gebhart/patrepeval huggingface dataset:
Investigation of Signals and Transcription Factors for The Generation of Female Germ-Like Cells. (2022)

<strong>Objective:</strong> Primordial germ cell (PGCs) lines are a source of a highly specialized type of cells, characteristically oocytes,<br />during female germline development in vivo. The oocyte growth begins in the transition from the primary follicle. It is<br />associated with dynamic changes in gene expression, but the gene-regulating signals and transcription factors that control oocyte growth remain unknown. We aim to investigate the differentiation potential of mouse bone marrow mesenchymal stem cells (mMSCs) into female germ-like cells by testing several signals and transcription factors.<br /><strong>Materials and Methods:</strong> In this experimental study, mMSCs were extracted from mice femur bone using the flushing<br />technique. The cluster-differentiation (CD) of superficial mesenchymal markers was determined with flow cytometric analysis. We applied a set of transcription factors including retinoic acid (RA), titanium nanotubes (TNTs), and fibrin such as TNT-coated fibrin (F+TNT) formation and (RA+F+TNT) induction, and investigated the changes in gene, MVH/ DDX4, expression and functional screening using an in vitro mouse oocyte development condition. Germ cell markers expression, (MVH / DDX4), was analyzed with Immunocytochemistry staining, quantitative transcription-polymerase chain reaction (RT-qPCR) analysis, and Western blots.<br /><strong>Results:</strong> The expression of CD was confirmed by flow cytometry. The phase determination of the TNTs and F+TNT were confirmed using x-ray diffraction (XRD) and scanning electron microscope (SEM), respectively. Remarkably, applying these transcription factors quickly induced pluripotent stem cells into oocyte-like cells that were sufficient to generate female germlike cells, growth, and maturation from mMSCs differentiation. These transcription factors formed oocyte-like cells specification of stem cells, epigenetic reprogramming, or meiosis and indicate that oocyte meiosis initiation and oocyte growth are not separable from the previous epigenetic reprogramming in stem cells in vitro.<br /><strong>Conclusion:</strong> Results suggested several transcription factors may apply for arranging oocyte-like cell growth and supplies an alternative source of in vitro maturation (IVM).
Simultaneous reconstruction of activity and attenuation in Time-of-Flight PET (2011)

In positron emission tomography (PET) and single photon emission tomography (SPECT), attenuation correction is necessary for quantitative reconstruction of the tracer distribution. Previously, several attempts have been undertaken to estimate the attenuation coefficients from emission data only. These attempts had limited success, because the problem does not have a unique solution, and severe and persistent “cross-talk” between the estimated activity and attenuation distributions was observed. In this paper, we show that the availability of TOF-information eliminates the cross-talk problem by destroying symmetries in the associated Fisher information matrix. We propose a maximum-a-posteriori reconstruction algorithm for jointly estimating the attenuation and activity distributions from TOF-PET data. The performance of the algorithm is studied with 2D simulations, and further illustrated with phantom experiments and with a patient scan. The estimated attenuation image is robust to noise, and does not suffer from the cross-talk that was observed in non-TOF PET. However, some constraining is still mandatory, because the TOF-data determine the attenuation sinogram only up to a constant offset.
Cloud computing: developing contemporary computer science curriculum for a cloud-first future (2018)

