bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomaterial surface energy-driven ligand assembly strongly regulates stem cell mechanosensitivity and fate on very soft substrates
Authors: Razafiarison Tojo , Holenstein Claude N. , Stauber Tino , Jovic Milan , Vertudes Edward , Loparic Marko , Kawecki Maciej , Bernard Laetitia , Silvan Unai , Snedeker Jess G. 
Published: April 2018

Significance
Cell instructive biomaterial cues are a major topic of interest in both basic and applied research. In this work, we clarify how surface energy of soft biomaterials can dramatically affect mesenchymal stem cell receptor recruitment and downstream signaling related to cell fate. We elucidate how surface protein self-assembly and the resulting surface topology can act to steer mechanotransduction and related biological response of attached cells. These findings fill a critical gap in our basic understanding of cell–biomaterial interaction and highlight soft biomaterial surface energy as a dominant design factor that should not be neglected.
Global shifts in the phenological synchrony of species interactions over recent decades
Authors: Kharouba Heather M. , Ehrlén Johan , Gelman Andrew , Bolmgren Kjell , Allen Jenica M. , Travers Steve E. , Wolkovich Elizabeth M. 
Published: April 2018

Significance
Shifts in the timing of species interactions are often cited as a consequence of climate change and, if present, are expected to have wide-reaching implications for ecological communities. Our knowledge about these shifts mostly comes from single systems, which have provided no clear picture, thus limiting our understanding of how species interactions may be responding overall. Using a new global database based on long-term data on the seasonal timing of biological events for pairwise species interactions, we find that the relative timing of interacting species has changed substantially in recent decades. The observed shifts are greater in magnitude than before recent climate change began, suggesting that there will be widespread warming-related shifts in the synchrony of species in the future.
Temperature accelerates the rate fields become forests
Authors: Fridley Jason D. , Wright Justin P. 
Published: April 2018

SignificanceThe transition of abandoned fields into forests (secondary succession) has long informed ecologists’ understanding of community assembly and species interactions. Intriguingly, rates of secondary succession show a striking latitudinal pattern, with dominance by woody species (>50% cover) taking less than a decade in the southern United States, and up to 60 years in New England. We used a large-scale experimental network to test how multiple drivers (climate, soils, and the identity of dominant species) influence field-to-forest transitions. We found consistent evidence that climate is the strongest driver of tree establishment, suggesting that temperature limitation of succession in northern latitudes is likely to be reduced under future warming, potentially increasing rates of carbon uptake on abandoned agricultural land.
An explainable deep machine vision framework for plant stress phenotyping
Authors: Ghosal Sambuddha , Blystone David , Singh Asheesh K. , Ganapathysubramanian Baskar , Singh Arti , Sarkar Soumik 
Published: April 2018

Significance
Plant stress identification based on visual symptoms has predominately remained a manual exercise performed by trained pathologists, primarily due to the occurrence of confounding symptoms. However, the manual rating process is tedious, is time-consuming, and suffers from inter- and intrarater variabilities. Our work resolves such issues via the concept of explainable deep machine learning to automate the process of plant stress identification, classification, and quantification. We construct a very accurate model that can not only deliver trained pathologist-level performance but can also explain which visual symptoms are used to make predictions. We demonstrate that our method is applicable to a large variety of biotic and abiotic stresses and is transferable to other imaging conditions and plants.
Characterization and engineering of a plastic-degrading aromatic polyesterase
Authors: Austin Harry P. , Allen Mark D. , Donohoe Bryon S. , Rorrer Nicholas A. , Kearns Fiona L. , Silveira Rodrigo L. , Pollard Benjamin C. , Dominick Graham , Duman Ramona , El Omari Kamel , Mykhaylyk Vitaliy , Wagner Armin , Michener William E. , Amore Antonella , Skaf Munir S. , Crowley Michael F. , Thorne Alan W. , Johnson Christopher W. , Woodcock H. Lee , McGeehan John E. , Beckham Gregg T. 
Published: April 2018

