bluuebunny/crossref_metadata_2025 huggingface dataset:
Fragility-based effectiveness evaluation of reinforced concrete bridge piers strengthened with UHPC jackets
Authors: Nguyen Hoang Vinh , Nguyen Dang D Nam , Phan Hoang Nam , Nguyen Minh Hai , Nguyen Van My , Hoang Phuong Hoa , Pham Duy Hoa
Published: August 2023

The use of ultra-high-performance concrete (UHPC) jackets as a seismic strengthening method for reinforced concrete structures has become increasingly prevalent. Specifically, these jackets are applied to plastic hinge regions of the structures to improve overall earthquake resistance. This study evaluates the effectiveness of UHPC jackets in strengthening reinforced concrete columns through fragility curves. The columns are modeled numerically, accounting for material nonlinearity, and various strengthening scenarios, including those without UHPC jackets and with UHPC jackets of different heights, are modeled and validated with cyclic loading tests. Subsequently, a case study of a two-column reinforced concrete bridge pier is examined. Time-history dynamics analyses are conducted on 140 ground motion records to develop probabilistic seismic demand models of the column with different strengthening designs. Fragility curves obtained using the cloud method indicate a significant impact of the strengthening method on the failure probability of the column. The research findings presented in this paper provide engineers with a basis for selecting appropriate UHPC jacket parameters, including thickness, height, and material strength in a rational manner.
Seismic performance of multi-span continuous reinforced concrete bridges considering flood-induced scour effects
Authors: Vinh Nguyen Hoang , Nam Phan Hoang , Hoa Pham Duy , Hoa Hoang Phuong
Published: August 2023

Flood-induced scours near the pier foundation are an adverse phenomenon that may cause the collapse of bridges. However, in the seismic design of bridges, the scour impact is commonly ignored when evaluating the seismic response. This study aims to quantify the effect of flood-induced scours on nonlinear static and dynamic behaviors of typical reinforced concrete bridges. For this regard, three-dimensional finite element models of two- and three-span bridges with a multi-cell box girder, circular column bent, and extended pile-shaft foundation are first developed, where the column bent is modeled considering the material and geometry nonlinearity. The interaction between the soil and structure is also accounted for by using soil spring models. By considering different scour depths, the modal, static pushover, and dynamic time-history analyses of the bridges in both directions are investigated. It is observed from the modal analysis that the fundamental periods of the bridges increase with the increase of scour depth. In addition, the results in terms of the column drift ratio show that scour may increase the seismic damage to the bridges, which transfers damage from the column bent to the pile-shaft foundation. The findings of this study exhibit the significant effect of the scour on the seismic damage of reinforced concrete bridges; therefore, it is recommended that this phenomenon should be considered in the bridge seismic design.
Modeling and Mapping of Flood Susceptibility at Que Son District, Quang Nam Province, Vietnam using CatBoost
Authors: Phong Tran Van , Nguyen Duc Dam , Pham Binh Thai
Published: August 2023

In this research, the main objective is to model and map flood susceptibility in Que Son district, Quang Nam province, Vietnam using one of the effective machine learning model namely CatBoost. With this purpose, a total of 96 flood and non-flood locations and a set of 10 conditioning factors were collected to construct the geospatial database. Thereafter, Shap feature importance method was used to validate and select the most important conditioning factors used for modeling of flood susceptibility, and the results showed that only 8 conditioning factors including aspect, slope, curvature, elevation, land cover, rainfall, distance to rivers, and Topographic Wetness Index (TWI) were selected for final modelling of flood susceptibility at the study area. Validation of the model was also done using various statistical indexes including area under the ROC curve (AUC). Validation results showed that the performance of CatBoost model (AUC = 0.96 for training and AUC = 0.94 for testing) is good for prediction of flood susceptibility of the study area. Thus, it can be concluded that CatBoost is valuable tool for flood susceptibility modeling which can be used to assess flood susceptibility in other flood prone areas of the world. In addition, flood susceptibility map generated from CatBoost model in this study might be helpful in development of better flood mitigation strategies at the study area.
A standards-based approach to enhancing interoperability of low-cost industrial IoT flood sensors for transportation system resilience
Authors: Umeike Chibuike R , Guo Xiaoming , Dao Thang , Croope Silvana , Hong Xiaoyan , Johnston Alan T
Published: August 2023

