bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of COVID-19 response actions on air quality in China
Authors: Marlier Miriam E , Xing Jia , Zhu Yifang , Wang Shuxiao
Published: July 2020

An outbreak of the novel coronavirus (COVID-19) was first reported in Wuhan, Hubei Province, China in December 2019. In late January 2020, the Chinese government implemented strict quarantine measures across Hubei Province and other parts of the country to limit the transmission of COVID-19. An effect of these quarantine measures was the reduction in economic activity and associated emissions that contribute to air pollution. In this study, we quantify the spatial extent and magnitude of changes in air pollution concentrations across China by comparing complementary satellite, ground-based, and modeled data from the first two months of 2019 and 2020. We find a 48% reduction in satellite-derived average fine particulate matter (PM2.5) concentrations in eastern China during a three-week period after the Lunar New Year (LNY) in 2020 compared to 2019, which follows significant declines in the pre-LNY period. We also observe a 49% and 11% decline in post-LNY satellite tropospheric column concentrations of nitrogen dioxide (NO2) and sulfur dioxide (SO2). These satellite-based results are in general agreement with data collected from ground monitoring stations across the country, which show a decline in post-LNY PM2.5, NO2, and SO2 concentrations. Our modeling analysis suggests that these observed air quality improvements are driven primarily by the reduction in NO2 emissions, which indicate reductions in transportation and industrial pollution sources during COVID-19, but unfavorable meteorological conditions weaken the role of emissions reduction. Finally, we estimate a reduction by 5%, 14%, and 18% of days in the post-LNY period for 2020 that exceed national PM2.5 air quality targets for the entire country, eastern China, and Hubei Province. As more information becomes available on population characteristics and air pollution exposure patterns, this analysis can be extended to quantify human health related impacts to sudden changes in air pollution in China and other locations around the world.
Incidence Correction Factors for Moderate and Severe Acute Child Malnutrition From 2 Longitudinal Cohorts in Mali and Burkina Faso
Authors: Barba Francisco M , Huybregts Lieven , Leroy Jef L
Published: July 2020

Child acute malnutrition (AM) is an important cause of child mortality. Accurately estimating its burden requires cumulative incidence data from longitudinal studies, which are rarely available in low-income settings. In the absence of such data, the AM burden is approximated using prevalence estimates from cross-sectional surveys and the incidence correction factor $K$, obtained from the few available cohorts that measured AM. We estimated $K$ factors for severe acute malnutrition (SAM) and moderate acute malnutrition (MAM) from AM incidence and prevalence using representative cross-sectional baseline and longitudinal data from 2 cluster-randomized controlled trials (Innovative Approaches for the Prevention of Childhood Malnutrition—PROMIS) conducted between 2014 and 2017 in Burkina Faso and Mali. We compared K estimates using complete (weight-for-length z score, mid-upper arm circumference (MUAC), and edema) and partial (MUAC, edema) definitions of SAM and MAM. $K$ estimates for SAM were 9.4 and 5.7 in Burkina Faso and in Mali, respectively; K estimates for MAM were 4.7 in Burkina Faso and 5.1 in Mali. The MUAC and edema–based definition of AM did not lead to different $K$ estimates. Our results suggest that $K$ can be reliably estimated when only MUAC and edema-based data are available. Additional studies, however, are required to confirm this finding in different settings.
Evaluation of Risks of Bias in Addiction Medicine Randomized Controlled Trials
Authors: Wayant Cole , Tritz Daniel , Horn Jarryd , Crow Matt , Vassar Matt
Published: July 2020

Aims

Perhaps the most important step when designing and conducting randomized controlled trials (RCTs) in addiction is to put methodological safeguards in place to minimize the likelihood for bias to affect trial outcomes. In this study, we applied the revised Cochrane risk of bias tool (ROB 2) to RCTs of drug, alcohol or tobacco interventions.

Methods

We searched for trials published in 15 addiction medicine journals over a 7-year period. Our primary endpoint is the risk of bias of included studies. We conducted a sensitivity analysis of publicly funded trials.

Results

Overall, included RCTs were most often at high risk of bias per our judgments (244/487, 50.1%). However, significant proportions of included RCTs were at low risk of bias (123/487, 25.3%) or some concerns for bias (120/497, 24.6%). RCTs with behavioral modification interventions (19/44, 43.2%) and alcohol interventions (80/150, 53.3%) had the highest proportion of high-risk judgments. In a sensitivity analysis of publicly funded RCTs), 195/386 (50.5%) were at high risk of bias.

