gebhart/patrepeval huggingface dataset:
Supplementary Methods, Figure Legends, Tables S1 - S3 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy (2023)

&lt;p&gt;Supplementary Table S1. Patient characteristics of the single-agent anti-PD-1 cohort. Supplementary Table S2. List of primers used for gene expression analysis by real-time PCR. Supplementary Table S3. List of autophagy-related genes for overexpressing experiment.&lt;/p&gt;
Possibilitats educatives del pensament complex (2009)

Aquest article preten contribuir a pensar sobre la nova cultura docent. S'hi reflexiona sobre les possibilitats educadores del pensament complex i sobre la necessitat de modificar la nostra relacio amb la natura. Tambe s'hi proposen alguns pensaments i algunes accions sobre l'educacio.
Early Squamous Lung Cancer and Longer Survival Rates (1993)

The criteria for early squamous lung cancer remain open to discussion as patients who have been treated for early stage lung cancer, such as T1N0M0, and appear to have been cured clinically may die from recurrent or metastatic tumors. We reviewed the pathological data on 242 surgical patients with squamous lung cancer and found 31 cases (13%) of early lung cancer, included were early lung cancer of the hilar type as a lesion restricted to the bronchial wall without lymph node involvement, and early lung cancer of the peripheral type as a lesion of less than 2 cm and surrounded by visceral pleura but without lymph node involvement. Of 89 patients with hilar-type squamous lung cancer, 17 (19%) had early lung cancer, and 14 (9%) of 153 patients with peripheral-type squamous lung cancer had early lung cancer (p < 0.05). For early lung cancer of the hilar type, all but 1 (94%) were detected using sputum cytologic study and bronchoscopy. For early lung cancer of the peripheral type, all were detected on chest X-ray, but 57% were cytologically proven to be malignant. The 5-year survival rate for patients with early lung cancer, according to this new criteria is 90%; 92% for the hilar type and 88% for the peripheral type. Thus, classification of early squamous lung cancer is pertinent for determining the prognosis and selection of treatment. We emphasize that efforts be made to detect early lung cancer.
Strain Monitoring of Combustible Gas Implosion Test Based on Fiber Bragg Grating (2019)

Strain measurement is an important component in model tests of combustible internal explosions. Strain gauges are used to measure strain in traditional electrical measurement methods and have some limitations, such as susceptibility to electromagnetic interference, short life, and inability to distribute. Fiber Bragg gratings (FBGs) are developing into useful sensing tools that can respond to changes in stress, strain, and temperature by changing wavelengths. FBGs have excellent sensing performance, such as long life, antielectromagnetic interference, easy networking, and good reusability. In this paper, FBG sensors are applied to strain monitoring in ethylene flammable implosion experiments. In the ethylene flammable implosion tests, an FBG was placed on the inner surface of the bottom plate of the rectangular steel test device near the detonation vent by the sticking method. The reliability and repeatability of the strain change of the FBG affected by detonation overpressure and combustion were tested at this point. Four explosion tests were carried out. The test results showed that FBG sensors could obtain stable and reliable strain data in all four tests. The strain variation reflects the development of overpressure and combustion in the whole process from ignition. For the strain amplitude formed by overpressure, the minimum was 1.449 με (the third test), and the maximum was 48.181 με (the fourth test).For the strain amplitude step change formed by the deflagration flame front passing the measurement points, the minimum was 1.673 με (the second test), and the maximum was 19.724 με (the fourth test).The strain amplitude produced by the deflagration temperature effect in the four tests ranged from 72.803 με (the first test) to 143.381 με (the fourth test).The results show that FBG sensors can provide reliable and effective strain monitoring data for the experimental study of flammable implosions.
Monotone Boolean Functions, Feasibility/Infeasibility, LP-type problems and MaxCon (2020)

This paper outlines connections between Monotone Boolean Functions, LP-Type problems and the Maximum Consensus Problem. The latter refers to a particular type of robust fitting characterisation, popular in Computer Vision (MaxCon). Indeed, this is our main motivation but we believe the results of the study of these connections are more widely applicable to LP-type problems (at least 'thresholded versions', as we describe), and perhaps even more widely. We illustrate, with examples from Computer Vision, how the resulting perspectives suggest new algorithms. Indeed, we focus, in the experimental part, on how the Influence (a property of Boolean Functions that takes on a special form if the function is Monotone) can guide a search for the MaxCon solution.
The Efficacy of Endovascular Stenting in the Treatment of Supraclinoid Internal Carotid Artery Blister Aneurysms Using a Stent-in-Stent Technique (2010)

