bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degraded RNA from human anterior cruciate ligaments yields valid gene expression profiles
Authors: Strawn Matthew D. , Fisher Geoffrey D. , Perry Cody J. , Hashemi Javad , Mansouri Hossein , Ferguson Matthew P. , Zumwalt Mimi , Brindley George W. , Slauterbeck James R. , Hardy Daniel M. 
Published: July 2022

ABSTRACTBackgroundCorrelating gene expression patterns with biomechanical properties of connective tissues provides insight into molecular processes underlying development and maintenance of the tissues’ physical characteristics. Cadaveric tissues such as human knees are widely considered suitable for biomechanical studies, but their usefulness for gene expression experiments is potentially limited by unavoidable, nuclease-mediated degradation of RNA.MethodsWe quantified mRNAs encoding 84 extracellular matrix components and five housekeeping proteins in intact and partially degraded RNA from human anterior cruciate ligaments (ACLs), and compared relative amounts of the individual mRNAs by regression analysis.ResultsHuman ACL RNA degraded in vitro by limited ribonuclease digestion (N=6) resembled degraded RNA isolated from cadaveric tissue. PCR threshold cycle (Ct) values from degraded RNAs ranged variably higher than values obtained from their corresponding non-degraded RNAs, reflecting both the expected loss of target templates in the degraded preparations as well as differences in the extent of degradation. Relative Ct values obtained for mRNA targets in degraded preparations correlated strongly with the corresponding target levels in non-degraded RNA, both for each ACL as well as for pooled results from all six ACLs. Nuclease-mediated degradation produced similar, strongly correlated losses of housekeeping and non-housekeeping gene mRNAs. Expression profiling of RNA degraded in situ yielded comparable results, confirming that in vitro digestion suitably mimicked degradation by endogenous ribonucleases in frozen and thawed ACL.ConclusionPCR-based expression analyses can yield valid mRNA profiles from partially degraded RNA preparations such as those obtained from cadaveric knees and other skeletal motion segments used in biomechanical studies. Legitimate comparisons between variably degraded tissues can be made by normalizing quantitative data to an appropriate housekeeping transcript.
Population Structure and Ecology of the African elephant (Loxodonta africana, Blumenbach, 1797) in Chebera Churchura National Park, Ethiopia
Authors: Tsegaye Adane , Bekele Afework , Atikem Anagaw 
Published: July 2022

AbstractAn investigation on population structure and ecology of the African elephants (Loxodonta africana) was carried out in Chebera Churchura National Park, Ethiopia during the wet and dry seasons of 2020 –2021. Sample counts using distance sampling of the African elephants were carried out in an area of 1, 410 km2. The total population estimated was 756 individuals, and the mean population density estimated was 0.53/km2. Among these, females constituted 52.12% and males 36.07%. The remaining 11.8% of the population was young of both sexes. It was difficult to categorize the young into male and female in the field, as their primary sexual characteristics were not easily visible.Male to female sex ratio was 1.00:-1.42. Age structure was dominated by adults, which constituted 53.83% of the total population. Sub-adults comprised 19.11%, juveniles contributed 15.18% and calves accounted for 12.11% of the population. The herd size ranged from 1 to 149 individuals and the mean herd size during wet and dry seasons were 16.5 and 50.25, respectively. The African elephants were distributed in four habitat types: grassland, woodland, montane forest and riverine habitats in the study area. They were observed more in the riverine vegetation types during the dry season. Relative abundance of food resources, green vegetation cover and water availability in the area were the major factors governing their distribution in the present study area.
A PAK kinase family member and the Hippo/Yorkie pathway modulate WNT signaling to functionally integrate body axes during regeneration
Authors: Doddihal Viraj , Mann Frederick G. , Ross Eric , McKinney Sean A. , Alvarado Alejandro Sánchez 
Published: July 2022

