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Generation of Shear Waves by Laser in Soft Media in the Ablative and Thermoelastic Re...
Pol Grasland-Mongrain
Yuankang Lu

Pol Grasland-Mongrain

and 1 more

January 07, 2016
This article describes the generation of elastic shear waves in a soft medium using a laser beam. Our experiments show two different regimes depending on laser energy. Physical modeling of the underlying phenomena reveals a thermoelastic regime caused by a local dilatation resulting from temperature increase, and an ablative regime caused by a partial vaporization of the medium by the laser. Computed theoretical displacements are close to experimental measurements. A numerical study based on the physical modeling gives propagation patterns comparable to those generated experimentally. These results provide a physical basis for the feasibility of a shear wave elastography technique (a technique which measures a soft solid stiffness from shear wave propagation) by using a laser beam.
Pharmit: Interactive Exploration of Chemical Space
Jocelyn Sunseri
David Koes

Jocelyn Sunseri

and 1 more

January 07, 2016
Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape, and energy minimization. Users can import, create, and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license.
Thermodynamics of the magnetocaloric effect in the swept field and stepped field meas...
Yasu Takano
Nathanael A. Fortune

Yasu Takano

and 1 more

November 14, 2015
ENERGY CONSERVATION IN SWEPT FIELD LIMIT For a calorimeter sample (plus addenda) weakly thermally linked to a temperature controlled reservoir, energy conservation implies -T dS = \kappa \Delta T dt + C_{} dT where κ is the sample to reservoir thermal conductance and addenda is the heat capacity of the actual addenda (such as the thermometer, heater, and glue or grease binding the sample to the sensors) plus the heat capacity of the sample lattice (due to phonons). The left hand side term is the heat released by the system — which in the case of a spin system, for example, would be the heat released by the spins — when the field is changed by dH. The minus sign indicates that system entropy decreases as heat is released. Most of the released heat flows to the reservoir but some fraction heats up the addenda (to the same temperature as the system). The first term on the right hand side describes heat flow to the reservoir. The second term describes the temperature rise of the addenda. In a non-adiabatic relaxation-time or ac-calorimeter like that used in our swept-field measurements , the first term dominates. In contrast, in an adiabatic measurement, the first term is negligible.
The Rainfall Annual Cycle Bias over East Africa in CMIP5 Coupled Climate Models
Wenchang Yang

Wenchang Yang

November 05, 2015
East Africa has two rainy seasons: the long rains (March–May, MAM) and the short rains (October–December, OND). Most CMIP3/5 coupled models overestimate the short rains while underestimating the long rains. In this study, the East African rainfall bias is investigated by comparing the coupled historical simulations from CMIP5 to the corresponding SST-forced AMIP simulations. Much of the investigation is focused on the MRI-CGCM3 model, which successfully reproduces the observed rainfall annual cycle in East Africa in the AMIP experiment but its coupled historical simulation has a similar but stronger bias as the coupled multimodel mean. The historical−AMIP monthly climatology rainfall bias in East Africa can be explained by the bias in the convective instability (CI), which is dominated by the near surface moisture static energy (MSE) and ultimately by the MSE’s moisture component. The near surface MSE bias is modulated by the sea surface temperature (SST) over the western Indian Ocean. The warm SST bias in OND can be explained by both insufficient ocean dynamical cooling and latent flux, while the insufficient short wave radiation and excess latent heat flux mainly contribute to the cool SST bias in MAM.
White matter connectivity differences converge with gene expression in a neurodevelop...
Joe Bathelt

