bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient storage of heterogeneous geospatial data in spatial databases
Authors: Sveen Atle Frenvik 
Published: November 2019

AbstractThe no-schema approach of NoSQL document stores is a tempting solution for importing heterogenous geospatial data to a spatial database. However, this approach means sacrificing the benefits of RDBMSes, such as existing integrations and the ACID principle. Previous comparisons of the document-store and table-based layout for storing geospatial data favours the document-store approach but does not consider importing data that can be segmented into homogenous datasets. In this paper we propose “The Heterogeneous Open Geodata Storage (HOGS)” system. HOGS is a command line utility that automates the process of importing geospatial data to a PostgreSQL/PostGIS database. It is developed in order to compare the performance of a traditional storage layout adhering to the ACID principle, and a NoSQL-inspired document store. A collection of eight open geospatial datasets comprising 15 million features was imported and queried in order to compare the differences between the two storage layouts. The results from a quantitative experiment are presented and shows that large amounts of open geospatial data can be stored using traditional RDBMSes using a table-based layout without any performance penalties.
New method of temperature and conductivity sensor calibration with improved efficiency for screening SBE41 CTD on Argo floats
Authors: Hosoda Shigeki , Hirano Mizue , Hashimukai Takayuki , Asai Satoko , Kawakami Noriko 
Published: November 2019

AbstractThe global ocean monitoring system would benefit from improvements in the efficiency of Conductivity, Temperature, and Depth Device (CTD) sensor screening. Here, we describe the development of a new screening system, J-Calibration, for use with the SBE41 CTD sensor on the Argo float (Sea Bird Scientific). This new system has crucial advantages over the traditional SBE-Calibration system. First, J-Calibration does not require removal of the CTD sensor unit from the Argo float body to operate in a laboratory. This feature enables technicians or operators to more efficiently check the Argo target accuracies (± 0.005 °C for temperature and ± 0.01 PSS-78 for salinity) and allows the manufacturer’s warranty to remain intact. This also allows for a more efficient basic screening system which maintains screening accuracy without the need for specialized technicians. J-Calibration reduces the screening time to 1/6th that of SBE-Calibration and does not require the preparation of large amounts of artificial seawater. J-Calibration uses 1/23rd of the volume of seawater compared to SBE-Calibration by examining calibration at only 1 temperature point (22 °C), whereas SBE-Calibration requires 7 points to achieve calibration. The J-Calibration system does require careful temperature control of the artificial seawater as it is critical to maintain a uniform water temperature throughout the experiments. To satisfy this, using a vinyl greenhouse and covering sensors with adiabatic materials and cooling packs are effective. In comparison with the accuracy and system stability of SBE-Calibration, we show that the J-Calibration system is non-inferior and therefore is suitable for use in laboratory screening prior to deployment. Based on these advantages, the J-Calibration system will make a strong contribution to the deployment of healthy Argo fleets and to the maintenance of uniform data in the global ocean.
Optical coherence tomography angiography in diabetic retinopathy: a review of current applications
Authors: Tey Kai Yuan , Teo Kelvin , Tan Anna C. S. , Devarajan Kavya , Tan Bingyao , Tan Jacqueline , Schmetterer Leopold , Ang Marcus 
Published: November 2019

AbstractBackgroundDiabetic retinopathy (DR) is a leading cause of vision loss in adults. Currently, the standard imaging technique to monitor and prognosticate DR and diabetic maculopathy is dye-based angiography. With the introduction of optical coherence tomography angiography (OCTA), it may serve as a potential rapid, non-invasive imaging modality as an adjunct.Main textRecent studies on the role of OCTA in DR include the use of vascular parameters e.g., vessel density, intercapillary spacing, vessel diameter index, length of vessels based on skeletonised OCTA, the total length of vessels, vascular architecture and area of the foveal avascular zone. These quantitative measures may be able to detect changes with the severity and progress of DR for clinical research. OCTA may also serve as a non-invasive imaging method to detect diabetic macula ischemia, which may help predict visual prognosis. However, there are many limitations of OCTA in DR, such as difficulty in segmentation between superficial and deep capillary plexus; and its use in diabetic macula edema where the presence of cystic spaces may affect image results. Future applications of OCTA in the anterior segment include detection of anterior segment ischemia and iris neovascularisation associated with proliferative DR and risk of neovascular glaucoma.ConclusionOCTA may potentially serve as a useful non-invasive imaging tool in the diagnosis and monitoring of diabetic retinopathy and maculopathy in the future. Future studies may demonstrate how quantitative OCTA measures may have a role in detecting early retinal changes in patients with diabetes.
Identification of novel citramalate biosynthesis pathways in Aspergillus niger
Authors: Hossain Abeer H. , Hendrikx Aiko , Punt Peter J. 
Published: November 2019

