bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliable multiplex generation of pooled induced pluripotent stem cells for genetic testing
Authors: Smullen Molly , Reichert Julia M , Dawes Pepper , Wang Qi , Readhead Benjamin , Church George M , Lim Elaine T , Chan Yingleong 
Published: August 2022

AbstractInducing somatic cells into pluripotent stem cells (iPSCs) provides an excellent model for studying systems in-vitro. Understanding the impact of individual donor genetic backgrounds on reprogramming ability would allow researchers to harness these genetic differences and increase the efficiency of the reprogramming process. To better understand the genetic basis of reprogramming cells into iPSCs, we present Induction of Pluripotency from Pooled Cells (iPPC) - an efficient, scalable, and reliable reprogramming procedure. Using our deconvolution algorithm that employs low-coverage pooled sequencing and single nucleotide polymorphisms (SNPs), we estimate individual donor proportions of cell lines within large cohorts. With iPPC, we concurrently reprogrammed over one hundred donor LCLs into iPSCs and found strong correlations of individual donors’ reprogramming ability across multiple experiments. We note that individual donors’ reprogramming ability remains consistent across both same-day replicates and multiple experimental runs, and that the expression of certain immunoglobulin precursor genes (IGLV10-54, IGLV3-9, IGLV1-17, IGLV1-6, and IGLV3-1) may impact reprogramming ability. Our process enables a multiplex framework to study the reprogramming ability of different donor cells into iPSCs and also provides a reliable method along with a pooled library of donor iPSCs for downstream research and investigation of other in-vitro phenotypes.
Spatio-temporal summation of perimetric stimuli in healthy observers
Authors: Montesano Giovanni , Mulholland Pádraig , Garway-Heath David F. , Evans Josephine , Ometto Giovanni , Crabb David P. 
Published: August 2022

AbstractSpatial summation of perimetric stimuli has been used to derive conclusions about the spatial extent of retinal-cortical convergence, mostly from the size of the critical area of summation (Ricco’s area, RA) and critical number of Retinal Ganglion Cells (RGCs). However, spatial summation is known to change dynamically with stimulus duration. Conversely, temporal summation and critical duration also vary with stimulus size. Such an important and often neglected spatio-temporal interaction has important implications for modelling perimetric sensitivity in healthy observers and for formulating hypotheses for changes measured in disease. In this work, we performed experiments on visually heathy observers confirming the interaction of stimulus size and duration in determining summation responses in photopic conditions. We then propose a simplified computational model that captures these aspects of perimetric sensitivity by modelling thetotal retinal input, the combined effect of stimulus size, duration and retinal cones-to-RGC ratio. We additionally show that, in the macula, the enlargement of RA with eccentricity might not correspond to a constant critical number of RGCs, as often reported, but to a constant criticaltotal retinal input. We finally compare our results with previous literature and show possible implications for modelling disease, especially glaucoma.
A Data-Driven Optimization Method for Coarse-Graining Gene Regulatory Networks
Authors: Caranica Cristian , Lu Mingyang 
Published: August 2022

AbstractOne major challenge in systems biology is to understand how various genes in a gene regulatory network (GRN) collectively perform their functions and control network dynamics. This task becomes extremely hard to tackle in the case of large networks with hundreds of genes and edges, many of which have redundant regulatory roles and functions. The existing methods for model reduction usually require the detailed mathematical description of dynamical systems and their corresponding kinetic parameters, which are often not available. Here, we present a data-driven method for coarse-graining large GRNs, named SacoGraci, using ensemble-based mathematical modeling, dimensionality reduction and gene circuit optimization by Markov Chain Monte Carlo methods. SacoGraci requires network topology as the only input and is robust against errors in GRNs. We benchmark and demonstrate its usage with synthetic, literature-based, and bioinformatics-derived GRNs. We hope SacoGraci will enhance our ability to model the gene regulation of complex biological systems.
The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome
Authors: Chase Madeline A. , Mugal Carina F. 
Published: August 2022