SummarySuccessful regeneration of missing tissues requires seamless integration of positional information along the body axes. Planarians, which regenerate from almost any injury, use conserved, developmentally important signaling pathways to pattern the body axes. However, the molecular mechanisms which facilitate crosstalk between these signaling pathways to integrate positional information remain poorly understood. Here, we report a p21-activated kinase (smed-pak1) which functionally integrates the anterior-posterior (AP) and the medio-lateral (ML) axes. pak1 inhibits WNT/β-catenin signaling along the AP axis and, functions synergistically with the β-catenin-independent WNT signaling of the ML axis. Furthermore, this functional integration is dependent on warts and merlin - the components of the Hippo/Yorkie (YKI) pathway. Hippo/YKI pathway is a critical regulator of body size in flies and mice, but our data suggest the pathway is required to pattern body axes in planarians. Our study provides a signaling network integrating positional information which can mediate coordinated growth and patterning during planarian regeneration.
Local fat content determines global and local stiffness in livers with simple steatosis
Authors: Li David , Janmey Paul A. , Wells Rebecca G. 
Published: July 2022

AbstractFat accumulation during liver steatosis precedes inflammation and fibrosis in fatty liver diseases, and is associated with disease progression. Despite a large body of evidence that liver mechanics play a major role in liver disease progression, the effect of fat accumulation by itself on liver mechanics remains unclear. Thus, we conducted ex vivo studies of liver mechanics in rodent models of simple steatosis to isolate and examine the mechanical effects of intrahepatic fat accumulation, and found that fat accumulation softens the liver. Using a novel adaptation of microindentation to permit association of local mechanics with microarchitectural features, we found evidence that the softening of fatty liver results from local softening of fatty regions rather than uniform softening of the liver. These results suggest that fat accumulation itself exerts a softening effect on liver tissue. This, along with the localized heterogeneity of softening within the liver, has implications in what mechanical mechanisms are involved in the progression of liver steatosis to more severe pathologies and disease. Finally, the ability to examine and associate local mechanics with microarchitectural features is potentially applicable to the study of the role of heterogeneous mechanical microenvironments in both other liver pathologies and other organ systems.
Heterogeneity of Tethered Agonist Signaling in Adhesion G Protein-Coupled Receptors
Authors: Dates Andrew N. , Jones Daniel T.D. , Smith Jeffrey S. , Skiba Meredith A. , Rich Maria F. , Burruss Maggie M. , Kruse Andrew C. , Blacklow Stephen C. 
Published: July 2022

AbstractAdhesion G Protein-Coupled Receptor (aGPCR) signaling influences development and homeostasis in a wide range of tissues. In the current model for aGPCR signaling, ligand binding liberates or unmasks a highly conserved tethered agonist (TA) that acts as an intramolecular ligand to stimulate G protein coupling. However, a systematic, comprehensive examination of signaling has not been performed for all aGPCR family members. Here, we report a platform for profiling TA-dependent activities of aGPCRs in several different assays and apply it to all 33 human family members. Activity profiling identified a heterogeneity of responses among these aGPCRs, with only ∼50% showing robust, TA-dependent signals. AlphaFold2 predictions assessing TA engagement in the predicted intramolecular binding pocket aligned with the TA-dependence of the cellular responses. The signaling information in this dataset is a comprehensive resource relevant for the investigation of all human aGPCRs and for targeting aGPCRs therapeutically.
Low-cost platform for multi-animal chronic local field potential video monitoring with graphical user interface (GUI) for seizure detection and behavioral scoring
Authors: Tarcsay Gergely , Boublil Brittney Lee , Ewell Laura A. 
Published: July 2022

