bluuebunny/crossref_metadata_2025 huggingface dataset:
Classification of surface condition of flexible road pavement using Naïve Bayes theorem
Authors: Olowosulu A T , Kaura J M , Murana A A , Adeke P T
Published: March 2021

Data collection, availability and accuracy on road pavement surface condition have been identified as the major setback for pavement management system in low and medium income countries. This situation necessitates the adoption of historic dataset which often is characterised by missing and noisy data elements. The Naïve Bayes theorem which depends on conditional probabilities of prior events or attributes for condition classification and prediction was used to investigate the authenticity of surface condition classification of flexible road pavement. Some selected links of Federal Highways in Nigeria based on the availability of historic dataset were considered. The Naïve Bayes theorem as a data mining approach was implemented using Waikato Environment for Knowledge Analysis (WEKA) software which performed satisfactorily in surface condition classification with minimal margin of errors due to its ability to handle challenges of missing and noisy dataset. Results of classifications indicated that; links 716, 5, 8, 22 and 136 in Borno, Kwara, Lagos, Oyo and Plateau states respectively had relatively high level of unworthiness as at the time the data was collected, hence call for immediate maintenance and rehabilitation actions, while links 89, 375, 370, 130, 17, 332, 138, 144 and 255 from Anambra, Bendel, Imo, Kaduna, Ogun, Plateau, Rivers and Sokoto states respectively were worthy and had no cause for immediate maintenance.
Investigating the suitability of sakasaka sand as replacement of natural aggregates in concrete for low volume pavement construction
Authors: Adegoke D D , Sani R O , Daramola K O
Published: March 2021

The demand for access roads to vital services is on the high side in rural areas. This demand face much challenge due to the cost of construction. However, having the opportunity to use non-conventional materials that are naturally available in meeting this demand will ease people living in such environs. It is on this note that an investigation was carried out on an indigenous, naturally available sand popularly known as Sakasaka by Ilesha indigenes to ascertain its suitability for pavement construction. The Sakasaka collected from Ilesha borrow site, Ilesha West Local Government Area of Osun State, was used to produce concrete cubes that were tested after curing for 7, 14, 21, 28, 56, and 112 days respectively to know the strength of the material and compared to theoretical strength. Prior to the cubes production, some investigations such as chemical analysis, Sieve analysis, Specific gravity and so on were carried out on the sand. The study investigates the physical properties, chemical components of Sakasaka as well as the compressive strength properties of the concrete produced at ratio 1:2:4 using Cements A, B, and C 3x brand. The total numbers of cubes cast were 162 with a concrete cube size of 150x150x150mm. Sieve analysis, specific gravity, slump tests were also carried out for different water-cement ratios for the three cement. The concrete cubes were tested at the ages of 7, 14, 21, 28, 56, and 112 days. The effects of cements (A, B, and C) on the all-in-aggregate was investigated with respect to compressive strength at different curing age. From the results obtained, the compressive strengths of cubes were 17.76 N/mm2, 19.92 N/mm2 and 20.5N/mm2 which was in line with the standard compressive strength of concrete mix 1:2:4 at 28days.
Protection performance of orange oil distillates on low carbon steel in dilute acid electrolytes
Authors: Loto R T , Mbah E H , Ugada J I
Published: March 2021

Orange essential oil distillate (OOE) was studied for its inhibition performance on low carbon steel in 0.5 M H2SO4and HCl aqueous electrolyte by electrochemical method and open circuit potential measurement. OOE performance was significantly proportional to it concentration with highest protection efficiency of 76.93% and 94.90% at optimal OOE concentration (10% OOE) in H2SO4and HCl electrolyte. The performance of OOE at low concentration in H2SO4was quite poor with inhibition efficiency values below 40%. OOE exhibited greater inhibition action in HCl solution with effective performance beginning at 4% OOE concentration compared to 6% concentration in H2SO4electrolyte. Corrosion potential deviated basically in the anodic direction signifying the dominant inhibition effect to be through surface coverage of the steel surface. OOE exhibited mixed type corrosion inhibition. Open circuit potential graphs show OOE increases the thermodynamic fluctuation of the carbon steel in H2SO4solution relative to the plots at 0% OOE, despite effective protection. In HCl, the open circuit potential plots were more electropositive relative to the plots at 0% OOE signifying decreased tendency to corrosion. Optical images of the carbon steel after evaluation with and without OOE significantly contrast each other.
Predicting the Compressive Strength of Concrete By Ultrasonic Pulse Velocity
Authors: Ofuyatan O , Olowofoyeku A , Oluwafemi J , Ighalo J
Published: March 2021

