters of these two descriptions have, up to now, only been related to each other using vague, effective-time-constant arguments. We show that these relations are invalid for the general case of time-varying stochastic photon rates and arbitrary detector impulse responses and derive generally valid linking equations for the ensemble average, the shot noise variance and the excess noise variance of the photon statistics and the photocurrent statistics due to a random optical field. The derivations are based on a general definition of the time average that allows an elegant treatment in the Fourier domain.
Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy (2012)

Autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN) is characterized by late onset (30-40 years old) cerebellar ataxia, sensory neuronal deafness, narcolepsy-cataplexy and dementia. We performed exome sequencing in five individuals from three ADCA-DN kindreds and identified DNMT1 as the only gene with mutations found in all five affected individuals. Sanger sequencing confirmed the de novo mutation p.Ala570Val in one family, and showed co-segregation of p.Val606Phe and p.Ala570Val, with the ADCA-DN phenotype, in two other kindreds. An additional ADCA-DN kindred with a p.GLY605Ala mutation was subsequently identified. Narcolepsy and deafness were the first symptoms to appear in all pedigrees, followed by ataxia. DNMT1 is a widely expressed DNA methyltransferase maintaining methylation patterns in development, and mediating transcriptional repression by direct binding to HDAC2. It is also highly expressed in immune cells and required for the differentiation of CD4+ into T regulatory cells. Mutations in exon 20 of this gene were recently reported to cause hereditary sensory neuropathy with dementia and hearing loss (HSAN1). Our mutations are all located in exon 21 and in very close spatial proximity, suggesting distinct phenotypes depending on mutation location within this gene.
USO DA SALIVA COMO AMOSTRA BIOLÓGICA NO DIAGNÓSTICO DA COVID-19 POR RT-PCR (2022)

O padrão-ouro para o diagnóstico de COVID-19 é o teste molecular que permite a detecção de ácidos nucleicos de SARS-CoV-2 em amostras de swab Nasofaríngeo (NPS). A detecção precoce seguida do isolamento dos indivíduos infectados desempenha um papel crucial para impedir a propagação da infecção e o controle da pandemia. No entanto, a coleta de NPS é invasiva e desconfortável para os pacientes, requer profissionais de saúde especializados e pode ser um risco de infecção cruzada para esses profissionais. Desta forma, avaliar outras fontes de material biológico, tal como a saliva, é fundamental para facilitar o diagnóstico de COVID-19. O objetivo deste trabalho foi avaliar o uso da saliva como amostra biológica para a detecção do RNA do SARS-CoV-2 e sua estabilidade pós coleta. Foram coletadas 954 amostras de saliva (5 mL) e de swab nasofaríngeo (NPS) de indivíduos entre dezembro de 2020 e fevereiro de 2021 e analisadas em diferentes tempos (24h, 48h, 72h, 5 dias e 10 dias) após a coleta. As amostras de saliva foram armazenadas em temperatura de 2° a 8°C e extraídas puras e diluídas em solução salina na proporção 1:1. A extração do RNA foi realizada em extrator automático de ácidos nucléicos (Extracta, Loccus) e o diagnóstico molecular do SARS-CoV-2 foi realizado com o kit Gene Finder™ COVID-19 Plus RealAmp (OSang Healthcare). A idade média dos participantes foi de 37 anos (8 a 83 anos de idade) e a maioria dos indivíduos 738 (77,3%) foram não-detectáveis e apenas 216 (22,7%) foram detectáveis para SARS-CoV-2. Entre os detectáveis, 96 (44,4%%) eram do sexo masculino e 120 (55,6%) do sexo feminino. A positividade na saliva foi posteriormente comparada com os resultados do NPS bem como a carga viral ou ciclo de limiar de amplificação (Ct). A análise dos testes com a saliva e NPS demonstrou concordância nos resultados de 210 (97%) pacientes detectáveis para COVID, em apenas 2,7 % (6/216) dos casos o SARS-CoV-2 foi detectado somente no NPS. Todos os participantes com resultado positivo para a RT-PCR apresentaram sintomas relacionados à COVID-19, sendo os mais comuns: tosse seca (19%), dor de cabeça (16%), coriza e dor de garganta (11%) e diarréia (8%). As amostras de salivas apresentaram estabilidade até o décimo dia após a coleta do material biológico, sem diferença de detecção do RNA viral entre a amostra de saliva pura e saliva diluída. Esses resultados demonstram que as amostras de saliva podem ser transportadas e armazenadas em temperatura de 2° a 8°C, e processadas em até 10 dias após a coleta. Os resultados mostraram que a saliva é uma alternativa para a detecção de SARS-CoV-2. É uma amostra biológica confiável, não invasiva, de fácil coleta e com resultados similares aos obtidos com amostras de NPS. É uma alternativa que facilitaria a coleta em lugares com baixo suprimento de swabs nasofaríngeos e regiões distantes de laboratórios especializados, uma vez que pode ser analisada até 10 dias após a coleta. Dessa forma, podemos concluir que a saliva pode ser utilizada com segurança para o diagnóstico de COVID-19.
Targeted gene disruption of methionine aminopeptidase 2 results in an embryonic gastrulation defect and endothelial cell growth arrest (2006)