ABSTRACTExperiments employing chronic monitoring of neurophysiological signals and video are commonly used in studies of epilepsy to characterize behavioral correlates of seizures. Our objective was to design a low-cost platform that enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real-time, and parses recorded data into manageable file sizes. We present a hardware solution leveraging Intan and Open Ephys acquisition systems and a software solution implemented in Bonsai. The platform was tested in 48-hour continuous recordings simultaneously from multiple mice (male and female) with chronic epilepsy. To enable seizure detection and scoring, we developed a graphical user interface (GUI) that reads the data produced by our workflow and allows a user with no coding expertise to analyze events. Our Bonsai workflow was designed to maximize flexibility for a wide variety of experimental applications, and our use of the Open Ephys acquisition board would allow for scaling recordings up to 128 channels per animal.SIGNIFICANCE STATEMENTWe present a low-cost hardware and software solution intended for multi-animal chronic seizure monitoring, that prioritizes experimental freedom, and requires no coding expertise of the user. We provide details for using an Intan adapter board to enable user freedom regarding the type of electrodes used. Video and local field potential data streams are synchronized and parsed in Bonsai – an open-source visual programming language that has pre-written libraries that allow our workflow to be adapted to other data types or to integrate with open-source toolboxes. Finally, for those intending to use our platform for seizure monitoring, we provide an accessible GUI to aid in seizure detection and behavioral scoring.
Functional characterization of multidomain protein Vip3Aa from Bacillus thuringiensis reveals a strategy to increase its insecticidal potency
Authors: Jiang Kun , Chen Zhe , Shi Yiting , Jiao Xuyao , Cai Jun , Gao Xiang 
Published: July 2022

AbstractMicrobially derived, protein-based biopesticides offer a more sustainable pest management alternative to synthetic pesticides. Vegetative insecticidal proteins (Vip3), multidomain proteins secreted by Bacillus thuringiensis, represent a second-generation insecticidal toxin that have been used in transgenic crops. However, the molecular mechanism underlying Vip3’s toxicity is poorly understood. Here, we determine the distinct functions and contributions of the domains of the Vip3Aa protein to its toxicity against Spodoptera frugiperda larvae. Vip3Aa domains II and III (DII-DIII) bind the midgut epithelium, while DI maintains the tetrameric state of the Vip3Aa protoxin, which is essential for its stability and toxicity. DI-DIII can be activated by midgut proteases, and exhibits ex vivo cytotoxicity similar to full-length Vip3Aa. We also determine that DV binds the peritrophic matrix via its glycan-binding activity, which is essential for Vip3Aa insecticidal activity. We further show that Vip3Aa has multiple protease activation sites and that introducing additional cleavage sites between DI and DII can increase the proteolysis efficiency and boost Vip3Aa insecticidal potency. This study provides insights into Vip3Aa’s mode-of-action and demonstrates a proof-of-concept strategy to enhance the insecticidal potency of Vip3Aa, which should significantly improve its application and development as a biopesticide.
Pangenome analysis of SARS-CoV2 strains to Identify Potential vaccine targets by Reverse Vaccinology
Authors: Haseeb Muhammad , Amir Afreenish , Irshad Hamza 
Published: July 2022

AbstractBackgroundCoronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) leads to respiratory failure and obstructive alveolar damage, which may be fatal in immunocompromised individuals. COVID-19 pandemic has severe global implications badly, and the situation in the world is depreciating with the emergence of novel variants. The aim of our study is to explore the genome of SARS-CoV2 followed by in silico reverse vaccinology analysis. This will help to identify the most putative vaccine candidate against the virus in a robust manner and enables cost-effective development of vaccines compared with traditional strategies.MethodsThe genomic sequencing data is retrieved from NCBI (Reference Sequence Number NC_045512.2). The sequences are explored through comparative genomics approaches by GENOMICS to find out the core genome. The comprehensive set of proteins obtained was employed in computational vaccinology approaches for the prediction of the best possible B and T cell epitopes through ABCpred and IEDB Analysis Resource, respectively. The multi-epitopes were further tested against human toll-like receptor and cloned in E. coli plasmid vector.FindingsThe designed Multiepitope Subunit Vaccine was non-allergenic, antigenic (0.6543), & non-toxic, with significant connections with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 84.38%. It has 276 amino acids, consisting of an adjuvant with the aid of EAAAK linker, AAY linkers used to join the 4 CTL epitopes, GPGPG linkers used to join the 3 HTL epitopes and KK linkers used to join the 7 B-cell epitopes. MESV docking with human pathogenic toll-like receptors-3 (TLR3) exhibited a stable & high binding affinity. An in-silico codon optimization approach was used in the codon system of E. coli (strain K12) to obtain the GC-Content of Escherichia coli (strain K12): 50.7340272413779 and CAI-Value of the improved sequence: 0.9542834278823386. The multi-epitope vaccine’s optimized gene sequence was cloned in-silico in E. coli plasmid vector pET-30a (+), BamHI and HindIII restriction sites were added to the N and C-terminals of the sequence, respectively.ConclusionThere is a pressing need to combat COVID-19 and we need quick and reliable approaches against Covid-19. By using In-silico approaches, we acquire an effective vaccine that could trigger adequate immune responses at the cellular and humoral level. The suggested sequences can be further validated through in vivo and in vitro experimentation.Statement of SignificanceCurrent developments in the immunological bioinformatics areas has resulted in different servers and tools that are cost and time efficient for the traditional vaccine development. Though for designing a multiple epitope vaccine the antigenic epitopes prediction of a relevant protein by immunoinformatic methods are very helpful.
Effects of trace elements Hf and Si on oxidation behavior of Co-Ni-Al-W-based superalloys at 900°C
Authors: Zhou Fanjie , Ma Chunmei , Zhang Yuheng , Wang Jialu , Fu Huadong 
Published: July 2022