Transportation infrastructure assets are particularly vulnerable to natural hazards, which are becoming more frequent and severe due to climate change and extreme weather conditions. Floods and flash floods are among the deadliest natural hazards, accounting for 50% of vehicle-related fatalities. This underscores the need for timely transportation flood detection systems adoption. However, current flood detection technologies are inadequate in terms of coverage, speed, geographical specificity, and interoperability, making it difficult for emergency managers to respond effectively to flood events. To address this issue, we propose a high-resolution network of low-cost Industrial Internet of Things (IIoT) sensing devices deployed at flood-prone transportation assets. These sensors collect location-specific data, which is then published in standardized formats, interfaces, and protocols, enabling other systems to generate flood forecasts, nowcasts, and warnings. A framework for Incident Management Systems (IMS) was also discussed to highlight the need for system interoperability during disaster management operations. Our solution employs standards-based interoperability, using the OIIE™ OpenO&M ecosystem architecture, to enable seamless interaction between interdependent systems and manages the risk to critical transportation infrastructure. The technology was tested at a microscale level to evaluate its performance. The model architecture supports scalable systems of systems interoperability for standardized use cases and common asset classes used in transportation, energy, facilities, and other critical infrastructure.
Axial and Flexural Performance of Discontinuously CFRP Strengthened Circularized and Square RC Columns
Authors: Mai A.D. , Sheikh M.N. , Hadi M.N.S. , Do H.T.G.
Published: August 2023

This study aims to evaluate the effect of the cross-section modification on the performance of square reinforced concrete (SRC) columns discontinuously strengthened with CFRP bands. In line with this research aim, the performance of SRC columns under eccentric and concentric compression was compared with that of circularized square RC (CSRC) columns. Six RC columns with 800 mm height including three SRC columns with 150 mm side length and three CSRC columns with 212 mm diameter were prepared and tested. The test results revealed that SRC columns achieved a substantial enhancement of strength and deformation by applying cross-section modification before strengthening with discontinuous CFRP bands. It was also found that SRC columns received a substantial improvement of deformation and considerable improvement of strength by strengthening with discontinuous CFRP bands.
An Assessment of the Algerian Trams and Subway Performance to Ensure an Efficient and a Sustainable Transport System
Authors: Khelf Mouloud
Published: August 2023

Since the beginning of the last decade, Algeria has given notable importance to sustainable transportation systems. The objective of this paper is to show the importance of two modern transportation means and to assess their operation. The methodology used in this work is based on the data recorded by the National Office of Statistics (ONS). The data analysis consists of two parts, the first part aims to show the importance of the subway and tram through an analysis of the passengers’ number who traveled by this two means in all cities. Then, the second part focuses on the Algiers subway and trams’ assessment by comparing the offered capacity and the passengers’ demand per year between 2017 and 2020. On the one hand, the results show that the number of users increased for the subway and trams except in 2020, due to the COVID-19 pandemic. On the other hand, the results show that the capacity offered for these two modes is high compared to the real passengers’ demand. This last finding can influence the sustainability criteria, especially for energy consumption. This contribution presents several recommendations for improving the subway and trams performance in Algeria.
A new approach to estimating link performance on Indonesian urban roads: deriving the BPR 1964 function
Authors: Rahman Aulia , Irawan Muhammad Zudhy , Amrozi Mukhammad Rizka Fahmi
Published: August 2023

Predictions of traffic volumes on road networks must be precise for transportation planning, and equilibrium trip assignment models based on the Volume Delay Function (VDF) are typically employed. In 1964, the U.S. Bureau of Public Roads (BPR) created a VDF widely used in many countries, including Indonesia. However, using capacity manuals from Western nations in Indonesia did not produce the desired results due to differences in traffic composition and driver behaviour. Using the Indonesian Highway Capacity Manual’s macroscopic fundamental diagram, this paper aims to derive a more accurate VDF for Indonesia. This method enables the development of a VDF tailored to the unique traffic conditions in Indonesia. It can enhance the precision of traffic volume forecasts in the region. The BPR function parameters tends to overestimate travel time delay, making the road network model flow misestimated. This is presumably caused by traffic count survey inability to record the build-up of traffic flow in the urban network during peak traffic periods.
Correlation analysis and regression of transit ridership by means of public buses – A preliminary data analysis
Authors: Karunakaran Ranjetha , Yuen Choon Wah , Chuah Joon Huang , Zainol Rosilawati , Goh Boon Hoe
Published: August 2023

Given ever-increasing private transportation ownership, a rising population, and unceasing mobility, it is crucial to ensure the usage and improvement of public transportation services. Therefore, it is important to review and understand relationships between variables affecting ridership to boost them. This paper acts as a preliminary data analysis in which correlation and multiple linear regression (MLR) analyses were constructed to examine bus transit ridership. The main goal of this study is to identify the variables that influence transit ridership and the degree to which they do so during a) peak hours and b) off-peak hours. Independent variables such as bus commercial speed, service frequency, in-vehicle travel time, bus stop distance, and rainfall were employed in this study. Results show that all the independent variables are significant and correlated with ridership. However, the regression models show that distance and travel time are not statistically significant during peak and off-peak hours, respectively. The findings of this study recommend the creation of relevant policy initiatives that can assist transit agencies in increasing ridership by analysing significant predictive factors. Additionally, the output from this study can be used in future works on designing efficient bus routes, stop locations, and even bus schedules.
Microscopic Simulation Model for Motorcycle Dominated Networks: A Case Study of a VISSIM Simulation Model for a Mixed Traffic Corridor
Authors: Vu Tam , Preston John
Published: August 2023

