bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decent Work Fundamentalism and Job Destruction in the South African Clothing Manufacturing Industry
Authors: Nattrass Nicoli , Seekings Jeremy 
Published: July 2019

AbstractChapter 6 reviews the history of collective bargaining in the South African clothing manufacturing industry. We show that its profoundly dualist character (high- and low-productivity firms co-existing) has historical and market-related roots and highlight the role of wage policy during and after apartheid in shaping the regional location of firms. The rise of China as a global producer of clothing had a profound impact on the South African industry—but it was the simultaneous introduction of national collective bargaining and the enforcement of minimum wages on relatively low-wage labour-intensive firms that drove the job losses. We describe the 2010/11 ‘compliance drive’ that resulted in legal action against the National Bargaining Council for the Clothing Manufacturing Industry by low-wage employers, including the Chinese firms (that is, owned by people who originated from Taiwan, Hong Kong, or China) in Newcastle seeking to obtain relief from the imposition of sector-wide minimum wages on their labour-intensive firms. Whilst trade union strategy as well as government policy adapted to some extent and many employers transformed their enterprises into workers’ co-operatives, that is to circumvent wage regulation, the outcome was nonetheless the preclusion of employment growth in this crucial sector.
The Political Economy of Upgrading
Authors: Nattrass Nicoli , Seekings Jeremy 
Published: July 2019

AbstractChapter 7 argues that the Southern African Clothing and Textile Workers Union (SACTWU) strategy was complicated by its dual role as a trade union and investment manager. Having taken advantage of investment opportunities provided through ‘black economic empowerment policies’ to grow substantial financial assets and later also direct investments in the clothing manufacturing industry, the union, in effect, was both a representative of labour as well as a capitalist. Its political connections meant that it was well positioned to take advantage of subsidies. The incentives and opportunities facing SACTWU were consistent with a union strategy to have a smaller body of better-paid workers rather than growing its membership of lower-wage workers through labour-intensive job creation. SACTWU is suspicious of the growth of workers’ co-operatives (seeing them as sham and designed solely to avoid minimum wage regulation). We argue that the potential for workers’ co-operatives to generate more transparent and inclusive productive and distributional practices is exciting and consistent with inclusive dualism.
A Mellow Bit of Rhythm
Authors: Burrows George 
Published: July 2019

Abstract
This concluding chapter considers the 1957 album, A Mellow Bit of Rhythm, as a Signifyin(g) form of musical recollection. It rounded off the recorded output of Kirk as a bandleader in a way that re-illuminated the earlier recordings made by his Clouds of Joy within a 1950s hot-jazz context. The retrospective album is shown to be as much a form of stylistic mask-play as the original recordings, as it served to represent a particular kind of ‘authentic’ black-jazz legacy for Andy Kirk and His Clouds of Joy within contemporary stylistic parameters and expectations. The bigger band and its more voluminous sound are considered relative to contemporary audio technologies and tastes and the louder big-band style is shown to re-present Kirk’s recordings of the previous two decades in fresh stylistic and racial garb. Exploring that album ultimately presents an opportunity to reflect on the whole race-political enterprise of the records of Kirk and his band.
TRANSIENT PARADOXICAL WORSENING OF VISION DUE TO GRAVITATIONAL SHIFT OF SUBRETINAL FLUID AFTER PHOTODYNAMIC THERAPY FOR CENTRAL SEROUS CHORIORETINOPATHY
Authors: Saengsirinavin Aim-On , Ma Dahui , Stewart Jay M. 
Published: July 2019

Purpose:
To report an atypical treatment-related complication from photodynamic therapy in central serous chorioretinopathy patient and explain its mechanism.

Methods:
History, physical examination, and imaging data were retrospectively reviewed and obtained from the electronic medical records of the patient.

