bluuebunny/crossref_metadata_2025 huggingface dataset:
Bipedal locomotion in zoo apes: Revisiting the hylobatian model for bipedal origins
Authors: Rosen Kyle H. , Jones Caroline E. , DeSilva Jeremy M.
Published: March 2022

Bipedal locomotion is a hallmark of being human. Yet the body form from which bipedalism evolved remains unclear. Specifically, the positional behaviour (i.e. orthograde vs. pronograde) and the length of the lumbar spine (i.e. long and mobile vs. short and stiff) of the last common ancestor (LCA) of the African great apes and humans require further investigation. While fossil evidence would be the most conclusive, the paucity of hominid fossils from 5–10 million years ago makes this field of research challenging. In their absence, extant primate anatomy and behaviour may offer some insight into the ancestral body form from which bipedalism could most easily evolve. Here, we quantify the frequency of bipedalism in a large sample (N =496) of zoo-housed hominoids and cercopithecines. Our results show that while each studied species of ape and monkey can move bipedally, hylobatids are significantly more bipedal and engage in bipedal locomotion more frequently and for greater distances than any other primate sampled. These data support hypotheses of an orthograde, long-backed and arboreal LCA, which is consistent with hominoid fossils from the middle-to-late Miocene. If true, knuckle-walking evolved in parallel inPanandGorilla, and the human body form, particularly the long lower back and orthograde posture, is conserved.
Modelling entrainment volume due to surface-parallel vortex interactions with an air–water interface
Authors: Hendrickson Kelli , Yu Xiangming , Yue Dick K.P.
Published: March 2022

We consider the entrainment volume that results from the quasi-two-dimensional interactions of rising surface-parallel vorticity with an air–water interface. Based on systematic (three-dimensional) direct numerical simulations (DNS) of the canonical problem of a rectilinear vortex pair impinging on and entraining air at the free surface, we develop a phenomenological model to predict the resulting entrainment volume in terms of four key parameters. We identify a new parameter, a circulation flux Froude number $Fr^2_\Xi =|\varGamma |W/a^2\,g$, that predicts the dimensionless volume $\forall$ of entrained air initiated by a coherent vortical structure of circulation $\varGamma$, effective radius $a$, vertical rise velocity $W$ with gravity $g$. For $Fr^2_\Xi$ below some critical value $Fr^2_{\Xi cr}$, no air is entrained. For $Fr^2_\Xi >Fr^2_{\Xi cr}$, the average initial entrainment $\overline {\forall }_o$ scales linearly with ($Fr^2_\Xi -Fr^2_{\Xi cr}$). We also find that $\overline {\forall }_o$ is linearly dependent on circulation Weber number $We_{\varGamma }$ for a range of vortex Bond number $5 \lesssim Bo_{\varGamma } \lesssim 50$, and parabolically dependent on circulation Reynolds $Re_{\varGamma }$ for $Re_{\varGamma }\lesssim 2580$. Outside of these ranges, surface tension and viscosity have little effect on the initial entrainment volume. For the canonical rectilinear vortex problem, the simple model predicts $\overline {\forall }_o$ extremely well for individual coherent structures over broad ranges of $Fr^2_\Xi$, $We_{\varGamma }$, $Bo_{\varGamma }$ and $Re_{\varGamma }$. We evaluate the performance of this parameterisation and phenomenological entrainment model for air entrainment due to the complex periodic vortex shedding and quasi-steady wave breaking behind a fully submerged horizontal circular cylinder. For the range of parameters we consider, the phenomenological model predicts the event-by-event dimensionless entrainment volume measured in the DNS satisfactorily for this complex application.
Dynamic stall at high Reynolds numbers induced by ramp-type pitching motions
Authors: Kiefer Janik , Brunner Claudia E. , Hansen Martin O.L. , Hultmark Marcus
Published: March 2022

The transient pressure field around a moderately thick airfoil is studied as it undergoes ramp-type pitching motions at high Reynolds numbers and low Mach numbers. A unique set of laboratory experiments were performed in a high-pressure wind tunnel to investigate dynamic stall at chord Reynolds numbers in the range of $0.5\times 10^6\leq Re _c\leq 5.5\times 10^6$ in the absence of compressibility effects. In addition to variations of mean angle and amplitude, pitching manoeuvres at reduced frequencies in the range of $0.01\leq k\leq 0.40$ were studied by means of surface-pressure measurements. Independently of the parameter variations, all test cases exhibit a nearly identical stall behaviour characterized by a gradual trailing-edge stall, in which the dynamic stall vortex forms approximately at mid-chord. The location of the pitching window with respect to the Reynolds-number-dependent static stall angle is found to define the temporal development of the stall process. The time until stall onset is characterized by a power law, where a small excess of the static stall angle results in a drastically prolonged stall delay. The reduced frequency exhibits a decrease in impact on the stall development in the case of angle-limited pitching manoeuvres. Beyond a critical reduced frequency, both load magnitudes and vortex evolution become reduced frequency independent and instead depend on the geometry of the motion and the convective time scale, respectively. Overall, the characteristics of vortex evolution induced by dynamic stall show remarkable similarities to the framework of optimal vortex formation reported in Gharib et al. (J. Fluid Mech., vol. 360, 1998, pp. 121–140). The data from this study are publicly available at https://doi.org/10.34770/b3vq-sw14.
A GENERALIZED CANTOR THEOREM IN
Authors: PENG YINHE , SHEN GUOZHEN
Published: March 2022