Abstract
Background
The filamentous fungus Aspergillus niger is frequently used for industrial production of fermentative products such as enzymes, proteins and biochemicals. Notable examples of industrially produced A. niger fermentation products are glucoamylase and citric acid. Most notably, the industrial production of citric acid achieves high titers, yield and productivities, a feat that has prompted researchers to propose A. niger to serve as heterologous production host for the industrial production of itaconic acid (IA), a promising sustainable chemical building-block for the fabrication of various synthetic resins, coatings, and polymers. Heterologous production of IA in A. niger has resulted in unexpected levels of metabolic rewiring that has led us to the identification of IA biodegradation pathway in A. niger. In this study we have attempted to identify the final product of the IA biodegradation pathway and analyzed the effect of metabolic rewiring on the bioproduction of 9 industrially relevant organic acids.

Results
IA biodegradation manifests in diminishing titers of IA and the occurrence of an unidentified compound in the HPLC profile. Based on published results on the IA biodegradation pathway, we hypothesized that the final product of IA biodegradation in A. niger may be citramalic acid (CM). Based on detailed HPLC analysis, we concluded that the unidentified compound is indeed CM. Furthermore, by transcriptome analysis we explored the effect of metabolic rewiring on the production of 9 industrially relevant organic acids by transcriptome analysis of IA producing and WT A. niger strains. Interestingly, this analysis led to the identification of a previously unknown biosynthetic cluster that is proposed to be involved in the biosynthesis of CM. Upon overexpression of the putative citramalate synthase and a genomically clustered organic acid transporter, we have observed CM bioproduction by A. niger.

Conclusion
In this study, we have shown that the end product of IA biodegradation pathway in A. niger is CM. Knock-out of the IA biodegradation pathway results in the cessation of CM production. Furthermore, in this study we have identified a citramalate biosynthesis pathway, which upon overexpression drives citramalate bioproduction in A. niger.
Relationship between retinal vessel tortuosity and oxygenation in sickle cell retinopathy
Authors: Khansari Maziyar M. , Garvey Sarah L. , Farzad Shayan , Shi Yonggang , Shahidi Mahnaz 
Published: November 2019

Abstract
Background
Reduced retinal vascular oxygen (O2) content causes tissue hypoxia and may lead to development of vision-threatening pathologies. Since increased vessel tortuosity is an early sign for some hypoxia-implicated retinopathies, we investigated a relationship between retinal vascular O2 content and vessel tortuosity indices.

Methods
Dual wavelength retinal oximetry using a commercially available scanning laser ophthalmoscope was performed in both eyes of 12 healthy (NC) and 12 sickle cell retinopathy (SCR) subjects. Images were analyzed to quantify retinal arterial and venous O2 content and determine vessel tortuosity index (VTI) and vessel inflection index (VII) in circumpapillary regions. Linear mixed model analysis was used to determine the effect of disease on vascular O2 content, VTI and VII, and relate vascular O2 content with VTI and VII. Models accounted for vessel type, fellow eyes, age and mean arterial pressure.

Results
Retinal arterial and venous O2 content were lower in SCR (O2A = 11 ± 4 mLO2/dL, O2V = 7 ± 2 mLO2/dL) compared to NC (O2A = 18 ± 3 mLO2/dL, O2V = 13 ± 3 mLO2/dL) subjects (p < 0.001). As expected, O2 content was higher in arteries (15 ± 5 mLO2/dL) than veins (10 ± 4 mLO2/dL) (p < 0.001), but not different between eyes (OD: 12 ± 5 mLO2/dL; OS:13 ± 5 mLO2/dL) (p = 0.3). VTI was not significantly different between SCR (0.18 ± 0.07) and NC (0.15 ± 0.04) subjects, or between arteries (0.18 ± 0.07) and veins (0.16 ± 0.04), or between eyes (OD: 0.18 ± 0.07, OS:0.17 ± 0.05) (p ≥ 0.06). VII was significantly higher in SCR (10 ± 2) compared to NC subjects (8 ± 1) (p = 0.003). VII was also higher in veins (9 ± 2) compared to arteries (8 ± 5) (p = 0.04), but not different between eyes (OD: 9 ± 2; OS: 9 ± 2) (p = 0.2). There was an inverse linear relationship between vascular O2 (13 ± 5 mLO2/dL) content and VII (9 ± 2) (β = −0.5; p = 0.02).

