bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concatenated 16S rRNA sequence analysis improves bacterial taxonomy
Authors: Paul Bobby 
Published: December 2022

Background: Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Advances in DNA sequencing and bioinformatics workflows have facilitated sophisticated genome-based methods for microbial taxonomy although sequencing of the 16S rRNA gene is widely employed to identify and classify the bacterial community as a cost-effective and single-gene approach. However, the 16S rRNA sequence-based species identification accuracy is limited by multiple copies of the gene and their higher sequence identity between closely related species. The availability of a large volume of bacterial whole-genome data provided an opportunity to develop comprehensive species-specific 16S rRNA reference libraries. Methods: The 16S rRNA copies were retrieved from the whole genomes in the complete stage at the Genome database. With defined rules, four 16S rRNA gene copy variants were concatenated to develop a species-specific reference library. The sequence similarity search was performed with a web-based BLAST program, and MEGA software was used to construct the phylogenetic tree. Results: Using this approach, species-specific 16S rRNA gene libraries were developed for four closely related Streptococcus species (S. gordonii, S. mitis, S. oralis, and S. pneumoniae). Sequence similarity and phylogenetic analysis using concatenated 16S rRNA copies yielded better resolution than single gene copy approaches. Conclusions: The approach is very effective in classifying genetically related species and may reduce misclassification of bacterial species and genome assemblies.
Driving event recognition using machine learning and smartphones
Authors: bin Jamal Mohd Lokman Eilham Hakimie , Goh Vik Tor , Yap Timothy Tzen Vun , Ng Hu 
Published: December 2022

Background: The lack of real-time monitoring is one of the reasons for the lack of awareness among drivers of their dangerous driving behavior. This work aims to develop a driver profiling system where a smartphone’s built-in sensors are used alongside machine learning algorithms to classify different driving behaviors. Methods: We attempt to determine the optimal combination of smartphone sensors such as accelerometer, gyroscope, and GPS in order to develop an accurate machine learning algorithm capable of identifying different driving events (e.g. turning, accelerating, or braking). Results: In our preliminary studies, we encountered some difficulties in obtaining consistent driving events, which had the potential to add “noise” to the observations, thus reducing the accuracy of the classification. However, after some pre-processing, which included manual elimination of extraneous and erroneous events, and with the use of the Convolutional Neural Networks (CNN), we have been able to distinguish different driving events with an accuracy of about 95%. Conclusions: Based on the results of preliminary studies, we have determined that the proposed approach is effective in classifying different driving events, which in turn will allow us to determine driver’s driving behavior.
Health Wearables, Gamification, and Healthful Activity
Authors: Hydari Muhammad Zia , Adjerid Idris , Striegel Aaron D. 
Published: December 2022

Health wearables in combination with gamification enable interventions that have the potential to increase physical activity—a key determinant of health. However, the extant literature does not provide conclusive evidence on the benefits of gamification, and there are persistent concerns that competition-based gamification approaches will only benefit those who are highly active at the expense of those who are sedentary. We investigate the effect of Fitbit leaderboards on the number of steps taken by the user. Using a unique data set of Fitbit wearable users, some of whom participate in a leaderboard, we find that leaderboards lead to a 370 (3.5%) step increase in the users’ daily physical activity. However, we find that the benefits of leaderboards are highly heterogeneous. Surprisingly, we find that those who were highly active prior to adoption are hurt by leaderboards and walk 630 fewer steps daily after adoption (a 5% relative decrease). In contrast, those who were sedentary prior to adoption benefited substantially from leaderboards and walked an additional 1,300 steps daily after adoption (a 15% relative increase). We find that these effects emerge because sedentary individuals benefit even when leaderboards are small and when they do not rank first on them. In contrast, highly active individuals are harmed by smaller leaderboards and only see benefit when they rank highly on large leaderboards. We posit that this unexpected divergence in effects could be due to the underappreciated potential of noncompetition dynamics (e.g., changes in expectations for exercise) to benefit sedentary users, but harm more active ones. This paper was accepted by Chris Forman, information systems. Funding: This work was supported by the National Institutes of Health [Grant 5R01HL117757]. Supplemental Material: The data and online appendix are available at https://doi.org/10.1287/mnsc.2022.4581 .
Cutting sinusoidal gratings to enhance light trapping in thin-film silicon solar cells
Authors: Chen Ke , He Jinyang , Zheng Nianhong , Wu Sheng , Zheng Hongmei 
Published: December 2022

