gebhart/patrepeval huggingface dataset:
Kinetics of Block Copolymer Phase Segregation during Sub-millisecond Transient Thermal Annealing (2016)

Early stage phase segregation of block copolymers (BCPs) critically impacts the material’s final structural properties, and understanding the kinetics of these processes is essential to intentional design of systems for practical applications. Using sub-millisecond lateral gradient laser spike annealing and microbeam grazing incidence small-angle X-ray scattering, the ordering and disordering kinetics of cylinder forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) were determined for peak annealing temperatures up to 550 °C for dwells (anneal durations) ranging from 250 μs to 10 ms. These temperatures, far in excess of the normal thermal decomposition limit, are enabled by the short time scales of laser annealing. From initially microphase-segregated films, disordering was observed near the equilibrium order–disorder transition temperature (TODT) for dwell times above 10 ms but was kinetically delayed by diffusion for shorter time scales, resulting in suppression of observed disordering by over 70 °C. The onset of ordering from initially disordered films was also kinetically limited for short dwells. For anneals with peak temperatures well above TODT, the block copolymer fully disorders and quenches to a history-independent final state determined by the quench rate. This kinetic behavior can be represented on an effective Tg and TODT phase map as a function of the heating time scale. These results then potentially enable BCP processing to retain or intentionally modify the initial state while accelerating kinetics for other chemical or structural alignment processes.
Analysis of Müller glia specific genes and their histone modification using Hes1-promoter driven EGFP expressing mouse (2017)

Retinal neurons and Müller glia are generated from a common population of multipotent retinal progenitor cells. We purposed to identify Müller glia-specific molecular signatures during retinal development. Using transgenic mice carrying the Hes1 promoter (pHes1) followed by EGFP, we purified EGFP-positive Müller glia and other EGFP-negative retinal cells from developing retinas and subjected them to RNA sequencing analysis. Gene expression pattern of EGFP-positive cell was similar to genes expressed in retinal progenitors, and they were downregulated in other cell lineages. Then, we examined the modification profiles of H3K27me3 and H3K4me3 by referring to chromatin immunoprecipitation-sequencing data of rods and other cells. Clustering of the H3K4me3 and H3K27me3 values followed by ontology analysis revealed a high incidence of transcription factors including Hes1 in clusters with high H3K27me3 levels. Hes1 expression level decreased dramatically, and the H3K27me3 level at the Hes1-locus was upregulated strongly during retinal development. Furthermore, the Hes1 expression level was upregulated in an Ezh2-knockout retina. These results suggest that downregulation of Müller glia-related genes in other lineage rather than upregulation of them in Müller glia contributed Müller-specific molecular features, and a role for modified H3K27me3 in suppressing Müller glia-related genes in other retinal cell lineages to avoid unfavorable expression.
Supplemental Figure Legends from Systemic Delivery of Microencapsulated 3-Bromopyruvate for the Therapy of Pancreatic Cancer (2023)

&lt;p&gt;This files contains the Supplemental Figure legends.&lt;/p&gt;
A microenvironment-inspired synthetic 3D model for pancreatic ductal adenocarcinoma organoids (2021)

Experimental in vitro models that accurately capture pathophysiological characteristics of human tumours are essential for basic and translational cancer biology. Here, we describe a fully synthetic hydrogel extracellular matrix, specifically designed to elicit key phenotypic traits of the pancreatic environment in culture. To enable the growth of normal and cancerous pancreatic organoids from murine genetically engineered models and human patients, essential adhesive cues were empirically defined and incorporated into the hydrogel scaffold, revealing a functional role of laminin – integrin a3/a6 signalling in adhesion and survival of pancreatic organoids. Altered tissue stiffness — a hallmark of pancreatic cancer — was recapitulated in culture by adjusting the hydrogel properties to engage mechano-signalling and alter organoid growth. Pancreatic stromal cells were readily incorporated and replicated phenotypic traits characteristic of the tumour environment in vivo. This model therefore recapitulates a pathologically remodelled tumour microenvironment for studies of normal and pancreatic cancer cells in vitro.
Solubilization of a π‐Conjugating Hydrophobic Dendrimer in Aqueous Media (2012)

