bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phagocytosis of Plasmodium falciparum ring-stage parasites predicts protection against malaria
Authors: Musasia Fauzia K. , Nkumama Irene N. , Frank Roland , Kipkemboi Victor , Schneider Martin , Mwai Kennedy , Odera Dennis O. , Rosenkranz Micha , Fürle Kristin , Kimani Domitila , Tuju James , Njuguna Patricia , Hamaluba Mainga , Kapulu Melissa C. , Wardemann Hedda ,   CHMI-SIKA Study Team, Abdi Abdirahman I. , Abebe Yonas , Bejon Philip , Billingsley Peter F. , Bull Peter C. , de Laurent Zaydah , Hoffman Stephen L. , James Eric R. , Kariuki Silvia , Kimathi Rinter , Kinyanjui Sam , Kivisi Cheryl , Makale Johnstone , Marsh Kevin , Mohammed Khadija Said , Mosobo Moses , Musembi Janet , Musyoki Jennifer , Muthui Michelle , Mwacharo Jedidah , Ndungu Francis , Ngoi Joyce M. , Ngoto Omar , Ogutu Bernhards , Olewe Fredrick , Omuoyo Donwilliams , Ong’echa John , Otieno Edward , Shangala Jimmy , Sim Betty Kim Lee , Richie Thomas L. , Wambua Juliana , Williams Thomas N. , Osier Faith H. A. 
Published: July 2022

AbstractRing-infected erythrocytes are the predominant asexual stage in the peripheral circulation but are rarely investigated in the context of acquired immunity against Plasmodium falciparum malaria. Here we compare antibody-dependent phagocytosis of ring-infected parasite cultures in samples from a controlled human malaria infection (CHMI) study (NCT02739763). Protected volunteers did not develop clinical symptoms, maintained parasitaemia below a predefined threshold of 500 parasites/μl and were not treated until the end of the study. Antibody-dependent phagocytosis of both ring-infected and uninfected erythrocytes from parasite cultures was strongly correlated with protection. A surface proteomic analysis revealed the presence of merozoite proteins including erythrocyte binding antigen-175 and −140 on ring-infected and uninfected erythrocytes, providing an additional antibody-mediated protective mechanism for their activity beyond invasion-inhibition. Competition phagocytosis assays support the hypothesis that merozoite antigens are the key mediators of this functional activity. Targeting ring-stage parasites may contribute to the control of parasitaemia and prevention of clinical malaria.
HRS phosphorylation drives immunosuppressive exosome secretion and restricts CD8+ T-cell infiltration into tumors
Authors: Guan Lei , Wu Bin , Li Ting , Beer Lynn A. , Sharma Gaurav , Li Mingyue , Lee Chin Nien , Liu Shujing , Yang Changsong , Huang Lili , Frederick Dennie T. , Boland Genevieve M. , Shao Guangcan , Svitkina Tatyana M. , Cai Kathy Q. , Chen Fangping , Dong Meng-Qiu , Mills Gordon B. , Schuchter Lynn M. , Karakousis Giorgos C. , Mitchell Tara C. , Flaherty Keith T. , Speicher David W. , Chen Youhai H. , Herlyn Meenhard , Amaravadi Ravi K. , Xu Xiaowei , Guo Wei 
Published: July 2022

AbstractThe lack of tumor infiltration by CD8+ T cells is associated with poor patient response to anti-PD-1 therapy. Understanding how tumor infiltration is regulated is key to improving treatment efficacy. Here, we report that phosphorylation of HRS, a pivotal component of the ESCRT complex involved in exosome biogenesis, restricts tumor infiltration of cytolytic CD8+ T cells. Following ERK-mediated phosphorylation, HRS interacts with and mediates the selective loading of PD-L1 to exosomes, which inhibits the migration of CD8+ T cells into tumors. In tissue samples from patients with melanoma, CD8+ T cells are excluded from the regions where tumor cells contain high levels of phosphorylated HRS. In murine tumor models, overexpression of phosphorylated HRS increases resistance to anti-PD-1 treatment, whereas inhibition of HRS phosphorylation enhances treatment efficacy. Our study reveals a mechanism by which phosphorylation of HRS in tumor cells regulates anti-tumor immunity by inducing PD-L1+ immunosuppressive exosomes, and suggests HRS phosphorylation blockade as a potential strategy to improve the efficacy of cancer immunotherapy.
Sub-nanometer mapping of strain-induced band structure variations in planar nanowire core-shell heterostructures
Authors: Martí-Sánchez Sara , Botifoll Marc , Oksenberg Eitan , Koch Christian , Borja Carla , Spadaro Maria Chiara , Di Giulio Valerio , Ramasse Quentin , García de Abajo F. Javier , Joselevich Ernesto , Arbiol Jordi 
Published: July 2022

