gebhart/patrepeval huggingface dataset:
Supplementary Figure 10 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC (2023)

&lt;p&gt;Supplementary Figure 10 - PDF file 333K, Analysis of multiple EGFR-related signaling pathways in parental NCI-H1975 and COR resistant clones by Western blotting&lt;/p&gt;
Robust Spatial Extent Inference with a Semiparametric Bootstrap Joint Testing Procedure (2018)

Spatial extent inference (SEI) is widely used across neuroimaging modalities to study brain-phenotype associations that inform our understanding of disease. Recent studies have shown that Gaussian random field (GRF) based tools can have inflated family-wise error rates (FWERs). This has led to fervent discussion as to which preprocessing steps are necessary to control the FWER using GRF-based SEI. The failure of GRF-based methods is due to unrealistic assumptions about the covariance function of the imaging data. The permutation procedure is the most robust SEI tool because it estimates the covariance function from the imaging data. However, the permutation procedure can fail because its assumption of exchangeability is violated in many imaging modalities. Here, we propose the (semi-) parametric bootstrap joint (PBJ; sPBJ) testing procedures that are designed for SEI of multilevel imaging data. The sPBJ procedure uses a robust estimate of the covariance function, which yields consistent estimates of standard errors, even if the covariance model is misspecified. We use our methods to study the association between performance and executive functioning in a working fMRI study. The sPBJ procedure is robust to variance misspecification and maintains nominal FWER in small samples, in contrast to the GRF methods. The sPBJ also has equal or superior power to the PBJ and permutation procedures. We provide an R package https://github.com/simonvandekar/pbj to perform inference using the PBJ and sPBJ procedures
The effect of the water/methane interface on methane hydrate cages: The potential of mean force and cage lifetimes (2008)

Molecular dynamics simulations were used to determine the influence of a methane-water interface on the position and stability of methane hydrate cages. A potential of mean force was calculated as a function of the separation of a methane hydrate cage and a methane-water interface. The hydrate cages are found to be strongly repelled from the methane gas into the water phase. At low enough temperatures, however, the most favorable location for the hydrate cage is at the interface on the water side. Cage lifetime simulations were performed in bulk water and near a methane-water interface. The methane-water interface increases the cage lifetime by almost a factor of 2 compared to cage lifetimes of cages in bulk water. The potential of mean force and the cage lifetime results give additional explanations for the proposed nucleation of gas hydrates at gas-water interfaces.
Mitochondria transplantation between living cells (2022)

Mitochondria and the complex endomembrane system are hallmarks of eukaryotic cells. To date, it has been difficult to manipulate organelle structures within single live cells. We developed a FluidFM-based approach to extract, inject, and transplant organelles from and into living cells with subcellular spatial resolution. The technology combines atomic force microscopy, optical microscopy, and nanofluidics to achieve force and volume control with real-time inspection. We developed dedicated probes that allow minimally invasive entry into cells and optimized fluid flow to extract specific organelles. When extracting single or a defined number of mitochondria, their morphology transforms into a pearls-on-a-string phenotype due to locally applied fluidic forces. We show that the induced transition is calcium independent and results in isolated, intact mitochondria. Upon cell-to-cell transplantation, the transferred mitochondria fuse to the host cells mitochondrial network. Transplantation of healthy and drug-impaired mitochondria into primary keratinocytes allowed monitoring of mitochondrial subpopulation rescue. Fusion with the mitochondrial network of recipient cells occurred 20 minutes after transplantation and continued for over 16 hours. After transfer of mitochondria and cell propagation over generations, donor mitochondrial DNA (mtDNA) was replicated in recipient cells without the need for selection pressure. The approach opens new prospects for the study of organelle physiology and homeostasis, but also for therapy, mechanobiology, and synthetic biology.
Recommendations of the 5th Canadian Consensus Conference on the diagnosis and treatment of dementia (2020)

