bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of an electron-ion coincidence apparatus for molecular-frame electron energy loss spectroscopy studies
Authors: Watanabe Noboru , Hirayama Tsukasa , Yamada So , Takahashi Masahiko
Published: April 2018

We report details of an electron-ion coincidence apparatus, which has been developed for molecular-frame electron energy loss spectroscopy studies. The apparatus is mainly composed of a pulsed electron gun, an energy-dispersive electron spectrometer, and an ion momentum imaging spectrometer. Molecular-orientation dependence of the high-energy electron scattering cross section can be examined by conducting measurements of vector correlation between the momenta of the scattered electron and fragment ion. Background due to false coincidences is significantly reduced by introducing a pulsed electron beam and pulsing scheme of ion extraction. The experimental setup has been tested by measuring the inner-shell excitation of N2 at an incident electron energy of 1.5 keV and a scattering angle of 10.2°.
Measurements of hydrogen gas stopping efficiency for tin ions from laser-produced plasma
Authors: Abramenko D. B. , Spiridonov M. V. , Krainov P. V. , Krivtsun V. M. , Astakhov D. I. , Medvedev V. V. , van Kampen M. , Smeets D. , Koshelev K. N.
Published: April 2018

Experimental studies of stopping of ion fluxes from laser-produced plasma by a low-pressure gas atmosphere are presented. A modification of the time-of-flight spectroscopy technique is proposed for the stopping cross-sectional measurements in the ion energy range of 0.1–10 keV. The application of the proposed technique is demonstrated for Sn ion stopping by H2 gas. This combination of elements is of particular importance for the development of plasma-based sources of extreme ultraviolet radiation for lithographic applications.
Gibbs measures based on 1d (an)harmonic oscillators as mean-field limits
Authors: Lewin Mathieu , Nam Phan Thành , Rougerie Nicolas
Published: April 2018

We prove that Gibbs measures based on 1D defocusing nonlinear Schrödinger functionals with sub-harmonic trapping can be obtained as the mean-field/large temperature limit of the corresponding grand-canonical ensemble for many bosons. The limit measure is supported on Sobolev spaces of negative regularity, and the corresponding density matrices are not trace-class. The general proof strategy is that of a previous paper of ours, but we have to complement it with Hilbert-Schmidt estimates on reduced density matrices.
Defect and grain boundary scattering in tungsten: A combined theoretical and experimental study
Authors: Lanzillo Nicholas A. , Dixit Hemant , Milosevic Erik , Niu Chengyu , Carr Adra V. , Oldiges Phil , Raymond Mark V. , Cho Jin , Standaert Theodorus E. , Kamineni Vimal K.
Published: April 2018

Several major electron scattering mechanisms in tungsten (W) are evaluated using a combination of first-principles density functional theory, a Non-Equilibrium Green's Function formalism, and thin film Kelvin 4-point sheet resistance measurements. The impact of grain boundary scattering is found to be roughly an order of magnitude larger than the impact of defect scattering. Ab initio simulations predict average grain boundary reflection coefficients for a number of twin grain boundaries to lie in the range r = 0.47 to r = 0.62, while experimental data can be fit to the empirical Mayadas-Schatzkes model with a comparable but slightly larger value of r = 0.69. The experimental and simulation data for grain boundary resistivity as a function of grain size show excellent agreement. These results provide crucial insights for understanding the impact of scaling of W-based contacts between active devices and back-end-of-line interconnects in next-generation semiconductor technology.
Hybrid forecasting of chaotic processes: Using machine learning in conjunction with a knowledge-based model
Authors: Pathak Jaideep , Wikner Alexander , Fussell Rebeckah , Chandra Sarthak , Hunt Brian R. , Girvan Michelle , Ott Edward
Published: April 2018

A model-based approach to forecasting chaotic dynamical systems utilizes knowledge of the mechanistic processes governing the dynamics to build an approximate mathematical model of the system. In contrast, machine learning techniques have demonstrated promising results for forecasting chaotic systems purely from past time series measurements of system state variables (training data), without prior knowledge of the system dynamics. The motivation for this paper is the potential of machine learning for filling in the gaps in our underlying mechanistic knowledge that cause widely-used knowledge-based models to be inaccurate. Thus, we here propose a general method that leverages the advantages of these two approaches by combining a knowledge-based model and a machine learning technique to build a hybrid forecasting scheme. Potential applications for such an approach are numerous (e.g., improving weather forecasting). We demonstrate and test the utility of this approach using a particular illustrative version of a machine learning known as reservoir computing, and we apply the resulting hybrid forecaster to a low-dimensional chaotic system, as well as to a high-dimensional spatiotemporal chaotic system. These tests yield extremely promising results in that our hybrid technique is able to accurately predict for a much longer period of time than either its machine-learning component or its model-based component alone.
Converging positive temperature equilibrium states in many-body bosonic quantum systems
Authors: Kim Meeri
Published: April 2018

Mathematicians take a step toward understanding how the impenetrable many-body problem can be solved with simplified equations.
Practical implications of mineral and vitamin imbalance in grazing sheep
Authors: Masters David G.
Published: April 2018

