bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ice front retreat reconfigures meltwater-driven gyres modulating ocean heat delivery to an Antarctic ice shelf
Authors: Yoon Seung-Tae , Lee Won Sang , Nam SungHyun , Lee Choon-Ki , Yun Sukyoung , Heywood Karen , Boehme Lars , Zheng Yixi , Lee Inhee , Choi Yeon , Jenkins Adrian , Jin Emilia Kyung , Larter Robert , Wellner Julia , Dutrieux Pierre , Bradley Alexander T. 
Published: January 2022

AbstractPine Island Ice Shelf (PIIS) buttresses the Pine Island Glacier, the key contributor to sea-level rise. PIIS has thinned owing to ocean-driven melting, and its calving front has retreated, leading to buttressing loss. PIIS melting depends primarily on the thermocline variability in its front. Furthermore, local ocean circulation shifts adjust heat transport within Pine Island Bay (PIB), yet oceanic processes underlying the ice front retreat remain unclear. Here, we report a PIB double-gyre that moves with the PIIS calving front and hypothesise that it controls ocean heat input towards PIIS. Glacial melt generates cyclonic and anticyclonic gyres near and off PIIS, and meltwater outflows converge into the anticyclonic gyre with a deep-convex-downward thermocline. The double-gyre migrated eastward as the calving front retreated, placing the anticyclonic gyre over a shallow seafloor ridge, reducing the ocean heat input towards PIIS. Reconfigurations of meltwater-driven gyres associated with moving ice boundaries might be crucial in modulating ocean heat delivery to glacial ice.
Hierarchically encapsulating enzymes with multi-shelled metal-organic frameworks for tandem biocatalytic reactions
Authors: Man Tiantian , Xu Caixia , Liu Xiao-Yuan , Li Dan , Tsung Chia-Kuang , Pei Hao , Wan Ying , Li Li 
Published: January 2022

AbstractBiocatalytic transformations in living organisms, such as multi-enzyme catalytic cascades, proceed in different cellular membrane-compartmentalized organelles with high efficiency. Nevertheless, it remains challenging to mimicking biocatalytic cascade processes in natural systems. Herein, we demonstrate that multi-shelled metal-organic frameworks (MOFs) can be used as a hierarchical scaffold to spatially organize enzymes on nanoscale to enhance cascade catalytic efficiency. Encapsulating multi-enzymes with multi-shelled MOFs by epitaxial shell-by-shell overgrowth leads to 5.8~13.5-fold enhancements in catalytic efficiencies compared with free enzymes in solution. Importantly, multi-shelled MOFs can act as a multi-spatial-compartmental nanoreactor that allows physically compartmentalize multiple enzymes in a single MOF nanoparticle for operating incompatible tandem biocatalytic reaction in one pot. Additionally, we use nanoscale Fourier transform infrared (nano-FTIR) spectroscopy to resolve nanoscale heterogeneity of vibrational activity associated to enzymes encapsulated in multi-shelled MOFs. Furthermore, multi-shelled MOFs enable facile control of multi-enzyme positions according to specific tandem reaction routes, in which close positioning of enzyme-1-loaded and enzyme-2-loaded shells along the inner-to-outer shells could effectively facilitate mass transportation to promote efficient tandem biocatalytic reaction. This work is anticipated to shed new light on designing efficient multi-enzyme catalytic cascades to encourage applications in many chemical and pharmaceutical industrial processes.
Asymmetric synthesis of N-bridged [3.3.1] ring systems by phosphonium salt/Lewis acid relay catalysis
Authors: Tan Jian-Ping , Li Kehan , Shen Boming , Zhuang Cheng , Liu Zanjiao , Xiao Kai , Yu Peiyuan , Yi Bing , Ren Xiaoyu , Wang Tianli 
Published: January 2022

