bluuebunny/crossref_metadata_2025 huggingface dataset:
Decadal Changes in Anthropogenic Inputs and Precipitation Influence Riverine Exports of Carbon, Nitrogen, and Phosphorus, and Alter Ecosystem Level Stoichiometry
Authors: Shousha Stéphanie , Maranger Roxane , Lapierre Jean‐François
Published: August 2023

Changes in precipitation and land use influence carbon (C), nitrogen (N), and phosphorus (P) exports from land to receiving waters. However, how these drivers differentially alter elemental inputs and impact subsequent ecosystem stoichiometry over time remains poorly understood. Here, we quantified long‐term (1979–2020) trends in C, N, and P exports at three sites along the mainstem of a north temperate river in Québec, Canada, that successively drains forested, urban, and more agriculturally impacted land‐use areas. Riverine N and to a lesser degree C exports tended to increase over time, with major inter‐annual variation largely resolved by changes in precipitation. Historical increases in net anthropogenic N inputs on land (NANI) also explained increases in riverine N exports, with about 35% of NANI reaching the river annually. Despite higher Net anthropogenic P inputs, NAPI, over time, P exports tended to decrease at all riverine sites. This decrease in P at the forested site was more gradual, whereas a precipitous drop was observed at the downstream urban site following legislated P removal in municipal wastewater. Changes in historical ecosystem stoichiometry reflected the differential elemental exports due to natural and anthropogenic drivers and ranged from 174: 23: 1 to 547: 76: 1 over the years. Our work shows how C, N, and P have responded to different drivers in the same catchment over the last four decades, and how their differential riverine exports have influenced ecosystem stoichiometry.
Subseasonal Prediction of Regional Antarctic Sea Ice by a Deep Learning Model
Authors: Wang Yunhe , Yuan Xiaojun , Ren Yibin , Bushuk Mitchell , Shu Qi , Li Cuihua , Li Xiaofeng
Published: August 2023

Antarctic sea ice concentration (SIC) prediction at seasonal scale has been documented, but a gap remains at subseasonal scale (1–8 weeks) due to limited understanding of ice‐related physical mechanisms. To overcome this limitation, we developed a deep learning model named Sea Ice Prediction Network (SIPNet) that can predict SIC without the need to account for complex physical processes. Compared to mainstream dynamical models like European Centre for Medium‐Range Weather Forecasts, National Centers for Environmental Prediction, and Seamless System for Prediction and Earth System Research developed at Geophysical Fluid Dynamics Laboratory, as well as a relatively advanced statistical model like the linear Markov model, SIPNet outperforms them all, effectively filling the gap in subseasonal Antarctic SIC prediction capability. SIPNet results indicate that autumn SIC variability contributes the most to sea ice predictability, whereas spring contributes the least. In addition, the Weddell Sea displays the highest sea ice predictability, while predictability is low in the West Pacific. SIPNet can also capture the signal of ENSO and SAM on sea ice.
Insulin-like growth factor 1 associated with altered immune responses in preterm infants and pigs
Authors: Bæk Ole , Rasmussen Martin Bo , Gerts Therese , Aunsholt Lise , Zachariassen Gitte , Sangild Per , Nguyen Duc Ninh
Published: August 2023

Background

Preterm infants show low blood levels of insulin-like growth factor 1 (IGF-1), known to be negatively correlated with Interleukin-6 (IL-6). We hypothesized that circulating IGF-1 is associated with systemic immune-markers following preterm birth and that exogenous IGF-1 supplementation modulates immune development in preterm pigs, used as model for preterm infants.

Methods

Plasma levels of IGF-1 and 29 inflammatory markers were measured in very preterm infants (n = 221). In preterm pigs, systemic immune development, assessed by in vitro challenge, was compared between IGF-1 treated (2.25 mg/kg/day) and control animals.

Results

Preterm infants with lowest gestational age and birth weight showed the lowest IGF-1 levels, which were correlated not only with IL-6, but a range of immune-markers. IGF-1 supplementation to preterm pigs reduced plasma IL-10 and Interferon-γ (IFN-γ), IL-2 responses to challenge and reduced expression of genes related to Th1 polarization. In vitro addition of IGF-1 (100 ng/mL) further reduced the IL-2 and IFN-γ responses but increased IL-10 response.

Conclusions

In preterm infants, plasma IGF-1 correlated with several immune markers, while supplementing IGF-1 to preterm pigs tended to reduce Th1 immune responses. Future studies should document whether IGF-1 supplementation to preterm infants affects immune development and sensitivity to infection.

Impact

Supplementation of insulin-like growth factor 1 (IGF-1) to preterm infants has been proposed to promote postnatal growth, but its impact on the developing immune system is largely unknown.

In a cohort of very preterm infants, low gestational age and birth weight were the primary predictors of low plasma levels of IGF-1, which in turn were associated with plasma immune markers. Meanwhile, in immature preterm pigs, experimental supplementation of IGF-1 reduced Th1-related immune responses in early life.

