bluuebunny/crossref_metadata_2025 huggingface dataset:
Swift J011511.0-725611: discovery of a rare Be star/white dwarf binary system in the SMC
Authors: Kennea J A , Coe M J , Evans P A , Townsend L J , Campbell Z A , Udalski A
Published: September 2021

We report on the discovery of Swift J011511.0-725611, a rare Be X-ray binary system (BeXRB) with a white dwarf (WD) compact object, in the Small Magellanic Cloud (SMC) by S-CUBED, a weekly X-ray/UV survey of the SMC by the Neil Gehrels Swift Observatory. Observations show an approximately 3 month outburst from Swift J011511.0-725611, the first detected by S-CUBED since it began in 2016 June. Swift J011511.0-725611 shows supersoft X-ray emission, indicative of a WD compact object, which is further strengthened by the presence of an 0.871 keV edge, commonly attributed to O viii K-edge in the WD atmosphere. Spectroscopy by South African Large Telescope confirms the Be nature of the companion star, and long term light curve by OGLE finds both the signature of a circumstellar disc in the system at outburst time, and the presence of a 17.4 day periodicity, likely the orbital period of the system. Swift J011511.0-725611 is suggested to be undergoing a Type-II outburst, similar to the previously reported SMC Be white dwarf binary (BeWD), Swift J004427.3-734801. It is likely that the rarity of known BeWD is in part due to the difficulty in detecting such outbursts due to both their rarity, and their relative faintness compared to outbursts in Neutron Star BeXRBs.
The global 21-cm signal of a network of cosmic string wakes
Authors: Hernández Oscar F
Published: September 2021

In previous works, we discussed the 21-cm signature of a single cosmic string wake. However, the 21-cm brightness temperature is influenced by a network of cosmic string wakes, and not one single wake. In this work, we consider the signal from a network of wakes laid down during the matter era. We also improve on the previous calculation of a single wake signature. Finally, we calculate the enhancement of the global 21-cm brightness temperature due to a network of wakes and discuss its affects of the signal measured in the Wouthuysen–Field absorption trough. We estimated that for string tensions between 10−8 and 10−7 there would be between a 10 per cent and a factor of 2 enhancement in the signal.
PS J1721+8842: a gravitationally lensed dual AGN system at redshift 2.37 with two radio components
Authors: Mangat C S , McKean J P , Brilenkov R , Hartley P , Stacey H R , Vegetti S , Wen D
Published: September 2021

Dual-Active Galactic Nuclei (AGN) are a natural consequence of the hierarchical structure formation scenario, and can provide an important test of various models for black hole growth. However, due to their rarity and difficulty to find at high redshift, very few confirmed dual-AGN are known at the epoch where galaxy formation peaks. Here we report the discovery of a gravitationally lensed dual-AGN system at redshift 2.37 comprising two optical/IR quasars separated by 6.5 ± 0.6 kpc, and a third compact (Reff = 0.45 ± 0.02 kpc) red galaxy that is offset from one of the quasars by 1.7 ± 0.1 kpc. From Very Large Array imaging at 3 GHz, we detect 600 and 340 pc-scale radio emission that is associated with both quasars. The 1.4 GHz luminosity densities of the radio sources are about 1024.35 W Hz−1, which is consistent with weak jets. However, the low brightness temperature of the emission is also consistent with star-formation at the level of 850 to 1150 M⊙ yr−1. Although this supports the scenario where the AGN and/or star-formation is being triggered through an ongoing triple-merger, a post-merger scenario where two black holes are recoiling is also possible, given that neither has a detected host galaxy.
Chronic E-Cigarette Exposure Alters Human Alveolar Macrophage Morphology and Gene Expression
Authors: Davis Eric S , Ghosh Arunava , Coakley Raymond D , Wrennall Joe A , Lubamba Bob A , Rowell Temperance R , Dang Hong , Pawlak Erica A , Li Quefeng , Alexis Neil E , Ribeiro Carla M P , Tarran Robert
Published: September 2021

Introduction

Alveolar macrophages (AMs) are lung-resident immune cells that phagocytose inhaled particles and pathogens, and help coordinate the lung’s immune response to infection. Little is known about the impact of chronic e-cigarette use (ie, vaping) on this important pulmonary cell type. Thus, we determined the effect of vaping on AM phenotype and gene expression.

Aims and Methods

We recruited never-smokers, smokers, and e-cigarette users (vapers) and performed research bronchoscopies to isolate AMs from bronchoalveolar lavage fluid samples and epithelial cells from bronchial brushings. We then performed morphological analyses and used the Nanostring platform to look for changes in gene expression.

Results

AMs obtained from smokers and vapers were phenotypically distinct from those obtained from nonsmokers, and from each other. Immunocytochemistry revealed that vapers AMs had significantly elevated inducible nitric oxide synthase (M1) expression and significantly reduced CD301a (M2) expression compared with nonsmokers or smokers. Vapers’ AMs and bronchial epithelia exhibited unique changes in gene expression compared with nonsmokers or smokers. Moreover, vapers’ AMs were the most affected of all groups and had 124 genes uniquely downregulated. Gene ontology analysis revealed that vapers and smokers had opposing changes in biological processes.

Conclusions

These data indicate that vaping causes unique changes to AMs and bronchial epithelia compared with nonsmokers and smokers which may impact pulmonary host defense.

