gebhart/patrepeval huggingface dataset:
Effects of Crystal Morphology on Singlet Exciton Fission in Diketopyrrolopyrrole Thin Films B (2016)

Singlet exciton fission (SF) is a promising strategy for increasing photovoltaic efficiency, but in order for SF to be useful in solar cells, it should take place in a chromophore that is air-stable, highly absorptive, solution processable, and inexpensive. Unlike many SF chromophores, diketopyrrolopyrrole (DPP) conforms to these criteria, and here we investigate SF in DPP for the first time. SF yields in thin films of DPP derivatives, which are widely used in organic electronics and photovoltaics, are shown to depend critically on crystal morphology. Time-resolved spectroscopy of three DPP derivatives with phenyl (3,6-diphenylpyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione, PhDPP), thienyl (3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione, TDPP), and phenylthienyl (3,6-di(5-phenylthiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione, PhTDPP) aromatic substituents in 100–200 nm thin films reveals that efficient SF occurs only in TDPP and PhTDPP (τSF = 220 ± 20 ps), despite the fact that SF is most exoergic in PhDPP. This result correlates well with the greater degree of π-overlap and closer π-stacking in TDPP (3.50 A) and PhTDPP (3.59 A) relative to PhDPP (3.90 A) and demonstrates that SF in DPP is highly sensitive to the electronic coupling between adjacent chromophores. The triplet yield in PhTDPP films is determined to be 210 ± 35% by the singlet depletion method and 165 ± 30% by the energy transfer method, showing that SF is nearly quantitative in these films and that DPP derivatives are a promising class of SF chromophores for enhancing photovoltaic performance.
A semantic regulatory framework for nanotechnology application in agri-food domain (2011)

Nanotechnology research and development in the agri-food sector is likely to facilitate and frame the next stage of development of genetically modified crops, chemical pesticides and design of less calorie-dense foods [1]. However, unlike other established domains, nanotechnology research and development has triggered serious calls for effective nano-specific regulatory arrangements and increased community participation in its infancy itself, as this discipline has a direct bearing on human life, environment and social issues [2]. The result is emergence of multiple stakeholders such as regulatory bodies, researchers, consumers and manufacturers seeking knowledge in this nascent area from a legal knowledge perspective. To the best of our knowledge, no transparent regulatory framework exists to cater to the knowledge needs of various stakeholders in this requirement intensive domain. To address this gap, we have developed an intelligent framework using which the stakeholders can collaboratively formulate regulations and get recommendations about their relevance and impact.
Toward Automated Provability-Based Semantic Interoperability Between Ontologies for the Intelligence Community (2007)

The need for interoperability is dire: Knowledge representation systems employ ontologies that use disparate formalisms to describe related domains; to be truly useful to the intelligence community, they must meaningfully share information. Ongoing research [3, 4, 7, 15] strives toward the holy grail of complete interoperability, but has been hindered by techniques that are specialized for particular ontologies, and that lack the expressivity needed to describe complex ontological relationships. In the sequel, we describe provability-based semantic interoperability (PBSI) [16], a means to surmount these hindrances; translation graphs, one of our key formalism for describing the complex relationships among arbitrary ontologies; and ways in which these techniques might be automated.
Biocatalytic Asymmetric Hydrocyanation in the Presence of (R)-Oxynitrilases Entrapped in Lens-Shaped Gels (2002)

This contribution contains a brief review of our results on the recent development of a cross-linked and subsequently polyvinylalcohol-entrapped (R)-oxynitrilase and its application in the asymmetric hydrocyanation. In the presence of this novel LentiKat ® entrapped oxynitrilase as a biocatalyst, and benzaldehyde as an aldehyde component, the desired (R)mandelonitrile was obtained in good yields and with high enantioselectivities. This new type of immobilized lens-shaped biocatalyst has a well-defined macroscopic size in mm-range, and can be re-used efficiently.
Micro- and Nanopatterning of Inorganic and Polymeric Substrates by Indentation Lithography (2010)

This paper describes the use of a nanoindenter, equipped with a diamond tip, to form patterns of indentations on planar substrates (epoxy, silicon, and SiO(2)). The process is called "Indentation Lithography" (IndL). The indentations have the form of pits and furrows, whose cross-sectional profiles are determined by the shapes of the diamond indenters, and whose dimensions are determined by the applied load and hardness of the substrate. IndL makes it possible to indent hard materials, to produce patterns with multiple levels of relief by changing the loading force, and to control the profiles of the indentations by using indenters with different shapes. This paper also demonstrates the transfer of indented patterns to elastomeric PDMS stamps for soft lithography, and to thin films of evaporated gold or silver. Stripping an evaporated film from an indented template produces patterns of gold or silver pyramids, whose tips concentrate electric fields. Patterns produced by IndL can thus be used as substrates for surface-enhanced Raman scattering (SERS) and for other plasmonic applications.
0.228 μm/sup 2/ trench cell technologies with bottle-shaped capacitor for 1 Gbit DRAMs (2002)

