bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decay and renormalization of a longitudinal mode in a quasi-two-dimensional antiferromagnet
Authors: Do Seung-Hwan , Zhang Hao , Williams Travis J. , Hong Tao , Garlea V. Ovidiu , Rodriguez-Rivera J. A. , Jang Tae-Hwan , Cheong Sang-Wook , Park Jae-Hoon , Batista Cristian D. , Christianson Andrew D. 
Published: September 2021

AbstractAn ongoing challenge in the study of quantum materials, is to reveal and explain collective quantum effects in spin systems where interactions between different modes types are important. Here we approach this problem through a combined experimental and theoretical study of interacting transverse and longitudinal modes in an easy-plane quantum magnet near a continuous quantum phase transition. Our inelastic neutron scattering measurements of Ba2FeSi2O7 reveal the emergence, decay, and renormalization of a longitudinal mode throughout the Brillouin zone. The decay of the longitudinal mode is particularly pronounced at the zone center. To account for the many-body effects of the interacting low-energy modes in anisotropic magnets, we generalize the standard spin-wave theory. The measured mode decay and renormalization is reproduced by including all one-loop corrections. The theoretical framework developed here is broadly applicable to quantum magnets with more than one type of low energy mode.
Aridity-driven shift in biodiversity–soil multifunctionality relationships
Authors: Hu Weigang , Ran Jinzhi , Dong Longwei , Du Qiajun , Ji Mingfei , Yao Shuran , Sun Yuan , Gong Chunmei , Hou Qingqing , Gong Haiyang , Chen Renfei , Lu Jingli , Xie Shubin , Wang Zhiqiang , Huang Heng , Li Xiaowei , Xiong Junlan , Xia Rui , Wei Maohong , Zhao Dongmin , Zhang Yahui , Li Jinhui , Yang Huixia , Wang Xiaoting , Deng Yan , Sun Ying , Li Hailing , Zhang Liang , Chu Qipeng , Li Xinwei , Aqeel Muhammad , Manan Abdul , Akram Muhammad Adnan , Liu Xianghan , Li Rui , Li Fan , Hou Chen , Liu Jianquan , He Jin-Sheng , An Lizhe , Bardgett Richard D. , Schmid Bernhard , Deng Jianming 
Published: September 2021

AbstractRelationships between biodiversity and multiple ecosystem functions (that is, ecosystem multifunctionality) are context-dependent. Both plant and soil microbial diversity have been reported to regulate ecosystem multifunctionality, but how their relative importance varies along environmental gradients remains poorly understood. Here, we relate plant and microbial diversity to soil multifunctionality across 130 dryland sites along a 4,000 km aridity gradient in northern China. Our results show a strong positive association between plant species richness and soil multifunctionality in less arid regions, whereas microbial diversity, in particular of fungi, is positively associated with multifunctionality in more arid regions. This shift in the relationships between plant or microbial diversity and soil multifunctionality occur at an aridity level of ∼0.8, the boundary between semiarid and arid climates, which is predicted to advance geographically ∼28% by the end of the current century. Our study highlights that biodiversity loss of plants and soil microorganisms may have especially strong consequences under low and high aridity conditions, respectively, which calls for climate-specific biodiversity conservation strategies to mitigate the effects of aridification.
Field-tunable toroidal moment in a chiral-lattice magnet
Authors: Ding Lei , Xu Xianghan , Jeschke Harald O. , Bai Xiaojian , Feng Erxi , Alemayehu Admasu Solomon , Kim Jaewook , Huang Fei-Ting , Zhang Qiang , Ding Xiaxin , Harrison Neil , Zapf Vivien , Khomskii Daniel , Mazin Igor I. , Cheong Sang-Wook , Cao Huibo 
Published: September 2021

