gebhart/patrepeval huggingface dataset:
Toxoplasma gondii autophagy-related protein ATG9 is crucial for the survival of parasites in their host (2016)

Autophagy is a conserved, life-promoting, catabolic process involved in the recycling of nonessential cellular components in response to stress. The parasite Toxoplasma gondii is an early-diverging eukaryote in which part of the autophagy machinery is not exclusively involved in a catabolic process but instead has been repurposed for an original function in organelle inheritance during cell division. This function, depending essentially on protein TgATG8 and its membrane conjugation system, is crucial for parasite survival and prevented an in depth study of autophagy in the mutants generated so far in Toxoplasma. Thus, in order to decipher the primary function of canonical autophagy in the parasites, we generated a cell line deficient for TgATG9, a protein thought to be involved in the early steps of the autophagy process. Although the protein proved to be dispensable for the development of these obligate intracellular parasites in vitro, the absence of TgATG9 led to a reduced ability to sustain prolonged extracellular stress. Importantly, depletion of the protein significantly reduced parasites survival in macrophages and markedly attenuated their virulence in mice. Altogether, this shows TgATG9 is important for the fate of Toxoplasma in immune cells and contributes to the overall virulence of the parasite, possibly through an involvement in a canonical autophagy pathway.
A sufficient condition for interference alignment (2015)

We consider the classical problem of spatial interference alignment (IA) in MIMO channels with constant channel coefficients through design of linear transmit precoders and receiver filters. Some easily (polynomial time) computable necessary conditions for IA have been derived in the literature [1], [2], [3]. Computable sufficient and necessary conditions that completely characterizes the feasibility of an IA problem have also been obtained [4], [2]. However, it has been shown that checking the feasibility of interference alignment when the number of antennas are more than two is NP-complete[3]. This result is inline with full characterization of the feasibility of IA as the sufficiency conditions require multiplication of Schubert cycles that becomes exhaustive as the dimensions grows. Naturally, the following questions may arise: “Is it possible to have a sufficiency condition for a general case of IA based on only the dimensions of the system (number of antennas at each node and degrees of freedom (DoF) per node [4]) that is simple (polynomial time) to compute?” and “How effective such sufficiency conditions would be?”. In this paper, we provide an affirmative answer to the first question and show the proposed sufficient condition is asymptotically optimal. The sufficiency conditions are expressed in terms of simple inequalities based on system dimensions. Unlike necessary conditions that are based on simple argument such as dimension counting [1], we have not yet been able to provide an elementary proof for the derived sufficiency conditions. The provided proof requires familiarity with Schubert calculus over complex Grassmannians.
Des-O-methylolivoretin C is a new member of the teleocidin class of tumor promoters. (1986)

Des-O-methylolivoretin C, a demethylated form of olivoretin C, is a naturally occurring compound in Streptomyces mediocidicus and Streptoverticillium olivoreticuli. Des-O-methylolivoretin C is a regioisomer of teleocidin B, which has the same activity as teleocidin. The tumor-promoting activity of des-O-methylolivoretin C was studied in a two-stage carcinogenesis experiment on mouse skin in comparison with that of teleocidin. Treatments with 7,12-dimethylbenz[a]anthracene (DMBA) plus des-O-methylolivoretin C and DMBA plus teleocidin induced tumors in 63.3% and 84.6% of the mice, respectively, in week 30. The difference in the tumor-promoting activities of des-O-methylolivoretin C and teleocidin is presumably related to the regioisomeric difference in the cyclohexene ring.
A Framework for Optimizing Multi-cell NOMA: Delivering Demand with Less Resource (2017)

