bluuebunny/crossref_metadata_2025_split huggingface dataset:
A minimal-length approach unifies rigidity in underconstrained materials
Authors: Merkel Matthias , Baumgarten Karsten , Tighe Brian P. , Manning M. Lisa 
Published: March 2019

Significance
What do a guitar string and a balloon have in common? They are both floppy unless rigidified by geometric incompatibility. The same kind of rigidity transition in underconstrained materials has more recently been discussed in the context of disordered biopolymer networks and models for biological tissues. Here, we propose a general approach to quantitatively describe such transitions. Based on a minimal length function, which scales linearly with intrinsic fluctuations in the system and quadratically with shear strain, we make concrete predictions about the elastic response of these materials, which we verify numerically and which are consistent with previous experiments. Finally, our approach may help develop methods that connect macroscopic elastic properties of disordered materials to their microscopic structure.
Gliogenesis in the outer subventricular zone promotes enlargement and gyrification of the primate cerebrum
Authors: Rash Brian G. , Duque Alvaro , Morozov Yury M. , Arellano Jon I. , Micali Nicola , Rakic Pasko 
Published: March 2019

Significance
The formation of cortical convolutions of primates, including humans, is one of the most important subjects in developmental neuroscience, but the underlying mechanisms—considered mostly solved toward the end of the 20th century—have become controversial in the last decade. Recent studies suggest that a stem cell zone called the outer subventricular zone (oSVZ) induces gyri to form directly through neurogenesis. Here, we provide evidence in macaque monkey demonstrating that oSVZ neurogenesis is actually complete before gyrification begins and that a major function of the oSVZ is to produce the glial cells associated with the rapid expansion and folding of the cortical surface.
Imaging flow cytometry facilitates multiparametric characterization of extracellular vesicles in malignant brain tumours
Authors: Ricklefs Franz L. , Maire Cecile L. , Reimer Rudolph , Dührsen Lasse , Kolbe Katharina , Holz Mareike , Schneider Enja , Rissiek Anne , Babayan Anna , Hille Claudia , Pantel Klaus , Krasemann Susanne , Glatzel Markus , Heiland Dieter Henrik , Flitsch Jörg , Martens Tobias , Schmidt Nils Ole , Peine Sven , Breakefield Xandra O. , Lawler Sean , Chiocca E. Antonio. , Fehse Boris , Giebel Bernd , Görgens André , Westphal Manfred , Lamszus Katrin 
Published: March 2019

ABSTRACTCells release heterogeneous nano‐sized vesicles either as exosomes, being derived from endosomal compartments, or through budding from the plasma membrane as so‐called microvesicles, commonly referred to as extracellular vesicles (EVs). EVs are known for their important roles in mammalian physiology and disease pathogenesis and provide a potential biomarker source in cancer patients. EVs are generally often analysed in bulk using Western blotting or by bead‐based flow‐cytometry or, with limited parameters, through nanoparticle tracking analysis. Due to their small size, single EV analysis is technically highly challenging. Here we demonstrate imaging flow cytometry (IFCM) to be a robust, multiparametric technique that allows analysis of single EVs and the discrimination of distinct EV subpopulations. We used IFCM to analyse the tetraspanin (CD9, CD63, CD81) surface profiles on EVs from human and murine cell cultures as well as plasma samples. The presence of EV subpopulations with specific tetraspanin profiles suggests that EV‐mediated cellular responses are tightly regulated and dependent on cell environment. We further demonstrate that EVs with double positive tetraspanin expression (CD63+/CD81+) are enriched in cancer cell lines and patient plasma samples. In addition, we used IFCM to detect tumour‐specific GFP‐labelled EVs in the blood of mice bearing syngeneic intracerebral gliomas, indicating that this technique allows unprecedented disease modelling. In summary, our study highlights the heterogeneous and adaptable nature of EVs according to their marker profile and demonstrates that IFCM facilitates multiparametric phenotyping of EVs not only in vitro but also in patient plasma at a single EV level, with the potential for future functional studies and clinically relevant applications.Abbreviation: EDTA = ethylenediamine tetraacetic acid
Linearity of photovoltaic devices: quantitative assessment with N-lamp method
Authors: Müllejans Harald , Salis Elena 
Published: March 2019