Rapid progress in research on mineral functions in biological systems over the past 20 years has provided new and unexplored implications for health and production in grazing livestock. The strong interaction among calcium (Ca), magnesium (Mg), phosphorus (P), sodium (Na), potassium (K) and vitamin D influences the absorption, utilisation and status of these nutrients, particularly Ca and Mg. An imbalanced intake of Ca, Mg, P, Na, K and vitamin D is common in ruminants grazing pastures and vegetative crops. The interaction may modify susceptibility to clinical hypocalcaemia, hypomagnesaemia and pregnancy toxaemia, or to subclinical and chronic deficiencies of Ca, Mg and Na. However, hypocalcaemia is also associated with endocrine failure. Whether this failure is susceptible to nutritional modulation or even whether supplements of Ca, Mg, Na and vitamin D reduce or exacerbate the risk of metabolic disease in sheep is unclear. Selenium, manganese, zinc, copper, sulfur, vitamin E and vitamin A play synergistic roles in the antioxidant defence mechanism and modulate the consequences of oxidative stress. In extensive grazing systems combined low intakes of these antioxidants are not unusual, particularly in seasonally dry environments and at a time coinciding with the increased oxidative stress that naturally occurs through the reproductive cycle. This oxidative stress is accentuated by heat stress and parasite infection. Oxidative stress in the short-term influences growth, reproduction, offspring survival and health. Long-term, oxidative damage to embryo DNA and changes in RNA expression, may influence lifetime performance of offspring. The high cost of providing mineral supplements to grazing sheep is a deterrence to addressing the implications of multiple mineral deficiencies. New herbaceous and shrub options to increase the botanical and nutritional diversity within pasture and crop-grazing systems may allow livestock to select a heterogeneous diet providing a more balanced mineral intake.
The efficacy of a cultured Synergistes jonesii inoculum to control hydroxypyridone toxicity in Bos indicus steers fed leucaena/grass diets
Authors: Halliday Michael J. , Giles Hayley E. , Padmanabha Jagadish , McSweeney Chris S. , Dalzell Scott A. , Shelton H. Max
Published: April 2018

An experiment was conducted to investigate the efficacy of a cultured Synergistes jonesii inoculum in degrading the Leucaena leucocephala (leucaena) toxins: 3-hydroxy-4(1H)-pyridone and 3-hydroxy-2(1H)-pyridone (3,4- and 2,3-DHP). Sixteen stall-housed Bos indicus steers naïve to leucaena were fed varying combinations of forage-harvested leucaena and Chloris gayana (Rhodes grass). Dietary treatments, offered at 25 g dry matter/kg LW.day, were: 25% leucaena; 50% leucaena; 100% leucaena; and 50% leucaena, switched to 50% Medicago sativa (lucerne) after 6 weeks at time of inoculation. The experiment was 10 weeks in duration, consisting of a 6-week pre-inoculation period, followed by inoculation with cultured S. jonesii, and a 4-week post-inoculation period. Mean daily dry matter intake was recorded. Twenty-four-hour urine collections and rumen fluid samples were obtained weekly for estimation of total urinary DHP, and detection of S. jonesii using nested polymerase chain reaction analysis including presence of single nucleotide polymorphisms (SNP), respectively. In the pre-inoculation period, total urinary DHP increased quickly to high levels, then gradually declined after Week 3 with 2,3-DHP the dominant isomer through to Week 6. Indigenous strains of S. jonesii were sporadically detected by PCR analysis, indicating S. jonesii was present before inoculation but at the lower limits of detection. After inoculation there was no change in the rate of total DHP degradation or the frequency of detection of S. jonesii, although there was increased rate of degradation of 2,3-DHP. SNP indicated the presence of different strains of S. jonesii in both indigenous and cultured S. jonesii. DMI was low, especially in the 100% treatment, due in part to the high stem content of the forage-harvested leucaena and probable DHP toxicosis. It was concluded that the cultured S. jonesii inoculum did not fully protect animals against leucaena toxicity.
Remembering the Spread of Western Science
Authors: Anderson Warwick
Published: April 2018

In the fifty years since publication of George Basalla's ‘The Spread of Western Science', historians of science have wavered between securely locating knowledge production in specific settings and trying to explain how scientific concepts and practices travel and come to appear universally applicable. As science has come to seem ever more ‘situated' and fragmented, we struggle to explain its obvious mobility and reproducibility. No single analytic framework seems plausibly to explain the globalization of science.
Ludwig Leichhardt: Four Previously Unknown Letters to John Nicholson and the Involvement of Ferdinand von Mueller in Publishing Leichhardt's Letters
Authors: Darragh Thomas A.
Published: April 2018

Two previously unknown letters written by Ludwig Leichhardt to his friend John Nicholson and sent to Ferdinand von Mueller were published in the Adelaide German newspaper Australische Zeitung in 1882. A third letter to Nicholson has been found as a copy in a Leichhardt diary and a fourth letter has been found in a volume of autograph letters in Brisbane. Translations of these letters are provided here and their significance indicated. The translation of another Leichhardt letter that proved to be controversial, and was attributed to Mueller, is shown not to have been translated by him. A transcription and translation of a previous unknown letter to Eduard Hallmann is provided in the Supplementary Material.
Chikungunya: treatments, opportunities and possibilities
Authors: Freitas Joseph R , Rao Shambhavi , Mahalingam Suresh
Published: April 2018