AbstractOptically pure pseudo-natural products (PNPs), particularly exemplified by azabicyclo[3.3.1]nonane molecules and their analogs provide an attractive platform for structure−activity relationship studies, and also lead new compound discovery in drug development. However, there are currently no examples of guiding catalytic asymmetric strategies available to construct such important PN-scaffolds, thus limiting their broad use. Here, we report a general and modular method for constructing these pseudo-natural N-bridged [3.3.1] ring systems via cascade process by bifunctional phosphonium salt/Lewis acid relay catalysis. A wide variety of substrates bearing an assortment of functional groups (59 examples) are compatible with this protocol. Other features include a [3 + 2] cyclization/ring-opening/Friedel-Crafts cascade pathway, excellent reactivities and stereoselectivities, easily available starting materials, step economy and scalability. The obtained enantioenriched products showed potential of preliminary anticancer activities. Insights gained from our studies are expected to advance general efforts towards the catalytic synthesis of challenging even unprecedented chiral PNPs, offering new opportunities for bioactive small-molecule discovery.
Iridium-catalyzed enantioconvergent hydrogenation of trisubstituted olefins
Authors: Peters Bram B. C. , Zheng Jia , Birke Norman , Singh Thishana , Andersson Pher G. 
Published: January 2022

AbstractAsymmetric hydrogenation of olefins constitutes a practical and efficient method to introduce chirality into prochiral substrates. However, the absolute majority of the developed methodologies is enantiodivergent and thus require isomerically pure olefins which is a considerable drawback since most olefination strategies produce (E/Z)-mixtures. Although some advances have been reported, a general enantioconvergent hydrogenation featuring a broad functional group tolerance remains elusive. Here, we report the development of a general iridium-catalyzed enantioconvergent hydrogenation of a broad range of functionalized trisubstituted olefins. The substitution pattern around the olefin is critical; whereas α-prochiral olefins can undergo an enantioconvergent hydrogenation, β-prochiral olefins react in an enantiodivergent manner. The presented methodology hydrogenates α-prochiral substrates with excellent control of enantioselection and high isolated yields. Most importantly, both isomerically pure alkenes as well as isomeric mixtures can be hydrogenated to yield the same major enantiomer in excellent enantiomeric excesses which is unusual in transition-metal catalyzed asymmetric hydrogenations.
The 21-gene recurrence score in early non-ductal breast cancer: a National Cancer Database analysis
Authors: Makower Della , Qin Jiyue , Lin Juan , Xue Xiaonan , Sparano Joseph A. 
Published: January 2022

AbstractThe 21-gene recurrence score (RS) is prognostic for recurrence and predictive of chemotherapy benefit in early estrogen receptor-positive (ER +) HER2-negative (HER2-) breast cancer (BCA). We evaluated clinicopathologic characteristics, RS and chemotherapy benefit in invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), and carcinomas of mixed histologies (ductal + lobular (DLC), ductal + other (DOC), lobular + other (LOC)). Women diagnosed between 1/1/2010 and 1/1/2014 with ER + HER2- BCA, measuring <5 cm, with 0–3 involved axillary nodes, surgery as first treatment, and available RS, were identified from the NCDB. Associations between categorical variables were examined using chi-square test. Cox proportional hazards model was used to examine overall survival (OS) differences among histology subtypes. IDC was associated with smaller size, high grade, and RS > 26. ILC was associated with larger size, and least likely to be high grade (p < 0.0001). Lobular histology was associated with lower incidence of RS > 26. IDC patients (pts) were more likely to receive chemotherapy than pts with other histologies (p < 0.0001). OS for IDC, ILC and DOC were similar. DLC was associated with improved OS (HR 0.82, p = 0.02). Adjuvant chemotherapy was associated with improved OS in IDC (HR = 0.76, p < 0.0001) but not in ILC (HR = 0.99, p = 0.93), DLC (HR = 1.04, p = 0.86), DOC (HR = 0.87, p = 0.71), or LOC (HR = 2.91, p = 0.10). Lobular and mixed BCA histologies have distinct clinicopathologic features compared with IDC, and are less likely to have high RS. OS is similar for IDC and ILC. Although chemotherapy benefit was seen only in IDC, benefit for ILC with RS > 26 cannot be excluded.
Comparative transcriptional analyses of preclinical models and patient samples reveal MYC and RELA driven expression patterns that define the molecular landscape of IBC
Authors: Rypens Charlotte , Bertucci François , Finetti Pascal , Robertson Fredika , Fernandez Sandra V. , Ueno Naoto , Woodward Wendy A. , Van Golen Kenneth , Vermeulen Peter , Dirix Luc , Viens Patrice , Birnbaum Daniel , Devi Gayathri R. , Cristofanilli Massimo , Van Laere Steven 
Published: January 2022