Cloud Computing adoption has seen significant growth over the last five years. It offers a diverse range of scalable and redundant service deployment models, including Infrastructure-as-a-Service (IaaS), Platform-as-a-Service (PaaS), Software-as-a-Service (SaaS), and Containers-as-a-Service (CaaS). These models are applied to areas such as IoT, Cyber-Physical Systems, Social Media, Data Science, Media Streaming, Ecommerce, and Health Informatics. The growth in cloud presents challenges for companies to source cloud expertise to support their business, particularly small and medium-sized enterprises with limited resources. The UK Government recently published the Digital Skills Crisis report, identifying skill-set challenges facing industry, with a shortage in cloud skills negatively impacting business. While cloud technologies have evolved at significant pace, the development of Computer Science curriculum in the further and higher education sector has lagged behind. The challenges faced in the sector includes the training of educators, institutional gaps (software and hardware policies), regulatory constraints, and access to cloud platforms. By embedding fundamental cloud skills throughout the educator and student journey, both stakeholders will be better positioned to understand and practically apply the use of appropriate cloud services, and produce graduates to support the needs of industry. This working group has carried out work to: i) assess current cloud computing curricula in CS and similar programs, ii) document industry needs for in-demand cloud skills, iii) identify issues and gaps around cloud curriculum uptake, and iv) develop solutions to meet the skill demands on core Cloud Computing topics, technical skills exercises, and modules for integration with contemporary Computer Science curricula.
In vivo footprints between the murine c-myc P1 and P2 promoters. (1992)

Assuming that when transcription starts at the P2 promoter of the c-myc gene sites located immediately upstream from P2 are occupied whereas in the absence of initiation they are not, the polymerase chain reaction (PCR)-based method of Mueller & Wold [(1989). Science, 246, 780-786] was used to map in vivo footprints upstream from the P2 promoter in various mouse cell lines. In cultured Friend erythroleukemic cells induced to differentiate with dimethysulfoxide (DMSO), a clear protection corresponding to ME1a2 and E2F sites was observed, consistent with in vitro band-shift and footprint data. However, in cell lines in which the gene was either silent or truncated the footprints were no longer visible. Friend c-myc transcripts decreased to a barely detectable level after 3 h of DMSO treatment. Transcription, as measured by in vitro run-on, was turned off at the level of RNA polymerase elongation rather than initiation [Mechti N., Piechaczyk, M. Blanchard, J.-M., Marty, L., Bonnieu, A., Jeanteur, Ph. & Lebler, B. (1986). Nucleic Acids Res., 24, 9653-9666]. The state of occupancy of the sites did not vary from the first hours up to 9 days of DMSO treatment, suggesting that DNA occupancy per se cannot explain premature termination, which rather would involve a more complex phenomenon.
A New Magnesium Alloy System: TEXAS (2013)

This chapter contains sections titled: Introduction Experimental Procedure Results and Discussion Conclusions
A geometrically based model for line-of-sight multipath radio channels (2002)

This paper provides a geometrically based model for single bounce multipath components in line-of-sight (LOS) microcell radiowave propagation channels. The model characterizes the excess delay, direction-of-arrival, and received power of multipath components and is particular useful for microcell and PCS systems with low transmitter and receiver antenna heights. The model includes analytical expressions for the probability density functions for all critical channel parameters and is thus useful for analytical purposes. The model is also useful for simulating both wideband and narrowband systems and in particular the model has been used extensively in a study of code division multiple access (CDMA) cellular radio systems employing adaptive antennas and switched beam systems at the base station.
Microexplosion Recording in Spin-Coated Polymer Films Including ZnO Nanoparticles for Three-Dimensional Optical Memory (2004)

As a microexplosion recording material, we propose polymer films including ZnO nanoparticles (ZnO polyester composite) for write-once multilayered recording media. These media with the ZnO composite material can be fabricated by a spin-coating method and can be read at the violet wavelength of 0.405 µm. By the electromagnetic analysis of diffraction loss, we clarified the pit design and the optical performance for void formation recording. From the results of experiments performed using three kinds of mode-locked pulsed lasers (pulse widths of 150 fs, 16 ps and 6 ns), with a clear reflection microscope image of submicrometer pits, the microexplosion sensitivity was confirmed to be greatly improved by 14, 38 and 50 times, respectively.
How to test graphical user interfaces (2003)

An approach for automatically testing GUIs in the MATLAB environment has been proposed. We developed a software tool that tests GUIs by simulating the user through an action recorder. We proposed a heuristic test procedure: providing random input to GUI, but guiding the randomness with predefined weights assigned to the user controls. The weights change during the testing process, as the controls are activated. The errors are collected for later investigation.
TGFβ Signaling Activated by Cancer-Associated Fibroblasts Determines the Histological Signature of Lung Adenocarcinoma (2021)