Microscopic traffic simulation packages, which were invented for car-based environments, have also been used for motorcycle-based environments. Because the interactions between several transport modes (e.g., buses, cars, and motorcycles) are different in these two environments, default parameters relating to these modes (e.g., acceleration, deceleration, speed) should be modified in the simulation of motorcycle-dominated networks. However, there seems to be very little evidence on the modification of these parameters in microscopic traffic simulation for these networks. To fill this gap in the literature, this research develops a VISSIM model (as one of the most appropriate microscopic simulation packages) for motorcycle-dominated mixed transport, which includes data collection, creation of a VISSIM model, and calibration and validation processes. For parameters which cannot be observed on-site, some values for each parameter are chosen based on the default values in VISSIM or local conditions. These values are then run in VISSIM models and tested in the calibration and validation processes to choose the values that best describe vehicle movements. By contrast, parameters that might be collected on-site are statistically analysed and inserted directly in to VISSIM. Acceleration and deceleration of motorcycles, the desired speed of car and bus, the desired speed of motorcycle, minimum lateral distance driving when overtaking vehicles on the same lane, and average standstill distance were applied for developing VISSIM models for a motorcycle-dominated mixed traffic corridor in Hanoi, Vietnam. Acceleration and deceleration surveys were carried out on-site by using the speed gun Stalker ATS. The results of statistical tests prove that the VISSIM models are sufficiently reliable to represent real traffic. Transport modellers can draw on the findings of this study. Desired acceleration and deceleration default values in VISSIM, which are for typical motorcycles used in Europe, should be replaced by local acceleration and deceleration rates. The methodology for developing a VISSIM model can be modified to suit other local motorcycle-dominated mixed traffic conditions.
Bus users’ behavior in using parking services and their expectations for the development of parking service quality at bus stations in Hanoi, Vietnam
Authors: Phuong Ngo Trung , Kojima Aya , Kubota Hisashi
Published: August 2023

Transportation Demand Management (TDM) has been introduced in Vietnam to keep the balance between the limited supply of road network, and the increase of private vehicles and Park & Ride (P&R) is one of TDM’s measures focused on the transition from private to public transport at stations. This research investigated the current situation of parking areas and bus users’ behavior in 4 main stations in Hanoi, Vietnam. Furthermore, bus users were asked in the assumption case that if they cannot use the bus, how much they will pay for the travel cost and time in that case compared to the actual case when they use the bus. The results have found that many people have accepted to travel in a longer time to save travel costs. This research also identified the factors which influence on using P&R services in station of bus users. Based on the Binary logistic regression model, the “Income” factor is one of the significant characteristics of bus users on selection use or not use of P&R services at the bus station. Finally, bus users’ expectations on the current situation of the parking services at stations gave some suggestions to improve the P&R services in bus stations in Hanoi.
Electrifying School Bus in Hanoi, Vietnam – What are Barriers and Enablers?
Authors: Truong Thi My Thanh , Nguyen Nga Thi
Published: August 2023

By the end of June 2022, Hanoi has 2,835 schools, nearly 70,200 classes, and more than 2.2 million students. More than one million children ride the bus to school, and 100% of these school buses run on diesel. Diesel exhaust has proven links to serious physical health issues as well as cognitive development impacts. Transitioning to electric school buses from traditional diesel-powered school buses can reduce students’ exposure to harmful pollutants that contribute to respiratory disease, heart disease, cancer and physical problems - and which can harm students’ cognitive development. However, the adoption of electric school buses concerns significant issues relating to the purchasing and operating costs, driving distance and charging systems. Therefore, the possibility of electric school buses remains unknown. The study used documents and semi-structured interviews with students, parents, school vehicle organizers, and bus service providers who involving in the decision-making of electric school bus adoption. The results show that the purchasing and operating cost, the driving distance and charging systems are major concerns and experiences by involved stakeholders are highly context-dependent. Financial and regulatory support from the national government, along with student demand and route characteristics had a significant influence on electric school bus adoption.
Analysis of service quality factors affecting passenger satisfaction with bus service based on a structural equation modeling: A case study of Ho Chi Minh City
Authors: Nguyen Xuan Long , Quach Bao Khang , Pham Chanh Toan , Nguyen Trong Thuc , Tran Thi Truc Lieu
Published: August 2023

This study aims to examine service quality factors and the extent of their influence on passenger satisfaction with public bus transport service. The study will describe the steps of creating a SEM (Structural Equation Modeling) model to demonstrate the service quality - satisfaction relations. Survey data conducted by the Ho Chi Minh Public Transport Management Centre in collaboration with the World Bank consultants from December 2019 to January 2020 includes 3,913 questionnaires on 25 subsidized bus routes. The analysis results from the SEM model indicate that the factors with the strongest impact on satisfaction are availability possibility, service information, fare, service attitude and friendliness with the environment. This result suggests that public transport should focus on improving these service quality factors to ensure a high level of passengers’ satisfaction.
Materials Characteristics of Soil-cement Samples under Various Maintenance Conditions
Authors: Vo Ba Huy , Dinh Hoai Luan , Dang Ngoc Loi
Published: August 2023