The natural progression of chikungunya virus (CHIKV) disease can consist of three stages – acute, post-acute and chronic, each having different clinical features. The acute phase (up to 3 weeks) is characterised by high viremia, fever, rash, polyarthralgia, synovitis and intense inflammation. Complete recovery is achieved in most symptomatic cases after this phase. However, in a large proportion of patients symptoms persist into a post-acute phase and in some may even continue to become chronic. In the post-acute phase, which can last up to 4 months, there is clinical persistence of joint inflammation or relapse after transient improvement. These can lead to musculoskeletal disorders and eventually chronicity of disease. The main symptoms being chronic inflammatory rheumatism that can last for several years in some cases. With the near global reach, debilitating nature and recent outbreaks of CHIKV there has been much research effort put towards combatting it. New antivirals and medications to counteract inflammation are being developed. Development of CHIKV vaccines is also an area with intense research focus.
A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy
Authors: Bauer Daniela , Meinhold Sarah , Jakob Roman P. , Stigler Johannes , Merkel Ulrich , Maier Timm , Rief Matthias , Žoldák Gabriel
Published: April 2018

Significance

Proteins with a similar structure can have largely different folding properties. Although some fold readily, others can only assume their native structure through the help of chaperone proteins. Partially folded intermediates play a key role in defining those folding differences. However, owing to their transient nature, they are not amenable to the structural investigation. Using a combination of single-molecule mechanics, protein engineering, and crystallography, we identified a stable native-like functional nucleus, which is a critical intermediate for spontaneous folding of the Hsp70 nucleotide-binding domain. Based on our findings, we engineered a chimera turning a homologous but folding-incompetent protein into a spontaneously folding protein that is enzymatically active. Our results have implications for the folding of actin from the same superfamily.
Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla
Authors: Metzger Michael J. , Paynter Ashley N. , Siddall Mark E. , Goff Stephen P.
Published: April 2018

Significance

An LTR retrotransposon,
Steamer
, was previously identified by virtue of high expression and dramatic amplification in a transmissible cancer in soft-shell clams (
Mya arenaria
). Here, we investigated genome sequences obtained from both physical collections of bivalves and genome databases and found evidence of horizontal transfer of
Steamer
-like transposons from one species to another, with jumps between bivalves and even between animals of completely different phyla. Some events were ancient, but some (in particular, those between bivalves) appear to be recent, as the elements are nearly identical in different species. These data show that horizontal transfer of LTR retrotransposons like
Steamer
has occurred and continues to occur frequently and that the marine environment may be particularly suitable for transfer of transposons.
Reduced vacuolar β-1,3-glucan synthesis affects carbohydrate metabolism as well as plastid homeostasis and structure in
Phaeodactylum tricornutum
Authors: Huang Weichao , Haferkamp Ilka , Lepetit Bernard , Molchanova Mariia , Hou Shengwei , Jeblick Wolfgang , Río Bártulos Carolina , Kroth Peter G.
Published: April 2018

Significance

Diatoms contribute considerably to the primary productivity of aquatic ecosystems. In diatoms, the principal storage polysaccharide is chrysolaminarin, consisting of branched β-1,3-glucans. The β-1,3-glucans are distributed widely in organisms and, besides starch and glycogen, represent major storage polysaccharides in nature. However, the synthesis pathway of storage β-1,3-glucans is still unclear. We report the localization of the glucan synthase, and thus the elongation of the glucan polymer, in the tonoplast membrane of the diatom
Phaeodactylum tricornutum
. Reduced expression of this glucan synthase results in various cellular effects. Our data indicate that the capacity of vacuolar polysaccharide storage substantially influences the photosynthetic performance of the plastid.
SAMHD1 enhances immunoglobulin hypermutation by promoting transversion mutation
Authors: Thientosapol Eddy Sanchai , Bosnjak Daniel , Durack Timothy , Stevanovski Igor , van Geldermalsen Michelle , Holst Jeff , Jahan Zeenat , Shepard Caitlin , Weninger Wolfgang , Kim Baek , Brink Robert , Jolly Christopher J.
Published: April 2018

Significance

Antibody affinity rises during immune responses to viruses via antibody gene somatic hypermutation and Darwinian selection of mutated B cells—in a time frame of days. The enzyme activation-induced deaminase (AID) initiates hypermutation by deaminating genomic cytosines. Mutation is exacerbated by noncanonical G
1
-phase DNA repair pathways that deploy error-prone polymerases, including Pol η (gene
Polh
). In G
1
phase, dNTP levels are restricted to inhibit viral replication. We derestricted G
1
-phase dNTP supply in hypermutating B cells, which increased virus susceptibility in vitro and caused changes in antibody hypermutation in vivo akin to
Polh
inactivation. We conclude that G
1
-phase dNTP paucity contributes to antibody hypermutation and that the evolution of antibody hypermutation included the repurposing of intracellular antivirus mechanisms based on dNTP starvation.
A selective class of inhibitors for the CLC-Ka chloride ion channel
Authors: Koster Anna K. , Wood Chase A. P. , Thomas-Tran Rhiannon , Chavan Tanmay S. , Almqvist Jonas , Choi Kee-Hyun , Du Bois J. , Maduke Merritt
Published: April 2018

