bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective gene expression prediction from sequence by integrating long-range interactions
Authors: Avsec Žiga , Agarwal Vikram , Visentin Daniel , Ledsam Joseph R. , Grabska-Barwinska Agnieszka , Taylor Kyle R. , Assael Yannis , Jumper John , Kohli Pushmeet , Kelley David R. 
Published: October 2021

AbstractHow noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction accuracy from DNA sequences through the use of a deep learning architecture, called Enformer, that is able to integrate information from long-range interactions (up to 100 kb away) in the genome. This improvement yielded more accurate variant effect predictions on gene expression for both natural genetic variants and saturation mutagenesis measured by massively parallel reporter assays. Furthermore, Enformer learned to predict enhancer–promoter interactions directly from the DNA sequence competitively with methods that take direct experimental data as input. We expect that these advances will enable more effective fine-mapping of human disease associations and provide a framework to interpret cis-regulatory evolution.
The Avian Diet Database as a source of quantitative information on bird diets
Authors: Hurlbert Allen H. , Olsen Aaron M. , Sawyer Melissa M. , Winner Patrick M. 
Published: October 2021

AbstractThis data paper describes a compilation of 73,075 quantitative diet data records for 759 primarily North American bird species, providing standardized information not just on the diet itself, but on the context for that diet information including the year, season, location, and habitat type of each study. The methods used for collecting and cleaning these data are described, and we present tools for summarizing and visualizing diet information by bird species or prey.
Dramatic increase in lever-pressing activity in rats after training on the progressive ratio schedule of cocaine self-administration
Authors: Tsibulsky Vladimir L. , Norman Andrew B. 
Published: October 2021

AbstractTransition from the highest rate of lever-pressing activity during the unloading (extinction) phase of a cocaine self-administration session to an extremely low activity rate during the remission phase is in many cases gradual. This makes it difficult to assess the duration of the unloading phase after a fixed ratio 1 (FR1) or breakpoint after a progressive-ratio (PR) self-administration session. In addition, 3–5 days of training under the PR schedule results in a dramatic and persistent increase in the rate of presses during PR sessions and in the unloading phase following FR1 self-administration sessions. The goals of this study were to find the definition of the last press demarcating the border between the unloading and remission phases of the session and to determine if this border was also affected by PR training. Rats were trained to self-administer cocaine under the FR1 schedule and then under the PR schedule of drug delivery. Distributions of inter-press intervals (IPIs) during the unloading phase in sessions before and after PR training were compared. It was found that the distribution of cocaine-induced IPIs during the unloading phase was lognormal, bimodal, and independent of previously injected cocaine unit doses. The first mode represented intervals within the short bouts of stereotypic presses and the second mode represented intervals between bouts. The two modes were approximately 0.7 s and 21 s during unloading prior to and 0.6 s and 1.5 s after PR self-administration training. The total number of presses per unloading phase increased eightfold. When the FR1 schedule was restored, the intervals between bouts remained very short for at least 7–10 days and only then started a gradual increase towards baseline levels. The last unloading press was defined as the press followed by the IPI longer than the defined criterion. PR training resulted in a substantial and long-lasting increase in lever-pressing activity during unloading. The duration of the unloading phase did not depend on the rate of lever-pressing activity.
Darcy–Forchheimer couple stress hybrid nanofluids flow with variable fluid properties
Authors: Saeed Anwar , Kumam Poom , Gul Taza , Alghamdi Wajdi , Kumam Wiyada , Khan Amir 
Published: October 2021

AbstractThe current study provides a detailed analysis of steady two-dimensional incompressible and electrically conducting magnetohydrodynamic flow of a couple stress hybrid nanofluid under the influence of Darcy–Forchheimer, viscous dissipation, joule heating, heat generation, chemical reaction, and variable viscosity. The system of partial differential equations of the current model (equation of motion, energy, and concentration) is converted into a system of ordinary differential equations by adopting the suitable similarity practice. Analytically, homotopy analysis method (HAM) is employed to solve the obtained set of equations. The impact of permeability, couple-stress and magnetic parameters on axial velocity, mean critical reflux condition and mean velocity on the channel walls are discussed in details. Computational effects show that the axial mean velocity at the boundary has an inverse relation with couple stress parameter while the permeability parameter has a direct relation with the magnetic parameter and vice versa. The enhancement in the temperature distribution evaluates the pH values and electric conductivity. Therefore, the $$SWCNTs\,\,{\text{and}}\,\,MWCNTs$$