Supplementation of IGF-1 to preterm infants may affect the developing immune system, which needs consideration when evaluating overall impact on neonatal health.
Peptidylarginine deiminase 2 plays a key role in osteogenesis by enhancing RUNX2 stability through citrullination
Authors: Kim Hyun-Jung , Shin Hye-Rim , Yoon Heein , Park Min-Sang , Kim Byung-Gyu , Moon Jae-I , Kim Woo-Jin , Park Seung Gwa , Kim Ki-Tae , Kim Ha-Neui , Choi Je-Yong , Ryoo Hyun-Mo
Published: August 2023

Peptidylarginine deiminase (PADI) 2 catalyzes the post-translational conversion of peptidyl-arginine to peptidyl-citrulline in a process called citrullination. However, the precise functions of PADI2 in bone formation and homeostasis remain unknown. In this study, our objective was to elucidate the function and regulatory mechanisms of PADI2 in bone formation employing global and osteoblast-specific Padi2 knockout mice. Our findings demonstrate that Padi2 deficiency leads to the loss of bone mass and results in a cleidocranial dysplasia (CCD) phenotype with delayed calvarial ossification and clavicular hypoplasia, due to impaired osteoblast differentiation. Mechanistically, Padi2 depletion significantly reduces RUNX2 levels, as PADI2-dependent stabilization of RUNX2 protected it from ubiquitin-proteasomal degradation. Furthermore, we discovered that PADI2 binds to RUNX2 and citrullinates it, and identified ten PADI2-induced citrullination sites on RUNX2 through high-resolution LC-MS/MS analysis. Among these ten citrullination sites, the R381 mutation in mouse RUNX2 isoform 1 considerably reduces RUNX2 levels, underscoring the critical role of citrullination at this residue in maintaining RUNX2 protein stability. In conclusion, these results indicate that PADI2 plays a distinct role in bone formation and osteoblast differentiation by safeguarding RUNX2 against proteasomal degradation. In addition, we demonstrate that the loss-of-function of PADI2 is associated with CCD, thereby providing a new target for the treatment of bone diseases.
CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology
Authors: Oppermann Henry , Marcos-Grañeda Elia , Weiss Linnea A. , Gurnett Christina A. , Jelsig Anne Marie , Vineke Susanne H. , Isidor Bertrand , Mercier Sandra , Magnussen Kari , Zacher Pia , Hashim Mona , Pagnamenta Alistair T. , Race Simone , Srivastava Siddharth , Frazier Zoë , Maiwald Robert , Pergande Matthias , Milani Donatella , Rinelli Martina , Levy Jonathan , Krey Ilona , Fontana Paolo , Lonardo Fortunato , Riley Stephanie , Kretzer Jasmine , Rankin Julia , Reis Linda M. , Semina Elena V. , Reuter Miriam S. , Scherer Stephen W. , Iascone Maria , Weis Denisa , Fagerberg Christina R. , Brasch-Andersen Charlotte , Hansen Lars Kjaersgaard , Kuechler Alma , Noble Nathan , Gardham Alice , Tenney Jessica , Rathore Geetanjali , Beck-Woedl Stefanie , Haack Tobias B. , Pavlidou Despoina C. , Atallah Isis , Vodopiutz Julia , Janecke Andreas R. , Hsieh Tzung-Chien , Lesmann Hellen , Klinkhammer Hannah , Krawitz Peter M. , Lemke Johannes R. , Jamra Rami Abou , Nieto Marta , Tümer Zeynep , Platzer Konrad
Published: August 2023

Heterozygous, pathogenic CUX1 variants are associated with global developmental delay or intellectual disability. This study delineates the clinical presentation in an extended cohort and investigates the molecular mechanism underlying the disorder in a Cux1+/− mouse model. Through international collaboration, we assembled the phenotypic and molecular information for 34 individuals (23 unpublished individuals). We analyze brain CUX1 expression and susceptibility to epilepsy in Cux1+/− mice. We describe 34 individuals, from which 30 were unrelated, with 26 different null and four missense variants. The leading symptoms were mild to moderate delayed speech and motor development and borderline to moderate intellectual disability. Additional symptoms were muscular hypotonia, seizures, joint laxity, and abnormalities of the forehead. In Cux1+/− mice, we found delayed growth, histologically normal brains, and increased susceptibility to seizures. In Cux1+/− brains, the expression of Cux1 transcripts was half of WT animals. Expression of CUX1 proteins was reduced, although in early postnatal animals significantly more than in adults. In summary, disease-causing CUX1 variants result in a non-syndromic phenotype of developmental delay and intellectual disability. In some individuals, this phenotype ameliorates with age, resulting in a clinical catch-up and normal IQ in adulthood. The post-transcriptional balance of CUX1 expression in the heterozygous brain at late developmental stages appears important for this favorable clinical course.
Critical dynamics arise during structured information presentation within embodied in vitro neuronal networks
Authors: Habibollahi Forough , Kagan Brett J. , Burkitt Anthony N. , French Chris
Published: August 2023

Understanding how brains process information is an incredibly difficult task. Amongst the metrics characterising information processing in the brain, observations of dynamic near-critical states have generated significant interest. However, theoretical and experimental limitations associated with human and animal models have precluded a definite answer about when and why neural criticality arises with links from attention, to cognition, and even to consciousness. To explore this topic, we used an in vitro neural network of cortical neurons that was trained to play a simplified game of ‘Pong’ to demonstrate Synthetic Biological Intelligence (SBI). We demonstrate that critical dynamics emerge when neural networks receive task-related structured sensory input, reorganizing the system to a near-critical state. Additionally, better task performance correlated with proximity to critical dynamics. However, criticality alone is insufficient for a neuronal network to demonstrate learning in the absence of additional information regarding the consequences of previous actions. These findings offer compelling support that neural criticality arises as a base feature of incoming structured information processing without the need for higher order cognition.
Acetylcholine modulates the temporal dynamics of human theta oscillations during memory
Authors: Gedankien Tamara , Tan Ryan Joseph , Qasim Salman Ehtesham , Moore Haley , McDonagh David , Jacobs Joshua , Lega Bradley
Published: August 2023