Conclusions
The findings augment knowledge of relationship between retinal vascular oxygenation and morphological changes and potentially contribute to identifying biomarkers for assessment of retinal hypoxia due to SCR and other retinopathies.
Use hierarchy for “liberating servant leadership” instead of controlling employees
Authors: Nobles Bill 
Published: November 2019

AbstractSince the Industrial Revolution, management has relied on hierarchy to control assets and employees. The negative impact of that hierarchical control on employee performance has long been recognized, yet in spite of expert and scholarly attempts to solve these problems hierarchical control generally continues to dominate management theory and practices. This article argues that is because these problems are rooted not in hierarchy, but rather in organizational expectations of hierarchy. Hierarchy emphasizing “liberating servant leadership” (Dr. Isaac Getz of the ESCP Business School in Paris introduced the term “liberating leadership,” the French equivalent of which “entreprise libérée” has become a household term in France. Max De Pree suggested the leader must become a servant in Leadership is an Art. This combines the two concepts.) instead of controlling employees can produce extraordinary business results. Eighteen innovative CEOs (The innovative CEOs and their successful companies in alphabetical order are Bill Gore, W.L. Gore Company; Bob Beyster, Science Applications International Corporation; Bob Davids, Radica Games & Sea Smoke Vineyard and Winery; Bob Koski, Sun Hydraulics; Bob Townsend, AVIS; David Kelley, IDEO; Garry Ridge, WD-40; Gordon Forward, Chaparral Steel; Harry Quadracci, Quad/Graphics; Herb Kelleher, Southwest Airlines; Jeff Westphal, Vertex; Ken Iverson, Nucor Steel; Kim Jordan, New Belgium Brewing; Max De Pree, Herman Miller; Paul Staley, PQ Corporation; Rich Teerlink, Harley Davidson; Robert McDermott, USAA Insurance; and Stan Richards, The Richards Group. Additional details about each leader can be found in the books Freedom, Inc. by Brian Carney and Isaac Getz and Questioning Corporate Hierarchy by Paul Staley and Bill Nobles.) whom I have studied discovered this by trial and error while trying to take advantage of Douglas McGregor’s Theory Y. Their leadership changed the design of their organizations. Believing that individuals can drive themselves more effectively than managers can, these CEOs sought to create conditions in which associates committed themselves to organizational objectives, and satisfied their ego and self-development needs. The CEOs relied on hierarchy to control financial assets, but fundamentally changed the human dimension. The organizational roles traditionally called “middle managers” responsible for controlling employees became “liberating servant leaders” responsible for ensuring that associates had everything needed to freely self-control and self-coordinate their efforts. The resulting self-motivated, creative employees played key roles in each CEO’s company being extraordinarily successful. These experiences provide a foundation for transforming the human role of hierarchy in organizational design.
Disease activity flares and pain flares in an early rheumatoid arthritis inception cohort; characteristics, antecedents and sequelae
Authors: McWilliams Daniel F. , Rahman Shimin , James Richard J. E. , Ferguson Eamonn , Kiely Patrick D. W. , Young Adam , Walsh David A. 
Published: November 2019

Abstract
Background
RA flares are common and disabling. They are described in terms of worsening inflammation but pain and inflammation are often discordant. To inform treatment decisions, we investigated whether inflammatory and pain flares are discrete entities.

Methods
People from the Early RA Network (ERAN) cohort were assessed annually up to 11 years after presentation (n = 719, 3703 person-years of follow up). Flare events were defined in 2 different ways that were analysed in parallel; DAS28 or Pain Flares. DAS28 Flares satisfied OMERACT flare criteria of increases in DAS28 since the previous assessment (≥1.2 points if active RA or ≥ 0.6 points if inactive RA). A ≥ 4.8-point worsening of SF36-Bodily Pain score defined Pain Flares. The first documented episode of each of DAS28 and Pain Flare in each person was analysed. Subgroups within DAS28 and Pain Flares were determined using Latent Class Analysis. Clinical course was compared between flare subgroups.

