bluuebunny/crossref_metadata_2025 huggingface dataset:
Uptake of home-initiated tuberculosis evaluation during household contact investigation in Kampala, Uganda: A mixed-methods study
Authors: Armstrong-Hough Mari , Ggita Joseph , Turimumahoro Patricia , Meyer Amanda , Ochom Emmanuel , Katamba Achilles , Davis J. Lucian
Published: January 2018

Background Home-initiated tuberculosis (TB) evaluation could improve test uptake and linkage to care among at-risk contacts of active TB index patients. However, there is a need to systematically explore why contacts accept, decline, or are unable to complete these services. We sought to describe the barriers to home-based sputum collection as part of enhanced household contact investigation for TB in Kampala, Uganda. Methods Using a parallel convergent mixed-methods design, we collected quantitative data describing home sputum collection among 82 household contacts of active TB patients and qualitative interviews from a sub-sample of 19 of those contacts. Data were analyzed in parallel to produce a more complete picture of the underlying barriers to home sputum collection. Results Men were significantly more likely than women to provide sputum when eligible (p=0.04). Contacts who reported risk factors for or symptoms of TB but no active cough where significantly less likely to provide sputum (p=0.05). Education level was not associated with differences in home sputum collection success. In interviews, contacts pointed to support from and for the index patient as a facilitator. Contacts were particularly enthusiastic about the convenience of home-based sputum collection compared to visiting a clinic. Lost or insufficient sputum containers, difficulty producing sputum on demand, and shame emerged as barriers to collecting sputum at home. Conclusions Uptake of sputum collection might be improved by addressing opportunity barriers prior to the visit, possibly through equipment checklists and improved community health worker training. More research is needed on the effects of TB stigma on willingness to produce sputum, even in the privacy of one’s own home.
Characterization of antimicrobial resistance genes in Haemophilus parasuis isolated from pigs in China
Authors: Zhao Yongda , Guo Lili , Li Jie , Huang Xianhui , Fang Binghu
Published: January 2018

Background: Haemophilus parasuis is a common porcine respiratory disease that causes high rates of morbidity and mortality in farmed swine. We performed a molecular characterization of antimicrobial resistance genes harbored by H. parasuis from pig farms in China.

Methods: We screened 143 H. parasuis isolates for the presence of 64 antimicrobial resistance genes by PCR amplification and DNA sequence analysis. We determined quinolone resistance determining region mutations of DNA gyrase (gyrA and gyrB) and topoisomerase IV (parC and parE). The genetic relatedness among the strains was analyzed by pulsed-field gel electrophoresis.

Results: We found 14 antimicrobial resistance genes were present in these isolates, including TEM-1, ROB-1.ermB,ermA ,flor, catl,tetB,tetC, rmtB, rmtD, aadA1, aac(3’)-ⅡC, sul1, and sul2 genes. Interestingly, one isolate carried 5 antibiotic resistance genes (tetB, tetC, flor, rmtB, sul1). The genes tetB, rmtB, and flor were the most prevalent resistance genes in H. parasuis in China. Alterations in the gyrA gene (S83F/Y, D87Y/N/H/G) were detected in 81% of the strains and parC mutations were often accompanied by a gyrA mutation. pulsed-field gel electrophoresis typing revealed 51 unique patterns in the isolates carrying antibiotic resistance genes indicating considerable genetic diversity and suggesting the genes were spread horizontally.

Discussion: The current study demonstrated that the high antibiotic resistance of H. parasuis in piglets is a combination of transferable antibiotic resistance genes and multiple target gene mutations. GyrA gene mutation also was the most important role in quinolone resistance. These data provide novel insights for the better understanding of the prevalence and epidemiology of antimicrobial resistance in H. parasuis.
Global epigenetic and metabolic changes accompany the alterations in fruit size and shape of Cucurbita pepo L. intra-species grafting
Authors: Xanthopoulou Aliki , Tsaballa Aphrodite , Ganopoulos Ioannis , Kapazoglou Aliki , Avramidou Evangellia , Aravanopoulos Filippos , Moysiadis Theodoros , Osathanunkul Maslin , Tsaftaris Athanasios , Doulis Andreas , Kalivas Apostolos , Sarrou Eirini , Martens Stefan , Nianiou- Obeidat Irini , Madesis Panagiotis
Published: January 2018

