bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation
Authors: Sillitoe Ian , Andreeva Antonina , Blundell Tom L , Buchan Daniel W A , Finn Robert D , Gough Julian , Jones David , Kelley Lawrence A , Paysan-Lafosse Typhaine , Lam Su Datt , Murzin Alexey G , Pandurangan Arun Prasad , Salazar Gustavo A , Skwark Marcin J , Sternberg Michael J E , Velankar Sameer , Orengo Christine 
Published: November 2019

Abstract
Genome3D (https://www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being ‘pushed’ to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms.
Necroptotic astrocytes contribute to maintaining stemness of disseminated medulloblastoma through CCL2 secretion
Authors: Liu Hailong , Sun Youliang , O’Brien Jenny A , Franco-Barraza Janusz , Qi Xueling , Yuan Hongyu , Jin Wei , Zhang Junping , Gu Chunyu , Zhao Zhenyu , Yu Chunjiang , Feng Shiyu , Yu Xinguang 
Published: November 2019

Abstract

Background
Medulloblastoma (MB) with metastases at diagnosis and recurrence correlates with poor prognosis. Unfortunately, the molecular mechanism underlying metastases growth has received less attention than primary therapy-naïve MB. Though astrocytes have been frequently detected in brain tumors, their roles in regulating the stemness properties of MB stem-like cells (MBSCs) in disseminated lesions remain elusive.

Methods
Effects of tumor-associated astrocyte (TAA)–secreted chemokine C-C ligand 2 (CCL2) on MBSC self-renewal was determined by immunostaining analysis. Necroptosis of TAA was examined by measuring necrosome activity. Alterations in Notch signaling were examined after inhibition of CCL2. Progression of MBSC-derived tumors was evaluated after pharmaceutical blockage of necroptosis.

Results
TAA, as the essential components of disseminated tumor, produced high levels of CCL2 to shape the inflammation microenvironment, which stimulated the enrichment of MBSCs in disseminated MB. In particular, CCL2 played a pivotal role in maintaining stem-like properties via Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3)–mediated activation of Notch signaling. Loss of CCL2/C-C chemokine receptor 2 (CCR2) function repressed the JAK2/STAT3-Notch pathway and impaired MBSC proliferation, leading to a dramatic reduction of stemness, tumorigenicity, and metastasizing capability. Furthermore, necroptosis-induced CCL2 release depended on activation of receptor-interacting protein 1 (RIP1)/RIP3/mixed lineage kinase domain-like pseudokinase (MLKL) in TAA, which promoted the oncogenic phenotype. Blockade of necroptosis resulted in CCL2 deprivation and compromised MBSC self-proliferation, indicating MBSCs outsourced CCL2 from necroptotic TAA. Finally, CCL2 was upregulated in high-risk stages of MB, further supporting its value as a prognostic indicator.

Conclusion
These findings highlighted the critical role of CCL2/CCR2 in Notch signaling activation in MBSCs and revealed a necroptosis-associated glial cytokine microenvironment driving stemness maintenance in disseminations.
Key Points
1. TAA-derived CCL2 promoted stemness in disseminated MBSCs through Notch signaling activation via the JAK2/STAT3 pathway.
2. TAA released CCL2 in a RIP1/RIP3/MLKL-dependent manner leading to necroptosis.
Visually constructing the chemical structure of a single molecule by scanning Raman picoscopy
Authors: Zhang Yao , Yang Ben , Ghafoor Atif , Zhang Yang , Zhang Yu-Fan , Wang Rui-Pu , Yang Jin-Long , Luo Yi , Dong Zhen-Chao , Hou J G 
Published: November 2019

