bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Post‐Assembly Modification of Western Laurentia by Back‐Arc Extension
Authors: Ekpo Johnson E. , Eaton D. W. , Nair R. 
Published: January 2022

AbstractThe crystalline crust that underlies the Western Canada Sedimentary Basin in northern Alberta is composed of tectonic domains that accreted to the margin of the Archean Rae province of western Laurentia, ca. 2.1‐1.8 Ga. Previous tectonic models in this region invoke complex plate dynamics, including oppositely verging subduction zones, to explain the assembly of various geologic domains. In this paper, we introduce a new tectonic model that invokes back‐arc extension within the Chinchaga Domain (CD). The basement crust in the CD hosts a vast, mid‐crustal reflection sequence (Winagami Reflection Sequence), previously interpreted as a mafic sill complex that intruded into an atypically wide domain of Paleoproterozoic arc magmatism. The latter has been interpreted to have formed during Paleoproterozoic tectonic assembly through near‐synchronous closure of multiple small oceanic basins and/or magmatism in a plate interior setting. Based on a reinterpretation of regional geophysical data and post‐compressional fabrics observed by re‐examination of drill cores, we propose that observed temporal relationships and present‐day configuration of Paleoproterozoic arcs is better explained by post‐assembly extension of the Chinchaga Domain. The proposed post‐assembly modification is analogous to the recent tectonic evolution of the Basin and Range and can be explained through back‐arc extension linked to slab rollback and/or a proximal coeval transform plate boundary. Our model implies a back‐arc setting for the Winagami sill complex; it also provides a tectonic framework for explaining the origin of an enigmatic low δ18O anomaly (Kimiwan anomaly) and reactivated basement faults associated with recent induced seismicity.
Application of Nonlinear Time Series and Machine Learning Algorithms for Forecasting Groundwater Flooding in a Lowland Karst Area
Authors: Basu Bidroha , Morrissey Patrick , Gill Laurence W. 
Published: January 2022

AbstractIn karst limestone areas interactions between ground and surface waters can be frequent, particularly in low lying areas, linked to the unique hydrogeological dynamics of that bedrock aquifer. In extreme hydrological conditions, however, this can lead to wide‐spread, long‐duration flooding, resulting in significant cost and disruption. This study develops and compares a nonlinear time‐series analysis based nonlinear autoregressive model with exogenous variables (NARX), machine learning based near support vector regression as well as a linear time‐series ARX model in terms of their performance to predict groundwater flooding in a lowland karst area of Ireland. The models have been developed upon the results of several years of field data collected in the area, as well as the outputs of a highly calibrated semi‐distributed hydraulic/hydrological model of the karst network. The prediction of total flooding volume indicates that the performances of all the models are similarly accurate up to 10 days into the future. A NARX model taking inputs of the past 5 days' flood volume; rainfall data and tidal amplitude data across the past 4 days, showed the best flood forecasting performance up to 30 days into the future. Existing real‐time telemetric monitoring of water level data at two points in the catchment can be fed into the model to provide an early warning flood warning tool. The model also predicts freshwater discharge from the inter‐tidal spring into the Atlantic Ocean which hitherto had not been possible to monitor.
Hyporheic Exchange Due to Cobbles on Sandy Beds
Authors: Lee Anzy , Aubeneau Antoine F. , Cardenas M. Bayani , Liu Xiaofeng 
Published: January 2022

AbstractHyporheic exchange induced by riverbed topography and roughness provides important ecosystem functions. We investigated how cobble clusters embedded in a finer‐grained sand bed affect the near‐bed channel flow and the exchange of surface and subsurface water. We tested how the spacing and embeddedness of cobbles altered hyporheic exchange through a three‐dimensional fully coupled surface‐subsurface model. The 3D modeling framework captured the full physics of the exchange process locating the lateral position of upwelling zones on the side of the cobble. As the cobbles protrude more into the channel, eddies appear downstream, with smaller vortices where cobbles are closer together. In our simulations, hyporheic exchange increased with the spacing and protrusion ratio. The travel time in the hyporheic zone also increased with the protrusion ratio because the hyporheic flow paths are longer when the cobble is more protruded. With different spacings at the highest protrusion ratio, the average slope of early time breakthrough curve was steeper for large spacing settings: the travel time increases as the spacing decreases.
Patterns of neutralizing humoral response to SARS-CoV-2 infection among hematologic malignancy patients reveal a robust immune response in anti-cancer therapy-naive patients
Authors: Borgogna Cinzia , Bruna Riccardo , Griffante Gloria , Martuscelli Licia , De Andrea Marco , Ferrante Daniela , Patriarca Andrea , Mahmoud Abdurraouf Mokhtar , Gaidano Valentina , Marchetti Monia , Rapezzi Davide , Lai Michele , Pistello Mauro , Ladetto Marco , Massaia Massimo , Gaidano Gianluca , Gariglio Marisa 
Published: January 2022