The cholinergic system is essential for memory. While degradation of cholinergic pathways characterizes memory-related disorders such as Alzheimer’s disease, the neurophysiological mechanisms linking the cholinergic system to human memory remain unknown. Here, combining intracranial brain recordings with pharmacological manipulation, we describe the neurophysiological effects of a cholinergic blocker, scopolamine, on the human hippocampal formation during episodic memory. We found that the memory impairment caused by scopolamine was coupled to disruptions of both the amplitude and phase alignment of theta oscillations (2–10 Hz) during encoding. Across individuals, the severity of theta phase disruption correlated with the magnitude of memory impairment. Further, cholinergic blockade disrupted connectivity within the hippocampal formation. Our results indicate that cholinergic circuits support memory by coordinating the temporal dynamics of theta oscillations across the hippocampal formation. These findings expand our mechanistic understanding of the neurophysiology of human memory and offer insights into potential treatments for memory-related disorders.
Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid
Authors: Pyne Michael E. , Bagley James A. , Narcross Lauren , Kevvai Kaspar , Exley Kealan , Davies Meghan , Wang Qingzhao , Whiteway Malcolm , Martin Vincent J. J.
Published: August 2023

Saccharomyces cerevisiae is a workhorse of industrial biotechnology owing to the organism’s prominence in alcohol fermentation and the suite of sophisticated genetic tools available to manipulate its metabolism. However, S. cerevisiae is not suited to overproduce many bulk bioproducts, as toxicity constrains production at high titers. Here, we employ a high-throughput assay to screen 108 publicly accessible yeast strains for tolerance to 20 g L−1 adipic acid (AA), a nylon precursor. We identify 15 tolerant yeasts and select Pichia occidentalis for production of cis,cis-muconic acid (CCM), the precursor to AA. By developing a genome editing toolkit for P. occidentalis, we demonstrate fed-batch production of CCM with a maximum titer (38.8 g L−1), yield (0.134 g g−1 glucose) and productivity (0.511 g L−1 h−1) that surpasses all metrics achieved using S. cerevisiae. This work brings us closer to the industrial bioproduction of AA and underscores the importance of host selection in bioprocessing.
Using a synthetic machinery to improve carbon yield with acetylphosphate as the core
Authors: Guo Likun , Liu Min , Bi Yujia , Qi Qingsheng , Xian Mo , Zhao Guang
Published: August 2023

In microbial cell factory, CO2 release during acetyl-CoA production from pyruvate significantly decreases the carbon atom economy. Here, we construct and optimize a synthetic carbon conserving pathway named as Sedoheptulose-1,7-bisphosphatase Cycle with Trifunctional PhosphoKetolase (SCTPK) in Escherichia coli. This cycle relies on a generalist phosphoketolase Xfspk and converts glucose into the stoichiometric amounts of acetylphosphate (AcP). Furthermore, genetic circuits responding to AcP positively or negatively are created. Together with SCTPK, they constitute a gene-metabolic oscillator that regulates Xfspk and enzymes converting AcP into valuable chemicals in response to intracellular AcP level autonomously, allocating metabolic flux rationally and improving the carbon atom economy of bioconversion process. Using this synthetic machinery, mevalonate is produced with a yield higher than its native theoretical yield, and the highest titer and yield of 3-hydroxypropionate via malonyl-CoA pathway are achieved. This study provides a strategy for improving the carbon yield of microbial cell factories.
Surpassing the nonlinear conversion efficiency of soliton microcombs
Authors: Helgason Óskar B. , Girardi Marcello , Ye Zhichao , Lei Fuchuan , Schröder Jochen , Torres-Company Victor
Published: August 2023

Laser frequency combs are enabling some of the most exciting scientific endeavours in the twenty-first century, ranging from the development of optical clocks to the calibration of the astronomical spectrographs used for discovering Earth-like exoplanets. Dissipative Kerr solitons generated in microresonators currently offer the prospect of attaining frequency combs in miniaturized systems by capitalizing on advances in photonic integration. Most of the applications based on soliton microcombs rely on tuning a continuous-wave laser into a longitudinal mode of a microresonator engineered to display anomalous dispersion. In this configuration, however, nonlinear physics precludes one from attaining dissipative Kerr solitons with high power conversion efficiency, with typical comb powers amounting to ~1% of the available laser power. Here we demonstrate that this fundamental limitation can be overcome by inducing a controllable frequency shift to a selected cavity resonance. Experimentally, we realize this shift using two linearly coupled anomalous-dispersion microresonators, resulting in a coherent dissipative Kerr soliton with a conversion efficiency exceeding 50% and excellent line spacing stability. We describe the soliton dynamics in this configuration and find vastly modified characteristics. By optimizing the microcomb power available on-chip, these results facilitate the practical implementation of a scalable integrated photonic architecture for energy-efficient applications.
First observation of 28O
Authors: Kondo Y. , Achouri N. L. , Falou H. Al , Atar L. , Aumann T. , Baba H. , Boretzky K. , Caesar C. , Calvet D. , Chae H. , Chiga N. , Corsi A. , Delaunay F. , Delbart A. , Deshayes Q. , Dombrádi Zs. , Douma C. A. , Ekström A. , Elekes Z. , Forssén C. , Gašparić I. , Gheller J.-M. , Gibelin J. , Gillibert A. , Hagen G. , Harakeh M. N. , Hirayama A. , Hoffman C. R. , Holl M. , Horvat A. , Horváth Á. , Hwang J. W. , Isobe T. , Jiang W. G. , Kahlbow J. , Kalantar-Nayestanaki N. , Kawase S. , Kim S. , Kisamori K. , Kobayashi T. , Körper D. , Koyama S. , Kuti I. , Lapoux V. , Lindberg S. , Marqués F. M. , Masuoka S. , Mayer J. , Miki K. , Murakami T. , Najafi M. , Nakamura T. , Nakano K. , Nakatsuka N. , Nilsson T. , Obertelli A. , Ogata K. , de Oliveira Santos F. , Orr N. A. , Otsu H. , Otsuka T. , Ozaki T. , Panin V. , Papenbrock T. , Paschalis S. , Revel A. , Rossi D. , Saito A. T. , Saito T. Y. , Sasano M. , Sato H. , Satou Y. , Scheit H. , Schindler F. , Schrock P. , Shikata M. , Shimizu N. , Shimizu Y. , Simon H. , Sohler D. , Sorlin O. , Stuhl L. , Sun Z. H. , Takeuchi S. , Tanaka M. , Thoennessen M. , Törnqvist H. , Togano Y. , Tomai T. , Tscheuschner J. , Tsubota J. , Tsunoda N. , Uesaka T. , Utsuno Y. , Vernon I. , Wang H. , Yang Z. , Yasuda M. , Yoneda K. , Yoshida S.
Published: August 2023

