bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solid-liquid interfacial energy of Al-Zn solid-solutions in equilibrium with Al-Zn liquid
Authors: Yılmaz E , Erol H , Acer Erol E , Gündüz M 
Published: May 2019

Abstract
The grain boundary groove method has been successfully used to measure solid-liquid interfacial energies, σSL, experimentally for binary eutectic and peritectic systems, multi-component systems as well as pure materials and for opaque materials as well as transparent materials. It was shown that the grain boundary groove method can be use to obtain σSL for any alloy system provided that the prepared alloy sample can be held at the evaluated temperature for a long enough time with a very stable temperature gradient. In order to show the applicability of the groove method to any system, a part of the Al-Zn phase diagram was chosen. Equilibrated grain boundary groove shapes for solid Alα solution (Al-30wt%Zn) in equilibrium with AlZn liquid (Al-60wt%Zn) have been directly observed with a radial heat flow apparatus. The Gibbs-Thomson coefficient, Γ, was determined with a numerical method using observed groove shapes. The measured thermal conductivities of the solid Alα solution and AlZn liquid phases and the temperature gradient in the solid phase at the solid-liquid interface were used for the calculation of Γ and then σSL was determined using the Gibbs-Thomson equation. The grain boundary energy for the same system was also obtained from the observed groove shapes. The results of the work were compared with the results of the related experimental works.
Random lattices, punctured tori and the Teichmüller distribution
Authors: Martin Gaven 
Published: May 2019

The moduli space of lattices of

C

\mathbb {C}

is a Riemann surface of finite hyperbolic area with the square lattice as an origin. We select a lattice from the induced uniform distribution and calculate the statistics of the Teichmüller distance to the origin. This in turn identifies distribution of the distance in Teichmüller space to the central “square” punctured torus in the moduli space of punctured tori. There are singularities in this p.d.f. arising from the topology of the moduli space. We also consider the statistics of the distance in Teichmüller space to the rectangular punctured tori and the p.d.f. and expected distortion of the extremal quasiconformal mappings.
Subconvexity for twisted 𝐿-functions on 𝐺𝐿₃ over the Gaussian number field
Authors: Qi Zhi 
Published: May 2019

Let

q
∈

Z

[
i
]

q \in \mathbb {Z} [i]

be prime, and let

χ
\chi

be the primitive quadratic Hecke character modulo

q
q

. Let

π
\pi

be a self-dual Hecke automorphic cusp form for

S
L

3

(

Z

[
i
]
)

\mathrm {SL}_3 (\mathbb {Z} [i] )

, and let

f
f

be a Hecke cusp form for

Γ
0

(
q
)
⊂

S
L

2

(

Z

[
i
]
)

\Gamma _0 (q) \subset \mathrm {SL}_2 (\mathbb {Z} [i])

. Consider the twisted

L
L

-functions

L
(
s
,
π
⊗
f
⊗
χ
)

L (s, \pi \otimes f \otimes \chi )

and

L
(
s
,
π
⊗
χ
)

L (s, \pi \otimes \chi )

on

G
L

3

×

G
L

2

\mathrm {GL}_3 \times \mathrm {GL}_2

and

G
L

3

\mathrm {GL}_3

. We prove the subconvexity bounds

L

(

1
2

,
π
⊗
f
⊗
χ

)

≪

ε
,
π
,
f

N

(
q

)

5

/

4
+
ε

,

L

(

1
2

+
i
t
,
π
⊗
χ

)

≪

ε
,
π
,
t

N

(
q

)

5

/

8
+
ε

\begin{equation*} L \big (\tfrac 1 2, \pi \otimes f \otimes \chi \big ) \ll _{\, \varepsilon , \pi , f } \mathrm {N} (q)^{5/4 + \varepsilon }, \quad L \big (\tfrac 1 2 + it, \pi \otimes \chi \big ) \ll _{\, \varepsilon , \pi , t } \mathrm {N} (q)^{5/8 + \varepsilon } \end{equation*}

for any

ε
>
0

\varepsilon > 0

.
Wage Compression within the Firm: Evidence from an Indexation Scheme
Authors: Leonardi Marco , Pellizzari Michele , Tabasso Domenico 
Published: May 2019