The key resolution of non-destructive methods applied to concrete structures is to offer a suitable estimate of the quality of the material. One of the modern methods used in the test of concrete strength is the non-destructive testing applying the ultrasonic pulse velocity (UPV). In this study, the ultrasonic pulse velocity technique as non-destructive testing of concrete was used to distinguish concrete mixture design and show the predictive relationship between compressive strength and UPV. The effect of various grades of concrete (M15, M20, M25, M30, and M35) with water to cement ratio (w/c) of 0.45 and 0.5 were examined. It was observed that grade M15 cubes had the lowest transit time (37.6 – 41.2 µs) and grade M35 cubes had the highest transit time (48.7 – 49.9 µs) showing that the concrete with short transit time generates the highest pulse velocity than that with low transit time. Grade M15 cubes had the highest pulse velocity (3.6 – 4.0 km/s) and grade M35 cubes had the lowest pulse velocity (3.0 – 3.1 km/s). M15 cubes had the lowest actual compressive strength (18.1 – 19.3 N/mm2) and grade M35 cubes have the highest actual compressive strength (34.6 – 36.0 N/mm2). There was a good correlation between compressive strength and UPV. The study furthermore revealed that UPV can be used to accurately predict the compressive strength of concrete. For all concrete grades, the percentage variation did not exceed ± 2.5%.
Effect of sorghum husk ash and calcium chloride on compressive strength of grade 20 concrete
Authors: Tijani M A , Olawale S O A , Abdullahi L , Aliyu M A , Ajagbe W O
Published: March 2021

This study examined the influence of sorghum husk ash (SHA) and calcium chloride (CaCl2) as fractional substitution of cement in grade 20 concrete. Sorghum husk Ash (SHA) was gotten by burning of sorghum husk at a regulated temperature. The substitution of cement by SHA were 0, 5, 10, 15, 20 and 25%. A fixed amount of 1% CaCl2 was mixed with Cement/SHA in all the test samples apart from control mixture. Sample sizes of 150 x 150 x 150 mm concrete cubes were cast and healed in water respectively for 7 as well as 28 days. The tests carried out on prepared fresh and hardened concrete were slump and compressive strength. The result of slump showed that the concrete turn out to be stiffer with increase in proportion of SHA. The 28 day compressive strengths result shows that 5%SHA/1%CaCl2 have the maximum strength of 26.45 N/mm2 followed by 10% (25.01 N/mm2), 0%SHA/1%CaCl2 (23.11 N/mm2), 15%SHA/1%CaCl2 (22.45 N/mm2), 20%SHA/1%CaCl2 (20.90 N/mm2) and 25%SHA/1%CaCl2 (18.13 N/mm2). This implies that the best addition of SHA/CaCl2 as fractional substitution for cement in concrete is in the range 0 - 20% since their compressive strength results were above 20 N/mm2 specified for grade 20 concrete. Incorporation of 5%SHA/1%CaCl2 and 10%SHA/1%CaCl2 substitution would yield a concrete of greater compressive strength than standard grade 20 concrete.
Performance evaluation of the mechanical and durability properties of concrete reinforced with hybridized fibers
Authors: Awolusi T F , Falana J N , Ajayi P O , Akinkurolere O O , Aluko O G
Published: March 2021

The hybridization of two different elements is done for synergy and better performance. This study investigates the effects of combining bamboo, steel, and carpet fibers, as reinforcement in concrete. The steel and carpet fibers were obtained from discarded tires, and carpets, respectively. The addition of fibers to the mixes was kept constant at 2% of the concrete volume. The first category concrete mix contained a hybrid of steel and carpet fibers at a fraction of 1.75% and 0.25%, respectively, the second category combined steel and bamboo fibers at a fraction of 1% - 1%. The third category contained only steel fibers at a 2% volumetric fraction. The mechanical property of the concrete was evaluated through compressive and flexural strengths, while the durability was examined through water absorption and the acid attack. The compressive strength results obtained for the three categories of fiber reinforced concrete ranged between 7.2 and 12.8 N/mm2, with the third category performing better. Also, the flexural strength results ranged between 5.37 and 7.47 N/mm2, with the first category having the best results. The second category had the least water absorption capacity, and the concrete reinforced with only steel fibers showed the best acid attack resistance. The results also confirmed that short discontinuous fibers are suitable strength and durability enhancers in producing durable eco-friendly concrete.
A review on the impact of information and communication technology in civil engineering practice
Authors: Oluwafemi J , Ede A , Ofuyatan O , Oyebisi S , Bankole D
Published: March 2021

Information and Communication Technology is playing a vital role in virtually almost every field of human operation such as education sector, medical field, banking sector, agricultural sector, field of engineering and more. Information and Communication Technology has substantially eased operations in several fields and has helped to save resources in the likes of labor, cost and time. It has also helped to drastically increase the speed at which work is done. This paper reviews the impact of information and communication technology in civil engineering practice and examines operations such as the construction industry, road transportation industry, engineering education, structural engineering, energy efficient buildings, building preservation and engineering design. Information and Communication Technology is seen to be very relevant for sustainability in civil engineering practices across literature.
Hazard Assessment and Implementation Strategies for Mitigating of Flood and Erosion in Nigeria
Authors: Oyebode O J
Published: March 2021

