bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating Machine Learning with Parametric Modeling Environments to Predict Building Daylighting Performance
Authors: Labib R
Published: September 2022

Buildings account for 30% of global energy consumption. To support the development of energy-efficient built environments and cities, architects, urban planners, and engineers have begun to utilize building performance simulation (BPS). Supporting decision-making and steering design toward high performance are crucial in the early design phase, when decisions have the biggest impact on the final product’s energy consumption and costs. Architects often assess the energy performance of hundreds of different design solutions and configurations in parametric environments to find the most energy-efficient solution. To adhere to strict project due dates, architects usually shorten the time required for BPS by reducing the number of variables or parameters for the building and facade design. This practice usually results in the elimination of design parameters that could potentially contribute to an energy-optimized design configuration. To achieve time-efficient BPS processes, recent research has focused on developing machine learning (ML) algorithms that can instantly predict the energy performance of buildings. Although ML has demonstrated high levels of accuracy, ML techniques are difficult to implement because they require technical knowledge of programming languages. Furthermore, these ML algorithms were developed as standalone applications, making them inappropriate for geometric modeling environments. This paper introduces a new ML tool that can be easily accessed within Grasshopper, a parametric modeling environment. The proposed tool can instantly predict the daylighting performance of building configurations.
Generating heat demand profiles of neighbourhoods
Authors: Koene F G H , Matthijssen E F , Menkveld M
Published: September 2022

To size future energy infrastructures, that may include energy storage or demand side management, insight in heat demand profiles of neighbourhoods is a prerequisite. TNO developed a tool to generate heat demand profiles. Using public sources, the tool makes an inventory of buildings in the neighbourhood. For each building, a building archetype that most closely resembles it is selected, and its space heating demand profile is simulated using a dynamic resistance capacitance (RC) building model. To this, a repetitive daily profile for domestic hot water (DHW) preparation and cooking is added. The heat demand profile of the neighbourhood is calculated by summing the profiles of buildings in it, taking a dispersion of thermostat times into account. The current version of the tool, which is still under development, was validated by comparing the annual gas consumption of a number of neighbourhoods with actual data. While the tool predicted annual gas consumption of pre-1960 neighbourhoods reasonably well, for more recent neighbourhoods, the tool underestimated the annual gas consumption by typically 30%.
The Dutch energy transition in practice
Authors: Looijen Bader E M , Oostra M A R
Published: September 2022

By 2050, the Netherlands aims to have created a natural gas-free built environment. It aims to do so in a combination of a neighbourhood approach and direct-targeting of owner-occupants. In order to realise this, broad support for the energy transition is required. Current experience shows this is not self-evident. This paper presents an analysis of the current situation in the Dutch energy transition at household level. What do the customer journeys look like that owner-occupants are going through? What barriers do residents experience? What are possible motivators? Aim of the research was to formulate lessons learned on barriers and motivators. There are clear issues emerge from the research that need addressing in order to bring the energy transition forward. Although market segmentation is used as an ingredient to target and service specific groups of residents, experience makes clear segmentation can help in developing different formulas in addressing private homeowners. Not being a panacea, an additional step needs development to facilitate people to take it up in a way that matches their own way, situation and preferences. There are substantial groups of people whose basic Maslow’s needs currently are not met. For these people it is too much to expect them to render their home more sustainable. Finally numerous people did already embark on a customer journey, and never made it to successful interventions to upgrade the energy performance of their house. They got lost along the route, did not get passed known danger zones and proved themselves to be unable to solve all the complex puzzles along the route.
Interactive feedback tool for occupants based on a tuned building energy model
Authors: Vijlbrief O , Mossallam B Eslami , Spiekman M E
Published: September 2022

It is a well-known fact that there is a gap between the theoretical energy performance and the actual energy use of a building. The behaviour of occupants has a large influence on this energy use. Within the BIM4Ren H2020 project we developed a feedback tool for occupants that gives insight in the effect of behaviour on the amount of energy use required for heating and cooling. The tool has a front-end in which the occupant can see their current behaviour, as well as their actual energy use. By changing their initial behaviour virtually, they will get feedback about the effect on their actual energy use. The back-end of the tool contains a reduced order simulation, based on the ISO 52016-1:2017 hourly method to calculate the energy needs. In deviation from the standard, the most important parameters that describe user behaviour are directly obtained from the occupants by a questionnaire. The model is tuned on the real situation using the behavioural data and measurement data. The feedback tool will help occupants understand better why their energy use is higher than expected despite the renovation, or help them save even more energy by educating them on the effect of their behaviour.
Requirements for renovating residential buildings in the Netherlands towards lower temperature supply from district heating.
Authors: Wahi P , Konstantinou T , Tenpierik M , Visscher H
Published: September 2022

