bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crustal Structure Beneath Mexico City From Joint Inversion of Receiver Functions and Dispersion Curves
Authors: Aguilar‐Velázquez Manuel J. , Pérez‐Campos Xyoli , Pita‐Sllim Olivia 
Published: July 2023

AbstractOver the years, it has been clear to seismologists that the crustal structure beneath Mexico City is highly complex. This fact may influence the seismic waves' behavior when traveling through it. Consequently, many studies have been done to understand this crustal structure. This article presents a high‐resolution S‐wave velocity model obtained from joint inversion of radial receiver functions and group‐velocity dispersion curves beneath Mexico City (VMRFDC). This model includes azimuthal variations observed with receiver functions, which may be interpreted as crustal discontinuities. Receiver functions were retrieved from velocity and acceleration records, and dispersion curves were collected from a previous tomographic study. We performed a geostatistical analysis that revealed a horizontal spatial correlation of the crustal structure for up to 7.5 km. This distance was obtained from the S‐wave velocity omnidirectional semivariogram range per depth. Using ordinary kriging, we utilized this spatial correlation to estimate S‐wave velocities per depth and introduced two novel techniques: a resolution test for kriging and a geostatistical‐dependent smoothing technique. Finally, we compare our results with previous works, making our model consistent with geological and geophysical features reported in the literature.
Strain Localization Patterns and Thrust Propagation in 3‐D Discrete Element Method (DEM) Models of Accretionary Wedges
Authors: del Castillo Enrique M. , Ferdowsi Behrooz , Rubin Allan M. , Schoene Blair 
Published: July 2023

AbstractHigh‐resolution three‐dimensional discrete element method (DEM) simulations of sandbox‐scale models of accretionary wedges suggest thrusts follow a variety of propagation processes and orientations depending on a number of factors. These include the stage of development of the wedge (precritical vs. critical), basal friction, and type of thrust (forward vs. backward‐vergent). In terms of propagation processes, two clear mechanisms are identified. The first involves propagation from the décollement to the wedge top, similar to the standard model of thrust propagation seen in many kinematic models, and in the second, thrusts grow downward from an initial nucleation point just below the top surface of the wedge as well as upward from the décollement joining in the middle. In terms of orientation, forward‐vergent thrusts initially form at Roscoe (θR = 45° − Ψ/2) or Arthur orientations (θA = 45° − (ϕ + Ψ)/4), and over greater shortening, rotate into Coulomb orientations (θC = 45° − ϕ/2). To arrive at these results, a wide array of continuum parameters and fields were extracted from the DEM simulations, including stress, strain, strain rate, kinetic energy, Mohr‐Coulomb parameters, and proximity to yielding using the Drucker‐Prager criterion to visualize thrust nucleation and propagation. Lastly, the advantages and disadvantages of these continuum proxies for discerning failure in the granular assembly are considered, and the spatial and temporal relationship between proximity to yielding and strain localization (both pre‐peak and subsequent persistent shear banding) in the granular model of an accretionary wedge is explored.
The Crustal and Uppermost Mantle Vs Structure of the Middle and Lower Reaches of the Yangtze River Metallogenic Belt: Implications for Metallogenic Process
Authors: Zhang Yongqian , Lü Qingtian , Shi Danian , Yang Yingjie , Afonso Juan Carlos , Xu Yao , Yan Jiayong , Gong Xuejing , Xu Tao 
Published: July 2023

