bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructional schemas in variation
Authors: Silvennoinen Olli O. 
Published: August 2018

AbstractThis paper discusses constructional variation in the domain of contrastive negation in English, using data from the British National Corpus. Contrastive negation refers to constructs with two parts, one negative and the other affirmative, such that the affirmative offers an alternative to the negative in the frame in question (e.g.shaken, not stirred;not once but twice;I don’t like it – I love it). The paper utilises multiple correspondence analysis to explore the degree of synonymy among the various constructional schemas of contrastive negation, finding that different schemas are associated with different semantic, pragmatic and extralinguistic contexts but also that certain schemas do not differ from each other in a significant way.
Particle drop of mimetics in Japanese
Authors: Toratani Kiyoko 
Published: August 2018

Abstract
Drawing on ideas from Discourse Grammar (Heine et al. 2013), this article examines characteristics of the Japanese reduplicated mimetics, arguing that they are transcategorial, able to function across different planes of grammar, either as mimetic adverbs belonging to Sentence Grammar (SG) or mimetic “theticals” belonging to Thetical Grammar (TG) (Kaltenböck et al. 2011: 879). The former expresses a manner of an action, typically occurring in the immediately preverbal position, as in
huwahuwa (to) uku [mim quot float] ‘float
lightly
’. By contrast the latter is the speaker’s re-enactment of the event, as in the case of “
Huwahuwa, shita de tsubuseru toohu gurai no katasa desu.” ‘Fluffy-fluffy, (the baby food should) have softness like tofu that can be crushed by (your) tongue.’, where the mimetic ‘re-enacts’ the speaker’s mouth feel (fluffiness) when she put the food into her mouth. The particle drop of the reduplicated mimetics is syntactically optional in SG, but obligatory in TG. The article suggests adding mimetics to the list of theticals, as the fronted zero-marked mimetics followed by a pause display three of the defining prototypical properties of theticals (Kaltenböck et al. 2011): (i) prosodic property (they display comma intonation), (ii) syntactic independence (they are not modifiers of the predicate), and (iii) semantic non-restrictiveness (they do not restrict the semantic content of the predicate).
Effect of Substrate Orientation on the Growth Direction of In
x
Ga1-x
As Nanowires (NWs)
Authors: Wibowo E , Ulya N , Othaman Z , Marwoto P , Sumpono I , Aji M P , Sulhadi  , Astuti B , Rokhmat M , Suwandi  , Ismardi A , Sutisna  
Published: August 2018

Abstract
We have grown the In
x
Gal-x
As NWs on GaAs(lll), GaAs(100) and Si(lll) substrates via Vapor-Solid-Solid (VSS) mode using MOCVD. We observed that the cylindrical NWs grow perpendicular to the GaAs(lll) substrate. The straight line NWs with an angle of 50.60° to the normal were occurred on GaAs(l00), while kinks NWs were perceived on Si(lll). We found that the growth direction of the In
x
Gal-x
As NWs can be easily controlled using certain orientation of the substrate by considering its lattice mismatch and its surface energy.
The Study of Mechanical Properties and Relaxation Time of Agar Hydrogel for Tissue Mimicking Phantom Material in Magnetic Resonance Imaging
Authors: Dwihapsari Y , Afriana R D , Darminto  
Published: August 2018

Abstract
Agar hydrogel is used for tissue mimicking phantom in magnetic resonance imaging studies. The spin-lattice relaxation time, T1 as an important parameter in Magnetic Resonance Imaging measurement was observed. The T1-value represents how fast the net spin magnetization vector recovers to its equilibrium after generation of magnetic field. To explore mechanical properties of agar, shear modulus was examined using a dynamic mechanical analyser. The relation between mechanical properties and spin-lattice relaxation time of agar hydrogel is discussed.
The Effect of Paramagnetic Agent on Relaxation and Mechanical Properties of Agar Hydrogel for Phantom in Magnetic Resonance Imaging
Authors: Dwihapsari Y , Maulidiyah N , Darminto  
Published: August 2018

