gebhart/patrepeval huggingface dataset:
Comparative chromosome painting in Spizaetus tyrannus and Gallus gallus with the use of macro- and microchromosome probes (2021)

Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes and many microchromosomes pairs, some groups, such as the Accipitriformes, are characterized by a large karyotypic reorganization, which resulted in complements with low diploid numbers, and a smaller number of microchromosomal pairs when compared to other birds. Among Accipitriformes, the Accipitridae family is the most diverse and includes, among other subfamilies, the subfamily Aquilinae, composed of medium to large sized species. The Black-Hawk-Eagle (Spizaetus tyrannus-STY), found in South America, is a member of this subfamily. Available chromosome data for this species includes only conventional staining. Hence, in order to provide additional information on karyotype evolution process within this group, we performed comparative chromosome painting between S. tyrannus and Gallus gallus (GGA). Our results revealed that at least 29 fission-fusion events occurred in the STY karyotype, based on homology with GGA. Fissions occurred mainly in syntenic groups homologous to GGA1-GGA5. On the other hand, the majority of the microchromosomes were found fused to other chromosomal elements in STY, indicating these rearrangements played an important role in the reduction of the 2n to 68. Comparison with hybridization pattern of the Japanese-Mountain-Eagle (Nisaetus nipalensis orientalis), the only Aquilinae analyzed by comparative chromosome painting previously, did not reveal any synapomorphy that could represent a chromosome signature to this subfamily. Therefore, conclusions about karyotype evolution in Aquilinae require additional painting studies.
Glioblastoma and glioblastoma stem cells are dependent on functional MTH1 (2017)

Glioblastoma multiforme (GBM) is an aggressive form of brain cancer with poor prognosis. Cancer cells are characterized by a specific redox environment that adjusts metabolism to its specific needs and allows the tumor to grow and metastasize. As a consequence, cancer cells and especially GBM cells suffer from elevated oxidative pressure which requires antioxidant-defense and other sanitation enzymes to be upregulated. MTH1, which degrades oxidized nucleotides, is one of these defense enzymes and represents a promising cancer target. We found MTH1 expression levels elevated and correlated with GBM aggressiveness and discovered that siRNA knock-down or inhibition of MTH1 with small molecules efficiently reduced viability of patient-derived GBM cultures. The effect of MTH1 loss on GBM viability was likely mediated through incorporation of oxidized nucleotides and subsequent DNA damage. We revealed that MTH1 inhibition targets GBM independent of aggressiveness as well as potently kills putative GBM stem cells <i>in vitro</i>. We used an orthotopic zebrafish model to confirm our results <i>in vivo</i> and light-sheet microscopy to follow the effect of MTH1 inhibition in GBM in real time. In conclusion, MTH1 represents a promising target for GBM therapy and MTH1 inhibitors may also be effective in patients that suffer from recurring disease.
Histopathological and immunohistochemical analysis of adenomatous hyperplasia and hepatocellular carcinoma: cellularity, thickness of cell cord, and Ki-67 proliferative activity. (1995)

To characterize adenomatous hyperplasia (AH) and hepatocellular carcinoma (HCC), and to establish their histopathological differences, morphometrical and immunohistochemical analyses, namely, cellularity, thickness of cell cord, and Ki-67 labeling index (Ki-67 LI) were done on surgically obtained hepatic lesions from patients with positive serum antibody against HCV. The hepatic lesions analyzed include chronic active hepatitis (CAH) (11 specimens), regenerative nodules of liver cirrhosis (LC) (29), AH (11), small HCC Edmondson's Grade I (GI) (19), GII (26), GIII (14). The results showed that AH has relatively high cellularity, and significantly greater thickness of cell cord than LC; whereas, HCC GI has significantly higher cellularity and Ki-67 LI than AH. From the data of these markers, and from the absence of conspicuous structural atypism, AH is considered to be in a different category from HCC GI. The premalignant potential of AH is supported only by its high incidence of coexistence adjacent to HCC GI or GII(6/11). Most lesions of HCC seem to develop from the liver tissue having a background of CAH or LC without passing through AH. Focal fatty changes are frequently observed within lesions of both AH and HCC GI (5/11, 8/19). When non-fatty regions of AH and HCC GI are compared, with respect to their markers, particularly Ki-67 LI, as well as the structural atypism, such as microacinus formation and pseudoglandular structure, and invasive growth into the surrounding liver parenchyma, HCC GI can be diagnosed as an early or well-differentiated malignant lesion.
The Focused Action of Surface Tension Versus the Brute Force of Turbulence – Scaleable Microchannel‐Based Process Intensification using Monoliths (2007)

