bluuebunny/crossref_metadata_2025 huggingface dataset:
Insight into the structure, physiological function, and role in cancer of m6A readers—YTH domain-containing proteins
Authors: Liao Jingyu , Wei Yi , Liang Junnan , Wen Jingyuan , Chen Xiaoping , Zhang Bixiang , Chu Liang
Published: March 2022

YT521-B homology (YTH) domain-containing proteins (YTHDF1-3, YTHDC1-2) are the most crucial part of N6-methyladenosine (m6A) readers and play a regulatory role in almost all stages of methylated RNA metabolism and the progression of various cancers. Since m6A is identified as an essential post-transcriptional type, YTH domain-containing proteins have played a key role in the m6A sites of RNA. Hence, it is of great significance to study the interaction between YTH family proteins and m6A-modified RNA metabolism and tumor. In this review, their basic structure and physical functions in RNA transcription, splicing, exporting, stability, and degradation as well as protein translation are introduced. Then we discussed the expression regulation of YTH domain-containing proteins in cancers. Furthermore, we introduced the role of the YTH family in cancer biology and systematically demonstrated their functions in various aspects of tumorigenesis and development. To provide a more institute understanding of the role of YTH family proteins in cancers, we summarized their functions and specific mechanisms in various cancer types and presented their involvement in cancer-related signaling pathways.
Coronavirus Host Genetics South Africa (COHG-SA) database—a variant database for gene regions associated with SARS-CoV-2 outcomes
Authors: Barmania Fatima , Mellet Juanita , Ryder Megan A. , Ford Graeme , Herd Candice L. , Tamuhla Tsaone , Hendricks Candice , Giles Rachel , Kalua Thumbiko , Joubert Fourie , Tiffin Nicki , Pepper Michael S.
Published: March 2022

The SARS-CoV-2 virus is responsible for the COVID-19 global public health emergency, and the disease it causes is highly variable in its clinical presentation. Clinical phenotypes are heterogeneous both in terms of presentation of symptoms in the host and response to therapy. Several studies and initiatives have been established to analyse and review host genetic epidemiology associated with COVID-19. Our research group curated these articles into a web-based database using the python application-server framework Django. The database provides a searchable research tool describing current literature surrounding COVID-19 host genetic factors associated with disease outcome. This paper describes the COHG-SA database and provides an overview of the analyses that can be derived from these data.
Effective viral-mediated lung gene therapy: is airway surface preparation necessary?
Authors: McCarron Alexandra , Cmielewski Patricia , Drysdale Victoria , Parsons David , Donnelley Martin
Published: March 2022

Gene-based therapeutics are actively being pursued for the treatment of lung diseases. While promising advances have been made over the last decades, the absence of clinically available lung-directed genetic therapies highlights the difficulties associated with this effort. Largely, progress has been hindered by the presence of inherent physical and physiological airway barriers that significantly reduce the efficacy of gene transfer. These barriers include surface mucus, mucociliary action, cell-to-cell tight junctions, and the basolateral cell membrane location of viral receptors for many commonly used gene vectors. Accordingly, airway surface preparation methods have been developed to disrupt these barriers, creating a more conducive environment for gene uptake into the target airway cells. The two major approaches have been chemical and physical methods. Both have proven effective for increasing viral-mediated gene transfer pre-clinically, although with variable effect depending on the specific strategy employed. While such methods have been explored extensively in experimental settings, they have not been used clinically. This review covers the airway surface preparation strategies reported in the literature, the advantages and disadvantages of each method, as well as a discussion about applying this concept in the clinic.
Wearable sensors during drawing tasks to measure the severity of essential tremor
Authors: Ali Sheik Mohammed , Arjunan Sridhar Poosapadi , Peters James , Perju-Dumbrava Laura , Ding Catherine , Eller Michael , Raghav Sanjay , Kempster Peter , Motin Mohammod Abdul , Radcliffe P. J. , Kumar Dinesh Kant
Published: March 2022

Commonly used methods to assess the severity of essential tremor (ET) are based on clinical observation and lack objectivity. This study proposes the use of wearable accelerometer sensors for the quantitative assessment of ET. Acceleration data was recorded by inertial measurement unit (IMU) sensors during sketching of Archimedes spirals in 17 ET participants and 18 healthy controls. IMUs were placed at three points (dorsum of hand, posterior forearm, posterior upper arm) of each participant’s dominant arm. Movement disorder neurologists who were blinded to clinical information scored ET patients on the Fahn–Tolosa–Marin rating scale (FTM) and conducted phenotyping according to the recent Consensus Statement on the Classification of Tremors. The ratio of power spectral density of acceleration data in 4–12 Hz to 0.5–4 Hz bands and the total duration of the action were inputs to a support vector machine that was trained to classify the ET subtype. Regression analysis was performed to determine the relationship of acceleration and temporal data with the FTM scores. The results show that the sensor located on the forearm had the best classification and regression results, with accuracy of 85.71% for binary classification of ET versus control. There was a moderate to good correlation (r2 = 0.561) between FTM and a combination of power spectral density ratio and task time. However, the system could not accurately differentiate ET phenotypes according to the Consensus classification scheme. Potential applications of machine-based assessment of ET using wearable sensors include clinical trials and remote monitoring of patients.
Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems
Authors: Guragain Manita , Schmidt John W. , Kalchayanand Norasak , Dickey Aaron M. , Bosilevac Joseph M.
Published: March 2022

