bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Asian gypsy moth (Lymantria disparL.) populations: resistance of eggs to extreme winter temperatures
Authors: Ananko G.G. , Kolosov A.V. 
Published: February 2021

ABSTRACTGypsy mothLymantria dispar(GM) is a polyphagous insect and one of the most significant pests in the forests of Eurasia and North America. Accurate information on GM cold hardiness is needed to improve methods for the prediction of population outbreaks, as well as for forecasting possible GM range displacements due to climate change.As a result of laboratory and field studies, we found that the lower lethal temperature (at which allL. dispar asiaticaeggs die) range from –29.0 °C to –29.9 °C for three studied populations, and no egg survived cooling to –29.9 °C. These limits agree to within one degree with the previously established cold hardiness limits of the European subspeciesL. dispar dispar, which is also found in North America. This coincidence indicates that the lower lethal temperature ofL. disparis conservative.Thus, we found that the Siberian populations of GM inhabit an area where winter temperatures go beyond the limits of egg physiological tolerance, because temperature often fall below –30 °C. Apparently, it is due to the flexibility of ovipositional behavior thatL. dispar asiaticasurvives in Siberia: the lack of physiological tolerance of eggs is compensated by choosing warm biotopes for oviposition. One of the most important factors contributing to the survival of GM eggs in Siberia is the stability of snow cover.SummaryWithin the geographical range of Siberian gypsy moth populations, extreme temperatures go beyond the limits of the physiological tolerance of wintering eggs (–29.9 °C), and their survival depends on the choice of warm biotopes for oviposition.
An endogenous basis for synchronization manners of the circadian rhythm in proliferatingLemna minorplants
Authors: Ueno Kenya , Ito Shogo , Oyama Tokitaka 
Published: February 2021

AbstractEndogenous circadian rhythms in plants play a role in adaptation to day-night cycles. The circadian clock is a cell-autonomous system that functions through the coordination of time information in the plant body. Synchronization of cellular clocks is based on coordination mechanisms; the synchronization manners in proliferating plants remain unclear. We performed spatiotemporal analysis of the circadian rhythm of fronds (leaf-like plant units) of proliferatingLemna minorplants carrying a circadian bioluminescence reporter,AtCCA1:LUC. Noninvasive observations of the bioluminescence of fast-growing two-dimensional plants allowed us to analyze the circadian rhythms at a cell-level resolution and obtain information regarding frond lineage. We focused on spontaneous circadian organization under constant light conditions for plants with light/dark treatment (LD-grown) or without it (LL-grown). Even fronds developing from an LL-grown parental frond showed coherent circadian rhythms among them. This allowed the maintenance of circadian rhythmicity in proliferating plants. Inside a frond, a centrifugal phase/period pattern was observed in LD-grown plants, whereas various phase patterns with traveling waves were formed in LL-grown plants. These patterns were model-simulated by local coupling of cellular circadian oscillators with different initial synchronous states in fronds. Taken together with similar patterning previously reported for detached leaves ofArabidopsis, it is strongly suggested that local coupling is the primary force for the development of these phase patterns in plants lacking long-distance communication. We propose a basic framework of spontaneous phase patterning with three stages of circadian organization: initial phasing, evolution of patterning, and desynchronization/randomizing of phase, in association with altering cell-cell coupling.
A Unit Pipe Pneumatic model to simulate gas kinetics during measurements of embolism in excised angiosperm xylem
Authors: Yang Dongmei , Pereira Luciano , Peng Guoquan , Ribeiro Rafael V. , Kaack Lucian , Jansen Steven , Tyree Melvin T. 
Published: February 2021

