bluuebunny/crossref_metadata_2025 huggingface dataset:
Research and application of stochastic resonance in quad-stable potential system
Authors: He Li-Fang , Liu Qiu-Ling , Zhang Tian-Qi
Published: December 2021

To solve the problem of low weak signal enhancement performance in the quad-stable system, a new quad-stable potential stochastic resonance (QSR) is proposed. Firstly, under the condition of adiabatic approximation theory, the stationary probability distribution (SPD), the mean first passage time (MFPT), the work (W), and the power spectrum amplification factor (SAF) are derived, and the impacts of system parameters on them are also extensively analyzed. Secondly, numerical simulations are performed to compare QSR with the classical Tri-stable stochastic resonance (CTSR) by using the genetic algorithm (GA) and the fourth-order Runge–Kutta algorithm. It shows that the signal-to-noise ratio (SNR) and mean signal-to-noise increase (MSNRI) of QSR are higher than CTSR, which indicates that QSR has superior noise immunity than CTSR. Finally, the two systems are applied in the detection of real bearing faults. The experimental results show that QSR is superior to CTSR, which provides a better theoretical significance and reference value for practical engineering application.
Beating standard quantum limit via two-axis magnetic susceptibility measurement
Authors: Wang Zheng-An , Peng Yi , Yu Dapeng , Fan Heng
Published: December 2021

We report a metrology scheme which measures the magnetic susceptibility of an atomic spin ensemble along the x and z directions and produces parameter estimation with precision beating the standard quantum limit. The atomic ensemble is initialized via one-axis spin squeezing with optimized squeezing time and parameter ϕ (to be estimated) assumed as uniformly distributed between 0 and 2π while fixed in each estimation. One estimation of ϕ can be produced with every two magnetic susceptibility data measured along the two axes respectively, which has an imprecision scaling (1.43 ± 0.02)/N
0.687±0.003 with respect to the number N of the atomic spins. The measurement scheme is easy to implement and is robust against the measurement fluctuation caused by environment noise and measurement defects.
Tri-hexagonal charge order in kagome metal CsV3Sb5 revealed by 121Sb nuclear quadrupole resonance
Authors: Mu Chao , Yin Qiangwei , Tu Zhijun , Gong Chunsheng , Zheng Ping , Lei Hechang , Li Zheng , Luo Jianlin
Published: December 2021

We report 121Sb nuclear quadrupole resonance (NQR) measurements on kagome superconductor CsV3Sb5 with T
c = 2.5 K. 121Sb NQR spectra split after a charge density wave (CDW) transition at 94 K, which demonstrates a commensurate CDW state. The coexistence of the high temperature phase and the CDW phase between 91 K and 94 K manifests that it is a first order phase transition. The CDW order exhibits tri-hexagonal deformation with a lateral shift between the adjacent kagome layers, which is consistent with 2 × 2 × 2 superlattice modulation. The superconducting state coexists with CDW order and shows a conventional s-wave behavior in the bulk state.
How to realize an ultrafast electron diffraction experiment with a terahertz pump: A theoretical study
Authors: Wang Dan , Wang Xuan , Liao Guoqian , Zhang Zhe , Li Yutong
Published: December 2021

To integrate a terahertz pump into an ultrafast electron diffraction (UED) experiment has attracted much attention due to its potential to initiate and detect the structural dynamics both directly. However, the deflection of the electron probe by the electromagnetic field of the terahertz pump alters the incident angle of the electron probe on the sample, impeding it from recording structural information afterwards. In this article, we studied this issue by a theoretical simulation of the terahertz-induced deflection effect on the electron probe, and came up with several possible schemes to reduce such effect. As a result, a terahertz-pump-electron-probe UED experiment with a temporal resolution comparable to the terahertz period is realized. We also found that MeV UED was more suitable for such terahertz pump experiment.
Assessing the effect of hydrogen on the electronic properties of 4H-SiC
Authors: Huang Yuanchao , Wang Rong , Zhang Yiqiang , Yang Deren , Pi Xiaodong
Published: December 2021

As a common impurity in 4H silicon carbide (4H-SiC), hydrogen (H) may play a role in tuning the electronic properties of 4H-SiC. In this work, we systemically explore the effect of H on the electronic properties of both n-type and p-type 4H-SiC. The passivation of H on intrinsic defects such as carbon vacancies (VC) and silicon vacancies (VSi) in 4H-SiC is also evaluated. We find that interstitial H at the bonding center of the Si–C bond (

H
i

bc

) and interstitial H at the tetrahedral center of Si (

H
i

Si
−
te

) dominate the defect configurations of H in p-type and n-type 4H-SiC, respectively. In n-type 4H-SiC, the compensation of

H
i

Si
−
te

is found to pin the Fermi energy and hinder the increase of the electron concentration for highly N-doped 4H-SiC. The compensation of

