bluuebunny/crossref_metadata_2025 huggingface dataset:
Fitting occupancy models with E-SURGE: Hidden Markov modelling of presence-absence data
Authors: Gimenez Olivier , Blanc Laetitia , Besnard Aurélien , Pradel Roger , Doherty Paul , Choquet Rémi
Published: January 2018

1. Occupancy – the proportion of area occupied by a species – is a key notion for addressing important questions in ecology, biogeography and conservation biology. Occupancy models allow estimating and inferring about species occurrence while accounting for false absences (or imperfect species detection). 2. Most occupancy models can be formulated as hidden Markov models (HMM) in which the state process captures the Markovian dynamic of the actual but latent states while the observation process consists of observations that are made from these underlying states. 3. We show how occupancy models can be implemented in program E-SURGE, which was initially developed to analyse capture-recapture data in the HMM framework. Replacing individuals by sites provides the user with access to several features of E-SURGE that are not available altogether or just not available in standard occupancy software: i) user-friendly model specification through a SAS/R-like syntax without having to write custom code, ii) decomposition of the observation and state processes in several steps to provide flexible parameterisation, iii) up-to-date diagnostics of model identifiability and iv) advanced numerical algorithms to produce fast and reliable results (including site random effects). 4. To illustrate E-SURGE features, we provide simulated data and the details of the implementation on the analysis of several occupancy models. These detailed examples are gathered in a companion wiki platform http://occupancyinesurge.wikidot.com/ .
Similarity thresholds used in short read assembly reduce the comparability of population histories across species
Authors: Harvey Michael G , Judy Caroline Duffie , Seeholzer Glenn F , Maley James M , Graves Gary R , Brumfield Robb T
Published: January 2018

Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted effects of evolutionary processes across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity thresholds allow the de novo assembly of short reads into loci for analysis, but the resulting datasets are sensitive to both the similarity threshold used and to the variation naturally present in the organism under study. Stringent thresholds as well as highly variable species may result in datasets in which divergent alleles are lost or divided into separate loci ('over-splitting'), whereas liberal thresholds increase the risk of paralogous loci being combined into a single locus (‘under-splitting’). Comparisons among datasets or species are therefore potentially biased if different similarity thresholds are applied or if the species differ in levels of genetic variation. We examine the impact of a range of similarity thresholds on assembly of empirical short read datasets from populations of four different non-model bird lineages (species or species pairs) with different levels of genetic divergence. We find that, in all species, stringent similarity thresholds result in fewer alleles per locus than more liberal thresholds, which appears to be the result of high levels of over-splitting at stringent thresholds. The frequency of putative under-splitting, conversely, is low at all thresholds. Inferred genetic distances between individuals, gene tree depths, and estimates of the ancestral mutation-scaled effective population size (θ) differ depending upon the similarity threshold applied. Relative differences in inferences across species differ even when the same threshold is applied, but may be dramatically different when datasets assembled under different thresholds are compared. We suggest some best practices for assembling short read data to maximize comparability, such as using more liberal thresholds and examining the impact of different thresholds on each dataset.
Redescription of Neochelys franzeni (Schleich, 1993) from the middle Eocene, Messel Pit, of Germany, and a revision of morphological characters with importance for Pleurodira phylogeny
Authors: Cadena Edwin
Published: January 2018

Background. Neochelys franzeni (Schelich, 1993) is the only pleurodire or side-necked turtle from the middle Eocene, Messel Pit (the first UNESCO, World Natural Heritage Site in Germany, since 1995). The original description of the species is based on two specimens SMF ME 1091 (Holotype) and 715 (Paratype) housed at the Senckenberg Museum Frankfurt. The excellent preservation of complete and articulated skeletons of this species makes it a key taxon for understanding the evolution and phylogeny of the European Neochelys genus and its relationships with South American and African-Madagascar podocnemidids. Methods. Seven specimens of Neochelys franzeni, including hatchlings, juveniles, and adults were studied, and the information obtained for this species was included in a new compiled character-taxon matrix of Pleurodira, built from previous studies and new observations. Phylogenetic analyses were run using Parsimony algorithm on PAUP version 4.0a136 obtaining strict consensus trees after 10000 random replicates, boostrap values and Decay indices were also calculated to support the topology of obtained clades. Results. A revised diagnosis for the species is defined here, indicating that Neochelys franzeni differs from other members of the genus by the presence of a basisphenoid with a very acute anterior tip; an interparietal scute with a heart-like shape with a deep concave anteromedial margin; and a ridge running along the neural series of the carapace. Discussion. The phylogenetical analysis indicates that Neochelys spp. group is better resolved as closer to Erymnochelys madagascariensis-Peltocephalus dumerilanus inside Podocnemididae.
Properties evaluation of silorane, low-shrinkage, non-flowable and flowable resin-based composites in dentistry
Authors: Maia Rodrigo , Reis Rodrigo S , Moro Andre FV , Perez Cesar , Pessôa Bárbara , Dias Katia RHC
Published: January 2018

