gebhart/patrepeval huggingface dataset:
Proof-of-concept demonstration of edge-illumination x-ray phase contrast imaging combined with tomosynthesis (2014)

In this note we present the first proof-of-concept results on the potential effectiveness of the edge-illumination x-ray phase contrast method (in its 'coded-aperture' based lab implementation) combined with tomosynthesis. We believe that, albeit admittedly preliminary (e.g. we only present phantom work), these results deserve early publication in a note primarily for four reasons. First, we fully modelled the imaging acquisition method, and validated the simulation directly with experimental results. This shows that the implementation of the method in the new geometry is understood, and thus that it will be possible to use the model to simulate more complex scenarios in the future. Secondly, we show that a strong phase contrast signal is preserved in the reconstructed tomosynthesis slices: this was a concern, as the high spatial frequency nature of the signal makes it sensitive to any filtration-related procedure. Third, we show that, despite the non-optimized nature of the imaging prototype used, we can perform a full angular scan at acceptable dose levels and with exposure times not excessively distant from what is required by clinical practice. Finally, we discuss how the proposed phase contrast method, unlike other approaches apart from free-space propagation (which however requires a smaller focal spot, thus reducing the flux and increasing exposure times), can be easily implemented in a tomosynthesis geometry suitable for clinical use. In summary, we find that these technical results indicate a high potential for the combination of the two methods. Combining slice separation with detail enhancement provided by phase effects would substantially increase the detectability of small lesions and/or calcifications, which we aim to demonstrate in the next steps of this study.
Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma (1998)

Inactivation of the genes involved in DNA mismatch repair is associated with microsatellite instability (MSI) in colorectal cancer. We report that hypermethylation of the 5' CpG island of hMLH1 is found in the majority of sporadic primary colorectal cancers with MSI, and that this methylation was often, but not invariably, associated with loss of hMLH1 protein expression. Such methylation also occurred, but was less common, in MSI- tumors, as well as in MSI+ tumors with known mutations of a mismatch repair gene (MMR). No hypermethylation of hMSH2 was found. Hypermethylation of colorectal cancer cell lines with MSI also was frequently observed, and in such cases, reversal of the methylation with 5-aza-2'-deoxycytidine not only resulted in reexpression of hMLH1 protein, but also in restoration of the MMR capacity in MMR-deficient cell lines. Our results suggest that microsatellite instability in sporadic colorectal cancer often results from epigenetic inactivation of hMLH1 in association with DNA methylation.
Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement (2013)

Complex and highly reticulated evolutionary relationships between Epichloë-Neotyphodium endophytes have been predicted on the basis of multiple nuclear genes and entire mitochondrial protein-coding gene complements, derived from independent assembly of whole genome sequence reads. The results are consistent with previous studies while also providing novel phylogenetic insights, particularly through inclusion of data from the endophyte lineage-specific gene, as well as affording evidence for the origin of cytoplasmic genomes. In particular, the results obtained from the present study imply the possible occurrence of at least two distinct E. typhina progenitors for heteropoid taxa, as well the ancestral contribution of an endophyte species distinct from (although related to) contemporary E. baconii to the extant hybrid species. Furthermore, the present study confirmed the distinct taxonomic status of the newly identified fescue endophyte taxa, FaTG-3-like and UNS, which are consequently proposed to be renamed FaTG4 and FaTG5, respectively.
Photoinduced Electron Transfer between Multifunctional Porphyrin and Ubiquinone Analogues Linked by Several Hydrogen‐Bonding Interactions (1996)

In only a few picoseconds the photoinduced electron transfer in the noncovalently linked complex between zinc porphyrin 1 and the quinone 2 is complete. Transient absorption spectra show the zinc porphyrin cation radical as typical intermediate of the electron transfer.
Accurate Measurement of Porous Low-k Thin-Films by Nanoindentation: Densification Scaling versus Substrate Effects (2017)

