Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Limitations of Using Ribosomal Genes as References for the Study of Codon Usage: A Rebuttal

In a recent paper published in PLOS ONE, Wang et al. challenge our finding that the identity of optimal codons in different genomes follows a set of clear rules. Here we provide a rebuttal of their paper and demonstrate that the results of our original PLOS Genetics paper stand. This provides us with an opportunity to bring up an aspect of how codon usage has been studied that should be of general interest. The Wang et al. study, as well as many other studies, used ribosomal genes as a reference set for the study of patterns of codon usage. We discuss here the assumptions that are made in order to justify using ribosomal genes to study codon bias, suggest that this practice can at times be problematic, and discuss its limitations.
ITIH5 induces a shift in TGF‐β superfamily signaling involving Endoglin and reduces risk for breast cancer metastasis and tumor death

ITIH5 has been proposed being a novel tumor suppressor in various tumor entities including breast cancer. Recently, ITIH5 was furthermore identified as metastasis suppressor gene in pancreatic carcinoma. In this study we aimed to specify the impact of ITIH5 on metastasis in breast cancer. Therefore, DNA methylation of ITIH5 promoter regions was assessed in breast cancer metastases using the TCGA portal and methylation‐specific PCR (MSP). We reveal that the ITIH5 upstream promoter region is particularly responsible for ITIH5 gene inactivation predicting shorter survival of patients. Notably, methylation of this upstream ITIH5 promoter region was associated with disease progression, for example, abundantly found in distant metastases. In vitro, stably ITIH5‐overexpressing MDA‐MB‐231 breast cancer clones were used to analyze cell invasion and to identify novel ITIH5‐downstream targets. Indeed, ITIH5 re‐expression suppresses invasive growth of MDA‐MB‐231 breast cancer cells while modulating expression of genes involved in metastasis including Endoglin (ENG), an accessory TGF‐β receptor, which was furthermore co‐expressed with ITIH5 in primary breast tumors. By performing in vitro stimulation of TGF‐β signaling using TGF‐β1 and BMP‐2 we show that ITIH5 triggered a TGF‐β superfamily signaling switch contributing to downregulation of targets like Id1, known to endorse metastasis. Moreover, ITIH5 predicts longer overall survival (OS) only in those breast tumors that feature high ENG expression or inversely regulated ID1 suggesting a clinical and functional impact of an ITIH5‐ENG axis for breast cancer progression. Hence, we provide evidence that ITIH5 may represent a novel modulator of TGF‐β superfamily signaling involved in suppressing breast cancer metastasis.
Adoption of Mobile Devices/Services &#8212; Searching for Answers with the UTAUT

The future of mobile telephony is expected to rely on mobile services and the use of mobile services will be an integral part of the revenues to be generated by third generation mobile telephony. The adoption of new mobile services contradicts this proposition as it has been much slower than expected, especially in Europe. Basic services such as SMS, ring tones, icons and logos are still the most popular services. Several reasons have been suggested for the slow adoption rate, ranging from cultural to business models. In this paper we are searching for answers to the adoption rates by testing the applicability of the Unified Theory of Acceptance and Use of Technology (UTAUT) to explain the acceptance of mobile devices/services. Based on our empirical evidence from a survey conducted in Finland, it seems that the UTAUT to some extent and with some reservations can be used as a starting point to find some explanations for the adoption of mobile devices/services.
Discovery of a faint R-band drop-out: A strongly reddened lensed star forming galaxy at z = 1.68