Conclusions

Approximately half of included drug, alcohol or tobacco RCTs in our sample were judged to be at high risk of bias with the most common reason being a lack of proper blinding or proper description of blinding. Key action items to reduce bias in future addiction RCTs include adequate randomization, blinding and inclusion of a trial registry number and protocol.
Pathogenetic profiling of COVID-19 and SARS-like viruses
Authors: Nain Zulkar , Rana Humayan Kabir , Liò Pietro , Islam Sheikh Mohammed Shariful , Summers Matthew A , Moni Mohammad Ali
Published: July 2020

The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA–DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein–chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein–chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.
qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets
Authors: Häkkinen Antti , Koiranen Juha , Casado Julia , Kaipio Katja , Lehtonen Oskari , Petrucci Eleonora , Hynninen Johanna , Hietanen Sakari , Carpén Olli , Pasquini Luca , Biffoni Mauro , Lehtonen Rainer , Hautaniemi Sampsa
Published: July 2020

Motivation

Non-parametric dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE), are the most frequently used methods in the exploratory analysis of single-cell datasets. Current implementations scale poorly to massive datasets and often require downsampling or interpolative approximations, which can leave less-frequent populations undiscovered and much information unexploited.

Results

We implemented a fast t-SNE package, qSNE, which uses a quasi-Newton optimizer, allowing quadratic convergence rate and automatic perplexity (level of detail) optimizer. Our results show that these improvements make qSNE significantly faster than regular t-SNE packages and enables full analysis of large datasets, such as mass cytometry data, without downsampling.

Availability and implementation

Source code and documentation are openly available at https://bitbucket.org/anthakki/qsne/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Tick-borne Pathogens Detected in the Blood of Immunosuppressed Norwegian Patients Living in a Tick-endemic Area
Authors: Quarsten Hanne , Salte Tore , Lorentzen Åslaug R , Hansen Inger J W , Hamre Runar , Forselv Kristine J N , Øines Øivind , Wennerås Christine , Noraas Sølvi
Published: July 2020

Background

The knowledge regarding the occurrence and the clinical implications of tick-borne infections in immunosuppressed patients living in tick-endemic areas is limited.

Methods

Adult patients with autoimmune conditions requiring immunosuppressive treatment such as infliximab and rituximab were invited to participate in the study when they attended the hospital for treatment and/or control of the disease. Whole-blood samples were analyzed by real-time polymerase chain reaction for Borrelia burgdorferi sensu lato, Borrelia miyamotoi, Anaplasma phagocytophilum, Rickettsia spp., Candidatus Neoehrlichia mikurensis, and Babesia spp.

Results

The occurrence of tick-borne pathogens in the blood of patients (n = 163) with autoimmune conditions requiring immunosuppressive treatment was evaluated. Pathogen DNA was detected in 8.6% (14/163) of the patients. The predominant pathogen was Ca. Neoehrlichia mikurensis (12/14), which was carried in the blood of infected patients for 10–59 days until treatment with doxycycline. B. burgdorferi s.l. and Rickettsia spp. were detected in 1 patient each. The B. burgdorferi–infected patient presented with fever, whereas the remaining patients were judged to have subclinical infections. B. miyamotoi, A. phagocytophilum, and Babesia spp. were not detected in any patient.

Conclusions

Patients treated with biologicals and living in a tick-endemic area seem to have a high risk of contracting Ca. Neoehrlichia mikurensis infection, which, if left untreated, could result in thromboembolic complications.
FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results
Authors: Harjes Janno , Link Anton , Weibulat Tanja , Triebel Dagmar , Rambold Gerhard
Published: July 2020

Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of ‘FAIR++’ digital objects is introduced.
Myocarditis in Crohn’s disease: a case report
Authors: McGrath-Cadell Lucy , Bart Nicole K , Lin Linda , Ghaly Simon , Holloway Cameron J
Published: July 2020

Background

Mobile valvular masses are often considered pathognomonic for infective endocarditis. We present a case of a young patient with mobile valvular masses in the context of myocarditis likely secondary to active ileal Crohn’s disease. Cardiac magnetic resonance (CMR) imaging was crucial in diagnosing and monitoring our patient.

Case summary

A 27-year-old woman presented with pleuritic chest pain, dyspnoea, and a 3-day history of fevers. She also reported a 2-month history of intermittent visual loss in her right eye. She had a history of histologically proven ileal Crohn’s disease, diagnosed 5 months prior. She was haemodynamically unstable on presentation. Abnormalities on a transthoracic echocardiogram necessitated a transoesophageal echocardiogram. After blood cultures were sent, the patient was commenced on empirical treatment for infective endocarditis with gentamicin and flucloxacillin. Eight days after her initial presentation, all blood cultures remained negative and she was changed to empirical treatment for culture negative endocarditis with ceftriaxone and vancomycin, according to local protocol. Despite 8 days of treatment for infective endocarditis she remained febrile. A CMR was organized on Day 9 and this showed myocarditis, which changed the treatment paradigm. She responded swiftly to steroids and anti-coagulation.