Implications

These data indicate that normal “healthy” vapers have altered AMs and may be at risk of developing abnormal immune responses to inflammatory stimuli.
Laron syndrome in three female siblings with the development of subclinical hypothyroidism and dyslipidemia in one case: first report of a Syrian family
Authors: Chreitah Ahmad , Hijazia Kheria , Doya Leen Jamel
Published: September 2021

Laron syndrome (LS) is a rare autosomal recessive disorder characterized by dwarfism and typical facial phenotype. This report is the first to present three cases of Laron syndrome affecting three female siblings from Syria. The index case presented at age of 8.5 years with severe short stature: low level of Insulin-like growth factor 1 (IGF-1), elevated levels of fasting and post-stimulation growth hormone (GH), consistent with the diagnosis of Laron syndrome. At the age of 9.5 years, she developed non-autoimmune subclinical hypothyroidism treated with Levothyroxine, then she developed dyslipidemia at the age of 11.3 years. Later, we identified two female siblings of the patient with Laron syndrome. Laron syndrome is a rare genetic disease, reporting of new cases of this rare syndrome must encourage pediatricians to develop high clinical suspicion if faced with patients with very short stature and typical facial features.
Colistin neurotoxicity mimicking Guillain-Barré syndrome in a patient with cystic fibrosis: case report and review
Authors: Camargo Celeste , Narula Tathagat , Jackson Daniel A , Padro Teresa , Freeman W David
Published: September 2021

Guillain-Barré syndrome (GBS) is an immune-mediated polyneuropathy, which is characterized by areflexia and ascending paresthesia which can progress to a respiratory failure. Certain conditions, such as vasculitis and heavy metal and drug toxicity, may have misleadingly similar clinical presentation to GBS. We describe a case of a patient with cystic fibrosis and intravenous colistin-induced neurotoxicity mimicking GBS. The patient had used inhaled colistin on five occasions with no adverse effects, however, developed symptoms on the second day of intravenous treatment. Overlapping findings between immune-mediated polyneuropathy and drug-induced neurotoxicity include limb paresthesia and decreased reflexes. Perioral tingling, however, is a common presentation of colistin-induced neurotoxicity, and therefore, is an important differentiating factor. Early diagnosis prevents further neurologic decline, extensive unnecessary workup and potentially harmful incorrect management.
Spontaneous retroperitoneal hematoma: a rare bleeding occurrence in COVID-19
Authors: Yeoh Whei Chuern , Lee Kee Tat , Zainul Nadiah Hanim , Syed Alwi Sharifah Baizura , Low Lee Lee
Published: September 2021

Emerging evidence suggest that COVID-19 is associated with hypercoagulability, predisposing patients to increase risk of thromboembolism. Anticoagulation is not without its risks of bleeding and decision to initiate anticoagulation should be carefully considered with close monitoring. Spontaneous retroperitoneal hematoma is a rare complication, and there are only a few documented reports implicating anticoagulant or antiplatelet agents as a potential cause. We report a 57-year-old gentleman with COVID-19 pneumonia who developed hypotension on Day 10 of illness while on prophylactic anticoagulation. Computed tomography scan of abdomen revealed a large right retroperitoneal and psoas muscle hematoma and he underwent surgical exploration to evacuate the hematoma. His condition improved and was discharged well. Although prophylactic anticoagulation may reduce thrombotic complications in severely ill COVID-19 patients, a high index of suspicion for rare bleeding complications should be maintained if patients become hemodynamically unstable. Early diagnosis and appropriate intervention may improve outcome and prevent mortality.
Early HER2-positive breast cancer arising from a fibroadenoma: a case report
Authors: Fujimoto Akihiro , Matsuura Kazuo , Kawasaki Tomonori , Ichinose Yuki , Nukui Asami , Hiratsuka Miyuki , Asano Aya , Shimada Hiroko , Osaki Akihiko , Saeki Toshiaki
Published: September 2021

Breast cancer arising from fibroadenoma (FA) is rare, in which almost all reported cases are human epidermal growth factor receptor 2 (HER2)-negative. This is the first report to describe a case of HER2-positive breast cancer arising from FA that was treated with chemotherapy plus anti-HER2 therapy. In this early case, upfront surgery outcomes guided the selection of appropriate systemic therapy. A 31-year-old woman previously diagnosed with FA experienced tumor growth. Core needle biopsy and imaging studies confirmed a diagnosis of stage IIA HER2-positive invasive ductal carcinoma (IDC) with no evidence of lymph node metastasis (cT2N0M0). Breast-conserving surgery was performed. Pathological diagnosis revealed stage IA IDC with a predominant intraductal component (pT1aN0M0), arising from FA. In conclusion, we encountered an extremely rare case of HER2-positive breast cancer arising from FA in which pathological infiltration was difficult to predict based on preoperative imaging.
Takotsubo syndrome during surgery for pheochromocytoma: an unexpected complication
Authors: Paraschiv Catalina , Trasca Livia F , Enciu Octavian , Balanescu Serban M , Miron Adrian
Published: September 2021

