bluuebunny/crossref_metadata_2025 huggingface dataset:
Teleconnections among tipping elements in the Earth system
Authors: Liu Teng , Chen Dean , Yang Lan , Meng Jun , Wang Zanchenling , Ludescher Josef , Fan Jingfang , Yang Saini , Chen Deliang , Kurths Jürgen , Chen Xiaosong , Havlin Shlomo , Schellnhuber Hans Joachim
Published: January 2023

Tipping elements are components of the Earth system that may shift abruptly and irreversibly from one state to another at specific thresholds. It is not well understood to what degree tipping of one system can influence other regions or tipping elements. Here, we propose a climate network approach to analyse the global impacts of a prominent tipping element, the Amazon Rainforest Area (ARA). We find that the ARA exhibits strong correlations with regions such as the Tibetan Plateau (TP) and West Antarctic ice sheet. Models show that the identified teleconnection propagation path between the ARA and the TP is robust under climate change. In addition, we detect that TP snow cover extent has been losing stability since 2008. We further uncover that various climate extremes between the ARA and the TP are synchronized under climate change. Our framework highlights that tipping elements can be linked and also the potential predictability of cascading tipping dynamics.
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses
Authors: Seong Kyungyong , Krasileva Ksenia V.
Published: January 2023

Elucidating the similarity and diversity of pathogen effectors is critical to understand their evolution across fungal phytopathogens. However, rapid divergence that diminishes sequence similarities between putatively homologous effectors has largely concealed the roots of effector evolution. Here we modelled the structures of 26,653 secreted proteins from 14 agriculturally important fungal phytopathogens, six non-pathogenic fungi and one oomycete with AlphaFold 2. With 18,000 successfully predicted folds, we performed structure-guided comparative analyses on two aspects of effector evolution: uniquely expanded sequence-unrelated structurally similar (SUSS) effector families and common folds present across the fungal species. Extreme expansion of lineage-specific SUSS effector families was found only in several obligate biotrophs,Blumeria graminisandPuccinia graminis. The highly expanded effector families were the source of conserved sequence motifs, such as the Y/F/WxC motif. We identified new classes of SUSS effector families that include known virulence factors, such as AvrSr35, AvrSr50 and Tin2. Structural comparisons revealed that the expanded structural folds further diversify through domain duplications and fusion with disordered stretches. Putatively sub- and neo-functionalized SUSS effectors could reconverge on regulation, expanding the functional pools of effectors in the pathogen infection cycle. We also found evidence that many effector families could have originated from ancestral folds conserved across fungi. Collectively, our study highlights diverse effector evolution mechanisms and supports divergent evolution as a major force in driving SUSS effector evolution from ancestral proteins.
Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase
Authors: Bloch Joël S. , John Alan , Mao Runyu , Mukherjee Somnath , Boilevin Jérémy , Irobalieva Rossitza N. , Darbre Tamis , Scott Nichollas E. , Reymond Jean-Louis , Kossiakoff Anthony A. , Goddard-Borger Ethan D. , Locher Kaspar P.
Published: January 2023

C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism. Here, we report cryogenic-electron microscopy structures of Caenorhabditiselegans CMT in four key states: apo, acceptor peptide-bound, donor-substrate analog-bound and as a trapped ternary complex with both peptide and a donor-substrate mimic bound. The structures indicate how the C-mannosylation sequon is recognized by this CMT and its paralogs, and how sequon binding triggers conformational activation of the donor substrate: a process relevant to all glycosyltransferase C superfamily enzymes. Our structural data further indicate that the CMTs adopt an unprecedented electrophilic aromatic substitution mechanism to enable the C-glycosylation of proteins. These results afford opportunities for understanding human disease and therapeutic targeting of specific CMT paralogs.
Human DNA-dependent protein kinase activation mechanism
Authors: Liang Shikang , Blundell Tom L.
Published: January 2023

DNA-dependent protein kinase (DNA-PK), a multicomponent complex including the DNA-PK catalytic subunit and Ku70/80 heterodimer together with DNA, is central to human DNA damage response and repair. Using a DNA-PK-selective inhibitor (M3814), we identified from one dataset two cryo-EM structures of the human DNA-PK complex in different states, the intermediate state and the active state. Here we show that activation of the kinase is regulated through conformational changes caused by the binding ligand and the string region (residues 802–846) of the DNA-PK catalytic subunit, particularly the helix-hairpin-helix motif (residues 816–836) that interacts with DNA. These observations demonstrate the regulatory role of the ligand and explain why DNA-PK is DNA dependent. Cooperation and coordination among binding partners, disordered flexible regions and mechanically flexible HEAT repeats modulate the activation of the kinase. Together with previous findings, these results provide a better molecular understanding of DNA-PK catalysis.
Functional group analyses of herpetofauna in South Korea using a large dataset
Authors: Jeon Jong Yoon , Lee Dong Kun , Kim Jae Hyun
Published: January 2023

