gebhart/patrepeval huggingface dataset:
p63 in Primary Cutaneous Carcinosarcoma (2007)

Primary cutaneous carcinosarcomas (PCCs) are rare malignant neoplasms that are characterized by biphasic epithelial and mesenchymal differentiation. When the biphasic nature is not evident, immunohistochemical studies may be important in the diagnosis of PCCs. Although AE1/AE3 is frequently used to demonstrate the epithelial component, it may not be strongly expressed in epithelial cells that are not well-differentiated. p63 is a protein homologue of p53 that is expressed in poorly differentiated epithelial cells. We report 3 cases of PCC. The clearly epithelial areas of each tumor were frequently positive for both markers, whereas the sarcomatous areas were negative for both markers. Epithelial cells that were poorly differentiated and not easily identifiable were positive for p63 but negative for AE1/AE3. Of interest, transitional areas showed positivity for p63 alone. These 3 cases suggest that the use of both p63 and routine cytokeratin markers such as AE1/AE3 can increase the sensitivity for distinguishing epithelial cells over a range of differentiation states, which we propose will aid in the diagnosis of PCCs. In addition, the staining pattern of AE1/AE3 and p63 in these cases further supports the conversion theory of PCC.
Moraxella catarrhalis evades neutrophil oxidative stress responses providing a safer niche for nontypeable Haemophilus influenzae (2022)

<i>Moraxella catarrhalis</i> and nontypeable <i>Haemophilus influenzae</i> (NTHi) are pathogenic bacteria frequently associated with exacerbation of chronic obstructive pulmonary disease (COPD), whose hallmark is inflammatory oxidative stress. Neutrophils produce reactive oxygen species (ROS) which can boost antimicrobial response by promoting neutrophil extracellular traps (NET) and autophagy. Here, we showed that <i>M. catarrhalis</i> induces less ROS and NET production in differentiated HL-60 cells compared to NTHi. It is also able to actively interfere with these responses in chemically activated cells in a phagocytosis and opsonin-independent and contact-dependent manner, possibly by engaging host immunosuppressive receptors. <i>M. catarrhalis</i> subverts the autophagic pathway of the phagocytic cells and survives intracellularly. It also promotes the survival of NTHi which is otherwise susceptible to the host antimicrobial arsenal. In-depth understanding of the immune evasion strategies exploited by these two human pathogens could suggest medical interventions to tackle COPD and potentially other diseases in which they co-exist.
ChemInform Abstract: MULTIPLE METAL‐CARBON BONDS. 16. TUNGSTEN‐OXO ALKYLIDENE COMPLEXES AS OLEFINS S METATHESIS CATALYSTS AND THE CRYSTAL STRUCTURE OF W(O)(CHCME3(PET3)CL2 (1980)

Abstract Ausgehend vom bekannten Komplex (Ia) werden bei Behandlung mit entsprechenden Olefinen CH2=CH‐R in Gegenwart von Spuren AlCl 3 die Analogen (Ib) erhalten.
Erratum to: Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at $$\sqrt{s}=8~$$ s = 8 TeV with the ATLAS detector (2015)

Author(s): Aad, G; Abbott, B; Abdallah, J; Abdel Khalek, S; Abdinov, O; Aben, R; Abi, B; Abolins, M; AbouZeid, OS; Abramowicz, H; Abreu, H; Abreu, R; Abulaiti, Y; Acharya, BS; Adamczyk, L; Adams, DL; Adelman, J; Adomeit, S; Adye, T; Agatonovic-Jovin, T; Aguilar-Saavedra, JA; Agustoni, M; Ahlen, SP; Ahmadov, F; Aielli, G; Akerstedt, H; Åkesson, TPA; Akimoto, G; Akimov, AV; Alberghi, GL; Albert, J; Albrand, S; Alconada Verzini, MJ; Aleksa, M; Aleksandrov, IN; Alexa, C; Alexander, G; Alexandre, G; Alexopoulos, T; Alhroob, M; Alimonti, G; Alio, L; Alison, J; Allbrooke, BMM; Allison, LJ; Allport, PP; Aloisio, A; Alonso, A; Alonso, F; Alpigiani, C; Altheimer, A; Alvarez Gonzalez, B; Alviggi, MG; Amako, K; Amaral Coutinho, Y; Amelung, C; Amidei, D; Amor Dos Santos, SP; Amorim, A; Amoroso, S; Amram, N; Amundsen, G; Anastopoulos, C; Ancu, LS; Andari, N; Andeen, T; Anders, CF; Anders, G; Anderson, KJ; Andreazza, A; Andrei, V; Anduaga, XS; Angelidakis, S; Angelozzi, I; Anger, P; Angerami, A; Anghinolfi, F; Anisenkov, AV; Anjos, N; Annovi, A; Antonelli, M; Antonov, A; Antos, J; Anulli, F; Aoki, M
Photo- and Radioluminescence of ZnO-Precipitated Glass-Ceramics (2015)