Purpose: This study tested the null hypothesis that different classes of direct restorative dental materials (silorane-based resin, low-shrinkage and conventional (non-flowable and flowable) resin-based composite (RBC)) do not differ from each other with regard to polymerization shrinkage, depth of cure, or microhardness. Methods: 140 RBC samples were fabricated and tested by one calibrated operator. Polymerization shrinkage was measured using a gas pycnometer both before and immediately after curing with 36 J/cm2 light energy density. Depth of cure was determined, using a penetrometer and the Knoop microhardness was tested from the top surface to a depth of 5 mm. Results: Considering polymerization shrinkage, the authors found significant differences (p<0,05) between different materials: non-flowable RBCs showed lower values, compared to flowable RBCs, with the silorane-based resin presenting the smallest shrinkage. The low shrinkage flowable composite performed similarly to non-flowable, with significant statistical differences compared to the two other flowable RBCs. Regarding to depth of cure, low-shrinkage flowable RBC were most effective compared to other groups. Microhardness was generally higher for the non-flowable vs. flowable RBCs (p<0.05). However, the values for low-shrinkage flowable did not differ significantly from those of non-flowable, but were significantly higher than those of the other flowable RBCs. Clinical Significance: RBCs have undergone many modifications as they have evolved and represent the most relevant restorative materials in today’s dental practice. This study of low-shrinkage RBCs, conventional RBCs (non-flowable and flowable) and silorane-based composite – by in vitro evaluation of volumetric shrinkage, depth of cure and microhardness – reveals that although filler content is an important determinant of polymerization shrinkage, it is not the only variable that affects properties of materials that were tested in this study.
A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae)
Authors: Kyrkou Ifigeneia , Iriondo José María , García-Fernández Alfredo
Published: January 2018

Silene ciliata Pourr. (Caryophyllaceae) is a species with a highly disjunct distribution that inhabits the alpine mountains of the Mediterranean Basin. We investigated the phylogeny and phylogeography of the species in an attempt to a) clarify the long suggested division of S. ciliata into two subspecies, b) evaluate its phylogenetic origin and c) assess whether the species´ diversification patterns were affected by the Mediterranean relief. For this purpose, we collected DNA from 25 populations of the species that inhabit the mountains of Portugal, Spain, France, Italy, FYROM, Bulgaria and Greece and studied the plastid regions rbcL, rps16 and trnL. Major intraspecific variation was supported by all analyses, while the possibility of existence of more varieties or subspecies was not favoured. Plastid DNA evidence, especially in the cases of rps16 and trnL markers, was in accordance with the division of S. ciliata into the two subspecies, one spreading west (Iberian Peninsula and Central Massif) and the other east of the Alps region (Italian and Balkan Peninsula). The present study proposes that this vicariance has probably derived from the Alps acting as a barrier to the species dispersal. The monophyletic origin of the species is highly supported. Plastid DNA patterns may have resulted from a combination of geographic factors providing links and barriers, climatic adversities and evolutionary processes that took place during Quaternary glaciations. The latter might include hybridization events for the western subspecies and mutational accumulation for the eastern ones.
Whale shark (Rhincodon typus) behavior: A multi-year analysis of individuals at Georgia Aquarium
Authors: Black Michael P , Grober Matthew , Schreiber Christian , Coco Chris , Dove Alistair
Published: January 2018

Background. From the coastal seas near Taiwan to the 6.3 million gallon Ocean Voyager habitat at Georgia Aquarium in Atlanta, Georgia, whale sharks, Rhincodon typus, were brought in stages: two females arrived in June 2006 and two males in June 2007. The behavioral observations described in this study began in 2008 as the first reported observations in captivity to assist in husbandry and better understand whale shark behavior variation between individuals and across time.

Methods. Two types of observations were made of the four sharks currently in the Georgia Aquarium Ocean Voyager habitat: 1) 15-minute focal observations throughout the day of individual sharks from a high gantry vantage point using Stopwatch+ software to time stamp all recorded behavior and 2) observations of swim speed, depth, and swimming direction for all sharks passing by a section of wall over longer periods of time (15 min-hours). Z-tests were used for inter-observer reliability.

Results. For most traits, whale sharks demonstrated unique behavioral profiles that were consistent over many years, but, over the course of years, some of these behavioral traits changed for individual sharks. There were also daily changes in behavior that were consistent across days. For instance, whale sharks showed a clear anticipation of feeding time marked by increases in swimming speed prior to obvious cues of the feed (i.e. 1 hour prior). During observations recorded during the day, whale sharks spent the majority of their time swimming at or near the surface. Most spent relatively equal times swimming clockwise as they did counterclockwise. Swim speeds observed in the habitat were similar to the range of those estimated from work in the field.

