bluuebunny/crossref_metadata_2025 huggingface dataset:
A recent weakening of winter temperature association between Arctic and Asia
Authors: Wu Bingyi , Li Zhenkun , Francis Jennifer A , Ding Shuoyi
Published: January 2022

Arctic warming and its association with the mid-latitudes has been a hot topic over the past two decades. Although many studies have explored these issues, it is not clear how their linkage has changed over time. The results show that winter low tropospheric temperatures in Asia experienced two phases over the past two decades. Phase I (2007/2008–2012/2013) was characterized by a warm Arctic and cold Eurasia, and phase II by a warm Arctic and warm Eurasia (2013/2014–2018/2019). A strengthened association in winter temperature between the Arctic and Asia occurred during phase I, followed by a weakened linkage during phase II. Simulation experiments forced by observed Arctic sea ice variability largely reproduce observed patterns, suggesting that Arctic sea ice loss contributes to phasic (or low-frequency) variations in winter atmosphere and makes the Arctic–Asia temperature association fluctuate over time. The weakening of the Arctic–Asia linkage post-2012/2013 was associated with amplified and expanded Arctic warming. The corresponding anomalies in sea level pressure resembled a positive-phase North Atlantic Oscillation during phase II. This study implies that the phasic warm Arctic—cold Eurasia and warm Arctic—warm Eurasia patterns would alternately happen in the context of Arctic sea ice loss, which increases the difficulty in correctly predicting Asian winter temperature.
How community forest management performs when REDD+ payments fail
Authors: Collins Amy C , Grote Mark N , Caro Tim , Ghosh Aniruddha , Thorne James , Salerno Jonathan , Mulder Monique Borgerhoff
Published: January 2022

The reduced emissions in deforestation and degradation (REDD+) initiative uses payments for ecosystem services as incentives for developing countries to manage and protect their forests. REDD+ initiatives also prioritize social (and environmental) co-benefits aimed at improving the livelihoods of communities that are dependent on forests. Despite the incorporation of co-benefits into REDD+ goals, carbon sequestration remains the primary metric for which countries can receive payments from REDD+, but after more than 10 years of REDD+, many site-specific programs have failed to complete the carbon verification process. Here, we examine whether the REDD+ social co-benefits alone are sufficient to have slowed deforestation in the absence of carbon payments on Pemba, Tanzania. Using satellite imagery (Landsat archive), we quantified forest cover change for the period before (2001–2010) and after (2010–2018) the launch in 2010–2011 of Pemba island’s REDD+ readiness project. We then compared rates of forest cover change between shehia (administrative units) that were part of REDD+ readiness intervention and those that were not, adjusting for confounding variables and the non-random selection of REDD+ shehia with a statistical matching procedure. Despite considerable variation in forest outcomes among shehia, the associated co-benefits with the Pemba REDD+ project had no discernible effect on forest cover change. Likewise, we did not detect an effect of socioecological covariates on forest cover change across all shehia, though island-wide human population growth since 2012 may have played a role. These findings are unsurprising given the failure to secure carbon payments on Pemba and indicate that co-benefits alone are insufficient to reduce deforestation. We conclude that better oversight of all-involved parties is needed to ensure that REDD+ interventions satisfactorily conclude the process of securing a mechanism for carbon payments, if slowing deforestation is to be achieved.
Classification of four qubit states and their stabilisers under SLOCC operations
Authors: Dietrich Heiko , de Graaf Willem A. , Marrani Alessio , Origlia Marcos
Published: January 2022

We classify four qubit states under SLOCC operations, that is, we classify the orbits of the group

S
L

(

2
,
C

)

4

on the Hilbert space

H

4

=

(

C

2

)

⊗
4

. We approach the classification by realising this representation as a symmetric space of maximal rank. We first describe general methods for classifying the orbits of such a space. We then apply these methods to obtain the orbits in our special case, resulting in a complete and irredundant classification of

S
L

(

2
,
C

)

4

-orbits on

H

4

. It follows that an element of

(

C

2

)

⊗
4

is conjugate to an element of precisely 87 classes of elements. Each of these classes either consists of one element or of a parameterised family of elements, and the elements in the same class all have equal stabiliser in

S
L

(

2
,
C

)

4

. We also present a complete and irredundant classification of elements and stabilisers up to the action of

S
y
m

4

⋉
S
L

(

2
,
C

)

4

where Sym4 permutes the four tensor factors of

(

C

2

)

⊗
4

.
Chaos in a deformed Dicke model
Authors: L Corps Ángel , Molina Rafael A , Relaño Armando
Published: January 2022