Phenylazomethine dendrimers, which can be used as the template for precise metal nanoparticles, are soluble only in aprotic media. The use of a specific surfactant enabled their solubilization in aqueous solutions. Under dilute condition, they formed discrete micelles with a size close to the that of the dendrimer. Condensation resulted in their aggregation; however, they remained in a homogeneous solution without precipitation. Furthermore, each micelle was well isolated. The triplet-excited state of the zinc porphyrin core in the micelles was significantly stable, suggesting the formation of rigid core-shell micelles preventing any external molecules from approaching to the core.
Characterization of solar-grade silicon produced by the SiF4-Na process (1986)

An atypical case of acute appendicitis is reported, in which the initial presentation was not suggestive of this diagnosis. A routine work-up revealed elevated levels of inflammatory markers, an ultrasonographically normal abdomen and normal endoscopic findings in the upper gastrointestinal tract. During colonoscopy, performed 3 days after admission, the inflamed appendiceal orifice was localized and intubated using an endoscopic retrograde cholangio-pancreatography (ERCP) catheter; pus was aspirated. Elective appendectomy was carried out 5 months later on the asymptomatic patient. Histological analysis revealed fibrous thickening of the appendiceal wall, correlating with an old inflammatory process, along with changes typical for acute ulcerophlegmonous appendicitis. To the best of our knowledge, this is the first case of an endoscopically diagnosed and treated acute ulcero-phlegmonous appendicitis. We draw the following conclusions: (1) Acute appendicitis may present atypically, leading to an extensive clinical work-up including gastroscopy and colonoscopy. (2) This condition may be effectively treated, at least temporarily, by colonoscopic suction of appendiceal pus, provided that clinical urgency for laparotomy is absent. (3) Histological changes typically associated with acute ulcero-phlegmonous appendicitis may be present in asymptomatic patients and in patients without fever and with normal erythrocyte sedimentation rates and blood leucocyte counts. (4) Elective appendectomy should be considered in patients with conservatively healed acute appendicitis or periappendiceal abscess.
A New and Efficient Method for the Preparation of S-Phenyl Carbothioates via Mixed Anhydrides Using Active Titanium(IV) Salts (1992)

Abstract In the presence of a catalytic amount of titanium(IV) salt, various S-phenyl carbothioates are prepared in excellent yields by the reaction of nearly equimolar amounts of silyl derivatives of carboxylic acids and benzenethiols with p-trifluoromethylbenzoic anhydride.
New Technology and Lunar Power Option for Power Beaming Propulsion (2004)

Orbit raising missions (LEO to GEO or beyond) are the only missions with enough current traffic to be seriously considered for near-term power beaming propulsion. Even these missions cannot justify the development expenditures required to deploy the required new laser, optical and propulsion technologies or the programmatic risks. To be deployed, the laser and optics technologies must be spin-offs of other funded programs. The manned lunar base nighttime power requirements may justify a major power beaming program with 2MW lasers and large optical systems. New laser and optical technologies may now make this mission plausible. If deployed these systems could be diverted for power beaming propulsion applications. Propulsion options include a thermal system with an Isp near 1000 sec., a new optical coupled thermal system with an Isp over 2000 sec. photovoltaic-ion propulsion systems with an Isp near 3000 sec., and a possible new optical coupled thermal system with an Isp over 2000 sec.
Photochemical syntheses, transformations, and bioorthogonal chemistry oftrans-cycloheptene and silatrans-cycloheptene Ag(i) complexes (2018)