Joe Bathelt

October 29, 2015
ABSTRACT Knowledge of genetic cause in neurodevelopmental disorders can highlight molecular and cellular processes critical for typical development. Furthermore, the relative homogeneity of neurodevelopmental disorders of known genetic origin allows the researcher to establish the subsequent neurobiological processes that mediate cognitive and behavioural outcomes. The current study investigated white matter structural connectivity in a group of individuals with intellectual disability due to mutations in _ZDHHC9_. In addition to shared cause of cognitive impairment, these individuals have a shared cognitive profile, involving oro-motor control difficulties and expressive language impairment. Analysis of structural network properties using graph theory measures showed global reductions in mean clustering coefficient and efficiency in the _ZDHHC9_ group, with maximal differences in frontal and parietal areas. Regional variation in clustering coefficient across cortical regions in _ZDHHC9_ mutation cases was significantly associated with known pattern of expression of _ZDHHC9_ in the normal adult human brain. The results demonstrate that a mutation in a single gene impacts upon white matter organisation across the whole-brain, but also shows regionally specific effects, according to variation in gene expression. Furthermore, these regionally specific patterns may link to specific developmental mechanisms, and correspond to specific cognitive deficits.
DNA barcoding and taxonomy: dark taxa and dark texts
Roderic Page

Roderic Page

October 20, 2015
Summary Both classical taxonomy and DNA barcoding are engaged in the task of digitising the living world. Much of the taxonomic literature remains undigitised. The rise of open access publishing this century, and the freeing of older literature from the shackles of copyright has greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late twentieth century remains offline ("dark texts"). DNA barcoding is generating a wealth of computable data that in many ways is much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These "dark taxa" hamper the classical method of integrating biodiversity data using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature, and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global "digital dashboard" to assess the extent to which biodiversity data is available online. Keywords: DNA barcoding, taxonomy, dark taxa, dark texts, digitisation
Curriculum Vitae: Alyssa A. Goodman
Alyssa Goodman

Alyssa Goodman

October 15, 2015
---------- ------------------------------------------ NAME Alyssa A. Goodman OFFICE Astronomy Department, Harvard University Cambridge, MA 02138, 617-495-9278 HOME 485 Concord Avenue, Lexington, MA 02421 WEB SITE scholar.harvard.edu/agoodman ORIGIN July 1, 1962, New York, New York ---------- ------------------------------------------
Fragment Oriented Molecular Shapes
Ethan Hain
Awaiting Activation

Ethan Hain

and 2 more

September 11, 2015
Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here we introduce and evaluate Fragment Oriented Molecular Shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of _shape constraints_, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search.
Open Source Molecular Modeling
David Koes
Somayeh Pirhadi

David Koes

and 2 more

August 27, 2015
The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry.
Asteroseismology Can Reveal Strong Internal Magnetic Fields in Red Giant Stars
Jim Fuller
Matteo Cantiello

Jim Fuller

and 4 more

July 21, 2015
_This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution. The definitive version was published in Science on Vol. 350 no. 6259 pp. 423-426 , DOI: 10.1126/science.aac6933_ Internal stellar magnetic fields are inaccessible to direct observations and little is known about their amplitude, geometry and evolution. We demonstrate that strong magnetic fields in the cores of red giant stars can be identified with asteroseismology. The fields can manifest themselves via depressed dipole stellar oscillation modes, which arises from a magnetic greenhouse effect that scatters and traps oscillation mode energy within the core of the star. The _Kepler_ satellite has observed a few dozen red giants with depressed dipole modes which we interpret as stars with strongly magnetized cores. We find field strengths larger than $\sim\! 10^5 \,{\rm G}$ may produce the observed depression, and in one case we infer a minimum core field strength of $\approx \! \! 10^7 \,{\rm G}$.
Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files
Jennifer Shelton
Sue Brown