AbstractInflammatory breast cancer (IBC) is an aggressive disease for which the spectrum of preclinical models was rather limited in the past. More recently, novel cell lines and xenografts have been developed. This study evaluates the transcriptome of an extended series of IBC preclinical models and performed a comparative analysis with patient samples to determine the extent to which the current models recapitulate the molecular characteristics of IBC observed clinically. We demonstrate that the IBC preclinical models are exclusively estrogen receptor (ER)-negative and of the basal-like subtype, which reflects to some extent the predominance of these subtypes in patient samples. The IBC-specific 79-signature we previously reported was retrained and discriminated between IBC and non-IBC preclinical models, but with a relatively high rate of false positive predictions. Further analyses of gene expression profiles revealed important roles for cell proliferation, MYC transcriptional activity, and TNFɑ/NFκB in the biology of IBC. Patterns of MYC expression and transcriptional activity were further explored in patient samples, which revealed interactions with ESR1 expression that are contrasting in IBC and nIBC and notable given the comparatively poor outcomes of ER+ IBC. Our analyses also suggest important roles for NMYC, MXD3, MAX, and MLX in shaping MYC signaling in IBC. Overall, we demonstrate that the IBC preclinical models can be used to unravel cancer cell intrinsic molecular features, and thus constitute valuable research tools. Nevertheless, the current lack of ER-positive IBC models remains a major hurdle, particularly since interactions with the ER pathway appear to be relevant for IBC.
Design of soft magnetic materials
Authors: Renuka Balakrishna Ananya , James Richard D. 
Published: January 2022

AbstractWe present a strategy for the design of ferromagnetic materials with exceptionally low magnetic hysteresis, quantified by coercivity. In this strategy, we use a micromagnetic algorithm that we have developed in previous research and which has been validated by its success in solving the “Permalloy Problem”—the well-known difficulty of predicting the composition 78.5% Ni of the lowest coercivity in the Fe–Ni system—and by the insight it provides into the “Coercivity Paradox” of W. F. Brown. Unexpectedly, the design strategy predicts that cubic materials with large saturation magnetization ms and large magnetocrystalline anisotropy constant κ1 will have low coercivity on the order of that of Permalloy, as long as the magnetostriction constants λ100, λ111 are tuned to special values. The explicit prediction for a cubic material with low coercivity is the dimensionless number $$({c}_{11}-{c}_{12}){\lambda }_{100}^{2}/(2{\kappa }_{1})=81$$

(

c

11

−

c

12

)

λ

100

2

/

(

2

κ

1

)

=
81
for 〈100〉 easy axes. The results would seem to have broad potential application, especially to magnetic materials of interest in energy research.
Unconventional superconductivity in magic-angle twisted trilayer graphene
Authors: Fischer Ammon , Goodwin Zachary A. H. , Mostofi Arash A. , Lischner Johannes , Kennes Dante M. , Klebl Lennart 
Published: January 2022

