bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep computational image analysis of immune cell niches reveals treatment-specific outcome associations in lung cancer
Authors: Barrera Cristian , Corredor Germán , Viswanathan Vidya Sankar , Ding Ruiwen , Toro Paula , Fu Pingfu , Buzzy Christina , Lu Cheng , Velu Priya , Zens Philipp , Berezowska Sabina , Belete Merzu , Balli David , Chang Han , Baxi Vipul , Syrigos Konstantinos , Rimm David L. , Velcheti Vamsidhar , Schalper Kurt , Romero Eduardo , Madabhushi Anant 
Published: June 2023

AbstractThe tumor immune composition influences prognosis and treatment sensitivity in lung cancer. The presence of effective adaptive immune responses is associated with increased clinical benefit after immune checkpoint blockers. Conversely, immunotherapy resistance can occur as a consequence of local T-cell exhaustion/dysfunction and upregulation of immunosuppressive signals and regulatory cells. Consequently, merely measuring the amount of tumor-infiltrating lymphocytes (TILs) may not accurately reflect the complexity of tumor-immune interactions and T-cell functional states and may not be valuable as a treatment-specific biomarker. In this work, we investigate an immune-related biomarker (PhenoTIL) and its value in associating with treatment-specific outcomes in non-small cell lung cancer (NSCLC). PhenoTIL is a novel computational pathology approach that uses machine learning to capture spatial interplay and infer functional features of immune cell niches associated with tumor rejection and patient outcomes. PhenoTIL’s advantage is the computational characterization of the tumor immune microenvironment extracted from H&E-stained preparations. Association with clinical outcome and major non-small cell lung cancer (NSCLC) histology variants was studied in baseline tumor specimens from 1,774 lung cancer patients treated with immunotherapy and/or chemotherapy, including the clinical trial Checkmate 057 (NCT01673867).
Abnormal thickness-dependent magneto-transport properties of vdW magnetic semiconductor Cr2Si2Te6
Authors: Li Yun , Chen Zheng , Wang Jie , li Teng , Tian Mingliang , Karel Julie , Suzuki Kiyonori 
Published: June 2023

AbstractCr2Si2Te6 (CST) is a van der Waals (vdW) ferromagnetic semiconductor. The unique spin model and temperature-dependent magnetic ordering of CST provide opportunities for the next generation of two-dimensional (2D) spintronic devices. Here, abnormal magneto-transport properties are found in CST nanoflakes with variations in thickness. Interestingly, the thickness-dependent magnetoresistance (MR) effect exhibits a nonlinear change as a function of the magnetic field, temperature, and thickness. At a certain temperature below Curie temperature (Tc), a sign reversal of MR ratio from positive to negative can even be detected with thickness reduction. At the temperature range from Tc to 60 K, the Hall effect also presents a transformation from nonlinear behavior in thick layer CST to linear behavior in thin layer CST. These distinctive magneto-transport properties are attributed to the variation of spin correlation with thickness in CST nanoflakes. These findings probe the unique magneto-transport properties of CST and associate it with ferromagnetic correlation, which provides a basis for subsequent spintronics device design based on this material. This work also offers new insights into the relationship between sample thickness, transport properties, and spin correlation of other vdW ferromagnets. It lays a foundation for future vdW magnet-based device fabrication and possible spintronic applications.
Production of recombinant human IgG1 Fc with beneficial N-glycosylation pattern for anti-inflammatory activity using genome-edited chickens
Authors: Park Jin Se , Choi Hee Jung , Jung Kyung Min , Lee Kyung Youn , Shim Ji Hyeon , Park Kyung Je , Kim Young Min , Han Jae Yong 
Published: June 2023

