Miracle-dz/UniFAR-FTUs huggingface dataset:
Preparation of MC3T3-E1 cell sheets through short-term osteogenic medium application

Abstract Cell sheet engineering is an emerging field based on the acquisition of cells together with their extracellular matrix (ECM) and is used not only in vitro but also in regeneration studies of various tissues in the clinic. Within this scope, wide variety of cell types have been investigated in terms of sheet formation and underlying mechanism. MC3T3-E1 is a mouse pre-osteoblast cell line that has greatly attracted researchers’ attention for bone tissue engineering (BTE) applications thanks to its high proliferation and differentiation properties. The potential of MC3T3-E1 cells on sheet formation and the effects of culture conditions have not been investigated in detail. This study aims to examine the effects of growth and osteogenic medium on cell sheet formation of MC3T3-E1. As a result of this study; intact, ECM-rich, transferable cell sheets at the beginning of the mineralization phase of the differentiation process were obtained by using osteogenic medium. Hereafter, 3D tissue model can be constructed by stacking MC3T3 cell sheets in vitro. This 3D model can conveniently be used for the development of novel biomaterials and in vitro drug screening applications to reduce the need for animal experiments.
Development of novel self-assembled polymeric micelles from partially hydrolysed poly(2-ethyl-2-oxazoline)-co-PEI-b-PCL block copolymer as non-viral vectors for plasmid DNA in vitro transfection

Abstract A new efficient, non-viral gene delivery cationic polymeric micellar system was developed by partial hydrolysis of poly(2-ethyl-2-oxazoline) (PEtOx) with two different hydrolysis percentages of PEtOx (30% and 60%) to reduce the disadvantages of the PEI. These self-assemble amphiphilic cationic micelles prepared from poly(2-ethyl-2-oxazoline)30%-co-poly(ethyleneimine)-block-poly(ɛ-caprolactone) (PEtOx30%-co-PEI-b-PCL) (PPP30) and poly(2-ethyl-2-oxazoline) 60%-co-poly(ethyleneimine)-block-poly(ɛ-caprolactone) (PEtOx60%-co-PEI-b-PCL) (PPP60) block copolymers were successfully condensed with pEGFP-C3 plasmid DNA via electrostatic interactions to form micelle/DNA complexes with desirable particle sizes. All formulations showed low critical micelle concentration (CMC) values that means highly stable in serum containing medium. Polymeric micelles were also evaluated for their stability in the presence of serum and nuclease as well as cytotoxicity and transfection efficiency. All our results proved that our novel polymeric micellar system prepared by PPP60 block copolymer offer to be an efficient promising carrier for gene delivery applications. Moreover, these findings contribute to design and development of novel gene vectors with tunable and functionality features and also to reduce the cytotoxicity of PEI by partial hydrolysis of PEtOx an alternative synthesis method to produce linear PEI.
Development and characterization of 15 polymorphic microsatellite loci isolated from Rafinesque's big‐eared bat, Corynorhinus rafinesquii

We developed and characterized 15 microsatellite markers for Rafinesque's big‐eared bat, Corynorhinus rafinesquii. In a population from Tennessee, the number of alleles per locus ranged from three to 13 and observed heterozygosities were 0.35 to 0.97 per locus. These loci will provide appropriate variability for estimation of population connectivity, demographic parameters, and genetic diversity for this species of concern.
DNA barcode accumulation curves for understudied taxa and areas

Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well‐known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment — parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha‐taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.
Moonlighting cytochrome P450 monooxygenases

Recently, cytochrome P450 170A1 (CYP170A1) has been found to be a bifunctional protein, which catalyzes both monooxygenase activity and terpene synthase activity by two distinct active sites in the well‐established P450 protein structure. Therefore, CYP170A1 is identified clearly as a moonlighting protein. The known activities of a small number of the 13,000 members of the P450 superfamily fall into two general classes: promiscuous enzymes that are not considered as moonlighting and forms that participate in biosynthesis of endogenous compounds, such as steroids, vitamins and play different roles in different tissues, sometimes being moonlighting enzymes. Here, we review examples of moonlighting P450, which add to our understanding of the large CYP superfamily. © 2011 IUBMB IUBMB Life, 63(7): 473–477, 2011
smogd: software for the measurement of genetic diversity

