bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated photonic devices in single crystal diamond
Authors: Mi Sichen , Kiss Marcell , Graziosi Teodoro , Quack Niels 
Published: June 2020

AbstractThe field of diamond photonics is reviewed, with a focus on recent experimental demonstrations of photonic integrated devices in a single crystal diamond. This field leverages the outstanding material properties of diamond with the aim to establish large-scale integrated photonics for applications in sensing, information and communication technologies, and optomechanics. Accordingly, this review introduces recent progress in scalable micro- and nano-fabrication techniques for single crystal diamond photonic integrated devices, and provides quantitative comparative evaluation of the performance of the state of the art devices. The review concludes with an outlook of the potential of photonic integrated circuits in single crystal diamond.
Thermal behavior of materials in laser-assisted extreme manufacturing: Raman-based novel characterization
Authors: Wang Ridong , Xu Shen , Yue Yanan , Wang Xinwei 
Published: June 2020

Abstract
Laser-assisted manufacturing (LAM) is a technique that performs machining of materials using a laser heating process. During the process, temperatures can rise above over 2000 °C. As a result, it is crucial to explore the thermal behavior of materials under such high temperatures to understand the physics behind LAM and provide feedback for manufacturing optimization. Raman spectroscopy, which is widely used for structure characterization, can provide a novel way to measure temperature during LAM. In this review, we discuss the mechanism of Raman-based temperature probing, its calibration, and sources of uncertainty/error, and how to control them. We critically review the Raman-based temperature measurement considering the spatial resolution under near-field optical heating and surface structure-induced asymmetries. As another critical aspect of Raman-based temperature measurement, temporal resolution is also reviewed to cover various ways of realizing ultrafast thermal probing. We conclude with a detailed outlook on Raman-based temperature probing in LAM and issues that need special attention.
Concordance of Embedded Performance and Symptom Validity Tests and Associations with Mild Traumatic Brain Injury and Posttraumatic Stress Disorder among Post-9/11 Veterans
Authors: Aase Darrin M , Soble Jason R , Shepard Paula , Akagi Kouri , Schroth Christopher , Greenstein Justin E , Proescher Eric , Phan K Luan 
Published: June 2020

Abstract

Objective
The present study explored both embedded symptom (SVT) and performance (PVT) validity test scores within a post-9/11 veteran sample to elucidate the degree to which there is concordance between validity indicators, as well as how frequently one SVT and four PVT indicators were failed in screened mild traumatic brain injury (mTBI) and diagnosed posttraumatic stress disorder (PTSD).

Method
A total of 114 post-9/11 veterans were evaluated utilizing the Neurobehavioral Symptom Inventory (NSI) Validity-10, four embedded PVTs, mTBI screening, and a diagnostic interview for PTSD.

Results
While we found concordance between embedded PVTs and the NSI Validity-10 at select cutoffs (i.e., ≥13, ≥19), symptom and performance validity indicators were clinically dissociable in that only SVT significantly predicted diagnosed PTSD and screened mTBI.

Conclusions
Dissociation between symptom and performance validity may be clinically useful when interpreting neuropsychological evaluation findings in post-9/11 veterans with a history of mTBI or PTSD.
Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development
Authors: Hsiao Yi , Su Bo-Han , Tseng Yufeng J 
Published: June 2020

Abstract
In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these preclinical endpoints have each been developed in the past decades. However, only a few web-based tools have integrated different models to provide a simple one-step platform to help researchers thoroughly evaluate potential drug candidates. To efficiently achieve this approach, a platform for preclinical evaluation must not only predict key ADMET (absorption, distribution, metabolism, excretion and toxicity) properties but also provide some guidance on structural modifications to improve the undesired properties. In this review, we organized and compared several existing integrated web servers that can be adopted in preclinical drug development projects to evaluate the subject of interest. We also introduced our new web server, Virtual Rat, as an alternative choice to profile the properties of drug candidates. In Virtual Rat, we provide not only predictions of important ADMET properties but also possible reasons as to why the model made those structural predictions. Multiple models were implemented into Virtual Rat, including models for predicting human ether-a-go-go-related gene (hERG) inhibition, cytochrome P450 (CYP) inhibition, mutagenicity (Ames test), blood–brain barrier penetration, cytotoxicity and Caco-2 permeability. Virtual Rat is free and has been made publicly available at https://virtualrat.cmdm.tw/.
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)
Authors: Touré Vasundra , Vercruysse Steven , Acencio Marcio Luis , Lovering Ruth C , Orchard Sandra , Bradley Glyn , Casals-Casas Cristina , Chaouiya Claudine , del-Toro Noemi , Flobak Åsmund , Gaudet Pascale , Hermjakob Henning , Hoyt Charles Tapley , Licata Luana , Lægreid Astrid , Mungall Christopher J , Niknejad Anne , Panni Simona , Perfetto Livia , Porras Pablo , Pratt Dexter , Saez-Rodriguez Julio , Thieffry Denis , Thomas Paul D , Türei Dénes , Kuiper Martin 
Published: June 2020

Abstract

Motivation
A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources.

