gebhart/patrepeval huggingface dataset:
An HMG1-like protein facilitates Wnt signaling in Caenorhabditis elegans (1999)

We show that during Caenorhabditis elegans male spicule development, the specification of a glial versus neuronal cell fate in a canonical neurogenic sublineage is dependent on Wnt signaling. Inactivation of a Wnt signaling pathway mediated by the Wnt receptor LIN-17 transforms the SPD sheath cell into its sister, the SPD neuron. We discovered a new mutant, son-1, that displays this same cell fate transformation. The son-1 mutation enhances the phenotypes of reduction-of-function lin-17 mutants in several developmental processes, including vulva development, somatic gonad development, and male tail patterning. son-1 encodes an HMG1/2-like DNA-binding protein and is localized in all cell nuclei through development as revealed by a GFP reporter construct. Disruption of son-1 function by RNA-mediated interference results in the same spicule defect as caused by overexpression of POP-1, a TCF/LEF class HMG protein known to act downstream of the Wnt signaling pathway. Our results provide in vivo evidence for the functional involvement of an HMG1/2-like protein, SON-1, in Wnt signaling. The sequence nonspecific HMG protein SON-1 and the sequence specific HMG protein POP-1 might both act in the Wnt responding cells to regulate gene transcription in opposite directions.
Reflective program generation with patterns (2006)

Runtime reflection facilities, as present in Java and .NET, are powerful mechanisms for inspecting existing code and metadata, as well as generating new code and metadata on the fly. Such power does come at a high price though. The runtime reflection support in Java and .NET imposes a cost on all programs, whether they use reflection or not, simply by the necessity of keeping all metadata around and the inability to optimize code because of future possible code changes. A second---often overlooked---cost is the difficulty of writing correct reflection code to inspect or emit new metadata and code and the risk that the emitted code is not well-formed.In this paper we examine a subclass of problems that can be addressed using a simpler mechanism than runtime reflection, which we call compile-time reflection. We argue for a high-level construct called a transform that allows programmers to write inspection and generation code in a pattern matching and template style, avoiding at the same time the complexities of reflection APIs and providing the benefits of staged compilation in that the generated code and metadata is known to be well-formed and type safe ahead of time.
Microelectromechanical Systems Resonator Utilizing Torsional-to-Transverse Vibration Conversion (2011)

A silicon microelectromechanical systems (MEMS) resonator utilizing the torsional-to-transverse vibration conversion is designed, fabricated and evaluated. The resonant frequency for the torsional modes mostly depends on only beam length, providing a large tolerance in the fabrication process. It has been, however, a critical issue to investigate the mechanism for generating the torsional vibration and the reduction of motional resistance. We propose a new beam structure, in which four torsion beams are vibrated by twist force generated by a transverse beam. The novel process for fabricating resonators provides a narrow gap surrounded by flat surfaces, which can reduce the motional resistance. The fabricated resonators are measured with a laser-Doppler (LD) vibrometer. The scanning function of the LD vibrometer confirms the torsional-to-transverse vibration conversion has been successfully achieved. The measured resonant frequency, 10.96 MHz, is in good agreement with the simulated one. The Q-factor has been also measured to be as high as 2.2 ×10 4 in vacuum. The electrical characteristic is evaluated with an impedance analyzer. At the resonant frequency, the extracted motional resistance for the 0.5-µm-gap resonator is 2.0 MΩ, which is greatly reduced, owing to the narrow gap effect, from that of the 1-µm-gap resonator. The temperature coefficient of the resonant frequency between -40 and 85 °C, has been measured to be -24.4 ppm/deg. The resonant frequency linearly decreases as the temperature rises.
Genetic analysis of the role of cAMP in mediating effects of interferon. (1982)