In the Netherlands, district heating with a lower temperature supply (<70°C) will play a crucial part in accomplishing the energy transition goals of delivering natural gas-free sustainable heating to dwellings. The existing dwellings often require energy renovations to make them suitable for lower temperature heating. However, choosing renovation strategies that promote the transition to lower temperature district heating while improving energy efficiency and thermal comfort is challenging. This study aims to identify minimum renovation requirements for comfortably heating homes using lower temperature heat from district heating. Identifying minimum renovation strategies to prepare existing dwellings for lower temperature district heating would be vital in addressing the European Renovation Wave’s target of improving worst-performing buildings. For the same, the study uses a typical intermediate terraced house built before 1945 as a case study to investigate renovation strategies based on four levels of renovation intervention (no renovation, basic, moderate and deep). The impact of renovations on space heating demand and thermal comfort was tested with medium (70/50°C) and low supply (55/35°C) temperatures against key performance indicators (KPIs) using dynamic simulation. The study found that for the case study dwelling, moderate renovation strategy of upgrading the building envelope insulation by 0.40 W/m2K for opaque parts and 1.5 W/m2K for glazing, improving the airtightness by 0.3h-1 and replacing existing radiators with LT radiators can be considered as a no-regret solution for comfortably heating homes with both medium and lower temperature supply from district heating.
A new framework for analysing local participation in community energy initiatives
Authors: Teladia A , der Windt H van
Published: September 2022

The Dutch Climate Agreement includes a 50 percent local ownership of energy production target. However, what is meant by “local,” “ownership” and “participation” is not strictly defined in the Agreement. Nevertheless, community energy initiatives are expected to be an integral part of the ‘local ownership’ goals listed in the Agreement. Consequently, there is a need for a robust framework which can capture local nuances, explain the role and degree of citizen participation in different contexts and areas of participation, and that will allow community energy initiatives to benchmark their participation levels in relation to ‘others’ and their own change over time. This paper proposes a new diagnostic framework which conceptualizes participation in the technical, political, and economic dimensions of local energy transitions and that can identify gaps and challenges in community energy initiatives in relation to local participation. We use the Socio-ecological Systems Framework (SESF) as a starting point and enrich the framework’s third and fourth tier variables using Arnstein’s ladder of participation along with other participatory literature. Our framework outlines the key variables for understanding the participatory environment in which participation occurs and links the environment to the levels of participation. The framework provides granularity and flexibility given its multi-tier and decomposable structure. Therefore, supporting gap analysis of local participation and comparison across diverse cases.
Policy instruments for energy-efficient renovations at district level
Authors: Mlecnik E , Hidalgo-Betanzos J M
Published: September 2022

IEA EBC Annex 75 aims to investigate, amongst other policy for reducing carbon emissions and energy use in buildings at district level, combining both energy efficiency measures and renewable energy measures. Particularly policy instruments deployed at the local level targeting owners and investors could increase residential building renovation and renewable energy systems to a district scale. A desk and empirical research using 38 expert interviews from 8 European countries was used to investigate the use and development of various types of policy instruments, including regulations, incentives, communication and facilitating instruments. The research confirms interest of frontrunners to use or develop specific policy instruments further, such as enforcement of energy standards and inspections, financial incentives for district stakeholders and for groups of homeowners, renovation services and energy desks, digital communication and network meetings in districts. It also finds that low relative advantage for some stakeholders, lack of good examples, an incompatible legal or national framework and high complexity are serious risks that can further hinder adoption of energy efficiency and renewable energy systems in districts. Renovations at district scale including energy efficiency and renewable energy can benefit from adapted or improved regulations, incentives, communication and facilitation to better support renovations at district scale including energy efficiency and renewable energy systems.
Chances for the upscaling of living-cost neutral renovations in the Netherlands
Authors: Mlecnik Erwin
Published: September 2022

Many multi-owned condominiums need an energy renovation, but in practice the number of such renovations is low. Dutch policy emphasizes the need to search for cost-neutral renovation solutions. This study therefore examined how the number of living-cost neutral renovations of buildings owned by assemblies of homeowners in the Netherlands can be increased by means of an integrated unburdening offer that includes energy performance guarantees and supply chain integration. The study uses scientific literature, project experiences and in-depth interviews with experts to examine how policy, demand and supply currently play a role in the upscaling of living-cost neutral renovations. The study finds that customized guidance is needed for condominium associations to steer their maintenance decision processes towards deep renovations. Also chances are detected to link living cost neutrality with energy neutrality, while developing an integrated supply chain that takes into account full process guidance including the provision of performance guarantees. This is now already successfully implemented in a new non-profit service desk and a new process model will be tested in multiple regions.
Designing hollow core nested anti-resonant fiber with ultra-low loss using finite difference eigen mode solver
Authors: Chatterjee Sudip K , Kaushalram Archana , Suchita  , Bhardwaj Asha
Published: September 2022