Subjecting a physical system to extreme conditions is one of the means often used to obtain a better understanding and deeper insight into its organization and structure. In the case of the atomic nucleus, one such approach is to investigate isotopes that have very different neutron-to-proton (N/Z) ratios than in stable nuclei. Light, neutron-rich isotopes exhibit the most asymmetricN/Zratios and those lying beyond the limits of binding, which undergo spontaneous neutron emission and exist only as very short-lived resonances (about 10−21 s), provide the most stringent tests of modern nuclear-structure theories. Here we report on the first observation of28O and27O through their decay into24O and four and three neutrons, respectively. The28O nucleus is of particular interest as, with theZ = 8 andN = 20 magic numbers1,2, it is expected in the standard shell-model picture of nuclear structure to be one of a relatively small number of so-called ‘doubly magic’ nuclei. Both27O and28O were found to exist as narrow, low-lying resonances and their decay energies are compared here to the results of sophisticated theoretical modelling, including a large-scale shell-model calculation and a newly developed statistical approach. In both cases, the underlying nuclear interactions were derived from effective field theories of quantum chromodynamics. Finally, it is shown that the cross-section for the production of28O from a29F beam is consistent with it not exhibiting a closedN = 20 shell structure.
Identification of an alternative triglyceride biosynthesis pathway
Authors: McLelland Gian-Luca , Lopez-Osias Marta , Verzijl Cristy R. C. , Ellenbroek Brecht D. , Oliveira Rafaela A. , Boon Nicolaas J. , Dekker Marleen , van den Hengel Lisa G. , Ali Rahmen , Janssen Hans , Song Ji-Ying , Krimpenfort Paul , van Zutphen Tim , Jonker Johan W. , Brummelkamp Thijn R.
Published: August 2023

Triacylglycerols (TAGs) are the main source of stored energy in the body, providing an important substrate pool for mitochondrial beta-oxidation. Imbalances in the amount of TAGs are associated with obesity, cardiac disease and various other pathologies1,2. In humans, TAGs are synthesized from excess, coenzyme A-conjugated fatty acids by diacylglycerol O-acyltransferases (DGAT1 and DGAT2)3. In other organisms, this activity is complemented by additional enzymes4, but whether such alternative pathways exist in humans remains unknown. Here we disrupt the DGAT pathway in haploid human cells and use iterative genetics to reveal an unrelated TAG-synthesizing system composed of a protein we called DIESL (also known as TMEM68, an acyltransferase of previously unknown function) and its regulator TMX1. Mechanistically, TMX1 binds to and controls DIESL at the endoplasmic reticulum, and loss of TMX1 leads to the unconstrained formation of DIESL-dependent lipid droplets. DIESL is an autonomous TAG synthase, and expression of human DIESL in Escherichiacoli endows this organism with the ability to synthesize TAG. Although both DIESL and the DGATs function as diacylglycerol acyltransferases, they contribute to the cellular TAG pool under specific conditions. Functionally, DIESL synthesizes TAG at the expense of membrane phospholipids and maintains mitochondrial function during periods of extracellular lipid starvation. In mice, DIESL deficiency impedes rapid postnatal growth and affects energy homeostasis during changes in nutrient availability. We have therefore identified an alternative TAG biosynthetic pathway driven by DIESL under potent control by TMX1.
DNA-PK and the TRF2 iDDR inhibit MRN-initiated resection at leading-end telomeres
Authors: Myler Logan R. , Toia Beatrice , Vaughan Cara K. , Takai Kaori , Matei Andreea M. , Wu Peng , Paull Tanya T. , de Lange Titia , Lottersberger Francisca
Published: August 2023

Telomeres replicated by leading-strand synthesis lack the 3′ overhang required for telomere protection. Surprisingly, resection of these blunt telomeres is initiated by the telomere-specific 5′ exonuclease Apollo rather than the Mre11–Rad50–Nbs1 (MRN) complex, the nuclease that acts at DNA breaks. Without Apollo, leading-end telomeres undergo fusion, which, as demonstrated here, is mediated by alternative end joining. Here, we show that DNA-PK and TRF2 coordinate the repression of MRN at blunt mouse telomeres. DNA-PK represses an MRN-dependent long-range resection, while the endonuclease activity of MRN–CtIP, which could cleave DNA-PK off of blunt telomere ends, is inhibited in vitro and in vivo by the iDDR of TRF2. AlphaFold-Multimer predicts a conserved association of the iDDR with Rad50, potentially interfering with CtIP binding and MRN endonuclease activation. We propose that repression of MRN-mediated resection is a conserved aspect of telomere maintenance and represents an ancient feature of DNA-PK and the iDDR.
A randomized vagus nerve stimulation study demonstrates that serum aldosterone levels decrease with age in women, but not in men
Authors: Veiz Elisabeth , Kieslich Susann-Kristin , Czesnik Dirk , Herrmann-Lingen Christoph , Meyer Thomas , Staab Julia
Published: August 2023

