bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel gapmer nanobiosensor for probing long noncoding RNAs (lncRNA) expression dynamics during osteogenic and adipogenic differentiation
Authors: Fasciano Samantha , Luo Shuai , Wang Shue 
Published: July 2023

AbstractLong non-coding RNAs (lncRNA) are non-protein coding RNA molecules that are longer than 200 nucleotides. lncRNA plays diverse roles in gene regulation, chromatin remodeling, and cellular processes, influencing various biological pathways. However, probing the complex dynamics of lncRNA in live cells is a challenging task. In this study, a double-stranded gapmer locked nucleic acid (ds-GapM-LNA) nanobiosensor is designed for visualizing the abundance and expression of lncRNA in live human bone-marrow-derived mesenchymal stem cells (hMSCs). The sensitivity, specificity, and stability were characterized. The results showed that this ds-GapM-LNA nanobiosensor has very good sensitivity, specificity, and stability, which allows for dissecting the regulatory roles of cellular processes during dynamic physiological events. By incorporating this nanobiosensor with living hMSCs imaging, we elucidated lncRNA MALAT1 expression dynamics during osteogenic and adipogenic differentiation. The data reveals that lncRNA MALAT1 expression is correlated with distinct sub-stages of osteogenic and adipogenic differentiation.
Relationship between luteal size and plasma progesterone concentration in pregnant and non-pregnant Indian crossbred dairy cows
Authors: Agarwal Sanjay , Gupta Harihar Prasad , Prasad Shiv , Khan Irfan Ahmad , Khanam Afroza , Khan Firdous Ahmad 
Published: July 2023

AbstractThe relationship between luteal size and plasma progesterone concentration in purebred cows has been investigated previously. However, there is limited information on this topic in Indian crossbred cows. This study aimed to evaluate the relationship between luteal size parameters (diameter and area) and plasma progesterone concentration in healthy pregnant and non-pregnant Indian crossbred cows. Fifty healthy lactating crossbred cows were artificially inseminated after estrus detection and retrospectively classified into pregnant (n=29) and non-pregnant (n=21) based on the results of ultrasonographic pregnancy diagnosis. Data on luteal diameter, luteal area, and plasma progesterone concentration collected on Days 7, 14, and 20 in non-pregnant cows and on Days 7, 14, 20, 25, 30, 35, 40, and 60 in pregnant cows were analyzed. Spearman’s correlation test was used to evaluate the association between the corpus luteum size parameters and the plasma progesterone concentration. Luteal area was positively correlated with plasma progesterone concentration in both pregnant (ρ=0.48, P<0.001) and non-pregnant (ρ=0.43, P=0.001) cows. Luteal diameter had a relatively weaker correlation with plasma progesterone concentration in both pregnant (ρ=0.45, P<0.001) and non-pregnant (ρ=0.24, P=0.058) cows. These results suggest that luteal area is a better indicator of CL function than luteal diameter in healthy Indian crossbred cows.
Improvement in Neoantigen Prediction via Integration of RNA Sequencing Data for Variant Calling
Authors: Nguyen Bui Que Tran , Tran Thi Phuong Diem , Nguyen Huu Thinh , Nguyen Thanh Nhan , Pham Thi Mong Quynh , Nguyen Hoang Thien Phuc , Tran Duc Huy , Nguyen Vy , Tran Thanh Sang , Pham Truong-Vinh Ngoc , Le Minh-Triet , Phan Minh-Duy , Giang Hoa , Nguyen Hoai-Nghia , Tran Le Son 
Published: July 2023

