bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of Ocean Circulation in the North Atlantic Ocean During the Miocene: Impact of the Greenland Ice Sheet and the Eastern Tethys Seaway
Authors: Pillot Q. , Donnadieu Y. , Sarr A.‐C. , Ladant J.‐B. , Suchéras‐Marx B.
Published: August 2022

The Modern Ocean is characterized by the formation of deep‐water in the North Atlantic Ocean (i.e., NADW). This feature has been attributed to the modern geography, in which the Atlantic Ocean is a large basin extending from northern polar latitudes to the Southern Ocean, the latter enabling the connection of the otherwise isolated Atlantic with the Pacific and Indian Oceans. Sedimentary data date the establishment of the NADW between the beginning of the Eocene (∼49 Ma) and the beginning of the Miocene (∼23 Ma). The objective of this study is to quantify the impact of Miocene geography (∼20 Ma) on NADW using new simulations performed with the Earth System Model IPSL‐CM5A2. We specifically focus on the closure of the Eastern Tethys Seaway (ETS), dated between 22 and 14 Ma, which allowed the connection between the Atlantic and Indian Oceans, and on the Greenland Ice Sheet, whose earliest onset remains open to discussion but for which evidence suggest a possible existence as early as the Eocene. Our results show that the closure of the ETS does not appear to impact the establishment of NADW, because waters from the Indian Ocean do not reach the NADW formation zone when the seaway is open. Conversely, the existence of an ice sheet over Greenland strengthens the formation of NADW owing to topography induced changes in wind patterns over the North Atlantic, which in turn, results in a salinification of the North Atlantic and Nordic Seas, and in an increase in deep‐water formation.
Resolving the High‐Latitude Ionospheric Irregularity Spectra Using Multi‐Point Incoherent Scatter Radar Measurements
Authors: Goodwin L. V. , Perry G. W.
Published: August 2022

To provide new insights into the relationship between geomagnetic conditions and plasma irregularity scale‐sizes, high‐latitude irregularity spectra are computed using a novel Incoherent Scatter Radar (ISR) technique. This new technique leverages: (a) the ability of phased array Advanced Modular ISR (AMISR) technology to collect volumetric measurements of plasma density, (b) the slow F‐region cross‐field plasma diffusion at scales greater than 10 km, and (c) the high dip angle of geomagnetic field lines at high‐latitudes. The resulting irregularity spectra are of a higher spatiotemporal resolution than what has been previously possible with ISRs. Spatial structures as small as 20 km are resolved in less than 2 minutes (depending on the radar mode). In this work, we focus on Resolute Bay ISR‐North (RISR‐N) observations operating in the “imaginglptight” mode. In addition to having an unprecedented view of the size and occurrence of irregularities as they traverse the polar cap, we find that as the F‐region plasma density decreases below approximately 2.5 × 1010 m−3 at 350 km altitude the spectral power shifts to scale‐sizes lower than 50 km. Additionally, near magnetic local noon, the spectral power shifts to scales greater than 50 km, and from 15 to 6 magnetic local time, the spectral power shifts to scales lower than 50 km. This reflects the role of photoionization dominating high‐latitude ionospheric structuring in the polar cap.
Diltiazem inhibits breast cancer metastasis via mediating growth differentiation factor 15 and epithelial-mesenchymal transition
Authors: Chen Yen-Chang , Wu Chen-Teng , Chen Jia-Hong , Tsai Cheng-Fang , Wu Chen-Yun , Chang Pei-Chun , Yeh Wei-Lan
Published: August 2022

Migration and metastasis commonly happen to triple-negative breast cancer (TNBC) patients with advanced diseases. In many studies, it has been suggested that epithelial-mesenchymal transition (EMT) is one of the key mechanisms triggering cancer metastasis. Accumulating evidence has proven that calcium channel blockers mediate cell motility. Therefore, we attempt to investigate the effects of diltiazem, which has been selected from several FDA-approved clinical calcium channel blockers, on EMT in TNBC. By using both mouse and human TNBC cell lines, we found that diltiazem decreases colony formation and cell migration in breast cancer cells. The expression of epithelial markers such as E-cadherin and ZO-1 were increased dose-dependently by diltiazem, while mesenchymal markers such as Snail and Twist were decreased. In addition, we found that the expression of growth differentiation factor-15 (GDF-15) was also increased by diltiazem. Administering recombinant GDF-15 also reverses EMT, inhibits colony formation and migration in breast cancer cells. Moreover, treatment with diltiazem in tumor-bearing mice also decreases cancer metastasis and nodule formation, with more GDF-15 expression in diltiazem-treated mice than saline-treated mice, respectively. These findings suggest that diltiazem regulates EMT and cell motility through elevating GDF-15 expression in breast cancers in vitro and in vivo.
Targeted therapeutics and novel signaling pathways in non-alcohol-associated fatty liver/steatohepatitis (NAFL/NASH)
Authors: Xu Xiaohan , Poulsen Kyle L. , Wu Lijuan , Liu Shan , Miyata Tatsunori , Song Qiaoling , Wei Qingda , Zhao Chenyang , Lin Chunhua , Yang Jinbo
Published: August 2022