Subsidence of embankment foundation at the approach roadway is quite common in South Vietnam because natural soil layers are high water content and low bearing capacity. Soil-cement columns could be a potential method to deal with foundation subsidence. A critical issue is to determine proper soil-cement mixtures, mainly depending on maintenance conditions. In this study, materials characteristics of soil-cement samples are experimentally tested under various maintenance conditions. To achieve the objective, first, we drill to get natural soil samples at various depths for different boreholes located in southern Vietnam. Second, soil samples are used to fabricate soil-cement cylinder samples. Third, a set of fabricated samples are maintained under various environmental conditions for 7, 14, and 28 days. Last, experimental tests are conducted to test axial compressive strength to evaluate the effects of environmental parameters on strength development. The result reveals that the proportion of soil cement should be properly designed for soil layers to maximize the performance of the soil-cement column.
Utilization of Slag as an Aggregate Replacement for Road Base/Subbase Layers
Authors: Al-Shamsi Khalid , Hassan Hossam , Al-Jabri Khalifa , Al-Alawi Mubarak
Published: August 2023

Ferrochrome and Steel slags are by-products of the stainless steel and steel production, respectively. The utilization of slag as an aggregate replacement to provide a sustainable solution has gained attention from the construction industry in recent years. By reducing the demand for natural aggregate and providing an alternative use for industrial waste products, the use of slag is an environmentally conscious and economically viable option. This paper focuses on the potential application of using slag as road base/subbase layers. The paper examines the physical and chemical properties of the slag and reports on the strength and toxic metal analysis results. Slag can be processed into a coarse and fine aggregate that satisfies the necessary standards for road base/subbase layers. The testing results highlight the successfulness of using slag as an aggregate replacement for base/subbase layers, making it a promising and sustainable solution for the construction industry.
Pavement sustainability: a tripartite analysis of natural stone pavements in Hanoi, Vietnam
Authors: Le Dinh-Phuoc , Do Minh-Huyen , Duong Ngoc-Oanh T.
Published: August 2023

As a basic component of the city’s structure and, particularly, an integral part of the transportation infrastructure, pavements fundamentally contribute to the city’s achievement of sustainability goals. This paper examines the environmental, societal, and economic impacts of using natural stone for the pavement to pursue an ideal image of Green-Clean-Beautiful city by the government in the burgeoning city of Hanoi, Vietnam. It addresses the urgent question of whether natural stone is a sustainable paving material in a tropical climate under the impacts of climate change. By analysing the published contents of the official press, supported by data and information gathered from interviews with key experts, stakeholders, and urban residents, this paper argues that the actual impacts of natural stone use for pavements on the environment, economy, and society are strongly negative, compared to the positivity initially perceived in Hanoi’s scheme of changing the pavement facelift. It shows that by overemphasising appearance and imagined nationalism values when selecting natural stone, Hanoi government shows a slow progress in improving and balancing functional, social, environmental, and economic dimensions. The paper is significant in contributing to knowledge on pavement sustainability and sustainable materials while shedding light on the challenges of applying these theoretical perspectives into real-life practice.
Influence of densified silica fume on engineering properties of concrete containing coal bottom ash aggregate.
Authors: Ban Cheah Chee , Ping Kevin Khaw Le , Lapongan Roysten Habirin , Jia Liew Jia
Published: August 2023

Coal bottom ash (CBA) is a significant waste produced by the coal manufacturing power plant, harming the environment. CBA has been used in many studies to replace sand in cementitious materials. However, few studies have investigated the use of CBA in concrete as a sand replacement with densified silica fume (DSF) as a cement replacement. DSF is a potential supplementary cementitious material (SCM) to combat the engineering properties of concrete that are typically decreased when CBA is used as a replacement for natural aggregate. Therefore, the present study aimed to evaluate the influence of DSF on the engineering properties of concrete containing different content of CBA as a partial replacement for natural sand. The mix design of the ordinary Portland cement (OPC) and binary blended concrete comprised 90% OPC and 10% DSF by total binder’s weight. The CBA as the fine aggregate replacement was used at 25%, 50%, 75%, and 100% by total aggregate volume. The mechanical, porosity, absorption performance of DSF and CBA (DSF+CBA) concrete containing CBA as partial aggregate replacement material were investigated. DSF+CBA with 50% CBA replacement showed improved mechanical strength performance than control by 15% at 28d and 5.6% at 56d of curing. However, the total porosity performance for DSF+CBA concrete decrease as CBA content increases. In conclusion, the DSF as SCM in binary blended concrete with CBA content up to 50% achieved a better performance in terms of mechanical properties even though the porosity was marginally increased.
Effect of pre-treated waste tire rubber on properties of concrete
Authors: Sidhu Amandeep Singh , Singla Ritika , Siddique Rafat
Published: August 2023

