bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of main energy parameters and efficiency of local energy system based on renewable energy sources
Authors: Urishev B , Kuvatov U , Umirov A 
Published: August 2022

Abstract
This article presents a methodology for determining the basic parameters of a local power system based on the use of wind, solar, hydropower devices and the hydraulic accumulation of some of their energy, including the maximum volume of the upper water basin. The results of calculations performed on the basis of this method determined the maximum volume of the water basin, which will allow to accumulate 14% of the energy produced in the local power system with a capacity of 18 MW. The cost-effectiveness and functional advantages of the method of hydraulic accumulation of energy adopted in this local power system over lithium-ion batteries have been identified.
Analysis of the impact of the energy industry on the environment
Authors: Zakharov S V , Lushpey V P , Abbasova L R , Zhongkai S 
Published: August 2022

Abstract
The article analyzes the issue of environmental pollution by the energy industry. Currently, the problems of environmental pollution are alarming, which is regularly discussed by the media and the scientific community. Over the past 20 years, many scientists have predicted death for the Earth if radical measures are not taken to save it. Due to the activities of enthusiasts and organizations, books and research papers have been written about pollution and its types; studies have been carried out on the consequences of environmental disasters in the world.
Environmental model using life cycle assessment and artificial intelligence techniques to predict impacts on industrial water treatment.
Authors: Jesus José de , Oliveira-Esquerre Karla , Medeiros Diego Lima 
Published: August 2022

Abstract
With the advancement of globalization, the growing demand for environmental resources in industrial processes and the increasing availability of data and information, the need to align data modeling concepts with Artificial Intelligence (AI) techniques and existing environmental tools has emerged. From a sustainability perspective, life cycle assessment (LCA) is an extremely important tool in ensuring adequate practices in environmental thinking. It is through the life cycle assessment (LCA) that it is possible to measure the environmental impacts from products and processes, as well as to make projections that minimize these impacts. This research employed an artificial intelligence (AI) methods, namely adaptive neurofuzzy inference system (ANFIS) model, to predict life cycle environmental impacts in industrial water treatment using aluminum sulfate and Tannin-Base biocoagulant. The results show that different AI algorithms are used to build LCA models. The AI algorithms in the studies work from problem identification to the solution stage, so the integration between AI and LCA makes it possible to build predictive machine learning models to enable assertiveness in decision making.
Mechanical Properties and Water Absorption of Glass Fiber Reinforced Composite Laminates made by Varying Stacking Sequence
Authors: Paglicawan Marissa A. , Emolaga Carlo S. , Custodio Cyron L. , Sudayon Johanna Marie B. , De Lara Ryan John L. 
Published: August 2022

Abstract
This study aims to demonstrate the effects of various stacking sequences of different glass fiber architecture forms on the mechanical properties of glass fibre reinforced polyester composites. The composites were manufactured by hand lay-up technique and its mechanical properties were characterized in terms of tensile, flexural, and drop-ball impact tests as well as water absorption. The mechanical properties of the glass fiber reinforced polyester were somewhat affected depending on the stacking sequences from single alternating order, double alternating order, and triple alternating order of chopped strand mat and plain-woven fabric piled in ten (10) to fourteen (14) layers. The laminates consisting of alternating sequence manner of plain-woven fabric and chopped strand mat stacked in different layers have no significant effect on the mechanical properties. Stacking sequence of double alternating layer piled in twelve (12) layers was found to have better tensile strength than single and double alternating order of two different glass fiber form while the triple alternating manner piled in twelve (12) layers resulted to higher tensile modulus. The double alternating order of different glass fiber forms stacked in twelve (12) layers resulted to an improvement in flexural properties. Some selected laminates exhibited no delamination in drop-ball impact test and minimal water absorption when immersed in water for 30 days for all the laminates.
Laser polarization driven micromanipulation and reorientation dynamics of an asymmetric shaped microscopic biomaterial using optical tweezers
Authors: D Chetana , P Praveen , B V Nagesh , Bhattacharya Sarbari , Ananthamurthy Sharath 
Published: August 2022

Abstract
We present measurements and a theoretical model that describes the dynamics of ellipsoidal shaped, chicken red blood cells (cRBCs) reorienting in an optical trap and demonstrates the ability to control their reorientation through changes in the intensity distribution that results from the different states of the polarization of the trapping laser. We have observed that in linearly polarized light, cRBC, a type of avian RBC, undergoes dual reorientation, with the first reorientation about the cell’s major axis and the second, about its short minor axis, with the major axis aligning with the laser propagation direction at equilibrium. We compute the work done for each of these reorientations and attribute the observed dynamics to a minimization of the energy cost for the particular sequence of the reorientations that we observe. Further, we achieve a controlled second orientation of the major axis along the laser propagation direction by varying the ellipticity of the polarization of the laser. We explain these partial second reorientation results by employing a geometrical optics-based model. Characterizing the dynamics and control of these regular-shaped natural soft materials through optical polarization is relevant in the context of current work in the design and development of microscopic artefacts such as lab-on-a-chip platforms.
Diffraction-free beam propagation at the exceptional point of non-Hermitian Glauber Fock lattices
Authors: Yuce Cem , Ramezani Hamidreza 
Published: August 2022

