Miracle-dz/UniFAR-FTUs huggingface dataset:
The Conjugation-Specific Die5 Protein Is Required for Development of the Somatic Nucleus in both Paramecium and Tetrahymena

ABSTRACT Development in ciliated protozoa involves extensive genome reorganization within differentiating macronuclei, which shapes the somatic genome of the next vegetative generation. Major events of macronuclear differentiation include excision of internal eliminated sequences (IESs), chromosome fragmentation, and genome amplification. Proteins required for these events include those with homology throughout eukaryotes as well as proteins apparently unique to ciliates. In this study, we identified the ciliate-specific Defective in IES Excision 5 (DIE5) genes of Paramecium tetraurelia (PtDIE5) and Tetrahymena thermophila (TtDIE5) as orthologs that encode nuclear proteins expressed exclusively during development. Abrogation of PtDie5 protein (PtDie5p) function by RNA interference (RNAi)-mediated silencing or TtDie5p by gene disruption resulted in the failure of developing macronuclei to differentiate into new somatic nuclei. Tetrahymena ΔDIE5 cells arrested late in development and failed to complete genome amplification, whereas RNAi-treated Paramecium cells highly amplified new macronuclear DNA before the failure in differentiation, findings that highlight clear differences in the biology of these distantly related species. Nevertheless, IES excision and chromosome fragmentation failed to occur in either ciliate, which strongly supports that Die5p is a critical player in these processes. In Tetrahymena, loss of zygotic expression during development was sufficient to block nuclear differentiation. This observation, together with the finding that knockdown of Die5p in Paramecium still allows genome amplification, indicates that this protein acts late in macronuclear development. Even though DNA rearrangements in these two ciliates look to be quite distinct, analysis of DIE5 establishes the action of a conserved mechanism within the genome reorganization pathway.
Shape Optimization of Bone-Bonding Subperiosteal Devices with Finite Element Analysis

Subperiosteal bone-bonding devices have been proposed for less invasive treatments in orthodontics. The device is osseointegrated onto a bone surface without fixation screws and is expected to rapidly attain a bone-bonding strength that successfully meets clinical performance. Hence, the device's optimum shape for rapid and strong bone bonding was examined in this study by finite element analyses. First, a stress analysis was performed for a circular rod device with an orthodontic force parallel to the bone surface, and the estimate of the bone-bonding strength based on the bone fracture criterion was verified with the results of an animal experiment. In total, four cross-sectional rod geometries were investigated: circular (Cr), elliptical (El), semicircular (Sc), and rectangular (Rc). By changing the height of the newly formed bone to mimic the progression of new bone formation, the estimation of the bone-bonding strength was repeated for each geometry. The rod with the Rc cross section exhibited the best performance, followed by those with the Sc, El, and Cr cross sections, from the aspects of the rapid acquisition of strength and the strength itself. Thus, the rectangular cross section is the best for rod-like subperiosteal devices for rapid bone bonding.
Ultrastructural Pathology of the Middle Ear Mucosa in Serous Otitis Media

Serous otitis media (SaM) is one of the most common childhood diseases. In spite of numerous investigations on the subject, its pathogenesis still remains obscure. Even the terminology sterile otitis, middle ear effusion, catarrhal otitis. and secretory otitis is diverse and confusing. However, it is generally agreed that the Eustachian tubal dysfunction is associated with this condition.
Mixing efficiency in a lock exchange experiment