Takotsubo syndrome is a rare cause of systolic dysfunction and can be found as a clinical manifestation of pheochromocytoma. We present a case of rapid onset of systolic dysfunction with cardiogenic shock, which developed after the surgical excision of an adrenal gland tumor in a 60-year-old male. Coronary angiography excluded coronary artery disease. The echocardiography and ventriculography images suggested Takotsubo cardiomyopathy pattern. Following 2 weeks of inotropic and vasopressor therapy, the left ventricular function gradually improved, until complete resolution.
Exploring remission concept in axial spondyloarthritis through the perception of rheumatologists using vignettes and priority ratings
Authors: Aouad Krystel , Wendling Daniel , Breban Maxime , Dadoun Sabrina , Hudry Christophe , Moltó Anna , Pertuiset Edouard , Gossec Laure
Published: September 2021

Objectives

The optimal treatment target in axial spondyloarthritis (axSpA) is remission; however, a consensual definition of remission is lacking. Our objective was to explore rheumatologists’ perception of remission using vignette cases and a priority exercise.

Methods

A cross-sectional survey of rheumatologists’ perceptions of remission in axSpA was performed in 2020 using (i) 36 vignette cases, with a single clinical picture and three varying parameters [axial pain (ranging from 2 to 5 on a 0–10 scale)], fatigue (2–8), and morning stiffness (<15 min, 30 min or 1 h), assessed as remission yes/no; and (ii) prioritization of elements to consider for remission from a list of 12 items: BASDAI, ASDAS, elements of BASDAI and ASDAS including CRP, NSAID use, extra-articular manifestations (EAMs), and other explanations of symptoms, e.g. fibromyalgia. Analyses were descriptive.

Results

Overall, 200 French rheumatologists participated in 2400 vignette evaluations. Of these, 463 (19%) were classified as remission. The six vignette cases representing 56% of all remission cases had <15 min duration of morning stiffness and axial pain ≤3/10, regardless of fatigue levels. Prioritized items for remission were: morning stiffness (75%), EAMs (75%), NSAID use (71%), axial pain (68%) and CRP (66%).

Conclusions

When conceptualizing remission in axSpA, rheumatologists took into account morning stiffness and axial pain as expected; the link between remission and fatigue was much weaker. Furthermore, rheumatologists also included EAMs and NSAID use in the concept of remission. Consensus is needed for definition of remission in axSpA.
UTERINE ARTERY EMBOLISATION: CONTINUOUS QUALITY IMPROVEMENT REDUCES RADIATION DOSE WHILE MAINTAINING IMAGE QUALITY
Authors: Nocum Don J , Robinson John , Halaki Mark , Båth Magnus , Mekiš Nejc , Liang Eisen , Thompson Nadine , Moscova Michelle , Reed Warren
Published: September 2021

The purpose of this study was to introduce a continuous quality improvement (CQI) program for radiation dose optimisation during uterine artery embolisation (UAE) and assess its impact on dose reduction and image quality. The CQI program investigated the effects of optimising radiation dose parameters on the kerma-area product (KAP) and image quality when comparing a ‘CQI intervention’ group (n = 50) and ‘Control’ group (n = 50). Visual grading characteristics (VGC) analysis was used to assess image quality, using the ‘Control’ group as a reference. A significant reduction in KAP by 17% (P = 0.041, d = 0.2) and reference air kerma (Ka, r) by 20% (P = 0.027, d = 0.2) was shown between the two groups. The VGC analysis resulted in an area under the VGC curve (AUCVGC) of 0.54, indicating no significant difference in image quality between the two groups (P = 0.670). The implementation of the CQI program and optimisation of radiation dose parameters improved the UAE radiation dose practices at our centre. The dose reduction demonstrated no detrimental effects on image quality.
Managing expectations in financial markets: voluntary accountability practices of capital market regulators in Spain and Turkey
Authors: Apaydin Fulya , Jordana Jacint
Published: September 2021

In recent decades, independent regulatory agencies (IRAs) have been introduced as part of public administration reforms around the world. Unlike traditional administrative agencies, most IRAs are not accountable to the executive and their accountability relationship to the legislative tends to be weak. Nevertheless, these agencies often engage in acts of voluntary explanation and justification of their decisions to stakeholders. Based on a comparative study of financial regulation agencies, this article shows that these IRAs resort more actively to voluntary accountability when the expectations of actors interacting with the agency are at conflict. Specifically, we argue that the agency’s ability to manage expectations is shaped by the level of agency independence and the degree of organizational capacity. Our findings contribute to the existing debates by conceptualizing voluntary accountability as a mechanism for managing stakeholders’ conflicting expectations through the lens of financial regulation based on original evidence from Spain and Turkey.
Comparison of self-reported and observed water contact measures in Schistosoma japonicum–endemic villages in Leyte, The Philippines
Authors: Falcone Bianca , Park Sangshin , Wu Hannah W , Leenstra Tjalling , Jiz Mario A , Jarilla Blanca , McGarvey Stephen T , Kurtis Jonathan D , Friedman Jennifer F
Published: September 2021

Background

We compared individuals’ self-reported water contact from a questionnaire to direct observation of water contact. Questionnaires that accurately capture water contact are necessary to risk-stratify individuals and communities at high risk for schistosomiasis.

Methods

Individuals (N=677) ages 7–30 y were included from three Schistosoma japonicum–endemic villages in Leyte, The Philippines. Each individual was observed for 12 d over the course of the 18-month study and the questionnaire was administered six times. A questionnaire index was derived that captured the number of self-reported contacts with water bodies for any purpose. An exposure index was created based on the sum of contacts that was weighted by the percentage of body surface area (BSA) exposed and exposure duration.