Since 1989, four Canadian Consensus Conferences on the Diagnosis and Treatment of Dementia (CCCDTD) have provided evidence-based dementia guidelines for Canadian clinicians and researchers. We present the results of the 5th CCCDTD, which convened in October 2019, to address topics chosen by the steering committee to reflect advances in the field, and build on previous guidelines. Topics included: (1) utility of the National Institute on Aging research framework for clinical Alzheimer's disease (AD) diagnosis; (2) updating diagnostic criteria for vascular cognitive impairment, and its management; (3) dementia case finding and detection; (4) neuroimaging and fluid biomarkers in diagnosis; (5) use of non-cognitive markers of dementia for better dementia detection; (6) risk reduction/prevention; (7) psychosocial and non-pharmacological interventions; and (8) deprescription of medications used to treat dementia. We hope the guidelines are useful for clinicians, researchers, policy makers, and the lay public, to inform a current and evidence-based approach to dementia.
SYNTHESIS OF CARBOCYCLIC NUCLEOTIDES AS POTENTIAL SUBSTRATES FOR THYMIDYLATE KINASE (2005)

Enantiomerically pure carbocyclic 2'-deoxy-3'-azidothymidine monophosphate (AZTMP) and carba-2'deoxy-3'-thiocyanatothymidine monophosphate were synthesized to study their behavior toward their phosphorylation by thymidylate kinase. The nucleotides were synthesized starting from the parent nucleosides by an alkaline hydrolysis of the corresponding cycloSal-phosphate triesters.
The rate distortion region for the multiple description problem (2002)

We derive the rate-distortion region for the two-channel multiple description problem on stationary discrete ergodic and nonergodic sources with alphabets admitting an ergodic decomposition. The results do not provide a single-letter representation for the rate-distortion region on i.i.d. sources.
Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA (2004)

Protein synthesis in all cells begins with recruitment of the small ribosomal subunit to the initiation codon in a messenger RNA. In some eukaryotic viruses, RNA upstream of the coding region forms an internal ribosome entry site (IRES) that directly binds to the 40S ribosomal subunit and enables translation initiation in the absence of many canonical translation initiation factors. The hepatitis C virus (HCV) IRES RNA requires just two initiation factors, eukaryotic initiation factor (eIF) 2 and eIF3, to form preinitiation 48S ribosomal complexes that subsequently assemble into translation-competent ribosomes. Using an RNA-based affinity purification approach, we show here that HCV IRES RNA facilitates eIF2 function through its interactions with eIF3 and the 40S ribosomal subunit. Although the wild-type IRES assembles normally into 48S and 80S ribosomal complexes in human cell extract, mutant IRES RNAs become trapped at the 48S assembly stage. Trapped 48S complexes formed by IRES mutants with reduced eIF3 binding affinity nonetheless contain eIF3, consistent with inherent eIF3-40S subunit affinity. Intriguingly, however, one of these IRES mutants prevents stable association of both eIF3 and eIF2, preventing initiator tRNA deposition and explaining the block in 80S assembly. In contrast, an IRES mutant unable to induce a conformational change in the 40S subunit, as observed previously by single-particle cryoelectron microscopy, blocks 80S formation at a later stage in assembly. These data suggest that the IRES RNA coordinates interactions of eIF3 and eIF2 on the ribosome required to position the initiator tRNA on the mRNA in the ribosomal peptidyl-tRNA site (P site).
First experimental demonstration of real-time neutron capture discrimination in helium and carbon ion therapy (2023)

Abstract This work provides the first experimental proof of an increased neutron capture photon signal following the introduction of boron to a PMMA phantom during helium and carbon ion therapies in Neutron Capture Enhanced Particle Therapy (NCEPT). NCEPT leverages 10B neutron capture, leading to the emission of detectable 478 keV photons. Experiments were performed at the Heavy Ion Medical Accelerator in Chiba, Japan, with two PMMA targets, one bearing a boron insert. The BeNEdiCTE gamma-ray detector measured an increase in the 478 keV signal of 45 ± 7% and 26 ± 2% for carbon and helium ion irradiation, respectively. Our Geant4 Monte Carlo simulation model, developed to investigate photon origins, found less than 30% of detected photons originated from the insert, while boron in the detector’s circuit boards contributed over 65%. Further, the model investigated detector sensitivity, establishing its capability to record a 10% increase in 478 keV photon detection at a target 10 B concentration of 500 ppm using spectral windowing alone, and 25% when combined with temporal windowing. The linear response extended to concentrations up to 20000 ppm. The increase in the signal in all evaluated cases confirm the potential of the proposed detector design for neutron capture quantification in NCEPT.
Providing end-to-end QoS assurances in a CORBA-based system (2002)

