bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tempo and drivers of plant diversification in the European mountain system
Authors: Smyčka Jan , Roquet Cristina , Boleda Martí , Alberti Adriana , Boyer Frédéric , Douzet Rolland , Perrier Christophe , Rome Maxime , Valay Jean-Gabriel , Denoeud France , Šemberová Kristýna , Zimmermann Niklaus E. , Thuiller Wilfried , Wincker Patrick , Alsos Inger G. , Coissac Eric ,   the PhyloAlps consortium, Roquet Cristina , Boleda Martí , Alberti Adriana , Boyer Frédéric , Douzet Rolland , Perrier Christophe , Rome Maxime , Valay Jean-Gabriel , Denoeud France , Zimmermann Niklaus E. , Thuiller Wilfried , Wincker Patrick , Alsos Inger G. , Coissac Eric , Lavergne Sébastien , Lavergne Sébastien 
Published: May 2022

AbstractThere is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.
Ultrafast orbital tomography of a pentacene film using time-resolved momentum microscopy at a FEL
Authors: Baumgärtner Kiana , Reuner Marvin , Metzger Christian , Kutnyakhov Dmytro , Heber Michael , Pressacco Federico , Min Chul-Hee , Peixoto Thiago R. F. , Reiser Mario , Kim Chan , Lu Wei , Shayduk Roman , Izquierdo Manuel , Brenner Günter , Roth Friedrich , Schöll Achim , Molodtsov Serguei , Wurth Wilfried , Reinert Friedrich , Madsen Anders , Popova-Gorelova Daria , Scholz Markus 
Published: May 2022

AbstractTime-resolved momentum microscopy provides insight into the ultrafast interplay between structural and electronic dynamics. Here we extend orbital tomography into the time domain in combination with time-resolved momentum microscopy at a free-electron laser (FEL) to follow transient photoelectron momentum maps of excited states of a bilayer pentacene film on Ag(110). We use optical pump and FEL probe pulses by keeping FEL source conditions to minimize space charge effects and radiation damage. From the momentum microscopy signal, we obtain time-dependent momentum maps of the excited-state dynamics of both pentacene layers separately. In a combined experimental and theoretical study, we interpret the observed signal for the bottom layer as resulting from the charge redistribution between the molecule and the substrate induced by excitation. We identify that the dynamics of the top pentacene layer resembles excited-state molecular dynamics.
The planarian wound epidermis gene equinox is required for blastema formation in regeneration
Authors: Scimone M. Lucila , Cloutier Jennifer K. , Maybrun Chloe L. , Reddien Peter W. 
Published: May 2022

AbstractRegeneration often involves the formation of a blastema, an outgrowth or regenerative bud formed at the plane of injury where missing tissues are produced. The mechanisms that trigger blastema formation are therefore fundamental for regeneration. Here, we identify a gene, which we named equinox, that is expressed within hours of injury in the planarian wound epidermis. equinox encodes a predicted secreted protein that is conserved in many animal phyla. Following equinox inhibition, amputated planarians fail to maintain wound-induced gene expression and to subsequently undergo blastema outgrowth. Associated with these defects is an inability to reestablish lost positional information needed for missing tissue specification. Our findings link the planarian wound epidermis, through equinox, to regeneration of positional information and blastema formation, indicating a broad regulatory role of the wound epidermis in diverse regenerative contexts.
Extensible and self-recoverable proteinaceous materials derived from scallop byssal thread
Authors: Zhang Xiaokang , Cui Mengkui , Wang Shuoshuo , Han Fei , Xu Pingping , Teng Luyao , Zhao Hang , Wang Ping , Yue Guichu , Zhao Yong , Liu Guangfeng , Li Ke , Zhang Jicong , Liang Xiaoping , Zhang Yingying , Liu Zhiyuan , Zhong Chao , Liu Weizhi 
Published: May 2022