It is proved in
$\mathsf {ZF}$
(without the axiom of choice) that, for all infinite sets M, there are no surjections from
$\omega \times M$
onto
$\operatorname {\mathrm {\mathscr {P}}}(M)$
.
TRIPHIODORUS’ SACK OF TROY AND THE POETICS OF CASSANDRA
Authors: Tsakiris Manos
Published: March 2022

This article explores Triphiodorus’ use of Cassandra in his brief epic Sack of Troy. An examination of the placing of the prophetess within the poem's plot and a comparison with previous literary attestations demonstrate that Triphiodorus makes extended use of the previously supplementary character. The reader is particularly invited to read Cassandra against the Cassandras of Euripides’ Trojan Women and Quintus Smyrnaeus’ Posthomerica, thus identifying ties with both epic and tragedy. Cassandra's speech alludes to the proem of the epic. At the same time, Cassandra's prophecy constitutes the key for understanding the connection between imagery deployed prior and subsequent to her presence, thus ensuring the thematic congruity of the poem. Triphiodorus’ Cassandra constitutes a doublet of the poet, depicted as imitating his poetic voice and effectively summarizing the entire epic in her speech; entwined in Triphiodorus’ poetic agenda, she also becomes its intradiegetic mouthpiece.
Protesting Precarity: South Korean Workers and the Labor of Refusal
Authors: Chun Jennifer Jihye
Published: March 2022

This essay examines the crisis of solidarity affecting workers who protest labor precarity under South Korea's capitalist democracy. Once considered foundational to the struggle for national democratization, the dramatic protests of aggrieved workers are frequently depicted as out of place and out of sync. Drawing upon ethnographic research on workers’ protest repertoires, this essay challenges prevailing explanations and instead argues that heightened forms of drama, ritual, and suffering in workers’ protests enact a willful politics of refusal. Moving beyond resistance as an all-encompassing frame, the labor of refusal foregrounds ways of being and becoming that are not rooted in the contractual fallacies of liberal capitalist democracy, but in the spaces of solidarity produced by social movement networks and grassroots communities of care. The labor of refusal may not always generate robust solidarity, but it challenges the structures of organized abandonment that treat workers as disposable under neoliberal capitalist rule.
Patient outcomes following thyroid surgery for thyrotoxicosis
Authors: Selwyn D , How-Hong E , Tan H , England R J
Published: March 2022

Objective

Total thyroidectomy can be used as a definitive treatment modality for thyrotoxicosis. This study assessed the outcomes of patients treated with surgery at a single secondary care site.

Method

A retrospective cohort study was conducted analysing consecutive patients who underwent thyroid surgery for thyrotoxicosis between 24 November 2000 and 26 April 2019 (n = 595).

Results

Total thyroidectomy was performed in 95.4 per cent of patients. Two-thirds of patients had Graves’ disease histology. Of patients, 22.8 per cent became transiently hypothyroid whilst on levothyroxine (thyroid hormone replacement therapy). Transient and persistent hypocalcaemia was present in 23.3 per cent and 2.8 per cent of patients respectively. Recurrent laryngeal nerve palsy was transient and persistent in 3.6 per cent and 0.3 per cent respectively. Of patients, 2.5 per cent developed post-operative haematomas that required surgical evacuation in the operating theatre.

Conclusion

The overall complication rate for thyroid surgery is higher in thyrotoxic than in euthyroid patients. Compared to other treatment modalities, total thyroidectomy appears to be the most effective, definitive means of managing Graves’ disease.
The foreign language effect on altruistic decision making: Insights from the framing effect
Authors: Liu Cong , Wang Han , Timmer Kalinka , Jiao Lu
Published: March 2022

The present study investigated the foreign language effect within an altruistic decision making process. Chinese–English bilinguals made altruistic decisions in their native (L1: Chinese) and second language (L2: English). The decisions were framed in two ways: either as “not to harm” (harm frame) or as “to help” the other person (help frame) at one's economic cost. Behavioral results suggest that bilinguals might behave more altruistically in the harm frame than the help frame (i.e., framing effect) in their native language but not in their foreign language. Electrophysiological results show that the modulation of the framing effect in the native versus foreign language originated in the early ERP components (N1 and N2) and did not present in the late positive potential (LPP). These findings suggest the foreign language effect most likely results from the reduced emotional reaction in a foreign compared to the native language.
A Physical Interpretation of Asymmetric Growth and Decay of the Geomagnetic Dipole Moment
Authors: Buffett B. A. , Avery M. S. , Davis W.
Published: March 2022