This chapter contains sections titled: Introduction Monoliths – A Scalable Microchannel Technology Power Required for Gas–Liquid Dispersion Turbulent Contactors Laminar Contactors Physical Adsorption of Oxygen Three-phase Processes Discussion Design Considerations for Intensified Monolith Processes Conclusions
Sequencing Analysis of Partial N gene of Feline Morbillivirus from Malaysia (2022)

Feline morbillivirus (FeMV) is a new emerging virus of domestic cats categorized under the genus of (Morbillivirus, associated with chronic kidney disease (CKD). The origin of the virus is yet to be determined, and whether it is caused by a spill-over event from wildlife or domestic cats remains speculative. Recombination event has been reported in FeMV isolate found in Japan; therefore, characterization of FeMV strains isolated in Malaysia (i.e., FeMV-Malaysia isolates) may provide some insight, thus adding some information on the viral evolution of FeMV. Therefore, this study aims to conduct a phylogenetic analysis and assess any genetic changes in the N gene of FeMV-Malaysia isolates. Through sequencing of N gene of seven isolates using three overlapping primer sets, the sequences spanning approximately 1.5kb of FeMV-N gene were obtained. DNA sequencing, nucleotide sequences, amino acid residues alignments, and phylogenetic analysis were performed. A nucleotide sequence alignment was also performed to compare the isolates obtained from two previous studies. From the alignment mentioned above, there were 19 variable sites of which there were absence of amino acid changes except for isolate UPM210 at position 806 and isolate UPM315 at position 823. Furthermore, protein alignment was done to compare FeMV-Malaysia isolates with FeMV strains from other countries, along with other morbillivirus-related isolates. From one of the conserved regions located within the N gene, similar amino acid sequences were detected across different morbilliviruses. Lastly, from the phylogenetic tree, it was illustrated that all partial FeMV-N gene Malaysia isolates sequenced in this study were clustered together in the same clade whereby these FeMV-N genes Malaysia isolates shared a common ancestor with isolates from Japan (SS3, MiJP003, ChJP073) and Thailand (Thai-U16, CTL16. CTL43).
Huygens Principle based technique for microwave imaging of objects with inclusions (2011)

A novel algorithm for use in a recently established technique for imaging based on ultrawideband (UWB) microwave signals is presented here. The method deals with Huygens Principle (HP), which removes the need to solve inverse problems and, consequently, the need for matrix generation/inversion. In addition to its simplicity, it is shown that HP enables the detection of the extent to which different tissues, or differing conditions of tissues, can be discriminated and render contrast in the final image. Moreover, UWB allows all the information in the frequency domain to be utilized by combining the signals from the individual frequencies to construct a consistent image. It follows that the methodology can identify the presence and location of significant scatterers inside a volume.
γ Chain-associated Cytokine Receptors Signal through Distinct Transducing Factors (1995)

The IL-2, IL-4, and IL-7 signaling pathways have been shown to utilize shared components. The receptors for these cytokines are composed of ligand-specific binding chains that associate with a shared signaling subunit, the common gamma (gamma c) chain. In addition, IL-2, IL-4, and IL-7 induce activation of a common set of nonreceptor tyrosine kinases, Jak-1 and Jak-3. We have further investigated the signaling events induced by these cytokines and find that the gamma c-associated receptors activate distinct signal transducing factors (STFs). In addition, we show that a 94-kDa STAT-related protein (p94) is activated in response to IL-2 and IL-7, but not IL-4. These data indicate that IL-2, IL-4, and IL-7 activate distinct signaling molecules which might be differentially recruited to the receptor complex by the ligand-specific units of the IL-2, IL-4, and IL-7 receptors.
State of the knowledge on European marine habitat mapping and degraded habitats (2017)