AbstractThe Middle and Lower Reaches of the Yangtze River metallogenic belt (MLYMB) is one of the most important Fe‐Cu polymetallic belts in China. However, the mechanism and deep geodynamical process for the formation of this belt are still controversial. Here, we obtain the crustal and the uppermost mantle structures using ambient noise data from a dense seismic profile. A low velocity zone is revealed beneath the Moho of MLYMB, interpreted as the source of the deep mineralization materials. In addition, a low velocity layer (LVL) and a high velocity layer (HVL) are observed in the crust of the southern segment of the profile. The LVL is interpreted as a tectonic detachment layer between the upper and the lower crust, and the HVL is interpreted as the aggregation zone for mineralizing melts or crystallized magma chambers. Based on the observed velocity features, we propose a three‐stage model for the formation of ore deposits in MLYMB. Our model suggests that an upwelling of asthenosphere triggered by the delamination of a previously thickened lithosphere leads to the partial melting of upper mantle rocks, which eventually ponders under the Moho. The magma then infiltrates through the ductile lower crust and reaches a depth of ∼7–13 km, forming a minerals‐enriched magma chamber. Minerals‐rich hot fluids originating from the magma chamber continue to move upward along the pre‐existent faults and the minerals finally precipitate in dense veinlets when reaching shallow depths, forming the ore deposits in and around the MLYMB.
ADAM12 expression is upregulated in cancer cells upon radiation and constitutes a prognostic factor in rectal cancer patients following radiotherapy
Authors: Piotrowski Krzysztof Bartłomiej , Blasco Laia Puig , Samsøe-Petersen Jacob , Eefsen Rikke Løvendahl , Illemann Martin , Oria Victor Oginga , Campos Karla Iveth Aguilera , Lopresti Alexia Mélanie , Albrechtsen Reidar , Sørensen Claus Storgaard , Sun Xiao-Feng , Kveiborg Marie , Gnosa Sebastian 
Published: July 2023

AbstractRadiotherapy is one of the most common cancer treatments, yet, some patients require high doses to respond. Therefore, the development of new strategies leans toward personalizing therapy to avoid unnecessary burden on cancer patients. This approach prevents the administration of ineffective treatments or uses combination strategies to increase the sensitivity of cancer cells. ADAM12 has been shown to be upregulated in many cancers and correlate with poor survival and chemoresistance, thus making it a potential candidate responsible for radioresistance. Here, we show that ADAM12 expression is upregulated in response to irradiation in both mouse and human cancer cells in vitro, as well as in tumor tissues from rectal cancer patients. Interestingly, the expression of ADAM12 following radiotherapy correlates with the initial disease stage and predicts the response of rectal cancer patients to the treatment. While we found no cell-autonomous effects of ADAM12 on the response of colon cancer cells to irradiation in vitro, depletion of ADAM12 expression markedly reduced the tumor growth of irradiated cancer cells when subcutaneously transplanted in syngeneic mice. Interestingly, loss of cancer cell-derived ADAM12 expression increased the number of CD31+FAP− cells in murine tumors. Moreover, conditioned medium from ADAM12−/− colon cancer cells led to increased tube formation when added to endothelial cell cultures. Thus, it is tempting to speculate that altered tumor vascularity may be implicated in the observed effect of ADAM12 on response to radiotherapy in rectal cancer. We conclude that ADAM12 represents a promising prognostic factor for stratification of rectal cancer patients receiving radiotherapy and suggest that targeting ADAM12 in combination with radiotherapy could potentially improve the treatment response.
Depletion of peroxiredoxin II promotes keratinocyte apoptosis and alleviates psoriatic skin lesions via the PI3K/AKT/GSK3β signaling axis
Authors: Han Ying-Hao , Feng Lin , Lee Seung-Jae , Zhang Yong-Qing , Wang Ai-Guo , Jin Mei-Hua , Sun Hu-Nan , Kwon Taeho 
Published: July 2023

