Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine structure and differentiation of ascidian muscle. II. Morphometrics and differentiation of the caudal muscle cells of Distaplia occidentalis tadpoles

The locomotor function of the caudal muscle cells of ascidian larvae is identical with that of lower vertebrate somatic striated (skeletal) muscle fibers, but other features, including the presence of transverse myomuscular junctions, an active Golgi apparatus, a single nucleus, and partial innervation, are characteristic of vertebrate myocardial cells.
Down-regulation of microRNA-34a* in rheumatoid arthritis synovial fibroblasts promotes apoptosis resistance.

OBJECTIVE To investigate the expression and effect of the microRNA-34 (miR-34) family on apoptosis in rheumatoid arthritis synovial fibroblasts (RASFs). METHODS Expression of the miR-34 family in synovial fibroblasts with or without stimulation with Toll-like receptor (TLR) ligands, tumor necrosis factor α (TNFα), interleukin-1β (IL-1β), hypoxia, or 5-azacytidine was analyzed by real-time polymerase chain reaction (PCR). Promoter methylation was studied by combined bisulfite restriction analysis. The effects of overexpression and silencing of miR-34a and miR-34a* on apoptosis were analyzed by annexin V/propidium iodide staining. Production of X-linked inhibitor of apoptosis protein (XIAP) was assessed by real-time PCR and immunohistochemistry analysis. Reporter gene assay was used to study the signaling pathways of miR-34a*. RESULTS Basal expression levels of miR-34a* were found to be reduced in synovial fibroblasts from RA patients compared to osteoarthritis patients, whereas levels of miR-34a, miR-34b/b*, and miR-34c/c* did not differ. Neither TNFα, IL-1β, TLR ligands, nor hypoxia altered miR-34a* expression. However, we demonstrated that the promoter of miR-34a/34a* was methylated and showed that transcription of the miR-34a duplex was induced upon treatment with demethylating agents. Enforced expression of miR-34a* led to an increased rate of FasL- and TRAIL-mediated apoptosis in RASFs. Moreover, levels of miR-34a* were highly correlated with expression of XIAP, which was found to be up-regulated in RA synovial cells. Finally, we identified XIAP as a direct target of miR-34a*. CONCLUSION Our data provide evidence of a methylation-specific down-regulation of proapoptotic miR-34a* in RASFs. Decreased expression of miR- 34a* results in up-regulation of its direct target XIAP, thereby contributing to resistance of RASFs to apoptosis.
Phenotypic comparison of Pseudomonas aeruginosa strains isolated from a variety of clinical sites

Pseudomonas aeruginosa elaborates a number of extracellular products which have been shown to play a role in the pathogenesis of disease caused by this organism. In this study, we showed that the host environment markedly affects the levels of exoproducts produced. We compared the phenotypes of a number of P. aeruginosa strains obtained from a variety of clinical sources, including burn wounds, skin wounds, urine, cystic fibrosis sputum, acute pneumonia sputum, and blood. The clinical isolates were examined quantitatively for levels of total protease, elastase, phospholipase C, exotoxin A, and exoenzyme S produced in vitro under defined conditions. The exoproduct levels varied significantly, depending on the site of isolation. Elevated levels of elastase were demonstrated in strains isolated from acute lung infections, phospholipase C levels were elevated in urinary tract and blood isolates, exotoxin A levels were elevated in blood isolates, and exoenzyme S levels were increased in acute pneumonia isolates. Isolates from cystic fibrosis sputum produced low amounts of virtually all of the tested exoproducts, particularly as compared with sputum isolates from acute P. aeruginosa lung infections.
Bladder neck contracture after robot-assisted laparoscopic radical prostatectomy: evaluation of incidence and risk factors and impact on urinary function.