There are notching unresolved issues and environmental hazards traceable to flood and erosion in major rural areas and notable communities in Nigeria. Researchers’ efforts on erosion control and flood mitigation have not yielded notable fruits due to inadequate planning and implementation strategies. Maintenance of roads and other infrastructures are the bed rock of any development round the globe. This paper assessed recent occurrence of flood and erosion. The study examined the causes, urban and regional planning of the affected area, construction practices, damages and maintenance practices. Questionnaires, field study and interview of experts were wont to elicit information from people within the affected location, officials from state and native government agencies charged with rehabilitation of affected areas. The research finding revealed that there are inadequate drainage systems, lack of enforcement of plan, corruptions, failure of systems, poor supervision, construction malpractices, lackadaisical attitude and lack of maintenance culture. Implementation strategies were highlighted to avert flood and erosion ravaging several areas of the country. The paper concluded that stakeholders, researchers, engineers should partner with government agencies within the planning, construction, management and maintenance of rural and concrete drainages for adequate funding and sustainable construction. It is recommended that strategies for alleviating flood and erosion should be implemented supported latest technology for sustainable infrastructural development. Periodic hazard assessment should be planned in various geopolitical zones especially Lagos, Niger delta and rain forest region of Nigeria. Land use control, landscape maintenance, weather stations, proper enforcement of construction works consistent with plan should be strategically put in situ for effective monitoring and alleviation of flood and erosion in Nigeria.
Corrosion inhibition and statistical data of thiocarbanilide and thiocarbanilide admixed with 4-hydroxy-3-methoxybenzaldehyde on carbon steel in dilute acid media
Authors: Loto R T , Loto C A
Published: March 2021

The inhibition performance of thiocarbanilide (TD) and thiocarbanilide admixed with 4-hydroxy-3-methoxybenzaldehyde (TDHM) on the corrosion of mild steel in 1M H2SO4 and HCl acid solutions was studied through coupon measurement. Data obtained showed the optimal performance of TD is 71.69% in H2SO4 and 83.14% HCl acid solution respectively. TDHM performed more effectively with optimal inhibition efficiency of 96.77% and 97.21% in both acids. The result showed the performance of corrosion inhibiting compounds improves through synergistic interaction with other compounds. However, exposure time and inhibitor concentration strongly influenced the performance of the compounds at varying degrees. Statistical data shows the standard deviation for inhibition efficiency of the compounds was significantly higher in H2SO4 compared to HCl due to the high degree of variation analogous to exposure time and stability of the inhibitor molecules. TD and TDHM generally showed lower standard of deviation, higher mean value, lower margin of error and higher proportion of inhibition efficiency data above 70% inhibition performance. Statistical data from analysis of variance depict both exposure time and inhibitor concentration is statistically relevant, and influences the inhibition performance of TD and TDHM compounds. However, the influence of concentration is significantly limited compared to exposure time with statistical relevance values above 60%
Correlating the thermomechanical indexes of concrete modified with anacardium occidentale nutshell ash using linear model polynomial analysis
Authors: Oyebisi S O , Igba U T , Ede A N , Oluwafemi J O , Mark G O
Published: March 2021

This study correlated the thermal and mechanical properties of concrete produced with anacardium occidentale (cashew) nutshell ash (AONA). Cashew nutshells, agricultural waste products, was valorized to obtain AONA. AONA was replaced at 5, 10, 15, and 20 wt% of cement to produce concrete grade 25 MPa. Density, compressive strength, and thermal conductivity of the concrete samples were determined at 28 days curing, and the results were correlated using regression model analysis. The experimental findings revealed that the compressive strength increased with increasing AONA content. Moreover, both density and thermal conductivity reduced as AONA content increased. Besides, the correlation yielded a high precision with 97% “R2”. Thus, AONA has proved to exhibit higher mechanical strength with excellent thermal insulation when utilized as supplementary cementitious material (SCM) in concrete production. The developed model can also be applied to the correlation of thermomechanical properties of concrete incorporating SCMs in that time, energy, and cost in conducting laboratory works would be reduced.
Effect of precursor ratio on the morphological and optical properties of CVD-grown monolayer MoS2 nanosheets
Authors: Zhu Zusong , You Jiancun , Zhu Dequan , Jiang Guisheng , Zhan Shengbao , Wen Jun , Xia Qiangsheng
Published: March 2021

Atmosphere pressure chemical vapor deposition (CVD) is one of the most powerful methods of synthesizing high quality and large area MoS2 films with a reasonable cost. In our work, the large-scale and high crystalline quality monolayer MoS2 nanosheets were synthesized on Silicon substrate with a 300 nm oxide layer using MoO3 and S powders as precursors by an atmosphere pressure CVD. The results suggest that the surface morphology, crystalline quality and luminescence of CVD-grown MoS2 nanosheets can be tunable by controlling the precursor ratio (the effective Mo: S ratio). Excessive S-rich atmosphere is favor to synthesize large-size and high crystalline quality monolayer MoS2 nanosheets with sharp corners and straight edges. This study may provide insight into the synthesis of large-scale and high crystalline quality MoS2 films.
Pore-level CFD investigation of velocity and pressure dispositions in microcellular structures
Authors: Otaru A J , Samuel M B
Published: March 2021

