bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoupled Finite Particle Method With Normalized Kernel (DFPM‐NK): A Computationally Efficient Method for Simulating Solute Transport in Heterogeneous Porous Media
Authors: Jiao Tian , Ye Ming , Jin Menggui , Yang Jing 
Published: August 2022

AbstractPrevious studies found that Finite Particle Method (FPM), an improved Smoothed Particle Hydrodynamics (SPH) method, yields more accurate solutions of the advection‐dispersion equation (ADE) than SPH method does when simulating solute transport in heterogeneous porous media. FPM however is computationally more expensive than SPH because FPM needs to solve a correction matrix equation for each particle. While decoupled FPM (DFPM) can reduce computational cost of FPM by using diagonal terms of the matrix equation, DFPM is less accurate than FPM due to discarding off‐diagonal terms of the matrix equation. This study develops the Decoupled Finite Particle Method with Normalized Kernel (DFPM‐NK) to improve computational accuracy of DFPM by using normalized kernels in DFPM. We evaluate computational performance of SPH, FPM, DFPM, and DFPM‐NK using two numerical experiments of ADE with non‐reactive and reactive solute transport in a heterogeneous aquifer. Results of the two experiments indicate that, among the four methods, SPH has the least computational time, but has the worst computational accuracy. DFPM‐NK is substantially more efficient than FPM, and has similar accuracy of FPM. On the other hand, DFPM‐NK and DFPM have similar computational cost, but DFMP‐NK is significantly more accurate than DFPM, especially for heterogeneous hydraulic conductivity fields. We thus recommend to use DFPM‐NK for computationally expensive ADE problems without sacrificing computational accuracy.
End-to-end learning of 3D phase-only holograms for holographic display
Authors: Shi Liang , Li Beichen , Matusik Wojciech 
Published: August 2022

AbstractComputer-generated holography (CGH) provides volumetric control of coherent wavefront and is fundamental to applications such as volumetric 3D displays, lithography, neural photostimulation, and optical/acoustic trapping. Recently, deep learning-based methods emerged as promising computational paradigms for CGH synthesis that overcome the quality-runtime tradeoff in conventional simulation/optimization-based methods. Yet, the quality of the predicted hologram is intrinsically bounded by the dataset’s quality. Here we introduce a new hologram dataset, MIT-CGH-4K-V2, that uses a layered depth image as a data-efficient volumetric 3D input and a two-stage supervised+unsupervised training protocol for direct synthesis of high-quality 3D phase-only holograms. The proposed system also corrects vision aberration, allowing customization for end-users. We experimentally show photorealistic 3D holographic projections and discuss relevant spatial light modulator calibration procedures. Our method runs in real-time on a consumer GPU and 5 FPS on an iPhone 13 Pro, promising drastically enhanced performance for the applications above.
AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis
Authors: Zhu Hong Jie , Zhang Bo , Wei Wanqing , Liu Shuang He , Xiang Lang , Zhu Jiapeng , Jiao Rui Hua , Igarashi Yasuhiro , Bashiri Ghader , Liang Yong , Tan Ren Xiang , Ge Hui Ming 
Published: August 2022

AbstractMacrocyclization is an important process that affords morphed scaffold in biosynthesis of bioactive natural products. Nature has adapted diverse biosynthetic strategies to form macrocycles. In this work, we report the identification and characterization of a small enzyme AvmM that can catalyze the construction of a 16-membered macrocyclic ring in the biosynthesis of alchivemycin A (1). We show through in vivo gene deletion, in vitro biochemical assay and isotope labelling experiments that AvmM catalyzes tandem dehydration and Michael-type addition to generate the core scaffold of1. Mechanistic studies by crystallography, DFT calculations and MD simulations of AvmM reveal that the reactions are achieved with assistance from the special tenuazonic acid like moiety of substrate. Our results thus uncover an uncharacterized macrocyclization strategy in natural product biosynthesis.
Selective separation of light rare-earth elements by supramolecular encapsulation and precipitation
Authors: O’Connell-Danes Joseph G. , Ngwenya Bryne T. , Morrison Carole A. , Love Jason B. 
Published: August 2022