H
i

bc

is negligible compared to that of VC on the p-type doping of Al-doped 4H-SiC. We further examine whether H can passivate VC and improve the carrier lifetime in 4H-SiC. It turns out that nonequilibrium passivation of VC by H is effective to eliminate the defect states of VC, which enhances the carrier lifetime of moderately doped 4H-SiC. Regarding the quantum-qubit applications of 4H-SiC, we find that H can readily passivate VSi during the creation of VSi centers. Thermal annealing is needed to decompose the resulting VSi–nH (n = 1–4) complexes and promote the uniformity of the photoluminescence of VSi arrays in 4H-SiC. The current work may inspire the impurity engineering of H in 4H-SiC.
Structural and thermodynamic properties of inhomogeneous fluids in rectangular corrugated nano-pores
Authors: Kang Yanshuang , Wang Haijun , Sun Zongli
Published: December 2021

Based on the free-energy average method, an area-weighted effective potential is derived for rectangular corrugated nano-pore. With the obtained potential, classical density functional theory is employed to investigate the structural and thermodynamic properties of confined Lennard–Jones fluid in rectangular corrugated slit pores. Firstly, influence of pore geometry on the adsorptive potential is calculated and analyzed. Further, thermodynamic properties including excess adsorption, solvation force, surface free energy and thermodynamic response functions are systematically investigated. It is found that pore geometry can largely modulate the structure of the confined fluids, which in turn influences other thermodynamic properties. In addition, the results show that different geometric elements have different influences on the confined fluids. The work provides an effective route to investigate the effect of roughness on confined fluids. It is expected to shed light on further understanding about interfacial phenomena near rough walls, and then provide useful clues for the design and characterization of novel materials.
Remembering Fritz Haake
Authors: Berry Michael V
Published: December 2021

Remarks at Conference in Memory of Fritz Haake, Bad Honnef , September 2021
Characteristics of nanopores in terrestrial low-maturity shale based on organic-inorganic interactions: A case study on the Shahejie Formation shale in the southern Bohai Bay Basin, Eastern China
Authors: Deliang Fu , Lina Sun , Guosheng Xu , Haoran Liang , Chen Zhang , Kefei Chen , Tao Tian , Fu Yang
Published: December 2021

In this study, the influence of organic matter and inorganic matter on the pore structure of the Shahejie Formation (E2-3S) shale in the Bohai Bay Basin, was analysed. The pore characteristics, including the BET surface area, BJH adsorption cumulative volume and average pore diameter of the original samples, extracted samples, H2O2-treated samples and kerogen samples, were analysed with low-pressure N2 adsorption experiment. The study showed that the soluble organic matter in low-maturity shale blocked a certain number of pores, which mainly had pore sizes below 5 nm. The solid organic matter mainly formed pore diameters of 1-2 nm and pore diameters larger than 10 nm. A large amount inorganic pore diameter in the ranges of less than 0.8 nm, 1-2 nm, and 2.3-20 nm was blocked by solid organic matter. The micropores formed by minerals were much more abundant than those formed by organic matter in the terrestrial low-maturity shale. The symbiotic relationship between the minerals and the organic matter led to a decrease in the specific surface area and pore volume of the terrestrial low-maturity shale.
Sustainability Group Status Analysis and The Role of Institution of Farmer Groups on The Income of Group Members
Authors: Sulaksana J , Dwirayani D
Published: December 2021

This research was conducted to find out how good institutional management and the benefits felt by members by joining farmer groups. The method used in this research is mix method and multiple regression analysis. The results showed that (1) the group had good institutional strength based on the process of group formation; (2) The group has a high institutional sustainability status which shows that the institutional management in the group has run well; (3) There are some factors that have influence to the group sustainability, namely member motivation, group leadership, knowledge of member, access to information, role of village apparatus, and role of member. The most influencer is access to information; (4)The group has a role in helping to solve farming problems, easy access to information, markets, technology and capital as well as resource efficiency and (5) Revenues received by the group in 2019 amounting to Rp. 785,497.5 / 100 kg of input with an R / C ratio of 1, 85 which means the coffee processing business is profitable and can continue to run.
Community participation form and level in the development of Geotourism in Wonocolo Village, Bojonegoro Regency
Authors: Idajati H , Calyandra A F , Nurliyana F U
Published: December 2021

Wonocolo Village is a village in Bojonegoro Regency with geology-based tourism potentials under development, i.e., Geopark Wonocolo, or commonly known as Teksas Wonocolo based on Bojonegoro Tourism Development Master Plan 2019-2034. Besides, this village has pokdarwis (tourism conscious group) as the tourism developer and manager in Wonocolo Village. However, under its development, several problems still exist. One of which is the constant local community participation condition because most of the community has not seen the potential. Also, the offered attractions are monotonous, e.g., it only has a tour guide and education activities in the Geopark museum. This study aimed to identify community participation forms and levels in Wonocolo Village concerning geotourism development. In determining community participation forms and levels, the qualitative descriptive analysis technique was used by involving stakeholders, which has been predetermined as respondents that consisted of governments, private sector, public sector, and the community. Based on the study results, community participation forms and levels were discovered.
Slope stability assessment and landslide vulnerability mapping of the Institut Teknologi Kalimantan area
Authors: Apriani D W , Mustofa U , Azhary M
Published: December 2021

