gebhart/patrepeval huggingface dataset:
Optical Field-Induced Mass Transport in Soft Materials (2013)

The dependence of the surface relief formation in amorphous chalcogenide (As2S3 and As-S-Se) and Disperse Red 1 dye grafted polyurethane polymer films on the polarization state of holographic recording light beams was studied. It is shown that the direction of lateral mass transport on the film surface is determined by the direction of light electric vector and photoinduced anisotropy in the film. We propose a photoinduced dielectropfhoretic model to explain the photoinduced mass transport in amorphous films. Model is based on the photoinduced softening of the matrix, formation of defects with enhanced or decreased polarizability, and their drift under the electrical field gradient of light.
Production and characterization of neutralizing and nonneutralizing monoclonal antibodies against listeriolysin O (1991)

Listeriolysin O (LLO) is a thiol-activated toxin secreted by the facultative intracellular pathogen Listeria monocytogenes. LLO is essential for the survival of the bacterium in the infected cell because it promotes lysis of the phagosome membrane and escape of the bacterium into the cytosol. LLO was used as an antigen for the production of nine monoclonal antibodies (MAbs) in mice. Three of these could inhibit the hemolytic activity of LLO. One of them inhibited binding of LLO to erythrocyte membranes. The two other antibodies blocked the activity of LLO at a step subsequent to membrane binding. Only two of the nine MAbs recognized three other purified SH-activated toxins, streptolysin O, alveolysin, and pneumolysin. Western blot (immunoblot) analysis of culture supernatants of Listeria ivanovii and Listeria seeligeri, two hemolytic species of the genus Listeria, revealed that two MAbs recognized ivanolysin and seeligerolysin. The latter was also recognized by two other MAbs, including one of the neutralizing antibodies. MAbs raised against a peptide, ECTG LAWEWWR, present in all thiol-activated toxins sequenced to date, recognized all toxins and were not neutralizing. Taken together, these results demonstrate the existence of regions important for hemolytic activity that are unique to hemolysins of the genus Listeria and show that regions outside the conserved peptide are important for activity of LLO.
Clinical genomic implications of transcriptional subtypes in pancreatic cancer. (2023)

4145 Background: Transcriptional profiling of pancreatic cancers (PC) has defined classical and basal subtypes; basal tumors have worse outcomes. Mesenchymal (MES) and neural-like progenitor (NRP) subtypes are increasingly recognized and enriched post-therapy. Initial data suggests worse outcomes to FOLFIRINOX (FFX) compared with gemcitabine nab-Paclitaxel (GnP) in basal tumors. Several clinical trials are ongoing to investigate this. Here, we examined the clinical implications of transcriptional subtypes in a large, real-world dataset. Methods: Retrospective IRB exempt, deidentified data was examined from NextGen DNA and RNA sequencing performed on PCs at Caris Life Sciences (Phoenix, AZ). Classical and basal cell states were identified using RNA-seq and the PurIST algorithm in a genomic cohort or GATA6 and KRT5 expression levels in a clinical cohort. Tumor microenvironment immune cell composition on RNA seq was performed using QuantiSeq. Survival was obtained from insurance claims data and calculated from first treatment date to last known contact. Kaplan-Meier estimates were calculated for patient cohorts. P values were adjusted using Benjamini-Hochberg correction. Results: A total of 7,250 PCs were profiled in the genomic cohort. 3,063 tumors (42.2%) were strongly classical (SC), 2,015 tumors (27.8%) were strongly basal (SB) and the remaining had mixed phenotypes. MES and NRP marker genes were significantly co-expressed with each other, with basal genes, and anti-correlated with classical genes. When compared to SC, SB had significantly higher mutation rates in KRAS (93% vs. 88%), TP53 (83% vs. 72%) and ARID1A (12% vs. 8%), whereas SMAD4 (23% vs. 17%) mutations were more common in SC (all q &lt; 0.05). There were no differences in mutation rates in homologous recombination or mismatch repair genes. SB had a significantly higher fraction of M1 macrophages (fold change [FC]: 1.14) and neutrophils (FC 1.16), whereas SC tumors had higher M2 macrophages (FC 1.18), NK (FC 1.2), and dendritic cells. Overall proportions of CD4/8 T cells were low and not different. Interestingly, SB had higher levels of PD-L1 by IHC (4.8% vs. 35%) and higher expression of immune exhaustion genes including CTLA4 (FC 1.19), TIM3 (FC 1.22) and PD-1 (FC 1.43) (all q &lt; 0.05). The clinical cohort had 1,623 patients. Basal tumors had an inferior survival (median survival: 8.2 months (mo) vs 13.3 mo (Hazard Ratio (HR) 0.67, p &lt; 0.00001)) and showed a significant improvement in outcomes when treated with upfront FFX vs GnP (n = 80 vs 90, Median: 15.8 vs 7.4 mos., HR 0.68, p = 0.021). This difference between FFX vs GnP was less pronounced in classical tumors (n = 70 vs 89, Median: 17.3 vs 15.4 mos, HR 0.70, p = 0.049). Conclusions: Our work represents the largest known real world molecular comparison of transcriptional subtypes of PC. Differential outcomes for patients with basal tumors treated with FFX versus GnP warrants further investigation in prospective studies.
Reporting Guidelines for Clinical Laboratory Reports in Surgical Pathology (2008)