Mixing Efficiency in a Lock Exchange Experiment Diane Micard 1 , Yvan Dossmann 2 , and Louis Gostiaux 1 LMFA, UMR CNRS 5509, Ecole Centrale de Lyon, France Laboratoire de Physique, UMR 5672, Ecole Normale Sup´erieure de Lyon, France diane.micard@doctorant.ec-lyon.fr Abstract We report on measurements of mixing efficiency in a lock-exchange laboratory experiment. Two reservoirs, separated by a small waterproof gate, are filled with salt water with different densities, and the gate is suddenly opened. All the energy injected into mixing derives from available potential energy. Mixing efficiency is defined as the ratio of the increase of background potential energy to the decrease of available potential energy after opening the gate. The background potential energy is the potential energy computed from cross-sorting density profiles over the two reservoirs. We were thus able to observed that mixing efficiency increases with the hydraulic Reynolds number which confirms the tendency observed by Prastowo et al [4]. Moreover, our method allows to compute the mixing efficiency in the general case where the initial state is composed of two different stratifications. We are also able to discretize the mixing process into elementary mixing events. Introduction Abyssal mixing is one of remaining uncertainties for whom wants to understand and predict heat and salt fluxes in the deep ocean. The water mass exchange between the deepest parts of ocean basins is sometimes hydraulically controlled, for instance when the flow is constrained by the geometry of the connections (fracture zones, sills, channels) and is driven by the density difference between water masses. Temperature and salinity fluxes occurring in these regions highly depends on turbulent mixing and entrainment at the fluid interface. As for global oceanic models, an important parameter needed to close the energy budget of the system is mixing efficiency η. The commonly used value is 0.17, obtained from laboratory experiments in the early 80’s [5]. Mixing efficiency measures the ratio the turbulent kinetic energy irreversibly transfered into potential energy. Direct measurement of total turbulent kinetic energy is very difficult in a real system, but it can be directly derived from the available potential energy in a lock-exchange experiment. This system is thus an elegant configuration to study mixing efficiency. Our set-up consists in a rectangular tank separated in two reservoirs by a waterproof wall, in the middle of which a gate has been installed. Inspired by Winters et al we propose to cross-sort the density profiles of the two reservoirs in order to define the reference (or background) potential energy [9]. From this quantity, the amount of irreversible mixing is evaluated, as well as mixing efficiency. This follows the work done by Prastowo et al [4] and extends it to the general case of lock-exchange between two arbitrarily stratified reservoirs. VIII th Int. Symp. on Stratified Flows, San Diego, USA, Aug. 29 - Sept. 1, 2016
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

MOTIVATION Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the 'local alignment' graph. RESULTS The algorithm is implemented in a program suite and web server called 'R3D Align'. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. AVAILABILITY R3D Align is freely available through a web server http://rna.bgsu. edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location.
P300, not feedback error-related negativity, manifests the waiting cost of receiving reward information

Previous studies have investigated how temporal discounting influences reward processing in the human brain; however, it remains unclear whether a short delay in presenting an outcome affects brain activity related to reward processing that is indexed by the two event-related potential components: the feedback error-related negativity (fERN) and P300 components. The present study used a revised simple gambling task and manipulated the waiting time before reward presentation. Behavioral data showed that participants did not respond differently between conditions; however, they reported more negative emotion under long-waiting conditions than under short-waiting conditions. Event-related potential results showed that fERN was not significantly different between the two conditions, whereas the short-waiting feedback elicited a notably larger P300 amplitude than the long-waiting feedback, particularly in frontal–central regions. The present study shows that P300, not fERN, reflects high-level motivated evaluation of waiting cost in such a decision-making task.
Business process reengineering: a survey of international experience

Despite the widespread adoption of business process re‐engineering (BPR), it has in many cases repeatedly failed to deliver its promised results. The lack of integrated implementation approach to exploiting BPR is seen as one of the important reasons amongst others, behind BPR failures. Yet, a relative void in the literature remains the scarcity of suitable models and frameworks that address the implementation issues surrounding BPR. This motivates the presented study to attempt to provide a “frame of reference” with which current practices can be re‐positioned. A survey was therefore designed to collect data from a sample of organizations in the USA and Europe. The survey assesses the level of importance placed on the essential elements of integrated BPR implementation. In doing so, the study was also able to identify the level of maturity of BPR concepts within organisations. Empirical findings are then discussed in the context of other studies.
The number and function of circulating CD34+CD133+ progenitor cells decreased in stable coronary artery disease but not in acute myocardial infarction

