Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of codon usage in beta-tubulin sequences of helminths.

Codon usage bias has been shown to be correlated with gene expression levels in many organisms, including the nematode Caenorhabditis elegans. Here, the codon usage (cu) characteristics for a set of currently available beta-tubulin coding sequences of helminths were assessed by calculating several indices, including the effective codon number (Nc), the intrinsic codon deviation index (ICDI), the P2 value and the mutational response index (MRI). The P2 value gives a measure of translational pressure, which has been shown to be correlated to high gene expression levels in some organisms, but it has not yet been analysed in that respect in helminths. For all but two of the C. elegans beta-tubulin coding sequences investigated, the P2 value was the only index that indicated the presence of codon usage bias. Therefore, we propose that in general the helminth beta-tubulin sequences investigated here are not expressed at high levels. Furthermore, we calculated the correlation coefficients for the cu patterns of the helminth beta-tubulin sequences compared with those of highly expressed genes in organisms such as Escherichia coli and C. elegans. It was found that beta-tubulin cu patterns for all sequences of members of the Strongylida were significantly correlated to those for highly expressed C. elegans genes. This approach provides a new measure for comparing the adaptation of cu of a particular coding sequence with that of highly expressed genes in possible expression systems.Finally, using the cu patterns of the sequences studied, a phylogenetic tree was constructed. The topology of this tree was very much in concordance with that of a phylogeny based on small subunit ribosomal DNA sequence alignments.
A Call for Specific Codes for Diabetes Foot and Eye Care

In this report, we propose new International Classification of Diseases (ICD) codes that could be incorporated into computer-based patient records or administrative data to monitor and improve diabetes care. Neither the ICD, 9th Revision, nor its imminent replacement, the ICD, 10th Revision, has specific codes for foot examinations and funduscopic examinations in the asymptomatic person, high-risk diabetic foot status, or clinically significant macular edema. Adoption of official codes for these procedures and conditions implemented in conjunction with computerized databases could be used for surveillance, program planning, and quality of care assessment. Computerized medical records could use the codes to monitor care and issue reminders to patients and providers. Payors could offer reimbursement incentives to encourage compliance with standard recommendations. These codesfor care procedures could be linked to outcomes, such as amputations and blindness, to improve our understanding of the etiology of blindness and the relationship between processand outcome. The uniform adoption of these codes would facilitate comparison between health care systems, geographic regions, and nations. The diabetes community should encouragethe National Center for Health Statistics to adopt new codes that could be used to monitor diabetes preventive care practices.
Lack of Association Between Hepatitis B Birth Immunization and Neonatal Death: A Population-Based Study From the Vaccine Safety Datalink Project

Background: There have been no population-based studies of the potential association between neonatal death and newborn immunization with hepatitis B vaccine (HBV). Methods: As part of the Vaccine Safety Datalink Project, we defined a birth cohort at Southern and Northern California Kaiser Permanente Health Plans of more than 350,000 live births from 1993 to 1998 and ascertained all deaths occurring under 29 days of age. We compared the proportions of deaths among birth HBV-vaccinated and unvaccinated newborns and reviewed the causes and circumstances of their deaths. We performed detailed clinical reviews of all HBV-vaccinated neonates who died and a sample of unvaccinated neonates who died and who were matched to vaccinated deaths for days of life, sex, birth year and site of care. To avoid confounding, we categorized the causes of death as either “expected” or “unexpected” and performed a stratified analysis to compare mortality with immunization status. Results: There were 1363 neonatal deaths during the study period. Whereas 67% of the entire birth cohort received HBV at birth, only 72 (5%) of the neonates who died were HBV-vaccinated at birth (P < 0.01). We found no significant difference in the proportion of HBV-vaccinated (31%) and unvaccinated (35%) neonates dying of unexpected causes (P = 0.6). Further we could not identify a plausible causal or temporal relationship between HBV administration and death for the 22 vaccinated neonates who died unexpectedly. Conclusions: A relationship between HBV and neonatal death was not identified.
Job Satisfaction and Dissatisfaction Among Journalism Graduates