Conclusion. Each shark in the habitat demonstrated a behavioral profile unique to that individual, and we have observed short-term and long-term consistent patterns as well as changes in some behavior. These observations increase our knowledge of whale shark behavior, assisting in the husbandry of these animals and giving a better understanding of individual differences, temporal changes, and interactions between sharks.
Colourless agar for enhanced colour contrast between microbial colonies and solid medium
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Solid medium enables spatially-resolved simultaneous cultivation of different microbes in a simple and relatively low-cost format useful for preliminary screening of microbial diversity. Lack of colour contrast between colonies and agar, however, hampers colony identification by automated image analysis – thus, presenting a challenge for phenotype screening experiments and viable cell counting. Since microbes secrete pigments of myriad hues, this research sought to develop a colourless agar - which when placed on coloured paper of suitable hue – would enhance the colour contrast between agar and colonies of any colour. Nevertheless, the concept is confounded by formation of coloured compounds between medium components during autoclave sterilisation, which, in this study, was prevented by dissolving glucose and ammonium chloride in two separate solutions containing other medium components. Upon mixing the two solutions after heat sterilisation, a colourless agar was obtained – which remained colourless even after adding sterile yeast extract (max: 1 g/L) for providing essential vitamins to microbes unable to synthesise them. Culture experiments revealed good growth of Escherichia coli DH5α (ATCC 53868), Pseudomonas protegens Pf-5 (ATCC BAA-477), Pseudomonas aeruginosa (ATCC 15442), and Bacillus subtilis (ATCC 8473) with cell yield positively correlated with yeast extract concentration. Additionally, identical viable cell concentration and colonies of similar morphologies were observed on both the colourless and LB agar; thus, suggesting that no inhibitory compounds were formed during agar preparation. Collectively, using commonly used buffer components, salts and nutrients, a colourless agar was prepared by segregating chromogenic compounds during heat sterilisation; thereby, opening up its potential use in enhancing colour contrast between colonies and agar medium for revealing finer details of pure culture colonies, or more accurate automated colony identification and counting in screening and viable cell count assays.
Zbrowse: an interactive GWAS results browser
Authors: Ziegler Greg R , Hartsock Ryan H , Baxter Ivan
Published: January 2018

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.
Kisspeptin receptor agonist (FTM080) increased plasma concentrations of luteinizing hormone in anestrous ewes
Authors: Whitlock Brian K , Daniel Joseph A , Amelse Lisa L , Tanco Valeria M , Chameroy Kelly A , Schrick F Neal
Published: January 2018

Kisspeptin receptor (KISS1R) agonists with increased half-life and similar efficacy to kisspeptin in vitro may provide beneficial applications in breeding management of many species. However, many of these agonists have not been tested in vivo. These studies were designed to test and compare the effects of a KISS1R agonist (FTM080) and kisspeptin on luteinizing hormone (LH) in vivo. In experiment 1 (pilot study), sheep were treated with FTM080 (500 pmol/kg BW) or sterile water (VEH) intravenosuly. Blood was collected every 15 min before (1 hr) and after (1 hr) treatment. In experiment 2, sheep were treated with KP-10 (human Metastin 45-54; 500 pmol/kg BW), one of three dosages of FTM080 [500 (FTM080:500), 2500 (FTM080:2500), or 5000 (FTM080:5000) pmol/kg BW], or VEH intravenously. Blood was collected every 15 min before (1 hr) and after (4 hr) treatment. In experiment 1, FTM080:500 increased (P < 0.05) plasma LH concentrations when compared to VEH. The area under the curve (AUC) of LH following FTM080:500 treatment was also increased (P < 0.05). In experiment 2, plasma LH concentrations increased (P < 0.05) following treatment with KP-10 and FTM080:5000 when compared to VEH and FTM080:500. The AUC of LH following KP-10 was greater than (P < 0.05) all other treatments and the AUC of LH following FTM080:5000 was greater than (P < 0.05) all treatments except KP-10. These data provide evidence to suggest that FTM080 stimulates the gonadotropic axis of ruminants in vivo. Any increased half-life and comparable efficacy of FTM080 to KP-10 in vitro does not appear to translate to in vivo in sheep.
Development of a web-based vegetation spectral library (VSL) for remote sensing research and applications
Authors: Goswami Santonu , Matharasi Kuldeep
Published: January 2018