In order to realize 1 Gbit DRAMs, we have developed a 0.228 /spl mu/m/sup 2/ trench type cell. Two methods are employed to shrink the memory cell size. One is a "bottle shaped" capacitor, which has a larger diameter than the opening for the storage node. For this capacitor structure, we have verified 30% capacitance increase keeping the trench opening, sufficiently high breakdown field of capacitor dielectric, and less than 1/1000 of a soft-error rate compared with the conventional one. The other is a 6F/sup 2/ cell layout suitable for an open-folded-bit-line architecture, which reduces to 75% for the conventional 8F/sup 2/ cell layout with the same feature size, F. We have also confirmed that a P/sup +/ poly gate transistor has a sufficient overlap tolerance (more than 0.1 /spl mu/m) between the transfer gate and the trench edge by using three-dimensional device simulator. These results strongly support feasibility of our novel cell.
NIR imaging the delivery of cathespin B probe to breast tumors (2003)

Proteases are involved in the invasion and metastasis of tumor cells. Cathepsin B overexpression has been shown in some neoplastic tissues. This study assesses the expression of Cathepsin B in the human fibrosarcoma (HT1080) in the mouse model by near-infrared (NIR) imaging. The nude mice were intravenously injected "a stealth probe" - an activable Cathepsin B sensing near-infrared fluorescence (NIRF) probe (24 hours before sacrifice) and the dye Cy5.5 (30 seconds before sacrifice). The animals were freeze-trapped and NIR images were obtained by the low temperature NIR scanner at the following excitation-emission wavelength pairs: 366, 450nm (NADH), 436, 520nm (FAD), and 670, 695nm (Cathepsin B probe). After imaging, the samples were submitted for histopathological evaluation. The tumor redox ratio NADH/(NADH+FAD) increased significantly because of the hypoxic state of tumor tissue with respect to normal tissue. The Cathepsin B probe was uniformly distributed throughout the tumor. This study indicated the efficient usage of the Cathepsin B probe in the molecular imaging for the detection of the early stage tumors.
In-vitro antimicrobial activity of the new fluoroquinolone, grepafloxacin, against pathogenic Nocardia spp. (1995)

Journal Article In-vitro antimicrobial activity of the new fluoroquinolone, grepafloxacin, against pathogenic Nocardia spp. Get access Katsukiyo Yazawa, Katsukiyo Yazawa Division of Experimental Chemotherapy, Research Centre for Pathogenic Fungi and Microbial Toxicoses, Chiba University1-8-1, Inohana, Chuo-ku, Chiba, Japan (260) Search for other works by this author on: Oxford Academic PubMed Google Scholar Yuzuru Mikami Yuzuru Mikami * Division of Experimental Chemotherapy, Research Centre for Pathogenic Fungi and Microbial Toxicoses, Chiba University1-8-1, Inohana, Chuo-ku, Chiba, Japan (260) *Corresponding author. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 35, Issue 4, April 1995, Pages 541–544, https://doi.org/10.1093/jac/35.4.541 Published: 01 April 1995 Article history Received: 13 June 1994 Accepted: 09 November 1994 Published: 01 April 1995
Synthesis of End-Functionalized Poly(norbornenes) and Poly(ethylidene norbornenes) Using a Pd(II) Catalyst in Combination with Chain Transfer Agents (2021)

Synthesis of end-functionalized poly(norbornenes) (PNBs) and poly(ethylidenenorbornenes) (PENBs) were prepared using the palladium catalyst tBu3PPdMeCl/NaBArf in combination with the chain transfer agents (CTAs) 4-penten-1-ol and 10-undecenal. These CTAs produce polymers end-capped with −OH and −CHO groups, respectively, in high yields with Mn values in the range of 6–17K, depending on the CTA:monomer molar ratio. End-functionalized PNBs and PENBs with precisely controlled Mn values and very narrow molecular weight distributions were accessed by using 4-penten-1-ol and 10-undecenal as chain-terminating agents following living polymerizations in which the monomer is completely consumed. The utility of the aldehyde-functionalized polymers is illustrated via coupling to a dye molecule and by the synthesis of ambiphilic diblock copolymers, PNB-b-PEG and PENB-b-PEG.
Comparative validation of the D. melanogaster modENCODE transcriptome annotation (2014)

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.
EXTRACTIVES FROM POPULUS TREMULOIDES HEARTWOOD: THE TRITERPENE ALCOHOLS (1963)