The critical behavior in an important class of excited state quantum phase transitions is signaled by the presence of a new constant of motion only at one side of the critical energy. We study the impact of this phenomenon in the development of chaos in a modified version of the paradigmatic Dicke model of quantum optics, in which a perturbation is added that breaks the parity symmetry. Two asymmetric energy wells appear in the semiclassical limit of the model, whose consequences are studied both in the classical and in the quantum cases. Classically, Poincaré sections reveal that the degree of chaos not only depends on the energy of the initial condition chosen, but also on the particular energy well structure of the model. In the quantum case, Peres lattices of physical observables show that the appearance of chaos critically depends on the quantum conserved number provided by this constant of motion. The conservation law defined by this constant is shown to allow for the coexistence between chaos and regularity at the same energy. We further analyze the onset of chaos in relation with an additional conserved quantity that the model can exhibit.
Large Eddy simulation of tracer gas dispersion in a cavity
Authors: McMullan W A
Published: January 2022

This paper assesses the prediction of inert tracer gas dispersion within a cavity of height (H) 1.0 m, and unity aspect ratio, using large Eddy simulation (LES). The flow Reynolds number was 67 000, based on the freestream velocity and cavity height. The flow upstream of the cavity was laminar, producing a cavity shear layer which underwent a transition to turbulence over the cavity. Three distinct meshes are used, with grid spacings of

H

/

100

(coarse),

H

/

200

(intermediate), and

H

/

400

(fine) respectively. The Smagorinsky, WALE, and Germano-Lilly subgrid-scale models are used on each grid to quantify the effects of subgrid-scale modelling on the simulated flow. Coarsening the grid led to small changes in the predicted velocity field, and to substantial over-prediction of the tracer gas concentration statistics. Quantitative metric analysis of the tracer gas statistics showed that the coarse grid simulations yielded results outside of acceptable tolerances, while the intermediate and fine grids produced acceptable output. Interrogation of the fluid dynamics present in each simulation showed that the evolution of the cavity shear layer is heavily influenced by the grid and subgrid scale model. On the coarse and intermediate grids the development of the shear layer is delayed, inhibiting the entrainment and mixing of the tracer gas into the shear layer, reducing the removal of the tracer gas from the cavity. On the fine grid, the shear layer developed more rapidly, resulting in enhanced removal of the tracer gas from the cavity. Concentration probability density functions showed that the fine grid simulations accurately predicted the range, and the most probable value, of the tracer gas concentration towards both walls of the cavity. The results presented in this paper show that the WALE and Germano-Lilly models may be advantageous over the standard Smagorinsky model for simulations of pollutant dispersion in the urban environment.
Plasmonic excitations in two-dimensional materials: effects of structural symmetry and material anisotropy
Authors: Ding Linhui , Wang Ningning , Chen Leiming , Han Kui , Shen Xiaopeng , Wang Weihua
Published: January 2022

Plasmonics in two-dimensional (2D) materials, an emerging direction of nano-optics, has attracted great attention recently, which exhibits unique properties than that in noble metals. Extending its advanced features by different manipulations is very beneficial for its promotion. In this paper, we study plasmonic excitations in graphene and black phosphorus (BP) nanostructures, where the effects of structural symmetry and material anisotropy are discussed. We show that the two factors are crucial to mode excitations, e.g. the extinction can be dominated by higher order modes rather than dipole resonance. The behavior occurs only in the direction hosting larger resonance frequencies, e.g. armchair (AC) direction of BP and shorter side of graphene rectangles. In BP rectangles along AC direction, the two factors are competing, and thus can be applied cooperatively to tune plasmonic resonance, from dipole to higher order excitations. Besides, the manipulation can also be achieved by designing BP square rings, in which the interaction between outer and inner edges show great impact on mode excitations. Our studies further promote the understanding of plasmonics in 2D materials, and will pave the way for particular plasmonic applications.
Optimal trap velocity in a dynamic holographic optical trap using a nematic liquid crystal spatial light modulator
Authors: Malik Karuna Sindhu , Boruah Bosanta R
Published: January 2022

A dynamic holographic optical trap uses a dynamic diffractive optical element such as a liquid crystal spatial light modulator to realize one or more optical traps with independent controls. Such holographic optical traps provide a number of flexibilities and conveniences useful in various applications. One key requirement for such a trap is the ability to move the trapped microscopic object from one point to the other with the optimal velocity. In this paper we develop a nematic liquid crystal spatial light modulator based holographic optical trap and experimentally investigate the optimal velocity feasible for trapped beads of different sizes, in such a trap. Our results show that the achievable velocity of the trapped bead is a function of size of the bead, step size, interval between two steps and power carried by the laser beam. We observe that the refresh rate of a nematic liquid crystal spatial light modulator is sufficient to achieve an optimal velocity approaching the theoretical limit in the respective holographic trap for beads with radius larger than the wavelength of light.
Designing spin-textured flat bands in twisted graphene multilayers via helimagnet encapsulation
Authors: Chen Guangze , Khosravian Maryam , Lado Jose L , Ramires Aline
Published: January 2022

