bluuebunny/crossref_metadata_2025 huggingface dataset:
Conditional valuation for combinations of goods in primates
Authors: Chung Hui-Kuan , Alós-Ferrer Carlos , Tobler Philippe N.
Published: January 2021

Valuing goods and selecting the one with the highest value forms the basis of adaptive behaviour across species. While it is obvious that the valuation of a given type of goods depends on ownership and availability of that type of goods, the effects of other goods on valuation of the original good are sometimes underappreciated. Yet, goods interact with each other, indicating that the valuation of a given good is conditional on the other goods it is combined with, both in the wild and the laboratory. Here, we introduce conditional valuation in the context of valuing multiple goods and briefly review how human and animal experimentalists can leverage economic tools for the study of interactions among goods. We then review evidence for conditional valuation for combined foods in both human and non-human primates. In the laboratory, non-human primates show increased valuation of certain combinations of foods but decreased valuation of other types of combinations. Thus, similarly to humans, monkeys appear to value combinations of goods in a conditional fashion. Additionally, both humans and monkeys appear to employ similar neural substrates for the valuation of single goods, such as the orbitofrontal cortex. Together, investigations of our evolutionary precursors may provide insights on how we value interacting goods.

This article is part of the theme issue ‘Existence and prevalence of economic behaviours among non-human primates’.
Non-human primates use combined rules when deciding under ambiguity
Authors: Romain A. , Broihanne M-H. , De Marco A. , Ngoubangoye B. , Call J. , Rebout N. , Dufour V.
Published: January 2021

Decision outcomes in unpredictable environments may not have exact known probabilities. Yet the predictability level of outcomes matters in decisions, and animals, including humans, generally avoid ambiguous options. Managing ambiguity may be more challenging and requires stronger cognitive skills than decision-making under risk, where decisions involve known probabilities. Here we compare decision-making in capuchins, macaques, orangutans, gorillas, chimpanzees and bonobos in risky and ambiguous contexts. Subjects were shown lotteries (a tray of potential rewards, some large, some small) and could gamble a medium-sized food item to obtain one of the displayed rewards. The odds of winning and losing varied and were accessible in the risky context (all rewards were visible) or partially available in the ambiguous context (some rewards were covered). In the latter case, the level of information varied from fully ambiguous (individuals could not guess what was under the covers) to predictable (individuals could guess). None of the species avoided gambling in ambiguous lotteries and gambling rates were high if at least two large rewards were visible. Capuchins and bonobos ignored the covered items and gorillas and macaques took the presence of potential rewards into account, but only chimpanzees and orangutans could consistently build correct expectations about the size of the covered rewards. Chimpanzees and orangutans combined decision rules according to the number of large visible rewards and the level of predictability, a process resembling conditional probabilities assessment in humans. Despite a low sample size, this is the first evidence in non-human primates that a combination of several rules can underlie choices made in an unpredictable environment. Our finding that non-human primates can deal with the uncertainty of an outcome when exchanging one food item for another is a key element to the understanding of the evolutionary origins of economic behaviour.

This article is part of the theme issue ‘Existence and prevalence of economic behaviours among non-human primates’.
Economic behaviours among non-human primates
Authors: Bourgeois-Gironde Sacha , Addessi Elsa , Boraud Thomas
Published: January 2021

Do we have any valid reasons to affirm that non-human primates display economic behaviour in a sufficiently rich and precise sense of the phrase? To address this question, we have to develop a set of criteria to assess the vast array of experimental studies and field observations on individual cognitive and behavioural competences as well as the collective organization of non-human primates. We review a sample of these studies and assess how they answer to the following four main challenges. (i) Do we see any economic organization or institutions emerge among groups of non-human primates? (ii) Are the cognitive abilities, and often biases, that have been evidenced as underlying typical economic decision-making among humans, also present among non-human primates? (iii) Can we draw positive lessons from performance comparisons among primate species, humans and non-humans but also across non-human primate species, as elicited by canonical game-theoretical experimental paradigms, especially as far as economic cooperation and coordination are concerned? And (iv) in which way should we improve models and paradigms to obtain more ecological data and conclusions? Articles discussed in this paper most often bring about positive answers and promising perspectives to support the existence and prevalence of economic behaviours among non-human primates.

This article is part of the theme issue ‘Existence and prevalence of economic behaviours among non-human primates’.
Corynebacterium anserum sp. nov., isolated from the faeces of greater white-fronted geese (Anser albifrons) at Poyang Lake, PR China
Authors: Liu Qian , Wu Kui , Fan Guoyin , Bai Xiangning , Yang Xi , Pan Yanyu , Cao Lijiao , Song Wentao , Chen Shengen , Xiong Yanwen , Chen Haiying
Published: January 2021

Two Gram-stain-positive, facultatively aerobic, non-motile and rod- to coccoid-shaped bacterial strains, 23H37-10T and 4HC-13, were isolated from the faeces of greater white-fronted geese (Anser albifrons) at Poyang Lake, Jiangxi Province, PR China. Optimal growth was observed at 35–37 °C, pH 7.0–8.0 and with 0.5–1.5 % (w/v) NaCl. The 16S rRNA gene sequences of strains 23H37-10T and 4HC-13 were identical. Phylogenetic and phylogenomic analyses indicated that strains 23H37-10T and 4HC-13 formed an independent cluster within the genus