The 'unsaturated alcohol fraction' from P. tremuloides heartwood (R. A. Abramovitch, R. G. Micetich, and S. J. Smith, Tappi, 46, 37 (1963)) has been found to contain α- and β-amyrin, butyrospermol, 24-methylenecycloartanol, lupeol, and α-amyrenonol. Some aspects of the infrared and n.m.r. spectra of these compounds are discussed and the suggestion is made that the tritisterols and orysterols may actually be C 31 H 52 O triterpenes containing a cyclopropane ring.
ChemInform Abstract: N,N‐Dibenzyl‐N′‐benzylidenehydrazines: Potent Competitive Glucose‐6‐phosphatase Catalytic Enzyme Inhibitors. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fully automatic measurements of axial vertebral rotation for assessment of spinal deformity in idiopathic scoliosis (2013)

Reliable measurements of spinal deformities in idiopathic scoliosis are vital, since they are used for assessing the degree of scoliosis, deciding upon treatment and monitoring the progression of the disease. However, commonly used two dimensional methods (e.g. the Cobb angle) do not fully capture the three dimensional deformity at hand in scoliosis, of which axial vertebral rotation (AVR) is considered to be of great importance. There are manual methods for measuring the AVR, but they are often time-consuming and related with a high intra- and inter-observer variability. In this paper, we present a fully automatic method for estimating the AVR in images from computed tomography. The proposed method is evaluated on four scoliotic patients with 17 vertebrae each and compared with manual measurements performed by three observers using the standard method by Aaro-Dahlborn. The comparison shows that the difference in measured AVR between automatic and manual measurements are on the same level as the inter-observer difference. This is further supported by a high intraclass correlation coefficient (0.971-0.979), obtained when comparing the automatic measurements with the manual measurements of each observer. Hence, the provided results and the computational performance, only requiring approximately 10 to 15 s for processing an entire volume, demonstrate the potential clinical value of the proposed method.
Correction: Massively Parallelized Pollen Tube Guidance and Mechanical Measurements on a Lab-on-a-Chip Platform (2017)

The images for Figs
A new plasmid vector for DNA delivery using lactococci (2009)

We showed the potential of an invasive L. lactis harbouring pValac to DNA delivery and subsequent triggering DNA expression by epithelial cells. Further work will be to examine whether these strains are able to deliver DNA in intestinal cells in vivo.
Visible Light Communications (2009)

This chapter contains sections titled: Introduction VLC Link Potential Applications Challenges Standardisation Conclusions References
Data from Ablative Tumor Radiation Can Change the Tumor Immune Cell Microenvironment to Induce Durable Complete Remissions (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The goals of the study were to elucidate the immune mechanisms that contribute to desirable complete remissions of murine colon tumors treated with single radiation dose of 30 Gy. This dose is at the upper end of the ablative range used clinically to treat advanced or metastatic colorectal, liver, and non–small cell lung tumors.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Changes in the tumor immune microenvironment of single tumor nodules exposed to radiation were studied using 21-day (&gt;1 cm in diameter) CT26 and MC38 colon tumors. These are well-characterized weakly immunogenic tumors.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We found that the high-dose radiation transformed the immunosuppressive tumor microenvironment resulting in an intense CD8&lt;sup&gt;+&lt;/sup&gt; T-cell tumor infiltrate, and a loss of myeloid-derived suppressor cells (MDSC). The change was dependent on antigen cross-presenting CD8&lt;sup&gt;+&lt;/sup&gt; dendritic cells, secretion of IFNγ, and CD4&lt;sup&gt;+&lt;/sup&gt;T cells expressing CD40L. Antitumor CD8&lt;sup&gt;+&lt;/sup&gt; T cells entered tumors shortly after radiotherapy, reversed MDSC infiltration, and mediated durable remissions in an IFNγ-dependent manner. Interestingly, extended fractionated radiation regimen did not result in robust CD8&lt;sup&gt;+&lt;/sup&gt; T-cell infiltration.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; For immunologically sensitive tumors, these results indicate that remissions induced by a short course of high-dose radiotherapy depend on the development of antitumor immunity that is reflected by the nature and kinetics of changes induced in the tumor cell microenvironment. These results suggest that systematic examination of the tumor immune microenvironment may help in optimizing the radiation regimen used to treat tumors by adding a robust immune response. &lt;i&gt;Clin Cancer Res; 21(16); 3727–39. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Fast image‐based mitral valve simulation from individualized geometry (2018)

The mitral valve simulation can help the surgeon understand valve behaviour and anticipate the outcome of a procedure.
Resistin Gene Expression is Downregulated in CD4+ T Helper Lymphocytes and CD14+ Monocytes in Rheumatoid Arthritis Responding to TNF‐α Inhibition (2016)

