bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative analysis of gradient effective refractive index in silicon nanowires for broadband light trapping and anti-reflective properties
Authors: Saini Sudhir Kumar , Nair Rajesh V.
Published: March 2019

Controlling the light reflection using vertically-aligned nanowires has great importance in fundamental research with interesting applications in photonic devices. Here, we discuss the spatial- and polarization-dependent reflectivity measurements from the cross-sectional as well as from the top surface of vertically-aligned disordered silicon nanowires. The gradient variation in an effective refractive index along the nanowire length is estimated using the cross-sectional reflectivity measurements. We have studied the gradient variation of an effective refractive index profile and its tunability with the nanowire length. The reflectivity is measured to be as low as 5% irrespective of spatial directions and the polarization of incident light in a broad wavelength range. This constitutes the signature of a broadband omnidirectional anti-reflector that is scalable with the nanowire length. The reflectivity measurements are in good agreement with theoretical calculations. Such omnidirectional anti-reflection in a broad wavelength range is useful for applications such as photon management in photovoltaic devices and disorder-induced light scattering.
Electrical transport in onion-like carbon—PMMA nanocomposites
Authors: Grimaldi Claudio , Kecsenovity Egon , Majidian Maryam , Kuznetsov Vladimir L. , Magrez Arnaud , Forró László
Published: March 2019

We report electrical conductivity measurements of polymethyl-methacrylate filled by onion-like carbon particles with a primary particle size of ≈5 nm. We show that the conductivity σ is exceptionally high even at very low loadings and that its low-temperature dependence follows a Coulomb gap regime at atmospheric pressure and an activated behavior at a pressure of 2 GPa. We interpret this finding in terms of the enhancement under the applied pressure of the effective dielectric permittivity within the aggregates of onion-like carbons, which improves the screening of the Coulomb interaction and reduces the optimal hopping distance of the electrons.
Symmetrical clock synchronization with time-correlated photon pairs
Authors: Lee Jianwei , Shen Lijiong , Cerè Alessandro , Troupe James , Lamas-Linares Antia , Kurtsiefer Christian
Published: March 2019

We demonstrate a point-to-point clock synchronization protocol based on bidirectionally exchanging photons produced in spontaneous parametric down conversion. The technique exploits tight timing correlations between photon pairs to achieve a precision of 51 ps in 100 s with count rates of order 200 s−1. The protocol is distance independent, is secure against symmetric delay attacks, and provides a natural complement to techniques based on Global Navigation Satellite Systems. The protocol works with mobile parties and can be augmented to provide authentication of the timing signal via a Bell inequality check.
Onset of transverse (shear) waves in strongly-coupled Yukawa fluids
Authors: Khrapak Sergey A. , Khrapak Alexey G. , Kryuchkov Nikita P. , Yurchenko Stanislav O.
Published: March 2019

A simple practical approach to describe transverse (shear) waves in strongly-coupled Yukawa fluids is presented. Theoretical dispersion curves, based on hydrodynamic consideration, are shown to compare favorably with existing numerical results for plasma-related systems in the long-wavelength regime. The existence of a minimum wave number below which shear waves cannot propagate and its magnitude are properly accounted in the approach. The relevance of the approach beyond plasma-related Yukawa fluids is demonstrated by using experimental data on transverse excitations in liquid metals Fe, Cu, and Zn, obtained from inelastic x-ray scattering. Some potentially important relations, scalings, and quasi-universalities are discussed. The results should be interesting for a broad community in chemical physics, materials physics, physics of fluids and glassy state, complex (dusty) plasmas, and soft matter.
Steering the outcome of a photochemical reaction—An
in silico
experiment on the H2CSO sulfine using few-femtosecond dump pulses
Authors: Mignolet Benoit , Curchod Basile F. E.
Published: March 2019

We propose a pump-dump control scheme using sub-10 fs pulses to enhance the photochemical formation of the three-membered C–S–O ring oxathiirane from the parent H2CSO sulfine molecule. The ultrashort nature of the pulses is essential to promptly alter the photoinduced dynamics, e.g., while a bond is elongating, which is key to selectively form the oxathiirane by radiative dumping. We carried out an in silico pump-dump experiment with excited-state dynamics simulations that include the interaction with electric field of the pump and dump pulses. By applying the dump pulse when the CS bond is elongating, the population transferred to the ground state will form the oxathiirane with a branching ratio of 4, much higher than the one solely due to nonradiative relaxation (0.66). The overall oxathiirane yield can be increased by up to 17% when the 6 fs IR dump pulse is applied at a delay time of 47 fs.
Cause and incidence of injuries experienced by children in remote Cape York Indigenous communities
Authors: West Caryn , Fitts Michelle S. , Rouen Chris , Muller Reinhold , Clough Alan R.
Published: March 2019

