bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropathologic findings in a patient with Parry-Romberg syndrome: active cerebral vasculitis and brain injury
Authors: Wappler-Guzzetta Edina A. , Hanak Brian W. , Bannout Firas , Harder Sheri L. , Deisch Jeremy K. 
Published: January 2024

Abstract
Purpose
Parry-Romberg syndrome (PRS) is a rare disorder characterized by slowly progressive hemifacial atrophy. Although the underlying etiology is unknown, proposed disease mechanisms which include autoimmune, infection, trauma, and other causes have been proposed as underlying disease mechanisms. Approximately, 10–20% of PRS patients have neurologic manifestations such as epilepsy, headaches, or associated vascular malformations. There are reports of PRS responsive to immunosuppressive medications, supporting the autoimmune hypothesis. Currently, the neuropathologic findings in patients with PRS are not well documented.

Methods
Herein, we present a case of a 19-year-old female with PRS, who underwent partial frontal lobectomy for intractable epilepsy.

Results
The resection specimen showed multifocal active lymphocytic (T-cell mediated) arteritis in midsized cortical arterioles, with the adjacent meninges showing fibrosis involving both the meningeal tissue and its vascular network. In addition, neuronal loss and gliosis were evident in the cortex, likely due to the associated vascular injury.

Conclusions
This report is the first to demonstrate active cerebral vasculitis in a patient with PRS, supporting the previous suspicion of inflammatory etiology in this disease. In addition, the widespread vascular fibrosis in the meningeal vessels and an area of cortical ischemia support the presence of previous inflammatory vascular processes in the area.
Intercomparison of Air Quality Models in a Megacity: Toward an Operational Ensemble Forecasting System for São Paulo
Authors: Deroubaix Adrien , Hoelzemann Judith J. , Ynoue Rita Yuri , Toledo de Almeida Albuquerque Taciana , Alves Rafaela Cruz , de Fatima Andrade Maria , Andreão Willian Lemker , Bouarar Idir , de Souza Fernandes Duarte Ediclê , Elbern Hendrik , Franke Philipp , Lange Anne Caroline , Lichtig Pablo , Lugon Lya , Martins Leila D. , de Arruda Moreira Gregori , Pedruzzi Rizzieri , Rosario Nilton , Brasseur Guy 
Published: January 2024

AbstractAn intercomparison of four regional air quality models is performed in the tropical megacity of São Paulo with the perspective of developing a forecasting system based on a model ensemble. Modeled concentrations of the main regulated pollutants are compared with combined observations in the megacity center, after analyzing the spatial scale of representativeness of air monitoring stations. During three contrasting periods characterized by different types of pollution events, the hourly concentrations of carbon monoxide (CO), nitrogen oxides (NOx), sulfur dioxide (SO2), and particulate matter (PM2.5 and PM10) modeled by the ensemble are in moderate agreement with observations. The median of the ensemble provides the best performance (R ≈ 0.7 for CO, 0.7 for NOx, 0.5 for SO2, 0.5 for PM2.5, and 0.4 for PM10) because each model has periods and pollutants for which it has the best agreement. NOx concentration is modeled with a large inter‐model variability, highlighting potential for improvement of anthropogenic emissions. Pollutants transported by biomass burning events strongly affect the air quality in São Paulo and are associated with significant inter‐model variability. Modeled hourly concentration of ozone (O3) is overestimated during the day (≈20 ppb) and underestimated at night (≈10 ppb), while nitrogen dioxide (NO2) is overestimated at night (≈20 ppb). The observed O3 concentration is best reproduced by the median of the ensemble (R ≈ 0.8), taking advantage of the variable performance of the models. Therefore, an operational air quality forecast system based on a regional model ensemble is promising for São Paulo.
Continental Scale Assessment of Variation in Floodplain Roughness With Vegetation and Flow Characteristics
Authors: Barinas Gabriel , Good Stephen P. , Tullos Desiree 
Published: January 2024

