Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Headgroup Chirality on the Mixing Behavior of Phosphatidylglycerol Mimics in Fluid Bilayers

The influence of headgroup chirality on the mixing behavior of a series of phosphatidylglycerol (PG) mimics has been investigated by use of the nearest-neighbor recognition method [Vigmond, S. J.; Dewa, T. ; Regen, S. L. J. Am. Chem. Soc. 1995, 117, 7838]. For this purpose, a series of disulfide-based phospholipid dimers 1−10 were synthesized from 1,2-dimyristoyl-sn-glycero-3-phosphate and 1,2-stearoyl-sn-glycero-3-phosphate, having the R-configuration at the sn-2 carbon, and either a R- or an S-configuration within the headgroup. Results of nearest-neighbor analyses indicate that chiral interactions between the headgroup and the glycerol backbone of neighboring PG mimics have a larger influence on lipid mixing than a chain length difference of four methylenes in analogous lipids, which are devoid of chirality and a hydroxymethylene moiety in the headgroup.
Applying the Nash Bargaining Solution for a Reasonable Royalty

There has been limited success applying the Nash Bargaining Solution (NBS) in assigning intellectual property damages due to the difficulty of applying it to the specific facts of the case. Because of this, parties are not taking advantage of Georgia-Pacific factor fifteen. The intent of this paper is to bring clarity to the NBS so it can be applied to the facts of a case. This paper normalizes the NBS and provides a methodology for determining the bargaining weight in Nash's solution. Several examples are shown demonstrating the use of this normalized form, and a nomograph is added for computational ease.
Spectral variability of the 3C 390.3 nucleus for more than 20 years – II.  Variability of the broad emission-line profiles and He ii λ4686 Å emission-line fluxes

Results of the analysis of the variability of the H$\beta$ and H$\alpha$ broad emission-line profiles and the He II $\lambda4686$A emission-line fluxes in the 3C 390.3 nucleus during 1992-2014 are present. The observed velocity-dependent lag for the Balmer lines is similar to that expected from the Keplerian disc configuration, although there are some differences. Probably, a radial infall motion can be present in the broad-line region of 3C 390.3 in addition to the Keplerian rotation. The lag of the broad He II line is $26\pm 8$d, significantly less than that of the Balmer lines, so the He II emission region is much smaller in size. In terms of the power-law relationship between line and optical continuum fluxes with slowly varying scalefactor $c(t)$: $F_{line}\propto c(t)\,F_{cont}^a$, the power $a$ is $1.03$ for the broad He II line, while according to Paper I the power is equal to $0.77$ and $0.54$ for the broad H$\beta$ and H$\alpha$ lines, respectively. It means that the variability amplitude is the largest in the He II, less in H$\beta$, and more less in H$\alpha$. However, the Balmer lines contain a long-term trend that is not seen in the helium line. The narrow He II line is variable with the amplitude (max-to-min ratio) $R_{max}\approx 3$ that is much greater than the variability amplitudes of both the narrow Balmer lines and the narrow [O III] $\lambda$5007A line.
Generating Question Titles for Stack Overflow from Mined Code Snippets

Stack Overflow has been heavily used by software developers as a popular way to seek programming-related information from peers via the internet. The Stack Overflow community recommends users to provide the related code snippet when they are creating a question to help others better understand it and offer their help. Previous studies have shown that a significant number of these questions are of low-quality and not attractive to other potential experts in Stack Overflow. These poorly asked questions are less likely to receive useful answers and hinder the overall knowledge generation and sharing process. Considering one of the reasons for introducing low-quality questions in SO is that many developers may not be able to clarify and summarize the key problems behind their presented code snippets due to their lack of knowledge and terminology related to the problem, and/or their poor writing skills, in this study we propose an approach to assist developers in writing high-quality questions by automatically generating question titles for a code snippet using a deep sequence-to-sequence learning approach. Our approach is fully data-driven and uses an attention mechanism to perform better content selection, a copy mechanism to handle the rare-words problem and a coverage mechanism to eliminate word repetition problem. We evaluate our approach on Stack Overflow datasets over a variety of programming languages (e.g., Python, Java, Javascript, C# and SQL) and our experimental results show that our approach significantly outperforms several state-of-the-art baselines in both automatic and human evaluation. We have released our code and datasets to facilitate other researchers to verify their ideas and inspire the follow up work.
A family of Vlasov–Maxwell equilibrium distribution functions describing a transition from the Harris sheet to the force-free Harris sheet