Results

Of 16 water contact activities, only bathing and washing clothes exhibited a significant, positive correlation between self-reported contacts and the observed exposure index related to those contacts.

Conclusions

We found that only the reported frequencies of bathing and washing clothes were significantly related to an individual's overall observed exposure index, while use of all reported contacts was not related to the observed exposure. This study further supports the need for questionnaires to be augmented by some measure of how much BSA is exposed and/or time is spent in the water on average for a specific activity.
The Epidemiology of Adult Tracheostomy in the United States 2002–2017: A Serial Cross-Sectional Study
Authors: Abril Maria K. , Berkowitz David M. , Chen Yunyun , Waller Lance A. , Martin Greg S. , Kempker Jordan A.
Published: September 2021

Objectives:

Describe the longitudinal national epidemiology of tracheostomies performed in acute care hospitals and describe the annual rate of tracheostomy performed for patients with respiratory failure with invasive mechanical ventilation.

DESIGN:

Serial cross-sectional study.

Setting:

The 2002–2014 and 2016–2017 Healthcare Utilization Project’s National Inpatient Sample datasets.

Patients:

Discharges greater than or equal to 18 years old, excluding those with head and neck cancer or transferred from another hospital. We used diagnostic and procedure codes from the International Classification of Diseases, 9th and 10th revisions to define cases of respiratory failure, invasive mechanical ventilation, and tracheostomy.

Interventions:

None.

Measurements and Main Results:

There were an estimated 80,612 tracheostomies performed in 2002, a peak of 89,545 tracheostomies in 2008, and a nadir of 58,840 tracheostomies in 2017. The annual occurrence rate was 37.5 (95% CI, 34.7–40.4) tracheostomies per 100,000 U.S. adults in 2002, with a peak of 39.7 (95% CI, 36.5–42.9) in 2003, and with a nadir of 28.4 (95% CI, 27.2–29.6) in 2017. Specifically, among the subgroup of hospital discharges with respiratory failure with invasive mechanical ventilation, an annual average of 9.6% received tracheostomy in the hospital. This changed over the study period from 10.4% in 2002, with a peak of 10.9% in 2004, and with a nadir of 7.4% in 2017. Among respiratory failure with invasive mechanical ventilation discharges with tracheostomy, the annual proportion of patients 50–59 and 60–69 years old increased, whereas patients from 70 to 79 and greater than or equal to 80 years old decreased. The mean hospital length of stay decreased, and in-hospital mortality decreased, whereas discharge to intermediate care facilities increased.

Conclusions:

Over the study period, there were decreases in the annual total case volume and adult occurrence rate of tracheostomy as well as decreases in the rate of tracheostomy among the subgroup with respiratory failure with invasive mechanical ventilation. There is some evidence of changing patterns of patient selection for in-hospital tracheostomy among those with respiratory failure with invasive mechanical ventilation with decreasing proportions of patients with advanced age.
Explainable Machine Learning on AmsterdamUMCdb for ICU Discharge Decision Support: Uniting Intensivists and Data Scientists
Authors: Thoral Patrick J. , Fornasa Mattia , de Bruin Daan P. , Tonutti Michele , Hovenkamp Hidde , Driessen Ronald H. , Girbes Armand R. J. , Hoogendoorn Mark , Elbers Paul W. G.
Published: September 2021

Objectives:

Unexpected ICU readmission is associated with longer length of stay and increased mortality. To prevent ICU readmission and death after ICU discharge, our team of intensivists and data scientists aimed to use AmsterdamUMCdb to develop an explainable machine learning–based real-time bedside decision support tool.

Derivation Cohort:

Data from patients admitted to a mixed surgical-medical academic medical center ICU from 2004 to 2016.

Validation Cohort:

Data from 2016 to 2019 from the same center.

Prediction Model:

Patient characteristics, clinical observations, physiologic measurements, laboratory studies, and treatment data were considered as model features. Different supervised learning algorithms were trained to predict ICU readmission and/or death, both within 7 days from ICU discharge, using 10-fold cross-validation. Feature importance was determined using SHapley Additive exPlanations, and readmission probability-time curves were constructed to identify subgroups. Explainability was established by presenting individualized risk trends and feature importance.

Results:

Our final derivation dataset included 14,105 admissions. The combined readmission/mortality rate within 7 days of ICU discharge was 5.3%. Using Gradient Boosting, the model achieved an area under the receiver operating characteristic curve of 0.78 (95% CI, 0.75–0.81) and an area under the precision-recall curve of 0.19 on the validation cohort (n = 3,929). The most predictive features included common physiologic parameters but also less apparent variables like nutritional support. At a 6% risk threshold, the model showed a sensitivity (recall) of 0.72, specificity of 0.70, and a positive predictive value (precision) of 0.15. Impact analysis using probability-time curves and the 6% risk threshold identified specific patient groups at risk and the potential of a change in discharge management to reduce relative risk by 14%.

