bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluid Drainage Leads to Thermal Decomposition of Wet Gouge During Experimental Seismic Slip
Authors: Nguyen Thi Trinh , Kuo Li‐Wei , Kong Qing‐En , Kuo Chia‐Wei , Dong Jia‐Jyun , Brown Dennis , Wang Huan , Kuo Szu‐Ting , Li Haibing , Si Jialiang 
Published: September 2024

AbstractSeveral borehole cores intersecting faults related to coseismic slip display high‐temperature features, including thermal decomposition of fault gouge. We present evidence that these features may be related to fluid drainage of the slip zone during seismic slip. We sheared water‐saturated kaolinite powders under both fluid drained and undrained conditions, expected for seismic slip at shallow crustal depths. Our results show typical dynamic weakening behavior regardless of conditions. Under fluid drained condition, restrengthening accompanied by the thermal decomposition of kaolinite occurs. In addition, thermal decomposition of kaolinite tends to be initiated at high normal stresses (>5 MPa) with short displacement (<5 m). We propose that thermal pressurization acts as a weakening mechanism but ceases because of fluid drainage, triggering kaolinite thermal decomposition. This finding explains seismic‐slip‐related clay anomalies at depth rather than at the surface, as observed in the borehole after the 1999 Mw 7.6 Chi‐Chi earthquake, Taiwan.
The Shortwave Cloud‐SST Feedback Amplifies Multi‐Decadal Pacific Sea Surface Temperature Trends: Implications for Observed Cooling
Authors: Espinosa Zachary I. , Zelinka Mark D. 
Published: September 2024

AbstractClimate models struggle to produce sea surface temperature (SST) gradient trends in the tropical Pacific comparable to those seen recently in nature. Here, we find that the magnitude of the cloud‐SST feedback in the subtropical Southeast Pacific is correlated across models with the magnitude of Eastern Pacific multi‐decadal SST variability. A heat‐budget analysis reveals coupling between cloud‐radiative effects, circulation, and SST gradients in driving multi‐decadal variability in the Eastern Pacific. Using this relationship and observed feedback estimates, we find that internal Eastern Pacific SST variability is underestimated in most models. Adjusting for model bias increases the likelihood of generating a cooling trend at least as large as observations in preindustrial control simulations by 56% on average. If models underestimate climate “noise,” as our results suggest, this bias should be accounted for when attributing the relative importance of forced versus unforced changes in the climate.
Tropical Aviation Turbulence Induced by the Interaction Between a Jet Stream and Deep Convection
Authors: Chen Haoming , Shi Xiaoming , Nie Xiuwen , Wang Yueya , Leung Christy Yan Yu , Cheung Ping , Chan Pak Wai 
Published: September 2024

AbstractOn 18 December 2022, Hawaiian Airlines flight HA35 encountered severe turbulence without warning in a cloud‐free height. We reproduced this incident using the Weather Research and Forecasting Model (WRF) at a convection‐permitting resolution. We found that this case of tropical upper‐level turbulence occurred primarily due to the fast‐growing convective tower in the unstable layer created by gravity wave breaking. At lower altitudes, a mesoscale convective system (MCS) caused a decrease in wind speed in both upstream and downstream regions. At upper levels, a large‐scale jet descended and accelerated after flowing over the top of the MCS, which acted like a barrier and produced a situation similar to a downslope windstorm due to mountain terrain. Upper‐level turbulence is 2–3 km higher than the top of the MCS. The critical level above the jet and the locally self‐induced critical level created the locally enhanced descending jet stream, which destabilized the flow through Kelvin–Helmholtz instabilities. The convective tower existed near the flight route and played an important role in triggering turbulence in the unstable environment through its convective gravity waves.
Vertical Profile Climatology of Polarimetric Radar Variables and Retrieved Microphysical Parameters in Synoptic and Lake Effect Snowstorms
Authors: Hu Jiaxi , Ryzhkov Alexander , Dunnavan Edwin L. 
Published: September 2024