Pore-level computational modelling and simulation have recently become the focus of considerable attention in the field of transport in porous media. This study presents pore-structure characterisation and computational fluid dynamics (CFD) modelling and simulation of fluid flow distribution across ‘real’ and ‘structure-adapted’ porous metallic structures derived from tomography datasets at the microscale level. The resulting CFD predicted pressure drop data as a function of superficial fluid velocity ranging between 0 and 6.0 m.s−1were used to account for the viscous (permeability,k0) and inertial (Form drag coefficient,C) terms of the porous samples. CFD modelling confidence was established by validating with experimental measurements for foam samples available in the literature. Exprerimental values ofk0were found to be consistent with values available in the literature, while observable deviations of experimental measurements ofCfrom predicted values (in some cases) strongly support the reliability of the inertial terms in superficial fluid flow velocity, nature of fluid, and level of extended tortuous pathway in porous metallic structures. The adaptation of the ‘real’ structures through erosion and dilation of their skeletal phases enabled the creation of ‘semi-virtual’ structures; thereby providing an in-depth understanding of the manifestation of flowing fluid from Darcy to inertial and a graphical relationship linking pore-structure related parameters and fluid flow properties of the porous media was substantiated.
Investigations on microstructural characteristics and mechanical properties of 316 L stainless steel welded joints using nickel coated filler material by gas tungsten arc welding
Authors: D Aravindkumar , R Thirumalai
Published: March 2021

The main objective of this present study is to weld the 316 L stainless steel (SS) joints by gas tungsten arc welding (GTAW) process using nickel coated filler materials. The existing modified filler metals with flux coatings used in GTAW are generally accompanied with more complications. Therefore it is essential to suppress complications and enhance the welding strength which significantly depends on filler metals properties. In this work, the filler materials used in GTAW are coated with nickel in several grades for welding process. The results of these filler metals are compared with the Plain-316 filler metal. Ni-304 filler metal shows better uniformed weldment and heat affected zone (HAZ) with less planer slip micorstrucutre on its surface. The tensile test results reveal that Ni-316, Ni-304 & Ni-308 filler metals produces fracture on the parent metal. Among the various filler metals used, Ni-304 filler metal shows the highest impact toughness of 69.10 J and it is 71% higher toughness than Plain-316 filler. Average hardness of Ni-308 filler metal is 2.78% higher than the Plain-316 filler metal. Scanning electron microscope (SEM) images of weldments and HAZ were analysed to investigate the effect of nickel on the microstructure changes.
Metal substitution in the metalloporphyrin linker of metal−organic framework PCN-601 for photocatalytic CO2 reduction
Authors: Liu Ting-Ting , Wu Xin-Ping , Gong Xue-Qing
Published: March 2021

Metalloporphyrinic metal–organic framework PCN-601 exhibits high photocatalytic performance for CO2 reduction. The photoreduction site was speculated to be the Ni atoms in the nodes and thus the single Ni atoms in the porphyrin centers are not effectively utilized. In this study, we applied Kohn–Sham density functional theory to investigate the effect of metal (Fe, Co, or Cu) substitution in the Ni-porphyrin linker of PCN-601 on the photocatalytic CO2 reduction. Our results show that the photocatalytic properties of Ni-porphyrin-based PCN-601, including photoexcitation, visible-light absorption, vacuum-aligned energy level, and CO2 adsorption strength and configuration, can be further optimized by Fe substitution in the Ni-porphyrin linker. In addition, Co-porphyrin-based PCN-601 is also found to be a promising candidate for CO2 photoreduction though its visible-light absorption is relatively weak in comparison with its Fe- and Ni-based analogs.
Anomaly detection in gravitational waves data using convolutional autoencoders
Authors: Morawski Filip , Bejger Michał , Cuoco Elena , Petre Luigia
Published: March 2021

As of this moment, 50 gravitational wave (GW) detections have been announced, thanks to the observational efforts of the LIGO-Virgo collaboration, working with the Advanced LIGO and the Advanced Virgo interferometers. The detection of signals is complicated by the noise-dominated nature of the data. Conventional approaches in GW detection procedures require either precise knowledge of the GW waveform in the context of matched filtering searches or coincident analysis of data from multiple detectors. Furthermore, the analysis is prone to contamination by instrumental or environmental artifacts called glitches which either mimic astrophysical signals or reduce the overall quality of data. In this paper, we propose an alternative generic method of studying GW data based on detecting anomalies. The anomalies we study are transient signals, different from the slow non-stationary noise of the detector. The anomalies presented in the manuscript are mostly based on the GW emitted by the mergers of binary black hole systems. However, the presented study of anomalies is not limited only to GW alone, but also includes glitches occurring in the real LIGO/Virgo dataset available at the Gravitational Waves Open Science Center. To search for anomalies we employ deep learning algorithms, namely convolutional autoencoders, which are trained on both simulated and real detector data. We demonstrate the capabilities of our deep learning implementation in the reconstruction of injected signals. We study the influence of the GW strength, defined in terms of matched filter signal-to-noise ratio, on the detection of anomalies. Moreover, we present the application of our method for the localization in time of anomalies in the studied time-series data. We validate the results of anomaly searches on real data containing confirmed gravitational wave detections; we thus prove the generalization capabilities of our method, towards detecting GWs unknown to our deep learning models during training.
Structural and mechanical properties of nanocrystalline Ga2O3 films made by pulsed laser deposition onto transparent quartz substrates
Authors: Zade Vishal , Makeswaran Nanthakishore , Boyce Brad L , Paraguay-Delgado Francisco , Ramana C V
Published: March 2021