Indigenous children experience a disproportionally high number of injuries, particularly in remote communities. This study aimed to investigate: (1) the causes of injury to children within three remote Indigenous communities of Cape York, Australia; (2) differences between communities; and (3) if strengthening of alcohol restrictions reduced the incidence of injury. An injury profile for children aged 0–14 years was constructed for the period 1 January 2006 to 31 December 2011 using clinical file audit data from Primary Health Care Clinics located in each community. Children aged <14 years were responsible for 1461 injury presentations among 563 individuals. Males were responsible for 58.7% of presentations and 38% (n = 214) of children presented on three or more occasions. The leading causes of injury were falls (including sports); cutting and piercing; animals, insects and plants; transport and assault. There were variations in the order of major injury causes across the three communities. As primary causes of injury, falls and transport-related injuries aligned with other child populations. Cutting and piercing; animals, insects and plants; and assault-related injuries were more prevalent compared with other child populations. There was a significant difference in injury rates between communities and no significant difference before and after the strengthening of alcohol restrictions.
Public perceptions of the health risks of extreme heat across US states, counties, and neighborhoods
Authors: Howe Peter D. , Marlon Jennifer R. , Wang Xinran , Leiserowitz Anthony
Published: March 2019

Extreme heat is the leading weather-related cause of death in the United States. Many individuals, however, fail to perceive this risk, which will be exacerbated by global warming. Given that awareness of one’s physical and social vulnerability is a critical precursor to preparedness for extreme weather events, understanding Americans’ perceptions of heat risk and their geographic variability is essential for promoting adaptive behaviors during heat waves. Using a large original survey dataset of 9,217 respondents, we create and validate a model of Americans’ perceived risk to their health from extreme heat in all 50 US states, 3,142 counties, and 72,429 populated census tracts. States in warm climates (e.g., Texas, Nevada, and Hawaii) have some of the highest heat-risk perceptions, yet states in cooler climates often face greater health risks from heat. Likewise, places with older populations who have increased vulnerability to health effects of heat tend to have lower risk perceptions, putting them at even greater risk since lack of awareness is a barrier to adaptive responses. Poorer neighborhoods and those with larger minority populations generally have higher risk perceptions than wealthier neighborhoods with more white residents, consistent with vulnerability differences across these populations. Comprehensive models of extreme weather risks, exposure, and effects should take individual perceptions, which motivate behavior, into account. Understanding risk perceptions at fine spatial scales can also support targeting of communication and education initiatives to where heat adaptation efforts are most needed.
Multiradionuclide evidence for an extreme solar proton event around 2,610 B.P. (∼660 BC)
Authors: O’Hare Paschal , Mekhaldi Florian , Adolphi Florian , Raisbeck Grant , Aldahan Ala , Anderberg Emma , Beer Jürg , Christl Marcus , Fahrni Simon , Synal Hans-Arno , Park Junghun , Possnert Göran , Southon John , Bard Edouard ,   ASTER Team, Muscheler Raimund , Aumaître Georges , Bourlès Didier L. , Keddadouche Karim
Published: March 2019

Significance

This study provides evidence of an enormous solar storm around 2,610 B.P. It is only the third such event reliably documented and is comparable with the strongest event detected at AD 774/775. The event of 2,610 years B.P. stands out because of its particular signature in the radionuclide data [i.e., carbon-14 (
14
C) data alone does not allow for an unequivocal detection of the event]. It illustrates that present efforts to find such events based solely on
14
C data likely lead to an underestimated number of such potentially devastating events for our society. In addition to
14
C data, high-resolution records of beryllium-10 and chlorine-36 are crucial for reliable estimates of the occurrence rate and the properties of past solar proton events.
Toddlers and infants expect individuals to refrain from helping an ingroup victim’s aggressor
Authors: Ting Fransisca , He Zijing , Baillargeon Renée
Published: March 2019

Significance

Adults are more likely to punish transgressions that do not affect them when these transgressions victimize ingroup members. Such third-party punishment (TPP) often takes an indirect form, such as the withholding of help. Building on these results, we showed 2.5- and 1-year-olds scenarios involving a wrongdoer, a victim, and a bystander, and we manipulated the minimal-group memberships of the wrongdoer and the victim relative to that of the bystander. When the victim belonged to the bystander’s group, children expected TPP: They detected a violation when the bystander chose to help the wrongdoer. When the victim did not belong to the bystander’s group, however, children no longer expected TPP. Young children thus selectively expect indirect TPP for harm to ingroup members.
Analysis of High School Physics National Examination questions based on Bloom Taxonomy and National Examination Question Standard in 2017/2018
Authors: Nurlailiyah A , Deta U A , Ain T N , Haq M S , Lestari N A , Yantidewi M
Published: March 2019

The National Examination is for measuring the success rate of student learning at school and mapping the quality of Education in Indonesia. To fulfill the objectives of the National Examination, an instrument is needed to represent the standards set by the Indonesian government. This research is a qualitative study that aims to analyze National Examination Questions in 2017/2018 based on Bloom’s taxonomy and National Examination Questions Standard. Data collected by analyzing the samples National Examination questions in 2017/2018 using operational verbs in Bloom’s taxonomy and grouping topics based the standard. Based on the research, it was found that most question is in the applying cognitive domain (C3), that is, 35 %, when the least question is in the creating cognitive domain (C6), that is, only 2.5%. According to the National Examination Questions Standard, the most topic in the National Examination in 2017/2018 are “Force and Motion” and “Electric, Magnet and Modern Physics” with the same amount of 22.5%. The National Examination Questions Standard is too general in writing down cognitive levels and the topics that appear on the question.
Behavioral diversity is maintained by a conditional strategy in a freshwater zooplankton
Authors: Meyer G Adam , Nelson William A
Published: March 2019

