bluuebunny/crossref_metadata_2025_split huggingface dataset:
Momentum space toroidal moment in a photonic metamaterial
Authors: Yang Biao , Bi Yangang , Zhang Rui-Xing , Zhang Ruo-Yang , You Oubo , Zhu Zhihong , Feng Jing , Sun Hongbo , Chan C. T. , Liu Chao-Xing , Zhang Shuang 
Published: March 2021

AbstractBerry curvature, the counterpart of the magnetic field in the momentum space, plays a vital role in the transport of electrons in condensed matter physics. It also lays the foundation for the emerging field of topological physics. In the three-dimensional systems, much attention has been paid to Weyl points, which serve as sources and drains of Berry curvature. Here, we demonstrate a toroidal moment of Berry curvature with flux approaching toπin judiciously engineered metamaterials. The Berry curvature exhibits a vortex-like configuration without any source and drain in the momentum space. Experimentally, the presence of Berry curvature toroid is confirmed by the observation of conical-frustum shaped domain-wall states at the interfaces formed by two metamaterials with opposite toroidal moments.
Prosocial and antisocial choices in a monogamous cichlid with biparental care
Authors: Satoh Shun , Bshary Redouan , Shibasaki Momoko , Inaba Seishiro , Sogawa Shumpei , Hotta Takashi , Awata Satoshi , Kohda Masanori 
Published: March 2021

AbstractHuman society is cooperative and characterized by spontaneous prosociality. Comparative studies on endotherm vertebrates suggest that social interdependence causes the evolution of proactive prosociality. To test the generality of this hypothesis, we modify a prosocial choice task for application to the convict cichlid,Amatitlania nigrofasciata, a monogamous fish with biparental care and a strong pair bond. We also affirm that male subjects learn to favor prosocial choices when their mates are the recipients in a neighboring tank. When the neighboring tank is empty, males choose randomly. Furthermore, in the absence of their mates, males behave prosocially toward a stranger female. However, if the mate of the subjects is also visible in the third tank, or if a male is a potential recipient, then subjects make antisocial choices. To conclude, fish may show both spontaneous prosocial and antisocial behaviors according to their social relationships with conspecifics and the overall social context.
R-loop resolution promotes co-transcriptional chromatin silencing
Authors: Xu Congyao , Wu Zhe , Duan Hong-Chao , Fang Xiaofeng , Jia Guifang , Dean Caroline 
Published: March 2021

AbstractRNA-mediated chromatin silencing is central to genome regulation in many organisms. However, how nascent non-coding transcripts regulate chromatin is poorly understood. Here, through analysis of Arabidopsis FLC, we show that resolution of a nascent-transcript-induced R-loop promotes chromatin silencing. Stabilization of an antisense-induced R-loop at the 3′ end of FLC enables an RNA binding protein FCA, with its direct partner FY/WDR33 and other 3′-end processing factors, to polyadenylate the nascent antisense transcript. This clears the R-loop and recruits the chromatin modifiers demethylating H3K4me1. FCA immunoprecipitates with components of the m6A writer complex, and m6A modification affects dynamics of FCA nuclear condensates, and promotes FLC chromatin silencing. This mechanism also targets other loci in the Arabidopsis genome, and consistent with this fca and fy are hypersensitive to a DNA damage-inducing drug. These results show how modulation of R-loop stability by co-transcriptional RNA processing can trigger chromatin silencing.
Dysregulation of mitochondria-lysosome contacts by GBA1 dysfunction in dopaminergic neuronal models of Parkinson’s disease
Authors: Kim Soojin , Wong Yvette C. , Gao Fanding , Krainc Dimitri 
Published: March 2021

AbstractMitochondria-lysosome contacts are recently identified sites for mediating crosstalk between both organelles, but their role in normal and diseased human neurons remains unknown. In this study, we demonstrate that mitochondria-lysosome contacts can dynamically form in the soma, axons, and dendrites of human neurons, allowing for their bidirectional crosstalk. Parkinson’s disease patient derived neurons harboring mutant GBA1 exhibited prolonged mitochondria-lysosome contacts due to defective modulation of the untethering protein TBC1D15, which mediates Rab7 GTP hydrolysis for contact untethering. This dysregulation was due to decreased GBA1 (β-glucocerebrosidase (GCase)) lysosomal enzyme activity in patient derived neurons, and could be rescued by increasing enzyme activity with a GCase modulator. These defects resulted in disrupted mitochondrial distribution and function, and could be further rescued by TBC1D15 in Parkinson’s patient derived GBA1-linked neurons. Together, our work demonstrates a potential role of mitochondria-lysosome contacts as an upstream regulator of mitochondrial function and dynamics in midbrain dopaminergic neurons in GBA1-linked Parkinson’s disease.
Asymmetric three-component olefin dicarbofunctionalization enabled by photoredox and copper dual catalysis
Authors: Wang Peng-Zi , Gao Yuan , Chen Jun , Huan Xiao-Die , Xiao Wen-Jing , Chen Jia-Rong 
Published: March 2021