Results
Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources.

Availability and implementation
The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST

Supplementary information
Supplementary data are available at Bioinformatics online.
Short-term resilience of Great Gray Owls to a megafire in California, USA
Authors: Siegel Rodney B , Eyes Stephanie A , Tingley Morgan W , Wu Joanna X , Stock Sarah L , Medley Joseph R , Kalinowski Ryan S , Casas Angeles , Lima-Baumbach Marcie , Rich Adam C 
Published: June 2020

ABSTRACT
Throughout western North America, longer, hotter fire seasons and dense fuels are yielding more frequent, larger, and higher-severity wildfires, including uncharacteristically large “megafires.” Wildlife species associated with late-seral forest characteristics may be particularly vulnerable to habitat loss stemming from changing fire regimes. The Great Gray Owl (Strix nebulosa) is a state-listed endangered species in California that typically nests in large snags in well-shaded forests adjacent to montane meadows. The 2013 Rim Fire burned 104,000 ha in Yosemite National Park and Stanislaus National Forest, making it the largest recorded fire in California’s Sierra Nevada. The fire perimeter contained 23 meadows known to be occupied by Great Gray Owls during the decade prior to the fire, representing nearly a quarter of all known or suspected territories in California at the time. We analyzed 13 yr (2004–2016) of Great Gray Owl detection/non-detection data from 144 meadows in the central Sierra Nevada, including meadows inside and outside the Rim Fire perimeter in Yosemite National Park and on Stanislaus National Forest. During 3 yr of surveys after the fire, Great Gray Owls were detected at 21 of 22 meadows surveyed within the fire perimeter that were occupied during the decade prior to the fire. Bayesian hierarchical modeling revealed that, rather than decreasing after the fire, persistence of owls at meadows actually increased on both National Park Service (NPS) and non-NPS lands, while colonization rates exhibited no significant change. Within the burned area, these dynamics were unrelated to forest structure variables describing post-fire stands around individual meadows. Notably, post-fire increases in owl persistence occurred both inside and outside the fire perimeter, suggesting factors other than the fire were likely favorable to Great Gray Owls during the post-fire years. Great Gray Owls appear to have been largely resilient to effects of the Rim Fire during the 3 yr after it burned.
Rapid development of visualization dashboards to enhance situation awareness of COVID-19 telehealth initiatives at a multihospital healthcare system
Authors: Dixit Ram A , Hurst Stephen , Adams Katharine T , Boxley Christian , Lysen-Hendershot Kristi , Bennett Sonita S , Booker Ethan , Ratwani Raj M 
Published: June 2020

Abstract
The COVID-19 pandemic has led to the rapid expansion of telehealth services as healthcare organizations aim to mitigate community transmission while providing safe patient care. As technology adoption rapidly increases, operational telehealth teams must maintain awareness of critical information, such as patient volumes and wait times, patient and provider experience, and telehealth platform performance. Using a model of situation awareness as a conceptual foundation and a user-centered design approach we describe our process for rapidly developing and disseminating dashboard visualizations to support telehealth operations. We used a 5-step process to gain domain knowledge, identify user needs, identify data sources, design and develop visualizations, and iteratively refine these visualizations. Through this process we identified 3 distinct stakeholder groups and designed and developed visualization dashboards to meet their needs. Feedback from users demonstrated the dashboard’s support situation awareness and informed important operational decisions. Lessons learned are shared to provide other organizations with insights from our process.
Modeling the Distribution of the Invasive Alien Cycad Aulacaspis Scale in Africa Under Current and Future Climate Scenarios
Authors: Kanle Satishchandra Nitin , Geerts Sjirk 
Published: June 2020

Abstract
The cycad aulacaspis scale, Aulacaspis yasumatsui Takagi (Hemiptera: Coccoidea: Diaspididae), is native to Southeast Asia but an invasive pest of the gymnosperm order Cycadales in many parts of the world. Aulacaspis yasumatsui was recently reported on the cycad genus Encephalartos in South Africa and is currently categorized as a ‘prohibited terrestrial invertebrate’ in the invasive species legislation, National Environmental Management: Biodiversity Act, 2004 (NEM:BA). Encephalartos is endemic to Africa, and 11 species are listed as critically endangered and four species as endangered. Seeing the limited distribution of A. yasumatsui in South Africa and only one unconfirmed record from the Ivory Coast, understanding the potential distribution range is essential for control and management. Here we model the potential distribution of A. yasumatsui under current and future climate scenarios in Africa, with a focus on South Africa. Future climatic scenarios were simulated using a bio-climatic software, CLIMEX. The model indicates that, under the current climatic scenario, all 17 African countries possessing Encephalartos are susceptible to A. yasumatsui establishment. However, under climatic change, the suitability decreases for large parts of Africa. In South Africa, 93% of the winter rainfall areas, and 90% of the temperate, summer rainfall areas are suitable for A. yasumatsui establishment. In this study, we highlight the urgent need for regulation, management, and research on A. yasumatsui in African countries with native cycads.
Cronyism in State Violence: Evidence from Labor Repression During Argentina's Last Dictatorship
Authors: Klor Esteban F , Saiegh Sebastian , Satyanath Shanker 
Published: June 2020

Abstract
We study whether crony governance can extend beyond economic policy to the targeting of state violence against citizens. Specifically, we examine the logic driving the choice of firm-level union representatives who were subjected to state repression by the 1976–1983 Argentine military junta. Using an original dataset, we find a positive, nonspurious, and robust correlation between labor repression and cronyism, measured by political, business, and social connections to the regime. Our results indicate that the number of firm-level union representatives victimized by the regime is three times higher for connected firms relative to nonconnected ones. The effect is pronounced in privately owned (as opposed to state-owned) firms, suggesting that the correlation is driven by cronyism for financial gain rather than ideology or information transmission. We show that connected firms benefited from violence against union representatives by subsequently having less strikes and a higher market valuation. Our findings highlight the pervasiveness of governmental cronyism, even in cases where one of the regime's main stated goals was to curb such behavior.
Behavior Training is Not Enough: Empowering Middle Managers by Shifting Mindset
Authors: Otocki Austin C , Turner Brian F 
Published: June 2020

Abstract
In most organizations, middle managers are expected to meet goals and expectations passed down from above while also connecting with and inspiring the frontline employees doing the work of the organization. Caught in the middle, they often receive training on competencies intended to help them manage issues that arise from this situation. Yet this training tends to be temporarily helpful at best—and harmful at worst. Competency training, because it focuses on changing behavior, fails to address a foundational element necessary to consistently and effectively resolve their challenges. That foundational element is mindset. Providing training and tools to shift their mindset regarding their management objectives better prepares mid-level leaders to be more effective in their challenging positions.
Pharmacological serum concentrations of epinephrine and norepinephrine do not affect growth rate, morphogenesis, stress tolerance, and virulence ofCandida albicans
Authors: Wurster Sebastian , Lyos Sebastian , Albert Nathaniel D , Kontoyiannis Dimitrios P 
Published: June 2020

AbstractVasopressors are frequently given in hemodynamically unstable patients with severe Candida sepsis. While catecholamines can aggravate sepsis-induced immune dysfunction and modulate bacterial virulence traits, their impact on fungal pathogenicity is poorly understood. Using IncuCyte time-lapse microscopy and a fruit fly candidiasis model, we studied growth rates, morphogenesis, stress tolerance, and virulence of C. albicans cocultured with epinephrine and norepinephrine. We found that pharmacologically attainable catecholamine serum concentrations caused minimal changes to in vitro growth kinetics, filamentation, and fungal resistance to thermal or oxidative stress. Similarly, exposure of C. albicans to catecholamines did not alter the survival of infected flies.
The Ophiuchus DIsc Survey Employing ALMA (ODISEA) – II. The effect of stellar multiplicity on disc properties
Authors: Zurlo Alice , Cieza Lucas A , Pérez Sebastián , Christiaens Valentin , Williams Jonathan P , Guidi Greta , Cánovas Hector , Casassus Simon , Hales Antonio , Principe David A , Ruíz-Rodríguez Dary , Fernandez-Figueroa Antonia 
Published: June 2020

ABSTRACT
We present adaptive optics (AO) near-infrared (NIR) observations using VLT/NACO and Keck/NIRC2 of Ophiuchus DIsc Survey Employing ALMA (ODISEA) targets. ODISEA is an ALMA survey of the entire population of circumstellar discs in the Ophiuchus molecular cloud. From the whole sample of ODISEA, we select all the discs that are not already observed in the NIR with AO and that are observable with NACO or NIRC2. The NIR-ODISEA survey consists of 147 stars observed in NIR AO imaging for the first time, as well as revisiting almost all the binary systems of Ophiuchus present in the literature (20 out of 21). In total, we detect 20 new binary systems and one triple system. For each of them, we calculate the projected separation and position angle of the companion, as well as their NIR and millimetre flux ratios. From the NIR contrast, we derived the masses of the secondaries, finding that nine of them are in the substellar regime (30–50 MJup ). Discs in multiple systems reach a maximum total dust mass of ∼50 M⊕, while discs in single stars can reach a dust mass of 200 M⊕. Discs with masses above 10 M⊕ are found only around binaries with projected separations larger than ∼110 au. The maximum disc size is also larger around single star than binaries. However, since most discs in Ophiuchus are very small and low-mass, the effect of visual binaries is relatively weak in the general disc population.
Distinguishing Felsenstein Zone from Farris Zone Using Neural Networks
Authors: Leuchtenberger Alina F , Crotty Stephen M , Drucks Tamara , Schmidt Heiko A , Burgstaller-Muehlbacher Sebastian , von Haeseler Arndt 
Published: June 2020

AbstractMaximum likelihood and maximum parsimony are two key methods for phylogenetic tree reconstruction. Under certain conditions, each of these two methods can perform more or less efficiently, resulting in unresolved or disputed phylogenies. We show that a neural network can distinguish between four-taxon alignments that were evolved under conditions susceptible to either long-branch attraction or long-branch repulsion. When likelihood and parsimony methods are discordant, the neural network can provide insight as to which tree reconstruction method is best suited to the alignment. When applied to the contentious case of Strepsiptera evolution, our method shows robust support for the current scientific view, that is, it places Strepsiptera with beetles, distant from flies.
Treatment outcomes in adult tuberculous meningitis: a systematic review and meta-analysis
Authors: Stadelman Anna M , Ellis Jayne , Samuels Thomas H A , Mutengesa Ernest , Dobbin Joanna , Ssebambulidde Kenneth , Rutakingirwa Morris , Tugume Lillian , Boulware David R , Grint Daniel , Cresswell Fiona V 
Published: June 2020

Abstract

Background
There is substantial variation in the reported treatment outcomes for adult tuberculous meningitis (TBM). Data on survival and neurological disability by continent and HIV serostatus are scarce.

Methods
We performed a systematic review and meta-analysis to characterize treatment outcomes for adult TBM. Following a systematic literature search (MEDLINE and EMBASE), studies underwent duplicate screening by independent reviewers in two stages to assess eligibility for inclusion. Two independent reviewers extracted data from included studies. We employed a random effects model for all meta-analyses. We evaluated heterogeneity by the I2 statistic.

Results
We assessed 2,197 records for eligibility; 39 primary research articles met our inclusion criteria reporting on treatment outcomes for 5,752 adults with TBM. The commonest reported outcome measure was six-month mortality. Pooled six-month mortality was 24% and showed significant heterogeneity (I2 &gt;95%; p&lt;0·01). Mortality ranged from 2% to 67% in Asian studies and from 23% to 80% in sub-Saharan African studies. Mortality was significantly worse in HIV-positive adults at 57% (95%CI; 48-67%), compared with 16% (95%CI; 10-24%) in HIV-negative adults (p&lt;0·01). Physical disability was reported in 32% (95%CI; 22-43%) of adult TBM survivors. There was considerable heterogeneity between studies in all meta-analyses with I2 statistics consistently &gt;50%.

Conclusions
Mortality in adult TBM is high and varies considerably by continent and HIV-status. The highest mortality is amongst HIV-positive adults in sub-Saharan Africa. Standardized reporting of treatment outcomes will be essential to improve future data quality and increase potential for data sharing, meta-analyses, and facilitating multi-center tuberculosis research to improve outcomes.
An “Infodemic”: Leveraging High-Volume Twitter Data to Understand Early Public Sentiment for the Coronavirus Disease 2019 Outbreak
Authors: Medford Richard J , Saleh Sameh N , Sumarsono Andrew , Perl Trish M , Lehmann Christoph U 
Published: June 2020

Abstract

Background
Twitter has been used to track trends and disseminate health information during viral epidemics. On January 21, 2020, the Centers for Disease Control and Prevention activated its Emergency Operations Center and the World Health Organization released its first situation report about coronavirus disease 2019 (COVID-19), sparking significant media attention. How Twitter content and sentiment evolved in the early stages of the COVID-19 pandemic has not been described.

Methods
We extracted tweets matching hashtags related to COVID-19 from January 14 to 28, 2020 using Twitter’s application programming interface. We measured themes and frequency of keywords related to infection prevention practices. We performed a sentiment analysis to identify the sentiment polarity and predominant emotions in tweets and conducted topic modeling to identify and explore discussion topics over time. We compared sentiment, emotion, and topics among the most popular tweets, defined by the number of retweets.

Results
We evaluated 126 049 tweets from 53 196 unique users. The hourly number of COVID-19-related tweets starkly increased from January 21, 2020 onward. Approximately half (49.5%) of all tweets expressed fear and approximately 30% expressed surprise. In the full cohort, the economic and political impact of COVID-19 was the most commonly discussed topic. When focusing on the most retweeted tweets, the incidence of fear decreased and topics focused on quarantine efforts, the outbreak and its transmission, as well as prevention.

Conclusions
Twitter is a rich medium that can be leveraged to understand public sentiment in real-time and potentially target individualized public health messages based on user interest and emotion.