Certain strains of Escherichia coli possess and express the toxin colibactin (Clb) which induces host mutations identical to the signature mutations of colorectal cancer (CRC) that lead to tumorigenic lesions. Since cattle are a known reservoir of several Enterobacteriaceae including E. coli, this study screened for clb amongst E. coli isolated from colons of cattle-at-harvest (entering beef processing facility; n = 1430), across the beef processing continuum (feedlot to finished subprimal beef; n = 232), and in ground beef (n = 1074). Results demonstrated that clb+E. coli were present in cattle and beef. Prevalence of clb+E. coli from colonic contents of cattle and ground beef was 18.3% and 5.5%, respectively. clb+E. coli were found susceptible to commonly used meat processing interventions. Whole genome sequencing of 54 bovine and beef clb+ isolates showed clb occurred in diverse genetic backgrounds, most frequently in phylogroup B1 (70.4%), MLST 1079 (42.6%), and serogroup O49 (40.7%).
Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing
Authors: Nousias O. , Oikonomou S. , Manousaki T. , Papadogiannis V. , Angelova N. , Tsaparis D. , Tsakogiannis A. , Duncan N. , Estevez A. , Tzokas K. , Pavlidis M. , Chatziplis D. , Tsigenopoulos C. S.
Published: March 2022

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity withDicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.
Evidence supporting a cultural evolutionary theory of prosocial religions in contemporary workplace safety data
Authors: Gu Yuqi , Mao Connie X. , Johnson Tim
Published: March 2022

A prominent line of cultural evolutionary theory hypothesizes that religiously inspired prosocial behavior enhances the fecundity of pious groups, causing them to outcompete non-religious communities and spread their prosocial values. We present evidence concerning contemporary workplace safety, in the United States, that unexpectedly tested implications of this cultural evolutionary hypothesis. Avoiding workplace injury requires cooperation and injury influences fitness, thus cultural evolutionary theory would anticipate that religious communities should exhibit fewer workplace injuries. Indeed, we find that the proportion of a community adhering to a religion correlates negatively with rates of workplace injury in its private-sector establishments. This correlation emerges primarily when secular workplace safety authorities are not prominent, thus echoing evidence that religiously inspired prosocial behavior mainly occurs absent “earthly” sanctioning authorities. Furthermore, the percent of religiously affiliated individuals in a community correlates with safety investments, suggesting that workplace injury reductions in religious communities result from individually costly, group-benefitting cooperation.
Elderly onset age is associated with low efficacy of first anti-tumor necrosis factor treatment in patients with inflammatory bowel disease
Authors: Amano Takahiro , Shinzaki Shinichiro , Asakura Akiko , Tashiro Taku , Tani Mizuki , Otake Yuriko , Yoshihara Takeo , Iwatani Shuko , Yamada Takuya , Sakakibara Yuko , Osugi Naoto , Ishii Shuji , Egawa Satoshi , Araki Manabu , Arimoto Yuki , Nakahara Masanori , Murayama Yoko , Kobayashi Ichizo , Kinoshita Kazuo , Ogawa Hiroyuki , Hiyama Satoshi , Shibukawa Narihiro , Komori Masato , Okuda Yorihide , Kizu Takashi , Yoshii Shunsuke , Tsujii Yoshiki , Hayashi Yoshito , Inoue Takahiro , Iijima Hideki , Takehara Tetsuo
Published: March 2022

The outcomes of patients with elderly onset (EO) inflammatory bowel disease (IBD) treated with anti-tumor necrosis factor (TNF) remains uncertain. The present study evaluated the efficacy and safety of anti-TNF treatment for bio-naïve EO-IBD. Elderly patients were defined as those 60 years and older, and further divided into those with EO (Elderly-EO) and those with non-elderly onset (Elderly-NEO). A total of 432 bio-naïve patients were enrolled in this multicenter observational study, comprising 55 with Elderly-EO (12.7%), 25 with Elderly-NEO (5.8%), and 352 under age 60 (Non-elderly, 81.5%). After 52 weeks of anti-TNF treatment, clinical and steroid-free remission rates were significantly lower in Elderly-EO than in Non-elderly (37.7% and 60.8%; P = 0.001, and 35.9% and 57.8%; P = 0.003, respectively), and comparable between Elderly-NEO and Non-elderly. Multivariate analysis revealed that elderly onset was a significant factor for both clinical remission (OR, 0.49, 95% CI 0.25–0.96) and steroid-free remission (OR, 0.51, 95% CI 0.26–0.99) after 52 weeks of anti-TNF treatment. The rate of cumulative severe adverse events was significantly higher in Elderly-EO than in Non-elderly (P = 0.007), and comparable between Elderly-NEO and Non-elderly. In conclusion, anti-TNF treatment for bio-naïve EO-IBD may be less effective and raise safety concerns.
Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex
Authors: Sridhara Sagar , Rai Jay , Whyms Charlisa , Goswami Hemant , He Huan , Woodside Walter , Terns Michael P. , Li Hong
Published: March 2022