Significance

Chloride ion channels and transporters (CLCs) are critical to cardiovascular, neurological, and musculoskeletal function. Small molecules capable of selectively inhibiting CLCs would serve as valuable tools for investigating CLC function and would have potential applications for treating CLC-related disorders. The lack of such agents has impeded efforts to study this family of proteins. This work introduces a class of inhibitors with unprecedented selectivity for a single CLC homolog, CLC-Ka. Insights gained through experiments to validate a predicted ligand binding site and to evaluate structure–activity relationships rationalize inhibitor potency and CLC-Ka selectivity. Our findings provide tools for studies of CLC-Ka function and will assist subsequent efforts to advance specific molecular probes for different CLC homologs.
Spelling-gate
Authors: Richardson Kay
Published: April 2018

Back in 2009, the Labour British Prime Minister Gordon Brown was attacked for “bad spelling” in a condolence letter written personally by him to the mother of a soldier who died in combat, and publicised by The Sun newspaper. “Spelling” here acts as a leveller of hierarchical differences in the national political culture, with ruler and subject both publicly disciplined by the same standard language ideology. Previous research on orthography as social practice has tended to focus on deliberate manipulation of fixed spellings; this article extends the approach to unconventional spellings that have come about ‘by mistake’, and also widens it, to consider aspects of orthography other than spelling, focusing on the look of the Prime Minister’s handwriting. At issue, semiotically, are meanings such as ‘the personal touch’ and ‘respect’.
Parasympathetic activity delayed after self‐paced exercise
Authors: Trojbicz Lucas Rosiello , Damasceno Mayara Vieira , Pasqua Leonardo Alves , Gáspari Arthur Fernandes , Lima‐Silva Adriano Eduardo , Bertuzzi Rômulo
Published: April 2018

The main purpose of this study was to compare the effect of the constant load and self‐paced exercise with similar total work on autonomic control after endurance exercise. Ten physically active men were submitted to (i) a maximal incremental exercise test, (ii) a 4‐km cycling time trial (4‐km TT), and (iii) a constant workload test with identical total external work performed at 4‐km TT. Gas exchange was measured throughout the tests, while blood lactate, heart rate, and heart rate variability (HRV) were measured during the passive recovery. Power output measured at the last lap (i.e. 3600–4000 m) of 4‐km TT (316 ± 89 W) was statistically higher than power output measured at the end of the constant workload exercise (211 ± 42 W). The 4‐km TT produced higher values of blood lactate concentration (8.8 ± 2.1 mmol L−1) than the constant workload test (7.8 ± 2.1 mmol L−1). The heart rate recovery measured at 60 s (constant workload: 37 ± 7 bpm; 4‐km TT: 30 ± 6) and 120 s (constant workload: 57 ± 9 bpm; 4‐km TT: 51 ± 9 bpm) were higher in the constant workload than in the self‐paced exercise. The HRV (i.e. RMSSD30s) was statistically higher in the constant load exercise measured at 120, 420, 450, 480, 540, and 570 s than the self‐paced exercise. These findings suggest that the autonomic control responses were dependent of the endurance exercise modalities, with parasympathetic activity being delayed after self‐paced exercise, as evidenced by post‐exercise heart rate indices.
Rethinking the left: a view from Latin America
Authors: Munck Ronaldo
Published: April 2018

The images of revolution in Latin America have long been part of the metropolitan left imagination. Yet there is not much input from the complex and grounded Latin American debates rethinking the left into the global discourse. I will develop an argument/analysis addressing that gap in three phases. First inTheoryI will seek to place the Latin American debates from a postcolonial perspective focusing on the reception of key debates in the global North. I then move on to the ‘left decade’ itself inPracticelaying out some of the basic parameters, its complexity and contradictions. Post 2000, Latin America became a laboratory of left experimentalism that deserves closer attention. Finally, inFuturesI cast a cold eye on alternative scenarios for the left with a view to going beyond the simplifications current in Northern left coverage. Any global rethinking on ‘augmenting the left’ would benefit from the various views from (not just on) Latin America. There is much to learn from debates which might help rethink a left strategy that is fit for purpose in the 21st century, learning from the mistakes of the past and from the now seemingly ebbing left decade or ‘pink tide’ in Latin America.
Superoxide dismutases: Dual roles in controlling ROS damage and regulating ROS signaling
Authors: Wang Ying , Branicky Robyn , Noë Alycia , Hekimi Siegfried
Published: April 2018

Superoxide dismutases (SODs) are universal enzymes of organisms that live in the presence of oxygen. They catalyze the conversion of superoxide into oxygen and hydrogen peroxide. Superoxide anions are the intended product of dedicated signaling enzymes as well as the byproduct of several metabolic processes including mitochondrial respiration. Through their activity, SOD enzymes control the levels of a variety of reactive oxygen species (ROS) and reactive nitrogen species, thus both limiting the potential toxicity of these molecules and controlling broad aspects of cellular life that are regulated by their signaling functions. All aerobic organisms have multiple SOD proteins targeted to different cellular and subcellular locations, reflecting the slow diffusion and multiple sources of their substrate superoxide. This compartmentalization also points to the need for fine local control of ROS signaling and to the possibility for ROS to signal between compartments. In this review, we discuss studies in model organisms and humans, which reveal the dual roles of SOD enzymes in controlling damage and regulating signaling.
SHP-1 regulates hematopoietic stem cell quiescence by coordinating TGF-β signaling
Authors: Jiang Linjia , Han Xue , Wang Jin , Wang Chen , Sun Xiaoqiang , Xie Jiayi , Wu Guojin , Phan Hiep , Liu Zhenguo , Yeh Edward T.H. , Zhang ChengCheng , Zhao Meng , Kang Xunlei
Published: April 2018