Non-orthogonal multiple access (NOMA) allows multiple users to simultaneously access the same time-frequency resource by using superposition coding and successive interference cancellation (SIC). Thus far, most papers on NOMA have focused on performance gain for one or sometimes two base stations. In this paper, we study multi-cell NOMA and provide a general framework for user clustering and power allocation, taking into account inter-cell interference, for optimizing resource allocation of NOMA in multi-cell networks of arbitrary topology. We provide a series of theoretical analysis, to algorithmically enable optimization approaches. The resulting algorithmic notion is very general. Namely, we prove that for any performance metric that monotonically increases in the cells' resource consumption, we have convergence guarantee for global optimum. We apply the framework with its algorithmic concept to a multi-cell scenario to demonstrate the gain of NOMA in achieving significantly higher efficiency.
Repairable replication-based storage systems using resolvable designs (2012)

We consider the design of regenerating codes for distributed storage systems at the minimum bandwidth regeneration (MBR) point. The codes allow for a repair process that is exact and uncoded, but table-based. These codes were introduced in prior work and consist of an outer MDS code followed by an inner fractional repetition (FR) code where copies of the coded symbols are placed on the storage nodes. The main challenge in this domain is the design of the inner FR code. In our work, we consider generalizations of FR codes, by establishing their connection with a family of combinatorial structures known as resolvable designs. Our constructions based on affine geometries, Hadamard designs and mutually orthogonal Latin squares allow the design of systems where a new node can be exactly regenerated by downloading β ≥ 1 packets from a subset of the surviving nodes (prior work only considered the case of β = 1). Our techniques allow the design of systems over a large range of parameters. Specifically, the repetition degree of a symbol, which dictates the resilience of the system can be varied over a large range in a simple manner. Moreover, the actual table needed for the repair can also be implemented in a rather straightforward way. Furthermore, we answer an open question posed in prior work by demonstrating the existence of codes with parameters that are not covered by Steiner systems.
Evaluation of three continuous glucose monitoring systems during exercise and meal challenges (2016)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Regional intracellular pH shift: a proposed new mechanism for radiopharmaceutical uptake in brain and other tissues. (1980)

This paper proposes a new mechanism for radiopharmaceutical uptake, which may be applicable to a variety of clinical studies. Many tissues and organs have low intracellular pH, either normally or as a result of various metabolic disturbances. We have developed a series of compounds that are neutral and lipid-soluble at blood pH. These molecules can diffuse freely into cells. In those regions where intracellular pH is low, they pick up a hydrogen ion and become charged. In this form they are no longer lipid-soluble and are trapped because they cannot diffuse out of the cell. Studies of the brain uptake of two compounds of this type, Se-75 labeled di-beta-(morpholinoethyl)-selenide (MOSE) and di-beta-(piperidinoethyl)-selenide (PIPSE), demonstrate the application of the principle.
Opposing effects of DNA on proteolysis of a replication initiator (2011)

DNA replication initiation proteins (Reps) are subjected to degradation by cellular proteases. We investigated how the formation of nucleoprotein complex, involving Rep and a protease, affects Rep degradation. All known Escherichia coli AAA+ cytosolic proteases and the replication initiation protein TrfA of the broad-host-range plasmid RK2 were used. Our results revealed that DNA influences the degradation process and that the observed effects are opposite and protease specific. In the case of ClpXP and ClpYQ proteases, DNA abolishes proteolysis, while in the case of ClpAP and Lon proteases it stimulates the process. ClpX and ClpY cannot interact with DNA-bound TrfA, while the ClpAP and Lon activities are enhanced by the formation of nucleoprotein complexes involving both the protease and TrfA. Lon has to interact with TrfA before contacting DNA, or this interaction can occur with TrfA already bound to DNA. The TrfA degradation by Lon can be carried out only on DNA. The absence of Lon results with higher stability of TrfA in the cell.
Optimisation conjointe d'un masque de phase et d'un algorithme de déconvolution pour l'augmentation de profondeur de champ (Orale) (2013)

National audience
Abstract 107: Laser Angioscopy Reveals Concealed Ulcers in Substenotic Carotid Plaques in Cryptogenic Stroke Patients: A Preclinical Study (2017)