AbstractIntravenous immunoglobulin (IVIG) is a plasma-derived polyclonal IgG used for treatment of autoimmune diseases. Studies show that α-2,6 sialylation of the Fc improves anti-inflammatory activity. Also, afucosylation of the Fc efficiently blocks FcγRIIIA by increasing monovalent affinity to this receptor, which can be beneficial for treatment of refractory immune thrombocytopenia (ITP). Here, we generated genome-edited chickens that synthesize human IgG1 Fc in the liver and secrete α-2,6 sialylated and low-fucosylated human IgG1 Fc (rhIgG1 Fc) into serum and egg yolk. Also, rhIgG1 Fc has higher affinity for FcγRIIIA than commercial IVIG. Thus, rhIgG1 Fc efficiently inhibits immune complex-mediated FcγRIIIA crosslinking and subsequent ADCC response. Furthermore, rhIgG1 Fc exerts anti-inflammatory activity in a passive ITP model, demonstrating chicken liver derived rhIgG1 Fc successfully recapitulated efficacy of IVIG. These results show that genome-edited chickens can be used as a production platform for rhIgG1 Fc with beneficial N-glycosylation pattern for anti-inflammatory activities.
Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales
Authors: Hong Zhou , Peng Dan , Tembrock Luke R. , Liao Xuezhu , Xu Daping , Liu Xiaojin , Wu Zhiqiang 
Published: June 2023

AbstractSandalwood is one of the most expensive woods in the world and is well known for its long-lasting and distinctive aroma. In our study, chromosome-level genome assemblies for two sandalwood species (Santalum album and Santalumyasi) were constructed by integrating NGS short reads, RNA-seq, and Hi-C libraries with PacBio HiFi long reads. The S. album and S. yasi genomes were both assembled into 10 pseudochromosomes with a length of 229.59 Mb and 232.64 Mb, containing 21,673 and 22,816 predicted genes and a repeat content of 28.93% and 29.54% of the total genomes, respectively. Further analyses resolved a Santalum-specific whole-genome triplication event after divergence from ancestors of the Santalales lineage Malania, yet due to dramatic differences in transposon content, the Santalum genomes were only one-sixth the size of the Malania oleifera genome. Examination of RNA-seq data revealed a suite of genes that are differentially expressed in haustoria and might be involved in host hemiparasite interactions. The two genomes presented here not only provide an important comparative dataset for studying genome evolution in early diverging eudicots and hemiparasitic plants but will also hasten the application of conservation genomics for a lineage of trees recovering from decades of overexploitation.
Structure-inducing pre-training
Authors: McDermott Matthew B. A. , Yap Brendan , Szolovits Peter , Zitnik Marinka 
Published: June 2023

AbstractLanguage model pre-training and the derived general-purpose methods have reshaped machine learning research. However, there remains considerable uncertainty regarding why pre-training improves the performance of downstream tasks. This challenge is pronounced when using language model pre-training in domains outside of natural language. Here we investigate this problem by analysing how pre-training methods impose relational structure in induced per-sample latent spaces—that is, what constraints do pre-training methods impose on the distance or geometry between the pre-trained embeddings of samples. A comprehensive review of pre-training methods reveals that this question remains open, despite theoretical analyses showing the importance of understanding this form of induced structure. Based on this review, we introduce a pre-training framework that enables a granular and comprehensive understanding of how relational structure can be induced. We present a theoretical analysis of the framework from the first principles and establish a connection between the relational inductive bias of pre-training and fine-tuning performance. Empirical studies spanning three data modalities and ten fine-tuning tasks confirm theoretical analyses, inform the design of novel pre-training methods and establish consistent improvements over a compelling suite of methods.
Multi-scale mapping of Australia’s terrestrial and blue carbon stocks and their continental and bioregional drivers
Authors: Walden Lewis , Serrano Oscar , Zhang Mingxi , Shen Zefang , Sippo James Z. , Bennett Lauren T. , Maher Damien T. , Lovelock Catherine E. , Macreadie Peter I. , Gorham Connor , Lafratta Anna , Lavery Paul S. , Mosley Luke , Reithmaier Gloria M. S. , Kelleway Jeffrey J. , Dittmann Sabine , Adame Fernanda , Duarte Carlos M. , Gallagher John Barry , Waryszak Pawel , Carnell Paul , Kasel Sabine , Hinko-Najera Nina , Hassan Rakib , Goddard Madeline , Jones Alice R. , Viscarra Rossel Raphael A. 
Published: June 2023