Abstract Context. —The surgical pathology report (SPR) is an essential part of patient care because it documents the pathologic findings in tissues removed from patients for diagnostic or therapeutic reasons. Despite the importance of the SPR, exhaustive guidelines outlining the various elements of the SPR have not, to our knowledge, been published. Objectives. —To outline recommendations delineating the required, preferred, and optional elements that should be included in the SPR. These guidelines, if implemented, will bring uniformity to the reporting of surgical pathology specimens. Data Sources. —The Surgical Pathology Resource Committee of the College of American Pathologists compiled and prioritized the elements that have been included in various institutional SPRs. Additional data sources include the College of American Pathologists Laboratory Accreditation Program checklists and the recommendations of the Association of Directors of Anatomic and Surgical Pathology. Each element was assigned a priority of required, preferred , or optional. These priorities were discussed and consensus was reached. This report does not address issues of formatting or style substantively. Conclusions. —These recommendations afford a framework for the creation of an SPR containing all of the components that are required or optimal for patient care.
Increased Expression of the Calcium‐Activated Chloride Channel in Hclca1 in Airways of Patients with Obstructive Chronic Bronchitis (2005)

Increased expression of IL-9, IL-9R and hCLCA1 in the bronchial mucosa of patients with obstructive CB suggests that mucus overproduction in this disease may be, at least in part, due to hCLCA1.
Organolanthanide-Mediated Silanolytic Chain Transfer Processes. Scope and Mechanism of Single Reactor Catalytic Routes to Silapolyolefins (1999)

This paper reports efficient and selective silanolytic (PhSiH3, n-BuSiH3, C6H5CH2SiH3) chain transfer in organolanthanide-catalyzed homogeneous ethylene polymerization and ethylene copolymerization with several α-olefins. The result is a series of silyl-capped polyolefins which have been characterized by 1H/13C NMR and IR spectroscopy as well as by GPC. In [(Me5C5)2LnH]2/[Me2Si(Me4C5)2LnH]2-mediated ethylene homopolymerization and ethylene copolymerization, both primary arylsilanes (PhSiH3) and alkylsilanes (n-BuSiH3, C6H5CH2SiH3) function as efficient chain-transfer agents. In the case of ethylene polymerization mediated by [(Me5C5)2SmH]2, the mechanism of chain transfer is supported by the observation that Mn of the capped polyethylenes formed at constant [catalyst], [PhSiH3], [ethylene] is inversely proportional to [PhSiH3]. Using silane-activated Me2Si(Me4C5)2LnCH(SiMe3)2 precatalysts, this chain-transfer process also efficiently produces silyl-endcapped ethylene + 1-hexene copolymers and ethylene + styrene copolymers.
Application-Defined Decentralized Access Control. (2014)