Our case series suggests that staged endovascular treatment entailing the use of a stent-in-stent technique, augmented with subsequent coil embolization as necessary for progressive disease, is a viable endovascular option for treating ruptured supraclinoid blister aneurysms, allowing for parent artery preservation.
Non-covalent calixarene-amino acid complexes formed by MALDI-MS (2002)

Non-covalent inclusion complexes formed between amino acids and derivatized calix[6]arenes are observed in MALDI mass spectrometry. The methyl, ethyl, and propyl ester derivatives of calix[6]arene yielded amino acid complexes, while the smaller calix[4]arene analogs did not. Similarly the underivatized calix[6]arene and calix[4]arene did not produce complexes. Amino acid complexes were observed for nearly all 20 amino acids in time-of-flight (TOF) analysis. In Fourier transform mass spectrometry (FTMS) analysis, however, only the most basic amino acids arginine, histidine, and lysine formed stable adducts. The complexes were abundant under matrix-assisted laser desorption ionization (MALDI) conditions, which suggested favorable interactions between host and guest.
Stenosis Detection of X-Ray Coronary Angiographic Image Sequence (2021)

Automatic lesion detection from coronary X-ray angiography images is important for the auxiliary diagnosis of coronary heart diseases. However, the current methods are inefficient, and the detection accuracy cannot meet the criteria of doctors. This paper proposes a two-step method including video phase partition and video stenosis detection to automatically identify coronary stenosis from the complete X-ray angiography (XRA) video. First, convolutional neural network and long short-term memory based spatial–temporal network are used to automatically extract a continuous video segment that is full of contrast agent. Second, a detection network for attention video object is used to accurately and efficiently discern coronary stenosis on the continuous video segment. In the experiment, 166 video data were used for training and testing. The accuracy of video phase partition network can reach 0.838, and the precision and F1 of video stenosis detection results are 0.8 and 0.76 respectively. This performance is the best among all comparison methods. Therefore, we have implemented a complete process for detecting stenoses from coronary XRA sequences.
Acylglucoses from Wild Tomatoes Alter Behavior and Reduce Growth and Survival of Helicoverpa zea and Spodoptera exigua (Lepidoptera: Noctuidae) (1994)

Journal Article Acylglucoses from Wild Tomatoes Alter Behavior and Reduce Growth and Survival of Helicoverpa zea and Spodoptera exigua (Lepidoptera: Noctuidae) Get access John A. Juvik, John A. Juvik Search for other works by this author on: Oxford Academic PubMed Google Scholar Joseph A. Shapiro, Joseph A. Shapiro Search for other works by this author on: Oxford Academic PubMed Google Scholar Todd E. Young, Todd E. Young Search for other works by this author on: Oxford Academic PubMed Google Scholar Martha A. Mutschler Martha A. Mutschler Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 87, Issue 2, 1 April 1994, Pages 482–492, https://doi.org/10.1093/jee/87.2.482 Published: 01 April 1994 Article history Received: 25 February 1993 Accepted: 05 October 1993 Published: 01 April 1994
Rigid E/spl I.oarr/-unifiability is DEXPTIME-complete (2002)

Proves that rigid E/spl I.oarr/-unifiability, a decision problem invented by Gallier et al. (1987) to extend first-order tableaux-like proof procedures to first-order logic with equality, is DEXPTIME-complete; and that, when restricted to monadic terms, it is PSPACE-complete.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-performance ultra-wideband tubular suspended stripline bandpass filter (2015)

A simple ultra-wideband (UWB) suspended stripline (SSL) bandpass filter based on the tubular filter structure is presented in this letter. In this design, the equivalent circuit of the proposed filter is considered as the tubular bandpass filter circuit. Then, the proposed filter could be realized by quasi-lumped elements using SSL easily. In the passband from 3.1 to 10.6 GHz, insertion loss is better than 0.5 dB, return loss is higher than 19 dB and the group delay variation is less than 0.7 ns. A good agreement between the simulation and measurement was observed.
In Vitro Development of Horse Oocytes Reconstructed with the Nuclei of Fetal and Adult Cells1 (2002)