Abstract
The short-circuit current output of photovoltaic (PV) reference device is typically used to determine the incident irradiance of natural or simulated sunlight. Normally the PV reference device is calibrated at standard test conditions and other irradiances are calculated based on a proportionality assumption (termed linearity) between short-circuit current output and incident irradiance. Here the linearity of PV devices is newly defined including a quantitative correction for non-linearity (NL) when measuring incident irradiance. Linearity can be determined experimentally by the flux addition principle such as in the two-lamp method. The latter provides information about linearity between two irradiance levels which differ by a factor of two, but no information on linearity inside this interval. Here this concept is extended to the N-lamp method. It is shown that this provides more detailed linearity information with low uncertainty. Measurements were made with an 11-lamp steady-state solar simulator and showed a NL deviation of 2% in the irradiance range from 100 W m−2 to 1100 W m−2 for the PV reference cell tested. The method is easily implemented, provides detailed quantitative linearity assessment at low cost and can be considered a primary method for linearity assessment, as it does not require any reference device.
Critical fields of Nb3Sn prepared for superconducting cavities
Authors: Keckert S , Junginger T , Buck T , Hall D , Kolb P , Kugeler O , Laxdal R , Liepe M , Posen S , Prokscha T , Salman Z , Suter A , Knobloch J 
Published: March 2019

Abstract
Nb3Sn is currently the most promising material other than niobium for future superconducting radiofrequency cavities. Critical fields above 120 mT in pulsed operation and about 80 mT in CW have been achieved in cavity tests. This is large compared to the lower critical field as derived from the London penetration depth, extracted from low field surface impedance measurements. In this paper direct measurements of the London penetration depth from which the lower critical field and the superheating field are derived are presented. The field of first vortex penetration is measured under DC and RF fields. The combined results confirm that Nb3Sn cavities are indeed operated in a metastable state above the lower critical field but are currently limited to a critical field well below the superheating field.
Energy-optimal strokes for multi-link microswimmers: Purcell's loops and Taylor's waves reconciled
Authors: Alouges François , DeSimone Antonio , Giraldi Laetitia , Or Yizhar , Wiezel Oren 
Published: March 2019

Abstract
Micron-scale swimmers move in the realm of negligible inertia, dominated by viscous drag forces. In this paper, we formulate the leading-order dynamics of a slender multi-link (N-link) microswimmer assuming small-amplitude undulations about its straight configuration. The energy-optimal stroke to achieve a given prescribed displacement in a given time period is obtained as the largest eigenvalue solution of a constrained optimal control problem. Remarkably, the optimal stroke is an ellipse lying within a two-dimensional plane in the (N – 1)-dimensional space of joint angles, where N can be arbitrarily large. For large N, the optimal stroke is a traveling wave of bending, modulo edge effects. If the number of shape variables is small, we can consider the same problem when the prescribed displacement in one time period is large, and not attainable with small variations of the joint angles. The fully nonlinear optimal control problem is solved numerically for the cases N = 3 (Purcell’s three-link swimmer) and N = 5 showing that, as the prescribed displacement becomes small, the optimal solutions obtained using the small-amplitude assumption are recovered. We also show that, when the prescribed displacements become large, the picture is different. For N = 3 we recover the non-convex planar loops already known from previous studies. For N = 5 we obtain non-planar loops, raising the question of characterizing the geometry of complex high-dimensional loops.
On-chip integration of single solid-state quantum emitters with a SiO2 photonic platform
Authors: Böhm Florian , Nikolay Niko , Pyrlik Christoph , Schlegel Jan , Thies Andreas , Wicht Andreas , Tränkle Günther , Benson Oliver 
Published: March 2019