A crystalline silicon thin-film solar cell with a three-layer sinusoidal grating
structure is studied. The structure has a double-layer antireflection
layer, and the three-layer grating is located in the double-layer
antireflection layer and the passivation layer, respectively. The
related parameters of the grating structure are optimized by scanning
using finite-difference time-domain. The optimization results show
that cutting the sinusoidal grating structure can significantly
improve the light absorption efficiency of the cell for near-infrared
light (750–1100 nm), and the enhancement effect is
mainly in the transverse electric (TE)-polarized light. This is
because the localized surface plasmon resonance and optical waveguide
mode under TE-polarized light can be fully excited after the
sinusoidal structure is cut. The short-circuit current density (

J

S
C

) of the optimized three-layer
sinusoidal grating structure is

19.82

m
A

/

c
m

2

, which is 112.43% higher than that of
the planar structure with the same parameters and 23.18% higher than
that of the uncut sinusoidal grating structure with the same
parameters.
Quality of life and well-being problems in secondary schoolgirls in Kenya: Prevalence, associated characteristics, and course predictors
Authors: Spinhoven Philip , Zulaika Garazi , Nyothach Elizabeth , van Eijk Anna Maria , Obor David , Fwaya Eunice , Mason Linda , Wang Duolao , Kwaro Daniel , Phillips-Howard Penelope A. 
Published: December 2022

Background
Adolescents in sub-Saharan Africa often report low levels of quality of life (QoL) and well-being, but reliable data are limited. This study examines which sociodemographic, health, and behavioral risk factors and adverse adolescent experiences are associated with, and predictive of, QoL in Kenyan secondary schoolgirls.

Methods and findings
3,998 girls at baseline in a randomised controlled trial in Siaya County, western Kenya were median age 17.1 years. Subjectively perceived physical, emotional, social and school functioning was assessed using the Pediatric Quality of Life (QoL) Inventory-23. Laboratory-confirmed and survey data were utilized to assess sociodemographic, health and behavioral characteristics, and adverse adolescent experiences. We identified a group of girls with Low QoL (n = 1126; 28.2%), Average QoL (n = 1445; 36.1%); and High QoL (n = 1427; 35.7%). Significantly higher scores on all well-being indicators in the LQoL compared with HQoL group indicated good construct validity (Odds Ratio’s (ORs) varying from 3.31 (95% CI:2.41–4.54, p < .001) for feeling unhappy at home to 11.88 (95%CI:7.96–17.74, p< .001) for PHQ9 defined possible caseness (probable diagnosis) of depression. Adverse adolescent experiences were independently statistically significant in the LQoL compared to the HQoL group for threats of family being hurt (aOR = 1.35,1.08–1.68, p = .008), sexual harassment out of school (aOR = 2.17,1.79–2.64, p < .001), and for menstrual problems like unavailability of sanitary pads (aOR = 1.23,1.05–1.44, p = .008) and stopping activities due to menstruation (aOR = 1.77,1.41–2.24, p < .001). After 2-years follow-up of 906 girls in the LQoL group, 22.7% persisted with LQoL. Forced sex (aOR = 1.56,1.05–2.32, p = .028) and threats of family being hurt (aOR = 1.98,1.38–2.82, p < .001) were independent predictors of persistent LQoL problems.

Conclusions
Persistent QoL problems in Kenyan adolescent girls are associated with adverse physical, sexual and emotional experiences and problems with coping with their monthly menstruation. A multi-factorial integral approach to reduce the rate of adverse adolescent experiences is needed, including provision of menstrual hygiene products.

Trial registration
ClinicalTrials.gov:NCT03051789.
Epidemiology and costs of dengue in Thailand: A systematic literature review
Authors: Thisyakorn Usa , Saokaew Surasak , Gallagher Elaine , Kastner Randee , Sruamsiri Rosarin , Oliver Louisa , Hanley Riona 
Published: December 2022

Background
Dengue is the fastest-spreading vector-borne viral disease worldwide. In Thailand, dengue is endemic and is associated with a high socioeconomic burden. A systematic literature review was conducted to assess and describe the epidemiological and economic burden of dengue in Thailand.