Invasive lung adenocarcinoma (LADC) can be classified histologically as lepidic, acinar, papillary, micropapillary, or solid. Most LADC tumors manifest several of these histological subtypes, with heterogeneity being related to therapeutic resistance. We report here that in immunodeficient mice, human LADC cells form tumors with distinct histological features, MUC5AC-expressing solid-type or cytokeratin 7 (CK7)-expressing acinar-type tumors, depending on the site of development, and that a solid-to-acinar transition (SAT) could be induced by the tumor microenvironment. The TGFβ-Smad signaling pathway was activated in both tumor and stromal cells of acinar-type tumors. Immortalized cancer-associated fibroblasts (CAF) derived from acinar-type tumors induced SAT in 3D cocultures with LADC cells. Exogenous TGFβ1 or overexpression of an active form of TGFβ1 increased CK7 expression and reduced MUC5AC expression in LADC cells, and knockdown of <i>Tgfb1</i> mRNA in CAFs attenuated SAT induction. RNA-sequencing analysis suggested that angiogenesis and neutrophil recruitment are associated with SAT <i>in vivo</i>. Our data indicate that CAF-mediated paracrine TGFβ signaling induces remodeling of tumor tissue and determines the histological pattern of LADC, thereby contributing to tumor heterogeneity. SIGNIFICANCE: CAFs secrete TGFβ to induce a solid-to-acinar transition in lung cancer cells, demonstrating how the tumor microenvironment influences histological patterns and tumor heterogeneity in lung adenocarcinoma.
Changes in somatic cell nuclei inserted into growing and maturing amphibian oocytes (1968)

ABSTRACT When somatic cell nuclei are injected into enucleated unfertilized eggs they very soon cease RNA synthesis (Gurdon &amp; Brown, 1965; Gurdon. 1967a), and commence DNA synthesis (Graham, Arms &amp; Gurdon, 1966). By means of such experiments it has been shown (i) that components of living egg cytoplasm can substantially change the nature of nuclear activity, (ii) that nuclear activity is altered in such a way as to conform to that of the host egg cell, and (iii) that these effects are obtained with the nuclei of adult as well as embryonic cells. The experiments to be reported here were designed to find out whether the same generalizations apply to nuclei inserted into cells other than eggs, and whether they are true of changes in nuclear activity other than the repression of RNA synthesis and the induction of DNA synthesis. For this purpose growing and maturing amphibian oocytes have been used. Growing oocytes are characterized by the very active synthesis of RNA (Brown &amp; Littna, 1964), and by the absence of nuclear DNA synthesis whether [3H]thymidine is supplied intraperitoneally (Izawa, Allfrey &amp; Mirsky, 1963a), or is injected directly into living oocytes (Gurdon, 1967b). Maturing oocytes are in the process of completing meiosis and contain condensed chromosomes inactive in both RNA and DNA synthesis. If cytoplasmic components are of general importance in controlling nuclear activity, it would be predicted that nuclei inactive in RNA synthesis, or unaccustomed to division, should display these activities following insertion, respectively, into growing or maturing oocytes. The results reported here show that this expectation is realized, and permit some general conclusions to be drawn on the widespread importance of the cytoplasmic control of nuclear activity during cell differentiation.
On $$L_p$$-solvability of stochastic integro-differential equations (2020)

Abstract A class of (possibly) degenerate stochastic integro-differential equations of parabolic type is considered, which includes the Zakai equation in nonlinear filtering for jump diffusions. Existence and uniqueness of the solutions are established in Bessel potential spaces.
Vortex-induced vibration measurements of seal whiskers using digital holography (2014)

