bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoemission oscillation in epitaxially grown van der Waals β-In2Se3WS2 heterobilayer bubbles*
Authors: Dong Jiyu , Lin Kang , Mu Congpu , Jia Zhiyan , Xu Jin , Nie Anmin , Wang Bochong , Xiang Jianyong , Wen Fusheng , Zhai Kun , Xue Tianyu , Liu Zhongyuan
Published: September 2021

Thin films of millimeter-scale continuous monolayer WS2 have been grown on SiO2/Si substrate, followed by the deposition of β-In2Se3 crystals on monolayer WS2 to prepare In2Se3/WS2 van de Waals heterostructures by a two-step chemical vapor deposition (CVD) method. After the growth of In2Se3 at elevated temperatures, high densities of In2Se3/WS2 heterostructure bubbles with monolayer to multilayer β-In2Se3 crystals atop are observed. Fluorescence of the resultant β-In2Se3/WS2 heterostructure is greatly enhanced in intensity upon the formation of bubbles, which are evidenced by the Newton’s rings in optical image owing to constructive and destructive interference. In photoluminescence (PL) mapping images of monolayer β-In2Se3/monolayer WS2 heterobilayer bubble, significant oscillatory behavior of emission intensity is demonstrated due to constructive and destructive interference. However, oscillatory behaviors of peak position are also observed and come from a local heating effect induced by an excitation laser beam. The oscillatory mechanism of PL is further verified by changing the exterior pressure of bubbles placed in a home-made vacuum chamber. In addition, redshifted in peak position and broadening in peak width are observed due to strain effect during decreasing the exterior pressure of bubbles.
2D measurements of parallel counter-streaming flows in the W7-X scrape-off layer for attached and detached plasmas
Authors: Perseo V. , Winters V. , Feng Y. , Reimold F. , Ford O.P. , König R. , Bozhenkov S.A. , Brunner K.J. , Burhenn R. , Drewelow P. , Ennis D.A. , Gao Y. , Gradic D. , Hacker P. , Hergenhahn U. , Jakubowski M.W. , Knauer J. , Kremeyer T. , Kriete D.M. , Krychowiak M. , Kwak S. , Niemann H. , Pavone A. , Pisano F. , Puig Sitjes A. , Schlisio G. , Svensson J. , Zhang D. , Sunn Pedersen T. ,   the W7-X Team
Published: September 2021

Investigations of particle parallel flow velocities have been carried out for the scrape-off layer (SOL) of the Wendelstein 7-X (W7-X) stellarator, in order to gain insights on the SOL transport properties during attached and detached plasma scenarios. The experimental evidence is based on the coherence imaging spectroscopy (CIS) diagnostic, able to measure 2D impurity emission intensity and flow velocity. The impurity monitored by CIS is C2+, characterized by a line-emission intensity observed to be linearly proportional to the total plasma radiated power in both attached and detached plasmas. The related C2+ velocity shows a strong dependence on the line-averaged electron density while remaining insensitive to the input power. During attached plasmas, the velocity increases with increasing line-averaged density. The tendency reverses in the transition to and during detachment, in which the velocity decreases by at least a factor of 2. The sharp drop in velocity, together with a rise in line-emission intensity, is reliably correlated to the detachment transition and can therefore be used as one of its signatures. The impurity flow velocity appears to be well coupled with the main ions’ one, thus implying the dominant role of impurity-main ion friction in the parallelimpurity transport dynamics. In view of this SOL impurity transport regime, the CIS measurement results are here interpreted with the help of EMC3-Eirene simulations, and their major trends are already explainable with a simple 1D fluid model.
MotorSkins—a bio-inspired design approach towards an interactive soft-robotic exosuit
Authors: Gutierrez Facundo , Razghandi Khashayar
Published: September 2021

The work presents a bio-inspired design approach to a soft-robotic solution for assisting the knee-bending in users with reduced mobility in lower limbs. Exosuits and fluid-driven actuators are fabric-based devices that are gaining increasing relevance as alternatives assistive technologies that can provide simpler, more flexible solutions in comparison with the rigid exoskeletons. These devices, however, commonly require an external energy supply or a pressurized-fluid reservoir, which considerably constrain the autonomy of such solutions. In this work, we introduce an event-based energy cycle (EBEC) design concept, that can harvest, store, and release the required energy for assisting the knee-bending, in a synchronised interaction with the user and the environment, thus eliminating any need for external energy or control input. Ice-plant hydro-actuation system served as the source of inspiration to address the specific requirements of such interactive exosuit through a fluid-driven material system. Based on the EBEC design concepts and the abstracted bio-inspired principles, a series of (material and process driven) design experimentations helped to address the challenges of realising various functionalities of the harvest, storage, actuation and control instances within a closed hydraulic circuit. Sealing and defining various areas of water-tight seam made out of thermoplastic elastomers provided the base material system to program various chambers, channels, flow-check valves etc of such EBEC system. The resulting fluid-driven EBEC-skin served as a proof of concept for such active exosuit, that brings these functionalities into an integrated ‘sense-acting’ material system, realising an auto-synchronised energy and information cycles. The proposed design concept can serve as a model for development of similar fluid-driven EBEC soft-machines for further applications. On the more general scheme, the work presents an interdisciplinary design-science approach to bio-inspiration and showcases how biological material solutions can be looked at from a design/designer perspective to bridge the bottom–up and top–down approach to bio-inspiration.
Superluminous supernovae: an explosive decade
Authors: Nicholl Matt
Published: September 2021