Discussion

In this case, echo-dense valvular lesions are not pathognomonic for infective endocarditis and a careful diagnostic process involving multi-modality imaging, including CMR, occurred to arrive at a diagnosis of myocarditis likely secondary to Crohn’s disease.
COVID-19 fulminant myocarditis: a case report
Authors: Bernal-Torres Wikler , Herrera-Escandón Álvaro , Hurtado-Rivera Manuel , Plata-Mosquera Carlos Andrés
Published: July 2020

Background

Fulminant myocarditis is a catastrophic disease with high mortality and complications. A viral aetiology is frequent and the implication of SARS-CoV-2 is not yet known.

Case summary

A 38-year-old woman who recently arrived from Spain presented with palpitations that started suddenly 3 days prior to presentation and were associated with haemodynamic instability, without dyspnoea or chest pain. We found features of myopericarditis on the electrocardiogram and severe systolic dysfunction on the echocardiogram. The chest tomography showed findings which suggested COVID-19 infection, and PCR for SARS-CoV-2 was positive. The cardiac magnetic resonance image showed Lake Louise criteria for myocarditis. The patient was treated with immunomodulatory, steroid, and immunoglobulin therapy, with a favourable clinical response.

Discussion

The importance of this case lies in highlighting the severe cardiac involvement in a young patient, without previous risk factors, positive for COVID-19, and the favourable response to the medical treatment given.
Triggering effect of CLIL practice on English as a lingua franca awareness
Authors: Yalçın Şebnem , Bayyurt Yasemin , Alahdab Benan Rifaioğlu
Published: July 2020

The present study explores whether/how CLIL practice at primary English language classrooms raises English language teachers’ awareness towards their language use from an English as a lingua franca (ELF)-aware perspective. English language teachers in a CLIL program completed a survey about their classroom practice and their opinions about their English language use in the classroom. They also shared their lesson plans to showcase their everyday teaching. The findings revealed that although CLIL practice presented challenges for language teachers, their experience enabled participants to conceptualize themselves as ‘competent English language users’ instead of non-native English language teachers. Moreover, the findings suggested that teachers’ CLIL experience enabled them to become aware of the three major components of ELF awareness; namely, awareness of language and language use, awareness of instructional practice, and awareness of learning.
Country of birth, time period of resettlement and subsequent treated common mental disorders in young refugees in Sweden
Authors: Amin Ridwanul , Rahman Syed , Dorner Thomas E , Björkenstam Emma , Helgesson Magnus , Norredam Marie L , Sijbrandij Marit , Sever Cansu Alozkan , Mittendorfer-Rutz Ellenor
Published: July 2020

Background

Little is known regarding treatment for common mental disorders (CMDs) in young refugees. We aimed to identify (i) if the risk of treatment for CMDs in young refugees varies by their country of birth, compared with the Swedish-born population and (ii) if time period of resettlement influences these possible associations.

Methods

All Swedish-born individuals and people who were granted refugee status, aged 16–25 years, living in Sweden on 31 December 1999, 2004 or 2009 (around 1 million people with 3–4% refugees in each cohort), were followed for 4 years for treated CMDs by linking register data. To facilitate stratified analyses by refugees’ country of birth, the 2009 cohort was followed for 7 years with regard to specialized healthcare and antidepressant prescription due to CMDs. Hazard ratios with 95% confidence intervals were computed in crude and adjusted models.

Results

Refugees in the 2009 cohort with 7-year follow-up had a 25% lower risk for treated CMDs, compared with the Swedish-born. Stratified analysis by country of birth showed a similarly lower risk regarding treated CMDs among refugees from all countries but Iran [hazard ratios (95% confidence intervals): 1.15 (1.05–1.26)] than their Swedish-born peers. No substantial effect of time period of resettlement was observed in the risk for treated CMDs in refugees.

Conclusions

Treatment for CMDs is lower in young refugees than in the majority population in Sweden, is stable across time, but varies with country of birth. Strategies to improve access to mental healthcare for young refugees are warranted.
Pleural infection—an indicator of morbidity and increased burden on health care
Authors: Lehtomäki Antti I , Nevalainen Riikka M , Toikkanen Vesa J , Pohja Emilia S , Nieminen Jaakko J , Laurikka Jari O , Khan Jahangir A
Published: July 2020

OBJECTIVES

Patients with pleural infections frequently have several comorbidities and inferior long-term survival. We hypothesized that these patients represent a vulnerable cohort with high rates of hospitalization and frequent use of healthcare services. This study aims to ascertain the need for and causes of treatment episodes after pleural infections during long-term follow-up.

METHODS

Patients treated for pleural infections at Tampere University Hospital between January 2000 and December 2008 (n = 191, 81% males, median age 58 years) were included and compared to a demographically matched population-based random sample of 1910 controls. Seventy percent of the pleural infections were caused by pneumonias and 80% of the patients underwent surgery. Information regarding later in-hospital periods and emergency room and out-patient clinic visits, as well as survival data, was obtained from national registries and compared between patients and controls.