Abstract
We revisit the role of labour market institutions by showing how they affect the sharing of firm-specific rents between employers and employees. We look at an Italian wage indexation mechanism (‘Scala Mobile’) that compressed the distribution of wages, imposing real wage increases at the bottom of the distribution. After developing a simplified version of a search model with intra-firm bargaining and on-the-job search, we document that skilled workers received lower wage adjustments when employed at firms with many unskilled workers and they tended to move towards more skill-intensive firms. Moreover, the system drove the least skill-intensive firms out of the market.
Ebola Response: A study of the Psychosocial Factors of Preparedness Among Commissioned Corps Officers of the United States Public Health Service
Authors: Sumter Jeffery L , Roberts Jill , Goodrich-Doctor Adrienne , Mason Thomas J 
Published: May 2019

AbstractIntroductionThe purpose of the cross-sectional study was to explore the relationships between occupational and general-self efficacy, and perceived preparedness among Commissioned Corps officers in the United States Public Health Service (Commissioned Corps). Commissioned Corps officers fight to protect the United States from diseases and care for the survivors of natural disasters and terrorist attacks. Commissioned Corps officers play a vital role in the fight to protect the United States from diseases and care for the survivors of natural disasters and terrorist attacks. The Commissioned Corps provided healthcare services in Liberia during the 2014 Ebola crisis that underscored the challenges of emerging diseases in a globalized community. It is imperative that these health professionals maintain a high level of self-efficacy and feel confident in their overall preparedness training as they respond to public health emergencies.Materials and MethodsThis study used assessment instruments derived from Albert Bandura’s concept of self-efficacy to analyze the occupational and general self-efficacy, and perceived preparedness levels of health services officers in the Commissioned Corps. 82 Commissioned Corps officers completed the assessment survey. To date, no study has examined the relationship between these constructs in this population.ResultsThere was a statistically significant relationship between feeling confident in one’s Commissioned Corps training and perceived preparedness (rs = 0.55, p &lt; 0.001).ConclusionThis study reflects the training perceptions and self-beliefs of Commissioned Corps officers, fills an important gap in the empirical research in this population, and advances previous investigations, which suffered from an underrepresentation of female service members.
Incidence of Hyperoxia in Combat Wounded in Iraq and Afghanistan: A Potential Opportunity for Oxygen Conservation
Authors: Schauer Steven G , April Michael D , Naylor Jason F , Mould-Millman Nee-Kofi , Bebarta Vikhyat S , Becker Tyson E , Maddry Joseph K , Ginde Adit A 
Published: May 2019

Abstract

Introduction
Oxygen supplementation is frequently used in critically injured trauma casualties in the combat setting. Oxygen supplies in the deployed setting are limited so excessive use of oxygen may unnecessarily consume this limited resource. We describe the incidence of supraphysiologic oxygenation (hyperoxia) within casualties in the Department of Defense Trauma Registry (DoDTR).

Methods
This is a subanalysis of previously published data from the DoDTR – we isolated casualties with a documented arterial blood gas (ABG) and categorized hyperoxia as an arterial oxygen &gt;100 mmHg and extreme hyperoxia &gt; 300 mmHg (a subset of hyperoxia). We defined serious injuries as those with an Abbreviated Injury Score (AIS) of 3 or greater. We defined a probable moderate traumatic brain injury of those with an AIS of 3 or greater for the head region and at least one Glasgow Coma Scale at 8 or less.