Abstract
Agar hydrogel is largely used in magnetic resonance imaging study as tissue mimicking phantom material for its cost-effectiveness and easy preparation. Spin-spin relaxation time, T2 is one important parameter in Magnetic Resonance Imaging study. However, T2 of agar sample is higher than those of human tissues. The addition of paramagnetic agent such as copper sulphate or CuSO4 had been observed to match T2-value of human tissues. In this study, the effect of CuSO4 on relaxation and mechanical properties of agar is observed.
DNA damaging agent-based antibody-drug conjugates for cancer therapy
Authors: Fu Ying , Ho Mitchell 
Published: August 2018

ABSTRACT
Currently, four antibody-drug conjugates (ADCs) are approved by the Food and Drug Administration or the European Medicine Agency to treat cancer patients. More than 60 ADCs are in clinical development for cancer therapy. More than 60% of ADCs in clinical trials employ microtubule inhibitors as their payloads. A better understanding of payloads other than microtubule inhibitors, especially DNA-damaging agents, is important for further development of ADCs. In this review, we highlight an emerging trend of using DNA-damaging agents as payloads for ADCs. This review summarizes recent advances in our understanding gained from ongoing clinical studies; it will help to define the utility of DNA-damaging payloads for ADCs as cancer therapeutics. Future directions of the development of ADCs are also discussed, focusing on targeting drug resistance and combination treatment with immunotherapy.
Computational determination of gene age and characterization of evolutionary dynamics in human
Authors: Yin Hongyan , Li Mengwei , Xia Lin , He Chaozu , Zhang Zhang 
Published: August 2018

AbstractGenes originate at different evolutionary time scales and possess different ages, accordingly presenting diverse functional characteristics and reflecting distinct adaptive evolutionary innovations. In the past decades, progresses have been made in gene age identification by a variety of methods that are principally based on comparative genomics. Here we summarize methods for computational determination of gene age and evaluate the effectiveness of different computational methods for age identification. Our results show that improved age determination can be achieved by combining homolog clustering with phylogeny inference, which enables more accurate age identification in human genes. Accordingly, we characterize evolutionary dynamics of human genes based on an extremely long evolutionary time scale spanning ~4,000 million years from archaea/bacteria to human, revealing that young genes are clustered on certain chromosomes and that Mendelian disease genes (including monogenic disease and polygenic disease genes) and cancer genes exhibit divergent evolutionary origins. Taken together, deciphering genes’ ages as well as their evolutionary dynamics is of fundamental significance in unveiling the underlying mechanisms during evolution and better understanding how young or new genes become indispensable integrants coupled with novel phenotypes and biological diversity.
HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels
Authors: Shen Jiangshan J , Yang Chao , Wang Yong-Fei , Wang Ting-You , Guo Mengbiao , Lau Yu Lung , Zhang Xuejun , Sheng Yujun , Yang Wanling 
Published: August 2018

Abstract

Summary
HLA allele imputation from SNP genotypes has become increasingly useful, but its accuracy is heavily dependent on the reference panels used. HLA-IMPUTER implements HIBAG algorithm for HLA imputation with different population specific reference panels, including a new Han Chinese reference panel derived from 10 689 samples. We provide a convenient platform for researchers to impute HLA alleles and perform association analysis.

Availability and implementation
http://wyanglab.org: 3838/RefPanelWebsite/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Understanding and predicting disease relationships through similarity fusion
Authors: Oerton Erin , Roberts Ian , Lewis Patrick S H , Guilliams Tim , Bender Andreas 
Published: August 2018

Abstract

Motivation
Combining disease relationships across multiple biological levels could aid our understanding of common processes taking place in disease, potentially indicating opportunities for drug sharing. Here, we propose a similarity fusion approach which accounts for differences in information content between different data types, allowing combination of each data type in a balanced manner.