Methods
Epidemiological and economic studies published in English and Thai between 2011–2019 and 2009–2019, respectively, were searched in MEDLINE, Embase, and Evidence-Based Medicines reviews databases. Reports published by the National Ministry of Public Health (MoPH) and other grey literature sources were also reviewed. Identified studies were screened according to predefined inclusion and exclusion criteria. Extracted data were descriptively summarised and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.

Results
A total of 155 publications were included in the review (39 journal articles and 116 grey literature). Overall, dengue incidence varied yearly, with the highest rates per 100,000 population in 2013 (dengue fever (DF) 136.6, dengue haemorrhagic fever (DHF) 100.9, dengue shock syndrome (DSS) 3.58) and 2015 (DF 133.1, DHF 87.4, DSS 2.14). Peak incidence coincided with the monsoon season, and annual mortality was highest for DSS, particularly in the age group 15–24-year-olds. The highest dengue incidence rates were reported in children (10–14-year-olds) and young adults (15-24-year-olds), irrespective of dengue case definition. Economic and societal burdens are extensive, with the average cost per case ranging from USD 41 to USD 261, total cost per year estimated at USD 440.3 million, and an average of 7.6 workdays lost for DHF and 6.6 days for DF.

Conclusions
The epidemiological, economic, and societal burden of dengue in Thailand is high and underreported due to gaps in national surveillance data. The use of expansion factors (EFs) is recommended to understand the true incidence of dengue and cost-benefit of control measures. Furthermore, as dengue is often self-managed and underreported, lost school and workdays result in substantial underestimation of the true economic and societal burden of dengue. The implementation of integrated strategies, including vaccination, is critical to reduce the disease burden and may help alleviate health disparities and equity challenges posed by dengue.
Identification of the parasite, Trypanosoma cruzi, in multiple tissues of epidemiological significance in the Virginia opossum (Didelphis virginiana): Implications for environmental and vertical transmission routes
Authors: Torhorst Carson W. , White Zoe S. , Bhosale Chanakya R. , Beatty Norman L. , Wisely Samantha M. 
Published: December 2022

Background
Trypanosoma cruzi, a parasitic protozoan, is endemic to the Americas and the causative agent of Chagas disease in humans. In South America, opossums facilitate transmission via infected anal gland secretions in addition to transmission via triatomine vectors. In North America, the Virginia opossum is a reservoir host for the parasite with transmission routes that are not clearly defined. The unique biology of this marsupial provides the opportunity to investigate vertical transmission in this wildlife species in situ. Our objectives were to investigate alternative routes of transmission that may facilitate spillover into other species and to determine if vertical transmission was evident.

Methodology/Principal findings
Virginia opossums were sampled at 10 trapping locations over a 10-month period in a 5-county region of north central Florida. Peripheral blood, fecal swabs, and anal gland secretions were collected from each adult individual, and peripheral blood was collected from joey opossums. Total DNA was extracted from each collected sample type, and T. cruzi infected individuals and the infecting Discrete Typing Unit (DTU) were identified using real time PCR methods. Adult Virginia opossums (n = 112) were infected with T. cruzi (51.8%, 95% CI [42.6–60.8%]) throughout the sampled period and at each location. T. cruzi DNA was found in each of the three biological sample types. Vertical transmission of T. cruzi was inferred in one litter of mother-dependent (n = 20, 5.0%, 95% CI [0.9–23.6%]) joey opossums where 2 joeys from this same litter were rtPCR positive for T. cruzi.

Conclusions/Significance
We inferred vertical transmission from mother to neonate which may serve to amplify the prevalence of T. cruzi in adult Virginia opossums. T. cruzi DNA was detected in the anal gland secretions of Virginia opossums. Infected anal gland secretions suggest a possible environmental route of transmission for T. cruzi via the deposition of contaminated feces and spraint at wildlife latrines. Only DTU1 was identified in the sampled population which is consistent with human autochthonous cases in the United States.
Photoacoustic tomography versus cone-beam computed tomography versus micro-computed tomography: Accuracy of 3D reconstructions of human teeth
Authors: Schneider Sonja Jasmin Maria , Höhne Christian , Schneider Martin , Schmitter Marc 
Published: December 2022

Objectives
In this in-vitro study, teeth were imaged using photoacoustic tomography (PAT), cone-beam computed tomography (CBCT), and micro-computed tomography (μ-CT). The study had aim: to identify the best wavelength for PAT images to determine the accuracy of the three imaging methods, and to determine whether PAT images of teeth can achieve acceptable reconstruction quality.