Software for the measurement of genetic diversity (SMOGD) is a web‐based application for the calculation of the recently proposed genetic diversity indices G′ST and Dest. SMOGD includes bootstrapping functionality for estimating the variance, standard error and confidence intervals of estimated parameters, and SMOGD also generates genetic distance matrices from pairwise comparisons between populations. SMOGD accepts standard, multilocus Genepop and Arlequin formatted input files and produces HTML and tab‐delimited output. This allows easy data submission, quick visualization, and rapid import of results into spreadsheet or database programs.
CVhaplot: a consensus tool for statistical haplotyping

Haplotypes contain genealogical information and play a prominent part in population genetic and evolutionary studies. However, haplotype inference is a complex statistical problem, showing considerable internal algorithm variability and among‐algorithm discordance. Thus, haplotypes inferred by statistical algorithms often contain hidden uncertainties, which may complicate and even mislead downstream analysis. Consensus strategy is one of the effective means to increase the confidence of inferred haplotypes. Here, we present a consensus tool, the CVhaplot package, to automate consensus techniques for haplotype inference. It generates consensus haplotypes from inferrals of competing algorithms to increase the confidence of haplotype inference results, while improving the performance of individual algorithms by considering their internal variability. It can effectively identify uncertain haplotypes potentially associated with inference errors. In addition, this tool allows file format conversion for several popular algorithms and extends the applicability of some algorithms to complex data containing triallelic polymorphic sites. CVhaplot is written in PERL and freely available at http://www.ioz. ac.cn/department/agripest/group/zhangdx/CVhaplot.htm.
Upstream sequences required for tissue‐specific activation of the cardiac actin gene in Xenopus laevis embryos.

The entire DNA sequence of the Xenopus laevis cardiac actin gene was determined. A recombinant plasmid comprising the cardiac actin gene promoter fused to the bacterial chloramphenicol acetyl transferase (CAT) gene is correctly regulated after introduction into fertilized Xenopus eggs. The fusion gene shows a temporal and tissue‐specific pattern of expression in the early embryo which is indistinguishable from that of the endogenous cardiac actin gene. The fusion gene is also activated in cultured embryo fragments that are induced by cell interactions to form embryonic muscle tissue. Tissue‐specific expression of the recombinant requires sequences between 217 and 416 nucleotides upstream from the transcription initiation site. In contrast, both the chimaeric gene and the entire cardiac actin gene are expressed at a basal level after microinjection into Xenopus oocytes, requiring only the presence of a TATA box upstream from the cap site.
Synergistic activation of transcription by the human estrogen receptor bound to tandem responsive elements.

The synergistic action of the human estrogen receptor (hER) has been investigated using minimal promoters containing a TATA region and one or two estrogen responsive elements (EREs). We find that paired perfectly palindromic EREs act additively and independently of their relative spacing when positioned close to the TATA box. However, when moved 175 bp further upstream, perfectly palindromic EREs act synergistically and in a stereoalignment‐dependent manner. Less efficient imperfectly palindromic EREs display a stereoalignment‐dependent synergism even when positioned close to the TATA box. Analysis of binding in vitro of the hER to perfectly or imperfectly palindromic EREs by gel retardation and nitrocellulose filter binding assays does not provide any evidence for cooperative DNA binding. Conversely, the human progesterone receptor (hPR) clearly shows cooperative binding to paired responsive elements (PREs) under similar conditions in vitro. Thus, hER molecules bound to adjacent EREs must be properly stereoaligned to activate transcription synergistically in vivo. However, our data suggest that this synergism is not primarily due to cooperative binding to the EREs.
RBANS factor structure in older adults with suspected cognitive impairment: Evidence for a 5-factor structure

ABSTRACT Previous research has yielded minimal empirical support for the theoretically formulated five-factor structure of the RBANS, a brief, yet comprehensive standardized neuropsychological test battery used to assess cognitive impairment. The present study tested the theoretically formulated five-factor structure, as well as three alternative factor solutions, using a combination of exploratory and confirmatory factor analytic approaches. The present study utilized archival data from a clinical sample of 150 older adults who were evaluated at an outpatient neuropsychological service. A total of four RBANS models were specified using confirmatory factor analysis. Results of the five-factor model demonstrated good to excellent fit following modifications to the model. Results of chi-square difference tests demonstrated that the five-factor model was statistically superior to the two- and three-factor models (p < .001). In summary, results provide support for the theoretically derived five-factor structure of the RBANS in a clinical sample of older adults. Cautious interpretation of the RBANS index scores as five distinct cognitive domains may be warranted, particularly when there is minimal discrepancy across performance on the tests that comprise each index.
Sperm whale population structure in the eastern and central North Pacific inferred by the use of single‐nucleotide polymorphisms, microsatellites and mitochondrial DNA