Twisted graphene multilayers provide tunable platforms to engineer flat bands and exploit the associated strongly correlated physics. The two-dimensional nature of these systems makes them suitable for encapsulation by materials that break specific symmetries. In this context, recently discovered two-dimensional helimagnets, such as the multiferroic monolayer NiI2, are specially appealing for breaking time-reversal and inversion symmetries due to their nontrivial spin textures. Here we show that this spin texture can be imprinted on the electronic structure of twisted bilayer graphene by proximity effect. We discuss the dependence of the imprinted spin texture on the wave-vector of the helical structure, and on the strength of the effective local exchange field. Based on these results we discuss the nature of the superconducting instabilities that can take place in helimagnet encapsulated twisted bilayer graphene. Our results put forward helimagnetic encapsulation as a powerful way of designing spin-textured flat band systems, providing a starting point to engineer a new family of correlated moire states.
Research on low cycle fatigue life prediction considering average strain
Authors: Peng Yan , Liu Yang , Li Haoran , Xing Jiankang
Published: January 2022

To address the difficult problems in the study of the effect of average strain on fatigue life under low-cycle fatigue loads, the effect of average strain on the low-cycle fatigue life of materials under different strain cycle ratios was discussed based on the framework of damage mechanics and its irreversible thermodynamics. By introducing the Ramberg-Osgood cyclic constitutive equation, a new low-cycle fatigue life prediction method based on the intrinsic damage dissipation theory considering average strain was proposed, which revealed the correlation between low-cycle fatigue strain life , material properties, and average strain. Through the analysis of the low-cycle fatigue test data of five different metal materials, the model parameters of the corresponding materials were obtained. The calculation results indicate that the proposed life prediction method is in good agreement with the test, and a reasonable characterization of the low-cycle fatigue life under the influence of average strain is realized. Comparing calculations with three typical low-cycle fatigue life prediction models, the new method is within two times the error band, and the prediction effect is significantly better than the existing models, which is more suitable for low-cycle fatigue life prediction. The low-cycle fatigue life prediction of different cyclic strain ratios based on the critical region intrinsic damage dissipation power method provides a new idea for the research of low-cycle fatigue life prediction of metallic materials.
Fiducial visibility on planar images during motion-synchronized tomotherapy treatments
Authors: Ferris William S , DeWerd Larry A , Culberson Wesley S
Published: January 2022

Objective. Synchrony® is a motion management system on the Radixact® that uses planar kV radiographs to locate the target during treatment. The purpose of this work is to quantify the visibility of fiducials on these radiographs. Approach. A custom acrylic slab was machined to hold 8 gold fiducials of various lengths, diameters, and orientations with respect to the imaging axis. The slab was placed on the couch at the imaging isocenter and planar radiographs were acquired perpendicular to the custom slab with varying thicknesses of acrylic on each side. Fiducial signal to noise ratio (SNR) and detected fiducial position error in millimeters were quantified. Main Results. The minimum output protocol (100 kVp, 0.8 mAs) was sufficient to detect all fiducials on both Radixact configurations when the thickness of the phantom was 20 cm. However, no fiducials for any protocol were detected when the phantom was 50 cm thick. The algorithm accurately detected fiducials on the image when the SNR was larger than 4. The MV beam was observed to cause RFI artifacts on the kV images and to decrease SNR by an average of 10%. Significance. This work provides the first data on fiducial visibility on kV radiographs from Radixact Synchrony treatments. The Synchrony fiducial detection algorithm was determined to be very accurate when sufficient SNR is achieved. However, a higher output protocol may need to be added for use with larger patients. This work provided groundwork for investigating visibility of fiducial-free solid targets in future studies and provided a direct comparison of fiducial visibility on the two Radixact configurations, which will allow for intercomparison of results between configurations.
MHD instability at the cathode spot as the origin of the vortex formation in high-intensity plasma arcs
Authors: Barati Hadi , Kharicha Abdellah , Al-Nasser Mohamad , Kreuzer Daniel , Hackl Gernot , Gruber Markus , Ishmurzin Anton , Redl Christian , Teplyakov Igor O , Wu Menghuai , Ludwig Andreas
Published: January 2022

Magnetohydrodynamic instability in a high-intensity arc, similar to typical arcs in DC electric arc furnaces, is simulated using an induction based model under 2D axisymmetric conditions. Time-averaged results show a good agreement with steady-state calculated results expected for a stable arc. The transient results declare that z-pinch close to the cathode, occurring due to the high electrical current density, is responsible for arc instability in this region. The unstable behavior of the arc can be evaluated in a periodic procedure. Moreover, correlations between the fluctuations in total voltage drop curve and the arc shape are investigated: when the arc is in form of column (or bell) the total voltage drop is on a minimum peak; if there is an irregular expansion of the arc in form of arms, the total voltage drop shows a maximum peak.
Deterministic loading of a single strontium ion into a surface electrode trap using pulsed laser ablation
Authors: Osada Alto , Noguchi Atsushi
Published: January 2022