AbstractThe soil in terrestrial and coastal blue carbon ecosystems is an important carbon sink. National carbon inventories require accurate assessments of soil carbon in these ecosystems to aid conservation, preservation, and nature-based climate change mitigation strategies. Here we harmonise measurements from Australia’s terrestrial and blue carbon ecosystems and apply multi-scale machine learning to derive spatially explicit estimates of soil carbon stocks and the environmental drivers of variation. We find that climate and vegetation are the primary drivers of variation at the continental scale, while ecosystem type, terrain, clay content, mineralogy and nutrients drive subregional variations. We estimate that in the top 0–30 cm soil layer, terrestrial ecosystems hold 27.6 Gt (19.6–39.0 Gt), and blue carbon ecosystems 0.35 Gt (0.20–0.62 Gt). Tall open eucalypt and mangrove forests have the largest soil carbon content by area, while eucalypt woodlands and hummock grasslands have the largest total carbon stock due to the vast areas they occupy. Our findings suggest these are essential ecosystems for conservation, preservation, emissions avoidance, and climate change mitigation because of the additional co-benefits they provide.
Past, present, and future of the Living Planet Index
Authors: Ledger Sophie E. H. , Loh Jonathan , Almond Rosamunde , Böhm Monika , Clements Christopher F. , Currie Jessica , Deinet Stefanie , Galewski Thomas , Grooten Monique , Jenkins Martin , Marconi Valentina , Painter Brett , Scott-Gatty Kate , Young Lucy , Hoffmann Michael , Freeman Robin , McRae Louise 
Published: June 2023

AbstractAs we enter the next phase of international policy commitments to halt biodiversity loss (e.g., Kunming-Montreal Global Biodiversity Framework), biodiversity indicators will play an important role in forming the robust basis upon which targeted, and time sensitive conservation actions are developed. Population trend indicators are one of the most powerful tools in biodiversity monitoring due to their responsiveness to changes over short timescales and their ability to aggregate species trends from global down to sub-national or even local scale. We consider how the project behind one of the foremost population level indicators - the Living Planet Index - has evolved over the last 25 years, its value to the field of biodiversity monitoring, and how its components have portrayed a compelling account of the changing status of global biodiversity through its application at policy, research and practice levels. We explore ways the project can develop to enhance our understanding of the state of biodiversity and share lessons learned to inform indicator development and mobilise action.
A large screen identifies beta-lactam antibiotics which can be repurposed to target the syphilis agent
Authors: Hayes Kathryn A. , Dressler Jules M. , Norris Steven J. , Edmondson Diane G. , Jutras Brandon L. 
Published: June 2023

AbstractSyphilis, caused by the spirocheteTreponema pallidumsubsp.pallidum(hereafter calledT. pallidum), is re-emerging as a worldwide sexually transmitted infection. A single intramuscular dose of benzathine penicillin G is the preferred syphilis treatment option. Both supply shortage concerns and the potential for acquired antibiotic resistance further the need to broaden the repertoire of syphilis therapeutics. We reasoned that other β-lactams may be equally or more effective at targeting the disease-causing agent,Treponema pallidum, but have yet to be discovered due to a previous lack of a continuous in vitro culture system. Recent technical advances with respect to in vitroT. pallidumpropagation allowed us to conduct a high-throughput screen of almost 100 β-lactams. Using several molecular and cellular approaches that we developed or adapted, we identified and confirmed the efficacy of several β-lactams that were similar to or outperformed the current standard, benzathine penicillin G. These options are either currently used to treat bacterial infections or are synthetic derivatives of naturally occurring compounds. Our studies not only identified additional potential therapeutics in the resolution of syphilis, but provide techniques to study the complex biology ofT. pallidum—a spirochete that has plagued human health for centuries.
Anchoring atomic antimony in an intercalative Mo–S frameworkviasoft covalent bonding for fast-charging and long-lived sodium ion batteries
Authors: Peng Baixin , Lv Zhuoran , Fang Yuqiang , Cai Tianxun , Shi Zhiyuan , Zhou Ce , Gao Yusha , Huang Fuqiang 
Published: June 2023

This work addresses the critical issue of volume expansion of alloy-type Sb anode by dispersing atomic Sb into a robust Mo–S framework via soft Mo–Sb bonds. 60C fast-charging over 10 000 cycles is achieved by utilizing this new Mo2SbS2 anode.
Lightweight image matting algorithm based on deep learning
Authors: Qin Xujia , Yang Guang , Shao Qin , Zheng Hongbo , Zhang Meiyu 
Published: June 2023

