gebhart/patrepeval huggingface dataset:
Nanoflares: Probes for Transfection and mRNA Detection in Living Cells* (2020)

Probes to visualize and detect intracellular RNA including those used for in situ staining [1], molecular beacons [2], and fluorescent resonance energy transfer (FRET) pairs [3] are important tools to measure and quantify activity in living systems in response to external stimuli [4]. However, these probes are often difficult to transfect, require additional agents for cellular internalization, and can be unstable in cellular environments. These factors can lead to 1718a high background signal and the inability to detect targets. Here we show how novel oligonucleotide-modified gold nanoparticle probes hybridized to fluorophore complements can be used as both transfection agents and cellular “nanoflares” for visualizing and quantifying RNA in living cells. Nanoflares take advantage of the highly efficient fluorescence-quenching properties of gold [5], cellular uptake of oligonucleotide nanoparticle conjugates without the use of transfection agents, and the enzymatic stability of such conjugates [6], thus overcoming many of the challenges to creating sensitive and effective intracellular probes. Specifically, nanoflares exhibit high signaling, have low background fluorescence, and are sensitive to changes in the number of RNA transcripts present in cells.
Beyond Li-ion batteries: novel concepts and designs (2019)

Efforts are being globally spent today to boost stored energy produced by renewable sources and to encourage a sustainable electric transportation. High-energy conversion systems like batteries can satisfy these demands in an efficient way. Although Li-ion batteries (LIBs) are the best batteries on the market in terms of energy content, a drastic change is desirable to increase both energy and power performance. In this context, Li/O2 is the next generation system due to the theoretical 10-fold higher specific energy than commercial LIBs (3500 vs. 250 Wh kg-1).&#13;\nThe aim of this PhD thesis is the development of novel concepts and cell designs with the purpose to increase the performance of the aprotic Li and Li/O2 batteries.&#13;\nSpecifically, a novel design of electrolyte (i.e. solvent-in-salt “SIS” solutions, where the salt-to-solvent ratio is higher than 1), and an innovative concept of semi-solid lithium redox flow air (O2) battery (SLRFAB) technology, based on the use of a O2-saturated semi-solid catholyte, have been proposed.
1) Gene Therapy as Future Medicine: from Regenerative Medicine to DNA Vaccine (2021)

The 48 th Scientific MeetingPerspectives of Internal MedicineGeneral internal medicine in the Reiwa era3. Future of gene and cell thera-pies1)Gene therapy as future medicine: from regenerative medicine to DNA vaccine.
Advances and issues in mantle cell lymphoma research: report of the 2014 Mantle Cell Lymphoma Consortium Workshop (2015)

Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma characterized by the t(11;14) chromosomal translocation and cyclin D1 over-expression. A biologically and clinically heterogeneous lymphoma, MCL, remains clinically challenging, with no proven curative therapy and no established standard of care. However, there have been considerable advances in the last several years in the treatment and understanding of MCL with the FDA approval of lenalidomide and ibrutinib, the development of other potentially active novel agents and the identification of recurrent mutations through new genomic sequencing approaches that may contribute to the biology of MCL and to therapeutic resistance. At the Lymphoma Research Foundation's 11th MCL Workshop, researchers gathered to discuss recent studies and current issues related to the biology of MCL, novel therapeutic targets and new treatment strategies. The presentations are summarized in this manuscript, which is intended to highlight areas of active investigation and identify topics for future research.
Enforcement or Fiction? Considering Grants of Authority Under the California Global Warming Solutions Act of 2006 and an Alternative to Compel Enforcement (2019)