Many populations have intraspecific diversity in phenotype and ecological strategy, but the mechanisms maintaining such diversity are not fully understood. Multiple behaviors can be maintained either as a conditional strategy, where fitness depends on an individual’s phenotype, or as a mixed strategy, where alternative behaviors have similar fitness independent of phenotype. Using high-resolution depth and time sampling, we characterize 2 distinct diel vertical migration behaviors in a population of freshwater zooplankton (Daphnia pulicaria). Individuals in this population differ in their color phenotype and migratory behavior with red morphs upregulating hemoglobin and undergoing a deep migration and pale morphs not producing hemoglobin and undergoing a shallow migration. We experimentally manipulated the behavior of each phenotype in the field and measured population growth in their natural migration behavior as well as population growth in their alternative behaviors. Experimental populations of pale and red morphs under their natural migrations had roughly equal fitness, despite vast differences in environmental conditions. When forced to switch behaviors, pale morphs suffered reduced fitness, whereas red morphs had similar fitness compared with their natural migration. Our results suggest that although behavioral diversity may be promoted by the opportunity for alternative behaviors of equal fitness, the distinct physiological conditions required for survival in alternative behaviors limit the capacity for individual behavioral switching and likely maintain behavioral diversity as a conditional strategy.
100 Years of evolving gene–disease complexities and scientific debutants
Authors: Zeeshan Saman , Xiong Ruoyun , Liang Bruce T , Ahmed Zeeshan
Published: March 2019

It’s been over 100 years since the word `gene’ is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it’s about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene–disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene–disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene–disease data.
Multiresolution correction of GC bias and application to identification of copy number alterations
Authors: Jang Ho , Lee Hyunju
Published: March 2019

Motivation

Whole-genome sequencing (WGS) data are affected by various sequencing biases such as GC bias and mappability bias. These biases degrade performance on detection of genetic variations such as copy number alterations. The existing methods use a relation between the GC proportion and depth of coverage (DOC) of markers by means of regression models. Nonetheless, severity of the GC bias varies from sample to sample. We developed a new method for correction of GC bias on the basis of multiresolution analysis. We used a translation-invariant wavelet transform to decompose biased raw signals into high- and low-frequency coefficients. Then, we modeled the relation between GC proportion and DOC of the genomic regions and constructed new control DOC signals that reflect the GC bias. The control DOC signals are used for normalizing genomic sequences by correcting the GC bias.

Results

When we applied our method to simulated sequencing data with various degrees of GC bias, our method showed more robust performance on correcting the GC bias than the other methods did. We also applied our method to real-world cancer sequencing datasets and successfully identified cancer-related focal alterations even when cancer genomes were not normalized to normal control samples. In conclusion, our method can be employed for WGS data with different degrees of GC bias.

Availability and implementation

The code is available at http://gcancer.org/wabico.

Supplementary information

Supplementary data are available at Bioinformatics online.
CABS-dock standalone: a toolbox for flexible protein–peptide docking
Authors: Kurcinski Mateusz , Pawel Ciemny Maciej , Oleniecki Tymoteusz , Kuriata Aleksander , Badaczewska-Dawid Aleksandra E , Kolinski Andrzej , Kmiecik Sebastian
Published: March 2019

CABS-dock standalone is a multiplatform Python package for protein–peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein–peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation—it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results.

Availability and implementation

CABS-dock standalone is distributed under the MIT licence, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use and installation instructions for Linux, macOS and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/cabsdock.
GToTree: a user-friendly workflow for phylogenomics
Authors: Lee Michael D
Published: March 2019

Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required—such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.—can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.

Availability and implementation

GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mimicry of lichens and cyanobacteria on tree-sized Amorphophallus petioles results in their masquerade as inedible tree trunks
Authors: Claudel Cyrille , Lev-Yadun Simcha , Hetterscheid Wilbert , Schultz Matthias
Published: March 2019

We revisit a case of mimicry in Amorphophallus involving visual mimicry of lichens and colonies of cyanobacteria on their tree-trunk sized petioles. We investigate the entire genus for similar defensive coloration types and report a defensive leaf coloration strategy in several Amorphophallus spp. that involves mimicry, camouflage and plant-mimicking that results in defensive visual masquerade. We propose that the visual expression of lichen and cyanobacteria mimicry enables the huge and fleshy petioles to look like solid non-edible tree trunks, a classic case of masquerade, probably as defence against herbivores. The results are discussed in a phylogenetic and evolutionary context.
Constructive Constitutionalism in Conservative and Unionist Political Thought, c.1885–1914
Authors: Jones Emily
Published: March 2019