The small RNA-mediated immunity in bacteria depends on foreign RNA-activated and self RNA-inhibited enzymatic activities. The multi-subunit Type III-A CRISPR-Cas effector complex (Csm) exemplifies this principle and is in addition regulated by cellular metabolites such as divalent metals and ATP. Recognition of the foreign or cognate target RNA (CTR) triggers its single-stranded deoxyribonuclease (DNase) and cyclic oligoadenylate (cOA) synthesis activities. The same activities remain dormant in the presence of the self or non-cognate target RNA (NTR) that differs from CTR only in its 3′-protospacer flanking sequence (3′-PFS). Here we employ electron cryomicroscopy (cryoEM), functional assays, and comparative cross-linking to study in vivo assembled mesophilic Lactococcus lactis Csm (LlCsm) at the three functional states: apo, the CTR- and the NTR-bound. Unlike previously studied Csm complexes, we observed binding of 3′-PFS to Csm in absence of bound ATP and analyzed the structures of the four RNA cleavage sites. Interestingly, comparative crosslinking results indicate a tightening of the Csm3-Csm4 interface as a result of CTR but not NTR binding, reflecting a possible role of protein dynamics change during activation.
Zinc(ii) phthalocyanine–viologen dyads: synthesis, electrochemistry, spectroelectrochemistry, electrodeposition, and electrochromism
Authors: Yıldız Burak , Ahmetali Erem , Budak Özlem , Koca Atıf , Şener M. Kasım
Published: March 2022

Electrochromic properties have been enriched by combining the anodic colorant zinc phthalocyanine and cathodic colorant viologen moieties into a dyad system via a flexible chain.
SARS-CoV-2 spike protein causes cardiovascular disease independent of viral infection
Authors: Imig John D.
Published: March 2022

The SARS-CoV-2 virus that results in COVID-19 has been found to damage multiple organs beyond the lung. Interestingly, the SARS-CoV-2 spike (S) protein can be found circulating in the blood of COVID-19 patients. Experimental findings are demonstrating that the circulating S protein can bind to receptors resulting in inflammation and cell, tissue, and organ damage. Avolio et al. previously determined that the S protein acting through the cluster of differentiation 147 (CD147) receptor, and another unknown mechanism had detrimental effects on human cardiac pericytes (Clin Sci (Lond) (2021) 135 (24): 2667–2689. DOI: 10.1042/CS20210735). These findings support the notion that circulating SARS-CoV-2 S protein could contribute to cardiovascular disease independent of viral infection. Future studies are needed to determine the effect of the S protein on pericytes in other organs and evaluate the effectiveness of CD147 receptor-blocking therapies to decrease organ damage caused by the S protein.
Load‐independent inverse class‐E ZVS inverter and its application to wireless power transfer systems
Authors: Komanaka Ayano , Zhu Wenqi , Wei Xiuqin , Nguyen Kien , Sekiya Hiroo
Published: March 2022

This paper proposes a load‐independent inverse class‐E zero‐voltage switching (ZVS) inverter. The proposed inverter achieves the constant output current and the ZVS at any load resistance without any control. The waveforms and design equations of the proposed inverter are shown. Besides, a wireless‐power‐transfer system was implemented using the proposed inverter. The designed WPT system kept the constant output voltage and the ZVS against load variations, which denoted the effectiveness of the proposed inverter and validities of the analytical equations.
A probabilistic uncertainty evaluation method for turbomachinery probe measurements
Authors: Behr Thomas , Kalfas Anestis I. , Abhari Reza S.
Published: March 2022

The paper presents a probabilistic uncertainty evaluation method described in the Guide to the Expression of Uncertainty in Measurement (GUM) [1] and its application to the field of Turbomachinery probe measurement techniques. All sources of uncertainties contributing to a measurement result are expressed in terms of probability distributions. Consequently, the overall standard uncertainty of the result can be calculated using the Gaussian error propagation formula. The result of the uncertainty evaluation yields the most probable value of the measurand and describes its distribution in terms of standard or extended uncertainties. A pneumatic five-hole-probe measurement technique has been chosen to show the principle of the probabilistic uncertainty evaluation method. The complete signal chain including the probe calibration, the modeling and the application in the turbine has been included in the analysis. The overall uncertainties of the measured flow angles and flow total and static pressures are presented as a function of the flow Mach number. In addition, the contribution of the individual sources of uncertainty to the overall standard uncertainty is shown. Based on this break down of uncertainties optimization options of the measurement chain are suggested.
Probing effect of solvation on photoexcited quadrupolar donor-acceptor-donor molecule via ultrafast Raman spectroscopy
Authors: Zhang Wei , Kong Jie , Xu Wenqi , Niu Xinmiao , Song Di , Liu Weimin , Xia Andong
Published: March 2022

