bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathway sensor-based functional genomics screening identifies modulators of neuronal activity
Authors: Herholt Alexander , Brankatschk Ben , Kannaiyan Nirmal , Papiol Sergi , Wichert Sven P. , Wehr Michael C. , Rossner Moritz J. 
Published: November 2018

AbstractNeuronal signal transduction shapes brain function and malfunction may cause mental disorders. Despite the existence of functional genomics screens for proliferation and toxicity, neuronal signalling has been difficult to address so far. To overcome this limitation, we developed a pooled screening assay which combines barcoded activity reporters with pooled genetic perturbation in a dual-expression adeno-associated virus (AAV) library. With this approach, termed pathScreener, we comprehensively dissect signalling pathways in postmitotic neurons. This overcomes several limitations of lentiviral-based screens. By applying first a barcoded and multiplexed reporter assay, termed cisProfiler, we identified the synaptic-activity responsive element (SARE) as top performance sensor of neuronal activity. Next, we targeted more than 4,400 genes and screened for modulatory effects on SARE activity in primary cortical neurons. We identified with high replicability many known genes involved in glutamatergic synapse-to-nucleus signalling of which a subset was validated in orthogonal assays. Several others have not yet been associated with the regulation of neuronal activity such as the hedgehog signalling membersPtch2andIft57. This assay thus enhances the toolbox for analysing regulatory processes during neuronal signalling and may help identifying novel targets for brain disorders.
Predicting Patient-ventilator Asynchronies with Hidden Markov Models
Authors: Marchuk Yaroslav , Magrans Rudys , Sales Bernat , Montanya Jaume , López-Aguilar Josefina , de Haro Candelaria , Gomà Gemma , Subirà Carles , Fernández Rafael , Kacmarek Robert M. , Blanch Lluis 
Published: November 2018

AbstractIn mechanical ventilation, it is paramount to ensure the patient’s ventilatory demand is met while minimizing asynchronies. We aimed to develop a model to predict the likelihood of asynchronies occurring. We analyzed 10,409,357 breaths from 51 critically ill patients who underwent mechanical ventilation >24 h. Patients were continuously monitored and common asynchronies were identified and regularly indexed. Based on discrete time-series data representing the total count of asynchronies, we defined four states or levels of risk of asynchronies, z1 (very-low-risk) – z4 (very-high-risk). A Poisson hidden Markov model was used to predict the probability of each level of risk occurring in the next period. Long periods with very few asynchronous events, and consequently very-low-risk, were more likely than periods with many events (state z4). States were persistent; large shifts of states were uncommon and most switches were to neighbouring states. Thus, patients entering states with a high number of asynchronies were very likely to continue in that state, which may have serious implications. This novel approach to dealing with patient-ventilator asynchrony is a first step in developing smart alarms to alert professionals to patients entering high-risk states so they can consider actions to improve patient-ventilator interaction.
Creation of Hollow Calcite Single Crystals with CQDs: Synthesis, Characterization, and Fast and Efficient Decontamination of Cd(II)
Authors: Yang Tianli , He Ren , Nie Guihua , Wang Wenlei , Zhang Gui , Hu Yunchu , Wu Lichao 
Published: November 2018

AbstractIn this work, carbon quantum dots were first prepared through one-pot hydrothermal route of the propyl aldehyde and sodium hydroxide via an aldol condensation reaction, and a novel solid-phase extraction adsorbent of hollow calcite single crystals was prepared via the precipitation of metal nitrates by the CO2 diffusion method in the presence of CQDs and further applied for excessive Cd(II) ions removal from water. The spectra and morphologies of the etched calcite were investigated by X-ray diffraction, Fourier transform infrared spectrometry, Scanning electron microscope, and Transmission electron microscopy. The results show that the CQDs etching technique successfully furnish a strategy for manufacturing interface defects onto the calcite crystal. Bath studies were done to evaluate the effects of the major parameters onto Cd(II) adsorption by the etched calcite, such as pH, contact time, and initial Cd(II) concentration. The Cd(II) adsorption onto the new adsorbent could reach a maximum adsorption amount of 66.68 mg/g at 120 min due to the abundant exterior adsorption sites on the adsorbent. The adsorption kinetics and adsorption isotherms of Cd(II) on the etched calcite were also investigated. The experimental datum showed that the adsorption kinetics and isotherms of Cd(II) on the etched calcite were well-fitted by the pseudo-second-order kinetic model and the Freundlich isotherm model respectively. The adsorption mechanisms could be primarily explained as the formation of Cd(OH)2 and CaxCd1−xCO3 solid solution on the adsorbent surface with the help of X-ray photoelectron spectroscopy.
Bovine neutrophils form extracellular traps in response to the gastrointestinal parasite Ostertagia ostertagi
Authors: Mendez Jonatan , Sun Donglei , Tuo Wenbin , Xiao Zhengguo 
Published: November 2018