AbstractPsoriasis is a chronic, systemic immune-mediated disease caused by abnormal proliferation, decreased apoptosis, and over-differentiation of keratinocytes. The psoriatic skin lesions due to abnormal keratinocytes are closely associated with ROS produced by inflammatory cells. Peroxiredoxin II (Prx II) is an efficient antioxidant enzyme, which were highly expressed in skin tissues of psoriasis patient. However, the detailed mechanical functions of Prx II on psoriatic skin remain to be elucidated. Present study showed that depletion of Prx II results in alleviation of symptoms of IMQ-induced psoriasis in mice, but no significant differences in the amounts of serum inflammatory factors. Prx II-knockdown HaCaT cells were susceptible to H2O2-induced apoptosis mediated by Ca2+ release from the endoplasmic reticulum through 1,4,5-triphosphate receptors (IP3Rs), the PI3K/AKT pathway and phosphorylated GSK3β (Ser9) were significant downregulated. Additionally, significantly reduced sensitivity of Prx II-knockdown HaCaT cells to apoptosis was evident post NAC, 2-APB, BAPTA-AM, SC79 and LiCl treated. These results suggest that Prx II regulated apoptosis of keratinocytes via the PI3K/AKT/GSK3β signaling axis. Furthermore, treatment with the Prx II inhibitor Conoidin A significantly alleviated psoriatic symptoms in IMQ model mice. These findings have important implications for developing therapeutic strategies through regulate apoptosis of keratinocytes in psoriasis, and Prx II inhibitors may be exploited as a therapeutic drug to alleviate psoriatic symptoms.
A phase 1 study of nivolumab in combination with interferon-gamma for patients with advanced solid tumors
Authors: Zibelman Matthew , MacFarlane Alexander W. , Costello Kimberly , McGowan Thomas , O’Neill John , Kokate Rutika , Borghaei Hossein , Denlinger Crystal S. , Dotan Efrat , Geynisman Daniel M. , Jain Angela , Martin Lainie , Obeid Elias , Devarajan Karthik , Ruth Karen , Alpaugh R. Katherine , Dulaimi Essel Al-Saleem , Cukierman Edna , Einarson Margret , Campbell Kerry S. , Plimack Elizabeth R. 
Published: July 2023

AbstractThis phase I, dose-escalation trial evaluates the safety of combining interferon-gamma (IFN-γ) and nivolumab in patients with metastatic solid tumors. Twenty-six patients are treated in four cohorts assessing increasing doses of IFN-γ with nivolumab to evaluate the primary endpoint of safety and determine the recommended phase two dose (RP2D). Most common adverse events are low grade and associated with IFN-γ. Three dose limiting toxicities are reported at the highest dose cohorts. We report only one patient with any immune related adverse event (irAE). No irAEs ≥ grade 3 are observed and no patients require corticosteroids. The maximum tolerated dose of IFN-γ is 75 mcg/m2, however based on a composite of safety, clinical, and correlative factors the RP2D is 50 mcg/m2. Exploratory analyses of efficacy in the phase I cohorts demonstrate one patient with a complete response, and five have achieved stable disease. Pre-planned correlative assessments of circulating immune cells demonstrate intermediate monocytes with increased PD-L1 expression correlating with IFN-γ dose and treatment duration. Interestingly, post-hoc analysis shows that IFN-γ induction increases circulating chemokines and is associated with an observed paucity of irAEs, warranting further evaluation. ClinicalTrials.gov Trial Registration: NCT02614456.
Geometric control of diffusing elements on InAs semiconductor surfaces via metal contacts
Authors: Benter Sandra , Jönsson Adam , Johansson Jonas , Zhu Lin , Golias Evangelos , Wernersson Lars-Erik , Mikkelsen Anders 
Published: July 2023

AbstractLocal geometric control of basic synthesis parameters, such as elemental composition, is important for bottom-up synthesis and top-down device definition on-chip but remains a significant challenge. Here, we propose to use lithographically defined metal stacks for regulating the surface concentrations of freely diffusing synthesis elements on compound semiconductors. This is demonstrated by geometric control of Indium droplet formation on Indium Arsenide surfaces, an important consequence of incongruent evaporation. Lithographic defined Aluminium/Palladium metal patterns induce well-defined droplet-free zones during annealing up to 600 °C, while the metal patterns retain their lateral geometry. Compositional and structural analysis is performed, as well as theoretical modelling. The Pd acts as a sink for free In atoms, lowering their surface concentration locally and inhibiting droplet formation. Al acts as a diffusion barrier altering Pd’s efficiency. The behaviour depends only on a few basic assumptions and should be applicable to lithography-epitaxial manufacturing processes of compound semiconductors in general.
MAPK inhibitor sensitivity scores predict sensitivity driven by the immune infiltration in pediatric low-grade gliomas
Authors: Sigaud Romain , Albert Thomas K. , Hess Caroline , Hielscher Thomas , Winkler Nadine , Kocher Daniela , Walter Carolin , Münter Daniel , Selt Florian , Usta Diren , Ecker Jonas , Brentrup Angela , Hasselblatt Martin , Thomas Christian , Varghese Julian , Capper David , Thomale Ulrich W. , Hernáiz Driever Pablo , Simon Michèle , Horn Svea , Herz Nina Annika , Koch Arend , Sahm Felix , Hamelmann Stefan , Faria-Andrade Augusto , Jabado Nada , Schuhmann Martin U. , Schouten-van Meeteren Antoinette Y. N. , Hoving Eelco , Brummer Tilman , van Tilburg Cornelis M. , Pfister Stefan M. , Witt Olaf , Jones David T. W. , Kerl Kornelius , Milde Till 
Published: July 2023