AbstractUnderstanding antibody-based SARS-CoV-2 immunity in hematologic malignancy (HM) patients following infection is crucial to inform vaccination strategies for this highly vulnerable population. This cross-sectional study documents the anti-SARS-CoV-2 humoral response and serum neutralizing activity in 189 HM patients recovering from a PCR-confirmed infection. The overall seroconversion rate was 85.7%, with the lowest values in patients with lymphoid malignancies or undergoing chemotherapy. Therapy-naive patients in the “watch and wait” status were more likely to seroconvert and display increased anti-s IgG titers. Enhanced serum neutralizing activity was observed in the following SARS-CoV-2-infected HM patient groups: (i) males; (ii) severe COVID-19; and (iii) “watch and wait” or “complete/partial response”. The geometric mean (GeoMean) ID50 neutralization titers in patients analyzed before or after 6 months post-infection were 299.1 and 306.3, respectively, indicating that >50% of the patients in either group had a neutralization titer sufficient to provide 50% protection from symptomatic COVID-19. Altogether, our findings suggest that therapy-naive HM patients mount a far more robust immune response to SARS-CoV-2 infection vs. patients receiving anti-cancer treatment, raising the important question as to whether HM patients should be vaccinated before therapy and/or receive vaccine formats capable of better recapitulating the natural infection.
Primary tumour immune response and lymph node yields in colon cancer
Authors: Lal Nikhil , Chan Dedrick Kok Hong , Ng Minn E , Vermeulen Louis , Buczacki Simon James Alexander 
Published: January 2022

Abstract
Background
The mechanism underlying improved survival in non-metastatic colon cancer with higher lymph node (LN) yield is unknown. This study aimed to identify whether molecular features in the primary tumour were predictive of LN yield.

Methods
Clinical, genomic, transcriptomic, proteomic and methylation data of non-metastatic, colon cancers studied in The Cancer Genome Atlas were interrogated for associations with LN yield. Based on maximal survival effects, patients were segregated into high (>15) and low (≤15) LN yield. Gene set enrichment analysis was performed on transcriptomic changes to identify biological processes associated with LN yield. Correlations were validated in an independent set of Stage II colon cancers.

Results
High LN yield was found predictive of overall and disease-free survival. There was no association of higher LN yield and increasing nodal positivity. High LN yield was strongly linked with gene expression changes associated with the adaptive and dendritic cell immune response. This association was most prominent in node-negative cancers. Analogous findings were reproduced in the validation dataset.

Conclusion
The study shows a strong association of an activated immune response in tumours with a high LN yield. Immunogenic tumours have a better prognosis, likely explaining the survival benefit with higher LN yields.
Integrative genomic and transcriptomic analysis reveals immune subtypes and prognostic markers in ovarian clear cell carcinoma
Authors: Ye Shuang , Li Qin , Wu Yutuan , Jiang Wei , Zhou Shuling , Zhou Xiaoyan , Yang Wentao , Tu Xiaoyu , Shan Boer , Huang Shenglin , Yang Huijuan 
Published: January 2022

Abstract
Background
We performed an integrative genomic and transcriptomic profiling to identify molecular subtypes and prognostic markers with special focus on immune-related pathways.

Methods
Totally, 50 Chinese patients were subjected to targeted next-generation sequencing and transcriptomic sequencing.