We report the discovery of an unusual emission line galaxy at redshift z=1.68 found from near-IR imaging and spectroscopic observations with ISAAC/VLT of a faint gravitationally lensed R-band drop-out behind the lensing cluster Abell 1835. From the emission lines of [O II] lambda 3727i, and Hβ this galaxy shows a moderate to high excitation and line equivalent widths typical of relatively metal-poor H II galaxies. Its apparent J magnitude translates to an absolute B-band magnitude MB ~ -16.4 once corrected for a gravitational magnification of 1.8 mag. This makes it one of the faintest intermediate redshift galaxies known so far. From the presence of emission lines and the available VRIJHK photometry we determine constraints on its dominant stellar population. The only viable fit found is for a fairly young ( ~ 6-9 Myr) burst suffering from a considerable extinction (AV ~ 1.2-1.8 mag). We find that this object resembles strongly H II galaxies and intermediate redshift compact emission line galaxies, albeit suffering from a larger extinction than usual. We also discuss the possible contamination introduced by such R-band drop-out galaxies in searches for z >~ 5 galaxies. Based on observations collected with the ESO VLT-UT1 Antu Telescope (70.A-0355, 271.A-5013), the Hubble Space Telescope (HST) and the Canada-France-Hawaii telescope.
Packing Tree Factors in Random and Pseudo-random Graphs

For a xed graph H with t vertices, an H-factor of a graph G with n vertices, where t divides n, is a collection of vertex disjoint (not necessarily induced) copies of H in G covering all vertices of G. We prove that for a xed tree T on t vertices and > 0, the random graph Gn;p, with n a multiple of t, with high probability contains a family of edge-disjoint T -factors covering all but an -fraction of its edges, as long as 4 np log 2 n. Assuming stronger divisibility conditions, the edge probability can be taken down to p > C logn n . A similar packing result is proved also for pseudorandom graphs, dened in terms of their degrees and co-degrees.
Homicide in Australia: 2004-05 National Homicide Monitoring Program Nhmp Annual Report

This report provides a statistical overview of the circumstances and characteristics of the incidents, victims and offenders of homicide in each of Australia's states and territories for 2001-2002. Statistics presented include incidence of homicide and percentage of incidents solved; single versus multiple victim / offender incidents; incidents by time of day, day of the week and location; incidents occurring during the course of another crime; trends in homicide victimisation, 1989-2002; age, gender, racial appearance, marital status and employment status of victims; percentage of victims by alcohol and/or drug use; motive; percentage of victims with a prior criminal history; percentage of victims killed by a mentally disordered offender; cause of death; type of weapon used, including handgun or other firearm; licence and registration status of firearms used; trends in homicide offending, 1989-2002; age, gender, racial appearance, marital status and employment status of offenders; percentage of offenders with a prior history of domestic violence; percentage of offenders by alcohol and/or illicit / prescription drug use; percentage of offenders who committed suicide; relationship between offender and victim; and relationship between offender and victim, by gender of offender. The report notes that there has been a 20% increase in homicide victimisation in 2001-2002, and a 25% decrease in the number of homicides involving a firearm - the lowest number and proportion since NHMP data collection began in 1989.
TRAM flap for immediate post mastectomy reconstruction: comparison between pedicled and free transfer.