A central concern of historical writing on the modern British Conservative Party has been that of adaptation and survival: to what extent, and in what ways, did the party appeal to new voters, in new areas, and on new terms? This article demonstrates, through an analysis of Conservative and Unionist intellectual culture, that the late Victorian and Edwardian period was a vital moment in which men and women, historians, novelists, journalists, MPs and peers were constructively re-envisaging what it meant to be a Conservative, or a Unionist, in the wake of the Third Reform Acts (1884–5) and the first Irish Home Rule Bill (1886). It argues that Conservative and Unionist intellectual culture evidences the constructive and imaginative ways in which the protection and ‘maintenance’ of the constitution was conceived both through the recognition and adoption of new modes of political legitimation and argument—including the referendum, Lords reform and women’s representation—and the construction of novel histories and genealogies. This was, therefore, a vital moment in the development of a modern ‘C/conservative’ tradition, as Conservatives and Unionists put pen to paper in order to express their C/conservative principles, as well as to inform and educate.
Bilateral internal thoracic artery versus radial artery multi-arterial bypass grafting: a report from the STS database†
Authors: Schwann Thomas A , Habib Robert H , Wallace Amelia , Shahian David , Gaudino Mario , Kurlansky Paul , Engoren Milo C , Tranbaugh Robert F , Schwann Alexandra N , Jacobs Jeffrey P
Published: March 2019

OBJECTIVES

Multi-arterial bypass grafting with bilateral internal thoracic (BITA-MABG) or radial (RA-MABG) arteries improves long-term survival, but its increased complexity raises perioperative safety concerns. We compared perioperative outcomes of RA-MABG and BITA-MABG using the Society of Thoracic Surgeons Adult Cardiac Surgery Database (STS-ACSD).

METHODS

We analysed the 2004–2015 BITA-MABG and RA-MABG experience in STS-ACSD. Primary end points were operative mortality (OM) and deep sternal wound infections (DSWI). Risk-adjusted odds ratios [AOR (95% confidence interval)] were derived via multivariable logistic regression. Sensitivity analyses were done in patient sub-cohorts and based on institutional BITA-utilization rates (<5%, 5–10%, 10–20%, 20–40% and >40%).

RESULTS

Eighty-five thousand nine hundred five RA-MABG (82.5% men; 61 years) and 61 336 BITA-MABG (85.1% men; 59 years) patients were analysed; 41.6% of BITA-MABG and 27.3% of RA-MABG cases came from institutions with low MABG utilization rates (<10%). Unadjusted OM was equivalent for both techniques (BITA-MABG versus RA-MABG: 1.3% vs 1.2%, P = 0.79), while DSWI was lower for RA-MABG (1.0% vs 0.6%, P < 0.001). RA-MABG was associated with lower adjusted OM [AOR = 0.80 (0.69–0.96)] and DSWI [AOR = 0.39 (0.32–0.46)]. Sensitivity analyses confirmed robustness of these findings. Equivalent outcomes were observed at high BITA-use institutions where BITA cases comprised >20% of all cases for OM and ≥40% for DSWI.

CONCLUSIONS

This analysis of the STS-ACSD showed that RA-MABG is a generally safer form of multi-arterial coronary artery bypass grafting surgery. However, this advantage is mitigated at institutions with substantial BITA experience.
Transthyretin cardiac amyloidosis in continental Western Europe: an insight through the Transthyretin Amyloidosis Outcomes Survey (THAOS)
Authors: Damy Thibaud , Kristen Arnt V , Suhr Ole B , Maurer Mathew S , Planté-Bordeneuve Violaine , Yu Ching-Ray , Ong Moh-Lim , Coelho Teresa , Rapezzi Claudio ,   THAOS Investigators
Published: March 2019

Aims

Transthyretin amyloidosis (ATTR amyloidosis) is a heterogeneous disorder with cardiac, neurologic, and mixed phenotypes. We describe the phenotypic and genotypic profiles of this disease in continental Western Europe as it appears from the Transthyretin Amyloidosis Survey (THAOS).

Methods and results

THAOS is an ongoing, worldwide, longitudinal, observational survey established to study differences in presentation, diagnosis, and natural history in ATTR amyloidosis subjects. At data cut-off, 1411 symptomatic subjects from nine continental Western European countries were enrolled in THAOS [1286 hereditary (ATTRm) amyloidosis; 125 wild-type ATTR (ATTRwt) amyloidosis]. Genotypes and phenotypes varied notably by country. Four mutations (Val122Ile, Leu111Met, Thr60Ala, and Ile68Leu), and ATTRwt, were associated with a mainly cardiac phenotype showing symmetric left ventricular (LV) hypertrophy, normal diastolic LV dimensions and volume, and mildly depressed LV ejection fraction (LVEF). Morphologic and functional abnormalities on echocardiogram were significantly more severe in subjects with cardiac (n‘= 210), compared with a mixed (n = 298), phenotype: higher median (Q1–Q3) interventricular septal thickness [18 (16–21) vs. 16 (13–20) mm; P = 0.0006]; and more frequent incidence of LVEF <50% (38.1 vs. 17.5%; P = 0.0008). Subjects with cardiac mutations or ATTRwt (or cardiac or mixed phenotype) had a lower survival rate than subjects in other genotype (or the neurologic phenotype) categories (P < 0.0001, for both).