AbstractThe intermolecular three-component alkene vicinal dicarbofunctionalization (DCF) reaction allows installation of two different carbon fragments. Despite extensive investigation into its ionic chemistry, the enantioseletive radical-mediated versions of DCF reactions remain largely unexplored. Herein, we report an intermolecular, enantioselective three-component radical vicinal dicarbofunctionalization reaction of olefins enabled by merger of radical addition and cross-coupling using photoredox and copper dual catalysis. Key to the success of this protocol relies on chemoselective addition of acyl and cyanoalkyl radicals, generated in situ from the redox-active oxime esters by a photocatalytic N-centered iminyl radical-triggered C-C bond cleavage event, onto the alkenes to form new carbon radicals. Single electron metalation of such newly formed carbon radicals to TMSCN-derived L1Cu(II)(CN)2 complex leads to asymmetric cross-coupling. This three-component process proceeds under mild conditions, and tolerates a diverse range of functionalities and synthetic handles, leading to valuable optically active β–cyano ketones and alkyldinitriles, respectively, in a highly enantioselective manner (>60 examples, up to 97% ee).
Breast adipocyte size associates with ipsilateral invasive breast cancer risk after ductal carcinoma in situ
Authors: Almekinders Mathilde M. M. , Schaapveld Michael , Thijssen Bram , Visser Lindy L. , Bismeijer Tycho , Sanders Joyce , Isnaldi Edoardo , Hofland Ingrid , Mertz Marjolijn , Wessels Lodewyk F. A. , Broeks Annegien , Hooijberg Erik , Zwart Wilbert , Lips Esther H. ,   Grand Challenge PRECISION Consortium, Desmedt Christine , Wesseling Jelle 
Published: March 2021

AbstractAlthough ductal carcinoma in situ (DCIS) is a non-obligate precursor to ipsilateral invasive breast cancer (iIBC), most DCIS lesions remain indolent. Hence, overdiagnosis and overtreatment of DCIS is a major concern. There is an urgent need for prognostic markers that can distinguish harmless from potentially hazardous DCIS. We hypothesised that features of the breast adipose tissue may be associated with risk of subsequent iIBC. We performed a case–control study nested in a population-based DCIS cohort, consisting of 2658 women diagnosed with primary DCIS between 1989 and 2005, uniformly treated with breast conserving surgery (BCS) alone. We assessed breast adipose features with digital pathology (HALO®, Indica Labs) and related these to iIBC risk in 108 women that developed subsequent iIBC (cases) and 168 women who did not (controls) by conditional logistic regression, accounting for clinicopathological and immunohistochemistry variables. Large breast adipocyte size was significantly associated with iIBC risk (odds ratio (OR) 2.75, 95% confidence interval (95% CI) = 1.25–6.05). High cyclooxygenase (COX)-2 protein expression in the DCIS cells was also associated with subsequent iIBC (OR 3.70 (95% CI = 1.59–8.64). DCIS with both high COX-2 expression and large breast adipocytes was associated with a 12-fold higher risk (OR 12.0, 95% CI = 3.10–46.3, P < 0.001) for subsequent iIBC compared with women with smaller adipocyte size and low COX-2 expression. Large breast adipocytes combined with high COX-2 expression in DCIS is associated with a high risk of subsequent iIBC. Besides COX-2, adipocyte size has the potential to improve clinical management in patients diagnosed with primary DCIS.
The obesity paradox in early and advanced HER2 positive breast cancer: pooled analysis of clinical trial data
Authors: Modi Natansh D. , Tan Jin Quan Eugene , Rowland Andrew , Koczwara Bogda , Abuhelwa Ahmad Y. , Kichenadasse Ganessan , McKinnon Ross A. , Wiese Michael D. , Sorich Michael J. , Hopkins Ashley M. 
Published: March 2021