In present day scenario the human activities have led to environmental degradation with increased urbanization contributing to many fold increase in constructing activities, which uses limited natural resources. Therefore, prevention of resource over-utilization and recycling of the waste is of utmost priority in construction sector. Waste tires rubber is one such potential material which can be used in concrete as replacement for fine aggregates replacement. This study represents the effect of addition of crumb rubber in concrete as sand replacement ranging from 5-20% on volume basis. The study evaluated the workability, compressive strength, ultrasonic pulse velocity (UPV), electrical resistivity and water permeability at 28 days. Tire rubber was also pre-treated with NaOH and KMnO4 as an effort to enhance its bonding characteristics. The contact angle was measure to test the efficacy of the treatment in reducing water hydrophobicity of crumb rubber. The treatment of tire rubber with NaOH and KMnO4 proved to be promising in regaining some of lost compressive strength and improved water permeability. However, both treatment processes didn’t have any significant effect on the workability. The NaOH treatment proved to be an overall better treatment than KMnO4 which was due to the reduced hydrophobicity as depicted by lower contact angle.
Fundamental study on rapid detection of the insufficient lateral resistance of ballasted railway tracks by dynamic loading
Authors: Xu C , Tada K , Nakamura T , Hayano K
Published: August 2023

To resume trains operation as soon as possible after disasters, it is necessary to quickly find out locations of ballasted railway with insufficient lateral ballast resistance. In this study, a new method was proposed to evaluate the lateral ballast resistance using dynamic lateral excitation. The dynamic method was performed on 1/9-scale ballasted railway models with ballast densities of 1.5 and 1.6 g/cm3. The simple harmonic excitation was generated from a pair of 20g flywheels, and the accelerations of the vibrator and the central sleeper were recorded by sensors attached on the central sleeper and the vibrator, respectively. Based on the obtained data sets, maximum accelerations as well as the maximum amplitudes of the lateral displacements of the vibrator and the central sleeper were analysed. It was found that the maximum accelerations of the vibrator were higher than those of the central sleepers. This was also true for the maximum amplitude of the lateral displacements. The ratio of the maximum amplitude of the lateral displacement of the central sleeper to that of the vibrator was evaluated. It was found that the amplitude ratio of the track model with the ballast density of 1.5 g/cm3 was higher than that with the ballast density of 1.6 g/cm3. This implies that the difference in the lateral ballast resistance owing to the difference in the ballast density may be detected based on the evaluation of the amplitude ratio.
Dynamically modulating the mid-infrared localized surface plasmon resonance of Al-doped ZnO nanocrystals
Authors: Jia Yan , Liu Dongqing , Wang Xinfei , Cheng Baizhang , Cheng Haifeng
Published: August 2023

The localized surface plasmon resonance (LSPR) regulation of semiconductor oxide nanocrystals (NCs) in the near-infrared region (0.8–2.5 μm) of the solar spectrum has attracted much attention for its potential in applications such as electrochromism and sensing. However, the LSPR modulation properties of doped semiconductor oxide NCs in the mid-infrared region (2.5–25 μm) have rarely been reported. Here, we synthesized aluminum-doped zinc oxide (AZO) NCs with various nominal Al doping contents (1–20at%). The LSPR absorption peaks of these films were regulated between ∼3.8 and 6.57 μm depending on the doping content. AZO NC films with 1at% nominal Al doping and a 1316 nm film thickness exhibited the highest electrochemical infrared absorption regulation, achieving 35.9% regulation at 3–5 μm and 32.5% at 7.5–13 μm. The infrared absorption regulation mechanism of the AZO NCs involved changes in the LSPR absorption intensity caused by electron injection/extraction into/from the surface depletion layer of the AZO NCs. After applying different voltages, the AZO NC film on the Al substrates exhibited different apparent temperatures, demonstrating its potential applications in infrared displays and camouflage.
The Impact of Rapid Drug Susceptibility Tests on Gonorrhea Burden and the Life Span of Antibiotic Treatments: A Modeling Study Among Men Who Have Sex With Men in the United States
Authors: Yaesoubi Reza , Xi Qin , Hsu Katherine , Gift Thomas L , St. Cyr Sancta B , Rönn Minttu M , Salomon Joshua A , Grad Yonatan H
Published: August 2023