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Application and characterization of crude fungal lipases used to degrade fat and oil wastes
Authors: Alabdalall Amira Hassan , Al-Anazi Norah A. , Aldakheel Lena A. , Amer Fatma H. I. , Aldakheel Fatimah A. , Ababutain Ibtisam M. , Alghamdi Azzah I. , Al-Khaldi Eida M. 
Published: October 2021

AbstractAspergillus niger MH078571.1 and A. niger MH079049.1 were identified previously as the two highest Aspergillus niger strains producing lipase. Biochemical characterizations of lipase activity and stability for these two strains were examined and revealed that the optimal temperature is 45 °C at pH 8for A. niger MH078571.1 and 55 °C for MH079049.1. The lipase production of both strains was studied on medium contains waste oil, as a cheap source to reduce the industrial cost, showed that the optimal incubation period for the enzyme production is 3 days. Moreover, an experiment on lipase activates in organic solvents demonstrated that 50% of acetone is the best solvent for the two strains. In the presence of surfactants, 0.1% of tween 80 surfactant showed the best lipase activities. Furthermore, Mg2+ and Zn2+ ions enhanced the lipase activity of A. niger MH078571.1, while Na2+ and Cu2+ enhanced the enzyme activity of A. niger MH079049.1. Lipase activity was also tested for industrial applications such as integrating it with different detergents. Maximum lipase activity was obtained with 1% of Omo as a powder detergent for both strains. In liquid detergent, 0.1% of Fairy showed maximum lipase activity in A. niger MH078571.1, while the lipase in A. niger MH079049.1 was more effective in 1% of Lux. Moreover, the degradation of natural animal fat with crude enzyme was tested using chicken and sheep fats. The results showed that more than 90% of fats degraded after 5 days of the incubation period.
Quantum semi-supervised generative adversarial network for enhanced data classification
Authors: Nakaji Kouhei , Yamamoto Naoki 
Published: October 2021

AbstractIn this paper, we propose the quantum semi-supervised generative adversarial network (qSGAN). The system is composed of a quantum generator and a classical discriminator/classifier (D/C). The goal is to train both the generator and the D/C, so that the latter may get a high classification accuracy for a given dataset. Hence the qSGAN needs neither any data loading nor to generate a pure quantum state, implying that qSGAN is much easier to implement than many existing quantum algorithms. Also the generator can serve as a stronger adversary than a classical one thanks to its rich expressibility, and it is expected to be robust against noise. These advantages are demonstrated in a numerical simulation.
g-C3N4/Ca2Fe2O5 heterostructures for enhanced photocatalytic degradation of organic effluents under sunlight
Authors: Vavilapalli Durga Sankar , Peri Raja Gopal , Sharma R. K. , Goutam U. K. , Muthuraaman B. , Ramachandra Rao M. S. , Singh Shubra 
Published: October 2021

Abstractg-C3N4/Ca2Fe2O5 heterostructures were successfully prepared by incorporating g-C3N4 into Ca2Fe2O5 (CFO). As prepared g-C3N4/CFO heterostructures were initially utilized to photodegrade organic effluent Methylene blue (MB) for optimization of photodegradation performance. 50% g-C3N4 content in CFO composition showed an enhanced photodegradation efficiency (~ 96%) over g-C3N4 (48.15%) and CFO (81.9%) due to mitigation of recombination of photogenerated charge carriers by Type-II heterojunction. The optimized composition of heterostructure was further tested for degradation of Bisphenol-A (BPA) under direct sunlight, exhibiting enhanced photodegradation efficiency of about 63.1% over g-C3N4 (17%) and CFO (45.1%). The photoelectrochemical studies at various potentials with and without light illumination showed significant improvement in photocurrent response for g-C3N4/Ca2Fe2O5 heterostructures (~ 1.9 mA) over CFO (~ 67.4 μA). These studies revealed efficient solar energy harvesting ability of g-C3N4/Ca2Fe2O5 heterostructures to be utilized for organic effluent treatment.
Subdiffraction-resolution fluorescence imaging of immunological synapse formation between NK cells and A. fumigatus by expansion microscopy
Authors: Trinks Nora , Reinhard Sebastian , Drobny Matthias , Heilig Linda , Löffler Jürgen , Sauer Markus , Terpitz Ulrich 
Published: October 2021