This study investigated the basic conditions required for the production of horse embryos by the transfer of the nuclei of fetal and adult fibroblast cells to enucleated oocytes. Cumulus-oocyte complexes were recovered from abattoir ovaries and matured in vitro in groups of 20-30 for 28-30 h in tissue culture medium 199 containing 20% v:v fetal bovine serum in coculture with equine oviduct epithelial cells. Fetal fibroblast cells (FFC) were derived from a 32-day-old Thoroughbred x Pony fetus, and adult skin fibroblast cells (SFC) were obtained from subdermal biopsies recovered from a 4-yr-old female Pony. The rates of fusion between the recipient cytoplasm with either FFC or SFC were significantly greater when the cells were treated with a combination of direct current (DC) pulses and Sendai virus rather than with DC pulses alone (81%-82% vs. 49%-57%, P < 0.05). There were no differences in the rates of nuclear reprogramming between FFC and SFC (88% vs. 84%), but the rate of cleavage of the resulting embryos to the 2-cell stage was higher when FFC were used (53%) than when SFC were used (35%). Blastocysts were obtained from oocytes reconstructed with both types of donor cells and after culture in vitro for 6-7 days, but the overall proportion of blastocysts produced was very low in both cases (FFC, 4%; SFC, 7%). These results demonstrate a very limited potential for in vitro development of horse embryos after nuclear reprogramming following the transfer of nuclei from either fetal or adult fibroblasts into recipient enucleated oocytes.
Campaigning for President in America, 1788–2016 (2016)

<JATS1:p>What does it take to get elected president of the United States—“leader of the free world”? This book gives readers insight into the major issues and events surrounding American presidential elections across more than two centuries, from the earliest years of the Republic through the campaigns of the 21st century.</JATS1:p> <JATS1:p>The race for the presidency encapsulates the broader changes in American democratic culture. This book provides insight into the major issues and events surrounding American presidential elections across more than two centuries, from the earliest years of the Republic through the campaigns of the 21st century. Readers will be able to see and understand how presidential campaigns have evolved over time, and how and why the current state of campaigning for president came into being.</JATS1:p>
Penicillanic Acid Sulfones Inactivate the Extended-Spectrum β-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of β-Lactamase Inhibition (2022)

β-Lactamases hydrolyze β-lactam antibiotics and are major determinants of antibiotic resistance in Gram-negative pathogens. Enmetazobactam (formerly AAI101) and tazobactam are penicillanic acid sulfone (PAS) β-lactamase inhibitors that differ by an additional methyl group on the triazole ring of enmetazobactam, rendering it zwitterionic. In this study, ultrahigh-resolution X-ray crystal structures and mass spectrometry revealed the mechanism of PAS inhibition of CTX-M-15, an extended-spectrum β-lactamase (ESBL) globally disseminated among <i>Enterobacterales</i>. CTX-M-15 crystals grown in the presence of enmetazobactam or tazobactam revealed loss of the Ser70 hydroxyl group and formation of a lysinoalanine cross-link between Lys73 and Ser70, two residues critical for catalysis. Moreover, the residue at position 70 undergoes epimerization, resulting in formation of a d-amino acid. Cocrystallization of enmetazobactam or tazobactam with CTX-M-15 with a Glu166Gln mutant revealed the same cross-link, indicating that this modification is not dependent on Glu166-catalyzed deacylation of the PAS-acylenzyme. A cocrystal structure of enmetazobactam with CTX-M-15 with a Lys73Ala mutation indicates that epimerization can occur without cross-link formation and positions the Ser70 Cβ closer to Lys73, likely facilitating formation of the Ser70-Lys73 cross-link. A crystal structure of a tazobactam-derived imine intermediate covalently linked to Ser70, obtained after 30 min of exposure of CTX-M-15 crystals to tazobactam, supports formation of an initial acylenzyme by PAS inhibitors on reaction with CTX-M-15. These data rationalize earlier results showing CTX-M-15 deactivation by PAS inhibitors to involve loss of protein mass, and they identify a distinct mechanism of β-lactamase inhibition by these agents. <b>IMPORTANCE</b> β-Lactams are the most prescribed antibiotic class for treating bacterial diseases, but their continued efficacy is threatened by bacterial strains producing β-lactamase enzymes that catalyze their inactivation. The CTX-M family of ESBLs are major contributors to β-lactam resistance in <i>Enterobacterales</i>, preventing effective treatment with most penicillins and cephalosporins. Combining β-lactams with β-lactamase inhibitors (BLIs) is a validated route to overcome such resistance. Here, we describe how exposure to enmetazobactam and tazobactam, BLIs based on a penicillanic acid sulfone (PAS) scaffold, leads to a protein modification in CTX-M-15, resulting in irremediable inactivation of this most commonly encountered member of the CTX-M family. High-resolution X-ray crystal structures showed that PAS exposure induces formation of a cross-link between Ser70 and Lys73, two residues critical to β-lactamase function. This previously undescribed mechanism of inhibition furthers our understanding of β-lactamase inhibition by classical PAS inhibitors and provides a basis for further, rational inhibitor development.
Surface Plasmon Resonance Imaging of Transcription Factor Proteins:  Interactions of Bacterial Response Regulators with DNA Arrays on Gold Films (2002)