During the last decades, several EU Directives and other international legislations have generated a large number of national initiatives (e.g. marine atlases) and EU programmes on habitat mapping. Nevertheless, the outcomes of these initiatives are fragmented and, to our best knowledge, to date there is no systematic assessment regarding the nature, quality and availability of information across the European seas. One of the main goals of the MERCES project (www.merces-project.eu) is to produce a census of available maps of European key marine habitats, along with their degradation status and restoration potential in the European Seas, providing a potential basis for future discussion on restoration activities.&#13;\nMERCES is producing a census of European marine key habitat maps, degraded habitat maps and investigating key habitat restoration potential. To do this MERCES has&#13;\ni. reviewed known existing habitat maps of European regional seas and provided source citations for all of the information&#13;\nii. reviewed degraded habitat map resources by regional sea and habitat type (e.g. seagrass, macroalgae, coral gardens, sponge aggregations, seamounts, vents), associated habitat deterioration (e.g. extent of decline), the most common human activities and pressures reported, and the recovery and restoration potential of these habitats&#13;\niii. reviewed 6 key habitats (including kelp and macroalgal forests, seagrass meadows, coralligenous assemblages, coral gardens and deep-sea bottom communities) and linked 6 major habitat features, such as dynamics, connectivity, structural complexity and vulnerability, to consequences for restoration and the likelihood of restoration success
The Impact of Green Activities on Stress and Depression in Senior Citizens (2015)

This study was performed to understand positive potential to provide green activities among leisure activity types of the senior citizens. The subjects were those more than 60 years old and participated in the festival of Cheonan Heung Taryeong and examined the level of stress and depression recognition. Questionnaire surveys were carried out and the pulse skin measurement index was used as the measurement of stress index. The types of leisure activities were classified with 'social meetings', 'travels', 'exercise' and 'green activities'. As a result of stress cognitive level analysis, 'exercise', 'travels' and 'green activities' were identified as a leisure program given vitality by lowering stress than social unions. According to depression cognitive level analysis, depression index of 'green activities group' was the lowest as 7.05 points. As a result of pulse skin measurements, stress index of the green activities group showed the lowest as 58.0 points. As to the cognitive level, the single-family houses and apartment residents housing form that garden activities were available had lower stress and depression than multi-family residential group. As shown in the figure above, 'stress' caused by the housing form and the leisure activities types, 'depression' and 'stress cognitive level' are arranged. And it shows a lower trend in the order of 'social meeting', 'green activities', 'travel', and âexerciseâ. From the result of depression cognitive level and pulse skin measurements, it is estimated that green activities have received a low sense of depression and stress compared to other leisure activities. Based on these results, it is determined to develope a variety of green programs in leisure activities for senior citizens. Keywords: Garden activities, Green programs, Pulse skin measurements, Stress index
Insecticidal Pyrroles (1992)

A series of new arylpyrrolecarbonitriles containing a trifluoromethyl group has been prepared. These compounds, based on a naturally occurring compound dioxapyrrolomycin, have broad spectrum insecticidal activity. This reports details the preparation of these compounds utilizing a new cycloaddition reaction. Preliminary structure-activity comparisons are also presented.
Red-Shifted Aminated Derivatives of GFP Chromophore for Live-Cell Protein Labeling with Lipocalins (2018)

Fluorogens are an attractive type of dye for imaging applications, eliminating time-consuming washout steps from staining protocols. With just a handful of reported fluorogen-protein pairs, mostly in the green region of spectra, there is a need for the expansion of their spectral range. Still, the origins of solvatochromic and fluorogenic properties of the chromophores suitable for live-cell imaging are poorly understood. Here we report on the synthesis and labeling applications of novel red-shifted fluorogenic cell-permeable green fluorescent protein (GFP) chromophore analogs.
Efficient Homology-directed Repair with Circular ssDNA Donors (2019)