Slope stability analysis was carried out in the Institut Teknologi Kalimantan which is an area with educational facilities that have a high risk of soil movement. The research area consists of slopes that often reported landslides, especially during the rains time. Evaluation is carried out to the important factors that affect slope stability such as slope geometry consist of 23 zones, soil parameters consist of 7 drilling holes, and past landslide occurrence. Slope stability was evaluated using back analysis based on soil parameters under critical conditions and field investigation and slope geometry using SLOPE/W software to obtain the safety factor (SF) of a certain slope. Landslide vulnerability maps are created based on the risk and potential landslide or landslide occurrence. Based on the results of the stability analysis, there are 6 zones with unstable conditions and a high potential for landslides and 4 zones in critical conditions with moderate landslide potential. The modeling also shows that in the same soil parameter value with a steep slope, the value of the safety factor is getting smaller. This means that the potential for soil movement is greater. Besides, the loading at the top of the slope also causes a reduced safety factor.
Modeling the effectiveness of the PSBB based on COVID-19 case in Greater Surabaya Area
Authors: Santoso E B , Siswanto V K , Umilia E , Syafitri R A W D , Desiana T A
Published: December 2021

East Java province with high mobility has a high case fatality rate of COVID-19. The core spread of COVID-19 is from the Greater Surabaya area following Surabaya, Sidoarjo, and Gresik districts. The East Java Government through Regulation No.18/2020 imposed a Large-Scale Social Restriction (PSBB) that is intended to support the effectiveness of the physical distancing strategy in addressing the emergency status of the COVID-19. But no official report has been found on the effectiveness of PSBB. Therefore, it is necessary to evaluate the effectiveness of PSBB, especially in Greater Surabaya. This research aims to know the model of PSBB policy to minimize the spread of COVID-19 in the greater Surabaya. The study focused on health facility (ventilator, ICU, non-ICU), population, case over a certain period, and positive case in care. This study analyzes the distribution pattern and models the effectiveness of PSBB against the spread of COVID-19 in Greater Surabaya. The data analysis used the COVID-19 Surge-CDC Model. The result of the research shows that the condition of COVID-19 cases increased significantly in the model without intervention. The sharp increase in cases is related to the anticipation of other policies related to the ability of regions to provide health facilities.
Identification of environmental conditions based on the carrying capacity and holding capacity analysis (case study: Kecamatan Barat, Magetan)
Authors: Idajati H , Umilia E , Nurliyana F U , Sianturi R
Published: December 2021

A rapid increase in population and unsustainable land use changes that are not following its capability are likely to lead to severe urban problems. An analysis of the carrying capacity and holding capacity of the environment is needed to determine whether lands can sustain the increasing population. The present research aims to identify the environmental conditions of the Kecamatan Barat based on the carrying capacity and holding capacity of land, water, and demography. Further, an overlay analysis is used to understand the overall carrying capacity level of the sub-district. Qualitative descriptive analysis is used to elaborate the study results. Two villages have deficits in the carrying capacity and capacity of land in West District in 2020, including Purwodadi and Tebon. Six villages are experiencing a water deficit in 2020, including Purwodadi, Karangsono, Bogorejo, Tebon, Manjung, and Mangge. All villages in Kecamatan Barat are still able to accommodate the projected population increase until 2042. The overlay of land, water, and demographic carrying capacity and water holding capacity shows 8, 4, and 2 villages with very high, high, and low overall carrying capacity values.
Development of set covering model for determining the open /closed facilities location and resizing capacity of fasilities
Authors: Linarti Utaminingsih , Fatonah Cahaya Annisa’ , Purwani Annie
Published: December 2021

Set Covering model determines the location of facilities that can be used that minimize the cost of assigning facilities to the point of request with the limitation that each facility was used for a number points of request. If there is an imbalance between the volume of demand points and the capacity of the facilities, it is necessary to open/closed facilities. In fact, facility location problem can extended for the decision not only open/closed but rezising area the existing facilities that can be adjusted considering the avaibility area of facilities location and demand points. This case has not been accommodated on the basic model of set covering. Not all the existing facilities can be resized. Rezising the area of facility location was assumed discrete. The aims of this study was optimized the alghorithm of set covering model. The solution this study was devided into two stages. The first stage was screening facilities that can be resized with survey location. The second stage was set covering model which the facilities will be close/opened and resize the existing facilities.
RETRACTED: Electrical and structural properties of pure and self-defected Bi1/2Na1/2TiO3 system: A DFT study
Authors: Lam Vu Tien
Published: December 2021