Trapped-ion quantum technologies have been developed for decades toward applications such as precision measurement, quantum communication and quantum computation. Coherent manipulation of ions’ oscillatory motions in an ion trap is important for quantum information processing by ions, however, unwanted decoherence caused by fluctuating electric-field environment often hinders stable and high-fidelity operations. One way to avoid this is to adopt pulsed laser ablation for ion loading, a loading method with significantly reduced pollution and heat production. Despite the usefulness of the ablation loading such as the compatibility with cryogenic environment, randomness of the number of loaded ions is still problematic in realistic applications where definite number of ions are preferably loaded with high probability. In this paper, we demonstrate an efficient loading of a single strontium ion into a surface electrode trap generated by laser ablation and successive photoionization. The probability of single-ion loading into a surface electrode trap is measured to be 82%, and such a deterministic single-ion loading allows for loading ions into the trap one-by-one. Our results open up a way to develop more functional ion-trap quantum devices by the clean, stable, and deterministic ion loading.
Infrastructure autopoiesis: requisite variety to engage complexity
Authors: Chester Mikhail V , Allenby Braden
Published: January 2022

Infrastructure systems must change to match the growing complexity of the environments they operate in. Yet the models of governance and the core technologies they rely on are structured around models of relative long-term stability that appear increasingly insufficient and even problematic. As the environments in which infrastructure function become more complex, infrastructure systems must adapt to develop a repertoire of responses sufficient to respond to the increasing variety of conditions and challenges. Whereas in the past infrastructure leadership and system design has emphasized organization strategies that primarily focus on exploitation (e.g., efficiency and production, amenable to conditions of stability), in the future they must create space for exploration, the innovation of what the organization is and does. They will need to create the abilities to maintain themselves in the face of growing complexity by creating the knowledge, processes, and technologies necessary to engage environment complexity. We refer to this capacity as infrastructure autopoiesis. In doing so infrastructure organizations should focus on four key tenets. First, a shift to sustained adaptation—perpetual change in the face of destabilizing conditions often marked by uncertainty—and away from rigid processes and technologies is necessary. Second, infrastructure organizations should pursue restructuring their bureaucracies to distribute more resources and decisionmaking capacity horizontally, across the organization’s hierarchy. Third, they should build capacity for horizon scanning, the process of systematically searching the environment for opportunities and threats. Fourth, they should emphasize loose fit design, the flexibility of assets to pivot function as the environment changes. The inability to engage with complexity can be expected to result in a decoupling between what our infrastructure systems can do and what we need them to do, and autopoietic capabilities may help close this gap by creating the conditions for a sufficient repertoire to emerge.
Recall of exposure in UK farmers and pesticide applicators: trends with follow-up time
Authors: Mueller William , Jones Kate , Mohamed Hani , Bennett Neil , Harding Anne-Helen , Frost Gillian , Povey Andrew , Basinas Ioannis , Kromhout Hans , van Tongeren Martie , Fuhrimann Samuel , Galea Karen S
Published: January 2022

Background

Occupational epidemiological studies on pesticide use commonly rely on self-reported questionnaire or interview data to assess exposure. Insight into recall accuracy is important, as misclassification of exposures due to imperfect recall can bias risk estimates.

Methods

We assessed the ability of workers in three UK cohorts (Prospective Investigation of Pesticide Applicators’ Health [PIPAH], Pesticide Users’ Health Study [PUHS], and Study of Health in Agricultural Work [SHAW]) to remember their working history related to pesticide exposure over time periods ranging from 3 to 14 years prior. During 2019–2020, cohort participants were re-surveyed using a similar questionnaire to that used previously. We compared recall of responses at follow-up to those reported at baseline related to crops/areas of work, use of personal protective equipment (PPE) items, hygiene habits, frequency of pesticide use, and application method. To assess the extent of recall, we used sensitivity, specificity, the percentage of overall agreement, and area under the curve (AUC) values. We also examined the presence of over or underestimation of recalled years, and days and hours per year, of working with pesticides using geometric mean ratios (GMR) and regression analysis to investigate any trends based on demographic characteristics.

Results

There were 643 individuals who completed both the baseline and follow-up surveys in the three cohorts with response rates ranging from 17 to 46%. There was a strong correlation (rho = 0.77) between the baseline and recalled years working with pesticides, though higher values were reported at follow-up (GMR = 1.18 [95% confidence interval: 1.07–1.30]) with no consistent differences by demographic characteristics. There was stronger agreement in the recalled days compared to hours per year in two of the cohorts. Recall for a number of exposure determinants across short and longer periods entailed overall agreement of >70%, though with some differences: for example, sensitivity for long-term recall of crops was poor (<43% in PUHS), whereas short-term recall of hygiene practices was good (AUC range = 0.65–1.00 in PIPAH).