Significance
Synthetic polymers are ubiquitous in the modern world but pose a global environmental problem. While plastics such as poly(ethylene terephthalate) (PET) are highly versatile, their resistance to natural degradation presents a serious, growing risk to fauna and flora, particularly in marine environments. Here, we have characterized the 3D structure of a newly discovered enzyme that can digest highly crystalline PET, the primary material used in the manufacture of single-use plastic beverage bottles, in some clothing, and in carpets. We engineer this enzyme for improved PET degradation capacity and further demonstrate that it can also degrade an important PET replacement, polyethylene-2,5-furandicarboxylate, providing new opportunities for biobased plastics recycling.
Vibrations of a molecule in an external force field
Authors: Okabayashi Norio , Peronio Angelo , Paulsson Magnus , Arai Toyoko , Giessibl Franz J. 
Published: April 2018

Significance
The vibration of a molecule adsorbed on a surface contains essential information on the molecule–surface bond, which is important to understand the surface reactions that occur, e.g., in catalytic reactions. Accessing the vibrational energies of a single molecule is possible by combining scanning tunneling microscopy with inelastic electron spectroscopy. However, the tip of a microscope exerts a force on a nearby molecule, and possibly even induces slight structural changes. To study this problem, we have further incorporated atomic force microscopy. The relationship between the exerted forces and vibrational energies is well reproduced by a classical mechanical model. This combined technique opens the possibility to study the atomic-scale interaction of a molecule on a surface with unprecedented precision.
The images in television programs and the potential for learning unknown words
Authors: Rodgers Michael P. H. 
Published: April 2018

Abstract
Previous studies have indicated the potential for incidental vocabulary learning through viewing television. The assumption has been that the imagery in television helps learners acquire vocabulary because when they hear an unfamiliar word, the on-screen images provide semantic support. However, the extent to which imagery in authentic television supports learners in this way is unclear. This study examines 90 target words occurring in single seasons of television, and the degree to which their aural occurrence matched the presentation of a potentially supporting image. Results indicate differences in the way imagery supports potential vocabulary learning in documentary television compared with narrative television, and that this supporting imagery occurred concurrently with the aural form more often in documentary television. Research and pedagogical implications are discussed in detail.
Effectiveness of a REDD+ Project in Reducing Deforestation in the Brazilian Amazon
Authors: Simonet Gabriela , Subervie Julie , Ezzine‐de‐Blas Driss , Cromberg Marina , Duchelle Amy E. 
Published: April 2018

AbstractWe estimate the early effects of the pilot project to Reduce Emissions from Deforestation and forest Degradation (REDD+) in the Brazilian Amazon. This project offers a mix of interventions, including conditional payments, to reduce deforestation by smallholders who depend on swidden agriculture and extensive cattle ranching. We collected original data from 181 individual farmers. We use difference‐in‐difference (DID) and DID‐matching approaches and find evidence that supports our identification strategy. We estimate that an average of 4 ha of forest were saved on each participating farm in 2014, and that this conservation came at the expense of pastures rather than croplands. This amounts to a decrease in the deforestation rate of about 50%. We find no evidence of within‐community spillovers.
A Comparison of the Diagnostic Accuracy of Common Office Blood Pressure Measurement Protocols
Authors: Kronish Ian M , Edmondson Donald , Shimbo Daichi , Shaffer Jonathan A , Krakoff Lawrence R , Schwartz Joseph E 
Published: April 2018

Abstract

BACKGROUND
The optimal approach to measuring office blood pressure (BP) is uncertain. We aimed to compare BP measurement protocols that differed based on numbers of readings within and between visits and by assessment method.

METHODS
We enrolled a sample of 707 employees without known hypertension or cardiovascular disease, and obtained 6 standardized BP readings during each of 3 office visits at least 1 week apart, using mercury sphygmomanometer and BpTRU oscillometric devices (18 readings per participant) for a total of 12,645 readings. We used confirmatory factor analysis to develop a model estimating “true” office BP that could be used to compare the probability of correctly classifying participants’ office BP status using differing numbers and types of office BP readings.