Conclusion

ATTR amyloidosis genotypes and phenotypes are highly heterogeneous in continental Western Europe. A geographic map of the different disease profiles and awareness that a subset of subjects have a dominant cardiac phenotype, mimicking hypertrophic cardiomyopathy, at presentation can facilitate the clinical recognition of this underdiagnosed disease.

Trial registration

ClinicalTrials.gov: NCT00628745.
Clinical impact of antithrombotic therapy in transvenous lead extraction complications: a sub-analysis from the ESC-EORP EHRA ELECTRa (European Lead Extraction ConTRolled) Registry
Authors: Di Cori Andrea , Auricchio Angelo , Regoli François , Blomström-Lundqvist Carina , Butter Christian , Dagres Nikolaos , Deharo Jean-Claude , Maggioni Aldo P , Kutarski Andrzej , Kennergren Charles , Laroche Cécile , Rinaldi Christopher A , Dovellini Emilio Vincenzo , Golzio Pier Giorgio , Thøgersen Anna Margrethe , Bongiorni Maria Grazia ,   ESC-EHRA ELECTRa Investigators
Published: March 2019

Aims

A sub-analysis of the ESC-EHRA European Lead Extraction ConTRolled (ELECTRa) Registry to evaluate the clinical impact of antithrombotic (AT) on transvenous lead extraction (TLE) safety and efficacy.

Methods and results

ELECTRa outcomes were compared between patients without AT therapy (No AT Group) and with different pre-operative AT regimens, including antiplatelets (AP), anticoagulants (AC), or both (AP + AC). Out of 3510 pts, 2398 (68%) were under AT pre-operatively. AT patients were older with more comorbidities (P < 0.0001). AT subgroups, defined as AP, AC, or AP + AC, were 1096 (31.2%), 985 (28%), and 317 (9%), respectively. Regarding AP patients, 1413 (40%) were under AP, 1292 (91%) with a single AP, interrupted in 26% about 3.8 ± 3.7 days before TLE. In total, 1302 (37%) patients were under AC, 881 vitamin K antagonist (68%), 221 (17%) direct oral anticoagulants, 155 (12%) low weight molecular heparin, and 45 (3.5%) unfractionated heparin. AC was ‘interrupted without bridging’ in 696 (54%) and ‘interrupted with bridging’ in 504 (39%) about 3.3 ± 2.3 days before TLE, and ‘continued’ in 87 (7%). TLE success rate was high in all subgroups. Only overall in-hospital death (1.4%), but not the procedure-related one, was higher in the AT subgroups (P = 0.0500). Age >65 years and New York Heart Association Class III/IV, but not AT regimens, were independent predictors of death for any cause. Haematomas were more frequent in AT subgroups, especially in AC ‘continued’ (P = 0.025), whereas pulmonary embolism in the No-AT (P < 0.01).

Conclusions

AT minimization is safe in patients undergoing TLE. AT does not seem to predict death but identifies a subset of fragile patients with a worse in-hospital TLE outcome.
A color-based competition assay for studying bacterial stress responses in Micrococcus luteus
Authors: Havis Spencer , Rangel Jonathan , Mali Sujina , Bodunrin Abiodun , Housammy Zina , Zimmerer Rene , Murphy Jesse , Widger William R , Bark Steven J
Published: March 2019

Competition assays measure differences between populations of bacteria after stress adaptation, populations of different bacteria and mutations in antibiotic resistance genes. We have developed a competition-based assay to evaluate if genes upregulated under starvation are important for bacterial survival. Stress responses are critical for survival in non-pathogenic and pathogenic bacteria alike including Mycobacterium tuberculosis, Enterococcus fecaelis, Escherichia coli and Staphylococcus aureus. Unfortunately, most stress-survival proteins are poorly understood because suitable model bacteria and techniques are limited. To address this problem, we have engineered Micrococcus luteus NCTC 2665 (M. luteus) for competition assays by inactivating the sarcinaxanthin biosynthesis gene crtE (ΔcrtE), changing M. luteus colonies from yellow to white. This change allows easy identification in mixed cultures. The crtE knockout is relatively neutral for growth in complex and minimal acetate media and shows a measured fitness of one in competition with yellow wild-type bacteria. The ΔcrtE M. luteus competition assay identified a competition defect in a M. luteus strain when a specific universal stress protein was inactivated, suggesting a negative survival phenotype for this protein. We anticipate this competition assay can identify defects in other gene knockouts and mutational studies in M. luteus and will enhance our understanding of bacterial survival mechanisms.
Size-independent sample complexity of neural networks
Authors: Golowich Noah , Rakhlin Alexander , Shamir Ohad
Published: March 2019