Abstract While genome editing has been revolutionized by the advent of CRISPR-based nucleases, difficulties in achieving efficient, nuclease-mediated, homology-directed repair (HDR) still limit many applications. Commonly used DNA donors such as plasmids suffer from low HDR efficiencies in many cell types, as well as integration at unintended sites. In contrast, single-stranded DNA (ssDNA) donors can produce efficient HDR with minimal off-target integration. Here, we describe the use of ssDNA phage to efficiently and inexpensively produce long circular ssDNA (cssDNA) donors. These cssDNA donors serve as efficient HDR templates when used with Cas9 or Cas12a, with integration frequencies superior to linear ssDNA (lssDNA) donors. To evaluate the relative efficiencies of imprecise and precise repair for a suite of different Cas9 or Cas12a nucleases, we have developed a modified Traffic Light Reporter (TLR) system [TLR-Multi-Cas Variant 1 (MCV1)] that permits side-by-side comparisons of different nuclease systems. We used this system to assess editing and HDR efficiencies of different nuclease platforms with distinct DNA donor types. We then extended the analysis of DNA donor types to evaluate efficiencies of fluorescent tag knock-ins at endogenous sites in HEK293T and K562 cells. Our results show that cssDNA templates produce efficient and robust insertion of reporter tags. Targeting efficiency is high, allowing production of biallelic integrants using cssDNA donors. cssDNA donors also outcompete lssDNA donors in template-driven repair at the target site. These data demonstrate that circular donors provide an efficient, cost-effective method to achieve knock-ins in mammalian cell lines.
Fibronectin receptor functions in embryonic cells deficient in alpha 5 beta 1 integrin can be replaced by alpha V integrins. (1996)

alpha 5 beta 1 integrin mediates cell adhesion to extracellular matrix by interacting with fibronectin (FN). Mouse lines carrying null mutations in genes encoding either the alpha 5 integrin subunit or FN have been generated previously. Both mutations are embryonic lethal with overlapping defects, but the defects of alpha 5-null embryos are less severe. Primary embryonic cells lacking alpha 5 beta 1 are able to adhere to FN, form focal contacts, migrate on FN, and assemble FN matrix. These results suggest the involvement of (an)other FN receptors(s). In this study, we examined functions of alpha 4 beta 1 and alpha V integrins in embryonic cells lacking alpha 5 beta 1. Our analysis of cells lacking both alpha 4 beta 1 and alpha 5 beta 1 showed that alpha 4 beta 1 is also not required for these FN-dependent functions. Using alpha V-specific blocking reagents, we showed that alpha V integrins are required for alpha 5-null cells, but not wild-type cells, to adhere and spread on FN. Our data also showed that, although the expression levels of alpha V integrins on the wild-type and alpha 5-null cells are similar, there is an increase in recruitment of alpha V integrins into focal contacts in alpha 5-null cells plated on FN, indicating that alpha V integrins can compensate functionally for the loss of alpha 5 beta 1 in focal contacts of alpha 5-null cells. Finally, our data suggested possible roles for alpha V integrins in replacing the role of alpha 5 beta 1 in FN matrix assembly in vitro and in FN-dependent embryonic functions in vivo.
Microclot array elastometry for integrated measurement of thrombus formation and clot biomechanics under fluid shear (2019)

Blood clotting at the vascular injury site is a complex process that involves platelet adhesion and clot stiffening/contraction in the milieu of fluid flow. An integrated understanding of the hemodynamics and tissue mechanics regulating this process is currently lacking due to the absence of an experimental system that can simultaneously model clot formation and measure clot mechanics under shear flow. Here we develop a microfluidic-integrated microclot-array-elastometry system (clotMAT) that recapitulates dynamic changes in clot mechanics under physiological shear. Treatments with procoagulants and platelet antagonists and studies with diseased patient plasma demonstrate the ability of the system to assay clot biomechanics associated with common antiplatelet treatments and bleeding disorders. The changes of clot mechanics under biochemical treatments and shear flow demonstrate independent yet equally strong effects of these two stimulants on clot stiffening. This microtissue force sensing system may have future research and diagnostic potential for various bleeding disorders.
Investigation of the formation of poly(ethylene terephthalate) with model molecules: Kinetics and mechanism of the catalytic esterification and alcoholysis reactions. I. Carboxylic acid catalysis (monofunctional reactants) (1988)