Cell cycle quiescence is critical for hematopoietic stem cell (HSC) maintenance. TGF-β signaling in bone marrow niche has been identified in regulating HSC quiescence; however, the intrinsic regulatory mechanisms remain unclear. This study reports that Shp-1 knockout HSCs have attenuated quiescence and impaired long-term self-renewal. SHP-1–activated HSCs are surrounded by megakaryocytes, which regulate HSC quiescence by producing TGF-β1. Mechanistically, SHP-1 interacts with the immunoreceptor tyrosine-based inhibition motif on TGF-β receptor 1 and is critical for TGF-β signaling activation in HSCs. Functionally, Shp-1 knockout HSCs do not respond to TGF-β–enforced HSC quiescence regulation, both in vitro and in vivo. Therefore, we identify TGF-β–SHP-1 as a novel intrinsic regulatory mechanism for HSC quiescence maintenance.
Calibration of mass and conventional mass of weights 2 kg, 1 kg, 200 g, 50 g, 1 g and 200 mg
Authors: Becerra Luis Omar , Peña Luis Manuel , Vargas Boris Escalante , Almonte Luz Cori , Martín Quiroga Rojas Aldo , Bermúdez Coronel lvaro , Soto Jhon J Escobar , Naula Wilson , Florencio Arnaldo , Valenzuela a Lourdes , Alfaro Olman Ramos , Peña Marcela Prenda
Published: April 2018

This report describes the results of a supplementary comparison between SIM NMIs, which was carried out to evaluate the consistency of the measurements of calibration in high accuracy mass standards using the normalized error criteria (2 kg, 1 kg, 200 g, 50 g, 1 g and 200 mg). The supplementary comparison was carried out from April 2012 to July 2013.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Projected Gromov-Witten varieties in cominuscule spaces
Authors: Buch Anders , Chaput Pierre–Emmanuel , Mihalcea Leonardo , Perrin Nicolas
Published: April 2018

A projected Gromov-Witten variety is the union of all rational curves of fixed degree that meet two opposite Schubert varieties in a homogeneous space

X
=
G

/

P

X = G/P

. When

X
X

is cominuscule we prove that the map from a related Gromov-Witten variety is cohomologically trivial. This implies that all (3-point, genus zero)

K
K

-theoretic Gromov-Witten invariants of

X
X

are determined by projected Gromov-Witten varieties, which extends an earlier result of Knutson, Lam, and Speyer, and provides an alternative version of the ‘quantum equals classical’ theorem. Our proof uses that any projected Gromov-Witten variety in a cominuscule space is also a projected Richardson variety.
An algebraic construction of a solution to the mean field equations on hyperelliptic curves and its adiabatic limit
Authors: Liou Jia-Ming (Frank) , Liu Chih-Chung
Published: April 2018

In this paper, we give an algebraic construction of the solution to the following mean field equation:

Δ
ψ
+

e

ψ

=
4
π

∑

i
=
1

2
g
+
2

δ

P

i

\begin{equation*} \Delta \psi +e^{\psi }=4\pi \sum _{i=1}^{2g+2}\delta _{P_{i}} \end{equation*}

on a genus

g
≥
2

g\geq 2

hyperelliptic curve

(
X
,
d

s

2

)

(X,ds^{2})

, where

d

s

2

ds^{2}

is a canonical metric on

X
X

and

{

P

1

,
⋯
,

P

2
g
+
2

}

\{P_{1},\cdots ,P_{2g+2}\}

is the set of Weierstrass points on

X
.

X.
Nondegeneracy of half-harmonic maps from ℝ into 𝕊¹
Authors: Sire Yannick , Wei Juncheng , Zheng Youquan
Published: April 2018

We prove that the standard half-harmonic map

U
:

R

→

S

1

U:\mathbb {R}\to \mathbb {S}^1

defined by

x
→

(

x
2

−
1

x
2

+
1

−
2
x

x
2

+
1

)

\begin{equation*} x\to \begin {pmatrix} \frac {x^2-1}{x^2+1} \\[4pt] \frac {-2x}{x^2+1} \end{pmatrix} \end{equation*}

is nondegenerate in the sense that all bounded solutions of the linearized half-harmonic map equation are linear combinations of three functions corresponding to rigid motions (dilation, translation, and rotation) of

U
U

.
Comparative analysis of tissue reconstruction algorithms for 3D histology
Authors: Kartasalo Kimmo , Latonen Leena , Vihinen Jorma , Visakorpi Tapio , Nykter Matti , Ruusuvuori Pekka
Published: April 2018

Motivation

Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking.

Results

We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.

Availability and implementation

Code: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702.

Supplementary information

Supplementary data are available at Bioinformatics online.
BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates
Authors: Goren Emily , Liu Peng , Wang Chao , Wang Chong
Published: April 2018

Motivation

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level.

Results

We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually.

Availability and implementation

Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R.