Results
We apply this method to six different types of biological data (ontological, phenotypic, literature co-occurrence, genetic association, gene expression and drug indication data) for 84 diseases to create a ‘disease map’: a network of diseases connected at one or more biological levels. As well as reconstructing known disease relationships, 15% of links in the disease map are novel links spanning traditional ontological classes, such as between psoriasis and inflammatory bowel disease. 62% of links in the disease map represent drug-sharing relationships, illustrating the relevance of the similarity fusion approach to the identification of potential therapeutic relationships.

Availability and implementation
Freely available under the MIT license at https://github.com/e-oerton/disease-similarity-fusion

Supplementary information
Supplementary data are available at Bioinformatics online.
Methods for automatic reference trees and multilevel phylogenetic placement
Authors: Czech Lucas , Barbera Pierre , Stamatakis Alexandros 
Published: August 2018

Abstract

Motivation
In most metagenomic sequencing studies, the initial analysis step consists in assessing the evolutionary provenance of the sequences. Phylogenetic (or Evolutionary) Placement methods can be employed to determine the evolutionary position of sequences with respect to a given reference phylogeny. These placement methods do however face certain limitations: The manual selection of reference sequences is labor-intensive; the computational effort to infer reference phylogenies is substantially larger than for methods that rely on sequence similarity; the number of taxa in the reference phylogeny should be small enough to allow for visually inspecting the results.

Results
We present algorithms to overcome the above limitations. First, we introduce a method to automatically construct representative sequences from databases to infer reference phylogenies. Second, we present an approach for conducting large-scale phylogenetic placements on nested phylogenies. Third, we describe a preprocessing pipeline that allows for handling huge sequence datasets. Our experiments on empirical data show that our methods substantially accelerate the workflow and yield highly accurate placement results.

Availability and implementation
Freely available under GPLv3 at http://github.com/lczech/gappa.

Supplementary information
Supplementary data are available at Bioinformatics online.
Robust prediction of clinical outcomes using cytometry data
Authors: Hu Zicheng , Glicksberg Benjamin S , Butte Atul J 
Published: August 2018

Abstract

Motivation
Flow cytometry and mass cytometry are widely used to diagnose diseases and to predict clinical outcomes. When associating clinical features with cytometry data, traditional analysis methods require cell gating as an intermediate step, leading to information loss and susceptibility to batch effects. Here, we wish to explore an alternative approach that predicts clinical features from cytometry data without the cell-gating step. We also wish to test if such a gating-free approach increases the accuracy and robustness of the prediction.

Results
We propose a novel strategy (CytoDx) to predict clinical outcomes using cytometry data without cell gating. Applying CytoDx on real-world datasets allow us to predict multiple types of clinical features. In particular, CytoDx is able to predict the response to influenza vaccine using highly heterogeneous datasets, demonstrating that it is not only accurate but also robust to batch effects and cytometry platforms.

Availability and implementation
CytoDx is available as an R package on Bioconductor (bioconductor.org/packages/CytoDx). Data and scripts for reproducing the results are available on bitbucket.org/zichenghu_ucsf/cytodx_study_code/downloads.

Supplementary information
Supplementary data are available at Bioinformatics online.
PDV: an integrative proteomics data viewer
Authors: Li Kai , Vaudel Marc , Zhang Bing , Ren Yan , Wen Bo 
Published: August 2018

Abstract

Summary
Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation of peptide identification results. Herein, we present PDV, an integrative proteomics data viewer that can be used to visualize a wide range of proteomics data, including database search results, de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from public proteomics repositories. PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes.

