gebhart/patrepeval huggingface dataset:
Cooperativity between an Upstream TATA-like Sequence and a CAA Repeated Element Mediates E1A-dependent Negative Repression of the H-2K Class I Gene (1995)

In primary rodent cells transformed by the E1A region of the highly oncogenic adenovirus type 12, repression of transcription mediated by the far upstream TATA-like element was observed only in conjunction with either possible juxtaposition of a CAA repeated element in the presence of E1A and was dependent upon the relative arrangement of both the TATA-like and CAA repeated motifs in both homologous and heterologous promoter constructs. A gel shift competition study demonstrated that the TATA-binding protein (TBP) or a TBP-like protein can bind to both the upstream TATA-like sequence and the regular TATA box on the H-2Kb basal promoter. Moreover, employing immunoselection and cyclic amplification and selection of targets (CASTing) methods with nuclear extracts derived from Ad12-E1A transformants, we have identified a high affinity binding site in the H-2Kb class I promoter for E1A-associated DNA-binding proteins. The sequences of the binding sites were identified and were found to contain both the upstream TATA-like motif and the CAA repeated motifs. Our results suggest that the TATA-like sequence in the far upstream region of the H-2Kb gene is one of the elements that is required for Ad12-E1A-mediated negative repression.
Computational holographic camera with a dielectric metasurface diffuser (2019)

We experimentally demonstrate computational complex optical field imaging by a metasurface diffuser and the speckle-correlation scattering matrix method. Thus, we show that the metasurface diffuser can outperform conventional scattering media in context of computational imaging. © 2019 The Author(s)
Tailoring Collagen to Engineer the Cellular Microenvironment (2018)

Collagen is the most abundant protein in the extracellular matrix (ECM), and it can direct the behavior of the neighboring cells. By customizing properties of collagen, it is possible to control the cells that interact with it. Utilizing a bottom-up strategy, modular gene fragments are assembled and recombinantly processed to create collagen-mimetic variants that modulate proteolytic degradation, cell adhesion, and mechanical characteristics. The removal of the native MMP cleavage site results in MMP-1 resistant collagen. By introducing additional MMP-susceptible sequences, the degradation characteristics of collagen molecules are modified. Additional non-native functionality is also introduced into the collagen, including the IKVAV sequence, which has been implicated in neurite outgrowth. This mutation, which disrupts the Gly-X-Y tripeptide repeat of collagen, does not prevent the formation of triple-helical collagen. Non-native cysteines and the integrin binding sequence GFOGER are combined in the collagen, and encapsulation of normal human lung fibroblasts within collagen hydrogels are tested. Cells remain spherical, when encapsulated within hydrogels of collagen variants in which the native integrin binding sites are removed, but cell adhesion is restored with the introduction of non-native GFOGER binding sequences. This modular collagen system allows for the combination of multiple functionalities, and it enables the production of biomimetic scaffolds with customizable characteristics to modulate cellular microenvironments.
Colour by correlation: a simple, unifying approach to colour constancy (1999)

In this paper we consider the problem of colour constancy; how given an image of a scene under an unknown illuminant can we recover an estimate of that light? Rather than recovering a single estimate of the illuminant as many previous authors have done, in the first instance we recover a measure of the likelihood that each possible illuminant was the scene illuminant. We do this by correlating image colours with the colours that can occur under each of a set of possible lights. We then recover an estimate of the scene illuminant based on these likelihoods. Computation is expressed and performed in a generic correlation framework which we develop in this paper. We develop a new probabilistic instantiation of this framework which delivers very good colour constancy on synthetic and real images. We show that the proposed framework is rich enough to allow many existing algorithms to be expressed within it; e.g. the grey-world and gamut mapping algorithms. We explore too the relationship of these algorithms to other probabilistic and neural network approaches.
Lomb-Wech periodogram for non-uniform sampling (2005)

