bluuebunny/crossref_metadata_2025 huggingface dataset:
Readiness of Malaysia’s construction industry in adopting green building rating tools
Authors: Razman R , Khaw S T , Md Noh N I F , Ng J L , Abd Wahid A Z , Yasin M N
Published: July 2023

Awareness on environmental issue is increasing along with the development of technology. People started to expand their efforts in reducing the environmental impact and buildings started to be recognized as major contributors to the world’s environmental issues. Green Building (GB) Practices are being promoted widely in construction industry. In conjunction with it, different countries including Malaysia started to introduce their own Green Building Rating Tools (GBRT) to meet the development of sustainable construction. This paper intents to study the current practices of Green Building Rating Tools adopting in Malaysia by identifying the barriers and success factors of the development of rating tools, and to propose strategies in promoting rating tools in construction industry. Throughout this study, the experts from construction industry limited to Klang Valley areas in Malaysia were selected as target respondents. Questionnaires were sent out to the list of respondents manually, as well as via e-mail. Out of 100 sets, a total of 83 (83%) set of questionnaires were respond. IBM SPSS software was adopted to analyse the data collected from the quantitative method. Based on result, Green Building Index (GBI) is the most commonly known and widely adopted rating tool in Malaysia. The main factors hindering the development of other rating tools mainly due to the financial problem of most companies and the lack of understanding by public. Strategies like education, workshop, collaboration and enforcement of building rules by government should be implemented immediately if the widely adoption of rating tools in Malaysia’s construction industry is to be achieved.
Identification of fall event and classification of the factors causing fall from height accidents in the construction industry
Authors: Samad Noratira Abd , Hasmori Muhammad Fikri , Ismail Radzi
Published: July 2023

Fall from height (FFH) accidents are common in the construction industry and cause many negative effects. This paper aims to identify the events of falls and causes of FFH accidents through a comprehensive literature review. The top three fall events that resulted in fatalities were falling from a ladder, falling from a scaffold, and falling through a roof surface. The causes of FFH accidents were classified into three categories: human factors, management factors, and environmental factors. The sub-factor for each factor is discovered and the most-cited causes of FFH accidents were identified. The most cited sub-factor for human factors is human behaviour, such as misjudgement, poor attitude, unsafe behaviour and carelessness, obliviousness, negligence, failure to wear personal protective equipment (PPE), as well as age or work experience. It is found that insufficient monitoring or inspection, lack of training programs, non-compliance with safety regulations, and cost-saving are the most-cited sub-factors in management factors. For environmental factors, the most cited sub-factors that cause FFH accidents are poor site management, which includes housekeeping, work platform heights, overexertion, and unusual positioning and bad weather. This research will serve as a foundation for the FFH accident field of study in Malaysia.
Energy transitioning school buildings in Peninsula Malaysia: A case study on the potential of photovoltaic power
Authors: Alwi N M , Flor J-F , Anuar N H , Hanafi N N H , Muhammad N H , Zain M H K M , Nasir M R M
Published: July 2023

This study builds on the ways design modifications can improve the integration of solar electric generation in Malaysian educational buildings. The study suggests the benefit of a solar installation at a standard school as both an educational and economic opportunity for a photovoltaic (PV) system can bring together classroom learning and energy supply. In analysing the existing design details of selected case study schools, this study aims to determine how the integration of this technology in the building design can be applied to the most basic education buildings in Malaysia. The existing design patterns of school classrooms with and without PV systems were logged and examined through a series of post-occupancy evaluation studies on selected schools. Basic energy requirements were summarized, and specific design modifications for the existing case study schools were proposed to adapt to the newer, modern classrooms. The results of this conceptual evaluation, coupled with energy simulations to model a reference case energy usage, provided the basis to predict PV outputs and future energy use for a modified classroom. Positive results from the solar analysis provided additional evidence about how alternative energy sources are beneficial in long term future-proofing schools.
Effect of Graphene Oxide on compressive strength of Shale Ceramsite high strength lightweight aggregate concrete
Authors: Hong Xiaojiang , Lee Jin Chai , Chu May Yen , Li Qiansha , Daze Xiaoli
Published: July 2023

The use of shale ceramsite to produce high-strength lightweight concrete (HSLWC) in the construction industry is an effective method for sustainable development and environmental protection. The growing demand for HSLWC has stimulated the development of nanomaterials to further enhance mechanical properties. This study investigated the effect of graphene oxide (GO) on the properties of HSLWC with shale ceramsite as a coarse and fine aggregate, including workability, density, compressive strength, and energy dispersive spectrometer (EDS) test. The control mixture was designed according to the standard of grade 40 high strength concrete, and four groups of mixtures were prepared by adding doses of GO at 0.00%, 0.02%, 0.04% and 0.06% by weight of cement to the control mixture. The experimental results showed that HSLWC with the 28-day compressive in the range of 43-54 MPa and the oven dry density of 1705-1783 kg/m3 could be produced by using shale ceramsite and shale pottery sand as coarse aggregate and fine aggregate, respectively. Simultaneously, adding a low content of GO to HSLWC could slightly increase the density, rationally reduce the slump, and significantly enhance the compressive strength. The EDS results showed that the reason for the increase in compressive strength was that GO could accelerate the cement hydration process and regulate the crystal morphology of the cement.
Viscoelastic damper for vibration mitigation of footbridges
Authors: Alhasa Abbas Ali , Vafaei Mohammadreza , Ali Sophia C. , Jian Tang Wei
Published: July 2023