Results:
A central serous chorioretinopathy patient with several focal leakage spots near the superotemporal arcade was treated with half-fluence verteporfin photodynamic therapy. The patient complained of worse vision after the treatment. Examination showed relocation of subretinal fluid from the superior macula to the central and submacular area, explained by a gravitational shift of subretinal fluid and the predisposing factor of a previously weakened junction between the retinal pigment epithelium and neurosensory retina. Without further treatment, the fluid reabsorbed, and the patient's vision returned to normal.

Conclusion:
This is the first report to describe this transient atypical adverse visual outcome early after photodynamic therapy in a central serous chorioretinopathy patient, caused by a gravitational shift of viscous subretinal fluid.
SPONTANEOUS RESOLUTION OF SUBMACULAR PERFLUOROCARBON LIQUIDS
Authors: Baumann Carmen , Cheng Clarissa , Jalil Assad , Patton Niall 
Published: July 2019

Purpose:
To demonstrate a case of spontaneous resolution of submacular heavy liquid.

Methods:
This is a case report analyzing consecutive data and optical coherence tomography scans of a patient who underwent revisional retinal detachment surgery with pars plana vitrectomy using perfluorocarbon liquid (PFCL) as an adjunct. Postoperatively submacular PFCL bubbles were noted, and after an only partially successful surgical attempt to remove them, the residual PFCL bubbles were monitored over the course of several months. The primary outcome measure was the anatomical appearance and size of the PFCL bubbles on optical coherence tomography. The secondary outcome measure was the functional outcome based on the best-corrected visual acuity.

Results:
We present a case of retained submacular PFCL after complex retinal detachment repair, which could only partially be removed surgically. However, the remaining PFCL droplets resolved spontaneously over several months, with partial anatomical restoration of the retinal layers and improvement in visual acuity.

Conclusion:
We hypothesize that the PFCL bubble was resorbed presumably by the retinal pigment epithelium.
EVALUATION OF SEGMENTAL RETINAL ARTERITIS WITH OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY
Authors: Tsui Edmund , Leong Belinda C. S. , Mehta Nitish , Gupta Akash , Goduni Lediana , Cunningham Emmett T. , Freund K. Bailey , Lee Gregory D. , Dedania Vaidehi S. , Yannuzzi Lawrence A. , Modi Yasha S. 
Published: July 2019

Purpose:
To describe the vascular anatomy and intraluminal flow characteristics of segmental retinal arteritis (SRA) using structural and angiographic optical coherence tomography (OCT).

Methods:
Retrospective case series of consecutive patients presenting with SRA. All patients were evaluated at presentation with fundus photography, spectral domain OCT, and OCT angiography. One patient was imaged with dense B-scan OCT angiography.

Results:
Three eyes of three male patients were evaluated. All examinations were consistent with reactivation of ocular toxoplasmosis with an area of active retinochoroiditis adjacent to a focal chorioretinal scar. Spectral domain OCT through areas of SRA noted on clinical examination demonstrated areas of hyperreflectivity circumscribing the affected vessel with a normoreflective lumen. Optical coherence tomography angiography and dense B-scan OCT angiography demonstrated narrowing of the intraluminal flow signal that correlated with areas of segmental hyperreflectivity on spectral domain OCT. Vascular sections proximal and distal to areas of SRA showed normal flow signal.

Conclusion:
Vessels with SRA demonstrated hyperreflectivity highlighting the vessel wall on spectral domain OCT. Optical coherence tomography angiography showed narrowing of the flow signal within these segments suggesting reduced lumen diameter. Coupling these finding with previous indocyanine green imaging findings in SRA, the collective data suggest the plaques are localized within the vessel wall to either the endothelium or the muscular tunica media without occlusion of the vessel lumen.
Neuroimaging biomarkers differentiate Parkinson disease with and without cognitive impairment and dementia
Authors: Owens-Walton Conor , Jakabek David , Power Brian D. , Walterfang Mark , Hall Sara , van Westen Danielle , Looi Jeffrey C.L. , Shaw Marnie , Hansson Oskar 
Published: July 2019

