bluuebunny/crossref_metadata_2025 huggingface dataset:
IGZO nanofiber photoelectric neuromorphic transistors with indium ratio tuned synaptic plasticity
Authors: Zhu Yixin , Peng Baocheng , Zhu Li , Chen Chunsheng , Wang Xiangjing , Mao Huiwu , Zhu Ying , Fu Chuanyu , Ke Shuo , Wan Changjin , Wan Qing
Published: September 2022

Synaptic plasticity divided into long-term and short-term categories is regarded as the origin of memory and learning, which also inspires the construction of neuromorphic systems. However, it is difficult to mimic the two behaviors monolithically, which is due to the lack of time-tailoring approaches for a certain synaptic device. In this Letter, indium-gallium-zinc-oxide (IGZO) nanofiber-based photoelectric transistors are proposed for realizing tunable photoelectric synaptic plasticity by the indium composition ratio. Notably, short-term plasticity to long-term plasticity transition can be realized by increasing the ratio of indium in the IGZO channel layer. The spatiotemporal dynamic logic and low energy consumption (<100 fJ/spike) are obtained in devices with low indium ratio. Moreover, the symmetric spike-timing-dependent plasticity is achieved by exploiting customized light and electric pulse schemes. Photoelectric long-term plasticity, multi-level characteristics, and high recognition accuracy (93.5%) are emulated in devices with high indium ratio. Our results indicate that such a composition ratio modulated method could enrich the applications of IGZO nanofiber neuromorphic transistors toward the photoelectric neuromorphic systems.
Imaging in reflecting spheres
Authors: Eckmann Jean-Pierre , Gunaratne Gemunu H. , Shulman Jason , Wood Lowell T.
Published: September 2022

We study the formation of images in a reflective sphere in three configurations using caustics on the field of light rays. The optical wavefront emerging from a source point reaching a subject following passage through the optical system is, in general, a Gaussian surface with partial focus along the two principal directions of the Gaussian surface; i.e., there are two images of the source point, each with partial focus. As the source point moves, the images move on two surfaces, referred to as viewable surfaces. In our systems, one viewable surface consists of points with radial focus and the other consists of points with azimuthal focus. The problems we study are (1) imaging of a parallel beam of light, (2) imaging of the infinite viewed from a location outside the sphere, and (3) imaging of a planar object viewed through the point of its intersection with the radial line normal to the plane. We verify the existence of two images experimentally and show that the distance between them agrees with the computations.
Magnomechanically induced absorption and switching properties in a dispersively coupled magnon-qubit system
Authors: Barbhuiya Sabur A. , Bhattacherjee Aranya B.
Published: September 2022

We theoretically study the non-linear behavior of a hybrid quantum magnomechanical system, where the system consisting of a superconducting qubit couples dispersively to a magnon–phonon mode. The magnetic excitations (magnons) can interact with the mechanical vibrations of the system via a magnomechanical interaction, which results in the formation of magnomechanically induced transparency in the output of the system. We investigate the system’s switching behavior in the dressed qubit anharmonicity of the system and shows the sharp bistable frequency switching of the magnon–excitons. The proposed model also shows a realistic scheme to measure the magnon-qubit dispersive shift in the absorption spectra of the probe field. The absorption spectrum induced by the dispersive coupling shows a series of asymmetric double Fano line shapes whose positions can be determined by the magnon-qubit driving field. Our results will provide a theoretical approach to understand the complex and dynamic non-linear interactions and may come up with great significance in the realization of quantum sensing applications of magnonic systems.
Landscape-scale concordance between local ecological knowledge for tropical wild species and remote sensing of land cover
Authors: Takasaki Yoshito , Coomes Oliver T. , Abizaid Christian , Kalacska Margaret
Published: September 2022

Monitoring the status of species is crucial for biodiversity conservation and sustainable resource management in tropical forests, but conventional in situ monitoring methods are impractical over large scales. Scientists have resorted to two potentially complementary approaches: local ecological knowledge (LEK) and remote sensing. To gauge the potential of combining LEK and remote sensing for assessing species status at landscape scales, a large-scale assessment of the reliability of both measures is critical but hampered by the lack of ground-level data. We conducted a landscape-scale assessment of LEK and remote sensing, using a survey of over 900 communities (a near census in our study area) and nearly 4,000 households in 235 randomly selected communities in the Peruvian Amazon—the largest LEK survey as yet undertaken in tropical forests. The survey collected LEK data on the presence of 20 indicator species from both community leaders/elders and randomly sampled households. We assessed LEK and remotely sensed land cover—forest cover and nonmain channel open water—as proxies for species habitat, across species (game, fish, and timber), over time (current and historical), and by indigeneity (Indigenous peoples and mestizos). Overall, LEK and remotely sensed land cover corroborate each other well. Concordance is highest for the current status of game species reported by sampled households, as is the concordance of historical LEK from Indigenous community leaders/elders. The results point to the promise of combining LEK and remote sensing in monitoring the status of species in data-poor tropical forests.
The contributions of positive outgroup and negative ingroup evaluation to implicit bias favoring outgroups
Authors: Calanchini Jimmy , Schmidt Kathleen , Sherman Jeffrey W. , Klein Samuel A. W.
Published: September 2022