The structural and electronic properties of the rhombohedral phase of the A-site-substituted perovskite Sodium bismuth titanate Bi1/2Na1/2TiO3 (BNT) were investigated via the density functional theory (DFT) that implemented in the CASTEP module in the Materials Studio software. I also investigated the impacts of atoms vacancy and oxygen-dopants on dielectric, electrical conductivity, and ferroelectric properties. The author expected that the defected on lead-free ferroelectric materials could extend the functional materials for innovative electronic applications.
Freestanding multi-gate IZO-based neuromorphic transistors on composite electrolyte membranes
Authors: Wang Xiangjing , Zhu Li , Chen Chunsheng , Mao Huiwu , Zhu Yixin , Zhu Ying , Yang Yang , Wan Changjin , Wan Qing
Published: December 2021

Brain-inspired neuromorphic computing would bring a breakthrough to the classical computing paradigm through its massive parallelism and potential low power consumption advantages. Introduction of flexibility may bring vitality to this area by expanding its application areas to such as wearable and implantable electronics. At present, the development of flexible neuromorphic devices makes it a choice with wide prospect for next-generation wearable artificial neuromorphic computing. In this study, a freestanding graphene oxide/polyvinyl alcohol composite solid electrolyte membrane is utilized as the gate dielectric and support material, and indium-zinc-oxide (IZO) neuromorphic transistors are fabricated on such membrane. Based on the in-plane gate modulation, many key synaptic plasticity behaviors have been successfully emulated, including excitatory postsynaptic current, paired-pulse facilitation, high-pass filtering, and spatiotemporal signal processing. Moreover, transition of the spiking logic and the superlinear and sublinear dendritic integration function are realized. Our results indicate that these freestanding IZO-based neuromorphic transistors may of great significance for future flexible anthropomorphic robots, wearable bionic perception.
Ten-year mortality and long-term visual acuity outcomes in patients with exudative age-related macular degeneration treated with intravitreal anti-vascular endothelial growth factor injections
Authors: Young Su Ling , Anderson Martin J , Borooah Shyamanga , Armbrecht Ana-Maria , Cackett Peter D
Published: December 2021

Purpose

There are limited real-world data on long-term mortality and visual outcomes in patients treated with anti-vascular endothelial growth factor (VEGF) for exudative age-related macular degeneration (exudative AMD). We assessed 10-year mortality and clinical outcomes in exudative AMD patients treated with intravitreal therapy (IVT) anti-VEGF injections on a pro-re-nata (PRN) regime following a standard loading regime.

Methods

Retrospective cohort study of the first 216 exudative AMD patients receiving IVT anti-VEGF for exudative AMD at a public tertiary referral hospital in Scotland. Main outcome measures were mortality, cause of death and best-corrected visual acuity (BCVA).

Results

A total of 216 patients were included. Mean age at presentation was 79.1 years [standard deviation (SD) 6.9]. Mean follow-up duration was 6.6 years (SD 3.2) during which there was a mean 24.3 Early Treatment Diabetic Retinopathy Study (ETDRS) letter loss in BCVA (P < 0.0001). Patients received a mean of 2.2 (SD 1.8) injections per year of follow-up. Overall, 52.6% (113/216) died during the period studied. Observed annual mortality incidence risk was 6.5% (SD 3.1) and was found to be significantly lower (P = 0.0064) than the expected annual death incidence risk (9.6%, SD 1.5) based on age and sex standardised Scottish mortality risk. The most common causes of death were malignancies (21.3%) and infection (20.0%).

Conclusions

This study highlights the relatively good long-term prognosis in vision and mortality in exudative AMD treated with a PRN regime in the real world. Although the majority lost vision, the rate of decline was significantly slower than that which would have been experienced in the pre-anti-VEGF era and reassuringly standardised mortality risk was lower than the national average.
Writing Accessible Theory in Ecology and Evolution: Insights from Cognitive Load Theory
Authors: Ou William J-A , Henriques Gil J B , Senthilnathan Athmanathan , Ke Po-Ju , Grainger Tess N , Germain Rachel M
Published: December 2021

Theories underpin science. In biology, theories are often formalized in the form of mathematical models, which may render them inaccessible to those lacking mathematical training. In the present article, we consider how theories could be presented to better aid understanding. We provide concrete recommendations inspired by cognitive load theory, a branch of psychology that addresses impediments to knowledge acquisition. We classify these recommendations into two classes: those that increase the links between new and existing information and those that reduce unnecessary or irrelevant complexities. For each, we provide concrete examples to illustrate the scenarios in which they apply. By enhancing a reader's familiarity with the material, these recommendations lower the mental capacity required to learn new information. Our hope is that these recommendations can provide a pathway for theoreticians to increase the accessibility of their work and for empiricists to engage with theory, strengthening the feedback between theory and experimentation.
Metabolic correlates of late midlife cognitive outcomes: findings from the 1946 British Birth Cohort
Authors: Green Rebecca , Lord Jodie , Xu Jin , Maddock Jane , Kim Min , Dobson Richard , Legido-Quigley Cristina , Wong Andrew , Richards Marcus , Proitsi Petroula
Published: December 2021