AbstractPediatric low-grade gliomas (pLGG) show heterogeneous responses to MAPK inhibitors (MAPKi) in clinical trials. Thus, more complex stratification biomarkers are needed to identify patients likely to benefit from MAPKi therapy. Here, we identify MAPK-related genes enriched in MAPKi-sensitive cell lines using the GDSC dataset and apply them to calculate class-specific MAPKi sensitivity scores (MSSs) via single-sample gene set enrichment analysis. The MSSs discriminate MAPKi-sensitive and non-sensitive cells in the GDSC dataset and significantly correlate with response to MAPKi in an independent PDX dataset. The MSSs discern gliomas with varying MAPK alterations and are higher in pLGG compared to other pediatric CNS tumors. Heterogenous MSSs within pLGGs with the same MAPK alteration identify proportions of potentially sensitive patients. The MEKi MSS predicts treatment response in a small set of pLGG patients treated with trametinib. High MSSs correlate with a higher immune cell infiltration, with high expression in the microglia compartment in single-cell RNA sequencing data, while low MSSs correlate with low immune infiltration and increased neuronal score. The MSSs represent predictive tools for the stratification of pLGG patients and should be prospectively validated in clinical trials. Our data supports a role for microglia in the response to MAPKi.
Exploring the configuration space of elemental carbon with empirical and machine learned interatomic potentials
Authors: Marchant George A. , Caro Miguel A. , Karasulu Bora , Pártay Livia B. 
Published: July 2023

AbstractWe demonstrate how the many-body potential energy landscape of carbon can be explored with the nested sampling algorithm, allowing for the calculation of its pressure-temperature phase diagram. We compare four interatomic potential models: Tersoff, EDIP, GAP-20 and its recently updated version, GAP-20U. Our evaluation is focused on their macroscopic properties, melting transitions, and identifying thermodynamically stable solid structures up to at least 100 GPa. The phase diagrams of the GAP models show good agreement with experimental results. However, we find that the models’ description of graphite includes thermodynamically stable phases with incorrect layer spacing. By adding a suitable selection of structures to the database and re-training the potential, we have derived an improved model — GAP-20U+gr — that suppresses erroneous local minima in the graphitic energy landscape. At extreme high pressure nested sampling identifies two novel stable structures in the GAP-20 model, however, the stability of these is not confirmed by electronic structure calculations, highlighting routes to further extend the applicability of the GAP models.
The Brief negative Symptom Scale (BNSS): a systematic review of measurement properties
Authors: Weigel Lucia , Wehr Sophia , Galderisi Silvana , Mucci Armida , Davis John , Giordano Giulia Maria , Leucht Stefan 
Published: July 2023

Abstract
Background
Negative symptoms of schizophrenia are linked with poor functioning and quality of life. Therefore, appropriate measurement tools to assess negative symptoms are needed. The NIMH-MATRICS Consensus defined five domains for negative symptoms, which The Brief Negative Symptom Scale (BNSS) covers.

Methods
We used the COSMIN guidelines for systematic reviews to evaluate the quality of psychometric data of the BNSS scale as a Clinician-Rated Outcome Measure (ClinROM).

Results
The search strategy resulted in the inclusion of 17 articles. When using the risk of bias checklist, there was a generally good quality in reporting of structural validity and hypothesis testing. Internal consistency, reliability and cross-cultural validity were of poorer quality. ClinROM development and content validity showed inadequate results. According to the updated criteria of good measurement properties, structural validity, internal consistency and interrater reliability showed good results, while hypothesis testing showed poorer results. Cross-cultural validity and test-retest reliability were indeterminate. The updated GRADE approach resulted in a moderate grade.