AbstractThe Pneumatic method has been introduced to quantify embolism resistance in plant xylem of various organs. Despite striking similarity in vulnerability curves between the Pneumatic and hydraulic methods, a modeling approach is highly needed to demonstrate that xylem embolism resistance can be accurately quantified based on gas diffusion kinetics.A Unit Pipe Pneumatic (UPPn) model was developed to estimate gas diffusion from intact conduits, which were axially interconnected by interconduit pit membranes. The physical laws used included Fick’s law for diffusion, Henry’s law for gas concentration partitioning between liquid and gas phases at equilibrium, and the ideal gas law.The UPPn model showed that 91% of the extracted gas came from the first two series of embolized, intact conduits, and only 9% from the aqueous phase after 15 s of simulation. Embolism resistance measured with a Pneumatic apparatus was systematically overestimated by 2 to 17%, corresponding to a typical measuring error of 0.11 MPa forP50(the water potential equivalent to 50% of the maximum amount of gas extracted).Because results from the UPPn model are supported by experimental evidence, there is a good theoretical and experimental basis for applying the pneumatic method to research on embolism resistance of angiosperms.
Multiplatform Computational Analysis of Mast Cells in Adrenocortical Carcinoma Tumor Microenvironment
Authors: Baechle Jordan J. , Hanna David N. , Sekhar Konjeti R. , Rathmell Jeffrey C. , Rathmell W. Kimryn , Baregamian Naira 
Published: February 2021

ABSTRACTIntroductionImmunotherapeutic response failure of adrenocortical carcinomas (ACC) highlights a need for novel strategies targeting immune cell populations in the tumor microenvironment (TME) to overcome tumor resistance and enhance therapeutic response. A recent study explored a new link between tumor mast cell (MC) infiltration and improved outcomes in patients with ACC. We further dissect the role of MC in TME of ACC by examining the tumor MC expression signatures and MC activity within TME to provide additional insight into potential novel immunotherapeutic targets.MethodsUsingCIBERSORTxcomputational immunogenomic deconvolution algorithm to analyze ACC tumor gene mRNA expression data (TCGA, N=79), we estimated the abundance of tumor immune infiltrating MC, and assessed prognostic potential of MC signaling genes as pro- or anti- tumor signatures, as well as the impact on overall (OS) and disease-free (DFS) survival.ResultsWe stratified MC signaling genes with survival prognostic values (OS, DFS, p<0.05) into anti-tumor (ALOX5, CCL2, CCL5, CXCL10, HDC, IL16, TNF, TPSAB1, VEGFD) and pro-tumor (CXCL1, CXCL3, CXCL8, IL4, IL13, PTGS3, TNSF4, VEGFD) groups. Anti-tumor MC signature, as the predominant phenotype, was associated with improved OS and DFS.ConclusionThe deconvolution analysis of TCGA data identified MC infiltration in ACC microenvironment as predominantly associated with anti-tumor activity. Future studies stemming from our findings may help define the role of MC in TME and the impact on patient survival in patients with ACC. Modulation of tumor MC infiltration may serve as a potential target for novel synergistic immunotherapies for the treatment and improved survival of patients with ACC.
Identification and Evaluation of a Panel of Strong Constitutive Promoters inListeria monocytogenesfor Improving the Expression of Foreign Antigens
Authors: Ma Junfei , Ji Qianyu , Wang Shuying , Qiu Jingxuan , Liu Qing 
Published: February 2021

AbstractAttenuatedListeria monocytogenes(L. monocytogenes) could be used as a vaccine vector for immunotherapy of tumors or pathogens. However, the lack of reliable promoters limits its ability to express foreign antigens. In this work, 21 promoters fromL. monocytogeneswere identified by RNA-seq analysis under two conditions of pH 7.4 and pH 5.5. Based on the constructed fluorescence report system, 7 constitutive promoters showed higher strength than that of Phelp, a previously reported strong promoter. Further, the selected 5 constitutive promoters also showed high activity in the production of UreB, a widely used antigen againstHelicobacter pylori(H. pylori). In particular, a well-characterized constitutive promoter P18, which performed best in both fluorescence intensity and UreB production, was proved to be highly active in vitro and in vivo. In summary, we provide a useful promoter library forListeriaspecies and offer a reference for constitutive promoter mining in other organisms.Key points21 promoters fromL. monocytogeneswere identified by RNA-seq.Fluorescent tracer ofL. monocytogenes(P18) was performed in vitro and in vivo.A well-characterized constitutive promoter P18could improve the expression level of a foreign antigen UreB inL. monocytogenes
Embedding of exogenous B cell epitopes on the surface of UreB structure generates a broadly reactive antibody response againstHelicobacter pylori
Authors: Ma Junfei , Wang Shuying , Ji Qianyu , Qiu Jingxuan , Liu Qing 
Published: February 2021