Ten years on from the discovery of mysterious events 100 times brighter than conventional stellar explosions, Matt Nicholl charts our understanding of superluminous supernovae
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2
Authors: Liu Qiaoming , Wan Jun , Wang Guohua
Published: September 2021

The outbreak of acute respiratory disease in 2019, namely Coronavirus Disease-2019 (COVID-19), has become an unprecedented healthcare crisis. To mitigate the pandemic, there are a lot of collective and multidisciplinary efforts in facilitating the rapid discovery of protein inhibitors or drugs against COVID-19. Although many computational methods to predict protein inhibitors have been developed [ 1– 5], few systematic reviews on these methods have been published. Here, we provide a comprehensive overview of the existing methods to discover potential inhibitors of COVID-19 virus, so-called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). First, we briefly categorize and describe computational approaches by the basic algorithms involved in. Then we review the related biological datasets used in such predictions. Furthermore, we emphatically discuss current knowledge on SARS-CoV-2 inhibitors with the latest findings and development of computational methods in uncovering protein inhibitors against COVID-19.
epitope3D: a machine learning method for conformational B-cell epitope prediction
Authors: da Silva Bruna Moreira , Myung YooChan , Ascher David B , Pires Douglas E V
Published: September 2021

The ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to guide rational vaccine development and immunotherapies, which are particularly relevant for rapid pandemic response. A range of computational tools has been developed over the past two decades to assist in epitope prediction; however, they have presented limited performance and generalization, particularly for the identification of conformational B-cell epitopes. Here, we present epitope3D, a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date. Our method uses the concept of graph-based signatures to model epitope and non-epitope regions as graphs and extract distance patterns that are used as evidence to train and test predictive models. We show epitope3D outperforms available alternative approaches, achieving Mathew’s Correlation Coefficient and F1-scores of 0.55 and 0.57 on cross-validation and 0.45 and 0.36 during independent blind tests, respectively.
PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics
Authors: Shi Xing-Xing , Wang Zhi-Zheng , Wang Yu-Liang , Huang Guang-Yi , Yang Jing-Fang , Wang Fan , Hao Ge-Fei , Yang Guang-Fu
Published: September 2021

Protein post-translational modifications (PTM) play vital roles in cellular regulation, modulating functions by driving changes in protein structure and dynamics. Exploring comprehensively the influence of PTM on conformational dynamics can facilitate the understanding of the related biological function and molecular mechanism. Currently, a series of excellent computation tools have been designed to analyze the time-dependent structural properties of proteins. However, the protocol aimed to explore conformational dynamics of post-translational modified protein is still a blank. To fill this gap, we present PTMdyna to visually predict the conformational dynamics differences between unmodified and modified proteins, thus indicating the influence of specific PTM. PTMdyna exhibits an AUC of 0.884 tested on 220 protein–protein complex structures. The case of heterochromatin protein 1α complexed with lysine 9-methylated histone H3, which is critical for genomic stability and cell differentiation, was used to demonstrate its applicability. PTMdyna provides a reliable platform to predict the influence of PTM on protein dynamics, making it easier to interpret PTM functionality at the structure level. The web server is freely available at http://ccbportal.com/PTMdyna.
DLAB: deep learning methods for structure-based virtual screening of antibodies
Authors: Schneider Constantin , Buchanan Andrew , Taddese Bruck , Deane Charlotte M
Published: September 2021

Motivation

Antibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time- and cost-intensive and heavily reliant on in vivo and in vitro high throughput screens. Here, we introduce a framework for structure-based deep learning for antibodies (DLAB) which can virtually screen putative binding antibodies against antigen targets of interest. DLAB is built to be able to predict antibody–antigen binding for antigens with no known antibody binders.

Results

We demonstrate that DLAB can be used both to improve antibody–antigen docking and structure-based virtual screening of antibody drug candidates. DLAB enables improved pose ranking for antibody docking experiments as well as selection of antibody–antigen pairings for which accurate poses are generated and correctly ranked. We also show that DLAB can identify binding antibodies against specific antigens in a case study. Our results demonstrate the promise of deep learning methods for structure-based virtual screening of antibodies.

Availability and implementation

The DLAB source code and pre-trained models are available at https://github.com/oxpig/dlab-public.

Supplementary information

Supplementary data are available at Bioinformatics online.
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures
Authors: Kaushik Rahul , Zhang Kam Y J
Published: September 2021

Motivation

An accurate estimation of the quality of protein model structures typifies as a cornerstone in protein structure prediction regimes. Despite the recent groundbreaking success in the field of protein structure prediction, there are certain prospects for the improvement in model quality estimation at multiple stages of protein structure prediction and thus, to further push the prediction accuracy. Here, a novel approach, named ProFitFun, for assessing the quality of protein models is proposed by harnessing the sequence and structural features of experimental protein structures in terms of the preferences of backbone dihedral angles and relative surface accessibility of their amino acid residues at the tripeptide level. The proposed approach leverages upon the backbone dihedral angle and surface accessibility preferences of the residues by accounting for its N-terminal and C-terminal neighbors in the protein structure. These preferences are used to evaluate protein structures through a machine learning approach and tested on an extensive dataset of diverse proteins.