Functional traits are characteristics of species that affect their fitness and ecosystem, and they greatly influence ecological niches. Thus, biodiversity assessment based on functional groups rather than species per se can more realistically reflect the ecological niche space. As essential players of ecosystem functions, herpetofauna are appropriate subjects of functional trait-based analyses. In this study, using a nationwide dataset and applying trait information and ecological niche modeling, the richness within each functional group, and the taxonomic and functional diversity indices of South Korean herpetofauna were visualized to identify and compare the geographic distributions. The results revealed that the reptile community seemed more locally diverse with more overlapping randomized patterns among groups than amphibians, while amphibians showed wider distributions and a higher within-grid occurrence ratio. Functional diversity indices of reptiles also showed more randomized geographic patterns with higher levels at Jejudo Island than amphibians. The findings of this study may help to identify biodiversity hot spots and understand its ecosystem health. Increasing survey data and trait information will improve the assessment.
Circulating microparticle proteins predict pregnancies complicated by placenta accreta spectrum
Authors: Yu Hope Y. , Gumusoglu Serena B. , Cantonwine David E. , Carusi Daniela A. , Gurnani Prem , Schickling Brandon , Doss Robert C. , Santillan Mark K. , Rosenblatt Kevin P. , McElrath Thomas F.
Published: January 2023

Placenta accreta spectrum (PAS) is characterized by abnormal attachment of the placenta to the uterus, and attempts at placental delivery can lead to catastrophic maternal hemorrhage and death. Multidisciplinary delivery planning can significantly improve outcomes; however, current diagnostics are lacking as approximately half of pregnancies with PAS are undiagnosed prior to delivery. This is a nested case–control study of 35 cases and 70 controls with the primary objective of identifying circulating microparticle (CMP) protein panels that identify pregnancies complicated by PAS. Size exclusion chromatography and liquid chromatography with tandem mass spectrometry were used for CMP protein isolation and identification, respectively. A two-step iterative workflow was used to establish putative panels. Using plasma sampled at a median of 26 weeks’ gestation, five CMP proteins distinguished PAS from controls with a mean area under the curve (AUC) of 0.83. For a separate sample taken at a median of 35 weeks’ gestation, the mean AUC was 0.78. In the second trimester, canonical pathway analyses demonstrate over-representation of processes related to iron homeostasis and erythropoietin signaling. In the third trimester, these analyses revealed abnormal immune function. CMP proteins classify PAS well prior to delivery and have potential to significantly reduce maternal morbidity and mortality.
The fabrication and growth mechanism of AlCrFeCoNiCu0.5 HEA thin films by substrate-biased cathodic arc deposition
Authors: Zhao Hong , Zheng Zhong , Akhavan Behnam , Tsoutas Kostadinos , Sun Lixian , Zhou Haoruo , Bilek Marcela M. , Liu Zongwen
Published: January 2023

AlCrFeCoNiCu0.5 thin films were fabricated by cathodic arc deposition under different substrate biases. Detailed characterization of the chemistry and structure of the film, from the substrate interface to the film surface, was achieved by combining high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, and atomic force microscopy. Computer simulations using the transport of ions in matter model were applied to understand the ion surface interactions that revealed the key mechanism of the film growth. The final compositions of the films are significantly different from that of the target used. A trend of elemental segregation, which was more pronounced with higher ion kinetic energy, was observed. The XPS results reveal the formation of $${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$$

Al
2

O
3

and $${\mathrm{Cr}}_{2}{\mathrm{O}}_{3}$$

Cr
2

O
3

on the thin film surface. The grain size is shown to increase with the increasing of the ion kinetic energy. The growth of equiaxed grains contributed to the formation of a flat surface with a relatively low surface roughness as shown by atomic force microscopy.
Correlation between CFTR variants and outcomes of ART in patients with CAVD in Central China
Authors: Qu Xiaowei , Li Lingyi , Cui Chenchen , Feng Ke , Xia Yanqing , Wan Feng , Zhang Cuilian , Guo Haibin
Published: January 2023

Biallelic variants in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) are the main pathogenic factor of congenital absence of the vas deferens (CAVD), including congenital bilateral absence of the vas deferens (CBAVD) and congenital unilateral absence of the vas deferens (CUAVD). However, there are few reports about the correlation between CFTR variant and outcomes of assisted reproductive technology (ART) in CAVD patients of China. In this study, 104 patients with CAVD were recruited in Central China, and provided gene detection by the whole-exome sequencing, among them 69% (72/104) carried at least one variant in CFTR and one carried adhesion G protein-coupled receptor G2 (ADGRG2) variant. A total of 81 CAVD patients were treated with ART, of which 21 and 60 carried none or at least one variant in CFTR, respectively. The fertilization rate, cleavage rate, effective embryo rate, implantation rate, clinical pregnancy rate and live birth rate per fresh embryo transfer were compared between patients with and without CFTR variants. It was found that the ART outcomes had no significant difference whether the patients carried the CFTR variant or not. In addition, all of the offspring were healthy after follow-up. In conclusion, rare CFTR variants may play a major role in patients with CAVD in Central China, which were greatly different from other descent. There was no significant difference in ART outcomes in CAVD patients with or without CFTR variants. The limitations of this study were that there was no statistical analysis of the sperm quality through TESA and conclusions were relatively limited due to the small sample size of the study.
A dual-mode neurostimulation approach to enhance athletic performance outcome in experienced taekwondo practitioners
Authors: Kamali Ali-Mohammad , Ijadi Mojtaba , Keshtkarhesamabadi Behnam , Kazemiha Milad , Mahmoudi Reza , Roozbehi Amrollah , Nami Mohammad
Published: January 2023

