bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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.
Self-similar grooving solutions to the Mullins’ equation
Authors: Kalantarova Habiba , Novick-Cohen Amy
Published: June 2020

In 1957, Mullins proposed surface diffusion motion as a model for thermal grooving. By adopting a small slope approximation, he reduced the model to the Mullins’ linear surface diffusion equation,

(

M
E

)

y
t

+
B

y

x
x
x
x

=
0
,

\begin{equation} \nonumber ({\mathrm {ME}})\quad \quad y_t + B y_{xxxx}=0, \end{equation}

known also more simply as the Mullins’ equation. Mullins sought self-similar solutions to (ME) for planar initial conditions, prescribing boundary conditions at the thermal groove, as well as far field decay. He found explicit series solutions which are routinely used in analyzing thermal grooving to this day.

While (ME) and the small slope approximation are physically reasonable, Mullins’ choice of boundary conditions is not always appropriate. Here we present an in depth study of self-similar solutions to the Mullins’ equation for general self-similar boundary conditions, explicitly identifying four linearly independent solutions defined on

R

∖
{
0
}

\mathbb {R}\setminus \{0\}

; among these four solutions, two exhibit unbounded growth and two exhibit asymptotic decay, far from the origin. We indicate how the full set of solutions can be used in analyzing the effective boundary conditions from experimental profiles and in evaluating the governing physical parameters.
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

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 < 0.001] and 0.95 vs 0.7 [P < 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

Typing 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

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

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

Theories 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

Heterochromatin 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

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

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

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 <20 IU/mL and quantitative HBsAg <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 < .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

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

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

This 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

Seismic 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.
Non-stability of the noise HVSR at sites near or on topographic heights
Authors: La Rocca M , Chiappetta G D , Gervasi A , Festa R L
Published: June 2020

The horizontal to vertical spectral ratio (HVSR) of seismic noise is often used to investigate site effects, and it is usually assumed to be a stable feature of the site considered. Here we show that such an assumption is not always justified, and may lead to incorrect conclusions. The HVSR analysis was performed on ambient seismic noise recordings lasting from weeks to months at many sites in Calabria, Italy. Results show a variety of site effects, from the resonance of a shallow sedimentary layer to the polarized amplification of horizontal ground motion associated with topographic effects. We describe the results of seven sites whose HVSR is characterized by dual content: one that is persistent, and another appearing only occasionally. Two sites very near the coast of the Tyrrhenian sea and five sites in the Calabrian Arc mountains show the most remarkable results. The shape of the HVSR changes significantly at these sites when the amplitude of background noise increases in a broad frequency band during periods of bad weather. The occasional contribution to the HVSR consists of one or more peaks, depending on the site, that appear only when the amplitude of ambient noise is higher than usual. The seven sites where we observe the HVSR variability are all located in complex geological environments, on mountains, ridges or foothills. A variation of the HVSR correlated with the day–night cycle is also observed at some of these sites.
A New Perspective on Female-to-Male Communication in Salamander Courtship
Authors: Staub Nancy L , Stiller Alexandrea B , Kiemnec-Tyburczy Karen M
Published: June 2020

Synopsis

Courtship behavior in salamanders is often complex and involves well-documented communication from males to females in multiple sensory modalities. Historically, behaviors exhibited during the major stages of courtship have been predominately framed as a male acting and signaling to “persuade” a passive female to participate in courtship and remain with him until sperm release is completed. In this review, we use courtship descriptions for lungless salamanders (Plethodontidae) as a case study to illustrate this historical bias of a male-centered perspective. We then re-examine the literature and summarize the many ways females are active participants during plethodontid courtships. We also relate female behaviors to the types of female-to-male communication that may occur. For example, females have been documented to approach a male and initiate courtship, participate in mutual head rubbing, and step astride the male’s tail to begin the tail-straddling walk (a key courtship behavior observed in all plethodontids). Additionally, females have glands that may produce chemical signals that males respond to during courtship. We conclude that communication during courtship is more accurately described as a two-way interaction where each partner’s behavior is coordinated with the other’s via multi-modal signaling. Shifting the lens through which we view courtship and behavior provides insight into which female behaviors and anatomical features are most likely to be used for communication with males.
Centers for Disease Control and Prevention 2019 novel coronavirus disease (COVID-19) information management: addressing national health-care and public health needs for standardized data definitions and codified vocabulary for data exchange
Authors: Garcia Macarena , Lipskiy Nikolay , Tyson James , Watkins Roniqua , Esser E Stein , Kinley Teresa
Published: June 2020