AbstractStrain relaxation mechanisms during epitaxial growth of core-shell nanostructures play a key role in determining their morphologies, crystal structure and properties. To unveil those mechanisms, we perform atomic-scale aberration-corrected scanning transmission electron microscopy studies on planar core-shell ZnSe@ZnTe nanowires on α-Al2O3 substrates. The core morphology affects the shell structure involving plane bending and the formation of low-angle polar boundaries. The origin of this phenomenon and its consequences on the electronic band structure are discussed. We further use monochromated valence electron energy-loss spectroscopy to obtain spatially resolved band-gap maps of the heterostructure with sub-nanometer spatial resolution. A decrease in band-gap energy at highly strained core-shell interfacial regions is found, along with a switch from direct to indirect band-gap. These findings represent an advance in the sub-nanometer-scale understanding of the interplay between structure and electronic properties associated with highly mismatched semiconductor heterostructures, especially with those related to the planar growth of heterostructured nanowire networks.
Electric-field control of nonlinear THz spintronic emitters
Authors: Agarwal Piyush , Huang Lisen , Ter Lim Sze , Singh Ranjan 
Published: July 2022

AbstractEnergy-efficient spintronic technology holds tremendous potential for the design of next-generation processors to operate at terahertz frequencies. Femtosecond photoexcitation of spintronic materials generates sub-picosecond spin currents and emission of terahertz radiation with broad bandwidth. However, terahertz spintronic emitters lack an active material platform for electric-field control. Here, we demonstrate a nonlinear electric-field control of terahertz spin current-based emitters using a single crystal piezoelectric Pb(Mg1/3Nb2/3)O3–PbTiO3 (PMN–PT) that endows artificial magnetoelectric coupling onto a spintronic terahertz emitter and provides 270% modulation of the terahertz field at remnant magnetization. The nonlinear electric-field control of the spins occurs due to the strain-induced change in magnetic energy of the ferromagnet thin-film. Results also reveal a robust and repeatable switching of the phase of the terahertz spin current. Electric-field control of terahertz spintronic emitters with multiferroics and strain engineering offers opportunities for the on-chip realization of tunable energy-efficient spintronic-photonic integrated platforms.
Adipocyte lysoplasmalogenase TMEM86A regulates plasmalogen homeostasis and protein kinase A-dependent energy metabolism
Authors: Cho Yoon Keun , Yoon Young Cheol , Im Hyeonyeong , Son Yeonho , Kim Minsu , Saha Abhirup , Choi Cheoljun , Lee Jaewon , Lee Sumin , Kim Jae Hyun , Kang Yun Pyo , Jung Young-Suk , Ha Hong Koo , Seong Je Kyung , Granneman James G. , Kwon Sung Won , Lee Yun-Hee 
Published: July 2022

AbstractDysregulation of adipose tissue plasmalogen metabolism is associated with obesity-related metabolic diseases. We report that feeding mice a high-fat diet reduces adipose tissue lysoplasmalogen levels and increases transmembrane protein 86 A (TMEM86A), a putative lysoplasmalogenase. Untargeted lipidomic analysis demonstrates that adipocyte-specific TMEM86A-knockout (AKO) increases lysoplasmalogen content in adipose tissue, including plasmenyl lysophosphatidylethanolamine 18:0 (LPE P-18:0). Surprisingly, TMEM86A AKO increases protein kinase A signalling pathways owing to inhibition of phosphodiesterase 3B and elevation of cyclic adenosine monophosphate. TMEM86A AKO upregulates mitochondrial oxidative metabolism, elevates energy expenditure, and protects mice from metabolic dysfunction induced by high-fat feeding. Importantly, the effects of TMEM86A AKO are largely reproduced in vitro and in vivo by LPE P-18:0 supplementation. LPE P-18:0 levels are significantly lower in adipose tissue of human patients with obesity, suggesting that TMEM86A inhibition or lysoplasmalogen supplementation might be therapeutic approaches for preventing or treating obesity-related metabolic diseases.
Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli
Authors: Gagarinova Alla , Hosseinnia Ali , Rahmatbakhsh Matineh , Istace Zoe , Phanse Sadhna , Moutaoufik Mohamed Taha , Zilocchi Mara , Zhang Qingzhou , Aoki Hiroyuki , Jessulat Matthew , Kim Sunyoung , Aly Khaled A. , Babu Mohan 
Published: July 2022