In this paper we describe the implementation of our end-to-end QoS-driven resource management scheme, called ERDoS, within a CORBA-compliant ORB that we call the ERDoS QoS ORB. Unlike other real-time CORBA implementations that focus on real-time support for simple client-server applications, our ERDoS QoS ORB provides end-to-end QoS support (i.e., QoS spanning computer network, and storage resources) to applications, while retaining the benefits of an open distributed object system. Specifically we present three contributions. First, we present a model for describing end-to-end applications as a combination of client-server interactions between CORBA objects. Second, we define a model for relating the user/application level QoS requirements to the corresponding resource demand requirements of these individual CORBA objects. Third, we suggest a framework for performing distributed resource management within the CORBA environment.
Scanning the controls: genomics and nanotechnology (2002)

We outline some of the possible applications of nanotechnology to modern molecular biology and discuss several technologies that can be used to make nanoscale confining environments (channels or post arrays) for long polymers such as DNA. A particular emphasis is placed on making large arrays using non-electron beam lithography methods. We then discuss how focused ion beam (FIB) milling can be used to construct nearfield slits for examining molecules.
Reovirus Infection in Psittacine Birds (Psittacus erithacus): Morphologic and Immunohistochemical Study (2002)

In this paper we report on an outbreak of reovirus, herpesvirus (Pacheco disease), and/or mycosis infection (Aspergillus spp. and Zygomyces spp.) affecting a batch of young African grey parrots (Psittacus erithacus), with 80% morbidity and 30% mortality. Study material was taken from five birds (four dead and one euthanatized) with a range of clinical symptoms (depression, diarrhea, respiratory symptoms). Diagnosis was confirmed by immunohistochemical detection of avian reovirus, electron microscopy, and virus isolation. Viral antigen of reovirus was detected mainly in large mononuclear cells in the bursa of Fabricius and the spleen, pancreas epithelial cells, and circulating cells; lymphoid organs displayed the largest number of immunopositive cells and severe lymphocyte depletion. Bacteriologic study was negative. Reovirus infection was common in all birds studied, whereas Pacheco disease and mycosis were found in only some, suggesting that reovirus could be the initial cause triggering the outbreak and facilitating infection by other agents and their swift spread through the batch.
Characterization of Canine Humoral Immune Responses to Outer Surface Protein Subunit Vaccines and to Natural Infection by Lyme Disease Spirochetes (1995)

Canine antibody responses to Lyme disease subunit vaccines and to natural borrelial infection were investigated. Vaccines were formulated with QS21 and outer surface proteins A (OspA) and B (OspB) derived from Borrelia burgdorferi B31. Vaccines containing QS21 and the lipoproteins gave 4-fold higher IgG1 and 8-fold higher IgG2 antibody responses than without QS21. Antisera to lipidated OspA or OspB vaccines containing QS21 had high antiborrelial activity against isolates B31 and CA-2-87, similar to those with a vaccine containing both OspA and OspB. Only the combination vaccine induced antiborrelial activity against heterologous isolates 24008 Fr and Borrelia garinii G25. Nonlipidated OspA- and OspB-based vaccines with QS21 elicited lower antibody and antiborrelial activity than did lipidated OspA and OspB vaccines; 49% of naturally exposed dogs had low titers to OspA or OspB. Thus, vaccines using lipidated OspA, OspB, and QS21 could induce higher antiborrelial activity than did natural exposure.
LeCroy MQT300-charge to time converter (2002)

