bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of density ratio on particle dispersion in a turbulent jet
Authors: Capone A. , Moscato G. , Romano G.
Published: January 2023

The behavior of dispersed particles in a turbulent round jet is experimentally investigated. The role of particle-to-fluid density ratio ρp/ρf is analyzed by inspecting particle velocity fields and preferential concentration at four different ratios, from 0.7 to 19.3. The jet near-field region, i.e., up to X/D=11, is analyzed and compared to the unladen case. Particle-to-fluid density ratio is reported to have a strong impact on particle velocity field structure, in terms of jet transition and self-similar region as well as on turbulent fluctuations. Concentrations of particles show that increasing particle density corresponds to larger departure from uniformity. This occurrence is limited to the region X/D<5, where also the largest differences of average and fluctuating velocities with respect to the unladen case are measured.
Reconfigurable phase contrast microscopy with correlated photon pairs
Authors: Hodgson Hazel , Zhang Yingwen , England Duncan , Sussman Benjamin
Published: January 2023

A phase-sensitive microscopy technique is proposed and demonstrated that employs the momentum correlations inherent in spontaneous parametric downconversion. One photon from a correlated pair is focused onto a microscopic target while the other is measured in the Fourier plane. This provides knowledge of the position and angle of illumination for every photon striking the target, allowing full post-production control of the illumination angle used to form an image. The versatility of this approach is showcased with asymmetric illumination and differential phase contrast imaging without any beam blocks or moving parts.
Analytical solution of supersonic axisymmetric flow around a sharp convex corner
Authors: Chen Kuangshi , Xu Jinglei , Qin Qihao , Huang Shuai
Published: January 2023

Supersonic axisymmetric expansion flow is a typical and fundamental issue in gas dynamics. It plays a vital role in the high-speed external and internal flow fields regarding the contour design and performance evaluation of supersonic/hypersonic vehicles and their propulsion systems. The supersonic two-dimensional (2D) planar expansion flow is dominated by the well-known Prandtl–Meyer (P–M) theory. However, no similar explicit relation exists for the supersonic axisymmetric expansion flow, and only the computational fluid dynamics results could be employed at present. Therefore, this work focuses on developing the analytical solution of supersonic axisymmetric flow around a sharp convex corner on the basis of the generic gasdynamic functions in a newly established coordinate system for addressing the aforementioned issue. Theoretical derivations and numerical results prove that the flow deflection angle and Mach number in supersonic axisymmetric flow around a sharp convex corner obey the identical law to the 2D planar situation, that is, the P–M theory, while the local axisymmetric expansion fan is not the simple wave flow despite the conical flow. Meanwhile, the method of characteristics is employed to further explicate the intrinsic connection and difference between the 2D and axisymmetric sharp convex corner flow. The equivalence of sharp corner and curved surface flows with the identical deflection angle is discussed, and three limitations of the proposed analytical solution are clarified.
Transition of natural convection of liquid metal in an annular enclosure under a magnetic field
Authors: Masuda Takuya , Tagawa Toshio , Alam M. M. A. , Hayamizu Yasutaka
Published: January 2023

Natural convection of a low-Prandtl-number conductive fluid driven by a horizontal temperature gradient in an annular enclosure with a square cross section was investigated. The surface temperatures of the inner and outer cylinders were differentially maintained. A static magnetic field was applied in the azimuthal direction. A three-dimensional (3D) numerical simulation was performed for a part of an annulus divided into 20 or 28 equal parts. The natural convection found changes on the order of a two-dimensional (2D) steady, a 3D steady, a 3D non-half-symmetric simply periodic oscillatory, a 3D indefinite oscillatory, a 3D half-symmetric simply periodic oscillatory, and a 3D aperiodic oscillatory flow as the Hartmann number decreases. This transition pattern is identical to that as the Rayleigh number increases in the same system without a magnetic field. In high Rayleigh numbers, the transition is accompanied by an axisymmetric oscillation. A disturbance causing the transition consists of three modes as a 3D steady, a 3D half-symmetric oscillatory, and a 2D axisymmetric oscillatory mode. The Nusselt numbers in most 3D flows are smaller at low Rayleigh numbers and larger at high Rayleigh numbers than that in 2D flows at a same condition, while the kinetic energy of a 3D flow is necessarily smaller than that of a 2D flow.
Biphasic concentration patterns in ionic transport under nanoconfinement revealed in steady-state and time-dependent properties
Authors: Queralt-Martín María , Pérez-Grau José J. , Alvero González Laidy M. , Perini D. Aurora , Cervera Javier , Aguilella Vicente M. , Alcaraz Antonio
Published: January 2023