Results
Our initial search yielded 28,222 casualties, of which 10,969 had at least one ABG available. Within the 10,969, the proportion of casualties experiencing hyperoxia in this population was 20.6% (2,269) with a subset of 4.1% (452) meeting criteria for extreme hyperoxia. Among those with hyperoxia, the median age was 25 years (IQR 21–30), most were male (96.8%), most frequently US forces (41.4%), injured in Afghanistan (68.3%), injured by explosive (61.1%), with moderate injury scores (median 17, IQR 10–26), and most (93.8%) survived to hospital discharge. A total of 17.8% (1,954) of the casualties underwent endotracheal intubation: 27.5% (538 of 1,954) prior to emergency department (ED) arrival and 72.5% (1,416 of 1,954) within the ED. Among those intubated in the prehospital setting, upon ED arrival 35.1% (189) were hyperoxic, and a subset of 5.6% (30) that were extremely hyperoxic. Among those intubated in the ED, 35.4% (502) were hyperoxic, 7.9% (112) were extremely hyperoxic. Within the 1,277 with a probable TBI, 44.2% (565) experienced hyperoxia and 9.5% (122) met criteria for extreme hyperoxia.

Conclusions
In our dataset, more than 1 in 5 casualties overall had documented hyperoxia on ABG measurement, 1 in 3 intubated casualties, and almost 1 in 2 TBI casualties. With limited oxygen supplies in theater and logistical challenges with oxygen resupply, efforts to avoid unnecessary oxygen supplementation may have material impact on preserving this scarce resource and avoid potential detrimental clinical effects from supraphysiologic oxygen concentrations.
CReasPy-cloning: a method for simultaneous cloning and engineering of megabase-sized genomes in yeast using the CRISPR-Cas9 system
Authors: Ruiz Estelle , Talenton Vincent , Dubrana Marie-Pierre , Guesdon Gabrielle , Lluch-Senar Maria , Salin Franck , Sirand-Pugnet Pascal , Arfi Yonathan , Lartigue Carole 
Published: May 2019

ABSTRACTOver the last decade a new strategy was developed to bypass the difficulties to genetically engineer some microbial species by transferring (or “cloning”) their genome into another organism that is amenable to efficient genetic modifications and therefore acts as a living workbench. As such, the yeastSaccharomyces cerevisiaehas been used to clone and engineer genomes from viruses, bacteria and algae. The cloning step requires the insertion of yeast genetic elements within the genome of interest, in order to drive its replication and maintenance as an artificial chromosome in the host cell. Current methods used to introduce these genetic elements are still unsatisfactory, due either to their random nature (transposon) or the requirement for unique restriction sites at specific positions (TAR cloning). Here we describe the CReasPy-Cloning, a new method that combines both the ability of Cas9 to cleave DNA at a user-specified locus and the yeast’s highly efficient homologous recombination to simultaneously clone and engineer a bacterial chromosome in yeast. Using the 0.816 Mbp genome ofMycoplasma pneumoniaeas a proof of concept, we demonstrate that our method can be used to introduce the yeast genetic element at any location in the bacterial chromosome while simultaneously deleting various genes or group of genes. We also show that CReasPy-cloning can be used to edit up to three independent genomic loci at the same time with an efficiency high enough to warrant the screening of a small (<50) number of clones, allowing for significantly shortened genome engineering cycle times.
Codon Use and Aversion is Largely Phylogenetically Conserved Across the Tree of Life
Authors: Miller Justin B. , McKinnon Lauren M. , Whiting Michael F. , Ridge Perry G. 
Published: May 2019

AbstractUsing parsimony, we analyzed codon usages across 12 337 species and 25 727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890 814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon’s congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25 771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1 109x more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs.AvailabilityAll scripts, a README, and necessary test files are freely available on GitHub at https://github.com/ridgelab/codon_congruenceContactperry.ridge@byu.edu
The plasma Factor XIII heterotetrameric complex structure: unexpected unequal pairing within a symmetric complex
Authors: Singh Sneha , Nazabal Alexis , Kaniyappan Senthilvelrajan , Pellequer Jean-Luc , Wolberg Alisa S. , Imhof Diana , Oldenburg Johannes , Biswas Arijit 
Published: May 2019