AbstractBiologically derived and biologically inspired fibers with outstanding mechanical properties have found attractive technical applications across diverse fields. Despite recent advances, few fibers can simultaneously possess high-extensibility and self-recovery properties especially under wet conditions. Here, we report protein-based fibers made from recombinant scallop byssal proteins with outstanding extensibility and self-recovery properties. We initially investigated the mechanical properties of the native byssal thread taken from scallopChlamys farreriand reveal its high extensibility (327 ± 32%) that outperforms most natural biological fibers. Combining transcriptome and proteomics, we select the most abundant scallop byssal protein type 5-2 (Sbp5-2) in the thread region, and produce a recombinant protein consisting of 7 tandem repeat motifs (rTRM7) of the Sbp5-2 protein. Applying an organic solvent-enabled drawing process, we produce bio-inspired extensible rTRM7 fiber with high-extensibility (234 ± 35%) and self-recovery capability in wet condition, recapitulating the hierarchical structure and mechanical properties of the native scallop byssal thread. We further show that the mechanical properties of rTRM7 fiber are highly regulated by hydrogen bonding and intermolecular crosslinking formed through disulfide bond and metal-carboxyl coordination. With its outstanding mechanical properties, rTRM7 fiber can also be seamlessly integrated with graphene to create motion sensors and electrophysiological signal transmission electrode.
Novel role of the synaptic scaffold protein Dlgap4 in ventricular surface integrity and neuronal migration during cortical development
Authors: Romero Delfina M. , Poirier Karine , Belvindrah Richard , Moutkine Imane , Houllier Anne , LeMoing Anne-Gaëlle , Petit Florence , Boland Anne , Collins Stephan C. , Soiza-Reilly Mariano , Yalcin Binnaz , Chelly Jamel , Deleuze Jean-François , Bahi-Buisson Nadia , Francis Fiona 
Published: May 2022

AbstractSubcortical heterotopias are malformations associated with epilepsy and intellectual disability, characterized by the presence of ectopic neurons in the white matter. Mouse and human heterotopia mutations were identified in the microtubule-binding protein Echinoderm microtubule-associated protein-like 1, EML1. Further exploring pathological mechanisms, we identified a patient with an EML1-like phenotype and a novel genetic variation inDLGAP4. The protein belongs to a membrane-associated guanylate kinase family known to function in glutamate synapses. We showed that DLGAP4 is strongly expressed in the mouse ventricular zone (VZ) from early corticogenesis, and interacts with key VZ proteins including EML1.In uteroelectroporation ofDlgap4knockdown (KD) and overexpression constructs revealed a ventricular surface phenotype including changes in progenitor cell dynamics, morphology, proliferation and neuronal migration defects. TheDlgap4KD phenotype was rescued by wild-type but not mutant DLGAP4. Dlgap4 is required for the organization of radial glial cell adherens junction components and actin cytoskeleton dynamics at the apical domain, as well as during neuronal migration. Finally,Dlgap4heterozygous knockout (KO) mice also show developmental defects in the dorsal telencephalon. We hence identify a synapse-related scaffold protein with pleiotropic functions, influencing the integrity of the developing cerebral cortex.
Phase transition and remodeling complex assembly are important for SS18-SSX oncogenic activity in synovial sarcomas
Authors: Cheng Yanli , Shen Zhongtian , Gao Yaqi , Chen Feilong , Xu Huisha , Mo Qinling , Chu Xinlei , Peng Chang-liang , McKenzie Takese T. , Palacios Bridgitte E. , Hu Jian , Zhou Hao , Long Jiafu 
Published: May 2022

AbstractOncoprotein SS18-SSX is a hallmark of synovial sarcomas. However, as a part of the SS18-SSX fusion protein, SS18’s function remains unclear. Here, we depict the structures of both human SS18/BRG1 and yeast SNF11/SNF2 subcomplexes. Both subcomplexes assemble into heterodimers that share a similar conformation, suggesting that SNF11 might be a homologue of SS18 in chromatin remodeling complexes. Importantly, our study shows that the self-association of the intrinsically disordered region, QPGY domain, leads to liquid-liquid phase separation (LLPS) of SS18 or SS18-SSX and the subsequent recruitment of BRG1 into phase-separated condensates. Moreover, our results show that the tyrosine residues in the QPGY domain play a decisive role in the LLPS of SS18 or SS18-SSX. Perturbations of either SS18-SSX LLPS or SS18-SSX’s binding to BRG1 impair NIH3T3 cell transformation by SS18-SSX. Our data demonstrate that both LLPS and assembling into chromatin remodelers contribute to the oncogenic activity of SS18-SSX in synovial sarcomas.
Highly efficient nonlinear optical emission from a subwavelength crystalline silicon cuboid mediated by supercavity mode
Authors: Panmai Mingcheng , Xiang Jin , Li Shulei , He Xiaobing , Ren Yuhao , Zeng Miaoxuan , She Juncong , Li Juntao , Lan Sheng 
Published: May 2022

