gebhart/patrepeval huggingface dataset:
Micropatterning of Ag and Au Nanoparticles by Microcontact Printing and Block Copolymer Micelles (2011)

Micropatterns of gold and silver nanoparticles were successfully obtained by combining microcontact printing and poly(2-vinylpyridine)-block-poly(cyclohexyl metharylate) (P2VP-b-PCHMA) diblock copolymer micelles with metal precursors. The metal ions were incorporated into poly(2-vinylpyridine) blocks and located into the core area of micelles. Then the metal-loaded micellar solutions were used as inks which were spin coated as thin layers onto polydimethylsiloxane stamps and transferred onto the substrates by stamping. Different morphologies of micellar aggregates were formed on the substrates depending on the stamp morphologies, and single layers of nanoparticles in the micropattern were obtained by the reducing process.
Identification of immediate early gene products of bovine herpes virus 1 (BHV-1) as dominant antigens recognized by CD8 T cells in immune cattle (2017)

In common with other herpes viruses, bovine herpes virus 1 (BHV-1) induces strong virus-specific CD8 T-cell responses. However, there is a paucity of information on the antigenic specificity of the responding T-cells. The development of a system to generate virus-specific CD8 T-cell lines from BHV-1-immune cattle, employing Theileria-transformed cell lines for antigen presentation, has enabled us to address this issue. Use of this system allowed the study to screen for CD8 T-cell antigens that are efficiently presented on the surface of virus-infected cells. Screening of a panel of 16 candidate viral gene products with CD8 T-cell lines from 3 BHV-1-immune cattle of defined MHC genotypes identified 4 antigens, including 3 immediate early (IE) gene products (ICP4, ICP22 and Circ) and a tegument protein (UL49). Identification of the MHC restriction specificities revealed that the antigens were presented by two or three class I MHC alleles in each animal. Six CD8 T-cell epitopes were identified in the three IE proteins by screening of synthetic peptides. Use of an algorithm (NetMHCpan) that predicts the peptide-binding characteristics of restricting MHC alleles confirmed and, in some cases refined, the identity of the epitopes. Analyses of the epitope specificity of the CD8 T-cell lines showed that a large component of the response is directed against these IE epitopes. The results indicate that these IE gene products are dominant targets of the CD8 T-cell response in BHV-I-immune cattle and hence are prime-candidate antigens for the generation of a subunit vaccine.
Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes (2020)

CAMKK2 is a serine/threonine kinase and an activator of AMPK whose dysregulation is linked with multiple diseases. Unfortunately, STO-609, the tool inhibitor commonly used to probe CAMKK2 signaling, has limitations. To identify promising scaffolds as starting points for the development of high-quality CAMKK2 chemical probes, we utilized a hinge-binding scaffold hopping strategy to design new CAMKK2 inhibitors. Starting from the potent but promiscuous disubstituted 7-azaindole GSK650934 (CAMKK2 IC50 = 3 nM), a total of 32 compounds, composed of single ring, 5,6-, and 6,6-fused heteroaromatic cores were synthesized. The compound set was specifically designed to probe interactions with the kinase hinge-binding residues. These compounds were evaluated in vitro in biochemical and cellular assays for CAMKK2 inhibition. Compared to GSK650394 and STO-609, thirteen of our compounds displayed similar or better CAMKK2 inhibitory potency in vitro, while compounds 13g and 45 had greatly improved selectivity for CAMKK2 across the kinome. Our systematic survey of hinge binding chemotypes identified several potent and selective inhibitors of CAMKK2 to serve as starting points for medicinal chemistry programs aimed at the identification of CAMKK2 chemical probes and clinical candidates
Supplementary Figures 1-3 from Oncogenic BRAF Is Required for Tumor Growth and Maintenance in Melanoma Models (2023)

Supplementary Figures 1-3 from Oncogenic BRAF Is Required for Tumor Growth and Maintenance in Melanoma Models
Structural analysis of 2-iodobenzamide and 2-iodo-<i>N</i>-phenylbenzamide (2018)

