gebhart/patrepeval huggingface dataset:
One Juliet and four Romeos: VeA and its methyltransferases (2015)

Fungal secondary metabolism has become an important research topic with great biomedical and biotechnological value. In the postgenomic era, understanding the diversity and the molecular control of secondary metabolites (SMs) are two challenging tasks addressed by the research community. Discovery of the LaeA methyltransferase 10 years ago opened up a new horizon on the control of SM research when it was found that expression of many SM gene clusters is controlled by LaeA. While the molecular function of LaeA remains an enigma, discovery of the velvet family proteins as interaction partners further extended the role of the LaeA beyond secondary metabolism. The heterotrimeric VelB-VeA-LaeA complex plays important roles in development, sporulation, secondary metabolism, and pathogenicity. Recently, three other methyltransferases have been found to associate with the velvet complex, the LaeA-like methyltransferase F and the methyltransferase heterodimers VipC-VapB. Interaction of VeA with at least four methyltransferase proteins indicates a molecular hub function for VeA that questions: Is there a VeA supercomplex or is VeA part of a highly dynamic cellular control network with many different partners?
Role of ambient temperature in modulation of behavior of vanadium dioxide volatile memristors and oscillators for neuromorphic applications (2022)

Volatile memristors are versatile devices whose operating mechanism is based on an abrupt and volatile change of resistivity. This switching between high and low resistance states is at the base of cutting edge technological implementations such as neural/synaptic devices or random number generators. A detailed understanding of this operating mechanisms is essential prerequisite to exploit the full potentiality of volatile memristors. In this respect, multi-physics device simulations provide a powerful tool to single out material properties and device features that are the keys to achieve desired behaviors. In this paper, we perform 3D electrothermal simulations of volatile memristors based on vanadium dioxide (VO[Formula: see text]) to accurately investigate the interplay among Joule effect, heat dissipation and the external temperature [Formula: see text] over their resistive switching mechanism. In particular, we extract from our simulations a simplified model for the effect of [Formula: see text] over the negative differential resistance (NDR) region of such devices. The NDR of VO[Formula: see text] devices is pivotal for building VO[Formula: see text] oscillators, which have been recently shown to be essential elements of oscillatory neural networks (ONNs). ONNs are innovative neuromorphic circuits that harness oscillators' phases to compute. Our simulations quantify the impact of [Formula: see text] over figures of merit of VO[Formula: see text] oscillator, such as frequency, voltage amplitude and average power per cycle. Our findings shed light over the interlinked thermal and electrical behavior of VO[Formula: see text] volatile memristors and oscillators, and provide a roadmap for the development of ONN technology.
LCSR Method to Verify the Attachment of Temperature Sensors and Strain Gauges to Solid Material (2003)

Resistance Temperature Detectors (RTDs) and thermocouples in some applications are attached to solid surfaces or imbedded in solid material for measurement of temperature of the solid material or the material within the solid boundary. For example, thermocouples are imbedded in the nozzle of Solid Rocket Motors (SRMs) to measure the temperature of the lining material of the nozzle. These thermocouples must remain intact during SRM firing tests to provide an accurate temperature profile especially under transient temperature conditions. This paper describes the Loop Current Step Response (LCSR) method that was developed for this and a number of other applications. This method is based on heating the thermocouple with an electric current to characterize the heat transfer condition around the measuring tip of the thermocouple. The same principle can also be used to verify the attachment of RTDs and strain gauges to solid surfaces. This is important in such applications as fuel leak detection in space shuttle engines, measurement of fluid temperatures within pressure sensing lines in nuclear power plants, and diagnostics of problems in instrumentation which involve strain gauges.
First principles study on electrochemical and chemical stability of solid electrolyte–electrode interfaces in all-solid-state Li-ion batteries (2015)

This study provides the understanding and design strategy of solid electrolyte–electrode interfaces to improve electrochemical performance of all-solid-state Li-ion batteries.
The SCUBA Half Degree Extragalactic Survey (SHADES) – IX. The environment, mass and redshift dependence of star formation (2008)