AbstractThe low quantum efficiency of silicon (Si) has been a long-standing challenge for scientists. Although improvement of quantum efficiency has been achieved in porous Si or Si quantum dots, highly efficient Si-based light sources prepared by using the current fabrication technooloy of Si chips are still being pursued. Here, we proposed a strategy, which exploits the intrinsic excitation of carriers at high temperatures, to modify the carrier dynamics in Si nanoparticles. We designed a Si/SiO2 cuboid supporting a quasi-bound state in the continuum (quasi-BIC) and demonstrated the injection of dense electron-hole plasma via two-photon-induced absorption by resonantly exciting the quasi-BIC with femtosecond laser pulses. We observed a significant improvement in quantum efficiency by six orders of magnitude to ~13%, which is manifested in the ultra-bright hot electron luminescence emitted from the Si/SiO2 cuboid. We revealed that femtosecond laser light with transverse electric polarization (i.e., the electric field perpendicular to the length of a Si/SiO2 cuboid) is more efficient for generating hot electron luminescence in Si/SiO2 cuboids as compared with that of transverse magnetic polarization (i.e., the magnetic field perpendicular to the length of a Si/SiO2 cuboid). Our findings pave the way for realizing on-chip nanoscale Si light sources for photonic integrated circuits and open a new avenue for manipulating the luminescence properties of semiconductors with indirect bandgaps.
Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation
Authors: Bensing Barbara A. , Stubbs Haley E. , Agarwal Rupesh , Yamakawa Izumi , Luong Kelvin , Solakyildirim Kemal , Yu Hai , Hadadianpour Azadeh , Castro Manuel A. , Fialkowski Kevin P. , Morrison KeAndreya M. , Wawrzak Zdzislaw , Chen Xi , Lebrilla Carlito B. , Baudry Jerome , Smith Jeremy C. , Sullam Paul M. , Iverson T. M. 
Published: May 2022

AbstractBacterial binding to host receptors underlies both commensalism and pathogenesis. Many streptococci adhere to protein-attached carbohydrates expressed on cell surfaces using Siglec-like binding regions (SLBRs). The precise glycan repertoire recognized may dictate whether the organism is a strict commensal versus a pathogen. However, it is currently not clear what drives receptor selectivity. Here, we use five representative SLBRs and identify regions of the receptor binding site that are hypervariable in sequence and structure. We show that these regions control the identity of the preferred carbohydrate ligand using chimeragenesis and single amino acid substitutions. We further evaluate how the identity of the preferred ligand affects the interaction with glycoprotein receptors in human saliva and plasma samples. As point mutations can change the preferred human receptor, these studies suggest how streptococci may adapt to changes in the environmental glycan repertoire.
Achieving high molecular alignment and orientation for CH$$_3$$F through manipulation of rotational states with varying optical and THz laser pulse parameters
Authors: Chordiya Kalyani , Simkó Irén , Szidarovszky Tamás , Upadhyay Kahaly Mousumi 
Published: May 2022

AbstractIncreasing interest in the fields of high-harmonics generation, laser-induced chemical reactions, and molecular imaging of gaseous targets demands high molecular “alignment” and “orientation” (A&O). In this work, we examine the critical role of different pulse parameters on the field-free A&O dynamics of the CH$$_3$$

3

F molecule, and identify experimentally feasible optical and THz range laser parameters that ensure maximal A&O for such molecules. Herein, apart from rotational temperature, we investigate effects of varying pulse parameters such as, pulse duration, intensity, frequency, and carrier envelop phase (CEP). By analyzing the interplay between laser pulse parameters and the resulting rotational population distribution, the origin of specific A&O dynamics was addressed. We could identify two qualitatively different A&O behaviors and revealed their connection with the pulse parameters and the population of excited rotational states. We report here the highest alignment of $$\langle {\mathrm{cos}^2\theta }\rangle = 0.843$$