The title compounds, 2-iodo-benzamide, C<sub>7</sub>H<sub>6</sub>INO (I), and 2-iodo-<i>N</i>-phenyl-benzamide, C<sub>13</sub>H<sub>10</sub>INO (II), were both synthesized from 2-iodo-benzoic acid. In the crystal structure of (I), N-H⋯O and hydrogen bonds form two sets of closed rings, generating dimers and tetra-mers. These combine with C-I⋯π(ring) halogen bonds to form sheets of mol-ecules in the <i>bc</i> plane. For (II), N-H⋯O hydrogen bonds form chains along the <i>a</i>-axis direction, while inversion-related C-I⋯π(ring) contacts supported by C-H⋯π(ring) interactions generate sheets of mol-ecules along the <i>ab</i> diagonal.
Intraoperative ultrasonography for the correction of brainshift based on the matching of hyperechogenic structures (2010)

In this paper, a global approach based on 3D freehand ultrasound imaging is proposed to (a) correct the error of the neuronavigation system in image-patient registration and (b) compensate for the deformations of the cerebral structures occurring during a neurosurgical procedure. The rigid and non rigid multimodal registrations are achieved by matching the hyperechogenic structures of brain. The quantitative evaluation of the non rigid registration was performed within a framework based on synthetic deformation. Finally, experiments were carried out on real data sets of 4 patients with lesions such as cavernoma and low-grade glioma. Qualitative and quantitative results on the estimated error performed by neuronavigation system and the estimated brain deformations are given.
The Development and Use of a DNA Polymerase Arrest Assay for the Evaluation of Parameters Affecting Intrastrand Tetraplex Formation (1996)

We show here that a K+-dependent block to DNA synthesis is a sensitive and specific indicator of intrastrand tetraplex formation that can be used, both to identify sequences with tetraplex-forming potential and to examine parameters that affect tetraplex formation. We show that tetraplex formation is determined by a complex combination of factors including the size and base composition of its constituent loops and stems. In the process of carrying out this study we have found that the number of sequences with the ability to form tetraplexes is larger than previously thought, and that such sequences are ubiquitous in eukaryote genomes.
UPDATE OF THE MECHANICAL DESIGN OF THE 650 MHZ BETA=0.9 CAVITIES FOR PROJECT X* (2013)

Abstract Not Provided
New Exploration of Chinese Herbal Medicines in Hepatology (2016)

Chronic liver diseases (CLD) are serious health-threatening problems worldwide. In particular, it is a significant healthcare burden in Southeast Asian countries where viral hepatitis is common. Regardless how the diseases are initiated, without proper intervention, CLD may gradually progress towards end-stage liver disease (ESLD), for which liver transplantation remains the only solution. Although this progression may be slow and gradual, there is no evidence showing that it could be reversed when cirrhosis has developed. Preventive intervention that may impede the progression of CLD is clinically favourable. Management of CLD depends on the etiology, and supporting treatment and hepatoprotective medicines are often provided. However, drug resistance and various adverse effects can lead to failure of treatment.
Supplementary Figure 4 from Dendritic Cells in Tumor-Associated Tertiary Lymphoid Structures Signal a Th1 Cytotoxic Immune Contexture and License the Positive Prognostic Value of Infiltrating CD8&lt;sup&gt;+&lt;/sup&gt; T Cells (2023)

&lt;p&gt;PDF file - 123K, CD62L- T cells represent the main T cell population in human lung tumors.&lt;/p&gt;
Contact mask optimization and SRAF design (2009)

Contact hole patterning and especially sub resolution assist feature (SRAF) insertion and optical proximity correction (OPC) have become an extremely critical element of enabling continued shrink of CMOS technology. These elements of mask generation are fundamental to the success of technology execution. As off-axis illumination modes have been introduced to resolve smaller pitches, forbidden pitches emerge that need to be considered in random logic layouts. Optimized placement of assist features for these pitches is extremely important for overall process window and tolerance budget considerations. Several techniques have recently been developed for model based SRAF optimization. These typically focus only on optimizing the aerial image through focus, but may not include sensitivity to mask error as well. These approaches will be evaluated and discussed. Total CD uniformity is presented as a metric for evaluation of mask solutions. This includes the impact of dose and focus, but also masks error in estimating the total CD variation of a contact patterning process. The SRAF solution with the lowest overall variation is the winner. This methodology is presented for parametric through pitch features, and logic patterns.
The role of electric field polarization of the incident laser beam in the short pulse damage mechanism of pulse compression gratings (2011)