AbstractTo solve the problem that the deep learning‐based image matting algorithm cannot balance accuracy and model size, a lightweight image matting algorithm based on deep learning is proposed. Considering the limitation of memory and computing resources, and aiming at lightweight. We construct a network and gradually improved it. Firstly, apply deep detachable convolution to deep image matting networks to form faster and stronger encoder and decoder networks. The simultaneous use of depth‐separable convolution can also reduce the number of corresponding model parameters and computation. And then attention mechanism is integrated into the model and SE Block was used to assign different weights to feature channels to improve the accuracy of the model. Finally, knowledge distillation scheme is designed in part of the encoder‐decoder structure, the corresponding loss function is proposed, and the method of knowledge distillation is used to improve the feature learning ability of the lightweight neural network. Compared with the original deep image matting model, the number of parameters in the new model is greatly reduced without too much loss of accuracy.
A note on the minimum‐norm in dual space approach to some classical linear optimal control problems
Authors: Zhou Yue , Kachroo Pushkin , Ozbay Kaan 
Published: June 2023

AbstractSome classical optimal control problems of linear systems can be characterized as finding minimum‐norm vectors from within linear varieties in appropriate dual spaces. Then, the solution to such an optimal control problem can be derived from the alignment between the optimal vector in the dual space and the optimal vector in the primal space, and the dual maximization problem of the minimum‐norm problem. This note presents a detailed introduction to this minimum‐norm in dual space approach by examples of minimum‐supremum‐norm, minimum‐energy, and minimum‐time optimal control problems of linear systems. Connections and differences between these problems in light of the introduced approach are discussed.
ATLASGAL: 3 mm class I methanol masers in high-mass star formation regions
Authors: Yang W. , Gong Y. , Menten K. M. , Urquhart J. S. , Henkel C. , Wyrowski F. , Csengeri T. , Ellingsen S. P. , Bemis A. R. , Jang J. 
Published: June 2023

Context. Class I methanol masers are known to be associated with shocked outflow regions around massive protostars, indicating a possible link between the maser properties and those of their host clumps.
Aims. The main goals of this study are (1) to search for new class I methanol masers, (2) to statistically study the relationship between class I masers and shock tracers, (3) to compare the properties between class I masers and their host clumps, also as a function of their evolutionary stage, and (4) to constrain the physical conditions that excite multiple class I masers simultaneously.
Methods. We analysed the 3 mm wavelength spectral line survey of 408 clumps identified by the APEX Telescope Large Area Survey of the Galaxy (ATLASGAL), which were observed with the IRAM 30-meter telescope, focusing on the class I methanol masers with frequencies near 84, 95, and 104.3 GHz.
Results. We detect narrow maser-like features towards 54, 100, and 4 sources in the maser lines near 84, 95, and 104.3 GHz, respectively. Among them, 50 masers at 84 GHz, 29 masers at 95 GHz, and 4 rare masers at 104.3 GHz are new discoveries. The new detections increase the number of known 104.3 GHz masers from five to nine. The 95 GHz class I methanol maser is generally stronger than the 84 GHz maser counterpart. We find nine sources showing class I methanol masers, but no SiO emission, indicating that class I methanol masers might be the only signpost of protostellar outflow activity in extremely embedded objects at the earliest evolutionary stage. Class I methanol masers that are associated with sources that show SiO line wings are more numerous and stronger than those without such wings. The total integrated intensity of class I methanol masers is well correlated with the integrated intensity and velocity coverage of the SiO (2−1) emission. The properties of class I methanol masers are positively correlated with the bolometric luminosity, clump mass, and peak H2 column density of their associated clumps, but are uncorrelated with the luminosity-to-mass ratio, dust temperature, and mean H2 volume density.
Conclusions. We suggest that the properties of class I masers are related to shocks traced by SiO. Based on our observations, we conclude that class I methanol masers at 84 and 95 GHz can trace a similar evolutionary stage to the H2O maser, and appear prior to 6.7 and 12.2 GHz methanol and OH masers. Despite their small number, the 104.3 GHz class I masers appear to trace a shorter and more evolved stage compared to the other class I masers.
Therapieoptionen von primären Motilitätsstörungen des Ösophagus
Authors: Denzer Ulrike , Müller Michaela , Kreuser Nicole , Thieme René , Hoffmeister Albrecht , Feisthammel Juergen , Niebisch Stefan , Gockel Ines 
Published: June 2023