Jennifer Shelton

and 1 more

July 16, 2015
As the sheer volume of bioinformatic sequence data increases, the only way to take advantage of this content is to more completely automate robust analysis workflows. Analysis bottlenecks are often mundane and overlooked processing steps. Idiosyncrasies in reading and/or writing bioinformatics file formats can halt or impair analysis workflows by interfering with the transfer of data from one informatics tools to another. Fasta-O-Matic automates handling of common but minor format issues that otherwise may halt pipelines. The need for automation must be balanced by the need for manual confirmation that any formatting error is actually minor rather than indicative of a corrupt data file. To that end Fasta-O-Matic reports any issues detected to the user with optionally color coded and quiet or verbose logs. Fasta-O-Matic can be used as a general pre-processing tool in bioinformatics workflows (e.g. to automatically wrap FASTA files so that they can be read by BioPerl). It was also developed as a sanity check for bioinformatic core facilities that tend to repeat common analysis steps on FASTA files received from disparate sources. Fasta-O-Matic can be set with format requirements specific to downstream tools as a first step in a larger analysis workflow. Fasta-O-Matic is available free of charge to academic and non-profit institutions at https://github.com/i5K-KINBRE-script-share/read-cleaning-format-conversion/tree/master/KSU_bioinfo_lab/fasta-o-matic.
Publication bias evaluations are not routinely conducted in clinical oncology systema...
David Herrmann
Sarah Khan

David Herrmann

and 4 more

July 13, 2015
Background: Publication bias (PB) can cause an exaggerated estimate of summary effects in systematic reviews (SR). The extent of PB assessment by SRs within oncology journals remains to be determined. Methods: This study looked at SRs from high impact factor oncology journals between 2007 and 2015 using a PubMed search. Articles were sorted and coded for PB. An additional assessment of BP from unevaluated SRs was performed using Egger’s regression and the trim-and-fill method. Findings: Of 182 included SRs, 52 preformed a PB assessment. The most common form of assessment was a funnel plot supplemented by Egger’s regression or Begg’s test (44%, 23/52). PB was a routine finding in these SRs (19%, 10/52). SRs that stated following a reporting guideline frequently failed to do so with regards to assessing PB. The magnitude of effect sizes generally decreased when conducting our independent assessments of PB among SRs in our sample that did not evaluate for it. Interpretation: Our study shows that there exists an underutilization of PB assessments by SRs in clinical oncology. Additionally the methodological validity of SRs can be increased by adhering to reporting guidelines, and through the search of grey literature and clinical trials registries. Funding: No external source of funding
Public-Friendly Open Science
Matteo Cantiello

Matteo Cantiello

July 10, 2015
PREVIOUS “A “MODERN SCIENTIST” MANIFESTO” In the 21st century science is growing more technical and complex, as we gaze further and further while standing on the shoulders of many generations of giants. The public has often a hard time understanding research and its relevance to society. One of the reasons for this is that scientists do not spend enough time communicating their findings outside their own scientific community. Obviously there are some exceptions, but THE RULE IS THAT SCIENTISTS WRITE CONTENT FOR SCIENTISTS. Academia is often perceived as an ivory tower, and when new findings are shared with the outside world, this is not done by scientists, but by the media or even the political class. The problem is that these external agents do not have the necessary background to digest and properly communicate this knowledge with the rest of society. They often misunderstand, over-hype and in some case even distort the results and views of the scientific community. IT’S IRONIC AND SOMEWHAT FRIGHTENING THAT THE DISCOVERIES AND RECOMMENDATIONS FOR WHICH SOCIETY INVESTS SUBSTANTIAL ECONOMIC AND HUMAN CAPITAL, ARE NOT DIRECTLY DISSEMINATED BY THE PEOPLE WHO REALLY UNDERSTAND THEM. At the same time transparency and reproducibility are at stake in the increasingly complex world of research, which is still using old-fashioned tools when packaging and sharing content. This is not only a big problem for research itself, but can give science a bad name in front of the public opinion, which increasingly does not understand and trust the work of scientists. To the average tax-payer science is often cryptic, with most recently published papers behind a pay-wall and the majority of research virtually inscrutable. In this scenario it is hard for the public to access and capture the relevance of scientists’ work. I strongly believe that a society that does not trust its scientists is set on a dangerous course. ACTION ITEMS. To improve the situation 21st century scientists need to: 1. Learn to efficiently share and communicate their research with the public at large. 2. Make their research more transparent and reproducible, so that it can be trusted and better understood by their peers and the public at large. 21st century scientists need to produce “PUBLIC-FRIENDLY OPEN SCIENCE” (PFOS).
From Walras’ auctioneer to continuous time double auctions: A general dynamic theory...
Jonathan Donier
Awaiting Activation