We discuss a family of Vlasov–Maxwell equilibrium distribution functions for current sheet equilibria that are intermediate cases between the Harris sheet and the force-free (or modified) Harris sheet. These equilibrium distribution functions have potential applications to space and astrophysical plasmas. The existence of these distribution functions had been briefly discussed by Harrison & Neukirch (Phys. Rev. Lett., vol. 102, (2009a), 135003), but here it is shown that their approach runs into problems in the limit where the guide field goes to zero. The nature of this problem will be discussed and an alternative approach will be suggested that avoids the problem. This is achieved by considering a slight variation of the magnetic field profile, which allows a smooth transition between the Harris and force-free Harris sheet cases.
Molecular and biochemical markers of some Vicia faba L. genotypes in response to storage insect pests infestation

Storage insect pests cause serious losses to all legume crops in both quality and quantity. This study was conducted to study some morphological characters and biochemical components in eight genotypes of faba bean to determine biochemical and molecular markers for resistance and susceptibility to infestation with stored insects. The results showed that chlorophyll content in leaves, phenol, tannin, peroxidase (POD), polyphenol oxidase (PPO), and protein content in leaves and seeds of faba bean plants either significantly or non significantly increased the effect of insect infestation in the resistance genotypes (L.551, L.512, L.153, NA112, and L.1) as compared with the susceptible genotypes (L.16 and T.W). Protein electrophoresis showed a wide variation between genotypes and determined some biochemical markers (sodium dodecyl sulfate poly acrylamide gel electrophoresis, SDS-PAGE). In addition, molecular genetic markers for stored insects' resistance were obtained using inter-simple sequence repeat polymerase chain reaction (ISSR-PCR) analyses.
A New Method for Sampling Spider Mites on Field Crops

Abstract. Multiple factors contribute to the significant challenge of obtaining an accurate assessment of infestations of spider mites under field conditions in field crops and trees. In addition, standard practices for counting spider mites do not provide a historical record of individual numbers. We developed and evaluated a new device, the “leaf inspector”, for sampling spider mites. Adhesive tape was pressed toward the underside of leaves of maize, Zea mays L. , and spider mites on pieces of tape were counted later with the aid of a stereoscope (16–25 magnification). Sampling spider mites using the leaf inspector in the field required 30–60 seconds per leaf, and subsequent counting of spider mites with the aid of a stereoscope required 8 minutes per piece of tape. We showed that: 1) absolute numbers of spider mites on maize leaves were positively correlated with those obtained with the leaf inspector, 2) leaf dimensions did not significantly affect performance of the leaf inspector, and 3) a residual but fairly constant percentage (about 20%) of spider mites was left behind after a maize leaf had been sampled with the leaf inspector. Thus, a more accurate estimation of spider mite abundance was obtained by adding 20% to each count based on using the leaf inspector.
Beware of commonly used approximations. Part II. Estimating systematic biases in the best-fit parameters