Investigating associations between metabolites and late midlife cognitive function could reveal potential markers and mechanisms relevant to early dementia. Here, we systematically explored the metabolic correlates of cognitive outcomes measured across the seventh decade of life, while untangling influencing life course factors. Using levels of 1019 metabolites profiled by liquid chromatography–mass spectrometry (age 60–64), we evaluated relationships between metabolites and cognitive outcomes in the British 1946 Birth Cohort (N = 1740). We additionally conducted pathway and network analyses to allow for greater insight into potential mechanisms, and sequentially adjusted for life course factors across four models, including sex and blood collection (Model 1), Model 1 + body mass index and lipid medication (Model 2), Model 2 + social factors and childhood cognition (Model 3) and Model 3 + lifestyle influences (Model 4). After adjusting for multiple tests, 155 metabolites, 10 pathways and 5 network modules were associated with cognitive outcomes. Of the 155, 35 metabolites were highly connected in their network module (termed ‘hub’ metabolites), presenting as promising marker candidates. Notably, we report relationships between a module comprised of acylcarnitines and processing speed which remained robust to life course adjustment, revealing palmitoylcarnitine (C16) as a hub (Model 4: β = −0.10, 95% confidence interval = −0.15 to −0.052, P = 5.99 × 10−5). Most associations were sensitive to adjustment for social factors and childhood cognition; in the final model, four metabolites remained after multiple testing correction, and 80 at P < 0.05. Two modules demonstrated associations that were partly or largely attenuated by life course factors: one enriched in modified nucleosides and amino acids (overall attenuation = 39.2–55.5%), and another in vitamin A and C metabolites (overall attenuation = 68.6–92.6%). Our other findings, including a module enriched in sphingolipid pathways, were entirely explained by life course factors, particularly childhood cognition and education. Using a large birth cohort study with information across the life course, we highlighted potential metabolic mechanisms associated with cognitive function in late midlife, suggesting marker candidates and life course relationships for further study.
Progressive increase of high-frequency EEG oscillations during meditation is associated with its trait effects on heart rate and proteomics: a study on the Tibetan Buddhist
Authors: Guo Xiaoli , Wang Meiyun , Wang Xu , Guo Menglin , Xue Ting , Wang Zhuo , Li Han , Xu Tianjiao , He Bin , Cui Donghong , Tong Shanbao
Published: December 2021

Meditation has been a spiritual and healing practice in the East for thousands of years. However, the neurophysiologic mechanisms underlying its traditional form remain unclear. In this study, we recruited a large sample of monks (n = 73) who practice Tibetan Buddhist meditation and compared with meditation-naive local controls (n = 30). Their electroencephalography (EEG) and electrocardiogram signals were simultaneously recorded and blood samples were collected to investigate the integrative effects of Tibetan Buddhist on brain, heart, and proteomics. We found that the EEG activities in monks shifted to a higher frequency from resting to meditation. Meditation starts with decrease of the (pre)frontal delta activity and increase of the (pre)frontal high beta and gamma activity; while at the deep meditative state, the posterior high-frequency activity was also increased, and could be specified as a biomarker for the deep meditation. The state increase of posterior high-frequency EEG activity was significantly correlated with the trait effects on heart rate and nueropilin-1 in monks, with the source of brain–heart correlation mainly locating in the attention and emotion networks. Our study revealed that the effects of Tibetan Buddhist meditation on brain, heart, and proteomics were highly correlated, demonstrating meditation as an integrative body–mind training.
An update of proliferative glomerulonephritis with monoclonal immunoglobulin deposits
Authors: Li Manna , Xu Gaosi
Published: December 2021

As aging increases, monoclonal gammopathy is becoming more common and monoclonal gammopathy of renal significance (MGRS) is gaining attention due to frequent renal involvement. Within MGRS, proliferative glomerulonephritis with monoclonal immunoglobulin deposits (PGNMID) is a special category. The disease was first described in 2004 and the research history on it is relatively short. Compared with other MGRS, the detection rate of circulating clones is lower in patients with PGNMID, which is easy to miss and misdiagnose in clinical work. In this review, the etiology and clinical features of PGNMID are discussed. It is noted that PGNMID is associated not only with MGRS, but also with malignancy, infection and other factors. PGNMID is not a disease exclusive to the elderly—young people can also develop this disease. Due to the low detection rate of circulating clones in most patients, confirmation of the disease needs to be combined with renal pathology, which emphasizes the importance of completing light and heavy chain subtype staining. Treatment options for patients with PGNMID differ by etiology. For MGRS-associated PGNMID, the current treatment is primarily empirical and more research evidence is needed to fill the treatment gap.
National Kidney Foundation Laboratory Engagement Working Group Recommendations for Implementing the CKD-EPI 2021 Race-Free Equations for Estimated Glomerular Filtration Rate: Practical Guidance for Clinical Laboratories
Authors: Miller W Greg , Kaufman Harvey W , Levey Andrew S , Straseski Joely A , Wilhelms Kelly W , Yu Hoi Ying (Elsie) , Klutts J Stacey , Hilborne Lee H , Horowitz Gary L , Lieske John , Ennis Jennifer L , Bowling James L , Lewis Mary Jane , Montgomery Elizabeth , Vassalotti Joseph A , Inker Lesley A
Published: December 2021