AbstractThis study derives polarimetric radar vertical profiles and microphysical retrievals for 25 Synoptic Snow (SS) and 23 Lake Effect Snow (LES) cases using the Range‐Defined Quasi‐Vertical Profiles (RD‐QVP), Columnar Vertical Profiles (CVP), and Process‐oriented Vertical Profiles (POVP) methods. For all vertical profile techniques, SS cases exhibit a near‐linear increase in reflectivity from −30 to 0°C whereas ZDR and Kdp locally peak in the dendritic growth layer. LES cases universally exhibit negative ZDR, rather high Z, negligible Kdp, and near‐unity ρhv. Ground measurements from the past OWLeS campaign provide direct evidence that conical graupel may strongly affect these polarimetric measurements in LES bands. Aggregation efficiencies for SS cases are estimated by optimizing the theoretical number concentration (Nt) and mean volume diameter (Dm) steady‐state vertical profiles against radar‐retrieved profiles derived from 20 of the 25 synoptic storm RD‐QVPs. The median estimated aggregation efficiency is approximately 0.15 with a relatively narrow interquartile range that spans from 0.1 to just over 0.2. Values of optimized aggregation efficiencies are nearly independent of the assumed gamma distribution shape parameter. These results are used to derive temperature‐dependent, climatological steady‐state relations for vertical profiles of Nt, Dm, and liquid‐equivalent snowfall rates. These results can be used in numerical weather prediction model aggregation parameterizations and can also provide climatologically representative vertical profiles of radar and microphysical quantities.
Transcriptomic profiles in major depressive disorder: the role of immunometabolic and cell-cycle-related pathways in depression with different levels of inflammation
Authors: Sforzini Luca , Marizzoni Moira , Bottanelli Chiara , Kunšteková Veronika , Zonca Valentina , Saleri Samantha , Kose Melisa , Lombardo Giulia , Mariani Nicole , Nettis Maria A. , Nikkheslat Naghmeh , Worrell Courtney , Zajkowska Zuzanna , Pointon Linda , Cowen Philip J. , Cavanagh Jonathan , Harrison Neil A. , Riva Marco A. , Mondelli Valeria , Bullmore Edward T. ,   the Neuroimmunology of Mood Disorders and Alzheimer’s Disease (NIMA) Consortium, Cattaneo Annamaria , Pariante Carmine M. 
Published: September 2024

AbstractTranscriptomic profiles are important indicators for molecular mechanisms and pathways involved in major depressive disorder (MDD) and its different phenotypes, such as immunometabolic depression. We performed whole-transcriptome and pathway analyses on 139 individuals from the observational, case-control, BIOmarkers in DEPression (BIODEP) study, 105 with MDD and 34 controls. We divided MDD participants based on levels of inflammation, as measured by serum high-sensitivity C-reactive protein (CRP), in n = 39 ‘not inflamed’ (CRP < 1 mg/L), n = 31 with ‘elevated CRP’ (1–3 mg/L), and n = 35 with ‘low-grade inflammation’ (>3 mg/L). We performed whole-blood RNA sequencing using Illumina NextSeq 550 and statistical analyses with the Deseq2 package for R statistics (RUV-corrected) and subsequent pathway analyses with Ingenuity Pathway Analysis. Immunometabolic pathways were activated in individuals with CRP > 1 mg/L, although surprisingly the CRP 1–3 group showed stronger immune activation than the CRP > 3 group. The main pathways identified in the comparison between CRP < 1 group and controls were cell-cycle-related, which may be protective against immunometabolic abnormalities in this ‘non-inflamed’ depressed group. We further divided MDD participants based on exposure and response to antidepressants (n = 47 non-responders, n = 37 responders, and n = 22 unmedicated), and identified specific immunomodulatory and neuroprotective pathways in responders (especially vs. non-responders), which could be relevant to treatment response. In further subgroup analyses, we found that the specific transcriptional profile of responders is independent of CRP levels, and that the inhibition of cell-cycle-related pathways in MDD with CRP < 1 mg/L is present only in those who are currently depressed, and not in the responders. The present study demonstrates immunometabolic and cell-cycle-related transcriptomic pathways associated with MDD and different (CRP-based and treatment-based) MDD phenotypes, while shedding light on potential molecular mechanisms that could prevent or facilitate an individual’s trajectory toward immunometabolic depression and/or treatment-non-responsive depression. The recognition and integration of these mechanisms will facilitate a precision-medicine approach in MDD.
Schizophrenia is associated with altered DNA methylation variance
Authors: Kiltschewskij Dylan J. , Reay William R. , Cairns Murray J. 
Published: September 2024