BACKGROUND AND PURPOSE Bladder neck contracture (BNC) after radical prostatectomy has been reported to occur in 5% to 32% of men after open retropubic prostatectomy (RRP) and in 0% to 3% after laparoscopic RRP. Optimal anastomotic closure involves creating a watertight, tension-free anastomosis with well-vascularized, mucosal apposition and correct realignment of the urethra. The cause of BNC is poorly understood; however, it is likely related to multiple factors, including excessive luminal narrowing at the site of reconstruction, local tissue ischemia, failed mucosal apposition, and urinary leakage. In this large series of patients who underwent robot-assisted laparoscopic radical prostatectomy (RLRP), we report the incidence of BNC, evaluate the influence of age, body mass index (BMI), estimated blood loss (EBL), surgical time, and prostate weight on its development and assess follow-up urinary function. METHODS Between February 2003 and July 2006, 650 consecutive men underwent RLRP at our institution. Patients with aborted or open conversion procedures were excluded from analysis. The mean overall follow-up for the remaining 634 patients was 19.5 months. Patients presenting with symptoms of outlet obstruction were evaluated with cystoscopy to confirm a BNC. Comparisons of age, BMI, EBL, operative time, and prostate weight were performed using the Student t-test and chi-square analysis. RESULTS BNC was the diagnosis in seven patients (1.1%) with a mean time of presentation of 4.8 (3-12) months postoperatively. The BNC patients had comparable mean age, BMI, prostate weight, and EBL to the non-BNC cohort. Their operative time, however, was significantly longer (283 v 225 min., P = 0.04). CONCLUSIONS The incidence of BNC after radical prostatectomy is 2.2% in a large series of men undergoing RLRP. The diagnosis was made within 1 year. No significant impact on urinary continence or quality-of-life urinary function was observed after BNC management. A running anastomosis, better visualization, improved instrument maneuverability, and decreased blood loss may account for such a low rate.
DIVERSITY IN CHILD CARE ASSISTANCE NEEDS: RELATED OUTCOMES EMPLOYEE PROBLEMS, PREFERENCES, AND WORK-

This research examines employee background variables moderating problems with child care arrangements and variance in work-related attitudes and behaviors. Gender, household employment configuration, dependents’ care profile, managerial status, and use of familial care arrangements help explain variance in child care problems, attitudes toward managing work and child care responsibilities, and the absence behavior of working parents in a public utility. The relationship between employee backgrounds and preferences for child care assistance is also examined. The study demonstrates that employees’ child care needs are diverse, multi-faceted, and changing. It is suggested that organizations consider developing several packages of child care assistance policies that can be responsive to changes in the mix of employees’ assistance needs and their work forces’ demographics over time. Although a growing number of U.S. employers (over 4,000 in 1989) provide some form of child care support to their employees, few firms conduct a needs assessment prior to adopting programs (Friedman, 1988; The Conference Board, 1989). As a consequence, there is limited understanding of the conditions related to variation in child care needs across diverse employee groups. This gap can be attributed partly to the fact that the dramatic increase in single parent and dual-career employees is a relatively new phenomenon. As Magid (1983) contends, companies have historically viewed child care as a “women’s issue,” and not as a mainstream employee relations matter. Also, the literature on
Analysis Technique for Asymmetrically Coupled Resonator Structures

Asymmetrical acoustically coupled structures are present in several acoustic applications. Specifically when they are used in filter design, some configurations provide unexplored and special response characteristics with high selectivity and relatively wide bandwidths. The relationships between geometries, configurations, and response specifications do not rely on a direct link. In this work, a novel approach to the analysis of these structures is presented as well as a model of an asymmetrical bulk acoustic wave coupled resonator filter obtained from the analysis presented.
[Decreased ATP-synthesis ability of brain mitochondria in spontaneously hypertensive rats].