Conclusions:

We developed an explainable machine learning model that may aid in identifying patients at high risk for readmission and mortality after ICU discharge using the first freely available European critical care database, AmsterdamUMCdb. Impact analysis showed that a relative risk reduction of 14% could be achievable, which might have significant impact on patients and society. ICU data sharing facilitates collaboration between intensivists and data scientists to accelerate model development.
A reliable diagnostic method of surgical site infection after posterior lumbar surgery based on serial C-reactive protein
Authors: Kim Min Hyung , Park Jong-Hyeok , Kim Jong Tae
Published: September 2021

Study design:

A observational study.

Purpose:

To evaluate the detection of surgical site infection (SSI) after posterior lumbar surgery by the laboratory parameters.

Materials and methods:

The study included 189 patients undergoing posterior lumbar fusion or decompression between January 2018 and December 2019. Patients with chronic renal disease, rheumatoid arthritis, hepatic disease were excluded. Patients with tumor, trauma, cervical and thoracic lesions were also excluded. Leukocyte counts, segmented neutrophils, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were evaluated preoperatively and on postoperative days 1 (POD1), 3 (POD3), 7 (POD7), 14 (POD14), and 30 (POD30). Surgical site infection was defined as (1) purulent discharge at incision site, (2) organisms isolated aseptically from the incision site, and (3) evidence of infection based on MRI. Increasing CRP (ICRP) and decreasing CRP (DCRP) groups were classified according to the value of CRP on POD7. The change rate in CRP was calculated using the formula: (Late value−Previous value/Previous value)×100. Receiver operating characteristic curves were used to validate laboratory data involving SSI.

Results:

The mean age was 64.5±12.5 years. Male to female ratio was 91–98. The incidence of SSI was 8.8%. Leukocyte count, segmented neutrophil, and ESR were not specific. ICRP group were 43 patients. SSI was found in 14% of ICRP group and 18.6% was associated with secondary infection. Even 7.7% of the infection in DCRP group was identified as SSI. Based on the change rate of CRP, −50% of decreasing rate of CRP in ICRP group between POD7 and POD14 showed the validity that sensitivity was 90.9% and specificity was 68.1%. In DCRP group, −43.3% of decreasing rate of CRP in DCRP group between POD7 and POD14 showed the validity that sensitivity and specificity were 83.3% and 82.4%, respectively. Only 43% of all patients showed normalization of CRP can rule out the SSI.

Conclusion:

The serial change rate of CRP is a reliable method for detecting SSI more than the criteria of normal value. Nevertheless, close monitoring of patient’s signs and symptoms is important to detect early SSI.
Chemical upcycling of polymers
Authors: Stadler Bernhard M. , de Vries Johannes G.
Published: September 2021

As the production volume of polymers increases, so does the amount of plastic waste. Plastic recycling is one of the concepts to address in this issue. Unfortunately, only a small fraction of plastic waste is recycled. Even with the development of polymers for closed loop recycling that can be in theory reprocessed infinitely the inherent dilemma is that because of collection, cleaning and separation processes the obtained materials simply are not cost competitive with virgin materials. Chemical upcycling, the conversion of polymers to higher valuable products, either polymeric or monomeric, could mitigate this issue. In the following article, we highlight recent examples in this young but fast-growing field.

This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 2)'.
Improved diagnosis of gastrointestinal infections using a semi-automated multiplex real-time PCR for detection of enteropathogens
Authors: Fidalgo Berta , Rubio Elisa , Pastor Victor , Parera Marta , Ballesté-Delpierre Clara , Fernández Mariana José , Chasco Genoveva Cuesta , Vergara Andrea , Zboromyrska Yuliya , Aylagas Cristian , Salvador Pilar , Fernández Adán , Valls M. Eugenia , Alvarez Martinez Míriam José , Mira Aurea , Marcos Maria Angeles , Vila Jordi , Martinez Miguel J. , Casals-Pascual Climent
Published: September 2021

Introduction. The identification of enteropathogens is critical for the clinical management of patients with suspected gastrointestinal infection. The FLOW multiplex PCR system (FMPS) is a semi-automated platform (FLOW System, Roche) for multiplex real-time PCR analysis.

Hypothesis/Gap Statement. FMPS has greater sensitivity for the detection of enteric pathogens than standard methods such as culture, biochemical identification, immunochromatography or microscopic examination.

Aim.The diagnostic performance of the FMPS was evaluated and compared to that of traditional microbiological procedures.

Methodology. A total of 10 659 samples were collected and analysed over a period of 7 years. From 2013 to 2018 (every July to September), samples were processed using standard microbiological culture methods. In 2019, the FMPS was implemented using real-time PCR to detect the following enteropathogens:

Shigella

spp., Salmonella spp., Campylobacter spp., Giardia intestinalis, Entamoeba histolytica, Blastocystis hominis, Cryptosporidum spp., Dientamoeba fragilis, adenovirus, norovirus and rotavirus. Standard microbiological culture methods (2013–2018) included stool culture, microscopy and immunochromatography.

Results. A total of 1078 stool samples were analysed prospectively using the FMPS from July to September (2019): bacterial, parasitic and viral pathogens were identified in 15.3, 9.71 and 5.29 % of cases, respectively. During the same period of 6 years (2013–2018), the proportion of positive identifications using standard microbiological methods from 2013 to 2018 was significantly lower. A major significant recovery improvement was observed for all bacteria species tested:

Shigella

spp./enteroinvasive

Escherichia coli

(EIEC) (P <0.05),

Salmonella

spp. (P <0.05) and

Campylobacter

spp. (P <0.05). Marked differences were also observed for the parasites G. intestinalis, Cryptosporidium spp. and D. fragilis.