Corynebacterium

and showed 98.8, 97.4, 97.4 and 97.2 % 16S rRNA gene sequence similarity to

Corynebacterium urogenitale

LMM 1652T,

Corynebacterium urealyticum

DSM 7109T,

Corynebacterium falsenii

DSM 44353T and

Corynebacterium jeikeium

NCTC 11913T, respectively. Cells contained C18 :1
ω9c, C18 : 0 and C16 : 0 as the major cellular fatty acids and MK-9 (H2) as the predominant respiratory quinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidyl inositol mannosides, two unidentified phospholipids, four unidentified glycolipids and one unidentified lipid. Strain 23H37-10T contained mycolic acids, with meso-diaminopimelic acid and arabinose as the major whole-cell hydrolysates. The genome G+C content of strains 23H37-10T and 4HC-13 was 55.2 mol%. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 23H37-10T and 4HC-13 were 94.4 and 99.6 %, respectively. Strains 23H37-10T and 4HC-13 had dDDH and ANI values of less than 70 and 96 % with all available genomes of the genus

Corynebacterium

, respectively. The differential genotypic inferences, together with phenotypic and biochemical characteristics, suggested that strains 23H37-10T and 4HC-13 represent a novel species within the genus

Corynebacterium

, for which the name Corynebacterium anserum sp. nov. is proposed. The type strain is 23H37-10T (=GDMCC 1.1737T=KACC 21672T).
The human papillomavirus oncoproteins: a review of the host pathways targeted on the road to transformation
Authors: Scarth James A. , Patterson Molly R. , Morgan Ethan L. , Macdonald Andrew
Published: January 2021

Persistent infection with high-risk human papillomaviruses (HR-HPVs) is the causal factor in over 99 % of cervical cancer cases, and a significant proportion of oropharyngeal and anogenital cancers. The key drivers of HPV-mediated transformation are the oncoproteins E5, E6 and E7. Together, they act to prolong cell-cycle progression, delay differentiation and inhibit apoptosis in the host keratinocyte cell in order to generate an environment permissive for viral replication. The oncoproteins also have key roles in mediating evasion of the host immune response, enabling infection to persist. Moreover, prolonged infection within the cellular environment established by the HR-HPV oncoproteins can lead to the acquisition of host genetic mutations, eventually culminating in transformation to malignancy. In this review, we outline the many ways in which the HR-HPV oncoproteins manipulate the host cellular environment, focusing on how these activities can contribute to carcinogenesis.
Weakly-Coupled Oscillators with Long-Distance Correlation as a Model of Human Atrial Fibrillation
Authors: Iravanian Shahriar
Published: January 2021

I.

Atrial Fibrillation (AF) is a chronic, progressive, and heterogeneous disease, which exhibits irregular and chaotic atrial electrical activity. The exact mechanisms of AF have remained elusive. The complexity of the atrial signals, irregular period, and the non-local nature of AF make it very difficult to characterize its spatiotemporal organization. This paper presents a set of data-processing tools to find and evaluate the intracardiac signals in AF based on synchronization theory. Specifically, a graph-theoretical algorithm is developed to prune spurious detections of atrial complexes (spikes). The processing pipeline was applied to 10 intracardiac recordings obtained during ablation procedures in patients with paroxysmal or persistent AF. The AF cases were classified into three main types. Type I (n=3) is defined as the presence of a single driver that dominates both atria and is consistent with the mother rotor hypothesis. The majority of the cases had more than one driver and were classified as types II (n=4) and III (n=3). The drivers, i.e., the interacting organized areas, in type II have significantly different peak frequencies and are only weakly coupled. The drivers in type III have close frequencies, are moderately interacting, and show evidence of transient intermittent phase-locking (intermittency). In addition, a long-distance correlation between channels from the left and right atria was observed. The theory of synchronization is a useful conceptual framework to process and analyze AF and can provide mechanistic insight into AF and the effect of various interventions.
Transcranial magnetic stimulation entrains alpha oscillatory activity in occipital cortex
Authors: Lin Yong-Jun , Shukla Lavanya , Dugué Laura , Valero-Cabré Antoni , Carrasco Marisa
Published: January 2021