AbstractQuantifying floodplain flows is critical to multiple river management objectives, yet how vegetation within floodplains dissipates flow energy lacks comprehensive characterization. Utilizing over 3.4 million discharge measurements, in conjunction with aboveground biomass and canopy height measurements from NASA's Global Ecosystem Dynamics Investigation (GEDI), this study characterizes the floodplain roughness coefficient Manning's n and its determinates across the continental United States. Estimated values of n show that flow resistance in floodplains decreases as flow velocity increases but increases with the fraction of vegetation inundated. A new function (RMSE = 0.024, r2 = 0.74) is proposed for predicting n based on GEDI vegetation characteristics and flow velocity, with GEDI derived n values improving predictions of discharge relative to those based only on land cover. This analysis provides evidence of key hydraulic patterns of energy dissipation in floodplains, and integration of the proposed function into flood and habitat models may reduce uncertainty.
Frictional Control on Accelerating Creep During the Slow‐To‐Fast Transition of Rainfall‐Induced Catastrophic Landslides
Authors: Paul Krishnendu , Bhattacharya Pathikrit , Misra Santanu 
Published: January 2024

AbstractSlow moving landslides regulated by precipitation/snowmelt induced subsurface pore‐pressure transients can sometimes accelerate to catastrophic failure causing loss of infrastructure and lives. Yet, unified theories of the transition of slow landslides into ultimately catastrophic ones in response to pore‐pressure changes remain relatively unexplored. Here, we use a simple gravity‐driven block‐slider model governed by laboratory‐derived rate‐and‐state friction (RSF) equations with velocity‐weakening parameters to analyze the mechanical progression of initially creeping landslides toward runaway acceleration. The rigid‐block approximation allows for exact or semi‐analytical estimates of the timescales over which such, potentially unstable, creeping landslides can be expected to transition to runaway acceleration in response to idealized pore‐pressure perturbation histories. We demonstrate that the duration of creep preceding catastrophic failure is critically sensitive to the RSF parameters, pore‐pressure variation amplitude and frequency, and background shear‐load and pore‐pressure levels through a set of non‐dimensional numbers. Our model predicts that slow landslides within velocity‐weakening clay‐rich soils can potentially creep for years to decades before transitioning to runaway failure when regulated by typical seasonal pore‐pressure transients. Remarkably, for much larger and rapid pore‐pressure changes, the same landslides can evolve to runaway failure over days to few tens of minutes. Being dependent purely on soil parameters that can be inferred from routine laboratory experiments, our model provides a theoretical framework that might be practically useful to understand the non‐linear and hysteretic response of landslide motion to pore‐pressure transients.
Biomarker Evidence for an MIS M2 Glacial‐Pluvial in the Mojave Desert Before Warming and Drying in the Late Pliocene
Authors: Peaple Mark D. , Bhattacharya Tripti , Tierney Jessica E. , Knott Jeffrey R. , Lowenstein Tim K. , Feakins Sarah J. 
Published: January 2024

AbstractAncient lake deposits in the Mojave Desert indicate that the water cycle in this currently dry place was radically different under past climates. Here we revisit a 700 m core drilled 55 years ago from Searles Valley, California, that recovered evidence for a lacustrine phase during the late Pliocene. We update the paleomagnetic age model and extract new biomarker evidence for climatic conditions from lacustrine deposits (3.373–2.706 Ma). The MBT′5Me temperature proxy detects present‐day conditions (21 ± 3°C, n = 2) initially, followed by warmer‐than‐present conditions (25 ± 3°C, n = 17) starting at 3.268 and ending at 2.734 Ma. Bacterial and archeal biomarkers reveal lake salinity increased after 3.268 Ma likely reflecting increased evaporation in response to higher temperatures. The δ13C values of plant waxes (−30.7 ± 1.4‰, n = 28) are consistent with local C3 taxa, likely expanded conifer woodlands during the pluvial with less C4 than the Pleistocene. δD values (−174 ± 5‰, n = 25) of plant waxes indicate precipitation δD values (−89 ± 5‰, n = 25) in the late Pliocene are within the same range as the late Pleistocene precipitation δD. Microbial biomarkers identify a deep, freshwater lake and a cooling that corresponds to the onset of major Northern Hemisphere glaciation at marine isotope stage marine isotope stages M2 (3.3 Ma). A more saline lake persisted for ∼0.6 Ma across the subsequent warmth of the late Pliocene (3.268–2.734 Ma) before the lake desiccated at the Pleistocene intensification of Northern Hemisphere Glaciation.
Posttraumatic stress disorder, trauma, and accelerated biological aging among post-9/11 veterans
Authors: Bourassa Kyle J. , Garrett Melanie E. , Caspi Avshalom , Dennis Michelle , Hall Katherine S. , Moffitt Terrie E. , Taylor Gregory A. ,   VA Mid Atlantic MIRECC Workgroup, Beckham Jean C. , Calhoun Patrick S. , Dedert Eric , Elbogen Eric B. , Hurley Robin A. , Kilts Jason D. , Kimbrel Nathan A. , Kirby Angela , Martindale Sarah L. , Marx Christine E. , McDonald Scott D. , Moore Scott D. , Morey Rajendra A. , Naylor Jennifer C. , Rowland Jared A. , Shura Robert , Swinkels Cindy , Van Voorhees Elizabeth E. , Wagner H. Ryan , Magnante Anna T. , O’Connor Victoria L. , Aurora Pallavi , Martinez Brandy S. , Halverson Tate F. , Ashley-Koch Allison E. , Beckham Jean C. , Kimbrel Nathan A. 
Published: January 2024