The indoor-outdoor (IO) status of mobile devices is fundamental information for various smart city applications.In this paper, we present NeuralIO, a neural-network-based method for dealing with the IO detection problem for smartphones.Multimodal data from various sensors on a smartphone are fused through neural network models to determine the IO status.A data set containing more than one million labeled samples is then constructed.We test the performance of an early fusion scheme in various settings.NeuralIO achieves an accuracy above 98% in 10-fold cross-validation and an accuracy above 90% in a real-world test.
Supplementary Figure 6 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;Supplementary Figure 6&lt;/p&gt;
335-LB: Towards Generating Spatiotemporal Multiscale Models of Pancreatic ß Cells (2019)

To characterize biology, we must consider how molecular machines and organelles within a cell interact and traffic, similar to the importance of understanding traffic patterns in major cities. We use an imaging across scales approach to understand architectural changes that occur in pancreatic β-cells during insulin secretion. β-cells produce and release insulin in response to glucose and are therefore a target for diabetes therapies. Diabetes is a worldwide problem affecting hundreds of millions of people with increasing patient numbers every year. To acquire cellular architectural information, we are integrating data from cryo-electron tomography, soft x-ray tomography (SXT), and fluorescence microscopy. We used multiple glucose and GPCR agonist concentrations to investigate the cellular organization changes induced during insulin vesicle biogenesis and trafficking. The SXT method allows for investigating the 3D cellular architecture and is an ideal method for investigating cell-to-cell variabilities. Additionally, we are using machine learning methods for image analysis and autosegmentation which increased the number of conditions and samples we can analyze rapidly. Furthermore, we can use the information from cryo-ET and SXT along with with live cell imaging to assemble a data-driven, dynamic model of insulin granules within pancreatic β-cells. Furthermore, the SXT method provides a unique opportunity for comparing cell-to-cell heterogeneity and will be a useful technique for comparing differences between rodent and human primary cell architectures. The integration of data from different time and spatial scales represents a sophisticated convergence of our understanding of cellular structure and function, which will revolutionize biological discovery, open new dimensions of research, and accelerate advancements in healthcare. Disclosure K.L. White: None. J. Singla: None. R.C. Stevens: Board Member; Self; BirdRock Bio, Danaher Corp. Funding University of Southern California
Active remote cloaking and optical transformations from a boundary element perspective (2009)

Recently, it was demonstrated that active sources can be used to cloak any objects that lie outside the cloaking devices [Phys. Rev. Lett. \textbf{103}, 073901 (2009)]. Here, we propose that active sources can create illusion effects, so that an object outside the cloaking device can be made to look like another object. invisibility is a special case in which the concealed object is transformed to a volume of air. From a boundary element perspective, we show that active sources can create a nearly silent domain which can conceal any objects inside and at the same time make the whole system look like an illusion of our choice outside a virtual boundary. The boundary element method gives the fields and field gradients (which can be related to monopoles and dipoles) on continuous curves which define the boundary of the active devices. Both the cloaking and illusion effects are confirmed by numerical simulations.
Efficiency of transduction of highly purified murine hematopoietic stem cells by lentiviral and oncoretroviral vectors under conditions of minimal in vitro manipulation (2005)

The development of leukemias in several children with severe combined immunodeficiency disease who were transplanted with retroviral vector-transduced bone marrow cells has renewed concerns about the risks associated with the random integration of proviral sequences into chromosomal DNA. One theoretical way to reduce the risks of insertional mutagenesis would be to employ transduction/transplantation protocols that minimize the total number of genetically modified cells and associated proviral integration "events" introduced into recipients. Toward this end, we have developed a transduction protocol that involves the short-term incubation of highly purified murine stem cells with high-titer recombinant lentivirus vectors in the presence of serum-free medium and the cytokines SCF and TPO. Competitive repopulation studies showed that stem cells transduced in this way possessed the same reconstitutive ability as fresh, unmanipulated cells. Animals transplanted with only 200-2000 transduced cells were efficiently reconstituted with the genetically modified cells, and most hematopoietic cells in the recipients expressed the transgene. In contrast, the use of high-titer oncoretroviral vectors in conjunction with the same transduction/transplantation protocol resulted in only low levels of gene marking in vivo. The use of a similar transduction/transplantation strategy in future clinical studies may offer distinct advantages over current protocols.
Synthesis and characterization of two novel star blocks: tCum[poly(isobutylene‐b‐norbornadiene)]3 and tCum[poly(norbornadiene‐b‐isobutylene)]3 (2003)