AbstractVarying combinations of genetic and environmental risk factors are thought to underpin phenotypic heterogeneity between individuals in psychiatric conditions such as schizophrenia. While epigenome-wide association studies in schizophrenia have identified extensive alteration of mean DNA methylation levels, less is known about the location and impact of DNA methylation variance, which could contribute to phenotypic and treatment response heterogeneity. To explore this question, we conducted the largest meta-analysis of blood DNA methylation variance in schizophrenia to date, leveraging three cohorts comprising 1036 individuals with schizophrenia and 954 non-psychiatric controls. Surprisingly, only a small proportion (0.1%) of the 213 variably methylated positions (VMPs) associated with schizophrenia (Benjamini-Hochberg FDR < 0.05) were shared with differentially methylated positions (DMPs; sites with mean changes between cases and controls). These blood-derived VMPs were found to be overrepresented in genes previously associated with schizophrenia and amongst brain-enriched genes, with evidence of concordant changes at VMPs in the cerebellum, hippocampus, prefrontal cortex, or striatum. Epigenetic covariance was also observed with respect to clinically significant metrics including age of onset, cognitive deficits, and symptom severity. We also uncovered a significant VMP in individuals with first-episode psychosis (n = 644) from additional cohorts and a non-psychiatric comparison group (n = 633). Collectively, these findings suggest schizophrenia is associated with significant changes in DNA methylation variance, which may contribute to individual-to-individual heterogeneity.
Metformin hydrolase is a recently evolved nickel-dependent heteromeric ureohydrolase
Authors: Sinn M. , Riede L. , Fleming J. R. , Funck D. , Lutz H. , Bachmann A. , Mayans O. , Hartig J. S. 
Published: September 2024

AbstractThe anti-diabetic drug metformin is one of the most widely prescribed medicines in the world. Together with its degradation product guanylurea, it is a major pharmaceutical pollutant in wastewater treatment plants and surface waters. An operon comprising two genes of the ureohydrolase family inPseudomonasandAminobacterspecies has recently been implicated in metformin degradation. However, the corresponding proteins have not been characterized. Here we show that these genes encode a Ni2+-dependent enzyme that efficiently and specifically hydrolyzes metformin to guanylurea and dimethylamine. The active enzyme is a heteromeric complex of α- and β- subunits in which only the α-subunits contain the conserved His and Asp residues for the coordination of two Ni2+ions in the active site. A crystal structure of metformin hydrolase reveals an α2β4stoichiometry of the hexameric complex, which is unprecedented in the ureohydrolase family. By studying a closely related but more widely distributed enzyme, we find that the putative predecessor specifically hydrolyzes dimethylguanidine instead of metformin. Our findings establish the molecular basis for metformin hydrolysis to guanylurea as the primary pathway for metformin biodegradation and provide insight into the recent evolution of ureohydrolase family proteins in response to an anthropogenic compound.
HIV-1 adapts to lost IP6 coordination through second-site mutations that restore conical capsid assembly
Authors: Kleinpeter Alex , Mallery Donna L. , Renner Nadine , Albecka Anna , Klarhof J. Ole , Freed Eric O. , James Leo C. 
Published: September 2024

AbstractThe HIV-1 capsid is composed of capsid (CA) protein hexamers and pentamers (capsomers) that contain a central pore hypothesised to regulate capsid assembly and facilitate nucleotide import early during post-infection. These pore functions are mediated by two positively charged rings created by CA Arg-18 (R18) and Lys-25 (K25). Here we describe the forced evolution of viruses containing mutations in R18 and K25. Whilst R18 mutants fail to replicate, K25A viruses acquire compensating mutations that restore nearly wild-type replication fitness. These compensating mutations, which rescue reverse transcription and infection without reintroducing lost pore charges, map to three adaptation hot-spots located within and between capsomers. The second-site suppressor mutations act by restoring the formation of pentamers lost upon K25 mutation, enabling closed conical capsid assembly both in vitro and inside virions. These results indicate that there is no intrinsic requirement for K25 in either nucleotide import or capsid assembly. We propose that whilst HIV-1 must maintain a precise hexamer:pentamer equilibrium for proper capsid assembly, compensatory mutations can tune this equilibrium to restore fitness lost by mutation of the central pore.
MASTER-NAADP: a membrane permeable precursor of the Ca2+ mobilizing second messenger NAADP
Authors: Krukenberg Sarah , Möckl Franziska , Weiß Mariella , Dekiert Patrick , Hofmann Melanie , Gerlach Fynn , Winterberg Kai J. , Kovacevic Dejan , Khansahib Imrankhan , Troost Berit , Hinrichs Macarena , Granato Viviana , Nawrocki Mikolaj , Hub Tobis , Tsvilovskyy Volodymyr , Medert Rebekka , Woelk Lena-Marie , Förster Fritz , Li Huan , Werner René , Altfeld Marcus , Huber Samuel , Clarke Oliver Biggs , Freichel Marc , Diercks Björn-Philipp , Meier Chris , Guse Andreas H. 
Published: September 2024