To further understand the impact of grafting on fruit characteristics and to comprehend the mechanisms involved in graft-induced changes we studied homo- and hetero- grafted Cucurbita pepo cultivars (cv.) that vary in fruit size and shape. C. pepo cv. ‘Munchkin’ (small fruit) and cv. ‘Big Moose’ (large fruit) as well as cv. ‘Round green’ (round fruit) and cv. ‘Princess’ (elongated fruit) were homografted and reciprocally heterografted. The results show significant changes in fruit size when ‘Big Moose’ was grafted onto ‘Munchkin’ rootstocks in comparison to homo-grafted controls. Moderate changes in fruit shape were observed when grafting of cv. ‘Round green’ and cv. ‘Princess’ were performed. This is the first report of such phenotypic changes after intra-species/inter-cultivar grafting in Cucurbitaceae. Additionally, we found significant changes in i) secondary metabolite profile, ii) global DNA methylation pattern and iii) miRNA expression patterns in grafted scions and iv) DNA methylation on graft-induced phenotypic changes in grafted plants. Our results contribute to further understanding graft-induced effects on fruit morphology in intra-species grafting. Furthermore, our results pave the way for understanding the role of phenolic metabolites and epigenetic molecular mechanisms on the phenotypic changes recorded.
Functional and morphometric analysis of a middle Miocene bandicoot (Marsupialia, Peramelemorphia) skeleton from the Riversleigh World Heritage Area, Australia
Authors: Black Karen H , Travouillon Kenny J , Myers Troy J , Archer Michael , Hand Suzanne J , Wilson Laura A B , Bevitt Joseph
Published: January 2018

Peramelemorphia comprises four families: the extant Peramelidae (bandicoots), and Thylacomyidae (bilbies); the recently extinct Chaeropodidae (pig-footed bandicoot); and the extinct Yaralidae; with at least ten fossil species of uncertain familial affinity designated as Perameloidea incertae sedis. Extant taxa (18 species) are characteristically omnivorous, small to medium sized (0.1-4.9 kg) semi-fossorial/fossorial marsupials with a quadrupedal bounding gait. They occupy varied habitats from desert to rainforest in Australia and New Guinea. Fourteen pre-Pliocene taxa are currently described on the basis of cranial and/or dental material, yet none is known from its postcranial skeleton. Here we use qualitative morphological and morphometric data to analyse a partial skeleton of a new species of bandicoot from a middle Miocene cave deposit, AL90 Site, in the Riversleigh World Heritage Area. AL90 has been radiometrically dated at 14.7-15.1 Ma, however the species is abundant in numerous early to middle Miocene deposits at Riversleigh The AL90 specimen preserves the skull and dentaries, the fore-and hindlimbs, and elements of the manus, pes and axial skeleton. The species is estimated to have weighed approximately 300g (based on predictive marsupial craniodental regression equations) which is comparable among extant bandicoots to Perameles bougainville (Western barred bandicoot). Unlike modern species, the appendicular skeleton of the fossil taxon is less well-adapted for scratch-digging and fossorial behaviours. A striking contrast is the relatively elongate, gracile bones of the antebrachium of the fossil taxon compared with the generally short, robust forearm of modern bandicoots. Collectively, our data indicate a more generalized niche for this species than crown group peramelemorphians and may support suggestions that archaic bandicoots filled an ecological niche later dominated by small dasyurids during the late Cainozoic.
Rapid lineage assignment for the influenza A internal genes
Authors: Dalby Andrew , Tinworth Lorna , Bhat Sushant , Iqbal Munir
Published: January 2018

The hemagglutinin subtypes from Influenza A can be divided into distinct lineages. This is important for tracing the evolutionary history of the gene. It allows regional lineages to be identified and studied. The process of lineage identification depends on phylogenetic analysis to identify the distinct clades within the data. Identification of lineages within the Influenza Internal genes would help to simplify the analysis of reassortment where these genes are transferred between subtypes. In this paper we show that a rapid clustering method can be used to assign lineages to the internal gene segments without the need for a full phylogenetic analysis.
An Indo-Pacific damselfish in the Gulf of Mexico: origin and mode of introduction
Authors: Robertson D Ross , Dominguez-Dominguez Omar , Victor Benjamin , Simoes Nuno
Published: January 2018

