gebhart/patrepeval huggingface dataset:
Different Follicle-Stimulating Hormone Exposure Regimens During Antral Follicle Growth Alter Gene Expression in the Cumulus-Oocyte Complex in Mice1 (2010)

Follicle-stimulating hormone (FSH) and oocyte-secreted factors influence granulosa cell differentiation and follicle development. Whereas FSH stimulates the expression of mural cell transcripts, oocyte-secreted factors regulate specific cumulus cell genes and suppress the appearance of mural cell transcripts. This study addresses the extent to which clinically relevant changes in FSH doses applied during antral follicle development in vitro could alter the expression of oocyte and cumulus cell transcripts. A 12-day culture system in which mouse ovarian preantral follicles can grow to preovulatory follicles was used. The following three FSH regimens were considered: 1) continuous exposure to an FSH level of 10 mIU/ml (control), 2) decreasing concentrations of FSH (low FSH), and 3) an FSH level of 25 mIU/ml (high FSH) as soon as the antrum is formed. Transcripts in oocytes (Gdf9, Bmp15, and Fgf8) and in cumulus cells (Amh, Lhcgr, Ar, and Pfkp) were quantified by real-time PCR. Under high FSH, the three oocyte transcripts were upregulated, while in cumulus cells a shutdown of the Amh signal and substantial increases in Lhcgr and Ar expression were measured. In contrast, low FSH tended to reduce Lhcgr to levels comparable to those in vivo. Levels of Pfkp were not affected by FSH doses. These results demonstrate that a 2.5-fold increase in FSH changes both oocyte and cumulus cell transcript levels. Conversely, a decrease in FSH does not affect transcript levels but seems to limit inappropriate Lhcgr expression. Modulating FSH within physiological ranges during the antral phase of culture alters cumulus cell differentiation.
3D Localization of ultracold atoms in a laser speckle (2012)

Oral
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma (2021)

Abstract Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand how the tumor microenvironment (TME) changes with transition to IBC, we used Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and a 37-plex antibody staining panel to analyze 140 clinically annotated surgical resections covering the full spectrum of breast cancer progression. We compared normal, DCIS, and IBC tissues using machine learning tools for multiplexed cell segmentation, pixel-based clustering, and object morphometrics. Transition from DCIS to IBC was found to occur along a trajectory marked by coordinated shifts in location and function of myoepithelium, fibroblasts, and infiltrating immune cells in the surrounding stroma. Taken together, this comprehensive study within the HTAN Breast PreCancer Atlas offers insight into the etiologies of DCIS, its transition to IBC, and emphasizes the importance of the TME stroma in promoting these processes.
Supplementary Figure 1 from Human T&lt;sub&gt;H&lt;/sub&gt;17 Immune Cells Specific for the Tumor Antigen MAGE-A3 Convert to IFN-γ–Secreting Cells as They Differentiate into Effector T Cells &lt;i&gt;In Vivo&lt;/i&gt; (2023)

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Heterogeneity within and across Pediatric Pulmonary Infections: From Bipartite Networks to At-Risk Subphenotypes. (2014)

Although influenza (flu) and respiratory syncytial virus (RSV) infections are extremely common in children under two years and resolve naturally, a subset develop severe disease resulting in hospitalization despite having no identifiable clinical risk factors. However, little is known about inherent host-specific genetic and immune mechanisms in this at-risk subpopulation. We therefore conducted a secondary analysis of statistically significant, differentially-expressed genes from a whole genome-wide case-control study of children less than two years of age hospitalized with flu or RSV, through the use of bipartite networks. The analysis revealed three clusters of cases common to both types of infection: core cases with high expression of genes in the network core implicated in hyperimmune responsiveness; periphery cases with lower expression of the same set of genes indicating medium-responsiveness; and control-like cases with a gene signature resembling that of the controls, indicating normal-responsiveness. These results provide testable hypotheses for at-risk subphenotypes and their respective pathophysiologies in both types of infections. We conclude by discussing alternate hypotheses for the results, and insights about how bipartite networks of gene expression across multiple phenotypes can help to identify complex patterns related to subphenotypes, with the translational goal of identifying targeted therapeutics.
Effect of diffusion on platinum coatings deposited on the surface of nickel based superalloy by the electroplating process (2010)