We investigate the short pulse laser induced damage initiation mechanism on multilayer dielectric pulse compression gratings. We report that damages initiate at the edge of the grating pillars opposite to the incoming wave. It demonstrates, at a nanometer scale, the role of the electric field in the damage process coupled with periodic ripple pattern developing along the polarization direction. We avoid the formation of ripples by illuminating the diffraction grating in TM polarization and measure a significantly improved laser induced damage threshold associated with a strong decrease of the electric field in the grating structure.
A trimodular bacterial enzyme combining hydrolytic activity with oxidative glycosidic bond cleavage efficiently degrades chitin (2020)

Findings from recent studies have indicated that enzymes containing more than one catalytic domain may be particularly powerful in the degradation of recalcitrant polysaccharides such as chitin and cellulose. Some known multicatalytic enzymes contain several glycoside hydrolase domains and one or more carbohydrate-binding modules (CBMs). Here, using bioinformatics and biochemical analyses, we identified an enzyme, <i>Jd</i>1381 from the actinobacterium <i>Jonesia denitrificans</i>, that uniquely combines two different polysaccharide-degrading activities. We found that <i>Jd</i>1381 contains an N-terminal family AA10 lytic polysaccharide monooxygenase (LPMO), a family 5 chitin-binding domain (CBM5), and a family 18 chitinase (Chi18) domain. The full-length enzyme, which seems to be the only chitinase produced by <i>J. denitrificans</i>, degraded both α- and β-chitin. Both the chitinase and the LPMO activities of <i>Jd</i>1381 were similar to those of other individual chitinases and LPMOs, and the overall efficiency of chitin degradation by full-length <i>Jd</i>1381 depended on its chitinase and LPMO activities. Of note, the chitin-degrading activity of <i>Jd</i>1381 was comparable with or exceeded the activities of combinations of well-known chitinases and an LPMO from <i>Serratia marcescens</i> Importantly, comparison of the chitinolytic efficiency of <i>Jd</i>1381 with the efficiencies of combinations of truncated variants-<i>Jd</i>LPMO10 and <i>Jd</i>CBM5-Chi18 or <i>Jd</i>LPMO10-CBM5 and <i>Jd</i>Chi18-indicated that optimal <i>Jd</i>1381 activity requires close spatial proximity of the LPMO10 and the Chi18 domains. The demonstration of intramolecular synergy between LPMOs and hydrolytic enzymes reported here opens new avenues toward the development of efficient catalysts for biomass conversion.
Advanced FO membranes from newly synthesized CAP polymer for wastewater reclamation through an integrated FO‐MD hybrid system (2012)

A new cellulose acetate propionate (CAP) polymer has been synthesized and used to prepare high‐performance forward osmosis (FO) membranes. With an almost equal degree of substitution of acetyl and propionyl groups, the CAP‐based dense membranes show more balanced physicochemical properties than conventional cellulose acetate (CA)‐based membranes for FO applications. The former have a lower equilibrium water content (6.6 wt. %), a lower salt diffusivity (1.6×10 14 m 2 s −1 ) and a much lower salt partition coefficient (0.013) compared with the latter. The as‐prepared and annealed CAP‐based hollow fibers have a rough surface with an average pore radius of 0.31 nm and a molecular weight cut off of 226 Da. At a transmembrane pressure of 1 bar, the dual‐layer CAP‐CA hollow fibers show a pure water permeability of 0.80 L m −2 h −1 bar −1 (LMH/bar) and a rejection of 75.5% to NaCl. The CAP‐CA hollow fibers were first tested for their FO performance using 2.0 M NaCl draw solution and deionized water feed. An impressive water flux of 17.5 L m −2 h −1 (LMH) and a reverse salt flux of 2.5 g m −2 h −1 (gMH) were achieved with the draw solution running against the active CAP layer in the FO tests. The very low reverse salt flux is mainly resulting from the low salt diffusivity and salt partition coefficient of the CAP material. In a hybrid system combining FO and membrane distillation for wastewater reclamation, the newly developed hollow fibers show very encouraging results, that is, water production rate being 13–13.7 LMH, with a MgCl 2 draw solution of only 0.5 M and an operating temperature of 343 K due to the incorporation of bulky propionyl groups with balanced physiochemical properties. © 2012 American Institute of Chemical Engineers AIChE J, 59: 1245–1254, 2013
Utility of Pouchoscopy Between J-Pouch Stages in Chronic Ulcerative Colitis (2015)