Purpose
This study aims to control the oxidation resistance of Co-based deformed superalloys by adding trace elements Hf and Si.

Design/methodology/approach
The effects and mechanism of trace elements Hf and Si on the oxidation behavior of Co-Ni-Al-W-based forged superalloys were investigated by cyclic oxidation at 900°C.

Findings
The results show that the addition of trace elements Hf and Si does not affect the type of surface oxides of Co-Ni-based superalloys, and the oxidation layers of the alloys are TiO2, spinel, Cr2O3, TaTiO4, Al2O3 and TiN from outside to inside. However, the addition of elements can affect the activity of Cr and Ti elements; decrease the formation of TiO2 and TaTiO4 layers, which are harmful to the oxidation performance; and then improve the oxidation resistance of the alloy.

Originality/value
The relevant research results can not only optimize the microalloying element content of Co-Ni-Al-W-based superalloys, but also provide a new perspective for the composition optimization design of superalloys.
Examining the dark side of using gamification elements in online community engagement: an application of PLS-SEM and ANN modeling
Authors: Srivastava Gautam , Bag Surajit , Rahman Muhammad Sabbir , Pretorius Jan Harm Christiaan , Gani Mohammad Osman 
Published: July 2022

PurposeThe negative influence of gamification on online communities has received little attention in the available literature. The study examines the adverse effects of gamification during engaging in online communities.Design/methodology/approachGap-spotting methods were used to develop the research questions, followed by model development using the social exchange and social-network theories. Data were collected from 429 samples. The study applied partial least squares structural equation modeling to test the research hypotheses followed by ANN application.FindingsThe study identified five factors related to gamification that have a significant adverse effect on the mental and emotional well-being of the users. Furthermore, the results of PLS-SEM were then compared through an artificial neural network (ANN) analytic process, revealing consistency for the model. This research presents a theoretical contribution by providing critical insights into online gamers' mental and emotional health. It implies that gamification can even bring mental and emotional disturbance. The resulting situation might lead to undesirable social consequences.Practical implicationsThe result highlights the managerial and social relevance from the perspective of a developing country. As respondents are becoming more engrossed in online gaming, managers and decision-makers need to take preventive measures to overcome the dark side of online gaming.Originality/valueThe present study shows that the dark side of gamification has some adverse effects on human mental and emotional health. The study's findings can be used to improve gamification strategies while engaging online communities.
Effectiveness of peer support to reduce depression, anxiety and stress among migrant construction workers in Singapore
Authors: Palaniappan Kavitha , Rajaraman Natarajan , Ghosh Santu 
Published: July 2022