AbstractSinceHelicobacter pylori(H. pylori) resistance to antibiotic regimens is increased, vaccination is becoming an increasingly important alternative therapy to controlH. pyloriinfection. UreB, FlaA, AlpB, SabA, and HpaA proteins ofH. pyloriwere previously proved to be used as candidate vaccine antigens. Here, we developed an engineered antigen based on a recombinant chimeric protein containing a structural scaffold from UreB and B cell epitopes from FlaA, AlpB, SabA, and HpaA. The multi-epitope chimeric antigen, named MECU, could generate a broadly reactive antibody response including antigen-specific antibodies and neutralizing antibodies againstH. pyloriurease and adhesins. Moreover, therapeutic immunization with MECU could reduceH. pyloricolonization in the stomach and protect the stomach in BALB/c mice. This study not only provides a promising immunotherapy to controlH. pyloriinfection, but also offers a reference for antigen engineering against other pathogens.
Characterization of a Novel Type Homoserine Dehydrogenase Only with High Oxidation Activity fromArthrobacter nicotinovorans
Authors: Liang Xinxin , Deng Huaxiang , Bai Yajun , Fan Tai-Ping , Zheng Xiaohui , Cai Yujie 
Published: February 2021

AbstractHomoserine dehydrogenase (HSD) is a key enzyme in the synthesis pathway of the aspartate family of amino acids. HSD can catalyze the reversible reaction of L-aspartate-β-semialdehyde (L-ASA) to L-homoserine (L-Hse). In direct contrast, growth characteristic studies of some bacterial such asArthrobacter nicotinovoransshowed that the bacterium could grow well in medium with L-homoserine as sole carbon, nitrogen and energy source, but the genes responsible for the degradation of L-Hse remain unknown. Based on the function and sequence analysis of HSD, one putative homoserine dehydrogenase fromA.nicotinovoranswas named AnHSD, which was different from those HSDs that from the aspartic acid metabolic pathway, might be responsible for the degradation of L-Hse. Surprisingly, the analysis showed that the purified AnHSD exhibited specific L-Hse oxidation activity without reducing activity. At pH 10.0 and 40 °C, TheKmandKcatof AnHSD was 6.30 ± 1.03 mM and 462.71 s-1, respectively. AnHSD was partiality for NAD+cofactor, as well as insensitive to feedback inhibition of downstream amino acids of aspartic acid family. The physiological role of AnHSD inA.nicotinovoransis discussed. These findings provide a novel insight for a better understanding of an alternative genetic pathway for L-Hse catabolism which was dominated by the novel HSD.ImportanceL-homoserine is an important building block for the synthesis of L-threonine, L-methionine, L-lysine which from aspartic acid family amino acids. However, some bacteria can make use of L-homoserine as a sole carbon and nitrogen source. Although the microbial degradation of L-homoserine has been studied several times, the genes involved and the molecular mechanisms remain unclear. In this study, we show that AnHSD responsible for the catabolism of L-homoserine in strainArthrobacter nicotinovorans, as a special homoserine dehydrogenase with high diversity exists inArthrobacter,Microbacterium,Rhizobium. We report for the first time that this novel homoserine dehydrogenase is now proposed to play a crucial role in that L-homoserine can use as a sole carbon and nitrogen source. This study is aimed at elucidating the enzymatic properties and function features of homoserine dehydrogenase fromArthrobacter nicotinovorans. These findings provide new insight into the catabolism of L-homoserine in bacteria.
Promises and pitfalls of Topological Data Analysis for brain connectivity analysis
Authors: Caputi Luigi , Pidnebesna Anna , Hlinka Jaroslav 
Published: February 2021