AbstractMild cognitive impairment in Parkinson disease places a high burden on patients and is likely a precursor to Parkinson disease-related dementia. Studying the functional connectivity and morphology of subcortical structures within basal ganglia-thalamocortical circuits may uncover neuroimaging biomarkers of cognitive dysfunction in PD. We used an atlas-based seed region-of-interest approach to investigate resting-state functional connectivity of important subdivisions of the caudate nucleus, putamen and thalamus, between controls (n = 33), cognitively unimpaired Parkinson disease subjects (n = 33), Parkinson disease subjects with mild cognitive impairment (n = 22) and Parkinson disease subjects with dementia (n = 17). We then investigated how the morphology of the caudate, putamen and thalamus structures and differed between groups. Results indicate that cognitively unimpaired Parkinson disease subjects, compared to controls, displayincreasedfunctional connectivity of the dorsal caudate, anterior putamen and mediodorsal thalamic subdivisions with areas across the frontal lobe, as well asreducedfunctional connectivity of the dorsal caudate with posterior cortical and cerebellar regions. Compared to cognitively unimpaired subjects, Parkinson disease subjects with mild cognitive impairment demonstratedreducedfunctional connectivity of the mediodorsal thalamus with midline nodes within the executive-control network. Compared to subjects with mild cognitive impairment, subjects with dementia demonstratedreducedfunctional connectivity of the mediodorsal thalamus with the posterior cingulate cortex, a key node within the default-mode network. Extensive volumetric and surface-based deflation was found in Parkinson disease subjects with dementia. Our research demonstrates how functional connectivity of the caudate, putamen and thalamus are implicated in the pathophysiology of cognitive impairment and dementia in Parkinson disease, with mild cognitive impairment and dementia in Parkinson disease associated with a breakdown in functional connectivity of the mediodorsal thalamus with para- and posterior cingulate regions of the brain.
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer
Authors: Rashid Rumana , Gaglia Giorgio , Chen Yu-An , Lin Jia-Ren , Du Ziming , Maliga Zoltan , Schapiro Denis , Yapp Clarence , Muhlich Jeremy , Sokolov Artem , Sorger Peter , Santagata Sandro 
Published: July 2019

ABSTRACTIn this data descriptor, we document a dataset of multiplexed immunofluorescence images and derived single-cell measurements of immune lineage and other markers in formaldehyde-fixed and paraffin-embedded (FFPE) human tonsil and lung cancer tissue. We used tissue cyclic immunofluorescence (t-CyCIF) to generate fluorescence images which we artifact corrected using the BaSiC tool, stitched and registered using the ASHLAR algorithm, and segmented using ilastik software and MATLAB. We extracted single-cell features from these images using HistoCAT software. The resulting dataset can be visualized using image browsers and analyzed using high-dimensional, single-cell methods. This dataset is a valuable resource for biological discovery of the immune system in normal and diseased states as well as for the development of multiplexed image analysis and viewing tools.METADATA SUMMARY
Identification of 2CS-CHXToperon signature of chlorhexidine tolerance amongEnterococcus faecium
Authors: Duarte Bárbara , Pereira Ana P. , Freitas Ana R. , Coque Teresa M. , Hammerum Anette M. , Hasman Henrik , Antunes Patrícia , Peixe Luísa , Novais Carla 
Published: July 2019

