bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binary-FRET reveals transient excited-state structure associated with activity-dependent CaMKII - NR2B binding and adaptation
Authors: Nguyen Tuan A. , Puhl Henry L. , Hines Kirk , Liput Daniel J. , Vogel Steven S. 
Published: October 2022

AbstractSynaptic functions are mediated and modulated by a coordinated choreography of protein conformational changes and interactions in response to intracellular calcium dynamics. Time-lapse Förster resonance energy transfer can be used to study the dynamics of both conformational changes and protein-protein interactions simultaneously under physiological conditions if two resonance energy transfer reactions can be multiplexed. Binary-FRET is a technique developed to independently monitor the dynamics of calcium-calmodulin dependent protein kinase-II catalytic-domain pair separation in the holoenzyme, and its role in establishing activity-dependent holoenzyme affinity for the NR2B binding fragment of the N-methyl-D-aspartate receptor. Here we show that a transient excited-state intermediate exists where paired catalytic-domains in the holoenzyme first separate prior to subsequent NR2B association. Additionally, at non-saturating free calcium concentrations, our multiplexed approach reveals that the holoenzyme exhibits a biochemical form of plasticity, calcium dependent adaptation of T-site ligand binding affinity.
Termination of the unfolded protein response is guided by ER stress-induced HAC1 mRNA nuclear retention
Authors: Matabishi-Bibi Laura , Challal Drice , Barucco Mara , Libri Domenico , Babour Anna 
Published: October 2022

AbstractCellular homeostasis is maintained by surveillance mechanisms that intervene at virtually every step of gene expression. In the nucleus, the yeast chromatin remodeler Isw1 holds back maturing mRNA ribonucleoparticles to prevent their untimely export, but whether this activity operates beyond quality control of mRNA biogenesis to regulate gene expression is unknown. Here, we identify the mRNA encoding the central effector of the unfolded protein response (UPR)HAC1, as an Isw1 RNA target. The direct binding of Isw1 to the 3’ untranslated region ofHAC1mRNA restricts its nuclear export and is required for accurate UPR abatement. Accordingly,ISW1inactivation sensitizes cells to endoplasmic reticulum (ER) stress while its overexpression reduces UPR induction. Our results reveal an unsuspected mechanism, in which binding of ER-stress induced Isw1 toHAC1mRNA limits its nuclear export, providing a feedback loop that fine-tunes UPR attenuation to guarantee homeostatic adaptation to ER stress.
Understanding the role of eye movement consistency in face recognition and autism through integrating deep neural networks and hidden Markov models
Authors: Hsiao Janet H. , An Jeehye , Hui Veronica Kit Sum , Zheng Yueyuan , Chan Antoni B. 
Published: October 2022

AbstractGreater eyes-focused eye movement pattern during face recognition is associated with better performance in adults but not in children. We test the hypothesis that higher eye movement consistency across trials, instead of a greater eyes-focused pattern, predicts better performance in children since it reflects capacity in developing visual routines. We first simulated visual routine development through combining deep neural network and hidden Markov model that jointly learn perceptual representations and eye movement strategies for face recognition. The model accounted for the advantage of eyes-focused pattern in adults, and predicted that in children (partially trained models) consistency but not pattern of eye movements predicted recognition performance. This result was then verified with data from typically developing children. In addition, lower eye movement consistency in children was associated with autism diagnosis, particularly autistic traits in social skills. Thus, children’s face recognition involves visual routine development through social exposure, indexed by eye movement consistency.
Ameliorative effect of oregano (Origanum vulgare) versus silymarin in experimentally induced hepatic encephalopathy
Authors: Abdelghffar Eman A. R. , El-Nashar Heba A. S. , Fayez Shaimaa , Obaid Wael A. , Eldahshan Omayma A. 
Published: October 2022