AbstractDeveloping sensitive and reliable methods to distinguish normal and abnormal brain states is a key neuroscientific challenge. Topological Data Analysis, despite its relative novelty, already generated many promising applications, including in neuroscience. We conjecture its prominent tool of persistent homology may benefit from going beyond analysing structural and functional connectivity to effective connectivity graphs capturing the direct causal interactions or information flows. Therefore, we assess the potential of persistent homology to directed brain network analysis by testing its discriminatory power in two distinctive examples of disease-related brain connectivity alterations: epilepsy and schizophrenia. We estimate connectivity from functional magnetic resonance imaging and electrophysiology data, employ Persistent Homology and quantify its ability to distinguish healthy from diseased brain states by applying a support vector machine to features quantifying persistent homology structure.We show how this novel approach compares to classification using standard undirected approaches and original connectivity matrices. In the schizophrenia classification, topological data analysis generally performs close to random, while classifications from raw connectivity perform substantially better; potentially due to topographical, rather than topological, specificity of the differences. In the easier task of seizure discrimination from scalp electroencephalography data, classification based on persistent homology features generally reached comparable performance to using raw connectivity, albeit with typically smaller accuracies obtained for the directed (effective) connectivity compared to the undirected (functional) connectivity. Specific applications for topological data analysis may open when direct comparison of connectivity matrices is unsuitable - such as for intracranial electrophysiology with individual number and location of measurements. While standard homology performed overall better than directed homology, this could be due to notorious technical problems of accurate effective connectivity estimation.
Up-regulation of bundle sheath electron transport capacity under limiting light in C4Setaria viridis
Authors: Ermakova Maria , Bellasio Chandra , Fitzpatrick Duncan , Furbank Robert T. , Mamedov Fikret , von Caemmerer Susanne 
Published: February 2021

AbstractC4photosynthesis is a biochemical pathway that operates across mesophyll and bundle sheath (BS) cells to increase CO2concentration at the site of CO2fixation. C4plants benefit from high irradiance but their efficiency decreases under shade causing a loss of productivity in crop canopies. We investigated shade acclimation responses of a model NADP-ME monocotSetaria viridisfocussing on cell-specific electron transport capacity. Plants grown under low light (LL) maintained CO2assimilation rates similar to high light plants but had an increased chlorophyll and light-harvesting-protein content, predominantly in BS cells. Photosystem II (PSII) protein abundance, oxygen-evolving activity and the PSII/PSI ratio all increased in LL BS cells indicating a higher capacity for linear electron flow. PSI, ATP synthase, Cytochromeb6fand the chloroplastic NAD(P) dehydrogenase complex, which constitute the BS cyclic electron flow machinery, were all upregulated in LL plants. A decline in PEP carboxylase activity in mesophyll cells and a consequent shortage of reducing power in BS chloroplasts was associated with the more oxidised redox state of the plastoquinone pool in LL plants and the formation of PSII - light-harvesting complex II supercomplexes with an increased oxygen evolution rate. Our results provide evidence of a redox regulation of the supramolecular composition of Photosystem II in BS cells in response to shading. This newly identified link contributes to understanding the regulation of PSII activity in C4plants and will support strategies for crop improvement including the engineering of C4photosynthesis into C3plants.Significance statementThe efficiency of C4photosynthesis decreases under low irradiance causing a loss of productivity in crop canopies. We investigate shade acclimation of a model NADP-ME monocot, analysing cell-specific protein expression and electron transport capacity. We propose a regulatory pathway controlling abundance and activity of Photosystem II in bundle sheath cells in response to irradiance.
Effects of Intravenous Magnesium Sulfate on Calcium-Regulating Hormones, Plasma and Urinary Electrolytes in Healthy Horses
Authors: Schumacher Stephen A. , Kamr Ahmed M. , Lakritz Jeffrey , Burns Teresa A. , Bertone Alicia L. , Toribio Ramiro E. 
Published: February 2021