Ion permeation across nanoscopic structures differs considerably from microfluidics because of strong steric constraints, transformed solvent properties, and charge-regulation effects revealed mostly in diluted solutions. However, little is known about nanofluidics in moderately concentrated solutions, which are critically important for industrial applications and living systems. Here, we show that nanoconfinement triggers general biphasic concentration patterns in a myriad of ion transport properties by using two contrasting systems: a biological ion channel and a much larger synthetic nanopore. Our findings show a low-concentration regime ruled by classical Debye screening and another one where ion–ion correlations and enhanced ion–surface interactions contribute differently to each electrophysiological property. Thus, different quantities (e.g., conductance vs noise) measured under the same conditions may appear contradictory because they belong to different concentration regimes. In addition, non-linear effects that are barely visible in bulk conductivity only in extremely concentrated solutions become apparent in nanochannels around physiological conditions.
Inertial migration of non-spherical particles in straight microfluidic channels
Authors: Hafemann T. , Fröhlich J.
Published: January 2023

The paper reports on simulations of particulate flows in square ducts with oblate and prolate particles at a bulk Reynolds number of 100 and dilute particle concentration. Inertial migration leads to focusing of particles in specific regions of the cross section. It is observed that these positions are different for the non-spherical particles compared to those obtained with spherical ones. Prolate particles exhibit Jeffery-type orbits, while oblate particles rotate around their axis of symmetry. As a result, the rotation-induced migration of prolates is much slower than for spheres and oblates. An analysis of the surrounding flow is used to show differences in the velocity field. In a second set of simulations, the particle concentration was increased by a factor of 4 with the same domain size, so that neighboring particles influence each other. The duration until focusing is achieved is substantially increased. The focusing position moves slightly to the wall, and further effects are generated. Steady particle oscillations in position are seen for spheres, and the formation of particle trains is observed in all cases. The interaction of prolate particles is particularly complex and addressed in substantial detail.
Enhanced light output of Eu, O-codoped GaN caused by reconfiguration of luminescent sites during post-growth thermal annealing
Authors: Iwaya T. , Ichikawa S. , Timmerman D. , Tatebayashi J. , Fujiwara Y.
Published: January 2023

Luminescence efficiency of Eu-related emission from Eu, O-codoped GaN (GaN:Eu, O) strongly depends on the local structure of Eu ions. Growth at relatively low temperature (∼960 °C) not only enables high Eu doping concentration but also elevates Eu-clustering due to its low diffusion coefficient, which results in formation of a large number of inefficient luminescent sites. We have studied the impact of post-growth thermal annealing at high temperatures on elimination of Eu clusters by photoluminescence measurements. These clarify that thermal annealing at high temperatures induces changes in the structural conformation and converts inefficient luminescent sites to efficient ones. As a result, the sample annealed at 1100 °C shows increased luminescence efficiency with a maximum of 5.1 times that of the as-grown sample. Post-growth thermal annealing offers a way to improve the efficiency of GaN:Eu, O further for practical application in III-nitride-based monolithic three-primary colors' light-emitting diodes.
HFIP-assisted Brønsted acid catalysed synthesis of furan derivatives
Authors: Pu Bonnie , Nguyen Thanh Vinh
Published: January 2023

The furan framework is ubiquitous in naturally occurring compounds, and furan-containing structures are also key intermediates to many industrially important chemicals and materials. There have been reports of numerous methods to synthesise furans, however most of them use transition metal catalysts or Brønsted acid catalysts under harsh conditions. This work describes the development of a new non-metal Brønsted acid catalytic method for the synthesis of 2-aryl-3-carboxylate ester furans and 2,3-diaryl furans from ynone substrates. The method was shown to be efficient under very mild reaction conditions with up to 94% product yields.
On the composition of
Authors: Westerman Michael , Umbrello Linette , Woolley Patricia A.
Published: January 2023

Morphological and molecular studies have consistently suggested that Sminthopsis, as currently defined, is rendered paraphyletic by the kultarr (Antechinomys laniger). They have also suggested a sister relationship between the kultarr and the long-tailed dunnart. Based on DNA sequence data from multiple mitochondrial and nuclear gene loci we reassign the long-tailed dunnart (formerly Sminthopsis longicaudata) to Antechinomys. Although there is good evidence of genetic structure within the kultarr (A. laniger), it does not correspond to the two currently recognised subspecies, viz A. laniger laniger and A. l. spenceri. We conclude that Antechinomys consists of two species, A. laniger and A. longicaudatus, consistent with morphology. We suggest that the observed genetic and morphological variation within A. laniger merits a more thorough investigation of more samples from across its range to resolve the taxonomy.
Distinct and opposite effects of leukemogenic
Idh
and
Tet2
mutations in hematopoietic stem and progenitor cells
Authors: Fortin Jerome , Chiang Ming-Feng , Meydan Cem , Foox Jonathan , Ramachandran Parameswaran , Leca Julie , Lemonnier François , Li Wanda Y. , Gams Miki S. , Sakamoto Takashi , Chu Mandy , Tobin Chantal , Laugesen Eric , Robinson Troy M. , You-Ten Annick , Butler Daniel J. , Berger Thorsten , Minden Mark D. , Levine Ross L. , Guidos Cynthia J. , Melnick Ari M. , Mason Christopher E. , Mak Tak W.
Published: January 2023

Mutations in
IDH1,
IDH2
, and
TET2
are recurrently observed in myeloid neoplasms.
IDH1
and
IDH2
encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic
IDH1/2
mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms,
IDH1
,
IDH2
, and
TET2
mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have distinct, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that

