bluuebunny/crossref_metadata_2025_split huggingface dataset:
An early-warning indicator for Amazon droughts exclusively based on tropical Atlantic sea surface temperatures
Authors: Ciemer Catrin , Rehm Lars , Kurths Jürgen , Donner Reik V , Winkelmann Ricarda , Boers Niklas 
Published: June 2020

Abstract
Droughts in tropical South America have an imminent and severe impact on the Amazon rainforest and affect the livelihoods of millions of people. Extremely dry conditions in Amazonia have been previously linked to sea surface temperature (SST) anomalies in the adjacent tropical oceans. Although the sources and impacts of such droughts have been widely studied, establishing reliable multi-year lead statistical forecasts of their occurrence is still an ongoing challenge. Here, we further investigate the relationship between SST and rainfall anomalies using a complex network approach. We identify four ocean regions which exhibit the strongest overall SST correlations with central Amazon rainfall, including two particularly prominent regions in the northern and southern tropical Atlantic. Based on the time-dependent correlation between SST anomalies in these two regions alone, we establish a new early-warning method for droughts in the central Amazon basin and demonstrate its robustness in hindcasting past major drought events with lead-times up to 18 months.
Entanglement entropy of two disjoint intervals separated by one spin in a chain of free fermion*
Authors: Brightmore L , Gehér G P , Its A R , Korepin V E , Mezzadri F , Mo M Y , Virtanen J A 
Published: June 2020

Abstract
We calculate the entanglement entropy of a non-contiguous subsystem of a chain of free fermions. The starting point is a formula suggested by Jin and Korepin, arXiv:1104.1004
, for the reduced density of states of two disjoint intervals with lattice sites P = {1, 2, …, m} ∪ {2m + 1, 2m + 2, …, 3m}, which applies to this model. As a first step in the asymptotic analysis of this system, we consider its simplification to two disjoint intervals separated just by one site, and we rigorously calculate the mutual information between these two blocks and the rest of the chain. In order to compute the entropy we need to study the asymptotic behaviour of an inverse Toeplitz matrix with Fisher–Hartwig symbol using the the Riemann–Hilbert method.
Comparison of rates of adherence to oral chemotherapy medications filled through an internal health-system specialty pharmacy vs external specialty pharmacies
Authors: McCabe Colleen C , Barbee Meagan S , Watson Marley L , Billmeyer Alyssa , Lee Collin E , Rupji Manali , Chen Zhengjia , Haumschild Ryan , El-Rayes Bassel 
Published: June 2020

Abstract

Purpose
The primary objective of the study described here was to compare rates of patient adherence to anticancer medications filled at an internal health system specialty pharmacy (HSSP) vs external specialty pharmacies. The primary outcome was the medication possession ratio (MPR), and the secondary outcomes included proportion of days covered (PDC), and time to treatment (TTT).

Methods
A retrospective chart review was conducted to compare the MPR, PDC, and TTT for patients who received oral anticancer therapy using prescriptions claim data. A t test or Wilcoxon test was used to explore the effect of demographic and other factors on adherence and TTT. A multiple regression model with backward elimination was used to analyze significant factors to identify covariates significantly associated with the outcomes.

Results
Of the 300 patients screened for study inclusion, 204 patients whose records had complete MPR and PDC data and 164 whose records had TTT data were included in the analysis. There were significant between-group differences in mean MPR and mean PDC with patient use of the HSSP vs external pharmacies (1.00 vs 0.75 [P &lt; 0.001] and 0.95 vs 0.7 [P &lt; 0.001], respectively). Pharmacy type (P = 0.024) and tumor type (P = 0.048) were significantly associated with TTT.