Purpose: In this paper the effect of diffusion on platinum coatings deposited on the surface of nickel based superalloy was evaluated. Design/methodology/approach: The platinum coatings with thickness of 3 mm and 7 mm were deposited by electroplating process on Inconel 713 LC Ni-base superalloy. The heat treatment of electroplating coatings at the temperature 1050 °C during 2h under argon atmosphere was performed. The microstructure investigations of the heat treated coatings were conducted by the use of optical microscope (Nikon Epiphot 300) and a scanning electron microscope (Hitachi S-3400N) equipped with an X-radiation detector EDS (VOYAGER of NORAN INSTRUMENTS). The phase composition was identified by X-ray (ARL X’TRAX) diffractometer. The surface roughness parameter - Ra was evaluated by Perthometer S2 MAHR equipment. Findings: The microstructure of platinum electroplating coating with thickness of 3 µm after diffusion treatment consists of two phases: γ-Ni and (Al0.25Pt0.75)Ni3. The increase of platinum thickness from 3 µm to 7 µm does not influence the phase composition of heat treated coatings. Heat treatment of platinum electroplating coatings causes the increase of surface roughness parameter as a result of unequal mass flow of platinum and nickel. Research limitations/implications: The results will be used in the future investigations to explain the mechanism of reaction of platinum as a modifier in aluminide coatings. Practical implications: The platinum electroplating coatings after diffusion treatment and aluminizing process are widely used as coatings for turbine blades of aircraft engines. Originality/value: The paper includes the results of microstructure and surface roughness investigations of platinum electroplating coatings with 3 mm and 7 µm thickness after diffusion treatment.
SbcCD-Mediated Processing of Covalent Gyrase-DNA Complex in Escherichia coli (2013)

Quinolones trap the covalent gyrase-DNA complex in Escherichia coli, leading to cell death. Processing activities for trapped covalent complex have not been characterized. A mutant strain lacking SbcCD nuclease activity was examined for both accumulation of gyrase-DNA complex and viability after quinolone treatment. Higher complex levels were found in ΔsbcCD cells than in wild-type cells after incubation with nalidixic acid and ciprofloxacin. However, SbcCD activity protected cells against the bactericidal action of nalidixic acid but not ciprofloxacin.
S/O-nanodispersion electrospun fiber mesh effective for sustained release of healthy plasmid DNA with the structural and functional integrity (2013)

Localized and sustained delivery of the therapeutic genes using a solid carrier matrix is a potential approach to develop highly curative treatments. Electrospun nanofiber mesh of biodegradable polymer has been applied extensively as a carrier for localized and sustained delivery of drugs, proteins, and DNA, but it remains difficult to release sufficient amounts of DNA while maintaining structural and functional integrity. To realize the stable sustained release of the healthy plasmid DNA (pDNA) from electrospun fiber mesh, a novel method was examined for loading pDNA into the fibers based on solid-in-oil (S/O) nanodispersion of pDNA in organic solvent for electrospinning polymer solution: S/O nanodispersion electrospinning. A prepared pDNA-loaded fiber mesh made of biodegradable polymer showed sustained release of pDNA without burst release. From luciferase activity-based in vitro transcription-translation assay, pDNA released from meshes of the S/O nanodispersion retained about 60% luciferase activity of control pDNA, whereas pDNA released from the meshes of simple mixing showed only about 5% activity, indicating that S/O nanodispersion electrospinning is effective for loading pDNA into electrospun fiber meshes while maintaining their healthy functions. Effectiveness of S/O nanodispersion electrospinning was verified for fabricating a sustained release carrier matrix for high molecular weight bioactives, including therapeutic genes.
A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages (2022)