Non-alcohol-associated fatty liver/steatohepatitis (NAFL/NASH) has become the leading cause of liver disease worldwide. NASH, an advanced form of NAFL, can be progressive and more susceptible to developing cirrhosis and hepatocellular carcinoma. Currently, lifestyle interventions are the most essential and effective strategies for preventing and controlling NAFL without the development of fibrosis. While there are still limited appropriate drugs specifically to treat NAFL/NASH, growing progress is being seen in elucidating the pathogenesis and identifying therapeutic targets. In this review, we discussed recent developments in etiology and prospective therapeutic targets, as well as pharmacological candidates in pre/clinical trials and patents, with a focus on diabetes, hepatic lipid metabolism, inflammation, and fibrosis. Importantly, growing evidence elucidates that the disruption of the gut–liver axis and microbe-derived metabolites drive the pathogenesis of NAFL/NASH. Extracellular vesicles (EVs) act as a signaling mediator, resulting in lipid accumulation, macrophage and hepatic stellate cell activation, further promoting inflammation and liver fibrosis progression during the development of NAFL/NASH. Targeting gut microbiota or EVs may serve as new strategies for the treatment of NAFL/NASH. Finally, other mechanisms, such as cell therapy and genetic approaches, also have enormous therapeutic potential. Incorporating drugs with different mechanisms and personalized medicine may improve the efficacy to better benefit patients with NAFL/NASH.
The dual action of glioma-derived exosomes on neuronal activity: synchronization and disruption of synchrony
Authors: Spelat Renza , Jihua Nie , Sánchez Triviño Cesar Adolfo , Pifferi Simone , Pozzi Diletta , Manzati Matteo , Mortal Simone , Schiavo Irene , Spada Federica , Zanchetta Melania Eva , Ius Tamara , Manini Ivana , Rolle Irene Giulia , Parisse Pietro , Millán Ana P. , Bianconi Ginestra , Cesca Fabrizia , Giugliano Michele , Menini Anna , Cesselli Daniela , Skrap Miran , Torre Vincent
Published: August 2022

Seizures represent a frequent symptom in gliomas and significantly impact patient morbidity and quality of life. Although the pathogenesis of tumor-related seizures is not fully understood, accumulating evidence indicates a key role of the peritumoral microenvironment. Brain cancer cells interact with neurons by forming synapses with them and by releasing exosomes, cytokines, and other small molecules. Strong interactions among neurons often lead to the synchronization of their activity. In this paper, we used an in vitro model to investigate the role of exosomes released by glioma cell lines and by patient-derived glioma stem cells (GSCs). The addition of exosomes released by U87 glioma cells to neuronal cultures at day in vitro (DIV) 4, when neurons are not yet synchronous, induces synchronization. At DIV 7–12 neurons become highly synchronous, and the addition of the same exosomes disrupts synchrony. By combining Ca2+ imaging, electrical recordings from single neurons with patch-clamp electrodes, substrate-integrated microelectrode arrays, and immunohistochemistry, we show that synchronization and de-synchronization are caused by the combined effect of (i) the formation of new neuronal branches, associated with a higher expression of Arp3, (ii) the modification of synaptic efficiency, and (iii) a direct action of exosomes on the electrical properties of neurons, more evident at DIV 7–12 when the threshold for spike initiation is significantly reduced. At DIV 7–12 exosomes also selectively boost glutamatergic signaling by increasing the number of excitatory synapses. Remarkably, de-synchronization was also observed with exosomes released by glioma-associated stem cells (GASCs) from patients with low-grade glioma but not from patients with high-grade glioma, where a more variable outcome was observed. These results show that exosomes released from glioma modify the electrical properties of neuronal networks and that de-synchronization caused by exosomes from low-grade glioma can contribute to the neurological pathologies of patients with brain cancers.
Elucidation of an mTORC2-PKC-NRF2 pathway that sustains the ATF4 stress response and identification of Sirt5 as a key ATF4 effector
Authors: Li Ruizhi , Wilson Kristin F. , Cerione Richard A.
Published: August 2022