Abstract
The strong spatial confinement of a nanocavity plasmonic field has made it possible to visualize the inner structure of a single molecule and even to distinguish its vibrational modes in real space. With such ever-improved spatial resolution, it is anticipated that full vibrational imaging of a molecule could be achieved to reveal molecular structural details. Here we demonstrate full Raman images of individual vibrational modes at the ångström level for a single Mg-porphine molecule, revealing distinct characteristics of each vibrational mode in real space. Furthermore, by exploiting the underlying interference effect and Raman fingerprint database, we propose a new methodology for structural determination, which we have called ‘scanning Raman picoscopy’, to show how such ultrahigh-resolution spectromicroscopic vibrational images can be used to visually assemble the chemical structure of a single molecule through a simple Lego-like building process.
A Retrospective Multisite Case-Control Series of Concomitant Use of Daptomycin and Statins and the Effect on Creatine Phosphokinase
Authors: Lehman Bethany , Neuner Elizabeth A , Heh Victor , Isada Carlos 
Published: November 2019

Abstract

Objective
Daptomycin has been associated with increased creatine phosphokinase (CPK) due to muscle injury leading to myalgias and muscle weakness. Statins have been proven to cause the same effects and it is recommended to discontinue the use of statins while on daptomycin. Evidence regarding this drug interaction is mixed. This study evaluated the risk of CPK elevation in concomitant use of daptomycin and statins compared to daptomycin alone.

Method
This is a multisite retrospective case-control study of patients who received daptomycin therapy with monitoring of CPK. Rates of CPK elevations were compared in patients receiving daptomycin with a statin versus daptomycin alone. To estimate the association between CPK elevation and daptomycin therapy controlling for other risk factors, logistic regression was used to analyze data. Statistical significance was determined at ɑ of 0.05.

Results
A total of 3658 patients were included in the study, with 2787 on daptomycin therapy alone and 871 with concurrent statin use. The incidence of CPK elevation was 90 events (3.2%) in the daptomycin group and 26 events (3.0%) in the concurrent statin group. Patients who received daptomycin therapy in addition to statins had no statistically significant difference from patients on daptomycin alone (hazard ratio, 1.05; P = .85; 95% confidence interval, 0.61–1.84). After adjusting for potential risk factors, the hazards ratio remained almost the same.

Conclusions
Concomitant use of daptomycin and statin did not show an increase risk of CPK elevation. Clinicians may consider concomitant use of daptomycin and statin therapy with weekly CPK monitoring.
Incidence and Predictive Risk Factors of Infective Events in Patients With Multiple Sclerosis Treated With Agents Targeting CD20 and CD52 Surface Antigens
Authors: Zappulo Emanuela , Buonomo Antonio Riccardo , Saccà Francesco , Russo Cinzia Valeria , Scotto Riccardo , Scalia Giulia , Nozzolillo Agostino , Lanzillo Roberta , Tosone Grazia , Gentile Ivan 
Published: November 2019

Abstract

Objective
Monoclonal antibodies (MAbs) directed against the CD20 and CD52 antigens are used increasingly in patients with multiple sclerosis (MS). Several life-threatening opportunistic infections have been reported in postmarketing case series. The aim of this study was to investigate the incidence of infections and associated prognostic factors during the first year of treatment in patients receiving anti-CD20 (ocrelizumab or rituximab) or anti-CD52 MAbs (alemtuzumab).

Methods
A retrospective study was conducted in patients with MS referring to the Neurodegenerative Diseases Center at the University of Naples Federico II who received MAbs between November 2015 and June 2018.

Results
A total of 163 patients were enrolled. Approximately 40% of patients experienced lymphocytopenia during treatment. Eighty-six infective events were reported in 67 patients (41%). Bacterial infections were significantly more frequent with anti-CD20, whereas viral infections prevailed with alemtuzumab. Cytomegalovirus reactivation rates were significantly higher in the alemtuzumab group than in patients on anti-CD20 (51% vs 6%, P < .001). The overall annualized infection rate was 1.1 per patient-year, higher in patients on anti-CD52 versus those on anti-CD20 regimens (1.5 vs 0.8 per patient-year). Alemtuzumab treatment, prior exposure to ≥2 MS drugs, and iatrogenic immune impairment significantly and independently predicted an infection event (adjusted hazard ratio [aHR], 2.7; P = .013; aHR, 1.7; P = .052; and aHR, 2.9; P = .004; respectively).