Abstract Two structurally closely related three‐arm star blocks were synthesized and characterized: tCum(PIB‐ b ‐PNBD) 3 and tCum(PNBD‐ b ‐PIB) 3 [where tCum (tricumyl) stands for the phenyl‐1,3,5‐tris(‐2‐propyl) fragment and PIB and PNBD are polyisobutylene and polynorbornadiene, respectively]. The syntheses were accomplished in two stages: (1) the preparation of the first (or inner) block fitted with appropriate chlorine termini capable of initiating the polymerization of the second (or outer) block with TiCl 4 and (2) the mediation of the polymerization of the second block. Therefore, the synthesis of tCum(PIB‐ b ‐PNBD) 3 was effected with tCum(PIB‐Cl t ) 3 [where Cl t is tert ‐chlorine and number‐average molecular weight ( M n ) = 102,000 g/mol] by the use of TiCl 4 and 30/70 CH 3 Cl/CHCl 3 solvent mixtures at −35 °C. PNBD homopolymer contamination formed by chain transfer was removed by selective precipitation. According to gel permeation chromatography, the M n 's of the star blocks were 107,300–109,200 g/mol. NMR spectroscopy (750 MHz) was used to determine structures and molecular weights. Differential scanning calorimetry (DSC) indicated two glass‐transition temperatures ( T g 's), one each for the PIB (−65 °C) and PNBD (232 °C) phases. Thermogravimetric analysis thermograms showed 5% weight losses at 293 °C in air and at 352 °C in N 2 . The synthesis of tCum(PNBD‐ b ‐PIB) 3 was achieved by the initiation of isobutylene polymerization with tCum(PNBD‐Cl sec ) 3 (where Cl sec is sec ‐chlorine and M n = 2900 g/mol) by the use of TiCl 4 in CH 3 Cl at −60 °C. DSC for this star block ( M n = 14,200 g/mol) also showed two T g 's, that is, at −67 and 228 °C for the PIB and PNBD segments, respectively. It is of interest that the Cl sec terminus of PNBD, , readily initiated isobutylene polymerization. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 740–751, 2003
Redox-Active Nitroxide Radical Polymers: From Green Catalysts to Energy Storage Devices (2009)

Robust but redox‐active radical polymers bearing 2, 2, 6, 6‐tetramethylpiperidin‐N‐oxy (TEMPO) were investigated as a metal‐free, green mediator/catalyst for the oxidation of alcohol derivatives, and as a new electrode‐active and charge‐storage material. The TEMPO‐mediated oxidation of the primary alcohol group of the natural cellulose improved the water‐dispersivity of cellulose, and the polymer‐supported catalysts or redox resins allow facile removal of catalysts from products by simple filtration. Other radical molecule (e.g. galvinoxyl) was also used as a mediator, which is coupled with the molecular oxygen. A reversible one‐electron redox reaction of TEMPO allowed its application as an electrode‐active material featuring high cyclability (>500 cycles), relatively high battery electrode capacity (100–135 mAh/g), and fast electrode kinetics, leading to the high power rate capability of the battery. The radical polymer‐based electrodes also provided good processability and shape flexibility, which promised the paper‐like and wearable energy‐storage devices.
Development, standardization and refinement of procedures for evaluating effects of endocrine active compounds on development and sexual differentiation of Xenopus laevis (2008)

Xenopus laevis has been introduced as a model to study effects of endocrine-active compounds (EAC) on development and sexual differentiation. However, variable and inconsistent data have raised questions about the reliability of the test methods applied. The current study was conducted in two laboratories to develop, refine, and standardize procedures and protocols. Larvae were exposed in flow-through systems to 17beta-estradiol (E2), at concentrations from 0.2 to 6.0 microg E2 L(-1) in Experiment 1A, and 0.015 to 2.0 microg E2 L(-1) in Experiment 1B. In both studies survival (92%, 99%) and percentage of animals that completed metamorphosis (97%, 99%) indicated reproducible biological performance. Furthermore, minor variations in husbandry led to significant differences in snout-to-vent length, weight, and gonad size. In Experiment 1A, almost complete feminization occurred in all E2 treatment groups whereas a concentration response was observed in Experiment 1B resulting in an EC(50) of 0.12 microg E2 L(-1). The final verified protocol is suitable for determining effects of EAC on development and sexual differentiation in X. laevis.
Caspase-1 targets the TLR adaptor Mal at a crucial TIR-domain interaction site (2010)