People sometimes prefer groups to which they do not belong (outgroups) over their own groups (ingroups). Many long-standing theoretical perspectives assume that this outgroup favorability bias primarily reflects negative ingroup evaluations rather than positive outgroup evaluations. To examine the contributions of negative ingroup versus positive outgroup evaluations to outgroup bias, we examined participants’ data (total
n
> 879,000) from Implicit Association Tests [A. G. Greenwald, D. E. McGhee, J. L. K. Schwartz,
J. Pers. Soc. Psychol.
74, 1464–1480 (1998)] measuring intergroup attitudes across four social domains in exploratory and preregistered confirmatory analyses. Process modeling [F. R. Conrey, J. W. Sherman, B. Gawronski, K. Hugenberg, C. J. Groom,
J. Pers. Soc. Psychol.
89, 469–487 (2005)] was applied to the responses of participants who demonstrated implicit outgroup bias to separately estimate the contributions of negative ingroup and positive outgroup evaluations. The outgroup biases of lower-status group members (i.e., Asian, Black, gay and lesbian, and older people) consistently reflected greater contributions of positive outgroup evaluations than negative ingroup evaluations. In contrast, the outgroup biases of higher-status group members (i.e., White, straight, and younger people) reflected a more varied pattern of evaluations. We replicated this pattern of results using explicitly measured intergroup evaluations. Taking these data together, the present research demonstrates a positive–negative asymmetry effect of outgroup bias, primarily among members of lower-status groups.
Changing patterns of genetic differentiation in the slender wild oat,Avena barbata
Authors: Latta Robert G. , Crosby Kate , Hamrick James L.
Published: September 2022

The slender wild oat (Avena barbata) was widely studied in California using allozymes in the 1970s and interpreted as a case of ecotypic adaptation to contrasting moisture environments. However, common garden studies suggested that the moist-associated (“mesic”) ecotype had high fitness in both moist and dry habitats, thus predicting an adaptive spread into areas occupied by the dry associated (“xeric”) ecotype. To test this prediction, we revisited 100 populations ofA. barbatathat were screened genetically 40 y ago. As expected, mesic allozyme and morphological markers are much more common than in the 1970s. The less-fit xeric ecotype, while still widespread, has declined markedly in range and frequency. Genotyping by sequencing of modern populations reveals striking genetic uniformity within each of the two ecotypes. In recombinants between the two ecotypes, the mesic allele at a major fitness quantitative trait locus (QTL) shows a high frequency but so do many other genomic regions not identified as fitness QTL. Additional introduced genotypes are diverse and more widespread than in the past, and our results show that these have spread into the former range of the xeric ecotype to an even greater extent than the mesic ecotype has. While these results confirm the prediction of contemporary evolution from common gardens, they also suggest that much of the change has been driven by additional waves of introduced genotypes.
Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics
Authors: Li Hong-Zhe , Yang Kai , Liao Hu , Lassen Simon Bo , Su Jian-Qiang , Zhang Xian , Cui Li , Zhu Yong-Guan
Published: September 2022

Antimicrobial resistance (AMR) in soils represents a serious risk to human health through the food chain and human–nature contact. However, the active antibiotic-resistant bacteria (ARB) residing in soils that primarily drive AMR dissemination are poorly explored. Here, single-cell Raman-D
2
O coupled with targeted metagenomics is developed as a culture-independent approach to phenotypically and genotypically profiling active ARB against clinical antibiotics in a wide range of soils. This method quantifies the prevalence (contamination degree) and activity (spread potential) of soil ARB and reveals a clear elevation with increasing anthropogenic activities such as farming and the creation of pollution, thereby constituting a factor that is critical for the assessment of AMR risks. Further targeted sorting and metagenomic sequencing of the most active soil ARB uncover several uncultured genera and a pathogenic strain. Furthermore, the underlying resistance genes, virulence factor genes, and associated mobile genetic elements (including plasmids, insertion sequences, and prophages) are fully deciphered at the single-cell level. This study advances our understanding of the soil active AMR repertoire by linking the resistant phenome to the genome. It will aid in the risk assessment of environmental AMR and guide the combat under the One Health framework.
The mismatch recognition protein MutSα promotes nascent strand degradation at stalled replication forks
Authors: Zhang Junqiu , Zhao Xin , Liu Lu , Li Hao-Dong , Gu Liya , Castrillon Diego H. , Li Guo-Min
Published: September 2022