Footbridges are among long-span light-weight structures that because of their low damping ratio are susceptible to vibration. Excessive vibration in footbridges usually occurs when they are subjected to rhythmic dynamic loads caused by human activities like walking and running. In order to mitigate the human induced vibrations in footbridges, an increase in the damping ratio is often suggested as the most economical approach. Tuned mass dampers have been widely used for this purpose, however, their installation and maintenance costs are high. This has encouraged researchers to examine the efficiency of the other types of dampers. Viscoelastic dampers have been successfully employed for vibration mitigation of structures against wind and earthquake loads. However, their efficiency for reducing human induced vibration in footbridges has not been addressed. In this study, a real footbridge with a free span of 22.5 m and a width of 2.3 m was selected for numerical investigations. SAP2000 program was used to establish the finite element (FE) model of the footbridge. The established FE model was validated by comparing its natural frequencies with those measured on the field. FE model results indicated that the acceleration response of the footbridge exceeded the code specified limit. Therefore, a viscoelastic damper was designed and installed under the footbridge in order to reduce the acceleration response below the allowable level. Installation of the viscoelastic damper significantly decreased the vibrations. It was concluded that viscoelastic dampers were an economical and efficient solution for vibration problems in footbridges.
Emerging Tenera oil palm shell concrete: Mix design and cost analyses
Authors: Hama Mohammed Fadhil , Anwar Mohammed Parvez , Lau Teck Leong , Ng Daryl Chun Pinn
Published: July 2023

The utilization of oil palm shell (OPS) in concrete dates back since four decades ago. While most research has only been done on the Dura-OPS as coarse aggregate in concrete, few research has been done on Tenera-OPS. The Tenera-OPS is obtained by a hybrid crossbreeding between Dura and Pisifera type fruits to obtain a thinner shell in the palm oil fruit to produce 30% more palm oil. Tenera-OPS has different physical properties compared to Dura-OPS, which could alter the mechanical behaviour of concrete. Therefore, this paper has studied mix designs of Tenera-OPS concrete (Tenera-OPSC) to investigate its physical characteristics, and compressive strength and has compared to those of Dura-OPSC from literature. It has been found that compressive strength of 20.24 MPa could only be produced with very high cement content of 1050 kg/m3. This study has shown that the compressive strength of Tenera-OPSC is reduced by 55 – 72% by using the most common acceptable mix design used for Dura-OPSC. It has been found that Tenera-OPS in concrete swells and shrinks during the hardening process which causes de-bonding between the Tenera-OPS and the cement matrix, which is believed to be the main reason for the lower compressive strength. A cost analysis was also done to compare the costs between Tenera-OPSC and normal weight concrete (NWC) of similar grade. The cost of Tenera-OPSC has been found to be 2% lower than that of NWC.
The influence of fuel pricing on the mode of transportation of travellers in rural areas
Authors: Zakaria H , Rohani M M , Rahimi N F L , Rahimi N I R
Published: July 2023

A great number of studies have consistently reported that people’s monthly incomes and salaries have a great influence on their mobility pattern. Fuel price increases have affected the monthly expenditure of certain people, which lead to the reduction of their travel frequency or change in their modes of transport. Rural people are believed to have fewer options for their mode of transportation in comparison to urban people, thus most of them use their own vehicles to travel. Therefore, there is a major difference in the travel patterns between rural and urban people, especially when travel costs increase due to the rising of fuel prices. This study aimed to examine the changes in mobility patterns of rural people as a result of fuel price fluctuations. The subject of this study were the respondents from rural Malaysia who lived in the state of Johor. The methodology was based on statistical analysis which had employed descriptive analysis and t-test. This study argued that the rising of fuel price did not give any significant changes (significance level, 0.05) towards the respondents’ mobility pattern.
Empirical correlation of uniaxial compressive and shear strength of jointed granitic rock
Authors: Ibrahim A , Ismail M K A , Sapawi Z
Published: July 2023

Shear Strength of jointed rock plays a significant role in the stability of rock mass structure especially if the developments plan to be constructed adjacent to this formation. However, to get the shear strength of the rock joints is quite costly and difficult to be identified directly at site. This research is conducted to establish the relationship between uniaxial compressive strength (UCS) and shear strength of jointed granitic rock. UCS parameters are quite easily identified and common practise in any construction project such as deep foundation and tunnelling. The result of uniaxial compressive strength test and direct shear test were plotted using 5 samples of cylindrical shape and 5 jointed rock samples respectively. The linear regression analysis produces meaningful correlation with R2 value of 0.8595 and a new correlation to estimate shear strength of jointed rock has been established.
Temperature susceptibility of asphalt binder modified with palm oil mill sludge
Authors: Sharulnizam N A , Kamaruddin N H M , Poharan A , Yunus K N M , Jusli E , Abdullah M E
Published: July 2023