Parieto-occipital alpha rhythms (8-12 Hz) underlie cortical excitability and influence visual performance. Whether the synchrony of intrinsic alpha rhythms in the occipital cortex can be entrained by transcranial magnetic stimulation (TMS) is an open question. We applied 4-pulse, 10-Hz rhythmic TMS to entrain intrinsic alpha oscillators targeting right V1/V2, and tested four predictions with concurrent electroencephalogram (EEG): (1) progressive enhancement of entrainment across time windows, (2) output frequency specificity, (3) dependence on the intrinsic oscillation phase, and (4) input frequency specificity to individual alpha frequency (IAF) in the neural signatures. Two control conditions with an equal number of pulses and duration were arrhythmic-active and rhythmic-sham stimulation. The results confirmed the first three predictions. Rhythmic TMS bursts significantly entrained local neural activity. Near the stimulation site, evoked oscillation amplitude and inter-trial phase coherence (ITPC) were increased for 2 and 3 cycles, respectively, after the last TMS pulse. Critically, ITPC following entrainment positively correlated with IAF rather than with the degree of similarity between IAF and the input frequency (10 Hz). Thus, we entrained alpha-band activity in occipital cortex for ~3 cycles (~300 ms), and IAF predicts the strength of entrained occipital alpha phase synchrony indexed by ITPC.
Structural basis for Potassium transport by KdpFABC
Authors: Sweet Marie E. , Larsen Casper , Zhang Xihui , Schlame Michael , Pedersen Bjørn P. , Stokes David L.
Published: January 2021

KdpFABC is an oligomeric K+transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the Superfamily of K+Transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryo-EM. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC and KdpF remain static. We observe a series of spherical densities that we assign as K+or water and which define a pathway for K+transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K+transfer between alternative sites in the membrane domain of KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K+to the cytoplasm.
Nitrogen availability drives gene length of dominant prokaryotes and diversity of genes acquiring Nitrogen-species in oceanic systems
Authors: Dlugosch Leon , Poehlein Anja , Wemheuer Bernd , Pfeiffer Birgit , Giebel Helge-A. , Daniel Rolf , Simon Meinhard
Published: January 2021

Nitrogen (N) is a key element for prokaryotes in the oceans and often limits phytoplankton primary production. An untested option to reduce prokaryotic N-demand under N-limitation is to reduce gene length. Here we show that in the sunlit Atlantic Ocean genes of the prokaryotic microbial communities in the permanently stratified N-limited (sub)tropics are up to 20% shorter than in N-replete regions further south and north. Average gene length (AGL) of major pelagic prokaryotic genera and two virus families correlated positively with nitrate concentrations. Further, the genomic G+C content of 60% of the taxa was lower and the gene repertoire to acquire inorganic and organic N-species higher in N-limited than in N-replete regions. A comparison of the N-demand by reducing gene length or G+C content showed that the former is much more efficient to save N. Our findings introduce a novel and most effective mode of evolutionary adaptation of prokaryotes to save resources including N and energy. They further show an enhanced diversification of genes acquiring N-species and -compounds in N-deplete relative to N-replete regions and thus add important information for a better understanding of the evolutionary adaptation of prokaryotes to N-availability in oceanic systems.
Occurrences of protonated base triples in RNA are determined by their cooperative binding energies and specific functional requirements
Authors: Halder Antarip , Jhunjhunwala Ayush , Bhattacharyya Dhananjay , Mitra Abhijit
Published: January 2021

With wide ranging diversity in their geometries, binding strengths and chemical properties, noncanonical base pairs are equipped to intricately regulate and control the structural dynamics of RNA molecules. Protonation of nucleobases adds to the diversity. Compared to the unprotonated scenario, on one hand they open up new alternatives for base pairing interactions (Class I) while on the other, they modulate the geometry and stability of existing base pairing interactions (Class II). In both cases, compensation of the energetic cost associated with nucleobase protonation at physiological pH, can be understood in terms of protonation induced restructuring of charge distribution. This not only leads to modifications in existing base-base interactions but often also leads to additional stabilizing interactions, resulting in the formation of protonated base triples. Here we report our detailed quantum chemical studies, in conjunction with structural bioinformatics based analysis of RNA crystal and NMR structure datasets, probing into the contribution of such protonated triples in the structural dynamics of RNA. Our studies revealed more than 55 varieties of protonated triples in RNA, some of which occur recurrently within conserved structural motifs present in rRNAs, tRNAs and in other synthetic RNAs. Our studies suggest that high occurrence frequencies are associated with protonated triples which satisfy the specific structural requirements of conserved motifs where they occur. For example, protonated triples with flexible geometries are involved in the formation of tertiary contacts between different distant motifs. Stabilization of protonated base pairs, through the induction of additional energetically cooperative interactions, appears to be another factor. These results provide significant insights into the sequence-structure-function relationships in RNA.
Simultaneous association of grip effort with snack food items does not change preferences
Authors: Aridan Nadav , Schonberg Tom
Published: January 2021

Effort is typically considered aversive such that rewards requiring less effort are preferred over identical value rewards that require greater effort, commonly referred to as “effort discounting”. Although effort has been repeatedly shown to be weighed as a cost, there are indications to suggest that under some conditions it may increase preferences. An example for how effort affects preferences is the ‘contrast effect’ were items that follow effort production gain value. In the current study we examined whether the association of grip effort with snack food items would change preferences. In four experiments, we first identified each participant’s individual preferences of snack food items and subjective maximal grip force. We then associated different effort levels with items of similar preference. Finally, we tested for changes in preferences following the effort association. Across the four studies, effort association had no effect on preferences. Using Bayesian analyses, we conclude that simultaneous association of effort does not change preferences in our studies and call for a replication effort of previous findings.
Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution
Authors: Wang Linhe , Li Jie , He Shuai , Chen Haitian , He Shujiao , Yin Meixian , Zou DaWei , Xu Jinghong , Chen Shirui , Luo Tao , Yu Xinyu , Bei Jinxin , Guo Zhiyong , He Xiaoshun
Published: January 2021