Results
Two distinct subgroups were identified as immune (22.0%) and non-immune (78.0%) based on the immune-pathway related hierarchical clustering. Surprisingly, patients with immune subtype had a significantly worse survival. The prognostic capacity was validated in external cohorts. The immune group had higher expression of genes involved in pro-inflammation and checkpoints. PD-1 signalling pathway was enriched in the immune subtype. Besides, the immune cluster presented enriched expression of genes involved in epithelial-mesenchymal transition, angiogenesis and PI3K-AKT-mTOR signalling, while the non-immune subtype had higher expression of metabolic pathways. The immune subtype had a higher mutation rate of PIK3CA though significance was not achieved. Lastly, we established a prognostic immune signature for overall survival. Interestingly, the immune signature could also be applied to renal clear cell carcinoma, but not to other histologic subtype of ovarian cancer.

Conclusions
An immune subtype of OCCC was identified with poor survival and enrichment of PD-1 and PI3K-AKT-mTOR signalling. We constructed and validated a robust prognostic immune signature of OCCC patients.
Tumour-infiltrating lymphocytes in oropharyngeal cancer: a validation study according to the criteria of the International Immuno-Oncology Biomarker Working Group
Authors: Almangush Alhadi , Jouhi Lauri , Atula Timo , Haglund Caj , Mäkitie Antti A. , Hagström Jaana , Leivo Ilmo 
Published: January 2022

Abstract
Background
The evaluation of immune response can aid in prediction of cancer behaviour. Here, we assessed the prognostic significance of tumour-infiltrating lymphocytes (TILs) in oropharyngeal squamous cell carcinoma (OPSCC).

Methods
A total of 182 patients treated for OPSCC were included in this study. Assessment of TILs was conducted on tumour sections stained with standard haematoxylin and eosin (HE) staining. We used the scoring criteria proposed by the International Immuno-Oncology Biomarker Working Group.

Results
The multivariable analysis showed that TILs associated with disease-specific survival with a hazard ratio (HR) of 2.13 (95% CI 1.14–3.96; P = 0.017). Similarly, TILs associated significantly with overall survival with HR of 1.87 (95% CI 1.11–3.13; P = 0.018). In a sub-analysis of HPV-positive and HPV-negative cases separately, TILs showed a significant prognostic value in both groups (P < 0.05).

Conclusion
The evaluation of TILs as proposed by the International Immuno-Oncology Biomarker Working Group is a simple and promising method in prediction of survival of OPSCC. It is easily applicable and after further validation can be implemented in the routine pathological report as a basic immune parameter.
Resolving the structure of phage–bacteria interactions in the context of natural diversity
Authors: Kauffman Kathryn M. , Chang William K. , Brown Julia M. , Hussain Fatima A. , Yang Joy , Polz Martin F. , Kelly Libusha 
Published: January 2022

AbstractMicrobial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.
Fate of dissolved black carbon in the deep Pacific Ocean
Authors: Yamashita Youhei , Nakane Motohiro , Mori Yutaro , Nishioka Jun , Ogawa Hiroshi 
Published: January 2022

AbstractBlack carbon (BC), a byproduct of biomass and fossil fuel combustion, may impact the climate because it can be stored on Earth’s surface for centuries to millennia. Dissolved BC (DBC) occurs ubiquitously in the ocean. However, the DBC cycle in the ocean has not been well constrained. Here, we show the basin-scale distribution of DBC in the Pacific Ocean and find that the DBC concentrations in the deep Pacific Ocean decrease along with deep-ocean meridional circulation. The DBC concentration is negatively correlated with apparent oxygen utilization, a proxy of the integrated flux of sinking particles, in the deep Pacific Ocean, implying that DBC is removed from the deep ocean to abyssal sediments through sorption onto sinking particles. The burial flux of BC to abyssal sediments is estimated to be 0.040–0.085 PgC yr−1, corresponding to 1.5–3.3% of the anthropogenic CO2uptake by the ocean.
Intensified continental chemical weathering and carbon-cycle perturbations linked to volcanism during the Triassic–Jurassic transition
Authors: Shen Jun , Yin Runsheng , Zhang Shuang , Algeo Thomas J. , Bottjer David J. , Yu Jianxin , Xu Guozhen , Penman Donald , Wang Yongdong , Li Liqin , Shi Xiao , Planavsky Noah J. , Feng Qinglai , Xie Shucheng 
Published: January 2022