The symmetric and quadrupolar donor-acceptor-donor (D-A-D) molecules usually exhibit excited-state charge redistribution process from delocalized intramolecular charge transfer (ICT) state to localized ICT state. Direct observation of such charge redistribution process in real-time has been intensively studied via various ultrafast time-resolved spectroscopies. Femtosecond stimulated Raman spectroscopy (FSRS) is one of the powerful methods which can be used to determine the excited state dynamics by tracking vibrational mode evolution of the specific chemical bonds within molecules. Herein, a molecule, 4,4′-(buta-1,3-diyne-1,4-diyl)bis(N,N-bis(4-methoxyphenyl)aniline), that consists of two central adjacent alkyne (-C≡C-) groups as electron-acceptors and two separated, symmetric N,N-bis(4-methoxyphenyl)aniline at both branches as electron-donors, is chosen to investigate the excited-state photophysical properties. It is shown that the solvation induced excited-state charge redistribution in polar solvents can be probed by using femtosecond stimulated Raman spectroscopy. The results provide a fundamental understanding of photoexcitation induced charge delocalization/localization properties of the symmetric quadrupolar molecules with adjacent vibrational markers located at central position.
QM/MM study on enzymatic mechanism in sinigrin biosynthesis
Authors: Guo Ya-Jie , Liu Ya-Jun
Published: March 2022

As the major and abundant type of glucosinolates (GL) in plants, sinigrin has potential functions in promoting health and insect defense. The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds, which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase (SOT). However, due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL, little is known about this sulfonation process. Fortunately, the crystal structure of SOT 18 from Arabidopsis thaliana (AtSOT18) containing the substance (sinigrin) similar to 3-methylthiopropyl GL has been determined. To understand the enzymatic mechanism, we employed molecular dynamics (MD) simulation and quantum mechanics combined with molecular mechanics (QM/MM) methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18. The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism. Moreover, Lys93, Thr96, Thr97, Tyr130, His155, and two enzyme peptide chains (Pro92-Lys93 and Gln95-Thr96-Thr97) play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry. Particularly, His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process. The presently proposed concerted dissociative mechanism explains the role of AtSOT18 in sinigrin biosynthesis, and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.
Development of a versatile micro-focused angle-resolved photoemission spectroscopy system with Kirkpatrick–Baez mirror optics
Authors: Kitamura Miho , Souma Seigo , Honma Asuka , Wakabayashi Daisuke , Tanaka Hirokazu , Toyoshima Akio , Amemiya Kenta , Kawakami Tappei , Sugawara Katsuaki , Nakayama Kosuke , Yoshimatsu Kohei , Kumigashira Hiroshi , Sato Takafumi , Horiba Koji
Published: March 2022

Angle-resolved photoemission spectroscopy using a micro-focused beam spot [micro-angle-resolved photoemission spectroscopy (ARPES)] is becoming a powerful tool to elucidate key electronic states of exotic quantum materials. We have developed a versatile micro-ARPES system based on the synchrotron radiation beam focused with a Kirkpatrick–Baez mirror optics. The mirrors are monolithically installed on a stage, which is driven with five-axis motion, and are vibrationally separated from the ARPES measurement system. Spatial mapping of the Au photolithography pattern on Si signifies the beam spot size of 10 µm (horizontal) × 12 µm (vertical) at the sample position, which is well suited to resolve the fine structure in local electronic states. Utilization of the micro-beam and the high precision sample motion system enables the accurate spatially resolved band-structure mapping, as demonstrated by the observation of a small band anomaly associated with tiny sample bending near the edge of a cleaved topological insulator single crystal.
Insight from high-pressure dielectric studies into molecular dynamics of the itraconazole-glycerol mixture in smectic and isotropic phases
Authors: Rams-Baron Marzena , Musiał Małgorzata , Kramarczyk Daniel , Paluch Marian
Published: March 2022

We present here the results of high-pressure broadband dielectric spectroscopy (BDS) measurements for a mixture of liquid-crystalline drug itraconazole (ITZ) and glycerol (GLY) at a critical concentration of 5% w/w in which the nematic order is eliminated. In the investigated system, smectic-A to isotropic phase transition leaves a clear fingerprint on the dielectric response, allowing for a phase diagram creation using BDS data. By following the α-relaxation dynamics under different thermodynamic conditions, we provide insights into the effect of pressure on temperature and the phenomenology of smectic-A to the isotropic phase transition. Additional measurements of specific volume as a function of pressure and temperature provide us with a deeper insight into material properties that could be analyzed comprehensively via the equation of state. We proved the validity of the density scaling concept, showing that the mixture’s complexity does not exclude thermodynamic scaling of dynamic properties related to the α-process in the smectic-A phase. The low value of scaling exponent γ = 2.00 ± 0.02 and a high ratio of the activation energy at constant volume, EV, to the activation enthalpy at constant pressure, HP, indicate that temperature is a dominant variable controlling α-relaxation dynamics in the ordered smectic-A phase of the ITZ-GLY mixture.
100-kT magnetic field generation using paisley targets by femtosecond laser–plasma interactions
Authors: Zosa M.-A. H. , Gu Y. J. , Murakami M.
Published: March 2022