DCAC is a practical OS-level access control system that supports application-defined principals. It allows normal users to perform administrative operations within their privilege, enabling isolation and privilege separation for applications. It does not require centralized policy specification or management, giving applications freedom to manage their principals while the policies are still enforced by the OS. DCAC uses hierarchically-named attributes as a generic framework for user-defined policies such as groups defined by normal users. For both local and networked file systems, its execution time overhead is between <i>0%-9%</i> on file system microbenchmarks, and under <i>1%</i> on applications. This paper shows the design and implementation of DCAC, as well as several real-world use cases, including sandboxing applications, enforcing server applications' security policies, supporting NFS, and authenticating user-defined sub-principals in SSH, all with minimal code changes.
Supplementary Figure Legend from Parathyroid Hormone–Related Protein Drives a CD11b&lt;sup&gt;+&lt;/sup&gt;Gr1&lt;sup&gt;+&lt;/sup&gt; Cell–Mediated Positive Feedback Loop to Support Prostate Cancer Growth (2023)

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Relationship Between BCC-Deformation, Transformation Temperature and Microstructure in ${\rm Nb}_{3}{\rm Al}$ Wires (2007)

The authors have been developing the Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Al conductors through transformation process, where the Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Al phase forms from the BCC (body-centered cubic) Nb(Al) supersaturated solid solution phase; the BCC phase is quenched by rapid-cooling from a temperature around 2000degC. It was reported several times that deformation to the quenched BCC Nb(Al) phase influences the superconducting properties, usually improving . But, the results have not been discussed in detail so far from a metallurgical viewpoint. This work investigates the fundamental relationship between the BCC-deformation, transformation temperature, microstructure and superconducting properties. The transformation temperature is identified by DTA measurement, detecting the release of the free energy between the BCC and the phases. It was found that the transformation temperature has a tendency of monotonic decrease with the deformation. But, the transformation temperature does not seem to go down below a temperature of about 720 degC even by strong deformation. The microstructures observed by FESEM suggests that the grain size is reduced almost proportionally with the deformation. In case of reduction in area of 99%, the grain size is reduced down to about 250 nm from 1.2mum . The increases with deformation, not showing a peak. The J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> of the wire (ME365) with reduction in area of 86% shows the best performance of the wire ever reported. But, at least high-field J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> seems to saturate at a certain value.
Detection of pollution sources using continuous mercury automobile survey (2001)

Overall picture of regional ecological situation shows that mercury is one of the most hazardous toxic elements in urban soils and sediments. The origins of mercury pollution at industrial and urban areas have been determined by exposure of many types of sources. A high proportion of mercury is transfered to deponent media through the atmosphere. Therefore, active sources of Hg emission can be found by mercury determination in ambient air. A portable Zeeman AAS RA-915 mercury analyzer of proprietary Lumex design has been used for continuous helicopter and automobile surveys of mercury distribution in ambient air. Carborne mercury surveys were carried out in cities and industrial areas in Russia, Ukraine, Kirgizia, Slovenia, Croatia and Czech Republic. The highest concentration of mercury in chimney plumes and the highest pollution of ambient air has been observed in the vicinity of operating mercury mines and smelters (Kirgizia), and at the premises of a chlor-alkali plant (Russia). High mercury concentration in the air was also observed around the Idrija mine and smelter (Slovenia), and chlor-alkali plant (Croatia), which were shut down for years. Around metropolitan areas which we studied (St. Petersburg, Zagreb, Ljubljana, Prague, et al.), the background mercury content in ambient air does not exceed 5 ng/m3. The local haloes, up to 300 ng/m3 and more, were recorded around plants which use mercury in technological processes, incinerators, over dumps and others contaminated sites. Our wide experience in continuous automobile mercury surveys in ambient air shows that it is the most rapid and effective method of detection and identification of active sources of mercury emission.
Measurement of complex permittivity of composite materials using waveguide method (2011)

Complex dielectric permittivity of 4 different composite materials has been measured using the transmissionline method. A waveguide fixture in L, S, C and X band was used for the measurements. Measurement accuracy is influenced by air gaps between test fixtures and the materials tested. One of the materials, unprotected glass fiber composite, has directional effects. All materials tested show low permittivity.
The influence of geometrical imperfections in micromachined cantilevers on the extracted Young's modulus using a simple model (2008)