Modification of asphalt binder is continuously gaining interest as a result of the depletion of this non-renewable materials and their expensive price. There is a drive to use modifiers in asphalt including agricultural waste. In this study, palm oil mill sludge (POMS) was employed. The penetration grade of 60/70 as base binder incorporating with 1%,2%,3%,4% and 5% POMS were investigated for temperature susceptibility. These modified binders were tested for penetration, softening point, and viscosity. Subsequently, the penetration index (PI), penetration-viscosity number (PVN), activation energy (Ea) and viscosity-temperature susceptibility (VTS) were used to analyze the effect of POMS on the temperature susceptibility of asphalt binder. The results showed that the addition of POMS to the asphalt binder under unaged circumstances increased the penetration value from 66.56 dmm to 80.08 dmm and decreased the softening point from 49.25°C to 45.6°C for 4% POMS which indicates the softening effect of the asphalt binder. In contrast, following short-term ageing, the penetration value decreased as the softening point increased, showing that the modified asphalt binder stiffened after aging. According to the PI, PVN, Ea and VTS values of the modified POMS asphalt binder, the addition of POMS decreased its temperature susceptibility. Based on the ranking, 4% POMS was found as the best concentration of asphalt binder modifier. In conclusion, the use of appropriate amounts of POMS as an asphalt modifier is possible and provides a possible way to reuse POMS.
Rethinking conservation of Malaysia world heritage site livability: The case of Chew Jetty, Penang
Authors: Mazlan I D , Shi B S , Wai L C
Published: July 2023

The designation of George Town, Penang as one of the world heritage sites has brought numerous impacts on the region and local communities. The main issue of world heritage sites includes livability and strict heritage management which produced challenges for the residents to sustain. This paper aims to study livability and heritage inheritance and rethink the conservation planning of the heritage site. It is imperative to understand the direct impact of tourism and strict rules and regulations pressure from the world heritage site designation on the livability of the residents in the heritage site and start addressing this livability issue to regain the balance and equilibrium between the residential and tourism sector. The Chew Jetty has been selected as the case study area. The research of the site is done by thorough site analysis including multiple contexts, which are historical context, physical context, sociocultural context, issues threats and challenges, and government policies and development plans using material and resources available online as well as in-depth interviews with residents. The paper shows that the conservation planning set by the authority has driven away the livability of Chew Jetty and is losing the intangible aspects of Chew Jetty.
Eco living – An effective interior spatial planning as an intervention towards healthy living environment
Authors: Nasir Siti Nuratirah Che Mohd , Ismail W Omar Ali Saifudin Wan , Aziz Salmiah , Anuar Nor Hafizah , Alwi Najah Md , Razali Noorul Huda Mohd
Published: July 2023

Healthy housing is a fundamental element for healthy community. It ensures the availability of safe, decent, and affordable housing that supports the health of its occupants. In addition, people spend more than 80% of their time inside the house. Unhealthy house can cause many diseases, health problems, injuries and many more. The aim of this research presented in this paper is to provide an information on the effective interior spatial planning where obviously it will impact people health and contribute to healthy living environment. The reasoning for this research originates from the perspective held by researcher that the place where we sleep, work, live have an impactful factor that will determine our daily basis health. To accomplish the target a blended method was utilized. The technique adopted incorporate questionnaire with homeowners including the case study of the chosen healthy home construction in Malaysia. Healthy home approach is not noticeably where some studies have conducted in Western countries in the field of medical healthcare. Thus, there is lack of deficient data in the field of built environment particularly in our developing countries. This research also seen as important in the wake of recent endemic COVID-19 that involved wellbeing inside house. Future investigation is necessary due to pervasive and recurring interior spatial planning deficiencies that can be drawn from this research for health fairness within the society and nation.
Sustainable living: Alternative green structure module design for home self-food production
Authors: Mahmud Nasrul-Arif , Sabil Azmal , Hisham Nadiyah Noor , Siraj Suhailah , Adnan Nor Azizah , Md Amin Noor Dina
Published: July 2023

Due to the increased food price volatility during the 2007-2008 food price crisis and its aftereffects, food self-sufficiency has been one of the policy priorities in various nations, including Senegal, India, the Philippines, Qatar, Bolivia, and Russia. In addition, the United Nations predicts that the global population will reach 9.7 billion by 2050, and that half of the land that may be utilised for crops and agriculture worldwide would be unusable for farming owing to climate change, soil degradation, and poverty. The world’s population is growing rapidly, and so is the demand for food. This highlights the importance of food self-sufficiency and the need to investigate and develop a comprehensive plan. This study explores food self-sufficiency and the concept of creating a modular and flexible self-produced food system that might potentially generate safe food from organic plants using environmentally aware farming practises and free of pesticide residues without the usage of arable land. The analysis phase comprises categorising the challenges, while the synthesis stage is when the efforts culminate in the creation of a remedy. Hence, more individuals may start growing their own food, with hydroponics being a popular choice.
Indoor level of BTEX and health risk assessment at science laboratories in a university
Authors: Hamid H H A , Nadzir M S M , Lee K E , Ayatillah A , Latif M T , Othman M
Published: July 2023