Historically, the integration of insulators with decreasing dielectric constants, k, has been critical in improving devices performance. The most efficient approach to decrease k is by introducing porosity. Since porosity directly impacts the Young's modulus, the accurate determination of the mechanical properties of porous dielectrics is essential in enabling their implementation into state-of-the-art devices. Currently, nanoindentation is the technique of choice, but as technology relevant thicknesses of dielectrics keep decreasing, substrate effects are unavoidably encountered. These issues have so far been circumvented by measuring bulk materials instead of their thin-film counterparts. This approach is, however, less than ideal as physical properties can be size-dependent. Moreover, pores densification also occurs, potentially leading to overestimated Young's modulus values. In this paper, we define a novel protocol based on ultra-low load, quasi-static nanoindentation to measure mechanical properties of porous thin-films as a function of porosity (0–60%) and thickness (150–700 nm). We could isolate materials densification from substrate effect, and we demonstrated that the former can be accounted for, while the latter does not happen until indentation depths are remarkably higher than the traditionally accepted indentation limit of 10% of the film thickness. Consequently, extremely accurate mechanical characterization of porous low-k thin-films is now possible.
Knockdown of RNA Interference Pathway Genes in Western Corn Rootworms (Diabrotica virgifera virgifera Le Conte) Demonstrates a Possible Mechanism of Resistance to Lethal dsRNA (2016)

RNA interference (RNAi) is being developed as a potential tool for insect pest management. Increased understanding of the RNAi pathway in target insect pests will provide information to use this technology effectively and to inform decisions related to resistant management strategies for RNAi based traits. Dicer 2 (Dcr2), an endonuclease responsible for formation of small interfering RNA's and Argonaute 2 (Ago2), an essential catalytic component of the RNA-induced silencing complex (RISC) have both been associated with the RNAi pathway in a number of different insect species including the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). We identified both genes from a transcriptome library generated from different tissues and developmental stages of the western corn rootworm, an important target pest for transgenic plants expressing dsRNA targeting essential genes. The expression of these genes was suppressed by more than 90% after injecting gene specific dsRNA into adult rootworms. The injected beetles were then fed vATPase A dsRNA which has previously been demonstrated to cause mortality in western corn rootworm adults. The suppression of both RNAi pathway genes resulted in reduced mortality after subsequent exposure to lethal concentrations of vATPase A dsRNA as well as increased vATPase A expression relative to control treatments. Injections with dsRNA for a non-lethal target sequence (Laccase 2) did not affect mortality or expression caused by vATPase A dsRNA indicating that the results observed with Argo and Dicer dsRNA were not caused by simple competition among different dsRNA's. These results confirm that both genes play an important role in the RNAi pathway for western corn rootworms and indicate that selection pressures that potentially affect the expression of these genes may provide a basis for future studies to understand potential mechanisms of resistance.
Mutation of the ATM Gene is Not Involved in the Pathogenesis of Either Follicle Center Lymphoma or its Transformation to Higher-grade Lymphoma (2002)

Loss of function of the ataxia-telangiectasia mutated (ATM) gene, located on human chromosome 11q22-23, is the cause of ataxia-telangiectasia (A-T), which is associated with an extremely high risk for lymphoma. Abnormalities in 11q22-23, including deletions and mutations of the ATM gene, have been reported in T-cell prolymphocytic leukemias, B-CLL and in mantle cell lymphoma. In a survey of gene expression in follicle center lymphomas (FCL) and diffuse large B-cell lymphomas (DLBCL), almost all FCL expressed significant levels of ATM and the majority of DLBCL expressed low levels of ATM. This finding raised the possibility that the transformation of some FCL to DLBCL might be associated with inactivation of the ATM gene. Therefore, we analyzed biopsy specimens of 17 patients with FCL obtained at the time of diagnosis, four subsequent biopsies obtained at the time of FCL relapse and seven subsequent biopsies at the time of transformation to DLBCL. A comprehensive analysis of the ATM gene was performed by denaturing high performance liquid chromatography and sequencing. The analysis covered all of the 66 exons including the 9168 base pairs of ATM coding sequence as well as 16,676 base pairs of non-coding sequence. Twenty-eight known polymorphisms and rare sequence variants were observed, but no classic A-T mutations were detected. In 11 tumors, both tumor B-cells and normal T-cells were sorted for separate examination, and in each case, polymorphisms and rare variants were present in both tumor and normal cells. No new ATM gene mutations were associated with transformation from FCL to DLBCL. Thus, ATM gene mutations do not play a pivotal role either in the pathogenesis of FCL or in its transformation to DLBCL.
ChemInform Abstract: Vortex Fluidic Promoted Diels—Alder Reactions in an Aqueous Medium. (2014)