Conclusions
Given their considerable infection risk, MS patients receiving MAbs should undergo timely follow up and tailored preventive interventions. Anti-CD52–based treatment, prior exposure to MS drugs, and on-treatment immune impairment are significant predictive factors of infection and their evaluation could help clinicians to stratify a patient’s risk of infection.
Factors Influencing the Delivery of Intensive Rehabilitation in Stroke: Patient Perceptions Versus Rehabilitation Therapist Perceptions
Authors: Janssen Jessie , Klassen Tara D , Connell Louise A , Eng Janice J 
Published: November 2019

Abstract

Background
Despite increasing evidence regarding the benefit of intensive task-specific practice and aerobic exercise in stroke rehabilitation, implementation remains difficult. The factors influencing implementation have been explored from therapists’ perspectives; however, despite an increased emphasis on patient involvement in research, patients’ perceptions have not yet been investigated.

Objective
The study aimed to investigate factors influencing implementation of higher intensity activity in people with stroke and to compare this with therapists’ perspectives.

Design
The design was a cross-sectional qualitative study.

Methods
The study used semistructured interviews with people with stroke who were part of a randomized clinical trial, the Determining Optimal post-Stroke Exercise study, which delivered a higher intensity intervention. An interview guide was developed and data analyzed using implementation frameworks. Factors emerging from interviews with people with stroke were compared and contrasted with factors perceived by rehabilitation therapists.

Results
Ten people with stroke were interviewed before data saturation was reached. Participants had a positive attitude regarding working hard and were satisfied with the graded exercise test, high intensity intervention, and the feedback-monitoring devices. Therapists and patients had contrasting perceptions about their beliefs regarding intensive exercise and the content of the intervention, with therapists more focused on the methods and patients more focused on the personal interactions stemming from the therapeutic relationship.

Conclusions
People with stroke perceived no barriers regarding the implementation of higher intensity rehabilitation in practice and were positive towards working at more intense levels. Contrastingly, from the therapists’ perspective, therapists’ beliefs about quality of movement and issues around staffing and resources were perceived to be barriers. In addition, therapists and people with stroke perceived the contents of the intervention differently, highlighting the importance of involving patients and clinicians in the development and evaluation of rehabilitation interventions.
Are Referees and Editors in Economics Gender Neutral?*
Authors: Card David , DellaVigna Stefano , Funk Patricia , Iriberri Nagore 
Published: November 2019

AbstractWe study the role of gender in the evaluation of economic research using submissions to four leading journals. We find that referee gender has no effect on the relative assessment of female- versus male-authored papers, suggesting that any differential biases of male referees are negligible. To determine whether referees as a whole impose different standards for female authors, we compare citations for female- and male-authored papers, holding constant referee evaluations and other characteristics. We find that female-authored papers receive about 25% more citations than observably similar male-authored papers. Editors largely follow the referees, resulting in a 1.7 percentage point lower probability of a revise and resubmit verdict for papers with female authors relative to a citation-maximizing benchmark. In their desk rejection decisions, editors treat female authors more favorably, though they still impose a higher bar than would be implied by citation maximization. We find no differences in the informativeness of female versus male referees or in the weight that editors place on the recommendations of female versus male referees. We also find no differences in editorial delays for female- versus male-authored papers.
A coaxially extruded heterogeneous core–shell fiber with Schwann cells and neural stem cells
Authors: Li Xinda , Zhou Dezhi , Jin Zhizhong , Chen Hongqing , Wang Xuanzhi , Zhang Xinzhi , Xu Tao 
Published: November 2019

Abstract
Cellular therapies play a critical role in the treatment of spinal cord injury (SCI). Compared with cell-seeded conduits, fully cellular grafts have more similarities with autografts, and thus might result in better regeneration effects. In this study, we fabricated Schwann cell (SC)-neural stem cell (NSC) core–shell alginate hydrogel fibers in a coaxial extrusion manner. The rat SC line RSC96 and mouse NSC line NE-4C were used in this experiment. Fully cellular components were achieved in the core portion and the relative spatial positions of these two cells partially mimic the construction of nerve fibers in vivo. SCs were demonstrated to express more genes of neurotrophic factors in alginate shell. Enhanced proliferation and differentiation tendency of NSCs was observed when they were co-cultured with SCs. This model has strong potential for application in SCI repair.
Enhanced osteogenesis of hydroxyapatite scaffolds by coating with BMP-2-loaded short polylactide nanofiber: a new drug loading method for porous scaffolds
Authors: Xu Taotao , Sheng Luyao , He Lei , Weng Jie , Duan Ke 
Published: November 2019