UNLABELLED It has been shown previously that a decrease of ATP amount and changed balance of other macroergic phosphates occurs in different tissues of spontaneously hypertensive rats (SHR) compared with control normotensive rats (WKY). AIM To assess the ability of SHR brain isolated mitochondria to synthesize ATP and to elucidate its relation to extramitochondrial calcium concentration. RESULTS The present work shows for the first time that SHR brain mitochondria initially differ from WKY ones by decreased (by 30%) ATP synthesis rate. When calcium concentration is increased up to 20 or 40 micromole/l ATP synthesis rates in WKY and SHR mitochondria are about one half compared with the condition when the medium does not contain calcium, but the differences between SHR and WKY remain the same. CONCLUSION Decreased ATP synthesis rate in SHR mitochondria may be considered as the main cause of cell energy deficiency observed in experimental variant of primary arterial hypertension.
Characterization of the Coronavirus Mouse Hepatitis Virus Strain A59 Small Membrane Protein E

ABSTRACT The small envelope (E) protein has recently been shown to play an essential role in the assembly of coronaviruses. Expression studies revealed that for formation of the viral envelope, actually only the E protein and the membrane (M) protein are required. Since little is known about this generally low-abundance virion component, we have characterized the E protein of mouse hepatitis virus strain A59 (MHV-A59), an 83-residue polypeptide. Using an antiserum to the hydrophilic carboxy terminus of this otherwise hydrophobic protein, we found that the E protein was synthesized in infected cells with similar kinetics as the other viral structural proteins. The protein appeared to be quite stable both during infection and when expressed individually using a vaccinia virus expression system. Consistent with the lack of a predicted cleavage site, the protein was found to become integrated in membranes without involvement of a cleaved signal peptide, nor were any other modifications of the polypeptide observed. Immunofluorescence analysis of cells expressing the E protein demonstrated that the hydrophilic tail is exposed on the cytoplasmic side. Accordingly, this domain of the protein could not be detected on the outside of virions but appeared to be inside, where it was protected from proteolytic degradation. The results lead to a topological model in which the polypeptide is buried within the membrane, spanning the lipid bilayer once, possibly twice, and exposing only its carboxy-terminal domain. Finally, electron microscopic studies demonstrated that expression of the E protein in cells induced the formation of characteristic membrane structures also observed in MHV-A59-infected cells, apparently consisting of masses of tubular, smooth, convoluted membranes. As judged by their colabeling with antibodies to E and to Rab-1, a marker for the intermediate compartment and endoplasmic reticulum, the E protein accumulates in and induces curvature into these pre-Golgi membranes where coronaviruses have been shown earlier to assemble by budding.
Social and Interpersonal Factors Relating to Adolescent Suicidality: A Review of the Literature

This article reviews the empirical literature concerning social and interpersonal variables as risk factors for adolescent suicidality (suicidal ideation, suicidal behavior, death by suicide). It also describes major social constructs in theories of suicide and the extent to which studies support their importance to adolescent suicidality. PsychINFO and PubMed searches were conducted for empirical studies focused on family and friend support, social isolation, peer victimization, physical/sexual abuse, or emotional neglect as these relate to adolescent suicidality. Empirical findings converge in documenting the importance of multiple social and interpersonal factors to adolescent suicidality. Research support for the social constructs in several major theories of suicide is summarized and research challenges are discussed.
Solder/adhesive bonding using simple planarization technique for 3D integration

This paper describes a hybrid solder/adhesive bonding method using a simple planarization technique for three-dimensional (3D) integration. With the hybrid bonding method, the chip bonding and encapsulation of underfill resin between chips is completed in one step. The simple planarization technique is used to planarize adhesive on a flat Si substrate coated with a release agent. The planarization technique is a simple and inexpensive operation compared to the conventional processes using Chemical Mechanical Polishing (CMP) or fly cutting. Since the CMP process has advantages for wafer-level fabrication, we also evaluated hybrid bonding using CMP. The results of the simple planarization process show that the spaces around the Cu/Sn bumps were fully filled with the adhesive, and the adhesive residual layer on the Cu/Sn bumps was removed by O2 plasma. A cross-sectional SEM image after the hybrid bonding using the proposed planarization process shows that the Cu/Sn solder had properly wetted the Au and the adhesive had uniformly filled the small gaps between the bonded chips. Solder/adhesive bonding using CMP was also succeeded. In addition, Au/adhesive bonding with 10-μm pitch Au bumps was realized.
Scoring Function Based Approach for Locating Binding Sites and Understanding Recognition Mechanism of Protein-DNA Complexes