The MQT300 was developed to offer high resolution (12 bit) and wide dynamic range (18 bit) with reasonable cost, high density and fast conversion time (<10 /spl mu/s). The reduced conversion time has allowed its first users the option of whether or not to develop a fast clear strategy as part of their trigger system. It can also be used, for chamber mounted applications allowing compact digital data cabling to the remote TDC. The MQT300 is a custom development produced in collaboration with the BELLE collaboration at KEK and the CLEO group at Cornell. In this collaboration Cornell and KEK were partners with LeCroy in both the specification and evaluation of the first prototypes. LeCroy (LRS division) has been responsible for the remainder of the project. The MQT300A will be available in LeCroy modules and also as a separate monolithic. The MQT300A was designed to take advantage of the latest generation of multi-hit TDCs, for example the LeCroy 1877S FASTBUS ADC. The 1877S was specifically optimized to improve conversion time and to intelligently minimize the data record size for the MQT300A application. A first prototype has been fabricated as a custom bipolar monolithic. Encouraging results are presented and have lead to design revisions that will be implemented on the next version the MQT300A. The validity of some of these revisions has been shown through both microsurgery of the existing die and extensive simulation.
Effects of Dialysate Flow Configurations in Continuous Renal Replacement Therapy on Solute Removal: Computational Modeling (2013)

Different dialysate flow configurations influence solute clearance and change major solute removal mechanisms in the proximal and distal parts of a hemodiafilter. Advantages of each configuration should be balanced against the overall performance of the treatment and its simplicity in terms of treatment delivery and circuit handling procedures.
Comparison of Voxel-Wise and Histogram Analyses of Glioma ADC Maps for Prediction of Early Therapeutic Change (2019)

Noninvasive imaging methods are sought to objectively predict early response to therapy for high-grade glioma tumors. Quantitative metrics derived from diffusion-weighted imaging, such as apparent diffusion coefficient (ADC), have previously shown promise when used in combination with voxel-based analysis reflecting regional changes. The functional diffusion mapping (fDM) metric is hypothesized to be associated with volume of tumor exhibiting an increasing ADC owing to effective therapeutic action. In this work, the reference fDM-predicted survival (from previous study) for 3 weeks from treatment initiation (midtreatment) is compared to multiple histogram-based metrics using Kaplan-Meier estimator for 80 glioma patients stratified to responders and nonresponders based on the population median value for the given metric. The ADC histogram metric reflecting reduction in midtreatment volume of solid tumor (ADC < 1.25 × 10<sup>-3</sup> mm<sup>2</sup>/s) by >8% population-median with respect to pretreatment is found to have the same predictive power as the reference fDM of increasing midtreatment ADC volume above 4%. This study establishes the level of correlation between fDM increase and low-ADC tumor volume shrinkage for prediction of early response to radiation therapy in patients with glioma malignancies.
High-performance computing with sparsity and structure (2010)

Computations involving sparse and structured matrices arise frequently in problems in operations research, science and engineering. Exploiting this structure has been a major contributor to the efficient application of past and current computing platforms, and will continue to play an important role for next-generation systems.
Design, Synthesis, and Biological Evaluation of Ganglioside Hp-s1 Analogues Varying at Glucosyl Moiety (2016)

Ganglioside Hp-s1 is isolated from the ovary of sea urchin Diadema setosum. It exhibited better neuritogenic activity than GM1 in pheochromocytoma 12 cells. To explore the roles of glucosyl moiety of Hp-s1 in contributing to the neurogenic activity, we developed feasible procedures for synthesis of Hp-s1 analogues (2a-2f). The glucosyl moiety of Hp-s1 was replaced with α-glucose, α-galactose, β-galactose, α-mannose, and β-mannose, and their biological activities on SH-SY5Y cells and natural killer T (NKT) cells were evaluated. We found that the orientation of C-2 hydroxyl group at glucosyl moiety of Hp-s1 plays an important role to induce neurite outgrowth of SH-SY5Y cells. Surprisingly, compound 2d could activate NKT cells to produce interleukin 2, although it did not show great activity on neurite outgrowth of SH-SY5Y cells. In general, the Hp-s1 might be considered as a lead compound for the development of novel drugs aimed at modulating the activity of neuronal cells.
Sharing multiple messages over mobile networks (2011)