A new technique is developed and shown capable of providing accurate measurements of vortex-induced vibrations (VIV) at small scales. The motions of three different objects are able to be fully resolved using a combination of digital holography and compressive sensing. The smallest object has a representative diameter of 1.25 mm, and is that of a harbor seal whisker. This ability to accurately measure the vibrations of whiskers at the original scale opens the door to conducting detailed studies on how the whiskers may serve as specialized flow sensors. Preliminary results reported here align with those found using traditional VIV measurements on whisker models at larger scales.
Organic Geochemistry of Upper JurassicCretaceous Sediments from Site 511, Leg 71, Western South Atlantic (1983)

Cretaceous and Jurassic sediments 435 m thick were drilled at Site 511, in the basin province of the Falkland Plateau, during DSDP Leg 71.
DNA methyltransferase DNMT3A associates with viral proteins and impacts HSV‐1 infection (2015)

Viral infections can alter the cellular epigenetic landscape, through modulation of either DNA methylation profiles or chromatin remodeling enzymes and histone modifications. These changes can act to promote viral replication or host defense. Herpes simplex virus type 1 (HSV-1) is a prominent human pathogen, which relies on interactions with host factors for efficient replication and spread. Nevertheless, the knowledge regarding its modulation of epigenetic factors remains limited. Here, we used fluorescently-labeled viruses in conjunction with immunoaffinity purification and MS to study virus-virus and virus-host protein interactions during HSV-1 infection in primary human fibroblasts. We identified interactions among viral capsid and tegument proteins, detecting phosphorylation of the capsid protein VP26 at sites within its UL37-binding domain, and an acetylation within the major capsid protein VP5. Interestingly, we found a nuclear association between viral capsid proteins and the de novo DNA methyltransferase DNA (cytosine-5)-methyltransferase 3A (DNMT3A), which we confirmed by reciprocal isolations and microscopy. We show that drug-induced inhibition of DNA methyltransferase activity, as well as siRNA- and shRNA-mediated DNMT3A knockdowns trigger reductions in virus titers. Altogether, our results highlight a functional association of viral proteins with the mammalian DNA methyltransferase machinery, pointing to DNMT3A as a host factor required for effective HSV-1 infection.
Software prefetching for indirect memory accesses (2017)

Many modern data processing and HPC workloads are heavily memory-latency bound. A tempting proposition to solve this is software prefetching, where special non-blocking loads are used to bring data into the cache hierarchy just before being required. However, these are difficult to insert to effectively improve performance, and techniques for automatic insertion are currently limited. This paper develops a novel compiler pass to automatically generate software prefetches for indirect memory accesses, a special class of irregular memory accesses often seen in high-performance workloads. We evaluate this across a wide set of systems, all of which gain benefit from the technique. We then evaluate the extent to which good prefetch instructions are architecture dependent. Across a set of memory-bound benchmarks, our automated pass achieves average speedups of 1.3x and 1.1x for an Intel Haswell processor and an ARM Cortex-A57, both out-of-order cores, and performance improvements of 2.1x and 3.7x for the in-order ARM Cortex-A53 and Intel Xeon Phi.
Planar laser induced fluorescence imaging of solid propellant flames (1988)

We have applied the PLIF technique to solid propellant ignition and deflagration flames to obtain temporally and spatially resolved images of species and temperature profiles. A CO2 laser was used to supply the igniting pyrolysis flux. A Nd-YAG pumped tunable dye laser beam was expanded into a sheet to excite fluorescence from transient species in the flame and the emitted fluorescence was imaged with a gated intensified diode array camera. Selection of the delay time between CO2 and diagnostic laser pulses allowed the time dependence of ignition events to be measured. We have studied NO2, NO, CN, CH, C2, NH, H2CO, OH, and OH rotational temperature in this manner. For HMX combustion, NO2 and NO are found to be primary decomposition products that form a expanding plume until a spherical ignition kernel occurs in the gas phase, which consumes the NO2 and NO and produces CN, NH, and OH. This kernel rapidly forms into a thin flame sheet which establishes a steep temperature rise to equilibrium values. CH was absent in HMX combustion flames and H2CO was seen only as a decomposition product of the PEG binder of composite propellants. The imaging PLIF technique has been found to be extremely useful even in very hostile combustion environments such as highly aluminized composite solid propellant flames.
Guest Editorial Mini-Special Issue on International Quantum Cascade Lasers School and Workshop (IQCLSW 2016) (2017)