Idh2
R172K

and
Tet2
loss-of-function have divergent consequences on the expression and activity of key hematopoietic and leukemogenic regulators. Notably, chromatin accessibility and transcriptional deregulation in

Idh2
R172K

cells were partially disconnected from DNA methylation alterations. These results highlight unanticipated divergent effects of
IDH1/2
and
TET2
mutations, providing support for the optimization of genotype-specific therapies.
Nitro-oleic acid regulates T cell activation through post-translational modification of calcineurin
Authors: Bago Ángel , Cayuela M. Laura , Gil Alba , Calvo Enrique , Vázquez Jesús , Queiro Antonio , Schopfer Francisco J. , Radi Rafael , Serrador Juan M. , Íñiguez Miguel A.
Published: January 2023

Nitro-fatty acids (NO
2
-FAs) are unsaturated fatty acid nitration products that exhibit anti-inflammatory actions in experimental mouse models of autoimmune and allergic diseases. These electrophilic molecules interfere with intracellular signaling pathways by reversible post-translational modification of nucleophilic amino-acid residues. Several regulatory proteins have been identified as targets of NO
2
-FAs, modifying their activity and promoting gene expression changes that result in anti-inflammatory effects. Herein, we report the effects of nitro-oleic acid (NO
2
-OA) on pro-inflammatory T cell functions, showing that 9- and 10-NOA, but not their oleic acid precursor, decrease T cell proliferation, expression of activation markers CD25 and CD71 on the plasma membrane, and IL-2, IL-4, and IFN-γ cytokine gene expressions. Moreover, we have found that NO
2
-OA inhibits the transcriptional activity of nuclear factor of activated T cells (NFAT) and that this inhibition takes place through the regulation of the phosphatase activity of calcineurin (CaN), hindering NFAT dephosphorylation, and nuclear translocation in activated T cells. Finally, using mass spectrometry-based approaches, we have found that NO
2
-OA nitroalkylates CaNA on four Cys (Cys129, 228, 266, and 372), of which only nitroalkylation on Cys372 was of importance for the regulation of CaN phosphatase activity in cells, disturbing functional CaNA/CaNB heterodimer formation. These results provide evidence for an additional mechanism by which NO
2
-FAs exert their anti-inflammatory actions, pointing to their potential as therapeutic bioactive lipids for the modulation of harmful T cell-mediated immune responses.
Dimerization of the Alzheimer’s disease pathogenic receptor SORLA regulates its association with retromer
Authors: Jensen Anne Mette G. , Kitago Yu , Fazeli Elnaz , Vægter Christian B. , Small Scott A. , Petsko Gregory A. , Andersen Olav M.
Published: January 2023

SORL1
, the gene encoding the large multidomain SORLA protein, has emerged as only the fourth gene that when mutated can by itself cause Alzheimer’s disease (AD), and as a gene reliably linked to both the early- and late-onset forms of the disease. SORLA is known to interact with the endosomal trafficking regulatory complex called retromer in regulating the recycling of endosomal cargo, including the amyloid precursor protein (APP) and the glutamate receptor GluA1. Nevertheless, SORLA’s precise structural–functional relationship in endosomal recycling tubules remains unknown. Here, we address these outstanding questions by relying on crystallographic and artificial-intelligence evidence to generate a structural model for how SORLA folds and fits into retromer-positive endosomal tubules, where it is found to dimerize via both SORLA’s fibronectin-type-III (3Fn)- and VPS10p-domains. Moreover, we identify a SORLA fragment comprising the 3Fn-, transmembrane, and cytoplasmic domains that has the capacity to form a dimer, and to enhance retromer-dependent recycling of APP by decreasing its amyloidogenic processing. Collectively, these observations generate a model for how SORLA dimer (and possibly polymer) formation can function in stabilizing and enhancing retromer function at endosome tubules. These findings can inform investigation of the many AD-associated
SORL1
variants for evidence of pathogenicity and can guide discovery of novel drugs for the disease.
Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation
Authors: Kuatsjah Eugene , Zahn Michael , Chen Xiangyang , Kato Ryo , Hinchen Daniel J. , Konev Mikhail O. , Katahira Rui , Orr Christian , Wagner Armin , Zou Yike , Haugen Stefan J. , Ramirez Kelsey J. , Michener Joshua K. , Pickford Andrew R. , Kamimura Naofumi , Masai Eiji , Houk K. N. , McGeehan John E. , Beckham Gregg T.
Published: January 2023

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of
erythro
-1,2-diguaiacylpropane-1,3-diol (
erythro
-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in
Novosphingobium aromaticivorans
. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts
erythro
-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the
N. aromaticivorans
LdpA and another homolog identified in
Sphingobium
sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C
1
reaction product, and we further demonstrated that both enantiomers of
erythro
-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.
Structure–function correlates of fibrinogen binding by
Acinetobacter
adhesins critical in catheter-associated urinary tract infections
Authors: Tamadonfar Kevin O. , Di Venanzio Gisela , Pinkner Jerome S. , Dodson Karen W. , Kalas Vasilios , Zimmerman Maxwell I. , Bazan Villicana Jesus , Bowman Gregory R. , Feldman Mario F. , Hultgren Scott J.
Published: January 2023