Conclusion

Results indicate that recall ability may deteriorate over a longer period. Although low-response rates may require these findings to be interpreted with caution, recall for a number of exposure determinants appeared reliable, such as crops and hygiene practices within 3 years, as well as days per year working with pesticides.
Ability’s Two Dimensions of Robustness
Authors: Kikkert Sophie
Published: January 2022

The actions of able agents are often reliably successful. I argue that their success may be modally robust along two dimensions. The first dimension helps distinguish the exercise of abilities, which requires local control, from lucky success. The second concerns the global availability of acts: agents with the ability to φ can φ across a variety of circumstances. I introduce a framework that captures the two dimensions and their interaction, and show how it bears on a disagreement about the modal force the robustness of ability requires: while local control involves a kind of local necessity, global availability does not.
SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants
Authors: Yang Yaning , Wang Xiaoqi , Zhou Deshan , Wei Dong-Qing , Peng Shaoliang
Published: January 2022

Although there are a large number of structural variations in the chromosomes of each individual, there is a lack of more accurate methods for identifying clinical pathogenic variants. Here, we proposed SVPath, a machine learning-based method to predict the pathogenicity of deletions, insertions and duplications structural variations that occur in exons. We constructed three types of annotation features for each structural variation event in the ClinVar database. First, we treated complex structural variations as multiple consecutive single nucleotide polymorphisms events, and annotated them with correlation scores based on single nucleic acid substitutions, such as the impact on protein function. Second, we determined which genes the variation occurred in, and constructed gene-based annotation features for each structural variation. Third, we also calculated related features based on the transcriptome, such as histone signal, the overlap ratio of variation and genomic element definitions, etc. Finally, we employed a gradient boosting decision tree machine learning method, and used the deletions, insertions and duplications in the ClinVar database to train a structural variation pathogenicity prediction model SVPath. These structural variations are clearly indicated as pathogenic or benign. Experimental results show that our SVPath has achieved excellent predictive performance and outperforms existing state-of-the-art tools. SVPath is very promising in evaluating the clinical pathogenicity of structural variants. SVPath can be used in clinical research to predict the clinical significance of unknown pathogenicity and new structural variation, so as to explore the relationship between diseases and structural variations in a computational way.
Compositional Data Analysis using Kernels in mass cytometry data
Authors: Rudra Pratyaydipta , Baxter Ryan , Hsieh Elena W Y , Ghosh Debashis
Published: January 2022

Motivation

Cell-type abundance data arising from mass cytometry experiments are compositional in nature. Classical association tests do not apply to the compositional data due to their non-Euclidean nature. Existing methods for analysis of cell type abundance data suffer from several limitations for high-dimensional mass cytometry data, especially when the sample size is small.

Results

We proposed a new multivariate statistical learning methodology, Compositional Data Analysis using Kernels (CODAK), based on the kernel distance covariance (KDC) framework to test the association of the cell type compositions with important predictors (categorical or continuous) such as disease status. CODAK scales well for high-dimensional data and provides satisfactory performance for small sample sizes (n < 25). We conducted simulation studies to compare the performance of the method with existing methods of analyzing cell type abundance data from mass cytometry studies. The method is also applied to a high-dimensional dataset containing different subgroups of populations including Systemic Lupus Erythematosus (SLE) patients and healthy control subjects.

Availability and implementation

CODAK is implemented using R. The codes and the data used in this manuscript are available on the web at http://github.com/GhoshLab/CODAK/.

Contact

prudra@okstate.edu

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
From viral evolution to spatial contagion: a biologically modulated Hawkes model
Authors: Holbrook Andrew J , Ji Xiang , Suchard Marc A
Published: January 2022

Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly relates a pathogen’s evolution to its spatial contagion dynamics—effectively combining the two epidemiological paradigms of phylogenetic inference and self-exciting process modeling—and apply this phylogenetic Hawkes process to a Bayesian analysis of 23 421 viral cases from the 2014 to 2016 Ebola outbreak in West Africa. The proposed model is able to detect individual viruses with significantly elevated rates of spatiotemporal propagation for a subset of 1610 samples that provide genome data. Finally, to facilitate model application in big data settings, we develop massively parallel implementations for the gradient and Hessian of the log-likelihood and apply our high-performance computing framework within an adaptively pre-conditioned Hamiltonian Monte Carlo routine.

Supplementary information

Supplementary data are available at Bioinformatics online.
Being ‘good enough’: Perfectionism and well-being in social workers
Authors: Kinman Gail , Grant Louise
Published: January 2022

Perfectionism refers to a tendency to set unrealistically high standards for oneself and others. Although often seen positively, perfectionism can threaten health, relationships and performance. This study examined the effects of three types of maladaptive perfectionism on burnout in 294 UK social workers: self-oriented (having excessively high standards for oneself), other-oriented (having excessively high expectations of others) and socially prescribed (perceiving external pressure to excel). In line with previous research, we predicted that socially prescribed perfectionism would have particularly powerful effects on well-being, but significant relationships with self and other-oriented perfectionism were also expected. We also examined whether maladaptive perfectionism intensified the negative impact of work-related emotional demands on burnout. Significant positive relationships were found between socially prescribed and other-oriented perfectionism and burnout. A higher level of socially prescribed perfectionism was found than self and other-oriented and its relationship with burnout was particularly strong. We found no evidence, however, that perfectionism was an additional risk factor for burnout when emotional demands were high. Early career social workers were found to be at greater risk of dysfunctional perfectionism and burnout. The implications of the findings for the well-being of social workers are considered and potential interventions outlined to reduce maladaptive perfectionism.
Seroprevalence and Risk Factors for Severe Acute Respiratory Syndrome Coronavirus 2 Among Incarcerated Adult Men in Quebec, Canada, 2021
Authors: Kronfli Nadine , Dussault Camille , Maheu-Giroux Mathieu , Halavrezos Alexandros , Chalifoux Sylvie , Sherman Jessica , Park Hyejin , Del Balso Lina , Cheng Matthew P , Poulin Sébastien , Cox Joseph
Published: January 2022