UNLABELLED Breast reconstruction after mastectomy is primarily carried out to improve the patients' quality of life. The most commonly used autologous tissue for reconstruction is the transverse rectus abdominis musculocutaneous flap (TRAM). The TRAM flap could be transferred either as pedicled or a free flap with microvascular anastomosis. The following work was carried out to evaluate the two techniques. PATIENTS AND METHODS Thirty-one female patients with operable breast cancer consented to immediate breast reconstruction during the period from June 1998 to December 2000. Fifteen patients had a free TRAM flap reconstruction. In sixteen patients, a pedicled TRAM flap was used. Three patients in the pedicled group underwent bilateral breast reconstruction, thus there were 19 pedicled flaps available for evaluation. Four patients in the pedicled flap group underwent reduction mammoplasty of the normal breast and in five other patients a bipedicled flap was used to achieve size matching with the reconstructed breast. Criteria for analysis included operative data, hospital stay, donor site morbidity, abdominal wall integrity, flap related complications, fat necrosis and final aesthetic result. RESULTS There was no difference between the two groups as regards age and, operative time. The pedicled flap group had shorter hospital stay and less blood loss than the free flap group, which was statistically significant (p=0.007 and p=0.001, respectively). In the pedicled flap group, two patients (10.5%) experienced partial flap loss and fat necrosis was detected in two other patients. For the free flap group, two patients (13.3%) developed complete flap loss, but none suffered fat necrosis. Donor site morbidity was equal in both groups. The total number of complications was higher in the pedicled group (7/19) (36.8.8%) than in the free flap group (5/15) (33.3 degrees k) but this was not statistically significant (p=0.27). None of the patients in both groups developed abdominal wall hernia, but abdominal wall weakness was evident in eight patients in the pedicled flap group that gradually improved over 2-3 months. Aesthetic results were comparable in both groups with a slightly better figure for the free flap group, but this was not statistically significant (p=0.23). IN CONCLUSION Although free TRAM flap seems to provide several advantages over the pedicled group, namely skin volume available for harvesting, preservation of abdominal wall integrity, and better flap contouring, yet the pedicled TRAM flap is a reliable and easy technique that will produce matching aesthetic results.
Detection of Tornado Frequency Trend Over Ontario, Canada

An upward trend in Ontario tornado frequency (about 1.6 tornadoes/decade with the statistically significant level at least at 95%) is identified using three independent approaches. The first method is the conventional linear regression method that had no disturbance to the original tornado time series. The second approach is to employ the Mann-Kendall test with consideration of removing a lag one autoregressive process. The trend is further firmed up using the Monte Carlo simulation. The robustness of the detected tornado frequency trend presented in this work offers an example for tornado frequency trend analysis over other regions of the world. It is shown in this study that the Ontario tornado frequency is linked to ENSO (El Nino/Southern Oscillation) signals with a statistically significant level at 99%.
Ultrastructural characterization of developmental and degenerative vitreo-retinal changes in the eyes of transgenic mice with a deletion mutation in type II collagen gene

Purpose. Molecular genetic analyses have clearly associated vitreoretinal degeneration with mutations in the type II collagen gene, but lack of experimental models has prevented systematic analyses of the occurrence of phenotypic changes and of the pathogenetic mechanisms involved. The present study is a detailed morphological and ultrastructural analysis of the vitreoretinal consequences of a small deletion mutation in the type II collagen gene. Methods. The eyes of Del1 mice carrying six copies of proa1(II) collagen transgene with a small deletion mutation were analyzed during embryonic development, postnatal growth and aging using their nontransgenic littermates as controls. Tissue samples were processed for light and electron microscopy for morphological and ultrastructural analyses. Transcription of proa1(II) collagen gene was localized by in situ hybridization, and type II collagen was detected by immunohistochemistry. Results. In this mouse model most components of the eye are ultrastructurally unaltered. However, the transgenes caused a dose-dependent dominant negative effect seen as a reduced number of type II collagen fibrils in the vitreous. In concert with this, dose-dependent accumulation of amorphous material was observed in the dilated rough endoplasmic reticulum of cells responsible for the production of type II collagen molecules. In mice homozygous for the transgene locus, the vitreoretinal degenerative lesions appeared already during late embryonic development. In mice heterozygous for the locus, such changes were milder and appeared only during postnatal growth and progressed gradually upon aging. Conclusions. The observed ultrastructural changes suggest that defective structure and function of collagen fibrils in Del1 mice result from a partial block in the post-translational processing and secretion of the mutated procollagen chains, and partly from secretion of mutated procollagen molecules which interfere with normal fibrillogenesis.
N‐13 Ammonia as an Indicator of Myocardial Blood Flow