A target using a paisley pattern generates 100-kT-level magnetic fields. Laser irradiation induces local charge separation on the target, which creates surface currents along the concave surface, generating a magnetic field. For a laser intensity of 1021 W cm−2, the target generates a 150-kT magnetic field. We developed a simple model to describe the magnetic field as a function of the laser intensity and target radius. A double paisley configuration extends the lifetime of the magnetic field to the picosecond scale. The paisley design generates comparable results even if it is simplified. Thus, it is a robust and modular target suitable for magnetic field applications such as 100-kT magnetic field generation and magnetic reconnection.
A 10-nm-thick silicon oxide based high switching speed conductive bridging random access memory with ultra-low operation voltage and ultra-low LRS resistance
Authors: Cao Haichao , Ren Hao
Published: March 2022

In this paper, a silicon oxide based conductive bridging random access memory (CBRAM) with an ultra-low operation voltage, a high switching speed, and an ultra-low resistance at low resistance state (LRS) is reported. The CBRAM has a sandwich structure with platinum and copper as electrode layers and an ultra-thin 10-nm-thick silicon oxide film as an insulating switching layer. The CBRAMs are fabricated with CMOS compatible materials and processes. DC I–V sweep characterizations show an ultra-low SET/RESET voltage of 0.35 V/−0.05 V, and the RESET voltage is the lowest among all ultra-low voltage CBRAMs. The CBRAM is capable of withstanding endurance tests with over 106 pulses of +0.4 V/−0.1 V with 1 μs pulse width, with the resistance at LRS maintaining at an ultra-low value of only 20 Ω, which is the lowest among all CBRAMs to date, and it is reduced by at least 2.95 times compared with prior studies. Meanwhile, the switching ratio between high resistance state and LRS is more than 1.49 × 104. Moreover, the switching time characterization of the CBRAM demonstrates an ultra-short SET/RESET time of 7/9 ns. The CBRAM has potential applications in high-speed, ultra-low voltage, and ultra-low power electronics.
A perspective on ultralong silicon nanowires for flexible sensors
Authors: Zhang Bingchang , Yu Jia , Zhang Xiaohong
Published: March 2022

Flexible sensitive materials are important for the development of flexible sensors. As a dominant semiconductor, silicon is an excellent sensitive material for fabricating traditional rigid sensors. However, its applications in flexible sensors have been hindered by the rigidity and brittleness of commonly used Si wafers. In this Perspective, we focus on ultralong silicon nanowires (SiNWs), which are a kind of flexible Si materials. The synthesis of ultralong SiNWs, fabrication of SiNW fabrics, and their applications in flexible sensors are discussed. We also point out some challenges and future directions in this field.
Gibbs spatial process for characterization of filament interaction in ReRAM devices via photon emission microscopy
Authors: Wu Ernest , Stellari Franco , Ocola Leonidas , Frank Martin , Song Peilin , Ando Takashi
Published: March 2022

In this work, we investigate spatial statistical properties of filament patterns in resistive random-access memory (ReRAM) devices measured from a newly developed near-infrared photon emission microscopy (PEM) [Stellari et al., IEEE Electron Device Lett. 42, 828 (2021); Stellari et al., in Proceedings of the 47th International Symposium for Testing and Failure Analysis Conference (ISTFA) (ASM International, 2021), pp. 115–121]. Unlike previous reports on uncorrelated filaments [Stellari et al., IEEE Electron Device Lett. 42, 828 (2021); Wu et al., Appl. Phys. Lett. 99, 093502 (2011)], we report a strong clustering and non-Poisson pattern of filaments constructed from individual devices. A Poisson-mixture model incorporating the clustering (attractive) effect is introduced with an excellent agreement with the PEM data for global and nearest-neighbor spatial statistics. On the other hand, a two-filament pattern is also detected within the ReRAM devices. We found that both attractive and repulsive interactions among the filaments are required in a Gibbs process to explain the filament spatial distribution. We implemented a birth-death algorithm using a Markov-chain Monte Carlo approach and achieve good agreement with the PEM data using a generalized Morse potential.
Tomographic entanglement indicators from NMR experiments
Authors: Sharmila B. , Krithika V. R. , Pal Soham , Mahesh T. S. , Lakshmibala S. , Balakrishnan V.
Published: March 2022

In recent years, the performance of different entanglement indicators obtained directly from tomograms has been assessed in continuous-variable and hybrid quantum systems. In this paper, we carry out this task in the case of spin systems. We compute the entanglement indicators from actual experimental data obtained from three liquid-state nuclear magnetic resonance (NMR) experiments and compare them with standard entanglement measures calculated from the corresponding density matrices, both experimentally reconstructed and numerically computed. The gross features of entanglement dynamics and spin squeezing properties are found to be reproduced by these entanglement indicators. However, the extent to which these indicators and spin squeezing track the entanglement during time evolution of the multipartite systems in the NMR experiments is very sensitive to the precise nature and strength of interactions as well as the manner in which the full system is partitioned into subsystems. We also use the IBM quantum computer to implement equivalent circuits that capture the dynamics of the multipartite system in one of the NMR experiments and carry out a similar comparative assessment of the performance of tomographic indicators. This exercise shows that these indicators can estimate the degree of entanglement without necessitating detailed state reconstruction procedures, establishing the advantage of the tomographic approach.
Learning-enabled recovering scattered data from twisted light transmitted through a long standard multimode fiber
Authors: Liu Yifan , Zhang Zhisen , Yu Panpan , Wu Yijing , Wang Ziqiang , Li Yinmei , Liu Wen , Gong Lei
Published: March 2022