California has long established itself as a leader in climate change policy, with a deeply entrenched and ever-developing regulatory framework. The state is home to some of the earliest research on, and regulations targeted at, mitigating the severe implications of greenhouse gas (GHG) emissions, like carbon dioxide (CO2), on Earth’s atmosphere. It is therefore unsurprising that California’s regulatory approaches for climate change mitigation and GHG emissions reductions influence local and national climate change law and policies. This influence also notably percolates international climate policy. However, before California may definitively proclaim itself as a global model for successful climate change efforts, it must first refine existing programs to ensure responsible regulatory authorities enforce statutory parameters on emissions. A series of recent cases illustrates the lack of demonstrable reductions in GHG emissions from regulated sources under California’s climate change legislation. These matters challenged different, but interrelated, aspects of CARB’s cap-and-trade policies to reduce GHGs under the California Global Warming Solutions Act of 2006, also known as Assembly Bill 32 (AB 32). Among the myriad of justifications necessitating a workable regulatory framework to reduce emissions, two are most crucial. First, because California’s climate policy is at least perceived a global exemplar, it is necessary to ensure the programs, compliance methodologies, and authorities deputized with such a significant task are the proper mechanisms to do so. Second, anthropogenic climate change—which is largely attributable to GHG emissions—is occurring at an unprecedented rate with devastating effects projected to exacerbate each year. Policies must, therefore, provide practicable methods to monitor emissions as well as avenues to guarantee compliance and enforcement beyond mere discretionary statutory guidelines.
A polylog(n)-competitive algorithm for metrical task systems (1997)

We present a randomized on-line algorithm for the Metrical Tti System problem that achieves a competitive ratio of O(log6 n) for arbitrary metric spaces, against art oblivious adversary. This is the first algorithm to achieve a sublinear competitive ratio for all mernc spaces. Our algorithm uses a recent result of Bart.al[Bar96] thatan arbitrarymetric space can be probabilistically approximated by a set of metric spaces called "k-hierarchical well-separated trees" (k-HST'S). Indeed, the main technical result of this paper is an 0(}og2 n)-competitive algorithm for fl(log2 n)-HST spaces. This, combined with the result of [Bar96], yields the general bound.
Cholesteric diffraction devices with a field-controlled grating vector (1998)

Electrically-controlled diffraction gratings are developed on the basis of a cholesteric liquid crystal confined between two transparent electrodes. The electrodes are coated with unidirectionally treated alignment layers. The initial state is planar, with the helix axis oriented normally to the electrodes. The applied field causes reorientation of molecules and creates structures modulated in the plane of the cell. Surface alignment provides unidirectional uniformity of the modulation. The parameters of the modulated structures and light diffraction are controlled by the cholesteric pitch, cell thickness and applied voltages. Diffraction regimes of both Raman-Nath and Bragg types are demonstrated. In the Raman-Nath regime, the electric field allows one to control continuously the deflection angle by changing the periodicity of modulations. This effect can be used in various beam steering devices. The variation in the diffracted beam direction can be more than 20 degrees. Typical working voltages are less than 10V. We present both the experimental results and 3D computer simulations of modulated structures caused by the field.
Heuristic Approaches with Energy Management for Node Placement in wireless Sensor Networks (2010)

In Wireless Sensor Network, Device placement is a key factor for determining the coverage, connectivity, and cost along with lifetime. Managing the sensor nodes is not much easier while comparing mobile Ad Hoc Networks. But the same approach can be implemented to manage the WSN. Addressing the management of the whole network is omitted and a probabilistic scheme where only a subset of nodes is managed is provided for light weight and efficient management. Relay node placement in heterogeneous WSN are formulated using a generalized node placement optimization problem to minimize the network cost with lifetime constraint, and connectivity. Based on the constraints two scenarios are used. In the first scenario relay nodes are not energy constrained, and in the second scenario all nodes are energy limited. As an optimal solution a two-phase approach is proposed. The placement of the first phase relay nodes (FPRN), which are directly connected to Sensor Nodes (SN), is modeled as a minimum set covering problem. To ensure the relaying of the traffic from the FPRN to the base station, three heuristic schemes are proposed to place the second phase relay nodes (SPRN). Some of the heuristic approaches available are Nearest to BS First algorithm (NTBF), Max Residual Capacity First algorithm (MRCF) and Best Effort Relaying algorithm (BER). Our contribution is centered on a distributed self organizing management algorithm at the application layer by organizing the management plane by extracting spatiotemporal components and by selecting manager nodes with several election mechanisms applied to wireless sensor nodes. Furthermore, a lower bound on the minimum number of SPRN required for connectivity is provided.
MYC-Driven Tumorigenesis Is Inhibited by WRN Syndrome Gene Deficiency (2012)