Jonathan Donier

and 1 more

July 08, 2015
In standard Walrasian auctions, the price of a good is defined as the point where the supply and demand curves intersect. Since both curves are generically regular, the response to small perturbations is linearly small. However, a crucial ingredient is absent of the theory, namely transactions themselves. What happens after they occur? To answer the question, we develop a dynamic theory for supply and demand based on agents with heterogeneous beliefs. When the inter-auction time is infinitely long, the Walrasian mechanism is recovered. When transactions are allowed to happen in continuous time, a peculiar property emerges: close to the price, supply and demand vanish quadratically, which we empirically confirm on the Bitcoin. This explains why price impact in financial markets is universally observed to behave as the square root of the excess volume. The consequences are important, as they imply that the very fact of clearing the market makes prices hypersensitive to small fluctuations.
Quality of systematic review and meta-analysis abstracts in oncology journals
Chelsea Koller
Sarah Khan

Chelsea Koller

and 6 more

July 04, 2015
Abstract Purpose: The purpose of this study was to evaluate the quality of reporting in the abstracts of oncology systematic reviews using PRISMA guidelines for abstract writing. Methods: Oncology systematic reviews and meta-analyses from four journals - The Lancet Oncology, Clinical Cancer Research, Cancer Research, and Journal of Clinical Oncology - were selected using a PubMed search. The resulting 337 abstracts were sorted for eligibility and 182 were coded based on a standardized abstraction manual constructed from the PRISMA criteria. Eligible systematic reviews were coded independently and later verified by a second coder, with disagreements handled by consensus. One hundred eighty-two abstracts comprised the final sample. Results: The number of included studies, information regarding main outcomes, and general interpretation of results were described in the majority of abstracts. In contrast, risk of bias or methodological quality appraisals, the strengths and limitations of evidence, funding sources, and registration information were rarely reported. By journal, the most notable difference was a higher percentage of funding sources reported in Lancet Oncology. No detectable upward trend was observed on mean abstract scores after publication of the PRISMA extension for abstracts. Conclusion: Overall, the reporting of essential information in oncology systematic review and meta-analysis abstracts is suboptimal and could be greatly improved. Keywords: Review, Systematic; Meta-Analysis; Cancer; Medical Oncology; Abstracting as Topic; Funding
Utilization of clinical trials registries in obstetrics and gynecology systematic rev...
Michael Bibens
A. Benjamin Chong

Michael Bibens

and 2 more

June 29, 2015
ABSTRACT Objectives: We evaluated the use of clinical trials registries in published obstetrics and gynecological systematic reviews and meta-analyses. Methods: A review of publications between January 1, 2007, and December 31, 2015, from six obstetrical and gynecological journals (_Obstetrics & Gynecology, Obstetrical & Gynecological Survey, Human Reproduction Update, Gynecologic Oncology, British Journal of Obstetrics and Gynaecology, and American Journal of Obstetrics & Gynecology_) was completed to identify eligible systematic reviews. All systematic reviews included after exclusions were independently reviewed to determine if clinical trials registries had been included as part of the search process. Studies that reported using a trials registry were further examined to determine whether trial data was included in the analysis. Results: Our initial search resulted in 292 articles, which was narrowed to 256 after exclusions. Of the 256 systematic reviews meeting our selection criteria, 47 utilized a clinical trials registry. Eleven of the 47 systematic reviews found unpublished data, and added the unpublished trial data into their results. Conclusion: A majority of systematic reviews in clinical obstetrics and gynecology journals do not conduct searches of clinical trials registries or do not make use of data obtained from these searches.
Factual errors in a recent paper by Westerhof, Segers and Westerhof in Hypertension
Kim H. Parker
Alun Hughes