Proliferating cancer cells are dependent on glutamine metabolism for survival when challenged with oxidative stresses caused by reactive oxygen species, hypoxia, nutrient deprivation and matrix detachment. ATF4, a key stress responsive transcription factor, is essential for cancer cells to sustain glutamine metabolism when challenged with these various types of stress. While it is well documented how the ATF4 transcript is translated into protein as a stress response, an important question concerns how the ATF4 message levels are sustained to enable cancer cells to survive the challenges of nutrient deprivation and damaging reactive oxygen species. Here, we now identify the pathway in triple negative breast cancer cells that provides a sustained ATF4 response and enables their survival when encountering these challenges. This signaling pathway starts with mTORC2, which upon sensing cellular stresses arising from glutamine deprivation or an acute inhibition of glutamine metabolism, initiates a cascade of events that triggers an increase in ATF4 transcription. Surprisingly, this signaling pathway is not dependent on AKT activation, but rather requires the mTORC2 target, PKC, which activates the transcription factor Nrf2 that then induces ATF4 expression. Additionally, we identify a sirtuin family member, the NAD+-dependent de-succinylase Sirt5, as a key transcriptional target for ATF4 that promotes cancer cell survival during metabolic stress. Sirt5 plays fundamental roles in supporting cancer cell metabolism by regulating various enzymatic activities and by protecting an enzyme essential for glutaminolysis, glutaminase C (GAC), from degradation. We demonstrate that ectopic expression of Sirt5 compensates for knockdowns of ATF4 in cells exposed to glutamine deprivation-induced stress. These findings provide important new insights into the signaling cues that lead to sustained ATF4 expression as a general stress-induced regulator of glutamine metabolism, as well as highlight Sirt5 an essential effector of the ATF4 response to metabolic stress.
XPC–PARP complexes engage the chromatin remodeler ALC1 to catalyze global genome DNA damage repair
Authors: Blessing Charlotte , Apelt Katja , van den Heuvel Diana , Gonzalez-Leal Claudia , Rother Magdalena B. , van der Woude Melanie , González-Prieto Román , Yifrach Adi , Parnas Avital , Shah Rashmi G. , Kuo Tia Tyrsett , Boer Daphne E. C. , Cai Jin , Kragten Angela , Kim Hyun-Suk , Schärer Orlando D. , Vertegaal Alfred C. O. , Shah Girish M. , Adar Sheera , Lans Hannes , van Attikum Haico , Ladurner Andreas G. , Luijsterburg Martijn S.
Published: August 2022

Cells employ global genome nucleotide excision repair (GGR) to eliminate a broad spectrum of DNA lesions, including those induced by UV light. The lesion-recognition factor XPC initiates repair of helix-destabilizing DNA lesions, but binds poorly to lesions such as CPDs that do not destabilize DNA. How difficult-to-repair lesions are detected in chromatin is unknown. Here, we identify the poly-(ADP-ribose) polymerases PARP1 and PARP2 as constitutive interactors of XPC. Their interaction results in the XPC-stimulated synthesis of poly-(ADP-ribose) (PAR) by PARP1 at UV lesions, which in turn enables the recruitment and activation of the PAR-regulated chromatin remodeler ALC1. PARP2, on the other hand, modulates the retention of ALC1 at DNA damage sites. Notably, ALC1 mediates chromatin expansion at UV-induced DNA lesions, leading to the timely clearing of CPD lesions. Thus, we reveal how chromatin containing difficult-to-repair DNA lesions is primed for repair, providing insight into mechanisms of chromatin plasticity during GGR.
Imbibition-induced selective wetting of liquid metal
Authors: Kim Ji-Hye , Kim Sooyoung , Kim Hyeonjin , Wooh Sanghyuk , Cho Jiung , Dickey Michael D. , So Ju-Hee , Koo Hyung-Jun
Published: August 2022

Herein, we present the imbibition-induced, spontaneous, and selective wetting characteristics of gallium-based liquid metal alloys on a metallized surface with micro-scale topographical features. Gallium-based liquid metal alloys are fascinating materials that have enormous surface tension; therefore, they are difficult to pattern into films. The complete wetting of eutectic alloy of gallium and indium is realized on microstructured copper surfaces in the presence of HCl vapor, which removes the native oxide from the liquid metal alloy. This wetting is numerically explained based on the Wenzel’s model and imbibition process, revealing that the dimensions of the microstructures are critical for effective imbibition-driven wetting of the liquid metal. Further, we demonstrate that the spontaneous wetting of the liquid metal can be directed selectively along the microstructured region on the metallic surface to create patterns. This simple process enables the uniform coating and patterning of the liquid metal over large areas without an external force or complex processing. We demonstrate that the liquid metal-patterned substrates maintain electrical connection even in a stretched state and after repetitive stretching cycles.
Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges
Authors: Wei Wen , Ho Wei-Chin , Behringer Megan G. , Miller Samuel F. , Bcharah George , Lynch Michael
Published: August 2022

Ecological and demographic factors can significantly shape the evolution of microbial populations both directly and indirectly, as when changes in the effective population size affect the efficiency of natural selection on the mutation rate. However, it remains unclear how rapidly the mutation-rate responds evolutionarily to the entanglement of ecological and population-genetic factors over time. Here, we directly assess the mutation rate and spectrum of Escherichia coli clones isolated from populations evolving in response to 1000 days of different transfer volumes and resource-replenishment intervals. The evolution of mutation rates proceeded rapidly in response to demographic and/or environmental changes, with substantial bidirectional shifts observed as early as 59 generations. These results highlight the remarkable rapidity by which mutation rates are shaped in asexual lineages in response to environmental and population-genetic forces, and are broadly consistent with the drift-barrier hypothesis for the evolution of mutation rates, while also highlighting situations in which mutator genotypes may be promoted by positive selection.
Anionic nanoplastic exposure induces endothelial leakiness
Authors: Wei Wei , Li Yuhuan , Lee Myeongsang , Andrikopoulos Nicholas , Lin Sijie , Chen Chunying , Leong David Tai , Ding Feng , Song Yang , Ke Pu Chun
Published: August 2022