Supplementary information

Supplementary data are available at Bioinformatics online.
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC
Authors: Liu Bin , Weng Fan , Huang De-Shuang , Chou Kuo-Chen
Published: April 2018

Motivation

DNA replication is the key of the genetic information transmission, and it is initiated from the replication origins. Identifying the replication origins is crucial for understanding the mechanism of DNA replication. Although several discriminative computational predictors were proposed to identify DNA replication origins of yeast species, they could only be used to identify very tiny parts (250 or 300 bp) of the replication origins. Besides, none of the existing predictors could successfully capture the ‘GC asymmetry bias’ of yeast species reported by experimental observations. Hence it would not be surprising why their power is so limited. To grasp the CG asymmetry feature and make the prediction able to cover the entire replication regions of yeast species, we develop a new predictor called ‘iRO-3wPseKNC’.

Results

Rigorous cross validations on the benchmark datasets from four yeast species (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis and Pichia pastoris) have indicated that the proposed predictor is really very powerful for predicting the entire DNA duplication origins.

Availability and implementation

The web-server for the iRO-3wPseKNC predictor is available at http://bioinformatics.hitsz.edu.cn/iRO-3wPseKNC/, by which users can easily get their desired results without the need to go through the mathematical details.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Effect of Antibiotic Selection Pressure on the Nasopharyngeal Macrolide Resistome: A Cluster-randomized Trial
Authors: Keenan Jeremy D , Chin Stephanie A , Amza Abdou , Kadri Boubacar , Nassirou Baido , Cevallos Vicky , Cotter Sun Y , Zhou Zhaoxia , West Sheila K , Bailey Robin L , Porco Travis C , Lietman Thomas M ,   Rapid Elimination of Trachoma (PRET) Study Group
Published: April 2018

Background

Frequent use of antibiotics is thought to create selection pressure by clearing susceptible bacteria and allowing resistant bacteria to spread in a community. A cluster-randomized trial comparing 2 different frequencies of mass azithromycin distributions for trachoma provided a convenient experiment for determining the causal relationship between antibiotic consumption and antibiotic resistance.

Methods

Twenty-four communities were randomized to either annual or biannual mass azithromycin distributions for trachoma. Randomization was stratified on health catchment area and trachoma prevalence. Swabs were processed for the genetic macrolide resistance determinants ermB and mefA/E in a masked fashion from a random sample of 120 preschool children before treatment and another 120 children after 2 years of mass antibiotics.

Results

Macrolide resistance determinants were similar in the 12 annually and 12 biannually treated communities before treatment, with a median prevalence among preschool children of 20% (interquartile range [IQR], 10%–40%) in each group. By 24 months, macrolide resistance determinants were found more commonly in the biannually treated communities (median, 60% [IQR, 50%–80%]) than the annually treated communities (median, 40% [IQR, 20%–40%]; P < .001). Adjusting for baseline, the 24-month prevalence of macrolide resistance determinants in the biannual group was 29.4% higher than that of the annual group (95% confidence interval, 10.5%–56.7%).

Conclusions

This randomized trial used direct genetic methods to confirm the causal relationship of community antibiotic consumption and antibiotic resistance. Communities randomized to less frequent use of antibiotics had a significantly lower prevalence of genetic antibiotic resistance determinants.

Clinical Trials Registration

NCT00792922.
Multiple Class I and Class II Haemophilus ducreyi Strains Cause Cutaneous Ulcers in Children on an Endemic Island
Authors: Grant Jacob C , González-Beiras Camila , Amick Kristen M , Fortney Kate R , Gangaiah Dharanesh , Humphreys Tricia L , Mitjà Oriol , Abecasis Ana , Spinola Stanley M
Published: April 2018

Background

Together with Treponema pallidum subspecies pertenue, Haemophilus ducreyi is a major cause of exudative cutaneous ulcers (CUs) in children. For H. ducreyi, both class I and class II strains, asymptomatic colonization, and environmental reservoirs have been found in endemic regions, but the epidemiology of this infection is unknown.

Methods

Based on published whole-genome sequences of H. ducreyi CU strains, a single-locus typing system was developed and applied to H. ducreyi–positive CU samples obtained prior to, 1 year after, and 2 years after the initiation of a mass drug administration campaign to eradicate CU on Lihir Island in Papua New Guinea. DNA from the CU samples was amplified with class I and class II dsrA-specific primers and sequenced; the samples were classified into dsrA types, which were geospatially mapped. Selection pressure analysis was performed on the dsrA sequences.

Results

Thirty-seven samples contained class I sequences, 27 contained class II sequences, and 13 contained both. There were 5 class I and 4 class II types circulating on the island; 3 types accounted for approximately 87% of the strains. The composition and geospatial distribution of the types varied little over time and there was no evidence of selection pressure.