Introduction: Creation of a J pouch is the current gold standard surgical intervention in patients with chronic ulcerative colitis (UC). Pouchoscopy prior to takedown of the loop ileostomy is commonly performed. We aim to describe the frequency, indication, and findings on pouchoscopy, and determine if pouchoscopy affects rates of complications after takedown. Methods: A retrospective chart review of all UC or indeterminate inflammatory bowel disease patients with a J pouch was conducted from Jan 1994-Dec 2014 at a single tertiary hospital. Cases were defined as having a pouchoscopy after J pouch creation but before ileostomy takedown. Controls were defined as having no pouchoscopy or pouchoscopy on the same day as ileostomy takedown. Statistical analysis was performed using STATA. Results: A total of 185 patients were included in the study, of which 152 (82.2%) were cases and 33 (17.8%) were controls. Of the controls, 21 patients (11.4%) had no endoscopy and 12 (6.5%) had pouchoscopy on the same day as ileostomy takedown. One case and one control had undergone J pouch creation but not ileostomy takedown. The most frequent indication for J pouch surgery was medically refractory disease. Cases and controls were similar in baseline characteristics; cases were more likely to have undergone stapled anastomoses and had a shorter duration of follow-up (Table 1). Most pouchoscopies were performed on a routine basis (n=145, 95.4%). Half (n=75) of all pouchoscopies were reported as normal. Common abnormal endoscopy findings included stricture (n=53, 35.3%), pouchitis (n=13, 8.7%), and cuffitis (n=1, 0.7%). All patients with strictures were dilated at the time. Length of stay during ileostomy takedown hospitalization was shorter for cases than controls. However, neither short- nor long-term complications were statistically different between cases and controls (Table 2). Additionally, abnormalities on pouchoscopy were not predictive for either short- (p=0.75) or long-term complications (p=0.57). Pouchoscopy delayed ileostomy takedown surgery in 4 patients, all of whom were symptomatic or had recognized complications prior to pouchoscopy.Table 1: Patient and Surgical CharacteristicsTable 2: Outcome MeasuresConclusion: Pouchoscopy prior to ileostomy takedown was common in our institutional experience. Although rates of abnormalities on pouchoscopy (mostly strictures) were frequent, ileostomy takedown was rarely delayed and there was no association with future complications. Pouchoscopy prior to ileostomy takedown probably has greatest utility in symptomatic patients.
The Plant Science Decadal Vision: Response to the Martin Commentary (2013)

The plant science community is being called upon as never before to carry out research that addresses challenges in food, climate, and health, to educate a populace inundated with science misinformation, and to excite and recruit a new generation of scientists from among that populace, all while investments in basic research are stagnant or even declining in many countries. The Decadal Vision (Plant Science Research Summit, 2013) represents a response from that community, one that launches a meaningful and ongoing dialogue about how best to accomplish these goals. In that spirit, we welcome this thoughtful commentary by Cathie Martin (Martin, 2013).
Interleukin-1 <i>β</i> enhances and interferon-<i>γ</i> suppresses activin A actions by reciprocally regulating activin A and follistatin secretion from bone marrow stromal fibroblasts (2001)

Activin A is a multi-functional cytokine with a potent stimulation on erythroid cell differentiation in the bone marrow. The actions of activin A are determined by a balance of the levels of activin A and its inhibitor, follistatin (FS). However, the regulation of its actions in the bone marrow has been unclear. Here we show that bone marrow-derived stromal fibroblasts are the major source of activin A and FS in the bone marrow, and that the production of activin A is enhanced by interleukin-1beta (IL-1beta) and lipopolysaccharide (LPS), whereas interferon-gamma (IFN-gamma) inhibits the secretion of activin A by stromal fibroblasts. Concomitantly, IL-1beta as well as LPS inhibits and IFN-gamma stimulates FS secretion from stromal fibroblasts. Thus, these cytokines potently regulate activin A actions by reciprocal modulation of activin A and FS secretion from stromal fibroblasts. Because activin A exhibits anti-inflammatory effects in various tissues, up-regulation of activin A actions by IL-1beta and endotoxin in the bone marrow may play a protective role against inflammatory processes as well as anaemia. The present results also suggest that the inhibitory effect of IFN-gamma on erythropoiesis is mediated at least in part by a suppression of activin A actions in bone marrow.
An experimental model of ischemia in rabbit hindlimb (2001)