AbstractOstertagia ostertagi (OO) is a widespread parasite that causes chronic infection in cattle and leads to annual losses of billions of dollars in the cattle industry. It remains unclear why cattle are unable to mount an effective immune response despite a large influx of immune cells to the infected abomasal mucosa and draining lymph nodes. Neutrophils, the immune system’s first responders, have the capacity to release neutrophil extracellular traps (NETs) to contain various pathogens, including some parasites. In the present study, the mechanisms by which O. ostertagi influences bovine NET formation were investigated. O. ostertagi larval soluble extract (OO extract) was able to induce typical NETs by purified neutrophils in vitro, confirmed by co-localization of extracellular DNA with typical NET-associated proteins histone and neutrophil elastase (NE). Consistent with existing literature, inhibition assays demonstrated that these OO extract-induced NETs were dependent upon the enzymes NADPH oxidase and myeloperoxidase (MPO). Live OO stage 4 larvae (L4) stimulated neutrophils to form NETs similar to those induced by OO extract. Bovine neutrophils also released NETs in response to Caenorhabditis elegans, a free-living soil nematode, suggesting that bovine NET production may be a conserved mechanism against a broad range of nematodes. This is the first report demonstrating O. ostertagi-induced NET formation by bovine neutrophils, a potentially underappreciated mechanism in the early immune response against nematode infections.
Aspartic and Glutamic Acid Templated Peptides Conjugation on Plasma Modified Nanofibers for Osteogenic Differentiation of Human Mesenchymal Stem Cells: A Comparative Study
Authors: Onak Günnur , Şen Mustafa , Horzum Nesrin , Ercan Utku Kürşat , Yaralı Ziyşan Buse , Garipcan Bora , Karaman Ozan 
Published: November 2018

AbstractOptimization of nanofiber (NF) surface properties is critical to achieve an adequate cellular response. Here, the impact of conjugation of biomimetic aspartic acid (ASP) and glutamic acid (GLU) templated peptides with poly(lactic-co-glycolic acid) (PLGA) electrospun NF on osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (hMSCs) was evaluated. Cold atmospheric plasma (CAP) was used to functionalize the NF surface and thus to mediate the conjugation. The influence of the CAP treatment following with peptide conjugation to the NF surface was assessed using water contact angle measurements, Fourier-Transform Infrared Spectroscopy (FTIR) and X-ray Photoelectron Spectroscopy (XPS). The effect of CAP treatment on morphology of NF was also checked using Scanning Electron Microscopy (SEM). Both the hydrophilicity of NF and the number of the carboxyl (-COOH) groups on the surface increased with respect to CAP treatment. Results demonstrated that CAP treatment significantly enhanced peptide conjugation on the surface of NF. Osteogenic differentiation results indicated that conjugating of biomimetic ASP templated peptides sharply increased alkaline phosphatase (ALP) activity, calcium content, and expression of key osteogenic markers of collagen type I (Col-I), osteocalcin (OC), and osteopontin (OP) compared to GLU conjugated (GLU-pNF) and CAP treated NF (pNF). It was further depicted that ASP sequences are the major fragments that influence the mineralization and osteogenic differentiation in non-collagenous proteins of bone extracellular matrix.
LRIG1 acts as a critical regulator of melanoma cell invasion, migration, and vasculogenic mimicry upon hypoxia by regulating EGFR/ERK-triggered epithelial–mesenchymal transition
Authors: Li Wei , Zhou Yubo 
Published: November 2018

Abstract
Intratumoral hypoxia is a well-known feature of solid cancers and constitutes a major contributor to cancer metastasis and poor outcomes including melanoma. Leucine-rich repeats and Ig-like domains 1 (LRIG1) participate in the aggressive progression of several tumors, where its expression is frequently decreased. In the present study, hypoxia exposure aggravated melanoma cell invasion, migration, vasculogenic mimicry (VM), and epithelial–mesenchymal transition (EMT). During this process, LRIG1 expression was also decreased. Importantly, overexpression of LRIG1 notably counteracted hypoxia-induced invasion, migration, and VM, which was further augmented after LRIG1 inhibition. Mechanism analysis corroborated that LRIG1 elevation muted hypoxia-induced EMT by suppressing E-cadherin expression and increasing N-cadherin expression. Conversely, cessation of LRIG1 further potentiated hypoxia-triggered EMT. Additionally, hypoxia stimulation activated the epidermal growth factor receptor (EGFR)/ERK pathway, which was dampened by LRIG1 up-regulation but further activated by LRIG1 inhibition. More important, blocking this pathway with its antagonist erlotinib abrogated LRIG1 suppression-induced EMT, and subsequently cell invasion, migration, and VM of melanoma cells under hypoxia. Together, these findings suggest that LRIG1 overexpression can antagonize hypoxia-evoked aggressive metastatic phenotype by suppressing cell invasion, migration, and VM via regulating EGFR/ERK-mediated EMT process. Therefore, these findings may provide a promising target for melanoma therapy.
Direct torque control strategy of five‐phase PMSM with load capacity enhancement
Authors: Zhou Yangzhong , Yan Zhen , Duan Qingtao , Wang Lingbo , Wu Xin 
Published: November 2018