Surface-micromachined test structures for material property characterization at the micro scale often have geometric imperfections. These imperfections make analytical modeling complex. Using an advanced fabrication process, test structures with minimal under-etching can be fabricated. With the use of these structures, straightforward and more accurate material parameter extraction is possible, as compared to test structures which are fabricated using conventional surface micromachining. This work investigates the influence of imperfections, such as under-etching and dishing, on the extracted Young's modulus using a simple model. The considered one-dimensional analytical model is that of a uniformly loaded cantilever beam with fixed boundary conditions. Very good agreement with this model is possible if the effect of bottom clamping, for which one can easily correct, is canceled out.
On the Therapeutic Potential of ERK4 in Triple-Negative Breast Cancer (2022)

ERK3 and ERK4 define a distinct and understudied subfamily of mitogen-activated protein kinases (MAPKs). Little is known about the physiological roles of these atypical MAPKs and their association with human diseases. Interestingly, accumulating evidence points towards a role for ERK3 and ERK4 signaling in the initiation and progression of various types of cancer. Notably, a recent study reported that ERK4 is expressed in a subset of triple-negative breast cancer (TNBC) cell lines and that this expression is critical for AKT activation and for sustaining TNBC cell proliferation in vitro and tumor growth in mice. The authors also showed that depletion of ERK4 sensitizes TNBC cells to phosphatidylinositol-3-kinase (PI3K) inhibitors. They concluded that ERK4 is a promising therapeutic target for TNBC and has potential for combination therapy with PI3K inhibitors. Here, we raise concerns about the cellular models and experimental approaches used in this study, which compromise the conclusions on the oncogenic role of ERK4 in TNBC.
Mutations in the UBIAD1 Gene, Encoding a Potential Prenyltransferase, Are Causal for Schnyder Crystalline Corneal Dystrophy (2007)

Schnyder crystalline corneal dystrophy (SCCD, MIM 121800) is a rare autosomal dominant disease characterized by progressive opacification of the cornea resulting from the local accumulation of lipids, and associated in some cases with systemic dyslipidemia. Although previous studies of the genetics of SCCD have localized the defective gene to a 1.58 Mbp interval on chromosome 1p, exhaustive sequencing of positional candidate genes has thus far failed to reveal causal mutations. We have ascertained a large multigenerational family in Nova Scotia affected with SCCD in which we have confirmed linkage to the same general area of chromosome 1. Intensive fine mapping in our family revealed a 1.3 Mbp candidate interval overlapping that previously reported. Sequencing of genes in our interval led to the identification of five putative causal mutations in gene UBIAD1, in our family as well as in four other small families of various geographic origins. UBIAD1 encodes a potential prenyltransferase, and is reported to interact physically with apolipoprotein E. UBIAD1 may play a direct role in intracellular cholesterol biochemistry, or may prenylate other proteins regulating cholesterol transport and storage.
ChemInform Abstract: Stereochemistry and Stereoelectronics of Azines. Part 3. Polymorphism and C=N‐N=C Conformational Isomers of Azines: X‐Ray Crystal and ab initio Structures of Two Rotational Isomers of Methyl (p‐Tolyl) Ketone Azine (I). (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
1. Pluripotent stem-cell-derived corneal cells (2019)