Conclusions
We can potentially recommend the use of the BNSS as a concise tool to rate negative symptoms. Due to weaknesses in certain domains further validations are warranted.
COVID-19 is linked to changes in the time–space dimension of human mobility
Authors: Santana Clodomir , Botta Federico , Barbosa Hugo , Privitera Filippo , Menezes Ronaldo , Di Clemente Riccardo 
Published: July 2023

AbstractSocio-economic constructs and urban topology are crucial drivers of human mobility patterns. During the coronavirus disease 2019 pandemic, these patterns were reshaped in their components: the spatial dimension represented by the daily travelled distance, and the temporal dimension expressed as the synchronization time of commuting routines. Here, leveraging location-based data from de-identified mobile phone users, we observed that, during lockdowns restrictions, the decrease of spatial mobility is interwoven with the emergence of asynchronous mobility dynamics. The lifting of restriction in urban mobility allowed a faster recovery of the spatial dimension compared with the temporal one. Moreover, the recovery in mobility was different depending on urbanization levels and economic stratification. In rural and low-income areas, the spatial mobility dimension suffered a more considerable disruption when compared with urbanized and high-income areas. In contrast, the temporal dimension was more affected in urbanized and high-income areas than in rural and low-income areas.
Extensive pedigrees reveal the social organization of a Neolithic community
Authors: Rivollat Maïté , Rohrlach Adam Benjamin , Ringbauer Harald , Childebayeva Ainash , Mendisco Fanny , Barquera Rodrigo , Szolek András , Le Roy Mélie , Colleran Heidi , Tuke Jonathan , Aron Franziska , Pemonge Marie-Hélène , Späth Ellen , Télouk Philippe , Rey Léonie , Goude Gwenaëlle , Balter Vincent , Krause Johannes , Rottier Stéphane , Deguilloux Marie-France , Haak Wolfgang 
Published: July 2023

AbstractSocial anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations1–4. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic around 4850–4500 bc. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality5. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.
Small protein modules dictate prophage fates during polylysogeny
Authors: Silpe Justin E. , Duddy Olivia P. , Johnson Grace E. , Beggs Grace A. , Hussain Fatima A. , Forsberg Kevin J. , Bassler Bonnie L. 
Published: July 2023

AbstractMost bacteria in the biosphere are predicted to be polylysogens harbouring multiple prophages1–5. In studied systems, prophage induction from lysogeny to lysis is near-universally driven by DNA-damaging agents6. Thus, how co-residing prophages compete for cell resources if they respond to an identical trigger is unknown. Here we discover regulatory modules that control prophage induction independently of the DNA-damage cue. The modules bear little resemblance at the sequence level but share a regulatory logic by having a transcription factor that activates the expression of a neighbouring gene that encodes a small protein. The small protein inactivates the master repressor of lysis, which leads to induction. Polylysogens that harbour two prophages exposed to DNA damage release mixed populations of phages. Single-cell analyses reveal that this blend is a consequence of discrete subsets of cells producing one, the other or both phages. By contrast, induction through the DNA-damage-independent module results in cells producing only the phage sensitive to that specific cue. Thus, in the polylysogens tested, the stimulus used to induce lysis determines phage productivity. Considering the lack of potent DNA-damaging agents in natural habitats, additional phage-encoded sensory pathways to lysis likely have fundamental roles in phage–host biology and inter-prophage competition.
Data scheme and data format for transferable force fields for molecular simulation
Authors: Kanagalingam Gajanan , Schmitt Sebastian , Fleckenstein Florian , Stephan Simon 
Published: July 2023

AbstractA generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and interoperable. A transferable force field is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a model for a given component. The data scheme proposed in this work (named TUK-FFDat) formalizes digitally these chemical construction plans, i.e. transferable force fields. It can be applied to all-atom as well as united-atom transferable force fields. The general applicability of the data scheme is demonstrated for different types of force fields (TraPPE, OPLS-AA, and Potoff). Furthermore, conversion tools for translating the data scheme between .xls spread sheet format and the SQL-based data format are provided. The data format can readily be integrated in existing workflows, simulation engines, and force field databases as well as for linking such.