bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal renormalization of multiscale systems
Authors: Price Jacob , Meuris Brek , Shapiro Madelyn , Stinis Panos 
Published: September 2021

Significance
Many systems involve more variables than can be reasonably simulated. Even when only some of these variables are of interest, they usually depend strongly on the other variables. Reduced order models of the relevant variables, which behave as those variables would in a full simulation, are of great interest. Many such models involve a “memory” term that is difficult to compute and can lead to instability if not properly approximated. We have developed a time-dependent renormalization approach to stabilize such models. We validate the approach on the inviscid Burgers equation. We use it to obtain a perturbative renormalization of the three-dimensional Euler equations of incompressible fluid flow including all the complex effects present in the dynamics.
Local thermodynamics govern formation and dissolution ofCaenorhabditiselegans P granule condensates
Authors: Fritsch Anatol W. , Diaz-Delgadillo Andrés F. , Adame-Arana Omar , Hoege Carsten , Mittasch Matthäus , Kreysing Moritz , Leaver Mark , Hyman Anthony A. , Jülicher Frank , Weber Christoph A. 
Published: September 2021

SignificanceLiving cells rely on a continuous flux of energy to spatially organize biochemical processes. It remains unclear whether cells can achieve this spatial organization via thermodynamic principles. Here, we report the striking behavior of a cold-blooded organism that reacts to environmental temperature changes similar to a thermodynamic system at local equilibrium. Our key finding is that protein-rich droplets form and dissolve reversibly with temperature due to changes in the organism’s entropy. We show that the organism uses a specific molecule to extend droplet stability to the natural temperature range of the organism’s habitat. Due to the relevance of such protein droplets for the organism’s fertility, our work sheds light on how molecular components could facilitate biological functions via thermodynamic principles.
IL-6 enhances CD4 cell motility by sustaining mitochondrial Ca2+through the noncanonical STAT3 pathway
Authors: Valença-Pereira Felipe , Fang Qian , Marié Isabelle J. , Giddings Emily L. , Fortner Karen A. , Yang Rui , Villarino Alejandro V. , Huang Yina H. , Frank David A. , Wen Haitao , Levy David E. , Rincon Mercedes 
Published: September 2021

SignificanceIn this manuscript, we identify a pathway involving mitochondrial Ca2+and mitochondrial Stat3 that strengthens the motility fitness of activated CD4 T cells. Considering that motility is essential for CD4 T cells to find and reach their targets and mediate pathogenesis, these findings could lead to the development of therapeutic strategies to intervene in CD4 T cell–mediated inflammatory diseases.
Mechanism of
Staphylococcus aureus
peptidoglycan
O
-acetyltransferase A as an
O
-acyltransferase
Authors: Jones Carys S. , Anderson Alexander C. , Clarke Anthony J. 
Published: September 2021

Significance
Enzymes comprised of membrane-spanning acyltransferase-3 (AT-3) domains catalyze the O-acetylation of diverse extracytoplasmic glycans in all forms of life. In many cases, such as peptidoglycan, these glycans represent important cell wall components, and their O-acetylation confers resistance to lytic enzymes. The enzyme responsible for peptidoglycan O-acetylation in gram-positive bacteria, OatA, is a single bimodal protein of an AT-3 domain fused to an SGNH domain. The AT-3 domain adopts a different topology to that predicted in silico. Moreover, its utilization of a unique mechanism for the translocation of acetyl groups across the cytoplasmic membrane for their transfer to peptidoglycan involving catalytic Tyr and Ser residues may be broadly applicable to homologs involved in the modification of other important cell wall glycans.
Prediction of arrhythmia susceptibility through mathematical modeling and machine learning
Authors: Varshneya Meera , Mei Xueyan , Sobie Eric A. 
Published: September 2021

SignificanceDespite our understanding of the many factors that promote ventricular arrhythmias, it remains difficult to predict which specific individuals within a population will be especially susceptible to these events. We present a computational framework that combines supervised machine learning algorithms with population-based cellular mathematical modeling. Using this approach, we identify electrophysiological signatures that classify how myocytes respond to three arrhythmic triggers. Our predictors significantly outperform the standard myocyte-level metrics, and we show that the approach provides insight into the complex mechanisms that differentiate susceptible from resistant cells. Overall, our pipeline improves on current methods and suggests a proof of concept at the cellular level that can be translated to the clinical level.
Tril dampens Nodal signaling through Pellino2- and Traf6-mediated activation of Nedd4l
Authors: Kim Hyung-Seok , Green Yangsook Song , Xie Yuanyuan , Christian Jan L. 
Published: September 2021