The Lomb-Scargle transform has been proposed for the direct evaluation, namely without interpolation, of non-uniformly sampled signals. In its current form, it is suitable only for single transform evaluation due to the implicit normalization. Enhancements of this transform are proposed to allow the evaluation of shorter transforms, combined with windows and averaging of overlapped records. This requires a de-normalization of the transform by a factor of 2(sigma)/sup 2//N, the use of equal time duration records, and multiplication by windows sampled at corresponding non-uniform time instances. This results in a Welch-like periodogram for non-uniform sampling.
Organic heterojunctions for direct solar fuel generation (2020)

Organic polymers have demonstrated promise as photocatalysts, but their photocatalytic efficiencies remain relatively low. Now, borrowing principles from organic photovoltaics, heterojunctions of polymer photocatalysts and small molecule acceptors have been shown to have excellent solar hydrogen production efficiencies. Organic polymers have demonstrated promise as photocatalysts, but their photocatalytic efficiencies remain relatively low. Now, borrowing principles from organic photovoltaics, heterojunctions of polymer photocatalysts and small molecule acceptors have been shown to have excellent solar hydrogen production efficiencies.
Abstract B231: Targeting Her2+ ductal breast cancer with PDL192, a novel humanized anti-TweakR monoclonal antibody (2009)

Abstract TWEAK receptor (TweakR), also known as Fn14, is a cell surface protein and member of the tumor necrosis factor receptor superfamily. TNFRSF family members are appealing therapeutic targets due to their expression and function in tumor cells. The goal of the current study was to examine the potential of TweakR as a therapeutic target in various subtypes of breast cancer by 1) determining expression of TweakR using immunohistochemistry (IHC) and 2) treating cells derived from breast cancer in vitro and in vivo with PDL192, a novel, humanized anti-TweakR mAb. Overexpression of TweakR protein in breast cancer was confirmed by IHC on formalin fixed paraffin embedded (FFPE) tissues. TweakR was elevated in infiltrating tumors when compared with normal adjacent tissues. 30 to 40% of various subtypes of invasive ductal breast cancer samples stained highly for TweakR; however, fewer than 5% of lobular breast cancer samples had high levels of TweakR. In addition, a strong positive correlation of TweakR and Her2 expression was observed, irrespective of ER status. More than 60% of Her2+ invasive ductal cancer exhibited elevated levels of TweakR. Strong TweakR expression was also observed in bone metastasis samples from primary breast cancer but rarely in benign tumors, such as DCIS. PDL192 inhibited the in vitro growth of various subtypes of TweakR-expressing breast cancer cell lines and this activity was augmented by crosslinking the mAb. In addition, PDL192 significantly inhibited the in vivo growth of a variant of the breast cancer xenograft model MDA-MB231 that exhibits metastatic potential. PDL192 administration exhibited a dose-dependent inhibition of primary tumor growth and lung metastasis and enhanced the anti-tumor activity of several chemotherapy agents currently used to treat breast cancer. These data provide the rationale to evaluate PDL192 as a potential therapy for the treatment of breast cancer. Currently, PDL192 is being tested in a phase I safety study for the treatment of patients with solid tumors. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B231.
Nucleosome Positioning on Episomal Human Papillomavirus DNA in Cultured Cells (2021)

Several human papillomaviruses (HPV) are associated with the development of cervical carcinoma. HPV DNA synthesis is increased during the differentiation of infected host keratinocytes as they migrate from the basal layer of the epithelium to the spinous layer, but the molecular mechanism is unclear. Nucleosome positioning affects various cellular processes such as DNA replication and repair by permitting the access of transcription factors to promoters to initiate transcription. In this study, nucleosome positioning on virus chromatin was investigated in normal immortalized keratinocytes (NIKS) stably transfected with HPV16 or HPV18 genomes to determine if there is an association with the viral life cycle. Micrococcal nuclease-treated DNA analyzed by Southern blotting using probes against HPV16 and HPV18 and quantified by nucleosome scanning analysis using real-time PCR revealed mononucleosomal-sized fragments of 140-200 base pairs that varied in their location within the viral genome according to whether the cells were undergoing proliferation or differentiation. Notably, changes in the regions around nucleotide 110 in proliferating and differentiating host cells were common to HPV16 and HPV18. Our findings suggest that changes in nucleosome positions on viral DNA during host cell differentiation is an important regulatory event in the viral life cycle.
Coverage enhancement for M2M communications using LTE (2014)