Toll-like receptors (TLRs) are crucial components of innate immunity, ensuring efficient responses against invading pathogens. After ligand binding, TLR signaling is initiated by recruitment of adaptor molecules, a step mediated by homotypic Toll-IL-1 receptor (TIR) domain interactions. Four TIR-containing TLR adaptor molecules are described, all of which are susceptible to modification and strict regulation. For example, caspase-1 is reported to cleave the TLR adaptor Mal at position D198, an event that is indispensible for Mal function. In this report, we use the mammalian two-hybrid technique MAPPIT to study the implications of Mal cleavage. We show that a Mal mutant, which mimics caspase-1 cleavage and a caspase-1-uncleavable MalD198A mutant, are abrogated in their bridging function and lose the ability to activate NF-kappaB. A MalD198E mutant is still fully functional, suggesting that caspase-1 cleavage of Mal is not necessary for Mal-mediated signaling. D198 of Mal is conserved in MyD88 and TLR4 TIR domains and the negatively charged amino acid at this position is crucial for the interactions and function of Mal, MyD88 and TLR4 TIR. Our data suggest an inhibitory, rather than an activating role for caspase-1 in Mal regulation, and show that the caspase-1 cleavage site in Mal is part of a TIR-domain interaction site.
PtMn-based spin-dependent tunneling materials with thin alumina barrier fabricated by two-step natural oxidation (2002)

Spin-dependent tunneling (SDT) materials with bottom-pinned structure (substrate/Ta/NiFeCr/PtMn/CoFe/t Al2O3/CoFe/NiFe/Ta) are fabricated by magnetron sputtering in ultrahigh vacuum. In this study, a two-step natural oxidation was used, in which the second Al layer was deposited and naturally oxidized after the natural oxidation of the first Al layer. The top and bottom leads were also patterned into bow-tie shaped structures. The two-step oxidation process results in a perfectly decoupled pinned and free layer in a film with a total as-deposited aluminum thickness of 7 Å, whereas, the one-step oxidation process gives rise to strongly coupled magnetic layers in a film with this thickness of aluminum. By using this two-step natural oxidation technique, an optimum tunneling magnetic resistance (TMR) ratio of 29.3% and resistance×area (RA) product of 34 Ω μm2 were achieved in junctions with 8 Å barrier (5+3 Å). In conclusion, a two-step oxidation process was used to fabricate spin-dependent tunneling devices with low RA product and high TMR ratio for head applications.
Full-Field Interferometric Imaging of Action Potentials (2019)

High-speed quantitative phase microscopy enables full-field imaging of cellular deformations during action potential. In spiking HEK cells, displacements of up to 3nm (0.9mrad) have been observed, and they match the time course electrical recordings.
Homogeneous catalytic hydrogenation of natural rubber using RhCl(PPh3)3 (1997)

Hydrogenation is an important method of chemical modification, which improves the physical, chemical, and thermal properties of diene elastomers. It is also a useful method for preparation of polymers with unusual monomer sequences. Natural rubber (NR) could be quantitatively hydrogenated to a strictly alternating ethylene-propylene copolymer using a homogeneous RhCl(PPh3)3 catalyst. The effect of concentration of rubber, catalyst and triphenyl phosphine, temperature, pressure, and solvent on the course of hydrogenation were evaluated. The thermal properties of the hydrogenated NR are compared with NR. © 1997 John Wiley & Sons, Inc. J. Appl Polym Sci 66: 1647–1652, 1997
Endoscopic full-thickness resection using an endoluminal-suturing device: a proof-of-concept study (2019)

<b>Background and study aims</b> Endoscopic full-thickness resection (EFTR) is used to achieve R0 resection in difficult situations and as a way to overcome the limitations of endoscopic submucosal dissection. Multiple techniques have been described but adequate tools are still under evaluation. In this study, we evaluated the safety and feasibility of non-exposed endoscopic full-thickness resection using a novel endoscopic suturing device. <b>Materials and methods</b> Full-thickness resections of gastric predetermined lesions were performed on five pigs using the Endomina platform. After creating virtual lesion > 20 mm, sutures were placed around it using this triangulation platform. After tightening the knots, the bulging lesion, internalized into the gastric lumen, was cut with a needle knife. <b>Results</b> R0 resections of large lesions (42 to 60 mm) were achieved in all cases. One perforation occurred and prompted us to improve the procedure by shortening the sutures for more maneuverability and reinforcing the suture line before section. Procedure duration dropped by 50 % between the first case and the fourth case. Histological analysis confirmed successful full-thickness resection of all resected specimens. <b>Conclusion</b> EFTR using this triangulation platform seems feasible for lesions > 20 mm. Additional possible improvements were identified to simplify the procedure before moving to human trials.
Optimizing the flattened test-generation model for very large designs (2002)