Kim H. Parker

and 1 more

June 16, 2015
But facts are chiels that winna ding An downa be disputed – from _A Dream_ by Robert Burns (1786) (But facts are fellows that will not be overturned, And cannot be disputed) _Wave separation, wave intensity, the reservoir-wave concept, and the instantaneous wave-free ratio (2015) N Westerhof, P Segers and BE Westerhof, Hypertension, DOI: 10.1161/HYPERTENSIONAHA.115.05567_ Hereinafter referred to as [WSW]. This paper by three distinguished workers in the field of cardiovascular mechanics, concludes that both the reservoir pressure and instantaneous wave-free ratio are ’... both physically incorrect, and should be abandoned’. These are very strong conclusions which, if they were opinions could only be debated. Reading the paper in detail, however, reveals that it contains numerous factual errors in their discussion of these two entities. Since facts are different from opinions, we believe that it is essential that these errors be corrected before they gain credence by repetition. False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for every one takes a salutary pleasure in proving their falseness. – Charles Darwin (1871) Because we are naturally prejudiced about the validity of both the reservoir pressure (Pres) and instantaneous wave-free ratio (iFR), having been involved in the conception and development of both ideas, we will try to present our arguments as transparently and fairly as possible. As far as possible we will demonstrate the errors by direct quotations from the paper. The whole paper¹ is available from the Hypertension web site and should be consulted directly if there are any questions about our treatment of the text. Approximately two thirds of the paper is taken up with a discussion of wave separation and wave intensity from the point of view of the more usual Fourier-based methods of analysing cardiovascular mechanics, frequently called the impedance method. This part of the paper is, as far as we can see, both insightful and free of major errors. We found some of the discussion about wave intensity analysis thought-provoking and agree with most of their conclusions. We recommend the first two-thirds of this paper to anyone interested in arterial mechanics. In contrast, the last third of the paper, starting with the final sentence of the section ’Summary of Wave Separation and WIA’ is riddled with errors of interpretation and, more importantly, contains a number of mistakes (or in Darwin’s terms ’false statements of fact’) that need to be corrected. Instead of dealing with these errors chronologically, we will point out the fundamental errors first and then deal with their sequelae.
Participatory action research about Figshare user experiences at the University of Me...
Cobi Calyx
Awaiting Activation

Cobi Calyx

and 1 more

June 11, 2015
Participation & feedback are welcome! Please email me on cobi.smith@unimelb.edu.au (which is treated as private unless you explicitly consent to sharing) or tweet [@cobismith](https://twitter.com/cobismith) (public) if you'd prefer not to comment on this working paper using Authorea's features. Please note this is an open notebook and is intended to be part of an open science research project, which means if you choose to share information here your contributions are in the public domain. See the University of Melbourne research protocols for more information: http://www.orei.unimelb.edu.au/content/when-approval-needed
Transcranial Direct Current Stimulation: Theory, Treatment of Major Depressive Disord...
Shan H. Siddiqi