Abstract
We construct localized beams in a non-Hermitian Glauber Fock (NGF) lattice of coupled waveguides and show that they can propagate over a long distance withalmost no diffraction. We specifically obtain the diffraction-free beams in a finite NGF lattice at the exceptional point (EP) by using the exact eigenstates of the semi-infinite unidirectional NGF lattice. We provide a numerical approach to finding other lattices that are capable of supporting non-diffracting beams at EPs.
PhenoComb: a discovery tool to assess complex phenotypes in high-dimensional single-cell datasets
Authors: Burke Paulo E P , Strange Ann , Monk Emily , Thompson Brian , Amato Carol M , Woods David M 
Published: August 2022

Abstract

Motivation
High-dimensional cytometry assays can simultaneously measure dozens of markers, enabling the investigation of complex phenotypes. However, as manual gating relies on previous biological knowledge, few marker combinations are often assessed. This results in complex phenotypes with the potential for biological relevance being overlooked. Here, we present PhenoComb, an R package that allows agnostic exploration of phenotypes by assessing all combinations of markers. PhenoComb uses signal intensity thresholds to assign markers to discrete states (e.g. negative, low, high) and then counts the number of cells per sample from all possible marker combinations in a memory-safe manner. Time and disk space are the only constraints on the number of markers evaluated. PhenoComb also provides several approaches to perform statistical comparisons, evaluate the relevance of phenotypes and assess the independence of identified phenotypes. PhenoComb allows users to guide analysis by adjusting several function arguments, such as identifying parent populations of interest, filtering of low-frequency populations and defining a maximum complexity of phenotypes to evaluate. We have designed PhenoComb to be compatible with a local computer or server-based use.

Results
In testing of PhenoComb’s performance on synthetic datasets, computation on 16 markers was completed in the scale of minutes and up to 26 markers in hours. We applied PhenoComb to two publicly available datasets: an HIV flow cytometry dataset (12 markers and 421 samples) and the COVIDome CyTOF dataset (40 markers and 99 samples). In the HIV dataset, PhenoComb identified immune phenotypes associated with HIV seroconversion, including those highlighted in the original publication. In the COVID dataset, we identified several immune phenotypes with altered frequencies in infected individuals relative to healthy individuals. Collectively, PhenoComb represents a powerful discovery tool for agnostically assessing high-dimensional single-cell data.

Availability and implementation
The PhenoComb R package can be downloaded from https://github.com/SciOmicsLab/PhenoComb.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
CellSium: versatile cell simulator for microcolony ground truth generation
Authors: Sachs Christian Carsten , Ruzaeva Karina , Seiffarth Johannes , Wiechert Wolfgang , Berkels Benjamin , Nöh Katharina 
Published: August 2022

Abstract

Summary
To train deep learning-based segmentation models, large ground truth datasets are needed. To address this need in microfluidic live-cell imaging, we present CellSium, a flexibly configurable cell simulator built to synthesize realistic image sequences of bacterial microcolonies growing in monolayers. We illustrate that the simulated images are suitable for training neural networks. Synthetic time-lapse videos with and without fluorescence, using programmable cell growth models, and simulation-ready 3D colony geometries for computational fluid dynamics are also supported.

Availability and implementation
CellSium is free and open source software under the BSD license, implemented in Python, available at github.com/modsim/cellsium (DOI: 10.5281/zenodo.6193033), along with documentation, usage examples and Docker images.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Identification of bacteriophage genome sequences with representation learning
Authors: Bai Zeheng , Zhang Yao-zhong , Miyano Satoru , Yamaguchi Rui , Fujimoto Kosuke , Uematsu Satoshi , Imoto Seiya 
Published: August 2022

