bluuebunny/crossref_metadata_2025_split huggingface dataset:
The powers of a social auditor in a global production network: the case of Verité and the exposure of forced labour in the electronics industry
Authors: Raj-Reichert Gale 
Published: October 2019

AbstractResearch on labour governance actors in global production networks (GPNs) has been limited to civil society organisations, firms and governments. Understanding the influence of actors in GPNs has been dealt with singular and overt modes of relational power. This paper contributes to both debates by examining an intermediary actor—the social auditing organisation Verité—and its exercise of multiple modes of overt and covert powers to illustrate the complex terrain of change in GPNs. Verité, whose exposure of forced labour in Malaysian electronics subsequently changed labour governance practices in the electronics industry, mobilised power resources of credible information to exercise powers of expert authority and acts of dissimulation across various networked relationships in the GPN. This paper puts forth a multi-power framework of analysis to understand the micro-politics of GPNs.
The Trick of the Hedgehog: Case Report and Short Review About Archaeopsylla erinacei (Siphonaptera: Pulicidae) in Human Health
Authors: Greigert Valentin , Brunet Julie , Ouarti Basma , Laroche Maureen , Pfaff Alexander W , Henon Nicolas , Lemoine Jean-Philippe , Mathieu Bruno , Parola Philippe , Candolfi Ermanno , Abou-Bacar Ahmed 
Published: October 2019

AbstractFleas are ectoparasites of various animals, including Homo sapiens Linnaeus, 1758 (Primates: Hominidae). Among the species relevant to the human health field, either due to their dermatopathological potential or because of their role as vectors of microorganisms responsible for infectious diseases, such as plague or murine typhus, are the human flea, oriental rat flea, closely related cat and dog fleas, and chigoe flea. However, other species can accidentally infest humans. We have herein reported two unusual cases of humans infested and bitten by Archaeopsylla erinacei, the hedgehog flea. This species has been identified using stereomicroscopy, on the base of key characteristics. Furthermore, a brief literature review has revealed that hedgehog fleas could carry human-infectious agents, such as Rickettsia felis Bouyer et al. 2001 (Rickettsiales: Rickettsiaceae) or Bartonella henselae Regnery et al.1992 (Rhizobiales: Bartonellaceae). Using molecular biology, we thus tested nine A. erinacei specimens taken from these patients, for several bacteria species commonly associated with hematophagous arthropods, implicated in human pathology. However, all our samples were proven negative. The role of A. erinacei in human epidemiology has never been evaluated to date. This report sought to remind us that these fleas can be accidental parasites in humans. In addition, recent findings pertaining to bacteria of medical interest that are present in these insects should be brought to the fore, given that the question of their role as vectors in human infections remains unanswered and deserves further investigation.
The Survival Job Trap: Explaining Refugee Employment Outcomes in Chicago and the Contributing Factors
Authors: Lumley-Sapanski Audrey 
Published: October 2019

AbstractRefugees resettled through the United States Refugee Admissions Program are expected to become economically self-sufficient by 90 days post arrival. To meet this expectation, refugee resettlement agencies attempt to place refugees in employment as rapidly as possible. Consequently, refugees are placed into pre-identified jobs—termed survival jobs—at partner employers in the secondary labour market largely irrespective of career background. This study examines the long-term employment and socio-economic outcomes of refugees given the agency approach and resulting initial job placement. To do so, I use individual employment records from a refugee resettlement agency in Chicago, semi-structured interviews with refugees and autoethnography conducted over an eight-year period (2008–16). I find that the initial employment placements made by the refugee resettlement agency in the immediate period post-arrival have long-term implications for economic integration. Refugees in general, but in particular those who arrive with less relevant human capital, remain in employment at agency partners five years after arrival. These positions offer limited opportunities for upward economic mobility, leaving many refugees at or near the Federal Poverty Line.
Deblending and classifying astronomical sources with Mask R-CNN deep learning
Authors: Burke Colin J , Aleo Patrick D , Chen Yu-Ching , Liu Xin , Peterson John R , Sembroski Glenn H , Lin Joshua Yao-Yu 
Published: October 2019

ABSTRACT
We apply a new deep learning technique to detect, classify, and deblend sources in multiband astronomical images. We train and evaluate the performance of an artificial neural network built on the Mask Region-based Convolutional Neural Network image processing framework, a general code for efficient object detection, classification, and instance segmentation. After evaluating the performance of our network against simulated ground truth images for star and galaxy classes, we find a precision of 92 per cent at 80 per cent recall for stars and a precision of 98 per cent at 80 per cent recall for galaxies in a typical field with ∼30 galaxies arcmin−2. We investigate the deblending capability of our code, and find that clean deblends are handled robustly during object masking, even for significantly blended sources. This technique, or extensions using similar network architectures, may be applied to current and future deep imaging surveys such as Large Synoptic Survey Telescope and Wide-Field Infrared Survey Telescope. Our code, astro r-cnn, is publicly available at https://github.com/burke86/astro_rcnn.
Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering
Authors: Zheng Yanli , Han Jiamei , Wang Baiyang , Hu Xiaoyun , Li Runxia , Shen Wei , Ma Xiangdong , Ma Lixin , Yi Li , Yang Shihui , Peng Wenfang 
Published: October 2019