The global-scale production of plastics has been instrumental in advancing modern society, while the rising accumulation of plastics in landfills, oceans, and anything in between has become a major stressor on environmental sustainability, climate, and, potentially, human health. While mechanical and chemical forces of man and nature can eventually break down or recycle plastics, our understanding of the biological fingerprints of plastics, especially of nanoplastics, remains poor. Here we report on a phenomenon associated with the nanoplastic forms of anionic polystyrene and poly(methyl methacrylate), where their introduction disrupted the vascular endothelial cadherin junctions in a dose-dependent manner, as revealed by confocal fluorescence microscopy, signaling pathways, molecular dynamics simulations, as well as ex vivo and in vivo assays with animal model systems. Collectively, our results implicated nanoplastics-induced vasculature permeability as primarily biophysical-biochemical in nature, uncorrelated with cytotoxic events such as reactive oxygen species production, autophagy, and apoptosis. This uncovered route of paracellular transport has opened up vast avenues for investigating the behaviour and biological effects of nanoplastics, which may offer crucial insights for guiding innovations towards a sustainable plastics industry and environmental remediation.
Gridded land use data for the conterminous United States 1940–2015
Authors: Mc Shane Caitlín , Uhl Johannes H. , Leyk Stefan
Published: August 2022

Multiple aspects of our society are reflected in how we have transformed land through time. However, limited availability of historical-spatial data at fine granularity have hindered our ability to advance our understanding of the ways in which land was developed over the long-term. Using a proprietary, national housing and property database, which is a result of large-scale, industry-fuelled data harmonization efforts, we created publicly available sequences of gridded surfaces that describe built land use progression in the conterminous United States at fine spatial (i.e., 250 m × 250 m) and temporal resolution (i.e., 1 year - 5 years) between the years 1940 and 2015. There are six land use classes represented in the data product: agricultural, commercial, industrial, residential-owned, residential-income, and recreational facilities, as well as complimentary uncertainty layers informing the users about quantifiable components of data uncertainty. The datasets are part of the Historical Settlement Data Compilation for the U.S. (HISDAC-US) and enable the creation of new knowledge of long-term land use dynamics, opening novel avenues of inquiry across multiple fields of study.
High frequency resistive switching behavior of amorphous TiO2 and NiO
Authors: Bulja Senad , Kopf Rose , Tate Al , Cappuzzo Mark , Kozlov Dmitry , Claussen Holger , Wiegner Dirk , Templ Wolfgang , Mirshekar-Syahkal Dariush
Published: August 2022

Resistive switching (RS) of Transition Metal Oxides (TMOs) has become not only an attractive choice for the development of next generation non-volatile memory, but also as a suitable family of materials capable of supporting high-frequency and high-speed switching needed for the next generation wireless communication technologies, such as 6G. The exact mechanism of RS is not yet clearly understood; however, it is widely accepted to be related to the formation and rupture of sub-stoichiometric conductive filaments (Magnéli phases) of the respective oxides upon activation. Here, we examine the switching behaviour of amorphous TiO2 and NiO both under the DC regime and in the high frequency mode. We show that the DC resistance of amorphous TiO2 is invariant of the length of the active region. In contrast, the resistance of the NiO samples exhibits a strong dependence on the length, and its DC resistance reduces as the length is increased. We further show that the high frequency switching characteristics of TiO2, reflected in insertion losses in the ON state and isolation in the OFF state, are far superior to those of NiO. Fundamental inferences stem from these findings, which not only enrich our understanding of the mechanism of conduction in binary/multinary oxides but are essential for the enablement of widespread use of binary/multinary oxides in emerging non-volatile memory and 6G mm-wave applications. As an example of a possible application supported by TMOs, is a Reflective-Type Variable Attenuator (RTVA), shown here. It is designed to operate at a centre frequency of 15 GHz. The results indicate that it has a dynamic range of no less than 18 dB with a maximum insertion loss of 2.1 dB.
User engagement in relation to effectiveness of a digital lifestyle intervention (the HealthyMoms app) in pregnancy
Authors: Henriksson Pontus , Migueles Jairo H. , Söderström Emmie , Sandborg Johanna , Maddison Ralph , Löf Marie
Published: August 2022

Although user engagement is generally considered important for the effectiveness of digital behavior change interventions, there is a lack of such data in pregnancy. The aim of this study was therefore to examine the associations of user engagement with the HealthyMoms app with gestational weight gain, diet quality and physical activity in pregnancy. The study involved secondary analyses of participant data from the intervention group (n = 134) in a randomized controlled trial to determine the effectiveness of a 6-month mHealth intervention (the HealthyMoms app) on gestational weight gain, diet quality and physical activity. In adjusted regression models, the total number of registrations from three self-monitoring features (i.e., for weight-, diet- and physical activity) was associated with lower gestational weight gain (β =  − 0.18, P = 0.043) and improved diet quality (β = 0.17, P = 0.019). These findings were mainly attributable to the associations of physical activity registrations with lower gestational weight gain (β =  − 0.20, P = 0.026) and improved diet quality (β = 0.20, P = 0.006). However, the number of app sessions and page views were not associated with any of the outcomes. Our results may motivate efforts to increase user engagement in digital lifestyle interventions in pregnancy. However, additional studies are needed to further elucidate the influence of different types of user engagement in digital pregnancy interventions on their effectiveness.