Introduction: Evidence suggests that a significant proportion of cryptogenic strokes may be due to artery-to-artery emboli from substenotic complicated carotid plaques. Thus, carotid artery disease not meeting etiological criteria for stroke (i.e. &lt;50% stenosis) could still harbor thrombo-emboligenic lesions undetectable by standard imaging modalities. We developed an ultrathin, high-resolution, laser-based angioscope (4.7F, 200.000 pixels), capable of detecting such lesions. Hypothesis: We hypothesized that, unlike conventional imaging modalities, high-definition angioscopy would accurately detect small thrombi and ulcers in non-stenosing complicated atherosclerotic plaques. Methods: After institutional approval, the carotid arteries from 2 patients with cryptogenic strokes were harvested post-mortem and endoluminal surface videos were obtained with multimodal SFA. Angioscopic findings were compared to 25 carotid arteries autopsied from subjects with and without atherosclerosis, and 5 carotid endarterectomy (CEA) specimens from symptomatic patients. After angioscopy, all specimens were processed for histology and blindly reviewed by a pathologist; lesions were then matched to endoscopic findings. Subsequently, we tested the SFA in an in vivo rabbit model of atherosclerosis. Results: Punched-out lesions with slightly raised, irregular bead-like borders were encountered in the ipsilateral substenotic carotid arteries (&lt;25%) of patients with cryptogenic stroke. This pathognomonic angioscopic architecture corresponded to ulcerated plaques, and was found exclusively in CEA specimens removed after stroke. As a prelude for clinical use, we demonstrated that SFA generates high quality images in vivo . Conclusions: Laser angioscopy reveals ulcerated plaques in carotid arteries with low-degree stenosis, obtained post-mortem from patients with cryptogenic strokes. Clinically, this novel platform could be used to identify ulcerated carotid plaques or intraluminal thrombi; such diagnostic resolution could help establish the etiology of a subset of cryptogenic strokes that present with low-degree carotid stenosis.
A small-molecule therapeutic lead for Huntington's disease: Preclinical pharmacology and efficacy of C2-8 in the R6/2 transgenic mouse (2007)

Huntington's disease (HD) is a progressive neurodegenerative disease caused by a glutamine expansion within huntingtin protein. The exact pathological mechanisms determining disease onset and progression remain unclear. However, aggregates of insoluble mutant huntingtin (mhtt), a hallmark of HD, are readily detected within neurons in HD brain. Although aggregated polyglutamines may not be inherently toxic, they constitute a biomarker for mutant huntingtin useful for developing therapeutics. We previously reported that the small molecule, C2-8, inhibits polyglutamine aggregation in cell culture and brain slices and rescues degeneration of photoreceptors in a Drosophila model of HD. In this study, we assessed the therapeutic potential of C2-8 in the R6/2 mouse model of HD, which has been used to provide proof-of-concept data in considering whether to advance therapies to human HD. We show that, at nontoxic doses, C2-8 penetrates the blood-brain barrier and is present in brain at a high concentration. C2-8-treated mice showed improved motor performance and reduced neuronal atrophy and had smaller huntingtin aggregates. There have been no prior drug-like, non-toxic, brain-penetrable aggregation inhibitors to arise from cell-based high-throughput screens for reducing huntingtin aggregation that is efficacious in preclinical in vivo models. C2-8 provides an essential tool to help elucidate mechanisms of neurodegeneration in HD and a therapeutic lead for further optimization and development.
Optimization of SEU emulation on SRAM FPGAs based on sensitiveness analysis (2015)

This paper presents a new and highly efficient approach for the estimation by fault injection of the sensitivity to Single Event Upsets of circuits implemented in Xilinx SRAM-based FPGAs. The proposed approach prioritizes fault injection in specific configuration bits subsets defined according to their contents and the type of FPGA resources that they are configuring. The new approach also allows maximizing either the number of critical bits flipped during the injection or the estimation accuracy of the critical bits number. The results show that the new approach outperforms the traditional random fault injection with speed up factors up to two orders of magnitude.
<title>Rapid multiexcitation spectrofluorimeter for in-vivo tissue diagnosis</title> (1997)