Objective

The 2019 novel coronavirus disease (COVID-19) outbreak progressed rapidly from a public health (PH) emergency of international concern (World Health Organization [WHO], 30 January 2020) to a pandemic (WHO, 11 March 2020). The declaration of a national emergency in the United States (13 March 2020) necessitated the addition and modification of terminology related to COVID-19 and development of the disease’s case definition. During this period, the Centers for Disease Control and Prevention (CDC) and standard development organizations released guidance on data standards for reporting COVID-19 clinical encounters, laboratory results, cause-of-death certifications, and other surveillance processes for COVID-19 PH emergency operations. The CDC COVID-19 Information Management Repository was created to address the need for PH and health-care stakeholders at local and national levels to easily obtain access to comprehensive and up-to-date information management resources.

Materials and Methods

We introduce the clinical and health-care informatics community to the CDC COVID-19 Information Management Repository: a new, national COVID-19 information management tool. We provide a description of COVID-19 informatics resources, including data requirements for COVID-19 data reporting.

Results

We demonstrate the CDC COVID-19 Information Management Repository’s categorization and management of critical COVID-19 informatics documentation and standards. We also describe COVID-19 data exchange standards, forms, and specifications.

Conclusions

This information will be valuable to clinical and PH informaticians, epidemiologists, data analysts, standards developers and implementers, and information technology managers involved in the development of COVID-19 situational awareness and response reporting and analytics.
Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes
Authors: Capstaff Nicola M , Morrison Freddie , Cheema Jitender , Brett Paul , Hill Lionel , Muñoz-García Juan C , Khimyak Yaroslav Z , Domoney Claire , Miller Anthony J
Published: June 2020

The use of potential biostimulants is of broad interest in plant science for improving yields. The application of a humic derivative called fulvic acid (FA) may improve forage crop production. FA is an uncharacterized mixture of chemicals and, although it has been reported to increase growth parameters in many species including legumes, its mode of action remains unclear. Previous studies of the action of FA have lacked appropriate controls, and few have included field trials. Here we report yield increases due to FA application in three European Medicago sativa cultivars, in studies which include the appropriate nutritional controls which hitherto have not been used. No significant growth stimulation was seen after FA treatment in grass species in this study at the treatment rate tested. Direct application to bacteria increased Rhizobium growth and, in M. sativa trials, root nodulation was stimulated. RNA transcriptional analysis of FA-treated plants revealed up-regulation of many important early nodulation signalling genes after only 3 d. Experiments in plate, glasshouse, and field environments showed yield increases, providing substantial evidence for the use of FA to benefit M. sativa forage production.
Comparison of Nucleic Acid Amplification and IgM Tests for the Diagnosis of Mycoplasma pneumoniae Infection in Children During a Recent Korean Outbreak
Authors: Lee Hye-Young , Sul Seunghwan , Lee Jeong Young , Kim Mi-Na , Yu Jinho , Sung Heungsup
Published: June 2020

Objective

In the absence of standardized methods for Mycoplasma pneumoniae detection, we evaluated the diagnostic value of polymerase chain reaction (PCR) and IgM assays for detecting M. pneumoniae infection in children during a recent Korean outbreak.

Methods

The diagnostic performances of PCR and IgM assays for M. pneumoniae in 1,109 clinical specimens were evaluated by the Japanese Respiratory Society (JRS) scoring system as an interim reference standard.

Results

The level of agreement between both tests was fair. As analyzed by the JRS scoring system, the sensitivity of PCR was 45.2% in the group aged <5 years, 86.8% in the group aged 5 years to 10 years group, and 72.2% in the group aged 10 years to 18 years; the sensitivity of the IgM assay was 66.8%, 71.4%, and 55.6% in each group, respectively.

Conclusion

The sensitivity of PCR is relatively low but is superior to that of IgM assays such that diagnostic performance can be improved by both test methods in patients aged <5 years.
Scatter in Sunyaev–Zel’dovich effect scaling relations explained by inter-cluster variance in mass accretion histories
Authors: Green Sheridan B , Aung Han , Nagai Daisuke , van den Bosch Frank C
Published: June 2020