Transcranial Direct Current Stimulation (tDCS) is a growing empirical approach to improve athletic performance. Some recent studies have investigated the effects of transcutaneous spinal direct current stimulation (tsDCS) on the motor performance such as reaction time. TDCS and tsDCS can lead to alteration of the spontaneous neural activity, and the membrane potentials of motor neurons in cerebral cortex and spinal interneurons, respectively. Given the paucity of experimental studies on the non-invasive brain stimulation in the field of sports neuroscience, especially martial sports, the present study aimed at investigating the effects of neurostimulation in potentiating the motor and cognitive functions in experienced taekwondo practitioners. The study sample included 15 experienced male taekwondo players who received real or sham direct current stimulation on the primary motor cortex (M1) and the lumbar spinal segment (T12-L2) over two sessions, 72 h apart. Next, the performance of the participants was evaluated through a simulation of taekwondo exercise directly after the sham and real sessions. Moreover, a cognitive platform (CBS: Cambridge Brain Science) was used to investigate the participants’ cognitive profile in each instance. Unlike sham stimulation, real tDCS was associated with improved selective attention and reaction time in both in the simulated task performance and cognitive examination. The concurrent cortical and trans-spinal tDCS was found to improve selective attention (31% performance improvement) (P < 0.0001) [EFFECT SIZE; 1.84]. and reduce reaction time (4.7% performance improvement) (P < 0.0001) [EFFECT SIZE; 0.02]. Meanwhile, the intervention failed to leave a significant change in cognitive functions evaluated through CBS (P > 0.05). As informed by our results, the present dual-mode neurostimulation could improve motor functions potentially through the effect of tsDCS over the spinal interneurons and tDCS over the primary motor cortex. Likewise, our findings suggested an improved performance in simulated taekwondo task after real- but not sham-stimulation. This study paves the way for designing neurostimulation protocols to improve the performance of professional athletes, namely martial art practitioners, including their accuracy and velocity of reactions. Such positive effects of neuostimulation in athletic performance as demonstrated in this research and similar reports are expected to enhance the athletes’ success in professional competitions.
Expanding repertoire of SARS-CoV-2 deletion mutations contributes to evolution of highly transmissible variants
Authors: Venkatakrishnan A. J. , Anand Praveen , Lenehan Patrick J. , Ghosh Pritha , Suratekar Rohit , Silvert Eli , Pawlowski Colin , Siroha Abhishek , Chowdhury Dibyendu Roy , O’Horo John C. , Yao Joseph D. , Pritt Bobbi S. , Norgan Andrew P. , Hurt Ryan T. , Badley Andrew D. , Halamka John , Soundararajan Venky
Published: January 2023

The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 countries/territories (up to June 2021) and performed whole-genome viral sequencing from 102 COVID-19 patients, including 43 vaccine breakthrough infections. We identified 92 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a 3-month window. Deletions in the Spike protein N-terminal domain were highly enriched for these ‘surge-associated mutations’ (Odds Ratio = 14.19, 95% CI 6.15–32.75, p value = 3.41 × 10–10). Based on a longitudinal analysis of mutational prevalence globally, we found an expanding repertoire of Spike protein deletions proximal to an antigenic supersite in the N-terminal domain that may be one of the key contributors to the evolution of highly transmissible variants. Finally, we generated clinically annotated SARS-CoV-2 whole genome sequences from 102 patients and identified 107 unique mutations, including 78 substitutions and 29 deletions. In five patients, we identified distinct deletions between residues 85–90, which reside within a linear B cell epitope. Deletions in this region arose contemporaneously on a diverse background of variants across the globe since December 2020. Overall, our findings based on genomic-epidemiology and clinical surveillance suggest that the genomic deletion of dispensable antigenic regions in SARS-CoV-2 may contribute to the evasion of immune responses and the evolution of highly transmissible variants.
Multi-objective predictive control based on the cutting tobacco outlet moisture priority
Authors: Fan Zhiping , Ren Zhengyun , Chen Angang
Published: January 2023

In this paper, we propose a new priority multi-objective optimization strategy of system output variables in cutting tobacco process. The proposed strategy focuses on the cutting tobacco moisture-controlled output variables optimization in feasible regions with two levels according to the priority. This study aims to provide a novel technical support for the chemical industry contained drying process. In order to alleviate the lack of degree of freedom of the system, strict set-point control is given, meanwhile, other output variables adopt zone control. Firstly, the system control output variables are optimized in ascending order of priority. Secondly, the specific lower-level target constraints are first relaxed. Finally, the relaxation of other high-priority target constraints is stopped when the optimization is feasible. Thus, the system control output variables move along the optimal target trajectory. From the perspective of practical application of engineering, under the condition of disturbance existing in the cutting tobacco drying process, the simulation shows that the proposed approach has good robustness when there is disturbance, and the previous method cannot meet the control requirement. The proposed strategy meanwhile has better tracking effect through single and multiple output variables simulation, which compared with traditional predictive control in real cutting tobacco drying process.
Plasma-enabled superhydrophobic coatings on mild steel
Authors: Hartl Hugo , Davies Joseph , Will Geoffrey , Ostrikov Kostya , MacLeod Jennifer
Published: January 2023

