bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of the Transition From Sevier‐ to Laramide‐Style Tectonism in Southwestern Montana Based on the Provenance of the Frontier Formation, North American Cordillera
Authors: Finzel E. S. , Rosenblume J. A. , Pearson D. M. , Zippi Pierre A. 
Published: July 2023

AbstractThe Upper Cretaceous Frontier Formation in southwestern Montana is coeval with the transition from Sevier‐ to Laramide‐style tectonism in the Idaho‐Montana sector of the North American Cordillera. To better constrain the timing of initial exhumation above the Laramide‐style Blacktail‐Snowcrest arch, we use biostratigraphic data, sandstone petrography, and detrital zircon (DZ) geochronology to determine the provenance and depositional age of the Frontier Formation. Near Lima Peaks, erosion of Lower Cretaceous strata from the frontal Sevier‐style Tendoy thrust sheet provided sediment to the foreland basin. In the Western Centennial Mountains, sediment sources included those same sources as well as Neoproterozoic and Cambrian strata and Mesoproterozoic plutons in the Belt basin. In contrast, near the Gravelly Range, sediment eroded from Pennsylvanian‐Upper Cretaceous strata atop the Blacktail‐Snowcrest basement‐cored uplift, documenting unroofing to Pennsylvanian‐Permian stratigraphic levels by 87–85 Ma. Palynology corroborates recycling into the Frontier Formation, including from the underlying Blackleaf Formation. The ubiquitous presence of 100–85 Ma DZ ages coupled with different interpreted source regions suggests that an ash‐fall source contributed young zircon grains to the Frontier Formation. The timing of exhumation above the Blacktail‐Snowcrest arch provided by these new data presented herein suggest that Laramide‐style tectonism in Idaho‐Montana may be unrelated to shallow‐angle subduction within a narrow corridor as envisioned by current models. Instead, upper plate controls, such as the locations of inherited faults and basement highs, the distribution and thickness of pre‐orogenic sedimentary cover, and the availability of detachment surfaces, may be responsible for Laramide‐style tectonism during early Late Cretaceous time.
Microenvironmental Snail1-induced immunosuppression promotes melanoma growth
Authors: Arumi-Planas Marta , Rodriguez-Baena Francisco Javier , Cabello-Torres Francisco , Gracia Francisco , Lopez-Blau Cristina , Nieto M. Angela , Sanchez-Laorden Berta 
Published: July 2023

AbstractMelanoma is an aggressive form of skin cancer due to its high metastatic abilities and resistance to therapies. Melanoma cells reside in a heterogeneous tumour microenvironment that acts as a crucial regulator of its progression. Snail1 is an epithelial-to-mesenchymal transition transcription factor expressed during development and reactivated in pathological situations including fibrosis and cancer. In this work, we show that Snail1 is activated in the melanoma microenvironment, particularly in fibroblasts. Analysis of mouse models that allow stromal Snail1 depletion and therapeutic Snail1 blockade indicate that targeting Snail1 in the tumour microenvironment decreases melanoma growth and lung metastatic burden, extending mice survival. Transcriptomic analysis of melanoma-associated fibroblasts and analysis of the tumours indicate that stromal Snail1 induces melanoma growth by promoting an immunosuppressive microenvironment and a decrease in anti-tumour immunity. This study unveils a novel role of Snail1 in melanoma biology and supports its potential as a therapeutic target.
The deubiquitinating enzyme OTUD7b protects dendritic cells from TNF-induced apoptosis by stabilizing the E3 ligase TRAF2
Authors: Harit Kunjan , Bhattacharjee Rituparna , Matuschewski Kai , Becker Jennifer , Kalinke Ulrich , Schlüter Dirk , Nishanth Gopala 
Published: July 2023