AbstractFactor XIII (FXIII) is a predominant determinant of clot stability, strength, and composition. Plasma FXIII circulates as a pro-transglutaminase with 2 catalytic A subunits and 2 carrier-protective B subunits in a heterotetramer (FXIII-A2B2). FXIII-A2and -B2subunits are synthesized separately and then assembled in plasma. Following proteolytic activation by thrombin and calcium-mediated dissociation of the B-subunits, activated FXIII (FXIIIa) covalently cross-links fibrin, promoting clot stability. The zymogen and active states of the FXIII-A subunits have been structurally characterized; however, the structure of FXIII-B subunits and the FXIII-A2B2complex have remained elusive. Using integrative hybrid approaches including atomic force microscopy, cross-linking mass spectrometry, and computational approaches, we have constructed the first all-atom model of the FXIII-A2B2complex. We also used molecular dynamic simulations in combination with isothermal titration calorimetry to characterize FXIII-A2B2assembly, activation, and dissociation. Our data reveal unequal pairing of individual subunit monomers in an otherwise symmetric complex, and suggest this unusual structure is critical for both assembly and activation of this complex. Our findings enhance understanding of mechanisms associating FXIII-A2B2mutations with disease and have important implications for the rational design of molecules to alter FXIII assembly and/or activity to reduce bleeding and thrombotic complications.
Brain age estimation is a sensitive marker of processing speed in the early course of multiple sclerosis
Authors: Høgestøl Einar A. , Nygaard Gro O. , Emhjellen Petter E. , Kaufmann Tobias , Beyer Mona K. , Sowa Piotr , Andreassen Ole A. , Celius Elisabeth G. , Landrø Nils Inge , Westlye Lars T. , Harbo Hanne F. 
Published: May 2019

ABSTRACTBackground and objectivesCognitive deficits in MS are common, also early in the disease course. We aimed to identify if estimated brain age from MRI could serve as an imaging marker for early cognitive symptoms in a longitudinal MS study.MethodsA group of 76 MS patients (mean age 34 years, 71% females, 96% relapsing-remitting) was examined 1, 2 and 5 years after diagnosis. A machine-learning model using Freesurfer-processed T1-weighted brain MRI data from 3208 healthy controls, was applied to develop a prediction model for brain age. The difference between estimated and chronological brain age was calculated (brain age gap). Tests of memory, attention and executive functions were performed. Associations between brain age gap and cognitive performance were assessed using linear mixed effects (LME) models and corrected for multiple testing.ResultsLME models revealed a significant association between the Color Naming condition of Color-Word Interference Test and brain age gap (t=2.84, p=0.005).ConclusionsIn this study, decreased information processing speed correlated with increased brain age gap. Our findings suggest that brain age estimation using MRI provides a useful semi-automated approach applying machine learning for individual level brain phenotyping and correlates with information processing speed in the early course of MS.
Selective autophagy, lipophagy and mitophagy, in the Harderian gland along the estrous cycle: a potential retrieval effect of melatonin
Authors: García-Macia Marina , Santos-Ledo Adrián , Caballero Beatriz , Rubio-González Adrián , de Luxán-Delgado Beatriz , Potes Yaiza , Rodríguez-González Susana , Boga José Antonio , Coto-Montes Ana 
Published: May 2019

ABSTRACTSexual dimorphism has been reported in many processes. However, sexual bias in favor of the use of males is very present in science. One of the main reasons is that the impact of hormones in diverse pathways and processes such as autophagy have not been properly addressed in vivo. The Harderian gland is a perfect model to study autophagic modulation as it exhibits important changes during the estrous cycle. The aim of this study is to identify the main processes behind Harderian gland differences under estrous cycle and their modulator. In the present study we show that redox-sensitive transcription factors have an essential role: NF-κB may activate SQSTM1/p62 in estrus, promoting selective types of autophagy: mitophagy and lipophagy. Nrf2 activation in diestrus, leads the retrieval phase and restoration of mitochondrial homeostasis. Melatonin’s receptors show higher expression in diestrus, leading to decreases in pro-inflammatory mediators and enhanced Nrf2 expression. Consequently, autophagy is blocked, and porphyrin release is reduced. All these results point to melatonin as one of the main modulators of the changes in autophagy during the estrous cycle.
Costs and benefits of giant sperm and sperm storage organs in Drosophila melanogaster
Authors: Zajitschek Susanne , Zajitschek Felix , Josway Sarah , Al Shabeeb Reem , Weiner Halli , Manier Mollie K. 
Published: May 2019