A photochemical synthesis of AgNO<sub>3</sub> complexes of <i>trans</i>-cycloheptene (TCH) and <i>trans</i>-1-sila-4-cycloheptene (Si-TCH) derivatives is described. A low temperature flow photoreactor was designed to enable the synthesis of carbocyclic TCH derivatives due to their thermal sensitivity in the absence of metal coordination. Unlike the free carbocycles, TCH·AgNO<sub>3</sub> complexes can be handled at rt and stored for weeks in the freezer (-18 °C). Si-TCH·AgNO<sub>3</sub> complexes are especially robust, and are bench stable for days at rt, and for months in the freezer. X-ray crystallography was used to characterize a Si-TCH·AgNO<sub>3</sub> complex for the first time. With decomplexation of AgNO<sub>3</sub><i>in situ</i>, metal-free TCO and Si-TCH derivatives can engage in a range of cycloaddition reactions as well as dihydroxylation reactions. Computation was used to predict that Si-TCH would engage in bioorthogonal reactions that are more rapid than the most reactive <i>trans</i>-cyclooctenes. Metal-free Si-TCH derivatives were shown to display good stability in solution, and to engage in the fastest bioorthogonal reaction reported to date (<i>k</i><sub>2</sub> 1.14 × 10<sup>7</sup> M<sup>-1</sup> s<sup>-1</sup> in 9 : 1 H<sub>2</sub>O : MeOH). Utility in bioorthogonal protein labeling in live cells is described, including labeling of GFP with an unnatural tetrazine-containing amino acid. The reactivity and specificity of the Si-TCH reagents with tetrazines in live mammalian cells was also evaluated using the HaloTag platform. The cell labeling experiments show that Si-TCH derivatives are best suited as probe molecules in the cellular environment.
Macro modeling of silent discharges and electrical characteristics of PDP discharge. (1999)

In order to design the driving electric circuits of PDPs, it is necessary to know how to treat the discharge as an electric circuit element. We have constructed a simple and novel discharge model which can be applied to general silent discharge phenomena. In this model, we treat the discharge as a resistor whose conductance changes with time. Using this macro-discharge model for silent discharges, not only we can know the electrical characteristics of PDP, but also we can understand the physical meaning of a PDP discharge, and general silent discharge phenomena systematically.
Complex technique of sound intensity measurements and properties of the basic sound fields (2012)

An overview of sensors and signal processing for the measurement of sound intensity and other energy related quantities such as reactive intensity, potential and kinetic energy is summarized. Many examples of energy propagation, vortices formation, radiationn from sources, sound interference and other acoustic phenomena are presented and analyzed.
CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1. (2015)

Supplementary data are available at Bioinformatics online.
Fragment screening for a protein-protein interaction inhibitor to WDR5 (2019)

The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of the "WIN" site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign-guided by a suite of high-resolution cocrystal structures with WDR5-progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time (<i>k</i> <sub>d</sub> = ∼0.06 s<sup>-1</sup>) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.
Identification, expression and chromosome localization of a human gene encoding a novel protein with similarity to the pilB family of transcriptional factors (pilin) and to bacterial peptide methionine sulfoxide reductases (1999)

Here we report the isolation, characterization and chromosome localization of a subtracted cDNA (CBS-1) isolated from the human ocular ciliary body which encodes a novel protein. As is deduced from the nucleotide sequence of the cDNA, CBS-1 contains an open reading frame consisting of 182 amino acids, with a molecular weight of 19.5kDa. CBS-1 shares significant nucleotide and amino acid sequence identities (residues 51 to 182) with a hypothetical 15.5kDa protein in the ANSA-GAP intergenic region (yeaA) of Escherichia coli, and the carboxyl terminal region of pilB, a transcription factor involved in the regulation of expression of pili, from Neisseria gonorrhoeae. Interestingly, CBS-1 also shares significant identity with the carboxyl terminus of the peptide-methionine sulfoxide reductase (MsrA), a repair enzyme, from Helicobacter pylori and Streptococcus pneumoniae. However, the amino terminal of CBS-1 (residues 23 to 43), which lacks homology to the amino terminal region of gonococcal pilB or pneumococcal MsrA, exhibits significant identity in a stretch of 20 amino acids, with glycine-rich proteins. By Northern blot, CBS-1, hybridized to a 0.6 to 0.7kb transcript in size, is expressed ubiquitously in many tissues, but most abundantly in the retina and ocular ciliary body, skeletal muscle and heart. An epitope-directed antibody to an amino acid sequence at the carboxyl terminus of CBS-1 recognized a main protein of 19.5kDa in ocular ciliary body extracts, and a 23kDa protein in total extracts from E. coli MC1061 cells, which expresses high levels of MsrA. The CBS-1 gene was mapped to human chromosome 10p12 between markers WI-8535 and WI-4724, and is tightly linked to the two STRP markers of D10S1789 and D10S550. We suggest that the CBS-1 gene encodes a mammalian transcription factor related to the bacterial pilB and certain bacterial MsrA homologues.
Structure Activity Relationship of 4-Amino-2-thiopyrimidine Derivatives as Platelet Aggregation Inhibitors (2019)