AbstractBacterial transcription factors (TFs) are widely studied inEscherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes inE. coliunder auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC,yneJ,ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization ofE. coliTFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits.
Ultraviolet supercontinuum generation driven by ionic coherence in a strong laser field
Authors: Lei Hongbin , Yao Jinping , Zhao Jing , Xie Hongqiang , Zhang Fangbo , Zhang He , Zhang Ning , Li Guihua , Zhang Qian , Wang Xiaowei , Yang Yan , Yuan Luqi , Cheng Ya , Zhao Zengxiu 
Published: July 2022

AbstractSupercontinuum (SC) light sources hold versatile applications in many fields ranging from imaging microscopic structural dynamics to achieving frequency comb metrology. Although such broadband light sources are readily accessible in the visible and near infrared regime, the ultraviolet (UV) extension of SC spectrum is still challenging. Here, we demonstrate that the joint contribution of strong field ionization and quantum resonance leads to the unexpected UV continuum radiation spanning the 100 nm bandwidth in molecular nitrogen ions. Quantum coherences in a bunch of ionic levels are found to be created by dynamic Stark-assisted multiphoton resonances following tunneling ionization. We show that the dynamical evolution of the coherence-enhanced polarization wave gives rise to laser-assisted continuum emission inside the laser field and free-induction decay after the laser field, which jointly contribute to the SC generation together with fifth harmonics. As proof of principle, we also show the application of the SC radiation in the absorption spectroscopy. This work offers an alternative scheme for constructing exotic SC sources, and opens up the territory of ionic quantum optics in the strong-field regime.
Rising ecosystem water demand exacerbates the lengthening of tropical dry seasons
Authors: Xu Hao , Lian Xu , Slette Ingrid J. , Yang Hui , Zhang Yuan , Chen Anping , Piao Shilong 
Published: July 2022

AbstractPrecipitation-based assessments show a lengthening of tropical dry seasons under climate change, without considering simultaneous changes in ecosystem water demand. Here, we compare changes in tropical dry season length and timing when dry season is defined as the period when precipitation is less than: its climatological average, potential evapotranspiration, or actual evapotranspiration. While all definitions show more widespread tropical drying than wetting for 1983-2016, we find the largest fraction (48.7%) of tropical land probably experiencing longer dry seasons when dry season is defined as the period when precipitation cannot meet the need of actual evapotranspiration. Southern Amazonia (due to delayed end) and central Africa (due to earlier onset and delayed end) are hotspots of dry season lengthening, with greater certainty when accounting for water demand changes. Therefore, it is necessary to account for changing water demand when characterizing changes in tropical dry periods and ecosystem water deficits.
Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries
Authors: Banday A. Rouf , Stanifer Megan L. , Florez-Vargas Oscar , Onabajo Olusegun O. , Papenberg Brenen W. , Zahoor Muhammad A. , Mirabello Lisa , Ring Timothy J. , Lee Chia-Han , Albert Paul S. , Andreakos Evangelos , Arons Evgeny , Barsh Greg , Biesecker Leslie G. , Boyle David L. , Brahier Mark S. , Burnett-Hartman Andrea , Carrington Mary , Chang Euijin , Choe Pyoeng Gyun , Chisholm Rex L. , Colli Leandro M. , Dalgard Clifton L. , Dude Carolynn M. , Edberg Jeff , Erdmann Nathan , Feigelson Heather S. , Fonseca Benedito A. , Firestein Gary S. , Gehring Adam J. , Guo Cuncai , Ho Michelle , Holland Steven , Hutchinson Amy A. , Im Hogune , Irby Les’Shon , Ison Michael G. , Joseph Naima T. , Kim Hong Bin , Kreitman Robert J. , Korf Bruce R. , Lipkin Steven M. , Mahgoub Siham M. , Mohammed Iman , Paschoalini Guilherme L. , Pacheco Jennifer A. , Peluso Michael J. , Rader Daniel J. , Redden David T. , Ritchie Marylyn D. , Rosenblum Brooke , Ross M. Elizabeth , Anna Hanaisa P. Sant , Savage Sharon A. , Sharma Sudha , Siouti Eleni , Smith Alicia K. , Triantafyllia Vasiliki , Vargas Joselin M. , Vargas Jose D. , Verma Anurag , Vij Vibha , Wesemann Duane R. , Yeager Meredith , Yu Xu , Zhang Yu , Boulant Steeve , Chanock Stephen J. , Feld Jordan J. , Prokunina-Olsson Ludmila 
Published: July 2022

AbstractThe chr12q24.13 locus encoding OAS1–OAS3 antiviral proteins has been associated with coronavirus disease 2019 (COVID-19) susceptibility. Here, we report genetic, functional and clinical insights into this locus in relation to COVID-19 severity. In our analysis of patients of European (n = 2,249) and African (n = 835) ancestries with hospitalized versus nonhospitalized COVID-19, the risk of hospitalized disease was associated with a common OAS1 haplotype, which was also associated with reduced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance in a clinical trial with pegIFN-λ1. Bioinformatic analyses and in vitro studies reveal the functional contribution of two associated OAS1 exonic variants comprising the risk haplotype. Derived human-specific alleles rs10774671-A and rs1131454-A decrease OAS1 protein abundance through allele-specific regulation of splicing and nonsense-mediated decay (NMD). We conclude that decreased OAS1 expression due to a common haplotype contributes to COVID-19 severity. Our results provide insight into molecular mechanisms through which early treatment with interferons could accelerate SARS-CoV-2 clearance and mitigate against severe COVID-19.
CRISPR–Cas12a-mediated DNA clamping triggers target-strand cleavage
Authors: Naqvi Mohsin M. , Lee Laura , Montaguth Oscar E. Torres , Diffin Fiona M. , Szczelkun Mark D. 
Published: July 2022

AbstractClustered regularly interspaced short palindromic repeats (CRISPR)–Cas12a is widely used for genome editing and diagnostics, so it is important to understand how RNA-guided DNA recognition activates the cleavage of the target strand (TS) following non-target-strand (NTS) cleavage. Here we used single-molecule magnetic tweezers, gel-based assays and nanopore sequencing to explore DNA unwinding and cleavage. In addition to dynamic and heterogenous R-loop formation, we also directly observed transient double-stranded DNA unwinding downstream of the 20-bp heteroduplex and, following NTS cleavage, formation of a hyperstable ‘clamped’ Cas12a–DNA intermediate necessary for TS cleavage. Annealing of a 4-nucleotide 3′ CRISPR RNA overhang to the unwound TS downstream of the heteroduplex inhibited clamping and slowed TS cleavage by ~16-fold. Alanine substitution of a conserved aromatic amino acid in the REC2 subdomain that normally caps the R-loop relieved this inhibition but favoured stabilisation of unwound states, suggesting that the REC2 subdomain regulates access of the 3′ CRISPR RNA to downstream DNA.
A europium metal–organic framework for dual Fe3+ ion and pH sensing
Authors: Rozenberga Linda , Skinner William , Lancaster David G. , Bloch Witold M. , Blencowe Anton , Krasowska M. , Beattie David A. 
Published: July 2022

AbstractMetal–organic frameworks (MOFs) with ratiometric sensing properties are desirable for many applications due to their intrinsic self-calibration. We report the re-assessment of the sensing properties of a MOF, originally reported as containing europium(III) and 2-hydroxyterephtalic acid, and having fluorescent ratiometric iron(III) sensing properties. Synchrotron single-crystal X-ray diffraction and proton nuclear magnetic resonance (1H NMR) spectroscopy revealed that the MOF is composed of 2-methoxyterephthalate, not 2-hydroxyterephthalate as originally reported. We found that the MOF exhibits a sensor turn-off response towards Fe3+ ion concentrations in the range 0.5–3.7 ppm (band 425 nm), and a turn-on response towards a decrease of pH from 5.4 to 3.0 (band 375 nm), both resulting from the addition of acidic Fe3+ salt solution to a MOF suspension. Thus, the ratiometric sensing properties and the originally proposed mechanism no longer apply; our work reveals a dynamic quenching mechanism for the fluorescence turn-off response due to the presence of Fe3+ ions, and a ligand protonation mechanism for the turn-on response to a decrease in pH. Our work highlights the importance of a thorough investigation of the structure of any newly synthesized MOF, and, in the case of potential sensors, their selectivity and any environmental effects on their sensing behavior.
Plant rarity in fire-prone dry sclerophyll communities
Authors: Sritharan Meena S. , Scheele Ben C. , Blanchard Wade , Foster Claire N. , Werner Patricia A. , Lindenmayer David B. 
Published: July 2022

AbstractUnderstanding the responses of rare species to altered fire disturbance regimes is an ongoing challenge for ecologists. We asked: are there associations between fire regimes and plant rarity across different vegetation communities? We combined 62 years of fire history records with vegetation surveys of 86 sites across three different dry sclerophyll vegetation communities in Booderee National Park, south-east Australia to: (1) compare associations between species richness and rare species richness with fire regimes, (2) test whether fire regimes influence the proportion of rare species present in an assemblage, and (3) examine whether rare species are associated with particular fire response traits and life history. We also sought to determine if different rarity categorisations influence the associations between fire regimes and plant rarity. We categorised plant rarity using three standard definitions; species' abundance, species' distribution, and Rabinowitz's measure of rarity, which considers a species' abundance, distribution and habitat specificity. We found that total species richness was negatively associated with short fire intervals but positively associated with time since fire and fire frequency in woodland communities. Total species richness was also positively associated with short fire intervals in forest communities. However, rare species richness was not associated with fire when categorised via abundance or distribution. Using Rabinowitz's measure of rarity, the proportion of rare species present was negatively associated with fire frequency in forest communities but positively associated with fire frequency in woodland communities. We found that rare species classified by all three measures of rarity exhibited no difference in fire response traits and serotiny compared to species not classified as rare. Rare species based on abundance differed to species not classified as rare across each life history category, while species rare by distribution differed in preferences for seed storage location. Our findings suggest that species categorised as rare by Rabinowitz's definition of rarity are the most sensitive to the effects of fire regimes. Nevertheless, the paucity of responses observed between rare species with fire regimes in a fire-prone ecosystem suggests that other biotic drivers may play a greater role in influencing the rarity of a species in this system.
Effectiveness of controlling COVID-19 epidemic by implementing soft lockdown policy and extensive community screening in Taiwan
Authors: Chan Ta-Chien , Chou Ching-Chi , Chu Yi-Chi , Tang Jia-Hong , Chen Li-Chi , Lin Hsien-Ho , Chen Kevin J. , Chen Ran-Chou 
Published: July 2022

AbstractStrict and repeated lockdowns have caused public fatigue regarding policy compliance and had a large impact on several countries’ economies. We aimed to evaluate the effectiveness of a soft lockdown policy and the strategy of active community screening for controlling COVID-19 in Taiwan. We used village-based daily confirmed COVID-19 statistics in Taipei City and New Taipei City, between May 2, 2021, and July 17, 2021. The temporal Gi* statistic was used to compute the spatiotemporal hotspots. Simple linear regression was used to evaluate the trend of the epidemic, positivity rate from community screening, and mobility changes in COVID-19 cases and incidence before and after a level three alert in both cities. We used a Bayesian hierarchical zero-inflated Poisson model to estimate the daily infection risk. The cities accounted for 11,403 (81.17%) of 14,048 locally confirmed cases. The mean effective reproduction number (Re) surged before the level three alert and peaked on May 16, 2021, the day after the level three alert in Taipei City (Re = 3.66) and New Taipei City (Re = 3.37). Mobility reduction and a lower positive rate were positively associated with a lower number of cases and incidence. In the spatiotemporal view, seven major districts were identified with a radial spreading pattern from one hard-hit district. Villages with a higher inflow degree centrality among people aged ≥ 60 years, having confirmed cases, specific land-use types, and with a higher aging index had higher infection risks than other villages. Early soft lockdown policy and detection of infected patients showed an effective strategy to control COVID-19 in Taiwan.
Broadband metasurface superstrate for polarization-independent wave focusing and gain enhancement at Ka-band
Authors: Lee Kanghyeok , Hong Ha Young , Lee Wonwoo , Jo Semin , Park Hong Soo , Yang Junhyuk , Park Changkun , Lee Hojin , Hong Sun K. 
Published: July 2022

AbstractA broadband metasurface flat lens is proposed as a polarization-independent wideband superstrate for wave focusing and gain enhancement at Ka-band. The proposed metasurface structure consists of four metal layers and is designed with diagonally symmetric unit cells to accommodate both the vertical and horizontal polarizations. The focusing ability of the proposed metasurface flat lens is validated via simulation and measurement, where normally incident plane waves are shown to be enhanced by up to 11 dB as a result of wave focusing. Also, the radiation gain enhancement due to the proposed metasurface flat lens is demonstrated via simulation and measurement, where a gain enhancement of up to 10.5 dB is achieved. The results show that the proposed structure maintains the wave focusing and gain enhancement characteristics over a bandwidth of 28–32 GHz. Furthermore, to demonstrate the utility of the proposed metasurface for circular polarization (CP), the gain enhancement of a CP patch antenna as a result of implementing the proposed metasurface as a superstrate is demonstrated via simulation and measurement. It is shown that the proposed metasurface superstrate provides a CP gain enhancement of nearly 10 dB.