Objective Circulating CD34+CD133+ cells are one of the main sources of circulating endothelial progenitor cells (EPCs). Age is inversely related to the number and function of CD34+CD133+ progenitor cells in stable coronary artery disease (CAD), but the relationship remains unclear in acute myocardial infarction (AMI). The authors aimed to clarify how ageing affects the number and function of mobilised CD34+CD133+ progenitor cells in AMI. Design and results Circulating CD34+CD133+ progenitor cells were measured by flow cytometry. Measurements were made at admission for CAD, or on day 7 after the onset of AMI. In stable CAD (n=131), circulating CD34+CD133+ cells decreased with age (r=−0.344, p<0.0001). In AMI, circulating CD34+CD133+ cells did not correlate with age (n=50), and multivariate analysis revealed that the decreased number of circulating CD34+CD133+ cells was associated with male sex and higher peak creatinine kinase. The ability to give rise to functional EPCs, which show good migratory and tube-forming capabilities, deteriorated among stable CAD subjects (n=10) compared with AMI subjects (N=6). Conclusions In stable CAD, the number and function of circulating CD34+CD133+ progenitor cells decreased with age, whereas those mobilised and circulating in AMI did not.
Strategies for the transformation of filamentous fungi

Molecular genetic manipulation of micro-organisms requires the development of plasmid-mediated transformation systems that include: (i) infusion of exogenous DNA into recipient cells; (ii) expression of genes present on the incoming DNA; and (iii) stable maintenance and replication of the inserted DNA, leading to expression of the desired phenotypic trait. Transformation systems have been developed for only a handful of fungi that are pathogenic to humans, including several species of filamentous fungi, and for a lot of filamentous fungi pathogenic to plants. Development of transformation systems in nearly all filamentous fungi has been delayed considerably, and has only been possible recently with the introduction of electroporation and biolistic methods. The fate of incoming DNA varies greatly among the species, regardless of their phylogenetic relationships. Understanding the fate of incoming DNA is critical for the construction of transforming vectors and the molecular manipulation of the fungi. In this review, recent advances in molecular genetics systems, selectable markers for transformation, the fate of incoming DNA, and further strategies for targeted integration, are discussed in relation to filamentous fungi.
Assessment of Mental Health Literacy among Perinatal Hispanic Adolescents

ABSTRACT According to the United States (U.S.) Census Bureau, Hispanics are the fastest growing ethnic minority in the U.S. As such, Hispanic females have the highest birth rate (35 per 1000) among adolescents between the ages of 15 and 19 years. Despite high fertility rates, there is limited mental health information among Hispanic adolescents during the perinatal period. Perinatal depression is a major concern as it poses health risks for both the mother and infant. Adverse outcomes such as preterm birth, low infant birth weight, and poor maternal-infant attachment may result from perinatal depression. However, less than half of Hispanic adolescent mothers who experience perinatal depression receive treatment. Previous research identified low mental health literacy (MHL) as one of the primary reasons for the limited use of mental health services among ethnic minorities. This study assessed the MHL of pregnant and postpartum Hispanic adolescents (n = 30) using a modified MHL scale. Implications for nursing practice are discussed to help improve mental health outcomes among pregnant and postpartum Hispanic adolescents.
The effect of a single infusion of zoledronic acid on early implant migration in total hip arthroplasty. A randomized, double-blind, controlled trial.