Abstract
Porous hydroxyapatite (HA) is widely used in porous forms to assist bone defect healing. However, further improvements in biological functions are desired for meeting complex clinical situations such as impaired bone regeneration in poor bone stock. The extracellular matrix (ECM) of human tissues is characterized by nanofibrous structures and a variety of signal molecules. Emulating these characteristics are expected to create a favorable microenvironment for cells and simultaneously allow release of osteogenic molecules. In this study, short polylactide fibers containing BMP-2 were prepared by electrospinning and coated on porous HA scaffolds. The coating did not affect porosity or pore interconnectivity of the scaffold but improved its compressive strength markedly. This fiber coating produced burst BMP-2 release in 1 day followed by a linear release for 24 days. The coating had a significantly lower rat calvarial osteoblasts (RCOBs) adhesion (vs. uncoated scaffold) but allowed normal proliferation subsequently. Bone marrow stem cells (MSCs) on the coated scaffolds expressed a significantly increased alkaline phosphatase activity relative to the uncoated ones. After implantation in canine dorsal muscles, the coated scaffolds formed significantly more new bone at Weeks 4 and 12, and more blood vessels at Week 12. This method offers a new option for drug delivery systems.
Is the Risk of Sea Level Rise Capitalized in Residential Real Estate?
Authors: Murfin Justin , Spiegel Matthew 
Published: November 2019

AbstractUsing a comprehensive database of coastal home sales merged with data on elevation relative to local tides, we compare prices for houses based on their inundation threshold under projections of sea level rise. The analysis separates the sensitivity of housing to rising seas from other confounding characteristics by exploiting cross-sectional differences in relative sea level rise due to vertical land motion. This provides variation in the expected time to inundation for properties of similar elevation and distance from the coast. In a variety of specifications and test settings, we find precisely estimated null results suggesting limited price effects.
Sectarianism, the Nonconformist Conscience, and ‘British Pluralism’: The Digital Humanities and the Language of Home Rule, c.1910–1914
Authors: Colbrook Stephen 
Published: November 2019

Abstract
In recent years, historians have reassessed the political importance of the third Home Rule Bill. Important works by G. K. Peatling, Daniel Jackson, and David Thackeray have overturned the once-dominant view that the measure was a straightforward distraction from social reform. Yet, this scholarship has focused almost exclusively on the response of Unionists to Home Rule, and few works discuss the measure’s significance for Edwardian Liberals. This article rectifies this historiographical oversight by comparing the Liberal and Unionist response to the third Home Rule Bill in Devonshire and Lancashire. Using techniques from the digital humanities, I have shown that the measure dominated the grassroots political discourse of both parties before the First World War.
Disentangling the Mechanisms of Retirement Adjustment: Determinants and Consequences of Subjective Well-Being
Authors: Hansson Isabelle , Buratti Sandra , Thorvaldsson Valgeir , Johansson Boo , Berg Anne Ingeborg 
Published: November 2019

AbstractRetirement from work is a major life event requiring adaptation to new life circumstances. The resource-based dynamic model of retirement adjustment suggests that well-being will change due to changes in individual resources. In the present study, we test this hypothesis by investigating longitudinal and bidirectional associations between life satisfaction and perceived resources (i.e., self-esteem, autonomy, social support, self-rated physical health, self-rated cognitive ability, and financial satisfaction) over a 4-year period in the transition from work to retirement. Our sample included annual assessment data from 497 older adults (aged 60–66) in the population-based HEalth, Ageing, and Retirement Transitions in Sweden (HEARTS) study. Results from bivariate latent change score models showed weak but consistent associations between changes in perceived resources and changes in life satisfaction over the retirement transition. Analyses of cross-lagged effects also revealed bidirectional associations. Self-esteem, self-rated physical health, and total resource capability were positively related to changes in life satisfaction, and life satisfaction was positively related to changes in self-esteem, autonomy, self-rated physical health, and self-rated cognitive ability. The total resource capability accounted for 12% of the changes in life satisfaction in the first years following retirement. Life satisfaction accounted for 16% of the changes in autonomy in the transition from work to retirement. Our findings demonstrate that perceived resources are important for life satisfaction in the retirement transition, at the same time as overall life satisfaction accounts for how we perceive and evaluate our own resources during this process.
Minute and diverse in fossil sticky stuff: Tanytarsini (Diptera: Chironomidae) from early Eocene Indian Cambay amber
Authors: Zakrzewska Marta , Singh Hukam , Wagner-Wysiecka Ewa , Giłka Wojciech 
Published: November 2019

Abstract
We here present a pioneering systematic review of fossil dipterans of the tribe Tanytarsini (family Chironomidae) discovered in Indian amber from Cambay. The specimens examined belong to five species: Gujaratomyia miripes,Stempellina stebneri sp. nov., Stempellinella pollex sp. nov., Tanytarsus forfex sp. nov. andTanytarsus ramus sp. nov., which are described. All species belong to the oldest known Tanytarsini and come from the Cambay shale formation in Tadkeshwar, dated to the early Eocene (~54 Mya). Displaying unusual characters/structures of diagnostic and phylogenetic importance, the specimens studied are discussed against the background of the evolution and systematics of the oldest fossil (Eocene) and extant representatives in the tribe. An updated checklist and key to the identification of genera and species of Tanytarsini from Eocene amber is also provided. The spectral characteristics and physical properties of Cambay amber are similar to those of glessite resins, which are discussed in detail in order to substantiate the identity of the amber and the origin of the inclusions studied.
Valuing Carbon Stocks across a Tropical Lagoon after Accounting for Black and Inorganic Carbon: Bulk Density Proxies for monitoring
Authors: Gallagher John Barry , Chew Swee-Theng , Madin John , Thorhaug Anitra 
Published: November 2019

ABSTRACTManaging seagrass and mangrove can be enhanced through carbon valued payment incentives schemes. Success will depend on the accuracy and extent of the carbon stock mitigation and accessible methods of monitoring and marking changes. In a relatively closed socioecological Southeast Asian lagoon we estimated the value of total organic carbon stocks (TOC) of both seagrass and mangroves. Mitigation corrections were also made for black carbon (BC) and calcareous inorganic carbon equivalents (PICequiv), and their sediment dry bulk density (DBD) tested as a cost effective means of both estimating those stock concepts and possible impacts outside their parameter confidence intervals. Overall, seagrass and mangroves TOC densities across the lower lagoon ranged from 15.3±4.3 and 124.3±21.1 Mg C ha-1respectively, 175.2±46.9 and 103.2±19.0 Mg C ha-1for seagrass and 355.0±24.8 and 350.3±35.2 Mg C ha-1) for mangroves across the two upper lagoon branches. Only mangrove biomass made significant additional contributions ranging from 178.5±62.3 to 120.7±94.8 Mg C ha-1for lower and upper regions respectively. The difference between the lagoons total seagrass and mangroves TOC stocks (5.98±0.69 and 390±33.22 GgC respectively) was further amplified by the lagoons’ larger mangrove area. When corrected for BC and PICequiv, the carbon stock mitigation was only reduced by a moderate 14.2%. Across the lagoon the sedimentary DBD showed strong (R2= 0.85,P< 0.001) to moderate (R2= 0.67,P< 0.001) linear correlations with seagrass and mangrove [TOC] respectively, moderate correlations with seagrass [PIC] (R2= 0.6,P< 0.001), but an invariant and relatively constant response to mangrove [PIC] (2.7 kg m-3± 0.07). Valuations as CO2ewas worth on average 0.44 million US$ y-1over 20 years; less than the total income of the indigenous users as potential custodians (1.8 and 7.4 million US$ y-1). Implications of this valuation was discussed.