These negative findings demonstrated that this heterocyclic nucleus is not a useful common pharmacophore for developing P2Y-dependent inhibitors of platelet aggregation. Nevertheless, compounds 2c and 2h could represent a new chemotype to further develop inhibitors of platelet aggregation.
User Perception and Preference in Model Mediated Telemanipulation (2007)

Model mediated teleoperation allows users to interact with a remote environment via a local rendition to mitigate the effects of large communication delays. As the slave encounters an environment a model is identified, transmitted to the master, then haptically and graphically recreated. Particular attention must be paid to the user interface when model information is updated, to avoid confusion or disruptive effects. This paper examines various transition methods from the perspective of user preferences and perception. Transitions are grouped according to three basic philosophies: hiding changes from the user, forcing changes upon the user, and alerting users to model updates. A user study is presented which evaluated subjects' performance and opinions for different approaches. We found transitions that gradually but actively presented information to be the most successful
Surface Patterning: Printing of Highly Integrated Crossbar Junctions (Adv. Funct. Mater. 6/2012) (2012)

On page 1129, Dirk Mayer and co-workers report the non-invasive assembly of highly integrated metal-bridge-metal crossbar junctions under ambient conditions by combining nanoimprint lithography and soft lithography. Different views of the printing process and ready assembled crossbar arrays are shown. Conductive polymer films are incorporated in the cross points to evaluate the utility and versatility of the soft lithography approach.
Multicenter trials using 18F-fluorodeoxyglucose (FDG) PET to predict chemotherapy response: Effects of differential measurement error and bias on power calculations for unselected and enrichment designs (2013)

Even moderate additional measurement error substantially reduced study power under both unselected and enrichment designs.
Profiling development of abdominal organs in the pig (2022)

The pig is an ideal model system for studying human development and disease due to its similarities to human anatomy, physiology, size, and genome. Further, advances in CRISPR gene editing have made genetically engineered pigs viable models for the study of human pathologies and congenital anomalies. However, a detailed atlas illustrating pig development is necessary for identifying and modeling developmental defects. Here we describe normal development of the pig abdominal system and show examples of congenital defects that can arise in CRISPR gene edited SAP130 mutant pigs. Normal pigs at different gestational ages from day 20 (D20) to term were examined and the configuration of the abdominal organs was studied using 3D histological reconstructions with episcopic confocal microscopy, magnetic resonance imaging (MRI) and necropsy. This revealed prominent mesonephros, a transient embryonic organ present only during embryogenesis, at D20, while the developing metanephros that will form the permanent kidney are noted at D26. By D64 the mesonephroi are absent and only the metanephroi remain. The formation of the liver and pancreas was observed by D20 and complete by D30 and D35 respectively. The spleen and adrenal glands are first identified at D26 and completed by D42. The developing bowel and the gonads are identified at D20. The bowel appears completely rotated by D42, and testes in the male were descended at D64. This atlas and the methods used are excellent tools for identifying developmental pathologies of the abdominal organs in the pig at different stages of development.
Effect of PET on Changes in the Structure of Coals Caking during Carbonization (2011)