With the widespread deployment of LTE 4G systems and large number of connected devices due to the Internet of Things, M2M services using LTE is under consideration by many cellular operators. To provide ubiquitous network coverage for M2M services, 3GPP will introduce coverage enhancement feature in Rel-13. In this paper we analyze features which will extend the range of an LTE system by up to 15dB. Performance analysis at both link and system levels will also be provided. We'll show that 15 dB coverage enhancement is feasible. The impact of this feature to system capacity depends on the fraction of UEs requiring coverage enhancement and their respective coverage shortfall.
Assessment of corticospinal tract dysfunction and disease severity in amyotrophic lateral sclerosis (2016)

The upper motor neuron dysfunction in amyotrophic lateral sclerosis was quantified using triple stimulation and more focal transcranial magnetic stimulation techniques that were developed to reduce recording variability. These measurements were combined with clinical and neurophysiological data to develop a novel random forest based supervised machine learning prediction model. This model was capable of predicting cross-sectional ALS disease severity as measured by the ALSFRSr scale with 97% overall accuracy and 99% precision. The machine learning model developed in this research provides a new, unique and objective diagnostic method for quantifying disease severity and identifying subtle changes in disease progression in ALS.
DC and Transient Performance of 4H-SiC Double-Implant MOSFETs (2008)

SiC vertical MOSFETs were fabricated and characterized, achieving blocking voltages around 1 kV and specific on-resistances as low as R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SP,ON</sub> =8.3 mOmegamiddotcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . DC and transient characteristics are shown. Room and elevated temperature (up to 200degC) 600 V/5 A inductive switching performance of the SiC MOSFETs are shown with turn-on and turn-off transients of approximately 20-40 ns.
Synthetic cells with self-activating optogenetic proteins communicate with natural cells (2022)

Development of regulated cellular processes and signaling methods in synthetic cells is essential for their integration with living materials. Light is an attractive tool to achieve this, but the limited penetration depth into tissue of visible light restricts its usability for in-vivo applications. Here, we describe the design and implementation of bioluminescent intercellular and intracellular signaling mechanisms in synthetic cells, dismissing the need for an external light source. First, we engineer light generating SCs with an optimized lipid membrane and internal composition, to maximize luciferase expression levels and enable high-intensity emission. Next, we show these cells' capacity to trigger bioprocesses in natural cells by initiating asexual sporulation of dark-grown mycelial cells of the fungus Trichoderma atroviride. Finally, we demonstrate regulated transcription and membrane recruitment in synthetic cells using bioluminescent intracellular signaling with self-activating fusion proteins. These functionalities pave the way for deploying synthetic cells as embeddable microscale light sources that are capable of controlling engineered processes inside tissues.
Solving the Navier-Lame Equation in Cylindrical Coordinates Using the\n Buchwald Representation: Some Parametric Solutions with Applications (2017)

Using a separable Buchwald representation in cylindrical coordinates, we show\nhow under certain conditions the coupled equations of motion governing the\nBuchwald potentials can be decoupled and then solved using well-known\ntechniques from the theory of PDEs. Under these conditions, we then construct\nthree parametrized families of particular solutions to the Navier-Lame equation\nin cylindrical coordinates. In this paper, we specifically construct solutions\nhaving 2pi-periodic angular parts. These particular solutions can be directly\napplied to a fundamental set of linear elastic boundary value problems in\ncylindrical coordinates and are especially suited to problems involving one or\nmore physical parameters. As an illustrative example, we consider the problem\nof determining the response of a solid elastic cylinder subjected to a\ntime-harmonic surface pressure that varies sinusoidally along its axis, and we\ndemonstrate how the obtained parametric solutions can be used to efficiently\nconstruct an exact solution to this problem. We also briefly consider\napplications to some related forced-relaxation type problems.\n
Efficient Dynamic Searchable Encryption with Forward Privacy (2018)