We report an optimized design of six-ring nodeless antiresonant fiber (NARF) in both single and nested ring configurations in the visible wavelength regime. Proposed fibers exhibit a record low loss of 6.7 × 10−4 dB km−1 at 630 nm with less than 1 dB km−1 over a broad 330 nm bandwidth, achieved by the incorporation and optimization of nested elements in the primary cladding tubes. A comprehensive analysis, utilizing finite difference algorithm, to study the role of structural parameters of the hollow core fiber viz. tube thickness and gaps between the tubes on the loss spectrum is also presented. A comparative analysis of NARF designs using tube thickness in different anti-resonant bands is also included. The bend robustness, polarization analysis, dispersion, and fabrication tolerances are investigated. Proposed low-loss fibers in the visible wavelength regime can drastically bring down the cost and complexity of quantum communication systems.
Optically induced changes in the band structure of the Weyl charge-density-wave compound

(TaSe4)2I
Authors: Crepaldi A , Puppin M , Gosálbez-Martínez D , Moreschini L , Cilento F , Berger H , Yazyev O V , Chergui M , Grioni M
Published: September 2022

Collective modes are responsible for the emergence of novel quantum phases in topological materials. In the quasi-one dimensional (1D) Weyl semimetal

(

T
a
S
e

4

)
2

I

, a charge density wave (CDW) opens band gaps at the Weyl points, thus turning the system into an axionic insulator. Melting the CDW would restore the Weyl phase, but 1D fluctuations extend the gapped regime far above the 3D transition temperature (T

C
D
W

= 263 K), thus preventing the investigation of this topological phase transition with conventional spectroscopic methods.

Here we use a non-equilibrium approach: we perturb the CDW phase by photoexcitation, and we monitor the dynamical evolution of the band structure by time- and angle-resolved photoelectron spectroscopy. We find that, upon optical excitation, electrons populate the linearly dispersing states at the Fermi level (E

F

), and fill the CDW gap. The dynamics of both the charge carrier population and the band gap renormalization (BGR) show a fast component with a characteristic time scale of a few hundreds femtoseconds. However, the BGR also exhibits a second slow component on the µs time scale. The combination of an ultrafast response and of persistent changes in the spectral weight at E

F

, and the resulting sensitivity of the linearly dispersing states to optical excitations, may explain the high performances of

(

T
a
S
e

4

)
2

I

as a material for broadband infrared photodetectors.
Electrostatic atomization minimum quantity lubrication machining: from mechanism to application
Authors: Xu Wenhao , Li Changhe , Zhang Yanbin , Ali Hafiz Muhammad , Sharma Shubham , Li Runze , Yang Min , Gao Teng , Liu Mingzheng , Wang Xiaoming , Said Zafar , Liu Xin , Zhou Zongming
Published: September 2022

Metal cutting fluids (MCFs) under flood conditions do not meet the urgent needs of reducing carbon emission. Biolubricant-based minimum quantity lubrication (MQL) is an effective alternative to flood lubrication. However, pneumatic atomization MQL has poor atomization properties, which is detrimental to occupational health. Therefore, electrostatic atomization MQL requires preliminary exploratory studies. However, systematic reviews are lacking in terms of capturing the current research status and development direction of this technology. This study aims to provide a comprehensive review and critical assessment of the existing understanding of electrostatic atomization MQL. This research can be used by scientists to gain insights into the action mechanism, theoretical basis, machining performance, and development direction of this technology. First, the critical equipment, eco-friendly atomization media (biolubricants), and empowering mechanisms of electrostatic atomization MQL are presented. Second, the advanced lubrication and heat transfer mechanisms of biolubricants are revealed by quantitatively comparing MQL with MCF-based wet machining. Third, the distinctive wetting and infiltration mechanisms of electrostatic atomization MQL, combined with its unique empowering mechanism and atomization method, are compared with those of pneumatic atomization MQL. Previous experiments have shown that electrostatic atomization MQL can reduce tool wear by 42.4% in metal cutting and improve the machined surface R
a by 47% compared with pneumatic atomization MQL. Finally, future development directions, including the improvement of the coordination parameters and equipment integration aspects, are proposed.
Preprocedural muscle strength and physical performance and the association with functional decline or mortality in frail older patients after transcatheter aortic valve implementation: a systematic review and meta-analysis
Authors: van Erck Dennis , Dolman Christine D , Limpens Jacqueline , Scholte op Reimer Wilma J M , Henriques José P , Delewi Ronak , Schoufour Josje D
Published: September 2022

Background

A significant number of older patients planned for transcatheter aortic valve implantation (TAVI) experience a decline in physical functioning and death, despite a successful procedure.

Objective

To systematically review the literature on the association of preprocedural muscle strength and physical performance with functional decline or long-term mortality after TAVI.