A direct torque control (DTC) strategy of five‐phase permanent magnet synchronous motor (PMSM) is proposed in this study. The proposed DTC scheme uses five‐phase inverter to output basic voltage vector or discrete synthesised voltage vectors in one control period to realise the direct control of torque and flux on the fundamental and third harmonic planes simultaneously, and then realise the third harmonic current injection to enhance the load capacity. In order to realise the third harmonic current injection with maximum torque outputting and minimum peak of stator current, the maximum torque per ampere (MTPA) scheme is proposed in which the minimum copper loss and the same phase relation between fundamental and third harmonic currents are taken as the constraint conditions, and the amplitude of the fundamental and third harmonic fluxes and the optimal torque distribution ratio are derived in MTPA. A TMS320F2812‐based digital controller is adopted as a core to construct the DTC experimental platform of the five‐phase PMSM with 800 W rated power. The results of experiment and simulation show that the proposed DTC strategy can improve the maximum load torque of the motor, reduce the flux density of the stator and improve the core utilisation rate of the stator.
Acute Liver Failure
Authors: Rajaram Priyanka , Subramanian Ram 
Published: November 2018

AbstractAcute liver failure (ALF) is a condition that can rapidly progress to multiorgan failure. This article focuses on the diagnosis and management of ALF. We provide a detailed review of the common etiologies of ALF, including acetaminophen overdose, viral hepatitis, drug-induced liver injury, Wilson's disease, and autoimmune hepatitis. The article then addresses how to recognize ALF and reviews the role of common laboratory and imaging tests in establishing this diagnosis. The remainder of the article details the management of hepatic and extrahepatic organ dysfunctions in ALF. The article concludes with a discussion regarding the prognostication of patients with ALF and the criteria for considering liver transplantation.
The syntax of Dutch gapping
Authors: Broekhuis Hans 
Published: November 2018

AbstractThis article takes as its point of departureNeijt’s (1979)claim that gapping is a rule of syntax with properties also found inwh-movement constructions. I will refine this proposal by concluding that gapping remnants are A′-moved into the clause-initial position (SpecCP) and/or the specifiers of functional projections such as TopP, FocP and NegP found in the middle field of the clause. I will further show that this approach sheds new light on various problems (such as the distribution of modal and polarity particles) not satisfactorily solved in earlier analyses.
Voice and information structure in Surinamese Javanese
Authors: Villerius Sophie 
Published: November 2018

Abstract
This paper examines the grammatical voice system of Indonesian and Surinamese Javanese speakers. Alongside Javanese, the Surinamese speakers also speak Sranantongo and Dutch. Studying the use of voice in both speaker groups shows that it depends both on givenness and animacy of arguments. This interacts with the speaker group. The Surinamese speakers were found to be less discourse-dependent, due to general language contact processes as well as convergence to Dutch and Sranantongo.
Charting the semantics of labour relations in House of Commons debates spanning two hundred years
Authors: Demmen Jane , Jeffries Lesley , Walker Brian 
Published: November 2018

Abstract
In this chapter we use new corpus linguistic software tools to investigate the discourse(s) of labour relations in UK House of Commons debates over the 19th and 20th centuries. Our data is from the Hansard Corpus (1803–2005), and benefits from the annotation of meaning and sense categories with the newly-developed Historical Thesaurus Semantic Tagger (Alexander et al. 2015; Piao et al. 2014). Using the bespoke corpus interface CQPweb Hansard, we carry out automated searches for words tagged with relevant semantic category codes. Our quantitative results enable us to chart the semantics of parliamentary discourse on labour relations over time, providing a detailed empirical basis which, we argue, would usefully support further qualitative analysis in linguistic and other research.
Cross-talk in political discourse
Authors: Toft Amoshaun 
Published: November 2018

Abstract
This chapter examines the ways that speakers connect movements through language use as they build support for their cause, and position it in a broader understanding of the political terrain. Using a corpus of spoken word transcripts aired between 2003–2013 from US broadcast news programme Democracy Now!, we developed a dictionary of named issue movements using corpus linguistics techniques. Semantic network analysis of issue-movement co-mentions revealed that the civil rights movement occupied a central role in facilitating cross-movement talk, and a purposive sub-sample of those stories was examined using qualitative discourse analysis tools to understand how and why. Several language strategies are explored that participants used to make relational connections between issue movements, and I offer some suggestions on how to approach the mixed methods analysis of cross-issue movement talk as political discourse.
Conceptual vs. inter-lexical polysemy
Authors: Evans Vyvyan 
Published: November 2018

