gebhart/patrepeval huggingface dataset:
P5-02-05: Real-Time Subcellular Imaging of Breast Cancer Cell Attachment in Blood Vessels Using GFP-Labeled Paxillin in Live Mice. (2011)

Abstract Background: Paxillin is involved in the assembly of focal adhesions. We wish to visualize paxillin behavior in breast cancer cells in vivo, as well as in vitro. Materials and Methods: Dual-photon confocal microscopy was used to image paxillin behavior by linking it to GFP. MDA-MB-231 human breast cancer cells expressing paxillin-GFP were imaged in vitro and in vivo adhering and trafficking in blood vessels in mice. 106 paxillin-GFP expressing breast cancer cells were injected in the epigastric cranialis vein. Results: In vitro, round breast cancer cells had greater paxillin movement than stretched cancer cells as seen by fluorescence imaging. Paxillin-GFP breast cancer cells in the epigastric cranialis vein were initially rounded and had GFP-expressing protrusions. At later timepoints, many paxillin-GFP-expressing breast cancer cells stretched. The breast cancer cells then extravasated and subsequently grew around the outer surface of the blood vessel after one week. Two weeks after injection, paxillin-GFP expressing breast cancer cells were imaged migrating along the vessel wall. Most of the paxillin-GFP expressing breast cancer cells were stretched and were not mobile. With anti-VEGF treatment, paxillin was observed in round structures within the cells rather than stretched structures and paxillin movement within the cell was arrested. Discussion: These results demonstrate that breast cancer cells brightly expressing paxillin-GFP and two-photon confocal microscopy can allow the visualization of the behavior of paxillin within breast cancer cells during adhesion and migration along the walls of blood vessels, as well as during anti-angiogenesis therapy. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-02-05.
Direct Estimation of the Vocal Tract Shape by Inverse Filtering of Acoustic Speech (1973)

This paper describes a new method for estimating the vocal tract area function directly from the acoustic speech waveform. Dynamic changes of the area functions and formants in voiced speech sounds are obtainable. The filtering processes of the inverse filter model and an acoustic tube model of speech are analyzed and they are shown to be identical, with the reflection coefficients in the acoustic tube model as a com- mon factor, thus making possible the extraction of the reflec- tion coefficients by the inverse filter processing of the speech signal. The discrete area function can easily be obtained from the set of reflection coefficients. Analysis examples for vowels, diphthongs, and consonants in vowel-consonant-vowel utterances are given.
Active sites in char gasification: Final technical report (1987)

Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.
Stable expression in mouse cells of nuclear neoantigen after transfer of a 3.4-megadalton cloned fragment of Epstein-Barr virus DNA. (1982)

All cells that harbor the Epstein-Barr virus (EBV) genome contain a neoantigen in the nucleus (EBNA). By transfection we located a segment of the genome that encodes or induces an antigen serologically related to EBNA. The responsible genes are found in the 3.4-megaldalton BamHI fragment K of EBV DNA, specifically in the left 1.9 megadaltons represented by HindIII fragment I1. Mouse LTK- cells were cotransformed with recombinant plasmids, containing the herpes simplex virus thymidine kinase gene and either EcoRI fragment B or BamHI fragment of K of EBV DNA. The TK+ cells surviving in selective medium were cloned. About 50% of the clones expressed the neoantigen in every nucleus. These mouse cells were used as antigens in immunofluorescence tests. Antibody to the nuclear antigen was found in 30 human sera known to contain antibody to EBNA; it was not detected in 18 sera that did not have antibody to EBNA. Mouse cells expressing EBNA as the result of acquisition of cloned EBV DNA fragments should prove useful in the characterization of the structure of this antigen and as reagents for the diagnosis of EBV infections.
Platelets have more than one binding site for von Willebrand factor. (1983)

The binding of 125I-von Willebrand factor (125I-vWF) to platelets stimulated by thrombin, ADP, and a combination of ADP + epinephrine (EPI) is specific, saturable, and reversible. Active platelet metabolism and divalent cations are required for binding induced by these stimuli, but not by ristocetin, suggesting the existence of different mechanisms involved in the vWF-platelet interaction. A monoclonal antibody directed against an epitope of membrane glycoprotein (GP) Ib had no effect on the binding of 125I-vWF to normal platelets stimulated by thrombin or a combination of ADP + EPI, but completely blocked ristocetin-induced binding. Binding induced by thrombin to GPIb-blocked platelets was specific. Moreover, thrombin-induced binding of 125I-vWF was increased, rather than decreased, in two patients with the Bernard-Soulier syndrome whose platelets lacked GPIb. Conversely, monoclonal antibodies directed against the GPIIb/IIIa complex had no effect on ristocetin-induced binding of 125I-v-WF to normal platelets, but blocked thrombin- and ADP + EPI-induced binding. To exclude effects mediated by the platelet Fc receptor, a monoclonal IgG directed against an epitope present on human B cells and monocytes, but not expressed on resting or stimulated platelets, was used. It did not affect 125I-vWF binding induced by any of the stimuli. These studies show that platelets have more than one binding site for vWF, and that they may be exposed by different stimuli.
Abstract 510: MicroRNA-8073 as a tumor suppressor and a potential diagnostic and therapeutic target (2018)