We present a comparison between the SCUBA (Submillimetre Common User Bolometer Array) Half Degree Extragalactic Survey (SHADES) at 450 and 850 μm in the Lockman Hole East with a deep Spitzer Space Telescope survey at 3.6–24 μm conducted in guaranteed time. Using stacking analyses we demonstrate a striking correspondence between the galaxies contributing the submm extragalactic background light, with those likely to dominate the backgrounds at Spitzer wavelengths. Using a combination BRIzK plus Spitzer photometric redshifts, we show that at least a third of the Spitzer-identified submm galaxies at 1 < z < 1.5 appear to reside in overdensities when the density field is smoothed at 0.5–2 Mpc comoving diameters, supporting the high-redshift reversal of the local star formation–galaxy density relation. We derive the dust-shrouded cosmic star formation history of galaxies as a function of assembled stellar masses. For model stellar masses <1011M⊙, this peaks at lower redshifts than the ostensible z∼ 2.2 maximum for submm point sources, adding to the growing consensus for ‘downsizing’ in star formation. Our surveys are also consistent with ‘downsizing’ in mass assembly. Both the mean star formation rates 〈dM*/dt〉 and specific star formation rates 〈(1/M*) d M*/d t〉 are in striking disagreement with some semi-analytic predictions from the Millenium Simulation. The discrepancy could either be resolved with a top-heavy initial mass function, or a significant component of the submm flux heated by the interstellar radiation field.
Scalable approximate Bayesian inference for particle tracking data (2018)

Abstract Many important datasets in physics, chemistry, and biology consist of noisy sequences of images of multiple moving overlapping particles. In many cases, the observed particles are indistinguishable, leading to unavoidable uncertainty about nearby particles’ identities. Exact Bayesian inference is intractable in this setting, and previous approximate Bayesian methods scale poorly. Non-Bayesian approaches that output a single “best” estimate of the particle tracks (thus discarding important uncertainty information) are therefore dominant in practice. Here we propose a flexible and scalable amortized approach for Bayesian inference on this task. We introduce a novel neural network method to approximate the (intractable) filter-backward-sample-forward algorithm for Bayesian inference in this setting. By varying the simulated training data for the network, we can perform inference on a wide variety of data types. This approach is therefore highly flexible and improves on the state of the art in terms of accuracy; provides uncertainty estimates about the particle locations and identities; and has a test run-time that scales linearly as a function of the data length and number of particles, thus enabling Bayesian inference in arbitrarily large particle tracking datasets.
Periphery‐Functionalized Porous Organic Cages (2016)

By synthesizing derivatives of a trans-1,2-diaminocyclohexane precursor, three new functionalized porous organic cages were prepared with different chemical functionalities on the cage periphery. The introduction of twelve methyl groups (CC16) resulted in frustration of the cage packing mode, which more than doubled the surface area compared to the parent cage, CC3. The analogous installation of twelve hydroxyl groups provided an imine cage (CC17) that combines permanent porosity with the potential for post-synthetic modification of the cage exterior. Finally, the incorporation of bulky dihydroethanoanthracene groups was found to direct self-assembly towards the formation of a larger [8+12] cage, rather than the expected [4+6], cage molecule (CC18). However, CC18 was found to be non-porous, most likely due to cage collapse upon desolvation.
Interstitial deletion of chromosome 12q: Genotype–phenotype correlation of two patients utilizing array comparative genomic hybridization (2005)

Interstitial deletions of chromosome 12q are rare, with only 11 reported cases in the literature. We recently described two cases with cytogenetically identical interstitial deletions of the long arm of chromosome 12. Here, we report on a third patient, a 26-month-old male with a cytogenetically-identical interstitial deletion: 46,XY,del(12)(q21.2q22). Phenotypic features of this male proband included craniofacial and ectodermal anomalies, genitourinary anomalies, minor cardiac abnormalities, mild ventriculomegaly on brain MRI, hyperopia, and developmental delay. To further define the extent of the chromosomal aberration, microarray-based comparative genomic hybridization (array CGH) analysis was performed and the array data was compared to one of our previously reported cases. Although cytogenetic analysis of the two patients was concordant, molecular analysis by array CGH revealed that the patients had discordant distal breakpoints. The determination of molecular breakpoints and phenotypic analyses in these two patients, in conjunction with previously reported cases, leads us to propose a 12q deletion phenotype and a possible genetic locus for hyperkeratosis pilaris/ulerythema ophryogenes.
Expression of an unusual T cell receptor (TCR)-V beta repertoire by Ly-6C+ subpopulations of CD4+ and/or CD8+ thymocytes. Evidence for a developmental relationship between Ly-6C+ thymocytes and CD4-CD8-TCR-alpha beta+ thymocytes (1991)