Results

The approach was extensively validated on a large test dataset (n = 25 005) of protein structures, comprising 23 661 models of 82 non-homologous proteins and 1344 non-homologous experimental structures. In addition, an external dataset of 40 000 models of 200 non-homologous proteins was also used for the validation of the proposed method. Both datasets were further used for benchmarking the proposed method with four different state-of-the-art methods for protein structure quality assessment. In the benchmarking, the proposed method outperformed some state-of-the-art methods in terms of Spearman’s and Pearson’s correlation coefficients, average GDT-TS loss, sum of z-scores and average absolute difference of predictions over corresponding observed values. The high accuracy of the proposed approach promises a potential use of the sequence and structural features in computational protein design.

Availability and implementation

http://github.com/KYZ-LSB/ProTerS-FitFun.

Supplementary information

Supplementary data are available at Bioinformatics online.
Early life predictors of late life cerebral small vessel disease in four prospective cohort studies
Authors: Backhouse Ellen V , Shenkin Susan D , McIntosh Andrew M , Bastin Mark E , Whalley Heather C , Valdez Hernandez Maria , Muñoz Maniega Susana , Harris Mathew A , Stolicyn Aleks , Campbell Archie , Steele Douglas , Waiter Gordon D , Sandu Anca-Larisa , Waymont Jennifer M J , Murray Alison D , Cox Simon R , de Rooij Susanne R , Roseboom Tessa J , Wardlaw Joanna M
Published: September 2021

Development of cerebral small vessel disease, a major cause of stroke and dementia, may be influenced by early life factors. It is unclear whether these relationships are independent of each other, of adult socio-economic status or of vascular risk factor exposures.

We examined associations between factors from birth (ponderal index, birth weight), childhood (IQ, education, socio-economic status), adult small vessel disease, and brain volumes, using data from four prospective cohort studies: STratifying Resilience And Depression Longitudinally (STRADL) (n = 1080; mean age = 59 years); the Dutch Famine Birth Cohort (n = 118; mean age = 68 years); the Lothian Birth Cohort 1936 (LBC1936; n = 617; mean age = 73 years), and the Simpson’s cohort (n = 110; mean age = 78 years). We analysed each small vessel disease feature individually and summed to give a total small vessel disease score (range 1–4) in each cohort separately, then in meta-analysis, adjusted for vascular risk factors and adult socio-economic status.

Higher birth weight was associated with fewer lacunes [odds ratio (OR) per 100 g = 0.93, 95% confidence interval (CI) = 0.88 to 0.99], fewer infarcts (OR = 0.94, 95% CI = 0.89 to 0.99), and fewer perivascular spaces (OR = 0.95, 95% CI = 0.91 to 0.99). Higher childhood IQ was associated with lower white matter hyperintensity burden (OR per IQ point = 0.99, 95% CI 0.98 to 0.998), fewer infarcts (OR = 0.98, 95% CI = 0.97 to 0.998), fewer lacunes (OR = 0.98, 95% CI = 0.97 to 0.999), and lower total small vessel disease burden (OR = 0.98, 95% CI = 0.96 to 0.999). Low education was associated with more microbleeds (OR = 1.90, 95% CI = 1.33 to 2.72) and lower total brain volume (mean difference = −178.86 cm3, 95% CI = −325.07 to −32.66). Low childhood socio-economic status was associated with fewer lacunes (OR = 0.62, 95% CI = 0.40 to 0.95).

Early life factors are associated with worse small vessel disease in later life, independent of each other, vascular risk factors and adult socio-economic status. Risk for small vessel disease may originate in early life and provide a mechanistic link between early life factors and risk of stroke and dementia. Policies investing in early child development may improve lifelong brain health and contribute to the prevention of dementia and stroke in older age.
Oral Fluoroquinolone Use and the Risk of Acute Liver Injury: A Nationwide Cohort Study
Authors: Nibell Olof , Svanström Henrik , Inghammar Malin
Published: September 2021

Background

Antibiotics are considered to be among the most frequent causes of drug-related acute liver injury (ALI). Although many ALIs have mild and reversible clinical outcomes, there is substantial risk of severe reactions leading to acute liver failure, need for liver transplant, and death. Recent studies have raised concerns of hepatotoxic potential related to the use of fluoroquinolones.

Methods

This study examined the risk of ALI associated with oral fluoroquinolone treatment compared with amoxicillin (419 930 courses, propensity score matched 1:1). The information on drug use was collected from a national, registry-based cohort derived from all Swedish adults aged 40–85 years.

Results

During a follow-up period of 60 days, users of oral fluoroquinolones had a >2-fold risk of ALI compared to users of amoxicillin (hazard ratio, 2.32 [95% confidence interval {CI}, 1.01–5.35). The adjusted absolute risk difference for use of fluoroquinolones as compared to amoxicillin was 4.94 (95% CI, .04–16.3) per 1 million episodes.