SignificanceA proper balance of Bmp and Tgf-ß/Nodal signaling is critical to ensure normal development and to prevent disease. Our studies identify a signaling cascade that functions to coordinately enhance Bmp signaling and reduce Nodal output by activating the ubiquitin ligase Nedd4l. Mutations inNEDD4Lthat lead to gain or loss of activity underlie congenital disorders and disease in humans. Understanding how Nedd4l activity is regulated in different contexts may provide insight into how mutations inNEDD4Lresult in human pathology.
DeepLINK: Deep learning inference using knockoffs with applications to genomics
Authors: Zhu Zifan , Fan Yingying , Kong Yinfei , Lv Jinchi , Sun Fengzhu 
Published: September 2021

SignificanceAlthough practically attractive with high prediction and classification power, complicated learning methods often lack interpretability and reproducibility, limiting their scientific usage. A useful remedy is to select truly important variables contributing to the response of interest. We develop a method for deep learning inference using knockoffs, DeepLINK, to achieve the goal of variable selection with controlled error rate in deep learning models. We show that DeepLINK can also have high power in variable selection with a broad class of model designs. We then apply DeepLINK to three real datasets and produce statistical inference results with both reproducibility and biological meanings, demonstrating its promising usage to a broad range of scientific applications.
Cyclodextrins increase membrane tension and are universal activators of mechanosensitive channels
Authors: Cox Charles D. , Zhang Yixiao , Zhou Zijing , Walz Thomas , Martinac Boris 
Published: September 2021

Significance
Mechanosensitive (MS) channels play a key role in the physiology of organisms from bacteria to man. Many prokaryotic and eukaryotic MS channels respond to membrane tension. Here, we show that cyclodextrin (CD)–mediated lipid removal induces membrane tension that activates not only the mechanosensitive channel of small conductance but the structurally unrelated mechanosensitive channel of large conductance, which gates at almost lytic membrane tensions. This finding suggests that for both functional and structural studies, provided that sufficient CD is added and enough lipids are removed, any tension-sensitive ion channel can be activated. Moreover, CDs may also prove useful for the in vitro study of other membrane proteins that are sensitive to mechanical forces.
MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells
Authors: Hornbachner Ruth , Lackner Andreas , Papuchova Henrieta , Haider Sandra , Knöfler Martin , Mechtler Karl , Latos Paulina A. 
Published: September 2021

Significance
The human placenta contains progenitors that give rise to highly specialized trophoblast cell types, and failures in their differentiation are associated with placental pathologies. Importantly, transcription factors controlling these cell fate decisions in humans are poorly understood. Here, we uncovered MSX2 as a human-specific regulator of trophoblast cell identity and implicate its role in placental development and disease. We found that MSX2 interacts and cobinds many target genes with components of the SWI/SNF chromatin remodeling complex, suggesting a mechanistic link. Given the critical function of SWI/SNF in gene expression, organogenesis, and disease, we provided characterization of its composition and possible role in the placental context.
Activation of Smad2/3 signaling by low fluid shear stress mediates artery inward remodeling
Authors: Deng Hanqiang , Min Elizabeth , Baeyens Nicolas , Coon Brian G. , Hu Rui , Zhuang Zhen W. , Chen Minghao , Huang Billy , Afolabi Titilayo , Zarkada Georgia , Acheampong Angela , McEntee Kathleen , Eichmann Anne , Liu Fang , Su Bing , Simons Michael , Schwartz Martin A. 
Published: September 2021