The antiangiogenic agent fumagillin (Fg) and its analog TNP-470 bind to intracellular metalloprotease methionine aminopeptidase-2 (MetAP-2) and inhibit endothelial cell growth in a p53-dependent manner. To confirm the role of MetAP-2 in endothelial cell proliferation and to validate it as a physiological target for the Fg class of antiangiogenic agents, we have generated a conditional MetAP-2 knockout mouse. Ubiquitous deletion of the MetAP-2 gene (MAP2) resulted in an early gastrulation defect, which is bypassed in double MetAP-2/p53 knockout embryos. Targeted deletion of MAP2 specifically in the hemangioblast lineage resulted in abnormal vascular development, and these embryos die at the midsomite stage. In addition, knockdown of MetAP-2 using small interfering RNA or homologous recombination specifically suppresses the proliferation of cultured endothelial cells. Together, these results demonstrate an essential role for MetAP-2 in angiogenesis and indicate that MetAP-2 is responsible for the endothelial cell growth arrest induced by Fg and its derivatives.
Degradation of polychlorinated biphenyl mixtures (Aroclors 1242, 1254, and 1260) by the white rot fungus Phanerochaete chrysosporium as evidenced by congener-specific analysis (1995)

Evidence for substantial degradation of polychlorinated biphenyl mixtures Aroclor 1242, 1254, and 1260 by the white rot fungus Phanerochaete chrysosporium, based on congener-specific gas chromatographic analysis, is presented. Maximal degradation (percent by weight) of Aroclors 1242, 1254, and 1260 was 60.9, 30.5, and 17.6%, respectively. Most of the congeners in Aroclors 1242 and 1254 were degraded extensively both in low-N (ligninolytic) as well as high-N (nonligninolytic) defined media. Even more extensive degradation of the congeners was observed in malt extract medium. Congeners with varying numbers of ortho, meta, and para chlorines were extensively degraded, indicating relative nonspecificity for the position of chlorine substitutions on the biphenyl ring. Aroclor 1260, which has not been conclusively shown to undergo aerobic microbial degradation, was shown to undergo substantial net degradation by P. chrysosporium. Maximal degradation of Aroclor 1260 was observed in malt extract medium (18.4% on a molar basis), in which most of the individual congeners were degraded.
Tuning the Photochromic Properties of a Flavylium Compound by pH (2004)

Abstract We studied the intricate pH‐ and light‐dependent network of the thermal and photochemical reactions of the 4′‐(dimethylamino)‐7‐hydroxyflavylium ion by continuous irradiation, flash photolysis, 1 H NMR spectroscopy, and stopped flow analysis. The distribution of the various forms at the pH‐dependent thermodynamic equilibrium and the rates of several interconversion processes were measured. The most interesting feature of this multistate/multifunctional system is related to the possibility of pH‐tuning the colour change caused by photoirradiation, because the cis ‐chalcone isomer, obtained from the photoisomerization of the trans ‐chalcone form, is spontaneously transformed into coloured species (flavylium cation and quinoidal base) at low values of pH, but reverts back to the uncoloured trans ‐chalcone at high values of pH because of the low energy barrier between the cis and trans chalcone isomers. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)