Conclusions

In this propensity score–matched study, fluoroquinolone treatment was associated with an increased risk of ALI in the first 2 months after starting treatment.
Diuretic vs. placebo in intermediate-risk acute pulmonary embolism: a randomized clinical trial
Authors: Lim Pascal , Delmas Clément , Sanchez Olivier , Meneveau Nicolas , Rosario Roger , Bouvaist Helene , Bernard Anne , Mansourati Jacques , Couturaud Francis , Sebbane Mustapha , Coste Pierre , Rohel Gwenole , Tardy Bernard , Biendel Caroline , Lairez Olivier , Ivanes Fabrice , Gallet Romain , Dubois-Rande Jean-Luc , Fard Damien , Chatelier Gilles , Simon Tabassome , Paul Muriel , Natella Pierre-André , Layese Richard , Bastuji-Garin Sylvie
Published: September 2021

Aims

The role of diuretics in patients with intermediate-risk pulmonary embolism (PE) is controversial. In this multicentre, double-blind trial, we randomly assigned normotensive patients with intermediate-risk PE to receive either a single 80 mg bolus of furosemide or a placebo.

Methods and results

Eligible patients had at least a simplified PE Severity Index (sPESI) ≥1 with right ventricular dysfunction. The primary efficacy endpoint assessed 24 h after randomization included (i) absence of oligo-anuria and (ii) normalization of all sPESI items. Safety outcomes were worsening renal function and major adverse outcomes at 48 hours defined by death, cardiac arrest, mechanical ventilation, or need of catecholamine. A total of 276 patients underwent randomization; 135 were assigned to receive the diuretic, and 141 to receive the placebo. The primary outcome occurred in 68/132 patients (51.5%) in the diuretic and in 49/132 (37.1%) in the placebo group (relative risk = 1.30, 95% confidence interval 1.04–1.61; P = 0.021). Major adverse outcome at 48 h occurred in 1 (0.8%) patients in the diuretic group and 4 patients (2.9%) in the placebo group (P = 0.19). Increase in serum creatinine level was greater in diuretic than placebo group [+4 µM/L (−2; 14) vs. −1 µM/L (−11; 6), P < 0.001].

Conclusion

In normotensive patients with intermediate-risk PE, a single bolus of furosemide improved the primary efficacy outcome at 24 h and maintained stable renal function. In the furosemide group, urine output increased, without a demonstrable improvement in heart rate, systolic blood pressure, or arterial oxygenation.

ClinicalTrials.gov identifier NCT02268903.
Aortic dissection and ruptures in adult congenital heart disease in Texas from 2009 to 2019
Authors: Well Andrew , Mizrahi Michelle , Johnson Gregory , Patt Hanoch , Fraser Charles D , Mery Carlos M , Beckerman Ziv
Published: September 2021

OBJECTIVES

Acute thoracic aortic dissection and rupture (TADR) has an incidence of 5–7 per 100 000-person years. Today, most children with congenital heart disease (CHD) survive to become adults with congenital heart disease (ACHD). This study evaluates TADR in patients with ACHD in a large, hospitalized patient population over 11 years to evaluate the incidence, risk factors and outcomes associated with TADR.

METHODS

This was a retrospective review of the Texas Inpatient Discharge Data Set from 1 January 2009 to 31 December 2019. All non-trauma discharges of patients ≥18 years were included. ACHD discharges were identified by International Classification of Diseases, 9th edition (ICD-9)/10 diagnosis codes. TADR were identified using 2 definitions: TADR1 is an ICD-9/10 code for TADR, and TADR2 is TADR1 with an ICD-9/10 procedure code for aortic intervention. Descriptive, univariate and logistic regression statistics were used.

RESULTS

A total of 22 154 664 eligible discharges were identified, of which 12 584 (0.06%) were TADR1 and a subgroup of 5699 (0.03%) were TADR2. CHD was more prevalent in TADR1 (0.2% vs 0.05%; P < 0.001) and TADR2 (0.3% vs 0.04%; P < 0.001). Adjusting for known TADR risk factors, CHD had an odds ratio of 1.69 (95% confidence interval: 1.09–2.63; P = 0.020) for TADR1 and an odds ratio of 1.69 (95% confidence interval: 0.99–2.88; P = 0.056) for TADR2. No in-hospital deaths were found in patients with CHD with TADR.

CONCLUSIONS

ACHD discharges had a higher frequency of TADR versus the general population (0.9–1.2 vs 0.3–0.6 per 1000 discharges). There is an indication that CHD confers an increased adjusted odds of TADR. As the ACHD population continues to grow in number as well as age, it will be important to continue to assess the risk of TADR from CHD and how traditional risk factors impact this risk.
‘I’m not an anti-vaxer!’—vaccine hesitancy among physicians: a qualitative study
Authors: Ecker Franziska , Kutalek Ruth
Published: September 2021

Background

Over the last years, research interest in vaccine hesitancy has increased. Studies usually focus on perceptions of parents and have largely neglected the group of health care providers. However, doctors’ notions on vaccination have a major impact on the decision-making process of their patients. We were interested to understand the phenomenon of vaccine hesitancy among physicians, with a particular focus on the measles vaccine. Furthermore, we aimed to understand the underlying perceptions of measles that may be associated with vaccine hesitant decisions.

Methods

In order to get an in-depth view, semi-structured interviews with physicians were conducted. Doctors were eligible for the study if they articulated vaccine hesitant views and/or demonstrated vaccine hesitancy in their medical practice.

Results

We interviewed 12 physicians, of whom 11 had a medical practice with no contract with the Austrian social insurance (‘Wahlarzt’) and additional training in complementary and alternative medicine. We found perceptions of immunology, health and illness that were discordant with evidence-based medicine and closely related to alternative and complementary medicine. All participants argued for a delayed administration of the measles vaccine. We found a consistent inclination towards ‘individual vaccination’, which was explained as empowering parents and to strengthen their decision-making competencies. Most participants expressed doubts about the reliability of vaccine studies and were concerned with possible long-term effects.