AbstractApplication of CRISPR-based technologies in non-model microorganisms is currently very limited. Here, we reported efficient genome engineering of an important industrial microorganism, Zymomonas mobilis, by repurposing the endogenous Type I-F CRISPR–Cas system upon its functional characterization. This toolkit included a series of genome engineering plasmids, each carrying an artificial self-targeting CRISPR and a donor DNA for the recovery of recombinants. Through this toolkit, various genome engineering purposes were efficiently achieved, including knockout of ZMO0038 (100% efficiency), cas2/3 (100%), and a genomic fragment of >10 kb (50%), replacement of cas2/3 with mCherry gene (100%), in situ nucleotide substitution (100%) and His-tagging of ZMO0038 (100%), and multiplex gene deletion (18.75%) upon optimal donor size determination. Additionally, the Type I-F system was further applied for CRISPRi upon Cas2/3 depletion, which has been demonstrated to successfully silence the chromosomally integrated mCherry gene with its fluorescence intensity reduced by up to 88%. Moreover, we demonstrated that genome engineering efficiency could be improved under a restriction–modification (R–M) deficient background, suggesting the perturbance of genome editing by other co-existing DNA targeting modules such as the R–M system. This study might shed light on exploiting and improving CRISPR–Cas systems in other microorganisms for genome editing and metabolic engineering practices.
ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology
Authors: Arnaiz Olivier , Meyer Eric , Sperling Linda 
Published: October 2019

AbstractParameciumDB (https://paramecium.i2bc.paris-saclay.fr) is a community model organism database for the genome and genetics of the ciliate Paramecium. ParameciumDB development relies on the GMOD (www.gmod.org) toolkit. The ParameciumDB web site has been publicly available since 2006 when the P. tetraurelia somatic genome sequence was released, revealing that a series of whole genome duplications punctuated the evolutionary history of the species. The genome is linked to available genetic data and stocks. ParameciumDB has undergone major changes in its content and website since the last update published in 2011. Genomes from multiple Paramecium species, especially from the P. aurelia complex, are now included in ParameciumDB. A new modern web interface accompanies this transition to a database for the whole Paramecium genus. Gene pages have been enriched with orthology relationships, among the Paramecium species and with a panel of model organisms across the eukaryotic tree. This update also presents expert curation of Paramecium mitochondrial genomes.
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update
Authors: Licata Luana , Lo Surdo Prisca , Iannuccelli Marta , Palma Alessandro , Micarelli Elisa , Perfetto Livia , Peluso Daniele , Calderone Alberto , Castagnoli Luisa , Cesareni Gianni 
Published: October 2019

Abstract
The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regulation) and to the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the up/down-regulation of the target entity. Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled. SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc. We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction. We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant formats, such as PSI-MI CausalTAB and GMT. The data are freely accessible and downloadable at https://signor.uniroma2.it/.
Dietary saturated fat and heart disease: a narrative review
Authors: Heileson Jeffery L 
Published: October 2019

AbstractThe American Heart Association (AHA) recently published a meta-analysis that confirmed their 60-year-old recommendation to limit saturated fat (SFA, saturated fatty acid) and replace it with polyunsaturated fat to reduce the risk of heart disease based on the strength of 4 Core Trials. To assess the evidence for this recommendation, meta-analyses on the effect of SFA consumption on heart disease outcomes were reviewed. Nineteen meta-analyses addressing this topic were identified: 9 observational studies and 10 randomized controlled trials. Meta-analyses of observational studies found no association between SFA intake and heart disease, while meta-analyses of randomized controlled trials were inconsistent but tended to show a lack of an association. The inconsistency seems to have been mediated by the differing clinical trials included. For example, the AHA meta-analysis only included 4 trials (the Core Trials), and those trials contained design and methodological flaws and did not meet all the predefined inclusion criteria. The AHA stance regarding the strength of the evidence for the recommendation to limit SFAs for heart disease prevention may be overstated and in need of reevaluation.
Migration of endothelial cells into photo-responsive hydrogels with tunable modulus under the presence of pro-inflammatory macrophages
Authors: Cao Wangbei , Li Xuguang , Zuo Xingang , Gao Changyou 
Published: October 2019