Surface plasmon resonance (SPR) imaging measurements have been used to study the sequence specific adsorption of response regulator proteins to DNA arrays constructed on gold thin films. Bacteria adapt to their environment primarily through two-component signal transduction systems that consist of an environmental sensor histidine kinase and a transcription activator response regulator DNA binding protein. DNA arrays were fabricated from oligonucleotide sequences of known DNA binding regions for two response regulators: OmpR, which controls gene expression of the outer membrane porin proteins in Escherichia coli, and VanR, which is involved in the antibiotic vancomycin resistance in Enterococcus faecium. The label-free method of SPR imaging was then used to monitor the sequence specific binding of these two response regulator proteins to the DNA arrays. The promoter regions from the ompF (F1 and F2) and ompC (C1) genes for the OmpR protein, and from the vanRS (R1) and vanHAX (H1 and H2) genes for the VanR protein were studied. SPR imaging was used to (i) monitor and compare the binding of both response regulators to various promoter regions on the DNA array, (ii) compare the binding of the OmpR response regulator protein in its phosphorylated and nonphosphorylated forms, and (iii) monitor the inhibition of VanR protein binding to the DNA arrays in the presence of a small molecule DNA binding inhibitor. The proteins exhibited specificity for the known binding sequences compared to control sequences on the DNA array. For the OmpR protein, the highest amount of binding was observed at the F1 site. When OmpR was phosphorylated by a small molecule phosphodonor, acetyl phosphate, there was on average a 42% increase in protein binding. In contrast, phosphorylated VanR binding decreased by an average of 40% in the presence of a known DNA binding inhibitor, (2,3,4-trifluorophenylisothiazolone). These measurements demonstrate that SPR imaging is an effective screening method for compounds that target DNA protein interactions and can serve as a useful tool for the discovery of new therapeutic molecules that target DNA binding proteins.
Scavenging of Atmospheric Particles by Ice Crystals (1967)

Ice crystals growing in supercooled clouds were studied in a Nakaya chamber to determine their ability to include foreign particles in their structure. In a series of experiments on wash-out ratios of condensing water and growing ice, ice crystals proved to be 16 times more efficient than water in capturing atmospheric particles. The existence of Facy's “dust-free space” around evaporating surfaces was confirmed. The dust-free space around supercooled droplets is considered, in connection with Stefan flow, to be an important mechanism in bringing particles toward ice surfaces, and may account for the observed wash-out efficiency of ice crystals.
Micro-modem - reliability solution for NoC communications (2005)

A new concept of micro-modem interface for reliable communications in networks on chip (NoC) is presented. The micro-modem addresses the major problems of sub-micron interconnect and contains techniques for reliability improvement. The architecture, data flow and components of the micro-modem are presented. Various techniques and processes are analyzed for compact on-chip implementation. Design and application considerations are discussed.
Optimization of sonochemical degradation of tetracycline in aqueous solution using sono-activated persulfate process (2015)