ABSTRACTNeoantigen-based immunotherapy has emerged as a promising strategy for improving the life expectancy of cancer patients. This therapeutic approach heavily relies on accurate identification of cancer mutations using DNA sequencing (DNAseq) data. However, current workflows tend to provide a large number of neoantigen candidates, of which only a limited number elicit efficient and immunogenic T-cell responses suitable for downstream clinical evaluation. To overcome this limitation and increase the number of high-quality immunogenic neoantigens, we propose integrating RNA sequencing (RNAseq) data into the mutation identification step in the neoantigen prediction workflow. In this study, we characterize the mutation profiles identified from DNAseq and/or RNAseq data in tumor tissues of 25 patients with colorectal cancer (CRC). We detected only 22.4% of variants shared between the two methods. In contrast, RNAseq-derived variants displayed unique features of affinity and immunogenicity. We further established that neoantigen candidates identified by RNAseq data significantly increased the number of highly immunogenic neoantigens (confirmed by ELISpot) that would otherwise be overlooked if relying solely on DNAseq data. In conclusion, this integrative approach holds great potential for improving the selection of neoantigens for personalized cancer immunotherapy, ultimately leading to enhanced treatment outcomes and improved survival rates for cancer patients.
In Vivo Three-dimensional Brain Imaging with Chemiluminescence Probes in Alzheimer’s Disease Models
Authors: Zhang Jing , Wickizer Carly , Ding Weihua , Van Richard , Yang Liuyue , Zhu Biyue , Yang Jun , Zhang Can , Shen Shiqian , Shao Yihan , Ran Chongzhao 
Published: July 2023

AbstractOptical three-dimensional (3D) molecular imaging is highly desirable for providing precise distribution of the target-of-interest in disease models. However, such 3D imaging is still far from wide applications in biomedical research; 3D brain optical molecular imaging, in particular, has rarely been reported. In this report, we designed chemiluminescence probes with high quantum yields (QY), relatively long emission wavelengths, and high signal-to-noise ratios (SNRs) to fulfill the requirements for 3D brain imaging in vivo. With assistance from density-function theory (DFT) computation, we designed ADLumin-Xs by locking up the rotation of the double-bond via fusing the furan ring to the phenyl ring. Our results showed that ADLumin-5 had a high quantum yield of chemiluminescence and could bind to amyloid beta (Aβ). Remarkably, ADLumin-5’s radiance intensity in brain areas could reach 4×107photon/s/cm2/sr, which is probably 100-fold higher than most chemiluminescence probes for in vivo imaging. Because of its strong emission, we demonstrated that ADLumin-5 could be used for in vivo 3D brain imaging in transgenic mouse models of Alzheimer’s disease (AD).Significance StatementAlthough MRI, PET, CT, and SPECT have been routinely used for 3D imaging, including 3D brain imaging, they are considerably expensive. Optical imaging is largely low-cost and high throughput. However, the 3D capacity of optical imaging is always limited. Obviously, optical 3D molecular imaging is highly challenging, particularly for 3D brain imaging. In this report, we provided the first example of 3D brain imaging with chemiluminescence probes ADLumin-Xs, which have advantages in quantum yields (QY), emission wavelengths, and signal-to-noise ratios (SNRs) to fulfill the requirements for 3D brain imaging. And we believe that such 3D capacity is potentially a game-changer for brain molecular imaging in preclinical studies.
Defining Dementia Subtypes Through Neuropsychiatric Symptom-Linked Brain Connectivity Patterns
Authors: Zhao Kanhao , Xie Hua , Fonzo Gregory A. , Carlisle Nancy , Osorio Ricardo S. , Zhang Yu 
Published: July 2023