Trial registration: ClinicalTrials.gov (NCT03298555); https://clinicaltrials.gov/ct2/show/NCT03298555 (date of registration: October 2, 2017; date of first enrolled participant: October 24, 2017).
Nonlinear spectral tunability of pulsed fiber laser with semiconductor optical amplifier
Authors: Bednyakova Anastasia , Khudozhitkova Daria , Turitsyn Sergei
Published: August 2022

We examine spectral properties of radiation in the pulsed fiber lasers using the semiconductor optical amplifier (SOA) as the gain medium. The complex light dynamics that result from the interplay between the fiber propagation effects in the cavity, the nonlinear effects in the SOA and spectral filtering, shift the generated radiation from the central wavelength of the filter. The resulting wavelength of the output radiation depends on the SOA pump power and the bandwidth of the intracavity filter. This offers the possibility of a spectral tunability of the generated pulses through nonlinear dynamics rather than the conventional use of a tunable filter.
Prenatal adherence to the Mediterranean diet decreases the risk of having a small-for-gestational-age baby, ECLIPSES study
Authors: Díaz-López Andrés , Díaz-Torres Sandra , Martín-Luján Francisco , Basora Josep , Arija Victoria
Published: August 2022

There is little evidence regarding the role that consuming a Mediterranean diet (MedDiet) during pregnancy plays in foetal growth. We therefore examined the relationship between maternal MedDiet adherence during pregnancy and anthropometric measures and small-for-gestational-age (SGA) at birth in a Spanish population on the north-eastern Mediterranean coast of Spain. Prospective analysis involved 614 mother–newborn pairs from the ECLIPSES study. Diet during pregnancy was assessed using a validated food frequency questionnaire, and a relative MedDiet score (rMedDiet) was calculated. Neonatal information, including weight, length, head circumference and SGA (< 10th percentile) at birth, was recorded. Multivariable logistic regression analyses were performed. The mean rMedDiet score was 9.8 (SD 2.1), ranging from 5 to 16 points. In the sample, 45% of the women had low (≤ 9 points), 32% had medium (10–11 points), and 22% had high (≥ 12 points) adherence to the rMedDiet. There was no association between rMedDiet and birth weight, length, head circumference or anthropometric indices (weight/length ratio and ponderal index). Pregnant women with a high rMedDiet score had a lower risk of delivering a SGA baby for weight (high vs low, OR = 0.36; 95% CI 0.16–0.79) and head circumference (high vs low, OR = 0.39; 95% CI 0.18–0.86), and a nonsignificant decrease in risk of SGA for length (high vs low, OR = 0.57; 95% CI 0.28–1.17). In conclusion, closer adherence to the MedDiet during pregnancy may have beneficial effects on foetal growth.
Male-female communication enhances release of extracellular vesicles leading to high fertility in Drosophila
Authors: Sanchez-Lopez Javier Arturo , Twena Shai , Apel Ido , Kornhaeuser Shani Chen , Chasnitsky Michael , Miklosi Andras G. , Vega-Dominguez Perla J. , Shephard Alex , Hefetz Amir , Heifetz Yael
Published: August 2022

The female reproductive tract (female-RT) must decipher the repertoire of molecular cues received from the male during copulation in order to activate and coordinate tract functionality necessary for high fertility. In Drosophila, this modulation is partially driven by spermathecal secretory cells (SSC). The SSC are a layer of cuboidal secretory glandular cells surrounding the spermatheca capsule where sperm is stored. It is unclear, however, how the SSC regulate the system’s activity. Here we show that mating activates the secretory machinery of the SSC. The SSC release a heterogeneous population of extracellular vesicles (EVs) which is involved in initiating and managing the increase in egg-laying, and possibly sperm storage. Moreover, sperm and male accessory gland proteins are essential for such mating-mediated SSC activity. Thus, mating regulates secretory/endocytic pathways required for trafficking of vesicles to SSC-female-RT target sites, which modulate and coordinate reproductive tract activity to achieve high fertility.
FACT modulates the conformations of histone H2A and H2B N-terminal tails within nucleosomes
Authors: Tsunaka Yasuo , Ohtomo Hideaki , Nishimura Yoshifumi
Published: August 2022