RESULTS

Patients treated for pleural infections had significantly higher rates of hospitalizations (8.19 vs 2.19), in-hospital days (88.5 vs 26.6), emergency room admissions (3.18 vs 1.45), out-patient clinic visits (41.1 vs 11.8) and procedures performed (1.26 vs 0.55) per 100 patient-months when compared to controls during 5-year follow-up, in addition to having increased mortality (30% vs 11%), P-value <0.00001 each. Particularly, episodes due to respiratory and digestive diseases, malignancies and mental disorders were more frequent. The patients’ comorbidities, such as alcoholism or chronic pulmonary disease, were associated with more frequent use of healthcare services.

CONCLUSIONS

Patients treated for pleural infections have high rates of hospitalizations, emergency room admissions and out-patient clinic visits during follow-up.
Transitional Justice and Temporal Parameters: Built-In Expiration Dates?
Authors: Horne Cynthia M
Published: July 2020

Temporal assumptions associated with personnel reforms, such as lustration and public disclosure programs, both prescribe the optimal timing for the onset of measures and proscribe a long duration for such measures. In the context of the post-communist transitions, these assumptions suggested that lustration and public disclosures should be enacted as soon as possible after a regime transition, with the legitimacy, motives, and legal appropriateness of delayed measures being questioned. In terms of duration, personnel reforms should have fixed time limits, often suggested as no more than a decade. This article critically explores the evolution of these temporal assumptions through an examination of the legal rulings, intergovernmental policies, and recommendations of the Parliamentary Assembly of the Council of Europe, the European Court of Human Rights, and the Venice Commission. The article illustrates the tension between the continued use of the measures by some post-communist states and international rulings signalling their expiration.
Demanding Truth: The Global Transitional Justice Network and the Creation of Truth Commissions
Authors: Zvobgo Kelebogile
Published: July 2020

Since 1970, scores of states have established truth commissions to document political violence. Despite their prevalence and potential consequence, the question of why commissions are adopted in some contexts, but not in others, is not well understood. Relatedly, little is known about why some commissions possess strong investigative powers while others do not. I argue that the answer to both questions lies with domestic and international civil society actors, who are connected by a global transitional justice (TJ) network and who share the burden of guiding commission adoption and design. I propose that commissions are more likely to be adopted where network members can leverage information and moral authority over governments. I also suggest that commissions are more likely to possess strong powers where international experts, who steward TJ best practices, advise governments. I evaluate these expectations by analyzing two datasets in the novel Varieties of Truth Commissions Project, interviews with representatives from international non-governmental organizations, interviews with Guatemalan non-governmental organization leaders, a focus group with Argentinian human rights advocates, and a focus group at the International Center for Transitional Justice. My results indicate that network members share the burden—domestic members are essential to commission adoption, while international members are important for strong commission design.
Drug repurposing: phosphate prodrugs of anticancer and antiviral FDA-approved nucleosides as novel antimicrobials
Authors: Pertusati Fabrizio , Pileggi Elisa , Richards Jennifer , Wootton Mandy , Van Leemputte Thijs , Persoons Leentje , De Coster David , Villanueva Xabier , Daelemans Dirk , Steenackers Hans , McGuigan Christopher , Serpi Michaela
Published: July 2020

Objectives

Following a drug repurposing approach, we aimed to investigate and compare the antibacterial and antibiofilm activities of different classes of phosphate prodrugs (HepDirect, cycloSal, SATE and mix SATE) of antiviral and anticancer FDA-approved nucleoside drugs [zidovudine (AZT), floxouridine (FUDR) and gemcitabine (GEM)] against a variety of pathogenic Gram-positive and -negative bacteria.

Methods

Ten prodrugs were synthesized and screened for antibacterial activity against seven Gram-negative and two Gram-positive isolates fully susceptible to traditional antibiotics, alongside six Gram-negative and five Gram-positive isolates with resistance mechanisms. Their ability to prevent and eradicate biofilms of different bacterial pathogens in relation to planktonic growth inhibition was also evaluated, together with their effect on proliferation, viability and apoptosis of different eukaryotic cells.

Results

The prodrugs showed decreased antibacterial activity compared with the parent nucleosides. cycloSal-GEM-monophosphate (MP) prodrugs 20a and 20b were the most active agents against Gram-positive bacteria (Enterococcus faecalis and Staphylococcus aureus) and retained their activity against antibiotic-resistant isolates. cycloSal-FUDR-MP 21a partially retained good activity against the Gram-positive bacteria E. faecalis, Enterococcus faecium and S. aureus. Most of the prodrugs tested displayed very potent preventive antibiofilm specific activity, but not curative. In terms of cytotoxicity, AZT prodrugs did not affect apoptosis or cell viability at the highest concentration tested, and only weak effects on apoptosis and/or cell viability were observed for GEM and FUDR prodrugs.