Methods

We followed the PRISMA guidelines and pre-registered this review at PROSPERO (CRD42020208032). A systematic search was conducted in MEDLINE and EMBASE from inception to 10 December 2021. Studies reporting on the association of preprocedural muscle strength or physical performance with functional decline or long-term (>6 months) mortality after the TAVI procedure were included. For outcomes reported by three or more studies, a meta-analysis was performed.

Results

In total, two studies reporting on functional decline and 29 studies reporting on mortality were included. The association with functional decline was inconclusive. For mortality, meta-analysis showed that low handgrip strength (hazard ratio (HR) 1.80 [95% confidence interval (CI): 1.22–2.63]), lower distance on the 6-minute walk test (HR 1.15 [95% CI: 1.09–1.21] per 50 m decrease), low performance on the timed up and go test (>20 s) (HR 2.77 [95% CI: 1.79–4.30]) and slow gait speed (<0.83 m/s) (HR 2.24 [95% CI: 1.32–3.81]) were associated with higher long-term mortality.

Conclusions

Low muscle strength and physical performance are associated with higher mortality after TAVI, while the association with functional decline stays inconclusive. Future research should focus on interventions to increase muscle strength and physical performance in older cardiac patients.
CITEdb: a manually curated database of cell–cell interactions in human
Authors: Shan Nayang , Lu Yao , Guo Hao , Li Dongyu , Jiang Jitong , Yan Linlin , Gao Jiudong , Ren Yong , Zhao Xingming , Hou Lin
Published: September 2022

Motivation

The interactions among various types of cells play critical roles in cell functions and the maintenance of the entire organism. While cell–cell interactions are traditionally revealed from experimental studies, recent developments in single-cell technologies combined with data mining methods have enabled computational prediction of cell–cell interactions, which have broadened our understanding of how cells work together, and have important implications in therapeutic interventions targeting cell–cell interactions for cancers and other diseases. Despite the importance, to our knowledge, there is no database for systematic documentation of high-quality cell–cell interactions at the cell type level, which hinders the development of computational approaches to identify cell–cell interactions.

Results

We develop a publicly accessible database, CITEdb (Cell–cell InTEraction database, https://citedb.cn/), which not only facilitates interactive exploration of cell–cell interactions in specific physiological contexts (e.g. a disease or an organ) but also provides a benchmark dataset to interpret and evaluate computationally derived cell–cell interactions from different tools. CITEdb contains 728 pairs of cell–cell interactions in human that are manually curated. Each interaction is equipped with structured annotations including the physiological context, the ligand–receptor pairs that mediate the interaction, etc. Our database provides a web interface to search, visualize and download cell–cell interactions. Users can search for cell–cell interactions by selecting the physiological context of interest or specific cell types involved. CITEdb is the first attempt to catalogue cell–cell interactions at the cell type level, which is beneficial to both experimental, computational and clinical studies of cell–cell interactions.

Availability and implementation

CITEdb is freely available at https://citedb.cn/ and the R package implementing benchmark is available at https://github.com/shanny01/benchmark.

Supplementary information

Supplementary data are available at Bioinformatics online.
Integrating phylogenetic and functional data in microbiome studies
Authors: Douglas Gavin M , Hayes Molly G , Langille Morgan G I , Borenstein Elhanan
Published: September 2022

Motivation

Microbiome functional data are frequently analyzed to identify associations between microbial functions (e.g. genes) and sample groups of interest. However, it is challenging to distinguish between different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed POMS, a package that implements multiple phylogeny-aware frameworks to more robustly identify enriched functions.

Results

The key contribution is an extended balance-tree workflow that incorporates functional and taxonomic information to identify functions that are consistently enriched in sample groups across independent taxonomic lineages. Our package also includes a workflow for running phylogenetic regression. Based on simulated data we demonstrate that these approaches more accurately identify gene families that confer a selective advantage compared with commonly used tools. We also show that POMS in particular can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome.

Availability and implementation

These workflows are freely available in the POMS R package at https://github.com/gavinmdouglas/POMS.

Supplementary information

Supplementary data are available at Bioinformatics online.
WMSA: a novel method for multiple sequence alignment of DNA sequences
Authors: Wei Yanming , Zou Quan , Tang Furong , Yu Liang
Published: September 2022

Motivation

Multiple sequence alignment (MSA) is a fundamental problem in bioinformatics. The quality of alignment will affect downstream analysis. MAFFT has adopted the Fast Fourier Transform method for searching the homologous segments and using them as anchors to divide the sequences, then making alignment only on segments, which can save time and memory without overly reducing the sequence alignment quality. MAFFT becomes slow when the dataset is large.