This work reports on the correlation between structure, surface/interface morphology and mechanical properties of pulsed laser deposited (PLD) β-Ga2O3 films on transparent quartz substrates. By varying the deposition temperature in the range of 25 °C–700 °C, ∼200 nm thick Ga2O3 films with variable microstructure and amorphous-to-nanocrystalline nature were produced onto quartz substrates by PLD. The Ga2O3 films deposited at room temperature were amorphous; nanocrystalline Ga2O3 films were realized at 700 °C. The interface microstructure is characterized with a typical nano-columnar morphology while the surface exhibits the uniform granular morphology. Corroborating with structure and surface/interface morphology, and with increasing deposition temperature, tunable mechanical properties were seen in PLD Ga2O3 films. At 700 °C, for nanocrystalline Ga2O3 films, the dense grain packing reduces the elastic modulus Er while improving the hardness. The improved crystallinity at elevated temperatures coupled with nanocrystallinity, the β-phase stabilization is accounted for the observed enhancement in the mechanical properties of PLD Ga2O3 films. The structure-morphology-mechanical property correlation in nanocrystalline PLD β-Ga2O3 films deposited on quartz substrates is discussed in detail.
Acute ethanol stress induces sumoylation of conserved chromatin structural proteins inSaccharomyces cerevisiae
Authors: Bradley Amanda I. , Marsh Nicole M. , Borror Heather R. , Mostoller Kaitlyn E. , Gama Amber I. , Gardner Richard G.
Published: March 2021

All organisms experience stress, and stress adaptation is essential to survival. Eukaryotes have evolved stress response mechanisms, many of which occur via posttranslational protein modifications. This study examines the effects of acute ethanol stress on protein sumoylation in Saccharomyces cerevisae.
Regulation of apical constriction via microtubule- and Rab11-dependent apical transport during tissue invagination
Authors: Le Thao Phuong , Chung SeYeon
Published: March 2021

During tissue invagination, contractile actomyosin structures generate the cellular forces that drive apical constriction. Using the Drosophila embryonic salivary gland as a model for epithelial tube formation, we show that microtubule- and Rab11-dependent apical transport is critical for regulating actomyosin networks during invagination.
Arf1 directly recruits the Pik1-Frq1 PI4K complex to regulate the final stages of Golgi maturation
Authors: Highland Carolyn M. , Fromme J. Christopher
Published: March 2021

Arf1 oversees a myriad of conserved processes at the Golgi complex. This work provides new insight into the relationship between Arf1 activity and PI4P synthesis in budding yeast by demonstrating that Arf1 directly recruits the Pik1-Frq1 PI 4-kinase complex to the Golgi. PI4P then primes the Golgi for the final stages of Golgi maturation.
Can person-centred care for people living with dementia be delivered in the acute care setting?
Authors: Abbott Rebecca A , Cheeseman Debbie , Hemsley Anthony , Thompson Coon Jo
Published: March 2021

The need to improve care for people living with dementia in the hospital setting has long been recognised. Person-centred care has the potential to improve the experience of care for persons living with dementia and their carers, and has been shown to improve the experiences of hospital staff caring for the persons living with dementia, however it remains challenging to deliver in a time- and task-focussed acute care setting. This commentary suggests that to embed person-centred care across the hospital environment, cultural changes are needed at organisational and ward levels. In particular there needs to be: leadership that supports and advocates for workforce capacity to recognise and meet both psychological and physical needs of people living with dementia, promotion of physical environments that support familiarisation and social interactions, an inclusive approach to carers and the development of a culture of sharing knowledge and information across hierarchies and roles. An evidence-based set of pointers for service change are described which highlight institutional and environmental practices and processes that need to be addressed in order for person-centred care to become part of routine care.
Invited Commentary: Code Review—An Important Step Toward Reproducible Research
Authors: Platt Robert W
Published: March 2021

In this issue of the Journal, Vable et al. (Am J Epidemiol. 2021;190(10):2172–2177) discuss a systematic approach to code review as a way to improve reproducibility in epidemiologic research. Reproducibility needs to become a cornerstone of our work. In the present commentary, I discuss some of the implications of their proposal, other methods to reduce coding mistakes, and other methods to improve reproducibility in research in general. Finally, I discuss the fact that no one of these approaches is sufficient on its own; rather, these different steps need to become part of a culture that prioritizes reproducibility in research.
Evaluation of the timing of MRSA PCR nasal screening: How long can a negative assay be used to rule out MRSA-positive respiratory cultures?
Authors: Turner Stephen C , Seligson Nathan D , Parag Bhavyata , Shea Katherine M , Hobbs Athena L V
Published: March 2021

Purpose

Previous studies indicate that the polymerase chain reaction (PCR) nasal assay for methicillin-resistant Staphylococcus aureus (MRSA) has a consistently high (>95%) negative predictive value (NPV) in ruling out MRSA pneumonia; however, optimal timing of PCR assay specimen and respiratory culture collection is unclear.