AbstractPeople who experience trauma and develop posttraumatic stress disorder (PTSD) are at increased risk for poor health. One mechanism that could explain this risk is accelerated biological aging, which is associated with the accumulation of chronic diseases, disability, and premature mortality. Using data from 2309 post-9/11 United States military veterans who participated in the VISN 6 MIRECC’s Post-Deployment Mental Health Study, we tested whether PTSD and trauma exposure were associated with accelerated rate of biological aging, assessed using a validated DNA methylation (DNAm) measure of epigenetic aging—DunedinPACE. Veterans with current PTSD were aging faster than those who did not have current PTSD, β = 0.18, 95% CI [0.11, 0.27], p < .001. This effect represented an additional 0.4 months of biological aging each year. Veterans were also aging faster if they reported more PTSD symptoms, β = 0.13, 95% CI [0.09, 0.16], p < 0.001, or higher levels of trauma exposure, β = 0.09, 95% CI [0.05, 0.13], p < 0.001. Notably, veterans with past PTSD were aging more slowly than those with current PTSD, β = -0.21, 95% CI [-0.35, -0.07], p = .003. All reported results accounted for age, gender, self-reported race/ethnicity, and education, and remained when controlling for smoking. Our findings suggest that an accelerated rate of biological aging could help explain how PTSD contributes to poor health and highlights the potential benefits of providing efficacious treatment to populations at increased risk of trauma and PTSD.
Cortical glutamate, Glx, and total N-acetylaspartate: potential biomarkers of repetitive transcranial magnetic stimulation treatment response and outcomes in major depression
Authors: Gonsalves Meghan A. , White Tara L. , Barredo Jennifer , DeMayo Marilena M. , DeLuca Emily , Harris Ashley D. , Carpenter Linda L. 
Published: January 2024

AbstractRepetitive transcranial magnetic stimulation (rTMS) is an effective treatment for individuals with major depressive disorder (MDD) who have not improved with standard therapies. However, only 30–45% of patients respond to rTMS. Predicting response to rTMS will benefit both patients and providers in terms of prescribing and targeting treatment for maximum efficacy and directing resources, as individuals with lower likelihood of response could be redirected to more suitable treatment alternatives. In this exploratory study, our goal was to use proton magnetic resonance spectroscopy to examine how glutamate (Glu), Glx, and total N-acetylaspartate (tNAA) predict post-rTMS changes in overall MDD severity and symptoms, and treatment response. Metabolites were measured in a right dorsal anterior cingulate cortex voxel prior to a standard course of 10 Hz rTMS to the left DLPFC in 25 individuals with MDD. MDD severity and symptoms were evaluated via the Inventory of Depression Symptomatology Self-Report (IDS-SR). rTMS response was defined as ≥50% change in full-scale IDS-SR scores post treatment. Percent change in IDS-SR symptom domains were evaluated using principal component analysis and established subscales. Generalized linear and logistic regression models were used to evaluate the relationship between baseline Glu, Glx, and tNAA and outcomes while controlling for age and sex. Participants with baseline Glu and Glx levels in the lower range had greater percent change in full scale IDS-SR scores post-treatment (p < 0.001), as did tNAA (p = 0.007). Low glutamatergic metabolite levels also predicted greater percent change in mood/cognition symptoms (p ≤ 0.001). Low-range Glu, Glx, and tNAA were associated with greater improvement on the immuno-metabolic subscale (p ≤ 0.003). Baseline Glu predicted rTMS responder status (p = 0.025) and had an area under the receiving operating characteristic curve of 0.81 (p = 0.009), demonstrating excellent discriminative ability. Baseline Glu, Glx, and tNAA significantly predicted MDD improvement after rTMS; preliminary evidence also demonstrates metabolite association with symptom subdomain improvement post-rTMS. This work provides feasibility for a personalized medicine approach to rTMS treatment selection, with individuals with Glu levels in the lower range potentially being the best candidates.
Varicella zoster virus glycoprotein E facilitates PINK1/Parkin-mediated mitophagy to evade STING and MAVS-mediated antiviral innate immunity
Authors: Oh Soo-Jin , Yu Je-Wook , Ahn Jin-Hyun , Choi Seok Tae , Park Hosun , Yun Jeanho , Shin Ok Sarah 
Published: January 2024