Availability and implementation
PDV software and the user manual are freely available at http://pdv.zhang-lab.org. The source code is available at https://github.com/wenbostar/PDV and is released under the GPL-3 license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Vertical distribution and active carbon transport by pelagic decapods in the North Pacific Subtropical Gyre
Authors: Pakhomov Evgeny A , Podeswa Yasha , Hunt Brian P V , Kwong Lian E 
Published: August 2018

Abstract
Pelagic decapods were sampled during August 2011 in the central North Pacific Subtropical Gyre (NPSG). Depth-stratified samples using a MOCNESS-10 (10 m2 Multiple Opening/Closing Net and Environmental Sensing System) were collected at two stations to the west and north of the Hawaiian island of Oahu: Station Kahe: 21°20.6′N–158°16.4′W and Station ALOHA: 22°45′N–158°00′W. Total decapod abundance and biomass were 4.3 ind. m−2 and 0.71 gDW m−2. While 40 decapod taxa were identified, only 22 species were sampled sufficiently to study quantitatively their vertical migrations. All species were classified into three migration groups: full migrators (6 species); partial migrators (13 species); and non-migrators (3 species). Using measured local temperature profiles along with decapod densities and published models of respiration, excretion and mortality as well as gut fullness data, the individual and total active downward carbon flux was calculated. Active carbon flux of migrating decapods ranged from 383 to 625 µgC m−2 day−1. This active flux was equal to 4.8–7.8% of passive flux at the mean nighttime residence depth of ∼711 m), 2.1–3.4% of passive flux at the mean daytime residence depth (∼262 m), and 1.5–2.4% of passive flux at the base of the euphotic zone (∼173 m). Mortality flux accounted for ∼70% of total active flux, followed by gut flux—∼18%.
Cloud services as the ultimate gate(keeper)
Authors: Lundqvist Björn 
Published: August 2018

Abstract
In the Internet of Things (IoT), the amount and smart use of data will determine whether or not a firm can compete successfully. Manufacturing firms will collect data through sensors in their devices and, at least in the cases of SMEs, likely store the collected data in the cloud, purchasing cloud services and storage from the large e-platform providers doubling as cloud providers. The e-platform providers will also collect data from users of their other services. These data are often generated by the same firms that purchase cloud services when they use the e-platforms to sell goods and services. Access to the data and to data analytics on fair business terms, and the possibility to switch cloud and service providers are vital for the SMEs and, in general, to create a competitive and vibrant IoT. However, cloud and e-platform customers seem to be facing difficulties. According to the EU Commission, SMEs are finding it particularly hard to engage cloud and e-platform providers, and to gain access to cloud services on reasonable, transparent terms. The contracts are skewed in favour of the cloud providers. The customers get locked in and may be obliged to agree not to assert any of their intellectual property rights vis-à-vis the cloud provider or the cloud provider’s network. Moreover, the cloud and e-platform providers may under certain circumstances access and make use of the users’ data, and that may give them a competitive advantage vis-à-vis the users, since the providers may have access to much more data, even data originating from the users’ competitors, suppliers, customers, etc. They can thus use all the data available to them to obtain a fuller picture of whole industries, and they may use that advantage in data to leverage and enter users’ markets. Indeed, they may use the data in the cloud for data-driven business strategies to enter the core market of the firms that have provided them with data in the first place. This article discusses whether competition law can address the conduct of the cloud and e-platform providers, so that firms may access and make use of all the possibilities that the IoT harbours.
‘They Say Our Work Is Not Halal’: Experiences and Challenges of Refugee Community Workers Involved in Gender-based Violence Prevention and Care in Dadaab, Kenya
Authors: Izugbara Chimaraoke , Muthuri Stella , Muuo Sheru , Egesa Carolyne , Franchi Giorgia , Mcalpine Alys , Bacchus Loraine , Hossain Mazeda 
Published: August 2018

Abstract
Notwithstanding the growing centrality of refugee community workers (RCWs) in the current response to gender-based violence (GBV) in the Dadaab refugee camps, they remain poorly studied. Using interview data, we explored the work-related experiences and challenges as well as GBV-related beliefs of RCWs. Whilst they demonstrated elevated knowledge of the forms and drivers of GBV in their community, some of the RCWs did not deem early marriage, female genital mutilation and wife-beating to be GBV acts. In their work, RCWs were motivated by compassion for survivors as well as a sense of community service, but they faced challenges such as insecurity; poor pay; opposition and violence by community members; tense relationships with and suspicion by professional providers; and limited skills and preparation in GBV management. RCWs’ GBV-related beliefs and work experiences underscore the challenges of programming in a complex humanitarian space and offer insights for strengthening their contribution in GBV care and service delivery.
Preoperative Planning Using 3-Dimensional Printing for Complex Paraspinal Schwannoma Resection: 2-Dimensional Operative Video
Authors: Stone Jonathan J , Matsumoto Jane M , Morris Jonathan M , Spinner Robert J 
Published: August 2018