PurposeThe aim of this study was to determine the effectiveness of promoting peer support to reduce depression, anxiety and stress among migrant construction workers in Singapore.Design/methodology/approachThis longitudinal study drew participants from migrant workers of various nationalities in the construction sector in Singapore. Baseline data pertaining to depression, anxiety and stress was established using the DASS-21 questionnaire, and salient covariates such as demographic factors and work environment factors recorded using suitable questionnaires. Intervention was training of participants on peer support techniques, supplemented by episodic support by trained counsellors. At the end of 6 months, DASS-21 was again deployed to obtain the post-results. Comparison of baseline with post-results data was performed to evaluate effectiveness of the peer support intervention.FindingsStatistically significant reduction was observed in measures of all the three parameters studied, namely, depression, anxiety and stress. A decrease of 3.3 (95% CI:2.3 to 4.3) points in mean depression score, a decrease of 2.6 (95% CI: 1.6 to 3.7) points in mean anxiety score and a decrease of 2.7 (with 95% CI: 1.6 to 4.0) points in mean stress scores on the DASS-21 scale were recorded. Conclusions: Peer support is effective in improving mental health of migrant workers in the construction sector in Singapore. This intervention should be considered among other measures to improve their welfare.Originality/valueThis is the first paper that talks about the mental health of migrant workers pre-COVID and hence would be a strong paper for the future comparative studies for pre-and post-COVID periods. This is the first paper that addresses the benefits of peer-support among migrant workers to improve their mental wellbeing.
Providing antibacterial properties to denim and non-denim trousers with encapsulation technology
Authors: İvedi İsmail , Güneşoğlu Bahadır , Karavana Sinem Yaprak , Erkan Gökhan , Kartal Gülşah Ekin , Sariisik Ayse Merih 
Published: July 2022

PurposeThe aim was to prepare antibacterial microcapsules and transferred to denim and non-denim (canvas) trousers.Design/methodology/approachFor this purpose, lavender and sweet almond oil as active agents were encapsulated with ethylcellulose shell with a spray dryer method and carried out capsule optimization studies.FindingsThe particle diameter of the capsules ranged between 0.61 and 8.76 µm, SPAN value was 1.608 and the mean particle size was 4 µm. The mass yields of capsules ranged between 35.0 and 75.4 %w/w. Denim fabrics were treated with prepared capsules by exhaustion and spraying methods. It was seen that microcapsules provided a reduction of bacteria by over 97% against both Staphylococcus aureus and Escherichia coli and the fabrics still showed an antibacterial effect after five washing cycles.Originality/valueWhen application methods were compared, the spraying method was found to be more sustainable process than exhaustion and could be used as an alternative for reducing energy consumption and capsules could provide antibacterial properties to the fabrics.
Secondary school organisation and home–school collaboration: a tale of two systems
Authors: Barnard Peter A. 
Published: July 2022

PurposeThis conceptual paper explores the relationship between school structure, organisation, and home–school collaboration. It argues that the traditional and dominant secondary school model based on same-age organisation acts in ways that constrain home–school collaboration while claiming to value it. The paper proposes an alternative model (vertical tutoring), one that relies on home–school collaboration and developing the capacity to absorb the complexity that collaboration createsDesign/methodology/approachModels of home–school collaboration abstracted from the research literature are set within a framework of organisational studies, complexity science, and systemic thinking, revealing incongruities between claimed values and operational practices. The paper contrasts the frailties endemic to same-age organisation with the advantages claimed by schools that have adopted a vertical tutoring (VT) systemFindingsThe choice of organisational structure is a major influence on a school's capacity to develop the home–school collaboration needed to liberate individual and organisational learning. Same-age organisational structure has a reduced capacity for building the collaborative partnerships needed to engage parents in their child's learning process. Multi-age organisation matches capacity with learning demand, enabling agency and liberating management.Research limitations/implicationsCurrent approaches to modelling rarely consider same-age operative structure and so are destined to restrict rather than enable home–school collaboration. The adoption of VT by schools broadens the scope of organisational analysis, positing a need for multi-disciplinary research able to link the form of school organisation to individual and organisational learning.Originality/valueVT is rarely mentioned in the research literature as an alternative to same-age structuration. This paper addresses this issue and draws upon complexity science, autopoietic theory, and systemic thinking to explain why current models of home–school collaboration are insufficiently situated in organisational practice.