Abstract Searchable symmetric encryption (SSE) enables a client to perform searches over its outsourced encrypted files while preserving privacy of the files and queries. Dynamic schemes, where files can be added or removed, leak more information than static schemes. For dynamic schemes, forward privacy requires that a newly added file cannot be linked to previous searches. We present a new dynamic SSE scheme that achieves forward privacy by replacing the keys revealed to the server on each search. Our scheme is efficient and parallelizable and outperforms the best previous schemes providing forward privacy, and achieves competitive performance with dynamic schemes without forward privacy. We provide a full security proof in the random oracle model. In our experiments on the Wikipedia archive of about four million pages, the server takes one second to perform a search with 100,000 results.
Influence of direct and indirect allorecognition pathways on CD4+CD25+regulatory T-cell function in transplantation (2007)

While both direct and indirect allorecognition are involved in allograft rejection, evidence to date suggests that tolerance is primarily dependent on indirect pathway-triggered CD4+CD25+ T cell-mediated immunoregulation. However, the precise influence of these two pathways on CD4+CD25+ T-cell function has not been addressed. In the current study, we have utilized an adoptive transfer model to assess selectively how the absence of either direct or indirect allorecognition affects CD4+CD25+ T-cell function. The effects of the loss of the direct pathway were assessed by transplanting skin grafts from minor histocompatibility mismatched B10.D2 (H-2d) donors onto Balb/c (H-2d) recipients, or by placing bone marrow chimeric DBA/2 (H-2d/H-2b) allografts onto C57BL/6 (H-2b) hosts. The requirement for indirect allorecognition was tested by grafting DBA/2 skin allografts onto either C57BL/6- or MHC-II-deficient C57BL/6 recipients. We report here that although CD4+CD25+ regulatory T cells can suppress both directly and indirectly generated alloresponses, immunoregulation is favored when indirect presentation is the sole mechanism of allorecognition. Hence, in the absence of indirect presentation, net CD4+CD25+ T cell-dependent immunoregulation is weak, and high ratios of CD4+CD25+ to CD4+CD25 T cells are required to ensure graft survival.
Modeling the Torque Requirement of a Blade Stirrer in Bulk Solids (2005)

Processing of solids is widely used in a variety of sectors, often requiring movement of the bulk material. The application of the particle-particle interaction model for a two blade stirrer geometry is presented. A qualitative model parameter study for the torque has been carried out and the theoretical data experimentally evaluated.
Direct Comb Vernier Spectroscopy for Fractional Isotopic Ratio Determinations (2021)

Accurate isotopic composition analysis of the greenhouse-gasses emitted in the atmosphere is an important step to mitigate global climate warnings. Optical frequency comb-based spectroscopic techniques have shown ideal performance to accomplish the simultaneous monitoring of the different isotope substituted species of such gases. The capabilities of one such technique, namely, direct comb Vernier spectroscopy, to determine the fractional isotopic ratio composition are discussed. This technique combines interferometric filtering of the comb source in a Fabry-Perot that contains the sample gas, with a high resolution dispersion spectrometer to resolve the spectral content of each interacting frequency inside of the Fabry-Perot. Following this methodology, simultaneous spectra of ro-vibrational transitions of 12C16O2 and 13C16O2 molecules are recorded and analyzed with an accurate fitting procedure. Fractional isotopic ratio 13C/12C at 3% of precision is measured for a sample of CO2 gas, showing the potentialities of the technique for all isotopic-related applications of this important pollutant.
Urinary Adenosine and Aminoimidazolecarboxamide Excretion in Methotrexate-Treated Patients With Psoriasis (1999)

Methotrexate treatment of patients with psoriasis inhibits AICA ribotide transformylase and adenosine metabolism. Since adenosine is a T-lymphocyte toxin, it may be partially responsible for the immunosuppressive effect.
Escherichia coli FolC Structure Reveals an Unexpected Dihydrofolate Binding Site Providing an Attractive Target for Anti-microbial Therapy (2005)