Significance
This paper analyzes the signaling network that regulates the size of artery lumens and thus their ability to transport blood to tissues. Lumen diameter is under close homeostatic regulation to match artery flow to the needs of downstream tissues. However, in atherosclerosis, this regulation is compromised, resulting in restricted blood flow and tissue ischemia. The elucidation of a Smad2/3 pathway that is specifically activated at low flow to trigger inward remodeling and thus restore normal shear stress levels not only reveals a mechanism of physiological regulation but also explains how activation of the same pathway by inflammatory factors in diseased arteries can lead to artery restriction.
All-or-none disconnection of pyramidal inputs onto parvalbumin-positive interneurons gates ocular dominance plasticity
Authors: Severin Daniel , Hong Su Z. , Roh Seung-Eon , Huang Shiyong , Zhou Jiechao , Bridi Michelle C. D. , Hong Ingie , Murase Sachiko , Robertson Sarah , Haberman Rebecca P. , Huganir Richard L. , Gallagher Michela , Quinlan Elizabeth M. , Worley Paul , Kirkwood Alfredo 
Published: September 2021

Significance
We report a unique form of neural plasticity in the visual cortex. Unlike well-known forms of neural plasticity, in which synaptic connections are slowly weakened or strengthened, we found that visual deprivation causes a rapid and transient “all-or-none” loss of local connections between pyramidal cells and parvalbumin-positive interneurons (Pyr→PV). After 1 d of visual deprivation, half of these connections are lost, whereas the spared ones remain unchanged; after 2 d of deprivation, the connectivity levels return to normal. Finally, we show that this early transient all-or-none loss of Pyr→PV connections is an obligatory step for subsequent changes in the cortical function induced by visual deprivation.
An Early Oligocene age for the oldest known monkeys and rodents of South America
Authors: Campbell Kenneth E. , O’Sullivan Paul B. , Fleagle John G. , de Vries Dorien , Seiffert Erik R. 
Published: September 2021

Significance
The Paleogene dispersals of monkeys and rodents from Africa to South America permanently and profoundly altered the composition of mammalian communities in the Neotropics, but the timing of these colonization events remains uncertain. Through a combination of geochronological analyses (detrital zircon dating of the Santa Rosa fossil locality in eastern Perú) and phylogenetic biochronological analyses (tip-dating age estimation of caviomorph rodents), we demonstrate that the oldest known primates and rodents of South America are unlikely to be older than Early Oligocene in age and are not Eocene in age as previously postulated. There are no grounds for rejecting the possibility of an earlier arrival for either clade, but at present the fossil record provides no evidence for earlier dispersals.
Discovery of complex oxides via automated experiments and data science
Authors: Yang Lusann , Haber Joel A. , Armstrong Zan , Yang Samuel J. , Kan Kevin , Zhou Lan , Richter Matthias H. , Roat Christopher , Wagner Nicholas , Coram Marc , Berndl Marc , Riley Patrick , Gregoire John M. 
Published: September 2021

Significance
Automation is accelerating the discovery of useful materials, yet testing even a small fraction of the billions of possible materials for a desired property is beyond the reach of workflows involving resource-intensive property measurements. Due to relationships among composition, structure, and properties, identifying a complex material with one interesting property makes it the proverbial needle in a haystack that merits testing for additional properties. We accelerate materials synthesis and optical characterization by employing physics-aware data science to identify materials for further investigation. With this approach, one does not need high-throughput methods for measuring every material property of interest since a single ultra-high–throughput workflow can guide material selection for other properties, which is a new paradigm for accelerated materials discovery.
Diffusion of a disordered protein on its folded ligand
Authors: Wiggers Felix , Wohl Samuel , Dubovetskyi Artem , Rosenblum Gabriel , Zheng Wenwei , Hofmann Hagen 
Published: September 2021

Significance
Flexibility in complexes between intrinsically disordered proteins and folded ligands is widespread in nature. However, timescales and spatial amplitudes of such dynamics remained unexplored for most systems. Our results show that the disordered cytoplasmic tail of the cell adhesion protein E-cadherin diffuses across the entire surface of its folded binding partner β-catenin at fast submillisecond timescales. The nanometer amplitude of these motions could allow kinases to access their recognition motifs without requiring a dissociation of the complex. We expect that the rugged energy landscape found in the E-cadherin/β-catenin complex is a defining feature of dynamic and partially disordered protein complexes.
Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens
Authors: Xu Shenyuan , McGinnis Kristen Rose , Liu Yang , Huang Pengwei , Tan Ming , Stuckert Michael Robert , Burnside Riley Erin , Jacob Elsa Grace , Ni Shuisong , Jiang Xi , Kennedy Michael A. 
Published: September 2021