Abstract Using an X-ray quantitative phase analysis, the effect of adding 2% polyethylene terephthalate on the course of structure changes of two orthocoking coals differing in maximum fluidity during their common carbonization was studied. Interplanar distances, height of crystallite, and quantity of crystalline phase were determined for the co-pyrolyzates obtained. The transformation of the texture of the material of the pore walls of co-pyrolyzates was investigated using scanning electron microscopy. In co-pyrolyzates, an addition of polyethylene terephthalate to coal of higher maximum fluidity was found to favor the formation of structure and texture of parameters similar to pyrolyzates of coal of lower maximum fluidity.
Supplementary Materials and Figure Legends 1-4 from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models (2023)

Supplementary Materials and Figure Legends 1-4 from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models
Differential expression of cytokine and chemokine transcripts in spleens and splenic macrophages of hamsters with VL. (2017)

&lt;p&gt;Heat maps showing the differential expression of selected transcripts in spleen tissue &lt;b&gt;(A)&lt;/b&gt; and splenic macrophages &lt;b&gt;(B)&lt;/b&gt; in uninfected (left side) and 28-day &lt;i&gt;L&lt;/i&gt;. &lt;i&gt;donovani&lt;/i&gt; infected (right side) hamsters (n = 4 per group). Transcripts down-regulated during infection are shown in green and upregulated transcripts are in red. The source or general function of the cytokine or chemokine is annotated to the left.&lt;/p&gt;
Circuit impact of device and interconnect parasitics in a complementary low-voltage organic thin-film technology (2011)

A simulation case study to indicate advancement opportunities for a low-voltage complementary organic thin-film transistor (OTFT) technology is presented. A 3-bit unary current-steering digital-to-analog converter (DAC) is used as circuit test vehicle. The study is based on accurate agreement of simulated and measured data, owing to optimized DC/AC SPICE models for both p- and n-type OTFTs. The model is validated by transient measurements of the driving complementary logic thermometer decoder up to a maximum operating frequency of 1 kHz. The case study shows that an improved circuit performance will result from a smaller source and drain overlap with the gate electrode particularly in the n-type OTFT, from avoiding metal interconnect crossings, and from increasing the channel carrier mobility of the n-type OTFT.
Pseudo Constant Time Implementations of TLS Are Only Pseudo Secure. (2018)

Today, about 10% of TLS connections are still using CBC-mode cipher suites, despite a long history of attacks and the availability of better options (e.g. AES-GCM). In this work, we present three new types of attack against four popular fully patched implementations of TLS (Amazon's s2n, GnuTLS, mbed TLS and wolfSSL) which elected to use constant countermeasures against the Lucky 13 attack on CBC-mode. Our attacks combine several variants of the PRIME+PROBE cache timing technique with a new extension of the original Lucky 13 attack. They apply in a cross-VM attack setting and are capable of recovering most of the plaintext whilst requiring only a moderate number of TLS connections. Along the way, we uncovered additional serious (but easy to patch) bugs in all four of the TLS implementations that we studied; in three cases, these bugs lead to Lucky 13 style attacks that can be mounted remotely with no access to a shared cache. Our work shows that adopting pseudo constant time countermeasures is not sufficient to attain real security in TLS implementations in CBC mode.
Drug Transport in the Kidney (2006)

This chapter contains sections titled: Introduction Molecular Identification of Renal Drug Transporters Regulation of Renal Drug Transporters Renal Handling of Selected Drugs Miscellaneous Aspects of Renal Drug Transporters Conclusions References
TUDCA Slows Retinal Degeneration in Two Different Mouse Models of Retinitis Pigmentosa and Prevents Obesity in Bardet-Biedl Syndrome Type 1 Mice (2011)

TUDCA treatment preserved ERG b-waves and the outer nuclear layer in Bbs1(M390R/M390R) mice, and prevented obesity assessed at P120. TUDCA treatment preserved ERG b-waves and the outer nuclear layer in the rd10 mice to P30. TUDCA is a prime candidate for treatment of humans with retinal degeneration, especially those with Bardet-Biedl syndrome, whom it may help not only with the vision loss, but with the debilitating obesity as well.