Conclusion. These results support the value of multiplex real-time PCR analysis for the detection of enteric pathogens in laboratory diagnosis with outstanding performance in identifying labile micro-organisms. The identification of unsuspected micro-organisms for less specific clinical presentations may also impact on clinical practice and help optimize patient management.
Integrating perspectives in actinomycete research: an ActinoBase review of 2020–21
Authors: Undabarrena Agustina , Pereira Camila F. , Kruasuwan Worarat , Parra Jonathan , Sélem-Mojica Nelly , Vind Kristiina , Schniete Jana K.
Published: September 2021

Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.
The tiered restrictions enforced in November 2020 did not impact the epidemiology of the second wave of COVID-19 in Italy
Authors: Rainisio Maurizio
Published: September 2021

In the attempt to counter the second COVID-19 wave in autumn 2020, the Italian government introduced a unique countrywide system of physical distancing measures organized in progressively restrictive tiers (coded as yellow, orange, and red) imposed on a regional basis according to epidemiological risk assessments. This followed a set of other scattered or limited measures described in full detail by Manica et al.1.

This paper concerns the introduction of the tiered restrictions. The data used to evaluate the impact of the restriction system on SARS-CoV-2 transmissibility and hospitalization burden in Italy is from the Italian COVID-19 integrated surveillance system.

The reproduction number R(t) estimated on the onset of COViD-19 symptoms constantly decreased during most of the observation period 04 October 2020 - 06 December 2020 than is centered on the date of introduction of the measures and includes the expected latency to reach an effect. The fastest decrease of R(t) occurred in the period preceding the introduction of the tiered restrictions. There was no evidence that introducing the tiered restrictions determined the reduction of R(t). An alternative analysis using the daily growth rate of the epidemic curve confirms these conclusions. Similar considerations are made concerning the health system burden, analyzing hospitalizations at country level.

The trend of R(t) tending to increase shortly after the measures became effective does not allow to exclude that the enforcement of such restrictions might have been counterproductive.

These results are instrumental in informing public health efforts aimed at attempting to manage the epidemic efficiently. Planning further use of the tiered restrictions and the associated containment measures should be carefully and critically revised to avoid a useless burden to the population with no advantage for the containment of the epidemic or a possible worsening.
The efficiency of dynamic regional lockdown approach in controlling the COVID-19 epidemic. Insights from the agent-based epidemiological model for Poland
Authors: Zieliński Jakub , Gruziel-Słomka Magdalena , Nowosielski Jȩdrzej M. , Bartczuk Rafał P. , Niedzielewski Karol , Semeniuk Marcin , Górski Łukasz , Kisielewski Jan , Moszyński Antoni , Radwan Maciej , Kaczorek Artur , Rakowski Franciszek
Published: September 2021

In this work properties of the dynamic regional lockdown approach to suppress the COVID-19 epidemic spread in Poland were investigated. In particular, an agent based model was used with the aim to indicate an optimal lockdown strategy, defined here as the one which minimizes mean lockdown time over regional unit provided health service is not overwhelmed. With this approach the lockdown extent was also considered by varying restrictions between complete regional school closure and/or significant social distancing in semi-public spaces. In result, a cooperative effect was discovered in the case when closure of schools was accompanied by severe restrictions of social contacts in semi-public spaces. Moreover, the regional lockdown approach implemented here on the level of counties (units of population around 100k) proofed to be successful, that is allowed to identify optimal entrance and release thresholds for lockdown. The authors believe that until significant portion of population is vaccinated such a strategy might be applied.
The 1st year of the COVID-19 epidemic in Estonia: an interrupted time series of population based nationwide cross-sectional studies
Authors: Uusküla Anneli , Kalda Ruth , Solvak Mihkel , Jürisson Mikk , Käärik Meelis , Fischer Krista , Keis Aime , Raudvere Uku , Vilo Jaak , Peterson Hedi , Käärik Ene , Metspalu Mait , Jürgenson Tuuli , Milani Lili , Kolberg Liis , Tiit Ene-Margit , Vassil Kristjan
Published: September 2021

Background

Decisions about the continued need for control measures and the effect of introducing COVID-19 vaccinations rely on accurate and population-based data on SARS-CoV-2 positivity and risk factors for testing positive.

Methods

In this interrupted time series of population-based nationwide cross-sectional studies, data from nasopharyngeal testing and questionnaires were used to estimate the SARS-CoV-2 RNA prevalence and factors associated with test positivity over the 1st year of the COVID-19 epidemic.

The study is registered with the ISRCTN Registry, ISRCTN10182320.

Results

Between April 23, 2020 and February 2, 2021, results were available from 34,915 individuals and 27,870 samples from 11 consecutive studies. The percentage of people testing positive for SARS-CoV-2 decreased from 0.27% (95% CI 0.10% - 0.59%) in April to 0.04% (95% CI 0.00% - 0.22%) by the end of May and remained very low (0.01%, 95% CI 0.00% - 0.17%) until the end of August, followed by an increase since November (0.37%, 95% CI 0.18% - 0.68%) that escalated to 2.69% (95% CI 2.08% - 2.69%) in January 2021. In addition to substantial change in time, an increasing number of household members (for one additional OR 1.15, 95% CI 1.02-1.29), reporting current symptoms of COVID-19 (OR 2.21, 95% CI 1.59-3.09), and completing questionnaire in the Russian language (OR 1.85, 95% CI 1.15-2.99) were associated with increased odds for SARS-CoV-2 RNA positivity.