Abstract
One important building block for future integrated nanophotonic devices is the scalable on-chip interfacing of single photon emitters and quantum memories with single optical modes. Here we present the deterministic integration of a single solid-state qubit, the nitrogen-vacancy (NV) center, with a photonic platform consisting exclusively of SiO2 grown thermally on a Si substrate. The platform stands out by its ultra-low fluorescence and the ability to produce various passive structures such as high-Q microresonators and mode-size converters. By numerical analysis an optimal structure for the efficient coupling of a dipole emitter to the guided mode could be determined. Experimentally, the integration of a preselected NV emitter was performed with an atomic force microscope and the on-chip excitation of the quantum emitter as well as the coupling of single photons to the guided mode of the integrated structure could be demonstrated. Our approach shows the potential of this platform as a robust nanoscale interface of on-chip photonic structures with solid-state qubits.
Hankel-total positivity of some sequences
Authors: Zhu Bao-Xuan 
Published: March 2019

The aim of this paper is to develop analytic techniques to deal with Hankel-total positivity of sequences.

We show two nonlinear operators preserving Stieltjes moment property of sequences. They actually both extend a result of Wang and Zhu that if

(

a
n

)

n
≥
0

(a_n)_{n\geq 0}

is a Stieltjes moment sequence, then so is

(

a

n
+
2

a

n

−

a

n
+
1

2

)

n
≥
0

(a_{n+2}a_{n}-a^2_{n+1})_{n\geq 0}

. Using complete monotonicity of functions, we also prove Stieltjes moment properties of the sequences

(

Γ
(

n

0

+
a
i
+
1
)

Γ
(

k

0

+
b
i
+
1
)

Γ
(
(

n
0

−

k
0

)
+
(
a
−
b
)
i
+
1
)

∏

j
=
0

m

1

d
j

i
+

e
j

)

i
≥
0

\left ( \frac {\Gamma (n_{0}+ai+1)}{{\Gamma (k_{0}+bi+1)} {\Gamma ((n_0-k_0)+(a-b)i+1)}}\prod _{j=0}^m\frac {1}{d_ji+e_j}\right )_{i\geq 0}

and

(

∑

k
≥
0

α
k

λ

k

n

)

n
≥
0

\left (\sum _{k\ge 0}\frac {\alpha _k}{\lambda _{k}^{n}}\right )_{n\geq 0}

. Particularly in a new unified manner our results imply the Stieltjes moment properties of binomial coefficients

(

p
n
+
r
−
1

n

)

\binom {pn+r-1}{n}

and Fuss-Catalan numbers

r

p
n
+
r

(

p
n
+
r

n

)

\frac {r}{pn+r}\binom {pn+r}{n}

proved by Mlotkowski, Penson, and Zyczkowski, and Liu and Pego, respectively, and also extend some results for log-convexity of sequences proved by Chen-Guo-Wang, Su-Wang, Yu, and Wang-Zhu, respectively.
The Difference Between Unfixed and Postfixation Placental Weight
Authors: Tambouret Rosemary , Jeck William R , Roberts Drucilla J 
Published: March 2019

ABSTRACT

Objectives
Reference values for placental weights correlated with gestational age are used in surgical pathology. Most reference values were established for fresh placentas. Some laboratories routinely fix all placentas, bringing into question the accuracy of the reference weight values. We wanted to determine the impact of fixation on placental weight.

Methods
One hundred placentas from uncomplicated pregnancies were weighed in the fresh state, after removal of the cord and membranes. After fixation in formalin for 1 day and 5 days, the placentas were reweighed. The change in weight for each placenta was analyzed by a two-tailed paired t test.

Results
Statistically, a small but significant gain in weight occurred after 24 hours (3.7%, P << .001), and there was no significant change identified in the additional 4 days (P = .51). Nine placentas lost weight with fixation; the weight of four was unchanged.

Conclusions
We consider formalin fixation to add a statistically significant but clinically negligible amount of weight to the placenta.
Ethnicity-Specific Changes in Cardiac Troponin T in Response to Acute Mental Stress and Ethnicity-Specific Cutpoints for the R Wave of the aVL Lead
Authors: Wentzel Annemarie , Malan Leoné , von Känel Roland , Malan Nicolaas T 
Published: March 2019