AbstractThe cytokine tumor necrosis factor (TNF) critically regulates the intertwined cell death and pro-inflammatory signaling pathways of dendritic cells (DCs) via ubiquitin modification of central effector molecules, but the intrinsic molecular switches deciding on either pathway are incompletely defined. Here, we uncover that the ovarian tumor deubiquitinating enzyme 7b (OTUD7b) prevents TNF-induced apoptosis of DCs in infection, resulting in efficient priming of pathogen-specific CD8+ T cells. Mechanistically, OTUD7b stabilizes the E3 ligase TNF-receptor-associated factor 2 (TRAF2) in human and murine DCs by counteracting its K48-ubiquitination and proteasomal degradation. TRAF2 in turn facilitates K63-linked polyubiquitination of RIPK1, which mediates activation of NF-κB and MAP kinases, IL-12 production, and expression of anti-apoptotic cFLIP and Bcl-xL. We show that mice with DC-specific OTUD7b-deficiency displayed DC apoptosis and a failure to induce CD8+ T cell-mediated brain pathology, experimental cerebral malaria, in a murine malaria infection model. Together, our data identify the deubiquitinating enzyme OTUD7b as a central molecular switch deciding on survival of human and murine DCs and provides a rationale to manipulate DC responses by targeting their ubiquitin network downstream of the TNF receptor pathway.
Genetic architecture of dispersal behaviour in the post-harvest pest and model organism Tribolium castaneum
Authors: Pointer Michael D. , Spurgin Lewis G. , Gage Matthew J. G. , McMullan Mark , Richardson David S. 
Published: July 2023

AbstractDispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world’s most species-rich order.
Combining amino acid PET and MRI imaging increases accuracy to define malignant areas in adult glioma
Authors: Harat Maciej , Rakowska Józefina , Harat Marek , Szylberg Tadeusz , Furtak Jacek , Miechowicz Izabela , Małkowski Bogdan 
Published: July 2023

AbstractAccurate determination of the extent and grade of adult-type diffuse gliomas is critical to patient management. In clinical practice, contrast-enhancing areas of diffuse gliomas in magnetic resonance imaging (MRI) sequences are usually used to target biopsy, surgery, and radiation therapy, but there can be discrepancies between these areas and the actual tumor extent. Here we show that adding 18F-fluoro-ethyl-tyrosine positron emission tomography (FET-PET) to MRI sequences accurately locates the most malignant areas of contrast-enhancing gliomas, potentially impacting subsequent management and outcomes. We present a prospective analysis of over 300 serial biopsy specimens from 23 patients with contrast-enhancing adult-type diffuse gliomas using a hybrid PET-MRI scanner to compare T2-weighted and contrast-enhancing MRI images with FET-PET. In all cases, we observe and confirm high FET uptake in early PET acquisitions (5–15 min after 18F-FET administration) outside areas of contrast enhancement on MRI, indicative of high-grade glioma. In 30% cases, inclusion of FET-positive sites changes the biopsy result to a higher tumor grade.
Preventing antimalarial drug resistance with triple artemisinin-based combination therapies
Authors: Nguyen Tran Dang , Gao Bo , Amaratunga Chanaki , Dhorda Mehul , Tran Thu Nguyen-Anh , White Nicholas J. , Dondorp Arjen M. , Boni Maciej F. , Aguas Ricardo 
Published: July 2023

AbstractIncreasing levels of artemisinin and partner drug resistance threaten malaria control and elimination globally. Triple artemisinin-based combination therapies (TACTs) which combine artemisinin derivatives with two partner drugs are efficacious and well tolerated in clinical trials, including in areas of multidrug-resistant malaria. Whether early TACT adoption could delay the emergence and spread of antimalarial drug resistance is a question of vital importance. Using two independent individual-based models of Plasmodium falciparum epidemiology and evolution, we evaluated whether introduction of either artesunate-mefloquine-piperaquine or artemether-lumefantrine-amodiaquine resulted in lower long-term artemisinin-resistance levels and treatment failure rates compared with continued ACT use. We show that introduction of TACTs could significantly delay the emergence and spread of artemisinin resistance and treatment failure, extending the useful therapeutic life of current antimalarial drugs, and improving the chances of malaria elimination. We conclude that immediate introduction of TACTs should be considered by policy makers in areas of emerging artemisinin resistance.
Guided construction of single cell reference for human and mouse lung
Authors: Guo Minzhe , Morley Michael P. , Jiang Cheng , Wu Yixin , Li Guangyuan , Du Yina , Zhao Shuyang , Wagner Andrew , Cakar Adnan Cihan , Kouril Michal , Jin Kang , Gaddis Nathan , Kitzmiller Joseph A. , Stewart Kathleen , Basil Maria C. , Lin Susan M. , Ying Yun , Babu Apoorva , Wikenheiser-Brokamp Kathryn A. , Mun Kyu Shik , Naren Anjaparavanda P. , Clair Geremy , Adkins Joshua N. , Pryhuber Gloria S. , Misra Ravi S. , Aronow Bruce J. , Tickle Timothy L. , Salomonis Nathan , Sun Xin , Morrisey Edward E. , Whitsett Jeffrey A. ,   NHLBI LungMAP Consortium, Lin Sara , Xu Yan 
Published: July 2023

AbstractAccurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.
Observation of geometry-dependent skin effect in non-Hermitian phononic crystals with exceptional points
Authors: Zhou Qiuyan , Wu Jien , Pu Zhenhang , Lu Jiuyang , Huang Xueqin , Deng Weiyin , Ke Manzhu , Liu Zhengyou 
Published: July 2023

AbstractExceptional points and skin effect, as the two distinct hallmark features unique to the non-Hermitian physics, have each attracted enormous interests. Recent theoretical works reveal that the topologically nontrivial exceptional points can guarantee the non-Hermitian skin effect, which is geometry-dependent, relating these two unique phenomena. However, such novel relation remains to be confirmed by experiments. Here, we realize a non-Hermitian phononic crystal with exceptional points, which exhibits the geometry-dependent skin effect. The exceptional points connected by the bulk Fermi arcs, and the skin effects with the geometry dependence, are evidenced in simulations and experiments. Our work, building an experimental bridge between the exceptional points and skin effect and uncovering the unconventional geometry-dependent skin effect, expands a horizon in non-Hermitian physics.
Kinetic drop friction
Authors: Li Xiaomei , Bodziony Francisco , Yin Mariana , Marschall Holger , Berger Rüdiger , Butt Hans-Jürgen 
Published: July 2023

AbstractLiquid drops sliding on tilted surfaces is an everyday phenomenon and is important for many industrial applications. Still, it is impossible to predict the drop’s sliding velocity. To make a step forward in quantitative understanding, we measured the velocity $$(U)$$

(

U

)

, contact width $$(w)$$

(

w

)

, contact length $$(L)$$

(

L

)

, advancing $$({\theta }_{{{{{{\rm{a}}}}}}})$$

(

θ

a

)

, and receding contact angle $$({\theta }_{{{{{{\rm{r}}}}}}})$$

(

θ

r

)

of liquid drops sliding down inclined flat surfaces made of different materials. We find the friction force acting on sliding drops of polar and non-polar liquids with viscosities ($${\eta }$$
η
) ranging from 10−3 to 1 $${{{{{\rm{Pa}}}}}}\cdot {{{{{\rm{s}}}}}}$$
Pa
⋅
s
can empirically be described by $${F}_{{{{{{\rm{f}}}}}}}(U)={F}_{0}+\beta w\eta U$$

F

f

(

U

)

=

F

0

+
β
w
η
U
for a velocity range up to 0.7 ms−1. The dimensionless friction coefficient $$(\beta )$$

(

β

)

defined here varies from 20 to 200. It is a material parameter, specific for a liquid/surface combination. While static wetting is fully described by $${\theta }_{{{{{{\rm{a}}}}}}}$$

θ

a

and $${\theta }_{{{{{{\rm{r}}}}}}}$$

θ

r

, for dynamic wetting the friction coefficient is additionally necessary.
Cryo-EM structure of a RAS/RAF recruitment complex
Authors: Park Eunyoung , Rawson Shaun , Schmoker Anna , Kim Byeong-Won , Oh Sehee , Song Kangkang , Jeon Hyesung , Eck Michael J. 
Published: July 2023

AbstractRAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF have focused on the isolated RAS-binding and cysteine-rich domains of RAF (RBD and CRD, respectively), which interact directly with RAS. Here we describe cryo-EM structures of a KRAS bound to intact BRAF in an autoinhibited state with MEK1 and a 14-3-3 dimer. Analysis of this KRAS/BRAF/MEK1/14-3-3 complex reveals KRAS bound to the RAS-binding domain of BRAF, captured in two orientations. Core autoinhibitory interactions in the complex are unperturbed by binding of KRAS and in vitro activation studies confirm that KRAS binding is insufficient to activate BRAF, absent membrane recruitment. These structures illustrate the separability of binding and activation of BRAF by RAS and suggest stabilization of this pre-activation intermediate as an alternative therapeutic strategy to blocking binding of KRAS.
An estimate of absolute shear-wave speed in the Earth’s inner core
Authors: Costa de Lima Thuany , Phạm Thanh-Son , Ma Xiaolong , Tkalčić Hrvoje 
Published: July 2023

AbstractObservations of seismic body waves that traverse the Earth’s inner core (IC) as shear (J) waves are critical for understanding the IC shear properties, advancing our knowledge of the Earth’s internal structure and evolution. Here, we present several seismological observations of J phases detected in the earthquake late-coda correlation wavefield at periods of 15–50 s, notably via the correlation feature I-J, found to be independent of the Earth reference velocity model. Because I-J is unaffected by compressional wave speeds of the Earth’s inner core, outer core, and mantle, it represents an autonomous class of seismological measurements to benchmark the inner core properties. We estimate the absolute shear-wave speed in the IC to be 3.39 ± 0.02 km/s near the top and 3.54 ± 0.02 km/s in the center, lower than recently reported values. This is a 3.4 ± 0.5% reduction from the Preliminary Reference Earth Model (PREM), suggesting a less rigid IC than previously estimated from the normal mode data. Such a low shear-wave speed requires re-evaluating IC composition, including the abundance of light elements, the atomic properties and stable crystallographic phase of iron, and the IC solidification process.
Encapsulation and adhesion of nanoparticles as a potential biomarker for TNBC cells metastatic propensity
Authors: Merkher Yulia , Kontareva Elizaveta , Bogdan Elizaveta , Achkasov Konstantin , Maximova Ksenia , Grolman Joshua M. , Leonov Sergey 
Published: July 2023

AbstractMetastasis is the main cause of cancer-related mortality; therefore, the ability to predict its propensity can remarkably affect survival rate. Metastasis development is predicted nowadays by lymph-node status, tumor size, histopathology, and genetic testing. However, all these methods may have inaccuracies, and some require weeks to complete. Identifying novel prognostic markers will open an essential source for risk prediction, possibly guiding to elevated patient treatment by personalized strategies. Cancer cell invasion is a critical step in metastasis. The cytoskeletal mechanisms used by metastatic cells for the invasion process are very similar to the utilization of actin cytoskeleton in the endocytosis process. In the current study, the adhesion and encapsulation efficiency of low-cost carboxylate-modified fluorescent nanoparticles by breast cancer cells with high (HM) and low metastatic potential (LM) have been evaluated; benign cells were used as control. Using high-content fluorescence imaging and analysis, we have revealed (within a short time of 1 h), that efficiency of nanoparticles adherence and encapsulation is sufficiently higher in HM cells compared to LM cells, while benign cells are not encapsulating or adhering the particles during experiment time at all. We have utilized custom-made automatic image analysis algorithms to find quantitative co-localization (Pearson’s coefficients) of the nanoparticles with the imaged cells. The method proposed here is straightforward; it does not require especial equipment or expensive materials nor complicated cell manipulations, it may be potentially applicable for various cells, including patient-derived cells. Effortless and quantitative determination of the metastatic likelihood has the potential to be performed using patient-specific biopsy/surgery sample, which will directly influence the choice of protocols for cancer patient’s treatment and, as a result, increase their life expectancy.
Functionalization of gutta-percha surfaces with argon and oxygen plasma treatments to enhance adhesiveness
Authors: Ferreira Inês , Lopes Cláudia , Rodrigues Marco S. , Rodrigues Pedro V. , Castro Cidália , Braga Ana Cristina , Lopes Maria , Vaz Filipe , Pina-Vaz Irene , Martín-Biedma Benjamin 
Published: July 2023