Observations of relative paleointensity reveal several forms of asymmetry in the time dependence of the virtual axial dipole moment (VADM). Slow decline of the VADM into a reversal is often followed by a more rapid rise back to a quasi‐steady state. Asymmetry is also observed in trends of VADM during times of stable polarity. Trends of increasing VADM over time intervals of a few 10s of kyr are more intense and less frequent than decreasing trends. We examine the origin of this behavior using stochastic models. The usual (Langevin) model can account for asymmetries during reversals, but it cannot reproduce the observed asymmetry in trends during stable polarity. Better agreement is achieved with a different class of stochastic models in which the dipole is generated by a series of impulsive events in time. The timing of each event occurs randomly as a Poisson process and the amplitude is also randomly distributed. Predicted trends replicate the observed asymmetry when the generation events are large and the recurrence time is long (typically longer than 3 kyr). Large and infrequent generation events argue against dipole generation by small‐scale turbulent flow. Instead, the observations favor a mechanism that relies on expulsion of poloidal magnetic field from the core.
Overturning Instabilities Across a Warm Core Ring From Glider Observations
Authors: Pérez J. G. C. , Pallàs‐Sanz E. , Tenreiro M. , Meunier T. , Jouanno J. , Ruiz‐Angulo A.
Published: March 2022

This work presents new evidence for conducive conditions for the existence of overturning instabilities in the mixed layer across a mesoscale anticyclonic Loop Current Eddy (LCE) and surrounding cyclonic eddies in the Gulf of Mexico (GoM). The LCE was intensively sampled using four gliders during 12 months. The LCE is characterized by a strong anomaly of fresh and warm water in the center and strong strain at the periphery. Mixed layers prone to overturning instabilities are diagnosed from the gradients of buoyancy. In the GoM, the reduction of potential vorticity (PV) in the mixed layer is driven by surface cooling by year‐round persistent negative turbulent heat fluxes, eventually reaching −700 W m−2 during extreme winter wind events. Lateral buoyancy gradients associated with submesoscale filaments and fronts at the periphery of the LCE enhance the frictional torque supplied by the wind stress when aligned with the geostrophic jet current. Negative PV in the mixed layer occurs simultaneously with negative turbulent heat fluxes and events of Ekman buoyancy fluxes that reduce the stratification. These regions are susceptible to mixed‐layer gravitational‐symmetric instability preferentially in winter. Extreme Ekman equivalent heat flux (≤−10,000 W m−2) associated with wind stress of 1.2 N m−2 coincides with the development of inertial‐symmetric instability across anticyclonic vorticity. These observations might have several implications for the restratification processes, kinetic energy budget, and biogeochemical cycles inside LCEs and can contribute to the formation of low‐PV waters that could feed mode water formation inside the GoM.
Locally Modified Winds Regulate Circulation in a Semi‐Enclosed Shelf Sea
Authors: Akpınar Anıl , Palmer Matthew R. , Inall Mark , Berx Barbara , Polton Jeff
Published: March 2022

Wind driven circulation in the North Sea is revisited with a specific focus on locally modified winds and their impacts. We show for the first time that local extrema of the wind stress curl (WSC), generated by orography and ocean‐atmosphere interactions, help regulate circulation in the northern North Sea. While calculated transports are strongly coupled with wind stress, which itself is driven by large‐scale forcing, transports through the Norwegian Trench have higher correlations with the WSC field due to local extrema. Such WSC extrema regulate the eddy activity around the Norwegian Trench. We conclude that orography and ocean‐atmosphere interaction are two important mechanisms contributing to the generation of the WSC extrema around the Norwegian coast. Ocean‐atmosphere interaction is considered a potential mechanism developing the WSC extrema. Our results show that local winds are more important than previously documented, with important implications for regional circulation likely to result from future changes to local surface gradients, such as may arise from changing meteorological or hydro‐climatic forcing. These are additional impacts on North Sea circulation that may not be accounted for from changes in wind stress alone.
Surface Kinetic Temperatures and Nontronite Single Scattering Albedo Spectra From Mars Reconnaissance Orbiter CRISM Hyperspectral Imaging Data Over Glen Torridon, Gale Crater, Mars
Authors: He L. , Arvidson R. E. , OʼSullivan J. A. , Morris R. V. , Condus T. , Hughes M. N. , Powell K. E.
Published: March 2022

The Mars Reconnaissance Orbiter Compact Imaging Spectrometer for Mars (CRISM) covers the spectral range from 0.362 to 3.92 μm with a midafternoon local solar time data acquisition. For equatorial to midlatitudes, depending on the season and surface materials, wavelengths longer than ∼2.65 μm exhibit spectral radiances on sensor that include sunlight and thermal‐emission related terms. We developed a radiative transfer based neural network approach to model both solar and emitted terms in which surface kinetic temperatures are retrieved for each image pixel, together with single scattering albedo spectra, over the full CRISM wavelength range. We applied the method to along‐track oversampled scene FRT00021C92 over Glen Torridon within Gale Crater, where the Curiosity rover traversed and acquired remote sensing and in‐situ data. Synergistic analysis of orbital and rover‐based data, coupled with laboratory analyses of ferric‐rich smectites, provide a self‐consistent set of results for the presence of desiccated nontronite associated with Murray formation mudstones exposed as periodic bedrock ridges located just to the south of Vera Rubin ridge. The desiccated nature is consistent with Curiosity's CheMin data, which for Glen Torridon drill samples indicate an abundance of nontronite having a collapsed structure resulting from loss of interlayer H2O.
Using an Explainable Machine Learning Approach to Characterize Earth System Model Errors: Application of SHAP Analysis to Modeling Lightning Flash Occurrence
Authors: Silva Sam J. , Keller Christoph A. , Hardin Joseph
Published: March 2022