Conclusions

Among the different prodrug approaches, the cycloSal prodrugs appeared the most effective. In particular, cycloSal (17a) and mix SATE (26) AZT prodrugs combine the lowest cytotoxicity with high and broad antibacterial and antibiofilm activity against Gram-negative bacteria.
Architectural Distortion on Digital Breast Tomosynthesis: Management Algorithm and Pathological Outcome
Authors: Samreen Naziya , Moy Linda , Lee Cindy S
Published: July 2020

Architectural distortion on digital breast tomosynthesis (DBT) can occur due to benign and malignant causes. With DBT, there is an increase in the detection of architectural distortion compared with 2D digital mammography, and the positive predictive value is high enough to justify tissue sampling when imaging findings are confirmed. Workup involves supplemental DBT views and ultrasound, with subsequent image-guided percutaneous biopsy using the modality on which it is best visualized. If architectural distortion is subtle and/or questionable on diagnostic imaging, MRI may be performed for problem solving, with subsequent biopsy of suspicious findings using MRI or DBT guidance, respectively. If no suspicious findings are noted on MRI, a six-month follow-up DBT may be performed. On pathology, malignant cases are noted in 6.8%–50.7% of the cases, most commonly due to invasive ductal carcinoma, followed by invasive lobular carcinoma. Radial scars are the most common benign cause, with stromal fibrosis and sclerosing adenosis being much less common. As there is an increase in the number of benign pathological outcomes for architectural distortion on DBT compared with 2D digital mammography, concordance should be based on the level of suspicion of imaging findings. As discordant cases have upgrade rates of up to 25%, surgical consultation is recommended for discordant radiologic-pathologic findings.
Partitioning beta diversity to unravel mechanisms underlying the distributions of nonvolant small mammls in Brazil’s Cerrado
Authors: Ribeiro Raquel , Ricklefs Robert E , Marinho-Filho Jader
Published: July 2020

Species distributions and the mechanisms that produce patterns in the occupation space are recurrent themes in community ecology. Here, we examine beta diversity among assemblages of small mammals in the Cerrado domain of Brazil to partition the effects of turnover and nestedness on species distributions. Our objective was to evaluate whether balanced spatial variation in abundance (β bal) and abundance gradients (β gra) are congruent within and among habitats and localities of the Brazilian Cerrado. In addition, we wanted to understand whether ecological mechanisms, such as dispersal limitation, habitat filtering, and species sorting, drive the distribution patterns of the Cerrado small mammals. We analyzed the occurrence and abundances of small mammals from 16 localities widely distributed across the Cerrado biome, and grouped our data with respect to two distinct spatial scales. Baselga’s Bray–Curtis index of dissimilarity and its respective partitions, i.e., balanced variation in abundance (β bal) and abundance gradients (β gra), were estimated between sampling units at the two spatial scales. Thus, we used exponential models to search for distance decay in species similarity between pairs of localities and between similar habitats. Our results show that differences between small mammal assemblages in the Cerrado are driven mainly by species replacement rather than independent gain or loss of species, both at small and large scales. The spatial turnover patterns of small mammals in the Cerrado biome are determined by a combination of large scale (biogeographic, spatial) and local mechanisms (low dispersal and habitat specificity). However, processes occurring at small scales seem to be more important in species sorting than processes occurring at large scales. The spatial configuration of the landscape and the extent and quality of habitats strongly influence the rate of species turnover in Cerrado. Thus, protecting the different types of habitats should be of prime importance to conserving the diversity of Cerrado small mammals.
Insulin protects against type 1 diabetes mellitus-induced ultrastructural abnormalities of pancreatic islet microcirculation
Authors: Wang Bing , Zhang Xu , Liu Mingming , Li Yuan , Zhang Jian , Li Ailing , Zhang Honggang , Xiu Ruijuan
Published: July 2020

Pancreatic islet microcirculation, consisting of pancreatic islet microvascular endothelial cells (IMECs) and pericytes (IMPCs), provides crucial support for the physiological function of pancreatic islet. Emerging evidence suggests that pancreatic islet microcirculation is impaired in type 1 diabetes mellitus (T1DM). Here, we investigated the potential ultrastructural protective effects of insulin against streptozotocin (STZ)-induced ultrastructural abnormalities of the pancreatic islet microcirculation in T1DM mouse model. For this purpose, pancreatic tissues were collected from control, STZ-induced T1DM and insulin-treated mice, and a pancreatic IMECs cell line (MS1) was cultured under control, 35 mM glucose with or without 10−8 M insulin conditions. Transmission and scanning electron microscopies were employed to evaluate the ultrastructure of the pancreatic islet microcirculation. We observed ultrastructural damage to IMECs and IMPCs in the type 1 diabetic group, as demonstrated by destruction of the cytoplasmic membrane and organelles (mainly mitochondria), and this damage was substantially reversed by insulin treatment. Furthermore, insulin inhibited collagenous fiber proliferation and alleviated edema of the widened pancreatic islet exocrine interface in T1DM mice. We conclude that insulin protects against T1DM-induced ultrastructural abnormalities of the pancreatic islet microcirculation.
β-Lactamase–Producing, Ciprofloxacin-Resistant Neisseria meningitidis Isolated From a 5-Month-Old Boy in the United States
Authors: Taormina Gillian , Campos Joseph , Sweitzer John , Retchless Adam C , Lunquest Kristy , McNamara Lucy A , Reese Natashia , Karlsson Maria , Hanisch Benjamin
Published: July 2020