AbstractCell migration in three-dimensional environment is extremely important for tissue regeneration and other biological processes. In this work, a model system was developed to study how endothelial cells (ECs) migrate into photo-responsive hydrogels under the presence of pro-inflammatory macrophages. The hydrogel was synthesized from hyaluronic acid grafted with coumarin and methacrylate moieties by both carbon–carbon covalent linking and coumarin dimerization under UV irradiation at 365 nm. The structure of the hydrogel was conveniently modulated by UV irradiation at 254 nm to decompose the coumarin dimers, leading to the significant decrease of modulus and increase of swelling ratio and mesh size. Under the presence of M1 macrophages, ECs were induced to migrate into the hydrogels with a different degree. A significant larger net displacement of ECs was found in the softer hydrogel obtained by irradiation with UV at 254 nm than in the stiffer original one at day 7.
Implementation of a Meaning-Centered Psychotherapy training (MCPT) program for oncology clinicians: a qualitative analysis of facilitators and barriers
Authors: Polacek Laura C , Reisch Sally , Saracino Rebecca M , Pessin Hayley , Breitbart William 
Published: October 2019

Abstract
The Meaning-Centered Psychotherapy training program (MCPT) is a multimodal, intensive, in-person program that trains cancer care providers in the evidence-based psychosocial treatment Meaning-Centered Psychotherapy (MCP). This analysis aimed to identify barriers and facilitators to clinical implementation (CI) at 1 year post-training. Trainee feedback regarding CI was collected via a mixed-methods questionnaire, including rating the ease of CI and free-text response identifying facilitators and barriers to CI. Descriptive statistics and thematic content analysis of follow-up data from the first five MCPT training cohorts (n = 55) were performed to assess CI and its facilitators and barriers. One third of participants indicated that it was at least somewhat difficult to implement MCP in clinical practice. Trainee-identified facilitators and barriers to CI were characterized within four main categories: program, patient, treatment, and institution. Within each of these factors, clinicians reported a variety of components that contributed to or hindered their ability to implement MCP. MCPT itself was reported as a facilitator. Patient access and interest were simultaneously identified as facilitators for some and barriers for others. Some trainees found the MCP treatment structure helpful in addressing important patient psychosocial needs, while others felt it was too restrictive. Institutional support played an important role in whether trainees felt hindered or helped to implement MCP. These initial results provide important insight into the program’s strengths and have fostered improvements to the MCPT program to better facilitate CI. Further study of MCPT CI is warranted, and theme refinement will be possible with a larger sample.
Patient-Level Value Analysis: An Innovative Approach to Optimize Care Delivery
Authors: McCreary Dylan L. , Dugarte Anthony J. , Vang Sandy , Plowman Brad , Williams Benjamin R. , Parikh Harsh R. , Cunningham Brian P. 
Published: October 2019

Background:
An increasing emphasis has been placed on developing value-based care delivery systems in orthopaedics to combat rising health care costs. The goal of these systems is to both measure and improve the provisional value of care. Patient-level value analysis creates a mechanism to quantify and optimize value within a procedure, in contrast to traditional methods, which only measures value. The purpose of this study was to develop a patient-level value analysis model and determine the efficacy of this model to improve value in orthopaedic care.

Methods:
Patients treated operatively for isolated closed ankle fractures at a single level 1 trauma center were prospectively identified. Short musculoskeletal function assessment was collected at the time of the initial clinical presentation and 6 months postoperatively. The cost of care was determined using time-driven activity-based costing, which included personnel, supplies, length of stay, implants, pharmacy, and radiology. Value was defined as each patient's change in the outcome score divided by their cost as determined by time-driven activity-based costing. A multiple linear regression was performed to determine which aspects of care significantly predicted value.

Results:
Forty-nine patients met inclusion/exclusion criteria. The multiple linear regression indicated treatment by physician D (β = −0.135, P = 0.04) and inpatient stay (β = −0.468, P < 0.01) were predictors of lesser value and represent areas for potential care pathway and value improvement.

Conclusions:
Patient-level value analysis represents a paradigm shift in the quantification of value. We recommend surgeons, practices, and health care systems begin implementing a system to quantify and optimize the value of care provided.

Level of Evidence:
Level III. See Instructions for Authors for a complete description of levels of evidence.
Long-Term Performance of Laboratory-Developed Liquid Chromatography–Tandem Mass Spectrometry Tests and a Food and Drug Administration–Approved Immunoassay for the Therapeutic Drug Monitoring of Everolimus
Authors: Schniedewind Björn , Meyer Eric J. , Christians Uwe 
Published: October 2019

Background:
Laboratory-developed tests (LDTs) are analytical tests developed and validated “in-house” for clinical diagnosis. Regulatory agencies, such as the United States Food and Drug Administration (FDA), encourage using regulatory-approved assays rather than LDTs. In the ongoing Zortracker everolimus study, samples were provided monthly to participating clinical laboratories that conduct therapeutic drug monitoring of everolimus. This allowed for the long-term (6-year) comparison of the performance of liquid chromatography–tandem mass spectrometry (LC-MS/MS) assays, which are LDTs, to the FDA-approved everolimus Quantitative Microsphere System (QMS).