Conclusions

Paying closer attention to doctors’ concerns on vaccination might help to design target-oriented interventions to specifically strengthen vaccine confidence.
Age-Friendly as Tranquilo Ambiente: How Sociocultural Perspectives Shape the Lived Environment of Latinx Older Adults
Authors: Plasencia Melanie Z
Published: September 2021

Background and Objectives

Researchers have increasingly considered the importance of age-friendly communities to improve the health and well-being of older adults. Studies have primarily focused on the built environment, such as community infrastructure, older adult behavior, and environmental expectations. Less is known about the role of cultural characteristics in shaping perceptions of age-friendly environments, especially among racial and ethnic minorities.

Research Design and Methods

Using an ethnographic methodological approach, including participant observation in a Latinx community near New York City and 72 semistructured interviews, this study examines how older Latinxs characterize age-friendly communities.

Results

Latinx older adults described their community as age-friendly through the concept Tranquilo Ambiente, translated as a calm or peaceful environment. More specifically, Tranquilo Ambiente includes (a) a sense of perceived personal safety, (b) ethnic and social connectedness, and (c) spatial and cultural accessibility.

Discussion and Implications

This study extends prior research that has largely considered structural or economic components to show how culture may also influence the well-being of older Latinxs, even if living in an underresourced area. The concept of Tranquilo Ambiente demonstrates that both structural and cultural environmental factors influence older Latinxs’ understandings of age-friendly communities. By utilizing a sociocultural lens, this research highlights how Latinx older adults benefit from an environment that supports their physical (e.g., well-lit and newly paved streets), social (e.g., city hall senior center), and cultural (e.g., events and programs that promote cultural heritage) needs.
The 2021 Historical Research lecture: Historians, accountabilities and judgement
Authors: Jordanova Ludmilla
Published: September 2021

‘Accountability’ may be a useful notion for reflecting on historians’ responsibilities, not just to students and peers but to their audiences, to ideas and to the past itself. The roles historians play in public life are of considerable interest given current controversies about ‘contested heritage’ that are strikingly polarized, with the lives of historical figures in the dock. To assess such roles, it is worth making comparisons with the situation a century ago, when the Institute of Historical Research was in its infancy. Furthermore, it may be productive to enlist the help of other disciplines. All such practices involve matters of judgement.
Four Lives, Two Cars, and a Colony
Authors: Lewis Su Lin , Bickers Robert
Published: September 2021

Prompted by the closure of archives and new ways of working during lockdown, Su Lin Lewis and Robert Bickers find an unexpected intersection in their own family histories. Photographs of their grandparents were taken a decade and a hundred miles apart but betray parallel histories of migration, war, and social aspiration amid the decolonization of Malaya and the birth of a new Malaysia. The car is a symbol of social mobility both forwards and up, in a colony whose wealth of natural resources helped fuel the postwar explosion of the global middle class. This piece reminds us that even when we are confined to our homes, with albums as our archives, we can also find new possibilities in the banality of everyday social histories, perhaps richer when woven together.
Antibody Responses to SARS-CoV-2 After Infection or Vaccination in Children and Young Adults With Inflammatory Bowel Disease
Authors: Dailey Joelynn , Kozhaya Lina , Dogan Mikail , Hopkins Dena , Lapin Blaine , Herbst Katherine , Brimacombe Michael , Grandonico Kristen , Karabacak Fatih , Schreiber John , Liang Bruce Tsan-Liang , Salazar Juan C , Unutmaz Derya , Hyams Jeffrey S
Published: September 2021

Background

Characterization of neutralization antibodies to SARS-CoV-2 infection or vaccination in children and young adults with inflammatory bowel disease (IBD) receiving biologic therapies is crucial.

Methods

We performed a prospective longitudinal cohort study evaluating SARS-CoV-2 spike protein receptor binding domain (S-RBD) IgG positivity along with consistent clinical symptoms in patients with IBD receiving infliximab or vedolizumab. Serum was also obtained following immunization with approved vaccines. The IgG antibody to the spike protein binding domain of SARS-CoV-2 was assayed with a fluorescent bead-based immunoassay that takes advantage of the high dynamic range of fluorescent molecules using flow cytometry. A sensitive and high-throughput neutralization assay that incorporates SARS-CoV-2 spike protein onto a lentivirus and measures pseudoviral entry into ACE2-angiotensin converting enzyme 2 (ACE2) expressing human embryonic kidney 293 (HEK-293) cells was used.

Results

There were 436 patients enrolled (mean age, 17 years, range 2–26 years; 58% male; 71% Crohn’s disease, 29% ulcerative colitis, IBD-unspecified). Forty-four (10%) of enrolled subjects had SARS-CoV-2 S-RBD IgG antibodies. Compared to non-IBD adults (ambulatory) and hospitalized pediatric patients with PCR documented SARS-CoV-2 infection, S-RBD IgG antibody levels were significantly lower in the IBD cohort and by 6 months post infection most patients lacked neutralizing antibody. Following vaccination (n = 33), patients had a 15-fold higher S-RBD antibody response in comparison with natural infection, and all developed neutralizing antibodies to both wild type and variant SARS-CoV-2.