AbstractDirect evidence of intense chemical weathering induced by volcanism is rare in sedimentary successions. Here, we undertake a multiproxy analysis (including organic carbon isotopes, mercury (Hg) concentrations and isotopes, chemical index of alteration (CIA), and clay minerals) of two well-dated Triassic–Jurassic (T–J) boundary sections representing high- and low/middle-paleolatitude sites. Both sections show increasing CIA in association with Hg peaks near the T–J boundary. We interpret these results as reflecting volcanism-induced intensification of continental chemical weathering, which is also supported by negative mass-independent fractionation (MIF) of odd Hg isotopes. The interval of enhanced chemical weathering persisted for ~2 million years, which is consistent with carbon-cycle model results of the time needed to drawdown excess atmospheric CO2 following a carbon release event. Lastly, these data also demonstrate that high-latitude continental settings are more sensitive than low/middle-latitude sites to shifts in weathering intensity during climatic warming events.
Brønsted acid-enhanced copper-catalyzed atroposelective cycloisomerization to axially chiral arylquinolizones via dearomatization of pyridine
Authors: Min Xiao-Long , Zhang Xiu-Lian , Yi Wenbin , He Ying 
Published: January 2022

AbstractThe construction of axially chiral N-heterobiaryls is of great interest as a result of their occurrence in organocatalysts, chiral ligands, natural products, and biologically active molecules. Despite remarkable achievements in this area, strategies for the preparation of new classes of axially chiral N-heterobiaryls remain to be further explored. Herein, we report the enantioselective synthesis of axially chiral arylquinolizones through an intramolecular atroposelective cycloisomerization. The reaction proceeds via the Brønsted acid-enhanced dearomatization of pyridine by a copper catalyst that allows for the formation of the desired products in excellent yields and enantioselectivities. The utility of this methodology is illustrated by a synthesis on gram scale production and transformation of the products into chiral thiourea catalysts. Mechanistic studies demonstrate that Brønsted acid plays a significant role in promoting the reactivity of the reaction, while both the steric and electronic effects of aryl substituents in substrate play a role in controlling the stereoselectivity.
One reaction to make highly stretchable or extremely soft silicone elastomers from easily available materials
Authors: Hu Pengpeng , Madsen Jeppe , Skov Anne Ladegaard 
Published: January 2022

AbstractHighly stretchable, soft silicone elastomers are of great interest for the fabrication of stretchable, soft devices. However, there is a lack of available chemistries capable of efficiently preparing silicone elastomers with superior stretchability and softness. Here we show an easy curing reaction to prepare silicone elastomers, in which a platinum-catalyzed reaction of telechelic/multi-hydrosilane (Si–H) functional polydimethylsiloxane (PDMS) in the presence of oxygen and water leads to slow crosslinking. This curing chemistry allows versatile tailoring of elastomer properties, which exceed their intrinsic limitations. Specifically, both highly stretchable silicone elastomers (maximum strain of 2800%) and extremely soft silicone elastomers (lowest shear modulus of 1.2 kPa) are prepared by creating highly entangled elastomers and bottle-brush elastomers from commercial precursor polymers, respectively.
Thermal assisted up-conversion electroluminescence in quantum dot light emitting diodes
Authors: Su Qiang , Chen Shuming 
Published: January 2022

AbstractUp-conversion electroluminescence, in which the energy of a emitted photon is higher than that of the excitation electron, is observed in quantum-dot light-emitting diodes. Here, we study its mechanism by investigating the effect of thermal energy on the charge injection dynamic. Based on the results of temperature-dependent electroluminescence and theoretical analysis, we reveal that at sub-bandgap voltage, holes can be successfully injected into quantum-dots via thermal-assisted thermionic-emission mechanism, thereby enabling the sub-bandgap turn-on and up-conversion electroluminescence of the devices. Further theoretical deduction and experimental results confirm that thermal-assisted hole-injection is the universal mechanism responsible for the up-conversion electroluminescence. This work uncovers the charge injection process and unlocks the sub-bandgap turn-on mechanism, which paves the road for the development of up-conversion devices with power conversion efficiency over 100%.
Recent upper Arctic Ocean warming expedited by summertime atmospheric processes
Authors: Li Zhe , Ding Qinghua , Steele Michael , Schweiger Axel 
Published: January 2022