Methods

A study including 736 patients from a community hospital system was conducted. Patients were included if they had undergone MRSA nasal screening with a PCR assay and had documented positive respiratory culture results.

Results

In the full cohort, the MRSA PCR nasal screen assay was demonstrated to have an NPV of 94.9% (95% confidence interval [CI], 92.8%-96.5%) in ruling out MRSA-positive respiratory cultures. When evaluating the NPV by level of care (ie, where the MRSA PCR nasal assay sample was collected), no significant difference between values for samples collected in an intensive care unit vs medical/surgical units was identified (NPV [95%CI], 94.9% [92.7%-96.6%] vs 95.3% [88.4%-98.7%]). Additionally, NPV remained high with use of both invasive (NPV [95%CI], 96.8% [92.7%-99.0%]) and noninvasive (NPV [95%CI], 94.5% [91.7%-96.2%]) respiratory sampling methods. Finally, when evaluating the effect of time between MRSA PCR nasal screening and respiratory sample collection, we found high NPVs for all evaluated timeframes: within 24 hours, 93.8% (90.1%-96.4%); within 25 to 48 hours, 98.6% (92.7%-100.0%); within 49 hours to 7 days, 95.7% (91.4%-98.3%); within 8 to 14 days, 92.9% (85.1%-97.3%); and after more than 14 days, 95.5% (84.5%-99.4%).

Conclusion

We report high NPVs for up to 2 weeks between specimen collections, which allows clinicians to use a negative MRSA PCR nasal screen assay to rule out MRSA pneumonia, potentially leading to decreased exposure to MRSA-active antibiotics.
Health Effects of Chronic Intermittent Hypoxia at a High Altitude among Chilean Miners: Rationale, Design, and Baseline Results of a Longitudinal Study
Authors: Muñoz Sergio , Nazzal Carolina , Jimenez Daniel , Frenz Patricia , Flores Patricia , Alcantara-Zapata Diana , Marchetti Nella
Published: March 2021

Objectives

This study aims to assess the health effects on mining workers of exposure to chronic intermittent hypoxia (CIH) at high- and very high-altitude mining compared with similar work at lower altitudes in Chile, and it also aims to constitute the baseline of a 5-year follow-up study.

Methods

We designed a cross-sectional study to assess health conditions in 483 miners working at 2 levels of altitude exposure: 336 working at a very high or high altitude (HA; 247 above 3900–4400 m, and 89 at 3000–3900 m), and 147 below 2400 m. Subjects were randomly selected in two stages. First, a selection of mines from a census of mines in each altitude stratum was made. Secondly, workers with less than 2 years of employment at each of the selected mines were recruited. The main outcomes measured at the baseline were mountain sickness, sleep alterations, hypertension, body mass index, and neurocognitive functions.

Results

Prevalence of acute mountain sickness (AMS) was 28.4% in the very high-altitude stratum (P = 0.0001 compared with the low stratum), and 71.7% experienced sleep disturbance (P = 0.02). The adjusted odds ratio for AMS was 9.2 (95% confidence interval: 5.2–16.3) when compared with the very high- and low-altitude groups. Motor processing speed and spatial working memory score were lower for the high-altitude group. Hypertension was lower in the highest-altitude subjects, which may be attributed to preoccupational screening even though this was not statistically significant.

Conclusions

Despite longer periods of acclimatization to CIH, subjects continue to present AMS and sleep disturbance. Compromise of executive functions was detected, including working memory at HA. Further rigorous research is warranted to understand long-term health impacts of high-altitude mining, and to provide evidence-based policy recommendations.
By the narrowest of margins: nano-scale modification of pit membranes and the fate of plants during drought. A commentary on: ‘Intervessel pit membrane thickness best explains variation in embolism resistance amongst stems ofArabidopsis thalianaaccessions’
Authors: Brodersen Craig R
Published: March 2021

This article comments on:

Ajaree Thonglim, Sylvain Delzon, Maximilian Larter, Omid Karami, Arezoo Rahimi, Remko Offringa, Joost J. B. Keurentjes, Salma Balazadeh, Erik Smets and Frederic Lens, Intervessel pit membrane thickness best explains variation in embolism resistance amongst stems of Arabidopsis thaliana accessions, Annals of Botany, Volume 128, Issue 2, 23 July 2021, Pages 171–182, 10.1093/aob/mcaa196
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization
Authors: Lou Shaoke , Li Tianxiao , Liu Jason , Gerstein Mark
Published: March 2021

Motivation

Traditionally, an individual can only query and retrieve information from a genome browser by using accessories such as a mouse and keyboard. However, technology has changed the way that people interact with their screens. We hypothesized that we could leverage technological advances to use voice recognition as an interactive input to query and visualize genomic information.

Results

We developed an Amazon Alexa skill called Gene Tracer that allows users to use their voice to find disease-associated gene information, deleterious mutations and gene networks, while simultaneously enjoy a genome browser-like visualization experience on their screen. As the voice can be well recognized and understood, Gene Tracer provides users with more flexibility to acquire knowledge and is broadly applicable to other scenarios.