AbstractWhile many studies have evaluated the relationship between BMI and breast cancer outcomes, it is unclear whether this relationship is consistent between early breast cancer (BC) and advanced BC. The study included 5099 patients with HER2 positive early BC (EBC) and 3496 with HER2 positive advanced BC (ABC). In the EBC cohort, higher BMI was associated with worse overall survival (OS) (HR [95% CI]: overweight = 1.30 [1.13–1.51]; obese = 1.37 [1.14–1.64], P = < 0.001), and worse disease-free survival (overweight = 1.10 [0.98–1.24]; obese = 1.20 [1.04–1.39], P = 0.061). In contrast, for the ABC cohort, higher BMI was significantly associated with improved OS (overweight = 0.85 [0.76–0.96]; obese = 0.82 [0.72–0.95], P = 0.014), and progression-free survival (overweight = 0.91 [0.83–1.01]; obese = 0.87 [0.77–0.98], P = 0.034). In this large high-quality dataset, higher BMI was independently associated with worse survival in EBC, paradoxically in ABC higher BMI was independently associated with improved survival.
A multiscale polymerization framework towards network structure and fracture of double-network hydrogels
Authors: Zhang Mingzhen , Zhang Dong , Chen Hong , Zhang Yanxian , Liu Yonglan , Ren Baiping , Zheng Jie 
Published: March 2021

AbstractDouble-network (DN) hydrogels, consisting of two contrasting and interpenetrating polymer networks, are considered as perhaps the toughest soft-wet materials. Current knowledge of DN gels from synthesis methods to toughening mechanisms almost exclusively comes from chemically-linked DN hydrogels by experiments. Molecular modeling and simulations of inhomogeneous DN structure in hydrogels have proved to be extremely challenging. Herein, we developed a new multiscale simulation platform to computationally investigate the early fracture of physically-chemically linked agar/polyacrylamide (agar/PAM) DN hydrogels at a long timescale. A “random walk reactive polymerization” (RWRP) was developed to mimic a radical polymerization process, which enables to construct a physically-chemically linked agar/PAM DN hydrogel from monomers, while conventional and steered MD simulations were conducted to examine the structural-dependent energy dissipation and fracture behaviors at the relax and deformation states. Collective simulation results revealed that energy dissipation of agar/PAM hydrogels was attributed to a combination of the pulling out of agar chains from the DNs, the disruption of massive hydrogen bonds between and within DN structures, and the strong association of water molecules with both networks, thus explaining a different mechanical enhancement of agar/PAM hydrogels. This computational work provided atomic details of network structure, dynamics, solvation, and interactions of a hybrid DN hydrogel, and a different structural-dependent energy dissipation mode and fracture behavior of a hybrid DN hydrogel, which help to design tough hydrogels with new network structures and efficient energy dissipation modes. Additionally, the RWRP algorithm can be generally applied to construct the radical polymerization-produced hydrogels, elastomers, and polymers.
Microbial interactions with silicate glasses
Authors: Weaver Jamie L. , DePriest Paula T. , Plymale Andrew E. , Pearce Carolyn I. , Arey Bruce , Koestler Robert J. 
Published: March 2021

AbstractGlass alteration in the presence of microorganisms has been a topic of research for over 150 years. Researchers from a variety of disciplines, including material science, biology, chemistry, geology, physics, and cultural heritage materials preservation have conducted experiments in this area to try and understand when, how, and why microorganism may interact and subsequently influence the alteration of glass. The breadth and depth of these studies are the topic of this review. This review presents a detailed history and a comprehensive overview of this field of research, while maintaining focus on the terrestrial alteration of anthropogenic silicate glasses. Within this manuscript is a schema for bio-interaction with silicate glasses and an outline of an evidence-based hypothesis on how these interactions may influence glass alteration processes. Topics discussed include microbial colonization of glass, development, and interactions of biofilms with glass surface, abiotic vs. biotic alteration processes, and signatures of bio-alteration. Future research needs and a discussion of practical drivers for this research are summarized.
A low-cost, low-density, and corrosion resistant AlFeMnSi compositionally complex alloy
Authors: O’Brien S. P. , Christudasjustus J. , Esteves L. , Vijayan S. , Jinschek J. R. , Birbilis N. , Gupta R. K. 
Published: March 2021