The levels of volatile organic compounds (VOCs) such as Benzene, Toluene, Ethylbenzene, and Xylene isomers (BTEX) are important parameters for an indoor air quality assessment. Exposure to BTEX in science laboratories in a university can potentially cause health risks to workers. Active sampling was carried out using Tenax® GR sorbent tubes and analyzed with thermal desorption gas chromatography-mass spectrometry (TD-GCMS) to measure the BTEX levels at selected indoor areas. The average concentration of individual BTEX at the laboratories complex were as follows: Benzene (1.76 ± 0.44 μg/m3), Toluene (8.15 ± 2.99 μg/m3), Ethylbenzene (3.75 ± 0.69 μg/m3), m, p-Xylene (6.07 ± 1.19 μg/m3) and o-Xylene (4.84 ± 0.43 μg/m3). The distribution of the BTEX components varied depending on the floor level, laboratory activities, laboratory size, and interior furniture. Non-cancer risk estimates based on hazard quotient value for BTEX were < 1, indicating unlikely non-cancer risk. Lifetime cancer risk estimates for Benzene were in the range of 1.16 × 10-6 – 2.54 × 10-6 indicating possible cancer risk at the sampled indoor locations. Therefore, science laboratories can potentially pose a health risk to workers from long-term exposure to BTEX.
Low energy ion-solid interactions: a quantitative experimental verification of binary collision approximation simulations
Authors: Hofsäss Hans , Junge Felix , Kirscht Patrick , van Stiphout Koen
Published: July 2023

Ultra-low energy ion implantation has become an attractive method for doping of two-dimensional materials and ultra-thin films. The new dynamic Monte Carlo program IMINTDYN based on the binary collision approximation allows a reliable prediction of low energy implantation profiles and target compositional changes, as well as efficient simulation of high energy light ion scattering. To demonstrate the quality of these predictions and simulations, we present a model case experiment where we implanted W ions into tetrahedral amorphous carbon with low (10 keV) and ultra-low (20 eV) ion energies and analyzed the W implantation profiles with high resolution Rutherford backscattering spectrometry (HR-RBS). This experiment is compared with a complete simulation of all aspects of ion-solid-interactions of the experiment using the new IMINTDYN program. A unique novel simulation option, also relevant for implantation into 2D materials, is the inclusion of the vacancy as target species with dynamic vacancy generation and annihilation. Whereas simulations neglecting vacancy formation cannot reproduce the measured implantation profiles, we find excellent agreement between simulated and measured HR-RBS spectra. We also demonstrate the important role of simultaneous weak collisions in the binary collision approximation at low projectile energies.
Geometries of topological groups
Authors: Rosendal Christian
Published: July 2023

The paper provides an overarching framework for the study of some of the intrinsic geometries that a topological group may carry. An initial analysis is based on geometric nonlinear functional analysis, that is, the study of Banach spaces as metric spaces up to various notions of isomorphism, such as bi-Lipschitz equivalence, uniform homeomorphism, and coarse equivalence. This motivates the introduction of the various geometric categories applicable to all topological groups, namely, their uniform and coarse structure, along with those applicable to a more select class, that is, (local) Lipschitz and quasimetric structure. Our study touches on Lie theory, geometric group theory, and geometric nonlinear functional analysis and makes evident that these can all be seen as instances of a single coherent theory.
Comprehensive evaluation of deep and graph learning on drug–drug interactions prediction
Authors: Lin Xuan , Dai Lichang , Zhou Yafang , Yu Zu-Guo , Zhang Wen , Shi Jian-Yu , Cao Dong-Sheng , Zeng Li , Chen Haowen , Song Bosheng , Yu Philip S , Zeng Xiangxiang
Published: July 2023

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug–drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, natural language processing based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction.
Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes
Authors: Dilliott Allison A , Kwon Seulki , Rouleau Guy A , Iqbal Sumaiya , Farhan Sali M K
Published: July 2023

Within recent years, there has been a growing number of genes associated with amyotrophic lateral sclerosis (ALS), resulting in an increasing number of novel variants, particularly missense variants, many of which are of unknown clinical significance. Here, we leverage the sequencing efforts of the ALS Knowledge Portal (3864 individuals with ALS and 7839 controls) and Project MinE ALS Sequencing Consortium (4366 individuals with ALS and 1832 controls) to perform proteomic and transcriptomic characterization of missense variants in 24 ALS-associated genes.