This study indicated that sono-activated persulfate process was found to be a promising method for the degradation of tetracycline.
CYRI1-mediated inhibition of RAC1 signalling restricts Salmonella Typhimurium infection (2017)

Abstract Salmonella presents a global public health concern. Central to Salmonella pathogenicity is an ability to subvert host defence mechanisms through bacterial effectors that target key host proteins implicated in restricting infection. Thus, to gain insight into host-pathogen interactions governing Salmonella infection, a thorough understanding of host defence mechanisms is needed. To tackle this, we performed an in vivo genome-wide ENU mutagenesis screen to uncover novel host defence proteins. Through this screen we identified an uncharacterised protein, which we name CYRI1 ( CY FIP-related R AC1 Interacting protein 1 ) that serves as a Salmonella resistance factor. We show that CYRI1 binds to the small GTPase RAC1 through a conserved domain present in CYFIP proteins, which are known RAC1 effectors that stimulate actin polymerisation. However, unlike CYFIP proteins, CYRI1 negatively regulates RAC1-driven actin cytoskeleton remodelling, thereby attenuating processes such as phagocytosis and cell migration. This, in turn, enables CYRI1 to counteract Salmonella at various stages of infection, including bacterial entry into epithelial cells, internalisation into myeloid-derived phagocytes as well as phagocyte-mediated bacterial dissemination. Together, this outlines a novel host defence mechanism that is crucial for determining bacterial fate.
Effect of Osimertinib on CTCs and ctDNA in EGFR Mutant Non-Small Cell Lung Cancer Patients: The Prognostic Relevance of Liquid Biopsy (2022)

The decrease in both CTCs and ctDNA occurring early during osimertinib treatment is predictive of better outcome, implying that liquid biopsy monitoring may be a valuable tool for the assessment of treatment efficacy.
Studies Towards Understanding the Biosynthesis of Methyl Phosphoramidates found in Campylobacter jejuni (2016)

The human pathogen Campylobacter jejuni is the leading cause of food-borne gastroenteritis, causing more foodborne illnesses than Salmonella, Shigella, and Listeria combined. Of the approximate 5.3 million people infected every year in North America alone, approximately 1/1000 will develop the post-infectious paralytic disorder Guillain–Barré syndrome. In addition, the Public Health Agency of Canada has recently reported that approximately 90% of all chickens in supermarkets are infected with C. jejuni. C. jejuni produces a capsular polysaccharide (CPS) that is an important virulence factor involved in colonization and invasion. The structure of C. jejuni CPS varies widely from strain to strain and is often functionalized with a range of phase-variable modifications. One of these unique and rare modifications is an O-methyl phosphoramidate (MeOPN) motif, which is found in over 70% of C. jejuni strains. The role of these MeOPNs is unknown, but recent studies have demonstrated that MeOPN-functionalized CPS plays a significant role in modulating several aspects of the immune response. Thus, there is good evidence for a biological role for the MeOPN group. Access to these MeOPN motifs could lead to the development of vaccines against C. jejuni and targeting the enzymes involved in its biosynthesis could lead to new therapeutic agents for the treatment of C. jejuni infections. However, before such agents can be identified, better characterization of these biosynthetic enzymes and their substrates are required. This thesis will focus on the MeOPN motif in two parts. The first part describes the development of a reliable method for the synthesis of the MeOPN motif and assess its stability through various chemical transformations. This will enable access to these rare and unique modifications for the potential development of vaccines against C. jejuni. Part two of this thesis will describe work directed at unraveling the biosynthesis of the MeOPN motifs. More specifically, we will describe work to demonstrate enzyme activity for the two phosphoramidate transferases found in the C. jejuni strain 11168H. This work, when complete, will provide insights that could be used to development of inhibitors against these proteins and possible new therapeutic agents against C. jejuni.
Spin–spin coupling constants as indicators of the conformation of anthrone in solution (1982)

The analyses of the 1 H nmr spectra of fluorene, 2,7-dibromofluorene, and anthrone are reported. The benzylic couplings in these compounds are compared with those in indene and toluene. It is argued that the six-bond and five-bond couplings in anthrone are more compatible with a nonplanar than a planar central ring. The spectrum of the 2,7-dibromofluorene suggest that couplings between protons in different benzenoid rings are small, perhaps no larger than 0.05 Hz.