Cosmological parameter estimation from forthcoming experiments promise to reach much greater precision than current constraints. As statistical errors shrink, the required control over systematic errors increases. Therefore, models or approximations that were sufficiently accurate so far, may introduce significant systematic biases in the parameter best-fit values and jeopardize the robustness of cosmological analyses. We generalize previously proposed expressions to estimate a priori the systematic error introduced in parameter inference due to the use of insufficiently good approximations in the computation of the observable of interest or the assumption of an incorrect underlying model. Although this methodology can be applied to measurements of any scientific field, we illustrate its power by studying the effect of modeling the angular galaxy power spectrum incorrectly. We also introduce Multi_CLASS, a new, public modification of the Boltzmann code CLASS, which includes the possibility to compute angular cross-power spectra for two different tracers. We find that significant biases in most of the cosmological parameters are introduced if one assumes the Limber approximation or neglects lensing magnification in modern galaxy survey analyses, and the effect is in general larger for the multi-tracer case, especially for the parameter controlling primordial non-Gaussianity of the local type, fNL.
Consistent ICA: Determined BSS Meets Spectrogram Consistency

Multichannel audio blind source separation (BSS) in the determined situation (the number of microphones is equal to that of the sources), or determined BSS, is performed by multichannel linear filtering in the time-frequency domain to handle the convolutive mixing process. Ordinarily, the filter treats each frequency independently, which causes the well-known permutation problem, i.e., the problem of how to align the frequency-wise filters so that each separated component is correctly assigned to the corresponding sources. In this paper, it is shown that the general property of the time-frequency-domain representation called spectrogram consistency can be an assistant for solving the permutation problem.
Applying the Transformer to Character-level Transduction

The transformer has been shown to outperform recurrent neural network-based sequence-to-sequence models in various word-level NLP tasks. Yet for character-level transduction tasks, e.g. morphological inflection generation and historical text normalization, there are few works that outperform recurrent models using the transformer. In an empirical study, we uncover that, in contrast to recurrent sequence-to-sequence models, the batch size plays a crucial role in the performance of the transformer on character-level tasks, and we show that with a large enough batch size, the transformer does indeed outperform recurrent models. We also introduce a simple technique to handle feature-guided character-level transduction that further improves performance. With these insights, we achieve state-of-the-art performance on morphological inflection and historical text normalization. We also show that the transformer outperforms a strong baseline on two other character-level transduction tasks: grapheme-to-phoneme conversion and transliteration.
AutoML Segmentation for 3D Medical Image Data: Contribution to the MSD Challenge 2018

Fueled by recent advances in machine learning, there has been tremendous progress in the field of semantic segmentation for the medical image computing community. However, developed algorithms are often optimized and validated by hand based on one task only. In combination with small datasets, interpreting the generalizability of the results is often difficult. The Medical Segmentation Decathlon challenge addresses this problem, and aims to facilitate development of generalizable 3D semantic segmentation algorithms that require no manual parametrization. Such an algorithm was developed and is presented in this paper. It consists of a 3D convolutional neural network with encoder-decoder architecture employing residual-connections, skip-connections and multi-level generation of predictions. It works on anisotropic voxel-geometries and has anisotropic depth, i.e., the number of downsampling steps is a task-specific parameter. These depths are automatically inferred for each task prior to training. By combining this flexible architecture with on-the-fly data augmentation and little-to-no pre-- or postprocessing, promising results could be achieved. The code developed for this challenge will be available online after the final deadline at: this https URL
Localization & Mitigation of Cascading Failures in Power Systems, Part I: Spectral Representation & Tree Partition

Cascading failures in power systems propagate non-locally, making the control of outages extremely difficult. In this work, we propose a new framework that offers strong analytical guarantees on both the localization and mitigation of cascading failures in power systems. The key component of this framework leverages the concept of tree partition, which characterizes regions of a power network inside which line failures are automatically localized. In Part I of this paper we establish a mathematical theory that underlies all the performance guarantees of tree partition, as well as its failure localization properties. This theory consists of a set of tools developed using the Laplacian matrix of the transmission network and reveals a novel perspective that precisely captures the Kirchhoff's Law in terms of topological structures. Our results show that the distribution of different families of subtrees of the transmission network plays a critical role on the patterns of power redistribution, and motivates tree partitioning of the network as a strategy to eliminate long-distance propagation of disturbances. These results are used in Parts II and III of this paper to design strategies to localize and mitigate line failures.
Real-Time Radar-Based Gesture Detection and Recognition Built in an Edge-Computing Platform