Multidrug-resistant 
Acinetobacter baumannii
infections are an urgent clinical problem and can cause difficult-to-treat nosocomial infections. During such infections, like catheter-associated urinary tract infections (CAUTI),
A. baumannii
rely on adhesive, extracellular fibers, called chaperone-usher pathway (CUP) pili for critical binding interactions. The
A. baumannii
uropathogenic strain, UPAB1, and the pan-European subclone II isolate, ACICU, use the CUP pili Abp1 and Abp2 (previously termed Cup and Prp, respectively) in tandem to establish CAUTIs, specifically to facilitate bacterial adherence and biofilm formation on the implanted catheter. Abp1 and Abp2 pili are tipped with two domain tip adhesins, Abp1D and Abp2D, respectively. We discovered that both adhesins bind fibrinogen, a critical host wound response protein that is released into the bladder upon catheterization and is subsequently deposited on the catheter. The crystal structures of the Abp1D and Abp2D receptor-binding domains were determined and revealed that they both contain a large, distally oriented pocket, which mediates binding to fibrinogen and other glycoproteins. Genetic, biochemical, and biophysical studies revealed that interactions with host proteins are governed by several critical residues in and along the edge of the binding pocket, one of which regulates the structural stability of an anterior loop motif. K34, located outside of the pocket but interacting with the anterior loop, also regulates the binding affinity of the protein. This study illuminates the mechanistic basis of the critical fibrinogen-coated catheter colonization step in
A. baumannii
CAUTI pathogenesis.
Spontaneous cortical dynamics from the first years to the golden years
Authors: Rempe Maggie P. , Ott Lauren R. , Picci Giorgia , Penhale Samantha H. , Christopher-Hayes Nicholas J. , Lew Brandon J. , Petro Nathan M. , Embury Christine M. , Schantell Mikki , Johnson Hallie J. , Okelberry Hannah J. , Losh Kathryn L. , Willett Madelyn P. , Losh Rebecca A. , Wang Yu-Ping , Calhoun Vince D. , Stephen Julia M. , Heinrichs-Graham Elizabeth , Kurz Max J. , Wilson Tony W.
Published: January 2023

In the largest and most expansive lifespan magnetoencephalography (MEG) study to date (n = 434, 6 to 84 y), we provide critical data on the normative trajectory of resting-state spontaneous activity and its temporal dynamics. We perform cutting-edge analyses to examine age and sex effects on whole-brain, spatially-resolved relative and absolute power maps, and find significant age effects in all spectral bands in both types of maps. Specifically, lower frequencies showed a negative correlation with age, while higher frequencies positively correlated with age. These correlations were further probed with hierarchical regressions, which revealed significant nonlinear trajectories in key brain regions. Sex effects were found in absolute but not relative power maps, highlighting key differences between outcome indices that are generally used interchangeably. Our rigorous and innovative approach provides multispectral maps indicating the unique trajectory of spontaneous neural activity across the lifespan, and illuminates key methodological considerations with the widely used relative/absolute power maps of spontaneous cortical dynamics.
Infection-elicited microbiota promotes host adaptation to nutrient restriction
Authors: De Siqueira Mirian Krystel , Andrade-Oliveira Vinicius , Stacy Apollo , Pedro Tôrres Guimarães João , Wesley Alberca-Custodio Ricardo , Castoldi Angela , Marques Santos Jaqueline , Davoli-Ferreira Marcela , Menezes-Silva Luísa , Miguel Turato Walter , Han Seong-Ji , Glatman Zaretsky Arielle , Hand Timothy Wesley , Olsen Saraiva Câmara Niels , Russo Momtchilo , Jancar Sonia , Morais da Fonseca Denise , Belkaid Yasmine
Published: January 2023

The microbiota performs multiple functions vital to host fitness, including defense against pathogens and adaptation to dietary changes. Yet, how environmental challenges shape microbiota resilience to nutrient fluctuation remains largely unexplored. Here, we show that transient gut infection can optimize host metabolism toward the usage of carbohydrates. Following acute infection and clearance of the pathogen, mice gained more weight as a result of white adipose tissue expansion. Concomitantly, previously infected mice exhibited enhanced carbohydrate (glucose) disposal and insulin sensitivity. This metabolic remodeling depended on alterations to the gut microbiota, with infection-elicited
Betaproteobacteria
being sufficient to enhance host carbohydrate metabolism. Further, infection-induced metabolic alteration protected mice against stunting in the context of limited nutrient availability. Together, these results propose that alterations to the microbiota imposed by acute infection may enhance host fitness and survival in the face of nutrient restriction, a phenomenon that may be adaptive in settings where both infection burden and food precarity are prevalent.
Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids
Authors: Costa Bruno , Li Calzi Marco , Castellano Mauricio , Blanco Valentina , Cuevasanta Ernesto , Litvan Irene , Ivanov Pavel , Witwer Kenneth , Cayota Alfonso , Tosar Juan Pablo
Published: January 2023