Rapid point-of-care tests that diagnose gonococcal infections and identify susceptibility to antibiotics enable individualized treatment. This could improve patient outcomes and slow the emergence and spread of antibiotic resistance. However, little is known about the long-term impact of such diagnostics on the burden of gonorrhea and the effective life span of antibiotics. We used a mathematical model of gonorrhea transmission among men who have sex with men in the United States to project the annual rate of reported gonorrhea cases and the effective life span of ceftriaxone, the recommended antibiotic for first-line treatment of gonorrhea, as well as 2 previously recommended antibiotics, ciprofloxacin and tetracycline, when a rapid drug susceptibility test that estimates susceptibility to ciprofloxacin and tetracycline is available. The use of a rapid drug susceptibility test with ≥50% sensitivity and ≥95% specificity, defined in terms of correct ascertainment of drug susceptibility and nonsusceptibility status, could increase the combined effective life span of ciprofloxacin, tetracycline, and ceftriaxone by at least 2 years over 25 years of simulation. If test specificity is imperfect, however, the increase in the effective life span of antibiotics is accompanied by an increase in the rate of reported gonorrhea cases even under perfect sensitivity.
Somatic mutation effects diffused over microRNA dysregulation
Authors: Yu Hui , Jiang Limin , Li Chung-I , Ness Scott , Piccirillo Sara G M , Guo Yan
Published: August 2023

Motivation

As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios.

Results

To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes’ mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA–miRNA network.

Availability and implementation

The data underlying this article are available in MutMix, at http://innovebioinfo.com/Database/TmiEx/MutMix.php.
Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis
Authors: Bedford James A , Carine Mark , Chapman Mark A
Published: August 2023

Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress–tolerant varieties and genes that could limit future climate-changed–induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change–resilient phenotypes.
Comparison of standard and modified human landing catching techniques for blackfly collection
Authors: Atekem Kareen , Nwane Philippe , Nditanchou Rogers , Jeyam Anita , Wilhelm Aude , Selby Richard , Hamill Louise , Schmidt Elena , Dixon Ruth , Boakye Daniel
Published: August 2023

Background

Human landing catches (HLCs) are required to collect blackflies for entomological evaluation to verify onchocerciasis elimination. However, there are ethical concerns regarding exposure of vector collectors to infectious blackflies and safer alternative methods are needed. This study evaluated a modified HLC technique where collectors wore coloured trousers (blue, black or blue-black), protecting them from bites during fly collection, and their performance was compared with the standard.

Methods

The study was conducted in Makouopsap, Cameroon, in the Massangam health district for 4 months. Four collector pairs—one ‘standard’ (bare-legged) and three modified—were placed 50 m apart along known breeding sites on the Mbam and Nja Rivers. Collections were performed from 07:00 to 17:00 h, 4 d/month. Hourly rates of flies caught were analysed using a negative binomial generalised linear model to explore associations between flies caught and collection techniques and seasons.

Results

Overall, 17 246 blackflies were caught. There was no significant statistical difference in the number of blackflies and parous flies caught between black trousers and the standard. Thus there is a strong indication that wearing black trousers is a viable non-inferior alternative to the standard HLC.

Conclusions

Further studies are needed to confirm generalisability in different ecozones and transmission environments and among different blackfly species.
The heterogeneous impacts of government on health system efficiency in China's new health reform, 2010–2019
Authors: Zhang Jianghua , Guo Baojie , Fu Xuemei , Feng Xing Lin
Published: August 2023

Background

Contextualizing in China's recent health reform, we empirically explore the heterogeneous effects of two distinct government roles, accommodating private hospitals vs investing in public hospitals, on health system efficiency.

Methods

We use panel data covering 31 provinces during 2010–2019 to assess health system efficiency. We incorporate health service volumes and population health outcomes to ascertain health system outputs, employing the non-radial directional distance function to estimate efficiency. We employ Bayesian Tobit quantile regression to explore the heterogeneous effects of the share of private hospitals and government subsidy to public providers on efficiency.

Results

China's health system inefficiency scores range from 0 to 0.45. The association between the share of private hospitals and inefficiency score are only significant in higher-inefficiency quantiles (coefficients −0.0258, −0.0315 and −0.0327 for quantiles 0.7, 0.8 and 0.9), meaning a heterogeneously positive impact for low-efficiency provinces. The association between government subsidy and inefficiency score are positive for all quantiles (from 0.0339 to 0.0567), meaning persistent negative impacts on efficiency.

Conclusions

The heterogeneous impacts of the share of private hospitals suggest that the government should accommodate more private hospitals in provinces with low efficiency. The persistent negative impacts of government subsidy suggest that the government investment seems not be subjected to economic objectives.
Concordance of emergency department physicians’ decisions on HIV post-exposure prophylaxis with national guidelines: results from a retrospective cohort study
Authors: Heck Johannes , Höner zu Siederdissen Christoph , Krause Olaf , Schröder Sebastian , Schulze Westhoff Martin , Strunz Patrick-Pascal , Schumacher Carsten , Stichtenoth Dirk O , Bosch Jacobus J , Pape Thorben , Koop Felix , Krichevsky Benjamin
Published: August 2023

Background

Post-exposure prophylaxis (PEP) is an effective tool to prevent infection with HIV. Patients seeking PEP after potential HIV exposure usually present to the emergency department (ED). Our study sought to determine the concordance of ED physicians’ decisions on HIV-PEP with national guidelines (primary objective) and to assess the clinical relevance of drug–drug interactions (DDIs) between the HIV-PEP regimen and patients’ concomitant medication (secondary objective).