AbstractChlorhexidine (CHX) is a broad-spectrum antiseptic widely used in community and clinical contexts for many years, recently acquiring higher relevance in nosocomial infections control worldwide. Despite of this, CHX tolerance has been poorly understood amongEnterococcus faecium, one of the leading agents causing nosocomial infections. This study provides new phenotypic and molecular data for a better identification of CHX tolerantE. faeciumsubpopulations in community and clinical contexts. MICCHXdistribution of 106E. faeciumsuggested the occurrence of tolerant subpopulations in diverse sources (human, animal, food, environment) and phylogenomic backgrounds (clades A1/A2/B), with predominance in clade A1. They carried a specific variant of 2CS-CHXToperon, here identified. It encodes a glucose and an amino-acid-polyamine-organocation family transporters, besides the DNA-binding-response-regulator ChtR with a P102H mutation previously described in only CHX tolerant clade A1E. faecium, and the ChtS sensor. Combined data from normal MIC distribution and 2CS-CHXToperon characterization supports a tentative epidemiological cut-off (ECOFF) of 8 mg/L to CHX, useful to detect tolerantE. faeciumpopulations in future surveillance studies. The spread of tolerantE. faeciumin diverse epidemiological backgrounds alerts for a prudent use of CHX in multiple contexts.ImportanceChlorhexidine is one of the substances included in the World Health Organization’s List of Essential Medicines which comprises the safest and most effective medicines needed in global health systems. Although it has been widely applied as a disinfectant and antiseptic since the 1950s in healthcare (skin, hands, mouthwashes, eye drops), its use in hospitals to prevent nosocomial infections has increased worldwide in recent years. Here we provide a comprehensive study on chlorhexidine tolerance amongEnterococcus faecium, one of the leading nosocomial agents worldwide, and identified a novel 2CS-CHXToperon as a signature of tolerant strains occurring in diverse phylogenomic groups. Finally, our data allowed to propose a tentative epidemiological cut-off of 8 mg/L, useful to detect tolerantE. faeciumpopulations in future surveillance studies in community and clinical contexts.
Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C
Authors: Belaghzal Houda , Borrman Tyler , Stephens Andrew D. , Lafontaine Denis L. , Venev Sergey V. , Weng Zhiping , Marko John F. , Dekker Job 
Published: July 2019

SUMMARYChromosomes are folded so that active and inactive chromatin domains are spatially segregated. Compartmentalization is thought to occur through polymer phase/microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci. Before fixation and Hi-C, chromosomes are fragmented removing the strong polymeric constraint to enable detection of intrinsic locus-locus interaction stabilities. Compartmentalization is stable when fragments are over 10-25 kb. Fragmenting chromatin into pieces smaller than 6 kb leads to gradual loss of genome organization. Dissolution kinetics of chromatin interactions vary for different chromatin domains. Lamin-associated domains are most stable, while interactions among speckle and polycomb-associated loci are more dynamic. Cohesin-mediated loops dissolve after fragmentation, possibly because cohesin rings slide off nearby DNA ends. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics.HighlightsLiquid chromatin Hi-C detects chromatin interaction dissociation rates genome-wideChromatin conformations in distinct nuclear compartments differ in stabilityStable heterochromatic associations are major drivers of chromatin phase separationCTCF-CTCF loops are stabilized by encirclement of loop bases by cohesin rings
Finding MEMo: Minimum sets of elementary flux modes
Authors: Röhl Annika , Bockmayr Alexander 
Published: July 2019

AbstractMetabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated.
Predicting mechanism of action of cellular perturbations with pathway activity signatures
Authors: Ren Yan , Sivaganesan Siva , Clark Nicholas A. , Zhang Lixia , Biesiada Jacek , Niu Wen , Plas David R. , Medvedovic Mario 
Published: July 2019