Results
DAS28 (45%) and Pain Flares (52%) were each common but usually discordant, with 60% of participants in DAS28 Flare not concurrently in Pain Flare, and 64% of those in Pain Flare not concurrently in DAS28 Flare. Three discrete DAS28 Flare subgroups were identified. One was characterised by increases in tender/swollen joint counts (14.4%), a second by increases in symptoms (13.1%), and a third displayed lower flare severity (72.5%). Two discrete Pain Flare subgroups were identified. One occurred following low disease activity and symptoms (88.6%), and the other occurred on the background of ongoing active disease and pain (11.4%). Despite the observed differences between DAS28 and Pain Flares, each was associated with increased disability which persisted beyond the flare episode.

Conclusion
Flares are both common and heterogeneous in people with RA. Furthermore our findings indicate that for some patients there is a discordance between inflammation and pain in flare events. This discrete flare subgroups might reflect different underlying inflammation and pain mechanisms. Treatments addressing different mechanisms might be required to reduce persistent disability after DAS28 and Pain Flares.
Effect of ionic liquids as entrainers on the dynamic behavior of ethanol-water extractive columns
Authors: Ramírez-Corona Nelly , Schramm-Flores Andrés , Reyes-Lombardo Sofía , Jiménez-Gutiérrez Arturo 
Published: November 2019

AbstractIonic liquids (ILs) have been recently considered as potential entrainers for extractive distillation. The use of ILs may affect the vapor-liquid properties to aid the separation of azeotropic mixtures. In particular, their effectiveness has been observed for ethanol dehydration, showing promising perspectives for their industrial implementation. However, there is still a lack of information about the effect of ILs on the system controllability. The objective of this work is to explore the dynamic implications of the use of two types of ionic liquids on the ethanol dehydration process. An equimolar feed mixture of ethanol and water was considered, and different IL concentrations were tested. The results show that changing the IL concentration affect the degree of stabilization of the product stream, even when smooth dynamic responses were in many cases observed.
Outcomes of Patients with Nelson’s Syndrome after Primary Treatment: A Multicenter Study from 13 UK Pituitary Centers
Authors: Fountas Athanasios , Lim Eugenie S , Drake William M , Powlson Andrew S , Gurnell Mark , Martin Niamh M , Seejore Khyatisha , Murray Robert D , MacFarlane James , Ahluwalia Rupa , Swords Francesca , Ashraf Muhammad , Pal Aparna , Chong Zhuomin , Freel Marie , Balafshan Tala , Purewal Tejpal S , Speak Rowena G , Newell-Price John , Higham Claire E , Hussein Ziad , Baldeweg Stephanie E , Dales Jolyon , Reddy Narendra , Levy Miles J , Karavitaki Niki 
Published: November 2019

AbstractContextLong-term outcomes of patients with Nelson’s syndrome (NS) have been poorly explored, especially in the modern era.ObjectiveTo elucidate tumor control rates, effectiveness of various treatments, and markers of prognostic relevance in patients with NS.Patients, design, and settingRetrospective cohort study of 68 patients from 13 UK pituitary centers with median imaging follow-up of 13 years (range 1–45) since NS diagnosis.ResultsManagement of Cushing’s disease (CD) prior to NS diagnosis included surgery+adrenalectomy (n = 30; eight patients had 2 and one had 3 pituitary operations), surgery+radiotherapy+adrenalectomy (n = 17; two received &gt;1 courses of irradiation, two had ≥2 pituitary surgeries), radiotherapy+adrenalectomy (n = 2), and adrenalectomy (n = 19). Primary management of NS mainly included surgery, radiotherapy, surgery+radiotherapy, and observation; 10-year tumor progression-free survival was 62% (surgery 80%, radiotherapy 52%, surgery+radiotherapy 81%, observation 51%). Sex, age at CD or NS diagnosis, size of adenoma (micro-/macroadenoma) at CD diagnosis, presence of pituitary tumor on imaging prior adrenalectomy, and mode of NS primary management were not predictors of tumor progression. Mode of management of CD before NS diagnosis was a significant factor predicting progression, with the group treated by surgery+radiotherapy+adrenalectomy for their CD showing the highest risk (hazard ratio 4.6; 95% confidence interval, 1.6–13.5). During follow-up, 3% of patients had malignant transformation with spinal metastases and 4% died of aggressively enlarging tumor.ConclusionsAt 10 years follow-up, 38% of the patients diagnosed with NS showed progression of their corticotroph tumor. Complexity of treatments for the CD prior to NS diagnosis, possibly reflecting corticotroph adenoma aggressiveness, predicts long-term tumor prognosis.
The fenestrae-associated protein Plvap regulates the rate of blood-borne protein passage into the hypophysis
Authors: Gordon Ludmila , Blechman Janna , Shimoni Eyal , Gur Dvir , Anand-Apte Bela , Levkowitz Gil 
Published: November 2019