Abstract
Acute mental stressor–induced cardiac stress responses might contribute to excessive myocardial strain and resultant cardiovascular episode risk. We assessed ethnicity-specific acute cardiac stress (by measuring cardiac troponin T (cTnT) and N-terminal prohormone of brain natriuretic peptide) related to hemodynamic activity. The prospective Sympathetic Activity and Ambulatory Blood Pressure in Africans (SABPA) study was conducted during 2007–2008 in South Africa. In the cross-sectional phase of the SABPA study, 388 black and white participants underwent a 1-minute acute mental stressor, during which blood pressure was continuously measured. Fasting blood samples for cardiac stress markers were obtained before and 10 minutes after stress (% change). Resting 10-lead electrocardiogram measured the R wave of the aVL lead (RaVL). Black participants exhibited greater cardiac stress responses (P &lt; 0.001), diastolic blood pressure, total peripheral resistance, and stroke volume compared with white participants, who displayed decreases in cardiac stress and increases in cardiac output. Prestress and stressor cTnT cutpoints of 4.2 pg/mL predicted 24-hour, daytime, and nighttime diastolic hypertension in black participants (P &lt; 0.001). These cTnT cutpoints were associated with an ethnicity-specific RaVL cutpoint of 0.28 mV (odds ratio = 3.49, 95% confidence interval: 2.18, 5.83; P = 0.021). Acute mental stress elicited an α-adrenergic activation pattern and cardiac stress hyperreactivity only in black participants. Mental stress might increase the black population’s risk for ischemic episodes and heart disease.
Qatar Biobank Cohort Study: Study Design and First Results
Authors: Al Thani Asma , Fthenou Eleni , Paparrodopoulos Spyridon , Al Marri Ajayeb , Shi Zumin , Qafoud Fatima , Afifi Nahla 
Published: March 2019

Abstract
We describe the design, implementation, and results of the Qatar Biobank (QBB) cohort study for the first 10,000 participants. QBB is a prospective, population-based cohort study in Qatar, established in 2012. QBB’s primary goal was to establish a cohort accessible to the local and international scientific community, providing adequate health data and biological samples to enable evidence-based research. The study design is based on an agnostic hypothesis, collecting data using questionnaires, biological samples, imaging data, and -omics. QBB aims to recruit 60,000 participants, men and women, adult (aged ≥18 years) Qataris or long-term residents (≥15 years living in Qatar) and follow up with them every 5 years. Currently, QBB has reached 28% (n = 17,065) of the targeted enrollee population and more than 2 million biological samples. QBB is a multinational cohort including 33 different nationalities, with a relatively young population (mean age, 40.5 years) of persons who are highly educated (50% university-educated) and have high monthly incomes. The 4 main noncommunicable diseases found among the QBB population are dyslipidemia, diabetes, hypertension, and asthma with prevalences of 30.1%, 17.4%, 16.8%, and 9.1%, respectively. The QBB repository can provide data and biological samples sufficient to demonstrate valid associations between genetic and/or environmental exposure and disease development to scientists worldwide.
SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing
Authors: Wylie Dennis C , Hofmann Hans A , Zemelman Boris V 
Published: March 2019

Abstract

Motivation
We set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score—fold-change, test-statistic, P-value—comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies non-parametric kernel smoothing to uncover promoter motif sites that correlate with elevated differential expression scores. SArKS detects motif k-mers by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motif sites can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.

Results
We applied SArKS to published gene expression data representing distinct neocortical neuron classes in Mus musculus and interneuron developmental states in Homo sapiens. When benchmarked against several existing algorithms using a cross-validation procedure, SArKS identified larger motif sets that formed the basis for regression models with higher correlative power.

Availability and implementation
https://github.com/denniscwylie/sarks.

Supplementary information
Supplementary data are available at Bioinformatics online.
PedigreeNet: a web-based pedigree viewer for biological databases
Authors: Braun Bremen L , Schott David A , Portwood John L , Andorf Carson M , Sen Taner Z 
Published: March 2019

AbstractMotivationPlant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data.ResultsAs a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships.Availability and implementationPedigreeNet is accessible at https://www.maizegdb.org/breeders_toolbox. The open source code is publically and freely available at GitHub: https://github.com/Maize-Genetics-and-Genomics-Database/PedigreeNet.Supplementary informationSupplementary data are available at Bioinformatics online.
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
Authors: Yin John , Zhang Chao , Mirarab Siavash 
Published: March 2019

Abstract

Motivation
Evolutionary histories can change from one part of the genome to another. The potential for discordance between the gene trees has motivated the development of summary methods that reconstruct a species tree from an input collection of gene trees. ASTRAL is a widely used summary method and has been able to scale to relatively large datasets. However, the size of genomic datasets is quickly growing. Despite its relative efficiency, the current single-threaded implementation of ASTRAL is falling behind the data growth trends is not able to analyze the largest available datasets in a reasonable time.