Conclusions

Multiple strains of H. ducreyi cause CU on an endemic island and coinfections are common. In contrast to recent findings with T. pallidum pertenue, strain composition is not affected by antibiotic pressure, consistent with environmental reservoirs of H. ducreyi. Such reservoirs must be addressed to achieve eradication of H. ducreyi.
Comparing plant and animal glutamate receptors: common traits but different fates?
Authors: Wudick Michael M , Michard Erwan , Oliveira Nunes Custódio , Feijó José A
Published: April 2018

Animal ionotropic glutamate receptors (iGluRs) are ligand-gated channels whose evolution is intimately linked to that of the nervous system, where the agonist glutamate and co-agonists glycine/d-serine act as neurotransmitters or neuromodulators. While iGluRs are specialized in neuronal communication, plant glutamate receptor-like (GLR) homologs have evolved many plant-specific physiological functions, such as sperm signaling in moss, pollen tube growth, root meristem proliferation, innate immune, and wound responses. GLRs have been associated with Ca2+ signaling by directly channeling its extracellular influx into the cytosol. Nevertheless, very limited information on functional properties of GLRs is available, and we mostly rely on structure/function data obtained for animal iGluRs to interpret experimental results obtained for plant GLRs. Yet, a deeper characterization and better understanding of plant GLRs is progressively unveiling original and different functions when compared with their mammalian counterparts. Here, we review the function of plant GLRs comparing their predicted structure and physiological roles with those of the well-documented roles of iGluRs. We conclude that interpreting GLR function based on comparison with their animal counterparts calls for caution, especially when presuming physiological roles and the mode of action for plant GLRs, and when comparing iGluRs in neuronal tissues with those in peripheral, non-neuronal tissues.
Very high-energy gamma-ray signature of ultrahigh-energy cosmic ray acceleration in Centaurus A
Authors: Joshi Jagdish C , Miranda Luis Salvador , Razzaque Soebur , Yang Lili
Published: April 2018

The association of at least a dozen ultrahigh-energy cosmic ray (UHECR) events with energy ≳ 55 EeV detected by the Pierre Auger Observatory from the direction of Centaurus-A, the nearest radio galaxy, supports the scenario of UHECR acceleration in the jets of radio galaxies. In this work, we model radio to very high energy (VHE,≳ 100 GeV) γ-ray emission from Cen A, including GeV hardness detected by Fermi–LAT and TeV emission detected by the High Energy Stereoscopic System (HESS). We consider two scenarios: (i) two-zone synchrotron self-Compton (SSC) and external-Compton (EC) models, (ii) two-zone SSC, EC, and photohadronic emission from cosmic ray interactions. The GeV hardness observed by Fermi–LAT can be explained using these two scenarios, where zone 2 EC emission is very important. Hadronic emission in scenario (ii) can explain VHE data with the same spectral slope as obtained through fitting UHECRs from Cen A. The peak luminosity in cosmic ray proton at 1 TeV, to explain the VHE γ-ray data is ≈2.5 × 1046 erg s−1. The bolometric luminosity in cosmic ray protons is consistent with the luminosity required to explain the origin of 13 UHECR signal events that are correlated with Cen A.
Evidence-Based Optimization of Post-Treatment Surveillance for Skull Base Chordomas Based on Local and Distant Disease Progression
Authors: Freeman Jacob L , Kaufmann Ascher B , Everson Richard G , DeMonte Franco , Raza Shaan M
Published: April 2018

BACKGROUND

There are no guidelines regarding post-treatment surveillance specific to skull base chordomas.

OBJECTIVE

To determine an optimal imaging surveillance schedule to detect both local and distant metastatic skull base chordoma recurrences.

METHODS

A retrospective review of 91 patients who underwent treatment for skull base chordoma between 1993 and 2017 was conducted. Time to and location of local and distant recurrence(s) were cataloged. Existing chordoma surveillance recommendations (National Comprehensive Cancer Network [NCCN], London and South East Sarcoma Network [LSESN], European Society for Medical Oncology [ESMO], Chordoma Global Consensus Group [CGCG]) were applied to our cohort to compare the number of recurrent patients and months of undiagnosed tumor growth between surveillances. These findings were used to inform the creation of a revised imaging surveillance protocol (MD Anderson Cancer Center Chordoma Imaging Protocol [MDACC-CIP]), presented here.

RESULTS

Thirty-four patients with 79 local/systemic recurrences met inclusion criteria. Mean age at diagnosis and follow-up time were 45 yr and 79 mo, respectively. The MDACC-CIP imaging protocol significantly reduced the time to diagnosis of recurrence compared with the LSESN and CGCG/ESMO imaging protocols for surveillance of local disease with a cumulative/average of 576/16.9 (LSESN), 336/9.8 (CGCG), and 170/5.0 (MDACC-CIP) months of undetected growth, respectively. The NCCN and MDACC-CIP guidelines for distant metastatic surveillance identified a cumulative/average of 65/6.5 and 51/5.1 mo of undetected growth, respectively, and were not significantly different.

CONCLUSION

The MDACC-CIP for skull base chordoma accounts for recurrence trends unique to this disease, including a higher rate of leptomeningeal spread than sacrococcygeal primaries, resulting in improved sensitivity and prompt diagnosis.
Planets around the evolved stars 24 Boötis and γ Libra: A 30 d-period planet and a double giant-planet system in possible 7:3 MMR
Authors: Takarada Takuya , Sato Bun’ei , Omiya Masashi , Harakawa Hiroki , Nagasawa Makiko , Izumiura Hideyuki , Kambe Eiji , Takeda Yoichi , Yoshida Michitoshi , Itoh Yoichi , Ando Hiroyasu , Kokubo Eiichiro , Ida Shigeru
Published: April 2018