AbstractViruses have evolved to control mitochondrial quality and content to facilitate viral replication. Mitophagy is a selective autophagy, in which the damaged or unnecessary mitochondria are removed, and thus considered an essential mechanism for mitochondrial quality control. Although mitophagy manipulation by several RNA viruses has recently been reported, the effect of mitophagy regulation by varicella zoster virus (VZV) remains to be fully determined. In this study, we showed that dynamin-related protein-1 (DRP1)-mediated mitochondrial fission and subsequent PINK1/Parkin-dependent mitophagy were triggered during VZV infection, facilitating VZV replication. In addition, VZV glycoprotein E (gE) promoted PINK1/Parkin-mediated mitophagy by interacting with LC3 and upregulating mitochondrial reactive oxygen species. Importantly, VZV gE inhibited MAVS oligomerization and STING translocation to disrupt MAVS- and STING-mediated interferon (IFN) responses, and PINK1/Parkin-mediated mitophagy was required for VZV gE-mediated inhibition of IFN production. Similarly, carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-mediated mitophagy induction led to increased VZV replication but attenuated IFN production in a three-dimensional human skin organ culture model. Our results provide new insights into the immune evasion mechanism of VZV gE via PINK1/Parkin-dependent mitophagy.
High-dimensional phenotyping to define the genetic basis of cellular morphology
Authors: Tegtmeyer Matthew , Arora Jatin , Asgari Samira , Cimini Beth A. , Nadig Ajay , Peirent Emily , Liyanage Dhara , Way Gregory P. , Weisbart Erin , Nathan Aparna , Amariuta Tiffany , Eggan Kevin , Haghighi Marzieh , McCarroll Steven A. , O’Connor Luke , Carpenter Anne E. , Singh Shantanu , Nehme Ralda , Raychaudhuri Soumya 
Published: January 2024

AbstractThe morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combine genomic sequencing and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identify novel associations between rare protein altering variants in WASF2, TSPAN15, and PRLR with several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirms their role in cell morphology. Analysis of common variants yields one significant association and nominate over 300 variants with suggestive evidence (P < 10−6) of association with one or more morphology traits. We then use these data to make predictions about sample size requirements for increasing discovery in cellular genetic studies. We conclude that, similar to molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.
Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe
Authors: Banerjee Samiran , Zhao Cheng , Garland Gina , Edlinger Anna , García-Palacios Pablo , Romdhane Sana , Degrune Florine , Pescador David S. , Herzog Chantal , Camuy-Velez Lennel A. , Bascompte Jordi , Hallin Sara , Philippot Laurent , Maestre Fernando T. , Rillig Matthias C. , van der Heijden Marcel G. A. 
Published: January 2024

AbstractSoil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
Production-induced seismicity indicates a low risk of strong earthquakes in the Groningen gas field
Authors: Boitz Nepomuk , Langenbruch Cornelius , Shapiro Serge A. 
Published: January 2024