,Journalism educators may occasionally find themselves wondering about the graduates they send out into professional journalism. How are they adjusting to their jobs? What do they find particularly satisfying? Or, heaven forbid, what dissatisfies them? Several researchers have attempted to answer such questions. Haberstroh uncovered high job satisfaction among a large group of advertising representatives with a strong correlation between income level and degree of satisfaction. ' McClain's study of Chicago advertising women indicated they held positive attitudes toward their jobs.2 A University of Wisconsin study revealed a higher degree of dissatisfaction among those newsmen who had the higher degree of professional orientation. ) A 1972 follow-up study of 1967 Michigan State University graduates showed a high degree ofjob satisfaction.4 In 1962 Samuelson and his colleagues at Stanford produced a standardized test to measure job satisfaction in the newsroom. An analysis of the responses of 200
Influence of serum on adult and fetal dermal fibroblast migration adhesion, and collagen expression

SummaryThe wound healing response to injury can be affected by many factors such as cell migration and extracellular matrix elaboration. The objective of this study was to examine the serum- and age-dependent effects on cell migration, adhesion, and collagen expression by skin fibroblasts. Dermal fibroblasts were isolated and plated with and without serum for up to 7 d. Cell migration was determined by quantitative image analysis, adhesion was quantified using a centrifugation assay, and collagen expression was assessed by PCR and immunohistochemical staining. Both adult and fetal fibroblasts migrated significantly faster in serum-containing medium compared to serum-free medium. There was no significant difference in migration between the two cell types in either serum-containing or serum-free medium. There was no significant difference in adhesion in the presence of serum, although there was a greater faction of adherent fetal skin fibroblasts than adult fibroblasts in serum-free medium. Moreover, the adherent fraction of fetal fibroblasts in serum-free medium was not significantly different from that in serum-containing medium, suggesting that fetal skin fibroblasts possess serum-independent adhesion properties. Collagen mRNA expression was significantly up-regulated in serum-free compared to serum-containing medium for both cell types. With respect to collagen immunohistochemistry, both dermal fibroblast populations exhibited greater type I collagen compared to type III collagen staining. Quantitative assessment of collagen staining indicated significantly enhanced type I collagen secretion in the presence of serum by fetal skin fibroblasts. These findings suggest that intrinsic cellular characteristics may govern the observed differences in adult and fetal wound healing.
Mental health problems in rural contexts: What are the barriers to seeking help from professional providers?

Abstract The aim of this review was to determine which sociodemographic, illness-related and psychological/attitudinal factors impact on a person's decision to seek help and the factors associated with attitudes to help-seeking in rural contexts. A computer search of the literature for 1990 – 2006 using the terms “help-seeking” and “mental” found 350 studies. Examination of the abstracts by one of the authors (AK) identified 20 relevant studies, which we review under two major headings: those papers dealing with help-seeking studies not specific to (but which may have included) rural settings; and a second group of studies conducted specifically in rural locations or that directly compared rural with urban locations. A number of factors were found consistently to be predictive of both mental health utilisation and attitudes toward formal help-seeking. They included sociodemographic factors such as gender, age, and marital status; illness-related factors such as having a mental disorder, comorbidity, and p.
Factors Related to Blood Loss During Fronto-Orbital Advancement