Protein-DNA recognition plays an essential role in the regulation of gene expression. Understanding the recognition mechanism of protein-DNA complexes is a challenging task in molecular and computational biology. In this work, a scoring function based approach has been developed for identifying the binding sites and delineating the important residues for binding in protein-DNA complexes. This approach considers both the repulsive interactions and the effect of distance between atoms in protein and DNA. The results showed that positively charged, polar, and aromatic residues are important for binding. These residues influence the formation of electrostatic, hydrogen bonding, and stacking interactions. Our observation has been verified with experimental binding specificity of protein-DNA complexes and found to be in good agreement with experiments. The comparison of protein-RNA and protein-DNA complexes reveals that the contribution of phosphate atoms in DNA is twice as large as in protein-RNA complexes. Furthermore, we observed that the positively charged, polar, and aromatic residues serve as hotspot residues in protein-RNA complexes, whereas other residues also altered the binding specificity in protein-DNA complexes. Based on the results obtained in the present study and related reports, a plausible mechanism has been proposed for the recognition of protein-DNA complexes.
Parathyroid hormone/parathyroid hormone‐related peptide modulates growth of avian sternal cartilage via chondrocytic proliferation

Parathyroid hormone (PTH; 10−7 to 10−15 M) decreased terminal chondrogenesis in the avian sterna. During the first half of an 8‐day culture, 100 nM PTH (1–34) significantly increased sternal length and downregulated the deposition of type X collagen and its mRNA expression. However, it remains unclear how PTH increased cartilaginous growth. In this study, we examined growth by both cell proliferation and analysis of cyclin d1 and collagen mRNA. Types II, IX, and X collagens and cyclin d1 mRNA were quantified through real‐time RT‐PCR, while Ki‐67 was used as an immunohistochemical proliferation marker. Extracellular matrix content was measured through mRNA quantification of types II, IX, and X collagen and observing deposition of the same collagens. PTH significantly increased the proliferation marker Ki‐67 in the sternal cephalic region. There was less type II and X collagen in PTH‐treated sterna with concomitant decreases in mRNA production, suggesting that proliferation was the major contributor to cartilage growth in the presence of PTH/PTH‐related peptide receptor activation. In conclusion, these experiments demonstrated that PTH increased cartilage growth by upregulating cell proliferation or other extracellular matrix components. Anat Rec, 290:155–167, 2007. © 2007 Wiley‐Liss, Inc.
Identification of differentially expressed genes through a meta-analysis approach for oral cancer classification

We propose a meta-analysis scheme for identifying differentially expressed genes in Oral Squamous Cell Carcinoma (OSCC) from different microarray studies. We detect a subset of relevant features and further classify samples under two experimental conditions (i.e healthy and cancer samples) for better patient stratification. A well-established meta-analysis method is adopted and gene expression data sets are derived from a public functional genomics data repository. Our primary aim is the accurate identification of up- and down-regulated genes in order to extract valuable biological information concerning the changes in expression between healthy and cancer samples. According to our results and the extracted informative gene list, a high classification accuracy of healthy and OSCC tumors is achieved with as few genes as possible. Furthermore, the proposed scheme implies that the combination of datasets from different origins may reduce the estimated percentage of false predictions, while the power of gene identification and disease classification is increased.
Interference competition and parasite virulence