Results

We made a software, WMSA, which uses the divide-and-conquer method to split the sequences into clusters, aligns those clusters into profiles with the center star strategy and then makes a progressive profile–profile alignment. The alignment is conducted by the compiled algorithms of MAFFT, K-Band with multithread parallelism. Our method can balance time, space and quality and performs better than MAFFT in test experiments on highly conserved datasets.

Availability and implementation

Source code is freely available at https://github.com/malabz/WMSA/, which is implemented in C/C++ and supported on Linux, and datasets are available at https://github.com/malabz/WMSA-dataset.

Supplementary information

Supplementary data are available at Bioinformatics online.
The influence of COVID-19 infection-associated immune response on the female reproductive system
Authors: Saadedine Mariam , El Sabeh Malak , Borahay Mostafa A , Daoud Georges
Published: September 2022

Coronavirus disease 2019 (COVID-19) is a multi-system disease that has led to a pandemic with unprecedented ramifications. The pandemic has challenged scientists for the past 2 years and brought back previously abandoned research topics. COVID-19 infection causes a myriad of symptoms ranging from mild flu-like symptoms to severe illness requiring hospitalization. Case reports showed multiple systemic effects of COVID-19 infection, including acute respiratory distress syndrome, fibrosis, colitis, thyroiditis, demyelinating syndromes, and mania, indicating that COVID-19 can affect most human body systems. Unsurprisingly, a major concern for women all over the globe is whether a COVID-19 infection has any long-term effects on their menstrual cycle, fertility, or pregnancy. Published data have suggested an effect on the reproductive health, and we hypothesize that the reported reproductive adverse effects are due to the robust immune reaction against COVID-19 and the associated cytokine storm. While the COVID-19 receptor (angiotensin converting enzyme, ACE2) is expressed in the ovaries, uterus, vagina, and placenta, we hypothesize that it plays a less important role in the adverse effects on the reproductive system. Cytokines and glucocorticoids act on the hypothalamo–pituitary gonadal axis, arachidonic acid pathways, and the uterus, which leads to menstrual disturbances and pregnancy-related adverse events such as preterm labor and miscarriages. This hypothesis is further supported by the apparent lack of long-term effects on the reproductive health in females, indicating that when the cytokine storm and its effects are dampened, the reproductive health of women is no longer affected.
Functional linear regression for discretely observed data: from ideal to reality
Authors: Zhou Hang , Yao Fang , Zhang Huiming
Published: September 2022

Despite extensive studies on functional linear regression, there exists a fundamental gap in theory between the ideal estimation from fully observed covariate functions and the reality that one can only observe functional covariates discretely with noise. The challenge arises when deriving a sharp perturbation bound for the estimated eigenfunctions in the latter case, which renders existing techniques for functional linear regression not applicable. We use a pooling method to attain the estimated eigenfunctions and propose a sample-splitting strategy to estimate the principal component scores, which facilitates the theoretical treatment for discretely observed data. The slope function is estimated by approximated least squares, and we show that the resulting estimator attains the optimal convergence rates for both estimation and prediction when the number of measurements per subject reaches a certain magnitude of the sample size. This phase transition phenomenon differs from the known results for the pooled mean and covariance estimation, and reveals the elevated difficulty in estimating the regression function. Numerical experiments, using simulated and real data examples, yield favourable results when compared with existing methods.
Propensity scores in the design of observational studies for causal effects
Authors: Rosenbaum P R , Rubin D B
Published: September 2022

The design of any study, whether experimental or observational, that is intended to estimate the causal effects of a treatment condition relative to a control condition refers to those activities that precede any examination of outcome variables. As defined in our 1983 article (Rosenbaum & Rubin, 1983), the propensity score is the unit-level conditional probability of assignment to treatment versus control given the observed covariates; so the propensity score explicitly does not involve any outcome variables, in contrast to other summaries of variables sometimes used in observational studies. Balancing the distributions of covariates in the treatment and control groups by matching or balancing on the propensity score is therefore an aspect of the design of the observational study. In this invited comment on our 1983 article, we review the situation in the early 1980s and recall some apparent paradoxes that propensity scores helped to resolve. We demonstrate that it is possible to balance an enormous number of low-dimensional summaries of a high-dimensional covariate, even though it is generally impossible to match individuals closely for all the components of a high-dimensional covariate. In a sense, there is only one crucial observed covariate, the propensity score, and there is one crucial unobserved covariate, the principal unobserved covariate. The propensity score and the principal unobserved covariate are equal when treatment assignment is strongly ignorable, that is, unconfounded. Controlling for observed covariates is a prelude to the crucial step from association to causation, the step that addresses potential biases from unmeasured covariates. The design of an observational study also prepares for the step to causation: by selecting comparisons to increase the design sensitivity, by seeking opportunities to detect bias, by seeking mutually supportive evidence affected by different biases, by incorporating quasi-experimental devices such as multiple control groups, and by including the economist’s instruments. All of these considerations reflect the formal development of sensitivity analyses that were largely informal prior to the 1980s.
Bioactive glass-based fibrous wound dressings
Authors: Homaeigohar Shahin , Li Meng , Boccaccini Aldo R
Published: September 2022