AbstractUpon stimulation of membrane receptors, nicotinic acid adenine dinucleotide phosphate (NAADP) is formed as second messenger within seconds and evokes Ca2+ signaling in many different cell types. Here, to directly stimulate NAADP signaling, MASTER-NAADP, a Membrane permeAble, STabilized, bio-rEversibly pRotected precursor of NAADP is synthesized and release of its active NAADP mimetic, benzoic acid C-nucleoside, 2’-phospho-3’F-adenosine-diphosphate, by esterase digestion is confirmed. In the presence of NAADP receptor HN1L/JPT2 (hematological and neurological expressed 1-like protein, HN1L, also known as Jupiter microtubule-associated homolog 2, JPT2), this active NAADP mimetic releases Ca2+ and increases the open probability of type 1 ryanodine receptor. When added to intact cells, MASTER-NAADP initially evokes single local Ca2+ signals of low amplitude. Subsequently, also global Ca2+ signaling is observed in T cells, natural killer cells, and Neuro2A cells. In contrast, control compound MASTER-NADP does not stimulate Ca2+ signaling. Likewise, in cells devoid of HN1L/JPT2, MASTER-NAADP does not affect Ca2+ signaling, confirming that the product released from MASTER-NAADP is a bona fide NAADP mimetic.
Impact and characterization of serial structural variations across humans and great apes
Authors: Höps Wolfram , Rausch Tobias , Jendrusch Michael ,   Human Genome Structural Variation Consortium (HGSVC), Ashraf Hufsah , Audano Peter A. , Austine Ola , Basile Anna O. , Beck Christine R. , Jan Bonder Marc , Byrska-Bishop Marta , Chaisson Mark J. P. , Chong Zechen , Corvelo André , Devine Scott E. , Ebert Peter , Ebler Jana , Eichler Evan E. , Gerstein Mark B. , Hallast Pille , Harvey William T. , Hasenfeld Patrick , Hastie Alex R. , Henglin Mir , Hoekzema Kendra , Hsieh PingHsun , Hunt Sarah , Konkel Miriam K. , Kordosky Jennifer , Lansdorp Peter M. , Lee Charles , Lee Wan-Ping , Lewis Alexandra P. , Li Chong , Lin Jiadong , Loftus Mark , Logsdon Glennis A. , Marschall Tobias , Mills Ryan E. , Mostovoy Yulia , Munson Katherine M. , Narzisi Giuseppe , Pang Andy , Porubsky David , Prodanov Timofey , Rodriguez-Martin Bernardo , Shi Xinghua , Surapaneni Likhitha , Talkowski Michael E. , Yilmaz Feyza , Yoo DongAhn , Zhou Weichen , Zody Michael C. , Korbel Jan O. , Sedlazeck Fritz J. 
Published: September 2024

AbstractModern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing a challenge for SV discovery. Here, we present NAHRwhals (https://github.com/WHops/NAHRwhals), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to haplotype-resolved human genomes from 28 individuals reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as the TPSAB1 gene, 8p23.1, 22q11 and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently, after the human-ape split, and involved non-repeat-mediated processes in addition to non-allelic homologous recombination. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and suggesting broader implications for disease.
Unipolar quantum optoelectronics for high speed direct modulation and transmission in 8–14 µm atmospheric window
Authors: Dely Hamza , Joharifar Mahdieh , Durupt Laureline , Ostrovskis Armands , Schatz Richard , Bonazzi Thomas , Maisons Gregory , Gacemi Djamal , Salgals Toms , Zhang Lu , Spolitis Sandis , Sun Yan-Ting , Bobrovs Vjačeslavs , Yu Xianbin , Sagnes Isabelle , Pantzas Konstantinos , Vasanelli Angela , Ozolins Oskars , Pang Xiaodan , Sirtori Carlo 
Published: September 2024