The two sequencing datasets were interrogated for missense variants in the 24 genes, and variants were annotated with gnomAD minor allele frequencies, ClinVar pathogenicity classifications, protein sequence features including Uniprot functional site annotations, and PhosphoSitePlus post-translational modification site annotations, structural features from AlphaFold predicted monomeric 3D structures, and transcriptomic expression levels from Genotype-Tissue Expression. We then applied missense variant enrichment and gene-burden testing following binning of variation based on the selected proteomic and transcriptomic features to identify those most relevant to pathogenicity in ALS-associated genes.

Using predicted human protein structures from AlphaFold, we determined that missense variants carried by individuals with ALS were significantly enriched in β-sheets and α-helices, as well as in core, buried or moderately buried regions. At the same time, we identified that hydrophobic amino acid residues, compositionally biased protein regions and regions of interest are predominantly enriched in missense variants carried by individuals with ALS. Assessment of expression level based on transcriptomics also revealed enrichment of variants of high and medium expression across all tissues and within the brain. We further explored enriched features of interest using burden analyses and identified individual genes were indeed driving certain enrichment signals. A case study is presented for SOD1 to demonstrate proof-of-concept of how enriched features may aid in defining variant pathogenicity.

Our results present proteomic and transcriptomic features that are important indicators of missense variant pathogenicity in ALS and are distinct from features associated with neurodevelopmental disorders.
Skin thermal recovery following cryotherapy: a comparison of liquid nitrogen and liquid nitrous oxide
Authors: Erdmann Sophie A B , Wokes James
Published: July 2023

Cryotherapy is a common technique used in the management of superficial skin lesions, with current advice on the correct timing for freeze–thaw cycles based on nonscientific visual skin appearances. We investigated the effect of cryotherapy on thermal thawing times by creating a porcine skin model in a laboratory setting maintained at normal skin temperature and comparing liquid nitrogen and liquid nitrous oxide. Thermal assessment was performed using a thermal camera attached to an iPhone 11Pro® smartphone. Liquid nitrogen reduced skin temperature to –60 °C after 5 s of application, recovering to 0 °C after 70 s. Liquid nitrous oxide reduced skin temperature to –34.8 °C after 5 s but had a faster recovery to 0 °C after only 20 s. Both cryogens required a thawing period of 5 min to recover to normal skin temperature. We therefore suggest that optimum cellular degradation should allow for 5-min freeze–thaw cryotherapy cycles; a slower thawing period than is in current common practice.
A global pause generates nonselective response inhibition during selective stopping
Authors: Wadsley Corey G , Cirillo John , Nieuwenhuys Arne , Byblow Winston D
Published: July 2023

Selective response inhibition may be required when stopping a part of a multicomponent action. A persistent response delay (stopping-interference effect) indicates nonselective response inhibition during selective stopping. This study aimed to elucidate whether nonselective response inhibition is the consequence of a global pause process during attentional capture or specific to a nonselective cancel process during selective stopping. Twenty healthy human participants performed a bimanual anticipatory response inhibition paradigm with selective stop and ignore signals. Frontocentral and sensorimotor beta-bursts were recorded with electroencephalography. Corticomotor excitability and short-interval intracortical inhibition in primary motor cortex were recorded with transcranial magnetic stimulation. Behaviorally, responses in the non-signaled hand were delayed during selective ignore and stop trials. The response delay was largest during selective stop trials and indicated that stopping-interference could not be attributed entirely to attentional capture. A stimulus-nonselective increase in frontocentral beta-bursts occurred during stop and ignore trials. Sensorimotor response inhibition was reflected in maintenance of beta-bursts and short-interval intracortical inhibition relative to disinhibition observed during go trials. Response inhibition signatures were not associated with the magnitude of stopping-interference. Therefore, nonselective response inhibition during selective stopping results primarily from a nonselective pause process but does not entirely account for the stopping-interference effect.
Digital PCR Partition Classification
Authors: Vynck Matthijs , Chen Yao , Gleerup David , Vandesompele Jo , Trypsteen Wim , Lievens Antoon , Thas Olivier , De Spiegelaere Ward
Published: July 2023

Background

Partition classification is a critical step in the digital PCR data analysis pipeline. A range of partition classification methods have been developed, many motivated by specific experimental setups. An overview of these partition classification methods is lacking and their comparative properties are often unclear, likely impacting the proper application of these methods.

Content

This review provides a summary of all available digital PCR partition classification approaches and the challenges they aim to overcome, serving as a guide for the digital PCR practitioner wishing to apply them. We additionally discuss strengths and weaknesses of these methods, which can further guide practitioners in vigilant application of these existing methods. This review provides method developers with ideas for improving methods or designing new ones. The latter is further stimulated by our identification and discussion of application gaps in the literature, for which there are currently no or few methods available.