We have designed, fabricated and tested a compact excitation-emission spectrofluorimeter with optical fiber light delivery and collection for use in rapid analysis of tissues in a clinical setting. This system provides ten different excitation wavelengths, permitting collection of all ten emission spectra from biological tissues in approximately 500 ms. It uses a nitrogen laser which pumps a sequence of dyes placed in cuvettes on a rotating wheel. All dye cuvettes utilize a common optical resonant cavity, which simplifies the coupling of the different excitation wavelengths into the delivery fiber of an optical fiber probe. A filter wheel containing one long-pass filter for each excitation wavelength is synchronized with the dye wheel for compactness and ease of control. A white light excitation source permits acquisition of the tissue diffuse reflectance spectrum on each cycle. The fiber optic probe is composed of seven optical fibers arranged at the distal tip in the form of a central delivery fiber surrounded by six collection fibers, with an optical shield. Return fluorescence and reflected light are dispersed by a small spectrograph and detected by a photodiode array detector. The system can collect a single shot spectrum from biological tissue with a signal-to-noise ratio in excess of 50:1. This unique design for providing rapidly variable excitation wavelengths facilitates the collection of multi- excitation fluorescence spectra for the diagnosis of diseases in vivo.
ChemInform Abstract: Synthesis and Characterization of Complexes of Trialkyl‐ and Triarylphosphine Gold(I) with Thiolated Purines and Pyrimidines: A Class of Bifunctional Compounds with Potential Antitumor Activity. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Antithrombogenic In Vivo Effects of Calcium Channel Blockers in Experimental Thrombosis in Mice (1987)

A new model of thrombotic challenge, well suited for screening agents and which acts primarily against platelet thromboembolism, has been used to test the in vivo anti-platelet effects of four calcium channel blockers (CCB). An i.v. injection of a mixture of collagen plus epinephrine (15 micrograms and 1.8 micrograms/mouse, respectively) was given to male mice. 94% control mice died or remained paralyzed for more than 15 minutes. The dihydropyridine agents, CRE-223 and Nifedipine, were highly protective against experimental thrombosis, whereas Verapamil had a weaker and much shorter effect and, on the other hand, Diltiazem had no protective effect over a range of doses. The activity on both dihydropyridines lasted for seven hours or even longer.
What Controls Deposition Rate in Electron-Beam Chemical Vapor Deposition? (2006)

The key physical processes governing electron-beam-assisted chemical vapor deposition are analyzed via a combination of theoretical modeling and supporting experiments. The scaling laws that define growth of the nanoscale deposits are developed and verified using carefully designed experiments of carbon deposition from methane onto a silicon substrate. The results suggest that the chamber-scale continuous transport of the precursor gas is the rate controlling process in electron-beam chemical vapor deposition.
Fractal Inductors (2013)

This paper investigates the performance of planar inductors based on space filling curves, a family of fractals with the property of completely filling a bounded area. Fractal-based inductor design is a method for obtaining a very long trace lengths-and thus inductance densities - in 2-D space as a replacement for the serpentines currently used in one layer inductors. Because of the intricate course created by a fractal curve, these types of inductors are particularly well suited for stretchable electronics, where a tortuous path relieves mechanical stress and creates a more compliant structure. Inductors based on seven common space filling curves, all bounded within a one square millimeter area, were both simulated and measured experimentally and found to vary between 3.0 and 7.1 nH. Lower order fractals were found to give comparable performance to serpentine inductors with similar inductance density. More complicated fractals, after more than two iterations, were found to have lower inductance density than similar resistance serpentines. Mechanical simulations demonstrate a reduction in stress by a factor of 10 or more compared with the loop and serpentine designs.
Palonosetron Exhibits Unique Molecular Interactions with the 5-HT3 Receptor (2008)

