Miracle-dz/UniFAR-FTUs huggingface dataset:
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction.

Froenicke et al. (2006) asked the question “Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? ” Their commentary seems to imply that cytogenetics is superior to “bioinformatics” when it comes to studies of ancestral mammalian genomes. But, comparing cytogenetics with other approaches to deriving ancestral genomic architectures (like MGR developed by Bourque and Pevzner 2002) on two very different data sets (80+ cytogenetic maps vs. four distantly related sequenced genomes) does not say much about the merits and demerits of the approaches; instead, it indirectly evaluates the quality of the input data sets. In this context, the main conclusion of Froenicke et al. (2006) amounts to the statement that 80+ cytogenetic maps lead to a more definitive reconstruction than four divergent genomes when it comes to low-resolution ancestral architectures. We never argued against this point in our publications and even advocated for the use of radiation hybrid mapping (as a trade-off in resolution between cytogenetic and sequencing data) to extend the number of analyzed genomes (Murphy et al. 2003, 2005). Indeed, with more taxon sampling, a rearrangementbased reconstruction with just seven genomes (Murphy et al. 2005) is already highly consistent with the cytogenetics reconstruction. Before we substantiate this convergence, we clarify the notion of weak associations, which was used in Bourque et al. (2005) to alert the reader that some of the adjacencies were left as unresolved in the ancestor. The discrepancies identified by Froenicke et al. (2006) all involve weak associations and point toward a misunderstanding more than a contradiction. Finally, we underline some of the important strengths exclusive to rearrangement-based approaches, such as the ability to detect smaller genomic segments, to handle fast evolving lineages, and to orient conserved segments in the ancestors.
Selenium Content in Blood of Donors from the North of Rio de Janeiro State, Brazil

Selenium is an element which participates in antioxidant enzymes. A medium and long term lack of such element is associated, mainly, with heart disease, joint and bone structure problems and thyroid activity. Selenium contents in blood reflect its ingestion and food content variation. It depends on soil characteristics, such as pH and selenium presence. There are few studies concerning selenium levels in food and blood in Brazil. Therefore, the objective of this research was to determine selenium content in a blood donor group in Rio de Janeiro state, conducted from December 2008 to March 2009. From the donated blood to Regional Blood Center of Campos dos Goytacazes, 4.0 mL were submitted to selenium analysis through atomic absorption spectrometry of hydride generation and organic matter oxidation wet basis with nitric and perchloric acid. Selenium content varied from 75 ± 16 ng·g-1 for females and 70 ± 21 ng·g-1 for males. There was no significant difference among selenium contents in blood from donors of different gender, age and residence. Seventy four percent of donors had selenium content in blood below 70 ng·mL-1, the lowest level for maximum selenoproteins production, according to the Nutritional Prevention Cancer.
Efficient Parallel 3-D Computation of Electrical Machines With Elmer

After its recent improvements described here, open source finite element software Elmer is shown to be a highly efficient option for electrical machine modeling. The parallelization of computational burden is shown to be a necessity. The methods implemented enable applying fully parallel computation to electrical machine models, including rotation and electrical circuits. Computational experiments performed demonstrate that Elmer can effectively utilize several hundreds of computational cores in parallel, making it an attractive alternative when computational speed is of high importance.
Pathologic prognostic factors in early stage adult‐type granulosa cell tumors of the ovary

Overall 10-year survival rates for patients with adulttype granulosa cell tumors of the ovary have been reported as being between 60 and 90%, but the 25-year survival rate is only in the region of 40—60% . The prognosis is stage-related but even for patients with stage I disease in whom the 10-year survival rate is between 85 and 95% the survival rate at 20 years is only between 60 and 75%. As 60—90% of patients present with stage I disease the definition of pathologic prognostic factors relates principally, perhaps solely, to stage I tumors. Studies aimed at defining prognostic factors in adult granulosa cell tumors have, however, commmonly been frustrated not only by their relative rarity but also by the very long period for which follow-up observation is required. These neoplasms tend to run an indolently malignant course and recurrences after initial therapy commonly occur after more than 5 years, not infrequently after more than 10 years, sometimes after 20 years, and very occasionally after more than 25 years; the longest recorded time interval between treatment and recurrence has been 37 years. Therefore even after a disease-free period of 20 years it is not possible to reassure the patient with absolute dogmatism that she is fully cured with no chance of recurrence. Hence, attempts to divide adult granulosa cell tumors of the ovary into benign and malignant categories are probably fruitless for all should be considered as being at least potentially malignant. Nevertheless most recurrences occur within the first 5—10 years after initial treatment and the aim of defining prognostic pathologic factors for adult granulosa cell tumors is not to identify those that are malignant but to distinguish those that are most likely to recur within 5—10 years, it probably being impossible to identify those neoplasms with a very long-term risk of recurrence.
Spatial and temporal oxygen isotope variability in northern Greenland – implications for a new climate record over the past millennium