In this paper, a real-time signal processing framework based on a 60 GHz frequency-modulated continuous wave (FMCW) radar system to recognize gestures is proposed. In order to improve the robustness of the radar-based gesture recognition system, the proposed framework extracts a comprehensive hand profile, including range, Doppler, azimuth and elevation, over multiple measurement-cycles and encodes them into a feature cube. Rather than feeding the range-Doppler spectrum sequence into a deep convolutional neural network (CNN) connected with recurrent neural networks, the proposed framework takes the aforementioned feature cube as input of a shallow CNN for gesture recognition to reduce the computational complexity. In addition, we develop a hand activity detection (HAD) algorithm to automatize the detection of gestures in real-time case. The proposed HAD can capture the time-stamp at which a gesture finishes and feeds the hand profile of all the relevant measurement-cycles before this time-stamp into the CNN with low latency. Since the proposed framework is able to detect and classify gestures at limited computational cost, it could be deployed in an edge-computing platform for real-time applications, whose performance is notedly inferior to a state-of-the-art personal computer. The experimental results show that the proposed framework has the capability of classifying 12 gestures in real-time with a high ${F}_{\sf 1}$ -score.
Citric Acid Fermentation and the Effects of Temperature

The temperature of the fermentation media heavily affects yields as well as rates of citric acid fermentations. At 26-28 °C, more than 40% of the available carbohydrate raw material is wasted, apparently through the respiratory activity of the fungus. At 30-32 °C, these losses are decreased to about 10%. The results thus emphasise the economic importance of adequate temperature control in industrial citric acid fermentation.
ς1 Receptor Agonist-Mediated Regulation ofN-Methyl-d-aspartate-Stimulated [3H]Dopamine Release Is Dependent upon Protein Kinase C

We have previously shown that ς1 receptor agonists inhibit N-methyl-d-aspartate (NMDA)-stimulated [3H]dopamine from slices of rat striatum in a concentration-related manner and that the inhibition is reversed by ς1 receptor-selective and nonsubtype-selective ς receptor antagonists. Based on previous evidence from our laboratory as well as other laboratories, we hypothesized that ς1 receptors might use a protein kinase C (PKC) signaling pathway to modulate stimulated dopamine release. We tested several inhibitors of PKC isozymes, as well as a phospholipase C inhibitor for their effects on ς1 receptor agonist-mediated regulation of [3H]dopamine release. Although none of the inhibitors tested affected the ability of NMDA to stimulate [3H]dopamine release, they all abolished regulation by the ς1 receptor agonist (+)-pentazocine in a concentration-related manner. We also found that prior exposure to 1 μM phorbol 2-myristate 13-acetate for 30 min abolished regulation by (+)-pentazocine. We concluded that an intact PKC system was required for ς1 agonist-mediated regulation of NMDA-stimulated [3H]dopamine release from rat striatal slices. Based on the pharmacological profile of the PKC inhibitors tested, as well as reports in the literature on PKC involvement in neurotransmitter release and ς receptor action, PKCβ seems most likely to be responsible, at least in part, for the effects of (+)-pentazocine on dopamine release.
The Use of Information Theory in Biology: Lessons from Social Insects

In this paper, I discuss how information theory has been used in the study of animal communication, as well as how these uses are justified. Biologists justify their use of Shannon’s information measures by the work they do in allowing for comparisons between different organisms and because they measure a quantity that is purported to be important for natural selection. I argue that there are problems with both sorts of justification. To make these difficulties clear, I focus on the use of Shannon’s information measures to quantify the amount of information transmitted by the fire ant’s odor trail and the honeybee’s waggle dance. Both of these systems are relatively simple and well understood, and the application of Shannon’s information measure to these systems initially seemed very promising and relatively straightforward. They are therefore particularly suitable for revealing the benefits and difficulties of applying Shannon’s information measures to biological systems in general, and animal communication systems in particular.
Seasonal cycles in the germination capacity of buried seeds of some Leguminosae (Fabaceae)