⟨

cos

2

θ

⟩
=
0.843

and orientation of $$\langle {\mathrm{cos}(\theta )}\rangle = 0.886$$

⟨

cos
(
θ
)

⟩
=
0.886

for CH$$_3$$

3

F molecule at 2 K using a single pulse. Our study should be useful to understand different aspects of laser-induced unidirectional rotation in heteronuclear molecules, and in understanding routes to tune/enhance A&O in laboratory conditions for advanced applications.
Improved simultaneous LET and dose measurements in proton therapy
Authors: Christensen Jeppe Brage , Togno Michele , Bossin Lily , Pakari Oskari Ville , Safai Sairos , Yukihara Eduardo Gardenali 
Published: May 2022

AbstractThe objective of this study was to improve the precision of linear energy transfer (LET) measurements using $$\text {Al}_2\text {O}_3\text {:C}$$

Al
2

O
3

:C

optically stimulated luminescence detectors (OSLDs) in proton beams, and, with that, improve OSL dosimetry by correcting the readout for the LET-dependent ionization quenching. The OSLDs were irradiated in spot-scanning proton beams at different doses for fluence-averaged LET values in the (0.4–6.5) $$\hbox {keV}\, \upmu \hbox {m}^{-1}$$

keV

μ

m

-
1

range (in water). A commercial automated OSL reader with a built-in beta source was used for the readouts, which enabled a reference irradiation and readout of each OSLD to establish individual corrections. Pulsed OSL was used to separately measure the blue (F-center) and UV ($$F^+$$

F
+

-center) emission bands of $$\text {Al}_2\text {O}_3\text {:C}$$

Al
2

O
3

:C

and the ratio between them (UV/blue signal) was used for the LET measurements. The average deviation between the simulated and measured LET values along the central beam axis amounts to 5.5% if both the dose and LET are varied, but the average deviation is reduced to 3.5% if the OSLDs are irradiated with the same doses. With the measurement procedure and automated equipment used here, the variation in the signals used for LET estimates and quenching-corrections is reduced from 0.9 to 0.6%. The quenching-corrected OSLD doses are in agreement with ionization chamber measurements within the uncertainties. The automated OSLD corrections are demonstrated to improve the LET estimates and the ionization quenching-corrections in proton dosimetry for a clinically relevant energy range up to 230 MeV. It is also for the first time demonstrated how the LET can be estimated for different doses.
Stretchable nanofibers of polyvinylidenefluoride (PVDF)/thermoplastic polyurethane (TPU) nanocomposite to support piezoelectric response via mechanical elasticity
Authors: Shehata Nader , Nair Remya , Boualayan Rabab , Kandas Ishac , Masrani Abdulrzak , Elnabawy Eman , Omran Nada , Gamal Mohammed , Hassanin Ahmed H. 
Published: May 2022

AbstractInterest in piezoelectric nanocomposites has been vastly growing in the energy harvesting field. They are applied in wearable electronics, mechanical actuators, and electromechanical membranes. In this research work, nanocomposite membranes of different blend ratios from PVDF and TPU have been synthesized. The PVDF is responsible for piezoelectric performance where it is one of the promising polymeric organic materials containing β-sheets, to convert applied mechanical stress into electric voltage. In addition, the TPU is widely used in the plastic industry due to its superior elasticity. Our work investigates the piezoresponse analysis for different blending ratios of PVDF/TPU. It has been found that TPU blending ratios of 15–17.5% give higher output voltage at different stresses conditions along with higher piezosensitivity. Then, TPU addition with its superior mechanical elasticity can partially compensate PVDF to enhance the piezoelectric response of the PVDF/TPU nanocomposite mats. This work can help reducing the amount of added PVDF in piezoelectric membranes with enhanced piezo sensitivity and mechanical elasticity.
Cytogenetic testing by fluorescence in situ hybridization is improved by plasma cell sorting in multiple myeloma
Authors: Ha Jihye , Cho Hyunsoo , Lee Taek Gyu , Shin Saeam , Chung Haerim , Jang Ji Eun , Kim Soo-Jeong , Cheong June-Won , Lee Seung-Tae , Kim Jin Seok , Choi Jong Rak 
Published: May 2022