Conclusion
The multiple regression analysis indicated that oncology patients who filled their anticancer medication precriptions at an internal HSSP at an academic medical center had significantly higher adherence, as measured by MPR and PDC, and quicker TTT than those who filled their prescriptions at an external specialty pharmacy.
Distance-based phylogenetic inference from typing data: a unifying view
Authors: Vaz Cátia , Nascimento Marta , Carriço João A , Rocher Tatiana , Francisco Alexandre P 
Published: June 2020

AbstractTyping methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. Moreover, their use is becoming standard, in particular with the introduction of high-throughput sequencing. On the other hand, the data being generated are massive and many algorithms have been proposed for a phylogenetic analysis of typing data, addressing both correctness and scalability issues. Most of the distance-based algorithms for inferring phylogenetic trees follow the closest pair joining scheme. This is one of the approaches used in hierarchical clustering. Moreover, although phylogenetic inference algorithms may seem rather different, the main difference among them resides on how one defines cluster proximity and on which optimization criterion is used. Both cluster proximity and optimization criteria rely often on a model of evolution. In this work, we review, and we provide a unified view of these algorithms. This is an important step not only to better understand such algorithms but also to identify possible computational bottlenecks and improvements, important to deal with large data sets.
Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies
Authors: Piñeiro César , Abuín José M , Pichel Juan C 
Published: June 2020

Abstract

Motivation
FastTree-2 is one of the most successful tools for inferring large phylogenies. With speed at the core of its design, there are still important issues in the FastTree-2 implementation that harm its performance and scalability. To deal with these limitations, we introduce VeryFastTree, a highly tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to boost performance.

Results
VeryFastTree is able to construct a tree on a standard server using double-precision arithmetic from an ultra-large 330k alignment in only 4.5 h, which is 7.8× and 3.5× faster than the sequential and best parallel FastTree-2 times, respectively.

Availability and implementation
VeryFastTree is available at the GitHub repository: https://github.com/citiususc/veryfasttree.

Supplementary information
Supplementary data are available at Bioinformatics online.
Molywood: streamlining the design and rendering of molecular movies
Authors: Wieczór Miłosz , Hospital Adam , Bayarri Genis , Czub Jacek , Orozco Modesto 
Published: June 2020

Abstract

Motivation
High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts—particularly, in structural biology—are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust and intuitive tool that builds on the capabilities of Visual Molecular Dynamics (VMD) to automate all stages of movie rendering.

Results
Molywood is a Python-based script that uses an integrated workflow to give maximal flexibility in movie design. It implements the basic concepts of actions, layers, grids and concurrency and requires no programming experience to run.

Availability and implementation
The script is freely available on GitLab (gitlab.com/KomBioMol/molywood) and PyPI (through pip), and features an extended documentation, tutorial and gallery hosted on mmb.irbbarcelona.org/molywood.
Crime Control in Japan: Exceptional, Convergent or What Else?
Authors: Brewster David 
Published: June 2020

AbstractTheories about crime control in Japan have largely been based around two opposing traditions. On the one hand, cultural explanations have emphasized the exceptional attributes of Japanese social relations that contribute towards shaming and re-integrative processes. On the other hand, more recent explanations assert that Japanese crime control is converging with other countries, particularly towards penal populism. Both approaches tend to reduce explanations to a monolithic characterization that disguises variegation within Japan. Through considering the governance of illegal drug use and the Kamagasaki area of Osaka, a ‘geo-historical’ perspective is advocated to better capture the complexity and contradictions of globalizing processes and social culture and their resulting manifestations in crime control within contemporary Japan.
Heterochromatin banding and rDNA physical mapping in 22Epimediumspecies and twoVancouveriaspecies: implications for evolution inEpimedium
Authors: Sheng Maoyin , Gao Mengdi , Wang Linjiao 
Published: June 2020

AbstractHeterochromatin banding patterns and the physical locations of 45S and 5S rDNA loci in mitotic metaphase chromosomes in 22 Epimedium spp. and two Vancouveria spp. species were studied using orcein staining and double-colour fluorescent in situ hybridization, respectively. Four types of chromosomal heterochromatin bands (satellite, centromeric, intercalary and terminal) were detected in all species, and there was clear variation in the number of bands and total length. In all species examined, at least one pair each of 45S and 5S rDNA signals was detected. The position of 5S rDNA is more conserved than that of 45S rDNA. The chromosomal distribution of 45S rDNA loci detected in Epimedium can be divided into three types. The chromosomal distributions of heterochromatin bands and 45S and 5S rDNA loci were closely related to the geographical distribution and may provide important evidence concerning the classification and systematics of Epimedium. Finally, based on results of the present study and pervious research, the centre of origin and formation of modern geographical distribution of Epimedium are discussed.
Sodium channel Nav1.6 in sensory neurons contributes to vincristine-induced allodynia
Authors: Chen Lubin , Huang Jianying , Benson Curtis , Lankford Karen L , Zhao Peng , Carrara Jennifer , Tan Andrew M , Kocsis Jeffery D , Waxman Stephen G , Dib-Hajj Sulayman D 
Published: June 2020