Methods:
Each laboratory received the same 3 blinded samples. LC-MS/MS and QMS assays were compared using Passing Bablok regression analysis. Data were analyzed in 12-month periods to detect trends over time.

Results:
The slopes of the Passing Bablok regression curves remained unchanged in 2013 and 2014 (reference LC-MS/MS; test QMS: slope = 0.934 and 1.008). However, by 2016, the slope increased significantly to between 1.111 and 1.320, then dropped to 0.980 in 2017 and 0.912 in 2018, suggestive of changes in QMS bias compared with LC-MS/MS over longer periods. Outliers did not affect these results. The interlaboratory variability of LC-MS/MS and QMS remained unchanged from 2013 to 2015, with coefficients of variation of 15.3%, 18.4%, and 17.2% for LC-MS/MS, and 13.0%, 13.1%, and 15.3% for QMS, respectively, per year. At the end of the observation period, the average coefficients of variation in LC-MS/MS laboratories dropped to 14.3%, 12.6%, and 14.2%, whereas the variability in QMS laboratories was 19.5%, 13.3%, and 19.6% in 2016, 2017, and 2018, respectively.

Conclusions:
Initially, QMS everolimus concentrations in patient samples were comparable with those detected in LC-MS/MS laboratories. However, concentration bias of the QMS assay significantly changed within 6 years, emphasizing the need for long-term, independent performance tracking of therapeutic drug monitoring assays, including FDA-approved assays.
Long-term research needed to avoid spurious and misleading trends in sustainability attributes of no-till
Authors: Cusser Sarah , Bahlai Christie , Swinton Scott M. , Robertson G. Philip , Haddad Nick M. 
Published: October 2019

ABSTRACTAgricultural management recommendations based on short-term studies can produce findings inconsistent with long-term reality. Here, we test the long-term relative profitability and environmental sustainability of continuous no-till agriculture practices on crop yield, soil moisture, and N2O fluxes. Using a moving window approach, we investigate the development and stability of several attributes of continuous no-till as compared to conventional till agriculture over a 29-year period at a site in the upper Midwest, U.S. We find that over a decade is needed to detect the consistent benefits of no-till on important attributes at this site. Both crop yield and soil moisture required periods 15 years or longer to generate patterns consistent with 29-year trends. Only marginally significant trends for N2O fluxes appeared in this period. Importantly, significant but misleading short-term trends appeared in more than 20% of the periods examined. Relative profitability analysis suggests that 10 years after initial implementation, 86% of periods recuperated the initial expense of no-till implementation, with the probability of higher relative profit increasing with longevity. Results underscore the essential importance of decade and longer studies for revealing the long-term dynamics and emergent outcomes of agricultural practices for different sustainability attributes and are consistent with recommendations to support the long-term adoption of no-till management.GRAPHICAL ABSTRACTHIGHLIGHTSWe test long-term effects of no-till on yield, soil moisture, and N2O fluxesWe examine 29 years of data with a moving window and relative profitability methodIt takes at least a decade to detect consistent benefits of no-tillShorter studies can produce significant but misleading findingsLong studies are essential to reveal the dynamics of agricultural management
Enhancing fMRI language lateralization indices by homotopic mapping
Authors: Pesci Matteo , van Steensel Mariska , Ramsey Nick , Raemaekers Mathijs 
Published: October 2019

AbstractThe non-invasive nature of fMRI would make it an excellent tool for determining language lateralization, potentially replacing the WADA test that is now considered the gold standard. However, while the result of the WADA test has 3 straightforward categories, i.e. left, right, or bilateral language lateralization, fMRI lateralization indices (LIs) are on a continuous scale between −1 (completely right lateralized) and 1 (completely left lateralized), requiring arbitrary thresholding to come to a useful clinical measure. We hypothesize that the absence of clear categories in fMRI LIs is in part linked to imperfect fMRI task control and/or homotopically mapped language activity in the non-dominant hemisphere. In this study we attempt to account for these sources of brain activity by making a detailed homotopic comparison between voxels in the language areas and their homologues, which is now possible using the Cgrid toolbox. 36 epilepsy were included who underwent presurgical fMRI including a picture naming and verb generation task, in addition to the WADA test, functional Transcranial Doppler sonography (fTCD), or Electrocortical stimulation (ECS). LIs were calculated using a traditional approach, and a novel approach based on the paired comparison between language voxels and their homologues. We observed that lateralization indices came in closer alignment with those established by the WADA test, ECS, of fTCD. Activity maps indicated that the accounting for imperfect fMRI task control was at least part of the reason for the improvement when using the new approach. This Cgrid based approach could help fMRI replacing the more invasive WADA test in the future.