AbstractExpansion microscopy (ExM) enables super-resolution fluorescence imaging on standard microscopes by physical expansion of the sample. However, the investigation of interactions between different organisms such as mammalian and fungal cells by ExM remains challenging because different cell types require different expansion protocols to ensure identical, ideally isotropic expansion of both partners. Here, we introduce an ExM method that enables super-resolved visualization of the interaction between NK cells and Aspergillus fumigatus hyphae. 4-fold expansion in combination with confocal fluorescence imaging allows us to resolve details of cytoskeleton rearrangement as well as NK cells’ lytic granules triggered by contact with an RFP-expressing A. fumigatus strain. In particular, subdiffraction-resolution images show polarized degranulation upon contact formation and the presence of LAMP1 surrounding perforin at the NK cell-surface post degranulation. Our data demonstrate that optimized ExM protocols enable the investigation of immunological synapse formation between two different species with so far unmatched spatial resolution.
Diurnal expansion and contraction of englacial fracture networks revealed by seismic shear wave splitting
Authors: Gajek Wojciech , Gräff Dominik , Hellmann Sebastian , Rempel Alan W. , Walter Fabian 
Published: October 2021

AbstractFractures contribute to bulk elastic anisotropy of many materials in the Earth. This includes glaciers and ice sheets, whose fracture state controls the routing of water to the base and thus large-scale ice flow. Here we use anisotropy-induced shear wave splitting to characterize ice structure and probe subsurface water drainage beneath a seismometer network on an Alpine glacier. Shear wave splitting observations reveal diurnal variations in S-wave anisotropy up to 3%. Our modelling shows that when elevated by surface melt, subglacial water pressures induce englacial hydrofractures whose volume amounts to 1-2 percent of the probed ice mass. While subglacial water pressures decrease, these fractures close and no fracture-induced anisotropy variations are observed in the absence of meltwater. Consequently, fracture networks, which are known to dominate englacial water drainage, are highly dynamic and change their volumes by 90-180 % over subdaily time scales.
A 5‐degrees of freedom hybrid excitation bearingless motor for vehicle flywheel battery
Authors: Yang Fan , Sun Yukun , Yuan Ye , Huang Yonghong 
Published: October 2021

AbstractTo deal with the restriction of vehicle space on a flywheel battery, a 5‐degrees of freedom (DOF) hybrid excitation bearingless motor (HEBM) was proposed. The 5‐DOF suspension force required for the flywheel battery is provided by HEBM. The use of a permanent magnet to provide a suspension bias magnetic field reduces power consumption. The relationship between the torque and suspension systems is weak coupling, which is beneficial to the decoupling control. To verify the aforementioned advantages of HEBM, its topology and principle are introduced, and its electromagnetic characteristics are analysed by finite element method. The HEBM is compared with the single‐winding bearingless switch reluctance motor by focusing on suspension loss and force density.
AKeplerK2 view of subdwarf A-type stars
Authors: Mösenlechner G. , Paunzen E. , Pelisoli I. , Seelig J. , Stidl S. , Maitzen H. M. 
Published: October 2021

Context.The spectroscopic class of subdwarf A-type (sdA) stars has come into focus in recent years because of their possible link to extremely low-mass white dwarfs, a rare class of objects resulting from binary evolution. Although most sdA stars are consistent with metal-poor halo main-sequence stars, the formation and evolution of a fraction of these stars are still matters of debate.Aims.The identification of photometric variability can help to put further constraints on the evolutionary status of sdA stars, in particular through the analysis of pulsations. Moreover, the binary ratio, which can be deduced from eclipsing binaries and ellipsoidal variables, is important as input for stellar models. In order to search for variability due to either binarity or pulsations in objects of the spectroscopic sdA class, we have extracted all available high precision light curves from theKeplerK2 mission.Methods.We have performed a thorough time series analysis on all available light curves, employing three different methods. Frequencies with a signal-to-noise ratio higher than four have been used for further analysis.Results.From the 25 targets, 13 turned out to be variables of different kinds (i.e., classical pulsating stars, ellipsoidal and cataclysmic variables, eclipsing binaries, and rotationally induced variables). For the remaining 12 objects, a variability threshold was determined.
One-Pot Synthesis of 3-(1,2,3,4-Tetrahydroisoquinolin-1-yl)-isoquinolin-1(2H)-ones by DEAD-Promoted Oxidative Ugi–Wittig ­Reaction Starting from Phosphonium Salt Precursors
Authors: Ding Ming-Wu , Zhao Long , Yang Mao-Lin , Sun Mei 
Published: October 2021