Ischemia-reperfusion injury (IRI) remains the major reason for impaired donor graft function and increased mortality post-liver transplantation. The mechanism of IRI involves multiple pathophysiological processes and numerous types of cells. However, a systematic and comprehensive single-cell transcriptional profile of intrahepatic cells during liver transplantation is still unclear. We performed a single-cell transcriptome analysis of 14,313 cells from liver tissues collected from pre-procurement, at the end of preservation and 2 h post-reperfusion. We made detailed annotations of mononuclear phagocyte, endothelial cell, NK/T, B and plasma cell clusters, and we described the dynamic changes of the transcriptome of these clusters during IRI and the interaction between mononuclear phagocyte clusters and other cell clusters. In addition, we found that TNFAIP3 interacting protein 3 (TNIP3), specifically and highly expressed in Kupffer cell clusters post-reperfusion, may have a protective effect on IRI. In summary, our study provides the first dynamic transcriptome map of intrahepatic cell clusters during liver transplantation at single-cell resolution.
Network centrality is the most important variable determining gene sequence evolution rates inSchizosaccharomyces pombe
Authors: Harnqvist Simon
Published: January 2021

Which variables determine the rate of gene and protein sequence evolution is a central question in evolutionary genomics. In the model organism fission yeast(Schizosaccharomyces pombe), the determinants of the rate of sequence evolution have yet to be determined. Previous studies in other organisms have typically found gene expression levels to be most significant, with numerous other variables identified as having a smaller impact. Here, partial least squares regression (PLS) and partial correlation analysis are used to model sequence evolution rates in the fission yeast genome by a range of variables. Variable importance in projection (VIP) scores as well as partial correlation coefficients are calculated for each variable, and used as estimates of the influence of each independent variable on sequence evolution rate. Unlike many previous studies in other organisms, centrality in the PPI network is shown to be the most important variable, and gene expression found to be less influential. Considerable heterogeneity is found in the influence of different gene ontology terms as well as amino acid composition. However, the majority of variance in constraint in fission yeast remains unexplained by this study, indicating that variables not yet considered and stochastics probably have considerable impact on the rate of molecular evolution.
Changes in Behavior and Salivary Serum Amyloid A in cows with Subclinical Mastitis
Authors: Caplen G. , Held S.D.E.
Published: January 2021

The aim of this study was to identify detailed changes in behavior, and in salivary serum amyloid A (SAA), associated with subclinical mastitis. This included standard sickness behaviors (which form part of an adaptive response to conserve energy, minimize heat loss and facilitate recovery following infection and inflammation) and lesser-studied behaviors, that are biologically predicted to change at low-level infection, and therefore particularly relevant for detecting subclinical mastitis (here labelled ‘luxury’ behaviors). SAA is a physiological marker of systemic inflammation, with levels in milk and serum already known to increase during subclinical mastitis. We investigated whether the same was true for SAA in cow saliva. Data were collected for n = 34 commercial barn-housed dairy cows, tested in 17 matched-pairs. Each pair comprised a cow with subclinical mastitis (SCM)and a healthy control (CTRL), identified using somatic cell count (SCC) (SCM: SCC >200 x1000 cells/ml; CTRL: SCC <100 x1000 cells/ml). SCM cows were selected for study ad-hoc, at which point they were paired with a CTRL cow, based upon parity and calving date; consequently, the full data set was accrued over several months. Data were collected for each pair over 3 days: SCC (l4:00-l5:00h) Day 1; behavior (24h from 00:00h) Day 2; salivary serum amyloid-A (SAA) Day 3. We report, for the first time, that an increase in salivary SAA occurs during subclinical mastitis; SAA was higher in SCM cows and demonstrated a positive (weak) correlation with SCC. The behavioral comparisons revealed that SCM cows had reductions in activity (behavioral transitions and distance moved), social exploration, social reactivity (here: likelihood to move away/be displaced following receipt of agonism), performance of social grooming and head butts, and the receipt of agonistic non-contact challenges. In addition, SCM cows received more head swipes, and spent a greater proportion of time lying with their head on their flank than CTRL cows. SCM cows also displayed an altered feeding pattern; they spent a greater proportion of feeding time in direct contact with two conspecifics, and a lower proportion of feeding time at self-locking feed barriers, than CTRL cows. Behavioral measures were found to correlate, albeit loosely, with serum SAA in a direction consistent with predictions for sickness behavior. These included positive correlations with both lying duration and the receipt of all agonistic behavior, and negative correlations with feeding, drinking, the performance of all social and all agonistic behavior, and social reactivity. We conclude that changes in salivary SAA, social behavior, and activity offer potential in the detection of subclinical mastitis and recommend further investigation to substantiate and refine our findings.
Estuarine molecular bycatch as a landscape-wide biomonitoring tool
Authors: Mariani S. , Harper L.R. , Collins R.A. , Baillie C. , Wangensteen O.S. , McDevitt A.D. , Heddell-Cowie M. , Genner M.J.
Published: January 2021