Palonosetron exhibited allosteric binding and positive cooperativity when binding to the 5-HT(3) receptor. Palonosetron also triggered functional effects that persisted beyond its binding to the 5-HT(3) receptor at the cell surface. Differences in binding and effects on receptor function may be relevant to the unique beneficial actions of palonosetron. To our knowledge, this is the first report showing palonosetron's interaction with the 5-HT(3) receptor at the molecular level, clearly differentiating it from other 5-HT(3)-RAs.
Brain-Reactive Antibodies and Disease (2013)

Autoimmune diseases currently affect 5-7% of the world's population; in most diseases there are circulating autoantibodies. Brain-reactive antibodies are present in approximately 2-3% of the general population but do not usually contribute to brain pathology. These antibodies penetrate brain tissue only early in development or under pathologic conditions. This restriction on their pathogenicity and the lack of correlation between serum titers and brain pathology have, no doubt, contributed to a delayed appreciation of the contribution of autoantibodies in diseases of the central nervous system. Nonetheless, it is increasingly clear that antibodies can cause damage in the brain and likely initiate or aggravate multiple neurologic conditions; brain-reactive antibodies contribute to symptomatology in autoimmune disease, infectious disease, and malignancy.
Novel single-atom and quasi phase-matching techniques at short wavelengths (2002)

Summary form only given. In the visible region of the spectrum, nonlinear conversion of light from one frequency to another is efficient because of phase matching. The phase velocity of the fundamental and nonlinear signal is matched such that the generated nonlinear signal sums coherently throughout the entire interaction region. At visible frequencies, this is accomplished by appropriate orientation of an anisotropic crystal. Alternatively, quasi-phase matching (QPM) techniques, which restrict nonlinear light generation to specific spatial regions, can be used. Both of these techniques rely on propagation effects. In this work, we present four new results. First, we present two new phase matching techniques that can be applied uniquely to extreme nonlinear optics, to upshift light into the XUV using high harmonic generation (HHG). The first uses a type of phase matching that can occur within single atoms. The second demonstrates a new type of QPM in the XUV based on amplitude modulation. We also show that these new techniques require an electron trajectory to be adjusted by 25 attoseconds. Finally, we demonstrate excellent agreement between theory and experiment for the first time in learning control of high-order nonlinear processes.
Early ADME/T Predictions: Toy or Tool? (2008)

The successful development of new drugs critically depends on the ability of researchers to predict the ADME/T (absorption, distribution, metabolism, excretion, and toxicity) properties of chemical compounds. These properties are important to narrow the search for New promising Chemical Entities (NC...
Characteristics of Pentacene on High-k Film for Flexible Organic Field Effect Transistor (2006)

We reported the grain growth of pentacone on film depending on OTS treatment. The hydrophilic thin film was changed into hydrophobic with less interface energy by OTS treatment. The grain size of pentacene on OTS/ film was increased from 50 nm to 90 nm with the variation of surface energy and the structure was maintained 3-dimensional island structure. Pentacene on OTS/ surface was directionally arrayed due to appearance of the only thin film phase without bulk phase by OTS treatment.
Design and synthesis of biobased epoxy thermosets from biorenewable resources (2017)

Biobased diepoxy synthons derived from isoeugenol, eugenol or resorcinol (DGE-isoEu, DGE-Eu and DGER, respectively) have been used as epoxy monomers in replacement of the diglycidyl ether of bisphenol A (DGEBA). Their curing with six different biobased anhydride hardeners leads to fully biobased epoxy thermosets. These materials exhibit interesting thermal and mechanical properties comparable to those obtained with conventional petrosourced DGEBA-based epoxy resins cured in similar conditions. In particular, a high T g in the range of 90–130 °C and instantaneous moduli higher than 4.3 GPa have been recorded. These good performances are very encouraging, making these new fully biobased epoxy thermosets compatible with the usual structural application of epoxy materials.
Figure S3 from A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma (2023)

&lt;p&gt;Controlling for MYCN amplification status increases the statistical significance of NE score vs. MYCN expression association.&lt;/p&gt;