AbstractA new one-pot synthesis of 3-(1,2,3,4-tetrahydroisoquinolin-1-yl)-isoquinolin-1(2H)-ones by DEAD-promoted oxidative Ugi–­Wittig reaction was developed. The sequential reactions of (2-carboxybenzyl)triphenylphosphonium salts, isocyanides, and N-aryl-1,2,3,4-tetrahydroisoquinolines produced 3-(1,2,3,4-tetrahydroisoquinolin-1-yl)-isoquinolin-1(2H)-ones in moderate to good overall yields in the presence of DEAD and Et3N.
Lockdown in a disneyfied city: Kraków Old Town and the first wave of the Covid-19 pandemic
Authors: Porębska Anna , Barnaś Krzysztof , Dendura Bartosz , Kania Olga , Łukasik Marta , Rogulska Aleksandra , Szpakowska-Loranc Ernestyna , Zieliński Miłosz 
Published: October 2021

AbstractThis paper presents the geography of the historic central district of Kraków, Poland before, during and after the first wave of the 2020 pandemic. It describes how the disneyfied main part of the UNESCO heritage site of universal values turned into a ghost town as functional changes were turning into physical ones amid restrictions. From the results of pre-pandemic processes (that, as we argue, turned the city into its disneyfied version), to the lockdown (that later revealed itself to be but the first one in a row), to the post-lockdown recovery, these changes are presented in modified figure-ground diagrams with accessibility being defined by both tangible and intangible properties. The results are set against the background of the city’s current policies regarding economic recovery, mobility and accessibility to urban green areas. As an attempt to address the present vulnerability of the once resilient historic city centres—of which Kraków Old Town is a luminous example—this paper tends to be a voice in the debate on the post-2020 planning and the strategies we will need to face the subsequent waves of this, or other, pandemics as well as consequences of climate change.
Development of scanning system for industrial accelerator
Authors: Dhavale A. S. , Sharma V. , Sharma A. 
Published: October 2021

A 10 MeV, 5 kW electron accelerator is being developed for industrial applications. A scanning system including an AC scan magnet and a triangular wave generating power supply is developed to scan the electron beam over a length of 1 m. About 1.7 kG magnetic field is required for the full scan. A scan magnet is designed using POISSON and CST Microwave studio. This paper presents simulation results, fabrication details of the magnet, and design and development of the power supply. Field measurement is taken using the DC power supply and AC power supply. The simulation and experimental results are in good agreement.
A time-shared switching scheme designed for multi-probe scanning tunneling microscope
Authors: Yan Jiahao , Ma Jiajun , Wang Aiwei , Ma Ruisong , Wu Liangmei , Wu Zebin , Liu Li , Bao Lihong , Huan Qing , Gao Hong-Jun 
Published: October 2021

We report the design of a time-shared switching scheme, aiming to realize the manipulation and working modes (imaging mode and transport measurement mode) switching between multiple scanning tunneling microscope (STM) probes one by one with a shared STM control system (STM CS) and an electrical transport characterization system. This scheme comprises three types of switch units, switchable preamplifiers (SWPAs), high voltage amplifiers, and a main control unit. Together with the home-made software kit providing the graphical user interface, this scheme achieves a seamless switching process between different STM probes. Compared with the conventional scheme using multiple independent STM CSs, this scheme possesses more compatibility, flexibility, and expansibility for lower cost. The overall architecture and technique issues are discussed in detail. The performances of the system are demonstrated, including the millimeter scale moving range and atomic scale resolution of a single STM probe, safely approached multiple STM probes beyond the resolution of the optical microscope (1.1 µm), qualified STM imaging, and accurate electrical transport characterization. The combinational technique of imaging and transport characterization is also shown, which is supported by SWPA switches with ultra-high open circuit resistance (909 TΩ). These successful experiments prove the effectiveness and the usefulness of the scheme. In addition, the scheme can be easily upgraded with more different functions and numbers of probe arrays, thus opening a new way to build an extremely integrated and high throughput characterization platform.
A flexible system-on-a-chip control hardware for atomic, molecular, and optical physics experiments
Authors: Trenkwalder A. , Zaccanti M. , Poli N. 
Published: October 2021