BackgroundBlood loss during fronto-orbital advancement (FOA) remains a significant potential source of morbidity. This study explored variables that might correlate with calculated blood loss (CBL) during this procedure. MethodsThe authors reviewed infants with craniosynostosis who underwent primary FOA (1997–2009). Patient demographics, operative time, and mean arterial pressure (MAP) were recorded. Serial MAPs were averaged for a MAPmean and subtracted from preoperative baseline to calculate MAP%decrease. This provided indicators of both absolute and relative hypotension, respectively. Calculated blood loss was based on preoperative/postoperative hemoglobin values and transfusion volumes and accounted for hemodilutional effects. ResultsNinety infants underwent FOA at an average age of 10.7 ±12.9 months and mean weight of 9.0 ± 7.0 kg. Average operative time was 4.2 hours, and intraoperative MAP was 56.1 mm Hg, 22.6% lower than baseline. Mean CBL was 259.3 mL, or 39.3% of estimated blood volume, negatively correlating with surgical age (r = −0.033, P < 0.05) and positively trending with operative time (r = 0.55, P < 0.05). Absolute hypotension was associated with greater blood loss, as demonstrated by an inverse relationship between CBL and MAPmean (r = −0.19, P < 0.05). From the perspective of relative hypotension, no association was found between CBL and MAP%decrease. ConclusionsGreater operative efficiency and deferring operative correction to a later age may diminish blood loss during FOA. The study results also raise serious concerns regarding the hemodynamic benefits of controlled systemic hypotension.
The Single IgG IL-1–Related Receptor Controls TLR Responses in Differentiated Human Intestinal Epithelial Cells

Intestinal epithelial cells (IECs) are constantly exposed to enteric microbes. Although IECs express TLRs that recognize bacterial products, the activation of these TLRs is strictly controlled through poorly understood mechanisms, producing a state of hyporesponsiveness and preventing unwanted inflammation. The single IgG IL-1–related receptor (Sigirr) is a negative regulator of TLRs that is expressed by IECs and was recently shown to inhibit experimental colitis. However, the importance of Sigirr in IEC hyporesponsiveness and its distribution within the human colon is unknown. In this study, we investigated the role of Sigirr in regulating epithelial-specific TLR responses and characterized its expression in colonic biopsy specimens. Transformed and nontransformed human IECs were cultured as monolayers. Transient gene silencing and stable overexpression of Sigirr was performed to assess innate IEC responses. Sigirr expression in human colonic biopsy specimens was examined by immunohistochemistry. Bacterial infection of IECs and exposure to flagellin transiently decreased Sigirr protein expression, concurrent with secretion of the neutrophil chemokine IL-8. Sigirr gene silencing augmented chemokine responses to bacterial flagellin, Pam3Cys, and the cytokine IL-1β. Conversely, stable overexpression of Sigirr diminished NF-κB–mediated IL-8 responses to TLR ligands. We also found that Sigirr expression increased as IECs differentiated in culture. This observation was confirmed in biopsy sections, in which Sigirr expression within colonic crypts was prominent in IECs at the apex and diminished at the base. Our findings show that Sigirr broadly regulates innate responses in differentiated human IECs; therefore, it may modulate epithelial involvement in infectious and inflammatory bowel diseases.
Theory, Method AND Triangulation IN THE Study OF Street Children

Comparative study of street children in three Latin American cities has led to a synergism between theory and method. Although the basic approach adopted is symbolic interactionism, a diversity of theories informs a variety of methods. Thus triangulation of methods allows a high degree of reliability in qualitative research that aims to explore children's own perspectives.
Modeling the impact of human spontaneity in mobile trajectories

Social mobility modeling has as motivation assist in developing mobile simulation environments, in order to provide better grounds for the evaluation of mobile networks. Being a new trend with roots on social network theory, these models are still unable to capture a few relevant characteristics of human movement, being one of them the impact of human spontaneity in mobile trajectories. This paper proposes a way to model such impact by providing nodes in movement with a mechanism that captures changes of target based on the notion of social attractiveness. We evaluate our proposal based on a social mobility model standalone simulator, against realistic traces.
On the effect of alkaline pH and cofactor availability in the conformational and oligomeric state of Escherichia coli glutamate decarboxylase