Conclusions

SARS-CoV-2 population prevalence needs to be carefully monitored as vaccine programmes are rolled out in order to inform containment decisions.

Strengths and limitations of this study

Our study relies upon nation-wide and population-based data on SARS-CoV-2 prevalence, and presents changes in prevalence over the whole 1st year of the Covid-19 epidemic.

Our analysis of SARS-CoV-2 infection risk factors is not limited to notification or health care-based case data.

Selection bias may have been introduced as a result of low response rate. The direction of bias is unclear, but most likely operates rather uniformly over the period of observation, though this presents less of a threat to the SARS-CoV-2 prevalence trend analysis.

Our data could be used to adequately project the future course of the SARS-CoV-2 epidemic and the effect of control measures.
Predicting the Effectiveness of Covid-19 Vaccines from SARS-CoV-2 Variants Neutralisation Data
Authors: Volkov Oleg , Borozdenkova Svetlana , Gray Alexander
Published: September 2021

Rapid and accurate prediction of Covid-19 vaccine effectiveness is crucial to response against SARS-CoV-2 variants of concern. Despite intensive research, several prediction tasks are not well supported, such as predicting effectiveness of partial vaccination, of vaccine boosters and in vaccinated subpopulations. This paper introduces a novel predictive framework to accommodate such tasks and improve prediction accuracy. It was developed for predicting the symptomatic effectiveness of the BNT162b2 (Comirnaty) and ChAdOx1 nCoV-19 (Vaxzevria) vaccines but could apply to other vaccines and effectiveness types. Direct prediction within the framework uses levels of vaccine-induced neutralising antibodies against SARS-CoV-2 variants to fit efficacy and effectiveness estimates from studies with a given vaccine. Indirect prediction uses a model fitted for one vaccine to predict the effectiveness of another. The directly predicted effectiveness of Comirnaty against the Delta variant was 44.8% (22, 69) after one and 84.6% (64, 97) after two doses, which is close to 45.6% and 85.5%, the average estimates from effectiveness studies with the vaccine. The corresponding direct predictions for Vaxzevria were 41.6% (18, 68) and 63.2% (37, 86); and the indirect predictions, from the model fitted to Comirnaty data, were 45.5% (23, 70) and 61.2% (37, 83). Both sets of predictions are comparable to the average estimates, 42.5% and 66.3%, from effectiveness studies with Vaxzevria. Further results are presented on age subgroups; prediction biases and their mitigation; and implications for vaccination policies.
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Authors: Obermeyer Fritz , Jankowiak Martin , Barkas Nikolaos , Schaffner Stephen F. , Pyle Jesse D. , Yurkovetskiy Lonya , Bosso Matteo , Park Daniel J. , Babadi Mehrtash , MacInnis Bronwyn L. , Luban Jeremy , Sabeti Pardis C. , Lemieux Jacob E.
Published: September 2021

Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR0, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR0to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR0forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as they emerge, and prioritizes mutations of biological and public health concern for functional characterization.

One Sentence summary

A Bayesian hierarchical model of all SARS-CoV-2 viral genomes predicts lineage fitness and identifies associated mutations.
Genome-wide association study of REM sleep behavior disorder identifies novel loci with distinct polygenic and brain expression effects
Authors: Krohn Lynne , Heilbron Karl , Blauwendraat Cornelis , Reynolds Regina H. , Yu Eric , Senkevich Konstantin , Rudakou Uladzislau , Estiar Mehrdad A. , Gustavsson Emil K. , Brolin Kajsa , Ruskey Jennifer A. , Freeman Kathryn , Asayesh Farnaz , Chia Ruth , Arnulf Isabelle , Hu Michele T.M. , Montplaisir Jacques Y. , Gagnon Jean-François , Desautels Alex , Dauvilliers Yves , Gigli Gian Luigi , Valente Mariarosaria , Janes Francesco , Bernardini Andrea , Högl Birgit , Stefani Ambra , Ibrahim Abubaker , Sonka Karel , Kemlink David , Oertel Wolfgang , Janzen Annette , Plazzi Giuseppe , Biscarini Francesco , Antelmi Elena , Figorilli Michela , Puligheddu Monica , Mollenhauer Brit , Trenkwalder Claudia , Sixel-Döring Friederike , De Cock Valérie Cochen , Monaca Christelle Charley , Heidbreder Anna , Ferini-Strambi Luigi , Dijkstra Femke , Viaene Mineke , Abril Beatriz , Boeve Bradley F. ,   23andMe Research Team, Scholz Sonja W. , Ryten Mina , Bandres-Ciga Sara , Noyce Alastair , Cannon Paul , Pihlstrøm Lasse , Nalls Mike A. , Singleton Andrew B. , Rouleau Guy A. , Postuma Ronald B. , Gan-Or Ziv
Published: September 2021