AbstractThe observed upper (0–50 m) Arctic Ocean warming since 1979 has been primarily attributed to anthropogenically driven changes in the high latitudes. Here, using both observational and modeling analyses, we demonstrate that a multiyear trend in the summertime large-scale atmospheric circulation, which we ascribe to internal variability, has played an important role in upper ocean warming in summer and fall over the past four decades due to sea ice-albedo effect induced by atmospheric dynamics. Nudging experiments in which the wind fields are constrained toward the observed state support this mechanism and suggest that the internal variability contribution to recent upper Arctic Ocean warming accounts for up to one quarter of warming over the past four decades and up to 60% of warming from 2000 to 2018. This suggests that climate models need to replicate this important internal process in order to realistically simulate Arctic Ocean temperature variability and trends.
OCT4-induced oligodendrocyte progenitor cells promote remyelination and ameliorate disease
Authors: Yun Wonjin , Choi Kyung-Ah , Hwang Insik , Zheng Jie , Park Minji , Hong Wonjun , Jang Ah-Young , Kim Jeong Hee , Choi Wonji , Kim Dae-Sung , Kim In Yong , Kim Yong Jun , Liu Ying , Yoon Byung Sun , Park Gyuman , Song Gwonhwa , Hong Sunghoi , You Seungkwon 
Published: January 2022

AbstractThe generation of human oligodendrocyte progenitor cells (OPCs) may be therapeutically valuable for human demyelinating diseases such as multiple sclerosis. Here, we report the direct reprogramming of human somatic cells into expandable induced OPCs (iOPCs) using a combination of OCT4 and a small molecule cocktail. This method enables generation of A2B5+(an early marker for OPCs) iOPCs within 2 weeks retaining the ability to differentiate into MBP-positive mature oligodendrocytes. RNA-seq analysis revealed that the transcriptome of O4+iOPCs was similar to that of O4+OPCs and ChIP-seq analysis revealed that putative OCT4-binding regions were detected in the regulatory elements of CNS development-related genes. Notably, engrafted iOPCs remyelinated the brains of adult shiverer mice and experimental autoimmune encephalomyelitis mice with MOG-induced 14 weeks after transplantation. In conclusion, our study may contribute to the development of therapeutic approaches for neurological disorders, as well as facilitate the understanding of the molecular mechanisms underlying glial development.
Ancestral SARS-CoV-2-specific T cells cross-recognize the Omicron variant
Authors: Gao Yu , Cai Curtis , Grifoni Alba , Müller Thomas R. , Niessl Julia , Olofsson Anna , Humbert Marion , Hansson Lotta , Österborg Anders , Bergman Peter , Chen Puran , Olsson Annika , Sandberg Johan K. , Weiskopf Daniela , Price David A. , Ljunggren Hans-Gustaf , Karlsson Annika C. , Sette Alessandro , Aleman Soo , Buggert Marcus 
Published: January 2022

AbstractThe emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (B.1.1.529) variant of concern (VOC) has destabilized global efforts to control the impact of coronavirus disease 2019 (COVID-19). Recent data have suggested that B.1.1.529 can readily infect people with naturally acquired or vaccine-induced immunity, facilitated in some cases by viral escape from antibodies that neutralize ancestral SARS-CoV-2. However, severe disease appears to be relatively uncommon in such individuals, highlighting a potential role for other components of the adaptive immune system. We report here that SARS-CoV-2 spike-specific CD4+ and CD8+ T cells induced by prior infection or BNT162b2 vaccination provide extensive immune coverage against B.1.1.529. The median relative frequencies of SARS-CoV-2 spike-specific CD4+ T cells that cross-recognized B.1.1.529 in previously infected or BNT162b2-vaccinated individuals were 84% and 91%, respectively, and the corresponding median relative frequencies for SARS-CoV-2 spike-specific CD8+ T cells were 70% and 92%, respectively. Pairwise comparisons across groups further revealed that SARS-CoV-2 spike-reactive CD4+ and CD8+ T cells were functionally and phenotypically similar in response to the ancestral strain or B.1.1.529. Collectively, our data indicate that established SARS-CoV-2 spike-specific CD4+ and CD8+ T cell responses, especially after BNT162b2 vaccination, remain largely intact against B.1.1.529.