Mismatch repair (MMR) is a replication-coupled DNA repair mechanism and plays multiple roles at the replication fork. The well-established MMR functions include correcting misincorporated nucleotides that have escaped the proofreading activity of DNA polymerases, recognizing nonmismatched DNA adducts, and triggering a DNA damage response. In an attempt to determine whether MMR regulates replication progression in cells expressing an ultramutable DNA polymerase ɛ (Polɛ), carrying a proline-to-arginine substitution at amino acid 286 (Polɛ-P286R), we identified an unusual MMR function in response to hydroxyurea (HU)-induced replication stress. Polɛ-P286R cells treated with hydroxyurea exhibit increased MRE11-catalyzed nascent strand degradation. This degradation by MRE11 depends on the mismatch recognition protein MutSα and its binding to stalled replication forks. Increased MutSα binding at replication forks is also associated with decreased loading of replication fork protection factors FANCD2 and BRCA1, suggesting blockage of these fork protection factors from loading to replication forks by MutSα. We find that the MutSα-dependent MRE11-catalyzed fork degradation induces DNA breaks and various chromosome abnormalities. Therefore, unlike the well-known MMR functions of ensuring replication fidelity, the newly identified MMR activity of promoting genome instability may also play a role in cancer avoidance by eliminating rogue cells.
Dissection of the long-range projections of specific neurons at the synaptic level in the whole mouse brain
Authors: Tian Jiaojiao , Ren Miao , Zhao Peilin , Luo Shukang , Chen Yingying , Xu Xiaofeng , Jiang Tao , Sun Qingtao , Li Anan , Gong Hui , Li Xiangning , Luo Qingming
Published: September 2022

Through synaptic connections, long-range circuits transmit information among neurons and connect different brain regions to form functional motifs and execute specific functions. Tracing the synaptic distribution of specific neurons requires submicron-level resolution information. However, it is a great challenge to map the synaptic terminals completely because these fine structures span multiple regions, even in the whole brain. Here, we develop a pipeline including viral tracing, sample embedding, fluorescent micro-optical sectional tomography, and big data processing. We mapped the whole-brain distribution and architecture of long projections of the parvalbumin neurons in the basal forebrain at the synaptic level. These neurons send massive projections to multiple downstream regions with subregional preference. With three-dimensional reconstruction in the targeted areas, we found that synaptic degeneration was inconsistent with the accumulation of amyloid-β plaques but was preferred in memory-related circuits, such as hippocampal formation and thalamus, but not in most hypothalamic nuclei in 8-month-old mice with five familial Alzheimer’s disease mutations. Our pipeline provides a platform for generating a whole-brain atlas of cell-type-specific synaptic terminals in the physiological and pathological brain, which can provide an important resource for the study of the organizational logic of specific neural circuits and the circuitry changes in pathological conditions.
Dynamic and stable population coding of attentional instructions coexist in the prefrontal cortex
Authors: Sapountzis Panagiotis , Paneri Sofia , Papadopoulos Sotirios , Gregoriou Georgia G.
Published: September 2022

A large body of recent work suggests that neural representations in prefrontal cortex (PFC) are changing over time to adapt to task demands. However, it remains unclear whether and how such dynamic coding schemes depend on the encoded variable and are influenced by anatomical constraints. Using a cued attention task and multivariate classification methods, we show that neuronal ensembles in PFC encode and retain in working memory spatial and color attentional instructions in an anatomically specific manner. Spatial instructions could be decoded both from the frontal eye field (FEF) and the ventrolateral PFC (vlPFC) population, albeit more robustly from FEF, whereas color instructions were decoded more robustly from vlPFC. Decoding spatial and color information from vlPFC activity in the high-dimensional state space indicated stronger dynamics for color, across the cue presentation and memory periods. The change in the color code was largely due to rapid changes in the network state during the transition to the delay period. However, we found that dynamic vlPFC activity contained time-invariant color information within a low-dimensional subspace of neural activity that allowed for stable decoding of color across time. Furthermore, spatial attention influenced decoding of stimuli features profoundly in vlPFC, but less so in visual area V4. Overall, our results suggest that dynamic population coding of attentional instructions within PFC is shaped by anatomical constraints and can coexist with stable subspace coding that allows time-invariant decoding of information about the future target.
Single p197 molecules of the mitochondrial genome segregation system of
Trypanosoma brucei
determine the distance between basal body and outer membrane
Authors: Aeschlimann Salome , Kalichava Ana , Schimanski Bernd , Berger Bianca Manuela , Jetishi Clirim , Stettler Philip , Ochsenreiter Torsten , Schneider André
Published: September 2022

The tripartite attachment complex (TAC) couples the segregation of the single unit mitochondrial DNA of trypanosomes with the basal body (BB) of the flagellum. Here, we studied the architecture of the exclusion zone filament (EZF) of the TAC, the only known component of which is p197, that connects the BB with the mitochondrial outer membrane (OM). We show that p197 has three domains that are all essential for mitochondrial DNA inheritance. The C terminus of p197 interacts with the mature and probasal body (pro-BB), whereas its N terminus binds to the peripheral OM protein TAC65. The large central region of p197 has a high α-helical content and likely acts as a flexible spacer. Ultrastructure expansion microscopy (U-ExM) of cell lines exclusively expressing p197 versions of different lengths that contain both N- and C-terminal epitope tags demonstrates that full-length p197 alone can bridge the ∼270-nm distance between the BB and the cytosolic face of the OM. Thus U-ExM allows the localization of distinct domains within the same molecules and suggests that p197 is the TAC subunit most proximal to the BB. In addition, U-ExM revealed that p197 acts as a spacer molecule, as two shorter versions of p197, with the repeat domain either removed or replaced by the central domain of the
Trypanosoma cruzi
p197 ortholog reduced the distance between the BB and the OM in proportion to their predicted molecular weight.
Super-enhancers conserved within placental mammals maintain stem cell pluripotency
Authors: Zhang Juqing , Zhou Yaqi , Yue Wei , Zhu Zhenshuo , Wu Xiaolong , Yu Shuai , Shen Qiaoyan , Pan Qin , Xu Wenjing , Zhang Rui , Wu Xiaojie , Li Xinmei , Li Yayu , Li Yunxiang , Wang Yu , Peng Sha , Zhang Shiqiang , Lei Anmin , Ding Xinbao , Yang Fan , Chen Xingqi , Li Na , Liao Mingzhi , Wang Wei , Hua Jinlian
Published: September 2022

Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals.
Reduced Satb1 expression predisposes CD4+T conventional cells to Treg suppression and promotes transplant survival
Authors: Gupta Pawan K. , Allocco Jennifer B. , Fraipont Jane M. , McKeague Michelle L. , Wang Peter , Andrade Michael S. , McIntosh Christine , Chen Luqiu , Wang Ying , Li Yan , Andrade Jorge , Conejo-Garcia José R. , Chong Anita S. , Alegre Maria-Luisa
Published: September 2022

Limiting CD4+T cell responses is important to prevent solid organ transplant rejection. In a mouse model of costimulation blockade-dependent cardiac allograft tolerance, we previously reported that alloreactive CD4+conventional T cells (Tconvs) develop dysfunction, losing proliferative capacity. In parallel, induction of transplantation tolerance is dependent on the presence of regulatory T cells (Tregs). Whether susceptibility of CD4+Tconvs to Treg suppression is modulated during tolerance induction is unknown. We found that alloreactive Tconvs from transplant tolerant mice had augmented sensitivity to Treg suppression when compared with memory T cells from rejector mice and expressed a transcriptional profile distinct from these memory T cells, including down-regulated expression of the transcription factor Special AT-rich sequence-binding protein 1 (Satb1). Mechanistically, Satb1 deficiency in CD4+T cells limited their expression of CD25 and IL-2, and addition of Tregs, which express higher levels of CD25 than Satb1-deficient Tconvs and successfully competed for IL-2, resulted in greater suppression of Satb1-deficient than wild-type Tconvs in vitro. In vivo, Satb1-deficient Tconvs were more susceptible to Treg suppression, resulting in significantly prolonged skin allograft survival. Overall, our study reveals that transplantation tolerance is associated with Tconvs’ susceptibility to Treg suppression, via modulated expression of Tconv-intrinsic Satb1. Targeting Satb1 in the context of Treg-sparing immunosuppressive therapies might be exploited to improve transplant outcomes.
Circadian clock controls rhythms in ketogenesis by interfering with PPARα transcriptional network
Authors: Mezhnina Volha , Ebeigbe Oghogho P. , Velingkaar Nikkhil , Poe Allan , Sandlers Yana , Kondratov Roman V.
Published: September 2022

Ketone bodies are energy-rich metabolites and signaling molecules whose production is mainly regulated by diet. Caloric restriction (CR) is a dietary intervention that improves metabolism and extends longevity across the taxa. We found that CR induced high-amplitude daily rhythms in blood ketone bodies (beta-hydroxybutyrate [βOHB]) that correlated with liver βOHB level. Time-restricted feeding, another periodic fasting–based diet, also led to rhythmic βOHB but with reduced amplitude. CR induced strong circadian rhythms in the expression of fatty acid oxidation and ketogenesis genes in the liver. The transcriptional factor peroxisome-proliferator-activated-receptor α (PPARα) and its transcriptional target hepatokine fibroblast growth factor 21 (FGF21) are primary regulators of ketogenesis.Fgf21expression and the PPARα transcriptional network became highly rhythmic in the CR liver, which implicated the involvement of the circadian clock. Mechanistically, the circadian clock proteins CLOCK, BMAL1, and cryptochromes (CRYs) interfered with PPARα transcriptional activity. Daily rhythms in the blood βOHB level and in the expression of PPARα target genes were significantly impaired in circadian clock–deficientCry1,2−/−mice. These data suggest that blood βOHB level is tightly controlled and that the circadian clock is a regulator of diet-induced ketogenesis.
Modulation of receptor-like transmembrane kinase 1 nuclear localization by DA1 peptidases in Arabidopsis
Authors: Gu Benguo , Dong Hui , Smith Caroline , Cui Guicai , Li Yunhai , Bevan Michael W.
Published: September 2022

The cleavage of intracellular domains of receptor-like kinases (RLKs) has an important functional role in the transduction of signals from the cell surface to the nucleus in many organisms. However, the peptidases that catalyze protein cleavage during signal transduction remain poorly understood despite their crucial roles in diverse signaling processes. Here, we report in the flowering plantArabidopsis thalianathat members of the DA1 family of ubiquitin-regulated Zn metallopeptidases cleave the cytoplasmic kinase domain of transmembrane kinase 1 (TMK1), releasing it for nuclear localization where it represses auxin-responsive cell growth during apical hook formation by phosphorylation and stabilization of the transcriptional repressors IAA32 and IAA34. Mutations inDA1family members exhibited reduced apical hook formation, and DA1 family-mediated cleavage of TMK1 was promoted by auxin treatment. Expression of the DA1 family-generated intracellular kinase domain of TMK1 by an auxin-responsive promoter fully restored apical hook formation in atmk1mutant, establishing the function of DA1 family peptidase activities in TMK1-mediated differential cell growth and apical hook formation. DA1 family peptidase activity therefore modulates TMK1 kinase activity between a membrane location where it stimulates acid cell growth and initiates an auxin-dependent kinase cascade controlling cell proliferation in lateral roots and a nuclear localization where it represses auxin-mediated gene expression and growth.
The Paf1 complex is required for RNA polymerase II removal in response to DNA damage
Authors: Chen Feilong , Liu Beibei , Zhou Hao , Long Jiafu
Published: September 2022