X-ray and microwave cluster scaling relations are immensely valuable for cosmological analysis. However, their power is limited by astrophysical systematics that bias mass estimates and introduce additional scatter. Turbulence injected into the intracluster medium via mass assembly contributes substantially to cluster non-thermal pressure support, a significant source of such uncertainties. We use an analytical model to compute the assembly-driven non-thermal pressure profiles of haloes based on Monte Carlo-generated accretion histories. We introduce a fitting function for the average non-thermal pressure fraction profile, which exhibits minimal dependence on redshift at fixed peak height. Using the model, we predict deviations from self-similarity and the intrinsic scatter in the Sunyaev–Zel’dovich effect observable-mass scaling relation (YSZ − M) due solely to inter-cluster variation in mass accretion histories. We study the dependence of YSZ − M on aperture radius, cosmology, redshift, and mass limit. The model predicts $5-9{{\ \rm per\ cent}}$ scatter in YSZ − M at z = 0, increasing as the aperture used to compute YSZ increases from R500c to 5R500c. The predicted scatter lies slightly below that of studies based on non-radiative hydro-simulations, illustrating that assembly history variance is likely responsible for a substantial fraction of scatter in YSZ − M. This should be regarded as a lower bound, which will likely increase with the use of an updated gas density model that incorporates a more realistic response to halo assembly. As redshift increases, YSZ − M deviates more from self-similarity and scatter increases. We show that the YSZ − M residuals correlate strongly with the recent halo mass accretion rate, potentially providing an opportunity to infer the latter.
Origin of star-forming rings around massive centres in massive galaxies at z < 4
Authors: Dekel Avishai , Lapiner Sharon , Ginzburg Omri , Freundlich Jonathan , Jiang Fangzhou , Finish Bar , Kretschmer Michael , Lin Doug , Ceverino Daniel , Primack Joel , Giavalisco Mauro , Ji Zhiyuan
Published: June 2020

Using analytic modelling and simulations, we address the origin of an abundance of star-forming clumpy extended gas rings about massive central bodies in massive galaxies at z < 4. Rings form by high-angular-momentum streams and survive in galaxies of Mstar > 109.5–10 M⊙ where merger-driven spin flips and supernova feedback are ineffective. The rings survive after events of compaction to central nuggets. Ring longevity was unexpected based on inward mass transport driven by torques from violent disc instability. However, evaluating the torques from a tightly wound spiral structure, we find that the time-scale for transport per orbital time is long and $\propto \! \delta _{\rm d}^{-3}$, with δd the cold-to-total mass ratio interior to the ring. A long-lived ring forms when the ring transport is slower than its replenishment by accretion and the interior depletion by star formation rate, both valid for δd < 0.3. The central mass that lowers δd is a compaction-driven bulge and/or dark matter, aided by the lower gas fraction at z < 4, provided that it is not too low. The ring is Toomre unstable for clump and star formation. The high-z dynamic rings are not likely to arise form secular resonances or collisions. Active galactic nucleus feedback is not expected to affect the rings. Mock images of simulated rings through dust indicate qualitative consistency with observed rings about bulges in massive z ∼ 0.5–3 galaxies, in H α and deep HST imaging. ALMA mock images indicate that z ∼ 0.5–1 rings should be detectable. We quote expected observable properties of rings and their central nuggets.
Radio afterglows of very high-energy gamma-ray bursts 190829A and 180720B
Authors: Rhodes L , van der Horst A J , Fender R , Monageng I M , Anderson G E , Antoniadis J , Bietenholz M F , Böttcher M , Bright J S , Green D A , Kouveliotou C , Kramer M , Motta S E , Wijers R A M J , Williams D R A , Woudt P A
Published: June 2020

We present high-cadence multifrequency radio observations of the long gamma-ray burst (GRB) 190829A, which was detected at photon energies above 100 GeV by the High Energy Stereoscopic System (H.E.S.S.). Observations with the Meer Karoo Array Telescope (MeerKAT, 1.3 GHz) and Arcminute Microkelvin Imager – Large Array (AMI-LA, 15.5 GHz) began one day post-burst and lasted nearly 200 d. We used complementary data from Swift X-Ray Telescope (XRT), which ran to 100 d post-burst. We detected a likely forward shock component with both MeerKAT and XRT up to over 100 d post-burst. Conversely, the AMI-LA light curve appears to be dominated by reverse shock emission until around 70 d post-burst when the afterglow flux drops below the level of the host galaxy. We also present previously unpublished observations of the other H.E.S.S.-detected GRB, GRB 180720B from AMI-LA, which shows likely forward shock emission that fades in less than 10 d. We present a comparison between the radio emission from the three GRBs with detected very high energy (VHE) gamma-ray emission and a sensitivity-limited radio afterglow sample. GRB 190829A has the lowest isotropic radio luminosity of any GRB in our sample, but the distribution of luminosities is otherwise consistent, as expected, with the VHE GRBs being drawn from the same parent distribution as the other radio-detected long GRBs.
Fe iii emission in quasars: evidence for a dense turbulent medium
Authors: Temple Matthew J , Ferland Gary J , Rankine Amy L , Hewett Paul C , Badnell N R , Ballance Connor P , Del Zanna Giulio , Dufresne Roger P
Published: June 2020