This work demonstrates a new pathway to the direct on-surface fabrication of a superhydrophobic surface coating on mild steel. The coating was formed using dielectric barrier discharge (DBD) plasma to convert a liquid small-molecule precursor (1,2,4-tricholorobenzene) to a solid film via plasma-assisted on-surface polymerization. Plasma treatments were performed under a nitrogen atmosphere with a variety of power levels and durations. Samples were analysed by optical and scanning electron microscopy (SEM), energy-dispersive x-ray spectroscopy (EDS), time-of-flight secondary ion mass spectrometry (ToF–SIMS), Raman spectroscopy, optical profilometry, contact angle measurement, and potentiodynamic polarisation tests. Wettability of the films varied with the plasma parameters, and through the inclusion of graphene nanoplatelets in the precursor. High-dose plasma exposures of the nanoplatelet-containing precursor created superhydrophobic films with water contact angles above 150°. Potentiodynamic polarisation tests revealed that the superhydrophobic coating provided little or no corrosion protection.
Genetic and phenotype recovery of Ananas comosus var. MD2 in response to ionizing radiation
Authors: Ma Siyuan , Mohd Raffi Anis Norsyahira , Rosli Muhamad Afiq , Mohd Zain Nurul Amalina , Ibrahim Mohd Hafiz , Karsani Saiful Anuar , Yaacob Jamilah Syafawati
Published: January 2023

Due to their sessile nature, plants are exposed to various environmental stressors such as exposure to high levels of harmful ultraviolet (UV), ionizing, and non-ionizing radiations. This exposure may result in various damages, ranging from DNA and chromosomal aberrations to phenotypic abnormalities. As an adaptation, plants have evolved efficient DNA repair mechanisms to detect and repair any damage caused by exposure to these harmful stressors to ensure their survival. In this study, the effects of gamma radiation (as a source of ionizing radiation) on clonal Ananas comosus var. MD2 was evaluated. The morphology and physiology of the clonal plantlets before and after exposure to gamma radiation were monitored at specific time intervals. The degree of genetic variation between the samples pre- and post-irradiation was also analyzed by using inter-simple sequence repeat (ISSR) markers. The resulting data revealed that the heights of the irradiated plantlets were significantly reduced (compared to control), but improved with the recovery period. Irradiated samples also exhibited relatively good photosynthetic efficiency that further improved as the plantlets recover. These observations were supported by the ISSR analysis, where the genetic dissimilarities between the irradiated samples and control were reduced by 0.1017, after 4 weeks of recovery. Overall, our findings suggested that the phenotype recovery of the clonal A. comosus var. MD2 plantlets was contributed by their ability to detect and repair the DNA lesions (as exemplified by the reduction in genetic dissimilarity after 4 weeks) and hence allow the plantlets to undergo phenotype reversion to normal plant stature.
Effects of exposure to immersive computer-generated virtual nature and control environments on affect and cognition
Authors: Mostajeran Fariba , Fischer Marvin , Steinicke Frank , Kühn Simone
Published: January 2023

Previous research has shown that exposure to immersive virtual nature environments is able to induce positive affective and physiological effects. However, research on the effects on cognitive performance is scarce. Additionally, the effects of virtual nature exposure compared to a virtual control environment with a comparable amount of virtual objects have not been examined so far. Therefore, we conducted an experiment with 27 participants to study the psychological effects of such exposure. The virtual nature consisted of a 3D model of a typical forest environment, whereas the control environment was an abstract replication of the virtual forest environment. In both environments, a virtual wooden cart was used to transport the users from the start to the end of the virtual road. The typical background noise of moving such a cart was integrated into both environments as well. In addition, the virtual nature environment included typical forest sounds in the background, whereas the control condition did not have such background sounds. Both environments were compared with regard to their effects on cognitive performance (using trail making tests (TMTA, TMTB, and TMTB-A) as well as digit span forward and digit span backward tests), perceived restorativeness, mood, stress, sense of presence, and simulator sickness. The results showed that in comparison to the control environment, exposure to the virtual nature resulted in significantly higher cognitive performance, higher perceived restorativeness, higher positive affect, higher sense of presence, lower perceived stress, and lower simulator sickness.
Microarray analysis identifies coding and non-coding RNA markers of liver injury in whole body irradiated mice
Authors: Aryankalayil Molykutty J. , Bylicky Michelle A. , Martello Shannon , Chopra Sunita , Sproull Mary , May Jared M. , Shankardass Aman , MacMillan Laurel , Vanpouille-Box Claire , Dalo Juan , Scott Kevin M. K. , Norman Coleman C.
Published: January 2023