Nonvesicular extracellular RNAs (nv-exRNAs) constitute the majority of the extracellular RNAome, but little is known about their stability, function, and potential use as disease biomarkers. Herein, we measured the stability of several naked RNAs when incubated in human serum, urine, and cerebrospinal fluid (CSF). We identified extracellularly produced tRNA-derived small RNAs (tDRs) with half-lives of several hours in CSF. Contrary to widespread assumptions, these intrinsically stable small RNAs are full-length tRNAs containing broken phosphodiester bonds (i.e., nicked tRNAs). Standard molecular biology protocols, including phenol-based RNA extraction and heat, induce the artifactual denaturation of nicked tRNAs and the consequent in vitro production of tDRs. Broken bonds are roadblocks for reverse transcriptases, preventing amplification and/or sequencing of nicked tRNAs in their native state. To solve this, we performed enzymatic repair of nicked tRNAs purified under native conditions, harnessing the intrinsic activity of phage and bacterial tRNA repair systems. Enzymatic repair regenerated an RNase R-resistant tRNA-sized band in northern blot and enabled RT-PCR amplification of full-length tRNAs. We also separated nicked tRNAs from tDRs by chromatographic methods under native conditions, identifying nicked tRNAs inside stressed cells and in vesicle-depleted human biofluids. Dissociation of nicked tRNAs produces single-stranded tDRs that can be spontaneously taken up by human epithelial cells, positioning stable nv-exRNAs as potentially relevant players in intercellular communication pathways.
SUMO/deSUMOylation of the BRI1 brassinosteroid receptor modulates plant growth responses to temperature
Authors: Naranjo-Arcos Maria , Srivastava Moumita , Deligne Florian , Bhagat Prakash Kumar , Mansi Mansi , Sadanandom Ari , Vert Grégory
Published: January 2023

Brassinosteroids (BRs) are a class of steroid molecules perceived at the cell surface that act as plant hormones. The BR receptor BRASSINOSTEROID INSENSITIVE1 (BRI1) offers a model to understand receptor-mediated signaling in plants and the role of post-translational modifications. Here we identify SUMOylation as a new modification targeting BRI1 to regulate its activity. BRI1 is SUMOylated in planta on two lysine residues, and the levels of BRI1 SUMO conjugates are controlled by the Desi3a SUMO protease. Loss of Desi3a leads to hypersensitivity to BRs, indicating that Desi3a acts as a negative regulator of BR signaling. Besides, we demonstrate that BRI1 is deSUMOylated at elevated temperature by Desi3a, leading to increased BRI1 interaction with the negative regulator of BR signaling BIK1 and to enhanced BRI1 endocytosis. Loss of Desi3a or BIK1 results in increased response to temperature elevation, indicating that BRI1 deSUMOylation acts as a safety mechanism necessary to keep temperature responses in check. Altogether, our work establishes BRI1 deSUMOylation as a molecular crosstalk mechanism between temperature and BR signaling, allowing plants to translate environmental inputs into growth response.
CBX5 loss drives EGFR inhibitor resistance and results in therapeutically actionable vulnerabilities in lung cancer
Authors: Bugide Suresh , Edwards Yvonne J. K. , Gupta Romi , Green Michael R. , Wajapeyee Narendra
Published: January 2023

Although epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (EGFRi) are approved for treating EGFR-mutant lung adenocarcinoma (LUAD), emergence of acquired resistance limits their clinical benefits. Several mechanisms for acquired resistance to EGFRi in LUAD have been identified; however, the molecular basis for this resistance remains unknown in ~30% of LUAD. Chromatin and DNA modifiers and their regulators play important roles in determining response to anticancer therapies. Therefore, to identify nongenetic mechanisms of EGFRi resistance in LUAD, we performed an epigenome-wide shRNA screen targeting 363 human epigenetic regulator genes. This screen identified loss of the transcriptional repressor chromobox homolog 5 (CBX5) as a driver of EGFRi resistance in EGFR-mutant LUAD. Loss of CBX5 confers resistance to multiple EGFRi in both cell culture and mice. We found that CBX5 loss in EGFR-mutant LUAD cells leads to increased expression of the transcription factor E2F1, which in turn stimulates expression of the antiapoptotic gene
BIRC5
(
survivin
). This E2F1-mediated upregulation of BIRC5 in
CBX5
-knockdown LUAD cells attenuates apoptosis induction following EGFRi treatment. Consistent with these results, knockdown of
E2F1
or
BIRC5
partly rescues
CBX5
-knockdown-induced EGFRi resistance in cell culture and mice. EGFRi-resistant LUAD cell lines show reduced CBX5 expression compared to parental lines; however, bromo- and extra-terminal (BET)-domain inhibitors (BETi) restore CBX5 expression in these cells and sensitize them to EGFRi/BETi combination therapy. Similarly, treatment with a BIRC5 inhibitor suppresses growth of EGFRi-resistant LUAD cells. Collectively, these studies identify CBX5 loss as a driver of EGFRi resistance and reveal therapeutic opportunities for treating EGFRi-resistant LUAD.
Serbian Clitics
Authors: Milićević Jasmina
Published: January 2023