ABSTRACTIn the Drosophila lineage, both sperm and the primary female sperm storage organ, the seminal receptacle (SR), may reach extraordinary lengths. In D. melanogaster, long SRs bias fertilization toward long sperm during the displacement stage of sperm competition. This sperm-SR interaction, together with a genetic correlation between the traits, suggests that the coevolution of exaggerated sperm and SR lengths may be driven by Fisherian runaway selection. To further understand the costs and benefits of long sperm and SR genotypes in both sexes, we measured male and female fitness in inbred lines of D. melanogaster derived from four populations previously selected for long sperm, short sperm, long SRs, or short SRs. We specifically asked: do long SRs impose costs or benefits on the females that bear them? Do genotypes that generate long sperm in males impose a fitness cost on females sharing those genotypes? Is long sperm an honest indicator of male viability and associated with increased fitness? And finally, are the benefits of long sperm restricted to competitive fertilization success, or do long-sperm males also have increased mating success and fecundity in single matings? We found that both sexes have increased longevity in long sperm and long SR genotypes, with fewer reproduction-related benefits and evidence for trade-offs in males, compared to females. Our results suggest that sperm length and SR length are both indicators of increased viability.
Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit
Authors: Malek Joel A. , Mathew Sweety , Mathew Lisa , Younuskunju Shameem , Mohamoud Yasmin A. , Suhre Karsten 
Published: May 2019

AbstractThe fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta-fructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future.
G-quadruplexes sequester free heme in living cells
Authors: Gray Lucas T. , Lombardi Emilia Puig , Verga Daniela , Guetta Corinne , Nicolas Alain , Teulade-Fichou Marie-Paule , Londoño-Vallejo Arturo , Maizels Nancy 
Published: May 2019

AbstractHeme is an essential cofactor for many enzymes, but free heme is toxic and its levels are tightly regulated. G-quadruplexes bind heme avidlyin vitro, raising the possibility that they may sequester hemein vivo. If so, then treatment that displaces heme from quadruplexes is predicted to induce expression of genes involved in iron and heme homeostasis. Here we show that PhenDC3, a G-quadruplex ligand structurally unrelated to heme, displaces quadruplex-bound hemein vitroand alters transcription in cultured human cells, up-regulating genes that support heme degradation and iron homeostasis, and most strikingly causing a 30-fold induction of heme oxidase 1, the key enzyme in heme degradation. We propose that G-quadruplexes sequester heme to protect cells from the pathophysiological consequences of free heme. This identifies a new function for G-quadruplexes and a new mechanism for protection of cells from heme.
Highly-connected, non-redundant microRNAs functional control in breast cancer molecular subtypes
Authors: de Anda-Jáuregui Guillermo , Espinal-Enríquez Jesús , Hernández-Lemus Enrique 
Published: May 2019

AbstractTranscriptional patterns are altered in breast cancer. These alterations capture the heterogeneity of breast cancer, leading to the emergence of molecular subtypes. Network biology approaches to study gene co-expression are able to capture the differences between breast cancer subtypes.Network biology approaches may be extended to include other co-expression patterns, like those found between genes and non-coding RNA: such as mi-croRNAs (miRs). Commodore miRs are microRNAs that, based on their connectivity and redundancy in co-expression networks, have been proposed as potential control elements of biological functions.In this work, we reconstructed miR-gene co-expression networks for each breast cancer molecular subtype. We identified Commodore miRs in three out of four molecular subtypes. We found that in each subtype, each cdre-miR had a different set of associated genes, as well as a different set of associated biological functions. We used a systematic literature validation strategy, and identified that the associated biological functions to these cdre-miRs are hallmarks of cancer.