All objects on the Earth's surface absorb and reflect portions of the electromagnetic spectrum. Depending on the composition of the material, every material has its characteristic spectral profile. The characteristic spectral profile for vegetation is often used to study how vegetation patterns at large spatial scales affect ecosystem structure and function. Analysis of spectroscopic data from the laboratory, and from various other platforms like aircraft or spacecraft, requires a knowledge base that consists of different characteristic spectral profiles for known different materials. This study reports on establishment of an online and searchable spectral library for a range of plant species and landcover types in the Arctic, Antarctic and Chihuahuan desert ecosystems. Field data were collected from Arctic Alaska, the Antarctic Peninsula and the Chihuahuan desert in the visible to near infrared (IR) range using a handheld portable spectrometer. The data have been archived in a database created using postgre sql with have been made publicly available on a plone web-interface.
Implicit value updating explains transitive inference performance: The betasort model
Authors: Jensen Greg , Muñoz Fabian , Alkan Yelda , Ferrera Vincent P , Terrace Herbert S
Published: January 2018

Transitive inference (the ability to infer that “B>D” given that “B>C” and “C>D”) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, the betasort algorithm, and Q-learning (an established RPE model). Of these, only Q-learning failed to respond above chance during critical test trials. Implications for cognitive/associative rivalries, as well as for the model-based/model-free dichotomy, are discussed.
Intrasaccadic perception triggers pupillary constriction
Authors: Mathôt Sebastiaan , Melmi Jean-Baptiste , Castet Eric
Published: January 2018

It is commonly believed that vision is impaired during saccadic eye movements. However, here we report that some visual stimuli are clearly visible during saccades, and trigger a constriction of the eye's pupil. Participants viewed sinusoid gratings that changed polarity 150 times per second (every 6.67 ms). At this rate of flicker, the gratings were perceived as homogeneous surfaces while participants fixated. However, the flickering gratings contained ambiguous motion: rightward and leftward motion for vertical gratings; upward and downward motion for horizontal gratings. When participants made a saccade perpendicular to the gratings' orientation (e.g., a leftward saccade for a vertical grating), the eye's peak velocity matched the gratings' motion. As a result, the retinal image was approximately stable for a brief moment during the saccade, and this gave rise to an intrasaccadic percept: A normally invisible stimulus became visible when eye velocity was maximal. Our results confirm and extend previous studies by demonstrating intrasaccadic perception using a reflexive measure (pupillometry) that does not rely on subjective report. Our results further show that intrasaccadic perception affects all stages of visual processing, from the pupillary response to visual awareness.
The association between sleep duration and obesity amongst Canadians aged 12 and over
Authors: Temkit Maha , Yaya Sanni
Published: January 2018

Obesity is a medical condition in which excess body fat has accumulated to the extent that it may trigger risk of chronic illness, reduce life expectancy, and affect quality of life. Body Mass Index (BMI), which relates the body’s weight with height, has been widely used and accepted as a simple method to classify medical risk by weight status. Several variables are thought to be correlated with obesity in Canadian children, adolescents, and adults. The objective of this project is to investigate the effect of sleep duration, leptin levels, and ghrelin levels on the prevalence of obesity in Canada. The number of hours spent sleeping per night and self-reported BMI data from the 2011-2012 Canadian Community Health Survey (CCHS) are analyzed. The CCHS covers approximately 98% of the Canadian population aged 12 and over. It is hypothesized that a lack of sleep and later bed times are associated with a greater daily energy intake, lower leptin levels, and higher ghrelin levels, ultimately leading to obesity. Data analysis indicates a negative correlation, thus the hypothesis is accepted.
Analysis of consistency in large multi-section courses using exploration of linked visual data summaries
Authors: Yalcin Mehmet Adil , Gardner Elizabeth E , Anderson Lindsey B , Kirby-Straker Rowie , Wolvin Andrew D. , Bederson Benjamin B
Published: January 2018

Higher education courses with large student enrollments are commonly offered in multiple sections by multiple instructors. Monitoring consistency of teaching activities across sections is crucial in achieving equity for all students, and in developing strategies in response to emerging patterns and outliers. To address this need, we present an approach to analyze the multivariate data of sections, assignments and student submissions collected by a learning management system (LMS) using a new data exploration framework that we call linked data summaries. Data summaries are a unit of exploration with uncluttered, analytical, comprehensible visualizations of aggregations of data records attributes. Data browsers link multiple summaries and record lists, and enable flexible and rapid data analysis through tightly coupled interaction. Our analysis approach, developed in collaboration between analytics researchers and university instructors, reveals patterns across many aspects, including assignment and section structures, submission grading and timeliness. We present findings from an analysis of three semesters of an introductory oral communication course with over 1,750 students and 90 sections per semester.
The social amplification of disaster: Policy implications for agroecological pandemics
Authors: Wallace Rodrick
Published: January 2018