This review provides an overview of digital PCR partition classification methods, their properties, and potential applications. Ideas for further advances are presented and may bolster method development.
PageRank centrality with non-local random walk-based teleportation
Authors: Bowater David , Stefanakis Emmanuel
Published: July 2023

PageRank is a popular measure of centrality that is often applied to rank nodes in real-world networks. However, in many cases, the notion of teleportation is counterintuitive because it implies that whatever is moving around the network will jump or ‘teleport’ directly from one node to any other, without considering how far apart the nodes are. To overcome this issue, we propose here a general measure of PageRank centrality whereby the teleportation probabilities depend, in some way, on the distance separating the nodes. We accomplish this by drawing upon recent advances in non-local random walks, which allow the proposed measure to be tailored for various real-world networks and applications. To illustrate the flexibility of the proposed measure and to demonstrate how it differs from PageRank centrality, we present and discuss experimental results for a selection of real-world spatial and social networks, including an air transportation network, a collaboration network and an urban street network.
Major Adverse Cardiovascular Events by Baseline Cardiovascular Risk in Patients with Ulcerative Colitis Treated with Tofacitinib: Data from the OCTAVE Clinical Programme
Authors: Schreiber Stefan , Rubin David T , Ng Siew C , Peyrin-Biroulet Laurent , Danese Silvio , Modesto Irene , Guo Xiang , Su Chinyu , Kwok Kenneth K , Jo Hyejin , Chen Yan , Yndestad Arne , Reinisch Walter , Dubinsky Marla C
Published: July 2023

Background and Aims

Patients with inflammatory bowel disease have increased risk of atherosclerotic cardiovascular [CV] disease [ASCVD]. Tofacitinib is an oral ﻿Janus kinase inhibitor for the treatment of ulcerative colitis [UC]. We report major adverse CV events [MACE] in the UC OCTAVE programme, stratified by baseline CV risk.

Methods

Rates of MACE were analysed by baseline [first tofacitinib exposure] CV risk profile: prior ASCVD, or 10-year ASCVD risk categories [low, borderline, intermediate, high].

Results

Of 1157 patients [2814.4 patient-years of exposure; ≤7.8 years’ tofacitinib treatment], 4% had prior ASCVD and 83% had no prior ASCVD and low–borderline baseline 10-year ASCVD risk. Eight [0.7%] patients developed MACE; one had prior ASCVD. Incidence rates [unique patients with events/100 patient-years of exposure; 95% confidence intervals] for MACE were: 0.95 [0.02–5.27] in patients with prior ASCVD; and 1.81 [0.05–10.07], 1.54 [0.42–3.95], 0.00 [0.00–2.85], and 0.09 [0.01–0.32] in patients without prior ASCVD and with high, intermediate, ­borderline, and low baseline 10-year ASCVD risk, respectively. For the 5/7 patients with MACE and without prior ASCVD, 10-year ASCVD risk scores were numerically higher [>1%] prior to MACE versus at baseline, primarily due to increasing age.

Conclusions

Most patients receiving tofacitinib in the UC OCTAVE programme had low baseline 10-year ASCVD risk. MACE were more frequent in patients with prior ASCVD and higher baseline CV risk. This analysis demonstrates potential associations between baseline CV risk and MACE in patients with UC, suggesting CV risk should be assessed individually in clinical practice.

ClinicalTrials.gov

NCT00787202; NCT01465763; NCT01458951; NCT01458574; NCT01470612.
Mediation analysis of the testosterone treatment effect to prevent type 2 diabetes in the Testosterone for Prevention of Type 2 Diabetes Mellitus trial
Authors: Robledo Kristy P , Marschner Ian C , Handelsman David J , Bracken Karen , Stuckey Bronwyn G A , Yeap Bu B , Inder Warrick , Grossmann Mathis , Jesudason David , Allan Carolyn A , Wittert Gary
Published: July 2023

Objective

To determine if testosterone treatment effect on glycaemia is mediated through changes in total fat mass, abdominal fat mass, skeletal muscle mass, non-dominant hand-grip, oestradiol (E2), and sex hormone-binding globulin (SHBG).

Design

Mediation analysis of a randomised placebo-controlled trial of testosterone.

Methods

Six Australian tertiary care centres recruited 1007 males, aged 50-74 years, with waist circumference ≥95 cm, serum total testosterone ≤14 nmol/L (immunoassay), and either impaired glucose tolerance or newly diagnosed type 2 diabetes on an oral glucose tolerance test (OGTT). Participants were enrolled in a lifestyle programme and randomised 1:1 to 3 monthly injections of 1000 mg testosterone undecanoate or placebo for 2 years. Complete data were available for 709 participants (70%). Mediation analyses for the primary outcomes of type 2 diabetes at 2 years (OGTT ≥ 11.1 mmol/L and change in 2-h glucose from baseline), incorporating potential mediators: changes in fat mass, % abdominal fat, skeletal muscle mass, non-dominant hand-grip strength, E2, and SHBG, were performed.

Results

For type 2 diabetes at 2 years, the unadjusted OR for treatment was 0.53 (95% CI:.35-.79), which became 0.48 (95% CI:.30-.76) after adjustment for covariates. Including potential mediators attenuated the treatment effect (OR 0.77; 95% CI:.44-1.35; direct effect) with 65% mediated. Only fat mass remained prognostic in the full model (OR: 1.23; 95% CI: 1.09-1.39; P < .001).