AbstractHepatic encephalopathy (HE) is a deterioration of brain function in patients suffering from chronic liver disease, cirrhosis as a result of elevated blood ammonia and the production of pseudo-neurotransmitters. Herein, we investigated the chemical composition of hexane extract fromOriganum vulgare(O. vulgare) leaves as well as its possible protective effects against thioacetamide (TAA)-induced HE in rats. GC–MS analysis of the extract revealed tentative identification of twenty-five compounds (82.93%), predominated by cholesten-3-one (27.30%), followed by γ-tocopherol (13.52%), α-tocopherol (5.01%), β-amyrin (5.24%) andα-amyrin (4.89%). Albino rats were distributed into seven groups (n = 7). G1served as negative control; G2and G3served as controls treated withO. vulgare(100 and 200 mg/kg/p.ob.w, respectively); G4served as TAA-positive control group (100 mg/kg/day/i.p., three alternative days per week for six weeks); G5, G6, and G7 served as TAA -induced HE rat model that receivedO. vulgare100,O. vulgare200, and silymarin (100 mg/kg of SILY, as standard drug), respectively. TAA showed depressive and anxiety-like behaviors in forced swimming test (FST) and reduction of cognitive score in elevated plus-maze test (EPMT) as well as impairment of locomotor and exploratory activities in open-field test (OFT). TAA caused a significant decline in body weight gain; however, the relative liver weight and brain water content were statistically increased. TAA-intoxicated rats showed significant increase of serum biomarker enzymes, proinflammatory cytokines, blood ammonia levels, brain serotonin, acetyl cholinesterase and cellular lipid peroxidation with significant decrease of brain dopamine, norepinephrine, antioxidant status. The hepatoprotective/neuro-protective activities ofO. vulgarewas found to be comparable with that of SILY in HE rats model. Where, treatment of TAA-intoxicated rats withO. vulgareattenuated anxiety, depressive-related behaviors, and reduced the biochemical changes in HE-induced by TAA. Therefore,O. vulgarecould be an excellent hepato-/neuroprotective against hepatic injury and HE via improving the oxidative/inflammatory status through its antioxidant and neuro-modulatory properties and its effect is equal to that of SILY.
Effects of carbon monoxide, nitrogen dioxide, and fine particulate matter on insect abundance and diversity in urban green spaces
Authors: Heidari Latibari Minoo , Moravvej Gholamhossein , Arias-Penna Diana Carolina , Ghafouri Moghaddam Mostafa 
Published: October 2022

AbstractThe impact of three air pollutants, carbon monoxide, nitrogen dioxide, and fine particulate matter (PM2.5) on the diversity and abundance of insect fauna associated with Chinese thuja, Platycladus orientalis, was evaluated for the first time in Iran. Sampling was performed in Lashkar, Sadaf, and Sajjad, three urban green spaces in Mashhad, a city located in Razavi Khorasan province. A total of 29 insect species including 16 natural enemies and 13 herbivores were identified. The results indicated that herbivore abundance was positively and significantly correlated with the level of carbon monoxide and nitrogen dioxide, but not with the level of fine particulate matter. In contrast, herbivore diversity was negatively and significantly correlated only with the level of carbon monoxide. As for natural enemies, abundance and diversity both were not significantly correlated with the levels of none of all three pollutants. The aphid, Cinara thujafilina Del Guercio was the most dominant herbivore species in all the sampling sites with a relative abundance of 86% at Lashkar, 93% at Sadaf, and 95% at Sajjad. Regarding natural enemies, the ladybird, Coccinella septempunctata was the most abundant species both at Lashkar (49%) and Sadaf (35%) while the ladybird, Oenopia conglubata was the most abundant at Sajjad (21%). The highest diversity of herbivores and natural enemies across the four seasons were at the Lashkar and Sadaf sites. The results highlight that of the three air pollutants, carbon monoxide is the one that affects both on abundance and diversity of herbivore guild associated with Platycladus orientalis in urban green spaces.
Explaining neural activity in human listeners with deep learning via natural language processing of narrative text
Authors: Russo Andrea G. , Ciarlo Assunta , Ponticorvo Sara , Di Salle Francesco , Tedeschi Gioacchino , Esposito Fabrizio 
Published: October 2022

AbstractDeep learning (DL) approaches may also inform the analysis of human brain activity. Here, a state-of-art DL tool for natural language processing, the Generative Pre-trained Transformer version 2 (GPT-2), is shown to generate meaningful neural encodings in functional MRI during narrative listening. Linguistic features of word unpredictability (surprisal) and contextual importance (saliency) were derived from the GPT-2 applied to the text of a 12-min narrative. Segments of variable duration (from 15 to 90 s) defined the context for the next word, resulting in different sets of neural predictors for functional MRI signals recorded in 27 healthy listeners of the narrative. GPT-2 surprisal, estimating word prediction errors from the artificial network, significantly explained the neural data in superior and middle temporal gyri (bilaterally), in anterior and posterior cingulate cortices, and in the left prefrontal cortex. GPT-2 saliency, weighing the importance of context words, significantly explained the neural data for longer segments in left superior and middle temporal gyri. These results add novel support to the use of DL tools in the search for neural encodings in functional MRI. A DL language model like the GPT-2 may feature useful data about neural processes subserving language comprehension in humans, including next-word context-related prediction.
Contrasting response of fungal versus bacterial residue accumulation within soil aggregates to long-term fertilization
Authors: Xu Yingde , Sun Liangjie , Gao Xiaodan , Wang Jingkuan 
Published: October 2022