The Indo-west Pacific (IWP) coral-reef damselfish Neopomacentrus cyanomos is well established across the southwest Gulf of Mexico (SwGoMx). Comparisons of mtDNA sequences of the SwGoMx population with those from conspecifics from 16 sites scattered across its native range show that the SwGoMx population is derived from two of four native lineages: one from the north-west Pacific Ocean, the other from the northern Indian Ocean. Three hypotheses address how this species was introduced to the SwGoMX: (1) aquarium release; (2) borne by cargo-ship; and (3) carried by offshore petroleum platform (petro-platform). The first is unlikely because this species rarely features in the aquarium trade, and “N. cyanomos” traded to the USA from the sole IWP source we are aware of are a misidentified congener, N. taeniurus. The second hypothesis is unlikely because shipping has not been associated with the introduction of alien damselfishes, there is little international shipping between the IWP and the SwGoMx, and voyages between those areas would be lengthy and along environmentally unfavorable routes. Various lines of evidence support the third hypothesis: (i) bio-fouled petro-platforms represent artificial reefs that can sustain large and diverse populations of tropical reef-fishes, including N. cyanomos in the SwGoMx; (ii) relocation of such platforms has been implicated in trans-ocean introductions leading to establishment of non-native populations of such fishes; and (iii) genetic characteristics of the SwGoMx population indicate that it was established by a large and diverse group of founders drawn from the regions where many SwGoMx petro-platforms originated.
Manipulating the alpha level cannot cure significance testing – comments on "Redefine statistical significance"
Authors: Trafimow David , Amrhein Valentin , Areshenkoff Corson N. , Barrera-Causil Carlos , Beh Eric J. , Bilgiç Yusuf , Bono Roser , Bradley Michael T. , Briggs William M. , Cepeda-Freyre Héctor A. , Chaigneau Sergio E. , Ciocca Daniel R. , Carlos Correa Juan , Cousineau Denis , de Boer Michiel R. , Dhar Subhra Sankar , Dolgov Igor , Gómez-Benito Juana , Grendar Marian , Grice James , Guerrero-Gimenez Martin E. , Gutiérrez Andrés , Huedo-Medina Tania B. , Jaffe Klaus , Janyan Armina , Karimnezhad Ali , Korner-Nievergelt Fränzi , Kosugi Koji , Lachmair Martin , Ledesma Rubén , Limongi Roberto , Liuzza Marco Tullio , Lombardo Rosaria , Marks Michael , Meinlschmidt Gunther , Nalborczyk Ladislas , Nguyen Hung T. , Ospina Raydonal , Perezgonzalez Jose D. , Pfister Roland , Rahona Juan José , Rodríguez-Medina David A. , Romão Xavier , Ruiz-Fernández Susana , Suarez Isabel , Tegethoff Marion , Tejo Mauricio , van de Schoot Rens , Vankov Ivan , Velasco-Forero Santiago , Wang Tonghui , Yamada Yuki , Zoppino Felipe C. , Marmolejo-Ramos Fernando
Published: January 2018

We argue that depending on p-values to reject null hypotheses, including a recent call for changing the canonical alpha level for statistical significance from .05 to .005, is deleterious for the finding of new discoveries and the progress of science. Given that blanket and variable criterion levels both are problematic, it is sensible to dispense with significance testing altogether. There are alternatives that address study design and determining sample sizes much more directly than significance testing does; but none of the statistical tools should replace significance testing as the new magic method giving clear-cut mechanical answers. Inference should not be based on single studies at all, but on cumulative evidence from multiple independent studies. When evaluating the strength of the evidence, we should consider, for example, auxiliary assumptions, the strength of the experimental design, or implications for applications. To boil all this down to a binary decision based on a p-value threshold of .05, .01, .005, or anything else, is not acceptable.
Current state of knowledge on Wolbachia infection among Coleoptera: a systematic review
Authors: Kajtoch Lukasz , Kotásková Nela
Published: January 2018

Background. Despite great progress in studies on Wolbachia infection in insects, the knowledge about its relations with beetle species, populations and individuals, and the effects of bacteria on these hosts is still unsatisfactory. In this review we summarize the current state of knowledge about Wolbachia occurrence and interactions with Coleopteran hosts. Methods. An intensive search of the available literature resulted in the selection of 57 publications that describe the relevant details about Wolbachia presence among beetles. These publications were then examined with respect to the distribution and taxonomy of infected hosts and diversity of Wolbachia found in beetles. Sequences of Wolbachia genes (16S rDNA, wsp and ftsZ) were used for the phylogenetic analyses. Results. The collected publications revealed that Wolbachia has been confirmed in 152 beetle species and that the estimated average prevalence of this bacteria across beetle species is 36% and varies greatly across families and genera (0-88% infected members) and is much lower (c. 13%) in geographic studies. The majority of the examined and infected beetles were from Europe and East Asia. The most intensively studied have been two groups of herbivorous beetles: Curculionidae and Chrysomelidae, followed by Hydraenidae and Buprestidae. Coleoptera harbor Wolbachia belonging to three supergroups: F found in only 3 species, and A and B found in similar numbers of beetles (including some doubly infected); however the latter two were most prevalent in different families. 65% of species with precise data were found to be totally infected. Single infections were found in 69% of species and others were doubly- or multiply-infected. Wolbachia caused numerous effects on its beetle hosts, including selective sweep with host mtDNA (found in 4% of species), cytoplasmic incompatibility (detected in c. 7% of beetles) and other effects related to reproduction or development (like male-killing, parthenogenesis reinforcement, possible haplodiploidy induction, and egg development). Phylogenetic reconstructions for Wolbachia genes rejected cospeciation between these bacteria and Coleoptera, with minor exceptions found in some closely related Hydraenidae and Chrysomelidae. In contrast, horizontal transmission of bacteria has been suspected or proven in numerous cases (e.g. among beetles sharing habitats and/or host plants). Discussion. The present knowledge about Wolbachia infection across beetle species and populations is very uneven. Even the basic data about infection status in species and frequency of infected species across genera and families is very superficial, as only c. 0.12% of all beetle species have been tested and/or examined so far. Future studies on Wolbachia in Coleoptera using next-generation sequencing technologies will be important for uncovering Wolbachia diversity and its relations with host evolution and ecology, as well as with other, co-occurring endosymbiotic bacteria.
Impact of STARD on reporting quality of diagnostic accuracy studies in a top Indian Medical Journal: A retrospective survey
Authors: Yellur Rajashree , Hassan Shabbeer
Published: January 2018