AbstractThe large mid-infrared (MIR) spectral region, ranging from 2.5 µm to 25 µm, has remained under-exploited in the electromagnetic spectrum, primarily due to the absence of viable transceiver technologies. Notably, the 8–14 µm long-wave infrared (LWIR) atmospheric transmission window is particularly suitable for free-space optical (FSO) communication, owing to its combination of low atmospheric propagation loss and relatively high resilience to turbulence and other atmospheric disturbances. Here, we demonstrate a direct modulation and direct detection LWIR FSO communication system at 9.1 µm wavelength based on unipolar quantum optoelectronic devices with a unprecedented net bitrate exceeding 55 Gbit s−1. A directly modulated distributed feedback quantum cascade laser (DFB-QCL) with high modulation efficiency and improved RF-design was used as a transmitter while two high speed detectors utilizing meta-materials to enhance their responsivity are employed as receivers; a quantum cascade detector (QCD) and a quantum-well infrared photodetector (QWIP). We investigate system tradeoffs and constraints, and indicate pathways forward for this technology beyond 100 Gbit s−1 communication.
Multistage lithospheric drips control active basin formation within an uplifting orogenic plateau
Authors: Andersen A. Julia , Göğüş Oguz Hakan , Pysklywec Russell N. , Şengül Uluocak Ebru , Santimano Tasca 
Published: September 2024

AbstractAccording to GNSS/INSAR measurements, the Konya Basin in Central Anatolia is undergoing rapid subsidence within an uplifting orogenic plateau. Further, geophysical studies reveal thickened crust under the basin and a fast seismic wave speed anomaly in the underlying mantle, in addition to a localised depression in calculated residual topography (down to 280 m) over the Konya Basin, based on gravity-topography considerations. Using scaled laboratory (analogue) experiments we show that the active formation of the Konya Basin may be accounted for by the descent of a mantle lithospheric drip causing local circular-shaped surface subsidence. We interpret that the Konya Basin is developing through a secondary drip pulse that is contemporaneous with broad plateau uplift caused by a larger-scale lithospheric drip since the Miocene. The research reveals that basin evolution and plateau uplift may be linked in a multistage process of lithospheric removal during episodic development of orogenic systems.
Cylindrical compression of thin wires by irradiation with a Joule-class short-pulse laser
Authors: Laso Garcia Alejandro , Yang Long , Bouffetier Victorien , Appel Karen , Baehtz Carsten , Hagemann Johannes , Höppner Hauke , Humphries Oliver , Kluge Thomas , Mishchenko Mikhail , Nakatsutsumi Motoaki , Pelka Alexander , Preston Thomas R. , Randolph Lisa , Zastrau Ulf , Cowan Thomas E. , Huang Lingen , Toncian Toma 
Published: September 2024

AbstractEquation of state measurements at Jovian or stellar conditions are currently conducted by dynamic shock compression driven by multi-kilojoule multi-beam nanosecond-duration lasers. These experiments require precise design of the target and specific tailoring of the spatial and temporal laser profiles to reach the highest pressures. At the same time, the studies are limited by the low repetition rate of the lasers. Here, we show that by the irradiation of a thin wire with single-beam Joule-class short-pulse laser, a converging cylindrical shock is generated compressing the wire material to conditions relevant to the above applications. The shockwave was observed using Phase Contrast Imaging employing a hard X-ray Free Electron Laser with unprecedented temporal and spatial sensitivity. The data collected for Cu wires is in agreement with hydrodynamic simulations of an ablative shock launched by highly impulsive and transient resistive heating of the wire surface. The subsequent cylindrical shockwave travels toward the wire axis and is predicted to reach a compression factor of 9 and pressures above 800 Mbar. Simulations for astrophysical relevant materials underline the potential of this compression technique as a new tool for high energy density studies at high repetition rates.
A sex-stratified analysis of the genetic architecture of human brain anatomy
Authors: Shafee Rebecca , Moraczewski Dustin , Liu Siyuan , Mallard Travis , Thomas Adam , Raznahan Armin 
Published: September 2024

AbstractLarge biobanks have dramatically advanced our understanding of genetic influences on human brain anatomy. However, most studies have combined rather than compared male and female participants. Here we screen for sex differences in the common genetic architecture of over 1000 neuroanatomical phenotypes in the UK Biobank and establish a general concordance between male and female participants in heritability estimates, genetic correlations, and variant-level effects. Notable exceptions include higher mean heritability in the female group for regional volume and surface area phenotypes; between-sex genetic correlations that are significantly below 1 in the insula and parietal cortex; and a common variant with stronger effect in male participants mapping to RBFOX1 - a gene linked to multiple neuropsychiatric disorders more common in men. This work suggests that common variant influences on human brain anatomy are largely consistent between males and females, with a few exceptions that will guide future research in growing datasets.