ABSTRACTRecombination is a central evolutionary process that reshuffles combinations of alleles along chromosomes, and consequently is expected to influence the efficacy of direct selection via Hill-Robertson interference. Additionally, the indirect effects of selection on neutral genetic diversity are expected to show a negative relationship with recombination rate, as background selection and genetic hitchhiking are stronger when recombination rate is low. However, owing to the limited availability of recombination rate estimates across divergent species, less is known about the impact of evolutionary changes in recombination rate on genomic signatures of selection. To address this question, we estimate recombination rate in two Ficedula flycatcher species, the taiga flycatcher (F. albicilla) and collared flycatcher (F. albicollis). We show that recombination rate is strongly correlated with signatures of indirect selection, and that evolutionary changes in recombination rate between species have observable impacts on this relationship. Conversely, signatures of direct selection on coding sequences show little to no relationship with recombination rate, even when restricted to genes where recombination rate is conserved between species. Thus, using measures of indirect and direct selection that bridge micro- and macro-evolutionary timescales, we demonstrate that the role of recombination rate and its dynamics varies for different signatures of selection.
A Phylogeny for Heterostraci (stem-gnathostomes)
Authors: Randle Emma , Keating Joseph N. , Sansom Robert S. 
Published: August 2022

AbstractThe armoured jawless fishes (ostracoderms) are major and widespread components of middle Palaeozoic ecosystems. As successive plesia on the gnathostome lineage, they reveal the early sequences of vertebrate evolution, including the assembly of the vertebrate skeleton. This is predicated however, on understanding of their diversity and interrelationships. The largest ostracoderm clade, the Pteraspidimorphi, is often reconstructed as sister taxon to other boney vertebrates yet they lack a phylogenetic framework, in particular the heterostracans. Problematic heterostracans with a tessellate headshield (‘tessellate-basal’ model) are often regarded as the plesiomorphic condition for the clade but no phylogenetic analysis has included these taxa. Here we review the Heterostraci and present their first comprehensive phylogenetic analysis (131 heterostracan taxa and 12 outgroup taxa). Heterostraci and Ordovician Pteraspidimorphi are recovered as sister-group to all other boney jawless vertebrates in parsimony analyses, however, in no instances do we recover a monophyletic Pteraspidimorphi. Tree visualization reveals lack of resolution results from two conflicting solutions for the heterostracan ‘root’. Stratigraphic congruences provides support for the macromeric Ctenaspisdidae as sister taxon to all other Heterostraci rather than the “tesselate-basal” model. The results presented here are the first phylogenetic hypotheses of heterostracan relationships and it is hoped a first step into an accurate interpretation of character evolution and polarity in this crucial episode of vertebrate evolution.
Urine γ-interferon-inducible protein (IP-10) as a biomarker of histological activity of lupus nephritis
Authors: Prasopsanti Karan , Supasiri Thanarat , Avihingsanon Yingyos , Iampenkhae Kroonpong , Surintrspanont Jerasit , Chongpisan Yuda , Promjean Chutipha , Suttichet Thitima Benjachat , Assawasaksakul Theerada , Oudomying Nont , Kittanamongkolchai Wonngarm 
Published: August 2022