AbstractSupramolecular chemical strategies for Rare Earth (RE) element separations are emerging which amplify the small changes in properties across the series to bias selectivity in extraction or precipitation. These advances are important as the REs are crucial to modern technologies yet their extraction, separation, and recycling using conventional techniques remain challenging. We report here a pre-organised triamidoarene platform which, under acidic, biphasic conditions, uniquely and selectively precipitates light RE nitratometalates as supramolecular capsules. The capsules exhibit both intra- and intermolecular hydrogen bonds that dictate selectivity, promote precipitation, and facilitate the straightforward release of the RE and recycling of the receptor. This work provides a self-assembly route to metal separations that exploits size and shape complementarity and has the potential to integrate into conventional processes due to its compatibility with acidic metal feed streams.
In mouse chronic pancreatitis CD25+FOXP3+ regulatory T cells control pancreatic fibrosis by suppression of the type 2 immune response
Authors: Glaubitz Juliane , Wilden Anika , Golchert Janine , Homuth Georg , Völker Uwe , Bröker Barbara M. , Thiele Thomas , Lerch Markus M. , Mayerle Julia , Aghdassi Ali A. , Weiss Frank U. , Sendler Matthias 
Published: August 2022

AbstractChronic pancreatitis (CP) is characterized by chronic inflammation and the progressive fibrotic replacement of exocrine and endocrine pancreatic tissue. We identify Treg cells as central regulators of the fibroinflammatory reaction by a selective depletion of FOXP3-positive cells in a transgenic mouse model (DEREG-mice) of experimental CP. In Treg-depleted DEREG-mice, the induction of CP results in a significantly increased stroma deposition, the development of exocrine insufficiency and significant weight loss starting from day 14 after disease onset. In CP, FOXP3+CD25+Treg cells suppress the type-2 immune response by a repression of GATA3+T helper cells (Th2), GATA3+innate lymphoid cells type 2 (ILC2) and CD206+M2-macrophages. A suspected pathomechanism behind the fibrotic tissue replacement may involve an observed dysbalance of Activin A expression in macrophages and of its counter regulator follistatin. Our study identified Treg cells as key regulators of the type-2 immune response and of organ remodeling during CP. The Treg/Th2 axis could be a therapeutic target to prevent fibrosis and preserve functional pancreatic tissue.
Cobalt-catalyzed branched selective hydroallylation of terminal alkynes
Authors: Chen Jieping , Ying Jiale , Lu Zhan 
Published: August 2022

AbstractHere, we reported a cobalt-hydride-catalyzed Markovnikov-type hydroallylation of terminal alkynes with allylic electrophile to access valuable and branched skipped dienes (1,4-dienes) with good regioselectivity. This operationally simple protocol exhibits excellent functional group tolerance and exceptional substrate scope. The reactions could be carried out in gram-scale with TON (turn over number) up to 1160, and the products could be easily derivatized. The preliminary mechanism of electrophilic allylation of α-selective cobalt alkenyl intermediate was proposed based on deuterium labeling experiment and kinetic studies.
Architecture and self-assembly of the jumbo bacteriophage nuclear shell
Authors: Laughlin Thomas G. , Deep Amar , Prichard Amy M. , Seitz Christian , Gu Yajie , Enustun Eray , Suslov Sergey , Khanna Kanika , Birkholz Erica A. , Armbruster Emily , McCammon J. Andrew , Amaro Rommie E. , Pogliano Joe , Corbett Kevin D. , Villa Elizabeth 
Published: August 2022

AbstractBacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction–modification and CRISPR–Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2–4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
A non-canonical vitamin K cycle is a potent ferroptosis suppressor
Authors: Mishima Eikan , Ito Junya , Wu Zijun , Nakamura Toshitaka , Wahida Adam , Doll Sebastian , Tonnus Wulf , Nepachalovich Palina , Eggenhofer Elke , Aldrovandi Maceler , Henkelmann Bernhard , Yamada Ken-ichi , Wanninger Jonas , Zilka Omkar , Sato Emiko , Feederle Regina , Hass Daniela , Maida Adriano , Mourão André Santos Dias , Linkermann Andreas , Geissler Edward K. , Nakagawa Kiyotaka , Abe Takaaki , Fedorova Maria , Proneth Bettina , Pratt Derek A. , Conrad Marcus 
Published: August 2022