Radiation injury from medical, accidental, or intentional sources can induce acute and long-term hepatic dysregulation, fibrosis, and cancer. This long-term hepatic dysregulation decreases quality of life and may lead to death. Our goal in this study is to determine acute changes in biological pathways and discover potential RNA biomarkers predictive of radiation injury. We performed whole transcriptome microarray analysis of mouse liver tissue (C57BL/6 J) 48 h after whole-body irradiation with 1, 2, 4, 8, and 12 Gray to identify significant expression changes in mRNAs, lncRNAs, and miRNAs, We also validated changes in specific RNAs through qRT-PCR. We used Ingenuity Pathway Analysis (IPA) to identify pathways associated with gene expression changes. We observed significant dysregulation of multiple mRNAs across all doses. In contrast, miRNA dysregulation was observed upwards of 2 Gray. The most significantly upregulated mRNAs function as tumor suppressors:Cdkn1a,Phlda3, andEda2r. The most significantly downregulated mRNAs were involved in hemoglobin synthesis, inflammation, and mitochondrial function including multiple members ofHbbandHba. The most significantly upregulated miRNA included: miR-34a-5p, miR-3102-5p, and miR-3960, while miR-342-3p, miR-142a-3p, and miR-223-3p were most significantly downregulated. IPA predicted activation of cell cycle checkpoint control pathways and inhibition of pathways relevant to inflammation and erythropoietin. Clarifying expression of mRNA, miRNA and lncRNA at a short time point (48 h) offers insight into potential biomarkers, including radiation markers shared across organs and animal models. This information, once validated in human models, can aid in development of bio-dosimetry biomarkers, and furthers our understanding of acute pathway dysregulation.
Modeling and optimization of bakery production scheduling to minimize makespan and oven idle time
Authors: Babor Majharulislam , Paquet-Durand Olivier , Kohlus Reinhard , Hitzmann Bernd
Published: January 2023

Makespan dominates the manufacturing expenses in bakery production. The high energy consumption of ovens also has a substantial impact, which bakers may overlook. Bakers leave ovens running until the final product is baked, allowing them to consume energy even when not in use. It results in energy waste, increased manufacturing costs, and CO2emissions. This paper investigates three manufacturing lines from small and medium-sized bakeries to find optimum makespan and ovens’ idle time (OIDT). A hybrid no-wait flow shop scheduling model considering the constraints that are most common in bakeries is proposed. To find optimal solutions, non-dominated sorting genetic algorithm (NSGA-II), strength Pareto evolutionary algorithm (SPEA2), generalized differential evolution (GDE3), improved multi-objective particle swarm optimization (OMOPSO), and speed-constrained multi-objective particle swarm optimization (SMPSO) were used. The experimental results show that the shortest makespan does not always imply the lowest OIDT. Even the optimized solutions have up to 231 min of excess OIDT, while the makespan is the shortest. Pareto solutions provide promising trade-offs between makespan and OIDT, with the best-case scenario reducing OIDT by 1348 min while increasing makespan only by 61 min from the minimum possible makespan. NSGA-II outperforms all other algorithms in obtaining a high number of good-quality solutions and a small number of poor-quality solutions, followed by SPEA2 and GDE3. In contrast, OMOPSO and SMPSO deliver the worst solutions, which become pronounced as the problem complexity grows.
Complete chloroplast genomes and comparative analysis of Ligustrum species
Authors: Long Lianxiang , Li Yongtan , Wang Shijie , Liu Zhenlin , Wang Jinmao , Yang Minsheng
Published: January 2023

In this study, we assembled and annotated the chloroplast (cp) genomes of four Ligustrum species, L. sinense, L. obtusifolium, L. vicaryi, and L. ovalifolium ‘Aureum’. Including six other published Ligustrum species, we compared various characteristics such as gene structure, sequence alignment, codon preference, and nucleic acid diversity, and performed positive-selection genes screening and phylogenetic analysis. The results showed that the cp genome of Ligustrum was 162,185–166,800 bp in length, with a circular tetrad structure, including a large single-copy region (86,885–90,106 bp), a small single-copy region (11,446–11,499 bp), and a pair of IRa and IRb sequences with the same coding but in opposite directions (31,608–32,624 bp). This structure is similar to the cp genomes of most angiosperms. We found 132–137 genes in the cp genome of Ligustrum, including 89–90 protein-coding genes, 35–39 tRNAs, and 8 rRNAs. The GC content was 37.93–38.06% and varied among regions, with the IR region having the highest content. The single-nucleotide (A/T)n was dominant in simple-sequence repeats of the Ligustrum cp genome, with an obvious A/T preference. Six hotspot regions were identified from multiple sequence alignment of Ligustrum; the ycf1 gene region and the clpP1 exon region can be used as potential DNA barcodes for the identification and phylogeny of the genus Ligustrum. Branch-site model and Bayes empirical Bayes (BEB) analysis showed that four protein-coding genes (accD, clpP, ycf1, and ycf2) were positively selected, and BEB analysis showed that accD and rpl20 had positively selected sites. A phylogenetic tree of Oleaceae species was constructed based on the whole cp genomes, and the results were consistent with the traditional taxonomic results. The phylogenetic results showed that genus Ligustrum is most closely related to genus Syringa. Our study provides important genetic information to support further investigations of the phylogenetic development and adaptive evolution of Ligustrum species.
Limits on phenological response to high temperature in the Arctic
Authors: Elmendorf Sarah C. , Hollister Robert D.
Published: January 2023