We study the sample complexity of learning neural networks by providing new bounds on their Rademacher complexity, assuming norm constraints on the parameter matrix of each layer. Compared to previous work, these complexity bounds have improved dependence on the network depth and, under some additional assumptions, are fully independent of the network size (both depth and width). These results are derived using some novel techniques, which may be of independent interest.
Quantum-Classical Correspondence on Associated Vector Bundles Over Locally Symmetric Spaces
Authors: Küster Benjamin , Weich Tobias
Published: March 2019

For a compact Riemannian locally symmetric space $\mathcal M$ of rank 1 and an associated vector bundle $\mathbf V_{\tau }$ over the unit cosphere bundle $S^{\ast }\mathcal M$, we give a precise description of those classical (Pollicott–Ruelle) resonant states on $\mathbf V_{\tau }$ that vanish under covariant derivatives in the Anosov-unstable directions of the chaotic geodesic flow on $S^{\ast }\mathcal M$. In particular, we show that they are isomorphically mapped by natural pushforwards into generalized common eigenspaces of the algebra of invariant differential operators $D(G,\sigma )$ on compatible associated vector bundles $\mathbf W_{\sigma }$ over $\mathcal M$. As a consequence of this description, we obtain an exact band structure of the Pollicott–Ruelle spectrum. Further, under some mild assumptions on the representations $\tau$ and $\sigma$ defining the bundles $\mathbf V_{\tau }$ and $\mathbf W_{\sigma }$, we obtain a very explicit description of the generalized common eigenspaces. This allows us to relate classical Pollicott–Ruelle resonances to quantum eigenvalues of a Laplacian in a suitable Hilbert space of sections of $\mathbf W_{\sigma }$. Our methods of proof are based on representation theory and Lie theory.
Triose phosphate utilization and beyond: from photosynthesis to end product synthesis
Authors: McClain Alan M , Sharkey Thomas D
Published: March 2019

During photosynthesis, plants fix CO2 from the atmosphere onto ribulose-bisphosphate, producing 3-phosphoglycerate, which is reduced to triose phosphates (TPs). The TPs are then converted into the end products of photosynthesis. When a plant is photosynthesizing very quickly, it may not be possible to commit photosynthate to end products as fast as it is produced, causing a decrease in available phosphate and limiting the rate of photosynthesis to the rate of triose phosphate utilization (TPU). The occurrence of an observable TPU limitation is highly variable based on species and especially growth conditions, with TPU capacity seemingly regulated to be in slight excess of typical photosynthetic rates the plant might experience. The physiological effects of TPU limitation are discussed with an emphasis on interactions between the Calvin–Benson cycle and the light reactions. Methods for detecting TPU-limited data from gas exchange data are detailed and the impact on modeling of some physiological effects are shown. Special consideration is given to common misconceptions about TPU.
Nitric oxide in plants: pro- or anti-senescence
Authors: Bruand Claude , Meilhoc Eliane
Published: March 2019

Senescence is a regulated process of tissue degeneration that can affect any plant organ and consists of the degradation and remobilization of molecules to other growing tissues. Senescent organs display changes at the microscopic level as well as modifications to internal cellular structure and differential gene expression. A large number of factors influencing senescence have been described including age, nutrient supply, and environmental interactions. Internal factors such as phytohormones also affect the timing of leaf senescence. A link between the senescence process and the production of nitric oxide (NO) in senescing tissues has been known for many years. Remarkably, this link can be either a positive or a negative correlation depending upon the organ. NO can be both a signaling or a toxic molecule and is known to have multiple roles in plants; this review considers the duality of NO roles in the senescence process of two different plant organs, namely the leaves and root nodules.
Chronic kidney disease, heart failure and neprilysin inhibition
Authors: Haynes Richard , Zhu Doreen , Judge Parminder K , Herrington William G , Kalra Philip A , Baigent Colin
Published: March 2019

Patients with chronic kidney disease are at increased risk of cardiovascular disease and this often manifests clinically like heart failure. Conversely, patients with heart failure frequently have reduced kidney function. The links between the kidneys and cardiovascular system are being elucidated, with blood pressure being a key risk factor. Patients with heart failure have benefitted from many trials which have now established a strong evidence based on which to base management. However, patients with advanced kidney disease have often been excluded from these trials. Nevertheless, there is little evidence that the benefits of such treatments are modified by the presence or absence of kidney disease, but more direct evidence among patients with advanced kidney disease is required. Neprilysin inhibition is the most recent treatment to be shown to improve outcomes among patients with heart failure. The UK HARP-III trial assessed whether neprilysin inhibition improved kidney function in the short- to medium-term and its effects on cardiovascular biomarkers. Although no effect (compared to irbesartan control) was found on kidney function, allocation to neprilysin inhibition (sacubitril/valsartan) did reduce cardiac biomarkers more than irbesartan, suggesting that this treatment might improve cardiovascular outcomes in this population. Larger clinical outcomes trials are needed to test this hypothesis.
Pharmacokinetics and Abuse Potential of Asalhydromorphone, a Novel Prodrug of Hydromorphone, After Intranasal Administration in Recreational Drug Users
Authors: Guenther Sven , Mickle Travis C , Barrett Andrew C , Smith Adam , Braeckman Rene , Kelsh Debra , Vince Bradley
Published: March 2019

Objectives

Hydromorphone (HM) is a potent μ-opioid receptor agonist with high susceptibility for abuse. A prodrug of hydromorphone, asalhydromorphone (ASAL-HM), has been designed to deter nonoral forms of abuse associated with hydromorphone. This study evaluated the intranasal (IN) pharmacokinetics and exploratory abuse potential of ASAL-HM compared with HM.