Rpb1, the largest subunit of RNA polymerase II (RNAPII), is rapidly polyubiquitinated and degraded in response to DNA damage; this process is considered to be a “mechanism of last resort’’ employed by cells. The underlying mechanism of this process remains elusive. Here, we uncovered a previously uncharacterized multistep pathway in which the polymerase-associated factor 1 (Paf1) complex (PAF1C, composed of the subunits Ctr9, Paf1, Leo1, Cdc73, and Rtf1) is involved in regulating the RNAPII pool by stimulating Elongin-Cullin E3 ligase complex-mediated Rpb1 polyubiquitination and subsequent degradation by the proteasome following DNA damage. Mechanistically, Spt5 is dephosphorylated following DNA damage, thereby weakening the interaction between the Rtf1 subunit and Spt5, which might be a key step in initiating Rpb1 degradation. Next, Rad26 is loaded onto stalled RNAPII to replace the Spt4/Spt5 complex in an RNAPII-dependent manner and, in turn, recruits more PAF1C to DNA lesions via the binding of Rad26 to the Leo1 subunit. Importantly, the PAF1C, assembled in a Ctr9-mediated manner, coordinates with Rad26 to localize the Elongin-Cullin complex on stalled RNAPII, thereby inducing RNAPII removal, in which the heterodimer Paf1/Leo1 and the subunit Cdc73 play important roles. Together, our results clearly revealed a new role of the intact PAF1C in regulating the RNAPII pool in response to DNA damage.
A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex
Authors: Huene Aidan L. , Sanders Steven M. , Ma Zhiwei , Nguyen Anh-Dao , Koren Sergey , Michaca Manuel H. , Mullikin James C. , Phillippy Adam M. , Schnitzler Christine E. , Baxevanis Andreas D. , Nicotra Matthew L.
Published: September 2022

Most colonial marine invertebrates are capable of allorecognition, the ability to distinguish between themselves and conspecifics. One long-standing question is whether invertebrate allorecognition genes are homologous to vertebrate histocompatibility genes. In the cnidarian
Hydractinia symbiolongicarpus,
allorecognition is controlled by at least two genes,
Allorecognition 1
(
Alr1
) and
Allorecognition 2
(
Alr2
), which encode highly polymorphic cell-surface proteins that serve as markers of self. Here, we show that
Alr1
and
Alr2
are part of a family of 41
Alr
genes, all of which reside in a single genomic interval called the Allorecognition Complex (ARC). Using sensitive homology searches and highly accurate structural predictions, we demonstrate that the Alr proteins are members of the immunoglobulin superfamily (IgSF) with V-set and I-set Ig domains unlike any previously identified in animals. Specifically, their primary amino acid sequences lack many of the motifs considered diagnostic for V-set and I-set domains, yet they adopt secondary and tertiary structures nearly identical to canonical Ig domains. Thus, the V-set domain, which played a central role in the evolution of vertebrate adaptive immunity, was present in the last common ancestor of cnidarians and bilaterians. Unexpectedly, several Alr proteins also have immunoreceptor tyrosine-based activation motifs and immunoreceptor tyrosine-based inhibitory motifs in their cytoplasmic tails, suggesting they could participate in pathways homologous to those that regulate immunity in humans and flies. This work expands our definition of the IgSF with the addition of a family of unusual members, several of which play a role in invertebrate histocompatibility.
The unusual convergence of steroid catabolic pathways in
Mycobacterium abscessus
Authors: Crowe Adam M. , Krekhno Jessica M. C. , Brown Kirstin L. , Kulkarni Jayesh A. , Yam Katherine C. , Eltis Lindsay D.
Published: September 2022