Since the discovery of silicate bioactive glass (BG) by Larry Hench in 1969, different classes of BGs have been researched over decades mainly for bone regeneration. More recently, validating the beneficial influence of BGs with tailored compositions on angiogenesis, immunogenicity and bacterial infection, the applicability of BGs has been extended to soft tissue repair and wound healing. Particularly, fibrous wound dressings comprising BG particle reinforced polymer nanofibers and cotton-candy-like BG fibers have been proven to be successful for wound healing applications. Such fibrous dressing materials imitate the physical structure of skin’s extracellular matrix and release biologically active ions e.g. regenerative, pro-angiogenic and antibacterial ions, e.g. borate, copper, zinc, etc., that can provoke cellular activities to regenerate the lost skin tissue and to induce new vessels formation, while keeping an anti-infection environment. In the current review, we discuss different BG fibrous materials meant for wound healing applications and cover the relevant literature in the past decade. The production methods for BG-containing fibers are explained and as fibrous wound dressing materials, their wound healing and bactericidal mechanisms, depending on the ions they release, are discussed. The present gaps in this research area are highlighted and new strategies to address them are suggested.
Japanese Encephalitis Emergence in Australia: The Potential Population at Risk
Authors: Yakob Laith , Hu Wenbiao , Frentiu Francesca D , Gyawali Narayan , Hugo Leon E , Johnson Brian , Lau Colleen , Furuya-Kanamori Luis , Magalhaes Ricardo Soares , Devine Gregor
Published: September 2022

In Australia, Japanese encephalitis virus circulated in tropical north Queensland between 1995 and 2005. In 2022, a dramatic range expansion across the southern states has resulted in 30 confirmed human cases and 6 deaths. We discuss the outbreak drivers and estimate the potential size of the human population at risk.
Neutral-Coating Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Top-Down Identification of Hemoglobin Variants
Authors: Luo Ruben Yiqi , Wong Carolyn , Xia James Qiangwei , Glader Bertil E , Shi Run-Zhang , Zehnder James L
Published: September 2022

Background

Identification of hemoglobin (Hb) variants is of significant value in the clinical diagnosis of hemoglobinopathy. However, conventional methods for identification of Hb variants in clinical laboratories can be inadequate due to the lack of structural characterization. We describe the use of neutral-coating capillary electrophoresis coupled with high-resolution mass spectrometry (CE-HR-MS) to achieve high-performance top-down identification of Hb variants.

Methods

An Orbitrap Q-Exactive Plus mass spectrometer was coupled with an ECE-001 capillary electrophoresis (CE) unit through an EMASS-II ion source. A PS1 neutral-coating capillary was used for CE. Samples of red blood cells were lysed in water and diluted in 10 mM ammonium formate buffer for analysis. Deconvolution of raw mass spectrometry data was carried out to merge multiple charge states and isotopic peaks of an analyte to obtain its monoisotopic mass.

Results

The neutral-coating CE could baseline separate individual Hb subunits dissociated from intact Hb forms, and the HR-MS could achieve both intact-protein analysis and top-down analysis of analytes. A number of patient samples that contain Hb subunit variants were analyzed, and the variants were successfully identified using the CE-HR-MS method.

Conclusions

The CE-HR-MS method has been demonstrated as a useful tool for top-down identification of Hb variants. With the ability to characterize the primary structures of Hb subunits, the CE-HR-MS method has significant advantages to complement or partially replace the conventional methods for the identification of Hb variants.
Case report on ambulatory pulmonary pressure monitoring: an attempt to reduce readmissions for heart failure with preserved ejection fraction
Authors: Angullo-Gómez María , Robles-Mezcua Ainhoa , Becerra-Muñoz Víctor Manuel , García-Pinilla José Manuel
Published: September 2022

Background

Despite many recent advances in heart failure (HF) therapies, there remains an unmet need in patients with HF with preserved ejection fraction (HFpEF) for adequate treatment and follow-up, with the potential to reduce associated mortality and morbidity. Increased intracardiac and intrapulmonary pressures have been shown to precede the onset of symptoms of decompensated HF by several days or even weeks, so there have been several attempts to influence the prognosis of HF by monitoring through various methods. One of these is ambulatory pulmonary pressure monitoring to guide treatment in anticipation of decompensation.

Case summary

We present the case of a 65-year-old woman with rheumatic valve disease and mechanical aortic and mitral prosthesis since 2003 and pacemaker since 2014, with development of severe tricuspid regurgitation in 2018 and with new valve implantation and multiple decompensations of HFpEF despite optimal medical treatment. Under follow-up in the Heart Failure Unit and after multiple unsuccessful treatment adjustments, it was decided to implant a pulmonary artery pressure monitoring device—CardioMEMS®—in order to optimize patient follow-up and treatment. The procedure was carried out without complications and early optimization of treatment was possible, resulting in a significant reduction in decompensations and admissions for HF.