Computational models of the Earth System are critical tools for modern scientific inquiry. Efforts toward evaluating and improving errors in representations of physical and chemical processes in these large computational systems are commonly stymied by highly nonlinear and complex error behavior. Recent work has shown that these errors can be effectively predicted using modern Artificial Intelligence (A.I.) techniques. In this work, we go beyond these previous studies to apply an explainable A.I. technique to not only predict model errors but also move toward understanding the underlying reasons for successful error prediction. We use XGBoost classification trees and SHapley Additive exPlanations analysis to explore the errors in the prediction of lightning occurrence in the NASA Goddard Earth Observing System model, a widely used Earth System Model. This explainable error prediction system can effectively predict the model error and indicates that the errors are strongly related to convective processes and the characteristics of the land surface.
A flexible, multifunctional, optoelectronic anticounterfeiting device from high-performance organic light-emitting paper
Authors: Pan Teng , Liu Shihao , Zhang Letian , Xie Wenfa , Yu Cunjiang
Published: March 2022

As a primary anticounterfeiting technology, most paper anticounterfeiting devices take advantage of photoresponsive behaviors of certain security materials or structures, thus featuring low-security threshold, which has been a critical global issue. To incorporate optoelectronic devices into existing anticounterfeiting technology suggests a feasible avenue to address this challenge. Here we report a high-performance organic light-emitting paper-based flexible anticounterfeiting (FAC) device with multiple stimuli-responsiveness, including light, electricity, and their combination. Without sacrificing the preexisted security information on the paper, we fabricate FAC device in a facile, low-cost yet high-fidelity fashion by integrating patterned electro-responsive and photo-responsive organic emitters onto paper substrates. By introducing optical microcavities, the FAC device shows considerable color shift upon different viewing angle and applied voltage, which is easily discernible by naked eyes. Notably, the FAC device is bendable, unclonable, and durable (a half-lifetime over 4000 hours at 100 cd m−2).
Evaluation of selective bone scan staging in prostate cancer – external validation of current strategies and decision-curve analysis
Authors: Hiwase Mrunal D. , Jay Alex , Bulamu Norma , Teh Johnathan , Paterson Felix , Kichenadasse Ganessan , Vincent Andrew D. , O’Callaghan Michael ,   South Australian Prostate Cancer Clinical Outcomes Collaborative (SA-PCCOC), Kopsaftis Tina , Walsh Scott
Published: March 2022

Background

Recommendations for staging newly diagnosed prostate cancer patients vary between guidelines and literature.

Methods

Our objective was to validate and compare prediction models selecting newly diagnosed prostate cancer patients for bone scan staging. To achieve this, we validated eleven models in a population-based cohort of 10,721 patients diagnosed with prostate cancer between 2005 and 2019. The primary outcome was net-benefit. This was assessed at different balances of conservatism and tolerance, represented by preference ratio and number-willing-to-test (NWT). Secondary outcomes included calibration slope, calibration-in-the-large (intercept), and discrimination measured by Area-under-the-receiver-operator-characteristics curve (AUC).

Results

For preference ratios less than 1:39 (NWT greater than 40), scanning everyone provided greater net-benefit than selective staging. For preference ratios 1:39 to 3:97 (NWT 33–40), the European Association of Urology (EAU) 2020 guideline recommendation was the best approach. For preference ratios 3:97–7:93 (NWT 14–33), scanning EAU high-risk patients only was preferable. For preference ratios 7:93–1:9 (NWT 10–13), scanning only Gnanapragasam Group 5 patients was best. All models had similar fair discrimination (AUCs 0.68–0.80), but most had poor calibration.

Conclusions

We identified three selective staging strategies that outperformed all other approaches but did so over different ranges of conservatism and tolerance. Scanning only EAU high-risk patients provided the greatest net-benefit over the greatest range of preference ratios and scenarios, but other options may be preferable depending upon the local healthcare system’s degree of conservatism and tolerance.
Autophagy-associated circRNA circATG7 facilitates autophagy and promotes pancreatic cancer progression
Authors: He Zhiwei , Cai Kun , Zeng Zhirui , Lei Shan , Cao Wenpeng , Li Xiaowu
Published: March 2022