Availabilityand implementation

Alexa skill store (https://www.amazon.com/LT-Gene-tracer/dp/B08HCL1V68/) and a demonstration video (https://youtu.be/XbDbx7JDKmI).

Supplementary information

Supplementary data are available at Bioinformatics online.
ASHLEYS: automated quality control for single-cell Strand-seq data
Authors: Gros Christina , Sanders Ashley D , Korbel Jan O , Marschall Tobias , Ebert Peter
Published: March 2021

Single-cell DNA template strand sequencing (Strand-seq) enables chromosome length haplotype phasing, construction of phased assemblies, mapping sister-chromatid exchange events and structural variant discovery. The initial quality control of potentially thousands of single-cell libraries is still done manually by domain experts. ASHLEYS automates this tedious task, delivers near-expert performance and labels even large datasets in seconds.

Availability and implementation

github.com/friendsofstrandseq/ashleys-qc, MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
Authors: Zhang Ruoshi , Mirdita Milot , Levy Karin Eli , Norroy Clovis , Galiez Clovis , Söding Johannes
Published: March 2021

SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.

Availability and implementation

SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS: https://github.com/soedinglab/spacepharer.

Supplementary information

Supplementary data are available at Bioinformatics online.
AASRA: an anchor alignment-based small RNA annotation pipeline†
Authors: Tang Chong , Xie Yeming , Guo Mei , Yan Wei
Published: March 2021

Small noncoding RNAs deep sequencing (sncRNA-Seq) has become a routine for sncRNA detection and quantification. However, the software packages currently available for sncRNA annotation can neither recognize sncRNA variants in the sequencing reads, nor annotate all known sncRNA simultaneously. Here, we report a novel anchor alignment-based small RNA annotation (AASRA) software package (https://github.com/biogramming/AASRA). AASRA represents an all-in-one sncRNA annotation pipeline, which allows for high-speed, simultaneous annotation of all known sncRNA species with the capability to distinguish mature from precursor microRNAs, and to identify novel sncRNA variants in the sncRNA-Seq sequencing reads.
Cortical inflammation and brain signs of high-risk atherosclerosis in a non-human primate model
Authors: Di Cataldo Vanessa , Debatisse Justine , Piraquive Joao , Géloën Alain , Grandin Clément , Verset Michaël , Taborik Fabrice , Labaronne Emmanuel , Loizon Emmanuelle , Millon Antoine , Mury Pauline , Pialoux Vincent , Serusclat André , Lamberton Franck , Ibarrola Danielle , Lavenne Franck , Le Bars Didier , Troalen Thomas , Confais Joachim , Crola Da Silva Claire , Mechtouff Laura , Contamin Hugues , Fayad Zahi A , Canet-Soulas Emmanuelle
Published: March 2021

Atherosclerosis is a chronic systemic inflammatory disease, inducing cardiovascular and cerebrovascular acute events. A role of neuroinflammation is suspected, but not yet investigated in the gyrencephalic brain and the related activity at blood−brain interfaces is unknown. A non-human primate model of advanced atherosclerosis was first established using longitudinal blood samples, multimodal imaging and gene analysis in aged animals. Non-human primate carotid lesions were compared with human carotid endarterectomy samples. During the whole-body imaging session, imaging of neuroinflammation and choroid plexus function was performed. Advanced plaques were present in multiple sites, premature deaths occurred and downstream lesions (myocardial fibrosis, lacunar stroke) were present in this model. Vascular lesions were similar to in humans: high plaque activity on PET and MRI imaging and systemic inflammation (high plasma C-reactive protein levels: 42 ± 14 µg/ml). We also found the same gene association (metabolic, inflammatory and anti-inflammatory markers) as in patients with similar histological features. Metabolic imaging localized abnormal brain glucose metabolism in the frontal cortex. It corresponded to cortical neuro-inflammation (PET imaging) that correlated with C-reactive protein level. Multimodal imaging also revealed pronounced choroid plexus function impairment in aging atherosclerotic non-human primates. In conclusion, multimodal whole-body inflammation exploration at the vascular level and blood−brain interfaces identified high-risk aging atherosclerosis. These results open the way for systemic and central inflammation targeting in atherosclerosis in the new era of immunotherapy.
Left ventricular free wall perforation by a right ventricular pacemaker lead: a case report
Authors: Satomi Natsuko , Enta Kenji , Otsuka Masato , Ishii Yasuhiro , Asano Ryota , Sawa Shigeharu
Published: March 2021

Background

Lead perforation is one of the major complications of pacemaker implantation, but cases of right ventricular (RV) lead perforation through the septum and left ventricle are rarely reported. We described a rare case of left ventricular (LV) free wall perforation by an RV lead and the management of this complication.

Case summary

An 84-year-old man was admitted with a dual-chamber pacemaker due to pacing failure caused by an RV lead fracture. New lead implantation was performed on the next day, but pacing failure occurred again on the second post-operative day (POD). We found the lead perforation on the fluoroscopy during temporary pacemaker insertion. Computed tomography scan and transthoracic echocardiogram showed that the added lead perforated through both the septum and LV free wall. A new lead was inserted on the fourth POD, and an off-pump open chest surgery for extraction of the penetrating lead was performed uneventfully on the 20th POD.