Background

People in prison are at increased risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We examined the seroprevalence of SARS-CoV-2 and associated carceral risk factors among incarcerated adult men in Quebec, Canada.

Methods

We conducted a cross-sectional seroprevalence study in 2021 across 3 provincial prisons, representing 45% of Quebec’s incarcerated male provincial population. The primary outcome was SARS-CoV-2 antibody seropositivity (Roche Elecsys serology test). Participants completed self-administered questionnaires on sociodemographic, clinical, and carceral characteristics. The association of carceral variables with SARS-CoV-2 seropositivity was examined using Poisson regression models with robust standard errors. Crude and adjusted prevalence ratios (aPR) with 95% confidence intervals (95% CIs) were calculated.

Results

Between 19 January 2021 and 15 September 2021, 246 of 1100 (22%) recruited individuals tested positive across 3 prisons (range, 15%–27%). Seropositivity increased with time spent in prison since March 2020 (aPR, 2.17; 95% CI, 1.53–3.07 for “all” vs “little time”), employment during incarceration (aPR, 1.64; 95% CI, 1.28–2.11 vs not), shared meal consumption during incarceration (“with cellmates”: aPR, 1.46; 95% CI, 1.08–1.97 vs “alone”; “with sector”: aPR, 1.34; 95% CI, 1.03–1.74 vs “alone”), and incarceration post-prison outbreak (aPR, 2.32; 95% CI, 1.69–3.18 vs “pre-outbreak”).

Conclusions

The seroprevalence of SARS-CoV-2 among incarcerated individuals was high and varied among prisons. Several carceral factors were associated with seropositivity, underscoring the importance of decarceration and occupational safety measures, individual meal consumption, and enhanced infection prevention and control measures including vaccination during incarceration.
Effusive–constrictive pericarditis after the second dose of BNT162b2 vaccine (Comirnaty): a case report
Authors: Viani Giacomo Maria , Pedrotti Patrizia , Seregni Romano , Antonio Brucato
Published: January 2022

Background

Whereas effusive–constrictive pericarditis (ECP) can rarely occur in coronavirus disease 2019 (COVID-19), to date no cases of ECP related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) vaccine have been documented.

Case summary

A 59-year-old Caucasian man presented to our emergency department with ECP. Symptoms occurred shortly after the second dose of BNT162b2 (Comirnaty) vaccine. No other aetiological causes were identified. Guidelines-directed therapy for acute pericarditis was implemented, with clinical benefit.

Discussion

Systemic inflammatory response to COVID-19 can rarely trigger pericarditis. In our case, a strong temporal relationship between the second dose of BNT162b2 vaccine and symptoms occurrence was documented, indicating a possible rare adverse reaction to the vaccine, similarly to natural infection. Further research is needed to confirm a causal relationship.
Marked recovery of cardiac function by chemotherapy and autologous stem cell transplantation of a patient with heart failure with preserved ejection fraction due to primary amyloid light-chain amyloidosis: a case report
Authors: Tanaka Hidekazu , Kitao Akihito , Minami Hironobu , Hirata Ken-Ichi
Published: January 2022

Background

Cardiac involvement of amyloid light-chain (AL) amyloidosis is strongly associated with poor outcome, but the early detection of cardiac involvement of AL amyloidosis can be challenging.

Case summary

We present a case of 49-year-old-female with heart failure with preserved ejection fraction. Echocardiography revealed normal left ventricular (LV) ejection fraction of 63% and an enlarged left atrium with a left atrial volume index (LAVI) of 54 mL/m2. Mild LV hypertrophy with an interventricular septum of 12.3 mm and posterior wall thickness of 11.0 mm was observed, and Doppler-derived LV diastolic filling showed a restrictive filling pattern. The conventional echocardiographic findings did not unequivocally indicate typical cardiac amyloidosis, but global longitudinal strain (GLS) was as low as 14.2%, and an apical sparing pattern was observed with relative apical longitudinal strain of 1.11. Finally, the patient was diagnosed as primary AL amyloidosis including histological examination of the endomyocardial specimen. After treatment with a regime of bortezomib and dexamethasone followed by high-dose melphalan followed by autologous peripheral blood stem cell transplantation (auto-PBSCT), Doppler-derived LV diastolic filling improved to normal filling pattern, and left atrial size had also decreased with an LAVI of 31 mL/m2. Moreover, GLS improved to 19.8%, and the apical sparing pattern had disappeared with relative apical longitudinal strain of 0.62. The patient has been asymptomatic during 18-month follow-up after auto-PBSCT, and recovered LV function has been maintained.