Discussion

Ambulatory pulmonary pressure monitoring is shown to be a safe and effective option to anticipate treatment of heart failure decompensation even with preserved left ventricular ejection fraction, with a significantly positive impact on hospital readmissions and consequent benefit on morbidity and mortality.
Effect of resected lung lobe on the prediction of postoperative pulmonary function
Authors: Shibazaki Takamasa , Mori Shohei , Noda Yuki , Tsukamoto Yo , Kato Daiki , Nakada Takeo , Yabe Mitsuo , Matsudaira Hideki , Hirano Jun , Ohtsuka Takashi
Published: September 2022

OBJECTIVES

This study examined whether a resected lung lobe can affect the accuracy of postoperative forced expiratory volume in 1 s (FEV1) predicted using the subsegment counting method and three-dimensional computed tomography (3D-CT) volumetry.

METHODS

Overall, 125 patients who underwent lobectomy through video-assisted thoracic surgery were enrolled in this retrospective study. Pulmonary function tests were performed preoperatively and postoperatively at 3 months. We defined the accuracy index as the ratio of predicted postoperative FEV1 to measured postoperative FEV1 and compared the accuracy index of the subsegment counting method and 3D-CT volumetry. Factors affecting the accuracy index were also examined.

RESULTS

The accuracy index of the subsegment counting method was 0.94 ± 0.12, versus 0.93 ± 0.11 for 3D-CT volumetry (P = 0.539). There was a significant difference among the resected lobes in the accuracy index of the subsegment counting method (P < 0.001) but not in that of 3D-CT volumetry (P = 0.370). The resected lobe, the number of staples used for interlobar dissection and interstitial pneumonia were significantly associated with the accuracy index of the subsegment counting method (all P < 0.001). The number of staples and interstitial pneumonia were significantly associated with the accuracy index of 3D-CT volumetry (P < 0.001, respectively), whereas the resected lobe was not a significant factor (P = 0.240).

CONCLUSIONS

The resected lobe affected the accuracy of the subsegment counting method but not that of 3D-CT volumetry. Furthermore, 3D-CT volumetry predicted postoperative FEV1 independent of the resected lobe.
Left main coronary disease: evolving management concepts
Authors: Armstrong Paul W , Bates Eric R , Gaudino Mario
Published: September 2022

Remarkable advances in the management of coronary artery disease have enhanced our approach to left main coronary artery (LMCA) disease. The traditional role of coronary artery bypass graft surgery has been challenged by the less invasive percutaneous coronary interventional approach. Additionally, major strides in optimal medical therapy now provide a rich menu of treatment choices in selected circumstances. Although a LMCA stenosis >70% is an acceptable threshold for revascularization, those patients with a LMCA narrowing between 40 and 69% present a more complex scenario. This review examines the relative merits of the different treatment options, addresses key diagnostic and therapeutic unknowns, and identifies future work likely to advance progress.
Parental alcohol and drug abuse and offspring mortality by age 10: a population-based register study
Authors: Berg Venla , Kuja-Halkola Ralf , Khemiri Lotfi , Larsson Henrik , Lichtenstein Paul , Latvala Antti
Published: September 2022

Background

Parental substance abuse (SA) of alcohol and drugs is associated with offspring mortality, including sudden infant death syndrome (SIDS), in infancy, but research on cause-specific mortality and mortality in later childhood is scarce.

Methods

Using population-based register data on all births in Sweden in 1973–2013 (N = 4.2 million) and Cox regressions, we examined the associations of mother’s and father’s SA registered between 2 years before and 12 years after the child birth with offspring all-cause and cause-specific mortality in infancy and childhood.

Results

Parental SA was associated with increased offspring all-cause and natural-cause mortality in infancy, but not in the neonatal period, and with external-cause mortality in ages 1–9. Risk of SIDS was 130–280% higher in infants with parental SA compared to infants with no parental SA. Adjusting for parental socioeconomic and immigrant status and severe psychiatric disorders, paternal SA was associated with 66% higher mortality due to communicable diseases and infections in infancy, and both maternal and paternal SA were associated with 40–174% higher mortality due to accidents in infancy and in ages 1–9. The associations between parental SA and offspring mortality were similar for male and female offspring.