Significance
Group A rotaviruses cause severe gastroenteritis in infants and young children worldwide, with P[II] genogroup rotaviruses (RVs) responsible for >90% of global cases. Existing RV vaccines are successful in many developed countries, but their efficacy remains poor in developing countries, which could be due to lack of cross protection between RV genotypes more common in developed countries and other P-type RVs less common in developed countries but common in developing countries. In this study, crystal structures of major P[II] genogroup VP8* receptor domains in complex with Lewis epitope–containing histo-blood group antigen (HBGA) glycans were determined, revealing the structural basis for RV HBGA receptor specificities that determine RV host ranges. The data should enable rationale design of next-generation RV vaccines.
Regulation of P2X1 receptors by modulators of the cAMP effectors PKA and EPAC
Authors: Fong Zhihui , Griffin Caoimhín S. , Large Roddy J. , Hollywood Mark A. , Thornbury Keith D. , Sergeant Gerard P. 
Published: September 2021

SignificanceP2X1 receptors are important for neurogenic contraction of smooth muscle, thrombus formation, and regulation of neutrophil migration. Knockdown of P2X1 causes a 90% reduction in male fertility, and up-regulation of P2X1 receptors is associated with inflammatory bladder conditions, such as interstitial cystitis and idiopathic detrusor instability. This study identifies EPAC as a negative regulator of P2X1 receptors, but a positive regulator of P2X2 receptors. Substitution of residues 21 to 23 on P2X1 receptors, for the equivalent residues on P2X2, protected P2X1 receptors from the inhibitory effects of EPAC activation. An inhibitor of the Rho GTPase, Rac1, also prevented the inhibitory effects of EPAC activation on P2X1 currents. Our findings demonstrate regulation of P2X1 and P2X2 receptors by EPAC.
Rising nonmarital first childbearing among college-educated women: Evidence from three national studies
Authors: Cherlin Andrew J. 
Published: September 2021

Significance
Until recently, one key way in which family formation in the United States was distinctive among college-educated young adults was their tendency to wait until after marriage to have a first birth. Even as nonmarital first childbearing became common among less-educated adults, levels among the college-educated remained very low. These levels now appear to be rising, according to data from three national surveys. The data suggest a change in the role of marriage in family formation among the college-educated population, although not necessarily a decline. Rather, the place of marriage in the sequence of life events that compose emerging adulthood may be shifting among college graduates: for a growing share, marriage may occur after a first birth rather than before.
Children’s text comprehension
Authors: Oakhill Jane 
Published: September 2021

Abstract
This paper first considers what is meant by good reading comprehension and makes a distinction between the product
of reading comprehension and the processes that are required to attain that product. It goes on to consider how less-skilled
comprehenders can be identified and provides a summary of the research into how less-skilled and skilled comprehenders differ in
terms of the skills and processes that they apply during text comprehension. Finally, the implications of these research findings
for instruction are considered, and generalizable research-based recommendations for teaching reading comprehension strategies are
considered.
Tunable enhanced Faraday rotation in a defected plasma photonic crystal under external magnetic field with different declinations
Authors: Pourali Nima , Alexander Kevon , Hessel Volker , Rebrov Evgeny V 
Published: September 2021

Abstract
Magneto-optical responses and the potential for tunability when changing the variables of a one-dimensional defected magnetized plasma photonic crystal have been studied using a transfer matrix method for operation in the mm-range wavelength region. The effect of the number and dielectric defect layer thickness as well as the intensity and declination angle of magnetic field on transmittance, Faraday rotation, and its ellipticity has been investigated. The results demonstrate the ability to alter the resonant modes frequency at multiple levels of precision. The structures with four, six, and eight defect layers have been investigated. The number of defect dielectric layers changes the number of resonance modes. A single defect mode appears within the photonic bandgap with four defect dielectric layers while two defect modes were observed with six layers, and three modes with eight layers. An increase in magnetic field declination decreased the Faraday rotation intensity and width of Faraday resonance mode.
Plasma-droplet interaction study to assess transport limitations and the role of ⋅OH, O⋅,H⋅,O2(a
1Δg),O3, He(23
S) and Ar(1s
5) in formate decomposition
Authors: Nayak Gaurav , Oinuma Gaku , Yue Yuanfu , Santos Sousa João , Bruggeman Peter J 
Published: September 2021