The effects of interferon (IFN) on Fc receptor-mediated phagocytosis, intracellular cAMP levels, antiviral activity, and growth inhibition were analyzed in a cloned macrophage-like cell line, J774.2, and variants derived from it. Purified IFN increased Fc receptor-mediated phagocytosis in J774.2 cells, and in cAMP-responsive nonphagocytic variants but was without effect in cAMP-unresponsive nonphagocytic variants, in adenylate cyclase-deficient variants, and in cAMP-dependent protein kinase-deficient variants. Under conditions in which IFN augmented phagocytosis, it increased intracellular levels of cAMP. Parental cells were highly sensitive to IFN-mediated growth inhibition. In contrast, cAMP-dependent protein kinase-deficient variants were only 1/100th as sensitive to growth inhibition by IFN. All cell lines tested, both responsive and unresponsive to cAMP, were equally protected by IFN against infection with vesicular stomatitis virus, demonstrating that the antiviral state was independent of cAMP. These results indicate that, in transformed macrophages, stimulation of phagocytosis and inhibition of growth by IFN are mediated through intracellular cAMP, whereas the antiviral state induced by IFN is independent of cAMP.
Speech recognition in the Waxholm dialog system (2009)

The speech recognition component in the KTH Waxholm dialog system is described. It will handle continuous speech with a vocabulary of about 1000 words. The output of the recogniser is fed to a pr ...
Timescales: the choreography of classical and unconventional computing (2023)

Tasks that one wishes to have done by a computer often come with conditions that relate to timescales. For instance, the processing must terminate within a given time limit; or a signal processing computer must integrate input information across several timescales; or a robot motor controller must react to sensor signals with a short latency. For classical digital computing machines such requirements pose no fundamental problems as long as the physical clock rate is fast enough for the fastest relevant timescales. However, when digital microchips become scaled down into the few-nanometer range where quantum noise and device mismatch become unavoidable, or when the digital computing paradigm is altogether abandoned in analog neuromorphic systems or other unconventional hardware bases, it can become difficult to relate timescale conditions to the physical hardware dynamics. Here we explore the relations between task-defined timescale conditions and physical hardware timescales in some depth. The article has two main parts. In the first part we develop an abstract model of a generic computational system that admits a unified discussion of computational timescales. This model is general enough to cover digital computing systems as well as analog neuromorphic or other unconventional ones. We identify four major types of timescales which require separate considerations: causal physical timescales; timescales of phenomenal change which characterize the ``speed'' of how something changes in time; timescales of reactivity which describe how fast a computing system can react to incoming trigger information; and memory timescales. In the second part we survey twenty known computational mechanisms that can be used to obtain desired task-related timescale characteristics from the physical givens of the available hardware.
Defect Engineering in Plasmonic Metal Oxide Nanocrystals (2016)

Defects may tend to make crystals interesting but they do not always improve performance. In doped metal oxide nanocrystals with localized surface plasmon resonance (LSPR), aliovalent dopants and oxygen vacancies act as centers for ionized impurity scattering of electrons. Such electronic damping leads to lossy, broadband LSPR with low quality factors, limiting applications that require near-field concentration of light. However, the appropriate dopant can mitigate ionized impurity scattering. Herein, we report the synthesis and characterization of a novel doped metal oxide nanocrystal material, cerium-doped indium oxide (Ce:In2O3). Ce:In2O3 nanocrystals display tunable mid-infrared LSPR with exceptionally narrow line widths and the highest quality factors observed for nanocrystals in this spectral region. Drude model fits to the spectra indicate that a drastic reduction in ionized impurity scattering is responsible for the enhanced quality factors, and high electronic mobilities reaching 33 cm(2)V(-1) s(-1) are measured optically, well above the optical mobility for tin-doped indium oxide (ITO) nanocrystals. We investigate the microscopic mechanisms underlying this enhanced mobility with density functional theory calculations, which suggest that scattering is reduced because cerium orbitals do not hybridize with the In orbitals that dominate the bottom of the conduction band. Ce doping may also reduce the equilibrium oxygen vacancy concentration, further enhancing mobility. From the absorption spectra of single Ce:In2O3 nanocrystals, we determine the dielectric function and by simulation predict strong near-field enhancement of mid-IR light, especially around the vertices of our synthesized nanocubes.
Optic Disc Classification by Deep Learning versus Expert Neuro‐Ophthalmologists (2020)

The performance of this deep learning system at classifying optic disc abnormalities was at least as good as 2 expert neuro-ophthalmologists. Future prospective studies are needed to validate this system as a diagnostic aid in relevant clinical settings. ANN NEUROL 2020;88:785-795.
In vitro Wear of Composite with Varied Cure, Filler Level, and Filler Treatment (1997)