AbstractAccurate detection of cytogenetic abnormalities has become more important for improving risk-adapted treatment strategies in multiple myeloma (MM). However, precise cytogenetic testing by fluorescence in situ hybridization (FISH) is challenged by the dilution effect of bone marrow specimens and poor growth of plasma cells ex vivo. It has been suggested that FISH should be performed in combination with plasma cell enrichment strategies. We examined cytogenetic abnormalities in newly diagnosed MM and compared the efficacy of three different enrichment modalities for FISH: direct FISH (n = 137), fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms (FICTION) technique (n = 224), and a plasma cell sorting FISH with fluorescence-activated cell sorter (FACS) (n = 132). FISH disclosed cytogenetic abnormalities in 38.0% of samples by direct FISH, 56.3% by FICTION, and 95.5% by FACS-FISH, and the percentage of cells with abnormal signals detected by FISH was significantly higher by FACS-FISH than direct FISH or FICTION. Our results suggest that the efficacy of FISH is dependent on the plasma cell enrichment modalities and reveal that plasma cell sorting FISH with FACS enables better detection of cytogenetic abnormalities in diagnostic MM samples.
ROV observations reveal infection dynamics of gill parasites in midwater cephalopods
Authors: Stenvers Vanessa I. , Sherlock Rob E. , Reisenbichler Kim R. , Robison Bruce H. 
Published: May 2022

AbstractGill parasites of coleoid cephalopods are frequently observed during remotely operated vehicle (ROV) dives in the Monterey Submarine Canyon. However, little knowledge exists on the identity of the parasite species or their effects on the cephalopod community. With the help of ROV-collected specimens and in situ footage from the past 27 years, we report on their identity, prevalence and potential infection strategy. Gill parasites were genetically and morphologically identified from collected specimens of Chiroteuthis calyx, Vampyroteuthis infernalis and Gonatus spp. In situ prevalence was estimated from video footage for C. calyx, Galiteuthis spp., Taonius spp. and Japetella diaphana, enabled by their transparent mantle tissue. The most common parasite was identified as Hochbergia cf. moroteuthensis, a protist of unresolved taxonomic ranking. We provide the first molecular data for this parasite and show a sister group relationship to the dinoflagellate genus Oodinium. Hochbergia cf. moroteuthensis was most commonly observed in adult individuals of all species and was sighted year round over the analyzed time period. In situ prevalence was highest in C. calyx (75%), followed by Galiteuthis spp. (29%), Taonius spp. (27%) and J. diaphana (7%). A second parasite, not seen on the in situ footage, but occurring within the gills of Gonatus berryi and Vampyroteuthis infernalis, could not be found in the literature or be identified through DNA barcoding. The need for further investigation is highlighted, making this study a starting point for unravelling ecological implications of the cephalopod-gill-parasite system in deep pelagic waters.
Comparing the natural progression and clinical features of keratoconus between pediatric and adult patients
Authors: Lin Ken-Kuo , Chen Yun-Wen , Yeh Chun-Ting , Li Pei-Ru , Lee Jiahn-Shing , Hou Chiun-Ho , Hsiao Ching-Hsi , See Lai-Chu 
Published: May 2022

AbstractTo present the natural course of keratoconus (KC) and compare pediatric and adult patients. Design A retrospective cohort study. Setting Hospital-based. Patient Population In total, 152 patients (288 eyes) diagnosed with KC at Chang Gung Memorial Hospital, Taiwan, were included. Previously managed patients and those with missing optical data were excluded. Observation Procedures Patients were divided into pediatric (≤ 18 years) and adult (> 18 years) groups. Demographics, clinical data, and optical variables were collected, including corrected distance visual acuity (CDVA), refractive error, and keratometric readings (K). Main Outcome Measure Optical variables at the final follow-up before aggressive treatment. Results In total, 20 pediatric (37 eyes) and 132 adults (251 eyes) patients were eligible for this study. The mean follow-up time was 2.98 years. Male predominance was observed in both groups. Both groups had similar clinical characteristics and optical variables at the initial diagnosis. Pediatric patients progressed significantly more rapidly in refractive errors, including spheres and cylinders, spherical equivalence, steep K, and flat K during the follow-up. However, significant change between the two study groups was only seen in sphere refractive error spherical equivalence. Conclusion Pediatric patients had more rapidly progressive KC than adult patients, so early detection and frequent follow-up for prompt interventions are necessary for these patients.