Design and test tools, such as automatic test-pattern generators (ATPG) and fault-simulators, work on a "flattened" simulation model of the entire design. Run-time performance is directly influenced by the number and complexity of simulation primitives in the flattened model. Moreover, the memory required to flatten and store the simulation model of current multi-million-gate designs may exceed the available address space of 32 bit computers. We present several model-optimization techniques that significantly reduce the number of simulation primitives and the associated memory usage while still preserving a complete, highly efficient flattened model. A commercial ATPG product implementing these techniques demonstrates fast simulation model construction for very large designs using a relatively small memory space.
Chronic sensitivity of white sturgeon (Acipenser transmontanus) and rainbow trout (Oncorhynchus mykiss) to cadmium, copper, lead, or zinc in laboratory water-only exposures (2014)

Chronic toxicity of cadmium, copper, lead, or zinc to white sturgeon (Acipenser transmontanus) and rainbow trout (Oncorhynchus mykiss) was evaluated in water-only exposures started with newly hatched larvae or approximately 1-mo-old juveniles. The 20% effect concentration (EC20) for cadmium from the sturgeon tests was higher than the EC20 from the trout tests, whereas the EC20 for copper, lead, or zinc for the sturgeon were lower than those EC20s for the trout. When the EC20s from the present study were included in compiled toxicity databases for all freshwater species, species mean chronic value for white sturgeon was in a relatively low percentile of the species sensitivity distribution for copper (9th percentile) and in the middle percentile for cadmium (55th percentile), zinc (40th percentile), or lead (50th percentile). However, the species mean chronic value for rainbow trout was in a high percentile for copper, lead, and zinc (∼68th-82nd percentile), but in a low percentile for cadmium (23rd percentile). The trout EC20s for each of the 4 metals and the sturgeon EC20s for cadmium or lead were above US Environmental Protection Agency chronic ambient water quality criteria (AWQC) or Washington State chronic water quality standards (WQS), whereas the sturgeon EC20s for copper or zinc were approximately equal to or below the chronic AWQC and WQS. In addition, acute 50% effect concentrations (EC50s) for copper obtained in the first 4 d of the chronic sturgeon test were below the final acute value used to derive acute AWQC and below acute WQS for copper.
Topical protection of human esophageal mucosal integrity (2015)

Patients with nonerosive reflux disease exhibit impaired esophageal mucosal integrity, which may underlie enhanced reflux perception. In vitro topical application of an alginate solution can protect mucosal biopsies against acid-induced changes in transepithelial electrical resistance (TER). We aimed to confirm this finding in a second model using 3D cell cultures and to assess prolonged protection in a biopsy model. We assessed the protective effect of a topically applied alginate solution 1 h after application. 3D cell cultures were grown by using an air-liquid interface and were studied in Ussing chambers. The apical surface was "protected" with 200 μl of either alginate or viscous control or was unprotected. The tissue was exposed to pH 3 + bile acid solution for 30 min and TER change was calculated. Distal esophageal mucosal biopsies were taken from 12 patients and studied in Ussing chambers. The biopsies were coated with either alginate or viscous control solution. The biopsies were then bathed in pH 7.4 solution for 1 h. The luminal chamber solution was replaced with pH 2 solution for 30 min. Percentage changes in TER were recorded. In five biopsies fluorescein-labeled alginate solution was used to allow immunohistological localization of the alginate after 1 h. In the cell culture model, alginate solution protected tissue against acid-induced change in TER. In biopsies, 60 min after protection with alginate solution, the acidic exposure caused a -8.3 ± 2.2% change in TER compared with -25.1 ± 4.5% change after protection with the viscous control (P < 0.05). Labeled alginate could be seen coating the luminal surface in all cases. In vitro, alginate solutions can adhere to the esophageal mucosa for up to 1 h and exert a topical protectant effect. Durable topical protectants can be further explored as first-line/add-on therapies for gastroesophageal reflux disease.