Abstract
In this chapter I consider two types of polysemy that have not received wide attention in the cognitive linguistics literature. First, I argue that polysemy can arise from the non-linguistic knowledge to which words facilitate access. This phenomenon I refer to as conceptual polysemy. I illustrate this with an analysis of the lexical item book. Moreover, polysemy also arises from different word forms, which, at least on first blush, appear to share a common semantic representation. This phenomenon I refer to as inter-lexical polysemy. I illustrate with a detailed case study involving an analysis of the prepositional forms in and on. I draw on the Theory of Lexical Concepts and Cognitive Models to account for these phenomena.
The use of hedging devices in L2 legal writing
Authors: Dolgova Jacobsen Natalia 
Published: November 2018

Abstract
The focus of this chapter is to determine the conceptual profile of the rhetorical phenomenon of hedging and to investigate how hedging devices are represented in legal memos produced by L2 writers of English. Because it addresses negotiation of various poles on the reality spectrum, hedging is crucial for the construction of an effective legal memo. A sample of 14 memos is analyzed utilizing a mixed method approach. The analysis demonstrates that the differences in the objective “success” of memos are conditioned by each writer’s textual and functional patterns of hedging. These conclusions elucidate the processes guiding legal memo writing and the longitudinal development of the hedging function in the writing patterns of non-native legal writers.
“A pretty village is a welcome sight”
Authors: Malamatidou Sofia 
Published: November 2018

Abstract
This paper analyses adjectival descriptions used to frame and promote physical space in tourism texts in English and in Greek, and
how any differences are negotiated in translation. A comparison is drawn across three categories of space (human-made, natural,
and abstract) to investigate how each locality affects and is affected by linguistic choices. Methodologically, a corpus
triangulation approach is employed, combining corpora created from three types of tourism websites: original or non-translated
Greek websites; their translations into English; and non-translated websites in English. Results reveal that, while important
differences are observed between English and Greek non-translated texts, translations tend to stay very close to their source
texts, with small differences observed across the three categories of space. This study contributes to both tourism and
translation studies by offering insight into how space is framed across languages, which can inform, and ultimately, transform,
translation practice.
TADOSS: computational estimation of tandem domain swap stability
Authors: Lafita Aleix , Tian Pengfei , Best Robert B , Bateman Alex 
Published: November 2018

Abstract

Summary
Proteins with highly similar tandem domains have shown an increased propensity for misfolding and aggregation. Several molecular explanations have been put forward, such as swapping of adjacent domains, but there is a lack of computational tools to systematically analyze them. We present the TAndem DOmain Swap Stability predictor (TADOSS), a method to computationally estimate the stability of tandem domain-swapped conformations from the structures of single domains, based on previous coarse-grained simulation studies. The tool is able to discriminate domains susceptible to domain swapping and to identify structural regions with high propensity to form hinge loops. TADOSS is a scalable method and suitable for large scale analyses.

Availability and implementation
Source code and documentation are freely available under an MIT license on GitHub at https://github.com/lafita/tadoss.

Supplementary information
Supplementary data are available at Bioinformatics online.
GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making
Authors: Schwarz Johanna , Heider Dominik 
Published: November 2018

Abstract

Motivation
Clinical decision support systems have been applied in numerous fields, ranging from cancer survival toward drug resistance prediction. Nevertheless, clinical decision support systems typically have a caveat: many of them are perceived as black-boxes by non-experts and, unfortunately, the obtained scores cannot usually be interpreted as class probability estimates. In probability-focused medical applications, it is not sufficient to perform well with regards to discrimination and, consequently, various calibration methods have been developed to enable probabilistic interpretation. The aims of this study were (i) to develop a tool for fast and comparative analysis of different calibration methods, (ii) to demonstrate their limitations for the use on clinical data and (iii) to introduce our novel method GUESS.

Results
We compared the performances of two different state-of-the-art calibration methods, namely histogram binning and Bayesian Binning in Quantiles, as well as our novel method GUESS on both, simulated and real-world datasets. GUESS demonstrated calibration performance comparable to the state-of-the-art methods and always retained accurate class discrimination. GUESS showed superior calibration performance in small datasets and therefore may be an optimal calibration method for typical clinical datasets. Moreover, we provide a framework (CalibratR) for R, which can be used to identify the most suitable calibration method for novel datasets in a timely and efficient manner. Using calibrated probability estimates instead of original classifier scores will contribute to the acceptance and dissemination of machine learning based classification models in cost-sensitive applications, such as clinical research.

Availability and implementation
GUESS as part of CalibratR can be downloaded at CRAN.