We have characterized N-13 ammonia as a myocardial blood flow imaging agent suitable for positron-emission computed tomography. However, the mechanisms of uptake and retention of this agent in myocardium are not known, and effects of altered metabolism were not considered. Therefore, we studied the uptake and retention of N-13 ammonia in myocardium under various hemodynamic and metabolic conditions in open-chest dogs. N-13 ammonia was extracted nearly 100% during its initial capillary transit, followed by metabolic trapping that competed with flow-dependent back diffusion. At control flows, the first capillary transit extraction fraction (E) of N-13 ammonia averaged 0.82 ± 0.06. It fell with higher flows by E = 1 − 0.607 exp − 125/F. Myocardial N-13 tissue clearance half-times were similarly inversely related to blood flow, and ranged from 110–642 minutes. Cardiac work and changes in the myocardial inotropic state induced by isoproterenol and propranolol did not affect E or the tissue clearance half-times. Low plasma pH reduced E by an average of 20%, while elevated plasma pH had no effect. Decreases in flow below control also were associated with a fall in E. Inhibition of glutamine synthetase with L-methionine sulfoximine impaired metabolic trapping of N-13 ammonia and implicates the glutamic acid-glutamine reaction as the primary mechanism for ammonia fixation. The product of E times flow predicts the myocardial N-13 tissue concentrations, which increased by 70% when flow was doubled. Thus, blood flow and metabolic trapping are the primary determinants of myocardial uptake and retention of N-13 ammonia. The relative constancy of metabolic trapping over a wide range of hemodynamic and metabolic conditions demonstrates the value of N-13 ammonia as a myocardial blood flow imaging agent.
Battle Management Language (BML) As an Enabler

According to its definition, a Battle Management Language (BML) is an unambiguous language used to command and control forces and equipment conducting military operations and to provide for situational awareness and a shared, common operational picture. In this paper, we will argue that the use of a BML enables military units to utilize state-of-the-art IT techniques for today's operations. In particular, we will discuss the benefits of using BML for military communications in multinational endeavors, for the use of simulation systems in staff training, for decision support, and for automatic information fusion.
A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure

The spatial patterns of microbial communities are largely determined by the combined effects of historical contingencies and contemporary environmental disturbances, but their relative importance remains poorly understood. Empirical biogeographic data currently available are mostly based on the traditional method of observational survey, which typically involves comparing indigenous microbial communities across spatial scales. Here, we report a long-term soil transplantation experiment, whereby the same two soils (red Acrisol and purple Cambisol from Yingtan) were placed into two geographic locations of ∼1000 km apart (i.e., Yingtan in the mid-subtropical region and Fengqiu in warm-temperate region; both located in China). Twenty years after the transplantation, the resulting soil microbial communities were subject to high-throughput 454 pyrosequencing analysis of 16S and 18S rRNA genes. Additionally, bacteria and archaea involved in nitrogen cycling were estimated using clone library analysis of four genes: archaeal amoA, bacterial amoA,nirK, and nifH. Data of subsequent phylogenetic analysis show that bacteria, fungi, and other microbial eukaryotes, as well as the nitrogen cycling genes, are grouped primarily by the factor of geographic location rather than soil type. Moreover, a shift of microbial communities toward those in local soil (i.e., Chao soil in Fengqiu) has been observed. The results thus suggest that the historical effects persistent in the soil microbial communities can be largely erased by contemporary disturbance within a short period of 20 years, implicating weak effects of historical contingencies on the structure and composition of microbial communities in the soil.
Graph Transformations , Proofs , and Grammars

Graph transformation systems or graph grammars are a generalization of formal grammars used in linguistics.One of principal differences is that the structures that are transformed by transformation rules are no more linear. In this paper we consider graph transformation systems in connection with proof theory. We develop the graph transformation framework, where the attributes are derivable judgments of some deductive system. The computation functions are represented by partial proofs. We consider the application of graph transformation systems to the description of Kleene-style permutation of rules, to the derivations with “distant links”, to “parallel derivations” and “presupposed judgements”. As a “feedback” to linguistics, we discuss applications to the linguistic derivations and their transformations, and some aspects of the notion of “presupposition”.
Influence of Strategy Fading and Progress Feedback on Children's Reading Comprehension and Self-Efficacy.