Abstract
Schwannomas are benign peripheral nerve sheath tumors that are typically round, smooth, and straightforward to resect. Occasionally they are more complicated to resect because of their size, location, degree of bony erosion, and vascular or neural compression. These complex lesions frequently require multidisciplinary surgical teams in order to decrease surgical morbidity. Historically, surgical planning consisted of imaging review and verbal communication among team members. 3-dimensional (3D) printing offers a new method for preoperative planning and is becoming more popular in Neurosurgery. This video demonstrates the use of 3D printing for complex paraspinal tumors in the cervical, thoracic, and sacral regions.
The Institutional Review Board Office for Human Research Protection does not require approval for single participant case studies, or a case series with multiple participants. The subjects involved in this study were not identifiable and the general surgical consent form included permission for intraoperative photos.
Minimally Invasive Single-Stage Removal of a Thoracic Dumbbell Tumor from a Posterior Approach: 2-Dimensional Operative Video
Authors: Landriel Federico , Hem Santiago , Yampolsky Claudio 
Published: August 2018

Abstract
Dumbbell-shaped thoracic tumors usually involve the spinal canal and the posterior thoracic cavity. Gross total resection is the treatment of choice, but techniques for surgical excision remain controversial. An anterolateral transthoracic approach may remove the paravertebral component of the tumor, but has limited or no control of the intracanal lesion. A combined posteroanterior approach requires a 2-stage surgery with significant morbidity. The preferred approach depends mainly on the tumor location, size, shape, and its specific anatomical relationship with the surrounding vital structures. We present a surgical video of a single-stage posterior minimally invasive approach for the management of a thoracic dumbbell tumor.
Microsurgical Excision of T12-L1 Pial Arteriovenous Malformation: 3-Dimensional Operative Video
Authors: Zeeshan Qazi , Cheng Chun-Yu , Ghodke Basavaraj V , Sekhar Laligam N 
Published: August 2018

Abstract
This 29-yr-old man presented with progressive paraparesis, sensory loss, allodynia, bowel, and bladder dysfunction for 9 mo, acutely exacerbated in the preceding 24 h. Magnetic resonance imaging scan showed multiple dilated vessels involving the thoracic cord. Spinal angiogram revealed a T12-L1 pial arteriovenous malformation (AVM)/arteriovenous fistula on the left side. It was fed by an L1 radicular artery that filled the anterior spinal artery, which in turn had multiple feeders to a pial AVM. Because of the supply from the anterior spinal artery with multiple feeders to the AVM, and the danger of infarction of the conus, embolization was not performed.
He underwent T11-L1 laminectomy laterally to the pedicles and excision of AVM. There was one large arterialized vein in the midline that had a fistulous connection with an artery coursing up from inferiorly. Despite occlusion of this fistula, the vein was still arterialized. On further exploration, there was a large artery coming in to the subarachnoid space at the T11 level and coursing inferiorly, and entering the intradural pial AVM with a glomus of vessels located at the T12 level in the left anterolateral subpial aspect of the cord. This major artery as well as multiple smaller vessels going into it were cauterized and divided, and the AVM was totally excised.
Postoperative angiogram showed complete excision of the nidus. At 1 mo follow-up, he had complete recovery of motor and bladder functions but bowel dysfunction persisted. He was independent for his daily activities.
Informed consent was obtained from the patient prior to the surgery that included videotaping of the procedure and its distribution for educational purposes. All relevant patient identifiers have also been removed from the video and accompanying radiology slides.