AbstractBACKGROUNDDementia is highly heterogeneous, with pronounced individual differences in neuropsychiatric symptoms (NPS) and neuroimaging findings. Understanding the heterogeneity of NPS and associated brain abnormalities is essential for effective management and treatment of dementia.METHODSUsing large-scale neuroimaging data from the Open Access Series of Imaging Studies (OASIS-3), we conducted a multivariate sparse canonical correlation analysis to identify functional connectivity-informed symptom dimensions. Subsequently, we performed a clustering analysis on the obtained latent connectivity profiles to reveal neurophysiological subtypes and examined differences in abnormal connectivity and phenotypic profiles between subtypes.RESULTSWe identified two reliable neuropsychiatric subsyndromes – behavioral and anxiety in the connectivity-NPS linked latent space. The behavioral subsyndrome was characterized by the connections predominantly involving the default mode and somatomotor networks and neuropsychiatric symptoms involving nighttime behavior disturbance, agitation, and apathy. The anxiety subsyndrome was mainly contributed by connections involving the visual network and the anxiety neuropsychiatric symptom. By clustering individuals along these two subsyndromes-linked connectivity latent features, we uncovered three subtypes encompassing both dementia patients and healthy controls. Dementia in one subtype exhibited similar brain connectivity and cognitive-behavior patterns to healthy individuals. However, dementia in the other two subtypes showed different dysfunctional connectivity profiles involving the default mode, frontoparietal control, somatomotor, and ventral attention networks, compared to healthy individuals. These dysfunctional connectivity patterns were associated with differences in baseline dementia severity and longitudinal progression of cognitive impairment and behavioral dysfunction.CONCLUSIONSOur findings shed valuable insights into disentangling the neuropsychiatric and brain functional heterogeneity of dementia, offering a promising avenue to improve clinical management and facilitate the development of timely and targeted interventions for dementia patients.
Polygenic basis of strong and rapid flowering time response to environment perturbations in wildArabidopsis thalianapopulation
Authors: Ji Yan , Han Yu , Dai Yifei , Hao Fan , Feng Xiao , Chen Qipian , Hao Ran , Chen Zhiqiang , Zhao Wei , Zhang Wenjia , Si Huan , Zan Yanjun 
Published: July 2023

AbstractDespite the importance in understanding the impact of climate change, the genetics of rapid response to changing environments and its role in adaptive evolution remains elusive. Here, we studied flowering time response to environment changes using 514Arabidopsis thalianaworldwide accessions with re-sequencing genomes and flowering time measurements from ten unique environments with variable temperature, drought, daylight and competition stresses. We revealed a polygenic basis of flowering time mean and plasticity, underpinned by 52 mean and plasticity QTL. Widespread interaction between mean QTL, polygenic background and surrounding environments considerably altered the amount of additive genetic variance and allelic effects of detected QTL. This caused variability in phenotype plasticity and across environment variation in genetic variance, resulting in rapid flowering time response to environment perturbations. In addition, the plastic alleles showed a higher correlation with the environment factors than that from randomly sampled alleles, suggesting a potential role in climate adaptation. We therefore proposed a polygenic interaction model, whereby large effect QTL and polygenic background simultaneously interacted with the surrounding environment, underlying rapid response to changing environments. Results from our study thus provided deeper insights into the genetics of plasticity, with potential benefit in genomic selection of crops in heterogeneous environments and predicting changes in species distribution and the evolutionary trajectory of wild populations.
Perception of COVID-19 rapid antigen testing approach prior to flight schedule among air travelers: a questionnaire-based study
Authors: Shahid Mohammed , Joji Ronni Mol , Prabu Kumar Archana , Almarabheh Amer , Kosaraju Kranthi , Almahmeed Ali , Deifalla Abdel Halim Salem 
Published: July 2023

PurposeThe COVID-19 pandemic had a huge impact on people's lives, air travel and tourism. The authors explored travelers' perceptions of COVID rapid antigen tests before boarding aircraft, willingness to fly and the precautionary actions for safe air travel.Design/methodology/approachAll the participants were asked to complete the survey while reflecting on their experiences of air travel during this COVID-19 pandemic. The questionnaire consisted of demographic information of the participants and air travel preferences during pandemic. The survey was conducted through Google Form in both English and Arabic language. The link was shared through emails and WhatsApp.FindingsIn this survey, majority had willingness to fly during pandemic. 45.2% preferred to undergo rapid test before boarding, while 41.9% refused owing to no added benefit (23.8%) and nasal discomfort (9.3%) among others. The best indicators to resume safe air travel were COVID-19 vaccination (80.4%), wearing face mask during flying hours (70.8%) and maintain social distancing with aircraft seating (49.6%).Research limitations/implicationsThe findings of the current survey could help the organizations and the biosecurity authorities to act and support accordingly and thus reduce passenger anxiety about resuming the flights, thereby increasing willingness to fly and preparing oneself and the aviation industry for future pandemics.Originality/valueThe findings of the current survey could help the organizations and the biosecurity authorities to act and support accordingly and thus reduce passenger anxiety about resuming the flights, thereby increasing willingness to fly, and preparing oneself and the aviation industry for future pandemics.
A risk assessment framework using neutrosophic theory for the halal supply chain under an uncertain environment
Authors: Khan Shahbaz , Haleem Abid , Khan Mohd Imran 
Published: July 2023