RESULTS
Averaging 2 systolic BP readings across 2 visits correctly classified participants as having BP below or above the 140 mm Hg threshold at least 95% of the time if the averaged reading was &lt;134 or &gt;149 mm Hg, respectively. Our model demonstrated that more confidence was gained by increasing the number of visits with readings than by increasing the number of readings within a visit. No clinically significant confidence was gained by dropping the first reading vs. averaging all readings, nor by measuring with a manual mercury device vs. with an automated oscillometric device.

CONCLUSIONS
Averaging 2 BP readings across 2 office visits appeared to best balance increased confidence in office BP status with efficiency of BP measurement, though the preferred measurement strategy may vary with the clinical context.
aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences
Authors: Glouzon Jean-Pierre Séhi , Ouangraoua Aïda 
Published: April 2018

Abstract

Motivation
Predicting the conserved secondary structure of homologous ribonucleic acid (RNA) sequences is crucial for understanding RNA functions. However, fast and accurate RNA structure prediction is challenging, especially when the number and the divergence of homologous RNA increases. To address this challenge, we propose aliFreeFold, based on a novel alignment-free approach which computes a representative structure from a set of homologous RNA sequences using sub-optimal secondary structures generated for each sequence. It is based on a vector representation of sub-optimal structures capturing structure conservation signals by weighting structural motifs according to their conservation across the sub-optimal structures.

Results
We demonstrate that aliFreeFold provides a good balance between speed and accuracy regarding predictions of representative structures for sets of homologous RNA compared to traditional methods based on sequence and structure alignment. We show that aliFreeFold is capable of uncovering conserved structural features fastly and effectively thanks to its weighting scheme that gives more (resp. less) importance to common (resp. uncommon) structural motifs. The weighting scheme is also shown to be capable of capturing conservation signal as the number of homologous RNA increases. These results demonstrate the ability of aliFreefold to efficiently and accurately provide interesting structural representatives of RNA families.

Availability and implementation
aliFreeFold was implemented in C++. Source code and Linux binary are freely available at https://github.com/UdeS-CoBIUS/aliFreeFold.

Supplementary information
Supplementary data are available at Bioinformatics online.
A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity
Authors: Petralia Francesca , Wang Li , Peng Jie , Yan Arthur , Zhu Jun , Wang Pei 
Published: April 2018

Abstract

Motivation
Tumor tissue samples often contain an unknown fraction of stromal cells. This problem is widely known as tumor purity heterogeneity (TPH) was recently recognized as a severe issue in omics studies. Specifically, if TPH is ignored when inferring co-expression networks, edges are likely to be estimated among genes with mean shift between non-tumor- and tumor cells rather than among gene pairs interacting with each other in tumor cells. To address this issue, we propose Tumor Specific Net (TSNet), a new method which constructs tumor-cell specific gene/protein co-expression networks based on gene/protein expression profiles of tumor tissues. TSNet treats the observed expression profile as a mixture of expressions from different cell types and explicitly models tumor purity percentage in each tumor sample.

Results
Using extensive synthetic data experiments, we demonstrate that TSNet outperforms a standard graphical model which does not account for TPH. We then apply TSNet to estimate tumor specific gene co-expression networks based on TCGA ovarian cancer RNAseq data. We identify novel co-expression modules and hub structure specific to tumor cells.

Availability and implementation
R codes can be found at https://github.com/petraf01/TSNet.

Supplementary information
Supplementary data are available at Bioinformatics online.
In silico read normalization using set multi-cover optimization
Authors: Durai Dilip A , Schulz Marcel H 
Published: April 2018

Abstract

Motivation
De Bruijn graphs are a common assembly data structure for sequencing datasets. But with the advances in sequencing technologies, assembling high coverage datasets has become a computational challenge. Read normalization, which removes redundancy in datasets, is widely applied to reduce resource requirements. Current normalization algorithms, though efficient, provide no guarantee to preserve important k-mers that form connections between regions in the graph.

Results
Here, normalization is phrased as a set multi-cover problem on reads and a heuristic algorithm, Optimized Read Normalization Algorithm (ORNA), is proposed. ORNA normalizes to the minimum number of reads required to retain all k-mers and their relative k-mer abundances from the original dataset. Hence, all connections from the original graph are preserved. ORNA was tested on various RNA-seq datasets with different coverage values. It was compared to the current normalization algorithms and was found to be performing better. Normalizing error corrected data allows for more accurate assemblies compared to the normalized uncorrected dataset. Further, an application is proposed in which multiple datasets are combined and normalized to predict novel transcripts that would have been missed otherwise. Finally, ORNA is a general purpose normalization algorithm that is fast and significantly reduces datasets with loss of assembly quality in between [1, 30]% depending on reduction stringency.

Availability and implementation
ORNA is available at https://github.com/SchulzLab/ORNA.

Supplementary information
Supplementary data are available at Bioinformatics online.
The evolution of entrepreneurial ecosystems and the critical role of migrants. A Phase-Model based on a Study of IT startups in the Greater Tel Aviv Area
Authors: Schäfer Susann , Henn Sebastian 
Published: April 2018

AbstractUnlike existing studies on entrepreneurial ecosystems that focus on the internal dynamics of such systems, this article argues that entrepreneurial ecosystems are linked to one another through economically specialised migrants that trigger their emergence and positively affect their future development. To illustrate the relation between migration and the dynamics of entrepreneurial ecosystems, a model is presented that distinguishes three different phases: (i) the remigration of highly skilled migrants, (ii) ‘sunshine return migration’ and (iii) the outmigration of local entrepreneurs to foreign entrepreneurial ecosystems. Even though the model is based on both existing literature and our own empirical findings in the Tel Aviv IT entrepreneurial ecosystem, it is argued that its implications also hold true for other regional contexts.
Feedback stabilization for unbounded bilinear systems using bounded control
Authors: El Ayadi Rachid , Ouzahra Mohamed 
Published: April 2018

Abstract
In this paper, we deal with the distributed bilinear system $ \frac{d z(t)}{d t}= A z(t) + v(t)Bz(t), $ where A is the infinitesimal generator of a semigroup of contractions on a real Hilbert space H. The linear operator B is supposed bounded with respect to the graph norm of A. Then we give sufficient conditions for weak and strong stabilizations. Illustrating examples are provided.
The Intracerebral Hemorrhage Score: A Self-Fulfilling Prophecy?
Authors: McCracken D Jay , Lovasik Brendan P , McCracken Courtney E , Frerich Jason M , McDougal Margaret E , Ratcliff Jonathan J , Barrow Daniel L , Pradilla Gustavo 
Published: April 2018

Abstract

BACKGROUND
The ICH Score has become the standard for risk-stratification of 30-d mortality in patients with intracerebral hemorrhage (ICH), but treatment has evolved over the last 17 yr since its inception. We sought to determine if the ICH Score remains an accurate predictor of 30-d mortality in these high acuity patients.

OBJECTIVE
To determine the role the ICH Score has on mortality in current treatment of patients.

METHODS
A retrospective review of 554 patients treated for acute, spontaneous ICH at 2 large academic institutions between 2010 and 2014 was carried out. Surgical intervention in the form of external ventricular drain or craniotomy was performed when indicated. All patients were managed medically until discharge or death.

RESULTS
Over half (53.6%) of the patients presented with ICH of the basal ganglia/thalamus and the majority (71%) presented with ICH Scores of 0 to 2. Overall mortality was 25.1%. Observed mortality in moderate grade ICH Score patients (3 and 4) was lower than expected (49% vs 72%, P < .001) and (71% vs 97%, P < .001) when compared to the original ICH Score results. Despite differences in ICH and intraventricular hemorrhage volume, and Glasgow Coma Scale there was no difference in surgical intervention (12.2% vs 11.8%, P = .94) between the two groups. Withdrawal of care was instituted in 56.6% of all patients who died and increased with ICH Score.

CONCLUSION
In our cohort, the original ICH score did not accurately predict the mortality rate. Patient survival exceeded ICH Score-predicted mortality regardless of surgical intervention. Reevaluation of predictive scores could be useful to aid in more accurate prognoses.
EMERGEncy ID NET: Review of a 20-Year Multisite Emergency Department Emerging Infections Research Network
Authors: Santibanez Scott , Fischer Leah S , Krishnadasan Anusha , Sederdahl Bethany , Merlin Toby , Moran Gregory J , Talan David A ,   for the EMERGEncy ID NET Study Group, Mower William , Sullivan Matthew , Abrahamian Fredrick M , Ong Sam , Gross Eric , Salhi Bisan , Heilpern Katherine , Hess Jeremy , Karras David , Biros Michelle , Dunbar Lala , Takhar Sukhjit , Pollack Charles , Runge Jeffrey , Cheney Paul , Rothrock Stephen , O’Brian John , Citron Diane , Goldstein Ellie , Finegold Sydney , Nakase Janet , Newdow Michael , Merchant Guy , Pathmarajah Kavitha , Gonzalez Eva , Mulrow Mary , Bussman Silas , Kalugdnan Vernon , Peterson Stephen , Pitts Seth , Narayan Kamil , Rubin Ada , Kemble Laurie , Beckham Danielle , Neal Niccole , Yagapen Annick , Von Hofen Carol , Hatala Kathleen , Fuentes Shelley , Sibley Debbi , Colucci Ashley , Hernandez Jackeline , Cruse Hope , Usher Sarah , Hendrickson Audrey , Dehnkamp Kimberly , Zeglin Britney , Jambaulikar Guruprasad , Gorwitz Rachel , Limbago Brandi , Kuehnert Matthew , Jarvis William , Slutsker Larry , Arvay Melissa , Conn Laura 
Published: April 2018

Abstract
As providers of frontline clinical care for patients with acute and potentially life-threatening infections, emergency departments (EDs) have the priorities of saving lives and providing care quickly and efficiently. Although these facilities see a diversity of patients 24 hours per day and can collect prospective data in real time, their ability to conduct timely research on infectious syndromes is not well recognized. EMERGEncy ID NET is a national network that demonstrates that EDs can also collect data and conduct research in real time. This network collaborates with the Centers for Disease Control and Prevention (CDC) and other partners to study and address a wide range of infectious diseases and clinical syndromes. In this paper, we review selected highlights of EMERGEncy ID NET’s history from 1995 to 2017. We focus on the establishment of this multisite research network and the network’s collaborative research on a wide range of ED clinical topics.
Cytomegalovirus (CMV) Disease Despite Weekly Preemptive CMV Strategy for Recipients of Solid Organ and Hematopoietic Stem Cell Transplantation
Authors: Lodding I P , da Cunha Bang C , Sørensen S S , Gustafsson F , Iversen M , Kirkby N , Perch M , Rasmussen A , Sengeløv H , Mocroft A , Lundgren J D 
Published: April 2018

Abstract

Background
Transplant recipients presenting with cytomegalovirus (CMV) disease at the time of diagnosis of CMV DNAemia pose a challenge to a preemptive CMV management strategy. However, the rate and risk factors of such failure remain uncertain.

Methods
Solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) recipients with a first episode of CMV polymerase chain reaction (PCR) DNAemia within the first year posttransplantation were evaluated (n = 335). Patient records were reviewed for presence of CMV disease at the time of CMV DNAemia diagnosis. The distribution and prevalence of CMV disease were estimated, and the odds ratio (OR) of CMV disease was modeled using logistic regression.

Results
The prevalence of CMV disease increased for both SOT and HSCT with increasing diagnostic CMV PCR load and with screening intervals &gt;14 days. The only independent risk factor in multivariate analysis was increasing CMV DNAemia load of the diagnostic CMV PCR (OR = 6.16; 95% confidence interval, 2.09–18.11). Among recipients receiving weekly screening (n = 147), 16 (10.8%) had CMV disease at the time of diagnosis of CMV DNAemia (median DNAemia load 628 IU/mL; interquartile range, 432–1274); 93.8% of these cases were HSCT and lung transplant recipients.

Conclusions
Despite application of weekly screening intervals, HSCT and lung transplant recipients in particular presented with CMV disease at the time of diagnosis of CMV DNAemia. Additional research to improve the management of patients at risk of presenting with CMV disease at low levels of CMV DNAemia and despite weekly screening is warranted.