Recent improvements to atomic energy-level data allow, for the first time, accurate predictions to be made for the Fe iii line emission strengths in the spectra of luminous, $L_\text{bol}\simeq 10^{46}\!-\!10^{48}\mbox{${\rm \, erg}{\rm \, s}^{-1}\, $}$, active galactic nuclei. The Fe iii emitting gas must be primarily photoionized, consistent with observations of line reverberation. We use cloudy models exploring a wide range of parameter space, together with ≃26 000 rest-frame ultraviolet spectra from the Sloan Digital Sky Survey, to constrain the physical conditions of the line emitting gas. The observed Fe iii emission is best accounted for by dense (nH ≃ 1014 cm−3) gas which is microturbulent, leading to smaller line optical depths and fluorescent excitation. Such high density gas appears to be present in the central regions of the majority of luminous quasars. Using our favoured model, we present theoretical predictions for the relative strengths of the Fe iii UV34 λλ1895, 1914, 1926 multiplet. This multiplet is blended with the Si iii] λ1892 and C iii] λ1909 emission lines and an accurate subtraction of UV34 is essential when using these lines to infer information about the physics of the broad line region in quasars.
Using a generic definition of cachexia in patients with kidney disease receiving haemodialysis: a longitudinal (pilot) study
Authors: McKeaveney Clare , Slee Adrian , Adamson Gary , Davenport Andrew , Farrington Ken , Fouque Denis , Kalantar-Zadeh Kamyar , Mallett John , Maxwell Alexander P , Mullan Robert , Noble Helen , O’Donoghue Donal , Porter Sam , Seres David S , Shields Joanne , Witham Miles , Reid Joanne
Published: June 2020

Background

Research indicates that cachexia is common among persons with chronic illnesses and is associated with increased morbidity and mortality. However, there continues to be an absence of a uniformed disease-specific definition for cachexia in chronic kidney disease (CKD) patient populations.

Objective

The primary objective was to identify cachexia in patients receiving haemodialysis (HD) using a generic definition and then follow up on these patients for 12 months.

Method

This was a longitudinal study of adult chronic HD patients attending two hospital HD units in the UK. Multiple measures relevant to cachexia, including body mass index (BMI), muscle mass [mid-upper arm muscle circumference (MUAMC)], handgrip strength (HGS), fatigue [Functional Assessment of Chronic Illness Therapy (FACIT)], appetite [Functional Assessment of Anorexia/Cachexia Therapy (FAACT)] and biomarkers [C-reactive protein (CRP), serum albumin, haemoglobin and erythropoietin resistance index (ERI)] were recorded. Baseline analysis included group differences analysed using an independent t-test, dichotomized values using the χ2 test and prevalence were reported using the Statistical Package for the Social Sciences 24 (IBM, Armonk, NY, USA). Longitudinal analysis was conducted using repeated measures analysis.

Results

A total of 106 patients (30 females and 76 males) were recruited with a mean age of 67.6 years [standard deviation (SD) 13.18] and dialysis vintage of 4.92 years (SD 6.12). At baseline, 17 patients were identified as cachectic, having had reported weight loss (e.g. >5% for >6 months) or BMI <20 kg/m2 and three or more clinical characteristics of cachexia. Seventy patients were available for analysis at 12 months (11 cachectic versus 59 not cachectic). FAACT and urea reduction ratio statistically distinguished cachectic patients (P = 0.001). However, measures of weight, BMI, MUAMC, HGS, CRP, ERI and FACIT tended to worsen in cachectic patients.

Conclusion

Globally, cachexia is a severe but frequently underrecognized problem. This is the first study to apply the defined characteristics of cachexia to a representative sample of patients receiving HD. Further, more extensive studies are required to establish a phenotype of cachexia in advanced CKD.
Trichomes at the Base of the Petal Are Regulated by the Same Transcription Factors as Cotton Seed Fibers
Authors: Tan Jiafu , Walford Sally-Anne , Dennis Elizabeth S , Llewellyn Danny J
Published: June 2020

Many polypetalous plants have a constriction at the base of the petal that leaves a small gap that can provide entry into the young flower bud before the reproductive organs are fully developed. In cotton (Gossypium hirsutum L.), this gap is occluded by tufts of short unicellular trichomes superficially resembling the fibers found on cotton seeds. We are just beginning to understand the developmental regulation of the seed fibers and have previously characterized several MIXTA-like MYB transcription factors (TFs) that are critical for correct seed fiber development but know little about the molecular regulation of other types of cotton trichomes. Here, using RNAi or dominant suppression transgenic cotton lines and natural fiber mutants, we investigated the development and regulation of the petal base trichomes. Petal base trichomes and seed trichomes were also examined across several different species within and outside of the Malvoideae. We found that the petal base trichomes are regulated by the same MYB TFs as cotton seed fibers and, since they are more widely distributed across different taxa than the seed fibers, could have preceded them in the evolution of these important textile fibers produced by some cotton species.
The use of an impact framework to evaluate the impact of research on policy and practice: Screening questionnaires for intellectual disability
Authors: McKenzie Karen , Murray Aja , Murray George , Martin Rachel
Published: June 2020

There is an increasing emphasis on the importance of research having an impact on policy and practice. This can be more difficult to evidence in intellectual disability services because of the wide range of stakeholders involved. We evaluated whether an impact questionnaire covering: knowledge production, capacity building, informing policy and practice, social and economic benefits could successfully be used to evaluate the impact of research into and use of two screening questionnaires: the Learning Disability Screening Questionnaire (LDSQ) and Child and Adolescent Intellectual Disability Screening Questionnaire (CAIDS-Q). We conducted an online search for published peer reviewed and grey literature, and Internet resources that referenced LDSQ and/or CAIDS-Q. The resultant literature and resources were assessed for relevance and organized according to the categories outlined in the impact questionnaire. Evidence was found for all the areas of impact, with the largest body of evidence being in relation to informing policy and practice and social benefits and the least for economic benefits. The impact questionnaire provided the basis for a comprehensive and useful evaluative framework to assess impact, although there was some overlap between the different categories. The process of using it highlighted some wider issues to consider when attempting to evaluate impact. The results indicated that the research underpinning the LDSQ and CAIDS-Q had resulted in significant, generally positive, and wide-reaching impact on policy and practice in intellectual disability and other services, resulting in a number of positive outcomes.
Decreased activation of ataxia telangiectasia mutated (ATM) in monocytes from patients with systemic sclerosis
Authors: Sakata Komei , Yasuoka Hidekata , Yoshimoto Keiko , Takeuchi Tsutomu
Published: June 2020

Objectives

The regulation system for oxidative stress in systemic sclerosis (SSc) remains unclear. This study aimed to clarify the possible involvement of ataxia telangiectasia mutated (ATM), which plays a key role in DNA repair and redox balance, in the pathogenesis of SSc.

Methods

Thirty patients with SSc and 15 healthy controls were enrolled. Expression of ATM and phosphorylated ATM (pATM), an activated form of ATM, in phagocytes in whole blood samples was analysed by FACS. Correlations between expression levels of ATM/pATM and clinical parameters of SSc patients were statistically analysed. Peripheral monocytes were cultured with an ATM-specific inhibitor (KU55933), and reactive oxygen species production in the cells was measured.

Results

Expression level of pATM in peripheral monocytes and neutrophils from SSc patients was significantly lower than those in healthy controls (P = 0.04 and P < 0.001, respectively), while no significant difference in total ATM expression was observed between SSc and healthy controls. In addition, pATM expression in monocytes of SSc patients with interstitial lung disease or digital pitting scar was remarkably lower than in the patients without these clinical features (P = 0.02 and P = 0.03), respectively. Moreover, pATM expression in monocytes positively correlated with forced vital capacity and negatively correlated with the serum Krebs von den Lungen-6 level. Notably, KU55933, an ATM-specific inhibitor, enhanced reactive oxygen species production by monocytes under oxidative stress.

Conclusion

Our data revealed that decreased ATM activation in monocytes was associated with SSc-interstitial lung disease and that impaired ATM activation in monocytes may contribute to the disease process of SSc via uncontrolled reactive oxygen species production.
Exploring Tropical Infections: A Focus on Cutaneous Larva Migrans
Authors: Gill Navdip , Somayaji Ranjani , Vaughan Stephen
Published: June 2020

Cutaneous larva migrans is a hookworm infection and one of the most common skin diseases of tourists in tropical countries. Most commonly, the infection is transmitted by contact with feces of dogs and cats containing hookworm eggs. This case-based review explores the epidemiology, diagnosis, clinical features, and management of cutaneous larva migrans infection.

GENERAL PURPOSE

To provide information about infection with cutaneous larva migrans (CLM).

TARGET AUDIENCE

This continuing education activity is intended for physicians, physician assistants, NPs, and nurses with an interest in skin and wound care.

LEARNING OBJECTIVES/OUTCOMES

After participating in this educational activity, the participant will:

1. Distinguish the clinical features, diagnosis, and management of CLM.

2. Explain the epidemiology of CLM.