Worldwide, there have been few reports of β-lactamases causing penicillin resistance in Neisseria meningitidis. The first known case of disease in the United States due to a β-lactamase-producing, ciprofloxacin-resistant N. meningitidis was recently identified. This has potential implications on standard laboratory testing and empiric management of meningococcal disease.
Guillain-Barré Syndrome Associated With Severe Acute Respiratory Syndrome Coronavirus 2 Detection and Coronavirus Disease 2019 in a Child
Authors: Khalifa Maher , Zakaria Fairouz , Ragab Yasser , Saad Ahmed , Bamaga Ahmed , Emad Yasser , Rasker Johannes J
Published: July 2020

Coronavirus disease (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Physicians in China reported what is believed to be the first adult case of a SARS-CoV-2 infection associated with acute Guillain-Barré syndrome (GBS), followed by 5 adult Italian patients and another case in the United States. In the current report, we present one of the first descriptions of an association of GBS and SARS-CoV-2 infection in a child. In our facility, an 11-year-old boy presented with typical features of GBS and, after 5 days, a morbilliform skin rash over the palms of both hands. Three weeks before the start of the neurological symptoms, the boy had experienced an episode of mild febrile illness with mild respiratory manifestations and a persistent cough. The diagnosis of SARS-CoV-2 infection was confirmed by oropharyngeal swab on reverse-transcription polymerase chain reaction assay. The disease course of our patient strongly suggests a possible relationship between the development of GBS and SARS-CoV-2 infection. The case is discussed in view of previous case reports regarding the association of GBS and COVID-19.
Radiation eye dose to medical staff during respiratory endoscopy under X-ray fluoroscopy
Authors: Haga Yoshihiro , Chida Koichi , Kimura Yuichiro , Yamanda Shinsuke , Sota Masahiro , Abe Mitsuya , Kaga Yuji , Meguro Taiichiro , Zuguchi Masayuki
Published: July 2020

Although the clinical value of fluoroscopically guided respiratory endoscopy (bronchoscopy) is clear, there have been very few studies on the radiation dose received by staff during fluoroscopically guided bronchoscopy. The International Commission on Radiological Protection (ICRP) is suggesting reducing the occupational lens dose limit markedly from 150 to 20 mSv/year, averaged over defined periods of five years. The purpose of this study was to clarify the current occupational eye dose of bronchoscopy staff conducting fluoroscopically guided procedures. We measured the occupational eye doses (3-mm-dose equivalent, Hp(3)) of bronchoscopy staff (physicians and nurses) over a 6-month period. The eye doses of eight physicians and three nurses were recorded using a direct eye dosimeter, the DOSIRIS. We also estimated eye doses using personal dosimeters worn at the neck. The mean ± SD radiation eye doses (DOSIRIS) to physicians and nurses were 7.68 ± 5.27 and 2.41 ± 1.94 mSv/6 months, respectively. The new lens dose limit, 20 mSv/year, may be exceeded among bronchoscopy staff, especially physicians. The eye dose of bronchoscopy staff (both physicians and nurses) was underestimated when measured using a neck dosimeter. Hence, the occupational eye dose of bronchoscopy staff should be monitored. To reduce the occupational eye dose, we recommend that staff performing fluoroscopically guided bronchoscopy wear Pb glasses. correct evaluation of the lens dose [Hp(3)] using an eye dosimeter such as the DOSIRIS is necessary for bronchoscopy staff.
Tonsillectomy as an effective treatment for arthralgia of SAPHO syndrome
Authors: Horiguchi Sena , Fujita Takeshi , Kinoshita Koji , Doi Katsumi
Published: July 2020

Synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome has been proposed to describe a clinicoradiological entity manifesting in the joints, skin and bones. We describe a patient with SAPHO syndrome for whom bilateral tonsillectomy was effective for the treatment of arthralgia, which was quantified using multiple pain scales.
Transcriptomic profiling identifies novel transcripts, isomorphs, and noncoding RNAs in Paracoccidioides brasiliensis
Authors: Menegidio Fabiano B , Aciole Barbosa David , Alencar Valquíria C , Vilas Boas Renata O , Costa de Oliveira Regina , Jabes Daniela L , Nunes Luiz R
Published: July 2020