Escherichia coli glutamate decarboxylase (EcGad) is a homohexameric pyridoxal 5'-phosphate (PLP)-dependent enzyme. It is the structural component of the major acid resistance system that protects E. coli from strong acid stress (pH < 3), typically encountered in the mammalian gastrointestinal tract. In fact EcGad consumes one proton/catalytic cycle while yielding γ-aminobutyrate and carbon dioxide from the decarboxylation of l-glutamate. Two isoforms of Gad occur in E. coli (GadA and GadB) that are 99% identical in sequence. GadB is the most intensively investigated. Prompted by the observation that some transcriptomic and proteomic studies show EcGad to be expressed in conditions far from acidic, we investigated the structural organization of EcGadB in solution in the pH range 7.5-8.6. Small angle X-ray scattering, combined with size exclusion chromatography, and analytical ultracentrifugation analysis show that the compact and entangled EcGadB hexameric structure undergoes dissociation into dimers as pH alkalinizes. When PLP is not present, the dimeric species is the most abundant in solution, though evidence for the occurrence of a likely tetrameric species was also obtained. Trp fluorescence emission spectra as well as limited proteolysis studies suggest that PLP plays a key role in the acquisition of a folding necessary for the canonical catalytic activity.
OpenADN: A Case for Open Application Delivery Networking

There are two key issues that prevent Application Service Providers (ASPs) from fully leveraging the cloud "advantage. " First, in modern enterprise and Internet-based application environments, a separate middlebox infrastructure for providing application delivery services such as security (e.g., firewalls, intrusion detection), performance (e.g., SSL off loaders), and scaling (e.g., load balancers) is deployed. In a cloud datacenter, the ASP does not have any control over the network infrastructure, thus making it hard for them to deploy middleboxes for their cloud-based application deployments. Second, modern services virtualize the application endpoint. A service can no longer be statically mapped to a single end host. Instead, the service is partitioned and replicated across multiple end hosts for better performance and scaling. In enterprise datacenters, service requests are intercepted by an application-level routing service (APR) in the data plane and dynamically mapped to the correct service partition and the best (e.g. least loaded) instance of that partition. However, although multi-cloud (or Inter-cloud) environments allow ASPs to globally distributed their applications over multiple cloud datacenters leased from multiple cloud providers, ASPs need support of a globally distributed APR infrastructure to intelligently route application traffic to the right service instance. But, since such an infrastructure would be extremely hard to own and mange, it is best to design a shared solution where APR could be provided as a service by a third party provider having a globally distributed presence, such as an ISP. Although these requirements seem separate, they can be converged into a single abstraction for supporting application delivery in the cloud context. A sample design of this abstraction is OpenADN, presented here.
Representing the Politics of Borders: Unorthodox Maps in Reclus, Mackinder and Others

The relationship between cartography and power has aroused much interest in recent years, stimulated by innovative critical approaches. The empiricist and neo-positivist paradigms, no longer satisfactory, have been abandoned, while the analysis has been extended to include not only state-sponsored, but also popular cartography. Regardless of the character of the map or its source, it continues to be inserted in the context of the modern territorial state, as it is perceived as a key instrument for conveying the state’s narrative. Seen in this light, cartography inevitably comes out on the subordinate end of this relationship, since it fully conforms to the orthodox state-centred world view that has dominated modernity. Overturning this mechanically deconstructionist approach, this paper proposes, instead, to apply a concept introduced by John Brian Harley, the father of critical cartography – that of the map’s internal power. This concept, usually considered a given and rarely tested in empirical studies, is evaluated here through an analysis of the border sign in a series of unorthodox maps (in the work of Reclus, Mackinder, Renner, Spykman, Horrabin, Radó, Ratzel, Kjèllen, Haushofer) which have received little scientific attention to date.
Environmental Sustainability and Behavioral Science

To provide practitioners with useful information about how to promote proenvironmental behavior (PEB), a meta-analysis was performed on 87 published reports containing 253 experimental treatments that measured an observed, not self-reported, behavioral outcome. Most studies combined multiple treatments, and this confounding precluded definitive conclusions about which individual treatments are most effective. Treatments that included cognitive dissonance, goal setting, social modeling, and prompts provided the overall largest effect sizes (Hedge’s g > 0.60). Further analyses indicated that different treatments have been more effective for certain behaviors. Although average effect sizes are based on small numbers of studies, effective combinations of treatments and behaviors are making it easy to recycle, setting goals for conserving gasoline, and modeling home energy conservation. The results also reveal several gaps in the literature that should guide further research, including both treatments and PEB that have not been tested.
Plasminogen-dependent and -independent Proteolytic Activity of Murine Endothelioma Cells with Targeted Inactivation of Fibrinolytic Genes