BACKGROUND Aseptic loosening is the most frequent cause of implant failure in total hip arthroplasty. While a direct link between aseptic loosening and periprosthetic bone loss remains elusive, there is plentiful evidence for a close association with early implant migration. The present trial was primarily designed to evaluate whether a single infusion of 4 mg of zoledronic acid prevented early implant migration in patients with osteonecrosis of the femoral head. METHODS Fifty patients were consecutively enrolled to receive either zoledronic acid or saline solution after cementless total hip arthroplasty. Radiographs, biochemical parameters of bone turnover, and the Harris hip-rating score were determined preoperatively and at each follow-up examination at seven weeks, six months, one year, and yearly thereafter. The median follow-up period was 2.8 years. RESULTS We found a significant subsidence of the stem of up to a mean (and standard deviation) of -1.2 +/- 0.6 mm at two years within the control group, and the cups had a mean medialization of 0.6 +/- 1.0 mm and a mean cranialization of 0.6 +/- 0.8 mm (p < 0.001). Treatment with zoledronic acid effectively minimized the migration of the cups in both the transverse and the vertical direction (mean, 0.15 +/- 0.6 mm and 0.06 +/- 0.6 mm, respectively; p < 0.05), while only a trend to decreased subsidence of the stem was detected. Finally, the Harris hip score rapidly increased over time in both treatment groups, although this increase was significantly more pronounced in the zoledronate-treated group than in the control group (analysis of variance, p = 0.008). CONCLUSIONS A single infusion of zoledronic acid shows promise in improving initial fixation of a cementless implant, which may improve the clinical outcome of total hip arthroplasty in patients with osteonecrosis of the femoral head.
Study on Topology Optimization Design, Manufacturability, and Performance Evaluation of Ti-6Al-4V Porous Structures Fabricated by Selective Laser Melting (SLM)

The combination of topology optimization (TOP) and selective laser melting (SLM) provides the possibility of fabricating the complex, lightweight and high performance geometries overcoming the traditional manufacturing “bottleneck”. This paper evaluates the biomechanical properties of porous structures with porosity from 40% to 80% and unit cell size from 2 to 8 mm, which are designed by TOP and manufactured by SLM. During manufacturability exploration, three typical structures including spiral structure, arched bridge structure and structures with thin walls and small holes are abstracted and investigated, analyzing their manufacturing limits and forming reason. The property tests show that dynamic elastic modulus and compressive strength of porous structures decreases with increases of porosity (constant unit cell size) or unit cell size (constant porosity). Based on the Gibson-Ashby model, three failure models are proposed to describe their compressive behavior, and the structural parameter λ is used to evaluate the stability of the porous structure. Finally, a numerical model for the correlation between porous structural parameters (unit cell size and porosity) and elastic modulus is established, which provides a theoretical reference for matching the elastic modulus of human bones from different age, gender and skeletal sites during innovative medical implant design and manufacturing.
Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene.

We have located a positive, cis-acting DNA sequence element within the 5' flanking DNA of the c-myc gene (-125 base pairs). This DNA sequence element has a large purine-pyrimidine strand asymmetry and can assume the H-DNA conformation. A factor with the properties of a ribonucleoprotein (RNP) interacts with this DNA region. The interaction of the c-myc DNA sequence element and the RNP involves an RNase H-sensitive mechanism and, therefore, may involve an RNA.DNA hybrid. In addition, a protein factor(s) binds to this DNA sequence element. DNA footprinting and mutant oligonucleotide binding/competition assays implicate a punctate, poly(G.C) recognition/binding sequence for the RNP factor, whereas the major protein factor requires two ACCCT sequence motifs for maximal binding. These results suggest that RNP and protein factors act as positive transcriptional regulators of the c-myc gene, perhaps by altering DNA topology.
Improving uptake of cervical cancer screening in women with prolonged history of non-attendance for screening: a randomized trial of enhanced invitation methods