Tundra plants are widely considered to be constrained by cool growing conditions and short growing seasons. Furthermore, phenological development is generally predicted by daily heat sums calculated as growing degree days. Analyzing over a decade of seasonal flower counts of 23 plant species distributed across four plant communities, together with hourly canopy-temperature records, we show that the timing of flowering of many tundra plants are best predicted by a modified growing degree day model with a maximum temperature threshold. Threshold maximums are commonly employed in agriculture, but until recently have not been considered for natural ecosystems and to our knowledge have not been used for tundra plants. Estimated maximum temperature thresholds were found to be within the range of daily temperatures commonly experienced for many species, particularly for plants at the colder, high Arctic study site. These findings provide an explanation for why passive experimental warming—where moderate changes in mean daily temperatures are accompanied by larger changes in daily maximum temperatures—generally shifts plant phenology less than ambient warming. Our results also suggest that many plants adapted to extreme cold environments may have limits to their thermal responsiveness.
Optimal design of dual air-gap closed-loop TMR current sensor based on minimum magnetic field uniformity coefficient
Authors: Yu Jicheng , Long Zhaozhi , Liang Siyuan , Yue Changxi , Yin Xiaodong , Zhou Feng
Published: January 2023

Advanced sensor technology provides accurate information for transparent monitoring and real-time control of the power grid. Tunnel magnetoresistance (TMR) elements with high sensitivity and linearity provide a new technical means for current measurement in medium-voltage DC power distribution systems. This paper proposes a dual air-gap closed-loop TMR current sensor and its optimal design method based on the magnetic field’s minimum uniformity coefficient. The dual air-gap structure reduces the measurement error caused by the eccentricity of the wire, and the theory and modelling of the minimum magnetic field uniformity coefficient optimise the key parameters, such as the inner radius of the magnetic core, the distance of the air-gap and the area size of the section side. Finally, a sensor prototype with a rated measurement current of ± 50 A was developed. The experiment results show that the relative error of the proposed TMR current sensor is less than 0.2% under the rated current. The conclusion can be drawn that the proposed sensor with the optimised design effectively improves the measurement accuracy.
Mediation of pain in the association of sleep problems with falls among older adults in India
Authors: Muhammad T. , Maurya Priya , Selvamani Y. , Kelekar Uma
Published: January 2023

Body pain, sleep problems and falls are commonly reported among the elderly population. This study aimed to explore the mediating role of pain in the association of sleep problems with fall-outcomes (falls, fall-injury, and multiple falls) among older adults. Cross-sectional data from the baseline survey of Longitudinal Aging Study in India (LASI), 2017–18 were used. The total sample size for the study was 28,285 older adults aged 60 years and above. Falls and fall-related injuries among older adults in the last two years were self-reported. The Jenkins Sleep Scale (JSS-4) was used to assess sleep problems while pain was assessed using questions on whether respondents reported that they were troubled by pain and they required some form of medication or treatment for the relief of pain. Multivariable logistic regression and mediation analyses were conducted to fulfill the study objectives. While 13% older adults suffered from sleep problems, 38.83% were troubled with pain. Additionally, 12.63%, 5.64% and 5.76% older adults reported falls, fall-injury and multiple falls respectively. Older adults who suffered from sleep problems had higher odds of falls [adjusted odds ratio (aOR): 1.43, confidence interval (CI): 1.30–1.58], fall-injuries, [aOR:1.50,CI:1.30–1.73] and multiple falls [aOR:1.41,CI:1.24–1.62]. Similarly, older adults who were troubled with pain were more likely to report falls [aOR:1.80, CI:1.67–1.95], fall-injuries [aOR:1.66, CI:1.48–1.87] and multiple falls [aOR:1.90,CI:1.69–2.12]. The percent of the mediated effect of pain when examining the association between sleep problems and fall outcomes were reported to be 17.10%, 13.56% and 18.78% in case of falls, fall-injuries and multiple falls respectively. The current study finds evidence that pain mediates the association of sleep problems and falls, fall-injuries, and multiple falls among older Indian adults. Both sleep problems and pain are modifiable risk factors that need attention for fall prevention strategies.
Third-order motifs are sufficient to fully and uniquely characterize spatiotemporal neural network activity
Authors: Deshpande Sarita S. , Smith Graham A. , van Drongelen Wim
Published: January 2023