Summary Plasminogen-dependent and -independent proteolytic activity of murine endothelioma (End) cells that were derived from mice with targeted inactivation of the tissue-type plasminogen activator (t-PA -/-), urokinase-type plasminogen activator (u-PA-/-) or plasminogen activator inhibitor-1 (PAI-1 -/- genes was studied with the use of fibrin and extracellular matrix degradation assays. In a buffer milieu, the activation rate of plasminogen (final concentration 0.25 µM) with wild-type and t-PA-/- End cells (3 X 104 to 4 X 106 cells/ml) was comparable, but it was about 4-fold reduced with u-PA -/- End cells and 3-fold enhanced with PAI-1End cells. Plasminogen activation was markedly reduced by addition of amiloride or of anti-murine u-PA antibodies but not by addition of anti-murine t-PA antibodies, and it was not stimulated by addition of fibrin. Lysis of125I-fibrin labeled matrix in the presence of plasminogen was comparable with wild-type, t-PA-/- and PAI-1-/- End cells (50% lysis in 3 h with 0.7 to 1.5 X 106 cells/ml), but was significantly reduced with u-PA-/- End cells (50% lysis in 20 h with 0.87 X 106 cells/ml). Lysis of3H-proline labeled extracellular matrix in the presence of plasminogen with wild-type, t-PA-/- and PAI-1-/- End cells (20% lysis in 48 h with 3 to 5 X 106 cells/ml) was comparable, but it was virtually abolished with u-PA-/- End cells. In the absence of plasminogen, lysis of both the fibrin and the extracellular matrix by all four cell types was drastically reduced and was virtually abolished by addition of phenylmethylsulfonylfluoride or 1,10 phenanthroline. These data indicate that the proteolytic activity of the transformed murine endothelioma cells, measured in plasminogen activation or matrix degradation assays, is essentially u-PA-related and largely plasminogen-dependent.
Self-regulation strategies used by student musicians during music practice

Individual music practice is a vital aspect of a student's development as a musician. Research indicates that expert music performers utilise substantial planning and a systematic approach to practice sessions, including problem identification, strategy planning and evaluation (Hallam 2001b), all of which are components of self-regulated thinking. The purpose of this study was to discover what self-regulating strategies adolescent instrumental musicians’ use during music practice. Sixteen middle school instrumental musicians were videotaped as they practiced a new piece of music. Immediately following the practice session, the student and researcher viewed the videotape of the session, and the student explained the strategies used during practice. Examination of the concurrent verbal report and music practice data revealed that repetition was referred to or used more frequently than other strategies. It is hoped that this study will aid in a better understanding of the self-regulation capabilities of student musicians.
Personality Development and the Person-Situation Debate: It's Déjà Vu All Over Again

In the two target articles and the series of perceptive responses we find a remarkable range of opinions on the empirical and conceptual viability of personality traits and about the nature of personality development. It seems we have stumbled upon the person-situation debate once again, this time in the context of personality development. We were under the impression that the person-situation debate was settled (Kenrick & Funder, 1988), but it appears to have been lying dormant. In this response we do three things. First, we rectify an omission on the part of the two target articles. Both target articles failed to cite critical empirical evidence demonstrating the continuity of temperaments and traits from childhood to adulthood. We attempt to briefly remedy this oversight. Second, we attend to several logical and methodological flaws in the situationist and contextualist criticisms of dispositional constructs that continue to plague the debate and unless dealt with directly will continue to do so. Third, we clarify our position on personality traits and argue that they should be included in the panoply of developmental constructs because they not only show remarkable levels of continuity, but they also demonstrate systematic changes throughout the life course.