Dysregulation of autophagy and circular RNAs (circRNAs) are involved in the pancreatic cancer (PC) progression. However, the regulatory network between circRNAs, autophagy, and PC progression remains unknown. Herein, we demonstrated that autophagy-associated circRNA circ-autophagy related 7 (circATG7) was elevated in PC tissues compared to adjacent tissues, and in PC cells treated with EBSS and hypoxia. circATG7 expression was positively associated with tumor diameter and lymph node invasion in patients with PC. circATG7 overexpression promoted PC cell proliferation, mobility, and autophagy in vitro, while circATG7 knockdown induced the opposite effects. ATG7 inhibition attenuated the effects of circATG7 on the biological functions of PC cells. CircATG7 is located in the cell cytoplasm and nucleus. Cytoplasmic circATG7 sponged miR-766-5p and decreased its expression, and increased the expression of ATG7, a target gene of miR-766-5p. Nuclear circATG7 acted as a scaffold to increase the interaction between the human antigen R protein and ATG7 mRNA and enhanced ATG mRNA stability. Furthermore, we demonstrated that circATG7 regulates PC cell proliferation and metastasis in vivo via ATG7-dependent autophagy. In conclusion, our results demonstrated that circATG7 accelerates PC progression via miR-766-5p/ATG7 and that HUR/ATG7 depends on autophagic flux. Thus, circATG7 may be a potential therapeutic target for PC.
A systematic review and meta-analysis of gene therapy with hematopoietic stem and progenitor cells for monogenic disorders
Authors: Tucci Francesca , Galimberti Stefania , Naldini Luigi , Valsecchi Maria Grazia , Aiuti Alessandro
Published: March 2022

Ex-vivo gene therapy (GT) with hematopoietic stem and progenitor cells (HSPCs) engineered with integrating vectors is a promising treatment for monogenic diseases, but lack of centralized databases is hampering an overall outcomes assessment. Here we aim to provide a comprehensive assessment of the short and long term safety of HSPC-GT from trials using different vector platforms. We review systematically the literature on HSPC-GT to describe survival, genotoxicity and engraftment of gene corrected cells. From 1995 to 2020, 55 trials for 14 diseases met inclusion criteria and 406 patients with primary immunodeficiencies (55.2%), metabolic diseases (17.0%), haemoglobinopathies (24.4%) and bone marrow failures (3.4%) were treated with gammaretroviral vector (γRV) (29.1%), self-inactivating γRV (2.2%) or lentiviral vectors (LV) (68.7%). The pooled overall incidence rate of death is 0.9 per 100 person-years of observation (PYO) (95% CI = 0.37–2.17). There are 21 genotoxic events out of 1504.02 PYO, which occurred in γRV trials (0.99 events per 100 PYO, 95% CI = 0.18–5.43) for primary immunodeficiencies. Pooled rate of engraftment is 86.7% (95% CI = 67.1–95.5%) for γRV and 98.7% (95% CI = 94.5–99.7%) for LV HSPC-GT (p = 0.005). Our analyses show stable reconstitution of haematopoiesis in most recipients with superior engraftment and safer profile in patients receiving LV-transduced HSPCs.
The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD
Authors: Günes Günsel Gizem , Conlon Thomas M. , Jeridi Aicha , Kim Rinho , Ertüz Zeynep , Lang Niklas J. , Ansari Meshal , Novikova Mariia , Jiang Dongsheng , Strunz Maximilian , Gaianova Mariia , Hollauer Christine , Gabriel Christina , Angelidis Ilias , Doll Sebastian , Pestoni Jeanine C. , Edelmann Stephanie L. , Kohlhepp Marlene Sophia , Guillot Adrien , Bassler Kevin , Van Eeckhoutte Hannelore P. , Kayalar Özgecan , Konyalilar Nur , Kanashova Tamara , Rodius Sophie , Ballester-López Carolina , Genes Robles Carlos M. , Smirnova Natalia , Rehberg Markus , Agarwal Charu , Krikki Ioanna , Piavaux Benoit , Verleden Stijn E. , Vanaudenaerde Bart , Königshoff Melanie , Dittmar Gunnar , Bracke Ken R. , Schultze Joachim L. , Watz Henrik , Eickelberg Oliver , Stoeger Tobias , Burgstaller Gerald , Tacke Frank , Heissmeyer Vigo , Rinkevich Yuval , Bayram Hasan , Schiller Herbert B. , Conrad Marcus , Schneider Robert , Yildirim Ali Önder
Published: March 2022