Conclusions

Child mortality is rare in contemporary Sweden, and parental SA has variable associations with elevated offspring mortality throughout the first 10 years of life, excluding the neonatal period, which is indicative of insufficient recognition of children at risk. Preventive measures should be long-term and targeted to both parental and offspring behaviour.
Demes: a standard format for demographic models
Authors: Gower Graham , Ragsdale Aaron P , Bisschop Gertjan , Gutenkunst Ryan N , Hartfield Matthew , Noskova Ekaterina , Schiffels Stephan , Struck Travis J , Kelleher Jerome , Thornton Kevin R
Published: September 2022

Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth rates, and continuous and pulse migrations between those populations over a number of epochs, which can require dozens of parameters to fully describe. There is currently no standard format to define such models, significantly hampering progress in the field. In particular, the important task of translating the model descriptions in published work into input suitable for population genetic simulators is labor intensive and error prone. We propose the Demes data model and file format, built on widely used technologies, to alleviate these issues. Demes provide a well-defined and unambiguous model of populations and their properties that is straightforward to implement in software, and a text file format that is designed for simplicity and clarity. We provide thoroughly tested implementations of Demes parsers in multiple languages including Python and C, and showcase initial support in several simulators and inference methods. An introduction to the file format and a detailed specification are available at https://popsim-consortium.github.io/demes-spec-docs/.
Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage
Authors: Rasmussen Malthe Sebro , Garcia-Erill Genís , Korneliussen Thorfinn Sand , Wiuf Carsten , Albrechtsen Anders
Published: September 2022

The site frequency spectrum is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the site frequency spectrum from called genotypes introduces bias when working with low-coverage sequencing data. Methods exist for addressing this issue but sometimes suffer from 2 problems. First, they can have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multidimensional site frequency spectrum estimation. In this article, we present a stochastic expectation–maximization algorithm for inferring the site frequency spectrum from NGS data that address these challenges. We show that this algorithm greatly reduces runtime and enables estimation with constant, trivial RAM usage. Furthermore, the algorithm reduces overfitting and thereby improves downstream inference. An implementation is available at github.com/malthesr/winsfs.
Five-Factor Model Personality Traits and the Trajectory of Episodic Memory: Individual-Participant Meta-Analysis of 471,821 Memory Assessments from 120,640 Participants
Authors: Sutin Angelina R , Brown Justin , Luchetti Martina , Aschwanden Damaris , Stephan Yannick , Terracciano Antonio
Published: September 2022

Objectives

Five-factor model (FFM) personality traits are associated with concurrent memory function and risk of incident dementia but are less consistently associated with the change in episodic memory. The present research analyzes multiple large-scale studies with a consistent analytic approach to evaluate the association between personality and change in episodic memory over time.

Method

Across nine public longitudinal data sets, 120,640 participants provided 471,821 memory assessments over up to 26 years (age range 18–108). FFM traits were tested as predictors of the average level (intercept) and change over time (slope) of episodic memory. Results from the individual samples were meta-analyzed to summarize the associations.

Results

Consistent with expectations for the intercept, higher neuroticism was associated with worse memory performance, whereas higher openness and conscientiousness were associated with better performance; extraversion and agreeableness were also associated with better performance. Higher neuroticism and lower conscientiousness were related to declines in memory only in samples with more than two assessments of memory. The other three traits were unrelated to memory slope. The pattern was similar when participants with dementia were excluded from the analysis, and the association with the slope was not moderated by age.

Discussion

FFM traits have a robust association with average memory performance. Higher neuroticism and lower conscientiousness were associated with declines in memory performance only among samples with more than two memory assessments. The heterogeneity across studies suggests that multiple memory assessments are needed to reliably detect change over time, which may be one reason for past inconsistencies across studies.
Complexity awareness among university students in Switzerland during the Covid-19 pandemic
Authors: Nigg Carina , Benkert Richard , Tadesse Lidya , Abel Thomas
Published: September 2022

Public health challenges relating to Covid-19 are highly complex and reasons behind preventive measures can be difficult to understand. Complexity awareness, an important part of healthy literacy, may help young people to understand the situation and act accordingly. However, we could not find any tools to assess complexity awareness during a pandemic in the literature. The purpose of this study was to develop pandemic-specific items to assess complexity awareness and explore relationships with sociodemographic characteristics in university students. Based on critical health literacy concepts and expert knowledge from public health, we developed four survey items, which were answered by 3616 Swiss university students online as part of the COVID-19 International Student Well-Being Study. Relationships between awareness and sociodemographic characteristics were explored using logistic regression and odds ratio (OR). Results showed that 49.6% of the students demonstrated limited and 50.4% demonstrated high complexity awareness. Being female (OR = 1.26; 95% CI 1.07–1.47), having highly educated parents (OR = 1.29; 95% CI 1.06–1.57), and being at a practically oriented university (OR = 0.79; 95% CI 0.64–0.97) was associated with high awareness. Covid-19-related complexity awareness varied significantly among university students, indicating that they have difficulties in dealing with complex information and processes in this pandemic. The results call for action to support students in understanding the complexity of this pandemic and to investigate complexity awareness in the general population.