AbstractSoil microorganisms are critical for soil carbon (C) cycling. They primarily regulate the turnover of the soil organic C (SOC) by adjusting their community structure, and contributing residues with a considerable amount to the resistant SOC. Nevertheless, how long-term fertilization (e.g., the combination of manure and chemical fertilizer) affects the spatial distribution of both living microbial communities and dead microbial residue within soil aggregate fractions remains largely unclear. In this study, we analyzed changes in microbial community (lipid biomarkers) and microbial residue retention (amino sugar biomarkers), and also calculated the contribution of microbial residue to organic C in bulk soil and different soil aggregates (> 2 mm, 1–2 mm, 0.25–1 mm, and < 0.25 mm) in Alfisols treated with 29 years fertilization or no fertilization (control). Our results showed that long-term fertilization significantly increased the mean weight diameter (MWD) of aggregates and organic C contents in all aggregate fractions. The fertilization treatment increased the contents of PLFAs and microbial residue C, but the relative contribution of microbial residue to SOC was higher in the control (56.8% vs. 49.0%), due to the low SOC background caused by much lower level of non-microbially derived C input. These results suggested that long-term fertilization could increase SOC by accumulating both plant- and microbial-derived C, while the C deficient soil is more dependent on the accumulation of microbial residues. Long-term fertilization promoted the enrichment of bacterial-derived muramic acid in micro aggregates, but increased the proportion of fungal-derived glucosamine in macro aggregates. Meanwhile, the contribution of bacterial residue to organic C in the fertilization treatment was higher in micro aggregates (7.6% for > 2 mm vs. 9.2% for < 0.25 mm aggregate), while the contribution of fungal residue was higher in macro aggregate fractions (40.9% for > 2 mm vs. 35.7% for < 0.25 mm aggregate). The above results indicated that long-term fertilization could drive the differentiation of heterogeneous microbial residue accumulation patterns that significantly alter the contribution of fungal- versus bacterial-derived C to organic C within soil aggregate fractions.
KUALA: a machine learning-driven framework for kinase inhibitors repositioning
Authors: De Simone Giada , Sardina Davide Stefano , Gulotta Maria Rita , Perricone Ugo 
Published: October 2022

AbstractThe family of protein kinases comprises more than 500 genes involved in numerous functions. Hence, their physiological dysfunction has paved the way toward drug discovery for cancer, cardiovascular, and inflammatory diseases. As a matter of fact, Kinase binding sites high similarity has a double role. On the one hand it is a critical issue for selectivity, on the other hand, according to poly-pharmacology, a synergistic controlled effect on more than one target could be of great pharmacological interest. Another important aspect of binding similarity is the possibility of exploit it for repositioning of drugs on targets of the same family. In this study, we propose our approach called Kinase drUgs mAchine Learning frAmework (KUALA) to automatically identify kinase active ligands by using specific sets of molecular descriptors and provide a multi-target priority score and a repurposing threshold to suggest the best repurposable and non-repurposable molecules. The comprehensive list of all kinase-ligand pairs and their scores can be found at https://github.com/molinfrimed/multi-kinases.
Effects of shady environments on fish collective behavior
Authors: Ribeiro Haroldo V. , Acre Matthew R. , Faulkner Jacob D. , da Cunha Leonardo R. , Lawson Katelyn M. , Wamboldt James J. , Brey Marybeth K. , Woodley Christa M. , Calfee Robin D. 
Published: October 2022

AbstractDespite significant efforts devoted to understanding the underlying complexity and emergence of collective movement in animal groups, the role of different external settings on this type of movement remains largely unexplored. Here, by combining time series analysis and complex network tools, we present an extensive investigation of the effects of shady environments on the behavior of a fish species (Silver CarpHypophthalmichthys molitrix) within earthen ponds. We find that shade encourages fish residence during daylight hours, but the degree of preference for shade varies substantially among trials and ponds. Silver Carp are much slower and exhibit lower persistence in their speeds when under shade than out of it during daytime and nighttime, with fish displaying the highest persistence degree and speeds at night. Furthermore, our research shows that shade affects fish schooling behavior by reducing their polarization, number of interactions among individuals, and the stability among local neighbors; however, fish keep a higher local degree of order when under shade compared to nighttime positions.
Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization
Authors: Kishi-Kaboshi Mitsuko , Tanaka Tsuyoshi , Sasaki Katsutomo , Noda Naonobu , Aida Ryutaro 
Published: October 2022

AbstractChrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading frames, and the combined dataset provided a more complete transcriptomic data than those produced from either SMRT-seq or RNA-seq-derived transcripts. We finally obtained ‘Sei Arabella’ transcripts containing 928,645 non-redundant mRNA, which showed 96.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) score. We also validated the reliability of the dataset by analyzing a mapping rate, annotation and transcript expression. Using the dataset, we searched anthocyanin biosynthesis gene orthologs and performed a qRT-PCR experiment to assess the usability of the dataset. The assessment of the dataset and the following analysis indicated that our dataset is reliable and useful for molecular biology. The combination of sequencing methods provided genetic information and a way to analyze the complicated C. morifolium transcriptome.
Salt stress decreases seed yield and postpones growth process of canola (Brassica napus L.) by changing nitrogen and carbon characters
Authors: Wang Long , Zuo Qingsong , zheng Jingdong , You Jingjing , Yang Guang , Leng Suohu 
Published: October 2022

AbstractSalt stress is a major challenge for plant growth and yield achievement in canola (Brassica napus L.). Nitrogen (N) is considered as an essential nutrient involved in many physiological processes, and carbon (C) is the most component of plant biomass. N and C assimilations of canola plants are always inhibited by salt stress. However, the knowledge of how salt stress affects biomass and seed yield through changing N and C characters is limited. A field experiment was conducted to investigate the growth process, N and C characters, photosynthetic performance, biomass accumulation and seed yield under the low and high soil salt-ion concentration conditions (LSSC and HSSC). The results indicated that HSSC postponed the time of early flowering stage and maturity stage by 4 ~ 5 days and 6 ~ 8 days, respectively, as compared with LSSC. Besides, HSSC decreased the N and C accumulation and C/N at both growing stages, suggesting that salt stress break the balance between C assimilation and N assimilation, with stronger effect on C assimilation. Although the plant N content under HSSC was increased, the photosynthesis rate at early flowering stage was decreased. The leaf area index at early flowering stage was also reduced. In addition, HSSC decreased N translocation efficiency especially in stem, and N utilization efficiency. These adverse effects of HSSC together resulted in reduced biomass accumulation and seed yield. In conclusion, the high soil salt-ion concentration reduced biomass accumulation and seed yield in canola through changing N and C characters.
The associations between stunting and wasting at 12 months of age and developmental milestones delays in a cohort of Cambodian children
Authors: Van Beekum Marion , Berger Jacques , Van Geystelen Judit , Hondru Gabriela , Som Somphos Vicheth , Theary Chan , Laillou Arnaud , Poirot Etienne , Bork Kirsten A. , Wieringa Frank T. , Fortin Sonia 
Published: October 2022

AbstractWorldwide, over 250 million children under 5 years do not reach their developmental potential due to several causes, including malnutrition. In Cambodia, the prevalence of stunting and wasting among children remains high. This prospective cohort study aimed to assess acquisition of motor and cognitive developmental milestones in early childhood and their associations with stunting and wasting. Children aged from 0 to 24 months were recruited from three provinces in Cambodia and followed up to seven times from March 2016 to June 2019, until their 5 years. Data collection included anthropometry and developmental milestones. Seven motor and seven cognitive milestones were evaluated using the Cambodian Development Milestone Assessment Tool. Associations were assessed with parametric survival models. Hazard ratios (HR) below 1 stood for lower probabilities for achieving developmental milestones. Data were available for 7394 children. At 12 months, the prevalence of stunting and wasting were 23.7% and 9.6% respectively. Both were consistently associated with delays in most motor and cognitive milestones. Stunting was strongly associated with delays in gross motor milestones (HR < 0.85;p < 0.001). Wasting was more strongly associated with delays in fine motor development and most cognitive milestones (HR < 0.75;p < 0.001). Promoting nutritional programs in the first 1000 days to prevent malnutrition is essential to further the optimal growth and motor and cognitive development of Cambodian children.
Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species
Authors: Geneva Anthony J. , Park Sungdae , Bock Dan G. , de Mello Pietro L. H. , Sarigol Fatih , Tollis Marc , Donihue Colin M. , Reynolds R. Graham , Feiner Nathalie , Rasys Ashley M. , Lauderdale James D. , Minchey Sergio G. , Alcala Aaron J. , Infante Carlos R. , Kolbe Jason J. , Schluter Dolph , Menke Douglas B. , Losos Jonathan B. 
Published: October 2022

AbstractRapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.
The role of thalamic group II mGlu receptors in health and disease
Authors: Copeland Caroline S. , Salt Thomas E. 
Published: October 2022

Abstract
The thalamus plays a pivotal role in the integration and processing of sensory, motor, and cognitive information. It is therefore important to understand how the thalamus operates in states of both health and disease. In the present review, we discuss the function of the Group II metabotropic glutamate (mGlu) receptors within thalamic circuitry, and how they may represent therapeutic targets in treating disease states associated with thalamic dysfunction.