ABSTRACTMotivationMisregulation of signaling pathway activity is etiologic for many human diseases, and modulating activity of signaling pathways is often the preferred therapeutic strategy. Understanding the mechanism of action (MOA) of bioactive chemicals in terms of targeted signaling pathways is the essential first step in evaluating their therapeutic potential. Changes in signaling pathway activity are often not reflected in changes in expression of pathway genes which makes MOA inferences from transcriptional signatures a difficult problem.ResultsWe developed a new computational method for implicating pathway targets of bioactive chemicals and other cellular perturbations by integrated analysis of pathway network topology, the LINCS transcriptional signatures of genetic perturbations of pathway genes and the transcriptional signature of the perturbation. Our methodology accurately predicts signaling pathways targeted by the perturbation when current pathway analysis approaches utilizing only a transcriptional signature of the perturbation fail.Availability and ImplementationOpen source R package paslincs is available at https://github.com/uc-bd2k/paslincs.
Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes
Authors: Holland Dominic , Frei Oleksandr , Desikan Rahul , Fan Chun-Chieh , Shadrin Alexey A. , Smeland Olav B. , Andreassen Ole A. , Dale Anders M. 
Published: July 2019

AbstractWe propose an extended Gaussian mixture model for the distribution of causal effects of common single nucleotide polymorphisms (SNPs) for human complex phenotypes that depends on linkage disequilibrium (LD) and heterozygosity (H), while also allowing for independent components for small and large effects. Using a precise methodology showing how genome-wide association studies (GWAS) summary statistics (z-scores) arise through LD with underlying causal SNPs, we applied the model to GWAS of multiple human phenotypes. Our findings indicated that causal effects are distributed with dependence on total LD and H, whereby SNPs with lower total LD and H are more likely to be causal with larger effects; this dependence is consistent with models of the influence of negative pressure from natural selection. Compared with the basic Gaussian mixture model it is built on, the extended model – primarily through quantification of selection pressure – reproduces with greater accuracy the empirical distributions of z-scores, thus providing better estimates of genetic quantities, such as polygenicity and heritability, that arise from the distribution of causal effects.
A canstatin-derived peptide provides insight into the role of Capillary Morphogenesis Gene 2 in angiogenic regulation and matrix uptake
Authors: Finnell Jordan G. , Tsang Tsz-Ming , Cryan Lorna , Garrard Samuel , Lee Sai-Lun , Ackroyd P. Christine , Rogers Michael S. , Christensen Kenneth A. 
Published: July 2019

AbstractCapillary Morphogenesis Gene 2 protein (CMG2) is a transmembrane, integrin-like receptor and the primary receptor for the anthrax toxin. In addition to its role as an anthrax toxin receptor, CMG2 has been repeatedly shown to play a role in angiogenic processes. However, the molecular mechanism mediating observed CMG2-related angiogenic effects has not been fully elucidated. Previous studies have found that CMG2 binds type IV collagen (Col-IV), a key component of the vascular basement membrane, as well as other ECM proteins. Currently, no link has been made between these CMG2-ECM interactions and angiogenesis; however, ECM fragments are known to play a role in regulating angiogenesis. Here, we further characterize the CMG2-Col-IV interaction and explore the effect of this interaction on angiogenesis. Using a peptide array, we observed that CMG2 preferentially binds peptide fragments of the NC1 (non-collagenous domain 1) domains of Col-IV. These domains are also known as the fragments arresten (from the α1 chain) and canstatin (from the α2 chain) and have documented antiangiogenic properties. A second peptide array was probed to map a putative binding epitope. A top hit from the initial array, a canstatin-derived peptide, binds to the CMG2 ligand-binding von Willebrand factor A (vWA) domain with sub-micromolar affinity (peptide S16, Kd= 400 ± 200 nM). This peptide competes with anthrax protective antigen (PA) for CMG2 binding, and does not bind CMG2 in the presence of EDTA. Together these data suggest that, like PA, S16 interacts with CMG2 at the metal-ion dependent adhesion site (MIDAS) of its vWA domain. We demonstrate that CMG2 specifically mediates endocytic uptake of S16, since CMG2-/- endothelial cells show markedly reduced S16 uptake, without reducing total endocytosis. Furthermore, we show that S16 reduces endothelial migration but not cell proliferation. Taken together, our data demonstrate that a Col IV-derived anti-angiogenic peptide acts via CMG2, suggesting a possible link between CMG2-Col IV interactions and angiogenesis.