In this randomized, sham-controlled study, we explored the effects of acute transcutaneous vagus nerve stimulation (tVNS) on serum aldosterone in 20 younger (21–26 years) and 19 older (40–70 years) healthy participants. Blood samples were collected on two different days before and after a 20-min application of active tVNS at the inner tragus or sham stimulation of the earlobe. Irrespective of the stimulation mode, aldosterone levels decreased from pre- to post-stimulation in both the young (active: β = − 1.610 (− 2.855, − 0.365), p = 0.022; sham: β = − 0.857 (− 2.102, 0.388), p = 0.257) and the old cohort (active: β = − 1.969 (− 3.234, − 0.703), p = 0.005; sham: β = − 1.334 (− 2.600, − 0.069), p = 0.063). Although this decline was significant during active tVNS, the difference in estimated β-coefficients between active and sham stimulation was not statistically significant in either cohort. Nevertheless, aldosterone concentrations showed a significant interaction effect between sex and age (p = 0.001). Among all study participants, younger women (23.3 ± 1.6 years) had the highest mineralocorticoid levels (pre active: 172.1 ± 102.0 pg/ml, pre sham: 214.3 ± 82.3 pg/ml), whereas the lowest were observed in older females (59.4 ± 9.4 years) (pre active: 104.9 ± 85.8 pg/ml, pre sham: 81.1 ± 53.8 pg/ml). This post hoc analysis did not suggest that active auricular tVNS reduces serum aldosterone levels compared to sham stimulation in healthy subjects. However, serum aldosterone levels differed among subjects depending on their age and sex, irrespective of tVNS.
X-ray free electron laser observation of ultrafast lattice behaviour under femtosecond laser-driven shock compression in iron
Authors: Sano Tomokazu , Matsuda Tomoki , Hirose Akio , Ohata Mitsuru , Terai Tomoyuki , Kakeshita Tomoyuki , Inubushi Yuichi , Sato Takahiro , Miyanishi Kohei , Yabashi Makina , Togashi Tadashi , Tono Kensuke , Sakata Osami , Tange Yoshinori , Arakawa Kazuto , Ito Yusuke , Okuchi Takuo , Sato Tomoko , Sekine Toshimori , Mashimo Tsutomu , Nakanii Nobuhiko , Seto Yusuke , Shigeta Masaya , Shobu Takahisa , Sano Yuji , Hosokai Tomonao , Matsuoka Takeshi , Yabuuchi Toshinori , Tanaka Kazuo A. , Ozaki Norimasa , Kodama Ryosuke
Published: August 2023

Over the past century, understanding the nature of shock compression of condensed matter has been a major topic. About 20 years ago, a femtosecond laser emerged as a new shock-driver. Unlike conventional shock waves, a femtosecond laser-driven shock wave creates unique microstructures in materials. Therefore, the properties of this shock wave may be different from those of conventional shock waves. However, the lattice behaviour under femtosecond laser-driven shock compression has never been elucidated. Here we report the ultrafast lattice behaviour in iron shocked by direct irradiation of a femtosecond laser pulse, diagnosed using X-ray free electron laser diffraction. We found that the initial compression state caused by the femtosecond laser-driven shock wave is the same as that caused by conventional shock waves. We also found, for the first time experimentally, the temporal deviation of peaks of stress and strain waves predicted theoretically. Furthermore, the existence of a plastic wave peak between the stress and strain wave peaks is a new finding that has not been predicted even theoretically. Our findings will open up new avenues for designing novel materials that combine strength and toughness in a trade-off relationship.
High N availability decreases N uptake and yield under limited water availability in maize
Authors: Flynn Nora E. , Comas Louise H. , Stewart Catherine E. , Fonte Steven J.
Published: August 2023

Water and nitrogen (N) are the most limiting factors to plant productivity globally, but we lack a critical understanding of how water availability impacts N dynamics in agricultural systems. Plant N requirements are particularly uncertain when water is limited because of the interactive effect of water and N on plant growth, N demand, and plant uptake. We investigated impacts of N application and water availability on plant growth and N movement, including above and belowground growth, water productivity, N productivity, N uptake, N recovery, and greenhouse gas emissions within a semi-arid system in northeastern Colorado, USA. Moderately high soil N availability depressed grain yield and shoot growth under both limited and full water availability, despite no indication of physical toxicity, and came with additional risk of deleterious N losses. Under low N availability, plant N concentrations in aboveground tissues showed greater recovery of N than what was applied in the low N treatments under both full and limited water availability. This enhanced recovery underscores the need to better understand both plant soil foraging and processes governing resource availability under these conditions. Finally, limited water availability reduced N uptake across all N treatments and left 30% more soil nitrate (NO3−) deep in the soil profile at the end of the season than under full water availability. Our results show that plant N needs are not linearly related to water use and emphasize the need for an integrated understanding of water and N interactions, plant foraging for these resources, and the dynamics of processes that make N available to plants.
Enhancing the accuracies by performing pooling decisions adjacent to the output layer
Authors: Meir Yuval , Tzach Yarden , Gross Ronit D. , Tevet Ofek , Vardi Roni , Kanter Ido
Published: August 2023