AbstractGutta-percha’s lack of adhesion has been presented as a drawback to avoid gaps at sealer/gutta-percha interface. Plasma treatments have been scarcely assessed on gutta-percha surfaces as a method of enhancing adhesiveness. This study aimed to evaluate the effect of low-pressure Argon and Oxygen plasma atmospheres on conventional and bioceramic gutta-percha standardized smooth discs, assessing their roughness, surface free energy, chemical structure, and sealer wettability. A Low-Pressure Plasma Cleaner by Diener Electronic (Zepto Model) was used. Different gases (Argon or Oxygen), powers (25 W, or 50 W), and exposure times (30 s, 60 s, 120 s, or 180 s) were tested in control and experimental groups. Kruskal–Wallis and Student's t-test were used in data analysis. Statistically significant differences were detected when P < 0.05. Both gases showed different behaviors according to the parameters selected. Even though chemical changes were detected, the basic molecular structure was maintained. Argon or Oxygen plasma treatments favoured the wetting of conventional and bioceramic gutta-perchas by Endoresin and AH Plus Bioceramic sealers (P < 0.001). Overall, the functionalization of gutta-percha surfaces with Argon or Oxygen plasma treatments can increase roughness, surface free energy and wettability, which might improve its adhesive properties when compared to non-treated gutta-percha.
Leishmania donovani persistence and circulation causing cutaneous leishmaniasis in unusual-foci of Nepal
Authors: Rai Tinmaya , Shrestha Srijan , Prajapati Sabita , Bastola Anup , Parajuli Niraj , Ghimire Pragya Gautam , Bhandari Parmananda , Pandey Kishor , Jain Manju , Matlashewski Greg , Bras-Goncalves Rachel , Manandhar Krishna Das 
Published: July 2023

AbstractCutaneous leishmaniasis cases have increased dramatically in recent years in Nepal. The study offers molecular identification of the Leishmania species using 40 patient’s aspiration biopsy samples, targeting markers kinetoplast minicircle DNA (kDNA) and internal transcribed spacer-1 (ITS1). Among molecularly diagnosed 22 cutaneous leishmaniasis cases, L. donovani complex was identified in 13 instances and L. major in 9 cases. The ITS1 PCR was positive in 12 of the positive nested- kDNA PCR cases (12/22), confirming L. donovani complex in seven of the cases and L. major in five of the cases. In addition, the study conclude that concurrent occurrence of atypical cutaneous infections caused by L. donovani parasite in 59.1% of cases and typical cutaneous infections caused by L. major parasite in 40.9% of cases. A Phylogentic analaysis showed that the detected L. donovani species present null genetic distances from seven references of L. donovani, but slight differences between ITS1 sequences and not grouped into a significant monophyletic cluster.
First estimates of fine root production in tropical peat swamp and terra firme forests of the central Congo Basin
Authors: Sciumbata Matteo , Wenina Yeto Emmanuel Mampouya , Mbemba Mackline , Dargie Greta C. , Baird Andy J. , Morris Paul J. , Ifo Suspense Averti , Aerts Rien , Lewis Simon L. 
Published: July 2023

AbstractTropical peatlands are carbon-dense ecosystems because they accumulate partially-decomposed plant material. A substantial fraction of this organic matter may derive from fine root production (FRP). However, few FRP estimates exist for tropical peatlands, with none from the world’s largest peatland complex in the central Congo Basin. Here we report on FRP using repeat photographs of roots from in situ transparent tubes (minirhizotrons), measured to 1 m depth over three one-month periods (spanning dry to wet seasons), in a palm-dominated peat swamp forest, a hardwood-dominated peat swamp forest, and a terra firme forest. We find FRP of 2.6 ± 0.3 Mg C ha−1 yr−1, 1.9 ± 0.5 Mg C ha−1 yr−1, and 1.7 ± 0.1 Mg C ha−1 yr−1 in the three ecosystem types respectively (mean ± standard error; no significant ecosystem type differences). These estimates fall within the published FRP range worldwide. Furthermore, our hardwood peat swamp estimate is similar to the only other FRP study in tropical peatlands, also hardwood-dominated, from Micronesia. We also found that FRP decreased with depth and was the highest during the dry season. Overall, we show that minirhizotrons can be used as a low-disturbance method to estimate FRP in tropical forests and peatlands.