PurposeThe complex network structure causes several disruptions in the supply chain that make risk management essential for supply chain management including halal supply chain (HSM). During risk management, several challenges are associated with the risk assessment phase, such as incomplete and uncertain information about the system. To cater this, the authors propose a risk assessment framework that addresses the issues of uncertainty using neutrosophic theory and demonstrated the applicability of the proposed framework through the case of halal supply chain management (HSCM).Design/methodology/approachThe proposed framework is using the capabilities of the neutrosophic number which can handle uncertain, vague and incomplete information. Initially, the risk related to the HSC is identified through a literature review and expert’s input. Further, the probability and impact of each HSM-related risk are assessed using experts’ input through linguistic terms. These linguistic values are transformed into single-value trapezoidal neutrosophic numbers (SVTNNs). Finally, the severity of each HSM-related risk is determined through the multiplication of the probability and impact of each risk and prioritised the risks based on their severity.FindingsA comprehensive risk assessment framework is developed that could be used under uncertainty. Initially, 16 risks are identified related to the HSM. Further, the identified risks are prioritised using the severity of the risks. The high-priority risk is “raw material status”, “raw material wholesomeness” and “origin of raw material” while “information integrity” and “people integrity” are low-priority risks.Practical implicationsHSM risk can be effectively assessed through the proposed framework. The proposed framework applied neutrosophic numbers to represent real-life situations, and it could be used for other supply chains as well.Originality/valueThe proposed method is effectively addressing the issue of linguistic subjectivity, inconsistent information and uncertainty in the expert’s opinion. A case study of the HSC is adopted to illustrate the efficiency and applicability of the proposed risk framework.
Implicit measures in leadership categorization theory: the case for using cognitive mapping and verbal protocols to study cross-categorization phenomena
Authors: Pitsi Safoora , Billsberry Jon , Barrett Mary 
Published: July 2023

PurposeThis paper contributes to leadership categorization theory by advocating a new method to surface people's implicit leadership theories. The purpose of this new approach is to simultaneously capture individual difference in how they conceptualize leadership but within a common framework to allow for comparison of within- and between-person effects.Design/methodology/approachThe authors conduct a narrative review of the implicit leadership theory, leadership categorization theory, cognitive mapping and verbal protocol literature with the purpose of surfacing a research method that will overcome the problems of over-simplification and over-individualization in existing methods.FindingsThe authors argue that using a combination of cognitive mapping and verbal protocols can capture the idiosyncrasies of individual lay theories of leadership while retaining the ability to compare people's responses through a common framework. The authors provide an example of how this method can be used to elicit people's perceptions of one aspect of implicit leadership theories, intelligence.Research limitations/implicationsThis new method will provide a methodology to test the subset propositions advocated by leadership categorization theory. These include the idea that subordinate level implicit leadership theories contain a subset of attributes found in the basic-level implicit leadership theories, that there is attribute integrity in superordinate implicit leadership theories through the levels, and the idea that people define leadership differently depending on the context they are observing.Originality/valueWhereas previous approaches to surfacing people's implicit leadership theories either heavily constrain their responses with a predetermined generic suite of attributes or are totally open-ended and idiosyncratic, the authors advocate an approach that combines the best of both.
Analysis of melting of phase change material inserted a block via impinging turbulent slot jet
Authors: Oztop Hakan F. , Gür Muhammed , Selimefendigil Fatih , Coşanay Hakan 
Published: July 2023