Learning classification tasks of $$({2}^{n}\times {2}^{n})$$

(

2

n

×

2

n

)

inputs typically consist of $$\le n(2\times 2$$

≤
n
(
2
×
2

) max-pooling (MP) operators along the entire feedforward deep architecture. Here we show, using the CIFAR-10 database, that pooling decisions adjacent to the last convolutional layer significantly enhance accuracies. In particular, average accuracies of the advanced-VGG with $$m$$
m
layers (A-VGGm) architectures are 0.936, 0.940, 0.954, 0.955, and 0.955 for m = 6, 8, 14, 13, and 16, respectively. The results indicate A-VGG8’s accuracy is superior to VGG16’s, and that the accuracies of A-VGG13 and A-VGG16 are equal, and comparable to that of Wide-ResNet16. In addition, replacing the three fully connected (FC) layers with one FC layer, A-VGG6 and A-VGG14, or with several linear activation FC layers, yielded similar accuracies. These significantly enhanced accuracies stem from training the most influential input–output routes, in comparison to the inferior routes selected following multiple MP decisions along the deep architecture. In addition, accuracies are sensitive to the order of the non-commutative MP and average pooling operators adjacent to the output layer, varying the number and location of training routes. The results call for the reexamination of previously proposed deep architectures and their accuracies by utilizing the proposed pooling strategy adjacent to the output layer.
Food additives and PAHO’s nutrient profile model as contributors’ elements to the identification of ultra-processed food products
Authors: Canella Daniela Silva , Pereira Montera Vanessa dos Santos , Oliveira Natália , Mais Laís Amaral , Andrade Giovanna Calixto , Martins Ana Paula Bortoletto
Published: August 2023

The NOVA classification system categorizes foods according to the extent and purpose of industrial processing. Ultra-processed food products (UPF) are frequently composed of excessive amounts of sugars, salt, oils, and fats, and cosmetic additives designed to make them palatable and/or appealing. We aimed to describe the presence of critical nutrients in excess and cosmetic additives in packaged foods and beverages and to evaluate the proportion of UPF that can be correctly identified through the presence of critical nutrients in excess or the presence of cosmetic additives in food products. A total of 9851 items available in Brazilian supermarkets containing lists of ingredients and nutrition facts panels were analyzed. Cosmetic additives and critical nutrients in excess, according to Pan American Health Organization (PAHO)’s nutrient profile model, were assessed. All food items were categorized into the four NOVA classification groups. Relative frequencies of items with at least one critical nutrient in excess and one type of cosmetic additive were estimated. For UPF, 82.1% had some cosmetic additive, and 98.8% had some cosmetic additive or a nutrient in excess. This combined criterion allowed the identification of 100.0% of sweet cookies, salted biscuits, margarine, cakes and sweet pies, chocolate, dairy beverages, and ice cream. Combining the presence of cosmetic additives and the PAHO’s nutrient profile model contributes to the identification of UPF.
Benchmarking of force fields to characterize the intrinsically disordered R2-FUS-LC region
Authors: Chan-Yao-Chong Maud , Chan Justin , Kono Hidetoshi
Published: August 2023

Intrinsically Disordered Proteins (IDPs) play crucial roles in numerous diseases like Alzheimer's and ALS by forming irreversible amyloid fibrils. The effectiveness of force fields (FFs) developed for globular proteins and their modified versions for IDPs varies depending on the specific protein. This study assesses 13 FFs, including AMBER and CHARMM, by simulating the R2 region of the FUS-LC domain (R2-FUS-LC region), an IDP implicated in ALS. Due to the flexibility of the region, we show that utilizing multiple measures, which evaluate the local and global conformations, and combining them together into a final score are important for a comprehensive evaluation of force fields. The results suggest c36m2021s3p with mTIP3p water model is the most balanced FF, capable of generating various conformations compatible with known ones. In addition, the mTIP3P water model is computationally more efficient than those of top-ranked AMBER FFs with four-site water models. The evaluation also reveals that AMBER FFs tend to generate more compact conformations compared to CHARMM FFs but also more non-native contacts. The top-ranking AMBER and CHARMM FFs can reproduce intra-peptide contacts but underperform for inter-peptide contacts, indicating there is room for improvement.
Intercellular cross-talk through lineage-specific gap junction of cancer-associated fibroblasts related to stromal fibrosis and prognosis
Authors: Cho Seong Ju , Oh Ji-Hye , Baek Jaehoon , Shin Yunsu , Kim Wonkyung , Ko Junsu , Jun Eunsung , Lee Dakeun , Kim Seok-Hyung , Sohn Insuk , Sung Chang Ohk
Published: August 2023

Stromal fibrosis in cancer is usually associated with poor prognosis and chemotherapy resistance. It is thought to be caused by fibroblasts; however, the exact mechanism is not yet well understood. The study aimed to identify lineage-specific cancer-associated fibroblast (CAF) subgroup and their associations with extracellular matrix remodeling and clinical significances in various tumor types using single-cell and bulk RNA sequencing data. Through unsupervised clustering, six subclusters of CAFs were identified, including a cluster with exclusively high gap junction protein beta-2 (GJB2) expression. This cluster was named GJB2-positive CAF. It was found to be a unique subgroup of terminally differentiated CAFs associated with collagen gene expression and extracellular matrix remodeling. GJB2-positive CAFs showed higher communication frequency with vascular endothelial cells and cancer cells than GJB2-negative CAFs. Moreover, GJB2 was poorly expressed in normal tissues, indicating that its expression is dependent on interaction with other cells, including vascular endothelial cells and cancer cells. Finally, the study investigated the clinical significance of GJB2 signature score for GJB2-positive CAFs in cancer and found a correlation with poor prognosis. These results suggest that GJB2-positive CAF is a unique fibroblast subtype involved in extracellular matrix remodeling, with significant clinical implications in cancer.
The elucidation of plasma lipidome profiles during severe influenza in a mouse model
Authors: Ohno Marumi , Gowda Siddabasave Gowda B. , Sekiya Toshiki , Nomura Naoki , Shingai Masashi , Hui Shu-Ping , Kida Hiroshi
Published: August 2023