AbstractA compositionally complex alloy was designed, consisting of equiatomic concentrations of four low-cost commodity elements (Al, Fe, Mn, and Si). The alloy was characterized using scanning electron microscopy and energy-dispersive X-ray spectroscopy. The corrosion of the AlFeMnSi alloy, as evaluated using potentiodynamic polarization tests and electrochemical impedance spectroscopy in 0.6 M NaCl solution, was comparable with that of stainless steel (SS) 304L. Detailed X-ray photoelectron spectroscopy analysis was carried out, including the determination of high-resolution spectra and surface sputtering. In addition, scanning transmission electron microscopy was also used to study the surface film(s) developed after constant immersion. The AlFeMnSi alloy exhibited a unique form of ‘passivity’ that arises from the development of a silicon-rich surface film from dynamic incongruent dissolution.
Clinical characteristics and factors associated with triple therapy use in newly diagnosed patients with COPD
Authors: Monteagudo Mònica , Barrecheguren Miriam , Solntseva Iryna , Dhalwani Nafeesa , Booth Alison , Nuñez Alexa , Lambrelli Dimitra , Miravitlles Marc 
Published: March 2021

AbstractThere is limited information about the initiation of triple therapy (TT) in patients with chronic obstructive pulmonary disease (COPD) in primary care. This was an observational, population-based study in patients identified from a primary care electronic medical records database in Catalonia from 2011 to 2015 aimed to identify the use of TT in patients with newly diagnosed COPD. A total of 69,668 newly diagnosed patients were identified of whom 11,524 (16.5%) initiated TT, of whom 8626 initiated TT at or immediately after COPD diagnosis. Among them, 72.3% were GOLD A/B, 14.6% were frequent exacerbators, and 7.1% had asthma–COPD overlap (ACO). Variables associated with TT initiation were: male sex, older age, previous exacerbations, ACO, a previous treatment regimen containing an inhaled corticosteroid, previous pneumonia, and history of lung cancer. A significant number of COPD patients in Primary Care initiated TT shortly after or even before an established COPD diagnosis.
Contributions of lipopolysaccharide and the type IVB secretion system to Coxiella burnetii vaccine efficacy and reactogenicity
Authors: Long Carrie M. , Beare Paul A. , Cockrell Diane C. , Fintzi Jonathan , Tesfamariam Mahelat , Shaia Carl I. , Heinzen Robert A. 
Published: March 2021

AbstractCoxiella burnetiiis the bacterial causative agent of the zoonosis Q fever. The current human Q fever vaccine, Q-VAX®, is a fixed, whole cell vaccine (WCV) licensed solely for use in Australia.C. burnetiiWCV administration is associated with a dermal hypersensitivity reaction in people with pre-existing immunity toC. burnetii, limiting wider use. Consequently, a less reactogenic vaccine is needed. Here, we investigated contributions of theC. burnetiiDot/Icm type IVB secretion system (T4BSS) and lipopolysaccharide (LPS) in protection and reactogenicity of fixed WCVs. A 32.5 kb region containing 23dot/icmgenes was deleted in the virulent Nine Mile phase I (NMI) strain and the resulting mutant was evaluated in guinea pig models ofC. burnetiiinfection, vaccination-challenge, and post-vaccination hypersensitivity. The NMI ∆dot/icmstrain was avirulent, protective as a WCV against a robustC. burnetiichallenge, and displayed potentially altered reactogenicity compared to NMI. Nine Mile phase II (NMII) strains ofC. burnetiithat produce rough LPS, were similarly tested. NMI was significantly more protective than NMII as a WCV; however, both vaccines exhibited similar reactogenicity. Collectively, our results indicate that, like phase I LPS, the T4BSS is required for full virulence byC. burnetii. Conversely, unlike phase I LPS, the T4BSS is not required for vaccine-induced protection. LPS length does not appear to contribute to reactogenicity while the T4BSS may contribute to this response. NMI ∆dot/icmrepresents an avirulent phase I strain with full vaccine efficacy, illustrating the potential of genetically modifiedC. burnetiias improved WCVs.
Human endogenous retrovirus-enveloped baculoviral DNA vaccines against MERS-CoV and SARS-CoV2
Authors: Cho Hansam , Jang Yuyeon , Park Ki-Hoon , Choi Hanul , Nowakowska Aleksandra , Lee Hee-Jung , Kim Minjee , Kang Min-Hee , Kim Jin-Hoi , Shin Ha Youn , Oh Yu-Kyoung , Kim Young Bong 
Published: March 2021