AbstractFerrotoroidal order, which represents a spontaneous arrangement of toroidal moments, has recently been found in a few linear magnetoelectric materials. However, tuning toroidal moments in these materials is challenging. Here, we report switching between ferritoroidal and ferrotoroidal phases by a small magnetic field, in a chiral triangular-lattice magnet BaCoSiO4 with tri-spin vortices. Upon applying a magnetic field, we observe multi-stair metamagnetic transitions, characterized by equidistant steps in the net magnetic and toroidal moments. This highly unusual ferri-ferroic order appears to come as a result of an unusual hierarchy of frustrated isotropic exchange couplings revealed by first principle calculations, and the antisymmetric exchange interactions driven by the structural chirality. In contrast to the previously known toroidal materials identified via a linear magnetoelectric effect, BaCoSiO4 is a qualitatively new multiferroic with an unusual coupling between several different orders, and opens up new avenues for realizing easily tunable toroidal orders.
Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling
Authors: van der Stel Anne-Xander , Gordon Emily R. , Sengupta Arnab , Martínez Allyson K. , Klepacki Dorota , Perry Thomas N. , Herrero del Valle Alba , Vázquez-Laslop Nora , Sachs Matthew S. , Cruz-Vera Luis R. , Innis C. Axel 
Published: September 2021

AbstractFree L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC–ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.
Treatment of skeletal and non-skeletal alterations of Mucopolysaccharidosis type IVA by AAV-mediated gene therapy
Authors: Bertolin Joan , Sánchez Víctor , Ribera Albert , Jaén Maria Luisa , Garcia Miquel , Pujol Anna , Sánchez Xavier , Muñoz Sergio , Marcó Sara , Pérez Jennifer , Elias Gemma , León Xavier , Roca Carles , Jimenez Veronica , Otaegui Pedro , Mulero Francisca , Navarro Marc , Ruberte Jesús , Bosch Fatima 
Published: September 2021

AbstractMucopolysaccharidosis type IVA (MPSIVA) or Morquio A disease, a lysosomal storage disorder, is caused byN-acetylgalactosamine-6-sulfate sulfatase (GALNS) deficiency, resulting in keratan sulfate (KS) and chondroitin-6-sulfate accumulation. Patients develop severe skeletal dysplasia, early cartilage deterioration and life-threatening heart and tracheal complications. There is no cure and enzyme replacement therapy cannot correct skeletal abnormalities. Here, using CRISPR/Cas9 technology, we generate the first MPSIVA rat model recapitulating all skeletal and non-skeletal alterations experienced by patients. Treatment of MPSIVA rats with adeno-associated viral vector serotype 9 encodingGalns(AAV9-Galns) results in widespread transduction of bones, cartilage and peripheral tissues. This led to long-term (1 year) increase of GALNS activity and whole-body correction of KS levels, thus preventing body size reduction and severe alterations of bones, teeth, joints, trachea and heart. This study demonstrates the potential of AAV9-Galnsgene therapy to correct the disabling MPSIVA pathology, providing strong rationale for future clinical translation to MPSIVA patients.
Fractionalized conductivity and emergent self-duality near topological phase transitions
Authors: Wang Yan-Cheng , Cheng Meng , Witczak-Krempa William , Meng Zi Yang 
Published: September 2021

AbstractThe experimental discovery of the fractional Hall conductivity in two-dimensional electron gases revealed new types of quantum particles, called anyons, which are beyond bosons and fermions as they possess fractionalized exchange statistics. These anyons are usually studied deep inside an insulating topological phase. It is natural to ask whether such fractionalization can be detected more broadly, say near a phase transition from a conventional to a topological phase. To answer this question, we study a strongly correlated quantum phase transition between a topological state, called a $${{\mathbb{Z}}}_{2}$$

Z

2

quantum spin liquid, and a conventional superfluid using large-scale quantum Monte Carlo simulations. Our results show that the universal conductivity at the quantum critical point becomes a simple fraction of its value at the conventional insulator-to-superfluid transition. Moreover, a dynamically self-dual optical conductivity emerges at low temperatures above the transition point, indicating the presence of the elusive vison particles. Our study opens the door for the experimental detection of anyons in a broader regime, and has ramifications in the study of quantum materials, programmable quantum simulators, and ultra-cold atomic gases. In the latter case, we discuss the feasibility of measurements in optical lattices using current techniques.
Saliva-derived microcosm biofilms grown on different oral surfaces in vitro
Authors: Li Xiaolan , Shang Lin , Brandt Bernd W. , Buijs Mark J. , Roffel Sanne , van Loveren Cor , Crielaard Wim , Gibbs Susan , Deng Dong Mei 
Published: September 2021