Gene expression is regulated by the modification and accessibility of histone tails within nucleosomes. The histone chaperone FACT (facilitate chromatin transcription), comprising SPT16 and SSRP1, interacts with nucleosomes through partial replacement of DNA with the phosphorylated acidic intrinsically disordered (pAID) segment of SPT16; pAID induces an accessible conformation of the proximal histone H3 N-terminal tail (N-tail) in the unwrapped nucleosome with FACT. Here, we use NMR to probe the histone H2A and H2B tails in the unwrapped nucleosome. Consequently, both the H2A and H2B N-tails on the pAID-proximal side bind to pAID with robust interactions, which are important for nucleosome assembly with FACT. Furthermore, the conformations of these N-tails on the distal DNA-contact site are altered from those in the canonical nucleosome. Our findings highlight that FACT both proximally and distally regulates the conformations of the H2A and H2B N-tails in the asymmetrically unwrapped nucleosome.
Learning the dynamics of metamaterials from diffracted waves with convolutional neural networks
Authors: Zhai Yuxin , Kwon Hyung-Suk , Choi Yunseok , Kovacevich Dylan , Popa Bogdan-Ioan
Published: August 2022

Conventional methods used to identify the dynamical properties of unknown media from scattered mechanical waves rely on analytical or numerical manipulations of the wave equation. These methods show their limitations in scenarios where the analyzed medium is moderately sized and the diffraction from the material edges influences the scattered fields significantly, such as non-destructive diagnostics and metamaterial characterization. Here, we show that convolutional neural networks can interpret the diffracted fields and learn the mapping between the scattered fields and all the effective material parameters including mass density and stiffness tensors from a small set of numerical simulations. Furthermore, networks trained with synthetic data can process physical measurements and are very robust to measurement errors. More importantly, the trained network provides insight into the dynamic behavior of matter including quantitative measures of the scattered field sensitivity to each material property and how the sensitivity changes depending on the material under test.
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
Authors: Crits-Christoph Alexander , Diamond Spencer , Al-Shayeb Basem , Valentin-Alvarado Luis , Banfield Jillian F
Published: August 2022

Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which species with this trait are widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We obtained high and medium-quality draft genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in five additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ metabolic activity and expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.
Pharmaceutical cocrystals of nomegestrol acetate with superior dissolution
Authors: Chen Xiaofeng , Ning Lifeng
Published: August 2022

The improvement of solubility and dissolution properties are the focus of research on poorly water-soluble APIs.
Improved visible light photocatalytic nitrogen fixation activity using a FeII-rich MIL-101(Fe): breaking the scaling relationship by photoinduced FeII/FeIII cycling
Authors: Guo Lijun , Li Feifei , Liu Jianxin , Jia Zehui , Li Rui , Yu Zhuobin , Wang Yawen , Fan Caimei
Published: August 2022

A FeII-rich MIL-101(Fe) was synthesized using a one-step solvent thermal method with ethylene glycol (EG) as a reducing agent, which can break the scaling relationship by photoinduced FeII and FeIII cycling.
Self-powered image array composed of touch-free sensors fabricated with semiconductor nanowires
Authors: Han Sangmoon , Lee Seoung-Ki , Kim Jong-Woong , Bae Sukang , Bae Sang-Hoon , Choi Kwang-Hun , Kim Jin Soo
Published: August 2022

The first demonstration of the image acquisition of a human hand in non-contact mode using a self-powered image array composed of touch-free sensors fabricated with InN nanowires.
Engineering of anchor sites and reaction time to efficiently synthesize high loading and stable sub-nanocluster catalysts
Authors: Wu Di , Zhang Dan , Wang Zuochao , Xu Jixiang , Chen Xilei , Lai Jianping , Wang Lei
Published: August 2022

A series of sub-nanoclusters (M/C-X, M = Pt, Pd, Ru. C = KB, CNT, rGO. X = O, N, S) synthesized by engineering anchor sites and reaction time. These materials have an excellent catalytic effect on the hydrogen evolution reaction.
A novel ionic liquid-based electrolyte assisting the high performance of low-temperature supercapacitors
Authors: Tang Xueqing , Xiao Dewei , Xu Zhenming , Liu Qingsheng , Ding Bing , Dou Hui , Zhang Xiaogang
Published: August 2022

A novel ionic liquid-based electrolyte with high conductivity and low freezing point assists carbon-based supercapacitors to exhibit superior low-temperature performance.
Modified unified power flow controller for medium voltage distribution networks
Authors: Abdelrahman Mohamed A. , Yang Peng , Ming Wenlong , Wu Jianzhong , Jenkins Nick
Published: August 2022

A conventional unified power flow controllers (UPFCs) can provide power flow control and voltage regulation in medium voltage (MV) distribution networks using partially rated converters. However, one of the main challenges of using the conventional UPFC is the unique design of the series interfacing transformer. This paper investigates a modified topology of a UPFC suitable for MV distribution networks. The modified UPFC does not need an interfacing series transformer. Hence, it offers a smaller size, lighter weight, and less cost than the conventional UPFC. It consists of single‐phase back‐to‐back series and shunt voltage source converters. The series converters are connected to a distribution network without a series transformer, while the shunt converters are interfaced using a three‐phase shunt transformer. The power ratings of the series and shunt converters were investigated considering a distribution network with a low X/R ratio. The modified UPFC was modelled in MATLAB Simulink and was connected to a two‐busbar distribution network and the enhanced IEEE 33‐bus distribution network. The results showed the ability of the modified UPFC to independently control active and reactive power in a distribution feeder by processing a fraction of the power transfer through the converters.
Active contour driven by adaptive‐scale local‐energy signed pressure force function based on bias correction for medical image segmentation
Authors: Liu Huaxiang , Fu Youyao , Zhang Shiqing , Liu Jun , Fang Jiangxiong
Published: August 2022