MYC-induced DNA damage is exacerbated in WRN-deficient cells, leading to replication stress and accelerated cellular senescence. To determine whether WRN deficiency impairs MYC-driven tumor development, we used both xenograft and autochthonous tumor models. Conditional silencing of WRN expression in c-MYC overexpressing non-small cell lung cancer xenografts impaired both tumor establishment and tumor growth. This inhibitory effect of WRN knockdown was accompanied by increased DNA damage, decreased proliferation, and tumor necrosis. In the Eμ-Myc mouse model of B-cell lymphoma, a germline mutation in the helicase domain of Wrn (Wrn(Δhel/Δhel)) resulted in a significant delay in emergence of lethal lymphomas, extending tumor-free survival by more than 30%. Analysis of preneoplastic B cells from Eμ-Myc Wrn mutant mice revealed increased DNA damage, elevation of senescence markers, and decreased proliferation in comparison with cells from age-matched Eμ-Myc mice. Immunohistochemical and global gene expression analysis of overt Eμ-Myc Wrn(Δhel/Δhel) lymphomas showed a marked increase in expression of the CDK inhibitor, p16(Ink4a), as well as elevation of TAp63, a known mediator of senescence. Collectively, these studies show that in the context of Myc-associated tumorigenesis, loss of Wrn amplifies the DNA damage response, both in preneoplastic and neoplastic tissue, engaging activation of tumor suppressor pathways. This leads to inhibition of tumor growth and prolonged tumor-free survival. Targeting WRN or its enzymatic function could prove to be an effective strategy in the treatment of MYC-associated cancers.
Improved pixel-by-pixel MRI R2* relaxometry by nonlocal means (2013)

Pixel-by-pixel fitting can skew MRI relaxometry. The NLM outperforms the conventional LPG filter and has the potential to provide more accurate pixel-by-pixel MRI relaxometry for improved tissue characterization.
Isotope-Selective Detection and Imaging of Organic Nanolayers (2009)

Magnetic resonance force microscopy (MRFM) makes use of the spectroscopic nature of magnetic resonance to add unambiguous elemental selectivity to scanning probe microscopy. We show isotopic selectivity of MRFM for three nuclei, (1)H, (31)P, and (13)C, in organic materials. We also detect a roughly 1 nm thick layer of naturally occurring adsorbates on a gold surface by measuring the magnetic resonance signal of the hydrogen contained in the layer. Finally, we detect the signal from hydrogen present on a carbon nanotube and use it to perform a three-dimensional magnetic resonance image of the 10 nm diameter object.
Copper-Catalyzed Coupling of Amides and Carbamates with Vinyl Halides (2003)

[reaction: see text] A general and efficient copper-catalyzed method for the amidation of vinyl bromides and iodides has been developed. This protocol uses a combination of 5 mol % copper iodide and 20 mol % N,N'-dimethyl ethylenediamine. Substrates bearing ester, silyl ether, and amino groups were successfully coupled under the reaction conditions. The double bond geometry of the vinyl halides was retained under the reaction conditions.
Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention (2018)

Translation into Russian:  Tomasetti, C. , Li, L. , & Vogelstein, B.  (2017).  Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention . Science ,  355 (6331), 1330-1334. DOI:  10.1126/science.aaf9011
Regulation of cranial neural crest cell fate by Irf6 and Twist1 interaction (2020)