AbstractIntroductionConventional markers are not reliable predictors of histological activity of lupus nephritis (LN). We aimed to examine the utility of urine γ-interferon-inducible protein (IP-10) in predicting LN flares, diagnosis of LN, and forecasting treatment response.MethodsSLE patients who fulfilled the ACR 1997 criteria with history of LN were enrolled. Urine IP-10 was measured at least once during routine quarterly visits, at the time of diagnosis of active LN, and monthly during induction therapy for 6 months.ResultsThere were 65 active LN and 46 inactive LN included. The mean urine IP-10 levels among the active and inactive LN were 2.69 (95%CI 2.53-2.86) and 2.18 (95%CI 1.96-2.39) log copies/mcg total RNA respectively (p-value < 0.0001). Clinicopathological discordance was observed in 9 of 55 (16%) biopsied patients (5 with proliferative LN without proteinuric flare and 4 with nephrotic-range proteinuria from glomerulosclerosis). Urine IP-10 predicted histological activity of LN with 91% accuracy, compared to 84% with proteinuric flare. Within two years, half of the clinically inactive LN patients with positive baseline urine IP-10 developed LN flare, whereas no flares were observed in patients with negative baseline urine IP-10. Urine IP-10 levels were not associated with treatment response at 6 months.ConclusionUrine IP-10 may reflect histological activity of LN more accurately than conventional markers, especially in patients with clinicopathologic discrepancy. Clinically inactive LN patients with positive urine IP-10 were at a higher risk of developing LN flare.Key messages-The majority of the studies on novel biomarkers in LN lacked renal biopsy and relied on clinical indicators to determine histological activity. As a result, the validity of these studies may be jeopardized.-According to this study, clinicopathological discordance was found in 16% of LN patients who underwent renal biopsy. Urine IP-10 outperformed urinary protein level in differentiating histologically active LN from inactive LN (accuracy 91% versus 84%).-Within two years, half of the clinically inactive LN patients who had positive urine IP-10 developed LN flares, whereas none of those who had negative urine IP-10 did.-Urine IP-10 may aid in the diagnosis of histologically active LN, particularly in patients with clinicopathologic discrepancy. Urine IP-10 monitoring in clinically inactive LN patients may predict the risk of future LN flares.
The Feasibility of a Smartphone-based Digital Therapeutics for Dysarthria after Stroke (DiDaS): Protocol for a pilot randomized controlled trial
Authors: Kim Yuyoung , Kim Minjung , Kim Jinwoo , Song Tae-Jin 
Published: August 2022

AbstractBackgroundDysarthria is a motor speech disorder occurring from neurological conditions such as stroke. It leads to serious problems in the intelligibility of patients’ speech, affecting their ability to communicate, quality of life, and emotional well-being. While digital therapeutic approaches for rehabilitation of dysarthria are increasing, clinical evidence of the effectiveness of digital therapeutics has been lacking. A mobile application, D-ST01, has the potential to enhance intensive and repetitive speech rehabilitation due to its high treatment accessibility and its incorporation of gamification, tailored feedback, and interactive functions.MethodsIn our trial, 60 stroke patients with dysarthria within 30 days following the occurrence of stroke will be recruited. In a 1:1 ratio, participants will be randomly assigned to either the intervention group (using D-ST01 for 60 minutes/day, five days/week along with usual stroke care) or the control group (usual stroke care only). This will be a single-blind study in which researchers will evaluate outcome measurements while masked to treatment allocation. After four weeks of treatment intervention, we will compare speech and psychological changes between the two groups.ConclusionsOur study will evaluate the feasibility of the speech treatment application D-ST01 for patients with post-stroke dysarthria. In addition, it will collect evidence for investigating the future efficacy of a large-scale randomized controlled trial.Trial registration numberClinicalTrial.gov #NCT05146765
Stock market prediction by applying big data mining
Authors: Alshammari Bedour M. , Aldhmour Fairouz , AlQenaei Zainab M. , Almohri Haidar 
Published: August 2022