Recognizing that race is a social and not a biological construct, healthcare professionals and the public have called for removal of race in clinical algorithms. In response, the National Kidney Foundation and the American Society of Nephrology created the Task Force on Reassessing the Inclusion of Race in Diagnosing Kidney Diseases to examine the issue and provide recommendations. The final report from the Task Force recommends calculating estimated glomerular filtration rate (eGFR) without a race coefficient using the recently published CKD-EPI 2021 creatinine (cr) and creatinine-cystatin C (cr-cys) equations. The Task Force recommends immediately replacing older eGFRcr equations (MDRD Study and CKD-EPI 2009) with the new CKD-EPI 2021 equation. In a 2019 survey by the College of American Pathologists, 23% of 6200 laboratories reporting eGFRcr used an incorrect equation that is not suitable for use with standardized creatinine measurements, 34% used the CKD-EPI 2009 equation and 43% used the MDRD Study 2006 equation re-expressed for standardized creatinine measurement. Rapid transition to using the CKD-EPI 2021 equation is an opportunity for laboratories to standardize to a single equation to eliminate differences in eGFRcr due to different equations used by different laboratories, and to report eGFR without use of race. We provide guidance to laboratories for implementing the CKD-EPI 2021 equations for both eGFRcr and eGFRcr-cys.
Cardiac arrest as first presentation of arrhythmogenic left ventricular cardiomyopathy due to Filamin C mutation: a case report
Authors: Kandhari Navneet , Khoury Shafik , Behr Elijah R , Miles Chris
Published: December 2021

Background

Arrhythmogenic left ventricular cardiomyopathy (ALVC) is a rare form of arrhythmogenic cardiomyopathy characterized by fibrofatty replacement of left ventricular myocardium, malignant arrhythmia, and sudden cardiac death. The definition incorporates several genetic causes, including pathogenic variation in the Filamin C gene (FLNC). Although awareness of ALVC has improved, identification remains challenging and diagnostic criteria continue to evolve.

Case summary

A 50-year-old athletic male was admitted following an out-of-hospital cardiac arrest due to ventricular tachycardia (VT) whilst playing football. Coronary angiography revealed unobstructed epicardial vessels and the diagnosis of ALVC was suggested by cardiovascular magnetic resonance imaging, which demonstrated a mildly dilated and moderately impaired left ventricle with epicardial late gadolinium enhancement in the basal to mid-lateral walls and subendocardial septum. Initial testing with a cardiomyopathy and arrhythmia gene panel was negative but extended testing uncovered a likely pathogenic variant in FLNC. Subsequently, the patient experienced a recurrence of sustained VT necessitating implantable cardioverter-defibrillator (ICD) therapies, ultimately undergoing a combined epicardial and endocardial VT ablation 4 years after presentation. Six months post-ablation, he was asymptomatic and his arrhythmia rendered quiescent.

Discussion

Arrhythmogenic cardiomyopathy should be considered in the evaluation of an initially unexplained cardiac arrest. This case characterizes the clinical features of a patient with FLNC cardiomyopathy and emphasizes the utility of genetic testing using modern gene panels in patients with comparable phenotypes. We also demonstrate that optimal medical therapy with antiarrhythmic drugs, exercise restriction, ICD insertion, and catheter ablation can be useful in the management of ALVC with positive outcomes
Predictors of non-participation in a cardiac telerehabilitation programme: a prospective analysis
Authors: Brouwers Rutger Willem Maurice , Brini Alberto , Kuijpers Robin Wilhelmus Franciscus Henricus , Kraal Jozua Johannes , Kemps Hareld Marijn Clemens
Published: December 2021

Aims 

Current cardiac telerehabilitation (CTR) interventions are insufficiently tailored to the preferences and competences of individual patients, which raises the question whether their implementation will increase overall participation and adherence to cardiac rehabilitation (CR). However, research on patient-specific factors that influence participation and adoption of CTR interventions is scarce. The aim of this study was to evaluate which patient-related characteristics influence participation in a novel CTR intervention in patients with coronary artery disease.

Methods and results 

This prospective observational substudy of the SmartCare-CAD randomized controlled trial evaluated patient characteristics of study participants as proxy for participation in a CTR intervention. We compared demographic, geographic, and health-related characteristics between trial participants and non-participants to determine which characteristics influenced trial participation. A total of 699 patients (300 participants and 399 non-participants; 84% male, mean age 64.3 ± 10.5 years) were included. Most of the non-participants refused participation because of insufficient technical skills or lack of interest in digital health (26%), or preferred centre-based CR (21%). Variables independently associated with non-participation included: higher age, lower educational level, shorter travelling distance, smoking, positive family history for cardiovascular disease, having undergone coronary artery bypass grafting; and a higher blood pressure, worse exercise capacity, and higher risk of depression before the start of CR.