Discussion

An earlier diagnosis of cardiac amyloidosis by using apical sparing may therefore allow for earlier treatment intervention for AL amyloidosis.
The autophagy-resistant Mycobacterium tuberculosis Beijing strain upregulates KatG to evade starvation-induced autophagic restriction
Authors: Siregar Tegar Adriansyah Putra , Prombutara Pinidphon , Kanjanasirirat Phongthon , Kunkaew Nawapol , Tubsuwan Alisa , Boonmee Atsadang , Palaga Tanapat , Khumpanied Tanawadee , Borwornpinyo Suparerk , Chaiprasert Angkana , Utaisincharoen Pongsak , Ponpuak Marisa
Published: January 2022

Mycobacterium tuberculosis utilizes several mechanisms to block phagosome–lysosome fusion to evade host cell restriction. However, induction of host cell autophagy by starvation was shown to overcome this block, resulting in enhanced lysosomal delivery to mycobacterial phagosomes and the killing of the M. tuberculosis reference strain H37Rv. Nevertheless, our previous studies found that strains belonging to the M. tuberculosis Beijing genotype can resist starvation-induced autophagic elimination, though the mycobacterial factors involved remain unclear. In this study, we showed that KatG expression is upregulated in the autophagy-resistant M. tuberculosis Beijing strain (BJN) during autophagy induction by the starvation of host macrophages, while such increase was not observed in the H37Rv. KatG depletion using the CRISPR-dCas9 interference system in the BJN resulted in increased lysosomal delivery to its phagosome and decreased its survival upon autophagy induction by starvation. As KatG functions by catabolizing ROS, we determined the source of ROS contributing to the starvation-induced autophagic elimination of mycobacteria. Using siRNA-mediated knockdown, we found that Superoxide dismutase 2, which generates mitochondrial ROS but not NADPH oxidase 2, is important for the starvation-induced lysosomal delivery to mycobacterial phagosomes. Taken together, these findings showed that KatG is vital for the BJN to evade starvation-induced autophagic restriction.
Microelectrode glucose biosensor based on nanoporous platinum/graphene oxide nanostructure for rapid glucose detection of tomato and cucumber fruits
Authors: Wu Binfang , Xu Haitao , Shi Yufeng , Yao Zhijie , Yu Jiayu , Zhou Hua , Li Yunpeng , Chen Qiulan , Long Yongbing
Published: January 2022

A microelectrode glucose biosensor based on a three-dimensional hybrid nanoporous platinum/graphene oxide nanostructure was developed for rapid glucose detection of tomato and cucumber fruits. The nanostructure was fabricated by a two-step modification method on a microelectrode for loading a larger amount of glucose oxidase. The nanoporous structure was prepared on the surface of the platinum microelectrode by electrochemical etching, and then graphene oxide was deposited on the prepared nanoporous electrode by electrochemical deposition. The nanoporous platinum/graphene oxide nanostructure had the advantage of improving the effective surface area of the electrode and the loading quantity of glucose oxidase. As a result, the biosensor achieved a wide range of 0.1–20.0 mmol/L in glucose detection, which had the ability to accurately detect the glucose content. It was found that the three-dimensional hybrid nanostructure on the electrode surface realized the rapid direct electrochemistry of glucose oxidase. Therefore, the biosensor achieved high glucose detection sensitivity (11.64 μA·L/(mmol·cm2), low detection limit (13 μmol/L) and rapid response time (reaching 95% steady-state response within 3 s), when calibrating in glucose standard solution. In agricultural application, the as-prepared biosensor was employed to detect the glucose concentration of tomato and cucumber samples. The results showed that the relative deviation of this method was less than 5% when compared with that of high-performance liquid chromatography, implying high accuracy of the presented biosensor in glucose detection in plants.
Comparative study of the characterisation and extraction techniques of polyphenolic compounds from Acacia seyal gum
Authors: Elnour Ahmed A M , Mirghani Mohamed E S , Kabbashi Nassereldeen A , Hamid Musa Khalid , Shahabipour Fahimeh , Ashammakhi Nureddin , Hamid Abdurahman Nour
Published: January 2022

Background

Acacia seyal gum (ASG) is an abundant source of natural polyphenolic compounds (NPPCs) and antioxidant activity with numerous benefits and is often used in cancer treatment. The type of extraction technique can significantly impact the yield and isolation of NPPCs from ASG. The traditional use of maceration extraction reportedly yields fewer NPPCs.

Objectives

This study investigated five extraction techniques for NPPCs and ASG antioxidant activity, namely: homogenisation, shaking, ultrasonication, magnetic stirring, and maceration.