Abstract Monofunctional compounds (benzoic acid, heptyl alcohol, and 2‐butoxy‐ethanol) were used to investigate the kinetics of the esterification and the alcoholysis reactions. Carboxylic acids (benzoic acid) are the only catalysts present in the reaction medium. The factors which influence the kinetics of the esterification reaction were studied: the nature of the carboxylic acid (substituents on the benzene ring), the nature of the alcohol, the composition of the reaction medium (alcohol alone or with another solvent, ester, or water). The results point out for an acyl type (A AC2 ) mechanism. The alcoholysis reaction needs the presence of carboxylic acid as a catalyst to occur significantly. A similar mechanism is proposed for both reactions: nucleophilic attack by the oxygen atom of the alcohol at the ion pair formed by protonation of the acid (esterification reaction) or by protonation of the ester (alcoholysis).
Expression of a homeo domain protein in noncontact-inhibited cultured cells and postmitotic neurons. (1987)

The murine Hox 1.3 gene is one of six homeo box genes clustered on chromosome 6. Our analysis of Hox 1.3 cDNA and genomic clones indicates that the gene is organized into two exons and encodes a 270-amino-acid homeo domain protein. The predicted protein is rich in serine, glycine, and proline residues, and its homeo domain is identical to the Hox 2.1 domain. During embryogenesis, the gene is maximally expressed at midgestation but is also expressed to a lesser extent in many adult tissues possessing different cell lineages. Hox 1.3 transcripts are also present in cultured fibroblasts. The Hox 1.3 protein accumulates in the nuclei of nonconfluent cultured fibroblasts but is greatly diminished in contact-inhibited nongrowing cells. Thus, the expression of the Hox 1.3 gene correlates with growth in embryos and cultured cells. Paradoxically, it is also expressed in certain subsets of postmitotic, fully differentiated neurons, most notably the Purkinje neurons of the cerebellum, the pyramidal and dentate neurons of the hippocampus, and the motor neurons of the spinal cord. This complex pattern of expression suggests that Hox 1.3 may provide a function required by many cell types in addition to any role it may have in morphogenesis.
Theoretical design of energy harvesting module or wireless power transmission receiver using magnetic field of 0.2 mT at 60 Hz (2013)

This paper presents a theoretical design method for a magnetic energy harvesting module. This module consists of an air-core coil and resonant capacitor. With a simple RLC circuit model, it can derive an equation of harvesting energy as a function of coil size. In order to demonstrate the magnetic field, a uniform magnetic field is generated by the developed coil system. From the experimented results, it is successfully demonstrated 100 mW of energy harvesting from a magnetic field of 0.09 mT at 60 Hz. This value is in good agreement with the estimated results. Harvested energy is proportional to the square of the magnetic flux density. However, ICNIRP2010 provides a guideline that an acceptable level for human health in a public space is 0.2 mT at power-line frequency. This paper also discuss the possibilities of several applications related with both magnetic energy harvesting and wireless power transmission.
Perovskite Micro Laser Arrays Using Scalable Lithography: Towards Integrated Perovskite Photonics (2019)

Low threshold Perovskite micro lasers are fabricated and characterized. These devices are realized using the first complete top-down lithography process of metal halide perovskites which presents a crucial step towards integrated perovskite photonics. © 2019 The Author(s)
Defect detection in food ingredients using Multilayer Perceptron Neural Network (2014)

Selection of healthy raw ingredient and similarly rejection of defective ones in an automatic and non-destructive way is becoming an essential job in food industry. In this paper, binary classification of raw food ingredients is presented using x-ray images of pistachio nuts. The objective is to develop an in-line defect detection system capable of detection and classification of raw food ingredients without any damage. A method is devised for detection and segmentation of each independent ingredient from the large x-ray image. For quality assessment, six textures properties from the images are calculated on global level, in addition to sixteen features, extracted by calculating the Gray Level Co-occurrence Matrices (GLCMs) at angles of 0, 45, 90 and 135 respectively. Artificial Neural Network (ANN) is used as classifier. Results are calculated using extracted features and presented in terms of accuracy, sensitivity and specificity. Later, Principal Component Analysis (PCA) is used in order to achieve discrimination among features. Results are calculated again using features obtained after PCA. Texture features with PCA out-performed previous outcomes, producing excellent classification results while achieving higher accuracy in comparison to similar approaches.