gebhart/patrepeval huggingface dataset:
Integrative physiological, biochemical and transcriptomic analysis of hexaploid wheat roots and shoots provides new insights into the molecular regulatory network during Fe & Zn starvation (2021)

Abstract In plants, iron (Fe) &amp; zinc (Zn) uptake and transportation from the rhizosphere to the grain is a critical process regulated by complex transcriptional regulatory networks. However, understanding the combined effect of Fe &amp; Zn starvation on their uptake and transportation and the molecular regulatory networks that control them lack in wheat. Here, we performed a comprehensive physiological, biochemical and transcriptome analysis in two bread wheat genotypes, i.e. Narmada 195 and PBW 502, differing in inherent Fe &amp; Zn content to understand the mechanism of Fe &amp; Zn homeostasis. Compared to PBW 502, Narmada 195 exhibited increased tolerance to Fe &amp; Zn withdrawal by an increased level of antioxidant enzymes and DPPH radical scavenging activity along with less malondialdehyde (MDA), H 2 O 2 level, increased PS accumulation and lower reduction of root and shoot Fe &amp; Zn content and length, leaf chlorosis, and leaf area. By integrating physiological and biochemical data along with co-expression &amp; functional genome annotation and gene expression analysis, we identified 25 core genes associated with four key pathways, i.e. Met cycle (10), PS biosynthesis (4), antioxidant (3) and transport system (8) that were significantly modulated by Fe &amp; Zn withdrawal in both the genotypes. Genes of these four pathways were more considerably up-regulated in Narmada 195, allowing better tolerance to Fe &amp; Zn withdrawal and efficient uptake and transportation of Fe &amp; Zn. Chromosomal distribution and sub-genome wise mapping of these genes showed a contribution from all the chromosomes except group 5 chromosomes with the highest number of genes mapped to chromosome 4 (24%) and sub-genome D (40%). Besides, we also identified 26 miRNAs targeting 14 core genes across the four pathways. Together, our work provides a crucial angle for an in-depth understanding of regulatory cross-talk among physiological, biochemical and transcriptional reprogramming underlying Fe &amp; Zn withdrawal in wheat. Core genes identified can serve as valuable resources for further functional research for genetic improvement of Fe &amp; Zn content in wheat grain. Highlight Our work provides a crucial angle for a comprehensive understanding of the regulatory mechanism underlying Fe &amp; Zn withdrawal associated with physiological, biochemical and transcriptional reprogramming in wheat.
Click on silica: systematic immobilization of Co(ii) Schiff bases to the mesoporous silica via click reaction and their catalytic activity for aerobic oxidation of alcohols (2010)

The systematic immobilization of cobalt(II) Schiff base complexes on SBA-15 mesoporous silica via copper catalyzed [3 + 2] azide-alkyne cycloaddition (CuAAC) "click reaction" involving either step-wise synthesis of silica-bound Schiff base ligand followed by its subsequent complexation with cobalt ions, or by the direct immobilization of preformed Co(II) Schiff base complex to the silica support is described. The catalytic activity of the prepared complexes was studied for the oxidation of alcohols to carbonyl compounds using molecular oxygen as oxidant. The immobilized complexes were recycled for several runs without loss in catalytic activity and no leaching was observed during this course.
Metabolic control of the cell cycle (2015)

Cell division is a metabolically demanding process, requiring the production of large amounts of energy and biomass. Not surprisingly therefore, a cell's decision to initiate division is co-determined by its metabolic status and the availability of nutrients. Emerging evidence reveals that metabolism is not only undergoing substantial changes during the cell cycle, but it is becoming equally clear that metabolism regulates cell cycle progression. Here, we overview the emerging role of those metabolic pathways that have been best characterized to change during or influence cell cycle progression. We then studied how Notch signaling, a key angiogenic pathway that inhibits endothelial cell (EC) proliferation, controls EC metabolism (glycolysis) during the cell cycle.
Heterogeneous disease progression and treatment response in a C3HeB/FeJ mouse model of tuberculosis (2015)