PurposeThere is a gap in knowledge about the Gulf Cooperation Council (GCC) because most studies are undertaken in countries outside the Gulf region – such as China, India, the US and Taiwan. The stock market contains rich, valuable and considerable data, and these data need careful analysis for good decisions to be made that can lead to increases in the efficiency of a business. Data mining techniques offer data processing tools and applications used to enhance decision-maker decisions. This study aims to predict the Kuwait stock market by applying big data mining.Design/methodology/approachThe methodology used is quantitative techniques, which are mathematical and statistical models that describe a various array of the relationships of variables. Quantitative methods used to predict the direction of the stock market returns by using four techniques were implemented: logistic regression, decision trees, support vector machine and random forest.FindingsThe results are all variables statistically significant at the 5% level except gold price and oil price. Also, the variables that do not have an influence on the direction of the rate of return of Boursa Kuwait are money supply and gold price, unlike the Kuwait index, which has the highest coefficient. Furthermore, the height score of the variable that affects the direction of the rate of return is the firms, and the accuracy of the overall performance of the four models is nearly 50%.Research limitations/implicationsSome of the limitations identified for this study are as follows: (1) location limitation: Kuwait Stock Exchange; (2) time limitation: the amount of time available to accomplish the study, where the period was completed within the academic year 2019-2020 and the academic year 2020-2021. During 2020, the coronavirus pandemic (COVID-19), which was a major obstacle, occurred during data collection and analysis; (3) data limitation: The Kuwait Stock Exchange data were collected from May 2019 to March 2020, while the factors affecting the stock exchange data were collected in July 2020 due to the corona pandemic.Originality/valueThe study used new titles, variables and techniques such as using data mining to predict the Kuwait stock market. There are no adequate studies that predict the stock market by data mining in the GCC, especially in Kuwait. There is a gap in knowledge in the GCC as most studies are in foreign countries, such as China, India, the US and Taiwan.
Experts' views onḥiyalin Malaysian Islamic banks: the case oftawarruq-based deposit products
Authors: Syahmi Muhammad Izzul , Mohamad Mohammad Taqiuddin , Ramli Mohd Anuar 
Published: August 2022

PurposeThere are two purposes to this study: first, to identify the status ofḥiyal(legal devices) in the offering of deposit products based on thetawarruqcontract in the Malaysian Islamic banking industry and second, to identify the reasons for the widespread offering oftawarruq-based deposit products by Malaysian Islamic banks (IBs).Design/methodology/approachThe study uses the qualitative method that involved interviews with Malaysian Sharī‘ah experts and Islamic banking operations experts.FindingsThe findings show that Malaysian IBs resolved to use thetawarruqmunaẓẓamcontract in deposit products due to several constraints in the existing banking system and in view of customer preferences.Research limitations/implicationsThis study solely focuses ontawarruq-based deposit products due to its extensive application in the Malaysian Islamic banking industry.Practical implicationsThe implication of the study is that more stringent procedures are required in the offering oftawarruq-based deposit products as they are extensively utilised and have sparked controversy among Sharī‘ah scholars. Moreover, to retain Malaysia's Islamic banking reputation and trustworthiness, new and less controversial contracts must be developed.Originality/valueThis paper discusses the extensive usage ofḥiyal-based contracts such astawarruqin Islamic banking institutions' deposit products, with justifications from Malaysian Islamic banking experts. The widespread use of thetawarruqmunaẓẓamcontract in deposit-based product offerings is based on a reasonable view considering the constraints that Malaysian Islamic banking is currently facing, with strict operation procedures by Bank Negara Malaysia to ensure real operations and to avoid fictitious elements. This paper reveals the use oftawarruqmunaẓẓamin deposit products which allows the Islamic banking industry to operate effectively under Malaysia's dominant conventional banking system.
Effects of cognitive-person factors on career choice of tertiary students: the moderating role of chance events
Authors: Osei Hannah Vivian , Tepprey Evaristus , Mensah Philip Opoku 
Published: August 2022

PurposeThis study aims to investigate the effects of several individual elements vis-a-vis the environment that affects students’ choice of a career. The study assesses the effects of cognitive-person factors on the career decision-making of tertiary students and analyses how chance events moderate these relationships.Design/methodology/approachThe study used the survey research design to gather data from 302 final-year tertiary students from four (4) Faculties and sixteen (16) academic departments of a Technical University in Ghana. Data were collected through self-administered questionnaires and analysed using the partial least square structural equation modelling (PLS-SEM).FindingsThe study reveals that students’ self-efficacy and outcome expectations are two cognitive-person factors that positively and significantly influence students’ career choices. However, chance events of tertiary students were found not to moderate the relationship between cognitive-person factors and students’ career choices.Practical implicationsUnderstanding how several cognitive-person factors influence the career choice of students through the lens of social career-cognitive theory could enable researchers to advance knowledge in the career choice process. Counselors and guidance coordinators need to motivate and encourage career/job exploration and development by identifying sources of psychosocial support available to students.Originality/valueThis study identifies the cognitive person factors that drive career decisions and provides one of the initial attempts to investigate how chance events moderate students’ cognitive-person career choice relationship.
Family formation and the career trajectories of women engineering PhDs
Authors: Main Joyce B. 
Published: August 2022