Design

Single-center, randomized, double-blind, crossover study.

Setting

Clinical research site.

Subjects

Healthy adult, nondependent recreational opioid users.

Methods

Subjects (N = 26) were randomized to receive IN administration of 16.1 mg of ASAL-HM and 8.0 mg of HM (molar-equivalent with respect to hydromorphone). Blood samples were taken through 24 hours postdose, and pharmacodynamic end points (Drug Liking, Feeling High, Take Drug Again, Overall Drug Liking) were assessed through eight hours postdose. Nasal irritation and safety were also assessed.

Results

Relative to IN HM, the rate (Cmax) and extent (area under the curve [AUC0-last, AUC0-inf]) of exposure to hydromorphone following IN ASAL-HM were reduced by ≥50%. Consistent with these findings, scores on “at-the-moment” (i.e., Drug Liking Emax, High Emax) and retrospective (i.e., Take Drug Again, Overall Drug Liking) end points were statistically significantly lower for IN ASAL-HM, with mean/median differences ranging from 11.4 to 25.0 points. ASAL-HM produced greater nasal-related effects, such as nasal burning and facial pain, and a lower incidence of typical opioid-related adverse events such as euphoria, pruritus, and somnolence.

Conclusions

The novel hydromorphone prodrug ASAL-HM produced marked reductions in hydromorphone exposure and abuse-related effects following IN administration compared with HM. ASAL-HM has desirable molecular features for incorporation into putative abuse-deterrent immediate-release and extended-release hydromorphone products.
Daily music listening to reduce work-related stress: a randomized controlled pilot trial
Authors: Raglio A , Bellandi D , Gianotti M , Zanacchi E , Gnesi M , Monti M C , Montomoli C , Vico F , Imbriani C , Giorgi I , Imbriani M
Published: March 2019

Background

Literature shows that music can reduce stress conditions. This pilot study investigated the effects of music listening on work-related stress and well-being in healthcare professionals.

Method

A total of 45 subjects were randomly assigned to three treatment groups: No Music, Individualized Music and Melomics-Health Listening. Music groups experienced a daily 30-min-playlist listening for 3 weeks at home. The Maugeri Stress Index-Revised (MASI-R) and the Psychological General Well-Being Index (PGWBI) were administered at baseline, after 3 weeks and after 7 weeks (follow-up). Longitudinal data were analyzed by means of a nested ANOVA model, testing the main effects of time and treatment and the interaction between them.

Results

MASI-R scores showed a positive trend in music groups and a worsening in the control group. Only the interaction time/treatment emerged as supporting a trend toward statistical significance (P = 0.07). PGWBI showed a stability in music groups and a clear decline in controls, without significant effects.

Conclusions

Results from the study support the need for a larger clinical trial: it is suggested that daily music listening could be implemented to reduce work-related stress and that the effects may be related, not only to individual musical preferences and familiarity, but also to specific music structures and parameters.
Negative Swap Spreads and Limited Arbitrage
Authors: J Jermann Urban
Published: March 2019

Since October 2008, fixed rates for interest rate swaps with a 30-year maturity have been mostly below Treasury rates with the same maturity. Under standard assumptions, this implies the existence of arbitrage opportunities. This paper presents a model for pricing interest rate swaps, where frictions for holding bonds limit arbitrage. I analytically show that negative swap spreads should not be surprising. In the calibrated model, swap spreads can reasonably match empirical counterparts without the need for large demand imbalances in the swap market. Empirical evidence is consistent with the relation between term spreads and swap spreads in the model.

Received April 16, 2017; editorial decision Januray 3, 2019 by Editor Stijn Van Nieuwerburgh.
The effect of cow udder score on cow/calf performance in the Nebraska Sandhills
Authors: Beard Joslyn K , Musgrave Jacki A , Funston Rick N , Mulliniks J Travis
Published: March 2019