AbstractFerroptosis, a non-apoptotic form of cell death marked by iron-dependent lipid peroxidation1, has a key role in organ injury, degenerative disease and vulnerability of therapy-resistant cancers2. Although substantial progress has been made in understanding the molecular processes relevant to ferroptosis, additional cell-extrinsic and cell-intrinsic processes that determine cell sensitivity toward ferroptosis remain unknown. Here we show that the fully reduced forms of vitamin K—a group of naphthoquinones that includes menaquinone and phylloquinone3—confer a strong anti-ferroptotic function, in addition to the conventional function linked to blood clotting by acting as a cofactor for γ-glutamyl carboxylase. Ferroptosis suppressor protein 1 (FSP1), a NAD(P)H-ubiquinone reductase and the second mainstay of ferroptosis control after glutathione peroxidase-44,5, was found to efficiently reduce vitamin K to its hydroquinone, a potent radical-trapping antioxidant and inhibitor of (phospho)lipid peroxidation. The FSP1-mediated reduction of vitamin K was also responsible for the antidotal effect of vitamin K against warfarin poisoning. It follows that FSP1 is the enzyme mediating warfarin-resistant vitamin K reduction in the canonical vitamin K cycle6. The FSP1-dependent non-canonical vitamin K cycle can act to protect cells against detrimental lipid peroxidation and ferroptosis.
Brown-fat-mediated tumour suppression by cold-altered global metabolism
Authors: Seki Takahiro , Yang Yunlong , Sun Xiaoting , Lim Sharon , Xie Sisi , Guo Ziheng , Xiong Wenjing , Kuroda Masashi , Sakaue Hiroshi , Hosaka Kayoko , Jing Xu , Yoshihara Masahito , Qu Lili , Li Xin , Chen Yuguo , Cao Yihai 
Published: August 2022

AbstractGlucose uptake is essential for cancer glycolysis and is involved in non-shivering thermogenesis of adipose tissues1–6. Most cancers use glycolysis to harness energy for their infinite growth, invasion and metastasis2,7,8. Activation of thermogenic metabolism in brown adipose tissue (BAT) by cold and drugs instigates blood glucose uptake in adipocytes4,5,9. However, the functional effects of the global metabolic changes associated with BAT activation on tumour growth are unclear. Here we show that exposure of tumour-bearing mice to cold conditions markedly inhibits the growth of various types of solid tumours, including clinically untreatable cancers such as pancreatic cancers. Mechanistically, cold-induced BAT activation substantially decreases blood glucose and impedes the glycolysis-based metabolism in cancer cells. The removal of BAT and feeding on a high-glucose diet under cold exposure restore tumour growth, and genetic deletion of Ucp1—the key mediator for BAT-thermogenesis—ablates the cold-triggered anticancer effect. In a pilot human study, mild cold exposure activates a substantial amount of BAT in both healthy humans and a patient with cancer with mitigated glucose uptake in the tumour tissue. These findings provide a previously undescribed concept and paradigm for cancer therapy that uses a simple and effective approach. We anticipate that cold exposure and activation of BAT through any other approach, such as drugs and devices either alone or in combination with other anticancer therapeutics, will provide a general approach for the effective treatment of various cancers.
OPERAnet, a multimodal activity recognition dataset acquired from radio frequency and vision-based sensors
Authors: Bocus Mohammud J. , Li Wenda , Vishwakarma Shelly , Kou Roget , Tang Chong , Woodbridge Karl , Craddock Ian , McConville Ryan , Santos-Rodriguez Raul , Chetty Kevin , Piechocki Robert 
Published: August 2022