We report the detection of planets around two evolved giant stars from radial velocity measurements at Okayama Astrophysical observatory. 24 Boo (G3 IV) has a mass of $0.99\,M_{\odot }$, a radius of $10.64\,R_{\odot }$, and a metallicity of [Fe/H] = −0.77. The star hosts one planet with a minimum mass of 0.91 MJup and an orbital period of 30.35 d. The planet has one of the shortest orbital periods among those ever found around evolved stars using radial-velocity methods. The stellar radial velocities show additional periodicity with 150 d, which can probably be attributed to stellar activity. The star is one of the lowest-metallicity stars orbited by planets currently known. γ Lib (K0 III) is also a metal-poor giant with a mass of $1.47\,M_{\odot }$, a radius of $11.1\,R_{\odot }$, and [Fe/H] = −0.30. The star hosts two planets with minimum masses of 1.02 MJup and 4.58 MJup, and periods of 415 d and 964 d, respectively. The star has the second-lowest metallicity among the giant stars hosting more than two planets. Dynamical stability analysis for the γ Lib system sets the minimum orbital inclination angle to be about 70° and suggests that the planets are in 7:3 mean-motion resonance, though the current best-fitting orbits for the radial-velocity data are not totally regular.
Development and Evaluation of the Boston University Osteoarthritis Functional Pain Short Form (BU-OA-FPS)
Authors: Goode Adam P , Ni Pengshend , Jette Alan , Fitzgerald G Kelley
Published: April 2018

Background

Pragmatic studies have gained popularity, thus emphasizing the need for patient-reported outcomes (PRO) to be integrated into electronic health records.

Objective

This study describes the development of a customized short form from the Boston University Osteoarthritis Functional Assessment PRO (BU-OA-PRO) for a specific pragmatic clinical trial.

Methods

A Functional Pain Short Form was created from an existing item bank of deidentified data in the BU-OA-PRO. Item response theory (IRT) methods were used to select items. Reliability was measured with the Cronbach alpha, then with IRT simulation methods. To examine validity, ceiling and floor effects, correlations between the short-form scores and scores from the BU-OA-PRO and the Western Ontario McMasters University Osteoarthritis Index (WOMAC) Pain and Difficulty subscales, and the area under the curve (AUC) were calculated. A minimum detectable change at 90% confidence (MDC90) was calculated based on a calibration sample.

Results

The BU-OA-PRO was reduced from 126 items to 10 items to create the BU-OA Functional Pain Short Form (BU-OA-FPS). The Cronbach alpha indicated high internal consistency (0.91), and reliability distribution estimates were 0.96 (uniform) and 0.92 (normal). Low ceiling effects (4.57%) and floor effects (0%) were found. Moderate-to-high correlations between the BU-OA-PRO and BU-OA-FPS were found with WOMAC Pain (BU-OA-FPS = 0.67; BU-OA-PRO = 0.64) and Difficulty (BU-OA-FPS = 0.73; BU-OA-PRO = 0.69) subscales. The correlation between the BU-OA-PRO and BU-OA-FPS was 0.94. The AUC ranged from 0.80 to 0.88. The MDC90 was approximately 6 standardized points.

Conclusions

The BU-OA-FPS provides reliable and valid measurement of functional pain. Pragmatic studies may consider the BU-OA-FPS for use in electronic health records to capture outcomes.
Effects of increasing dietary level of a commercial liquid supplement on growth performance and carcass characteristics in feedlot steers
Authors: Felix Tara L , Long Chloe J , Stierwalt Madeline R , Carvalho Pedro H V , Blalock Howard M
Published: April 2018

Feeding cattle liquid supplements has become increasingly popular in the feedlot industry; however, optimal inclusion of liquid supplements in feedlot cattle diets is not known. The objectives of this study were to determine the optimal inclusion of liquid supplementation to maximize growth performance and improve carcass characteristics, as well as estimate the energy value of liquid supplementation when used as a direct corn replacement, for feedlot steers fed a concentrate-based diet. Two hundred and eighty steer calves were stratified by BW into light (BW = 208 ± 9 kg; n = 24) and heavy (BW = 275 ± 8 kg; n = 16) pens. Pens within BW block were randomly assigned to 1 of 4 supplements: 1) dry at 4.5% inclusion (0LIQ), 2) liquid (a proprietary blend from Quality Liquid Feeds; Dodgeville, WI) at 4.5% inclusion (4.5LIQ), 3) liquid at 9% inclusion (9LIQ), or 4) liquid at 13.5% inclusion (13.5LIQ). The remainder of the diet was 47.5% to 55.5% dry rolled corn, 20% corn silage, and 20% modified wet distillers grains with solubles (DM basis). Data were analyzed as a randomized complete block design and linear and quadratic were examined to determine effects of increasing dietary concentrations of liquid. Steers fed 4.5LIQ and 9LIQ had greater (quadratic; P ≤ 0.05) final BW, HCW, and NEm and NEg, and less DMI as a percent of BW compared to steers fed 13.5LIQ. Steers fed 0LIQ were intermediate and not different from other treatments. However, ADG and total BW gain did not differ (P ≥ 0.15) among treatments. Despite the lack of treatment effect on live measures of gain, feeding steers 4.5LIQ and 9LIQ resulted in greater carcass ADG (quadratic; P = 0.03), total carcass gain (quadratic; P = 0.04), and more efficient carcass gain (quadratic; P ≤ 0.01) compared to carcasses from steers fed 13.5LIQ. Feeding steers a liquid supplement at 9% of the diet, DM allowed for the greatest final BW and ADG in this study; however, there was no benefit of increasing liquid to 13.5%.