Information dissemination in a large network is typically achieved when each user shares its own information or resources with each other user. Consider n users randomly located over a fixed region, and k of them wish to flood their individual messages among all other users, where each user only has knowledge of its own contents and state information. The goal is to disseminate all messages using a low-overhead strategy that is one-sided and distributed while achieving an order-optimal spreading rate over a random geometric graph. In this paper, we investigate the random-push gossip-based algorithm where message selection is based on the sender's own state in a random fashion. It is first shown that random-push is inefficient in static random geometric graphs. Specifically, it is Ω(√n) times slower than optimal spreading. This gap can be closed if each user is mobile, and at each time moves “locally” using a random walk with velocity v(n). We propose an efficient dissemination strategy that alternates between individual message flooding and random gossiping. We show that this scheme achieves the optimal spreading rate as long as the velocity satisfies v(n) = ω(√log n/k). The key insight is that the mixing introduced by this velocity-limited mobility approximately uniformizes the locations of all copies of each message within the optimal spreading time, which emulates a balanced geometry-free evolution over a complete graph.
Three-dimensional polarization ray-tracing calculus II: retardance (2011)

The concept of retardance is critically analyzed for ray paths through optical systems described by a three-by-three polarization ray-tracing matrix. Algorithms are presented to separate the effects of retardance from geometric transformations. The geometric transformation described by a "parallel transport matrix" characterizes nonpolarizing propagation through an optical system, and also provides a proper relationship between sets of local coordinates along the ray path. The proper retardance is calculated by removing this geometric transformation from the three-by-three polarization ray-tracing matrix. Two rays with different ray paths through an optical system can have the same polarization ray-tracing matrix but different retardances. The retardance and diattenuation of an aluminum-coated three fold-mirror system are analyzed as an example.
Broadband amplification by picosecond OPCPA in DKDP pumped at 515 nm (2012)

On the quest towards reaching petawatt-scale peak power light pulses with few-cycle duration, optical parametric chirped pulse amplification (OPCPA) pumped on a time scale of a few picoseconds represents a very promising route. Here we present an experimental demonstration of few-ps OPCPA in DKDP, in order to experimentally verify the feasibility of the scheme. Broadband amplification was observed in the wavelength range of 830-1310 nm. The amplified spectrum supports two optical cycle pulses, at a central wavelength of ~920 nm, with a pulse duration of 6.1 fs (FWHM). The comparison of the experimental results with our numerical calculations of the OPCPA process showed good agreement. These findings confirm the reliability of our theoretical modelling, in particular with respect to the design for further amplification stages, scaling the output peak powers to the petawatt scale.
Beam-shaping condenser lenses for full-field transmission X-ray microscopy (2007)

A new type of diffractive X-ray optical elements is reported, which have been used as beam-shaping condenser lenses in full-field transmission X-ray microscopes. These devices produce a square-shaped flat-top illumination on the sample matched to the field of view. The size of the illumination can easily be designed depending on the geometry and requirements of the specific experimental station. Gold and silicon beam-shapers have been fabricated and tested in full-field microscopes in the hard and soft X-ray regimes, respectively.
A Practical Iron Loss Calculation for AC Filter Inductors Used in PWM Inverters (2009)

A novel iron loss calculation method is proposed based on an iron loss map for an AC filter inductor used in a pulsewidth-modulation (PWM) inverter. The iron loss map, previously reported by the authors, is created by measuring the dynamic minor loop on the B-H plane, and this is used for the calculation of inductor iron loss in the dc chopper circuit. However, in the case of an AC filter inductor used in a PWM inverter, the iron loss map cannot be directory applied to the iron loss calculation. In this paper, an iron loss calculation for an ac filter inductor is presented by expanding the loss map method. We describe the principle of expansion and the practical procedure for the calculation, which utilizes the loss map and a conventional circuit simulator. Iron loss for the ac filter inductor under some typical modulation methods of the PWM inverter are calculated and discussed with regard to the relation between the modulation methods and iron loss. The calculated results are verified using experimental results from a 500-W inverter setup. The inductor loss and conversion efficiency of the PWM inverter are measured for each modulation method.