Clitics, those “funny little words” like English contracted future tense and pluperfect tense/conditional mood markers (’ll and ’d) or French pronominal objects (le ‘him’, la ‘her’, lui ‘to him/her’, etc.), have long been a source of fascination for linguists. Lacking an inherent stress that characterizes “well-behaved” words, clitics prosodically depend on a stressed sentence element, called their host, which makes them look and, in some contexts, behave like affixes (parts of words). Some clitics, Serbian second-position clitics being the case in point, also obey stringent linear ordering rules, different from those holding for fully-fledged sentence elements. This monograph offers a comprehensive formalized description of second-position clitics in standard Serbian from the viewpoint of the Meaning-Text theory, an approach relying on syntactic dependencies and oriented towards speech production, which sets it apart from most contemporary frameworks. It will be of interest for general linguists, Slavists, and advanced learners of Serbian.
On the use of there-clefts with zero subject relativizer
Authors: Kaltenböck Gunther
Published: January 2023

This chapter investigates the use of there-clefts without a subject relativizer (e.g. There’s a man came into the bar) in contemporary British English, a much neglected construction that is often dismissed as non-standard. Using data from the Spoken British National Corpus 2014, the study shows that it is clearly attested, with a total of 170 instances, and thus more than just a marginal syntactic anomaly. Omission of the relativizer is most frequent with the presentational-eventive type, which narrowly outnumbers the specificational type (viz. enumerative-specificational and quantifying-specificational). The relative frequency of the former is attributed to its unique pragmatic function, combining a new predication with a new referent. Structurally, this type is analysed as mono-clausal with an invariable existential prefix there’s.
Atopicality as the unmarked logical structure in Scottish Gaelic
Authors: Bartlett Tom
Published: January 2023

In this paper I argue that the canonical clause structure in Scottish Gaelic does not select an element as topical, but that marked structures are available to do so under specific discursive conditions. As such, Scottish Gaelic represents a previously unrecognised typological category in terms of text-organisational preferences. To make this argument I draw on discussions concerning the structure of marked atopical utterances crosslinguistically and compare these with the unmarked Gaelic structure. I draw a distinction, however, between the unmarked atopical clause in Gaelic, which I analyse as event-scoped, and the marked atopical clauses discussed in the literature, which are analysed as sentence-focused. I then demonstrate that Gaelic employs marked structures for the purposes of both topicalisation and sentence focus.
Community Engagement in Research & Policy Development: A One Health Approach to the Control of Ticks and Tick-borne Diseases in Eastern Bhutan
Authors: Namgyal Jamyang , Chedup Kinzang , Couloigner Isabelle , Cork Susan
Published: January 2023

Livestock farming plays an important role in supporting the livelihood of resource-poor subsistence farmers in Bhutan. However, ticks and tick-borne diseases (TBDs) are major constraints on livestock farming due to their negative effect on health and production. In this case study, we illustrate how we engaged communities, academic partners from the University of Calgary (UoC), and the experts and policy makers from the Royal Government of Bhutan (RGoB) to conduct research and develop policies regarding ticks and TBDs in Bhutan. The team used a transdisciplinary approach to design and conduct an active field-surveillance programme. Live ticks were collected from cattle to determine tick species diversity, infestation prevalence and geographic distribution. Habitat suitability models were also developed for four common tick species identified in Bhutan by engaging environmental modellers from UoC. Further, we conducted face-to-face interviews with 246 farmers in eastern Bhutan to understand their knowledge, management practices and perspectives on ticks and TBDs. Five genera and 13 species of ixodid ticks were identified. Despite a high level of acaricide usage among farmers, we found that the level of knowledge about ticks and TBDs was low. The research results were shared with the communities and other stakeholders to inform and initiate the development and adoption of effective tick prevention and control measures. We conclude that such collaborative research projects using an interdisciplinary approach and involving communities have huge potential to transfer research findings into policy and practice.
Effect of selective attention on auditory brainstem response
Authors: Kumar Sathish , Nayak Srikanth , Pitchai Muthu Arivudai Nambi
Published: January 2023

Introduction

Auditory selective attention can enhance the processing of relevant information and inhibit irrelevant information. The attentional modulation of auditory processing is evidenced through cortical auditory event-related potentials and frequency following response. On the other hand, such attentional effects on brainstem evoked potentials showed mixed results. Hence, the current study aimed to investigate the effect of selective attention on Auditory Brainstem Response.

Methods

Sixteen young adults with bilateral normal hearing sensitivity were recruited for the study, and their auditory brainstem responses were recorded using IHS Smart EP version 3.92 for active listening, passive listening with the visual task, and passive listening with visual distracter conditions.

Results

The statistical analysis of the wave-V latency and amplitude obtained from three conditions revealed no effect on the latency; however, peak V amplitude was lower in passive listening with visual distractor condition than in active listening and passive listening with visual task condition. Further attentional modulation was seen only on the contralateral montage and not on the ipsilateral montage.