Abstract MicroRNAs (miRNAs) generated inside cells are also present in peripheral blood. MiR-8073 has been studied in various disease model, but its molecular function had been unknown. In this study, we demonstrated that miR-8073 regulates target genes that participate in cell survival and works as a tumor suppressor controlling only cancer cells. First, we observed that miR-8073 expression was evidently decreased in multiple types of cancer cells compared to normal cells, but was increased in cancer exosome secreted into cultured supernatant. We then transfected synthetic miR-8073 mimic into various cancer cell lines and found dramatic reduction in cell proliferation, which was not detected in normal cells. Additionally, in tumor xenograft mice model, three-time subcutaneous injections of miR-8073 mimic at 2nM suppressed 57% growth of colorectal tumor weight. Through mRNA expression analysis and in silico sequence analysis, we further identified five potential miR-8073 targets that plays critical roles in regulation of cell proliferation, cycle and apoptosis, and demonstrated that miR-8073 indeed bound with the 3'-UTR of these target mRNAs and reduced both mRNA and protein expression. These results suggest that miR-8073 is a potential tumor suppressor, possibly discarded from cancer cells for their survival out to extracellular space, and circulates in bloodstream in the form of exosome. Our findings promise miR-8073 as a novel cancer diagnostic and therapeutic target. Citation Format: Atsuko Mizoguchi, Aiko Takayama, Taiga Arai, Yuho Kida, Junpei Kawauchi, Hiroko Sudo. MicroRNA-8073 as a tumor suppressor and a potential diagnostic and therapeutic target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 510.
MIMO Systems for Military Communications (2006)

Since the seminal work of Foschini, Gans and Teletar, the research community has generated a large body of work dealing with various aspects and benefits of MIMO for wireless data communications in civilian and commercial systems. Here we focus on the use of MIMO for military communication. In particular the effectiveness of MIMO for: (a) communications under very high mobility such as UAV based communication and, (b) the use of multi antenna techniques for covert (LPD) communications. Our results show the ability to operate at speeds of up to 200 mph, and a 17 dB reduction in the required TX power for covert, LPD communications, in addition to an interference/jammer mitigation technique based on MIMO eigen beam-nulling.
Columbia Suicide Severity Rating Scale (C-SSRS): Development and Uses (2010)

Brain-derived neurotrophic factor (BDNF) is a preferred ligand for a member of the tropomyosin-related receptor family, trkB. Activation of trkB is implicated in various activity-independent as well as activity-dependent growth processes in many developing and mature neural systems. In the subcortical visual system, where electrical activity has been implicated in normal development, both differential survival, as well as remodeling of axonal arbors, have been suggested to contribute to eye-specific segregation of retinal ganglion cell inputs. Here, we tested whether BDNF is required for eye-specific segregation of visual inputs to the lateral geniculate nucleus and the superior colliculus, and two other major subcortical target fields in mice. We report that eye-specific patterning is normal in two mutants that lack BDNF expression during the segregation period: a germ-line knockout for BDNF, and a conditional mutant in which BDNF expression is absent or greatly reduced in the central nervous system. We conclude that the availability of BDNF is not necessary for eye-specific segregation in subcortical visual nuclei.
Visualization and Quantification of Electrochemical H2 Bubble Nucleation at Pt, Au, and MoS2 Substrates (2020)

Electrolytic gas evolution is a significant phenomenon in many electrochemical technologies from water splitting, chloralkali process to fuel cells. Although it is known that gas evolution may substantially affect the ohmic resistance and mass transfer, studies focusing on the electrochemistry of individual bubbles are critical but also challenging. Here, we report an approach using scanning electrochemical cell microscopy (SECCM) with a single channel pipet to quantitatively study individual gas bubble nucleation on different electrode substrates, including conventional polycrystalline Pt and Au films, as well as the most interesting two-dimensional semiconductor MoS<sub>2</sub>. Due to the confinement effect of the pipet, well-defined peak-shaped voltammetric features associated with single bubble nucleation and growth are consistently observed. From stochastic bubble nucleation measurement and finite element simulation, the surface H<sub>2</sub> concentration corresponding to bubble nucleation is estimated to be ∼218, 137, and 157 mM, with critical nuclei contact angles of ∼156°, ∼161°, and ∼160° at polycrystalline Pt, Au, and MoS<sub>2</sub> substrates, respectively. We further demonstrated the surface faceting at polycrystalline Pt is not specifically correlated with the bubble nucleation behavior.
Olaparib in HR-deficient (HRD), metastatic triple-negative breast cancer (TNBC) and relapsed ovarian cancer (ROC) without germline mutations in BRCA1 or BRCA2: Phase 2 EMBRACE trial. (2023)

e15079 Background: Homologous recombination deficiency (HRD) caused by germline BRCA1/2 mutations (gBRCAm) sensitize high grade serous ovarian cancers (HGSOC) and TNBC to PARP inhibitors (PARPi) such as olaparib. Loss of function of BRCA1 or RAD51C, due to promoter methylation or mutation of non-BRCA HR genes may also confer sensitivity to PARPi. This investigator-initiated, proof-of-concept trial evaluated olaparib in platinum(Pt)-sensitive, relapsed HGSOC and metastatic TNBC, with HRD due to mechanisms other than gBRCAm. EMBRACE is the first trial evaluating PARPi in loss of function of BRCA1/ RAD51C by promoter methylation. Methods: Single-arm, phase 2 trial of olaparib 300 mg orally twice daily in adults with metastatic TNBC or Pt-sensitive relapsed HGSOC and HRD due to mechanisms other than gBRCAm. 1 line of prior Pt-chemotherapy was allowed (HGSOC); additional lines of non-Pt therapy were allowed (TNBC). Tumor BRCA1/RAD51C promoter methylation was determined by methylation-sensitive high-resolution melting PCR and next generation sequencing (NGS, Pillar Biosciences BRCA1 &amp; RAD51C Methylation test, high methylation threshold 70%). Unmethylated cases underwent NGS HR gene mutation testing (Pillar Biosciences HRD test, paired tumor/normal). The primary outcome was objective tumor response rate (OTRR) at 6 months(m). Secondary objectives: progression-free survival (PFS), OTRR according to HR gene mutation type, safety. Tertiary: associations between biomarkers and clinical outcomes. Results: 22 participants (15 HGSOC, 7 TNBC) enrolled from 208 screened (Sep 2018 - Mar 2022). Methylation was detected in 8/15 HGSOC (all BRCA1) and 5/7 TNBC (4 BRCA1, 1 RAD51C). Both cohorts included mutations in gBRIP1 (1), gPALB2 (1), gRAD51C (3), sBRCA1 (2), with 1 COSMIC mutational signature 3, and 1 positive HRD score in HGSOC. OTRR at 6m was 40% in HGSOC (6/15: 5 partial, 1 complete), and 0% in TNBC (0/7). OTRR was 38% (3/8) in methylated tumors vs 43% (4/7) with other HRD. Stable disease at 6m was 47% (7) in HGSOC and 43% (3) in TNBC durations were 7m in HGSOC and 3m in TNBC. PFS was 53% at 6m and 25% at 12m in HGSOC, vs 17% at 6m and NE at 12m in TNBC. TNBC 2-3 prior lines of therapy. Conclusions: Olaparib demonstrated clinically relevant activity in HGSOC without gBRCAm. Objective responses were seen in HGSOC with methylated BRCA1. Olaparib had limited activity in heavily pre-treated TNBC. Further research is needed into the effects of non-Pt chemotherapy on methylation of BRCA1/RAD51C to improve selection of HGSOC and TNBC for PARPi. (ANZCTRN12617000855325) Acknowledgements: Funding from Cancer Australia and the NBCF(PS-15-048), provision of study drug plus an untied educational grant from AstraZeneca and its group of companies. EMBRACE was led by the NHMRC CTC, University of Sydney in collaboration with ANZGOG, BCT-ANZ, and GCCTI. Clinical trial information: ACTRN12617000855325 .
Fluids in ARDS (2014)

Lung edema is likely the single pathogenic factor more relevant for ARDS severity and outcome. Fluid overload must be avoided. Several monitoring techniques are available to reach this target. No specific studies are available to recommend a given fluid composition in ARDS. In our opinion, the general recommendations for fluid composition suggested for severe sepsis and septic shock should be applied to ARDS that may be considered an organ-confined sepsis.
A secreted WNT-ligand-binding domain of FZD5 generated by a frameshift mutation causes autosomal dominant coloboma (2016)

Ocular coloboma is a common eye malformation resulting from incomplete fusion of the optic fissure during development. Coloboma is often associated with microphthalmia and/or contralateral anophthalmia. Coloboma shows extensive locus heterogeneity associated with causative mutations identified in genes encoding developmental transcription factors or components of signaling pathways. We report an ultra-rare, heterozygous frameshift mutation in FZD5 (p.Ala219Glufs*49) that was identified independently in two branches of a large family with autosomal dominant non-syndromic coloboma. FZD5 has a single-coding exon and consequently a transcript with this frameshift variant is not a canonical substrate for nonsense-mediated decay. FZD5 encodes a transmembrane receptor with a conserved extracellular cysteine rich domain for ligand binding. The frameshift mutation results in the production of a truncated protein, which retains the Wingless-type MMTV integration site family member-ligand-binding domain, but lacks the transmembrane domain. The truncated protein was secreted from cells, and behaved as a dominant-negative FZD5 receptor, antagonizing both canonical and non-canonical WNT signaling. Expression of the resultant mutant protein caused coloboma and microphthalmia in zebrafish, and disruption of the apical junction of the retinal neural epithelium in mouse, mimicking the phenotype of Fz5/Fz8 compound conditional knockout mutants. Our studies have revealed a conserved role of Wnt-Frizzled (FZD) signaling in ocular development and directly implicate WNT-FZD signaling both in normal closure of the human optic fissure and pathogenesis of coloboma.
Modelling and simulation of electronic and optical responses of quantum well infrared photodetectors (QWIPs) (2006)

A first principles theory of electronic transport in quantum well infrared photodetectors (QWIPs) is presented. The model is based on the cascade scattering rate equations approach and uses the translation symmetry to reduce the computational cost of the problem. The model delivers a non-equilibrium electron distribution in both dark conditions and under illumination. The model was tested by simulating a non-conventional broadband InGaAs/AlGaAs QWIP and good agreement with experimental data available in the literature was achieved. The model can be applied to any QWIP structure and can be used for extending the range of materials employed.
Identification of Oil/Gas and water zones in geological logging with Support-vector Machine (2012)

Support Vector Machines (SVM) is systematic and properly motivated by Statistical Learning Theory (SLT). Training involves separating the classes with a surface that maximizes the margin between them. An interesting property of this approach is that it is an approximate implementation of Structural Risk Minimization (SRM) induction principle, therefore, SVM is more generalized performance and accurate as compared to artificial neural network which embodies the Embodies Risk Minimization (ERM) principle. The theory and method of Support Vector Machines based the Statistical Learning Theory and proposed a pattern recognition method based Support Vector Machine to determine oil, gas and water zones in geological logging are studied. The outline of the method is as follows: First, the basic parameters of the gasometry logging and geochemistry logging, and induced some significant parameters, such as hydrocarbon moistness index, pyrolysis hydrocarbon equilibrium index, gasometry hydrocarbon equilibrium index ,etc. are researched, which can help to distinguish the feature of reservoir; then the Support Vector Machine to study the relationship of those parameters is used, and the recognition mode and develop its program to determine of oil, gas and water zones are set up. Application and analysis of the experimental results in Xinjiang oilfield proved that SVM can achieve greater accuracy than the BP neural network does. It proved that identification of oil/gas and water zones in geological logging with SVM is reliable, adaptable, precise and easy to operate.
Study of geometry footprints origin from the physical modeling data (2011)

Acquisition footprint is a new concept of seismic noise, which appears in 90s of last century when seismic exploration has carried out in complex area. It was called “Acquisition artifacts” firstly (Gulunay, 1994). Its impacts are found in marine streamer survey and complex surface survey on land. Marine plume cable and surface obstacles will make spatial sampling of receiver irregular, which causes uneven properties distribution among underground panels. When data is applied 3D DMO or 3D pre‐stack migration, this impact will be enhanced. This has been thought of the reason for acquisition footprint. However, with improving of seismic imaging resolution in the lithologicalreservoirs and subtle reservoirs, people find that regular 3D geometry and spatial sampling will produce acquisition footprints also, which have bad influence on the high‐precision imaging quality of target zone, so this problem has been a focus of 3D seismic exploration. Acquisition footprints include geometry acquisition footprints and non‐geometry acquisition footprints. Most of the latter are irregular, caused by the equipment, complex surface, weather etc., which have been considered by the routine processing. Now attentions are on the geometry acquisition, and because it is relative with geometry, its rules can be cognized. During last few years of 20th century, many papers about this problem have appeared and can be divided into two parts. One is theory analysis, using numerical simulation and physical modeling simulation to study the feature and origin of footprints and optimize geometry design. Another part is application, whose aim is attenuation and even removal of acquisition footprints to improve imaging quality. There are not many good results in numerical analysis because of its large computation. If we apply 3D wave equation with field design 3D geometry on the layered models to analyze acquisition footprints, computer skill cannot meet the capacity now. To this point, physical modeling study shows its advantages. In recent years, CNPC Key Laboratory of Geophysical Exploration where the author is has carried out some 3D seismic physical modeling simulation experiments with different 3D geometry. This paper chooses 2 physical models with three kinds of geometries to analyze footprints features. On the basis of Xiong's results, the author defines two new concepts: static acquisition footprints and dynamic acquisition footprints. And then shows their features and origin separately.