Conclusion

Participation in CTR is strongly influenced by demographic and health-related factors such as age, educational level, smoking status, and both physical and mental functioning. Cardiac telerehabilitation interventions should therefore be redesigned with the involvement of these currently underrepresented patient subgroups.
No Evidence That Genetic Variation at the Klotho Locus Is Associated With Longevity in Caucasians from the Newcastle 85+ Study and the UK Biobank
Authors: Amin Hasnat A , Cordell Heather J , Martin-Ruiz Carmen , Robinson Louise , Kirkwood Tom , Blakemore Alexandra I , Drenos Fotios
Published: December 2021

The demographics of Western populations are changing, with an increase in the proportion of older adults. There is evidence to suggest that genetic factors may influence the aging process: studying these may lead to interventions to help individuals live a longer and healthier life. Evidence from several groups indicates that Klotho (KL), a gene encoding a single-pass transmembrane protein that acts as an FGF23 co-receptor, may be associated with longevity and healthy aging. We aimed to explore this area further by comparing the genotype counts in 642 long-lived individuals from the Newcastle 85+ Study with 18 295 middle-aged Newcastle-based controls from the UK Biobank to test whether variants at the KL gene locus are over- or under-represented in older individuals. If KL is associated with longevity, then we would expect the genotype counts to differ between the 2 cohorts. We found that the rs2283368 CC genotype and the rs9536338 C allele, but not the KL-VS haplotype, were associated with reaching very old age. However, these associations did not replicate in the remainder of the UK Biobank cohort. Thus, our results do not reliably support the role of KL as a longevity factor.
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects
Authors: Sheffield Nathan C , Stolarczyk Michał , Reuter Vincent P , Rendeiro André F
Published: December 2021

Background

Organizing and annotating biological sample data is critical in data-intensive bioinformatics. Unfortunately, metadata formats from a data provider are often incompatible with requirements of a processing tool. There is no broadly accepted standard to organize metadata across biological projects and bioinformatics tools, restricting the portability and reusability of both annotated datasets and analysis software.

Results

To address this, we present the Portable Encapsulated Project (PEP) specification, a formal specification for biological sample metadata structure. The PEP specification accommodates typical features of data-intensive bioinformatics projects with many biological samples. In addition to standardization, the PEP specification provides descriptors and modifiers for project-level and sample-level metadata, which improve portability across both computing environments and data processing tools. PEPs include a schema validator framework, allowing formal definition of required metadata attributes for data analysis broadly. We have implemented packages for reading PEPs in both Python and R to provide a language-agnostic interface for organizing project metadata.

Conclusions

The PEP specification is an important step toward unifying data annotation and processing tools in data-intensive biological research projects. Links to tools and documentation are available at http://pep.databio.org/.
A high-throughput multiplexing and selection strategy to complete bacterial genomes
Authors: Arredondo-Alonso Sergio , Pöntinen Anna K , Cléon François , Gladstone Rebecca A , Schürch Anita C , Johnsen Pål J , Samuelsen Ørjan , Corander Jukka
Published: December 2021

Background

Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections.

Results

Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library.

Conclusions

The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
Long-term Disease Behavior and Surgical Intervention Analysis in Hospitalized Patients With Crohn’s Disease in China: A Retrospective Cohort Study
Authors: Bai Xiaoyin , Zhang Huimin , Ruan Gechong , Lv Hong , Li Yue , Li Ji , Tan Bei , Zheng Weiyang , Jin Meng , Xu Hui , Yang Hong , Qian Jiaming
Published: December 2021

Background

There is lack of real-world data for disease behavior and surgery of Crohn’s disease (CD) from large-scale Chinese cohorts.

Methods

Hospitalized patients diagnosed with CD in our center were consecutively included from January 2000 to December 2018. Disease behavior progression was defined as the initial classification of B1 to the progression of B2 or B3. Clinical characteristics including demographics, disease classification and activity, medical therapy, development of cancers, and death were collected.

Results

Overall, 504 patients were included. Two hundred thirty-one (45.8%) patients were initially classified as B1; 30 (13.0%), 71 (30.7%), and 95 (41.1%) of them had disease progression at the 1-year follow-up, 5-year follow-up, and overall, respectively. Patients without location transition before behavior transition were less likely to experience behavior progression. However, patients without previous exposure to a corticosteroid, immunomodulator, or biological agent had a greater chance of experiencing behavior progression. When the long-term prognosis was evaluated, 211 (41.9%) patients underwent at least 1 CD-related surgery; 108 (21.4%) and 120 (23.8%) of these patients underwent surgery before and after their diagnosis, respectively. An initial classification as B1, no behavior transition, no surgery prior to diagnosis, and previous corticosteroid exposure during follow-up were associated with a lower risk of undergoing surgery.