It is well understood that a vast spectrum of RNA virus types is undergoing rapid genetic reassortment and evolution in large-scale animal monoculture facilities, increasingly likely to entrain newer pathogens from neoliberally 'developing' areas to produce a massively fatal human pandemic that will overwhelm even the best possible health system responses. In such a pandemic -- that a mathematical model suggests can penetrate far more deeply than the 1918 event -- the USA and the PRC, which are parallel in animal monoculture structures, could lose a significant fraction of their populations to direct disease. Here, we examine powerful but less understood mechanisms of social amplification that can greatly raise the ultimate loss of life, roughly similar to the impact of the 'stabbed in the back' myth that emerged in Germany after WW I. It is obvious that effective programs to contain these threats must include -- or even begin with -- establishment of a close collaboration between interests in the USA and the PRC, where most large-scale animal monoculture is either located or from which it is managed.
The evolution of the fifth cervical vertebrae in Pelomedusoides (Testudines, Pleurodira): a preliminary analysis
Authors: Mariani Thiago F , Romano Pedro S R
Published: January 2018

Background. Crown-Pleurodira (i.e.: Cheloides and Pelomedusoides) possess a side-necked retraction mode with specialized cervical vertebrae (CV) anatomy. Moreover, there are distinctive ecological features among its lineages, as the convergent long neck in species of Chelidae and in the extinct pelomedusoid Araripemydidae. Also, the CV5-CV6 articulation is the major point of flexure in neck retraction and reflects a key point for the evolution of Pleurodira. Here we evaluated CV5 shape variation within some Pleurodira groups with emphasis on some Brazilian fossil species. Methods. We analyzed the fifth CV of eight species and 14 specimens comprising four pleurodiran clades (Chelidae, Araripemydidae, Bothremydidae and Podocnemididae) in order to assess the shape variation via geometric morphometry. All specimens were photographed in caudal view under the same protocol, and eight landmarks (LM) were picked at the left side of each vertebrae using TPSDig2. Data were Procrustes superimposed and a Relative Warps Analysis (RWA) was performed using TPSRelw v1.49. Results. RW1 and RW2 summarized 68.63% of the shape variance. The scatter of the specimens revealed distinctiveness between Podocnemidoidea (Podocnemididae+Bothremydidae) and Araripemys+Chelidae paraphyletic group. Such variation is due to (1) a medial contraction of the surface of the postzygapophysis, (2) a taller neural spine and (3) a more rounded vertebral condile towards Podocnemidoidea. Podocnemididae showed greater variation: a Podocnemis sextuberculata specimen (MZSP3218) is more alike to Cearachelys placidoi (Procrustes Distances, PD=0.17) than other podocnemidids and Bauruemys elegans resembles P. unifilis (PD=0.11). Also, other P. sextuberculata specimen (MZSP3217) is more alike to the Araripemys-Chelidae group. Discussion. Previous works have noticed the anatomical similarities between both longnecked chelids and A. barretoi, considering it as a convergence since they are from different clades. Our data showed the same pattern and, assuming the current phylogenetic relationships of Pleurodira, this might indicates similar feeding behavior between living Hydromedusa and Chelus and Araripemys. The Podocnemidoidea morphospace variation is consistent with the phylogeny, since C. placidoi is nested among Podocnemis spp., and this might indicate a more specialized CV5 for the former and a possible convergence with some Podocnemis species. Also, the resemblance of P. unifilis CV5 with B. elegans seems to indicate a morphotype similar to the podocnemidid ancestor for this living species. Despite our scanty sample, it shows a notable variation in Podocnemis spp. and at least two convergences among CV5 within Pleurodira. Further studies with additional sampling might shed light on a more complex evolution of CV specializations in side-necked turtles than previously assumed.
Runtime metric meets developer - Building better cloud applications using feedback
Authors: Cito Jürgen , Leitner Philipp , Gall Harald C. , Dadashi Aryan , Keller Anne , Roth Andreas
Published: January 2018

A unifying theme of many ongoing trends in software engineering is a blurring of the boundaries between building and operating software products. In this paper, we explore what we consider to be the logical next step in this succession: integrating runtime monitoring data from production deployments of the software into the tools developers utilize in their daily workflows (i.e., IDEs) to enable tighter feedback loops. We refer to this notion as feedback-driven development (FDD). This more abstract FDD concept can be instantiated in various ways, ranging from IDE plugins that implement feedback-driven refactoring and code optimization to plugins that predict performance and cost implications of code changes prior to even deploying the new version of the software. We demonstrate existing proof-of-concept realizations of these ideas and illustrate our vision of the future of FDD and cloud-based software development in general. Further, we discuss the major challenges that need to be solved before FDD can achieve mainstream adoption.
Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes
Authors: Renema Willem , Cotton Laura
Published: January 2018

Larger benthic foraminifera (LBF) are an important tool for the biostratigraphy of (sub)tropical shallow marine deposits. In Paleogene the genus Nummulites is an important genus for biostratigraphical zonation schemes. However, classification is Europe centered and based on external characters and equatorial thin sections. New results from regions outside the northern Tethys shows that a more rigid framework for the classification of nummulites is needed.