We have implemented a control system core for experiments in atomic, molecular, and optical physics based on a commercial low-cost board, featuring a field-programmable gate array as part of a system-on-a-chip on which a Linux operating system is running. The board features Gigabit Ethernet, allowing for fast data transmission and operation of remote experimental systems. A single board can control a set of devices generating digital, analog, and radio frequency signals with precise timing given either by an external or internal clock. Contiguous output and input sampling rates of up to 40 MHz are achievable. Several boards can run synchronously with a timing error approaching 1 ns. For this purpose, a novel auto-synchronization scheme is demonstrated, with possible application in complex distributed experimental setups with demanding timing requests.
A digital feedback system for advanced ion manipulation techniques in Penning traps
Authors: Herkenhoff Jost , Door Menno , Filianin Pavel , Huang Wenjia , Kromer Kathrin , Lange Daniel , Schüssler Rima X. , Schweiger Christoph , Eliseev Sergey , Blaum Klaus 
Published: October 2021

The possibility of applying active feedback to a single ion in a Penning trap using a fully digital system is demonstrated. Previously realized feedback systems rely on analog circuits that are susceptible to environmental fluctuations and long term drifts, as well as being limited to the specific task they were designed for. The presented system is implemented using a field-programmable gate array (FPGA)-based platform (STEMlab), offering greater flexibility, higher temporal stability, and the possibility for highly dynamic variation of feedback parameters. The system’s capabilities were demonstrated by applying feedback to the ion detection system primarily consisting of a resonant circuit. This allowed shifts in its resonance frequency of up to several kHz and free modification of its quality factor within two orders of magnitude, which reduces the temperature of a single ion by a factor of 6. Furthermore, a phase-sensitive detection technique for the axial ion oscillation was implemented, which reduces the current measurement time by two orders of magnitude, while simultaneously eliminating model-related systematic uncertainties. The use of FPGA technology allowed the implementation of a fully-featured data acquisition system, making it possible to realize feedback techniques that require constant monitoring of the ion signal. This was successfully used to implement a single-ion self-excited oscillator.
Thiophene- and selenophene-based conjugated polymeric mixed ionic/electronic conductors
Authors: Sachinthani K. A. Niradha , Panchuk Jenny R. , Wang Yuhang , Zhu Tong , Sargent Edward H. , Seferos Dwight S. 
Published: October 2021

Mixed ionic/electronic conductors (MIECs) are desirable materials for next-generation electronic devices and energy storage applications. Polymeric MIECs are attractive from the standpoint that their structure can be controlled and anticipated to have mechanically robust properties. Here, we prepare and investigate conjugated copolymers containing thiophene and selenophene repeat units and their homopolymer counterparts. Specifically, thiophene bearing a triethylene glycol (EG3) side chain was polymerized and copolymerized with dodecyl thiophene/selenophene monomers. The synthesis leads to a class of copolymers that contain either S or Se and are blocky in nature. The Li-ion conductivity of ionically doped copolymers, P3DDT-s-P3(EG3)T and P3DDS-s-P3(EG3)T (9.7 × 10−6 and 8.2 × 10−6 S/cm, respectively), was 3–4 fold higher than that of the ionically doped constituent homopolymer, P3(EG3)T (2.2 × 10−6 S/cm), at ambient conditions. The electronic conductivity of the oxidatively doped copolymers was significantly higher than that of the constituent homopolymer P3(EG3)T, and most notably, P3DDS-s-P3(EG3)T reached ∼7 S/cm, which is the same order of magnitude as poly(3-dodecylthiophene) and poly(3-dodecylselenophene), which are the highest oxidatively doped conductors based on control experiments. Our findings provide implications for designing new MIECs based on copolymerization and the incorporation of heavy atom heterocycles.