Methods
Nineteen human mandibular single-rooted incisors were extracted from patients with trauma or periodontitis. To determine the best wavelength for acquiring photoacoustic images, all 19 teeth were scanned in vitro with PAT, using different laser wavelengths between 680 and 960 nm. The images were analyzed using image analysis software. To assess the accuracy of PAT and compare it with the accuracy of CBCT, each tooth was also scanned in vitro using CBCT and the reference standard technique of μ-CT. Subsequently, three different three-dimensional models, one for each imaging technique, were created for each tooth. Finally, the three different three-dimensional models acquired for the same tooth were matched and analyzed regarding volume and surface.

Results
The highest quality tooth images were achieved using the 680 nm wavelength, which showed the best contrast ratio. The full geometry of the dental root (μ-CT compared with PAT) could be visualized with relative standard deviations of 0.12 mm for the surface and −7.33 mm3 for the volume (n = 19). The full geometry of the dental root (μ-CT compared with CBCT) could be visualized with relative standard deviations of 0.06 mm for the surface and −14.56 mm3 for the volume (n = 19). The difference between the PAT–μ-CT group and CBCT–μ-CT group regarding the total average of the root surface area was not significant (p>0.06).

Conclusion
Images, which were acquired using PAT at 680nm showed the best contrast ration, enabling the identification of dentin, cementum and the dental pulp. No significant differences were found between the PAT–μ-CT group and CBCT–μ-CT group regarding the total average of the RSA and the total volume. Thus, three-dimensional reconstructions based on in-vitro PAT are already of acceptable reconstruction quality.
Changes of bacterial and fungal communities and relationship between keystone taxon and physicochemical factors during dairy manure ectopic fermentation
Authors: Gong Ping , Gao Daoyu , Hu Xiuzhong , Tan Junjun , Wu Lijun , Liu Wu , Yang Yu , Jin Erguang 
Published: December 2022

Background
Due to interactions with variety of environmental and physicochemical factors, the composition and diversity of bacteria and fungi in manure ectopic fermentation are constantly changing. The purpose of this study was to investigated bacterial and fungal changes in dairy manure ectopic fermentation, as well as the relationships between keystone species and physicochemical characteristics.

Methods
Ectopic fermentation was carried out for 93 days using mattress materials, which was combined with rice husk and rice chaff (6:4, v/v), and dairy waste mixed with manure and sewage. Physicochemical characteristics (moisture content, pH, NH4+-N (NN), total organic carbon (TO), total nitrogen (TN) and the C/N ratio) of ectopic fermentation samples were measured, as well as enzymatic activity (cellulose, urease, dehydrogenase and alkaline phosphatase). Furthermore, the bacterial and fungal communities were studied using 16S rRNA and 18S rRNA gene sequencing, as well as network properties and keystone species were analyzed.

Results
During the ectopic fermentation, the main pathogenic bacteria reduced while fecal coliform increased. The C/N ratio gradually decreased, whereas cellulase and dehydrogenase remained at lower levels beyond day 65, indicating fermentation maturity and stability. During fermentation, the dominant phyla were Chloroflexi, Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria of bacteria, and Ascomycota of fungi, while bacterial and fungal community diversity changed dramatically and inversely. The association between physicochemical characteristics and community keystone taxon was examined, and C/N ratio was negative associated to keystone genus.

Conclusion
These data indicated that microbial composition and diversity interacted with fermentation environment and parameters, while regulation of keystone species management of physicochemical factors might lead to improved maturation rate and quality during dairy manure ectopic fermentation. These findings provide a reference to enhance the quality and efficiency of waste management on dairy farm.
Comparison of refractive and visual acuity results after Contoura® Vision topography-guided LASIK planned with the Phorcides Analytic Engine to results after wavefront-optimized LASIK in eyes with oblique astigmatism
Authors: Brunson Phillip , Mann Paul M. , Mann Paul Michael , Potvin Richard 
Published: December 2022

Purpose
To compare visual acuity and refractive results between topography-guided laser in situ keratomileusis (LASIK) planned with the Phorcides Analytic Engine (PAE) to results after wavefront-optimized (WFO) LASIK in subjects with preoperative oblique astigmatism in their manifest refraction.