A novel thymocyte subpopulation expressing an unusual TCR repertoire was identified by high surface expression of the Ly-6C Ag. Ly-6C+ thymocytes were distributed among all four CD4/CD8 thymocyte subsets, and represented a readily identifiable subpopulation within each one. Ly-6C+ thymocytes express TCR-alpha beta, arise late in ontogeny, and appear in the CD4/CD8 developmental pathway after birth in a sequence that resembles that followed by conventional Ly-6C- cells during fetal ontogeny. Most interestingly, adult Ly-6C+ thymocytes express an unusual TCR-V beta repertoire that is identical to that expressed by CD4-CD8-TCR-alpha beta+ thymocytes in its overexpression of TCR-V beta 8 and in its expression of some potentially autoreactive TCR-V beta specificities. This unusual TCR-V beta repertoire was even expressed by Ly-6C+ thymocytes contained within the CD4+ CD8- 'single positive' thymocyte subset. Thus, expression of this unusual TCR-V beta repertoire is not limited to CD4-CD8-thymocytes, and is unlikely to be a consequence of their double negative phenotype. Rather, we think that Ly-6C+TCR-alpha beta+ thymocytes and CD4-CD8-TCR-alpha beta+ are developmentally interrelated, a conclusion supported by several lines of evidence including the selective failure of both Ly-6C+ and CD4-CD8-TCR-alpha beta+ thymocyte subsets to appear in TCR-beta transgenic mice. In contrast, peripheral Ly-6C+ T cells are developmentally distinct from Ly-6C+ thymocytes in that peripheral Ly-6C+ T cells expressed a conventional TCR-V beta repertoire and developed normally in TCR-beta transgenic mice in which Ly-6C+ thymocytes failed to arise. We conclude that: 1) expression of a skewed TCR-V beta repertoire is a characteristic of Ly-6C+TCR-alpha beta+ thymocytes as well as CD4-CD8-TCR-alpha beta+ thymocytes, and is not unique to thymocytes expressing neither CD4 nor CD8 accessory molecules; and 2) Ly-6C+ thymocytes are developmentally linked to CD4-CD8-TCR-alpha beta+ thymocytes, but not to Ly-6C+ peripheral T cells. We suggest that Ly-6C+TCR-alpha beta+ thymocytes are not the developmental precursors of Ly-6C+ peripheral T cells, but rather may be the developmental precursors of CD4-CD8-TCR-alpha beta+ thymocytes.
A Single Chip 1 W CMOS Audio Power Amplifier with Pseudo Buffer Analog and Class D Switching Mixed Mode for Mobile Application (2005)

A single chip analog and class D switching mixed mode audio power amplifier using 0.35 μm CMOS process is presented in this paper. It has on-chip power MOSFET's and adopts a novel reverse recovery current free gate control that can reduce EMI noise and current stress of the power MOSFETs. It shows about 0.1% THD at 1 kHz and up to 87% efficiency at 4 Ω BTL at 3.3 V single power supply.
Interrelationship of Velocity and Chest Compression in Blunt Thoracic Impact to Swine (1981)

&lt;div class="htmlview paragraph"&gt;As part of a continuing study of thoracic injury resulting from blunt frontal loading, the interrelationship of velocity and chest compression was investigated in a series of animal experiments. Anesthetized male swine were suspended in their natural posture and subjected to midsternal, ventrodorsad impact. Twelve animals were struck at a velocity of 14.5 ± 0.9 m/s and experienced a controlled thoracic compression of either 15, 19, or 24%. Six others were impacted at 9.7 ± 1.3 m/s with a greater mean compression of 27%.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;For the 14.5 m/s exposures the severity of trauma increased with increasing compression, ranging from minor to fatal. Injuries included skeletal fractures, pulmonary contusions, and cardiovascular ruptures leading to tamponade and hemothorax. Serious cardiac arrhythmias also occurred, including one case of lethal ventricular fibrillation. The 9.7 m/s exposures produced mainly pulmonary contusion, ranging in severity from moderate to critical. Cardiac arrhythmias occurred but were typically minor. In contrast to the lower compression impacts at 14.5 m/s, there were no rib fractures or cardiovascular ruptures. In general, peak sternal acceleration and applied force correlated with impact velocity but not with normalized compression; and spinal acceleration did not correlate with any parameter.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Overall, the high velocity exposures, produced higher mechanical responses, more severe gross trauma and more serious cardiac arrhythmias despite lower compression levels. The results of this study while reconfirming normalized compression as one correlate of injury, emphasize the importance of loading velocity in determining the overall severity of blunt thoracic impact.&lt;/div&gt;
SCRF-DFT and NMR Comparison of Tetracycline and 5a,6-Anhydrotetracycline in Solution (2006)