Neuroscientific analyses balance between capturing the brain’s complexity and expressing that complexity in meaningful and understandable ways. Here we present a novel approach that fully characterizes neural network activity and does so by uniquely transforming raw signals into easily interpretable and biologically relevant metrics of network behavior. We first prove that third-order (triple) correlation describes network activity in its entirety using the triple correlation uniqueness theorem. Triple correlation quantifies the relationships among three events separated by spatial and temporal lags, which are triplet motifs. Classifying these motifs by their event sequencing leads to fourteen qualitatively distinct motif classes that embody well-studied network behaviors including synchrony, feedback, feedforward, convergence, and divergence. Within these motif classes, the summed triple correlations provide novel metrics of network behavior, as well as being inclusive of commonly used analyses. We demonstrate the power of this approach on a range of networks with increasingly obscured signals, from ideal noiseless simulations to noisy experimental data. This approach can be easily applied to any recording modality, so existing neural datasets are ripe for reanalysis. Triple correlation is an accessible signal processing tool with a solid theoretical foundation capable of revealing previously elusive information within recordings of neural networks.
High-resolution processing and sigmoid fusion modules for efficient detection of small objects in an embedded system
Authors: Kim Mingi , Kim Heegwang , Sung Junghoon , Park Chanyeong , Paik Joonki
Published: January 2023

Recent advances in deep learning realized accurate, robust detection of various types of objects including pedestrians on the road, defect regions in the manufacturing process, human organs in medical images, and dangerous materials passing through the airport checkpoint. Specifically, small object detection implemented as an embedded system is gaining increasing attention for autonomous vehicles, drone reconnaissance, and microscopic imagery. In this paper, we present a light-weight small object detection model using two plug-in modules: (1) high-resolution processing module (HRPM ) and (2) sigmoid fusion module (SFM). The HRPM efficiently learns multi-scale features of small objects using a significantly reduced computational cost, and the SFM alleviates mis-classification errors due to spatial noise by adjusting weights on the lost small object information. Combination of HRPM and SFM significantly improved the detection accuracy with a low amount of computation. Compared with the original YOLOX-s model, the proposed model takes a two-times higher-resolution input image for higher mean average precision (mAP) using 57% model parameters and 71% computation in Gflops. The proposed model was tested using real drone reconnaissance images, and provided significant improvement in detecting small vehicles.
Investigating active area dependent high performing photoresponse through thin films of Weyl Semimetal WTe2
Authors: Verma Sahil , Yadav Reena , Pandey Animesh , Kaur Mandeep , Husale Sudhir
Published: January 2023

WTe2 is one of the wonder layered materials, displays interesting overlapping of electron–hole pairs, opening of the surface bandgap, anisotropy in its crystal structure and very much sought appealing material for room temperature broadband photodection applications. Here we report the photoresponse of WTe2 thin films and microchannel devices fabricated on silicon nitride substrates. A clear sharp rise in photocurrent observed under the illumination of visible (532 nm) and NIR wavelengths (1064 nm). The observed phoresponse is very convincing and repetitive for ON /OFF cycles of laser light illumination. The channel length dependence of photocurrent is noticed for few hundred nanometers to micrometers. The photocurrent, rise & decay times, responsivity and detectivity are studied using different channel lengths. Strikingly microchannel gives few orders of greater responsivity compared to larger active area investigated here. The responsivity and detectivity are observed as large as 29 A/W and 3.6 × 108 Jones respectively. The high performing photodetection properties indicate that WTe2 can be used as a broad band material for future optoelectronic applications.
A possible unique ecosystem in the endoglacial hypersaline brines in Antarctica
Authors: Guglielmin M. , Azzaro M. , Buzzini P. , Battistel D. , Roman M. , Ponti S. , Turchetti B. , Sannino C. , Borruso L. , Papale M. , Lo Giudice A.
Published: January 2023

Here, we present the results related to a new unique terrestrial ecosystem found in an englacial hypersaline brine found in Northern Victoria Land (Antarctica). Both the geochemistry and microbial (prokaryotic and fungal) diversity revealed an unicity with respect to all the other known Antarctic brines and suggested a probable ancient origin mainly due a progressive cryoconcentration of seawater. The prokaryotic community presented some peculiarities, such as the occurrence of sequences of Patescibacteria (which can thrive in nutrient-limited water environments) or few Spirochaeta, and the presence of archaeal sequences of Methanomicrobia closely related toMethanoculleus,a methanogen commonly detected in marine and estuarine environments. The high percentage (35%) of unassigned fungal taxa suggested the presence of a high degree of undiscovered diversity within a structured fungal community (including both yeast and filamentous life forms) and reinforce the hypothesis of a high degree of biological uniqueness of the habitat under study.
External validation of binary machine learning models for pain intensity perception classification from EEG in healthy individuals
Authors: Mari Tyler , Asgard Oda , Henderson Jessica , Hewitt Danielle , Brown Christopher , Stancak Andrej , Fallon Nicholas
Published: January 2023