ZusammenfassungÖsophagusmotilitätsstörungen sind Erkrankungen, bei denen es aufgrund einer Veränderung der neuromuskulären Strukturen zu Fehlfunktionen des Schluckakts kommt. Das Leitsymptom ist daher die Dysphagie für feste und/oder flüssige Speisen, häufig begleitet von Symptomen wie Thoraxschmerz, Regurgitation, Sodbrennen, und Gewichtsverlust. Die Ösophagusmanometrie ist der Goldstandard in der Diagnostik. Endoskopie und Radiologie dienen dem Ausschluss entzündlicher oder maligner Veränderungen.Durch die Einführung der hochauflösenden Ösophagusmanometrie (HRM) hat sich die Diagnostik der Ösophagusmotilitätsstörungen verbessert und mit der Chicago-Klassifikation zu einer neuen Einteilung geführt, die im letzten Jahrzehnt mehrfach modifiziert wurde, zuletzt 2020 mit der Chicago-Klassifikation v4.0. Verglichen mit der Vorversion v3.0 finden sich einige wichtige Änderungen, die anhand der im klinischen Alltag wichtigsten Ösophagusmotilitätsstörungen vorgestellt werden.
Divergent Synthesis of Isochroman-4-ols, 1,3-Dihydroisobenzo­furans, and Tetrahydro-2H-indeno[2,1-b]furan-2-ones via Epoxidation/Cyclization Strategy of (E)-(2-Stilbenyl/Styrenyl)methanols
Authors: Ploypradith Poonsakdi , Jongcharoenkamol Jira , Jancharoen Kitsana , Batsomboon Paratchata , Ruchirawat Somsak 
Published: June 2023

AbstractStarting from (E)-(2-stilbenyl/styrenyl)methanols, two distinct scaffolds, namely isochroman-4-ols and 1,3-dihydroisobenzofurans (phthalans), could be synthesized via an epoxidation/cyclization strategy. Indenes, readily accessible from the same starting materials, could undergo epoxidation/ring-opening/cyclization to provide tetrahydro-2H-indeno[2,1-b]furan-2-ones. Stilbene/styrene/indene epoxidation by m-CPBA or DMDO converted the nucleophilic olefin into the electrophilic epoxide, which subsequently underwent the regioselective ring-opening either by the hydroxy or the ester group to furnish the corresponding products with stereocontrol at the newly formed stereogenic centers. The reaction proceeded under substrate control to yield each product type exclusively.
Perforator-Based Propeller Flap with Additional Venous Pedicle for Lower Limb Reconstruction
Authors: Mishra Jiten Kumar , Sahu Shamendra Anand , Bodhey Narendra Kuber , Sindhuja Abi , V. Abhijith 
Published: June 2023

AbstractPropeller flaps are effective reconstructive tools for small-to-medium sized defects of the lower limb and a reasonable alternative to free flaps. A major vessel of the lower limb remains undisturbed while raising the flap and the flap donor and recipient areas are addressed in the same operative field. Perforator-based propeller flaps are based on single perforator arising from a major vessel and during rotation of the larger paddle there is a possibility of kink in the venous component leading to congestion of flap. In our modification, one superficial vein of the lower limb namely the great saphenous or short saphenous vein was included in the flap territory to enhance the retrograde or antegrade venous drainage of the flap. We observed, no flap congestion or necrosis in the postoperative period. Also, the patency of the incorporated vein was confirmed using handheld and color Doppler.
PMM2-CDG T237M Mutation in a Patient with Cerebral Palsy-Like Phenotypes Reported from South India
Authors: Sreedevi N. , Swapna N. , Maruthy Santosh , Meghavathi H.S. , Sylvester Charles 
Published: June 2023

AbstractCongenital disorder of glycosylation (CDG) is an autosomal recessively inherited disorder. Hypotonia, stroke-like episodes, and peripheral neuropathy are also associated with the condition that typically develops during infancy. The patient, a 12-year-old girl born to healthy consanguineous parents, was diagnosed with cerebral palsy as a child. The affected patient has hypotonia, inadequate speech, strabismus, and developmental delay with mild mental retardation, which are key symptoms of CDG. Whole-exome sequencing (WES) identified the known missense pathogenic variant PMM2 c.710 C > T, p.T237M in the patient coding for the phosphomannomutase 2 (PMM2) confirming molecular testing of CDG. The patient's parents carried heterozygous PMM2 c.710 C > T variants. This study highlights the importance of WES in patients with a developmental disability or other neurological conditions, which is also useful in screening risk factors in couples with infertility or miscarriage issues.