A combination of structures, energies, and spectral data calculated using density functional theory (DFT) with experimental NMR data has been used to assign conformational equilibria for tetracycline and 5a,6-anhydrotetracycline in water at pH 1, 7, and 10 and in chloroform (5a,6-anhydrotetracycline) and methanol (tetracycline). The results suggest that tetracycline always prefers the extended conformation but that 5a,6-anhydrotetracycline exists in water as a mixture of the two conformers and in chloroform exclusively in the twisted conformation. The conformational equilibria are also shown to be pH dependent.
Synthesis of Benzimidazole-Fused Heterocycles by Intramolecular Oxidative C-N Bond Formation Using Hypervalent Iodine Reagents (2011)

A straightforward approach by dehydrogenative C-N coupling between aryl C-H and N-H bonds using a hypervalent iodine reagent under mild conditions offers a versatile and convenient method for synthesizing various benzimidazole-fused heterocycles.
Background memory area estimation for multidimensional signal processing systems (1995)

Memory cost is responsible for a large amount of the chip and/or board area of customized video and image processing system realizations. In this paper, we present a novel technique-founded on data-flow analysis which allows one to address the problem of background memory size evaluation for a given nonprocedural algorithm specification, operating on multidimensional signals with affine indexes. Most of the target applications are characterized by a huge number of signals, so a new polyhedral data-flow model operating on groups of scalar signals is proposed. These groups are obtained by a novel analytical partitioning technique, allowing to select a desired granularity, depending on the application complexity. The method incorporates a way to tradeoff memory size with computational and controller complexity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Facilitated Glutamatergic Transmission in the Striatum of D2Dopamine Receptor-Deficient Mice (2001)

Dopamine (DA) receptors play an important role in the modulation of excitability and the responsiveness of neurons to activation of excitatory amino acid receptors in the striatum. In the present study, we utilized mice with genetic deletion of D2 or D4 DA receptors and their wild-type (WT) controls to examine if the absence of either receptor subtype affects striatal excitatory synaptic activity. Immunocytochemical analysis verified the absence of D2 or D4 protein expression in the striatum of receptor-deficient mutant animals. Sharp electrode current- and whole cell patch voltage-clamp recordings were obtained from slices of receptor-deficient and WT mice. Basic membrane properties were similar in D2 and D4 receptor-deficient mutants and their respective WT controls. In current-clamp recordings in WT animals, very little low-amplitude spontaneous synaptic activity was observed. The frequency of these spontaneous events was increased slightly in D2 receptor-deficient mice. In addition, large-amplitude depolarizations were observed in a subset of neurons from only the D2 receptor-deficient mutants. Bath application of the K+ channel blocker 4-aminopyridine (100 microM) and bicuculline methiodide (10 microM, to block synaptic activity due to activation of GABA(A) receptors) markedly increased spontaneous synaptic activity in receptor-deficient mutants and WTs. Under these conditions, D2 receptor-deficient mice displayed significantly more excitatory synaptic activity than their WT controls, while there was no difference between D4 receptor-deficient mice and their controls. In voltage-clamp recordings, there was an increase in frequency of spontaneous glutamate receptor-mediated inward currents without a change in mean amplitude in D2 receptor-deficient mutants. In WT mice, activation of D2 family receptors with quinpirole decreased spontaneous excitatory events and conversely sulpiride, a D2 receptor antagonist, increased activity. In D2 receptor-deficient mice, sulpiride had very little net effect. Morphologically, a subpopulation of medium-sized spiny neurons from D2 receptor-deficient mice displayed decreased dendritic spines compared with cells from WT mice. These results provide evidence that D2 receptors play an important role in the regulation of glutamate receptor-mediated activity in the corticostriatal or thalamostriatal pathway. These receptors may function as gatekeepers of glutamate release or of its subsequent effects and thus may protect striatal neurons from excessive excitation.
Synthese von O‐Acetyl‐N‐(4‐biphenylyl)hydroxylamin („N‐Acetoxy‐4‐aminobiphenyl”), einem entscheidenden Metaboliten des carcinogenen 4‐Aminobiphenyls, und seine Reaktion mit Desoxyguanosin (1989)