AbstractThe microbial composition of a specific oral niche could be influenced by initial bacterial adherence, nutrient and physiological property of the local surface. To investigate the influence of nutrient and surface properties on microbial composition, saliva-derived biofilms were grown in agar on three substrata: Reconstructed Human Gingiva (RHG), a hydroxyapatite (HAP) surface, and a titanium (TI) surface. Agar was mixed with either Brain Heart Infusion (BHI) or Thompson (TP) medium. After 1, 3, or 5 days, biofilm viability (by colony forming units) and microbiome profiles (by 16 S rDNA amplicon sequencing) were determined. On RHG, biofilm viability and composition were similar between BHI and TP. However, on the abiotic substrata, biofilm properties greatly depended on the type of medium and substratum. In BHI, the viability of HAP-biofilm first decreased and then increased, whereas that of TI-biofilm decreased in time until a 6-log reduction. In TP, either no or a 2-log reduction in viability was observed for HAP- or TI-biofilms respectively. Furthermore, different bacterial genera (or higher level) were differentially abundant in the biofilms on 3 substrata: Haemophilus and Porphyromonas for RHG; Bacilli for HAP and Prevotella for TI. In conclusion, RHG, the biotic substratum, is able to support a highly viable and diverse microbiome. In contrast, the viability and diversity of the biofilms on the abiotic substrata were influenced by the substrata type, pH of the environment and the richness of the growth media. These results suggest that the host (oral mucosa) plays a vital role in the oral ecology.
Interim clinical trial analysis of intraoperative mass spectrometry for breast cancer surgery
Authors: Basu Sankha S. , Stopka Sylwia A. , Abdelmoula Walid M. , Randall Elizabeth C. , Gimenez-Cassina Lopez Begoña , Regan Michael S. , Calligaris David , Lu Fake F. , Norton Isaiah , Mallory Melissa A. , Santagata Sandro , Dillon Deborah A. , Golshan Mehra , Agar Nathalie Y. R. 
Published: September 2021

AbstractOptimal resection of breast tumors requires removing cancer with a rim of normal tissue while preserving uninvolved regions of the breast. Surgical and pathological techniques that permit rapid molecular characterization of tissue could facilitate such resections. Mass spectrometry (MS) is increasingly used in the research setting to detect and classify tumors and has the potential to detect cancer at surgical margins. Here, we describe the ex vivo intraoperative clinical application of MS using a liquid micro-junction surface sample probe (LMJ-SSP) to assess breast cancer margins. In a midpoint analysis of a registered clinical trial, surgical specimens from 21 women with treatment naïve invasive breast cancer were prospectively collected and analyzed at the time of surgery with subsequent histopathological determination. Normal and tumor breast specimens from the lumpectomy resected by the surgeon were smeared onto glass slides for rapid analysis. Lipidomic profiles were acquired from these specimens using LMJ-SSP MS in negative ionization mode within the operating suite and post-surgery analysis of the data revealed five candidate ions separating tumor from healthy tissue in this limited dataset. More data is required before considering the ions as candidate markers. Here, we present an application of ambient MS within the operating room to analyze breast cancer tissue and surgical margins. Lessons learned from these initial promising studies are being used to further evaluate the five candidate biomarkers and to further refine and optimize intraoperative MS as a tool for surgical guidance in breast cancer.
Multimodal liquid biopsy for early monitoring and outcome prediction of chemotherapy in metastatic breast cancer
Authors: Bortolini Silveira Amanda , Bidard François-Clément , Tanguy Marie-Laure , Girard Elodie , Trédan Olivier , Dubot Coraline , Jacot William , Goncalves Anthony , Debled Marc , Levy Christelle , Ferrero Jean-Marc , Jouannaud Christelle , Rios Maria , Mouret-Reynier Marie-Ange , Dalenc Florence , Hego Caroline , Rampanou Aurore , Albaud Benoit , Baulande Sylvain , Berger Frédérique , Lemonnier Jérôme , Renault Shufang , Desmoulins Isabelle , Proudhon Charlotte , Pierga Jean-Yves 
Published: September 2021

AbstractCirculating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are two cancer-derived blood biomarkers that inform on patient prognosis and treatment efficacy in breast cancer. We prospectively evaluated the clinical validity of quantifying both CTCs (CellSearch) and ctDNA (targeted next-generation sequencing). Their combined value as prognostic and early monitoring markers was assessed in 198 HER2-negative metastatic breast cancer patients. All patients were included in the prospective multicenter UCBG study COMET (NCT01745757) and treated by first-line chemotherapy with weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline and before the second cycle of chemotherapy. At baseline, CTCs and ctDNA were respectively detected in 72 and 74% of patients and were moderately correlated (Kendall’s τ = 0.3). Only 26 (13%) patients had neither detectable ctDNA nor CTCs. Variants were most frequently observed in TP53 and PIK3CA genes. KMT2C/MLL3 variants detected in ctDNA were significantly associated with a lower CTC count, while the opposite trend was seen with GATA3 alterations. Both CTC and ctDNA levels at baseline and after four weeks of treatment were correlated with survival. For progression-free and overall survival, the best multivariate prognostic model included tumor subtype (triple negative vs other), grade (grade 3 vs other), ctDNA variant allele frequency (VAF) at baseline (per 10% increase), and CTC count at four weeks (≥5CTC/7.5 mL). Overall, this study demonstrates that CTCs and ctDNA have nonoverlapping detection profiles and complementary prognostic values in metastatic breast cancer patients. A comprehensive liquid-biopsy approach may involve simultaneous detection of ctDNA and CTCs.
Proteomics-derived basal biomarker DNA-PKcs is associated with intrinsic subtype and long-term clinical outcomes in breast cancer
Authors: Asleh Karama , Riaz Nazia , Cheng Angela S. , Gao Dongxia , Leung Samuel C. Y. , Anurag Meenakshi , Nielsen Torsten O. 
Published: September 2021

AbstractPrecise biomarkers are needed to guide better diagnostics and therapeutics for basal-like breast cancer, for which DNA-dependent protein kinase catalytic subunit (DNA-PKcs) has been recently reported by the Clinical Proteomic Tumor Analysis Consortium as the most specific biomarker. We evaluated DNA-PKcs expression in clinically-annotated breast cancer tissue microarrays and correlated results with immune biomarkers (training set:n = 300; validation set:n = 2401). Following a pre-specified study design per REMARK criteria, we found that high expression of DNA-PKcs was significantly associated with stromal and CD8 + tumor infiltrating lymphocytes. Within the basal-like subtype, tumors with low DNA-PKcs and high tumor-infiltrating lymphocytes displayed the most favourable survival. DNA-PKcs expression by immunohistochemistry identified estrogen receptor-positive cases with a basal-like gene expression subtype. Non-silent mutations inPRKDCwere significantly associated with poor outcomes. Integrating DNA-PKcs expression with validated immune biomarkers could guide patient selection for DNA-PKcs targeting strategies, DNA-damaging agents, and their combination with an immune-checkpoint blockade.
Plasma-assisted multiscale topographic scaffolds for soft and hard tissue regeneration
Authors: Kim Woochan , Gwon Yonghyun , Kim Yang-Kyung , Park Sunho , Kang Sung-Ju , Park Hyeng-Kyu , Kim Myung-Sun , Kim Jangho 
Published: September 2021

AbstractThe design of transplantable scaffolds for tissue regeneration requires gaining precise control of topographical properties. Here, we propose a methodology to fabricate hierarchical multiscale scaffolds with controlled hydrophilic and hydrophobic properties by employing capillary force lithography in combination with plasma modification. Using our method, we fabricated biodegradable biomaterial (i.e., polycaprolactone (PCL))-based nitrogen gas (N-FN) and oxygen gas plasma-assisted flexible multiscale nanotopographic (O-FMN) patches with natural extracellular matrix-like hierarchical structures along with flexible and controlled hydrophilic properties. In response to multiscale nanotopographic and chemically modified surface cues, the proliferation and osteogenic mineralization of cells were significantly promoted. Furthermore, the O-FMN patch enhanced regeneration of the mineralized fibrocartilage tissue of the tendon–bone interface and the calvarial bone tissue in vivo in rat models. Overall, the PCL-based O-FMN patches could accelerate soft- and hard-tissue regeneration. Thus, our proposed methodology was confirmed as an efficient approach for the design and manipulation of scaffolds having a multiscale topography with controlled hydrophilic property.
Immobilization of active ammonia-oxidizing archaea in hydrogel beads
Authors: Landreau Matthieu , You HeeJun , Stahl David A. , Winkler Mari K. H. 
Published: September 2021