Methods

We conducted a retrospective cohort study at the ED of Hannover Medical School, Germany. Between 1 January 2018 and 31 December 2019, 113 of 11 246 screened patients presented to the ED after potential HIV exposure and were enrolled in the study.

Results

The median age of the patients (82.3% male) was 30 y (IQR 25–35.5), 85.8% of potential HIV exposures were characterised as sexual and 85.0% presented within 72 h. ED physicians’ decisions on HIV-PEP were concordant with national guidelines in 93.8%. No clinically relevant DDIs were detected.

Conclusions

ED physicians’ decisions on HIV-PEP were highly concordant with national guidelines. Approximately 1% of patient presentations to the ED were related to HIV exposure; therefore, training ED physicians on HIV transmission risk assessment and indications/contraindications for HIV-PEP is paramount.
Evaluation of in vitro pharmacodynamic drug interactions of ceftazidime/avibactam and fosfomycin in Escherichia coli
Authors: Kroemer Niklas , Martens Miklas , Decousser Jean-Winoc , Grégoire Nicolas , Nordmann Patrice , Wicha Sebastian G
Published: August 2023

Background

Combination therapy can increase efficacy of antibiotics and prevent emergence of resistance. Ceftazidime/avibactam and fosfomycin may be empirically combined for this purpose, but a systematic and quantitative evaluation of this combination is needed.

Objectives

In this study, a systematic analysis of the pharmacodynamic interactions of ceftazidime/avibactam and fosfomycin in clinical and isogenic Escherichia coli strains carrying genes coding for several carbapenemases or ESBLs was performed and pharmacodynamic interactions were quantified by modelling and simulations.

Methods

Pharmacodynamic interactions were evaluated in ‘dynamic’ chequerboard experiments with quantification of viable bacteria in eight isogenic and six clinical E. coli strains. Additionally, supplemental time–kill experiments were performed and genomic analyses were conducted on representative fosfomycin-resistant subpopulations. Models were fitted to all data using R and NONMEM®.

Results

Synergistic drug interactions were identified for 67% of the clinical and 75% of the isogenic isolates with a mean EC50 reduction of >50%. Time–kill experiments confirmed the interactions and modelling quantified EC50 reductions up to 97% in combination and synergy prevented regrowth of bacteria by enhanced killing effects. In 9 out of 12 fosfomycin-resistant mutants, genomic analyses identified previously reported mutations.

Conclusions

The broad synergistic in vitro activity of ceftazidime/avibactam and fosfomycin confirms the potential of the application of this drug combination in clinics. The substantial reduction of the EC50 in combination may allow use of lower doses or treatment of organisms with higher MIC values and encourage further research translating these findings into the clinical setting.
Chemokine Cxcl1–Cxcl2 heterodimer is a potent neutrophil chemoattractant
Authors: Sawant Kirti V , Sepuru Krishna Mohan , Penaranda Brigith , Lowry Emily , Garofalo Roberto P , Rajarathnam Krishna
Published: August 2023

Microbial infection is characterized by release of multiple proinflammatory chemokines that direct neutrophils to the insult site. How collective function of these chemokines orchestrates neutrophil recruitment is not known. Here, we characterized the role for heterodimer and show that the Cxcl1–Cxcl2 heterodimer is a potent neutrophil chemoattractant in mice and can recruit more neutrophils than the individual chemokines. Chemokine-mediated neutrophil recruitment is determined by Cxcr2 receptor signaling, Cxcr2 endocytosis, and binding to glycosaminoglycans. We have now determined heterodimer's Cxcr2 activity using cellular assays and Cxcr2 density in blood and recruited neutrophils in heterodimer-treated mice. We have shown that the heterodimer binds glycosaminoglycans with higher affinity and more efficiently than Cxcl1 or Cxcl2. These data collectively indicate that optimal glycosaminoglycan interactions and dampened receptor activity acting in concert in a dynamic fashion promote heterodimer-mediated robust neutrophil recruitment. We propose that this could play a critical role in combating infection.
Frozen shoulder. An overview of pathology and biology with hopes to novel drug therapies
Authors: Tamai Kazuya , Hamada Junichiro , Nagase Yuichi , Morishige Masahiko , Naito Masashi , Asai Hideaki , Tanaka Sakae
Published: August 2023