Die Carcinogenität aromatischer Amine ist seit 1895 bekannt. Welches Schicksal haben diese Verbindungen im Organismus? In vitro ließ sich das aus 4‐Aminobiphenyl 1 erzeugte Hydroxylamin‐Derivat jetzt erstmals in die kristalline Titelverbindung 2 umwandeln. 2 reagiert mit Desoxyguanosin zu den gleichen „Addukten”︁, die z. B. auch erhalten werden, wenn man 1 Hunden verabreicht und die DNA anschließend enzymatisch spaltet (Aryl=4‐Biphenylyl). magnified image
NASTransfer: Analyzing Architecture Transferability in Large Scale Neural Architecture Search (2021)

Neural Architecture Search (NAS) is an open and challenging problem in machine learning. While NAS offers great promise, the prohibitive computational demand of most of the existing NAS methods makes it difficult to directly search the architectures on large-scale tasks. The typical way of conducting large scale NAS is to search for an architectural building block on a small dataset (either using a proxy set from the large dataset or a completely different small scale dataset) and then transfer the block to a larger dataset. Despite a number of recent results that show the promise of transfer from proxy datasets, a comprehensive evaluation of different NAS methods studying the impact of different source datasets has not yet been addressed. In this work, we propose to analyze the architecture transferability of different NAS methods by performing a series of experiments on large scale benchmarks such as ImageNet1K and ImageNet22K. We find that: (i) The size and domain of the proxy set does not seem to influence architecture performance on the target dataset. On average, transfer performance of architectures searched using completely different small datasets (e.g., CIFAR10) perform similarly to the architectures searched directly on proxy target datasets. However, design of proxy sets has considerable impact on rankings of different NAS methods. (ii) While different NAS methods show similar performance on a source dataset (e.g., CIFAR10), they significantly differ on the transfer performance to a large dataset (e.g., ImageNet1K). (iii) Even on large datasets, random sampling baseline is very competitive, but the choice of the appropriate combination of proxy set and search strategy can provide significant improvement over it. We believe that our extensive empirical analysis will prove useful for future design of NAS algorithms.
Melting line of the Lennard-Jones system, infinite size, and full potential (2007)

Literature estimates of the melting curve of the Lennard-Jones system vary by as much as 10%. The origin of such discrepancies remains unclear. We present precise values for the Lennard-Jones melting temperature, and we examine possible sources of systematic errors in the prediction of melting points, including finite-size and interaction-cutoff effects. A hypothetical thermodynamic integration path is used to find the relative free energies of the solid and liquid phases, for various system sizes, at constant cutoff radius. The solid-liquid relative free energy and melting temperature scale linearly as the inverse of the number of particles, and it is shown that finite-size effects can account for deviations in the melting temperature (from the infinite-size limit) of up to 5%. An extended-ensemble density-of-states method is used to determine free energy changes for each phase as a continuous function of the cutoff radius. The resulting melting temperature predictions exhibit an oscillatory behavior as the cutoff radius is increased. Deviations in the melting temperature (from the full potential limit) arising from a finite cutoff radius are shown to be of comparable magnitude as those resulting from finite-size effects. This method is used to identify melting temperatures at five different pressures, for the infinite-size and full potential Lennard-Jones system. We use our simulation results as references to connect the Lennard-Jones solid equation of state of van der Hoef with the Lennard-Jones fluid equation of state of Johnson. Once the references are applied the two equations of state are used to identify a melting curve. An empirical equation that fits this melting curve is provided. We also report a reduced triple point temperature T(tr)=0.694.