Discussion

We considered that some features of the lead (SelectSecure 3830-69, Medtronic) may be related to this complication, as the lead was very thin, had a non-retractable bare screw and was inserted with a dedicated delivery catheter. We have to be careful when performing implantation of this kind of lead to avoid such a rare complication.
Effects of sheared chromatin length on ChIP-seq quality and sensitivity
Authors: Keller Cheryl A , Wixom Alexander Q , Heuston Elisabeth F , Giardine Belinda , Hsiung Chris C -S , Long Maria R , Miller Amber , Anderson Stacie M , Cockburn April , Blobel Gerd A , Bodine David M , Hardison Ross C
Published: March 2021

Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focused on sonication, a user-controlled variable, to produce sheared chromatin. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measuring the distribution of resultant fragment lengths prior to ChIP-seq. This systematic study was complemented with a retrospective analysis of additional experiments. We found that the level of sonication had a pronounced impact on the quality of ChIP-seq signals. Over-sonication consistently reduced quality, while the impact of under-sonication differed among transcription factors, with no impact on sites bound by CTCF but frequently leading to the loss of sites occupied by TAL1 or bound by POL2. The bound sites not observed in low-quality datasets were inferred to be a mix of both direct and indirect binding. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in rare, primary hematopoietic progenitor cells. Our observation that the amount of chromatin sonication is a key variable in success of ChIP-seq experiments indicates that monitoring the level of sonication can improve ChIP-seq quality and reproducibility and facilitate ChIP-seq in rare cell types.
Uniform error estimates for artificial neural network approximations for heat equations
Authors: Gonon Lukas , Grohs Philipp , Jentzen Arnulf , Kofler David , Šiška David
Published: March 2021

Recently, artificial neural networks (ANNs) in conjunction with stochastic gradient descent optimization methods have been employed to approximately compute solutions of possibly rather high-dimensional partial differential equations (PDEs). Very recently, there have also been a number of rigorous mathematical results in the scientific literature, which examine the approximation capabilities of such deep learning-based approximation algorithms for PDEs. These mathematical results from the scientific literature prove in part that algorithms based on ANNs are capable of overcoming the curse of dimensionality in the numerical approximation of high-dimensional PDEs. In these mathematical results from the scientific literature, usually the error between the solution of the PDE and the approximating ANN is measured in the $L^p$-sense, with respect to some $p \in [1,\infty )$ and some probability measure. In many applications it is, however, also important to control the error in a uniform $L^\infty $-sense. The key contribution of the main result of this article is to develop the techniques to obtain error estimates between solutions of PDEs and approximating ANNs in the uniform $L^\infty $-sense. In particular, we prove that the number of parameters of an ANN to uniformly approximate the classical solution of the heat equation in a region $ [a,b]^d $ for a fixed time point $ T \in (0,\infty ) $ grows at most polynomially in the dimension $ d \in {\mathbb {N}} $ and the reciprocal of the approximation precision $ \varepsilon> 0 $. This verifies that ANNs can overcome the curse of dimensionality in the numerical approximation of the heat equation when the error is measured in the uniform $L^\infty $-norm.
The Birth of “Religion and International Relations”: Questions of Scale
Authors: Adams Nicholas
Published: March 2021

The field religion and international relations (IR) has been established over the last twenty years within the discipline of IR. It marks a new (largely twenty-first century) set of interdisciplinary engagements, bringing together political science and the sociology of religion. “Religion and IR” and “religious studies” continue to conduct their business independently, in different conferences, journals, and book series, but their interests increasingly overlap. This enquiry interprets religion and IR as a “turn to the local.” This is displayed in its concern with events at the local level that have significance that travels up the scale of levels of analysis to events that have international significance. The turn to the local offers compelling arguments for shifting the focus in IR away from states and on to relations between local, national, and international actors. Engaging here with influential works in religion and IR published over the last fifteen years, I argue that it is the turn to the local that offers the most scope for collaboration between scholars of religion and IR and scholars in religious studies.
Education: An overview from the author of ‘Cefiderocol as rescue therapy for Acinetobacter baumannii and other carbapenem-resistant Gram-negative infections in intensive care unit patients’
Authors: Falcone Marco
Published: March 2021

This video is a presentation from Professor Marco Falcone from the University Hospital Pisa, Italy, originally presented at the BSAC conference ‘Into clinical practice: Meeting the challenges of Gram-negative infection management’ on 14 October 2020. Professor Falcone highlights the cefiderocol compassionate use case series that has been published in Clinical Infectious Diseases (Falcone M, Tiseo G, Nicastro M et al. Cefiderocol as rescue therapy for Acinetobacter baumannii and other carbapenem-resistant Gram-negative infections in intensive care unit patients. Clin Infect Dis 2020; doi: 10.1093/cid/ciaa1410). The prescribing information for cefiderocol is available at: https://shionogi-eu-content.com/gb/fetcroja/pi.