Environmental DNA analysis is rapidly transforming biodiversity monitoring and bolstering conservation applications worldwide. This approach has been assisted by the development of metabarcoding PCR primers that are suited for detection of a wide range of taxa. However, little effort has gone into exploring the value of the non-target DNA sequences that are generated in every survey, but subsequently discarded. Here we demonstrate that fish-targeted markers widely employed in aquatic biomonitoring can also detect birds and mammals present in the surrounding habitats. We showcase this feature in three temperate estuaries over multiple seasons, where dozens of bird and mammal species offer valuable insights into spatial and temporal faunal variation. Our results indicate that existing metabarcode sequence data sets are suitable for mining and exploration of this ‘molecular by-catch’, and that any future eDNA-based surveys can be designed to accommodate this enhanced property of this widely applicable tool.
Computational identification and characterization of antigenic properties of Rv3899c ofMycobacterium tuberculosisand its interaction with Human leukocyte antigen (HLA)
Authors: Das Ritam , Eniyan Kandasamy , Bajpai Urmi
Published: January 2021

Tuberculosis (TB) is the second largest infectious disease that kills 1.2 million people annually worldwide. A rise in drug-resistant TB cases demands continued efforts towards the discovery & development of drugs and vaccines. In the recent past, though novel drugs have been added to the current TB regimen [1], research on new vaccine candidates needs a greater thrust. Secretory proteins of H37Rv are frequently studied for their antigenicity and their scope as protein subunit vaccines decrees further analysis. In this study, Rv3899c of H37Rv emerges as a potential vaccine candidate on its evaluation by several bioinformatics tools. It is a non-toxin, secretory protein with an ‘immunoglobulin-like’ fold which does not show similarity with a human protein. We found Rv3899c homologs in several mycobacterial species and its antigenic score (0.54) to compare well with the known immunogens such as ESAT-6 (0.56) and Rv1860 (0.52). Structural examination of Rv3899c predicted ten antigenic peptides, an accessibility profile of the antigenic determinants constituting B-cell epitope rich regions and a low Abundance of Antigenic Regions (AAR) value. Significantly, our study shows ESX-2 secretion system proteins and antigenic PE/PPE proteins of H37Rv as the interacting partners of Rv3899c. Further, molecular docking predicted Rv3899c to interact with human leukocyte antigen HLA-DRB1*04:01 through its antigenically conserved motif (RAAEQQRLQRIVDAVARQEPRISWAAGLRDDGTT). Interestingly, the binding affinity was observed to increase on citrullation of its Arg1 residue. Taken together, the computational characterization and predictive information suggest Rv3899c to be a promising TB vaccine candidate, which should be examined and validated experimentally.
Molecular population genetics ofSex-lethal(Sxl) in theD. melanogasterspecies group - a locus that genetically interacts withWolbachia pipientisinDrosophila melanogaster
Authors: Bauer DuMont Vanessa L. , White Simone L. , Zinshteyn Daniel , Aquadro Charles F.
Published: January 2021

Sex-lethal(Sxl)is the sex determination switch inDrosophila, and also plays a critical role in germ-line stem cell (GSC) daughter differentiation inDrosophila melanogaster. Three female-sterile alleles atSxlinDrosophila melanogasterwere previously shown to genetically interact to varying degrees with the maternally inherited endosymbiontWolbachia pipientis.Given this genetic interaction andW. pipientis’ability to manipulate reproduction inDrosophila, we carried out a careful study of both the population genetics (within fourDrosophilaspecies) and molecular evolutionary analysis (across 20Drosophilaspecies) ofSxl. Consistent with earlier studies, we find that selective constraint has played a prominent role inSxl’smolecular evolution withinDrosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection atSxl. The episodic nature ofSxl’sprotein evolution is discussed in light of its genetic interaction withW. pipientis.
MBASR: Workflow-simplified ancestral state reconstruction of discrete traits with MrBayes in the R environment
Authors: Heritage Steven
Published: January 2021

Ancestral state reconstruction (ASR) is a critical tool in comparative biology. Given a phylogenetic tree and observed trait states for taxa at the tree’s tips, ASR aims to model ancestral trait states at the tree’s internal nodes. Thus, the pattern, tempo, and frequency of a character’s evolution can be considered in a phylogenetic framework. Software programs that perform discrete trait ASR analyses are variably complex in terms of workflow steps, input formats, user interfaces, settings and execution commands, and the organization of output.MBASR(acronym forMrBayes Ancestral States with R) is an R language toolkit that highly automates the ASR workflow and uses the machinery of the popular phylogenetics software MrBayes. Input data files are simple, analysis can be setup and run with a single R function, and statistical output is concisely organized and immediately interpretable. Use requires minimal knowledge of the most basic R commands and no experience with the MrBayes program. TheMBASRtoolkit can be freely downloaded from GitHub.
Imaging cytoplasmic lipid dropletsin vivowith fluorescent perilipin 2 and perilipin 3 knockin zebrafish
Authors: Wilson Meredith H. , Ekker Stephen C. , Farber Steven A.
Published: January 2021