Objective: To compare the effectiveness and cost-effectiveness of three methods of inviting women with a long history of non-attendance to undergo cervical screening. Methods: Randomized controlled trial and cost-effectiveness analysis. In all, 1140 women were identified from routine NHS screening records as having no smear for at least 15 years and randomly allocated to receive a telephone call from a nurse, a letter from a well-known celebrity (Claire Rayner) or letter from the local NHS Cervical Screening Commissioner. Uptake of screening was measured using routine data and attributed to interventions if occurring within three months. Uptake was compared with a control group. Costs of carrying out the interventions were noted from the perspective of the NHS and cost-effectiveness, as cost per additional attender, calculated. Results: Uptake following all interventions was low: telephone call (1.4, 95% confidence interval [CI] 0.38–3.6%); celebrity letter (1.8, 95% CI 0.57–4.0%); commissioner letter (4.6, 95% CI 2.5–7.7%); control group (1.8, 95% CI 0.57–4.0%). There were no significant differences between groups. Telephone intervention was not possible in a quarter of women whose numbers were unlisted. Telephone intervention was the most expensive and least effective of the interventions. The commissioner letter yielded an additional attender within three months at an incremental cost of £23.21 compared with taking no action. Conclusions: Neither a telephone call from a nurse nor a letter from a celebrity to encourage attendance for cervical screening were effective or cost-effective in women with a prolonged history of non-participation in the screening programme. A letter from the local cervical screening programme commissioner resulted in a small, non-significant increase in uptake. The low cost and ease of implementation of this intervention supports further research into its use in routine practice.
1 A novel splicing variant encoding putative catalytic subunit of maize protein kinase CK 2

A cDNA highly homologous to the known catalytic α subunit of protein kinase CK2 was cloned from maize (Zea mays). It was designated ZmCK2-4 (accession no. AAF76187). Sequence analysis shows that ZmCK2-4 and the previously identified ZmCK2-1 (accession no. X61387) are transcribed from the same gene, ZmPKCK2AL (accession no. Y11649), but at different levels in various maize organs and at different stages of development. The cDNA encoding ZmCK2-4 has three potential translation initiation sites. The three putative variants of ZmCK2-4 were expressed in Escherichia coli as glutathione S-transferase (GST)-fusion proteins and purified from bacterial extracts. In contrast to the previously characterized ZmCK2s, the obtained GST:ZmCK2-4 proteins were catalytically inactive as monomers or in the presence of equimolar amounts of the human CK2β. However, GST:ZmCK2α-4 did phosphorylate casein in the presence of a large excess of the β subunit. The activity of ZmCK2α-4 toward casein could also be stimulated by increasing ATP concentration. Modeling studies have shown that there is no interaction between the N-terminal segment of ZmCK2α-4 and the activation loop responsible for constitutive catalytic activity of CK2. Preliminary results suggest that ZmCK2α-4 may function as a negative regulator of other CK2s, and at certain circumstances as a holoenzyme which catalytic activity is stimulated by specific regulatory subunit(s). Abbreviations: AS, alternative splicing; AFEs, alternative first exons; CK2, caseine kinase 2.
Radiological Bile Acid Absorption Test 75SeHCAT in Patients with Diarrhoea of Unknown Cause

Purpose: The purpose with this study was to investigate the usefulness of the 75SeHCAT test in patients suffering from “functional” diarrhoea and to disclose earlier radiological investigations performed in the course of disease. Material and Methods: Twenty patients with chronic diarrhoea of unknown cause were investigated with the 75SeHCAT test. The cholestyramine test and an estimation of oro-caecal transit time (OCTT) were also performed in 13 and 10 patients respectively. Results: Ten patients had low 7-day retention (≤15%). Nine of these were tested with cholestyramine and 8 showed complete relief from the diarrhoea. The cholestyramine test had no effect on the 4 patients with normal bile acid retention. No correlation was found between the retention of 75SeHCAT and OCCT. A total of 80 inconclusive gastrointestinal barium examinations were performed during the course of disease. Conclusion: Pathological bile acid retention, studied with the radiological 75SeHCAT test, is common in patients with diarrhoea of unknown cause. The test should be performed earlier in the course of disease in order to prevent unnecessary radiological investigations and to reduce patient suffering and distress.