A wide variety of common craniofacial birth defects and pediatric cancers arise from errors in the development of cranial neural crest cells (CNCC) that give rise to craniofacial skeletal and peripheral nervous systems. Identification of the genetic and environmental factors that regulate cell fate of CNCCs is crucial for uncovering the causes behind craniofacial disorders. Our lab has identified a dual‐transcription factor pathway that regulates CNCCs during EMT and migration. Initially, we identified a causative mutation in a TWIST1 binding site within an Interferon Regulatory Factor 6 ( IRF6 ) enhancer in a multi‐generational family affected with syndromic cleft lip and palate called Van der Woude syndrome. Our subsequent animal work has shown that Twist1 and Irf6 genetically interact during early craniofacial development, and that the compound heterozygotes exhibit craniofacial abnormalities. We recently demonstrated that Irf6 is required for neural tube and CNCC development and that it interacts with Twist1 during EMT and migration of CNCCs. We also showed that TWIST1 is highly phosphorylated in CNCCs and its phosphorylation is crucial for regulating Irf6 and potentially miR10 family members in CNCC‐derived craniofacial tissues. Our recent in‐vivo and neural tube explants using dual fluorescent cell tracing system showed that Twist1 conditional knockout (CKO) in CNCCs significantly reduced cell delamination and disrupted EMT. The detached Twist1 CKO in CNCCs retained their epithelial signatures and migrated as clusters of epithelial‐like cells over significantly shorter distances. Finally, Twist1 phospho‐incompetent mice for two serine residues were recently generated to determine their impact on TWIST1 activity. Our preliminary results showed that Twist1 S68A/S68A phospho‐mutant mice have craniofacial bone defects and forebrain hemorrhage. Support or Funding Information UTHealth start‐up funds and a small grant from the Rolanette and Berdon Lawrence Bone Disease Program of Texas
Sensory eye balance in surgically corrected intermittent exotropes with normal stereopsis (2015)

Surgery to align a deviated or strabismic eye is often done for both functional as well as cosmetic reasons. Although amblyopia is often an impediment to regaining full binocularity in strabismics in general, intermittent exotropes, because their deviation is intermittent, have no amblyopia and some degree of stereopsis. Binocular function, including a balanced ocular dominance, could be expected to be normal after surgical correction if normal levels of stereopsis and visual acuity are postsurgically achieved. Here we used a binocular phase combination paradigm to quantitatively assess the ocular dominance in a group of surgically corrected intermittent exotropes who have normal stereo and visual acuity as defined clinically. Interestingly, we found significant interocular imbalance (balance point < 0.9) in most of the surgically treated patients (8 out 10) but in none of the controls. We conclude that the two eyes may still have a residual sensory imbalance in surgically corrected strabismus even if stereopsis is within normal limits. Our study opens the possibility that a further treatment aimed at re-balancing the ocular dominance might be necessary in surgically treated intermittent exotropia to provide more efficient binocular processing in the long term.
A fast randomized incremental gradient method for decentralized non-convex optimization (2020)

We study decentralized non-convex finite-sum minimization problems described over a network of nodes, where each node possesses a local batch of data samples. In this context, we analyze a single-timescale randomized incremental gradient method, called GT-SAGA. GT-SAGA is computationally efficient as it evaluates one component gradient per node per iteration and achieves provably fast and robust performance by leveraging node-level variance reduction and network-level gradient tracking. For general smooth non-convex problems, we show the almost sure and mean-squared convergence of GT-SAGA to a first-order stationary point and further describe regimes of practical significance where it outperforms the existing approaches and achieves a network topology-independent iteration complexity respectively. When the global function satisfies the Polyak-Lojaciewisz condition, we show that GT-SAGA exhibits linear convergence to an optimal solution in expectation and describe regimes of practical interest where the performance is network topology-independent and improves upon the existing methods. Numerical experiments are included to highlight the main convergence aspects of GT-SAGA in non-convex settings.
Comparative Aspects of Prostatic Growth and Androgen Metabolism with Aging in the Dog Versus the Rat* (1984)