Conclusions

This study depicts the clinical features and factors associated with behavior progression and surgery among hospitalized CD patients in a Chinese center. Behavior progression is associated with a higher probability of CD-related surgery, and strengthened therapies are necessary for them in the early phase.
Treatment Decision-making in Chinese Inflammatory Bowel Disease Patients
Authors: Yang Li , Song Xiaomei , Chen Yan , Li Yue , Gu Yubei , Wang Xinying , Zhu Liangru , Zhi Min , Ouyang Chunhui , Guo Hong
Published: December 2021

Background

Inflammatory bowel disease (IBD) is rising in China, and the tendency for lifelong recurrence decreases patients’ quality of life. However, no studies on treatment decision-making in Chinese patients with IBD exist. Thus, this study aimed to determine the actual and ideal decision-making, as well as factors affecting decision-making in Chinese IBD patients.

Methods

A multicenter online questionnaire was distributed among patients diagnosed with IBD. To assess factors that influence treatment decision-making, univariate and multivariate logistic regression analyses were performed.

Results

From March 20, 2018, to May 20, 2018, a total of 866 patients completed the questionnaires, including 222 patients with ulcerative colitis, 588 patients with Crohn’s disease, and 56 patients with unclassified IBD. There was a significant difference between ideal and actual decision-making in Chinese IBD patients (P < .005). The factors affecting ideal decision-making included income, education, illness severity, religiosity, the importance of the treatment decision, the employment situation, and occupation area. The factors affecting actual decision-making included age, illness severity, religiosity, the employment situation, economic anxiety, concern about the side effects, and the importance of the treatment decision.

Conclusions

There is a significant difference between ideal and actual decision-making in IBD patients in China. That is, the economy, religiosity, illness severity, and concern about the side effects of treatment are the most important factors affecting treatment decisions in Chinese IBD patients.
Maternal respiratory health and intrauterine exposure-driven birthweight: a two-sample Mendelian randomization study
Authors: He Baoting , Kwok Man Ki , Chan Io Ieong , Schooling C Mary
Published: December 2021

Background

Observationally, poorer maternal respiratory health is associated with poorer birth outcomes, possibly confounded by socioeconomic position and other maternal attributes. We used multivariable Mendelian randomization (MR) to obtain unconfounded estimates of effect of maternal lung function on birthweight, independent of maternal height.

Methods

Single nucleotide polymorphisms (SNPs) for forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) in women were obtained from publicly available summary statistics from the UK Biobank. SNPs for asthma were obtained from the Trans-National Asthma Genetic consortium. SNPs for height in women were obtained from the Genetic Investigation of Anthropometric Traits consortium and the genetic estimates were obtained the UK Biobank. The genetic associations with maternally-driven birthweight were obtained from the Early Growth Genetics consortium. Multivariable MR estimates were obtained using inverse variance weighting with multivariable MR-Egger as sensitivity analysis.

Results

Maternal lung capacity, as indicated by FVC, was positively associated with maternally-driven birthweight (0.08 per standard deviation, 95% confidence interval 0.01 to 0.15) independent of maternal height, whereas no clear such associations were shown for maternal airway function, indicated by FEV1 and peak expiratory flow, or for asthma, on maternally-driven birthweight. Similar findings were shown using MR-Egger.

Conclusions

These findings suggest that maternal lung function, especially lung capacity independent of maternal height, is directly associated with maternally-driven birthweight, and highlights the importance of maternal respiratory health in fetal growth.
Soybean-BioCro: a semi-mechanistic model of soybean growth
Authors: Matthews Megan L , Marshall-Colón Amy , McGrath Justin M , Lochocki Edward B , Long Stephen P
Published: December 2021

Soybean is a major global source of protein and oil. Understanding how soybean crops will respond to the changing climate and identifying the responsible molecular machinery are important for facilitating bioengineering and breeding to meet the growing global food demand. The BioCro family of crop models are semi-mechanistic models scaling from biochemistry to whole crop growth and yield. BioCro was previously parameterized and proved effective for the biomass crops Miscanthus, coppice willow and Brazilian sugarcane. Here, we present Soybean-BioCro, the first food crop to be parameterized for BioCro. Two new module sets were incorporated into the BioCro framework describing the rate of soybean development and carbon partitioning and senescence. The model was parameterized using field measurements collected over the 2002 and 2005 growing seasons at the open air [CO2] enrichment (SoyFACE) facility under ambient atmospheric [CO2]. We demonstrate that Soybean-BioCro successfully predicted how elevated [CO2] impacted field-grown soybean growth without a need for re-parameterization, by predicting soybean growth under elevated atmospheric [CO2] during the 2002 and 2005 growing seasons, and under both ambient and elevated [CO2] for the 2004 and 2006 growing seasons. Soybean-BioCro provides a useful foundational framework for incorporating additional primary and secondary metabolic processes or gene regulatory mechanisms that can further aid our understanding of how future soybean growth will be impacted by climate change.