Here we present a new tool for achieving this goal. We visualise 3D chamber shape of Nummulites djodjokartae and compare these to traditional morphometrical characters. To achieve this goal we use computed microtomography of well preserved Nummulites tests.

We find that despite the regular shape in equatorial and axial thin section 3D chamber shape is not predicted by these sections. We argue that 3D reconstructions of Nummulites tests will be a great aid in improving our understanding lineages within the genus Nummulites, and to elucidate its evolutionary and biogeographical history.
Temperature drives asymmetric competition between alien and indigenous freshwater snails (Physa acuta vs. Physa fontinalis)
Authors: Früh Denise , Haase Peter , Stoll Stefan
Published: January 2018

Biological invasion represent one of the major threats to global biodiversity as alien species often displace indigenous species. However, knowledge of the mechanisms behind such displacements and the driving factors of the competitive superiority of the alien species still remain rare. In our study we combined analysis of field data and laboratory experiments examining species interactions, to investigate the impact of temperature in the case of the alien freshwater snail Physa acuta that is held responsible for the decline of indigenous snail Physa fontinalis in Europe. From field data, we identified higher temperature as the most important difference between sites populated by alien P. acuta and those where indigenous P. fontinalis occurred. Results of the species interaction experiment conducted at 15, 20, and 25°C confirmed the hypothesis that the competitive superiority of P. acuta over P. fontinalis increases at warmer temperatures. In single species treatments, increasing temperature stimulated both species to grow faster and reach greater shell heights. Coexistence treatments revealed an asymmetric competitive interaction between the two snail species. In both species, the density of conspecifics did not affect snail growth; however, density of heterospecifics affected the growth. At 15°C, the presence of heterospecifics stimulated the growth of both species, while at higher temperatures the presence of heterospecifics stimulated the growth in P. acuta, but inhibited in P. fontinalis. Our study shows that temperature can be a powerful driver of the outcomes of alien and indigenous species’ competition by driving asymmetric interaction. Further our results point up that the environmental context cannot be disregarded when investigating the interaction between alien and indigenous species, and predict alien species success and impact.
Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytesin vitro
Authors: Subhan Fazli , Shahzad Raheem , Tauseef Isfahan , Haleem Kashif Syed , Rehman Atta-Ur , Mahmood Sajid , Lee In-Jung
Published: January 2018

Background

Beaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand.

Method

This study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified asPseudomonas stutzeriusing 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession numberMF599548. The isolatedP. stutzeribacterium was cultured in Luria–Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect ofP. stutzerion human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay.

Result

The crudeP. stutzeriextract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract ofP. stutzeriFSRS had a strong pathological effect on human skin cells.

Discussion

Beach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacteriumP. stutzerimay, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach.
RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration
Authors: Zhang Jing , Storey Kenneth B.
Published: January 2018

Background

With the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis.

Methods

The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs.

Results

By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow.

Conclusions

With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865).
What Is Allergic Rhinitis?
Authors: Voelker Rebecca
Published: October 2024

This JAMA Patient Page describes allergic rhinitis and its risk factors, diagnosis, and treatment.
Safety of Simultaneous Vaccination With Adjuvanted Zoster Vaccine and Adjuvanted Influenza Vaccine
Authors: Schmader Kenneth E. , Walter Emmanuel B. , Talaat Kawsar R. , Rountree Wes , Poniewierski Marek , Randolph Emily , Leng Sean X. , Wunderlich Bettina , McNeil Michael M. , Museru Oidda , Broder Karen R.
Published: October 2024

Importance

Quadrivalent adjuvanted inactivated influenza vaccine (aIIV4) and adjuvanted recombinant zoster vaccine (RZV) contain novel adjuvants. Data are limited on the comparative safety, reactogenicity, and health-related quality of life (HRQOL) effects of the simultaneous administration of these vaccines.

Objective

To compare the safety and reactogenicity after simultaneous doses of RZV and aIIV4 administration (opposite arms) with simultaneous doses of RZV with quadrivalent high-dose inactivated influenza vaccine [HD-IIV4]).

Design, Setting, and Participants

This randomized blinded clinical trial was conducted during the 2021-2022 and 2022-2023 influenza seasons at 2 centers in the US among community-dwelling adults aged 65 years or older. Analysis was performed on an intention-to-treat basis.

Intervention

Simultaneous intramuscular administration of RZV dose 1 and aIIV4 or HD-IIV4 in opposite arms after age stratification (65-69 and ≥70 years) and randomization.