Abstract The reaction is performed in a vortex fluidic device (VFD), a thin film microfluidic platform, at a 45° tilt angle and 5000 rpm in the absence of a catalyst.
Improved Top-Down Techniques in Differential Cryptanalysis. (2015)

Abstract. The fundamental problem of differential cryptanalysis is to find the highest entries in the Difference Distribution Table (DDT) of a given mapping F over n-bit values, and in particular to find the highest diagonal entries which correspond to the best iterative characteristics of F. The standard bottom-up approach to this problem is to consider all the internal components of the mapping along some differential char-acteristic, and to multiply their transition probabilities. However, this can provide seriously distorted estimates since the various events can be dependent, and there can be a huge number of low probability charac-teristics contributing to the same high probability entry. In this paper we use a top-down approach which considers the given mapping as a black box, and uses only its input/output relations in order to obtain direct experimental estimates for its DDT entries which are likely to be much more accurate. In particular, we describe three new techniques which reduce the time complexity of three crucial aspects of this prob-
Co‐continuous Nanostructured Blend by Reactive Blending: Incorporation of High Molecular Weight Polymers (2010)

Abstract One of the most challenging issues remaining in the design and the synthesis of robust nanostructured polymers blends is incorporating long crystallizable chains while preserving the co‐continuity of the phases. Here, we demonstrate that by reactive blending of functionalized polyolefin and polyamides such co‐continuous structures can be obtained provided that a bimodal mixture of short and long polyamides is used. The short chains react more readily to form graft copolymers that facilitate both grafting of long chains and formation of nanostructures. We discuss different mixing strategies, characterize, and compare reacted products and resulting blend structures. magnified image
High aspect ratio diamond nanosecond laser machining (2023)

The online version contains supplementary material available at 10.1007/s00339-023-06755-2.
Human Immunodeficiency Virus Type 1 Envelope Epitope-Specific CD4+T Lymphocytes in Simian/Human Immunodeficiency Virus-Infected and Vaccinated Rhesus Monkeys Detected Using a Peptide-Major Histocompatibility Complex Class II Tetramer (2000)

A tetrameric recombinant major histocompatibility complex (MHC) class II-peptide complex was used to quantitate human immunodeficiency virus type 1 (HIV-1) envelope (Env)-specific CD4(+) T cells in vaccinated and in simian/human immunodeficiency virus (SHIV)-infected rhesus monkeys. A rhesus monkey MHC class II DR molecule, Mamu-DR*W201, and an HIV-1 Env peptide (p46) were employed to construct this tetrameric complex. A p46-specific proliferative response was seen in sorted, tetramer-binding, but not nonbinding, CD4(+) T cells, directly demonstrating that this response was mediated by the epitope-specific lymphocytes. Although staining of whole blood from 10 SHIV-infected Mamu-DR*W201(+) rhesus monkeys failed to demonstrate tetramer-binding CD4(+) T cells (<0.02%), p46-stimulated peripheral blood mononuclear cells (PBMCs) from 9 of these 10 monkeys had detectable p46 tetramer-binding cells, comprising 0.5 to 15.2% of the CD4(+) T cells. p46-stimulated PBMCs from 7 of 10 Mamu-DR*W201(+) monkeys vaccinated with a recombinant canarypox virus-HIV-1 env construct also demonstrated p46 tetramer-binding cells, comprising 0.9 to 7.2% of the CD4(+) T cells. Thus, Env p46-specific CD4(+) T cells can be detected by tetrameric Mamu-DR*W201-p46 complex staining of PBMCs in both SHIV-infected and vaccinated rhesus monkeys. These epitope-specific cell populations appear to be present in peripheral blood at a very low frequency.
Faculty Opinions recommendation of Natural killer cells distinguish innocuous and destructive forms of pancreatic islet autoimmunity. (2004)