Mycobacterium abscessus
, an opportunistic pathogen responsible for pulmonary infections, contains genes predicted to encode two steroid catabolic pathways: a cholesterol catabolic pathway similar to that of
Mycobacterium tuberculosis
and a 4-androstenedione (4-AD) catabolic pathway. Consistent with this prediction,
M. abscessus
grew on both steroids. In contrast to
M. tuberculosis
,
Rhodococcus jostii
RHA1, and other Actinobacteria, the cholesterol and 4-AD catabolic gene clusters of the
M. abscessus
complex lack genes encoding HsaD, the
meta
-cleavage product (MCP) hydrolase. However,
M. abscessus
ATCC 19977 harbors two
hsaD
homologs elsewhere in its genome. Only one of the encoded enzymes detectably transformed steroid metabolites. Among tested substrates, HsaD
Mab
and HsaD
Mtb
of
M. tuberculosis
had highest substrate specificities for MCPs with partially degraded side chains thioesterified with coenzyme A (
k
cat
/
K
M
= 1.9 × 10
4
and 5.7 × 10
3
mM
−1
s
−1
, respectively). Consistent with a dual role in cholesterol and 4-AD catabolism, HsaD
Mab
also transformed nonthioesterified substrates efficiently, and a Δ
hsaD
mutant of
M. abscessus
grew on neither steroid. Interestingly, both steroids prevented growth of the mutant on acetate. The Δ
hsaD
mutant of
M. abscessus
excreted cholesterol metabolites with a fully degraded side chain, while the corresponding RHA1 mutant excreted metabolites with partially degraded side chains. Finally, the Δ
hsaD
mutant was not viable in macrophages. Overall, our data establish that the cholesterol and 4-AD catabolic pathways of
M. abscessus
are unique in that they converge upstream of where this occurs in characterized steroid-catabolizing bacteria. The data further indicate that cholesterol is a substrate for intracellular bacteria and that cholesterol-dependent toxicity is not strictly dependent on coenzyme A sequestration.
Rpd3 regulates single-copy origins independently of the rDNA array by opposing Fkh1-mediated origin stimulation
Authors: He Yiwei , Petrie Meghan V. , Zhang Haiyang , Peace Jared M. , Aparicio Oscar M.
Published: September 2022

Eukaryotic chromosomes are organized into structural and functional domains with characteristic replication timings, which are thought to contribute to epigenetic programming and genome stability. Differential replication timing results from epigenetic mechanisms that positively and negatively regulate the competition for limiting replication initiation factors. Histone deacetylase Sir2 negatively regulates initiation of the multicopy (∼150) rDNA origins, while Rpd3 histone deacetylase negatively regulates firing of single-copy origins. However, Rpd3’s effect on single-copy origins might derive indirectly from a positive function for Rpd3 in rDNA origin firing shifting the competitive balance. Our quantitative experiments support the idea that origins compete for limiting factors; however, our results show that Rpd3’s effect on single-copy origin is independent of rDNA copy-number and of Sir2’s effects on rDNA origin firing. WhereasRPD3deletion andSIR2deletion alter the early S phase dynamics of single-copy and rDNA origin firings in opposite fashion, unexpectedly onlyRPD3deletion suppresses overall rDNA origin efficiency across S phase. Increased origin activation inrpd3Δrequires Fkh1/2, suggesting that Rpd3 opposes Fkh1/2-origin stimulation, which involves recruitment of Dbf4-dependent kinase (DDK). Indeed, Fkh1 binding increases at Rpd3-regulated origins inrpd3Δcells in G1, supporting a mechanism whereby Rpd3 influences initiation timing of single-copy origins directly through modulation of Fkh1-origin binding. Genetic suppression of aDBF4hypomorphic mutation byRPD3deletion further supports the conclusion that Rpd3 impedes DDK recruitment by Fkh1, revealing a mechanism of Rpd3 in origin regulation.
Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism
Authors: Yoshihara Takeshi , Miller Nathan D. , Rabanal Fernando A. , Myles Hannah , Kwak Il-Youp , Broman Karl W. , Sadkhin Boris , Baxter Ivan , Dilkes Brian P. , Hudson Matthew E. , Spalding Edgar P.
Published: September 2022

Plants typically orient their organs with respect to the Earth’s gravity field by a dynamic process called gravitropism. To discover conserved genetic elements affecting seedling root gravitropism, we measured the process in a set ofZea mays(maize) recombinant inbred lines with machine vision and compared the results with those obtained in a similar study ofArabidopsis thaliana. Each of the several quantitative trait loci that we mapped in both species spanned many hundreds of genes, too many to test individually for causality. We reasoned that orthologous genes may be responsible for natural variation in monocot and dicot root gravitropism. If so, pairs of orthologous genes affecting gravitropism may be present within the maize andArabidopsisQTL intervals. A reciprocal comparison of sequences within the QTL intervals identified seven pairs of such one-to-one orthologs. Analysis of knockout mutants demonstrated a role in gravitropism for four of the seven:CCT2functions in phosphatidylcholine biosynthesis,ATG5functions in membrane remodeling during autophagy,UGP2produces the substrate for cellulose and callose polymer extension, andFAMAis a transcription factor. Automated phenotyping enabled this discovery of four naturally varying components of a conserved process (gravitropism) by making it feasible to conduct the same large-scale experiment in two species.
In vivo 3D profiling of site-specific human cancer cell morphotypes in zebrafish
Authors: Segal Dagan , Mazloom-Farsibaf Hanieh , Chang Bo-Jui , Roudot Philippe , Rajendran Divya , Daetwyler Stephan , Fiolka Reto , Warren Mikako , Amatruda James F. , Danuser Gaudenz
Published: September 2022

Tissue microenvironments affect the functional states of cancer cells, but determining these influences in vivo has remained a challenge. We present a quantitative high-resolution imaging assay of single cancer cells in zebrafish xenografts to probe functional adaptation to variable cell-extrinsic cues and molecular interventions. Using cell morphology as a surrogate readout of cell functional states, we examine environmental influences on the morphotype distribution of Ewing Sarcoma, a pediatric cancer associated with the oncogene EWSR1-FLI1 and whose plasticity is thought to determine disease outcome through non-genomic mechanisms. Computer vision analysis reveals systematic shifts in the distribution of 3D morphotypes as a function of cell type and seeding site, as well as tissue-specific cellular organizations that recapitulate those observed in human tumors. Reduced expression of the EWSR1-FLI1 protein product causes a shift to more protrusive cells and decreased tissue specificity of the morphotype distribution. Overall, this work establishes a framework for a statistically robust study of cancer cell plasticity in diverse tissue microenvironments.
Killing tensors in Koutras–Mcintosh spacetimes
Authors: Kruglikov Boris , Steneker Wijnand
Published: September 2022