This paper describes a transcriptomic profiling of Paracoccidioides brasiliensis (Pb) performed with the aid of an RNA-seq-based approach, aimed at characterizing the general transcriptome in this human pathogenic fungus, responsible for paracoccidioidomycosis (PCM). Results confirm that ∼75% of the genes currently annotated in the P. brasiliensis genome are, in fact, transcribed in vivo and that ∼19% of them may display alternative isomorphs. Moreover, we identified 627 transcripts that do not match any gene currently mapped in the genome, represented by 114 coding transcripts (probably derived from previously unmapped protein-coding genes) and 513 noncoding RNAs (ncRNAs), including 203 long-noncoding RNAs (lncRNAs).
Chemo-dynamics of outer halo dwarf stars, including Gaia-Sausage and Gaia-Sequoia candidates
Authors: Monty Stephanie , Venn Kim A , Lane James M M , Lokhorst Deborah , Yong David
Published: July 2020

The low-metallicity, kinematically interesting dwarf stars studied by Stephens & Boesgaard (2002, SB02) are re-examined using Gaia DR2 astrometry, and updated model atmospheres and atomic line data. New stellar parameters are determined based on the Gaia DR2 parallactic distances and Dartmouth Stellar Evolution Database isochrones. These are in excellent agreement with spectroscopically determined stellar parameters for stars with [Fe/H] > −2; however, large disagreements are found for stars with [Fe/H] ≤ −2, with offsets as large as ΔTeff ∼ +500 K and Δlog g ∼ +1.0. A subset of six stars (test cases) are analysed ab initio using high-resolution spectra with Keck HIRES and Gemini GRACES. This sub-sample is found to include two α-challenged dwarf stars, suggestive of origins in a low-mass, accreted dwarf galaxy. The orbital parameters for the entire SB02 sample are re-determined using Gaia DR2 data. We find 11 stars that are dynamically coincident with the Gaia-Sausage accretion event and another 17 with the Gaia-Sequoia event in action space. Both associations include low-mass, metal-poor stars with isochrone ages older than 10 Gyr. Two dynamical subsets are identified within Gaia-Sequoia. When these subsets are examined separately, a common knee in [α/Fe] is found for the Gaia-Sausage and low orbital energy Gaia-Sequoia stars. A lower metallicity knee is tentatively identified in the Gaia-Sequoia high orbital energy stars. If the metal-poor dwarf stars in these samples are true members of the Gaia-Sausage and Gaia-Sequoia events, then they present a unique opportunity to probe the earlier star formation histories of these systems.
Radio variability from corotating interaction regions threading Wolf–Rayet winds
Authors: Ignace Richard , St-Louis Nicole , Prinja Raman K
Published: July 2020

The structured winds of single massive stars can be classified into two broad groups: stochastic structure and organized structure. While the former is typically identified with clumping, the latter is typically associated with rotational modulations, particularly the paradigm of corotating interaction regions (CIRs). While CIRs have been explored extensively in the ultraviolet band, and moderately in the X-ray and optical, here we evaluate radio variability from CIR structures assuming free–free opacity in a dense wind. Our goal is to conduct a broad parameter study to assess the observational feasibility, and to this end, we adopt a phenomenological model for a CIR that threads an otherwise spherical wind. We find that under reasonable assumptions, it is possible to obtain radio variability at the 10 per cent level. The detailed structure of the folded light curve depends not only on the curvature of the CIR, the density contrast of the CIR relative to the wind, and viewing inclination, but also on wavelength. Comparing light curves at different wavelengths, we find that the amplitude can change, that there can be phase shifts in the waveform, and the entire waveform itself can change. These characterstics could be exploited to detect the presence of CIRs in dense, hot winds.
Dynamics of black hole–neutron star binaries in young star clusters
Authors: Rastello Sara , Mapelli Michela , Di Carlo Ugo N , Giacobbo Nicola , Santoliquido Filippo , Spera Mario , Ballone Alessandro , Iorio Giuliano
Published: July 2020

Young star clusters are likely the most common birthplace of massive stars across cosmic time and influence the formation of compact binaries in several ways. Here, we simulate the formation of black hole–neutron star binaries (BHNSs) in young star clusters, by means of the binary population synthesis code MOBSE interfaced with the N-body code NBODY6++GPU. BHNSs formed in young star clusters (dynamical BHNSs) are significantly more massive than BHNSs formed from isolated binaries (isolated BHNSs): ∼40 per cent of the dynamical BHNS mergers have a total mass of >15 M⊙, while only ∼0.01 per cent of the isolated BHNS mergers have mass in excess of this value. Hence, our models strongly support a dynamical formation scenario for GW190814, given its total mass of ∼26 M⊙, if this event is a BHNS merger. All our dynamical BHNSs are ejected from their parent star cluster before they reach coalescence. Thus, a significant fraction of BHNS mergers occurring in the field might have originated in a young star cluster. The mass spectrum of BHNS mergers from gravitational-wave detections will provide a clue to differentiate between dynamical and isolated formation of BHNSs.
Weak-lensing observables in relativistic N-body simulations
Authors: Lepori Francesca , Adamek Julian , Durrer Ruth , Clarkson Chris , Coates Louis
Published: July 2020