Purpose
The underrepresentation of women in engineering has important consequences for meeting the need for a larger, talented scientific and technological labor force. Increasing the proportion of women faculty in engineering will help increase the persistence probabilities of women undergraduate and graduate students in engineering, as well as contribute to the range and diversity of ideas toward innovations and solutions to the greatest engineering challenges. This study aims to examine the association among gender, family formation and post-PhD employment patterns of a cohort of engineering doctorates.

Design/methodology/approach
Using the National Science Foundation’s Survey of Doctorate Recipients data, 2001–2010, descriptive and multinomial logit regression analyses are conducted to illustrate the career trajectories of engineering PhDs over a ten-year period.

Findings
The career trajectories of engineering PhDs are nonlinear, and transitions between employment sectors commonly occur over the ten-year time period studied. Although women engineering PhDs with young dependents are less likely to be employed initially after PhD completion, they tend to enter the workforce in the academic sector as time progresses. Early post-PhD employment as a postdoctoral researcher or in the academic sector contributes to the pursuit of the professoriate downstream.

Originality/value
While previous studies tend to focus on the early career outcomes of science and engineering students, this study contributes to the literature by focusing on the long-term career outcomes of engineering doctorates. Research findings provide engineering PhD students and PhDs with more information regarding potential post-PhD career trajectories, highlighting the multitude of career options and transitions that occur over time. Research findings also provide higher education administrators and doctoral program stakeholders with foundational information toward designing and revitalizing professional development programs to help PhD students prepare for the workforce. The findings have the potential to be applied toward helping increase diversity by shaping policies and programs to encourage multiple alternative career pathways to the professoriate.
Explosive wind‐pollination in a monoecious plant, Laportea bulbifera (Urticaceae)
Authors: Tsujimoto Ryutaro , Ohara Masashi 
Published: August 2022

AbstractLaportea bulbifera (Ulticaceae) is a monoecious plant that has a unique sexual expression: female flowers form on the upper part and male flowers on the lower part on an individual shoot. Therefore, for the seed reproduction, pollen needs to be transferred from the lower (male) to the upper (female) flowers. Our observations of male flowers confirmed that pollen was dispersed upward by “explosive wind pollination.” A male flower has five stamens, and when the petals are open, the stamens are caught in a pistillode. With the growth of the stamens, they are released from the pistillode and then straightened with a spring‐like movement of the filament. At the same time, the anthers dehisce, and the pollen is dispersed. The explosive release of pollen from the anthers and light wind in the habitat (forest edge or gap) contributes to wind pollination in L. bulbifera.
Co‐design or top‐down welfare conditionality? An analysis of the impact of Aboriginal and Torres Strait Islander submissions to six parliamentary inquiries into the Cashless Debit Card
Authors: Mendes Philip , Roche Steven , Conway Lisa , Castan Lani 
Published: August 2022

AbstractThe former Coalition Commonwealth Government consistently asserted that representative Aboriginal and Torres Strait Islander (hereafter Indigenous) organisations supported the introduction of the Cashless Debit Card (CDC) in multiple trial sites. Consequently, they depicted the CDC policy as an alleged exemplar of a co‐designed policy model based on partnership with Indigenous community groups. This article examines the validity of this argument by analysing the views expressed by Indigenous organisations via written and oral submissions to the six parliamentary inquiries into the CDC from 2015 to 2020. Our findings suggest that with the exception of the first inquiry, most Indigenous submissions opposed the introduction or the expansion of the CDC. Yet, these critical views received only limited acknowledgement in the inquiry reports, and seem to have little or no impact on government policy concerning the CDC. It appears that the CDC policy is more accurately identified as a top‐down policy imposed by government on local Aboriginal communities which, with some exceptions, neither requested nor consented to the policy.