AbstractIntravenous magnesium sulfate (MgSO4) is used in equine practice to treat hypomagnesemia, dysrhythmias, neurological disorders, and calcium dysregulation. MgSO4is also used as a calming agent in equestrian events. Hypercalcemia affects calcium-regulating hormones, as well as plasma and urinary electrolytes; however, the effect of hypermagnesemia on these variables is unknown. The goal of this study was to investigate the effect of hypermagnesemia on blood parathyroid hormone (PTH), calcitonin (CT), ionized calcium (Ca2+), ionized magnesium (Mg2+), sodium (Na+), potassium (K+), chloride (Cl-) and their urinary fractional excretion (F) after intravenous administration of MgSO4in healthy horses. Twelve healthy female horses of 4-18 years of age and 432-600 kg of body weight received a single intravenous dose of MgSO4(60 mg/kg) over 5 minutes, and blood and urine samples were collected at different time points over 360 minutes. Plasma Mg2+concentrations increased 3.7-fold over baseline values at 5 minutes and remained elevated for 120 minutes (P < 0.05), Ca2+concentrations decreased from 30-60 minutes (P < 0.05), but Na+, K+and Cl-concentrations did not change. Serum PTH concentrations dropped initially to rebound and remain elevated from 30 to 60 minutes, while CT concentrations increased at 5 minutes to return to baseline by 10 minutes (P < 0.05). The FMg, FCa, FNa, FK, and FCl increased, while urine osmolality decreased from 30-60 minutes compared baseline (P < 0.05). Experimental hypermagnesemia alters calcium-regulating hormones (PTH, CT), reduces plasma Ca2+concentrations, and increases the urinary excretion of Mg2+, Ca2+, K+, Na+and Cl-in healthy horses. This information has clinical implications on the short-term effects of hypermagnesemia on calcium-regulating hormones as well as plasma and urine electrolytes.
NeuronMotif: Deciphering transcriptional cis-regulatory codes from deep neural networks
Authors: Wei Zheng , Hua Kui , Wei Lei , Ma Shining , Jiang Rui , Li Yanda , Wong Wing Hung , Wang Xiaowo 
Published: February 2021

AbstractDiscovering DNA regulatory sequence motifs and their relative positions are vital to understand the mechanisms of gene expression regulation. Such complicated motif grammars are difficult to be summarized from shallow models. Although Deep Convolutional Neural Network (DCNN) achieved great success in annotating cis-regulatory elements, few combinatorial motif grammars have been accurately interpreted due to the mixed signal in DCNN. To address this problem, we proposed NeuronMotif, a general backward decoupling algorithm, to reveal the homo-/hetero-typic motif combinations and arrangements embedded in convolutional neurons. We applied NeuronMotif on several widely-used DCNN models. Many uncovered motif grammars of deep convolutional neurons are supported by literature or ATAC-seq footprinting. We further diagnosed the sick neurons that are sensitive to adversarial noises, which can guide DCNN architecture optimization for better prediction performance and motif feature extraction. Overall, NeuronMotif enables decoding cis-regulatory codes from deep convolutional neurons and understanding DCNN from a novel perspective.
Vocal plasticity in harbour seal pups
Authors: Borda Laura Torres , Jadoul Yannick , Rasilo Heikki , Casals Anna Salazar , Ravignani Andrea 
Published: February 2021

ABSTRACTVocal plasticity can occur in response to environmental and biological factors, including conspecifics’ vocalisations and noise. Pinnipeds are one of the few mammalian groups capable of vocal learning, and are therefore relevant to understanding the evolution of vocal plasticity in humans and other animals. Here, we investigate the vocal plasticity of harbour seals (Phoca vitulina), a species with vocal learning abilities attested in adulthood but not puppyhood. To zoom into early mammalian vocal development, we tested 1-3 weeks old seal pups. We tailored noise playbacks to this species and age to induce seal pups to shift their fundamental frequency (F0), rather than adapt call amplitude or temporal characteristics. We exposed individual pups to bandpass-filtered noise, which purposely spanned – and masked – their typical range of F0s, and simultaneously recorded pups’ spontaneous calls. Seals were able to modify their vocalisations quite unlike most mammals: They lowered their F0 in response to increased noise. This modulation was punctual and adapted to the particular noise condition. In addition, higher noise induced less dispersion around the mean F0, suggesting that pups may have been actively focusing their phonatory efforts to target lower frequencies. Noise masking did not seem to affect call amplitude. However, one seal showed two characteristics of the Lombard effect known for human speech in noise: significant increase in call amplitude and flattening of spectral tilt. Our relatively low noise levels may have favoured F0 shifts while inhibiting amplitude adjustments. This lowering of F0 is quite unusual, as other animals commonly display no F0 shift independently of noise amplitude. Our data represents a relatively rare case in mammalian neonates, and may have implications for the evolution of vocal plasticity across species, including humans.