Multiplexing multiple orbital angular momentum (OAM) modes of light has proven to be an effective way to increase data capacity in fiber-optic communications. However, existing techniques for distributing the OAM modes rely on specially designed fibers or couplers. Direct transmission of multiplexed OAM modes through a long standard multimode fiber remains challenging because the strong mode coupling in fibers disables OAM demultiplexing. Here, we propose a deep-learning-based approach to recover the scattered data from multiplexed OAM channels without measuring any phase information. Over a 1-km-long standard multimode fiber, our method is able to identify different OAM modes with an accuracy of more than 99.9% in the parallel demultiplexing of 24 scattered OAM channels. To demonstrate the transmission quality, color images are encoded in multiplexed twisted light and our method achieves decoding the transmitted data with an error rate of 0.13%. Our work shows that the artificial intelligence algorithm could benefit the use of OAM multiplexing in commercial fiber networks and high-performance optical communication in turbulent environments.
Impact of feeding volumes on performance and bone characteristics of Embrapa 051 laying hens housed in a cage-free system
Authors: Forgiarini Juliana , Krabbe Everton Luis , Alves Débora Aline , Silveira de Ávila Valdir , Nunes da Silva Suelen , Xavier Eduardo Gonçalves , Rutz Fernando , Büttow Roll Victor Fernando
Published: March 2022

Context Few studies have been conducted with the Brazilian Embrapa 051 hens to improve the feed conversion rate and control skeletal health in this breed. Aims To determine how different feeding volumes affect the laying rate and bone quality of the Embrapa 051 (E051) strain in comparison with Lohmann Brown (LB). Methods In total, 600 E051 and 200 LB hens were subjected to the following treatments: (1) control (LB fed 100% of their dietary requirements), (2) E051 fed 93% of the control diet, (3) E051 fed 100% of the control diet, and (4) E051 fed 107% of the control diet. Key results Throughout the 37–72 weeks of age, LB hens presented a higher egg production rate than E051 hens (P < 0.05). The bodyweight and egg production rate were lower in E051 when hens received 93% of the E051 control diet. The E051 hens achieved higher values for tibia weight and length and Seedor index than did LB hens (P < 0.05). At Week 40, the E051 hens fed 93% of the control diet presented a greater tibia weight (12.6 vs 11.5 g), length (124.5 vs 118.9 mm) and strength (21.9 vs 15.5 kgf), Seedor index (101.7 vs 96.13), and ash (33.0 vs 29.6%), calcium (11.1 vs 9.8%) and phosphorus (4.9 vs 4.5%) concentrations than did LB hens. However, at 73 weeks of age, the only differences observed in favour of E051 hens fed 93% of the control diet were for tibia weight, tibia length and tibia strength in comparison with LB hens (P < 0.05). Conclusions LB hens showed a higher performance, but lower bone quality than did E051 hens. E051 receiving 7% less feed showed a reduced laying rate but, in contrast, better bone quality. This study showed that the best feeding strategy for Embrapa 051 hens was to use the same feeding volume as recommended for Lohmann Brown hens. Implications Despite E051 hens showing a lower laying rate than that of LB hens, especially when receiving a restricted amount of feed, E051 is an accessible alternative breed with excellent bone quality for free-range systems in Brazil.
Dissecting the difference in tree species richness between Africa and South America
Authors: Silva de Miranda Pedro Luiz , Dexter Kyle G. , Swaine Michael D. , de Oliveira-Filho Ary Teixeira , Hardy Olivier J. , Fayolle Adeline
Published: March 2022

Significance

Our full-scale comparison of Africa and South America’s lowland tropical tree floras shows that both Africa and South America’s moist and dry tree floras are organized similarly: plant families that are rich in tree species on one continent are also rich in tree species on the other continent, and these patterns hold across moist and dry environments. Moreover, we confirm that there is an important difference in tree species richness between the two continents, which is linked to a few families that are exceptionally diverse in South American moist forests, although dry formations also contribute to this difference. Plant families only present on one of the two continents do not contribute substantially to differences in tree species richness.
Revealing the catalytic kinetics and dynamics of individual Pt atoms at the single-molecule level
Authors: Liu Xiaodong , Ge Xin , Cao Jing , Xiao Yi , Wang Yan , Zhang Wei , Song Ping , Xu Weilin
Published: March 2022

Significance

Here, with single-molecule fluorescence microscopy, we study the catalytic behavior of individual Pt atoms at single-turnover resolution, and then reveal the unique catalytic properties of Pt single-atom catalyst and the difference in catalytic properties between individual Pt atoms and Pt nanoparticles. Further density functional theory calculation indicates that unique catalytic properties of Pt single-atom catalyst could be attributed intrinsically to the unique surface properties of Pt
1
-based active sites.
Structural insights into the activation of autoinhibited human lipid flippase ATP8B1 upon substrate binding
Authors: Cheng Meng-Ting , Chen Yu , Chen Zhi-Peng , Liu Xin , Zhang Zhiyong , Chen Yuxing , Hou Wen-Tao , Zhou Cong-Zhao
Published: March 2022