ABSTRACT
To maintain body homeostasis, endocrine systems must detect and integrate blood-borne peripheral signals. This is mediated by fenestrae, specialized permeable pores in the endothelial membrane. Plasmalemma vesicle-associated protein (Plvap) is located in the fenestral diaphragm and is thought to play a role in the passage of proteins through the fenestrae. However, this suggested function has yet to be demonstrated directly. We studied the development of fenestrated capillaries in the hypophysis, a major neuroendocrine interface between the blood and brain. Using a transgenic biosensor to visualize the vascular excretion of the genetically tagged plasma protein DBP-EGFP, we show that the developmental acquisition of vascular permeability coincides with differential expression of zebrafish plvap orthologs in the hypophysis versus brain. Ultrastructural analysis revealed that plvapb mutants display deficiencies in fenestral diaphragms and increased density of hypophyseal fenestrae. Measurements of DBP-EGFP extravasation in plvapb mutants provided direct proof that Plvap limits the rate of blood-borne protein passage through fenestrated endothelia. We present the regulatory role of Plvap in the development of blood-borne protein detection machinery at a neuroendocrine interface through which hormones are released to the general circulation.
Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm
Authors: Linneberg-Agerholm Madeleine , Wong Yan Fung , Romero Herrera Jose Alejandro , Monteiro Rita S. , Anderson Kathryn G. V. , Brickman Joshua M. 
Published: November 2019

ABSTRACT
Embryonic stem cells (ESCs) exist in at least two states that transcriptionally resemble different stages of embryonic development. Naïve ESCs resemble peri-implantation stages and primed ESCs the pre-gastrulation epiblast. In mouse, primed ESCs give rise to definitive endoderm in response to the pathways downstream of Nodal and Wnt signalling. However, when these pathways are activated in naïve ESCs, they differentiate to a cell type resembling early primitive endoderm (PrE), the blastocyst-stage progenitor of the extra-embryonic endoderm. Here, we apply this context dependency to human ESCs, showing that activation of Nodal and Wnt signalling drives the differentiation of naïve pluripotent cells toward extra-embryonic PrE, or hypoblast, and these can be expanded as an in vitro model for naïve extra-embryonic endoderm (nEnd). Consistent with observations made in mouse, human PrE differentiation is dependent on FGF signalling in vitro, and we show that, by inhibiting FGF receptor signalling, we can simplify naïve pluripotent culture conditions, such that the inhibitor requirements closer resemble those used in mouse. The expandable nEnd cultures reported here represent stable extra-embryonic endoderm, or human hypoblast, cell lines.
This article has an associated ‘The people behind the papers’ interview.
Thrust generation during steady swimming and acceleration from rest in anguilliform swimmers
Authors: Du Clos Kevin T. , Dabiri John O. , Costello John H. , Colin Sean P. , Morgan Jennifer R. , Fogerson Stephanie M. , Gemmell Brad J. 
Published: November 2019

ABSTRACTEscape swimming is a crucial behavior by which undulatory swimmers evade potential threats. The hydrodynamics of escape swimming have not been well studied, particularly for anguilliform swimmers, such as the sea lamprey Petromyzon marinus. For this study, we compared the kinematics and hydrodynamics of larval sea lampreys with those of lampreys accelerating from rest during escape swimming. We used experimentally derived velocity fields to calculate pressure fields and distributions of thrust and drag along the body. Lampreys initiated acceleration from rest with the formation of a high-amplitude body bend at approximately one-quarter body length posterior to the head. This deep body bend produced two high-pressure regions from which the majority of thrust for acceleration was derived. In contrast, steady swimming was characterized by shallower body bends and negative-pressure-derived thrust, which was strongest near the tail. The distinct mechanisms used for steady swimming and acceleration from rest may reflect the differing demands of the two behaviors. High-pressure-based mechanisms, such as the one used for acceleration from rest, could also be important for low-speed maneuvering during which drag-based turning mechanisms are less effective. The design of swimming robots may benefit from the incorporation of such insights from unsteady swimming.