Methods
This was a retrospective chart review of clinical results from eyes treated with topography-guided LASIK planned with PAE compared to eyes treated with WFO LASIK using the same Wavelight® excimer laser system. All included subjects had preoperative oblique astigmatism. Residual refractive error and visual acuity (uncorrected and corrected) were the measures of interest, at the visit closest to 90 days postoperative.

Results
A matched data set from 100 WFO and 97 PAE eyes was extracted from clinical records. At the postoperative visit the PAE group showed lower residual refractive cylinder (p = 0.04), uncorrected distance visual acuity (UDVA) (-0.06 PAE vs. -0.02 WFO, p < 0.01) and distance corrected visual acuity (CDVA) (p < 0.01). The percentage of eyes with a mean refraction spherical equivalent (MRSE) magnitude within 0.25 D and 0.50 D of plano was statistically significantly higher in the PAE group (p = 0.04 and 0.01, respectively). A statistically significantly higher percentage of eyes in the PAE group had UDVA better than or equal to -0.10 logMAR (20/16 Snellen, 36% vs 22%, p = 0.04). More eyes gained CDVA after surgery in the PAE group (53% vs 32%, p < 0.01). There were five enhancements in the WFO group versus none in the PAE group, a statistically significant difference (p = 0.03).

Conclusions
Visual acuity and refractive outcomes after LASIK using PAE in eyes with oblique astigmatism in their preoperative refraction were statistically significantly better than those obtained when WFO treatment was used. The number of refractive outliers and the number of retreatments were also significantly lower with PAE treatment.
Deméter y la revisión de los mitos clásicos: madres soñadas y madres cotidianas en la poesía contemporánea en lengua inglesa
Authors: Salcedo González Cristina 
Published: December 2022

Este trabajo investiga la presencia de la figura de Deméter en la poesía inglesa contemporánea, con el fin de identificar qué modelos de madre se ofrecen a partir del recurso al mito clásico de Deméter. Para ello, se analizan las fuentes clásicas que más importancia conceden al vínculo madre-hija, y cuya descripción de la madre imprime una huella imborrable en el imaginario occidental. Después, se estudian cuatro acercamientos al mito (uno ensayístico y tres literarios) que son representativos de las principales tendencias en la representación de Deméter en la poesía inglesa actual. A través del estudio de los mecanismos de recepción del mito clásico y de la representación de Deméter en cada ejemplo, se llega a la conclusión de que existen dos lecturas diferenciadas de Deméter (ya como la madre soñada, ya como la madre cotidiana), que hacen referencia a dos formas distintas de entender la maternidad. En último término, se pone de manifiesto la capacidad del mito de Perséfone y Deméter para dar voz a la vivencia de las madres en épocas diferentes y bajo prismas diversos.
Radio over plastic optical fibers – a tutorial and review
Authors: Adnan Usama , Abbas Zaheer , Gulistan Aamir , Ghafoor Salman 
Published: December 2022

Abstract
In this paper, recent advancements in radio over plastic optical fibers are reviewed. Plastic fibers are used in short-range, high data rate communication systems and are considered to be consumer-friendly as they are simpler to install, easy to maintain and its associated components are inexpensive. A few of the challenges faced in employing plastic fibers are its high attenuation and modal dispersion, which limits the transmission range. However, plastic fibers are considered to be a low-cost alternative to be employed in short-range fiber-to-the-home (FTTH) networks as compared to the commonly known silica optical fiber. Advancement from 4G to 5G has paved a way for plastic fiber, which can be employed for simultaneous multi-format transmissions supporting 5G networks. In this paper, the evolution of multi-format transmission and its challenges are also discussed, along with the applications of plastic fibers in systems employing various techniques. Furthermore, the paper discusses the challenges and future prospects of radio over plastic fibers to guide a way for further research in this domain for improving the quality of transmission and linking it with other cutting-edge technologies such as machine learning and blockchain.