This paper presents an active contour model driven by an adaptive‐scale local‐energy signed pressure force (ALSPF) function based on bias correction for segmenting medical images with intensity inhomogeneity. Firstly, a local energy‐driven signed pressure force (LESPF) function is designed as the driving force to extract local image features, which can effectively deal with intensity inhomogeneity. Secondly, to avid selecting the neighbourhood size in the LESPF function, a multi‐scale adaptive selection schema is put forward to adaptively choose the local window size according to the degree of intensity inhomogeneity. Finally, a novel single‐well potential function proved to be a strictly monotonic function is designed to ensure the stable movement of the neighbourhood points in the vicinity of the evolution curve, which can not only avoid the re‐initialization process but also enhance. Experiments on synthetic and medical images demonstrate that the proposed model is more robust than the popular ACMs for segmenting images with intensity inhomogeneity. The code is available at the website: https://github.com/HuaxiangLiu/ALSPF
Wave interaction and energy absorption from arrays of complex-shaped point absorbers
Authors: Liu Yingyi , Zheng Siming , Liang Hui , Cong Peiwen
Published: August 2022

Water wave interactions with arrays of wave energy converters are numerically investigated based on the interaction theory. The converter is a heaving point absorber that can harness the ocean wave energy through up-and-down movements. A semi-analytical hybrid method is developed that combines the boundary element method and the interaction theory. The developed numerical method is verified against theoretical solutions for arrays of truncated vertical circular cylinders. Three different array layouts are studied in detail. It is found that trapped waves exist at critical wave numbers just below the cutoff values, and the peak load on the middle device increases with the number of devices in head waves. With the increase in the complexity of the array layout, significant wave force enhancement is observed, leading to a broader range of magnitude and stronger variations over the frequency band in beam waves. Moreover, variations of the q-factor show that there are some remarkable “bright spot” regions, indicating that the wave energy absorption there is locally optimized against wave conditions. By arranging the layout in a more randomized way, the optimal conditions for maximized power output can be hard to achieve, but the maximum power output can increase to a higher level.
Structural analogue-based protein structure domain assembly assisted by deep learning
Authors: Peng Chun-Xiang , Zhou Xiao-Gen , Xia Yu-Hao , Liu Jun , Hou Ming-Hua , Zhang Gui-Jun
Published: August 2022

Motivation

With the breakthrough of AlphaFold2, the protein structure prediction problem has made remarkable progress through deep learning end-to-end techniques, in which correct folds could be built for nearly all single-domain proteins. However, the full-chain modelling appears to be lower on average accuracy than that for the constituent domains and requires higher demand on computing hardware, indicating the performance of full-chain modelling still needs to be improved. In this study, we investigate whether the predicted accuracy of the full-chain model can be further improved by domain assembly assisted by deep learning.

Results

In this article, we developed a structural analogue-based protein structure domain assembly method assisted by deep learning, named SADA. In SADA, a multi-domain protein structure database was constructed for the full-chain analogue detection using individual domain models. Starting from the initial model constructed from the analogue, the domain assembly simulation was performed to generate the full-chain model through a two-stage differential evolution algorithm guided by the energy function with an inter-residue distance potential predicted by deep learning. SADA was compared with the state-of-the-art domain assembly methods on 356 benchmark proteins, and the average TM-score of SADA models is 8.1% and 27.0% higher than that of DEMO and AIDA, respectively. We also assembled 293 human multi-domain proteins, where the average TM-score of the full-chain model after the assembly by SADA is 1.1% higher than that of the model by AlphaFold2. To conclude, we find that the domains often interact in the similar way in the quaternary orientations if the domains have similar tertiary structures. Furthermore, homologous templates and structural analogues are complementary for multi-domain protein full-chain modelling.

Availability and implementation

http://zhanglab-bioinf.com/SADA

Supplementary information

Supplementary data are available at Bioinformatics online.
How is Social Care Provided in Adult Prisons in England and Wales?
Authors: Walton Holly , Tomini Sonila M , Sherlaw-Johnson Chris , Ng Pei Li , Fulop Naomi J
Published: August 2022

There is variation in provision of social care in prisons. Our research aimed to understand variation across adult prisons in England and Wales, including: (1) what social care is provided? (2) who delivers social care? (3) what peer support initiatives are used? (4) what social care indicators are relevant? and (5) are there differences between prison type and social care provision? We analysed Her Majesty’s Inspectorate of Prisons (HMIP) reports (published 2017–2020) from 102 prisons. From these reports we extracted and analysed data on social care provision. Elements of social care are not consistently delivered; need assessments (81.4 per cent) and referrals (75.5 per cent) were most frequently reported. Different providers (health care/social care/prison) deliver social care. Forty-one prisons (40.2 per cent) included peer support (formal to informal). We found no notable differences between prison categories and social care delivery, although, within category D prisons, a significantly larger proportion of those with a disability reported receiving support they needed. Inspection reports highlighted that prison social care should mirror community social care, but we could not fully evaluate this due to reporting issues. Social care provision varies; effectiveness of different models is not yet known. We provide recommendations to improve social care reporting within HMIP reports.
Quantifying research interests in 7,521 mammalian species with h-index: a case study
Authors: Tam Jessica , Lagisz Malgorzata , Cornwell Will , Nakagawa Shinichi
Published: August 2022