We use mitochondrial DNA (mtDNA) (400 bp), six microsatellites and 36 single‐nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long‐term studies of globally distributed species such as sperm whales, a species of conservation concern because of both historical and contemporary impacts. We estimate genetic differentiation among three strata in the temperate to tropical waters where females are found: California Current, Hawai`i and the eastern tropical Pacific. We then consider how males on sub‐Arctic foraging grounds assign to these strata. The California Current stratum was differentiated from both the other strata (P < 0.05) for mtDNA, microsatellites and SNPs, suggesting that the region supports a demographically independent population and providing the first indication that males may exhibit reproductive philopatry. Comparisons between the Hawai`i stratum and the eastern tropical Pacific stratum are not conclusive at this time. Comparisons with Alaska males were statistically significant, or nearly so, from all three strata and individuals showed mixed assignment to, and few exclusions from, the three potential source strata, suggesting widespread origin of males on sub‐Arctic feeding grounds. We show that SNPs have sufficient power to detect population structure even when genetic differentiation is low. There is a need for better analytical methods for SNPs, especially when linked SNPs are used, but SNPs appear to be a valuable marker for long‐term studies of globally dispersed and highly mobile species.
Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa

The limitations intrinsic to morphology‐based identification systems have created an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species, particularly those that are prone to overexploitation and/or market substitution. The aim of this study was to develop a comprehensive reference library of DNA sequence data to allow the explicit identification of 53 commercially available fish species in South Africa, most of which were locally caught marine species. Sequences of approximately 655 base pairs were generated for all species from the cytochrome c oxidase I (COI) gene, the region widely adopted for DNA barcoding. Specimens of the genus Thunnus were examined in further detail, employing additional mitochondrial DNA control region sequencing. Cumulative analysis of the sequences from the COI region revealed mean conspecific, congeneric and confamilial Kimura 2‐parameter distances of 0.10%, 4.58% and 15.43%, respectively. The results showed that the vast majority (98%) of fish species examined could be readily differentiated by their COI barcodes, but that supplementary control region sequencing was more useful for the discrimination of three Thunnus species. Additionally, the analysis of COI data raised the prospect that Thyrsites atun (snoek) could constitute a species pair. The present study has established the necessary genetic information to permit the unambiguous identification of 53 commonly marketed fish species in South Africa, the applications of which hold a plethora of benefits relating to ecology research, fisheries management and control of commercial practices.
Application of multiplex PCR approaches for shark molecular identification: feasibility and applications for fisheries management and conservation in the Eastern Tropical Pacific

Here we describe the application of new and existing multiplex PCR methodologies for shark species molecular identification. Four multiplex systems (group ID, thresher sharks, hammerhead sharks and miscellaneous shark) were employed with primers previously described and some designed in this study, which allow for species identification after running PCR products through an agarose gel. This system was implemented for samples (bodies and fins) collected from unidentified sharks landed in the port of Buenaventura and from confiscated tissues obtained from illegal fishing around the Malpelo Island Marine Protected Area, Pacific Coast of Colombia. This method has allowed reliable identification, to date, of 407 samples to the genus and/or species levels, most of them (380) identified as the pelagic thresher shark (Alopias pelagicus). Another seven samples were identified as scalloped hammerhead sharks (Sphyrna lewini). This is an easy‐to‐implement and reliable identification method that could even be used locally to monitor shark captures in the main fishing ports of developed and developing countries.
Characterization of nerve growth factor‐induced mechanical and thermal hypersensitivity in rats

Injection of nerve growth factor (NGF) produces mechanical and thermal hypersensitivity in rodents and humans. Treatment with sequestering antibodies demonstrates the importance of NGF in various pain states, with efficacy seen in a number of animal pain models and in painful human conditions. However, these phenomena have not been evaluated in the context of using NGF‐induced hypersensitivities as a model of pain.
Thinking aloud during idea generating and planning before written translation: Developmental changes from ages 10 to 12 in expressing and defending opinions