For the clinical wear of composite filing materials to be reduced, compositional factors such as degree of cure, filler level, and silanation level should be optimized. An oral-wear-stimulating machine was used to explore the effects of these factors on abrasion and attrition wear as well as on opposing enamel wear. The composites were made from Sr glass (1-2 micron avg) and a 50/50 Bis-GMA/TEGDMA resin. Series I (A-D, E) were light-cured (Triad II) for 9, 12, 25, and 40 sec/side to produce degree of cure (DC) as measured by FTIR of 56, 60, 61, and 63%, respectively. E received an additional heat cure (120 degrees C for 10 min) to reach a DC of 66%. Series II (D, F-I) were filled to 62, 53, 48, 37, and 28 vol%, respectively. In series III (D, J-M), the portion of fillers treated with a silane coupler (MPS) was 100, 80, 60, 40, and 20%, respectively. Samples were cycled 50,000 times against an enamel antagonist in a poppy seed/PMMA slurry in the oral wear simulator to produce abrasion (load = 20 N) and attrition (load = 70 N) simultaneously. Wear depth (micron: n = 5) was measured by profilometry. Results for each series were analysed by ANOVA/Turkey's (p < or = 0.05). The wear depths did reflect cure values, though only the abrasion difference for E < A was significant. Greater wear was correlated with lower filler levels (r2 = 0.88; p < 0.05), significantly increasing below 48 vol% (G). Wear increased linearly as the percent of silane-treated fillers was reduced (r2 = 0.99; p < 0.05). Abrasion and attrition did not differ significantly for any composite. Wear of the opposing enamel was largely unchanged by these factors. Compositional factors including degree of cure, filler level, and silanation directly affected the wear resistance of dental composites evaluated in an oral wear simulator.
ChemInform Abstract: Amidation of Esters Assisted by Mg(OCH3)2 or CaCl2. (2010)

Abstract The title reagents facilitate the direct aminolysis of various esters by NH 3 (or NH 4 Cl) and amine hydrochlorides.
The YEATS family member GAS41 interacts with the general transcription factor TFIIF (2010)

Our results demonstrate binding between endogenous GAS41 and the endogenous TFIIF subunits (RAP30 and RAP74). Since we did not find evidence for a binding of GAS41 to TBP or RNA polymerase II, GAS41 seems to preferentially bind to TFIIF. GAS41 that does not contain a DNA-binding domain appears to be a co-factor of TFIIF.
Systematic examination of carrier polarity in composition spread ZnO thin films codoped with Ga and N (2002)

We have grown high-crystallinity ZnO thin films on lattice-matched ScAlMgO4 substrates by pulsed-laser deposition with doping donor (Ga) and acceptor (N) simultaneously. Alternating ablation of ceramics with concentrated Ga addition and highly pure single crystal targets yielded in a controlled Ga concentration (CGa) in a wide range of 1018–1020 cm−3 with minimal contamination of undesired impurities such as Al and Si. The use of the originally developed temperature-gradient method, where controlled and continuous gradient of the growth temperature is given to the single substrate with a range of about 50–200 °C, results in a continuous spread of N concentration (CN) in a controlled fashion. Therefore, the ratio of CN/CGa can be varied continuously in a wide range for each film, assuring that a region satisfying p-type codoping condition predicted by T. Yamamoto and H. K. Yoshida [Jpn. J. Appl. Phys., Part 2 38, L166 (1999)] is included in the sample. The electrical properties were measured for over thousand specimens of lithographically patterned Hall bars without observing any sign of p-type conduction.
Sampling at the rate of innovation: theory and applications (2012)

Parametric signals, such as streams of short pulses, appear in many applications including bio-imaging, radar, and spread-spectrum communication. The recently developed finite rate of innovation (FRI) framework has paved the way to low-rate sampling of such signals, by exploiting the fact that only a small number of parameters per unit of time are needed to fully describe them. For example, a stream of pulses can be uniquely defined by the time delays of the pulses and their amplitudes, which leads to far fewer degrees of freedom than the signal's Nyquist rate samples. This chapter provides an overview of FRI theory, algorithms, and applications. We begin by discussing theoretical results and practical algorithms allowing perfect reconstruction of FRI signals from a minimal number of samples. We then turn to treat recovery from noisy measurements. Finally, we overview a diverse set of applications of FRI theory, in areas such as super-resolution, radar, and ultrasound.
Transport of ultrasmall gold nanoparticles (2 nm) across the blood–brain barrier in a six-cell brain spheroid model (2020)