Abstract
Vincristine, a widely used chemotherapeutic agent, produces painful peripheral neuropathy. The underlying mechanisms are not well understood. In this study, we investigated whether voltage-gated sodium channels are involved in the development of vincristine-induced neuropathy. We established a mouse model in which repeated systemic vincristine treatment results in the development of significant mechanical allodynia. Histological examinations did not reveal major structural changes at proximal sciatic nerve branches or distal toe nerve fascicles at the vincristine dose used in this study. Immunohistochemical studies and in vivo two-photon imaging confirmed that there is no significant change in density or morphology of intra-epidermal nerve terminals throughout the course of vincristine treatment. These observations suggest that nerve degeneration is not a prerequisite of vincristine-induced mechanical allodynia in this model. We also provided the first detailed characterization of tetrodotoxin-sensitive (TTX-S) and resistant (TTX-R) sodium currents in dorsal root ganglion neurons following vincristine treatment. Accompanying the behavioural hyperalgesia phenotype, voltage-clamp recordings of small and medium dorsal root ganglion neurons from vincristine-treated animals revealed a significant upregulation of TTX-S Na+ current in medium but not small neurons. The increase in TTX-S Na+ current density is likely mediated by Nav1.6, because in the absence of Nav1.6 channels, vincristine failed to alter TTX-S Na+ current density in medium dorsal root ganglion neurons and, importantly, mechanical allodynia was significantly attenuated in conditional Nav1.6 knockout mice. Our data show that TTX-S sodium channel Nav1.6 is involved in the functional changes of dorsal root ganglion neurons following vincristine treatment and it contributes to the maintenance of vincristine-induced mechanical allodynia.
Human Immunodeficiency Virus Continuum of Care in 11 European Union Countries at the End of 2016 Overall and by Key Population: Have We Made Progress?
Authors: Vourli Georgia , Noori Teymur , Pharris Anastasia , Porter Kholoud , Axelsson Maria , Begovac Josip , Cazein Francoise , Costagliola Dominique , Cowan Susan , Croxford Sara , d’Arminio Monforte Antonella , Delpech Valerie , Díaz Asunción , Girardi Enrico , Gunsenheimer-Bartmeyer Barbara , Hernando Victoria , Leierer Gisela , Lot Florence , Nunez Olivier , Obel Niels , Op de Coul Eline , Paraskeva Dimitra , Patrinos Stavros , Reiss Peter , Schmid Daniela , Sonnerborg Anders , Suligoi Barbara , Supervie Virginie , van Sighem Ard , Zangerle Robert , Touloumi Giota ,   the European HIV Continuum of Care Working Group
Published: June 2020

Abstract

Background
High uptake of antiretroviral treatment (ART) is essential to reduce human immunodeficiency virus (HIV) transmission and related mortality; however, gaps in care exist. We aimed to construct the continuum of HIV care (CoC) in 2016 in 11 European Union (EU) countries, overall and by key population and sex. To estimate progress toward the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 target, we compared 2016 to 2013 estimates for the same countries, representing 73% of the population in the region.

Methods
A CoC with the following 4 stages was constructed: number of people living with HIV (PLHIV); proportion of PLHIV diagnosed; proportion of those diagnosed who ever initiated ART; and proportion of those ever treated who achieved viral suppression at their last visit.

Results
We estimated that 87% of PLHIV were diagnosed; 92% of those diagnosed had ever initiated ART; and 91% of those ever on ART, or 73% of all PLHIV, were virally suppressed. Corresponding figures for men having sex with men were: 86%, 93%, 93%, 74%; for people who inject drugs: 94%, 88%, 85%, 70%; and for heterosexuals: 86%, 92%, 91%, 72%. The proportion suppressed of all PLHIV ranged from 59% to 86% across countries.

Conclusions
The EU is close to the 90-90-90 target and achieved the UNAIDS target of 73% of all PLHIV virally suppressed, significant progress since 2013 when 60% of all PLHIV were virally suppressed. Strengthening of testing programs and treatment support, along with prevention interventions, are needed to achieve HIV epidemic control.
Entecavir Plus Pegylated Interferon and Sequential Hepatitis B Virus Vaccination Increases Hepatitis B Surface Antigen Seroclearance: A Randomized Controlled Proof-of-Concept Study
Authors: Lee Jeong-Hoon , Lee Yun Bin , Cho Eun Ju , Yu Su Jong , Yoon Jung-Hwan , Kim Yoon Jun 
Published: June 2020

Abstract

Background
Hepatitis B surface antigen (HBsAg) seroclearance is considered a functional cure for patients with chronic hepatitis B, but is rarely achievable with oral nucleos(t)ide analogues alone. We conducted a randomized controlled proof-of-concept trial to evaluate the impact of adding pegylated interferon (peg-IFN) alfa-2a plus sequential or concomitant hepatitis B virus (HBV) vaccination.

Methods
A total of 111 patients who achieved serum HBV DNA &lt;20 IU/mL and quantitative HBsAg &lt;3000 IU/mL with entecavir were randomly assigned (1:1:1) to the E + sVIP group (entecavir + peg-IFN alfa-2a [180 µg every week over 48 weeks] plus sequential HBV vaccination [20 µg of HBsAg on weeks 52, 56, 60, and 76]), the E + cVIP group (entecavir + peg-IFN alfa-2a + concomitant HBV vaccination [weeks 4, 8, 12, and 28]), or the control group (entecavir only). The primary endpoint was HBsAg seroclearance at week 100, and secondary endpoints included safety.

Results
No differences in baseline quantitative HBsAg were observed among the groups. The E + sVIP group in the intention-to-treat analysis showed a significantly higher chance of HBsAg seroclearance during week 100 than the control group (16.2% vs 0%; P = .025), but the E + cVIP group (5.4%) failed to reach a significant difference (P = .54). Adverse events were significantly more frequent in the E + sVIP (81.1%) and E + cVIP group (70.3%) than the control group (2.7%) (both P &lt; .0001). However, the frequency of serious adverse events did not differ significantly among the 3 groups (2.7%, 5.4%, and 2.7%, respectively; P = 1.00).

Conclusions
Entecavir plus an additional peg-IFN alfa-2a treatment followed by sequential HBV vaccination under an intensified schedule significantly increases the chance of HBsAg seroclearance compared to entecavir alone.

Clinical Trials Registration
NCT02097004.
A Randomized Controlled Trial of Isoniazid to Prevent Mycobacterium tuberculosis Infection in Kenyan Human Immunodeficiency Virus–Exposed Uninfected Infants
Authors: LaCourse Sylvia M , Richardson Barbra A , Kinuthia John , Warr A J , Maleche-Obimbo Elizabeth , Matemo Daniel , Cranmer Lisa M , Mecha Jerphason , Escudero Jaclyn N , Hawn Thomas R , John-Stewart Grace 
Published: June 2020

Abstract

Background
Human immunodeficiency virus (HIV)–exposed uninfected (HEU) infants in endemic settings are at high risk of tuberculosis (TB). For infants, progression from primary Mycobacterium tuberculosis (Mtb) infection to TB disease can be rapid. We assessed whether isoniazid (INH) prevents primary Mtb infection.

Methods
We conducted a randomized nonblinded controlled trial enrolling HEU infants 6 weeks of age without known TB exposure in Kenya. Participants were randomized (1:1) to 12 months of daily INH (10 mg/kg) vs no INH. Primary endpoint was Mtb infection at end of 12 months, assessed by interferon-γ release assay (QuantiFERON-TB Gold Plus) and/or tuberculin skin test (TST, added 6 months after first participant exit).

Results
Between 15 August 2016 and 6 June 2018, 416 infants were screened, with 300 (72%) randomized to INH or no INH (150 per arm); 2 were excluded due to HIV infection. Among 298 randomized HEU infants, 12-month retention was 96.3% (287/298), and 88.9% (265/298) had primary outcome data. Mtb infection prevalence at 12-month follow-up was 10.6% (28/265); 7.6% (10/132) in the INH arm and 13.5% (18/133) in the no INH arm (7.0 vs 13.4 per 100 person-years; hazard ratio, 0.53 [95% confidence interval {CI}, .24–1.14]; P = .11]), and driven primarily by TST positivity (8.6% [8/93] in INH and 18.1% [17/94] in no INH; relative risk, 0.48 [95% CI, .22–1.05]; P = .07). Frequency of severe adverse events was similar between arms (INH, 14.0% [21/150] vs no INH, 10.7% [16/150]; P = .38), with no INH-related adverse events.

Conclusions
Further studies evaluating TB preventive therapy to prevent or delay primary Mtb infection in HEU and other high-risk infants are warranted.

Clinical Trials Registration
NCT02613169.
From ontological orientation to axiomatic habitus? An historical reappraisal of contemporary political economy from a Marxian angle
Authors: Lampa Roberto , Abeles Martín 
Published: June 2020

Abstract
An accurate analysis of Marx’s early works reveals the pivotal role of ontology in defining his critical research project, which culminated with the publication of Capital. By re-assessing Marx’s critical project in such terms, a careful review of the ontological conceptions of contemporary heterodox economics becomes possible, revealing a paradoxical situation. By focussing exclusively on mainstream’s logical inconsistencies, a branch of heterodox economics converged towards the same ontological assumptions as mainstream economics. These economists fall into the ‘axiomatic habitus’ of mimicking, at times unconsciously, the same stances as mainstream economics. By contrast, segments of mainstream economics (new political economy and neo-institutionalist economics) are more aware of the nature of the social reality to be investigated, introducing an axiomatised history within their framework. A careful review of Karl Marx’s ontological rupture then becomes an inescapable reference in order to amend both heterodox and orthodox economics, challenging the increasing insularity of our discipline.
Institutional Fields as Arenas of Rhetorical Engagement: Convergence, Conflict, and Divergence Between Competing Logics in the Field of Finance
Authors: Just Sine N , Dahlman Sara , Mouton Nicolaas TO 
Published: June 2020

AbstractThis article contributes to the theory of rhetorical institutionalism ( Green & Li, 2011) by considering the relationship between institutional entrepreneurs and the institutional fields in which they operate as configured by rhetorical strategies. Thus, we posit that the legitimacy of institutional entrepreneurs and institutional fields, respectively, is an inherently rhetorical construct ( Suddaby & Greenwood, 2005), whereby rhetorical engagement becomes central to the establishment, maintenance, and reform of institutions ( Brown, Ainsworth & Grant, 2012; Green, Babb & Alpaslan, 2008). Working with an illustrative case of the Co-operative Bank's financial distress and leadership scandal, we identify three particular strategies of rhetorical engagement with competing institutional logics, which we label convergence, conflict, and divergence. Thus, we add to the theory of rhetorical institutionalism by arguing, broadly, that institutional fields are arenas of rhetorical engagement between competing institutional logics and identifying, more specifically, three rhetorical strategies for constituting institutional legitimacy.
3-D joint inversion of seismic waveform and airborne gravity gradiometry data
Authors: Jiang Wenbin 
Published: June 2020

SUMMARYSeismic full waveform inversion (FWI) is a robust velocity model building technique for hydrocarbon exploration. However, the density reconstruction within the framework of multiparameter FWI leads to more degrees of freedom in the parametrization, and the sensitivity of the inversion change significantly from velocity to density, thereby increasing the ill-posedness of the inverse problem. Gravity gradiometry data inversion is an effective method for resolving density distribution. Combining gravity gradiometry data in FWI could alleviate the non-linearity of the inversion by contributing additional density information for the velocity model building. I develop a 3-D joint seismic waveform and gravity gradiometry inversion method for estimating the velocity and density distribution in the subsurface. The method alternatingly minimizes the waveform and gravity gradiometry misfit. The cross-gradient constraint is applied to enhance the structural similarity between the density and velocity models. The effectiveness of the joint inversion algorithm is demonstrated by a 3-D checkerboard model and 3-D SEAM model. Synthetic examples demonstrate that the joint inversion can improve the image quality in geologically complex areas. A case study from the South China Sea shows that the joint inversion improves the velocity and density solutions compared to a standalone seismic FWI. The joint inversion results are consistent with the pre-stack depth migration section and the shape of the salt body is well resolved.