Corneal dystrophies are the leading cause of corneal transplantations performed in the United States each year. Although keratoplasty has been successful at visual rehabilitation, graft rejection and lack of suitable donor tissue for transplantation are among the obstacles to reduce cornea-related blindness worldwide. As an alternative to donor corneal transplantation for corneal epithelium dysfunction, cultured limbal stem cell (LSC) transplantation has been performed successfully for the treatment of LSC deficiency to replace the degenerated corneal epithelium. Stromal scarring because of trauma, surgery, or infection is responsible for a significant portion of the corneal blindness worldwide. At present, deep anterior lamellar keratoplasty is the only option to treat corneal stromal disease. The therapeutic potential of stromal keratocytes by differentiating adult dental pulp stem cells, human embryonic stem cells (hESCs), and mesenchymal stem cells for corneal stromal dysfunctions have been reported. In contrast to the epithelium, corneal endothelial cells (CECs) have limited proliferative capability in vivo, which is the driving force for efforts to generate CECs from pluripotent stem cells. Several groups used hESCs and induced pluripotent stem cells (iPSCs) to generate CECs and characterized the differentiated CECs through next-generation based RNA-sequencing (RNA-Seq) and mass-spectrometry-based proteome sequencing. We previously reported the generation and proteome profiling of CECs using the peripheral blood mononuclear cell (PBMC)-originated, iPSCs and recently extended our analysis through RNA-Seq-based transcriptome profiling of hESC- and iPSC-derived CECs. As an alternative to donor corneas, multiple therapeutic options for corneal endothelial dysfunction, including cultured CECs and hESC- and iPSC-derived CECs, are currently under investigation. Different preclinical studies demonstrated the regeneration of corneal endothelium following the injection of a cultured and pluripotent stem-cell-derived CECs, in combination with a Rho kinase (ROCK) inhibitor. Recently, a clinical trial using human cultured CECs supplemented with a ROCK inhibitor reported an increased CEC density in 11 patients with bullous keratopathy. In this chapter, we will discuss efforts by various research groups to generate pluripotent stem-cell-derived corneal cells and their possible therapeutic applications in corneal dystrophies.
In-Plane Printed Batteries Based on Mxenes (2022)

In the era of miniaturization, micro energy storage devices become an essential part of the progress in many fields starting from simple sensors to medical devices. However upcoming developments in all these fields are restricted to finding safe, reliable and high-performance micro batteries with the shapes that is not limited only to rectangles, cylinders, and pouches. The research is confronted with challenges of fitting a battery into a microdevice. Lithium-ion batteries (LIBs), a mature energy storage technology, are a leading candidate for the development of micro batteries that can be easily integrated into microelectronic devices. However, despite significant achievements in the field of micro batteries, limitations in areal capacity and in power densities still motivate the search for alternative designs and novel concepts in the battery field. Insufficient areal energy density from planar micro batteries has inspired a search for three-dimensional micro batteries. The power output of a three-dimensional micro battery is expected to be higher than that of a two-dimensional battery of equal size, as a result of the higher ratio of electrode-surface-area to volume and lower Ohmic losses. Within a battery electrode, the 3D architecture provides large surface area, increasing power by reducing the diffusion path for Li ions. Additive manufacturing, also known as 3D printing, has appeared as a novel class of free form fabrication technologies that have a variety of possibilities for the rapid creation of complex architectures at lower cost than conventional methods. 3D printing enables the controlled creation of functional materials with three-dimensional architectures, representing a promising approach for the fabrication of next-generation electrochemical energy-storage devices and has many unique advantages over conventional manufacturing methods. In this work, printer is employed to print a 3D micro battery with MXene electrodes that can be printed easily and can be fitted into any small device.
Activated Mutants of SHP-2 Preferentially Induce Elongation of <i>Xenopus</i> Animal Caps (2000)

In Xenopus ectodermal explants (animal caps), fibroblast growth factor (FGF) evokes two major events: induction of ventrolateral mesodermal tissues and elongation. The Xenopus FGF receptor (XFGFR) and certain downstream components of the XFGFR signal transduction pathway (e.g., members of the Ras/Raf/MEK/mitogen-activated protein kinase [MAPK] cascade) are required for both of these processes. Likewise, activated versions of these signaling components induce mesoderm and promote animal cap elongation. Previously, using a dominant negative mutant approach, we showed that the protein-tyrosine phosphatase SHP-2 is necessary for FGF-induced MAPK activation, mesoderm induction, and elongation of animal caps. Taking advantage of recent structural information, we now have generated novel, activated mutants of SHP-2. Here, we show that expression of these mutants induces animal cap elongation to an extent comparable to that evoked by FGF. Surprisingly, however, activated mutant-induced elongation can occur without mesodermal cytodifferentiation and is accompanied by minimal activation of the MAPK pathway and mesodermal marker expression. Our results implicate SHP-2 in a pathway(s) directing cell movements in vivo and identify potential downstream components of this pathway. Our activated mutants also may be useful for determining the specific functions of SHP-2 in other signaling systems.