Materials and methods

The evaluation of the antioxidant activity (AoA) of the extracted NPPCs from ASG used five assays, namely: total flavonoids content, Folin–Ciocalteu index, 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity, ferric reducing antioxidant power, and cupric reducing antioxidant capacity.

Results

To minimise the data set dimensionality requires principal component analysis. The ultrasonic and maceration techniques were the best techniques to extract NPPCs and examine the AoA of ASG, with a high correlation between the NPPCs and AoA. However, the maceration process was slow (12 h) compared to ultrasonication (1 h). Slow extraction can result in a decline of the NPPCs due to polyphenol oxidase–enzyme and impact productivity.

Conclusions

These findings provide an essential guide for the choice of extraction techniques for the effective extraction of NPPCs from ASG and other plant materials.
Multidimensional Social Network Types and Their Correlates in Older Americans
Authors: Ali Talha , Elliott Michael R , Antonucci Toni C , Needham Belinda L , Zelner Jon , Mendes de Leon Carlos F
Published: January 2022

Background and Objectives

Social support networks of older adults have been linked to their health and well-being; however, findings regarding the effects of specific network characteristics have been mixed. Additionally, due to demographic shifts increasing numbers of older adults live outside of traditional family structures. Previous studies have not systematically examined the resulting complexity and heterogeneity of older adults’ social networks. Our objectives were to examine this complexity and heterogeneity by developing a multidimensional typology of social networks that simultaneously considers multiple structural and functional network characteristics, and to examine differences in network type membership by sociodemographic characteristics, health characteristics, and birth cohort.

Research Design and Methods

Participants included 5,192 adults aged 57–85 years in the National Social Life, Health, and Aging Project at rounds 1 (2005–2006) and 3 (2015–2016). Data were collected on social relationships including network size, diversity, frequency of contact, and perceived support and strain in relationships. We used latent class analysis to derive the network typology and multinomial logistic regression to examine differences in network type membership by sociodemographic characteristics, health characteristics, and birth cohort.

Results

Older adults were classified into 5 distinct social network types: (i) large, with strain; (ii) large, without strain; (iii) small, diverse, low contact; (iv) small, restricted, high contact; and (v) medium size and support. Membership in these network types varied by age, gender, marital status, race/ethnicity, education, mental health, and birth cohort.

Discussion and Implications

Network typologies can elucidate the varied interpersonal environments of older adults and identify individuals who lack social connectedness on multiple network dimensions and are therefore at a higher risk of social isolation.
Halvade somatic: Somatic variant calling with Apache Spark
Authors: Decap Dries , de Schaetzen van Brienen Louise , Larmuseau Maarten , Costanza Pascal , Herzeel Charlotte , Wuyts Roel , Marchal Kathleen , Fostier Jan
Published: January 2022

Background

The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired. In turn, this leads to large volumes of raw sequencing data to process and hence, large computational requirements. For example, calling the somatic variants according to the GATK best practices guidelines requires days of computing time for a typical whole-genome sequencing sample.

Findings

We introduce Halvade Somatic, a framework for somatic variant calling from DNA sequencing data that takes advantage of multi-node and/or multi-core compute platforms to reduce runtime. It relies on Apache Spark to provide scalable I/O and to create and manage data streams that are processed on different CPU cores in parallel. Halvade Somatic contains all required steps to process the tumor and matched normal sample according to the GATK best practices recommendations: read alignment (BWA), sorting of reads, preprocessing steps such as marking duplicate reads and base quality score recalibration (GATK), and, finally, calling the somatic variants (Mutect2). Our approach reduces the runtime on a single 36-core node to 19.5 h compared to a runtime of 84.5 h for the original pipeline, a speedup of 4.3 times. Runtime can be further decreased by scaling to multiple nodes, e.g., we observe a runtime of 1.36 h using 16 nodes, an additional speedup of 14.4 times. Halvade Somatic supports variant calling from both whole-genome sequencing and whole-exome sequencing data and also supports Strelka2 as an alternative or complementary variant calling tool. We provide a Docker image to facilitate single-node deployment. Halvade Somatic can be executed on a variety of compute platforms, including Amazon EC2 and Google Cloud.

Conclusions

To our knowledge, Halvade Somatic is the first somatic variant calling pipeline that leverages Big Data processing platforms and provides reliable, scalable performance. Source code is freely available.
High Degree of Practice Variability in Colonic Dysplasia Surveillance for Patients With Inflammatory Bowel Disease
Authors: Lewis James D , Cross Raymond K , Long Millie , Singh Siddharth , Herfarth Hans , Weiss Alexandra , Buchner Anna
Published: January 2022

Lay Summary

Dysplasia surveillance practice varies widely among high-volume inflammatory bowel disease providers. We surveyed high-volume inflammatory bowel disease providers about practice patterns to detect dysplasia. Regular use of dye-based chromoendoscopy was reported by 20%, virtual chromoendoscopy by 27%, and random biopsies by 58%.