Within–host competition between parasites, a consequence of infection by multiple strains, is predicted to favour rapid host exploitation and greater damage to hosts (virulence). However, the inclusion of biological variables can drastically change this relationship. For example, if competing parasite strains produce toxins that kill each other (interference competition), their growth rates and virulence may be reduced relative to single–strain infections. Bacteriocins are antimicrobial toxins produced by bacteria that target closely related strains and species, and to which the producing strain is immune. We investigated competition between bacteriocin–producing, insect–killing bacteria (Photorhabdus and Xenorhabdus) and how this competition affected virulence in caterpillars. Where one strain could kill the other, and not vice versa, the non–killing strain was competitively excluded, and insect mortality was the same as that of the killing strain alone. However, when caterpillars were multiply infected by strains that could kill each other, we did not observe competitive exclusion and their virulence was less than single–strain infections. The ubiquity and diversity of bacteriocins among pathogenic bacteria suggest mixed infections will be, on average, less virulent than single infections.
Chemical and physical changes observed in poly(oxy-1,4 phenylsulfonyl-1,4 phenylene) following electrical stressing

High voltage insulation failure can arise because of the physical and chemical properties of the material and intrinsic changes through use, aging and weathering. Overall aging is believed to produce localised defects and structural points which eventually fail under electrical stressing. This paper will present FT-IR and AFM evidence to show some of the chemical and physical changes in the insulating polymer, poly(oxy-1,4 phenylsulfonyl-1,4 phenylene) (PES) when subjected to short duration high voltage electric discharge activity in the air above the surface of the polymer film.
Young Children’s Digital Literacy Practices in the Home: A Review of the Literature

This paper reports a review of research literature on young children’s (aged 0-8 years old) digital literacy practices in the home. The review contributes to one of the aims of the COST DigiLitEY programme by identifying the current state of knowledge on young children’s digital literacy and multimodal practices in homes and communities, including synthesising research on parental support of children’s digital literacy development” (WG1 Mission Statement). Accordingly, the purpose of this review is to 1) summarise current research knowledge in the area of young children’s digital literacy practices in the home, 2) identify key messages for educational researchers, parents and policy makers, and 3) propose key research questions in the field for future study. A total of 33 studies published between 2005 and 2015 were selected for the review. Informed by a descriptive and narrative approach, the review revealed three leading themes that emerged from the analysis, namely; Parental mediation of children’s digital literacy practices in homes, Children’s media engagement and literacy learning in homes, and home-school knowledge exchange of children’s digital literacy practices. The major findings of these themes are highlighted and the review ends with key messages for parents; educational policy and practice, and educational researchers.
Calcifying Matrix Vesicles and Atherosclerosis

Artery calcification is a well-recognized predictor of late atherosclerotic complications. In the intima media, calcification starts with apoptosis of vascular smooth muscle cells (VSMCs) and the release of calcifying matrix vesicles with diameter of 0.5–15 μm that can be observed microscopically. In complicated plaques, calcification is generally less frequent. Calcifying vesicles are released by proatherosclerotic VSMCs into the collagen-rich matrix. The vesicles can penetrate into the intima media and protrude into the arterial lumen and thereby may represent a potential cause of atherothrombosis. In calcified fibrolipid plaques, the rate of calcification is increased but is followed with healing of a lesion rupture and exhibited by further erosion and/or intimal thickening. Generally, calcification directly correlates with the apoptosis of VSMCs and macrophages accompanied by the release of osteogenic matrix vesicles. This is a hallmark of atherosclerosis-related apoptosis of VSMCs that is commonly released in plaque stabilization.
Orthogonality of the mean and error distribution in generalized linear models

ABSTRACT We show that the mean-model parameter is always orthogonal to the error distribution in generalized linear models. Thus, the maximum likelihood estimator of the mean-model parameter will be asymptotically efficient regardless of whether the error distribution is known completely, known up to a finite vector of parameters, or left completely unspecified, in which case the likelihood is taken to be an appropriate semiparametric likelihood. Moreover, the maximum likelihood estimator of the mean-model parameter will be asymptotically independent of the maximum likelihood estimator of the error distribution. This generalizes some well-known results for the special cases of normal, gamma, and multinomial regression models, and, perhaps more interestingly, suggests that asymptotically efficient estimation and inferences can always be obtained if the error distribution is non parametrically estimated along with the mean. In contrast, estimation and inferences using misspecified error distributions or variance functions are generally not efficient.