Mice are the most commonly used species for non-clinical evaluations of drug efficacy against tuberculosis (TB). Unlike commonly used strains, C3HeB/FeJ mice develop caseous necrosis in the lung, which might alter the representation of drug efficacy in a way that is more like human TB. Because the development of such pathology requires time, we investigated the effect of infection incubation period on the activity of six drugs in C3HeB/FeJ and BALB/c mice. Mice were aerosol infected and held for 6, 10 or 14 weeks before receiving therapy with rifampin (RIF), rifapentine (RPT), pyrazinamide (PZA), linezolid (LZD), sutezolid (PNU) or metronidazole (MTZ) for 4-8 weeks. Outcomes included pathological assessments, pH measurements of liquefied caseum and assessment of colony-forming unit (CFU) counts from lung cultures. Remarkable heterogeneity in the timing and extent of disease progression was observed in C3HeB/FeJ mice, largely independent of incubation period. Likewise, drug efficacy in C3HeB/FeJ mice was not affected by incubation period. However, for PZA, LZD and PNU, dichotomous treatment effects correlating with the presence or absence of large caseous lesions were observed. In the case of PZA, its poor activity in the subset of C3HeB/FeJ mice with large caseous lesions might be explained by the pH of 7.36±0.09 measured in liquefied caseum. This study highlights the potential value of C3HeB/FeJ mice for non-clinical efficacy testing, especially for investigating the interaction of lesion pathology and drug effect. Careful use of this model could enhance the bridging of non-clinical results with clinical outcomes.
EBR-II and TREAT Digitization Project (2015)

Digitizing the technical drawings for EBR-II and TREAT provides multiple benefits. Moving the scanned or hard copy drawings to modern 3-D CAD (Computer Aided Drawing) format saves data that could be lost over time. The 3-D drawings produce models that can interface with other drawings to make complex assemblies. The 3-D CAD format can also include detailed material properties and parametric coding that can tie critical dimensions together allowing easier modification. Creating the new files from the old drawings has found multiple inconsistencies that are being flagged or corrected improving understanding of the reactor(s).
Tunable Ionic Control of Polymeric Films for Inkjet Based 3D Printing (2018)

Inkjet printing is a powerful additive manufacturing (AM) technique to generate advanced and complex geometries. However, requirements of low viscosity and surface tension are limiting the range of functional inks available, thus hindering the development of novel applications and devices. Here, we report a method to synthesize materials derived from highly viscous or even solid monomers in a simple, flexible fashion and with the potential to be integrated in the printing process. Polymerizable ionic liquids (PILs) have been employed as a proof of principle due to the broad range of properties available upon fine-tuning of the anion-cation pair and the high viscosity of the monomers. The method consists of the deposition and polymerization of a PIL precursor, followed sequentially by quaternization and anion metathesis of the films. The fine control over the mechanical and superficial properties of inkjet printable polymeric films of neutral and cationic nature by postpolymerization reactions is demonstrated for the first time. A family of different polycationic materials has been generated by modification of cross-linked copolymers of butyl acrylate and vinyl imidazole with liquid solutions of functional reagents. The variation in the mechanical, thermal, and surface properties of the films demonstrates the success of this approach. The same concept has been applied to a modified formulation, designed for optimal inkjet printing. This work will pave the way for a broad range of applications of inkjet printing, with a plethora of anion–cation combinations characteristic of PILs, thus enormously broadening the range of applications available in additive manufacturing.
Overview of TREC-6 Very Large Collection Track. (1997)

In line with the wishes of last year&amp;apos;s participants, this year&amp;apos;s VLC track was essentially a re-run of last year&amp;apos;s with a five-fold increase in data size. The data used was a completely new 100-gigabyte collection of Web documents (the VLC2) whose characteristics are presented here. This time, two orders of magnitude scale-up was investigated using 1%, and 10% samples as well as the full collection. Six groups managed to complete the full VLC task, of which five completed last year&amp;apos;s track. An overview is given of the track participants, the methods used and the results obtained. One group of participants, using hardware costing less than $US10,000, have shown that a hundred gigabyte collection can be indexed in less than ten hours and that quite good rankings (better than several well-known search engines) can be produced from queries processed in less than one second. 1 Background and Motivation The arguments for test collection sizes representative of the data sizes encountered in ...
Critical Undercooling in DNA-Mediated Nanoparticle Crystallization (2015)

The nucleation of DNA-functionalized nanoparticle superlattices is observed to exhibit a temperature hysteresis between melting (superlattice dissociation) and freezing (particle association) transitions that allows for the study of nucleation thermodynamics. Through detailed study of the assembly of these particles, which can be considered programmable atom equivalents (PAEs), we identify this hysteresis as critical undercooling-a phase transition phenomenon related to a thermodynamic barrier to nucleation. The separable nature of the DNA bonding elements and nanoparticle core enables the PAE platform to pose unique questions about the microscopic dependencies of critical undercooling and, ultimately, to control the nucleation pathway. Specifically, we find that the undercooling required to initiate nucleation increases as the nanoparticle coordination number increases (number of particles to which a single particle can bind).
Corrigenda (1989)