Conclusions

The lower and less durable SARS-CoV-2 S-RBD IgG response to natural infection in IBD patients receiving biologics puts them at risk of reinfection. The robust response to immunization is likely protective.
Reduced mortality during the COVID-19 outbreak in Japan, 2020: a two-stage interrupted time-series design
Authors: Onozuka Daisuke , Tanoue Yuta , Nomura Shuhei , Kawashima Takayuki , Yoneoka Daisuke , Eguchi Akifumi , Ng Chris Fook Sheng , Matsuura Kentaro , Shi Shoi , Makiyama Koji , Uryu Shinya , Kawamura Yumi , Takayanagi Shinichi , Gilmour Stuart , Hayashi Takehiko I , Miyata Hiroaki , Sera Francesco , Sunagawa Tomimasa , Takahashi Takuri , Tsuchihashi Yuuki , Kobayashi Yusuke , Arima Yuzo , Kanou Kazuhiko , Suzuki Motoi , Hashizume Masahiro
Published: September 2021

Background

Coronavirus disease 2019 (COVID-19) continues to be a major global health burden. This study aims to estimate the all-cause excess mortality occurring in the COVID-19 outbreak in Japan, 2020, by sex and age group.

Methods

Daily time series of mortality for the period January 2015–December 2020 in all 47 prefectures of Japan were obtained from the Ministry of Health, Labour and Welfare, Japan. A two-stage interrupted time-series design was used to calculate excess mortality. In the first stage, we estimated excess mortality by prefecture using quasi-Poisson regression models in combination with distributed lag non-linear models, adjusting for seasonal and long-term variations, weather conditions and influenza activity. In the second stage, we used a random-effects multivariate meta-analysis to synthesize prefecture-specific estimates at the nationwide level.

Results

In 2020, we estimated an all-cause excess mortality of −20 982 deaths [95% empirical confidence intervals (eCI): −38 367 to −5472] in Japan, which corresponded to a percentage excess of −1.7% (95% eCI: −3.1 to −0.5) relative to the expected value. Reduced deaths were observed for both sexes and in all age groups except those aged <60 and 70–79 years.

Conclusions

All-cause mortality during the COVID-19 outbreak in Japan in 2020 was decreased compared with a historical baseline. Further evaluation of cause-specific excess mortality is warranted.
A global assessment of distance pharmacy education amid COVID-19: teaching, assessment and experiential training
Authors: Alzubaidi Hamzah , Jirjees Feras Jassim , Franson Kari L , Saidawi Ward , Othman Amna M , Rabeeah Zainab H , Al-Obaidi Hala Jehad , Hatahet Taher , Caliph Suzanne
Published: September 2021

Objectives

To explore pharmacy colleges’ experiences and challenges worldwide with the transition to online teaching during the coronavirus disease 2019 (COVID-19) pandemic.

Methods

From the six World Health Organization regions, 28 countries with the highest number of COVID-19 cases were identified, and 111 pharmacy colleges were randomly selected from these countries. Two online surveys were sent to faculty members and senior administrators. They assessed changes in teaching and learning, experiential training, assessment, readiness for and challenges with distance e-learning and work-related stress.

Key findings

Data were collected from 46 colleges. The majority (80.4%) of colleges transitioned to distance e-learning. On-site experiential training was discontinued in 55.5% of colleges and 25.0% redesigned on-site training into remote learning experiences. Assessments were modified in 75.9% of colleges. Assuring the integrity of assessments and delivering practical classes were the most prominent faculty challenges. The majority of faculty (75.0%) and administrators (61.9%) reported moderate work-related stress. Nevertheless, most academics felt that they received adequate support from their institutions and had positive perceptions of the transition to distance e-learning during the pandemic.

Conclusions

The COVID-19 pandemic required drastic changes for most programs’ teaching methods. Our results showed that educational institutions were somewhat able to support faculty and the needs of educational programs were largely met. However, academic rigour and provision of experiential training can be improved. Faculty emotional support and training needs were not fully addressed in these difficult times. These results shed light on how the global pharmacy academy has addressed the COVID-19 pandemic and help rethink crisis response models.
A low-order divergence-free H(div)-conforming finite element method for Stokes flows
Authors: Li Xu , Rui Hongxing
Published: September 2021

In this paper, we propose a ${\textbf{P}_{1}^{c}}\oplus{RT0}-P0$ discretization of the Stokes equations on general simplicial meshes in two/three dimensions, which yields an exactly divergence-free and pressure-independent velocity approximation with optimal order. Our method has the following features. First, the global number of the degrees of freedom (DOFs) of our method is the same as the low-order Bernardi and Raugel ($B$-$R$) finite element method (Bernardi & Raugel, 1985, Analysis of some finite elements for the Stokes problem. Math. Comp., 44, 71–79), while the number of the nonzero entries of the former is about half of the latter in the velocity–velocity region of the coefficient matrix. Secondly, the ${\textbf{P}_{1}^{c}}$ component of the velocity, the $RT0$ component of the velocity and the pressure seem to solve a popular ${\textbf{P}_{1}^{c}}-{RT0}-P0$ discretization of a poroelastic-type system formally. Finally, our method can be easily transformed into a pressure-robust and stabilized ${\textbf{P}_{1}^{c}}-P0$ discretization for the Stokes problem via the static condensation of the $RT0$ component, which has a much smaller number of global DOFs. Numerical experiments illustrating the robustness of our method are also provided.
Quantifying Ethanol in Ethanol-Based Hand Sanitizers by Headspace Gas Chromatography with Flame Ionization Detector (HS-GC/FID)
Authors: Costa Bruno Ruiz Brandão da , Haddad Lohanna Pereira El , Caleffo Piva Bigão Vítor Luiz , Martinis Bruno Spinosa De
Published: September 2021

Background

The COVID-19 pandemic sharply increased the demand for ethanol-based gel hand sanitizers, leading to a shortage of these products. Consequently, regulatory health agencies worldwide have altered their regulatory guidelines on ethanol quality to meet this high demand, raising concerns about product quality.