AbstractMagic-angle twisted trilayer graphene (MATTG) recently emerged as a highly tunable platform for studying correlated phases of matter, such as correlated insulators and superconductivity. Superconductivity occurs in a range of doping levels that is bounded by van Hove singularities, which stimulates the debate of the origin and nature of superconductivity in this material. In this work, we discuss the role of spin-fluctuations arising from atomic-scale correlations in MATTG for the superconducting state. We show that in a phase diagram as a function of doping (ν) and temperature, nematic superconducting regions are surrounded by ferromagnetic states and that a superconducting dome with Tc ≈ 2 K appears between the integer fillings ν = −2 and ν = −3. Applying a perpendicular electric field enhances superconductivity on the electron-doped side which we relate to changes in the spin-fluctuation spectrum. We show that the nematic unconventional superconductivity leads to pronounced signatures in the local density of states detectable by scanning tunneling spectroscopy measurements.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Authors: Viana Raquel , Moyo Sikhulile , Amoako Daniel G. , Tegally Houriiyah , Scheepers Cathrine , Althaus Christian L. , Anyaneji Ugochukwu J. , Bester Phillip A. , Boni Maciej F. , Chand Mohammed , Choga Wonderful T. , Colquhoun Rachel , Davids Michaela , Deforche Koen , Doolabh Deelan , du Plessis Louis , Engelbrecht Susan , Everatt Josie , Giandhari Jennifer , Giovanetti Marta , Hardie Diana , Hill Verity , Hsiao Nei-Yuan , Iranzadeh Arash , Ismail Arshad , Joseph Charity , Joseph Rageema , Koopile Legodile , Kosakovsky Pond Sergei L. , Kraemer Moritz U. G. , Kuate-Lere Lesego , Laguda-Akingba Oluwakemi , Lesetedi-Mafoko Onalethatha , Lessells Richard J. , Lockman Shahin , Lucaci Alexander G. , Maharaj Arisha , Mahlangu Boitshoko , Maponga Tongai , Mahlakwane Kamela , Makatini Zinhle , Marais Gert , Maruapula Dorcas , Masupu Kereng , Matshaba Mogomotsi , Mayaphi Simnikiwe , Mbhele Nokuzola , Mbulawa Mpaphi B. , Mendes Adriano , Mlisana Koleka , Mnguni Anele , Mohale Thabo , Moir Monika , Moruisi Kgomotso , Mosepele Mosepele , Motsatsi Gerald , Motswaledi Modisa S. , Mphoyakgosi Thongbotho , Msomi Nokukhanya , Mwangi Peter N. , Naidoo Yeshnee , Ntuli Noxolo , Nyaga Martin , Olubayo Lucier , Pillay Sureshnee , Radibe Botshelo , Ramphal Yajna , Ramphal Upasana , San James E. , Scott Lesley , Shapiro Roger , Singh Lavanya , Smith-Lawrence Pamela , Stevens Wendy , Strydom Amy , Subramoney Kathleen , Tebeila Naume , Tshiabuila Derek , Tsui Joseph , van Wyk Stephanie , Weaver Steven , Wibmer Constantinos K. , Wilkinson Eduan , Wolter Nicole , Zarebski Alexander E. , Zuze Boitumelo , Goedhals Dominique , Preiser Wolfgang , Treurnicht Florette , Venter Marietje , Williamson Carolyn , Pybus Oliver G. , Bhiman Jinal , Glass Allison , Martin Darren P. , Rambaut Andrew , Gaseitsiwe Simani , von Gottberg Anne , de Oliveira Tulio 
Published: January 2022

AbstractThe SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
Comprehensive diffusion MRI dataset for in vivo human brain microstructure mapping using 300 mT/m gradients
Authors: Tian Qiyuan , Fan Qiuyun , Witzel Thomas , Polackal Maya N. , Ohringer Ned A. , Ngamsombat Chanon , Russo Andrew W. , Machado Natalya , Brewer Kristina , Wang Fuyixue , Setsompop Kawin , Polimeni Jonathan R. , Keil Boris , Wald Lawrence L. , Rosen Bruce R. , Klawiter Eric C. , Nummenmaa Aapo , Huang Susie Y. 
Published: January 2022

AbstractStrong gradient systems can improve the signal-to-noise ratio of diffusion MRI measurements and enable a wider range of acquisition parameters that are beneficial for microstructural imaging. We present a comprehensive diffusion MRI dataset of 26 healthy participants acquired on the MGH-USC 3 T Connectome scanner equipped with 300 mT/m maximum gradient strength and a custom-built 64-channel head coil. For each participant, the one-hour long acquisition systematically sampled the accessible diffusion measurement space, including two diffusion times (19 and 49 ms), eight gradient strengths linearly spaced between 30 mT/m and 290 mT/m for each diffusion time, and 32 or 64 uniformly distributed directions. The diffusion MRI data were preprocessed to correct for gradient nonlinearity, eddy currents, and susceptibility induced distortions. In addition, scan/rescan data from a subset of seven individuals were also acquired and provided. The MGH Connectome Diffusion Microstructure Dataset (CDMD) may serve as a test bed for the development of new data analysis methods, such as fiber orientation estimation, tractography and microstructural modelling.
Landscape Dynamics (landDX) an open-access spatial-temporal database for the Kenya-Tanzania borderlands
Authors: Tyrrell Peter , Amoke Irene , Betjes Koen , Broekhuis Femke , Buitenwerf Robert , Carroll Sarah , Hahn Nathan , Haywood Daniel , Klaassen Britt , Løvschal Mette , Macdonald David , Maiyo Karen , Mbithi Hellen , Mwangi Nelson , Ochola Churchil , Odire Erick , Ondrusek Victoria , Ratemo Junior , Pope Frank , Russell Samantha , Sairowua Wilson , Sigilai Kiptoo , Stabach Jared A. , Svenning Jens-Christian , Stone Elizabeth , du Toit Johan T. , Western Guy , Wittemyer George , Wall Jake 
Published: January 2022