We present a numerical weak-lensing analysis that is fully relativistic and non-perturbative for the scalar part of the gravitational potential and first order in the vector part, frame dragging. Integrating the photon geodesics backwards from the observer to the emitters, we solve the Sachs optical equations and study in detail the weak-lensing convergence, ellipticity and rotation. For the first time, we apply such an analysis to a high-resolution relativistic N-body simulation, which consistently includes the leading-order corrections due to general relativity on both large and small scales. These are related to the question of gauge choice and to post-Newtonian corrections, respectively. We present the angular power spectra and one-point probability distribution functions for the weak-lensing variables, which we find are broadly in agreement with comparable Newtonian simulations. Our geometric approach, however, is more robust and flexible, and can therefore be applied consistently to non-standard cosmologies and modified theories of gravity.
Role of cosmic rays in the early stages of galactic outflows
Authors: Jana Ranita , Gupta Siddhartha , Nath Biman B
Published: July 2020

Using an idealized set-up, we investigate the dynamical role of cosmic rays (CRs) in the early stages of galactic outflows for galaxies of halo masses 108, 1011, and 1012 M⊙. The outflow is launched from a central region in the galactic disc where we consider three different constant star formation rates (0.1, 1, and 10 $\mathrm{M}_\odot \, \mathrm{yr}^{-1}$) over a dynamical time-scale of 50 Myr. We determine the temperature distribution of the gas and find that CRs can reduce the temperature of the shocked gas, which is consistent with previous results. However, we show that CRs do not have any noticeable effect on the mass loading by the outflow. We find that CRs can reduce the size of the outflow, which contradicts previous claims of efficient dynamical impact of CRs; however, it is consistent with earlier theoretical models of CR-driven blastwave as well as stellar wind. We discuss the dependence of our results on CR injection prescriptions and compare them with earlier studies. We conclude that in the early stages of galactic outflows the dynamical role of CRs is not important.
ExoMol line lists – XL. Rovibrational molecular line list for the hydronium ion (H3O+)
Authors: Yurchenko S N , Tennyson Jonathan , Miller Steve , Melnikov V V , O’Donoghue J , Moore L
Published: July 2020

A new line list for hydronium (H316O+) is computed. The line list is based on a new ab initio dipole moment surface (CCSD(T)/aug-cc-pVQZ) and a new empirical potential energy surface (PES). The empirical PES of H3O+ was obtained by refining an ab initio surface through a global fit to the experimentally determined rovibrational energies collected from the literature covering the ground, $\nu _1^{\pm }$, $\nu _2^{\pm }$, $2\nu _2^{\pm }$, $\nu _3^{\pm }$, and $\nu _4^{\pm }$ vibrational states. The line list covers the wavenumber range up to 10 000 cm−1 (wavelengths $\gt 1 \, \mu$m) and should be complete for temperatures up to T = 1500 K. This is the first comprehensive line list for H3O+ with extensive wavenumber coverage and accurate transitional probabilities. Prospects of detection of hydronium in spectra of Solar system giant planets as well as exoplanets are discussed. The eXeL line list is publicly available from the ExoMol and CDS data bases.
Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen
Authors: Andras Jason P , Fields Peter D , Du Pasquier Louis , Fredericksen Maridel , Ebert Dieter
Published: July 2020

Knowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host–pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen of planktonic crustaceans that has been established as a model for studies of Red Queen host–pathogen coevolution. We sequenced the genomes of a geographically, phenotypically, and genetically diverse collection of P. ramosa strains and performed a genome-wide association study to identify genetic correlates of infection phenotype. We found multiple polymorphisms within a single gene, Pcl7, that correlate perfectly with one common and widespread infection phenotype. We then confirmed this perfect association via Sanger sequencing in a large and diverse sample set of P. ramosa clones. Pcl7 codes for a collagen-like protein, a class of adhesion proteins known or suspected to be involved in the infection mechanisms of a number of important bacterial pathogens. Consistent with expectations under Red Queen coevolution, sequence variation of Pcl7 shows evidence of balancing selection, including extraordinarily high diversity and absence of geographic structure. Based on structural homology with a collagen-like protein of Bacillus anthracis, we propose a hypothesis for the structure of Pcl7 and the physical location of the phenotype-associated polymorphisms. Our results offer strong evidence for a gene governing infectivity and provide a molecular basis for further study of Red Queen dynamics in this model host–pathogen system.