The Koutras–McIntosh family of metrics include conformally flat pp-waves and the Wils metric. It appeared in a paper of 1996 by Koutras–McIntosh as an example of a pure radiation spacetime without scalar curvature invariants or infinitesimal symmetries. Here we demonstrate that these metrics have no ‘hidden symmetries’, by which we mean Killing tensors of low degrees. For the particular case of Wils metrics we show the nonexistence of Killing tensors up to degree 6. The technique we use is the geometric theory of overdetermined PDEs and the Cartan prolongation–projection method. Application of those allows to prove the nonexistence of polynomial in momenta integrals for the equation of geodesics in a mathematical rigorous way. Using the same technique we can completely classify all lower degree Killing tensors and, in particular, prove that for generic conformally flat pp-waves all Killing tensors of degree 3 and 4 are reducible.
In-band Radar Cross Section reduction for electromagnetic window by simultaneously enhancing transmission and coding reflection
Authors: Li Tiefu , Li Songyan , Wang Jiafu , Xia Song , Li Lei , Chu Zuntian , Yan Mingbao , Qu Shaobo
Published: September 2022

For electromagnetic windows (EWs), although the in-band transmission is satisfactory, reflection always exists at interfaces, which leads to considerable in-band RCS, especially for large-size EWs. The conventional manner of reducing the in-band RCS is focused on enhancing transmission, which is always limited by the unavoidable impedance mismatch at interfaces. To overcome this limit, in this paper, we propose to reduce the in-band RCS of EWs by simultaneously enhancing transmission and coding reflection using dimer metasurfaces. The dimer structure is composed of two unidentical meta-atoms patterned on the front and back surfaces of the EW, respectively, which can enhance the transmission in the band of interest. More importantly, when the dimer structure is flipped, the transmission is unaffected due to reciprocity, whereas the reflection will be different. Therefore, by coding the reflection phase, the in-band backward reflection can be further reduced due to scattering cancellation. Proof-of-principle prototypes were designed, fabricated and measured to verify this strategy. The experimental results are consistent with the simulation results, which proves the feasibility of this strategy. This work provides an alternative way of reducing the in-band RCS of EWs and may find practical applications in radomes, lenses and other areas.
Comparative studies on superconductivity in Cr3Ru compounds with bcc and A15 structures
Authors: Zhu Zhengyan , Zhang Ying-Jie , Li Yiwen , Li Qing , Duan Wen , Wen Hai-Hu
Published: September 2022

Chromium (Cr) is a transition metal element with 3d orbital electrons. In most compounds containing Cr, due to the correlation effect, twofold features, namely localization and itinerancy are expected. The localization gives rise to a magnetic moment, while the latter exhibits as the effective coherent weight for conductivity. Here we report the physical properties of Cr3Ru compounds with body-centered cubic (bcc) and A15 structures by using multiple experimental tools. The resistivity measurements show sharp superconducting transitions at

T

c

= 2.77 K and

T

c

= 3.37 K for the bcc and A15 structures, respectively. A high residual resistivity exists in both phases. Magnetization measurements also show rather narrow superconducting transitions, with a clear hump feature in the intermediate temperature region (about 150 K), which may be ascribed to the remaining antiferromagnetic spin fluctuations. A pronounced second peak effect has been observed in magnetization hysteresis loops in the superconducting state only for samples with bcc structure. The specific heat coefficient reveals a clear jump at critical temperatures (

T

c

). We find that s-wave gaps can be adopted to fit the low temperature specific heat data of both samples yielding ratios of

2
Δ

/

k

B

T

c

about 3.6, indicating a moderate pairing strength. Interestingly, the Wilson ratios

R

W

=
A

χ

0

/

γ
n

are 3.81 and 3.62 for the bcc and A15 phases, suggesting a moderate correlation effect of conducting electrons in the normal state. Besides, for samples with A15 structure, another specific heat anomaly occurs at about 0.85 K and is sensitive to magnetic fields. In addition, by applying high pressures, both systems will exhibit an enhancement of

T

c

with a rate of about 0.019 K GPa−1 and 0.013 K GPa−1 for the bcc and A15 phases, respectively. Our combinatory results point to unusual behavior of both superconducting and normal states in these two Cr based alloys.
Calibration-free pH long-time measurement method based on electrode potential drift dynamic compensation-applying self-adaptive dynamic optimization exponential smoothing method
Authors: Zhao Xueliang , Chen Ying , Xu Chongxuan , Wei Guanghua , Yuan Aijun
Published: September 2022

The long-term in-situ accurate measurement of pH value is an urgent need for environmental water quality monitoring without calibration of pH electrodes. The nonlinearity and potential drift of pH electrode is the main problem which restricts long-term continuous monitoring. The characteristic rules including electrode potential, zero value, electrode slope coefficient, and electrode potential drift for pH electrode are analyzed in detail under the condition of long-term continuous use. The exponential smoothing potential drift prediction model with self-adaptive dynamic optimization smoothing order and smoothing coefficient is established. Combining electrode potential drift threshold judgment and Nernst equation, calibration-free dynamic calculation mathematical model of pH long-term monitoring is established. Indoor simulation and field test indicate that the measurement absolute error caused by electrode drift is within 0.01 pH and the specified measurement error for pH monitoring instrument is always within 0.1 pH. The proposed method is very suitable for the terminal of pH detector with the advantages of good portability for the MCU chip, small samples, high-precision and fast running speed. Furthermore, the life of pH electrode can be prolonged significantly. It is also proved that the proposed method has a good application prospect.
Prognosis of rotor parts fly-off based on cascade classification and online prediction ability index
Authors: Shen Yingjun , Song Zhe , Kusiak Andrew , Zhan Zhiyong
Published: September 2022

Large rotating machines are critical equipment in many process industries, such as energy, chemical, and power generation. Due to high rotating speed and tremendous momentum of the rotor, the centrifugal force may lead to flying apart of the rotor parts, which brings a great threat to the operation safety. Early detection and prediction of potential failures could prevent catastrophic plant downtime and economic loss. In this paper, we divide the operational states of a rotating machine into normal, risky, and high-risk ones based on the time to the moment of failure. Then, a cascade classification algorithm is proposed to predict the states in two steps; first, we determine whether the machine is in normal or abnormal condition; for time periods predicted as abnormal, we further classify them into risky or high-risk state. Moreover, traditional classification model evaluation metrics, such as confusion matrix and true–false accuracy, are static and neglect online prediction dynamics and uneven error-prediction prices. An online prediction ability index is proposed to select prediction models with consistent online predictions and smaller close-to-downtime prediction errors. Real-world data and computational experiments are used to verify the effectiveness of the proposed method.
An indirect flow measurement based high-precision slide valve grinding mechanism for hydraulic servo valve
Authors: Fan Zeming , Fan Jing , Yu Xiaojun
Published: September 2022

As a crucial power amplifying component for electro-hydraulic servo valves, the servo-valve spool valve largely determines the overall performance of an electro-hydraulic servo system. Due to the machining errors during the servo-valve manufacturing process, however, it is extremely difficult to characterize such response characteristics in engineering practice, and thus, there may exist certain nonlinearity between the flow rate and valve spool displacement caused by the spool and valve sleeve overlap. To accurately characterize the relationship between the flow rate and spool displacement to facilitate servo-valve production, an indirect flow measurement-based servo-valve spool valve grinding (FM-SVG) scheme is proposed in this study. Specifically, a valve spool overlap measurement mechanism is presented first based on the valve spool grinding principle, and then a data processing method is devised to eliminate the errors introduced by the fluctuations of differential pressure at the valve ports. Meanwhile, a closed-loop control system is also devised to maintain a constant differential pressure at the servo-valve ports. Finally, the FM-SVG scheme is embedded onto a lab-customized electro-hydraulic servo valve platform, and experiments are conducted to verify the feasibility and effectiveness of the FM-SVG scheme. Results show that, by utilizing the devised control scheme to maintain a differential pressure around 2.00 MP, the proposed grinding scheme helps achieve a grinding accuracy of 2.0 μm. With only grinding process needed, such a grinding scheme helps improve both grinding accuracy and production efficiency in practice.
First-principles study of O-functionalized two-dimensional AsP monolayers: electronic structure, mechanical, piezoelectric, and optical properties
Authors: Zhao Jun , Jin Xuehu , Yao Can , Zeng Hui
Published: September 2022

Using density functional theory, we investigated the geometrical properties, electronic structures, carrier mobilities, piezoelectric coefficients, and optical absorption behaviors of three O-functionalized β-phase AsP structures (b-AsPO-FO, b-AsPO-As-SO and b-AsPO-P-SO). It is shown that three O-functionalized monolayers are all indirect semiconductors with bandgaps of 0.21, 0.67, and 0.80 eV, respectively. Our calculations demonstrated that the pristine AsP monolayer and these O-functionalized AsP monolayers have strongly anisotropic carrier mobilities, allowing their potential applications for in-plane anisotropic electronic device. The bandgaps of three functionalized nanomaterials exhibit non-monotonic variations under the biaxial strains changing from −0.10 to +0.10, all experiencing metal-indirect bandgap-direct bandgap transition. The calculated in-plane Young’s modulus results suggest that they are fairly flexible to allow the application of large elastic strains on the chemically functionalized AsP monolayers. Furthermore, the b-AsPO-FO monolayer exhibits excellent anisotropic light-harvesting behavior (absorption peak: 2.36 and 2.76 eV along x and 2.37 eV along y direction) in visible light region. The b-AsPO-As-SO and b-AsPO-P-SO monolayers have strong absorption peak at 2.60 eV and 2.87 eV, respectively. The tunable electronic structures, anisotropic carrier mobility, and excellent optical absorption properties may facilitate practical applications of O-functionalized b-AsP monolayers in nanoelectronics and photovoltaics.