S. S. Rahman, B. J. Wakefield, S. M. Roberts, M. D. Dowle, D. Crich, D. Batty and S. M. Fortt, J. Chem. Soc., Chem. Commun., 1989, 1696 DOI: 10.1039/C39890001696
CMOS and BiCMOS class AB structures for switched-current applications (2002)

The performance limitations of SI-circuits is essentially related to the non-linear behavior of SI-memory cells. Three CMOS and one BiCMOS class AB current memory cells for SI applications are proposed. The main advantages of the class AB cells are error linearization, high dynamic range and low consumption.
An Information-Theoretic View of Cloud Workloads (2014)

Analytics-as-a-service is emerging as a key offering for cloud systems, however in the petascale regime, data transfer bottlenecks are a limiting factor. Often information has to be transmitted to the cloud by physical transportation. Efficient information representations that leverage the functional purpose of data for the analytics service to be offered can serve to ameliorate many of these information flow bottlenecks. In this paper, we provide an information-theoretic view on optimal information representations for big data analytics in the cloud. We also provide some structural design principles for building a petascale analytics appliance.
Supplementary Table S2 from The Genomic Landscape of Pediatric Ewing Sarcoma (2023)

&lt;p&gt;Mutations identified from WES and WGS of 26 tumors with paired normals.&lt;/p&gt;
Non-invasive Cardiovascular Disease Assessment with Miniaturized Multi-beam Laser Doppler Vibrometry (2018)

A miniaturized 2×6-beam laser Doppler vibrometry sensor for non-invasive detection of cardiovascular disease is demonstrated. The pulse wave velocity is retrieved from preliminary experiments both on phantoms and on human subjects.
Insight toward Early Diagnosis of Leprosy through Analysis of the Developing Antibody Responses of Mycobacterium leprae -Infected Armadillos (2010)

Leprosy is a debilitating chronic disease caused by infection with Mycobacterium leprae. A World Health Organization-directed control strategy based upon the identification and treatment of patients has resulted in a marked reduction in the number of registered worldwide leprosy cases over the last 20 years. Despite these efforts, the number of new leprosy cases detected each year now remains relatively stable, and M. leprae infection continues to pose a health problem. It is suggested that earlier diagnosis is required to strengthen control programs. In this study, we have examined the development of antigen-specific immunoglobulin responses within armadillos experimentally infected with M. leprae to identify those responses that develop most rapidly and robustly following infection. Antibody responses to the M. leprae-specific phenolic glycolipid I and several protein antigens previously demonstrated to have diagnostic potential were assessed. Our results identify several antigens that can provide early diagnosis of M. leprae infection but also indicate considerable variability in the development of antigen-specific antibodies. Our data suggest that a combination of antigens is likely required to provide accurate and early leprosy diagnosis.
Genetically-determined cytokine programs of human NK cells uncover a novel mechanism of NK cells and Killer cell IgG-like Receptor genes in Crohn’s Disease susceptibility (P3262) (2013)

Abstract Mucosal innate lymphocyte subsets have emerged as an important new factor in CD pathogenesis, but the role of NK cells is poorly understood. A recent genetic study identified the KIR gene KIR2DL2/3 as a risk factor for CD in the genetic context of its ligand HLA-C1. However, the biologic mechanism of this genetic contribution is unknown. NK cells are mainly known for their cytolytic function, but recent work indicates that strong KIR/HLA interactions that induce NK "licensing" augment NK cytotoxicity but also IFN-γ production. We therefore tested the hypothesis that human NK licensing by KIR2DL2/3 and HLA-C1 induces a broader cytokine program that modifies the threshold of pro-inflammatory T cell activation. Single cell multiplex functional proteomics revealed that licensed and unlicensed NK cells had strikingly distinct cytokine programs. Licensed NK cells were distinguished by high-output, proinflammatory, poly-cytokine expression. Select cytokine among this output fully accounted for their unique capacity, unlike unlicensed NK cells, to efficiently augment antigenic CD4+ T cell proliferation and induce CD4+ T cell IL-17A production. In conclusion, NK licensing mediated by KIR2DL2/3 and HLA-C1 elicits a novel cytokine program of NK cells that activates and induces pro-inflammatory CD4+ T cells, and therefore provides a predisposing biologic mechanism for this KIR-associated susceptibility to CD and other chronic inflammatory syndromes.
Reduction of Cable Shield Currents Generated by High Field Body Coils at 3 Tesla and Above (2002)

Induced currents can flow on the outside shield of a coaxial cable when no methods are used to suppress them. This is apart from the signal current flowing on the center conductor of the cable. These currents may be generated by the local receive coil or by the surrounding transmit coil. Prior work (1) has demonstrated that the use of balanced matching schemes and cable traps can reduce shield currents if the local coil is considered the source. This work focuses on the measurement and reduction of shield currents that are induced by a surrounding body coil.
Phenotype, function, and differentiation potential of human monocyte subsets (2017)

Human monocytes have been grouped into classical (CD14++CD16-), non-classical (CD14dimCD16++), and intermediate (CD14++CD16+) subsets. Documentation of normal function and variation in this complement of subtypes, particularly their differentiation potential to dendritic cells (DC) or macrophages, remains incomplete. We therefore phenotyped monocytes from peripheral blood of healthy subjects and performed functional studies on high-speed sorted subsets. Subset frequencies were found to be tightly controlled over time and across individuals. Subsets were distinct in their secretion of TNFα, IL-6, and IL-1β in response to TLR agonists, with classical monocytes being the most producers and non-classical monocytes the least. Monocytes, particularly those of the non-classical subtype, secreted interferon-α (IFN-α) in response to intracellular TLR3 stimulation. After incubation with IL-4 and GM-CSF, classical monocytes acquired monocyte-derived DC (mo-DC) markers and morphology and stimulated allogeneic T cell proliferation in MLR; intermediate and non-classical monocytes did not. After incubation with IL-3 and Flt3 ligand, no subset differentiated to plasmacytoid DC. After incubation with GM-CSF (M1 induction) or macrophage colony-stimulating factor (M-CSF) (M2 induction), all subsets acquired macrophage morphology, secreted macrophage-associated cytokines, and displayed enhanced phagocytosis. From these studies we conclude that classical monocytes are the principal source of mo-DCs, but all subsets can differentiate to macrophages. We also found that monocytes, in particular the non-classical subset, represent an alternate source of type I IFN secretion in response to virus-associated TLR agonists.
Differentiation of hepatic metastases from hepatic hemangiomas and cysts by using MR imaging (1988)

T1-weighted and T2-weighted pulse sequences were employed for MR imaging of hepatic metastatic tumors (98 patients), hemangiomas (24 patients), and cysts (seven patients); a 0.6-T superconducting magnet was used. In a retrospective study, signal intensity and morphology were used to establish criteria for differentiating metastases from hemangiomas and cysts. The signal intensity of the lesion alone failed to be an etiologic discriminator because over 96% of all masses had a signal intensity less than that of liver on T1-weighted sequences, and at least 90% had a signal intensity greater than that of liver on T2-weighted sequences. Morphologic features depicted on T2-weighted images were more specific than those depicted on T1-weighted images in differential diagnosis. Amorphous, target, and halo signs and a change in morphology were present only in metastatic disease, with a frequency of 45%, 27%, 13%, and 12%, respectively. Two other morphologic patterns--doughnut and lightbulb signs--were found to have overlapping causes. Overall, at least one of the specific signs was observed in 92% of patients with metastatic disease. These data suggest that T2-weighted pulse sequences are essential for discriminating between hepatic metastases and hepatic hemangiomas and cysts. MR imaging is a promising technique for distinguishing these lesions.
Supplementary Figure 6 from PlGF/VEGFR-1 Signaling Promotes Macrophage Polarization and Accelerated Tumor Progression in Obesity (2023)

&lt;p&gt;Effects of VEGFR-1 signaling ablation on glucose/insulin tolerance and insulin production by the pancreas during obesity.&lt;/p&gt;
Differential amplification and expression of c-myb oncogene in Zajdela ascitic hepatoma. (1990)

Organisation and expression of c-myb protooncogene have been studied in a heterogeneous tumour the Zajdela ascitic hepatoma (ZAH). The myb gene is selectively amplified in the more tumorigenic subpopulation of the tumour while the non-lethal subpopulation does not show any change. Analysis of transcripts of the myb gene in tumorigenic versus nontumorigenic cells shows that the level of amplification of the gene does not correspond to the level of its transcription. Results have been discussed in the light of existing evidence regarding the role of c-myb gene expression during cell cycle.
Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase (2017)

Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
Aggregation of amphiphiles in nonaqueous media (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAggregation of amphiphiles in nonaqueous mediaE. Ruckenstein and R. NagarajanCite this: J. Phys. Chem. 1980, 84, 11, 1349–1358Publication Date (Print):May 1, 1980Publication History Published online1 May 2002Published inissue 1 May 1980https://pubs.acs.org/doi/10.1021/j100448a013https://doi.org/10.1021/j100448a013research-articleACS PublicationsRequest reuse permissionsArticle Views464Altmetric-Citations125LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Ionic Liquids for Soft Functional Materials with Carbon Nanotubes (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.