Main Outcomes and Measures

The primary outcome was the proportions of participants with 1 or more severe solicited reactions during days 1 to 8, using a noninferiority test (10% noninferiority margin). Additional measures included serious adverse events and adverse events of clinical interest during days 1 to 43 of the study period.

Results

A total of 267 adults (median age, 71 years [range, 65-92 years]; 137 men [51.3%]) were randomized; 130 received simultaneous RZV and aIIV4, and 137 received simultaneous RZV and HD-IIV4. The proportion of patients reporting 1 or more severe reactions after simultaneous administration of RZV and aIIV4 (15 of 115 [11.5%]) was noninferior compared with simultaneous RZV and HD-IIV4 (17 of 119 [12.5%]) (absolute difference, −1.0% [95% CI, −8.9% to 7.1%]). There were no significant differences in the number of serious adverse events or adverse events of clinical interest between the groups.

Conclusions and Relevance

In this clinical trial of simultaneous doses of RZV and aIIV4 compared with simultaneous doses of RZV and HD-IIV4, overall safety findings were similar between groups. From a safety standpoint, this study supports the simultaneous administration of RZV and aIIV4 among older adults.

Trial Registration

ClinicalTrials.gov Identifier: NCT05007041
Prolonging Endothelial Cell Survival with Thermoresponsive Peptide‐Functionalized Hydrogels Improves Ischemic Limb Tissue Regeneration and Function
Authors: Wang Huifeng , Dang Caitlyn , Rivera‐Bolanos Nancy , Tong Ophelia , Wang Xinlong , Chen Guo , Riter Rebecca L. , Chin Yuan‐Ho , Duan Chongwen , Zhang Xiaomin , Haney Chad R. , Ameer Guillermo , Jiang Bin
Published: October 2024

Critical limb ischemia (CLI) presents a significant clinical challenge, leading to tissue ischemia and potentially resulting in limb necrosis or amputation. Cell‐based regenerative therapies offer promise for improving outcomes in CLI, but their effectiveness is often limited by poor cell survival and engraftment. This study hypothesized that a thermo‐responsive polymer, poly(polyethylene glycol citrate‐co‐N‐isopropylacrylamide) (PPCN), combined with pro‐survival bioactive peptides, can create a protective microenvironment to improve endothelial cell survival and function after their delivery. Through in vitro and in vivo experiments, laminin‐derived peptide A5G81 and vascular endothelial growth factor (VEGF)‐derived peptide QK are identified as effective in promoting endothelial cell spreading, proliferation, and prolonged survival. PPCN's viscoelastic properties protected against shear stress during injection, while the peptides supported endothelial cell behavior through distinct molecular pathways. Importantly, delivery of endothelial cells with PPCN‐A5G81 and PPCN‐QK in a murine hindlimb ischemia model resulted in significant improvements in limb perfusion, tissue preservation, and functional outcomes compared to controls. Additionally, this approach enhanced skeletal muscle remodeling following ischemic injury. This innovative biomaterial platform represents a versatile solution for addressing cell survival challenges and advancing regenerative therapies in CLI and other ischemic conditions.
Stabilizing 2D Pt‐Based Halide Perovskites via Solvent Lone Pair Donation
Authors: Liu Huilong , Biswas Maitreyo , Smith Walter J. , Barnard Edward , Beechem Thomas , Mannodi‐Kanakkithodi Arun , Bansal Shubhra
Published: October 2024

Platinum‐based halide perovskites exhibit promising optoelectronic properties along with merits of low‐temperature processing and stability. Current research on Pt halide perovskites is limited to 0D A2BX6 structure as the ABX3 3D structure is thermodynamically unstable. Herein, the study reports the stabilization of the ABX3 structure into a 2D layered phase, CsPtI3(DMSO), that is stable up to 181.5 °C. The 2D phase shows an excitonic peak at the absorption edge of 600 nm, indicating quantum confinement. It also exhibits a large Stokes shift due to intersystem crossing (ISC), with a quenched singlet excitonic fluorescence at 610 nm and strong triplet emission at 852 nm. Pt(II) co‐ordinates with dimethyl sulfoxide (DMSO) via σ‐donation of S lone‐pair electrons and π‐ back donation from Pt to S, stabilizing CsPtI3(DMSO) layered structure. The strong electronic interaction between DMSO and Pt(II) and orbital mixing lead to spin‐orbit‐coupling, facilitating ISC and singlet‐to‐triplet exciton energy transfer. The interaction of Pt and DMSO is further confirmed by addition of thioacetamide (TAA), a strong S‐donor, which retards the formation of 2D layered structure, and directly results in Cs2PtI6 and Pt.
Electronic Modulation of RuCo Catalysts on TiO2 Nanotubes Promoting Durable Acidic Overall Water Splitting
Authors: Chen Hengyi , Gao Zehua , Ren Shijie , Gao Rui‐Ting , Wu Limin , Wang Lei
Published: October 2024