Rapid eye movement (REM) sleep behavior disorder (RBD), enactment of dreams during REM sleep, is an early clinical symptom of alpha-synucleinopathies. RBD also defines more severe forms of alpha-synucleinopathies. The genetic background of RBD and its underlying mechanisms are not well understood. Here, we performed the first genome-wide association study of RBD, identifying five RBD risk loci. Expression analyses highlight SNCA-AS1 and SCARB2 differential expression in different brain regions in RBD, with SNCA-AS1 further supported by colocalization analyses. Genetic risk score and other analyses provide further insights into RBD genetics, highlighting RBD as a unique subpopulation that will allow future early intervention.
SARS-CoV-2 variant exposures elicit antibody responses with differential cross-neutralization of established and emerging strains including Delta and Omicron
Authors: Laurie Matthew T , Liu Jamin , Sunshine Sara , Peng James , Black Douglas , Mitchell Anthea M , Mann Sabrina A , Pilarowski Genay , Zorn Kelsey C , Rubio Luis , Bravo Sara , Marquez Carina , Sabatino Joseph J , Mittl Kristen , Petersen Maya , Havlir Diane , DeRisi Joseph
Published: September 2021

The wide spectrum of SARS-CoV-2 variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of the immune response to different spike protein versions. Here, we compare the neutralization of variants of concern, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure. We also observe that exposure to multiple spike variants increases the breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.

This study characterizes neutralization of eight different SARS-CoV-2 variants, including Delta and Omicron, with respect to nine different prior exposures, including vaccination, booster, and infections with Delta, Epsilon, and others. Different exposures were found to confer substantially differing neutralization specificity.
Impact of direct-acting antiviral treatment of hepatitis C on the quality of life of adults in Ukraine
Authors: Benade M , Rosen S , Antoniak S , Chasela C , Stopolianska Y , Barnard T , Gandhi MM , Ivanchuk I , Tretiakov V , Dible J , Minior T , Chew KW , van der Horst C , Tsenilova Z , Sanne I ,   for EQUIP Health
Published: September 2021

Background

Direct-acting antivirals (DAAs) are highly effective in achieving sustained virologic response among those with chronic hepatitis C virus (HCV) infection. Quality of life (QOL) benefits for an HCV-infected population with high numbers of people who inject drugs and people living with HIV (PLHIV) in Eastern Europe have not been explored. We estimated such benefits for Ukraine.

Methods

Using data from a demonstration study of 12-week DAA conducted in Kyiv, we compared self-reported QOL as captured with the MOS-SF20 at study entry and 12 weeks after treatment completion (week 24). We calculated domain scores for health perception, physical, role and social functioning, mental health and pain to at entry and week 24, stratified by HIV status.

Results

Among the 857 patients included for the final analysis, health perception was the domain that showed the largest change, with an improvement of 85.7% between entry and week 24. The improvement was larger among those who were HIV negative (104.4%) compared to those living with HIV (69.9%). Other domains that showed significant and meaningful improvements were physical functioning, which improved from 80.5 (95% CI: 78.9-82.1) at study entry to 89.4 (88.1-90.7) at 24 weeks, role functioning (64.5 [62.3-66.8] to 86.5 [84.9-88.2], social functioning (74.2 [72.1-76.2] to 84.8 [83.2-86.5] and bodily pain (70.1 [68.2-72.0] to 89.8 [88.5-91.1]). Across all domains, QOL improvements among PLHIV were more modest than among HIV-negative participants.

Conclusion

QOL improved substantially across all domains between study entry and week 24. Changes over the study period were smaller among PLHIV.
‘Citizens’ Attitudes Under Covid19’: a cross-country panel survey of public opinion in 11 democracies
Authors: Brouard Sylvain , Foucault Martial , Michel Elie , Becher Michael , Vasilopoulos Pavlos , Bono Pierre-Henri , Sormani Nicolas
Published: September 2021

This article introduces data collected in the Citizens’ Attitudes Under Covid-19 Project (CAUCP), which surveyed public opinion throughout the Covid-19 pandemic in 11 countries between March to December 2020. In this paper, we present a unique cross-country panel survey of citizens’ attitudes and behaviors during a worldwide unprecedented health, governance, and economic crisis. This dataset allows to examine the behavioral and attitudinal consequences of crisis across time and contexts. In this paper, we describe the set-up of the CAUCP and the main features of the dataset and we present promising research prospects.
Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences
Authors: Borcard Loïc , Gempeler Sonja , Terrazos Miani Miguel A. , Baumann Christian , Grädel Carole , Dijkman Ronald , Suter-Riniker Franziska , Leib Stephen L , Bittel Pascal , Neuenschwander Stefan , Ramette Alban
Published: September 2021

We are reporting on the observation of a large, under-sequenced region of the S gene of the SARS-CoV2 Delta variant genomes, identified in sequences originating from various sequencing centres worldwide (e.g. USA, India, England, Switzerland, France, Germany). This poorly sequenced region was identified from the early phases of the Delta variant spread and the phenomenon is still ongoing. As many commonly-used protocols rely on amplicon-based sequencing procedures, we investigated the likely origin of the issue. We established its biological origin as resulting from mutations in the viral genomes at primer binding sites. We designed and evaluated new PCR primers to circumvent this issue in order to complement the ARTIC v3 set, and validated their performance for the sequencing of circulating Delta variants.