Significance

ATP8B1 is a P4 ATPase that maintains membrane asymmetry by transporting phospholipids across the cell membrane. Disturbance of lipid asymmetry will lead to the imbalance of the cell membrane and eventually, cell death. Thus, defects in ATP8B1 are usually associated with severe human diseases, such as intrahepatic cholestasis. The present structures of ATP8B1 complexed with its auxiliary noncatalytic partners CDC50A and CDC50B reveal an autoinhibited state of ATP8B1 that could be released upon substrate binding. Moreover, release of this autoinhibition could be facilitated by the bile acids, which are key factors that alter the membrane asymmetry of hepatocytes. This enabled us to figure out a feedback loop of bile acids and lipids across the cell membrane.
A new mode of swimming in singly flagellated
Pseudomonas aeruginosa
Authors: Tian Maojin , Wu Zhengyu , Zhang Rongjing , Yuan Junhua
Published: March 2022

Significance

The monotrichous
Pseudomonas aeruginosa
was usually thought to swim in a pattern of “run and reverse” (possibly with pauses in between), where straight runs alternated with reverses with angular changes of swimming direction near 180°. Here, by simultaneously tracking the cell swimming and the morphology of its flagellum, we discovered a swimming mode in
P. aeruginosa
—the wrap mode, during which the flagellar filament wrapped around the cell body and induced large fluctuation of the body orientation. The wrap mode randomized swimming direction, resulting in a broad distribution of angular changes over 0 to 180° with a peak near 90°. This allowed the bacterium to explore the environment more efficiently, which we confirmed by stochastic simulations of
P. aeruginosa
chemotaxis.
Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor
Authors: Zhou Jian , Lai Junpeng , Menda Gil , Stafstrom Jay A. , Miles Carol I. , Hoy Ronald R. , Miles Ronald N.
Published: March 2022

Significance

The sense of hearing in all known animals relies on possessing auditory organs that are made up of cellular tissues and constrained by body sizes. We show that hearing in the orb-weaving spider is functionally outsourced to its extended phenotype, the proteinaceous self-manufactured web, and hence processes behavioral controllability. This finding opens new perspectives on animal extended cognition and hearing—the outsourcing and supersizing of auditory function in spiders. This study calls for reinvestigation of the remarkable evolutionary ecology and sensory ecology in spiders—one of the oldest land animals. The sensory modality of outsourced hearing provides a unique model for studying extended and regenerative sensing and presents new design features for inspiring novel acoustic flow detectors.
The solute carrier SLC15A4 is required for optimal trafficking of nucleic acid–sensing TLRs and ligands to endolysosomes
Authors: Rimann Ivo , Gonzalez-Quintial Rosana , Baccala Roberto , Kiosses William B. , Teijaro John R. , Parker Christopher G. , Li Xiaohong , Beutler Bruce , Kono Dwight H. , Theofilopoulos Argyrios N.
Published: March 2022

Significance

A large body of evidence has indicated that recognition of self-nucleic acids by endosomal toll-like receptors (TLRs) is central to the pathogenesis of lupus-like systemic autoimmunity in spontaneous mouse models, and the solute carrier SLC15A4 is required for this recognition. Here we describe a mechanism in which SLC15A4 is a major contributor to the proper trafficking of TLRs and their ligands to endolysosomes, wherein recognition and signaling is initiated. This finding supports ongoing efforts to identify pharmacologic inhibitors for this carrier as a means to treat lupus and other inflammatory disorders.
CT-based detection of material flow in friction stir welding of dissimilar Al/Mg alloys with and without ultrasonic assistance
Authors: Wang Tao , Wu ChuanSong , Shi Lei
Published: March 2022

Comparative experiments of friction stir welding (FSW) of Al/Mg alloys were conducted with and without ultrasonic assistance. The copper powders were preset inside the workpieces as the marker material, and computer tomography technique was employed to obtain the three-dimensional information of material flow around the tool. The top view of copper powders distribution inside the weldments shows that the distribution zones of marker material at the retreating side and the trailing side were all widened by the exerted ultrasonic vibration (UV). The front view and side view of marker material distribution demonstrated that UV also enhanced the vertical material flow. Such detection results are helpful to elucidate the mechanism of ultrasonic-assisted FSW of dissimilar Al/Mg alloys.
Calcium current modulation by the γ1 subunit depends on alternative splicing of CaV1.1
Authors: El Ghaleb Yousra , Ortner Nadine J. , Posch Wilfried , Fernández-Quintero Monica L. , Tuinte Wietske E. , Monteleone Stefania , Draheim Henning J. , Liedl Klaus R. , Wilflingseder Doris , Striessnig Jörg , Tuluc Petronel , Flucher Bernhard E. , Campiglio Marta
Published: March 2022