AbstractThis paper presents a comprehensive dataset intended to evaluate passive Human Activity Recognition (HAR) and localization techniques with measurements obtained from synchronized Radio-Frequency (RF) devices and vision-based sensors. The dataset consists of RF data including Channel State Information (CSI) extracted from a WiFi Network Interface Card (NIC), Passive WiFi Radar (PWR) built upon a Software Defined Radio (SDR) platform, and Ultra-Wideband (UWB) signals acquired via commercial off-the-shelf hardware. It also consists of vision/Infra-red based data acquired from Kinect sensors. Approximately 8 hours of annotated measurements are provided, which are collected across two rooms from 6 participants performing 6 daily activities. This dataset can be exploited to advance WiFi and vision-based HAR, for example, using pattern recognition, skeletal representation, deep learning algorithms or other novel approaches to accurately recognize human activities. Furthermore, it can potentially be used to passively track a human in an indoor environment. Such datasets are key tools required for the development of new algorithms and methods in the context of smart homes, elderly care, and surveillance applications.
Development of a diagnostic assay by three-tube multiplex real-time PCR for simultaneous detection of nine microorganisms causing acute respiratory infections
Authors: Jiang Xi-Wen , Huang Tao-Sheng , Xie Long , Chen Si-Ze , Wang Shi-Dong , Huang Zhi-Wen , Li Xin-Yu , Ling Wei-Ping 
Published: August 2022

AbstractAcute respiratory infections are widespread in vulnerable populations of all ages and are characterized by a variety of symptoms. The underlying infection can be caused by a multitude of microorganisms, including viruses and bacteria. Early detection of respiratory infections through rapid pathogen screening is vital in averting infectious respiratory disease epidemics. This study utilized a multiplex real-time PCR system to develop a three-tube reverse transcription-PCR (RT-PCR) assay, enabling simultaneously detect nine respiratory pathogens, including: influenza A and B, adenovirus, respiratory syncytial virus (RSV), Streptococcus pneumoniae, Legionella pneumophila, Haemophilus influenzae, Chlamydia pneumoniae, and Mycoplasma pneumoniae. This technique utilizes a one-step assay, with specifically designed TaqMan primer–probe sets combined in the same tube. This assay provided rapid and simplified detection of the nine prevalent pathogens, as well as increased sensitivity and reduced cross-contamination. This assay was evaluated using 25 related viral/bacterial strains as positive references, the other 25 irrelevant strains as negative controls, and clinical specimens from 179 patients. All positive strains were detected with no amplification of the non-target microorganism mixtures and the assay’s detection limits ranged between 250–500 copies/ml (1.25–2.5 copies/reaction). A total of 167 (93.3%) samples tested positive for at least one of the pathogens identified; 109 of these samples were from patients confirmed to have RSV infections. The diagnostic accuracy of our assay was further confirmed by matching results from classical direct immunofluorescence assay and nucleotide sequencing. These data demonstrate the innovative multiplex real-time PCR assay as a promising alternative to the current approaches used for early screening of acute respiratory infections.
Linking personality traits and reproductive success in common marmoset (Callithrix jacchus)
Authors: Masilkova Michaela , Boukal David , Ash Hayley , Buchanan-Smith Hannah M. , Konečná Martina 
Published: August 2022

AbstractAnimal personality can affect individual fitness and population growth. Personality traits of either parent or parents’ combination may facilitate reproduction and offspring survival across species. However, previous studies focused mainly on the role of only one sex, and the link between personality and fitness has not been confirmed in primates. We examined this link in both sexes of captive common marmosets (Callithrix jacchus), a cooperatively breeding primate with extensive paternal care. We studied the effects of five personality traits of the parents (Agreeableness, Assertiveness, Conscientiousness, Inquisitiveness, and Patience), including their absolute and directional differences within pairs, on key components of reproductive performance. We expected pairs with more similar personality scores to have higher reproductive success as found in other species with long-term pairs and biparental care, but found no evidence for this hypothesis. Instead, we detected strong effects of female traits on inter-birth intervals, which were shorter in more agreeable females, and fecundity rates, which were higher in more inquisitive females. Male traits appeared to have only a limited effect on reproductive success of the pair. Our study demonstrates that various aspects of animal personality underpin reproductive performance in captive common marmosets and provides novel insights into the possible ultimate causes of personality in cooperatively breeding species.
Plume–MOR decoupling and the timing of India–Eurasia collision
Authors: Sehsah Haytham , Furnes Harald , Pham Luan Thanh , Eldosouky Ahmed M. 
Published: August 2022