Objective

The aim of this study was to quantify ethanol content and to qualitatively assess common impurities in ethanol-based gel hand sanitizers by headspace (HS) gas chromatography (GC) with flame ionization detector (FID).

Methods

To quantify the ethanol content, 0.10 g of the sample was weighed in a 20 mL HS vial and 5 mL of deionized water was added. Regarding the qualitative approach, 0.25 g of the sample was weighed and 4 mL of deionized water was added. The samples were incubated and then 400 µL of the HS was injected into the GC/FID. Forty-eight products purchased in Brazil were analyzed.

Results

Thirteen products presented at least one nonconformity regarding the ethanol quantity. Two samples presented an average ethanol concentration below the lower limit considered effective. Twelve samples presented acetaldehyde or ethyl acetate.

Conclusion

The huge demand for ethanol-based gel hand sanitizers may have impacted their quality. Because concern with proper hand hygiene tends to remain an issue for a long period, more studies about quality control of hand sanitizers will be needed.

Highlights

A simple and fast HS-GC/FID method to quantify ethanol in ethanol-based gel hand sanitizers was developed, validated, and applied to commercial samples in Brazil. The regulatory authorities must be more vigilant to ensure that the commercially available products meet the recommended specifications.
Rethinking the (CP)TPP as a Model for Regulation of Chinese State-Owned Enterprises
Authors: Zhou Weihuan
Published: September 2021

This paper challenges the widespread view that the Comprehensive and Progressive Agreement for Trans-Pacific Partnership (CPTPP) provides the most advanced rules for regulating China’s state-owned enterprises (SOEs). It argues that compared to China’s existing World Trade Organization (WTO) obligations, particularly those specifically tailored to it, the CPTPP SOE chapter does not provide more rigorous or workable rules but rather has narrower applications and more carve-outs. More recent US/EU free trade agreements (FTAs) are largely based on the CPTPP SOE chapter. While these FTAs also seek to address some deficiencies in the CPTPP SOE chapter and gradually expand the rules on subsidies and SOEs, the expanded rules are balanced by the inclusion of extensive exceptions. This balanced approach may be used to facilitate multilateral negotiations of SOE rules, but if this approach is adopted, WTO Members will need to be prepared to negotiate with China on replacing the potentially very broad and rigid China-specific WTO rules with more balanced new rules that apply to all members. The likely consequence would be softer rather than stronger disciplines on Chinese SOEs.
Biophysical Settings that Influenced Plantation Survival During the 2015 Wildfires in Northern Rocky Mountain Moist Mixed-Conifer Forests
Authors: Jain Theresa B , Nelson Andrew S , Bright Benjamin C , Byrne John C , Hudak Andrew T
Published: September 2021

Fire suppression and the loss of western white pine (WWP) have made northern Rocky Mountain moist mixed-conifer forests less disturbance resilient. Although managers are installing hundreds of plantations, most of these plantations have not experienced wildfire since establishment. In 2015, wildfires burned through 100 WWP plantations in this region, providing an opportunity to evaluate the effects of wildfires on sapling survival. A Weibull distribution approach was used to characterize the variation of fire severity pixels, as indicated by the differenced normalized burn ratio. The distribution parameters provided a method to identify the biophysical setting and plantation characteristics influencing fire severity and sapling survival. Plantations located on lower slope positions were more resistant to wildfires than plantations located midslope or close to the ridges. Snow water equivalent was positively correlated with wildfire resistance and resilience. Results will help focus reforestation efforts and identify locations where future plantations can potentially survive wildfires.
Use of a pacemaker magnet to remove a broken suture needle during a laparoscopic cholecystectomy
Authors: Titus Derek , Rifenbery James
Published: September 2021

Prompt removal of unintended surgical foreign bodies is essential for prevention of adverse consequences of retained surgical foreign bodies postop. Current practices utilizing radiographic images in combination with visual inspection and palpation to remove foreign bodies can lead to increased surgical times and tissue damage. A suture needle fragment broke off during a laparoscopic cholecystectomy performed on a morbidly obese adult female. After being unable to retrieve the fragment by increasing the midline incision by ~7 cm and undergoing an additional ~1 of intraoperative time, a pacemaker magnet wrapped in sterilized plastic was able to instantaneously remove the shard. Techniques utilizing magnetism could be researched and developed for the removal of surgical foreign bodies both intraoperatively and postop.
A rare lipoma site in a 1-year-old boy
Authors: Maree Gulan , Gawrieh Bardisan , Omran Ammar , Ali Wajih
Published: September 2021