In some bacteria, such as Escherichia coli, the addition of L-glutamate to dihydropteroate (dihydrofolate synthetase activity) and the subsequent additions of L-glutamate to tetrahydrofolate (folylpolyglutamate synthetase (FPGS) activity) are catalyzed by the same enzyme, FolC. The crystal structure of E. coli FolC is described in this paper. It showed strong similarities to that of the FPGS enzyme of Lactobacillus casei within the ATP binding site and the catalytic site, as do all other members of the Mur synthethase superfamily. FolC structure revealed an unexpected dihydropteroate binding site very different from the folate site identified previously in the FPGS structure. The relevance of this site is exemplified by the presence of phosphorylated dihydropteroate, a reaction intermediate in the DHFS reaction. L. casei FPGS is considered a relevant model for human FPGS. As such, the presence of a folate binding site in E. coli FolC, which is different from the one seen in FPGS enzymes, provides avenues for the design of specific inhibitors of this enzyme in antimicrobial therapy.
Input conditions for continuous-time adaptive system problems (1983)

The exponential convergence of certain algorithms used in continuous-time adaptive identification and control is investigated by deriving persistence of excitation conditions which depend on the system inputs exclusively. Stable plants and unstable plants with external stabilizing control are considered in the identification study. For the control algorithm considered, it is shown that in the absence of foreknowledge of a gain parameter, exponential stability is impossible to claim.
A Flexibility Metric and Optimization Methods for Mixed Numerologies in 5G and Beyond (2018)

Mixed numerology-based frame structures will be a part of 5G systems in order to enhance overall flexibility and user satisfaction. However, inter-numerology interference, spectral efficiency reduction, complexity, and signaling overhead type of issues arise in such structures. It is needed to limit the number of numerologies used together. In this paper, a novel heuristic method is developed to find the efficient number of mixed numerologies. The proposed method aims to control overheads in systems using multi-numerology structures. Analysis of the trade-offs and relationships between different services and user requirements are also presented. The designed algorithm employs a new flexibility function and performance metric. Simulation results are shown for three different numerology sets, which include 5G numerologies.
Transdifferentiation potential of human mesenchymal stem cells derived from bone marrow (2004)

Transdifferentiation is a process whereby one cell type committed to and progressing along a specific developmental lineage switches into another cell type of a different lineage through genetic reprogramming. Even though this process has been well studied and established in amphibian systems, it is unclear if mammalian cells possess the same potential. Recent in vivo transplantation studies showed that adult mesenchymal stem cells (MSCs) were able to differentiate into mesoderm-derived cell types as well as cells with neuroectodermal and endodermal characteristics, suggesting that transdifferentiation occurs in mammalian systems. However, there are concerns over these findings because of the possibility of progenitor cell contamination and cell fusion. In this study, we have developed an in vitro differentiation strategy to assess if human MSCs that have differentiated into a given mesenchyme cell lineage can transdifferentiate into other cell types in response to inductive extracellular cues. Our results showed that fully differentiated cells from hMSCs were capable of dedifferentiation and transdifferentiation into cells of another developmental lineage at single cell levels.
Human Hair Derived Keratins Mediate Schwann Cell Behavior in vitro and Facilitate Rapid Peripheral Nerve Regeneration in vivo (2007)

Nerve defects are a common result of peripheral nerve injury and present a significant challenge clinically. Keratins extracted from human hair fiber are a novel group of biomaterials with superior biocompatibility to many synthetic and naturally derived scaffolds. The specific aims of this study were to investigate the ability of human hair keratins to mediate Schwann cell behavior in vitro and to determine whether keratin scaffolds are capable of accelerating functional nerve regeneration in vivo. Using a variety of in vitro assays we have found that keratins increase Schwann cell proliferation, migration and attachment. In addition, keratins have the ability to self‐assemble into fibrous and highly porous scaffolds suitable for cell infiltration and axonal growth. To determine whether a keratin hydrogel scaffold could facilitate functional nerve regeneration in vivo, a tibial nerve axotomy mouse model was employed. After 6 weeks, the extent of regeneration was evaluated using electrophysiology and muscle force testing. Functional testing showed that keratin filled conduits significantly enhanced the nerve regeneration process in comparison to empty conduit controls, and were comparable to autograft. This data demonstrates that keratin hydrogels serve as effective scaffolds for neural tissue engineering and may facilitate functional nerve regeneration by acting on Schwann cells.