Conclusion

The current study results demonstrate the attentional modulation at earlier stages of auditory processing as evidenced by the increased amplitude of peak V.
Characterization of factors influencing absorbance measurements in LED-based colorimeters
Authors: Dangkulwanich Manchuta , Thitaparun Porntida , Yimkosol Warangkana , Chalermsongsak Tara
Published: January 2023

Homemade colorimeters using simple parts are excellent in undergraduate teaching labs as they allow students to learn instrument components and principles behind absorbance measurements. However, the absorbance values measured from such instruments often differ from those determined by commercial spectrophotometers. This work provides a step-by-step calculation of absorbance, taking into account the properties of each component. Using a Si-photodiode detector and a light-dependent resistor, we show how the absorbance measurements depend on the spectral irradiance of the light source, the absorption spectrum of the sample, and the responsivity of the detectors. The provided calculation can help undergraduate students visualize how these factors contribute to optical measurements. It can serve as an experiment to introduce concepts of instrumentation and analysis of its performance.
Beyond Stevin’s law: the Janssen effect
Authors: Ivchenko Vladimir
Published: January 2023

We give a detailed derivation of the equation describing the height distribution of the vertical pressure in both cylindrical and conical vessels filled with granular material. It is surprising that for a convergent hopper, the vertical pressure can reach a maximum at some intermediate depth (the enhanced Janssen effect). The consideration of this problem will be useful for undergraduates, who study the statics of heterogeneous media.
Study on low rate of change characteristics of saturation output current of 28 nm UTBB FDSOI at 300 °C high-temperature
Authors: Xu L D , Gao L C , Ni T , Wang J J , Zhao S S , Zhang H Y , Li Y F , Wang R J , Li X J , Yan W W , Li D L , Bu J H , Zeng C B , Li B , Wang Z J , Zhao F Z , Luo J J , Han Z S
Published: January 2023

Partially-depleted silicon-on-insulator (PDSOI) MOSFETs with full dielectric isolation structure are widely used in the high temperature field of 225 °C, but affected by the threshold voltage and carrier mobility, the saturated output current has a rate of change as high as 24.9% at 25 °C–300 °C, which will reduce the working speed and accuracy of the analog circuit. This paper studies the high temperature output current characteristics of ultra-thin body and buried oxide (UTBB) fully-depleted silicon-on-insulator (FDSOI) MOSFETs with the 28 nm low voltage threshold structure. The experimental results show that when the gate voltage of the device is constant, the saturation current change of 28 nm short-channel FDSOI device is 1.93% in the temperature range from 25 °C to 300 °C, which is 12.9 times more stable than that of 0.13 μm PDSOI device, 4.5 times and 8.4 times higher than that of 0.3 μm and 2 μm long-channel FDSOI device. When the gate voltage of the device drifts from the zero-temperature coefficient (ZTC) point by ±10%–±20%, the output current change of the short-channel FDSOI device is still the lowest. It is proved by theory and simulation that the low temperature change rate of the carrier velocity of the short-channel FDSOI device is the main factor affecting the stability of the output current. From the analysis of the saturation current model and the ZTC operating point, reducing the gate operating voltage of the device or increasing the threshold voltage of the device can further improve the stability of the output current at high temperatures. The research in this paper proves that the 28 nm UTBB FDSOI device has good high temperature saturation current stability, which can well meet the output current stability requirements of high temperature analog circuits.
A 2π-periodic anisotropic magnetoresistance in multi-Weyl semimetals
Authors: Zhang J X , Wang C M
Published: January 2023

A 2π-periodic anisotropic magnetoresistance (AMR) violating the classical two-fold symmetry is found in the multi-Weyl semimetals. It is induced by the intrinsic magnetization due to the magnetic doping. The monopole charge influences the novel AMR, strongly. For single- and triple-Weyl semimetals, tilt along the x-direction or equivalently along the y-direction is indispensable in the nonzero AMR. However, the AMR with 2π period even exists for the untilted double-Weyl case. The oscillation of the conductivity for the triple one is out-of-phase compared to the other two. We decompose the conductivity into the π and 2π parts. The amplitude of the dominant 2π contribution increases almost linearly with the magnetization for all three cases. Moreover, the strength of the magnetic scattering strongly affects the magnitudes. Our work will contribute to a deeper understanding of the AMR in multi-Weyl semimetals.
RETRACTED: An unsupervised anomaly detection approach for pre-seismic ionospheric total electron content
Authors: Shi Wen , Peng Zhiyu , Huang Yongming , Zhang Guobao , Wang Cunsong
Published: January 2023

This paper focuses on the anomaly detection for ionospheric total electron content (TEC) before earthquakes. In this paper, a novel unsupervised approach is proposed. First, interval-based method is employed to granulate the TEC series. Justifiable granularity principle is utilized to construct interval information granules (IGs) for representing TEC series. Second, high-order difference method is introduced to construct rectangle IGs and cube IGs for obtaining the new representation of TEC. Third, corresponding similarity measurement method is designed to calculate the anomaly score of each IG, which is the evaluation criterion for detecting the anomalies. Finally, experimental results using real TEC datasets validate the effectiveness of the proposed approach. Compared with the existing major approaches, because the proposed approach can capture more morphological details and variation trend of TEC series, it can achieve a higher detection accuracy.
Dimensionality reduction method based on multiple feature-space collaborative discriminative projection for rotor fault diagnosis
Authors: Dong Xiaoxin , Zhao Rongzhen , Yuan Jianhui , Chen Pengfei , He Tianjing , Wei Kongyuan
Published: January 2023