Conclusion

At least part of the testosterone treatment effect was found to be mediated by changes in fat mass, abdominal fat, skeletal muscle mass, grip strength, SHBG, and E2, but predominantly by changes in fat mass.
Digest: Trilobites to vertebrates: how development influences the evolution of segmental patterning
Authors: Verma Neeharika
Published: July 2023

How has the evolution of segment size patterning been developmentally regulated and what does the trilobite fossil record tell us about these ancestral control mechanisms? Nikolic et al. relate the evolutionary and developmental mechanisms of segmentation in extinct trilobites to those seen in extant arthropods and vertebrates to examine how ontogenic renovations are echoed in the phylogeny of segmental patterning.
Diversity and succession of chemolithoautotrophic microbial community along a recently deglaciation chronosequence on the Tibetan Plateau
Authors: Khan Ajmal , Kong Weidong , Khan Sardar , Nawab Javed , Khan Muhammad Israr
Published: July 2023

Glaciers in high-altitude mountain regions are retreating rapidly due to global warming, exposing deglaciated soils to extreme environmental conditions, and microbial colonization. However, knowledge about chemolithoautotrophic microbes, which play important roles in the development of oligotrophic deglaciated soils prior to plant colonization, remains elusive in deglaciated soils. Using real-time quantitative PCR and clone library methods, the diversity and succession of the chemolithoautotrophic microbial community harboring the cbbM gene across a 14-year deglaciation chronosequence on the Tibetan Plateau were determined. The abundance of the cbbM gene remained stable for the first 8 years after deglaciation and then increased significantly, ranging from 105 to 107 gene copies g−1 soil (P < 0.001). Soil total carbon increased gradually to 5-year deglaciation and then decreased. While total nitrogen and total sulfur levels were low throughout the chronosequence. Chemolithoautotrophs were related to Gammaproteobacteria and Betaproteobacteria, with the former dominating early deglaciated soils and the latter dominating older deglaciated soils. The diversity of chemolithoautotrophs was high in mid-age deglaciated soils (6-year-old) and was low in early (3-year-old) and older deglaciated soils (12-year-old). Our findings revealed that chemolithoautotrophic microbes colonize deglaciated soils quickly and follow a clear successional pattern across recently deglaciated chronosequences.
Data management strategy for a collaborative research center
Authors: Mittal Deepti , Mease Rebecca , Kuner Thomas , Flor Herta , Kuner Rohini , Andoh Jamila
Published: July 2023

The importance of effective research data management (RDM) strategies to support the generation of Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience data grows with each advance in data acquisition techniques and research methods. To maximize the impact of diverse research strategies, multidisciplinary, large-scale neuroscience research consortia face a number of unsolved challenges in RDM. While open science principles are largely accepted, it is practically difficult for researchers to prioritize RDM over other pressing demands. The implementation of a coherent, executable RDM plan for consortia spanning animal, human, and clinical studies is becoming increasingly challenging. Here, we present an RDM strategy implemented for the Heidelberg Collaborative Research Consortium. Our consortium combines basic and clinical research in diverse populations (animals and humans) and produces highly heterogeneous and multimodal research data (e.g., neurophysiology, neuroimaging, genetics, behavior). We present a concrete strategy for initiating early-stage RDM and FAIR data generation for large-scale collaborative research consortia, with a focus on sustainable solutions that incentivize incremental RDM while respecting research-specific requirements.
Vietnam's prudent pivot to the rules-based international order
Authors: Do Thuy T
Published: July 2023

Vietnam's conceptualization of the international and regional orders has changed remarkably over the past decades. Previously an outsider if not a challenger of the western-crafted liberal order, Vietnam has in recent years increasingly leaned toward a rules-based international order. This article argues that the reason for Vietnam's changing perceptions about the liberal international order is largely threefold: domestic reform and modernization; deepened integration into the international political economy; as well as growing strategic concerns over great power coercion stemming from China's rise. Vietnam's pivot to the rules-based international order, however, is cautious given Hanoi's lingering worry over western intentions to undermine Vietnam's socialist orientation, the path dependence of Vietnam's relationships with its traditional partners as well as the occasional clashes between the old, conservative worldview and the new, open-minded thinking in shaping its foreign policy. As a result, Vietnam's vision for a rules-based international order emphasizes universally negotiated rules and institutions, rather than western-dominated ones, with a focus on the rules and norms promoted by the United Nations and ASEAN. Amid the current power shift, Vietnam supports an emerging multi-polar and multi-center order in which small and medium states like itself would have a bigger voice and greater agency.
Non-Torpid Heterothermy in Mammals: Another Category along the Homeothermy–Hibernation Continuum
Authors: Levesque Danielle L , Breit Ana M , Brown Eric , Nowack Julia , Welman Shaun
Published: July 2023