Extravasation of monocytes into tissue and to the site of injury is a fundamental immunological process, which requires rapid responses via post translational modifications (PTM) of proteins. Protein arginine methyltransferase 7 (PRMT7) is an epigenetic factor that has the capacity to mono-methylate histones on arginine residues. Here we show that in chronic obstructive pulmonary disease (COPD) patients, PRMT7 expression is elevated in the lung tissue and localized to the macrophages. In mouse models of COPD, lung fibrosis and skin injury, reduced expression of PRMT7 associates with decreased recruitment of monocytes to the site of injury and hence less severe symptoms. Mechanistically, activation of NF-κB/RelA in monocytes induces PRMT7 transcription and consequential mono-methylation of histones at the regulatory elements of RAP1A, which leads to increased transcription of this gene that is responsible for adhesion and migration of monocytes. Persistent monocyte-derived macrophage accumulation leads to ALOX5 over-expression and accumulation of its metabolite LTB4, which triggers expression of ACSL4 a ferroptosis promoting gene in lung epithelial cells. Conclusively, inhibition of arginine mono-methylation might offer targeted intervention in monocyte-driven inflammatory conditions that lead to extensive tissue damage if left untreated.
Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
Authors: Pacheco Javier Martínez , Ranocha Philippe , Kasulin Luciana , Fusari Corina M. , Servi Lucas , Aptekmann Ariel. A. , Gabarain Victoria Berdion , Peralta Juan Manuel , Borassi Cecilia , Marzol Eliana , Rodríguez-Garcia Diana Rosa , del Carmen Rondón Guerrero Yossmayer , Sardoy Mariana Carignani , Ferrero Lucía , Botto Javier F. , Meneses Claudio , Ariel Federico , Nadra Alejandro D. , Petrillo Ezequiel , Dunand Christophe , Estevez José M.
Published: March 2022

Root Hairs (RHs) growth is influenced by endogenous and by external environmental signals that coordinately regulate its final cell size. We have recently determined that RH growth was unexpectedly boosted whenArabidopsis thalianaseedlings are cultivated at low temperatures. It was proposed that RH growth plasticity in response to low temperature was linked to a reduced nutrient availability in the media. Here, we explore the molecular basis of this RH growth response by using a Genome Wide Association Study (GWAS) approach usingArabidopsis thaliananatural accessions. We identify the poorly characterized PEROXIDASE 62 (PRX62) and a related protein PRX69 as key proteins under moderate low temperature stress. Strikingly, a cell wall protein extensin (EXT) reporter reveals the effect of peroxidase activity on EXT cell wall association at 10 °C in the RH apical zone. Collectively, our results indicate that PRX62, and to a lesser extent PRX69, are key apoplastic PRXs that modulate ROS-homeostasis and cell wall EXT-insolubilization linked to RH elongation at low temperature.
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
Authors: Liu Yunxi , Kearney Joshua , Mahmoud Medhat , Kille Bryce , Sedlazeck Fritz J. , Treangen Todd J.
Published: March 2022

Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of intra-host variants with low allele frequencies remains an open challenge with no viable computational solutions available. In response to this need, we present Variabel, a novel approach and first method designed for rescuing low frequency intra-host variants from ONT data alone. We evaluate Variabel on both synthetic data (SARS-CoV-2) and patient derived datasets (Ebola virus, norovirus, SARS-CoV-2); our results show that Variabel can accurately identify low frequency variants below 0.5 allele frequency, outperforming existing state-of-the-art ONT variant callers for this task. Variabel is open-source and available for download at: www.gitlab.com/treangenlab/variabel.
Mucospheres produced by a mixotrophic protist impact ocean carbon cycling
Authors: Larsson Michaela E. , Bramucci Anna R. , Collins Sinead , Hallegraeff Gustaaf , Kahlke Tim , Raina Jean-Baptiste , Seymour Justin R. , Doblin Martina A.
Published: March 2022

Mixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)—are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich ‘mucospheres’ that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17–1.24 mg m−2 d−1 of particulate organic carbon, or 0.02–0.15 Gt to the biological pump annually, which represents 0.1–0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean.
Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2
Authors: Sangree Annabel K. , Griffith Audrey L. , Szegletes Zsofia M. , Roy Priyanka , DeWeirdt Peter C. , Hegde Mudra , McGee Abby V. , Hanna Ruth E. , Doench John G.
Published: March 2022

Numerous rationally-designed and directed-evolution variants of SpCas9 have been reported to expand the utility of CRISPR technology. Here, we assess the activity and specificity of WT-Cas9 and 10 SpCas9 variants by benchmarking their PAM preferences, on-target activity, and off-target susceptibility in cell culture assays with thousands of guides targeting endogenous genes. To enhance the coverage and thus utility of base editing screens, we demonstrate that the SpCas9-NG and SpG variants are compatible with both A > G and C > T base editors, more than tripling the number of guides and assayable residues. We demonstrate the performance of these technologies by screening for loss-of-function mutations in BRCA1 and Venetoclax-resistant mutations in BCL2, identifying both known and new mutations that alter function. We anticipate that the tools and methodologies described here will facilitate the investigation of genetic variants at a finer and deeper resolution for any locus of interest.
Quantifying and comparing radiation damage in the Protein Data Bank
Authors: Shelley Kathryn L. , Garman Elspeth F.
Published: March 2022

Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
Universality, criticality and complexity of information propagation in social media
Authors: Notarmuzi Daniele , Castellano Claudio , Flammini Alessandro , Mazzilli Dario , Radicchi Filippo
Published: March 2022