The papers in this special section were presented at the International Quantum Cascade Lasers School and Workshop (IQCLSW 2016). Quantum cascade lasers (QCLs) are unipolar optoelectronic devices that exploit optical transitions between engineered electronic subbands created in multiple coupled semiconductor quantum wells. The large number of nano metre thick semiconductor layers and the complexity of the overall structure, makes the QCL the most impressive demonstration of the capabilities offered by band structure engineering and state-of-the-art materials growth technologies.
Prognostic and therapeutic implications of measurable residual disease in acute myeloid leukemia (2021)

Quantification of measurable residual disease (MRD) provides critical prognostic information in acute myeloid leukemia (AML). A variety of platforms exist for MRD detection, varying in their sensitivity and applicability to individual patients. MRD detected by quantitative polymerase chain reaction, multiparameter flow cytometry, or next-generation sequencing has prognostic implications in various subsets of AML and at various times throughout treatment. While it is overwhelmingly evident that minute levels of remnant disease confer increased risk of relapse and shortened survival, the therapeutic implications of MRD remain less clear. The use of MRD as a guide to selecting the most optimal post-remission therapy, including hematopoietic stem cell transplant or maintenance therapy with hypomethylating agents, small molecule inhibitors, or immunotherapy is an area of active investigation. In addition, whether there are sufficient data to use MRD negativity as a surrogate endpoint in clinical trial development is controversial. In this review, we will critically examine the methods used to detect MRD, its role as a prognostic biomarker, MRD-directed therapeutics, and its potential role as a study endpoint.
Hybrid Self-Backhaul and Cache Assisted Millimeter Wave Two-Tier Heterogeneous Networks With MIMO Equipped Backhaul Access Points (2019)

This paper focuses on effective content delivering over the co-channel and full millimeter-wave (mm-Wave) heterogeneous networks (HetNets) by using hybrid self-backhaul and cache-assisted (HSBC-assisted) content delivering. Especially, the small base stations (SBSs) are equipped with a single antenna, a portion of which has the capacity-limited cache and the remaining of which has not to cache. The macro base stations (MBSs) are equipped with multiple antennas or even massive MIMO, which provide the wireless self-backhaul for the SBSs without cache. Instead of the oversimplified flat-top mm-Wave antenna pattern, a more actual and accurate one for the uniform linear array at MBSs is used. By modeling the locations of line-of-sight (LoS) and non-LoS base stations as independent Poisson point processes, this paper first presents the downlink content delivering model as well as the distributions of interferences. Then, to explore the impact of the specific MIMO self-backhaul on content delivering, a comprehensive investigation is conducted in terms of the coverage probability, achievable average area rate (AAR), average delay (AD), and energy effective (EE). The analytical and numerical results show that the utilization of multi-antenna MBSs not only improves the AAR and AD of self-backhaul transmission from MBS to SBS but also does the ones of cache and non-cache access links due to narrow beam and direction transmission decreasing interference. The results also show that in the proposed HSBC-assisted HetNets, under the scenario where the low-resolution antenna array is used and the cache capacity is large, the effect of hardware power consumption on the aggregate EE is negligible. This result shows a trade-off between AD and EE. With a projected EE, the joint utilization of cache and low-resolution antenna array allows more antennas equipped at MBSs so that the near-field propagation loss is compensated by the higher gain of directional antennas. Meanwhile, the results show that the achieved performance gain by the HSBC-assisted system over the traditional self-backhaul (TSB)-assisted greatly depends on the system parameters. With this observation, an adaptive TSB-HSBC-assisted system model is proposed. When the ratio factor of cache-assisted SBSs is less than the threshold, the sole TSB-assisted model is selected; otherwise, the HSBC-assisted model is used.