Cytoplasmic lipid droplets are highly dynamic storage organelles; their rapid synthesis, expansion, and degradation, as well as their varied interactions with other organelles allow cells to maintain lipid homeostasis. While the molecular details of lipid droplet dynamics are currently a very active area of investigation, this work has been primarily performed in cultured cells andin vitrosystems. By taking advantage of the powerful transgenic andin vivoimaging opportunities afforded by the zebrafish model system, we have built a suite of tools to allow lipid droplets to be studied in real-time from the subcellular to the whole organism level. Fluorescently-tagging the lipid droplet associated proteins, perilipin 2 and perilipin 3, in the endogenous loci, permits visualization of lipid droplets in the intestine, liver, lateral line and adipose tissue. Using these transgenic lines we have found that perilipin 3 is rapidly loaded on intestinal lipid droplets following a high fat meal and then largely replaced by perilipin 2 a few hours later. These powerful new tools will facilitate studies on the role of lipid droplets in different tissues and under different genetic and physiological manipulations.
Non-targeted multimodal metabolomics data from ovine rumen fluid fractions
Authors: Palevich Nikola , Maclean Paul H. , Cao Mingshu
Published: January 2021

From an animal production and health perspective, our understanding of the metabolites in ruminant biofluids, particularly rumen fluid across different host species is poorly understood. Metabolomics is a powerful and sensitive approach for investigating low molecular weight metabolite profiles present in rumen biofluids. It can be used to identify potential roles of metabolites in the rumen microbiome and provide and understanding of host-level regulatory mechanisms associated with animal production. The rumen is a strictly anaerobic environment enriched with a complex community of bacteria, protozoa, fungi, archaea and bacteriophages. Here, we present a metabolomic dataset generated using hydrophilic interaction liquid chromatography (HILIC) and semi-polar (C18) chromatography methods coupled to high resolution mass spectrometry (MS), collected in both positive and negative ionization modes, of ovine rumen samples that were fractionated based on molecular weight (20 kDa, 8-10 kDa and 100 Da). This study highlights the potential of HILIC and C18 chromatography combined with non-targeted mass spectrometric methods to detect the polar and semi-polar metabolite species of the ruminal fluid metabolome.
Natural protection from type 1 diabetes in Non Obese Diabetic (NOD) mice is characterised by a unique pancreatic islet phenotype
Authors: Boldison Joanne , Thayer Terri C. , Davies Joanne , Wong F. Susan
Published: January 2021

The non-obese diabetic (NOD) mouse develops spontaneous type 1 diabetes, with some features of disease that are very similar to the human disease. However, a proportion of NOD mice are naturally-protected from developing diabetes, and currently studies characterising this cohort are very limited. Here, using both immunofluorescence and multi-parameter flow cytometry we focus on the pancreatic islet morphology and immune infiltrate observed in naturally-protected NOD mice. We show that naturally-protected NOD mice are characterised by an increased frequency of insulin-containing, smaller sized, pancreatic islets. Although mice remain diabetes free, florid immune infiltrate remains. However, this immune infiltrate is skewed towards a regulatory phenotype in both T and B-cell compartments. Pancreatic islets have an increased frequency of IL-10 producing B cells and associated cell surface markers. Resident memory CD69+CD8+T cells show a significant shift towards reduced CD103 expression, while CD4+T cells have increased FoxP3+CTLA4+expression. These data indicate that naturally-protected NOD mice have a unique islet signature and provide new insight into regulatory mechanisms within pancreatic islets.
GeneFriends 2021: Updated co-expression databases and tools for human and mouse genes and transcripts
Authors: Raina Priyanka , Lopes Inês , Chatsirisupachai Kasit , Farooq Zoya , de Magalhães João Pedro
Published: January 2021

Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have updated the GeneFriends database. Here, we present the latest version of GeneFriends, which includes updated gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples. GeneFriends is freely available athttp://www.genefriends.org/
Quaternary and quinary molecular solids based on structural inequivalence and combinatorial approaches: 2-nitroresorcinol and 4,6-dichlororesorcinol
Authors: Rajkumar Madhu , Desiraju Gautam R.
Published: January 2021