Summary High-throughput RNA sequencing offers unprecedented opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered &gt;2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology.
Wave refocusing for linear diffractor using the time‐reversal principle (2019)

ABSTRACT One of the problems encountered in a variety of near‐surface investigations is detecting and mapping localized heterogeneities. The heterogeneities may be classified under two kinds of objects: (1) a point diffractor that can be considered as an approximation of a small quasi‐isometric, such as small karstic cavities and caves; (2) a linear diffractor roughly approximating an elongated object, such as a tube or fault plane. The point and linear diffractors generate two types of seismic diffraction: tip and edge waves, respectively. During the last few decades, different methods were proposed by many researchers for detecting these heterogeneities utilizing seismic waves diffracted by them. An alternative method for detecting point diffractors using a time‐reversal principle combined with focusing analysis is proposed in this study: we present an extension of the time‐reversal method for linear diffractors. It consists of a coherent summation of seismic energy along edge‐diffraction traveltimes. Real data examples show the feasibility and efficiency of the proposed method.
PDLIM4, An Actin Binding Protein, Suppresses Prostate Cancer Cell Growth (2009)

We investigated the molecular function of PDLIM4 in prostate cancer cells. PDLIM4 mRNA and protein-expression levels were reduced in LNCaP, LAPC4, DU145, CWR22, and PC3 prostate cancer cells. The re-expression of PDLIM4 in prostate cancer cells has significantly reduced the cell growth and clonogenicity with G1 phase of cell-cycle arrest. We have shown the direct interaction of PDLIM4 with F-actin. Restoration of PDLIM4 expression resulted in reduction of tumor growth in xenografts. These results suggest that PDLIM4 may function as a tumor suppressor, involved in the control of cell proliferation by associating with actin in prostate cancer cells.
In-Situ Measurement of Power Loss for Crystalline Silicon Modules Undergoing Thermal Cycling and Mechanical Loading Stress Testing (2020)

An in-situ method is proposed for monitoring and estimating the power degradation of mc-Si photovoltaic (PV) modules undergoing thermo-mechanical degradation tests that primarily manifest through cell cracking, such as mechanical load tests, thermal cycling and humidity freeze tests. The method is based on in-situ measurement of the module’s dark current-voltage (I-V) characteristic curve during the stress test, as well as initial and final module flash testing on a Sun simulator. The method uses superposition of the dark I-V curve with final flash test module short-circuit current to account for shunt and junction recombination losses, as well as series resistance estimation from the in-situ measured dark I-Vs and final flash test measurements. The method is developed based on mc-Si standard modules undergoing several stages of thermo-mechanical stress testing and degradation, for which we investigate the impact of the degradation on the modules light I-V curve parameters, and equivalent solar cell model parameters. Experimental validation of the method on the modules tested shows good agreement between the in-situ estimated power degradation and the flash test measured power loss of the modules, of up to 4.31 % error (RMSE), as the modules experience primarily junction defect recombination and increased series resistance losses. However, the application of the method will be limited for modules experiencing extensive photo-current degradation or delamination, which are not well reflected in the dark I-V characteristic of the PV module.
Benefit of a Sharp Computed Tomography Angiography Reconstruction Kernel for Improved Characterization of Intracranial Aneurysms (2013)

H60f sharp CTA kernel reconstruction provides more accurate anatomic characterization of cerebral aneurysms than the H20f smooth kernel at the expense of less visually pleasing reconstructions. Because it does not require additional contrast, radiation, or imaging hardware and is more similar to 3DRA, it may aid in selecting the appropriate treatment strategy before to evaluation by catheter-based angiography.
A hybrid VBR/ABR service for scalable MPEG2 video networking: a simulation-based analysis (2002)

The available bit rate (ABR) will be one of the primary available ATM service for carrying data. Since it is based on the use of excess bandwidth in the network, it is expected to have a lower usage cost. Although, it is intended for non-real time applications, the inclusion of a minimum cell rate (MCR) makes it an attractive and economical candidate for the transmission of delay tolerant video applications. Therefore, we evaluate the effectiveness of a hybrid ATM service, composed of a dual VBR/ABR connection, for the transport of a 2-layer MPEG2 encoded application. We compare the ABR binary feedback and explicit rate mechanisms in the transmission of an enhancement video sublayer for various data partitioning configurations. To carry out the comparison, we consider the variations of the switches buffer occupancy, the end-to-end cell transfer delay (CTD), and the 2-point cell delay variation (CDV). We show that for one-way video applications, the mean end-to-end delay is below the recommended 1 second but at the cost of a large buffer at the destination due to excessive jitter.
Planternes produktive potentiale (2014)

Den næste industrielle revolution vil lede til biologisk baseret produktion af alt fra eksempelvis kræftmedicin til flybrændstof.
Spin polarization of 23Mg in 24Mg+Au, Cu, and Al collisions at 91 A MeV (1995)

Spin polarization of beta‐emitting fragment 23Mg(Iπ=3/2+, T1/2=11.3 s) produced through the projectile fragmentation process in 24Mg+Au, Cu, and Al collisions has been observed at 91 AMeV. General trend in the observed momentum dependence of polarization is reproduced well qualitatively by a simple fragmentation model based on the participant‐spectator picture, for heavy and light targets. However the polarization behavior differs from this model in terms of zero crossing momentum, which become prominent in the case of Cu target, where the polarization is not monotone function of the fragment momentum.
Corrosion of Titanium Matrix Composites (2002)

The corrosion behavior of unalloyed Ti and titanium matrix composites containing up to 20 vol% of TiC or TiB{sub 2} was determined in deaerated 2 wt% HCl at 50, 70, and 90 degrees C. Corrosion rates were calculated from corrosion currents determined by extrapolation of the tafel slopes. All curves exhibited active-passive behavior but no transpassive region. Corrosion rates for Ti + TiC composites were similar to those for unalloyed Ti except at 90 degrees C where the composites were slightly higher. Corrosion rates for Ti + TiB{sub 2} composites were generally higher than those for unalloyed Ti and increased with higher concentrations of TiB{sub 2}. XRD and SEM-EDS analyses showed that the TiC reinforcement did not react with the Ti matrix during fabrication while the TiB{sub 2} reacted to form a TiB phase.
A scalable algorithmic framework for row-based power-gating (2008)

Leakage power is a serious concern in nanometer CMOS technologies. In this paper we focus on leakage reduction through automatic insertion of sleep transistors for power gating in standard cell based designs. In particular, we propose clustering algorithms for row-based power-gating methodology which is based on using rows of the layout as the granularity for clustering. Our clustering methodology does timing and area constraint driven power-gating in contrast to only timing driven power-gating as proposed in the previous works. We present two distinct clustering algorithms with different accuracy-efficiency trade-off. An optimal one, which exploits a 0--1 or Binary Integer Programming approach, and a heuristic one, which resorts to an implicit enumeration of the layout rows.
Power-efficient time-to-digital converter for all-digital frequency locked loops (2015)

An 8-bit time-to-digital converter (TDC) for all-digital frequency-locked loops is presented. The selected architecture uses a Vernier delay line where the commonly used D flip-flops are replaced with a single enable transistor in the delay elements. This architecture allows for an area efficient and power efficient implementation. The dynamic range of the TDC is extended by using a 6-bit gray counter. A prototype chip has been implemented in a 65 nm CMOS process with an active core area of 75μm × 120μm. The time resolution is 5.7 ps with a power consumption of 1.85 mW measured at 50 MHz sampling frequency.
Fasting induces anti-Warburg effect that increases respiration but reduces ATP-synthesis to promote apoptosis in colon cancer models (2015)

Tumor chemoresistance is associated with high aerobic glycolysis rates and reduced oxidative phosphorylation, a phenomenon called "Warburg effect" whose reversal could impair the ability of a wide range of cancer cells to survive in the presence or absence of chemotherapy. In previous studies, Short-term-starvation (STS) was shown to protect normal cells and organs but to sensitize different cancer cell types to chemotherapy but the mechanisms responsible for these effects are poorly understood. We tested the cytotoxicity of Oxaliplatin (OXP) combined with a 48hour STS on the progression of CT26 colorectal tumors. STS potentiated the effects of OXP on the suppression of colon carcinoma growth and glucose uptake in both in vitro and in vivo models. In CT26 cells, STS down-regulated aerobic glycolysis, and glutaminolysis, while increasing oxidative phosphorylation. The STS-dependent increase in both Complex I and Complex II-dependent O(2) consumption was associated with increased oxidative stress and reduced ATP synthesis. Chemotherapy caused additional toxicity, which was associated with increased succinate/Complex II-dependent O(2) consumption, elevated oxidative stress and apoptosis .These findings indicate that the glucose and amino acid deficiency conditions imposed by STS promote an anti-Warburg effect characterized by increased oxygen consumption but failure to generate ATP, resulting in oxidative damage and apoptosis.
Rhodium-Catalyzed Carbonylation of Methyl Acetate (1992)

In principle, the rhodium-catalyzed carbonylation of methyl acetate involves the types of transformations found in the conversion of methanol to acetic acid, namely the activation of a normally unreactive methyl group, insertion of carbon monoxide, and recombination with the initial leaving group. However, several significant differences become apparent upon switching from the well-documented aqueous methanol carbonylation to the anhydrous methyl acetate carbonylation to acetic anhydride. A mechanism based primarily upon high-pressure kinetic and infrared data is proposed. The operational and mechanistic similarities and differences involved in the carbonylation of methanol to acetic acid and the carbonylation of methyl acetate to acetic anhydride will be discussed, as well as the historical development of the process.
OV$^{2}$SLAM: A Fully Online and Versatile Visual SLAM for Real-Time Applications (2021)

Many applications of Visual SLAM, such as augmented reality, virtual reality, robotics or autonomous driving, require versatile, robust and precise solutions, most often with real-time capability. In this work, we describe OV <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> SLAM, a fully online algorithm, handling both monocular and stereo camera setups, various map scales and frame-rates ranging from a few Hertz up to several hundreds. It combines numerous recent contributions in visual localization within an efficient multi-threaded architecture. Extensive comparisons with competing algorithms shows the state-of-the-art accuracy and real-time performance of the resulting algorithm. For the benefit of the community, we release the source code: https://github.com/ov2slam/ov2slam.
Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of <i>Plasmodium vivax</i> from Unprocessed Clinical Samples (2017)

Malaria is a disease caused by Plasmodium parasites that caused 214 million symptomatic cases and 438,000 deaths in 2015. Plasmodium vivax is the most widely distributed species, causing the majority of malaria infections outside sub-Saharan Africa. Whole-genome sequencing (WGS) of Plasmodium parasites from clinical samples has revealed important insights into the epidemiology and mechanisms of drug resistance of malaria. However, WGS of P. vivax is challenging due to low parasite levels in humans and the lack of a routine system to culture the parasites. Selective whole-genome amplification (SWGA) preferentially amplifies the genomes of pathogens from mixtures of target and host gDNA. Here, we demonstrate that SWGA is a simple, robust method that can be used to enrich P. vivax genomic DNA (gDNA) from unprocessed human blood samples and dried blood spots for cost-effective, high-quality WGS.
Severity Index for Estimating the Impact of Wind Generation on System Vulnerability (2007)

This paper proposes a severity index for estimating the impact of penetration of wind energy on the vulnerability of a power system. This index is the risk of not meeting the load and is in fact the risk of failure of the probability distributions of the system load and the system generation including the wind penetration. This probabilistic approach is appropriate for a system with large wind generation installation due to the random nature of the wind generation output. The severity index is proposed to recognize the possible existence of an area of vulnerability at the point of common coupling (PCC). This approach does not preclude applying this methodology to a specific PCC bus in order to verify the impact on the security at each PCC bus in the planning stage and to alert the system operator of any possible shortfall of generation. A case study is provided to demonstrate the proposed approach.