The development of efficient and durable bifunctional electrocatalysts is essential for hydrogen production from acidic water splitting. Herein, a TiO2 nanotube‐loaded Co‐doped Ru nanoparticle catalyst (RuCo/TiO2 NTs) is reported that exhibits excellent activity and stability toward acidic oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). The Ru─O─Ti bonding is enhanced by Co doping, and the metal carrier interaction between Ru nanoparticles and TiO2 NTs is enhanced, which effectively stabilizes Ru species during OER and initiates hydrogen spillover accelerating HER kinetics. As a result, RuCo/TiO2 NTs catalyst requires only 156 mV OER overpotential and 17 mV HER overpotential to achieve a current density of 10 mA cm−2 with a stability more than 500 h in acidic conditions. More importantly, benefiting from the excellent bifunctional activities, the proton exchange membrane electrolyte assembled from RuCo/TiO2 NTs has excellent activity and robust stability (1000 h). This work opens a new avenue for the efficient energy conversion devices.
Co‐inoculation with Rhizobium, Azospirillum, and microalgae increases common bean yield and profitability
Authors: de Oliveira Karen Sinéia , Volsi Bruno , Telles Tiago Santos , Mendes Aretusa Daniela Resende , Yunes João Sarkis , Andrade Diva Souza
Published: October 2024

Widely used as inoculants in agriculture, nitrogen‐fixing bacteria can be associated with other plant growth‐promoting microorganisms (PGPMs) to increase crop grain yield. This study aimed to evaluate whether co‐inoculation with Rhizobium tropici and Azospirillum brasilense associated with microalgae or cyanobacteria enhances common bean (Phaseolus vulgaris) grain yield and its economic gains in contrasting sandy and clayey soils. Water‐soluble protein content and indole‐3‐acetic acid (IAA) production of two cyanobacteria (Anabaena cylindrica and Calotrix brevissima) and six Chlorophyta microalgae (Nannochloropsis oculata, Haematococcus pluvialis, Muriellopsis sphaerica, Chlorella protothecoides, Chlorella vulgaris, and Botryococcus braunii) were determined. Anabaena cylindrica and C. brevissima had the highest IAA production, 336.7 ± 44.7 and 94.1 ± 11.8 µg IAA mg−1 of protein, respectively. Two field experiments were carried out to evaluate the triple inoculation of these Chlorophyta microalgae and cyanobacteria associated with R. tropici plus A. brasilense on the agronomic efficiency and profitability of common bean. Co‐inoculation of C. vulgaris plus R. tropici and A. brasilense in common bean had grain yield of 1277.5 kg ha−1 in clayey soil and 2960.3 kg ha−1 in sandy soil, increasing by 219.7 and 656.0 kg ha−1, respectively, in relation to double inoculation of R. tropici + A. brasilense. In the sandy soil, common bean with triple co‐inoculation had the highest profit ($956 ha−1), which was 25.6% higher than the N fertilized plants. Co‐inoculation with PGPMs generated the highest economic gains, and in addition, it is an eco‐friendly agronomic practice for sustainable food production.
Direct Epitaxial Growth of Polycrystalline MOF Membranes on Cu Foils for Uniform Li Deposition in Long‐life Anode‐free Li Metal Batteries
Authors: Wu Haiyang , Wu Langyuan , Li Yang , Dong Wendi , Ma Wenyu , Li Shaopeng , Xiao Dewei , Huang Peng , Zhang Xiaogang
Published: October 2024

Anode‐free Li‐metal battery (AFLMB) is being developed as the next generation of advanced energy storage devices. However, the low plating and stripping reversibility of Li on Cu foil prevents its widespread application. A promising avenue for further improvement is to enhance the lithophilicity of Cu foils and optimise their surfaces through a metal–organic framework (MOF) functional layer. However, excessive binder usage in the current approaches obscures the active plane of the MOF, severely limiting its performance. In response to this challenge, MOF polycrystalline membrane technology has been integrated into the field of AFLMB in this work. The dense and seamless HKUST‐1 polycrystalline membrane was deposited on Cu foil (HKUST‐1 M@Cu) via an epitaxial growth strategy. In contrast to traditional MOF functional layers, this binder‐free polycrystalline membrane fully exposes lithophilic sites, effectively reducing the nucleation overpotential and optimising the deposition quality of Li. Consequently, the Li plating layer becomes denser, eliminating the effects of dendrites. When coupled with LiFePO4 cathodes, the battery based on the HKUST‐1 membrane exhibits excellent rate performance and cycling stability, achieving a high reversible capacity of approximately 160 mAh g−1 and maintaining a capacity retention of 80.9 % after 1100 cycles.