Discrimination of pain intensity using machine learning (ML) and electroencephalography (EEG) has significant potential for clinical applications, especially in scenarios where self-report is unsuitable. However, existing research is limited due to a lack of external validation (assessing performance using novel data). We aimed for the first external validation study for pain intensity classification with EEG. Pneumatic pressure stimuli were delivered to the fingernail bed at high and low pain intensities during two independent EEG experiments with healthy participants. Study one (n = 25) was utilised for training and cross-validation. Study two (n = 15) was used for external validation one (identical stimulation parameters to study one) and external validation two (new stimulation parameters). Time–frequency features of peri-stimulus EEG were computed on a single-trial basis for all electrodes. ML training and analysis were performed on a subset of features, identified through feature selection, which were distributed across scalp electrodes and included frontal, central, and parietal regions. Results demonstrated that ML models outperformed chance. The Random Forest (RF) achieved the greatest accuracies of 73.18, 68.32 and 60.42% for cross-validation, external validation one and two, respectively. Importantly, this research is the first to externally validate ML and EEG for the classification of intensity during experimental pain, demonstrating promising performance which generalises to novel samples and paradigms. These findings offer the most rigorous estimates of ML’s clinical potential for pain classification.
Residential green environments are associated with human milk oligosaccharide diversity and composition
Authors: Lahdenperä Mirkka , Galante Laura , Gonzales-Inca Carlos , Vahtera Jussi , Pentti Jaana , Rautava Samuli , Käyhkö Niina , Yonemitsu Chloe , Gupta Julia , Bode Lars , Lagström Hanna
Published: January 2023

Increased exposure to greener environments has been suggested to lead to health benefits in children, but the associated mechanisms in early life, particularly via biological mediators such as altered maternal milk composition, remain largely unexplored. We investigated the associations between properties of the mother’s residential green environment, measured as (1) greenness (Normalized Difference Vegetation index, NDVI), (2) Vegetation Cover Diversity (VCDI) and (3) Naturalness Index (NI), and human milk oligosaccharides (HMOs), known for their immune- and microbiota-related health effects on the infant (N = 795 mothers). We show that HMO diversity increases and concentrations of several individual HMOs and HMO groups change with increased VCDI and NI in residential green environments. This suggests that variation in residential green environments may influence the infant via maternal milk through modified HMO composition. The results emphasize the mediating role of breastfeeding between the residential green environments and health in early life.
Reproducibility of the computational fluid dynamic analysis of a cerebral aneurysm monitored over a decade
Authors: Paritala Phani Kumari , Anbananthan Haveena , Hautaniemi Jacob , Smith Macauley , George Antony , Allenby Mark , Mendieta Jessica Benitez , Wang Jiaqiu , Maclachlan Liam , Liang EeShern , Prior Marita , Yarlagadda Prasad K. D. V. , Winter Craig , Li Zhiyong
Published: January 2023

Computational fluid dynamics (CFD) simulations are increasingly utilised to evaluate intracranial aneurysm (IA) haemodynamics to aid in the prediction of morphological changes and rupture risk. However, these models vary and differences in published results warrant the investigation of IA-CFD reproducibility. This study aims to explore sources of intra-team variability and determine its impact on the aneurysm morphology and CFD parameters. A team of four operators were given six sets of magnetic resonance angiography data spanning a decade from one patient with a middle cerebral aneurysm. All operators were given the same protocol and software for model reconstruction and numerical analysis. The morphology and haemodynamics of the operator models were then compared. The segmentation, smoothing factor, inlet and outflow branch lengths were found to cause intra-team variability. There was 80% reproducibility in the time-averaged wall shear stress distribution among operators with the major difference attributed to the level of smoothing. Based on these findings, it was concluded that the clinical applicability of CFD simulations may be feasible if a standardised segmentation protocol is developed. Moreover, when analysing the aneurysm shape change over a decade, it was noted that the co-existence of positive and negative values of the wall shear stress divergence (WSSD) contributed to the growth of a daughter sac.
Subtle changes in perivascular endometrial mesenchymal stem cells after local endometrial injury in recurrent implantation failure
Authors: Fan Yiping , Lee Ryan Wai Kheong , Ng Xiang Wen , Gargett Caroline E. , Chan Jerry Kok Yen
Published: January 2023

Improvements in reproductive techniques have resulted in the live birth rates from IVF procedures increasing from 5% to approximately 30% in recent decades but has plateaued since. Emerging preclinical and clinical data implicates endometrial receptivity deficiencies in patients with recurrent implantation failure (RIF) as the predominant factor hindering successful implantation. Mechanisms on how local endometrial injury (LEI) improves implantation rates in patients with RIF are currently unknown. We hypothesized that LEI may influence perivascular endometrial mesenchymal stem/progenitor cells (eMSCs) which are thought to regenerate the stromal vascular component of the functional layer every month. Here, we assessed the effect of LEI on the proportion and function of eMSCs present in consecutive LEI biopsies. Consecutive paired mid-luteal phase endometrial biopsies obtained from patients with RIF were digested to single cells and the proportion of SUSD2-expressing cells determined. Growth kinetics and decidualization were compared between the consecutive LEI samples. A mid-luteal LEI altered the decidualization capacity of SUSD2+ eMSCs in women with RIF, but not their proportion or clonogenicity. With the potential of LEI to improve IVF outcomes in women with RIF, additional investigations are needed to understand the impact of the altered decidualization response in eMSCs.