The effects of strategy fading and progress feedback on children's achievement outcomes were investigated. Forty-four fifth graders with reading-skills deficiencies from 2 elementary schools received instruction on locating main ideas. Children were taught and verbalized a strategy, and some faded the verbalizations to inner speech. Half of the children in the fading and nc fading conditions periodically received progress feedback linking strategy use with improved performance. The no fading/no feedback condition scored significantly lower than did the other three conditions on posttest self-efficacy, comprehension skills, and self-reported strategy use. Fading plus feedback led to higher reported strategy use compared with the fading-only and feedback-only conditions and to higher comprehension skills compared with the feedback-only conditions. These results support the idea that students receiving remedial reading services benefit from procedures requiring extensive cognitive activity and informing them about strategy usefulness. A table of means and standard deviations from the study and a 60-item list of references are included. (Author/SLD) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. ***********************************************************************
Incapacity for work in elective orthopaedic surgery: a study of occurrence and the probability of returning to work after treatment.

STUDY OBJECTIVE--The extent to which patients undergoing elective surgery for orthopaedic disorders were incapacitated for work while they were on the waiting list and whether they were able to return to work after surgery were studied. DESIGN--This was a prospective cohort study of patients admitted to hospital for elective orthopaedic surgery. Main outcome measures were occurrence of sickness certification during the waiting time, and whether those incapacitated for work at the time of surgery returned to work during the first year after treatment. Multivariate logistic regression was used to estimate adjusted odds ratios for factors influencing return to work. SETTING--Orthopaedic department in charge of all elective orthopaedic surgery in a population of 197,354 persons in central Norway. SUBJECTS--All 2803 patients admitted to hospital for chronic orthopaedic disorders in the defined population between 1 September 1988 and 31 August 1990 were included in the study. MAIN RESULTS--Of the 1333 patients who were employed, 42% had been certified sick due to the orthopaedic disorder for some period of the waiting time. Sickness benefits from the national insurance scheme (paid from the 15th day of sickness certification) had been received by 33% and were received by 29% at the time of surgery. Of 380 patients incapacitated for work at the time of surgery, 53% returned to work within the first year after surgery. Using those treated within one month of being placed on the waiting list as the reference group, the adjusted odds ratios for not returning to work during the first year after surgery were 9.2 (p < 0.0001) for those who waited more than a year for surgery, 6.2 (p = 0.002) for those waiting nine to 12 months, and 4.9 (p = 0.02) for those waiting for six to nine months. CONCLUSIONS--A high proportion of these patients were incapacitated for work, 53% of those incapacitated returned to work within the first year after surgery. The probability of returning to work after surgery is strongly influenced by the length of time on the waiting list. Waiting for more than one year, compared with immediate treatment, was associated with an adjusted odds ratio of 9.2 for not returning to work.
The Comparison of Facial Estethics between Orthodontically Treated Patients and Their Parents

Orthodontists emphasize the importance of facial esthetics while planning a treatment, and orthodontist state that orthodontics have more than expected effects on dentofacial esthetics. The facial esthetics of treated patients and their parents was analyzed and compared to define facial growth and to use in forensic sciences. Our study was applied to 45 orthodontic patients who were treated in our clinic and their untreated parents. The patients were divided into Classes I, II, and III groups according to their malocclusions. Pre- and posttreatment changes, pretreatment facial esthetics of the paitents and its accordance with their parents, and the calculation of heritability tests were performed. After the statistics, for pre- and posttreatment changes, all the groups except Class I revealed significant changes. There were significant correlations of patients for the heritability values and pretreatment esthetic in accordance with parents, but there were more correlations of fathers when compared to mothers. The facial esthetics in adolescences is related with so many factors, not only related with one factor. The facial esthetics in fact includes the aim of evaluation of facial properties partly or totally. Because orthodontic treatments affect facial esthetics, performing similar studies for the treatment outcomes, capabilities, and borders is important.