At present, the trend for complex and intelligent rotating machinery and equipment, which generate a large amount of high-dimensional and nonlinear fault monitoring data that is difficult to handle, is becoming more and more apparent. This makes the traditional dimensionality reduction algorithms based on point-to-point metrics or a small number of graph-embedding structures lose their utility. To solve this problem, a multiple feature-space collaborative discriminative projection (MFSCDP) algorithm for rotor fault data set dimensionality reduction is proposed. The algorithm first improves the projection metric from sample point to feature space into the median metric in order to achieve the effect of weakening the extrapolation error of the algorithm, and based on this, we propose a sample point-to-point guided nearest-neighbor feature space selection method to improve the construction efficiency of the feature space embedding graph. Then, we use Relief F to indirectly construct the reduced dimensional projection matrix with multiple feature space of collaboration. Finally, the proposed MFSCDP algorithm is used for the dimensionality reduction process of a rotor fault data set. The algorithm’s performance was verified using experimental information from rotor failure simulations of two different structural types. The results show that the algorithm can reduce the difficulty of fault classification and improve the accuracy of identification.
Improving distance relay performance for heavily distorted voltage and current by accurate signal reconstruction using extended Kalman filter
Authors: Nair Shivani H , K Devika M , Raj Aswin , Bernard Bensen , V Vinod , P R Sunil Kumar
Published: January 2023

Distance relay plays a pivotal role in the detection of faults and subsequent isolation in transmission lines. However, severe distortion in the measured voltage and current waveforms (such as due to current transformer (CT) saturation), affects their performance. This paper focuses on a compensation method for signal reconstruction using extended Kalman filter (EKF) algorithm to improve relay functioning, enhancing the safety of transmission lines. The proposed fault detection scheme was tested extensively by running simulations using PSCAD and MATLAB for different types of faults at various distances and CT burden. The CT model in PSCAD was developed based on the Jiles–Atherton phenomenological theory in order to closely resemble a real-time CT with its saturation effects. The simulation results show that the proposed method is highly efficient in determining the exact fault point with improved zone approaching times even with measured signals having high noise and harmonic content. In cases where the conventional relay fails to detect the fault in the correct zone, the compensated data from the proposed method accurately detects the zone. Hardware experimental tests were carried out to further verify the effectiveness of the scheme in real-time, where the EKF based algorithm was implemented using a DSP-based microcontroller.
10-kHz-rate two-color dual-plane stereo-PIV using an optical parametric oscillator
Authors: Jiang Naibo , Hsu Paul S , Fugger Christopher A , Schmidheiser Sara E , Emerson Benjamin L , Lieuwen Timothy C , Roy Sukesh
Published: January 2023

10 kHz-rate dual-plane stereoscopic particle-image velocimetry (DSPIV) was applied in a swirling jet flame measurement simultaneously with hydroxyl planar laser-induced fluorescence (OH-PLIF). A high-speed burst-mode laser system with an optical parametric oscillator were used in double-pulse laser generation of 532 nm for one plane and 607 nm for the second plane. Temporally-resolved particle image velocimetry (PIV) image sequences, nine-component velocity gradient tensor, and simultaneous OH-PLIF images are presented. Flow vorticities and strain rates are also obtained with the measured velocity gradients. Compared with previous polarization-based dual-plane PIV technique, two-color based DSPIV measurement has distinctive advantages in elimination of signal interference from different PIV plane due to polarization leakage and hence improves measurement accuracy.
Study of the oxidation process of bismuth nanoparticles using NaClO
Authors: Flores Castañeda M , Camacho-López S , Castrejón-Sánchez V H , Morales-Ramos C B , Camacho-López M
Published: January 2023

Bismuth nanoparticles (NPs) colloids synthesized in deionized water by laser ablation of solids in liquids technique (LASL) were oxidized using NaClO solutions at different concentrations. Oxidized nanomaterials were characterized using several techniques. The crystalline phases of the bismuth compound were determined using Raman microspectroscopy, and the crystallographic structure was identified by x-ray diffraction (XRD). The size and morphology of the obtained nanomaterials were studied by transmission electron microscopy (TEM). The chemical states were determined using x-ray photoelectron spectroscopy (XPS), and the optical properties of the colloids were characterized by UV–vis spectroscopy. The absorption spectra were analyzed using the Tauc method to determine the band gaps of the obtained nanomaterials. Our results showed morphological changes, starting from small nanoparticles to nanosheets and a mixture of nanosheets with hollow nanoparticles. Two kinds of nanomaterials were found depending on the NaClO solution concentration: Bi2O2CO3 single phase and a mixture of δ-Bi2O3 and Bi2O2CO3. Some samples were tested as photocatalysts and showed good performance in the degradation of methylene blue in solution. To the best of our knowledge, this is the first study on the oxidation process of bismuth colloidal nanoparticles at room temperature.