Although influenza virus infection has been shown to affect lipid metabolism, details remain unknown. Therefore, we elucidated the kinetic lipid profiles of mice infected with different doses of influenza virus A/Puerto Rico/8/34 (H1N1) (PR8) by measuring multiple lipid molecular species using untargeted lipidomic analysis. C57BL/6 male mice were intranasally infected with PR8 virus at 50 or 500 plaque-forming units to cause sublethal or lethal influenza, respectively. Plasma and tissue samples were collected at 1, 3, and 6 days post-infection (dpi), and comprehensive lipidomic analysis was performed using high-performance liquid chromatography–linear trap quadrupole–Orbitrap mass spectrometry, as well as gene expression analyses. The most prominent feature of the lipid profile in lethally infected mice was the elevated plasma concentrations of phosphatidylethanolamines (PEs) containing polyunsaturated fatty acid (PUFA) at 3 dpi. Furthermore, the facilitation of PUFA-containing phospholipid production in the lungs, but not in the liver, was suggested by gene expression and lipidomic analysis of tissue samples. Given the increased plasma or serum levels of PUFA-containing PEs in patients with other viral infections, especially in severe cases, the elevation of these phospholipids in circulation could be a biomarker of infection and the severity of infectious diseases.
Genome-wide study of longitudinal brain imaging measures of multiple sclerosis progression across six clinical trials
Authors: Loomis Stephanie J. , Sadhu Nilanjana , Fisher Elizabeth , Gafson Arie R. , Huang Yunfeng , Yang Chengran , Hughes Emily E. , Marshall Eric , Herman Ann , John Sally , Runz Heiko , Jia Xiaoming , Bhangale Tushar , Bronson Paola G.
Published: August 2023

While the genetics of MS risk susceptibility are well-described, and recent progress has been made on the genetics of disease severity, the genetics of disease progression remain elusive. We therefore investigated the genetic determinants of MS progression on longitudinal brain MRI: change in brain volume (BV) and change in T2 lesion volume (T2LV), reflecting progressive tissue loss and increasing disease burden, respectively. We performed genome-wide association studies of change in BV (N = 3401) and change in T2LV (N = 3513) across six randomized clinical trials from Biogen and Roche/Genentech: ADVANCE, ASCEND, DECIDE, OPERA I & II, and ORATORIO. Analyses were adjusted for randomized treatment arm, age, sex, and ancestry. Results were pooled in a meta-analysis, and were evaluated for enrichment of MS risk variants. Variant colocalization and cell-specific expression analyses were performed using published cohorts. The strongest peaks were in PTPRD (rs77321193-C/A, p = 3.9 × 10–7) for BV change, and NEDD4L (rs11398377-GC/G, p = 9.3 × 10–8) for T2LV change. Evidence of colocalization was observed for NEDD4L, and both genes showed increased expression in neuronal and/or glial populations. No association between MS risk variants and MRI outcomes was observed. In this unique, precompetitive industry partnership, we report putative regions of interest in the neurodevelopmental gene PTPRD, and the ubiquitin ligase gene NEDD4L. These findings are distinct from known MS risk genetics, indicating an added role for genetic progression analyses and informing drug discovery.
Frequency and risk factors of H. pylori infection among dental students: an observational cross-sectional study
Authors: Mikhail Christine Raouf George , Abd El Maksoud Mohamed Abeer , Shaker Olfat Gamil , EL Desouky Eman , Shalaby Rania Hassan
Published: August 2023

Despite Helicobacter pylori infection remains asymptomatic in most people, it is associated with an increased risk of gastric cancer. Considering Egypt had the highest prevalence of H. pylori in healthy asymptomatic population in adults and pediatric age in past studies and currently salivary ELISA could be used for diagnosis of Oral H. pylori infection. Moreover, some researchers speculated that dentists and dental students might be at a higher risk for oral H. pylori infection because they are the most frequently exposed ones to saliva and dental plaque. This study aimed to determine risk factors associated with frequency of H. pylori among a sample of dental students for better management of the disease. 83 participants, with age (21–25 years), attending Faculty of Dentistry, Fayoum University were recruited. A structured questionnaire was used to collect information on sociodemographic parameters and risk factors for H. pylori. Direct inquiry about dyspeptic symptoms were done. Saliva samples were collected and tested for H. pylori antibodies. Overall seroprevalence was 22.9%. Participants in internship were more prone to be positive (p = 0.005). 32.6% of urban residents versus 10.8% of rural were H. pylori positive (p = 0.019). 75.0% of previous history of H. pylori infection versus 14.1% of those with no history were H. pylori positive p < 0.001. 70% of positive H. pylori participants reported positive clinical symptoms that were statistically significant. This study suggests that middle income, previous history of H. pylori and clinical symptoms of dyspepsia are risk factors of oral H. pylori with a decline in its prevalence in Egypt.
Reliability and performance evaluation of a solar PV-powered underground water pumping system
Authors: Ahmed Nesma Mohamed , Hassan Ahmed Mahrous , Kassem Mohamed Abdelwahab , Hegazi Ahmed Mahmoud , Elsaadawi Youssef Fayez
Published: August 2023