AbstractMotivationBacteriophages/phages are the viruses that infect and replicate within bacteria and archaea, and rich in human body. To investigate the relationship between phages and microbial communities, the identification of phages from metagenome sequences is the first step. Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Database-based methods typically use a large number of sequences as references; alignment-free methods usually learn the features of the sequences with machine learning and deep learning models.ResultsWe propose INHERIT which uses a deep representation learning model to integrate both database-based and alignment-free methods, combining the strengths of both. Pre-training is used as an alternative way of acquiring knowledge representations from existing databases, while the BERT-style deep learning framework retains the advantage of alignment-free methods. We compare INHERIT with four existing methods on a third-party benchmark dataset. Our experiments show that INHERIT achieves a better performance with the F1-score of 0.9932. In addition, we find that pre-training two species separately helps the non-alignment deep learning model make more accurate predictions.Availability and implementationThe codes of INHERIT are now available in: https://github.com/Celestial-Bai/INHERIT.Supplementary informationSupplementary data are available at Bioinformatics online.
Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet
Authors: Hardisty Alex R , Ellwood Elizabeth R , Nelson Gil , Zimkus Breda , Buschbom Jutta , Addink Wouter , Rabeler Richard K , Bates John , Bentley Andrew , Fortes José A B , Hansen Sara , Macklin James A , Mast Austin R , Miller Joseph T , Monfils Anna K , Paul Deborah L , Wallis Elycia , Webster Michael 
Published: August 2022

Abstract
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
Culture and Quality Matter in Building Effective Mentorship Relationships with Native STEM Scholars
Authors: Estrada Mica , Young Gerald , Flores Lilibeth , Hernandez Paul R , Hosoda K Kanoho , DeerInWater Kathy 
Published: August 2022

Abstract
Native peoples (Native American, Alaskan Native, Native Hawaiian) are underrepresented in academia; they represent 2% of the US population but 0.01% of enrolled undergraduate students. Native peoples share the experiences of colonization and forced assimilation, resulting in the loss of ancestral knowledge, language, and cultural identity. Recognizing history and the literature on social integration and mentorship, we followed 100 Native science and engineering scholars across a year of participation in the hybrid American Indian Science and Engineering Society mentorship program. The results showed that high-quality faculty mentorship predicted persistence a year later. Furthermore, mentors who shared knowledge of Native culture—through experience or shared heritage—uniquely contributed to the Native scholars’ social integration and persistence through scientific community values in particular. Therefore, Native scholars may benefit from mentorship supporting the integration of their Native culture and discipline rather than assimilation into the dominant disciplinary culture.
Coronavirus Disease 19 (COVID-19) Vaccine Effectiveness Against Symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Delta-Dominant and Omicron-Dominant Periods in Japan: A Multicenter Prospective Case-control Study (Factors Associated with SARS-CoV-2 Infection and the Effectiveness of COVID-19 Vaccines Study)
Authors: Arashiro Takeshi , Arima Yuzo , Muraoka Hirokazu , Sato Akihiro , Oba Kunihiro , Uehara Yuki , Arioka Hiroko , Yanai Hideki , Kuramochi Jin , Ihara Genei , Chubachi Kumi , Yanagisawa Naoki , Nagura Yoshito , Kato Yasuyuki , Ueda Akihiro , Numata Akira , Kato Hideaki , Ishii Koji , Ooki Takao , Oka Hideaki , Nishida Yusuke , Stucky Ashley , Smith Chris , Hibberd Martin , Ariyoshi Koya , Suzuki Motoi 
Published: August 2022

Abstract

Background
Although several coronavirus disease 2019 (COVID-19) vaccines initially showed high efficacy, there have been concerns because of waning immunity and the emergence of variants with immune escape capacity.

Methods
A test-negative design case-control study was conducted in 16 healthcare facilities in Japan during the Delta-dominant period (August-September 2021) and the Omicron-dominant period (January-March 2022). Vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 infection was calculated for 2 doses for the Delta-dominant period and 2 or 3 doses for the Omicron-dominant period compared with unvaccinated individuals.

Results
The analysis included 5795 individuals with 2595 (44.8%) cases. Among vaccinees, 2242 (55.8%) received BNT162b2 and 1624 (40.4%) received messenger RNA (mRNA)-1273 at manufacturer-recommended intervals. During the Delta-dominant period, VE was 88% (95% confidence interval [CI], 82–93) 14 days to 3 months after dose 2 and 87% (95% CI, 38–97) 3 to 6 months after dose 2. During the Omicron-dominant period, VE was 56% (95% CI, 37–70) 14 days to 3 months since dose 2, 52% (95% CI, 40–62) 3 to 6 months after dose 2, 49% (95% CI, 34–61) 6+ months after dose 2, and 74% (95% CI, 62–83) 14+ days after dose 3. Restricting to individuals at high risk of severe COVID-19 and additional adjustment for preventive measures (ie, mask wearing/high-risk behaviors) yielded similar estimates, respectively.