Improper reporting of diagnostic studies leads to an incorrect assessment of their clinical performance. STARD (Standards for Reporting of Diagnostic Accuracy Studies) checklist was launched in 2003 with the intention of improving reporting quality in diagnostic accuracy studies. The main aim of this study was to check the extent to which published diagnostic accuracy studies follow the 28-item STARD checklist. We conducted a literature survey of diagnostic studies published in Indian Journal of Medical Research (IJMR) between the years 1995-2013 for the evaluating their reporting quality by checking their adherence to STARD. Relevant studies (N=76) were retrieved from IJMR website and data extraction was performed by two authors simultaneously. A simple pre-post analysis found that there was no overall change in the reporting quality before and after STARD was released. Though some STARD items like description of participant sampling (χ2 = 5.712, p = 0.0169), clinical applicability of study findings (χ2 = 9.704, p = 0.0018) had a significant increase in post-STARD period. To take into account any underlying trend we conducted an interrupted time-series was done. We found a significant increase in the reporting quality after publication of STARD (β3 = 0.215 ± 0.068, p = 0.034). The overall reporting quality of diagnostic accuracy studies have improved since the introduction of STARD, however, error/defects in many sections remain as before.
Hi-MC: A novel method for high-throughput mitochondrial haplogroup classification
Authors: Mitchell Sabrina L , Farber-Eger Eric H , Veatch Olivia J , Goodloe Robert J , Wells Quinn S , Murdock Deborah G , Crawford Dana C
Published: January 2018

Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms (SNPs) that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. The source code is freely available at https://github.com/vserch/himc .
Inability to completely remove trace contaminants from drinking water by adsorption
Authors: Ng Wenfa
Published: January 2018

Trace contaminant removal is of contemporary concern in drinking water and wastewater treatment, given increasing evidence of potential toxicity of various heavy metals and metalloids in water at parts per billion (ppb) concentration levels. Currently, only high pressure reverse osmosis is able to reliably remove trace concentration contaminants from water but with high energy cost. Thus, the search is on for techniques and methods able to remove trace concentration contaminants with a lower energy footprint. Adsorption, a low energy technique for water and wastewater treatment is one possibility, which when coupled with the use of low cost biomass as adsorbent, would further improve process efficiency. This synopsis describes work done on examining the use of local marine seaweed, Sargassum sp. for removing copper at low (4 to 20 ppm, parts per million) and trace concentration (< 1000 ppb), with and without ammonium ion interference at different solution pH. Specifically, to reduce organic leaching and improve mechanical stability, formaldehyde crosslinking was used and was effective in enhancing stability of seaweed between pH 3 and 9. But, residual organic leaching of ~ 4 ppm meant that modified seaweed was not suitable for drinking water treatment. Batch kinetic and equilibrium studies revealed that up to a threshold ammonium concentration of 50 ppm [NH4+-N], there was good sorption of copper on formaldehyde crosslinked seaweed (treated seaweed), with residual copper concentration of 0.5 ppm. Residual copper concentration increased with increase in ammonium concentration (up to 2500 ppm [NH4+-N]); thereby, highlighting a competitive binding effect for treated seaweed’s surface functional groups. Attempts to remove trace concentration copper highlighted feasibility of the approach. However, significant residual equilibrium concentration of copper remained in the solution. More importantly, thermodynamic considerations point to the existence of a finite residual equilibrium concentration for copper in water; thereby, making adsorption not feasible as a method for completely removing trace concentration copper. Additionally, surface concentration of copper at the adsorbent might, in some cases, be higher than the bulk solution; thus, leading to desorption of copper from the seaweed surface back to the solution. Collectively, adsorption is not capable of completely removing a contaminant such as is the case for reverse osmosis where the non-porous membrane serves as barrier separating treated water from raw influent.
Enhancing knowledge of head and neck anatomy in preclinical medical students using low fidelity simulation
Authors: Buckley Lisa , St. Hilaire Rose Clarie , Gilbert Gregory , Leighton Kim , Barremkala Mallikarjuna , Callender Diana , Pederson David
Published: January 2018

Background: Simulation-based medical education is more prevalent in undergraduate preclinical medical education and acts as a foundation for clinical learning in years three and four. Currently, there is a call to teach clinical application of basic science material in preclinical years one and two.

Methods: Two groups of students participated in this investigation; a historical control of 270 students from the 2010 matriculating class and students receiving the intervention (anatomy lecture plus airway management simulation) from the 2012 matriculating class (n=337). Descriptive statistics were calculated for demographic and academic performance variables. Unadjusted and adjusted odds of passage of mid-term and final assessment were calculated. The final assessment was defined as one correct, two correct, and all three questions correct.

Results: Adjusted odds of passage of mid-term exam for the control group were 3.9 (95% CI: 2.7-5.9), virtually unchanged from the unadjusted odds of passage. Control group results for final exam passage as defined as one correct increased from .7 to .9 when adjusted for variables (95% CI:.3-2.5). Odds of passage of final assessment, for the control group, for adjusted models for two or greater correct increased from 4.1 to 5.6 (95% CI:2.6-13.7) and from 34.1 to 44.0 (95% CI: 21.7-102.5) when three answers (or 100%) are needed for passage.

Conclusions: When passage criteria for the final exam were defined as one correct, addition of a simulation exercise to the anatomy lecture increased the rate of passage by 11% after adjusting for covariates. However, when passage criteria for the final exam was defined as two or three correct, addition of a simulation exercise to the anatomy lecture decreased the rate of passage.
NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
Authors: Hatcher Eneida , Bao Yiming , Amedeo Paolo , Blinkova Olga , Cochrane Guy , Fedorova Nadia , Gruner William , Leipe Detlef , Nakamura Yasukazu , Ostapchuk Yuri , Palanigobu Vasuki , Sanders Robert , Schoch Conrad , Smith Catherine , Wentworth David , Yankie Linda , Zhdanov Sergey , Karsch-Mizrachi Ilene , Brister J. Rodney
Published: January 2018

Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy database and unique taxonomy identifiers generated. This added layer of manual processing is unique to influenza virus and prevents automatization of the flu sequence submission process. Here we outline a new NCBI policy that normalizes influenza virus taxonomy processing but maintains features supported by the previous approach. This change will reduce the amount of manual handling necessary for flu submissions and pave the way for increased automation of the submissions process. While this automation may disrupt some historic practices, it will better align influenza virus data processing with other viruses and ultimately lower the submission burden on data providers.
Cancer growth, metastasis and control likewise Go gaming: an Ising model approach
Authors: Barradas-Bautista Didier , Alvarado Matías , Cocho Germinal , Agostino Mark
Published: January 2018

This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones play first, could correspond to metastasis of cancer. Moreover, playing white stones on the second turn would correspond to the inhibition of cancer invasion. Mathematical modeling and algorithmic simulation of Go may, therefore, benefit the efforts to deploy therapies to surpass cancer illness by providing insight into the cellular growth and expansion over a tissue area. In this paper, we use the Ising Hamiltonian, an energy model to describe the energy exchange in interacting particles, to propose the modeling of cancer dynamics. Parameters in the energy function refer the biochemical elements that induce cancer metastasis; as well as, the biochemical immune system process of response.
A review of existing 4-bit crypto S-box cryptanalysis techniques and two new techniques with 4-bit Boolean functions for cryptanalysis of 4-bit crypto S-boxes
Authors: Dey Sankhanil , Ghosh Ranjan
Published: January 2018

4-bit Linear Relations play an important role in Cryptanalysis of 4-bit Bijective Crypto S-boxes. 4-bit finite differences also a major part of cryptanalysis of 4-bit substitution boxes. Count of existence of all 4-bit linear relations, for all of 16 input and 16 output 4-bit bit patterns of 4-bit bijective crypto S-boxes said as S-boxes has been reported in Linear Cryptanalysis of 4-bit S-boxes. Count of existing finite differences from each element of output S-boxes to distant output S-boxes have been noted in Differential Cryptanalysis of S-boxes. In this paper a brief review of these cryptanalytic methods for 4-bit S-boxes has been introduced in a very lucid and conceptual manner. Two new Analysis Techniques, one to search for the existing Linear Approximations among the input Boolean Functions (BFs) and output BFs of a particular 4-bit S-Box has also been introduced in this paper. The search is limited to find the existing linear relations or approximations in the contrary to count the number existent linear relations among all 16 4-bit input and output bit patterns within all possible linear approximations. Another is to find number of balanced 4-bit BFs in difference output S-boxes. Better the number of Balanced BFs, Better the security.
Paleontology of the Bears Ears National Monument: history of exploration and designation of the monument
Authors: Uglesich Jessica , Gay Robert J , Stegner M. Allison
Published: January 2018

Bears Ears National Monument (BENM) is a new, landscape-scale national monument jointly administered by the Bureau of Land Management and the Forest Service in southeastern Utah as part of the National Conservation Lands system. As initially designated, BENM encompasses 1.3 million acres of land with exceptionally fossiliferous rock units. These units comprise a semi-continuous depositional record from the Pennsylvanian Period through the middle of the Cretaceous Period. Additional Quaternary and Holocene deposits are known from unconsolidated river gravels and cave deposits. The fossil record from BENM provides unique insights into several important paleontological periods of time, including the Pennsylvanian-Permian transition from fully aquatic to more fully terrestrial tetrapods; the rise of the dinosaurs following the Triassic-Jurassic extinction; and the response of ecosystems in dry climates to sudden temperature increases at the end of the last ice age and across the Holocene. While the paleontological resources of BENM are extensive, they have historically been under-studied. Here we summarize prior paleontological work in BENM and review the data used to support paleontological resource protection in the 2016 BENM proclamation.
Aminopeptidase activity is related to the amino acids composition of the food in passerine birds
Authors: Garro Cintia , Brun Antonio , Karasov William , Caviedes-Vidal Enrique
Published: January 2018

Background. Passerine birds exploit different kinds of feeding habits and they have to face seasonal changes in food availability. Therefore, the composition of the principal nutrient in their food differs from the usual. In consequence the digestive function – enzyme hydrolysis and absorption – have to adapt to these nutrients. These changes in digestive physiology could respond to the adaptive modulation hypothesis which postulated that the activities of digestive enzymes should match the levels of their substrates in their diet so energy is not wasted on enzymes that are no need. Thus, we decide to measure intestinal enzymes activities of two species of passerine birds that differ in natural diet. Overall we hypothesized that species with different feeding habits present enzyme activity according to the mainly component of the diet (e.g., carbohydrates, proteins). Our prediction is that the individuals will present enzyme activity proportionally to the primary components of the diets. Methods. We select for study: red ovenbirds (Furnarius rufus), which are strict insectivores and zebra finches (Taeniopygia guttata), which are specialist granivores. We complete the analysis with publish data for house sparrows (Passser domesticus) feed on high starch from the literature. To examine intestinal enzyme activities, we measured the activity of two disaccharidases (sucrase-isomaltase and maltase-glucoamilase) and one dipeptidase (aminopeptidase-N). Results. The average intestinal activity of sucrase shows that the omnivorous P. domesticus presents almost 4 times more activity than the granivorous T. guttata and more than 11 times than the insectivorous F. rufus. This difference is also reflected in the total sucrase hydrolytic capacity where P. domesticus has roughly 10 times more than the other two birds. Surprisingly in F. rufus we found maltase and aminopeptidase activity while sucrase activity was close to zero. In the case of the average activity of maltase for the omnivorous P. domesticus is approximately 40 % more than the granivorous T. guttata and more than 5 times than the insectivorous F. rufus. Although the total maltase hydrolytic capacity of P. domesticus is 5 times more than T. guttata and F. rufus. The average of aminopeptidase-N activity for F. rufus and T. guttata almost doubled the P. domesticus ones. Also F. rufus roughly doubles the other two birds in total aminopeptidase hydrolytic capacity. Discussion. This study has shown that exist a relationship between the levels of amino acids in the diet and the total aminopeptidase capacity, but in the case of carbohydrates this relationship is not evident.
Aminopeptidase activity is related to the amino acids composition of the food in passerine birds
Authors: Garro Cintia , Brun Antonio , Caviedes-Vidal Enrique
Published: January 2018

Background. Passerine birds exploit different kinds of feeding habits and they have to face seasonal changes in food availability. Therefore, the composition of the principal nutrient in their food differs from the usual. In consequence the digestive function – enzyme hydrolysis and absorption – have to adapt to these nutrients. These changes in digestive physiology could respond to the adaptive modulation hypothesis which postulated that the activities of digestive enzymes should match the levels of their substrates in their diet so energy is not wasted on enzymes that are no need. Thus, we decide to measure intestinal enzymes activities of two species of passerine birds that differ in natural diet. Overall we hypothesized that species with different feeding habits present enzyme activity according to the mainly component of the diet (e.g., carbohydrates, proteins). Our prediction is that the individuals will present enzyme activity proportionally to the primary components of the diets. Methods. We select for study: red ovenbirds (Furnarius rufus), which are strict insectivores and zebra finches (Taeniopygia guttata), which are specialist granivores. We complete the analysis with publish data for house sparrows (Passser domesticus) feed on high starch from the literature. To examine intestinal enzyme activities, we measured the activity of two disaccharidases (sucrase-isomaltase and maltase-glucoamilase) and one dipeptidase (aminopeptidase-N). Results. The average intestinal activity of sucrase shows that the omnivorous P. domesticus presents almost 4 times more activity than the granivorous T. guttata and more than 11 times than the insectivorous F. rufus. This difference is also reflected in the total sucrase hydrolytic capacity where P. domesticus has roughly 10 times more than the other two birds. Surprisingly in F. rufus we found maltase and aminopeptidase activity while sucrase activity was close to zero. In the case of the average activity of maltase for the omnivorous P. domesticus is approximately 40 % more than the granivorous T. guttata and more than 5 times than the insectivorous F. rufus. Although the total maltase hydrolytic capacity of P. domesticus is 5 times more than T. guttata and F. rufus. The average of aminopeptidase-N activity for F. rufus and T. guttata almost doubled the P. domesticus ones. Also F. rufus roughly doubles the other two birds in total aminopeptidase hydrolytic capacity. Discussion. This study has shown that exist a relationship between the levels of amino acids in the diet and the total aminopeptidase capacity, but in the case of carbohydrates this relationship is not evident.
Ecological divergence of burying beetles into the forest canopy
Authors: Wettlaufer Jillian D , Burke Kevin W , Schizkoske Adam , Beresford David V , Martin Paul R
Published: January 2018

Closely related species with overlapping geographic ranges encounter a significant challenge: they share many ecological traits and preferences but must partition resources to coexist. In Ontario, potentially eleven species of carrion beetles (Coleoptera: Silphidae) live together and require vertebrate carrion for reproduction. Their reliance on an ephemeral and uncommon resource that is unpredictable in space and time is thought to create intense intra- and interspecific competition. Evidence suggests that burying beetle species reduce competition by partitioning carrion for breeding across different habitats, temperatures, and seasons. Here, we test predictions of an alternative axis for partitioning carrion: vertical partitioning between the ground and forest canopy. We conducted a survey of carrion beetles from May to July 2016 at the Queen’s University Biological Station across 50 randomly generated points using baited lethal traps at 0m and 6m. Ground traps yielded more species and individuals compared to those in the canopy, and the number of individuals and species caught increased through the season in both trap types. Ground and canopy traps were accurately distinguished by the presence or absence of three predictor species: ground traps contained more Nicrophorus orbicollis and Necrophila americana, while canopy traps contained more Nicrophorus pustulatus. Indeed, we trapped 253 N. pustulatus in the canopy, but only 60 on the ground; N. pustulatus was the most common species in the canopy, and the only species that was more common in the 6m traps than on the ground. N. pustulatus is thought to be rare across its geographic range, but our results suggest instead that N. pustulatus is uniquely common in canopy habitats, demonstrating a vertical partitioning of habitat and resources between N. pustulatus and other co-occurring burying beetles. Our results are consistent with N. pustulatus having diverged into canopy habitats as a strategy to coexist with closely related sympatric species when competing for similar resources. We still, however, do not know the traits that allow N. pustulatus to flourish in the canopy, exactly how N. pustulatus uses canopy resources for breeding, or the factors that restrict the expansion of other burying beetles into this habitat.
A possible bivoltine development of several bumblebee species in Europe
Authors: Potapov Grigory , Kolosova Yulia , Bolotov Ivan
Published: January 2018

This article is devoted to an analysis of the possible bivoltine development of several bumblebee species in Europe. This study is based on materials collected by the authors in European countries and in the European North of Russia. Our records reveal that several bumblebee species may have at least two generations per season. We found the possibility of bivoltine development for the following species: Bombus hortorum (Slovakia and France), B. terrestris (Slovakia, France and the Isle of Crete off the east coast of Greece), B. pratorum (France and European North of Russia), and B. jonellus (European North of Russia).
MCLEAN: Multilevel Clustering Exploration As Network
Authors: Alcaide Daniel , Aerts Jan
Published: January 2018

Finding useful patterns in datasets has attracted considerable interest in the field of visual analytics. One of the most common tasks is the identification and representation of clusters. However, this is non-trivial in heterogeneous datasets since the data needs to be analyzed from different perspectives. Indeed, highly variable patterns may mask underlying trends in the dataset. Dendrograms are graphical representations resulting from agglomerative hierarchical clustering and provide a framework for viewing the clustering at different levels of detail. However, dendrograms become cluttered when the dataset gets large, and the single cut of the dendrogram to demarcate different clusters can be insufficient in heterogeneous datasets.

In this work, we propose a visual analytics methodology called MCLEAN that offers a general approach for guiding the user through the exploration and detection of clusters. Powered by a graph-based transformation of the relational data, it supports a scalable environment for representation of heterogeneous datasets by changing the spatialization. We thereby combine multilevel representations of the clustered dataset with community finding algorithms. Our approach entails displaying the results of the heuristics to users, providing a setting from which to start the exploration and data analysis.

To evaluate our proposed approach, we conduct a qualitative user study, where participants are asked to explore a heterogeneous dataset, comparing the results obtained by MCLEAN with the dendrogram. These qualitative results reveal that MCLEAN is an effective way of aiding users in the detection of clusters in heterogeneous datasets. The proposed methodology is implemented in an R package available at https://bitbucket.org/vda-lab/mclean
Divergent and convergent evolution of housekeeping genes in human-pig lineage
Authors: Wei Kai , Zhang Tingting , Ma Lei
Published: January 2018

Housekeeping genes are ubiquitously expressed and maintain basic cellular function across tissue/cell types conditions. The present study aimed to develop a set of pig housekeeping genes and compare characteristics of structure, evolution and function of housekeeping genes in the human-pig lineage. Using RNA sequencing data, we identified a list of 3,136 pig housekeeping genes. Comparing to human homologous counterparts, we found pig housekeeping genes were longer and subjected to slight weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, have stronger purifying selection than species-specific genes. But pig-specific and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein-active sites or structure, such as classical catalytic serine-histidine-aspartate triad and zinc finger features, implying that they have converged for maintaining the basic cellular function, which led to equivalent solutions for adapting to the environment. Human and pig housekeeping genes have varied in their structure and gene list, but they have converged on the maintenance of basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results shed light on the evolutionary dynamics of housekeeping genes.
Threatened plants species of Guinea-Conakry: A preliminary checklist
Authors: Couch Charlotte , Magassouba Sekou , Rokni Saba , Cheek Martin
Published: January 2018

Guinea-Conakry has one of the highest plant diversities in Sub-Saharan West Africa and is part of the Upper Guinean Forest ecoregion and the Guinean Forests of West Africa biodiversity hotspot. Guinea is a major supplier of the world’s bauxite and has significant reserves of high grade iron ore, it also has small reserves of diamonds, gold and uranium. As a result large areas of open cast mining exist in the country and pressure on habitats and vegetation are increasing with the need to bring revenue into the country; this is in addition to unsustainable slash and burn agriculture and a growing population. An initial list of 482 was drawn up from the Flore de Guinée, subsequent discussion and screening reduced the list to 253 which is presented here. It is estimated that c. 10% of the countries flora is threatened. Rediscoveries and new species are being made in Guinea, but they are often already threatened having been discovered as part of Environmental Impact Assessments. A comprehensive red list of threatened species is much needed to support the country’s environmental policy as well as their international obligations.
Average deviation for measuring variation in data in small samples (n < 5)
Authors: Ng Wenfa
Published: January 2018

Good control of experiment variability is critical to experiment success, and many methods are available for quantifying variation in data. Popular methods for measuring variability in data typically uses a statistical distribution such as a standard normal distribution, but these distributions are designed for large sample size with n > 30. However, experiments typically generate less than 5 replicates (n < 5). Thus, the key requirement for the use of standard normal distribution is not satisfied, which bring forth the need for the development of alternative ways of quantifying the variation in collected data for small sample size. This abstract describes a new statistic, average deviation, that aims to quantify the variation of repeated measurements of a variable. By taking an average of the sum of the differences between the mean and all measurements, average deviation provides a better representation of the variation in data around a mean, while capturing the impact of significant deviation from the mean by individual measurement. However, division of the sum of deviation of all measurements from the mean by the sample size meant that the presence of outlier measurement may not be fully represented by the calculated average deviation. Thus, the new statistic is better used with a small sample size of less than 5, which helps reduce the extent in which an outlier’s influence on the average deviation would be diluted. In summary, for small sample size, average deviation better represents the deviation between each measurement and the mean compared to statistical distribution-based approaches such as standard error. However, desire to not dilute the impact of outlier measurement on the calculated average deviation meant that the new statistic is only suitable for sample size less than 5.
Bacteria as “ink” for writing the initials of names on agar
Authors: Ng Wenfa
Published: January 2018

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created, to help them remember the strong friendships that they had fostered with their fellow course-mates during their final year research projects. Besides the fun activity of “Bacterial Calligraphy,” the surface patterning technique can also serve as a simple and relatively low-cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates for investigating possible interactions between different microbial species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students,” has been published in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, and is available at http://jmbe.asm.org/index.php/jmbe/article/view/414 as an open-access article.
Socratic approach for unlocking creative potential in undergraduate research students
Authors: Ng Wenfa
Published: January 2018

The final year research project aims to introduce undergraduates to scientific research as well as encourage them to think creatively and critically about problems from different angles. However, most courses in earlier parts of the curriculum focus on well defined problems with clear answers; thus, a huge gap exists between a research project’s desired educational outcomes and the students’ preparation. As a result, students experience significant difficulties in handling ambiguities (i.e., no defined answers) inherent in research, which leads to lack of motivation or trepidation at their projects. Is the above due to students’ lack of creativity? Or does it have more to do with the difficulty of sparking students’ imagination? One possibility for igniting students’ imagination and fascination for their chosen research topic is in using common lab observations and experiences to unlock students’ creative potential. In this abstract preprint, I describe a simple pedagogical tool for helping ignite creative and critical thinking processes in students. Specifically, the Socratic approach of question and answer, used in guiding students to answer their own questions rather than having answers provided to them, helped initiate, in the students, deductive and inductive thinking processes critical to tackling any research problem. This also helps increase students’ self confidence in problem solving. More importantly, the tentative steps taken in independent thinking also helped debunk their misconception that there exists a single correct answer for every research question. Collectively, through simple pedagogical tools such as question and answer, students can be guided to explore different perspectives in problem solving; thus, improving their creative and critical thinking skills.