Abstract This interdisciplinary research, drawing on cognitive psychology and linguistics, extended to middle childhood past research during early childhood or adulthood on thinking aloud prior to written composing. In year 5 of a longitudinal study of typical writing, when cohort 1 was in grade 5 (n = 110 ten year-olds) and cohort 2 in grade 7 (n = 97 twelve year-olds), a cross-sectional study was conducted. Children were first asked to think aloud while they generated ideas and second while they planned their essays to express and defend their opinions on a controversial topic in the region of the United States where they lived. Third, they wrote their essays. Their think-aloud protocols were audio-recorded and later transcribed into writing for analysis. The authors developed and applied rating scales for quality of idea generating and planning in the written transcriptions and quality of opinion expression, opinion defense, organization, and content in the essays children wrote after thinking aloud; total number of words in essays was also counted. Seventh graders scored significantly higher than fifth graders on quality of idea generation but not planning, and higher on all variables rated for quality in the written essays including length. Quality of expressing opinions and defending opinions were uncorrelated in grade 5, but moderately correlated in grade 7. Whether idea generating or planning quality explained unique variance in essays varied with coded written essay variables and grade. Educational applications of results for assessment, assessment-instruction links, instruction in social studies, and theory of mind in persuasive essay writing are discussed.
After‐effects of cognitive control on pain

The higher order processes involved in self‐regulation are generally thought to depend on cognitive (attentional/executive) functions with limited resources. Experimental studies further show that exerting self‐control in a first task results in decreased performance in other following self‐control tasks, which may be interpreted as the consequence of either effective or perceived resource depletion outlasting the first task. Given that higher order cognitive/attentional processes are also considered to be involved in pain modulatory mechanisms, we tested the idea that pain could be influenced by prior mobilization of cognitive resources.
Establishing Rapport: Interactional Skills and Occupational Therapy

A good relationship between occupational therapist and patient contributes fundamentally to the effectiveness of treatment. Indeed, the quality of the relationship can often determine the duration and course of the re-adaptation process. The subject of rapport and how it is attained may not generally be taught to occupational therapy students in any systematic way. Its desirability is recognised, stressed, even laboured, by both staff and students, without taking part in any form of training specifically directed towards learning the requisite skills-for skills are what is required rather than possession of a particular personality type. Furthermore, similar skills are often required in order to establish a helpful and co-operative working relationship with colleagues in multi-disciplinary teams. Rapport is clearly essential but how does one go about achieving it with a colleague or client and how, as a skill, can it be taught?
Issues in the Hierarchy of Study Design, Hypothesis Testing, and Presentation of Results

Summary: Although evidence-based orthopaedics is sometimes perceived as a strict adherence to information obtained from randomized trials, it more accurately involves informed and effective use of all types of clinical evidence. However, any study that compares 2 or more treatments (ie, comparative study: randomized trial, observational study with control group, case–control) can be subject to the following errors in hypothesis testing: 1) A true positive result (ie, the study correctly identifies a true difference between treatments); 2) a true negative result (ie, the study correctly identifies no difference between treatment); 3) a false negative result–type II (beta) error (ie, the study incorrectly concludes no difference between treatments when a difference really exists); and 4) a false positive result–type I (alpha) error (ie, the study incorrectly concludes a difference between treatments when no difference exists). Understanding the principles of research design can limit errors and improve the validity of a study's results.
Model organoids provide new research opportunities for ductal pancreatic cancer

We recently established organoid models from normal and neoplastic murine and human pancreas tissues. These organoids exhibit ductal- and disease stage-specific characteristics and, after orthotopic transplantation, recapitulate the full spectrum of tumor progression. Pancreatic organoid technology provides a novel platform for the study of tumor biology and the discovery of potential biomarkers, therapeutics, and personalized medicine strategies.
Occupational Therapy to Optimise Independence in Parkinson's Disease: The Designing and Recording of a Randomised Controlled Trial Intervention

PDOT (Parkinson's Disease Occupational Therapy) was a pilot randomised controlled trial investigating occupational therapy for people with Parkinson's disease (PD) exhibiting difficulties with activities of daily living (ADL). This article describes the process undertaken to design and record the intervention. Intervention development was informed by the current evidence base and practice consensus. An expert steering group synthesised this information to develop an intervention framework. A recording tool was identified from a previous occupational therapy trial and adopted for PDOT. This was completed for all participants receiving the intervention, capturing the dose and content of therapy delivered. Nineteen participants received occupational therapy. A mean number of 5.7 visits was delivered over 60.3 days, with the initial visit lasting 60 minutes (median) and subsequent visits lasting 50 minutes (median). The intervention log demonstrated that a large proportion of therapist visits involved equipment provision/environmental adaptation, mobility/transfers/ADL training, review/discussion, and the teaching of techniques/provision of education. The intervention developed was found to be feasible and acceptable, and the findings of PDOT have been used to inform a phase III rehabilitation trial (PD REHAB). The intervention log has been revised in light of the findings and will be used within this trial.