Synopsis

Variability in body temperature is now recognized to be widespread among whole-body endotherms with homeothermy being the exception rather than the norm. A wide range of body temperature patterns exists in extant endotherms, spanning from strict homeothermy, to occasional use of torpor, to deep seasonal hibernation with many points in between. What is often lost in discussions of heterothermy in endotherms are the benefits of variations in body temperature outside of torpor. Endotherms that do not use torpor can still obtain extensive energy and water savings from varying levels of flexibility in normothermic body temperature regulation. Flexibility at higher temperatures (heat storage or facultative hyperthermia) can provide significant water savings, while decreases at cooler temperatures, even outside of torpor, can lower the energetic costs of thermoregulation during rest. We discuss the varying uses of the terms heterothermy, thermolability, and torpor to describe differences in the amplitude of body temperature cycles and advocate for a broader use of the term “heterothermy” to include non-torpid variations in body temperature.
Topological information retrieval with dilation-invariant bottleneck comparative measures
Authors: Cao Yueqi , Monod Anthea , Vlontzos Athanasios , Schmidtke Luca , Kainz Bernhard
Published: July 2023

Appropriately representing elements in a database so that queries may be accurately matched is a central task in information retrieval; recently, this has been achieved by embedding the graphical structure of the database into a manifold in a hierarchy-preserving manner using a variety of metrics. Persistent homology is a tool commonly used in topological data analysis that is able to rigorously characterize a database in terms of both its hierarchy and connectivity structure. Computing persistent homology on a variety of embedded datasets reveals that some commonly used embeddings fail to preserve the connectivity. We show that those embeddings which successfully retain the database topology coincide in persistent homology by introducing two dilation-invariant comparative measures to capture this effect: in particular, they address the issue of metric distortion on manifolds. We provide an algorithm for their computation that exhibits greatly reduced time complexity over existing methods. We use these measures to perform the first instance of topology-based information retrieval and demonstrate its increased performance over the standard bottleneck distance for persistent homology. We showcase our approach on databases of different data varieties including text, videos and medical images.
Cumulative incidence of anal cancer since HIV or AIDS diagnosis in the United States
Authors: Haas Cameron B , Engels Eric A , Horner Marie-Josèphe , Pfeiffer Ruth M , Luo Qianlai , Kreimer Aimée R , Palefsky Joel M , Shiels Meredith S
Published: July 2023

Treatment of screen-detected anal high-grade squamous intraepithelial lesions has been shown to effectively reduce the incidence of invasive anal cancer in people with HIV. We provide population-based estimates of cumulative incidence of anal cancer by risk group and age at HIV or AIDS diagnosis. The 0- to 10-year cumulative incidence of anal cancer for men who have sex with men and are younger than 30 years of age at HIV diagnosis was 0.17% (95% confidence interval [CI] = 0.13% to 0.20%) compared with 0.04% (95% CI = 0.02% to 0.06%) in other men and 0.03% (95% CI = 0.01% to 0.04%) in women. For men who have sex with men and have a diagnosis of AIDS and are younger than 30 years of age, the 0- to 10-year cumulative incidence was 0.35% (95% CI = 0.28% to 0.41%). Among people with HIV, men who have sex with men are at the greatest risk of anal cancer, and those with a diagnosis of AIDS had higher risk than those without AIDS. These estimates may inform recommendations for priority populations that could benefit most from anal cancer screening and treatment.
MEN1 is a regulator of alternative splicing and prevents R-loop-induced genome instability through suppression of RNA polymerase II elongation
Authors: Jin Bangming , Zhu Jiamei , Pan Ting , Yang Yunqiao , Liang Li , Zhou Yuxia , Zhang Tuo , Teng Yin , Wang Ziming , Wang Xuyan , Tian Qianting , Guo Bing , Li Haiyang , Chen Tengxiang
Published: July 2023

The fidelity of alternative splicing (AS) patterns is essential for growth development and cell fate determination. However, the scope of the molecular switches that regulate AS remains largely unexplored. Here we show that MEN1 is a previously unknown splicing regulatory factor. MEN1 deletion resulted in reprogramming of AS patterns in mouse lung tissue and human lung cancer cells, suggesting that MEN1 has a general function in regulating alternative precursor mRNA splicing. MEN1 altered exon skipping and the abundance of mRNA splicing isoforms of certain genes with suboptimal splice sites. Chromatin immunoprecipitation and chromosome walking assays revealed that MEN1 favored the accumulation of RNA polymerase II (Pol II) in regions encoding variant exons. Our data suggest that MEN1 regulates AS by slowing the Pol II elongation rate and that defects in these processes trigger R-loop formation, DNA damage accumulation and genome instability. Furthermore, we identified 28 MEN1-regulated exon-skipping events in lung cancer cells that were closely correlated with survival in patients with lung adenocarcinoma, and MEN1 deficiency sensitized lung cancer cells to splicing inhibitors. Collectively, these findings led to the identification of a novel biological role for menin in maintaining AS homeostasis and link this role to the regulation of cancer cell behavior.