In both human patients and murine models, the progression from insulitis to diabetes is neither immediate nor inevitable, as illustrated by the innocuous versus destructive infiltrates of BDC2.5 transgenic mice on the nonobese diabetic (NOD) versus C57BL/6.H-2g7 genetic backgrounds. Natural killer (NK)-cell-specific transcripts and the proportion of NK cells were increased in leukocytes from the aggressive BDC2.5/B6.H-2g7 lesions. NK cell participation was also enhanced in the aggressive lesions provoked by CTLA-4 blockade in BDC2.5/NOD mice. In this context, depletion of NK cells significantly inhibited diabetes development. NOD and B6.H-2g7 mice exhibit extensive variation in NK receptor expression, reminiscent of analogous human molecules. NK cells can be important players in type 1 diabetes, a role that was previously underappreciated. PMID: 15141080 Funding information This work was supported by: NIAID NIH HHS, United States Grant ID: P01 AI39671-08 NIAID NIH HHS, United States Grant ID: P01 AI039671 NIDDK NIH HHS, United States Grant ID: P30 DK036836 NIAID NIH HHS, United States Grant ID: P01 AI054904 NIDDK NIH HHS, United States Grant ID: 2 P30 DK36836-17 NIAID NIH HHS, United States Grant ID: P01 AI54904-01 More Less keyboard_arrow_down
Density of amorphous sputtered Ge2Sb2Te5 thin films (2023)

The density, crystallinity, and microstructure of reactively sputtered amorphous Ge2Sb2Te5 thin films have been assessed as a function of deposition temperature. The continuous density increase was observed with increasing substrate temperature between room temperature and 200 °C. The films deposited at room temperature are amorphous and exhibit a columnar structure with a lateral size of cells in the 10–15 nm range. Cells consist of high-density interior with boundaries with the density lower by ∼9% due to incorporation of pores. The pores and the columnar microstructure can be eliminated by deposition at 80 °C while still preserving the amorphous phase. The density of pore- and stress-free amorphous Ge2Sb2Te5 is 6.16 g/cm3 and is only 1.5% lower than the crystalline Ge2Sb2Te5 with NaCl structure.
Data from Delivery of Telomerase Reverse Transcriptase Small Interfering RNA in Complex with Positively Charged Single-Walled Carbon Nanotubes Suppresses Tumor Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To determine whether -CONH-(CH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;6&lt;/sub&gt;-NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; functionalized single-walled carbon nanotubes (SWNT) carrying complexed small interfering RNA (siRNA) can enter into tumor cells, wherein they release the siRNA to silence the targeted gene.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; -CONH-(CH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;6&lt;/sub&gt;-NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; was used to mediate the conjugation of telomerase reverse transcriptase (TERT) siRNA to SWNTs. The ability of TERT siRNA delivered via SWNT complexes to silence the expression of TERT was assessed by their effects on the proliferation and growth of tumor cells both &lt;i&gt;in vitro&lt;/i&gt; and in mouse models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The functionalized SWNTs -CONH-(CH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;6&lt;/sub&gt;-NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; could facilitate the coupling of siRNAs that specifically target murine TERT expression to form the mTERT siRNA:SWNT+ complex. These functionalized SWNTs rapidly entered three cultured murine tumor cell lines, suppressed mTERT expression, and produced growth arrest. Injection of mTERT siRNA:SWNT+ complexes into s.c. Lewis lung tumors reduced tumor growth. Furthermore, human TERT siRNA:SWNT+ complexes also suppressed the growth of human HeLa cells both &lt;i&gt;in vitro&lt;/i&gt; and when injected into tumors in nude mice.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; -CONH-(CH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;6&lt;/sub&gt;-NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; functionalized SWNTs carry complexed siRNA into tumor cells, wherein they release the siRNA from the nanotube sidewalls to silence the targeted gene. The -CONH-(CH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;6&lt;/sub&gt;-NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; functionalized SWNTs may represent a new class of molecular transporters applicable for siRNA therapeutics.&lt;/p&gt;&lt;/div&gt;
Distinctive Subpopulations of Stromal Cells Are Present in Human Lymph Nodes Infiltrated with Melanoma (2020)