Results
ASTRAL uses dynamic programing and is not trivially parallel. In this paper, we introduce ASTRAL-MP, the first version of ASTRAL that can exploit parallelism and also uses randomization techniques to speed up some of its steps. Importantly, ASTRAL-MP can take advantage of not just multiple CPU cores but also one or several graphics processing units (GPUs). The ASTRAL-MP code scales very well with increasing CPU cores, and its GPU version, implemented in OpenCL, can have up to 158× speedups compared to ASTRAL-III. Using GPUs and multiple cores, ASTRAL-MP is able to analyze datasets with 10 000 species or datasets with more than 100 000 genes in &lt;2 days.

Availability and implementation
ASTRAL-MP is available at https://github.com/smirarab/ASTRAL/tree/MP.

Supplementary information
Supplementary data are available at Bioinformatics online.
High burden of drug therapy in adult congenital heart disease: polypharmacy as marker of morbidity and mortality
Authors: Woudstra Odilia I , Kuijpers Joey M , Meijboom Folkert J , Post Marco C , Jongbloed Monique R M , Duijnhouwer Anthonie L , van Dijk Arie P J , van Melle Joost P , Konings Thelma C , Zwinderman Aeilko H , Mulder Barbara J M , Bouma Berto J 
Published: March 2019

Abstract

Aims
To assess medication use in adult congenital heart disease (ACHD) patients compared to the age- and sex-matched general population, identify patterns of pharmacotherapy, and analyse associations between pharmacotherapy and adverse outcomes in ACHD.

Methods and results
Data of 14 138 ACHD patients from the CONCOR registry [35 (24–48) years, 49% male] and age- and sex-matched referents (1:10 ratio) were extracted from the Dutch Dispensed Drug Register for the years 2006–14. Adult congenital heart disease patients had more cardiovascular and non-cardiovascular drugs than referents (median 3 vs. 1, P < 0.001). Polypharmacy, defined as ≥5 dispensed drug types yearly, was present in 30% of ACHD and 15% of referents {odds ratio [OR] = 2.47 [95% confidence interval (CI) 2.39–2.54]}. Polypharmacy was independently associated with female sex [OR = 1.92 (95% CI 1.88–1.96)], older age [for men: OR = 2.3/10 years (95% CI 2.2–2.4) and for women: OR = 1.6/10 years (95% CI 1.5–1.6); Pinteraction < 0.001], and ACHD severity [mild: OR = 2.51 (95% CI 2.40–2.61), moderate: OR = 3.22 (95% CI 3.06–3.40), severe: OR = 4.87 (95% CI 4.41–5.38)]. Cluster analysis identified three subgroups with distinct medication patterns; a low medication use group (8-year cumulative survival: 98%), and a cardiovascular and comorbidity group with lower survival (92% and 95%, respectively). Cox regression revealed a strong association between polypharmacy and mortality [hazard ratio (HR) = 3.94 (95% CI 3.22–4.81)], corrected for age, sex, and defect severity. Polypharmacy also increased the risk of hospitalization for adverse drug events [HR = 4.58 (95% CI 2.04–10.29)].

Conclusion
Both cardiovascular and non-cardiovascular medication use is high in ACHD with twice as much polypharmacy compared with the matched general population. Patients with polypharmacy had a four-fold increased risk of mortality and adverse drug events. Recognition of distinct medication patterns can help identify patients at highest risk. Drug regimens need repeating evaluation to assess the appropriateness of all prescriptions. More high-quality studies are needed to improve ACHD care with more evidence-based pharmacotherapy.