AbstractThe debatable timing of India–Eurasia collision is based on geologic, stratigraphic, kinematic, and tectonic evidence. However, the collision event disturbed persistent processes, and the timing of disturbance in such processes could determine the onset of India–Eurasia collision precisely. We use the longevity of Southeast Indian Ridge (SEIR)—Kerguelen mantle plume (KMP) interaction cycles along the Ninetyeast ridge (NER) as a proxy to determine the commencement of India–Eurasia collision. The geochemical signature of the KMP tail along the NER is predominantly that of long-term coupling cycles, that was perturbed once by a short-term decoupling cycle. The long-term coupling cycles are mainly of enriched mid-ocean ridge basalts (E-MORBs). The short-term decoupling cycle is mostly derived from two distinct sources, MOR and plume separately, whereas the KMP is still being on-axis. The onset of India–Eurasia collision led to continental materials recycling into the mantle; hence the abrupt enrichment in incompatible elements at ca. 55 Ma, the MOR–plume on-axis decoupling, and the abrupt slowdown in the northward drift of the Indian plate was induced by the onset of India–Eurasia collision, thereafter MOR–plume recoupled.
Long-term trends in storm surge climate derived from an ensemble of global surge reconstructions
Authors: Tadesse Michael Getachew , Wahl Thomas , Rashid Md Mamunur , Dangendorf Sönke , Rodríguez-Enríquez Alejandra , Talke Stefan Andreas 
Published: August 2022

AbstractWe address the challenge, due to sparse observational records, of investigating long-term changes in the storm surge climate globally. We use two centennial and three satellite-era daily storm surge time series from the Global Storm Surge Reconstructions (GSSR) database and assess trends in the magnitude and frequency of extreme storm surge events at 320 tide gauges across the globe from 1930, 1950, and 1980 to present. Before calculating trends, we perform change point analysis to identify and remove data where inhomogeneities in atmospheric reanalysis products could lead to spurious trends in the storm surge data. Even after removing unreliable data, the database still extends existing storm surge records by several decades for most of the tide gauges. Storm surges derived from the centennial 20CR and ERA-20C atmospheric reanalyses show consistently significant positive trends along the southern North Sea and the Kattegat Bay regions during the periods from 1930 and 1950 onwards and negative trends since 1980 period. When comparing all five storm surge reconstructions and observations for the overlapping 1980–2010 period we find overall good agreement, but distinct differences along some coastlines, such as the Bay of Biscay and Australia. We also assess changes in the frequency of extreme surges and find that the number of annual exceedances above the 95th percentile has increased since 1930 and 1950 in several regions such as Western Europe, Kattegat Bay, and the US East Coast.
Assessing the impact of long-term exposure to nine outdoor air pollutants on COVID-19 spatial spread and related mortality in 107 Italian provinces
Authors: Perone Gaetano 
Published: August 2022

AbstractThis paper investigates the air quality in 107 Italian provinces in the period 2014–2019 and the association between exposure to nine outdoor air pollutants and the COVID-19 spread and related mortality in the same areas. The methods used were negative binomial (NB) regression, ordinary least squares (OLS) model, and spatial autoregressive (SAR) model. The results showed that (i) common air pollutants—nitrogen dioxide (NO2), ozone (O3), and particulate matter (PM2.5and PM10)—were highly and positively correlated with large firms, energy and gas consumption, public transports, and livestock sector; (ii) long-term exposure to NO2, PM2.5, PM10, benzene, benzo[a]pyrene (BaP), and cadmium (Cd) was positively and significantly correlated with the spread of COVID-19; and (iii) long-term exposure to NO2,O3, PM2.5, PM10, and arsenic (As) was positively and significantly correlated with COVID-19 related mortality. Specifically, particulate matter and Cd showed the most adverse effect on COVID-19 prevalence; while particulate matter and As showed the largest dangerous impact on excess mortality rate. The results were confirmed even after controlling for eighteen covariates and spatial effects. This outcome seems of interest because benzene, BaP, and heavy metals (As and Cd) have not been considered at all in recent literature. It also suggests the need for a national strategy to drive down air pollutant concentrations to cope better with potential future pandemics.