The blood-brain barrier (BBB) is an efficient barrier for molecules and drugs. Multicellular 3D spheroids display reproducible BBB features and functions. The spheroids used here were composed of six brain cell types: Astrocytes, pericytes, endothelial cells, microglia cells, oligodendrocytes, and neurons. They form an in vitro BBB that regulates the transport of compounds into the spheroid. The penetration of fluorescent ultrasmall gold nanoparticles (core diameter 2 nm; hydrodynamic diameter 3-4 nm) across the BBB was studied as a function of time by confocal laser scanning microscopy, with the dissolved fluorescent dye (FAM-alkyne) as a control. The nanoparticles readily entered the interior of the spheroid, whereas the dissolved dye alone did not penetrate the BBB. We present a model that is based on a time-dependent opening of the BBB for nanoparticles, followed by a rapid diffusion into the center of the spheroid. After the spheroids underwent hypoxia (0.1% O<sub>2</sub>; 24 h), the BBB was more permeable, permitting the uptake of more nanoparticles and also of dissolved dye molecules. Together with our previous observations that such nanoparticles can easily enter cells and even the cell nucleus, these data provide evidence that ultrasmall nanoparticle can cross the blood brain barrier.
New Paradigms in the Continuum of Spine Care: From Newborns to Elderly Patients. (2019)

The evaluation and management of spinal disorders is complex and constantly evolving. Back pain and spinal deformity are substantial contributors to hospital and outpatient physician visits even for young patients. With new insights into the etiology, clinical presentation, and evaluation, children can be more accurately diagnosed and treated. Patients with adolescent idiopathic scoliosis may undergo selective fusion to preserve motion segments, and in some cases, vertebral body tethering or other growth-modification techniques may provide correction with motion preservation in this rapidly changing specialty. The understanding of spinopelvic parameters (pelvic incidence, pelvic tilt, sacral slope) and sagittal balance as they relate to clinical health status has provided surgeons with valuable guidance when managing pediatric and adult spinal deformity. An evidence-based approach to the management of spinal disorders across the continuum of ages has the goal of improving the value of care through optimization of outcomes and limitation of costs and complications. There are new paradigms in the management of spinal disorders and evidence-based approaches to the evaluation and management of patients across the ages.
[Analysis of plasmid pUDKH by anion-exchange high performance liquid chromatogaphy]. (2004)

pUDKH, a new plasmid DNA comprising human hepatocyte growth factor (HGF), was developed as a potential genetherapeutic product for peripheral arterial disease. An anion-exchange high performance liquid chromatographic (HPLC) method was developed to determine the proportion of plasmid DNA in both opened and supercoiled forms. A TSK gel DNA-NPR column was equilibrated with 50% buffer A (20 mmol/L Tris-HCl, pH 8.8) and 50% buffer B (buffer A with 1 mol/L NaCl added). pUDKH was analyzed by using a gradient HPLC with a mobile phase from 50% B to 80% B and with a UV detection at 260 nm. The flow rate was 0.5 mL/min. The method was also used to monitor the production procedures.
Tapentadol hydrochloride: A next-generation, centrally actinganalgesic with two mechanisms of action in a single molecule (2009)

Tapentadol exerts its analgesic effects through micro opioid receptor agonism and noradrenaline reuptake inhibition in the central nervous system. Preclinical studies demonstrated that tapentadol is effective in a broad range of pain models, including nociceptive, inflammatory, visceral, mono- and polyneuropathic models. Moreover, clinical studies showed that tapentadol effectively relieves moderate to severe pain in various pain care settings. In addition, it was reported to be associated with significantly fewer treatment discontinuations due to a significantly lower incidence of gastrointestinal-related adverse events compared with equivalent doses of oxycodone. The combination of these reduced treatment discontinuation rates and tapentadol efficacy for the relief of moderate to severe nociceptive and neuropathic pain may offer an improvement in pain therapy by increasing patient compliance with their treatment regimen.
Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae (2012)