A synthetic strategy for the formation of stoichiometric quaternary and nonstoichiometric quinary solids is outlined. A series of 2-nitroresorcinol-based quaternary cocrystals were developed from binary precursors in two conceptual stages. In the first stage, ternary solids are synthesized based on the structural inequivalence at two recognition sites in the binary. In the second stage, the ternary is homologated into a stoichiometric quaternary based on the same concept. Any cocrystal without an inequivalence becomes a synthetic dead end. The combinatorial approach involves lower cocrystal systems with different structural environments and preferred synthon selection from a synthon library in solution. Such are the stepping stones for the isolation of higher cocrystals. In addition, a quaternary cocrystal of 4,6-dichlororesorcinol is described wherein an unusual synthon is observed with two resorcinol molecules in a closed loop with two different ditopic bases. The concept of the virtual synthon in binaries with respect to isolated ternaries is validated for the 4,6-dichlororesorcinol system. It is possible that only some binary systems are amenable to homologation into higher cocrystals. The reasons for this could have to do with the existence of preferred synthon modules, in other words, the critical components of the putative higher assembly that cannot be altered. Addition of the third and fourth component might be more flexible, and the choices of these components, possible from a larger pool of chemically related molecules.
Prognostic value of liver and kidney function parameters and their correlation with the ratio of urine‐to‐plasma paraquat in patients with paraquat poisoning
Authors: Zhang Shuangyang , Song Shuai , Luo Xuemei , Liu Jianfeng , Liu Mouze , Li Wenqun , Cao Ting , Li Nana , Zeng Cuirong , Zhang Bikui , Cai Hualin
Published: January 2021

Acute paraquat poisoning resulting from multiple organ failure usually has a high mortality rate. Liver and kidney, as the key oranges of paraquat detoxification and elimination, their injuries may suppress toxin excretion and enhance the toxicity of paraquat in other organs and worsen the prognosis. Therefore, we intended to explore the prognostic value of liver and kidney function parameters, and further evaluate their correlation with a more stable index urine‐to‐plasma paraquat (urine paraquat concentrations/plasma paraquat concentrations) instead of considering paraquat concentrations in plasma or urine alone. The study included 33 patients with acute paraquat poisoning admitted to four centres in China from January 2018 to December 2019. Seventeen patients (10 male/7 female) survived, whereas 16 patients (7 male/9 female, 48.48%) died from paraquat poisoning. Alanine aminotransferase (ALT) and the blood urea nitrogen (BUN) represent liver and kidney function parameters, respectively. The ratio of urine‐to‐plasma paraquat is negatively correlated with ALT (r = −0.94, P = 0 .02) and BUN (r = −0.82, P = 0.03). For receiver operating characteristic curve (ROC) analysis, ALT, BUN and urine‐to‐plasma paraquat have an AUC over 0.80. The study shows that the functional indexes of liver and kidney, as well as the ratio of urine‐to‐plasma paraquat, could be considered for evaluating the extent of organ injury and excretion rate of paraquat.
A retrospective analysis of the optimal time and psychological impact of decoronation in children and adolescents
Authors: Zhang Lili , Wang Meng , Xue Liang , Zhou Weiwei , Zhang Xin , Jin Luyuan , Xia Dengsheng , Gong Yi
Published: January 2021

Background/Aims

Decoronation offers one of the best and most predictable clinical outcomes for dentoalveolar ankylosis. The aim of this study was to determine the factors associated with the efficacy and psychological impact of decoronation for bone preservation.

Materials and Methods

The study included 42 paediatric patients with 42 infrapositioned replanted permanent teeth. Twelve of these teeth were decoronated. Variables such as the time of injury, stage of root development and the extent of infraposition were analysed. The vertical changes in the alveolar bone level of the decoronated teeth were assessed on radiographs using a three‐point scoring system. Parents of 30 patients with teeth that were not decoronated completed a questionnaire addressing their considerations and concerns regarding the treatment of infraposition.

Results

Teeth with root development in stages 2 and 3 showed a significantly higher rate of severe infraposition during the follow‐up visits. Decoronation was performed on 12 teeth within 1.5–5 years (mean 3.8 ± 1.3 years) after replantation and 11 of these cases developed a considerable alveolar bone level. The alveolar bone levels of boys and girls showed improvements of 2.2 and 3.2 mm, respectively. The optimal age for decoronation to have a considerable increase in bone level was 12.12 ± 0.83 years for boys and 11.25 ± 1.77 years for girls. Complicated treatments, followed by parents’ lack knowledge regarding decoronation, children's fear, follow‐up times, and cost were the major concerns regarding decoronation.

Conclusion

The optimal time for decoronation should be decided after considering the age, gender, skeletal growth pattern, and the degree of infraposition at the time of decoronation.
Pruritus Intensity Scales across Europe: a prospective validation study
Authors: Storck M. , Sandmann S. , Bruland P. , Pereira M.P. , Steinke S. , Riepe C. , Soto‐Rey I. , Garcovich S. , Augustin M. , Blome C. , Bobko S. , Legat F.J. , Potekaev N. , Lvov A. , Misery L. , Weger W. , Reich A. , Şavk E. , Streit M. , Serra‐Baldrich E. , Szepietowski J.C. , Dugas M. , Ständer S. , Zeidler C.
Published: January 2021

Background

Chronic pruritus (CP) is a subjective symptom, and it is necessary to assess its intensity with validated patient‐reported outcome tools in order to allow determination of the treatment course.

Objectives

So far, the itch intensity scales were validated in small cohorts and in single languages. Here, we report the validation of the numerical rating scale, the verbal rating scale and the visual analogue scale for the worst and average pruritus intensity in the last 24h in several languages across Europe and across different pruritic dermatoses.

Methods

After professional translation, the intensity scales were digitized for use as a tablet computer application. Validation was performed in clinics for Dermatology in Austria, France, Germany, Italy, Poland, Russia, Spain, Switzerland and Turkey.

Results

A total of 547 patients with contact dermatitis, chronic nodular prurigo, psoriasis vulgaris, lichen planus or cutaneous T‐cell lymphoma were included. The intensity scales showed a high level of reproducibility and inter‐correlations with each other. The correlation with the Dermatology Life Quality Index was weak to strong in nearly all countries and dermatoses with the exception of France and patients with chronic nodular prurigo, for which no statistically significant correlations were found.

Conclusions

The numerical rating scale, the verbal rating scale und the visual analogue scales are valid instruments with good reproducibility and internal consistency in German (Germany, Austria, Switzerland), French, Italian, Polish, Russian, Spanish and Turkish for different pruritic dermatoses. VAS worst was the best reproducible and consistent measuring instrument in all countries.
Assortment Optimization under a Single Transition Choice Model
Authors: Nip Kameng , Wang Zhenbo , Wang Zizhuo
Published: January 2021

In this study, we consider a new customer choice model which we call the single transition choice model. In this model, there is a universe of products and customers arrive at each product with a certain probability. If the arrived product is unavailable, then the seller can recommend a subset of available products and the customer will purchase one of the recommended products or choose not to purchase with certain transition probabilities. The distinguishing features of the model are that the seller can control which products to recommend depending on the arrived product, and each customer either purchases a product or leaves the market after one transition. We study the assortment optimization problem under this model. Particularly, we show that it is NP‐Hard even if the customer can transition from each product to at most two products. Despite the computational complexity, we provide polynomial time algorithms or approximation algorithms for several special cases, such as when the customer can only transition from each product to at most a given number of products and the size of each recommended set is bounded. Our approximation algorithms are developed by invoking the submodularity arguments, or connecting the problem with maximum constraint satisfaction problem and applying randomized rounding techniques to its semidefinite programming relaxation. We also provide a tight worst‐case performance bound for revenue‐ordered assortments. In addition, we propose a compact mixed‐integer program formulation, which is efficient for moderate size problems. Finally, we conduct numerical experiments to demonstrate the effectiveness of the proposed algorithms.
Same Game, Different Players: Emerging Pathogens of the CF Lung
Authors: Gannon Alexa D. , Darch Sophie E.
Published: January 2021

Incidences of non-tuberculosis mycobacteria (NTM) and
Aspergillus fumigatus
have increased around the world over the past decade and have become a significant health threat to immunocompromised individuals such as those with cystic fibrosis (CF). CF is characterized by the buildup of mucus in the lungs which become chronically infected by a myriad of pathogens.
Atypical Ebola Virus Disease in a Nonhuman Primate following Monoclonal Antibody Treatment Is Associated with Glycoprotein Mutations within the Fusion Loop
Authors: Banadyga Logan , Zhu Wenjun , Kailasan Shweta , Howell Katie A. , Franaszek Krzysztof , He Shihua , Siragam Vinayakumar , Cheng Keding , Yan Feihu , Moffat Estella , Cao Wenguang , Leung Anders , Embury-Hyatt Carissa , Aman M. Javad , Qiu Xiangguo
Published: January 2021

Ebola virus remains a global threat to public health and biosecurity, yet we still know relatively little about its pathogenesis and the complications that arise following recovery. With nearly 20,000 survivors from the 2013–2016 West African outbreak, as well as over 1,000 survivors of the recent outbreak in the DRC, we must consider the consequences of virus persistence and recrudescent disease, even if they are rare.
Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers Retain Activity against Multidrug-Resistant Pseudomonas aeruginosa
In Vitro
and
In Vivo
Authors: Moustafa Dina A. , Wu Ashley W. , Zamora Danniel , Daly Seth M. , Sturge Carolyn R. , Pybus Christine , Geller Bruce L. , Goldberg Joanna B. , Greenberg David E.
Published: January 2021

Numerous Gram-negative bacteria are becoming increasingly resistant to multiple, if not all, classes of existing antibiotics. Multidrug-resistant
Pseudomonas aeruginosa
bacteria are a major cause of health care-associated infections in a variety of clinical settings, endangering patients who are immunocompromised or those who suffer from chronic infections, such as people with cystic fibrosis (CF).
Direct Intracellular Visualization of Ebola Virus-Receptor Interaction by
In Situ
Proximity Ligation
Authors: Mittler Eva , Alkutkar Tanwee , Jangra Rohit K. , Chandran Kartik
Published: January 2021

Ebola virus causes episodic but increasingly frequent outbreaks of severe disease in Middle Africa, as shown by the recently overcome second largest outbreak on record in the Democratic Republic of Congo. Despite considerable effort, FDA-approved antifiloviral therapeutics or targeted interventions are not available yet.
Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in
Pseudomonas
Authors: Trouillon Julian , Ragno Michel , Simon Victor , Attrée Ina , Elsen Sylvie
Published: January 2021

Bacteria of the
Pseudomonas
genus, including the major human pathogen
Pseudomonas aeruginosa
, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized.