bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological roles and potential applications of immune cell‐derived extracellular vesicles
Authors: Wen Chuan , Seeger Robert C. , Fabbri Muller , Wang Larry , Wayne Alan S. , Jong Ambrose Y. 
Published: November 2017

ABSTRACTExtracellular vesicles (EVs) deliver bioactive macromolecules (i.e. proteins, lipids and nucleic acids) for intercellular communication in multicellular organisms. EVs are secreted by all cell types including immune cells. Immune cell‐derived EVs modulate diverse aspects of the immune system to either enhance or suppress immune activities. The extensive effects of immune cell‐derived EVs have become the focus of great interest for various nano‐biomedical applications, ranging from the medical use of nanoplatform‐based diagnostic agents to the development of therapeutic interventions as well as vaccine applications, and thus may be ideal for ‘immune‐theranostic’. Here, we review the latest advances concerning the biological roles of immune cell‐derived EVs in innate and acquired immunity. The intercellular communication amongst immune cells through their EVs is highlighted, showing that all immune cell‐derived EVs have their unique function(s) in immunity through intricate interaction(s). Natural‐killer (NK) cell‐derived EVs, for example, contain potent cytotoxic proteins and induce apoptosis to targeted cancer cells. On the other hand, cancer cell‐derived EVs bearing NK ligands may evade immune surveillance and responses. Finally, we discuss possible medical uses for the immune cell‐derived EVs as a tool for immune‐theranostic: as diagnostic biomarkers, for use in therapeutic interventions and for vaccination.
Comparison study on flexible pavement design using FAA (Federal Aviation Administration) and LCN (Load Classification Number) code in Ahmad Yani international airport’s runway
Authors: Santoso S E , Sulistiono D , Mawardi A F 
Published: November 2017

Abstract
FAA code for airport design has been broadly used by Indonesian Ministry of Aviation since decades ago. However, there is not much comprehensive study about its relevance and efficiency towards current situation in Indonesia. Therefore, a further comparison study on flexible pavement design for airport runway using comparable method has become essential.
The main focus of this study is to compare which method between FAA and LCN that offer the most efficient and effective way in runway pavement planning. The comparative methods in this study mainly use the variety of variable approach. FAA code for instance, will use the approach on the aircraft’s maximum take-off weight and annual departure. Whilst LCN code use the variable of equivalent single wheel load and tire pressure. Based on the variables mentioned above, a further classification and rated method will be used to determine which code is best implemented. According to the analysis, it is clear that FAA method is the most effective way to plan runway design in Indonesia with consecutively total pavement thickness of 127cm and LCN method total pavement thickness of 70cm. Although, FAA total pavement is thicker that LCN its relevance towards sustainable and pristine condition in the future has become an essential aspect to consider in design and planning.
Differences among Thai Agricultural Workers’ Health, Working Conditions, and Pesticide Use by Farm Type
Authors: Kongtip Pornpimol , Nankongnab Noppanun , Mahaboonpeeti Redeerat , Bootsikeaw Sasivimol , Batsungnoen Kiattisak , Hanchenlaksh Chalalai , Tipayamongkholgul Mathuros , Woskie Susan 
Published: November 2017

Abstract
More than 11 million Thai people (38%) work in agriculture, but since most are in the informal sector, government enforcement and support are very limited. As a result, working conditions on Thai farms vary greatly, putting the health of many agricultural workers at risk. A cross-sectional study in three Thai provinces collected information on the work activities and conditions of 424 farmers representing five farm types: rice, vegetable, flower, rice/vegetable, and flower/vegetable. The agricultural workers were mainly women (60%); their average age was 53 but ranged from 18 to 87 years. More than 64% worked more than 5 days/week. Seventy-four percent of them had only primary school education. A number of the health and hazardous working conditions surveyed were significantly different by farm type. Rice farmers were found to have the highest prevalence of allergies, nasal congestion, wheezing, and acute symptoms after pesticide use, while flower farmers had the lowest prevalence of these health outcomes. Rice farmers reported the highest prevalence of hazardous working conditions including high noise levels, working on slippery surfaces, sitting or standing on a vibrating machine, spills of chemicals/pesticides, and sharp injuries. The lowest prevalence of these working conditions (except noise) was reported by flower farmers. Vegetable farmers reported the highest prevalence knee problems, while rice farmers had the lowest prevalence. Among these farmers, more than 27 different types of pesticides were reported in use during the past year, with the majority reporting use once a month. The flower/vegetable farming group reported the highest frequency of good exposure prevention practices during pesticide use. They were the most likely to report using cotton or rubber gloves or a disposable paper masks during insecticide spraying. Those farmers who only grew vegetables had the lowest frequency of good exposure prevention practices, including use of personal protective equipment. The economic cost of work-related injuries and illnesses among informal sector agricultural workers in Thailand is unknown and in need of study. Gaps in the regulations covering pesticide sales allow farmers to purchase pesticides without adequate training in their safe use. Training targeted to farm type regarding safe pesticide use and the prevention of accidents and musculoskeletal disorders is needed. Studies of chronic health effects among Thai farmers are needed, with special emphasis on respiratory, metabolic disease and cancer.
Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network
Authors: Ramírez Carlos , Mendoza Luis 
Published: November 2017

Abstract

Motivation
Blood cell formation has been recognized as a suitable system to study celular differentiation mainly because of its experimental accessibility, and because it shows characteristics such as hierarchical and gradual bifurcated patterns of commitment, which are present in several developmental processes. Although hematopoiesis has been extensively studied and there is a wealth of molecular and cellular data about it, it is not clear how the underlying molecular regulatory networks define or restrict cellular differentiation processes. Here, we infer the molecular regulatory network that controls the differentiation of a blood cell subpopulation derived from the granulocyte-monocyte precursor (GMP), comprising monocytes, neutrophils, eosinophils, basophils and mast cells.

Results
We integrate published qualitative experimental data into a model to describe temporal expression patterns observed in GMP-derived cells. The model is implemented as a Boolean network, and its dynamical behavior is studied. Steady states of the network can be clearly identified with the expression profiles of monocytes, mast cells, neutrophils, basophils, and eosinophils, under wild-type and mutant backgrounds.

Availability and implementation
All scripts are publicly available at https://github.com/caramirezal/RegulatoryNetworkGMPModel

Supplementary information
Supplementary data are available at Bioinformatics online.
GDSCTools for mining pharmacogenomic interactions in cancer
Authors: Cokelaer Thomas , Chen Elisabeth , Iorio Francesco , Menden Michael P , Lightfoot Howard , Saez-Rodriguez Julio , Garnett Mathew J 
Published: November 2017

Abstract

Motivation
Large pharmacogenomic screenings integrate heterogeneous cancer genomic datasets as well as anti-cancer drug responses on thousand human cancer cell lines. Mining this data to identify new therapies for cancer sub-populations would benefit from common data structures, modular computational biology tools and user-friendly interfaces.

Results
We have developed GDSCTools: a software aimed at the identification of clinically relevant genomic markers of drug response. The Genomics of Drug Sensitivity in Cancer (GDSC) database (www.cancerRxgene.org) integrates heterogeneous cancer genomic datasets as well as anti-cancer drug responses on a thousand cancer cell lines. Including statistical tools (analysis of variance) and predictive methods (Elastic Net), as well as common data structures, GDSCTools allows users to reproduce published results from GDSC and to implement new analytical methods. In addition, non-GDSC data resources can also be analysed since drug responses and genomic features can be encoded as CSV files.

Supplementary information
Supplementary data are available at Bioinformatics online.
FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web
Authors: Probst Daniel , Reymond Jean-Louis 
Published: November 2017

Abstract

Motivation
During the past decade, big data have become a major tool in scientific endeavors. Although statistical methods and algorithms are well-suited for analyzing and summarizing enormous amounts of data, the results do not allow for a visual inspection of the entire data. Current scientific software, including R packages and Python libraries such as ggplot2, matplotlib and plot.ly, do not support interactive visualizations of datasets exceeding 100 000 data points on the web. Other solutions enable the web-based visualization of big data only through data reduction or statistical representations. However, recent hardware developments, especially advancements in graphical processing units, allow for the rendering of millions of data points on a wide range of consumer hardware such as laptops, tablets and mobile phones. Similar to the challenges and opportunities brought to virtually every scientific field by big data, both the visualization of and interaction with copious amounts of data are both demanding and hold great promise.

Results
Here we present FUn, a framework consisting of a client (Faerun) and server (Underdark) module, facilitating the creation of web-based, interactive 3D visualizations of large datasets, enabling record level visual inspection. We also introduce a reference implementation providing access to SureChEMBL, a database containing patent information on more than 17 million chemical compounds.

Availability and implementation
The source code and the most recent builds of Faerun and Underdark, Lore.js and the data preprocessing toolchain used in the reference implementation, are available on the project website (http://doc.gdb.tools/fun/).
An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition
Authors: Luo Ling , Yang Zhihao , Yang Pei , Zhang Yin , Wang Lei , Lin Hongfei , Wang Jian 
Published: November 2017

Abstract

Motivation
In biomedical research, chemical is an important class of entities, and chemical named entity recognition (NER) is an important task in the field of biomedical information extraction. However, most popular chemical NER methods are based on traditional machine learning and their performances are heavily dependent on the feature engineering. Moreover, these methods are sentence-level ones which have the tagging inconsistency problem.

Results
In this paper, we propose a neural network approach, i.e. attention-based bidirectional Long Short-Term Memory with a conditional random field layer (Att-BiLSTM-CRF), to document-level chemical NER. The approach leverages document-level global information obtained by attention mechanism to enforce tagging consistency across multiple instances of the same token in a document. It achieves better performances with little feature engineering than other state-of-the-art methods on the BioCreative IV chemical compound and drug name recognition (CHEMDNER) corpus and the BioCreative V chemical-disease relation (CDR) task corpus (the F-scores of 91.14 and 92.57%, respectively).

Availability and implementation
Data and code are available at https://github.com/lingluodlut/Att-ChemdNER.

Supplementary information
Supplementary data are available at Bioinformatics online.
Local sympathetic denervation attenuates myocardial inflammation and improves cardiac function after myocardial infarction in mice
Authors: Ziegler Karin A , Ahles Andrea , Wille Timo , Kerler Julia , Ramanujam Deepak , Engelhardt Stefan 
Published: November 2017

Abstract

Aims
Cardiac inflammation has been suggested to be regulated by the sympathetic nervous system (SNS). However, due to the lack of methodology to surgically eliminate the myocardial SNS in mice, neuronal control of cardiac inflammation remains ill-defined. Here, we report a procedure for local cardiac sympathetic denervation in mice and tested its effect in a mouse model of heart failure post-myocardial infarction.

Methods and results
Upon preparation of the carotid bifurcation, the right and the left superior cervical ganglia were localized and their pre- and postganglionic branches dissected before removal of the ganglion. Ganglionectomy led to an almost entire loss of myocardial sympathetic innervation in the left ventricular anterior wall. When applied at the time of myocardial infarction (MI), cardiac sympathetic denervation did not affect acute myocardial damage and infarct size. In contrast, cardiac sympathetic denervation significantly attenuated chronic consequences of MI, including myocardial inflammation, myocyte hypertrophy, and overall cardiac dysfunction.

Conclusion
These data suggest a critical role for local sympathetic control of cardiac inflammation. Our model of myocardial sympathetic denervation in mice should prove useful to further dissect the molecular mechanisms underlying cardiac neural control.
The effect of descriptive age norms on the motivation to exercise among older adults
Authors: Pelssers Johan , Fransen Katrien , Vanbeselaere Norbert , Boen Filip 
Published: November 2017

SummaryBased on the principles of the Social Identity Approach (SIA), the present experiment aimed to examine the impact of communicating descriptive age norms on older adults’ autonomous motivation to exercise. Under the cover of a marketing study, older adults (n = 120; age = 65–70 years) participated in a newly created exercise activity, ‘Pattern Stepping’. This activity was framed as an activity that was descriptively normative either for older adults, for younger adults, for both groups, or for none. Repeated measures ANOVAs revealed that participants felt greater satisfaction of their basic psychological needs and were more autonomously motivated to exercise if Pattern Stepping was framed as an activity popular among the young, rather than among older adults. These findings suggest that framing an exercise as descriptively normative for the elderly can thwart older adults’ autonomous motivation if they do not identify as an older adult.
Neuroprotection for Traumatic Brain Injury
Authors: Ratcliff Jonathan J. , Wright David W. 
Published: November 2017

Abstract
Traumatic brain injury (TBI) is a common, clinically complex, heterogeneous global public health problem. Neuroprotection strategies focus on preventing secondary injury by creating a physiologic environment devoid of extremes while targeting normal physiologic parameters. Careful attention must be paid to aggressively avoid and treat hypoxia, hypotension, hypoglycemia, intracranial hypertension, and cerebral hypoperfusion (low cerebral perfusion pressure). Aggressive management of intracranial pressure and cerebral perfusion pressure through optimal patient positioning, appropriate use of sedation and analgesia, and administration of hyperosmolar therapy remain the hallmark for the care of the TBI patient. Surgical decompressive craniectomy and hypothermia hold promise but remain controversial and should be used in carefully selected clinical situations. Early identification of injury progression is aided through careful monitoring by clinical examination and cerebral physiological monitoring. Multimodal monitoring provides an early warning system to guide appropriate clinical responses to identified deranged physiology.
Neuroprotection for Acute Ischemic Stroke
Authors: Mayor Diana , Tymianski Michael 
Published: November 2017

Abstract
Acute ischemic stroke (AIS) is the leading cause of acquired neurological disability worldwide. AIS most commonly occurs when a cerebral artery is occluded, leading to irreversible brain injury and neurologic disability. Acute supportive physiological interventions and close monitoring on a stroke unit are beneficial to optimize overall recovery and functional outcome. Phamacological treatment options are limited though as the only FDA-approved therapy for AIS is the thrombolytic agent intravenous recombinant tissue plasminogen activator (Alteplase, rtPA), which improves functional outcome in therapeutic time windows ranging up to 3–4.5 hours. Several clinical trials assessing the efficacy of endovascular therapy have shown a benefit in carefully selected patients with a documented large vessel occlusion (LVO), and subsequently are becoming part of the standard practice in this AIS subset. Clinical trials using various imaging paradigms to enhance patient selection for thrombolytic therapy, endovascular therapy and neuroprotection therapies are all progressing.
Neuroprotection for Vascular and Endovascular Neurosurgery
Authors: Ladner Travis R , Kumar Nishant Ganesh , He Lucy , Mocco J 
Published: November 2017

Abstract
The complexity of neurovascular disease presents a challenge to the surgical and anesthesia teams managing patients with such conditions. With open or endovascular techniques, abrupt changes in hemodynamic status and intracranial pressure are an ever-present concern throughout the perioperative period. Monitoring of neurological status, hemodynamic parameters, and intracranial pressure are important adjuncts. Targeted physiologic and pharmacological interventions are critical to ensuring safe completion of complex procedures and the prevention secondary injury. This chapter reviews common complications of cerebrovascular and endovascular operations and their risk factors and summarize clinical principles, strategies, and considerations for maximizing neuroprotection in the treatment of neurovascular disease.
Non-linear acceleration at supernova remnant shocks and the hardening in the cosmic ray spectrum
Authors: Recchia S , Gabici S 
Published: November 2017

Abstract
In the last few years, several experiments have shown that the cosmic ray spectrum below the knee is not a perfect power law. In particular, the proton and helium spectra show a spectral hardening by ∼0.1–0.2 in spectral index at particle energies of ∼ 200–300 GeV nucleon−1. Moreover, the helium spectrum is found to be harder than that of protons by ∼0.1 and some evidence for a similar hardening was also found in the spectra of heavier elements. Here, we consider the possibility that the hardening may be the result of a dispersion in the slope of the spectrum of cosmic rays accelerated at supernova remnant shocks. Such a dispersion is indeed expected within the framework of non-linear theories of diffusive shock acceleration, which predict steeper (harder) particle spectra for larger (smaller) cosmic ray acceleration efficiencies.
Germline SUFU mutation carriers and medulloblastoma: clinical characteristics, cancer risk, and prognosis
Authors: Guerrini-Rousseau Léa , Dufour Christelle , Varlet Pascale , Masliah-Planchon Julien , Bourdeaut Franck , Guillaud-Bataille Marine , Abbas Rachid , Bertozzi Anne-Isabelle , Fouyssac Fanny , Huybrechts Sophie , Puget Stéphanie , Bressac-De Paillerets Brigitte , Caron Olivier , Sevenet Nicolas , Dimaria Marina , Villebasse Sophie , Delattre Olivier , Valteau-Couanet Dominique , Grill Jacques , Brugières Laurence 
Published: November 2017

Abstract

Background
Germline mutations of suppressor of fused homolog (SUFU) predispose to sonic hedgehog (SHH) medulloblastoma. Germline SUFU mutations have been reported in nevoid basal cell carcinoma syndrome (NBCCS), but little is known about the cancer risk and clinical spectrum.

Methods
We performed a retrospective review of all patients with medulloblastoma and a germline SUFU mutation in France.

Results
Twenty-two patients from 17 families were identified with medulloblastoma and a germline SUFU mutation (median age at diagnosis: 16.5 mo). Macrocrania was present in 20 patients, but only 5 met the diagnostic criteria for NBCCS. Despite treatment with surgery and chemotherapy, to avoid radiotherapy in all patients except one, the outcome was worse than expected for SHH medulloblastoma, due to the high incidence of local relapses (8/22 patients) and second malignancies (n = 6 in 4/22 patients). The 5-year progression-free survival and overall survival rates were 42% and 66%. Mutations were inherited in 79% of patients, and 34 additional SUFU mutation carriers were identified within 14 families. Medulloblastoma penetrance was incomplete, but higher than in Patched 1 (PTCH1) mutation carriers. Besides medulloblastoma, 19 other tumors were recorded among the 56 SUFU mutation carriers, including basal cell carcinoma (BCC) in 2 patients and meningioma in 3 patients.

Conclusion
Germline SUFU mutations strongly predispose to medulloblastoma in the first years of life, with worse prognosis than usually observed for SHH medulloblastoma. The clinical spectrum differs between SUFU and PTCH1 mutation carriers, and BCC incidence is much lower in SUFU mutation carriers. The optimal treatment of SUFU mutation–associated medulloblastoma has not been defined.
Single cell transcriptomics of regulatory T cells reveals trajectories of tissue adaptation
Authors: Miragaia Ricardo J , Gomes Tomás , Chomka Agnieszka , Jardine Laura , Riedel Angela , Hegazy Ahmed N. , Lindeman Ida , Emerton Guy , Krausgruber Thomas , Shields Jacqueline , Haniffa Muzlifah , Powrie Fiona , Teichmann Sarah A. 
Published: November 2017

SummaryNon-lymphoid tissues (NLTs) harbour a pool of adaptive immune cells, the development and phenotype of which remains largely unexplored. Here, we used single-cell RNA-seq to characterise CD4+regulatory (Treg) and memory (Tmem) T cells in mouse skin and colon, the respective draining lymph nodes and spleen. From this data, we modelled a continuous lymphoid-to-NLT trajectory for Treg, and reconstructed the mechanisms of cell migration and NLT adaption. This revealed a shared transcriptional programme of NLT priming in both skin and colon-associated lymph nodes, followed by tissue-specific adaptation. Predicted migration kinetics were validated using a melanoma-induction model, emphasizing the relevance of key regulators and receptors, includingBatf, Rora, Ccr8, Samsn1. Finally, we profiled human blood and NLT Treg and Tmem cells, identifying cross-mammalian conserved tissue signatures. In summary, we have identified molecular signals mediating NLT Treg recruitment and tissue adaptation through the combined use of computational prediction andin vivovalidation.