Rheumatoid arthritis (RA) is caused by complex interactions between immune cells and sustained by Th1 response cytokines. Resistin [resistance to insulin; (RETN)] is an inflammatory cytokine, first discovered in murine adipocytes. In man, RETN is mainly secreted by monocytes. The distinct role of RETN in the immune reaction is uncertain; however, RETN has pro-inflammatory, pro-fibrotic and possibly tolerogenic properties. The aim was to assess the reaction of RETN gene expression to TNF-α inhibition (I) in pathogenetic immune cell subsets in RA, in the context of Th1, inflammatory and regulatory cytokine gene expressions. Accordingly, we measured RETN, IFN-γ, TNF-β, IL-1β, TNF-α, TGF-β and IL-10 gene expressions in CD14(+) monocytes, CD4(+) T helper (Th) lymphocytes (ly), CD8(+) T cytotoxic (Tc) ly and CD19(+) B ly in active RA before and 3 months after start of TNF-αI. Leucocyte subsets were separated by specific monoclonal antibody-covered beads, RNA extracted and levels of RETN, Th1 response, inflammatory and regulatory cytokine mRNAs measured by quantitative reverse transcription-polymerase chain reaction technique. We found that TNF-αI caused a significant downregulation of RETN gene expression in CD14(+) monocytes and CD4(+) Th ly and was unchanged in CD8(+) Tc ly and CD19(+) B ly. Both in active RA and during TNF-αI, RETN mRNA levels were significantly higher in CD14(+) monocytes than in all other examined cell types. In monocytes, fold change in RETN and TGF-β gene expressions upon TNF-αI correlated significantly. Our findings indicate that RETN has pro-inflammatory as well as proresolving roles in active RA.
Digital Subcarrier Multiplexing in Optically Routed Networks (2017)

We examine the benefit of digital subcarrier multiplexing in optically routed networks. We show that optimizing the number of subcarriers not only improves system tolerance to nonlinearities, but also induces smaller performance variations in various network scenarios.
Creating femtosecond-laser-hyperdoped silicon with a homogeneous doping profile (2015)

Femtosecond-laser hyperdoping of sulfur in silicon typically produces a concentration gradient that results in undesirable inhomogeneous material properties. Using a mathematical model of the doping process, we design a fabrication method consisting of a sequence of laser pulses with varying sulfur concentrations in the atmosphere, which produces hyperdoped silicon with a uniform concentration depth profile. Our measurements of the evolution of the concentration profiles with each laser pulse are consistent with our mathematical model of the doping mechanism, based on classical heat and solute diffusion coupled to the far-from-equilibrium dopant incorporation. The use of optimization methods opens an avenue for creating controllable hyperdoped materials on demand.
Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC (2015)

Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.
Watson syndrome: is it a subtype of type 1 neurofibromatosis? (1991)

Over 20 years ago, Watson described three families with a condition characterised by pulmonary valvular stenosis, café au lait patches, and dull intelligence. Short stature is an additional feature of this autosomal dominant condition. A fourth family with Watson syndrome has since been reported. We have had the opportunity to review members of three of these four families. The clinical phenotype of Watson syndrome has been expanded to include relative macrocephaly and Lisch nodules in the majority of affected subjects, and neurofibromas in one-third of family members. Because the additional clinical findings enhance the similarity between Watson syndrome and neurofibromatosis 1, molecular linkage studies have been performed using probes flanking the NF1 gene on chromosome 17. Probe HHH202 showed the tightest linkage to Watson syndrome with a maximum lod score of 3.59 at phi = 0.0 (95% confidence limits of phi = 0.0-0.15). This suggests either that Watson syndrome and neurofibromatosis 1 are allelic, or that there is a series of contiguous genes for pulmonary stenosis, neurocutaneous anomalies, short stature, and mental retardation on 17q.
[Cutaneous manifestations of mediterranean periodic disease. Concerning an observation. Review of the literature (author's transl)]. (1981)

Méditerranean Periodic Disease is frequently encountered in non-aschenazic Jews and in Armenians. Aside from the classic triad of pseudo-palustral febrile crises, paroxysms of abdominal and articular pain, and a biological syndrome of inflammation; cutaneous manifestations were noted in 25 to 35% of the cases according to various authors. The most commonly encountered lesions consisted of erysipel-like plaques and subcutaneous nodules. We observed the case of a 47 years old Armenian male, afflicted with Mediterranean Periodic Disease for 30 years in which the dermatologic symptoms are quite classic aside from a vitiligo having progressively appeared since 15 years. Possibly a coincidental association, but to the best of our knowledge, which has not as yet been reported.