Abstract
Plasmas interacting with liquid microdroplets are gaining momentum due to their ability to significantly enhance the reactivity transfer from the gas phase plasma to the liquid. This is, for example, critically important for efficiently decomposing organic pollutants in water. In this contribution, the role of ⋅OH as well as non-⋅OH-driven chemistry initiated by the activation of small water microdroplets in a controlled environment by diffuse RF glow discharge in He with different gas admixtures (Ar, O2 and humidified He) at atmospheric pressure is quantified. The effect of short-lived radicals such as O⋅ and H⋅ atoms, singlet delta oxygen (O2(a
1Δg)), O3 and metastable atoms of He and Ar, besides ⋅OH radicals, on the decomposition of formate dissolved in droplets was analyzed using detailed plasma diagnostics, droplet characterization and ex situ chemical analysis of the treated droplets. The formate decomposition increased with increasing droplet residence time in the plasma, with ∼70% decomposition occurring within ∼15 ms of the plasma treatment time. The formate oxidation in the droplets is shown to be limited by the gas phase ⋅OH flux at lower H2O concentrations with a significant enhancement in the formate decomposition at the lowest water concentration, attributed to e−/ion-induced reactions. However, the oxidation is diffusion limited in the liquid phase at higher gaseous ⋅OH concentrations. The formate decomposition in He/O2 plasma was similar, although with an order of magnitude higher O⋅ radical density than the ⋅OH density in the corresponding He/H2O plasma. Using a one-dimensional reaction–diffusion model, we showed that O2(a
1Δg) and O3 did not play a significant role and the decomposition was due to O⋅, and possibly ⋅OH generated in the vapor containing droplet-plasma boundary layer.
Synthesis of yttrium aluminum garnet (Y3Al5O12, YAG) powder with nano and submicro size and high infrared transmittance using flame aerosol synthesis method
Authors: Tian Hui , Wang Lei , Yang Taisheng , Zhang Zili 
Published: September 2021

Abstract
In this study, the flame aerosol synthesis (FAS) method was used to synthesize a yttrium aluminum garnet (Y3Al5O12, YAG) nanopowder. The dominant reaction route in the FAS method is the liquid route; this shaped the primary morphology of the YAG nanopowder into hollow and solid spheres. The effects of precursor concentration and annealing parameters were systematically investigated. At a precursor concentration of 0.4 mol L−1 and an annealing temperature of 1400 °C, the YAG nanopowder exhibited excellent infrared transmittance. Compared to other conventional synthesis methods, the FAS method has the advantages of high yield, low cost, and ease of obtaining a nanosized powder. The FAS method is thought to be one of the best choices for the large-scale production of YAG powders.
Geriatric medicine in the era of climate change
Authors: Davies Bethan , Bhutta Mahmood F 
Published: September 2021

Abstract
Climate change has been termed the greatest threat to human health of the 21st century. Older people and those living with frailty are more vulnerable to the effects of climate change including heatwaves and extreme weather events, and therefore, we have a responsibility to advocate for action on the climate emergency and take steps to reduce the environmental impact of our care provision. The NHS contributes 5.7% to the carbon footprint of the UK, and by reviewing the financial costs associated with frailty, we estimate the carbon footprint of frailty to be 1.7 MtCO2e, or 7% of the total NHS carbon footprint. Resource use also increases with age with particular interventions and medical equipment such as hearing and mobility aids being predominantly associated with the care of older people. The NHS has committed to net zero carbon emissions by 2045 and in order to achieve this we all need to act—balancing the triple bottom line of environmental, social and financial impacts alongside outcomes for patients and populations when making decisions about care. The principles of sustainable healthcare are already embedded in the geriatrician’s holisitic approach to the care of older people and those living with frailty, and the imperative to reduce the carbon footprint of healthcare should add weight to the argument for extending the role of the geriatrician into other specialties. It is time to begin our journey to net-zero geriatric medicine.