AbstractThe savannas of the Kenya-Tanzania borderland cover >100,000 km2and is one of the most important regions globally for biodiversity conservation, particularly large mammals. The region also supports >1 million pastoralists and their livestock. In these systems, resources for both large mammals and pastoralists are highly variable in space and time and thus require connected landscapes. However, ongoing fragmentation of (semi-)natural vegetation by smallholder fencing and expansion of agriculture threatens this social-ecological system. Spatial data on fences and agricultural expansion are localized and dispersed among data owners and databases. Here, we synthesized data from several research groups and conservation NGOs and present the first release of the Landscape Dynamics (landDX) spatial-temporal database, covering ~30,000 km2of southern Kenya. The data includes 31,000 livestock enclosures, nearly 40,000 kilometres of fencing, and 1,500 km2of agricultural land. We provide caveats and interpretation of the different methodologies used. These data are useful to answer fundamental ecological questions, to quantify the rate of change of ecosystem function and wildlife populations, for conservation and livestock management, and for local and governmental spatial planning.
Mendelian randomisation analyses of UK Biobank and published data suggest that increased adiposity lowers risk of breast and prostate cancer
Authors: Amin Hasnat A. , Kaewsri Pimpika , Yiorkas Andrianos M. , Cooke Heather , Blakemore Alexandra I. , Drenos Fotios 
Published: January 2022

AbstractBreast (BCa) and prostate (PrCa) cancer are the first and second most common types of cancer in women and men, respectively. We aimed to explore the causal effect of adiposity on BCa and PrCa risk in the UK Biobank and published data. We used Mendelian randomisation (MR) to assess the causal effect of body mass index (BMI), body fat percentage (BFP), waist circumference (WC), hip circumference (HC), and waist-to-hip ratio (WHR) on BCa and PrCa risk. We found that increased BMI, WC and HC decreased the risk of breast cancer (OR 0.70 per 5.14 kg/m2 [0.59–0.85, p = 2.1 × 10–4], 0.76 per 12.49 cm [60–0.97, p = 0.028] and 0.73 per 10.31 cm [0.59–0.90, p = 3.7 × 10–3], respectively) and increased WC and BMI decreased the risk of prostate cancer (0.68 per 11.32 cm [0.50–0.91, p = 0.01] and 0.76 per 10.23 kg/m2 [0.61–0.95, p = 0.015], respectively) in UK Biobank participants. We confirmed our results with a two-sample-MR of published data. In conclusion, our results suggest a protective effect of adiposity on the risk of BCa and PrCa highlighting the need to re-evaluate the role of adiposity as cancer risk factor.
A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data
Authors: Li Ziyi , Feng Hao 
Published: January 2022

AbstractThe fast-advancing single cell RNA sequencing (scRNA-seq) technology enables researchers to study the transcriptome of heterogeneous tissues at a single cell level. The initial important step of analyzing scRNA-seq data is usually to accurately annotate cells. The traditional approach of annotating cell types based on unsupervised clustering and marker genes is time-consuming and laborious. Taking advantage of the numerous existing scRNA-seq databases, many supervised label assignment methods have been developed. One feature that many label assignment methods shares is to label cells with low confidence as “unassigned.” These unassigned cells can be the result of assignment difficulties due to highly similar cell types or caused by the presence of unknown cell types. However, when unknown cell types are not expected, existing methods still label a considerable number of cells as unassigned, which is not desirable. In this work, we develop a neural network-based cell annotation method called NeuCA (Neural network-based Cell Annotation) for scRNA-seq data obtained from well-studied tissues. NeuCA can utilize the hierarchical structure information of the cell types to improve the annotation accuracy, which is especially helpful when data contain closely correlated cell types. We show that NeuCA can achieve more accurate cell annotation results compared with existing methods. Additionally, the applications on eight real datasets show that NeuCA has stable performance for intra- and inter-study annotation, as well as cross-condition annotation. NeuCA is freely available as an R/Bioconductor package at https://bioconductor.org/packages/NeuCA.