The operation and effectiveness of a solar-powered underground water pumping system are affected by many environmental and technical factors. The impact of these factors must be investigated to be considered when developing these systems and to ensure their dependability. This study evaluated the dependability and performance of photovoltaic water pumping system (PVWPS) under real operating conditions by examining the effects of solar irradiance, panels’ temperature, and components' efficiency. From December 2020 to June 2021, experiments were conducted on a 10 hp PVWPS located in Bani Salamah, Al-Qanater-Giza Governorate, Egypt, at latitude 30.3° N, longitude 30.8° E, and 19 m above sea level. The irradiance values reached 755.7, 792.7, and 805.7 W/m2at 12:00 p.m. in December, March, and June, respectively. Furthermore, the irradiance has a significant impact on the pump flow rate, as the amount of pumped water during the day reached 129, 164.1, and 181.8 m3/day, respectively. The panels' temperatures rose to 35.7 °C, 39.9 °C, and 44 °C, respectively. It was observed that when the temperature rises by 1 degree Celsius, efficiency falls by 0.48%. The average efficiency of photovoltaic solar panels reached its highest value in March (13.8%) and its lowest value in December (13%).
Optimized time dependent exfoliation of graphite for fabrication of Graphene/GO/GrO nanocomposite based pseudo-supercapacitor
Authors: Zainab Sana , Fraz Sajal , Awan Saif Ullah , Hussain Danish , Rizwan Syed , Mehmood Waqar
Published: August 2023

High capacitance devices (Supercapacitors) fabricated using two-dimensional materials such as Graphene and its composites are attracting great attention of the research community, recently. Synthesis of 2D materials and their composites with high quality is desirable for the fabrication of 2D materials-based supercapacitors. Ultrasonic Assisted Liquid Phase Exfoliation (UALPE) is one of the widely used techniques for the synthesis of graphene. In this article, we report the effect of variation in sonication time on the exfoliation of graphite powder to extract a sample with optimal properties well suited for supercapacitors applications. Three different graphite powders (hereafter termed as sample A, sample B, and sample C) were sonicated for duration of 24 h, 48 h and 72 h at 60 °C. The exfoliation of graphite powder into graphene, GO and GrO was studied using XRD and RAMAN. AFM and SEM were further used to examine the layered structure of the synthesized nanocomposite. UV–visible spectroscopy and cyclic voltammetery were used to measure the band gaps, and capacitive behavior of the samples. Sample B exhibited a remarkable specific capacitance of 534.53 F/g with charge specific capacity of 530.1 C/g at 1 A/g and energy density of 66 kW/kg. Power density varied 0.75 kWh/kg to 7.5 kWh/kg for a variation in current density from 1 to 10 A/g. Sample B showed capacitive retention of 94%, the lowest impedance and highest degree of exfoliation and conductivity as compared to the other two samples.
Two-step hot isostatic pressing densification achieved non-porous fully-densified wood with enhanced physical and mechanical properties
Authors: Maturana J. C. , Guindos P. , Lagos J. , Arroyave C. , Echeverría F. , Correa E.
Published: August 2023

A new two-step densification method for wooden materials entitled hot isostatic pressing (HIP) is proposed. This method has the advantage over previous densification methods that can achieved almost the full densification of wood, reaching values up to 1.47 kg/m3, which exceeds any value ever reported for a hardwood species. Furthermore, it can preserve about 35% of the original volume, in comparison to other methods which typically can preserve only 20% of the volume. Although not tested in this investigation, in principle, the HIP method should be capable of densifying any shape of wood including circular and tubular cross sections because the main densification mechanism is based on gas pressure that is equally exerted in the entire surface, rather than localized mechanical compression, which can only be effective with rectangular cross sections. In the first stage of the two-step proposed method, the compressive strength of the anatomical wood structure is reduced by delignification, and, in the second, a full densification is achieved by hot isostatic pressing under argon atmosphere. Three tropical hardwood species with distinct anatomical characteristics and properties were used to test the method. The HIP-densified wood’s microstructural, chemical, physical, and mechanical properties were assessed. Apart from the high densification values and volume preservation, the results indicate that proposed method was effective for all the tested species, showing homogenous density patterns, stable densification without noticeable shape recovery, and enhanced mechanical properties. Future research should test the HIP method in softwoods and consider the ring orientation in order to enhance the control of the densified geometry.
The association between working memory precision and the nonlinear dynamics of frontal and parieto-occipital EEG activity
Authors: Chang Wen-Sheng , Liang Wei-Kuang , Li Dong-Han , Muggleton Neil G. , Balachandran Prasad , Huang Norden E. , Juan Chi-Hung
Published: August 2023

Electrophysiological working memory (WM) research shows brain areas communicate via macroscopic oscillations across frequency bands, generating nonlinear amplitude modulation (AM) in the signal. Traditionally, AM is expressed as the coupling strength between the signal and a prespecified modulator at a lower frequency. Therefore, the idea of AM and coupling cannot be studied separately. In this study, 33 participants completed a color recall task while their brain activity was recorded through EEG. The AM of the EEG data was extracted using the Holo-Hilbert spectral analysis (HHSA), an adaptive method based on the Hilbert-Huang transforms. The results showed that WM load modulated parieto-occipital alpha/beta power suppression. Furthermore, individuals with higher frontal theta power and lower parieto-occipital alpha/beta power exhibited superior WM precision. In addition, the AM of parieto-occipital alpha/beta power predicted WM precision after presenting a target-defining probe array. The phase-amplitude coupling (PAC) between the frontal theta phase and parieto-occipital alpha/beta AM increased with WM load while processing incoming stimuli, but the PAC itself did not predict the subsequent recall performance. These results suggest frontal and parieto-occipital regions communicate through theta-alpha/beta PAC. However, the overall recall precision depends on the alpha/beta AM following the onset of the retro cue.