Statistical laws of information avalanches in social media appear, at least according to existing empirical studies, not robust across systems. As a consequence, radically different processes may represent plausible driving mechanisms for information propagation. Here, we analyze almost one billion time-stamped events collected from several online platforms – including Telegram, Twitter and Weibo – over observation windows longer than ten years, and show that the propagation of information in social media is a universal and critical process. Universality arises from the observation of identical macroscopic patterns across platforms, irrespective of the details of the specific system at hand. Critical behavior is deduced from the power-law distributions, and corresponding hyperscaling relations, characterizing size and duration of avalanches of information. Statistical testing on our data indicates that a mixture of simple and complex contagion characterizes the propagation of information in social media. Data suggest that the complexity of the process is correlated with the semantic content of the information that is propagated.
Norway spruce postglacial recolonization of Fennoscandia
Authors: Nota Kevin , Klaminder Jonatan , Milesi Pascal , Bindler Richard , Nobile Alessandro , van Steijn Tamara , Bertilsson Stefan , Svensson Brita , Hirota Shun K. , Matsuo Ayumi , Gunnarsson Urban , Seppä Heikki , Väliranta Minna M. , Wohlfarth Barbara , Suyama Yoshihisa , Parducci Laura
Published: March 2022

Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Oxidative metabolisms catalyzed Earth’s oxygenation
Authors: Shang Haitao , Rothman Daniel H. , Fournier Gregory P.
Published: March 2022

The burial of organic carbon, which prevents its remineralization via oxygen-consuming processes, is considered one of the causes of Earth’s oxygenation. Yet, higher levels of oxygen are thought to inhibit burial. Here we propose a resolution of this conundrum, wherein Earth’s initial oxygenation is favored by oxidative metabolisms generating partially oxidized organic matter (POOM), increasing burial via interaction with minerals in sediments. First, we introduce the POOM hypothesis via a mathematical argument. Second, we reconstruct the evolutionary history of one key enzyme family, flavin-dependent Baeyer–Villiger monooxygenases, that generates POOM, and show the temporal consistency of its diversification with the Proterozoic and Phanerozoic atmospheric oxygenation. Finally, we propose that the expansion of oxidative metabolisms instigated a positive feedback, which was amplified by the chemical changes to minerals on Earth’s surface. Collectively, these results suggest that Earth’s oxygenation is an autocatalytic transition induced by a combination of biological innovations and geological changes.
Photoinduced bond oscillations in ironpentacarbonyl give delayed synchronous bursts of carbonmonoxide release
Authors: Banerjee Ambar , Coates Michael R. , Kowalewski Markus , Wikmark Hampus , Jay Raphael M. , Wernet Philippe , Odelius Michael
Published: March 2022

Early excited state dynamics in the photodissociation of transition metal carbonyls determines the chemical nature of short-lived catalytically active reaction intermediates. However, time-resolved experiments have not yet revealed mechanistic details in the sub-picosecond regime. Hence, in this study the photoexcitation of ironpentacarbonyl Fe(CO)5 is simulated with semi-classical excited state molecular dynamics. We find that the bright metal-to-ligand charge-transfer (MLCT) transition induces synchronous Fe-C oscillations in the trigonal bipyramidal complex leading to periodically reoccurring release of predominantly axial CO. Metaphorically the photoactivated Fe(CO)5 acts as a CO geyser, as a result of dynamics in the potential energy landscape of the axial Fe-C distances and non-adiabatic transitions between manifolds of bound MLCT and dissociative metal-centered (MC) excited states. The predominant release of axial CO ligands and delayed release of equatorial CO ligands are explained in a unified mechanism based on the σ*(Fe-C) anti-bonding character of the receiving orbital in the dissociative MC states.
Al13− and B@Al12− superatoms on a molecularly decorated substrate
Authors: Shibuta Masahiro , Inoue Tomoya , Kamoshida Toshiaki , Eguchi Toyoaki , Nakajima Atsushi
Published: March 2022

Aluminum nanoclusters (Aln NCs), particularly Al13− (n = 13), exhibit superatomic behavior with interplay between electron shell closure and geometrical packing in an anionic state. To fabricate superatom (SA) assemblies, substrates decorated with organic molecules can facilitate the optimization of cluster–surface interactions, because the molecularly local interactions for SAs govern the electronic properties via molecular complexation. In this study, Aln NCs are soft-landed on organic substrates pre-deposited with n-type fullerene (C60) and p-type hexa-tert-butyl-hexa-peri-hexabenzocoronene (HB-HBC, C66H66), and the electronic states of Aln are characterized by X-ray photoelectron spectroscopy and chemical oxidative measurements. On the C60 substrate, Aln is fixed to be cationic but highly oxidative; however, on the HB-HBC substrate, they are stably fixed as anionic Aln− without any oxidations. The results reveal that the careful selection of organic molecules controls the design of assembled materials containing both Al13− and boron-doped B@Al12− SAs through optimizing the cluster–surface interactions.
Selection rules in symmetry-broken systems by symmetries in synthetic dimensions
Authors: Tzur Matan Even , Neufeld Ofer , Bordo Eliyahu , Fleischer Avner , Cohen Oren
Published: March 2022