AbstractHere we report a recombinant baculoviral vector-based DNA vaccine system against Middle East respiratory syndrome coronavirus (MERS-CoV) and the severe acute respiratory syndrome coronavirus-2 (SARS-CoV2). A non-replicating recombinant baculovirus expressing the human endogenous retrovirus envelope gene (AcHERV) was constructed as a DNA vaccine vector for gene delivery into human cells. For MERS-CoV vaccine construction, DNA encoding MERS-CoV S-full, S1 subunit, or receptor-binding domain (RBD) was inserted into the genome of AcHERV. For COVID19 vaccine construction, DNA encoding SARS-CoV2 S-full or S1 or a MERS-CoV NTD domain-fused SARS-CoV2 RBD was inserted into the genome of AcHERV. AcHERV-DNA vaccines induce high humoral and cell-mediated immunity in animal models. In challenge tests, twice immunized AcHERV-MERS-S1 and AcHERV-COVID19-S showed complete protection against MERS-CoV and SARS-CoV2, respectively. Unlike AcHERV-MERS vaccines, AcHERV-COVID19-S provided the greatest protection against SARS-CoV2 challenge. These results support the feasibility of AcHERV-MERS or AcHERV-COVID19 vaccines in preventing pandemic spreads of viral infections.
High turbidity levels alter coral reef fish movement in a foraging task
Authors: Newport Cait , Padget Oliver , de Perera Theresa Burt 
Published: March 2021

AbstractSensory systems allow animals to detect and respond to stimuli in their environment and underlie all behaviour. However, human induced pollution is increasingly interfering with the functioning of these systems. Increased suspended sediment, or turbidity, in aquatic habitats reduces the reactive distance to visual signals and may therefore alter movement behaviour. Using a foraging task in which fish (Rhinecanthus aculeatus) had to find six food sites in an aquarium, we tested the impact of high turbidity (40–68 NTU; 154 mg/L) on foraging efficiency using a detailed and novel analysis of individual movements. High turbidity led to a significant decrease in task efficacy as fish took longer to begin searching and find food, and they travelled further whilst searching. Trajectory analyses revealed that routes were less efficient and that fish in high turbidity conditions were more likely to cover the same ground and search at a slower speed. These results were observed despite the experimental protocol allowing for the use of alternate sensory systems (e.g. olfaction, lateral line). Given that movement underlies fundamental behaviours including foraging, mating, and predator avoidance, a reduction in movement efficiency is likely to have a significant impact on the health and population dynamics of visually-guided fish species.
Discovering environmental management opportunities for infectious disease control
Authors: Beltrame Ludovica , Rose Vineer Hannah , Walker Josephine G. , Morgan Eric R. , Vickerman Peter , Wagener Thorsten 
Published: March 2021

AbstractClimate change and emerging drug resistance make the control of many infectious diseases increasingly challenging and diminish the exclusive reliance on drug treatment as sole solution to the problem. As disease transmission often depends on environmental conditions that can be modified, such modifications may become crucial to risk reduction if we can assess their potential benefit at policy-relevant scales. However, so far, the value of environmental management for this purpose has received little attention. Here, using the parasitic disease of fasciolosis in livestock in the UK as a case study, we demonstrate how mechanistic hydro-epidemiological modelling can be applied to understand disease risk drivers and the efficacy of environmental management across a large heterogeneous domain. Our results show how weather and other environmental characteristics interact to define disease transmission potential and reveal that environmental interventions such as risk avoidance management strategies can provide a valuable alternative or complement to current treatment-based control practice.
Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma
Authors: Roberts Hannah E. , Lopopolo Maria , Pagnamenta Alistair T. , Sharma Eshita , Parkes Duncan , Lonie Lorne , Freeman Colin , Knight Samantha J. L. , Lunter Gerton , Dreau Helene , Lockstone Helen , Taylor Jenny C. , Schuh Anna , Bowden Rory , Buck David 
Published: March 2021

AbstractRecent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from specific chromosomes of the long-read data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialised joint calling algorithms. We find the comparative genome-wide performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6 Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans.