bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated fluorescence intensity and gradient analysis enables detection of rare fluorescent mutant cells deep within the tissue of RaDR mice
Authors: Wadduwage Dushan N. , Kay Jennifer , Singh Vijay Raj , Kiraly Orsolya , Sukup-Jackson Michelle R. , Rajapakse Jagath , Engelward Bevin P. , So Peter T. C. 
Published: August 2018

AbstractHomologous recombination (HR) events are key drivers of cancer-promoting mutations, and the ability to visualize these events in situ provides important information regarding mutant cell type, location, and clonal expansion. We have previously created the Rosa26Direct Repeat (RaDR) mouse model wherein HR at an integrated substrate gives rise to a fluorescent cell. To fully leverage this in situ approach, we need better ways to quantify rare fluorescent cells deep within tissues. Here, we present a robust, automated event quantification algorithm that uses image intensity and gradient features to detect fluorescent cells in deep tissue specimens. To analyze the performance of our algorithm, we simulate fluorescence behavior in tissue using Monte Carlo methods. Importantly, this approach reduces the potential for bias in manual counting and enables quantification of samples with highly dense HR events. Using this approach, we measured the relative frequency of HR within a chromosome and between chromosomes and found that HR within a chromosome is more frequent, which is consistent with the close proximity of sister chromatids. Our approach is both objective and highly rapid, providing a powerful tool, not only to researchers interested in HR, but also to many other researchers who are similarly using fluorescence as a marker for understanding mammalian biology in tissues.
A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Authors: Engelmann Brett W. , Hsiao Chiaowen Joyce , Blischak John D. , Fourne Yannick , Khan Zia , Ford Michael , Gilad Yoav 
Published: August 2018

AbstractPhosphorylation of proteins on serine, threonine, and tyrosine residues is a ubiquitous post-translational modification that plays a key part of essentially every cell signaling process. It is reasonable to assume that inter-individual variation in protein phosphorylation may underlie phenotypic differences, as has been observed for practically any other molecular regulatory phenotype. However, we do not know much about the extent of inter-individual variation in phosphorylation because it is quite challenging to perform a quantitative high throughput study to assess inter-individual variation in any post-translational modification. To test our ability to address this challenge with SILAC-based mass spectrometry, we quantified phosphorylation levels for three genotyped human cell lines within a nested experimental framework, and found that genetic background is the primary determinant of phosphoproteome variation. We uncovered multiple functional, biophysical, and genetic associations with germline driven phosphopeptide variation. Variants affecting protein levels or structure were among these associations, with the latter presenting, on average, a stronger effect. Interestingly, we found evidence that is consistent with a phosphopeptide variability buffering effect endowed from properties enriched within longer proteins. Because the small sample size in this ‘pilot’ study may limit the applicability of our genetic observations, we also undertook a thorough technical assessment of our experimental workflow to aid further efforts. Taken together, these results provide the foundation for future work to characterize inter-individual variation in post-translational modification levels and reveal novel insights into the nature of inter-individual variation in phosphorylation.
Lake sediment fecal and biomass burning biomarkers provide direct evidence for prehistoric human-lit fires in New Zealand
Authors: Argiriadis E. , Battistel D. , McWethy D. B. , Vecchiato M. , Kirchgeorg T. , Kehrwald N. M. , Whitlock C. , Wilmshurst J. M. , Barbante C. 
Published: August 2018

AbstractDeforestation associated with the initial settlement of New Zealand is a dramatic example of how humans can alter landscapes through fire. However, evidence linking early human presence and land-cover change is inferential in most continental sites. We employed a multi-proxy approach to reconstruct anthropogenic land use in New Zealand’s South Island over the last millennium using fecal and plant sterols as indicators of human activity and monosaccharide anhydrides, polycyclic aromatic hydrocarbons, charcoal and pollen as tracers of fire and vegetation change in lake-sediment cores. Our data provide a direct record of local human presence in Lake Kirkpatrick and Lake Diamond watersheds at the time of deforestation and a new and stronger case of human agency linked with forest clearance. The first detection of human presence matches charcoal and biomarker evidence for initial burning at c. AD 1350. Sterols decreased shortly after to values suggesting the sporadic presence of people and then rose to unprecedented levels after the European settlement. Our results confirm that initial human arrival in New Zealand was associated with brief and intense burning activities. Testing our approach in a context of well-established fire history provides a new tool for understanding cause-effect relationships in more complex continental reconstructions.
The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines
Authors: Payelleville Amaury , Legrand Ludovic , Ogier Jean-Claude , Roques Céline , Roulet Alain , Bouchez Olivier , Mouammine Annabelle , Givaudan Alain , Brillard Julien 
Published: August 2018

AbstractDNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium’s lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.
Palaeozoic giant dragonflies were hawker predators
Authors: Nel André , Prokop Jakub , Pecharová Martina , Engel Michael S. , Garrouste Romain 
Published: August 2018

AbstractThe largest insects to have ever lived were the giant meganeurids of the Late Palaeozoic, ancient stem relatives of our modern dragonflies. With wingspans up to 71 cm, these iconic insects have been the subject of varied documentaries on Palaeozoic life, depicting them as patrolling for prey through coal swamp forests amid giant lycopsids, and cordaites. Such reconstructions are speculative as few definitive details of giant dragonfly biology are known. Most specimens of giant dragonflies are known from wings or isolated elements, butMeganeurites gracilipespreserves critical body structures, most notably those of the head. Here we show that it is unlikely it thrived in densely forested environments where its elongate wings would have become easily damaged. Instead, the species lived in more open habitats and possessed greatly enlarged compound eyes. These were dorsally hypertrophied, a specialization for long-distance vision above the animal in flight, a trait convergent with modern hawker dragonflies. Sturdy mandibles with acute teeth, strong spines on tibiae and tarsi, and a pronounced thoracic skewness are identical to those specializations used by dragonflies in capturing prey while in flight. The Palaeozoic Odonatoptera thus exhibited considerable morphological specializations associated with behaviours attributable to ‘hawkers’ or ‘perchers’ among extant Odonata.
Isoform-Specific Compensation of Cyclooxygenase (Ptgs) Genes during Implantation and Late-Stage Pregnancy
Authors: Li Xinzhi , Ballantyne Laurel L. , Crawford Mackenzie C. , FitzGerald Garret A. , Funk Colin D. 
Published: August 2018

AbstractThe participation of cyclooxygenase (COX) in embryo implantation and parturition has been studied extensively. However, the distinct role of the two COX isoforms in these processes still remains unclear. Using three characterized mouse lines where the Ptgs1 and Ptgs2 genes substitute for one another, this study focused on the reproductive significance of their distinct roles and potential biological substitution. In both non-gravid and gravid uteri, the knock-in COX-2 is expressed constitutively, whereas the knock-in COX-1 is slightly induced in early implantation. The delayed onset of parturition previously found in COX-1 null mice was corrected by COX-2 exchange in COX-2>COX-1 mice, with normal term pregnancy, gestation length and litter size. In contrast, loss of native COX-2 in COX-1>COX-2 mice resulted in severely impaired reproductive functions. Knock-in COX-1 failed to substitute for the loss of COX-2 in COX-1>COX-2 mice during implantation, indicating that COX-1 may be replaced by COX-2, but not vice versa. A panel of prostaglandins detected in uterus and ovary demonstrates that prostaglandin biosynthesis preferentially depends on native COX-1, but not COX-2. More interestingly, preferential compensations by the COX isoforms were sustained despite weak dependency on their role in prostaglandin biosynthesis in the uterus and ovary.
Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach
Authors: Leasi Francesca , Sevigny Joseph L. , Laflamme Eric M. , Artois Tom , Curini-Galletti Marco , de Jesus Navarrete Alberto , Di Domenico Maikon , Goetz Freya , Hall Jeffrey A. , Hochberg Rick , Jörger Katharina M. , Jondelius Ulf , Todaro M. Antonio , Wirshing Herman H. , Norenburg Jon L. , Thomas W. Kelley 
Published: August 2018

AbstractAccurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.
Frequency tunable graphene metamaterial reflectarray for terahertz applications
Authors: Zainud‐Deen Saber H. , Mabrouk Ahmed M. , Malhat Hend A. 
Published: August 2018

A graphene‐based metamaterial (GMM) reflectarray antenna with frequency tunable radiation characteristics has been investigated in this study. The unit‐cell element consists of graphene split‐ring‐resonator (SRR) with two gaps printed on a grounded SiO2 substrate. The electrical properties of the metamaterial unit‐cell have been determined at different graphene chemical potentials and different SRR gaps using the waveguide simulator. The metamaterial unit‐cell element introduces negative ɛ r and μ r over a wide frequency band starting from 390 to 550 GHz. A reflectarray unit‐cell element based on the GMM is designed at different frequencies. The phase compensation of the reflected waves is achieved by changing the SRR gap width. Reflection coefficient phase variations for 0°–301° with a variable slope are obtained for different graphene conductivities. Three different 13 × 13 GMM reflectarrays are designed and analysed at different graphene chemical potentials. A maximum gain of 22.6, 19, and 21.5 dB with side lobe level (SLL) is 11.31/9.15, 10.98/5.31, and 7.31/8.45 dB in an E/H‐plane for the reflectarray arrangements (I), (II) and (III), respectively. An averaging phase curve is calculated to construct a single structure GMM reflectarray with frequency tunable radiation characteristics. A maximum gain of 21.8 ± 1 dB with improved SLL of 13 dB was achieved.
Stability analysis of platinum nanoparticles prepared by ESDM in deionised water
Authors: Tseng Kuo‐Hsiung , Lin Yu‐Hung , Tien Der‐Chi , Ku Hsueh‐Chien , Stobinski Leszek 
Published: August 2018

Electrical discharge machine was used to prepare platinum nanocolloid by electric spark discharge method (ESDM) at room temperature. Preparation of platinum nanocolloid needed only traditional electrical discharge machine, platinum wire (99.5%) and magnet mixer. Then verify whether platinum nanoparticles be could successfully prepared under different preparation and their suspension stability. The optical properties and zeta potential were measured by UV–vis and Zetasizer, and their characteristic peaks (surface plasmon resonant), while suspension stability was analysed. The results of transmission electron microscope showed size, shape and dispersibility of platinum nanoparticles with a size of mostly <10 nm. X‐ray diffraction was used to measure crystal lattice structure and component of platinum nanoparticles. In this work, platinum nanocolloid in conditions of normal and centrifuge were analysed. Zeta potential of normal colloid was decreased from −29.5 to −18.8 mV after precipitation, while zeta potential of the centrifuged colloid still maintained at −40 mV, confirming the good suspension stability of platinum nanocolloid prepared by ESDM after centrifugation.
Antibiotic Susceptibility Profile of ‘Vibrio Cholerae O1 Biotype El Tor Serotype Ogawa’ Outbreak in North Delhi, India
Authors: Jena Pragnya , Sharma Abha , Duggal Shalini , Bharara Tanisha , Gur Renu 
Published: August 2018

Background Cholera remains a public health issue, especially in developing countries. We report a cholera outbreak in North Delhi.
Objective To report the causative agent of outbreak and to characterize, biotype, and analyze antimicrobial resistance pattern of V. cholerae isolated from cholera patients admitted to our hospital. The outbreak occurred from July 2016 to August 2016.
Materials and Methods A total of 179 stool samples from pediatrics department were received and processed according to the current Clinical and Laboratory Standards Institute (CLSI) guidelines.
Results Out of 179 stool samples received by the laboratory, 26 samples grew Vibrio cholerae O1 Biotype El Tor. Cefotaxime and ceftriaxone were the most sensitive drugs. All isolates were resistant to cotrimoxazole followed by tetracycline.
Conclusion According to the World Health Organization (WHO), cholera is becoming endemic in Delhi. Emergence of multiple antibiotic-resistant cholera isolates is a concern. Prompt identification and notification of cholera are the key measures to avert cholera outbreak. Clean water supply and improved sanitation measures should be taken for prevention of cholera.
The aerodynamic stability of a new type of Multi-tower cable-stayed bridge with rhombic stiffening cables
Authors: Wang Xiaowei , Li Yingmin , Song Weiju 
Published: August 2018

Abstract
Aerodynamic stability is an important problem in the design and research of long-span multi-tower cable-stayed Bridges. The three-dimensional nonlinear aerodynamic stability analysis method is used to qualitatively analyze the aerodynamic stability of a new type of rhombic stiffened cable-stayed bridge in this paper, and compared with conventional cable-stayed bridges. The results show that the new rhombus stiffener can greatly increase the longitudinal stiffness of the structure and reduce the vibration period of the structure. The maximum lateral displacement, vertical displacement and torsion Angle of the structure under wind load are reduced, and the critical unstable wind speed of the structure is increased. It can be seen that the aerodynamic stability of the new type of rhombus cable-stayed bridge is better than conventional cable-stayed bridge.
An adaptive variational procedure for a two-phase model with variable density and viscosity
Authors: Yang Min 
Published: August 2018

Abstract
In this paper we present an adaptive variational procedure to solve a two-phase field model with variable density, viscosity. The model is a couple system that consists of incompressible Navier-Stokes equations and Allen-Cahn equation. In the scheme the projection method based on pressure is used to deal with the Navier-Stokes equations and stabilization approach is used for the Allen-Cahn equation. By some subtle explicit-implicit treatments, the proposed scheme is energy stable. In particular the adaptive refinement/coarsening is carried out by evaluating the residual error indicators on the error estimates of the Allen-Cahn equation. Some numerical examples are performed to show the accuracy and efficiency.
Four-variable expanders over the prime fields
Authors: Koh Doowon , Mojarrad Hossein , Pham Thang , Valculescu Claudiu 
Published: August 2018

Let

F

p

\mathbb {F}_p

be a prime field of order

p
>
2

p>2

, and let

A
A

be a set in

F

p

\mathbb {F}_p

with very small size in terms of

p
p

. In this note, we show that the number of distinct cubic distances determined by points in

A
×
A

A\times A

satisfies
\[

|

(
A
−
A

)
3

+
(
A
−
A

)
3

|

≫

|

A

|

8

/

7

,

|(A-A)^3+(A-A)^3|\gg |A|^{8/7},

\]
which improves a result due to Yazici, Murphy, Rudnev, and Shkredov. In addition, we investigate some new families of expanders in four and five variables. We also give an explicit exponent of a problem of Bukh and Tsimerman, namely, we prove that
\[

max

{

|

A
+
A

|

,

|

f
(
A
,
A
)

|

}

≫

|

A

|

6

/

5

,

\max \left \lbrace |A+A|, |f(A, A)|\right \rbrace \gg |A|^{6/5},

\]
where

f
(
x
,
y
)

f(x, y)

is a quadratic polynomial in

F

p

[
x
,
y
]

\mathbb {F}_p[x, y]

that is not of the form

g
(
α
x
+
β
y
)

g(\alpha x+\beta y)

for some univariate polynomial

g
g

.
Dietary Phosphorus and Ambulatory Blood Pressure in African Americans: The Jackson Heart Study
Authors: Olivo Robert E , Hale Sarah L , Diamantidis Clarissa J , Bhavsar Nrupen A , Tyson Crystal C , Tucker Katherine L , Carithers Teresa C , Kestenbaum Bryan , Muntner Paul , Tanner Rikki M , Booth John N , Mwasongwe Stanford E , Pendergast Jane , Boulware L Ebony , Scialla Julia J 
Published: August 2018

Abstract

BACKGROUND
Higher dietary phosphorus is associated with left ventricular hypertrophy and mortality, which are blood pressure (BP)-related outcomes. For this reason, we hypothesized that dietary phosphorus may be associated with adverse clinic and ambulatory BP patterns.

METHODS
Our study included 973 African American adults enrolled in the Jackson Heart Study (2000–2004) with 24-hour ambulatory BP monitoring (ABPM) data at baseline. We quantified dietary phosphorus from a validated Food Frequency Questionnaire as follows: (i) absolute daily intake, (ii) ratio of phosphorus-to-protein intake, (iii) phosphorus density, and (iv) energy-adjusted phosphorus intake. Using multivariable linear regression, we determined associations between dietary phosphorus intake and systolic blood pressure (SBP), diastolic blood pressure (DBP), and pulse pressure in clinic and over daytime, nighttime, and 24-hour periods from ABPM. Extent of nocturnal BP dipping was also assessed. Using logistic regression, we modeled relationships between dietary phosphorus intake and clinically relevant qualitative BP phenotypes, such as masked, sustained, or white-coat hypertension and normotension.

RESULTS
There were no statistically significant associations between phosphorus intake and SBP or pulse pressure in adjusted models. Most metrics of higher phosphorus intake were associated with lower daytime, nighttime, and clinic DBP. Higher phosphorus intake was not associated with clinic or ABPM-defined hypertension overall, but most metrics of higher phosphorus intake were associated with lower odds of sustained hypertension compared to sustained normotension, white-coat hypertension, and masked hypertension. There were no associations between dietary phosphorus and nocturnal BP dipping.

CONCLUSIONS
These data do not support a role for higher phosphorus intake and higher BP in African Americans.
On entropy and information in gene interaction networks
Authors: Wallace Z S , Rosenthal S B , Fisch K M , Ideker T , Sasik R 
Published: August 2018

AbstractMotivationModern biological experiments often produce candidate lists of genes presumably related to the studied phenotype. One can ask if the gene list as a whole makes sense in the context of existing knowledge: Are the genes in the list reasonably related to each other or do they look like a random assembly? There are also situations when one wants to know if two or more gene sets are closely related. Gene enrichment tests based on counting the number of genes two sets have in common are adequate if we presume that two genes are related only when they are in fact identical. If by related we mean well connected in the interaction network space, we need a new measure of relatedness for gene sets.ResultsWe derive entropy, interaction information and mutual information for gene sets on interaction networks, starting from a simple phenomenological model of a living cell. Formally, the model describes a set of interacting linear harmonic oscillators in thermal equilibrium. Because the energy function is a quadratic form of the degrees of freedom, entropy and all other derived information quantities can be calculated exactly. We apply these concepts to estimate the probability that genes from several independent genome-wide association studies are not mutually informative; to estimate the probability that two disjoint canonical metabolic pathways are not mutually informative; and to infer relationships among human diseases based on their gene signatures. We show that the present approach is able to predict observationally validated relationships not detectable by gene enrichment methods. The converse is also true; the two methods are therefore complementary.Availability and implementationThe functions defined in this paper are available in an R package, gsia, available for download at https://github.com/ucsd-ccbb/gsia.