Selection rules are often considered a hallmark of symmetry. Here, we employ symmetry-breaking degrees of freedom as synthetic dimensions to demonstrate that symmetry-broken systems systematically exhibit a specific class of symmetries and selection rules. These selection rules constrain the scaling of a system’s observables (non-perturbatively) as it transitions from symmetric to symmetry-broken. Specifically, we drive bi-elliptical high harmonic generation (HHG), and observe that the scaling of the HHG spectrum with the pump’s ellipticities is constrained by selection rules corresponding to symmetries in synthetic dimensions. We then show the generality of this phenomenon by analyzing periodically-driven (Floquet) systems subject to two driving fields, tabulating the resulting synthetic symmetries for (2 + 1)D Floquet groups, and deriving the corresponding selection rules for high harmonic generation (HHG) and other phenomena. The presented class of symmetries and selection rules opens routes for ultrafast spectroscopy of phonon-polarization, spin-orbit coupling, symmetry-protected dark bands, and more.
Tough, stable and self-healing luminescent perovskite-polymer matrix applicable to all harsh aquatic environments
Authors: Liu Yuncong , Chen Tao , Jin Zhekai , Li Mengxue , Zhang Dongdong , Duan Lian , Zhao Zhiguo , Wang Chao
Published: March 2022

Gelatinous underwater invertebrates such as jellyfish have organs that are transparent, luminescent and self-healing, which allow the creatures to navigate, camouflage themselves and, indeed, survive in aquatic environments. Artificial luminescent materials that can mimic such functionality can be used to develop aquatic wearable/stretchable displays and water-resistant devices. Here, a luminescent composite that is simultaneously transparent, tough and can autonomously self-heal in both dry and wet conditions is reported. A tough, self-healable fluorine elastomer with dipole–dipole interactions is synthesized as the polymer matrix. It exhibits excellent compatibility with metal halide perovskite quantum dots. The composite possesses a toughness of 19 MJ m−3, maximum strain of 1300% and capability to autonomously self-heal underwater. Notably, the material can withstand extremely harsh aqueous conditions, such as highly salty, acidic (pH = 1) and basic (pH = 13) environment for more than several months with almost no decay in mechanical performance or optical properties.
High-resolution population estimation using household survey data and building footprints
Authors: Boo Gianluca , Darin Edith , Leasure Douglas R. , Dooley Claire A. , Chamberlain Heather R. , Lázár Attila N. , Tschirhart Kevin , Sinai Cyrus , Hoff Nicole A. , Fuller Trevon , Musene Kamy , Batumbo Arly , Rimoin Anne W. , Tatem Andrew J.
Published: March 2022

The national census is an essential data source to support decision-making in many areas of public interest. However, this data may become outdated during the intercensal period, which can stretch up to several decades. In this study, we develop a Bayesian hierarchical model leveraging recent household surveys and building footprints to produce up-to-date population estimates. We estimate population totals and age and sex breakdowns with associated uncertainty measures within grid cells of approximately 100 m in five provinces of the Democratic Republic of the Congo, a country where the last census was completed in 1984. The model exhibits a very good fit, with anR2value of 0.79 for out-of-sample predictions of population totals at the microcensus-cluster level and 1.00 for age and sex proportions at the province level. This work confirms the benefits of combining household surveys and building footprints for high-resolution population estimation in countries with outdated censuses.
Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics
Authors: Ma Duo , Li Yuexin , Wu Kaiyue , Yan Zhaoqing , Tang Anli A. , Chaudhary Soma , Ticktin Zachary M. , Alcantar-Fernandez Jonathan , Moreno-Camacho José L. , Campos-Romero Abraham , Green Alexander A.
Published: March 2022

Applications of RNA-based molecular logic have been hampered by sequence constraints imposed on the input and output of the circuits. Here we show that the sequence constraints can be substantially reduced by appropriately encoded multi-arm junctions of single-stranded RNA structures. To conditionally activate RNA translation, we integrated multi-arm junctions, self-assembled upstream of a regulated gene and designed to unfold sequentially in response to different RNA inputs, with motifs of loop-initiated RNA activators that function independently of the sequence of the input RNAs and that reduce interference with the output gene. We used the integrated RNA system and sequence-independent input RNAs to execute two-input and three-input OR and AND logic in Escherichia coli, and designed paper-based cell-free colourimetric assays that accurately identified two human immunodeficiency virus (HIV) subtypes (by executing OR logic) in amplified synthetic HIV RNA as well as severe acute respiratory syndrome coronavirus-2 (via two-input AND logic) in amplified RNA from saliva samples. The sequence-independent molecular logic enabled by the integration of multi-arm junction RNAs with motifs for loop-initiated RNA activators may be broadly applicable in biotechnology.
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning
Authors: Athiyannan Naveenkumar , Abrouk Michael , Boshoff Willem H. P. , Cauet Stéphane , Rodde Nathalie , Kudrna David , Mohammed Nahed , Bettgenhaeuser Jan , Botha Kirsty S. , Derman Shannon S. , Wing Rod A. , Prins Renée , Krattinger Simon G.
Published: March 2022

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance geneYr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance.Yr27is allelic to the leaf rust resistance geneLr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineeringYr27alleles with multiple recognition specificities in the future.