Metastasis of human tumors to lymph nodes (LN) is a universally negative prognostic factor. LN stromal cells (SC) play a crucial role in enabling T-cell responses, and because tumor metastases modulate their structure and function, this interaction may suppress immune responses to tumor antigens. The SC subpopulations that respond to infiltration of malignant cells into human LNs have not been defined. Here, we identify distinctive subpopulations of CD90<sup>+</sup> SCs present in melanoma-infiltrated LNs and compare them with their counterparts in normal LNs. The first population (CD90<sup>+</sup> podoplanin<sup>+</sup> CD105<sup>+</sup> CD146<sup>+</sup> CD271<sup>+</sup> VCAM-1<sup>+</sup> ICAM-1<sup>+</sup> α-SMA<sup>+</sup>) corresponds to fibroblastic reticular cells that express various T-cell modulating cytokines, chemokines, and adhesion molecules. The second (CD90<sup>+</sup> CD34<sup>+</sup> CD105<sup>+</sup> CD271<sup>+</sup>) represents a novel population of CD34<sup>+</sup> SCs embedded in collagenous structures, such as the capsule and trabeculae, that predominantly produce extracellular matrix. We also demonstrated that these two SC subpopulations are distinct from two subsets of human LN pericytes, CD90<sup>+</sup> CD146<sup>+</sup> CD36<sup>+</sup> NG2<sup>-</sup> pericytes in the walls of high endothelial venules and other small vessels, and CD90<sup>+</sup> CD146<sup>+</sup> NG2<sup>+</sup> CD36<sup>-</sup> pericytes in the walls of larger vessels. Distinguishing between these CD90<sup>+</sup> SC subpopulations in human LNs allows for further study of their respective impact on T-cell responses to tumor antigens and clinical outcomes.
Network Reconfiguration for Electrical Loss Minimization (2011)

Increasing requirements of urbanization, industrialization and modernization demands further expansion and development of the national power grid and nonetheless, with a better efficiency and an enhanced voltage stability. The aim of this project is to conceptualize and realize an electric transmission and distribution network with improved efficiency and voltage stability that will contribute to the substantial reduction in the involved operational costs. Network Reconfiguration Methodology has been used. The study of this work was conducted on IEEE 14 bus network with Matlab tool using Newton-Raphson Method. The study also deals with how this technique can practically be implemented using Artificial Neural Network and sensors.
AAV9-mediated gene delivery of MCT1 to oligodendrocytes does not provide a therapeutic benefit in a mouse model of ALS (2021)

Oligodendrocyte dysfunction has been implicated in the pathophysiology of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder characterized by progressive motor neuron loss. The failure of trophic support provided by oligodendrocytes is associated with a concomitant reduction in oligodendroglial monocarboxylate transporter 1 (MCT1) expression and is detrimental for the long-term survival of motor neuron axons. Therefore, we established an adeno-associated virus 9 (AAV9)-based platform by which MCT1 was targeted mostly to white matter oligodendrocytes to investigate whether this approach could provide a therapeutic benefit in the SOD1G93A mouse model of ALS. Despite good oligodendrocyte transduction and AAV-mediated MCT1 transgene expression, the disease outcome of SOD1G93A mice was not altered. Our study further increases our current understanding about the complex nature of oligodendrocyte pathology in ALS and provides valuable insights into the future development of therapeutic strategies to efficiently modulate these cells. Oligodendrocyte dysfunction has been implicated in the pathophysiology of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder characterized by progressive motor neuron loss. The failure of trophic support provided by oligodendrocytes is associated with a concomitant reduction in oligodendroglial monocarboxylate transporter 1 (MCT1) expression and is detrimental for the long-term survival of motor neuron axons. Therefore, we established an adeno-associated virus 9 (AAV9)-based platform by which MCT1 was targeted mostly to white matter oligodendrocytes to investigate whether this approach could provide a therapeutic benefit in the SOD1G93A mouse model of ALS. Despite good oligodendrocyte transduction and AAV-mediated MCT1 transgene expression, the disease outcome of SOD1G93A mice was not altered. Our study further increases our current understanding about the complex nature of oligodendrocyte pathology in ALS and provides valuable insights into the future development of therapeutic strategies to efficiently modulate these cells.