AbstractThe maximum possible earthquake related to gas production in Western Europe’s largest gas field, Groningen, Netherlands, is an urgent practical question. Here we show how to distinguish between induced and triggered tectonic earthquakes. We estimate the maximum possible induced magnitude in the Groningen gas field to be around Mw = 4. We extend the concept of the seismogenic index to gas-production, and calculate the worst-case probability of triggering a larger-magnitude tectonic earthquake in a continuum. The probability of a Mw5.5 earthquake at Groningen is significantly higher than at Pohang Geothermal System (South Korea), where a Mw5.5 earthquake was actually triggered. Due to a long history of production in Groningen, our model estimates that strong earthquakes (Mw ≥ 4) must have occurred there several times, in disagreement with the observations. This indicates that the Groningen gas field is inherently stable and the physical conditions to trigger large tectonic earthquakes likely do not exist.
Theory predicts 2D chiral polaritons based on achiral Fabry–Pérot cavities using apparent circular dichroism
Authors: Salij Andrew H. , Goldsmith Randall H. , Tempelaar Roel 
Published: January 2024

AbstractRealizing polariton states with high levels of chirality offers exciting prospects for quantum information, sensing, and lasing applications. Such chirality must emanate from either the involved optical resonators or the quantum emitters. Here, we theoretically demonstrate a rare opportunity for realizing polaritons with so-called 2D chirality by strong coupling of the optical modes of (high finesse) achiral Fabry–Pérot cavities with samples exhibiting “apparent circular dichroism” (ACD). ACD is a phenomenon resulting from an interference between linear birefringence and dichroic interactions. By introducing a quantum electrodynamical theory of ACD, we identify the design rules based on which 2D chiral polaritons can be produced, and their chirality can be optimized.
Active machine learning model for the dynamic simulation and growth mechanisms of carbon on metal surface
Authors: Zhang Di , Yi Peiyun , Lai Xinmin , Peng Linfa , Li Hao 
Published: January 2024

AbstractSubstrate-catalyzed growth offers a highly promising approach for the controlled synthesis of carbon nanostructures. However, the growth mechanisms on dynamic catalytic surfaces and the development of more general design strategies remain ongoing challenges. Here we show how an active machine-learning model effectively reveals the microscopic processes involved in substrate-catalyzed growth. Utilizing a synergistic approach of molecular dynamics and time-stamped force-biased Monte Carlo methods, augmented by the Gaussian Approximation Potential, we perform fully dynamic simulations of graphene growth on Cu(111). Our findings accurately replicate essential subprocesses–from the preferred diffusion of carbon monomer/dimer, chain or ring formations to edge-passivated Cu-aided graphene growth and bond breaks by ion impacts. Extending our simulations to carbon deposition on metal surfaces like Cu(111), Cr(110), Ti(001), and oxygen-contaminated Cu(111), our results align closely with experimental observations, providing a practical and efficient approach for designing metallic or alloy substrates to achieve desired carbon nanostructures and explore further reaction possibilities.
Controllable strain-driven topological phase transition and dominant surface-state transport in HfTe5
Authors: Liu Jinyu , Zhou Yinong , Yepez Rodriguez Sebastian , Delmont Matthew A. , Welser Robert A. , Ho Triet , Sirica Nicholas , McClure Kaleb , Vilmercati Paolo , Ziller Joseph W. , Mannella Norman , Sanchez-Yamagishi Javier D. , Pettes Michael T. , Wu Ruqian , Jauregui Luis A. 
Published: January 2024

AbstractThe fine-tuning of topologically protected states in quantum materials holds great promise for novel electronic devices. However, there are limited methods that allow for the controlled and efficient modulation of the crystal lattice while simultaneously monitoring the changes in the electronic structure within a single sample. Here, we apply significant and controllable strain to high-quality HfTe5 samples and perform electrical transport measurements to reveal the topological phase transition from a weak topological insulator phase to a strong topological insulator phase. After applying high strain to HfTe5 and converting it into a strong topological insulator, we found that the resistivity of the sample increased by 190,500% and that the electronic transport was dominated by the topological surface states at cryogenic temperatures. Our results demonstrate the suitability of HfTe5 as a material for engineering topological properties, with the potential to generalize this approach to study topological phase transitions in van der Waals materials and heterostructures.