Frozen shoulder (FS) is a common disorder characterized by spontaneous onset of shoulder pain accompanied by progressive loss of range-of-motions. The cause of FS is still unclear, and radical therapy has not been established. With the final aim of preventing or curing FS at an earlier stage, we reviewed the pathological and biological features of this disease. Many studies indicate that the main pathology of FS is inflammation initially and fibrosis later. There are inflammatory cytokines, immune cells, fibrotic growth factors, and type-III collagen in the synovium and the joint capsule. The immune cell landscape switches from the macrophages to T cells. Activated fibroblasts seem to regulate the inflammatory and fibrotic processes. The imbalance between matrix metalloproteinases and tissue inhibitors of metalloproteases might promote fibrosis. Additionally, advanced glycation end-products are noted in the FS synovium. Diabetes mellitus and hypothyroidism are closely related to the development of FS. In terms of nonsurgical treatment, oral or intra-articular glucocorticoids are the only drugs that provide early benefit. Some other anti-inflammatory or antifibrotic drugs may potentially control the FS, but have not been proven effective in the clinical setting. Future studies should be targeted to develop steroid-sparing agents that inhibit biological events in FS.
Empirical comparisons between the past 5000 years of European and Eastern Mediterranean history and precipitation as recorded by ice accumulation in the GISP2 (Greenland) ice core
Authors: Holdaway Richard N
Published: August 2023

Adequate and regular levels of precipitation are fundamental to the sustained success of civilizations based on early agricultural production technologies, but palaeoclimate studies have concentrated on temperature. Potentially important insights into the fates of early civilization can be gained, however, from long term records of precipitation. Patterns in precipitation over the past 5000 years recorded by the ice accumulation balance in the GISP 2 ice core on the Greenland plateau appear to be correlated with major events in European and Mediterranean history. Near Greenland, Viking raids coincided with a major step-wise precipitation increase after 600 CE. Viking settlement of Greenland coincided with a precipitation low. During the Egyptian Old Kingdom period of pyramid-building precipitation was higher than when the New Kingdom tombs were excavated. The Old Kingdom and Akkadian Empire both failed as precipitation descended into the same prolonged precipitation low. The end of the New Kingdom and of the other Bronze Age civilizations in the eastern Mediterranean and around the Aegean Sea coincided with the lowest ice accumulation rate in the past 5000 years. The Roman ‘Imperial Good Times’ coincided with a precipitation high. The brief 2nd century imperial reigns and those of late New Kingdom pharaohs accompanied precipitation lows, as did the Antonine and Justinianic plagues. A trans-Alpine ‘production see-saw’ hypothesis, in which the same precipitation levels generated opposite effects, fits the sequence of successes and failures of western civilizations.
Molecular hydrogen positively regulates nitrate uptake and seed size by targeting nitrate reductase
Authors: Cheng Pengfei , Wang Yueqiao , Cai Chenxu , Li Longna , Zeng Yan , Cheng Xu , Shen Wenbiao
Published: August 2023

Although the sources of molecular hydrogen (H2) synthesis in plants remain to be fully elucidated, ample evidence shows that plant-based H2 can regulate development and stress responses. Here, we present genetic and molecular evidence indicating that nitrate reductase (NR) might be a target of H2 sensing that positively regulates nitrogen use efficiency (NUE) and seed size in Arabidopsis (Arabidopsis thaliana). The expression level of NR and changes of NUE under control and, in particular, low nitrogen supply were positively associated with H2 addition supplied exogenously or through genetic manipulation. The improvement in nitrate assimilation achieved by H2 was also mediated via NR dephosphorylation. H2 control of seed size was impaired by NR mutation. Further genetic evidence revealed that H2, NR, and nitric oxide can synergistically regulate nitrate assimilation in response to N starvation conditions. Collectively, our data indicate that NR might be a target for H2 sensing, ultimately positively regulating nitrate uptake and seed size. These results provide insights into H2 signaling and its functions in plant metabolism.
Pyrenoid-core CO2-evolving machinery is essential for diatom photosynthesis in elevated CO2
Authors: Shimakawa Ginga , Okuyama Akane , Harada Hisashi , Nakagaito Shuko , Toyoshima Yui , Nagata Kazuya , Matsuda Yusuke
Published: August 2023

Marine diatoms are responsible for up to 20% of the annual global primary production by performing photosynthesis in seawater where CO2 availability is limited while HCO3− is abundant. Our previous studies have demonstrated that solute carrier 4 proteins at the plasma membrane of the diatom Phaeodactylum tricornutum facilitate the use of the abundant seawater HCO3−. There has been an unconcluded debate as to whether such HCO3− use capacity may itself supply enough dissolved inorganic carbon (DIC) to saturate the enzyme Rubisco. Here, we show that the θ-type carbonic anhydrase, Ptθ-CA1, a luminal factor of the pyrenoid-penetrating thylakoid membranes, plays an essential role in saturating photosynthesis of P. tricornutum. We isolated and analyzed genome-edited mutants of P. tricornutum defective in Ptθ-CA1. The mutants showed impaired growth in seawater aerated with a broad range of CO2 levels, from atmospheric to 1%. Independently of growth CO2 conditions, the photosynthetic affinity measured as K0.5 for DIC in mutants reached around 2 mm, which is about 10 times higher than K0.5[DIC] of high-CO2–grown wild-type cells that have repressed CO2-concentrating mechanism levels. The results clearly indicate that diatom photosynthesis is not saturated with either seawater-level DIC or even under a highly elevated CO2 environment unless the CO2-evolving machinery is at the core of the pyrenoid.