Shan H. Siddiqi

June 04, 2015
BACKGROUND AND THEORY The use of non-invasive brain stimulation for the treatment of various neuropsychiatric disorders, including major depressive disorder (MDD), has rapidly expanded recently. Transcranial direct current electrical stimulation (tDCS), variants of which have been used experimentally for psychiatric , neurologic , and physical rehabilitation applications, has garnered a great deal of attention. While it is not yet FDA-approved for any indication, its promise is related to its low cost and wide range of applications; although the breadth of its applicability has been questioned due to heterogeneous data , this heterogeneity has been attributed to methodological variability . The safety and tolerability of tDCS were outlined by an early study including 567 sessions in 102 patients. The most common adverse effects were mild tingling/itching at the stimulation site and moderate fatigue. Less frequent effects included headaches (11.8%), nausea (2.9%), and insomnia (0.98%), all of which were mild and transient . The underlying theory is that tDCS modulates the excitability of certain cortical regions by passage of a small electrical current through conducting pads applied to the scalp in a minimally painful manner. While the precise mechanism is not fully understood, it likely enhances cortical excitability at the anode and depresses it at the cathode . Proposed mechanisms have been based on data demonstrating relationships between tDCS stimulation and neuropharmacologic effects, cortical electrophysiology, and functional neuroimaging changes. Effects of tDCS on neuroplasticity and cortical excitability have been shown to be differentially modulated by agents affecting neurotransmission via serotonin (citalopram), dopamine (L-dopa), NMDA (dextromethorphan and d-cycloserine), and GABA (lorazepam). Electrophysiologic changes include differential modulation in the presence of agents that modulate sodium channels (carbamazepine) and calcium channels (flunarizine) . Active tDCS shows significant increases in prefrontal cortex activity as measured by functional near infrared spectroscopy (fNIRS), a technique used to measure cortical oxygenation, during and after stimulation – notably, fNIRS measurements may be limited by interference due extracranial blood flow and inability to assess deeper structures, so they merely approximate the functional magnetic resonance imaging (fMRI) signal in superficial structures . Stimulation also increases fMRI activation and connectivity of the underlying cortical regions and hippocampi, though the clinical significance of this is uncertain given that this same study found no behavioral changes .
A Framework for Mitigating the Biases in Barometric Dust Devil Surveys...
Brian Jackson

Brian Jackson

May 27, 2015
BACKGROUND Dust devils are small-scale (few to many tens of meters) low-pressure vortices rendered visible by lofted dust. They usually occur in arid climates on the Earth and ubiquitously on Mars. Martian dust devils have been studied with orbiting and landed spacecraft and were first identified on Mars using images from the Viking Orbiter . On Mars, dust devils may dominate the supply of atmospheric dust and influence climate , pose a hazard for human exploration , and they may have lengthened the operational lifetime of Martian rovers . On the Earth, dust devils significantly degrade air quality in arid climates and may pose an aviation hazard . The dust-lifting capacity of dust devils seems to depend sensitively on their structures, in particular on the pressure wells at their centers , so the dust supply from dust devils on both planets may be dominated by the seldom-observed larger devils. Using a martian global climate model, showed that observed seasonal variations in Mars’ near-surface temperatures could not be reproduced without including the radiative effects of dust and estimated the dust contributes more than 10 K of heating to the heating budget. Thus, elucidating the origin, evolution, and population statistics of dust devils is critical for understanding important terrestrial and Martian atmospheric properties and for in-situ exploration of Mars. Studies of Martian dust devils have been conducted through direct imaging of the devils and identification of their tracks on Mars’ dusty surface \citep[cf.][]{Balme_2006}. Studies with in-situ meteorological instrumentation have also identified dust devils, either via obscuration of the Sun by the dust column or their pressure signals . Studies have also been conducted of terrestrial dust devils and frequently involve in-person monitoring of field sites. Terrestrial dust devils are visually surveyed , directly sampled , or recorded using in-situ meteorological equipment . As noted in , in-person visual surveys are likely to be biased toward detection of larger, more easily seen devils. Such surveys would also fail to recover dustless vortices . Recently, terrestrial surveys similar to Martian dust devil surveys have been conducted using in-situ single barometers and photovoltaic sensors . These sensor-based terrestrial surveys have the advantage of being directly analogous to Martian surveys and are highly cost-effective compared to the in-person surveys (in a dollars per data point sense). In single-barometer surveys, a sensor is deployed in-situ and records a pressure time series at a sampling period ≲1 s. Since it is a low-pressure convective vortex, a dust devil passing nearby will register as pressure dip discernible against a background ambient (but not necessarily constant) pressure. Figure [fig:conditioning_detection_b_inset] from shows a time-series with a typical dust devil signal.
How structure-directing agents control nanocrystal shape: PVP-mediated growth of Ag n...
Tonnam Balankura