Purpose
The purpose of this study is to do a numerical analysis of the jet to a body filled with phase change material (PCM). The melting of the PCM filled body was investigated by the hot jet flow. Four different values of the Reynolds number were taken, ranging from 5 × 103 = Re = 12.5 103. Water, Al2O3 1%, Al2O3 2% and hybrid nanofluid (HNF; Al2O3–Ag mixture) were used as fluid types and the effects of fluid type on melting were investigated. At 60 °C, the jet stream was impinged on the PCM filled body at different Reynolds numbers.

Design/methodology/approach
Two-dimensional analysis of melting of PCM inserted A block via impinging turbulent slot jet is numerically studied. Governing equations for turbulent flow are solved by using the finite element method via analysis and system fluent R2020.

Findings
The obtained results showed that the best melting occurred when the Reynolds number increased and the HNF was used. However, the impacts of using alumina-water nanofluid were slight. At Re = 12,500, phase completion time was reduced by about 13.77% when HNF was used while this was only 3.93% with water + alumina nanofluid as compared to using only water at Re = 5,000. In future studies, HNF concentrations will change the type of nanoenhanced PCMs. In addition, the geometry and jet parameters of the PCM-filled cube can be changed.

Originality/value
Effects of impinging jet onto PCM filled block and control of melting via impinging hot jet of PCM. Thus, novelty of the work is to control of melting in a block by impinging hot jet and nanoparticles.
Cavitation characteristics and energy loss in high-pressure differential control valve
Authors: Jin Haozhe , Wen Ruoshuang , Wang Chao , Liu Xiaofei 
Published: July 2023

Purpose
The purpose of this study is to determine the cavitation flow characteristics of the high-pressure differential control valve. The relationship between cavitation, flow coefficient and spool angle is obtained. By analyzing the relationship between different spool angles and energy loss, the energy loss at different spool angles is predicted.

Design/methodology/approach
A series of numerical simulations were performed to study the cavitation problem of a high-pressure differential control valve using the RNG k–e turbulence model and the Zwart cavitation model. The flow states and energy distribution at different spool angles were analyzed under specific working conditions.

Findings
The cavitation was the weakest when the spool angle was 120° or the outlet pressure was 8 MPa. The pressure and speed fluctuations of the valve in the throttle section were greater than those at other locations. By calculating the entropy production rate, the reason and location of valve energy loss are analyzed. The energy loss near the throttling section accounts for about 92.7% of the total energy loss. According to the calculated energy loss relationship between different regions of the spool angle, the relationship between any spool angle and energy loss in the [80,120] interval is proposed.

Originality/value
This study analyzes the cavitation flow characteristics of the high-pressure differential control valve and provides the law of energy loss in the valve through the analysis method of entropy. The relationship between spool angle and energy loss under cavitation is finally proposed. The research results are expected to provide a theoretical basis for the optimal design of valves.
Project managers' ability to explore and exploit predictive and iterative best practices
Authors: Marnewick Carl , Marnewick Annlizé L. 
Published: July 2023

Purpose Project managers face decisions every day and those decisions result in an “either or” situation. This is also true when it comes to the choice of a project management approach, i.e. predictive versus iterative. A case is made in this article that project managers should be ambidextrous and apply practices that are beneficial to the project, irrespective of the origin of the practices.Design/methodology/approach This study is based on a questionnaire focussing on six themes. The results of 290 projects were analysed using ANOVA and boxplots to test for skewness and variances.Findings Based on the analysis of 117 practices, most of these projects could be classified as either hybrid or iterative projects. The results indicate that irrespective of the classification of the projects or the industry, projects are managed using a hybrid approach, with a tendency to incorporate more iterative practices than predictive practices.Originality/value This article contributes to the current debate on which approach is the best given certain circumstances.