The skeletal muscle voltage-gated calcium channel (CaV1.1) primarily functions as a voltage sensor for excitation–contraction coupling. Conversely, its ion-conducting function is modulated by multiple mechanisms within the pore-forming α1S subunit and the auxiliary α2δ-1 and γ1 subunits. In particular, developmentally regulated alternative splicing of exon 29, which inserts 19 amino acids in the extracellular IVS3-S4 loop of CaV1.1a, greatly reduces the current density and shifts the voltage dependence of activation to positive potentials outside the physiological range. We generated new HEK293 cell lines stably expressing α2δ-1, β3, and STAC3. When the adult (CaV1.1a) and embryonic (CaV1.1e) splice variants were expressed in these cells, the difference in the voltage dependence of activation observed in muscle cells was reproduced, but not the reduced current density of CaV1.1a. Only when we further coexpressed the γ1 subunit was the current density of CaV1.1a, but not that of CaV1.1e, reduced by >50%. In addition, γ1 caused a shift of the voltage dependence of inactivation to negative voltages in both variants. Thus, the current-reducing effect of γ1, unlike its effect on inactivation, is specifically dependent on the inclusion of exon 29 in CaV1.1a. Molecular structure modeling revealed several direct ionic interactions between residues in the IVS3-S4 loop and the γ1 subunit. However, substitution of these residues by alanine, individually or in combination, did not abolish the γ1-dependent reduction of current density, suggesting that structural rearrangements in CaV1.1a induced by inclusion of exon 29 may allosterically empower the γ1 subunit to exert its inhibitory action on CaV1.1 calcium currents.
Simple traversable wormholes violating energy conditions only near the Planck scale
Authors: Maeda Hideki
Published: March 2022

We present a static and axisymmetric traversable wormhole spacetime with vanishing Arnowitt-Deser-Misner (ADM) mass which is characterized by a length parameter l and a deformation parameter a and reduces to the massless Kerr vacuum wormhole as l → 0. The spacetime is analytic everywhere and regularizes a ring-like conical singularity of the massless Kerr wormhole by virtue of a localized exotic matter which violates the standard energy conditions only near the wormhole throat. In the spherically symmetric case (a = 0), the areal radius of the wormhole throat is exactly l and all the standard energy conditions are respected outside the proper radial distance approximately 1.60l from the throat. While the curvature at the throat is beyond the Planck scale if l is identical to the Planck length l
p, our wormhole may be a semi-classical model for l ≃ 10l
p. With l = 10l
p, the total amount of the negative energy supporting this wormhole is only E ≃ −26.5m
p
c
2, which is the rest mass energy of about −5.77 × 10−4 g. It is shown that the geodesic behavior on the equatorial plane does not qualitatively change by the localization of an exotic matter.
Theoretical calculation of characteristic radiation: multiconfiguration Dirac–Hartree–Fock calculations in scandium K

α
and K

β
Authors: Dean J W , Pushkarna P , Melia H A , Nguyen T V B , Chantler C T
Published: March 2022

The characteristic x-ray spectra of 3d transition metals are a constant source of advances in atomic physics, x-ray spectrometry, and quantum mechanics. Prior to this work, there was a discrepancy of 0.549 eV between theoretical and experimental results for the scandium Kα
1 peak energy, representing a 55σ discrepancy using the experimental uncertainty. This work improves this to a 0.330 eV discrepancy with only a 4σ error between experiment and theory. Furthermore, we add considerable evidence that asymmetries in x-ray spectra are described by shake events. This work provides ab initio calculations for the diagram and shake-off satellite lines of Sc Kα and Kβ and makes significant improvement on the previous fitting between theory and experiment, from a

χ

r

2

of 7.35 and 20.85 to 1.60 and 1.45 for Kα and Kβ, respectively. Therefore, we make a strong claim that the asymmetries in scandium x-ray lines exist due to satellite lines with very little room for other hypothesised phenomena to exist, such as Kondo-like interactions and Doniac–Sunjic asymmetries. By fitting to the best experimental data for Sc Kα, β we obtain values for the width and intensity of the satellite lines which enable us to reconstruct the Kα, Kβ profiles.
A high-speed single-photon detection scheme based on frequency domain filtering
Authors: Wu Jin , Rong Yue , Wan Chenggong , Shi Yumeng , Sun Xingsheng , Zheng Lixia , Sun Weifeng
Published: March 2022

This paper presents a high-speed integrated circuit for narrow-gated single-photon detection. Due to the parasitic capacitor that exists in the avalanche photo-diode (APD), the avalanche signal pulse triggered by the received photon is easily mixed with unavoidable spike noise arising from the gated clock. The traditional double-ended architecture extracts avalanche signals by suppressing common-mode noise. In order to overcome the shortcomings of high cost and mismatch in the traditional architecture, this paper adopts a single-ended detection architecture and deals with the problem of spike noise from the perspective of the frequency domain. According to the difference between the frequency characteristics of the spike noise and the avalanche signal, the effective separation of the two signals can be realized in the frequency domain by a low-pass filter with a specific cut-off frequency. The signal-to-noise ratio of the detection system is improved by using the subsequent amplification and discrimination circuit, so as to realize sensitive detection of the avalanche signals. The proposed circuit is implemented in 180 nm complementary metal oxide semiconductor technology and occupies an effective area of 2.6 mm2. The test results show that the single-ended detection system can sensitively discriminate photon signals with an emission frequency below 20 MHz when the whole circuit, including the APD, is operated at room temperature, where the minimum voltage amplitude converted from the avalanche current of the APD is around 20 mV, and the stopband attenuation of the filter at 1 GHz frequency is −58.8 dB.