Poor udder and teat confirmation decreases profitability due to decreased calf weaning weight, increased incidence of mastitis and labor, and decreased cow lifetime productivity. Therefore, the objective of this retrospective study was to evaluate the effect of beef cow udder score on cow performance and pre- and postweaning progeny performance. In a 5-yr study, crossbred cows at the Gudmundsen Sandhills Laboratory, Whitman, NE, were assigned an udder score each year at calving, from 1 to 5, using an udder and teat combination score. Cows were grouped by udder scores and classified as either low udder score (LUS, udder score 1 or 2; n = 223) or high udder score (HUS, udder score 3 or 4; n = 1,742). The udder score combines udder conformation and a teat scoring system. Low udder scores consisted of pendulous udders and large teats, whereas HUS consisted of tight udders and small, symmetrical teats. Mixed models were used to evaluate udder score on cow performance and calf pre- and postweaning performance. Cow body weight (BW) at prebreeding and weaning was greater (P < 0.01) in LUS cows compared with HUS counterparts. Pregnancy rate was not different (P = 0.35) between udder classification groups. Calf BW at birth (P = 0.95), weaning (P = 0.40), and adjusted 205-d BW (P = 0.28) were not different between udder groups. Cow udder score did not influence feedlot entry (P = 0.41) and final BW (P = 0.30), dry matter intake (P = 0.53), average daily gain (P = 0.60), and gain:feed ratio (P = 0.85) of steer progeny. However, steers from HUS dams had greater hot carcass weight (HCW; P = 0.04) and backfat thickness (P = 0.02) compared with LUS counterparts. Results from this study suggest cows with less desirable udder structure may not have a negative impact on calf preweaning growth and performance; however, backfat thickness and HCW in the finishing phase were lower in steers from cows with a lower udder score.
Effect of increased inclusion of dried distillers grain supplement on adaptation, intake, digestibility, and rumen parameters in steers consuming bermudagrass round bale silage
Authors: Alava Erin N , Alava Eduardo I , Welchons Cody A , Yelich Joel V , Hersom Matthew J
Published: March 2019

Eight ruminally cannulated beef steers were used to evaluate forage intake and physiological response during adaptation to a diet consisting of bermudagrass round bale silage (RBS) and dried distillers grains (DDG) and in a second experiment the effect of level of DDG supplementation on RBS forage intake, digestibility, and rumen parameters. The adaptation experiment was designed to simulate a 14-d step-up process. Initially steers received ad libitum RBS, on d 4 steers were offered 1.13 kg of DDG daily and every 4 d daily DDG offered was increased by 1.13 kg. Blood and rumen fluid samples were collected before feeding (0 h) and 6, 12, 24 (before feeding), and 36 h after every diet change. The digestibility experiment was conducted as an 8 × 4 Latin square with four periods. Treatments included RBS only and DDG supplement levels of 0.33%, 0.66%, and 1.0% of body weight (RBS + 0.33, +0.66, and 1.0, respectively). Collection periods consisted of 21 d to determine dry matter intake [DMI], digestibility, and collect rumen fluid samples. During adaptation, level of DDG did not (P = 0.42) affect RBS DMI. Mean ruminal pH was greater (P < 0.05) for RBS only compared with diets with DDG. When steers were offered 3.39 or 4.52 kg/d of DDG rumen NH3-N concentration was greater (P ≤ 0.05) compared with other levels of DDG or RBS alone. Mean nonesterified fatty acid and plasma urea N concentrations varied among levels of DDG offered. In the digestibility experiment forage DMI, total DMI, and total tract apparent digestibility exhibited a quadratic (P ≤ 0.05) response to level of DDG offered. Mean ruminal pH responded in a quadratic manner (P = 0.03) and was greater for RBS only compared with RBS plus DDG at any level. Mean ruminal NH3-N concentration tended (P = 0.07) to respond in a cubic manner as DDG amount offered increased. Physiological responses during adaptation to DDG over 14 d resembled responses previously observed after long-term DDG supplementation. Offering DDG up to 1% of body weight did depress forage DMI and ruminal pH but increased total DMI, diet digestibility, and ruminal NH3-N concentration.
Embryo and cow factors affecting pregnancy per embryo transfer for multiple-service, lactating Holstein recipients
Authors: Estrada-Cortés Eliab , Ortiz William G , Chebel Ricardo C , Jannaman Elizabeth A , Moss James I , de Castro Fernanda Cavallari , Zolini Adriana M , Staples Charles R , Hansen Peter J
Published: March 2019

The objective was to determine whether pregnancy success after embryo transfer (ET) during heat stress in multi-service Holstein cows depends upon characteristics of the embryo or recipient. Female embryos produced in vitro were cultured with either 0.0 (control) or 1.8 mM choline chloride and transferred fresh. Fresh embryos of undetermined breed and frozen Holstein embryos were used when experimental embryos were insufficient. Embryos were transferred 8 d after the last GnRH injection of an ovulation synchronization program. Embryo type [frozen vs. fresh, choline vs. control, unknown breed vs. (control + choline)] and characteristics of recipients (average of 190 d in milk at transfer) were evaluated. Pregnancy per ET was lower for cows receiving frozen embryos (7.0%; 3/43) than for cows receiving fresh embryos (26.7%; 32/120) but there were no differences between various types of fresh embryo. Pregnancy per ET was lower for cows diagnosed with metritis in the early postpartum period (7.1%; 2/28) than for cows without metritis (24.4%; 33/135). In conclusion, the use of frozen/thawed embryos produced in vitro and recipients which had metritis in the early postpartum period reduced the success of ET in multiple-service Holstein cows.