Tonnam Balankura

May 25, 2015
KINETIC WULFF PLOT Away from equilibrium, the NC shape is governed by the kinetics of inter- and intrafacet atom diffusion, as well as by the kinetics of deposition to various facets. At nonequilibrium growth conditions, the resulting shapes are expected to be different from the thermodynamic shapes. Examples of well-known kinetic shapes include nanowires and highly branched (bi- and tripods) structures . When NCs grow beyond a critical size, the relative atom deposition rate to various facets becomes a major influence in the NC shape. In this kinetically-controlled growth regime, the kinetic Wulff construction can predict the shape evolution of faceted crystal growth based on the surface kinetics . Using 3-dimensional shape evolution calculation method , we correlate the relative flux of Ag atom deposition to {111} and {100} facets $}{F_{100}}$ and the resulting kinetic Wulff shape in the reversible octahedron-to-cube transformation. This transformation is observed in the seed-mediated growth of Ag NCs , in which the shape-controlling parameter is the concentration of poly(vinylpyrrolidone) (PVP) in the solution. The constructed kinetic Wulff plot is shown in Fig. [fig:kinetic-wulff]. The construction of the kinetic Wulff plot is described in the supporting information. When the relative flux to {111} facets is less than half of the flux to {100} facets, the octahedra is predicted as the kinetic Wulff shape. As $}{F_{100}}$ increases, we observe a shape progression from octahedra to cubo-octahedra, then to truncated cubes, and eventually to cubes at $}{F_{100}} \geq $. To study the mechanism by which SDAs impart shape selectivity, we use the seed-mediated Ag polyol synthesis in the presence of PVP as our model. We utilize large-scale MD simulations to quantify F₁₀₀ and F₁₁₁ using _in-silico_ deposition and potential of mean force calculation.
Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaf...
Jennifer Shelton
Cassondra Coleman

Jennifer Shelton

and 7 more

May 20, 2015
BACKGROUND: Genome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes. RESULTS: We used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the _Tribolium castaneum_ genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the _T. castaneum_ sequence assembly, more than tripling its N50 with the program Stitch. CONCLUSIONS: In this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the _T. castaneum_ genome. KEYWORDS: Genome map; BioNano; Genome scaffolding; Genome validation; Genome finishing
A prevalence of dynamo-generated magnetic fields in the cores of intermediate-mass st...
Dennis
Matteo Cantiello

Dennis

and 4 more

May 17, 2015
_This is the author’s version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Nature on 04 January 2016, DOI:10.1038/nature16171_ Magnetic fields play a role in almost all stages of stellar evolution . Most low-mass stars, including the Sun, show surface fields that are generated by dynamo processes in their convective envelopes . Intermediate-mass stars do not have deep convective envelopes , although 10% exhibit strong surface fields that are presumed to be residuals from the stellar formation process . These stars do have convective cores that might produce internal magnetic fields , and these might even survive into later stages of stellar evolution, but information has been limited by our inability to measure the fields below the stellar surface . Here we use asteroseismology to study the occurrence of strong magnetic fields in the cores of low- and intermediate-mass stars. We have measured the strength of dipolar oscillation modes, which can be suppressed by a strong magnetic field in the core , in over 3,600 red giant stars observed by . About 20% of our sample show mode suppression but this fraction is a strong function of mass. Strong core fields only occur in red giants above 1.1 solar masses (1.1), and the occurrence rate is at least 60% for intermediate-mass stars (1.6–2.0), indicating that powerful dynamos were very common in the convective cores of these stars.
Reanalyzing Head et al. (2015): No widespread p-hacking after all?
C.H.J. Hartgerink

C.H.J. Hartgerink

May 06, 2015
Statistical significance seeking (i.e., p-hacking) is a serious problem for the validity of research, especially if it occurs frequently. Head et al. provided evidence for widespread p-hacking throughout the sciences, which would indicate that the validity of science is in doubt. Previous substantive concerns about their selection of p-values indicated they were too liberal in selecting all reported p-values, which would result in including results that would not be interesting to have been p-hacked. Despite this liberal selection of p-values Head et al. found evidence for p-hacking, which raises the question why p-hacking was detected despite it being unlikely a priori. In this paper I reanalyze the original data and indicate Head et al. their results are an artefact of rounding in the reporting of p-values.
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