AbstractAmmonia-oxidizing archaea (AOA) are major players in the nitrogen cycle but their cultivation represents a major challenge due to their slow growth rate and limited tendency to form biofilms. In this study, AOA was embedded in small (~2.5 mm) and large (~4.7 mm) poly(vinyl alcohol) (PVA)—sodium alginate (SA) hydrogel beads cross-linked with four agents (calcium, barium, light, or sulfate) to compare the differences in activity, the diffusivity of nitrogen species (NH4+, NO2−, and NO3−), and polymer leakage in batch systems over time. Sulfate-bound PVA-SA beads were the most stable, releasing the lowest amount of polymer without shrinking. Diffusion coefficients were found to be 2 to 3 times higher in hydrogels than in granules, with ammonium diffusivity being ca. 35% greater than nitrite and nitrate. Despite a longer lag phase in small beads, embedded AOA sustained a high per volume rate of ammonia oxidation compatible with applications in research and wastewater treatment.
Prognostic role of Ki-67 in glioblastomas excluding contribution from non-neoplastic cells
Authors: Dahlrot Rikke H. , Bangsø Julie A. , Petersen Jeanette K. , Rosager Ann Mari , Sørensen Mia D. , Reifenberger Guido , Hansen Steinbjørn , Kristensen Bjarne W. 
Published: September 2021

AbstractSurvival of glioblastoma patients varies and prognostic markers are important in the clinical setting. With digital pathology and improved immunohistochemical multiplexing becoming a part of daily diagnostics, we investigated the prognostic value of the Ki-67 labelling index (LI) in glioblastomas more precisely than previously by excluding proliferation in non-tumor cells from the analysis. We investigated the Ki-67 LI in a well-annotated population-based glioblastoma patient cohort (178 IDH-wildtype, 3 IDH-mutated). Ki-67 was identified in full tumor sections with automated digital image analysis and the contribution from non-tumor cells was excluded using quantitative double-immunohistochemistry. For comparison of the Ki-67 LI between WHO grades (II-IV), 9 IDH-mutated diffuse astrocytomas and 9 IDH-mutated anaplastic astrocytomas were stained. Median Ki-67 LI increased with increasing WHO grade (median 2.7%, 6.4% and 27.5%). There was no difference in median Ki-67 LI between IDH-mutated and IDH-wildtype glioblastomas (p = 0.9) and Ki-67 LI was not associated with survival in glioblastomas in neither univariate (p = 0.9) nor multivariate analysis including MGMT promoter methylation status and excluding IDH-mutated glioblastomas (p = 0.2). Ki-67 may be of value in the differential diagnostic setting, but it must not be over-interpreted in the clinico-pathological context.
Impact of overlapping risks of type 2 diabetes and obesity on coronavirus disease severity in the United States
Authors: Ando Wataru , Horii Takeshi , Uematsu Takayuki , Hanaki Hideaki , Atsuda Koichiro , Otori Katsuya 
Published: September 2021

AbstractThe impact of overlapping risk factors on coronavirus disease (COVID-19) severity is unclear. To evaluate the impact of type 2 diabetes (T2D) and obesity on COVID-19 severity, we conducted a cohort study with 28,095 anonymized COVID-19 patients using data from the COVID-19 Research Database from January 1, 2020 to November 30, 2020. The mean age was 50.8 ± 17.5 years, and 11,802 (42%) patients were male. Data on age, race, sex, T2D complications, antidiabetic medication prescription, and body mass index ≥ 30 kg/m2 (obesity) were analysed using Cox proportional hazard models, with hospitalization risk and critical care within 30 days of COVID-19 diagnosis as the main outcomes. The risk scores were 0–4 for age ≥ 65 years, male sex, T2D, and obesity. Among the participants, 11,294 (61.9%) had obesity, and 4445 (15.8%) had T2D. T2D, obesity, and male sex were significantly associated with COVID-19 hospitalization risk. Regarding hospitalization risk scores, compared with those for hospitalization risk score 0 and critical care risk score 0, hazard ratios [95% confidence intervals] were 19.034 [10.470–34.600] and 55.803 [12.761–244.015] (P < 0.001) (P < 0.001), respectively, for risk score 4. Complications from diabetes and obesity increased hospitalization and critical care risks for COVID-19 patients.