This study was performed to establish an experimental model of ischemia for the investigation of new treatment modality of limb-threatening ischemia. We produced ischemia in the hindlimbs of 8 New Zealand white rabbits. Under general anesthesia, the left femoral artery was exposed, freed, and excised from distal external iliac artery to proximal popliteal and saphenous arteries. And then both hindlimbs were serially examined to assess the ischemia according to the time table until postoperative 6 weeks. We assessed clinical observation, blood pressure, radioisotopic perfusion scan, and angiography. Clinical ischemic changes of the operated feet were observed in 63%. The blood pressure of left calves was measurable on postoperative day 3 (p<0.05, vs preoperative day 2) and then gradually increased to reach a plateau in postoperative week 6. Radioisotopic arterial perfusion showed similar profiles as in blood pressure. Angiography of ischemic hindlimbs demonstrated a few collateral vessels arising from the internal iliac artery with the reconstitution of the posterior tibial artery in postoperative week 2. In postoperative week 6, collaterals remained the same in number. However, these became dilated and tortuous and showed reconstitution in distal hindleg. In conclusion, this is a reproducible, measurable, and economical animal model of hind limb ischemia.
Expanding the bandwith of MDOF road reproductions (2006)

This paper describes the use of a high-frequency 6-DOF shaker table for the reproduction of multiple degree of freedom (MDOF) road input measurements in the frequency range up to 300 Hz. Results are discussed for 3-DOF tire patch excitation and 3-DOF spindle excitation. It is shown that the typical bandwidth from tests on a fourposter or axle testrig, can be expanded into this range by use of the shaker table if, depending on the target spectrum, measures are taken to ensure sufficient accuracy trough out the frequency range. Especially the typical low energy band (165-220 Hz) in the tire response spectrum requires further work. © (2006) by the Katholieke Universiteit Leuven Department of Mechanical Engineering All rights reserved.
Synthesis and Structure of a Propeller-Shaped Polycyclic Aromatic Hydrocarbon Containing Seven-Membered Rings (2018)

The synthesis and structure of a C<sub>3</sub>-symmetric propeller-shaped polycyclic aromatic hydrocarbon that bears three seven-membered rings is reported. The synthesis was accomplished in three steps from benzo[ c]naphtho[2,1- p]chrysene, including a Pd-catalyzed intramolecular C-H arylation for the formation of the seven-membered rings. The combination of the helicities ( P/ M) of the three seven-membered-ring moieties and three [4]helicene moieties affords 24 possible conformers, and two relatively stable conformations were observed by <sup>1</sup>H NMR spectroscopy.
SU‐F‐T‐451: Doses to Organs‐At‐Risk in the Presence and Absence of a 1.5 T Magnetic Field for NSCLC Patients Undergoing SABR (2016)

Purpose: To determine whether the electron return effect (ERE) has deleterious effects on lung SABR plans optimized in the presence of an orthogonal 1.5 T magnetic field. Methods: Data from five NSCLC‐SABR patients were used. The Dose was modeled with a 2.5 mm dose grid in the presence and absence of a magnetic field using the Monaco (Elekta) TPS with the Monte Carlo GPUMCD (v5.1) algorithm. For each patient, two plans were generated, one using our conventional Elekta Agility linac beam model and another using the Elekta MRI Linac (MRL) model. Both plans were generated on the average CT using similar dose constraints and a 5 mm PTV. The optimization was performed using our clinic's planning criteria, with normalization of the targets such that their V99% was equal to 99%. The OAR DVHs were compared for each patient. Results: The DVH plots revealed that there were limited differences when optimizing plans in the presence or absence of the magnetic field. The mean of the absolute differences, between the two planning types, in the equivalent uniform doses (EUDs) for the OARs were: 0.3 Gy (range of 0.0 ‐ 1.0 Gy) for the esophagus, 0.6 Gy (range of 0.1 – 1.9 Gy) for the heart, 0.5 Gy (range of 0.2 – 0.8 Gy) for the lungs, and 0.6 Gy (range of 0.2 – 1.5 Gy) for the spinal canal. Regarding the maximum doses to the serial organs, the mean of the differences were 3.0 Gy (esophagus) and 0.9 Gy (spinal canal). No trends in the differences were observed. Conclusion: This study has demonstrated that there were no major differences between plans optimized using a conventional linac and those optimized using an MRI linac with an orthogonal 1.5 T magnetic field. This is attributed to the consideration of the ERE in the optimization. This project was made possible with the financial support of Elekta