Background

Taxonomic bias is a known issue within the field of biology, causing scientific knowledge to be unevenly distributed across species. However, a systematic quantification of the research interest that the scientific community has allocated to individual species remains a big data problem. Scalable approaches are needed to integrate biodiversity data sets and bibliometric methods across large numbers of species. The outputs of these analyses are important for identifying understudied species and directing future research to fill these gaps.

Findings

In this study, we used the species h-index to quantity the research interest in 7,521 species of mammals. We tested factors potentially driving species h-index, by using a Bayesian phylogenetic generalized linear mixed model (GLMM). We found that a third of the mammals had a species h-index of zero, while a select few had inflated research interest. Further, mammals with higher species h-index had larger body masses; were found in temperate latitudes; had their humans uses documented, including domestication; and were in lower-risk International Union for Conservation of Nature Red List categories. These results surprisingly suggested that critically endangered mammals are understudied. A higher interest in domesticated species suggested that human use is a major driver and focus in mammalian scientific literature.

Conclusions

Our study has demonstrated a scalable workflow and systematically identified understudied species of mammals, as well as identified the likely drivers of this taxonomic bias in the literature. This case study can become a benchmark for future research that asks similar biological and meta-research questions for other taxa.
Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform
Authors: Wing Kevin , Grint Daniel J , Mathur Rohini , Gibbs Hamish P , Hickman George , Nightingale Emily , Schultze Anna , Forbes Harriet , Nafilyan Vahé , Bhaskaran Krishnan , Williamson Elizabeth , House Thomas , Pellis Lorenzo , Herrett Emily , Gautam Nileesa , Curtis Helen J , Rentsch Christopher T , Wong Angel Y S , MacKenna Brian , Mehrkar Amir , Bacon Seb , Douglas Ian J , Evans Stephen J W , Tomlinson Laurie , Goldacre Ben , Eggo Rosalind M
Published: August 2022

Background

Ethnic differences in the risk of severe COVID-19 may be linked to household composition. We quantified the association between household composition and risk of severe COVID-19 by ethnicity for older individuals.

Methods

With the approval of NHS England, we analysed ethnic differences in the association between household composition and severe COVID-19 in people aged 67 or over in England. We defined households by number of age-based generations living together, and used multivariable Cox regression stratified by location and wave of the pandemic and accounted for age, sex, comorbidities, smoking, obesity, housing density and deprivation. We included 2 692 223 people over 67 years in Wave 1 (1 February 2020–31 August 2020) and 2 731 427 in Wave 2 (1 September 2020–31 January 2021).

Results

Multigenerational living was associated with increased risk of severe COVID-19 for White and South Asian older people in both waves [e.g. Wave 2, 67+ living with three other generations vs 67+-year-olds only: White hazard ratio (HR) 1.61 95% CI 1.38–1.87, South Asian HR 1.76 95% CI 1.48–2.10], with a trend for increased risks of severe COVID-19 with increasing generations in Wave 2. There was also an increased risk of severe COVID-19 in Wave 1 associated with living alone for White (HR 1.35 95% CI 1.30–1.41), South Asian (HR 1.47 95% CI 1.18–1.84) and Other (HR 1.72 95% CI 0.99–2.97) ethnicities, an effect that persisted for White older people in Wave 2.

Conclusions

Both multigenerational living and living alone were associated with severe COVID-19 in older adults. Older South Asian people are over-represented within multigenerational households in England, especially in the most deprived settings, whereas a substantial proportion of White older people live alone. The number of generations in a household, number of occupants, ethnicity and deprivation status are important considerations in the continued roll-out of COVID-19 vaccination and targeting of interventions for future pandemics.
Non-dissipative and structure-preserving emulators via spherical optimization
Authors: Dai Dihan , Epshteyn Yekaterina , Narayan Akil
Published: August 2022

Approximating a function with a finite series, e.g., involving polynomials or trigonometric functions, is a critical tool in computing and data analysis. The construction of such approximations via now-standard approaches like least squares or compressive sampling does not ensure that the approximation adheres to certain convex linear structural constraints, such as positivity or monotonicity. Existing approaches that ensure such structure are norm-dissipative and this can have a deleterious impact when applying these approaches, e.g., when numerical solving partial differential equations. We present a new framework that enforces via optimization such structure on approximations and is simultaneously norm-preserving. This results in a conceptually simple convex optimization problem on the sphere, but the feasible set for such problems can be very complex. We establish well-posedness of the optimization problem through results on spherical convexity and design several spherical-projection-based algorithms to numerically compute the solution. Finally, we demonstrate the effectiveness of this approach through several numerical examples.