In untreated rats and dogs, there is a species-specific time period when proliferative growth of the prostate normally occurs during which the gland grows to its maximum normal cellular content. In both species, after the prostate has reached its maximum normal cellular content, which requires 1 yr for the rat and 2 yr for the dog, net proliferative prostatic growth ceases and is replaced by a steady state maintenance of the gland. When 2-yr-old dogs with starting prostates already at their maximum normal cellular content are subsequently treated for 4 months with dihydrotestosterone (DHT), such treatment induces an additional 2-fold abnormal proliferative increase in prostatic cell number above that seen in normal glands from untreated dogs of any age. In direct contrast to the dog, when rats are treated with exogenous DHT for as long as 650 days, such treatment cannot induce any abnormal overgrowth of the gland above the maximum size normally obtained by 365 days of life in untreated control rats. Studies of prostatic androgen metabolism suggest that the differential susceptibility of the dog and rat prostate to DHT-induced abnormal hyperplasia is related to the differential ability of DHT treatment to increase the gland's ability for net DHT formation. This suggestion is based upon the fact that only in the DHT-treated dog, and not the rat, can such DHT treatment induce changes in several of the prostatic activities of DHT metabolism resulting in a 2.5-fold increase in the gland's overall ability for net DHT formation. These results indicate that changes in prostatic DHT metabolism which result in an increased prostatic ability for net DHT formation may be essential in abnormal hyperplasia of the prostate.
Suspensions of Polymer Hydrogel Microparticles with Highly Sensitive Detectability of Glucose (2021)

In this study, we synthesized the glucose-responsive hydrogel microparticles containing phenylboronic acid units by emulsion polymerization. The diameters of hydrogel microparticles could be controlled in the range between 133 nm and 199 nm by changing the surfactant concentration in emulsion polymerization. As-prepared hydrogel microparticles showed the coefficient of variation with approximately 10% in particle diameter regardless of the difference particle diameters, implying the relative monodispersity of microparticles. When glucose was added to the aqueous suspensions of hydrogel microparticles, the visible Bragg reflection visually appeared under alkaline conditions due to the formation of colloidal crystals caused by the increase of particle diameter triggered by the binding of glucose to the particles. Since the critical glucose concentrations to show a visible Bragg reflection were dependent on the concentration or diameter of microparticles, these hydrogel microparticles can be applied to the diabetic detectors and sugar sensors.
Molecular Mechanisms of Cell Cycle Arrest and Apoptosis by Dideoxypetrosynol A, a Polyacetylene from the Sponge Petrosia sp., in Human Monocytic Leukemia Cells (2006)

Dideoxypetrosynol A, a polyacetylene from the marine sponge Petrosia sp., is known to exhibit significant selective cytotoxic activity against a small panel of human tumor cell lines, however, the mechanisms of which are poorly understood. In the present study, it was investigated the further possible mechanisms by which dideoxytetrosynol A exerts its anti-proliferative action in cultured human leukemia cell line U937. We observed that the proliferation-inhibitory effect of dideoxypetrosynol A was due to the induction of G1 arrest of the cell cycle and apoptosis, which effects were associated with up-regulation of cyclin D1 and down-regulation of cyclin E without any change in cyclin-dependent-kinases (Cdks) expression. Dideoxypetrosynol A markedly induced the levels of Cdk inhibitor p16/INK4a expression. Furthermore, down-regulation of phosphorylation of retinoblastoma protein (pRB) by this compound was associated with enhanced binding of pRB and the transcription factor E2F-1. The increase in apoptosis was associated with a dose-dependent up-regulation in pro-apoptotic Bax expression and activation of caspase-3 and caspase-9. Dideoxytetrosynol A decreased the levels of cyclooxygenase (COX)-2 mRNA and protein expression without significant changes in the levels of COX-1, which was correlated with a decrease in prostaglandin E2 (PGE2) synthesis. Furthermore, dideoxytetrosynol A treatment markedly inhibited the activity of telomerase, and the expression of human telomerase reverse transcriptase (hTERT), a main determinant of the telomerase enzymatic activity, was progressively down-regulated by dideoxytetrosynol A treatment in a dose-dependent fashion. Taken together, these findings provide important new insights into the possible molecular mechanisms of the anti-cancer activity of dideoxytetrosynol A.
ChemInform Abstract: Reaction of 5‐Substituted 2‐Methoxy‐1,4‐quinones with Boron Tribromide. (1987)

Abstract The methoxyquinones (Ia) ‐ (Id) react consecutively with boron tribromide and acetic anhydride to give the reduction products (II) and the benzoxocins (III).