Lipomas are benign tumors composed of mature adipocytes. A 1-year-old-male baby was admitted to the hospital with a history of an abdominal mass, which had been incidentally detected by a local pediatrician. upon examining the child for a complaint of distention and chronic diarrhea. An ultrasound and computed tomography scan were performed, and findings revealed a fat mass, which was confirmed by laparotomy and microscopic results. At laparotomy, a soft yellow mass was found attached to the mesentery of the jejunum. The mass was enucleated without anastomosis, and the patient was followed up 4 months postoperatively with regular clinical examination and abdominal ultrasonography. This case was examined and reported in this study because lipomas are very rarely present in the mesentery of the intestine, especially at this early age.
The Definiteness Marker of Cypriot Arabic: A Phonological Account
Authors: Christodoulou Charalambos , Armostis Spyros , Karyolemou Marilena
Published: September 2021

This paper presents a description and analysis of both the morphophonological processes in which the definiteness marker /l/ of Cypriot Arabic is involved, and the rules that are proposed to describe these processes. More specifically, we offer a thorough account of the allomorphs of this marker and of its phonological behaviour regarding the preceding or the following word. The analysis was primarily based on naturalistic data obtained from interviews with native speakers.
Ammonium nutrition interacts with iron homeostasis in Brachypodium distachyon
Authors: De la Peña Marlon , Marín-Peña Agustín Javier , Urmeneta Leyre , Coleto Inmaculada , Castillo-González Jorge , van Liempd Sebastiaan M , Falcón-Pérez Juan M , Álvarez-Fernández Ana , González-Moro María Begoña , Marino Daniel
Published: September 2021

Most plant species develop stress symptoms when exposed to high ammonium (NH4+) concentrations. The root is the first organ in contact with high NH4+ and therefore the first barrier to cope with ammonium stress. In this work, we focused on root adaptation to ammonium nutrition in the model plant Brachypodium distachyon. Proteome analysis revealed changes associated with primary metabolism, cell wall remodelling, and redox homeostasis. In addition, it showed a strong induction of proteins related to methionine (Met) metabolism and phytosiderophore (PS) synthesis in ammonium-fed plants. In agreement with this, we show how ammonium nutrition impacts Met/S-adenosyl-Met and PS metabolic pathways together with increasing root iron content. Nevertheless, ammonium-fed plants displayed higher sensitivity to iron deficiency, suggesting that ammonium nutrition triggers impaired iron utilization and root to shoot transport, which entailed an induction in iron-related responses. Overall, this work demonstrates the importance of iron homeostasis during ammonium nutrition and paves a new way to better understand and improve ammonium use efficiency and tolerance.
Modelling spin evolution of magnetars
Authors: Jawor Jedrzej A , Tauris Thomas M
Published: September 2021

The origin and fate of magnetars [young, extremely magnetized neutron stars (NSs)] remains unsolved. Probing their evolution is therefore crucial for investigating possible links to other species of isolated NSs, such as the X-ray dim NSs (XDINSs) and rotating radio transients (RRATs). Here, we investigate the spin evolution of magnetars. Two avenues of evolution are considered: one with exponentially decaying B-fields, the other with sub- and superexponential decay. Using Monte Carlo methods, we synthesize magnetar populations using different input distributions and physical parameters, such as for the initial spin period, its time derivative, and the B-field decay time-scale. Additionally, we introduce a fade-away procedure that can account for the fading of old magnetars, and we briefly discuss the effect of alignment of the B-field and spin axes. Imposing the Galactic core-collapse supernova rate of ∼20 kyr−1 as a strict upper limit on the magnetar birthrate and comparing the synthetic populations to the observed one using both manual and automatic optimization algorithms for our input parameter study, we find that the B-field must decay exponentially or superexponentially with a characteristic decay time-scale of 0.5−10 kyr (with a best value of ∼4 kyr). In addition, the initial spin period must be less than 2 s. If these constraints are kept, we conclude that there are multiple choices of input physics that can reproduce the observed magnetar population reasonably well. We also conclude that magnetars may well be evolutionary linked to the population of XDINSs, whereas they are in general unlikely to evolve into RRATs.
Electrically charged black holes and the Blandford–Znajek mechanism
Authors: Komissarov Serguei S
Published: September 2021

Recently, it was claimed by King & Pringle that accretion of electric charge by a black hole (BH) rotating in an aligned external magnetic field results in a ‘dead’ vacuum magnetosphere, where the electric field is totally screened, no vacuum breakdown is possible, and the Blandford–Znajek mechanism cannot operate. Here, we study in details the properties of the Wald solution for electrically charged BHs discussed in their paper. Our results show that the claim is erroneous as in the solution with the critical charge q0 = 2aB0, there exists a drop of electrostatic potential along all magnetic field lines except the one coinciding with the symmetry axis. It is also found that while uncharged rotating BHs expel external vacuum magnetic field from their event horizon (the Meissner effect), electric charging of BHs pulls the magnetic field lines back on it, resembling what has been observed in some previous force-free, Relativistic Magnetohydrodynamics (RMHD), and Particle-in-Cell (PIC) simulations of BH magnetospheres. This suggests that accretion of electric charge may indeed be a feature of the BH electrodynamics. However, our analysis shows that the value q0 of the BH charge given by Wald is likely to be only an upper limit, and that the actual value depends of the details of the magnetospheric physics.