A novel obligately anaerobic, mesophilic, organotrophic bacterium, strain P3M-1(T), was isolated from a microbial mat formed in a wooden bath filled with hot water emerging from a 2775 m-deep well in the Tomsk region of western Siberia, Russia. Cells of strain P3M-1(T) were rod-shaped, 0.3-0.7 µm in width and formed multicellullar filaments that reached up to 400 µm in length. Strain P3M-1(T) grew optimally at 42-45 °C, pH 7.5-8.0, and with 0.1% (w/v) NaCl. Under optimal conditions, the doubling time was 6 h. The isolate was able to ferment a variety of proteinaceous substrates and sugars, including microcrystalline cellulose. Acetate, ethanol and H(2) were the main products of glucose fermentation. The genomic DNA G+C content was 55 mol%. 16S rRNA gene sequence-based phylogenetic analyses showed that strain P3M-1(T) was a member of the class Anaerolinea, with 92.8 % sequence similarity to Levilinea saccharolytica KIBI-1(T). Based on phylogenetic analysis and physiological properties, strain P3M-1(T) represents a novel species in a new genus, for which the name Ornatilinea apprima gen. nov., sp. nov. is proposed; the type strain of O. apprima is P3M-1(T) (= DSM 23815(T)=VKM B-2669(T)).
Abstract 3965: An algorithm to detect somatic mutations in cancer specimens using mass spectrometric genotyping (2012)

Abstract Although advances in technology and the biological understanding of cancer pathogenesis have brought the goal of personalized cancer medicine closer, important challenges remain in several areas. One such challenge is the reliable and sensitive detection of somatic mutations in clinical tumor specimens. Somatic mutation detection in clinical tumor specimens is confounded by biological variables such as the percentage of tumor cells in a specimen, stromal contamination, sequence quality (particularly in DNA derived from formalin-fixed clinical samples), tumor heterogeneity and ploidy considerations. These and other experimental factors can lead to allele signal ratios very different from the 1:0, 1:1 or 0:1 ratio expected for a classically-defined SNP. Germline genotyping using the Sequenom MALDI-TOF mass spectrometry platform has been used to reliably detect single-nucleotide polymorphisms (SNPs) in a wide variety of samples. The automated genotype calling algorithm included with the Sequenom platform falters, however, when the ratio of allele peak signals for a given assay in a specific sample do not approximate the native algorithm's expectations of frequency, confounding accurate genotype calling by the system. We report here a cancer-specific algorithm for sensitive genotype calling of somatic mutations, based on an independent clustering of raw allele peak data for each assay run, and the identification and stratification of outliers from an empirical background (‘wildtype’) cluster of genotypes. Outliers from this cluster are then evaluated using a number of criteria to determine the quality and performance of the overall assay run, as well as the individual call; these factors include the relative signal-to-noise ratio (SNR) of each allele peak, the ratio of variant allele peak height to peak area, the percentage of signal lost in unextended probe (UEP) and relative distance of a putative mutation call from the wildtype cluster In a scatter plot of peak area values. Based on these criteria, a confidence value is assigned to each candidate outlier, allowing for stratification and prioritization of these candidates for validation. We applied the algorithm to samples run against the our OncoMap genotyping panel, comprised of 460 assays interrogating mutations in 33 cancer-associated genes. Candidate mutations produced by this algorithm correlate strongly with those called by users manually, and use of the algorithm increases the sensitivity and reliability of the OncoMap platform to detect somatic mutations in clinical tumor samples, particularly in FFPE-derived material. The algorithm code and documentation will be made publicly available in a form compatible with most Sequenom genotyping platform installations. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3965. doi:1538-7445.AM2012-3965
Supplementary Table 1 from Cancer-Associated Fibroblasts Promote Aggressive Gastric Cancer Phenotypes via Heat Shock Factor 1–Mediated Secretion of Extracellular Vesicles (2023)

&lt;p&gt;Clinical characteristics of the gastric cancer patient cohort&lt;/p&gt;