Conclusions
In Japan, where most are infection-naïve, and strict prevention measures are maintained regardless of vaccination status, 2-dose mRNA vaccines provided high protection against symptomatic infection during the Delta-dominant period and moderate protection during the Omicron-dominant period. Among individuals who received an mRNA booster dose, VE recovered to a high level.
Coenzyme Q10 Levels Associated With Cognitive Functioning and Executive Function in Older Adults
Authors: Fernández-Portero Cristina , Amián Josué G , Bella Rocío de la , López-Lluch Guillermo , Alarcón David 
Published: July 2022

Abstract
Brain deterioration with age is associated with inflammation and oxidative stress that result in structural and functional changes. Recent studies have indicated that coenzyme Q10 (CoQ10) is associated with neurological oxidative stress and cognitive impairment. Studies with older people have shown a relationship between neurodegenerative diseases and CoQ10 levels. However, no studies have analyzed the relationship between CoQ10 and cognitive functioning in older adults. The aim of this study was to analyze the association between CoQ10 and cognitive functioning in an older adult sample, controlling for other factors that may influence aging, such as the level of physical activity and nutritional status. The sample consisted of 64 older adults aged 65–99 years (76.67 ± 8.16 years), among whom 48 were women (75%). The participants were recruited among those who attended community centers to voluntarily participate in leisure activities. According to previous studies, physical activity and nutritional status are positively associated with cognitive functioning. However, the main finding of this study was that plasma CoQ10, controlling for other measures, was significantly associated with cognitive functioning and executive function. The current findings suggest that a decline in cognitive capacities may be related to reduced antioxidant defenses, as reflected by low CoQ10 levels in older adults.
Perceptions on Oral Care Needs, Barriers, and Practices Among Managers and Staff in Long-Term Care Settings for Older People in Flanders, Belgium: A Cross-sectional Survey
Authors: Palmers Ellen , Janssens Lynn , Phlypo Inès , Vanhaecht Kris , De Almeida Mello Johanna , De Visschere Luc , Declerck Dominique , Duyck Joke 
Published: August 2022

Abstract

Background and Objectives
This study aimed to explore oral health perception and oral care needs, barriers, and current practices as perceived by managers and staff in long-term care organizations for older people in Flanders.

Research Design and Methods
This is a cross-sectional study where 2 questionnaires were developed, one for managers and one for caregivers, and were validated in Flemish long-term care organizations. Descriptive analyses and multivariable generalized linear models evaluated the main outcomes and their associations with determinants such as the size of the organization, the presence of an oral health policy, collaboration with a dentist, among others.

Results
A total of 145 managers and 197 caregivers completed the questionnaire. More than 50% of caregivers and managers perceived their residents’ oral health as mediocre to good. Collaboration with a dentist (B = 0.84) and oral health care involvement (B = 0.08) within the organization showed a strong association with a positive perception of oral health. Lack of time (57%) and care resistance (70%) were the most important barriers perceived by caregivers. Guidelines concerning oral care were not available or were unknown to 52% of the caregivers. Having an oral health policy within the organization was strongly associated with the correct use of guidelines for daily care of natural teeth (B = 1.25) and of dental prosthesis (B = 1.15).

Discussion and Implications
The results emphasize that collaborating with a dentist and the presence of an oral health policy in care organizations are important for a positive perception of the oral health of the residents and for the adoption of guidelines by caregivers and managers. In addition, training on handling care refusal should be included in the overall training. These results are crucial input for the development of a methodology for implementing a structured oral care policy in long-term care facilities.
What are the tuberculosis care practices of informal healthcare providers? A cross-sectional study from Eastern India
Authors: Thapa Poshan , Hall John J , Jayasuriya Rohan , Mukherjee Partha Sarathi , Beek Kristen , Das Dipesh Kr , Mandal Tushar , Narasimhan Padmanesan 
Published: August 2022

Abstract
India is the highest TB burden country, accounting for an estimated 26% of the global TB cases. Systematic engagement of the private sector is a cornerstone of India’s National Strategic Plan for TB Elimination (2017–25). However, informal healthcare providers (IPs), who are the first point of contact for a large number of TB patients, remain significantly underutilized in the National TB Elimination Program of India. Non-prioritization of IPs has also resulted in a limited understanding of their TB care practices in the community. We, therefore, undertook a descriptive study to document IPs’ TB care practices, primarily focusing on their approach to screening, diagnosis, treatment and referral. This cross-sectional study was carried out from February to March 2020 in the Birbhum District of West Bengal, India. Interviews were conducted utilizing the retrospective case study method. A total of 203 IPs participated who reported seeing at least one confirmed TB patient in 6 months prior to the study. In that duration, IPs reported interacting with an average of five suspected TB cases, two of which were later confirmed as having TB. Antibiotic use was found to be common among IPs (highest 69% during the first visit); however, they were prescribed before the patient was suspected or confirmed as having TB. We noted the practice of prolonged treatment among IPs as patients were prescribed medicines until the second follow-up visit. Referral was the preferred TB case management approach among IPs, but delayed referral was observed, with only one-third (34%) of patients being referred to higher health facilities during their first visit. This study presents important findings on IPs’ TB care practices, which have consequences for achieving India’s national goal of TB elimination.