Summary • The influence of seasonal factors on the germination of impermeable seeds of Fabaceae was studied. Seeds of 14 herbaceous species were buried for up to 2.5 yr and exposed to natural seasons. At regular intervals, seeds were exhumed and germination was tested in four different temperature regimes. Some species had a very low percentage germination regardless of season, others germinated predominantly in the autumn. • Six species showed a marked seasonal cycle with high germination percentages in spring and very low percentages in other seasons. The results of the burial experiment were similar to the pattern of seedling emergence in field conditions. • High percentage germination in spring could be simulated in controlled conditions for Melilotus albus, Medicago lupulina, Lotus corniculatus, Trifolium pratense and T. repens. Seeds of T. pratense had a high percentage germination after cold treatment, whereas seeds of the other four species were brought to germination by chilling for 8 wk followed by exposure to daily alternating temperatures (15/6°C or 20/10°C). Without previous chilling, these seeds did not respond to the alternating temperatures. • At least for some legume species, a combination of temperature treatments may act as a signal for seeds and induce water uptake and germination. If the temperature requirements are not fulfilled, seeds remain impermeable and dormant until the next favourable season.
Big boys on top: effects of body size, sex and reproductive state on perching behaviour in the tropical rock dragon, Psammophilus dorsalis

Perching behaviour, in relation to sex, body size and reproductive phases, was studied in the field in a population of the tropical rock lizard, Psammophilus dorsalis. Adult lizards (n = 14 males and 16 females) were marked by toe clipping in November 2001. They were observed at intervals (n = 10 times) over the next 18 months encompassing post-breeding (December-early March), recrudescence (late March-April) and breeding (May-August) phases. In the post-breeding phase, males perched at lower heights. They began perching higher during the recrudescence phase with the highest perches in the breeding phase. In comparison to females, the males perched higher than females all year round and showed greater among-individual variations in perch height. The bigger males perched at greater heights compared to smaller ones during recrudescence and breeding phases. No such trend was evident during the post-breeding phase and perch height was not related to body size. Females moved within a narrow range of heights from the substrata and showed no size-specific relationship in perch selection throughout the reproductive cycle. Selection of higher perches by the males, despite high predation risk, possibly helps in territory defence, courtship displays and in advertising their presence to conspecifics. Further, size-specific perch selection prior to and during the breeding period, suggests that size vis-a-vis age and reproductive cycle also influences selection of perch height in males. In females perching close to the substrata, refuge sites and food sources, seems to be associated with escape from predators, foraging benefits and, in turn, reproductive fitness. Thus, in the seasonally breeding P. dorsalis, sex and reproductive status determine the complex pattern of perching behaviour and, possibly, circulating levels of androgens drive the bigger boys on top in accordance with their size or age.
Quantum reflections of nonlocal optical solitons in a cold Rydberg atomic gas

Quantum reflection refers to a non-vanishing reflection probability in the absence of a classically turning point. Much attention has been paid to such reflections due to their fundamental, intriguing physics and potential practical applications. Here we propose a scheme to realize a quantum reflection of nonlocal nonlinear optical beams in a cold Rydberg atomic gas via electromagnetically induced transparency working in a dispersion regime. Based on the long-range interaction between Rydberg atoms, we found that the system supports low-power nonlocal optical solitons. Such nonlocal solitons can display a sharp transition between reflection, trapping, and transmission when scattered by a linear attractive potential, created by gate photons stored in another Rydberg state. Different from conventional physical systems explored up to now, the quantum reflection of the nonlocal optical solitons in the Rydberg atomic gas exhibits interesting anomalous behaviors, which can be actively manipulated by tuning the incident velocity and intensity of the probe field, as well as the nonlocality of the Kerr nonlinearity inherent in the Rydberg atomic gas. The results reported here are not only useful for developing Rydberg nonlinear optics but also helpful for characterizing the physical property of the Rydberg gas and for designing novel nonlinear optical devices.