Abstract. We present for the first time all 12 δ18O records obtained from ice cores drilled in the framework of the North Greenland Traverse (NGT) between 1993 and 1995 in northern Greenland. The cores cover an area of 680 km × 317 km, 10 % of the Greenland ice sheet. Depending on core length (100–175 m) and accumulation rate (90–200 kg m−2 a−1) the single records reflect an isotope–temperature history over the last 500–1100 years. Lowest δ18O mean values occur north of the summit and east of the main divide as a consequence of Greenland's topography. In general, ice cores drilled on the main ice divide show different results than those drilled east of the main ice divide that might be influenced by secondary regional moisture sources. A stack of all NGT records and the NGRIP record is presented with improved signal-to-noise ratio. Compared to single records, this stack represents the mean δ18O signal for northern Greenland that is interpreted as proxy for temperature. Our northern Greenland δ18O stack indicates distinctly enriched δ18O values during medieval times, about AD 1420 ± 20 and from AD 1870 onwards. The period between AD 1420 and AD 1850 has depleted δ18O values compared to the average for the entire millennium and represents the Little Ice Age. The δ18O values of the 20th century are comparable to the medieval period but are lower than that about AD 1420.
Molecular typing of Shigella sonnei isolates circulating in Nanjing, China, 2007-2011.

INTRODUCTION Shigellosis is a major public health concern worldwide. This study intended to assess the baseline genotyping data among local Shigella sonnei strains spanning over five years. METHODOLOGY Fifty non-repeat clinical strains of S. sonnei isolated from stools of patients in different hospitals in Nanjing, China, were studied. Three subtyping tools, pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable-number tandem-repeat (VNTR) analysis (MLVA), were used for routinely subtyping local S. sonnei. RESULTS DNA sequencing only identified two sequence types (STs) among the 50 isolates in the MLST profiles, whereas PFGE and MLVA both showed suitable discriminatory power and yielded 19 and 30 different patterns, respectively. The major PFGE pattern comprised 21 strains isolated from different years. A total of four complexes were identified by MLVA, with the isolates differing by a single locus (single-locus variants). CONCLUSIONS The S. sonnei strains circulating in Nanjing, China, in 2007-2011 originated from different clones with a degree of diversity. Most of the clones were closely related to each other. Overall, the strains were distinguishable by PFGE and MLVA. MLVA based on eight selected VNTR loci represented a more favorable degree of discrimination than did PFGE and may be a reliable complement for PFGE for routine subtyping of S. sonnei. The problems of MLST in subtyping regarding S. sonnei were also demonstrated.
Mechanisms of interaction between polycyclic aromatic hydrocarbons and dissolved organic matters

Binding of phenanthrene and fluorene to a number of humic and fulvic substances isolated from various sources as well as a commercially available humic acid, was investigated using a fluorescence quenching approach. The observed fluorescence quenching indicated by linear Stern-Volmer plots and high bimolecular quenching rate constant was induced by a static interaction process. A significant correlation of binding constants with aromaticity and polarity of dissolved organic matter (DOM) was observed. It is hypothesized that the binding of polycyclic aromatic hydrocarbons (PAHs) by DOM is due to both π-π interactions and hydrophobic interactions. In addition, energy transfer from PAHs to DOM occurs because of the significant overlap between the absorbance spectra of DOM and emission spectra of PAHs. Thus, dipole-dipole interaction may also play an important role in the binding mechanism between PAHs and DOM.
TITLE: Identification of Pro-differentiation p53 Target Genes and E valuation of Expression in Normal and Malignant Mammary Gland

Tumor stem cell theory implies that causative lesions underlying human malignancies occur and are harbored in multi-potent progenitors with retained proliferative capacity and a prolonged lifespan. Transcriptional profiling of human breast cancers has identified five distinct subtypes of which the basal-epithelial subtype is most aggressive, correlates with poor prognosis, and lacks established molecular targets such as ERα, PR and Her2overexpression. These tumors display a high degree of cellular heterogeneity suggesting that they may arise as the result of unregulated self-renewal in a multipotent cell. Clinically basal epithelial tumors are recognized by their negativity for ERα, PR and Her2, suggesting that the identification and validation of markers that definitively define this subtype will improve the diagnosis of these tumors. We present evidence that nestin, a previouslydescribed neural progenitor marker is expressed in basal epithelia of the normal human mammary gland. Co-localization studies indicate two distinct populations of nestin-positive cells; one that expresses cytokeratin 14 and p63 and another that expresses desmin. Oncogenic transformation of a mammary progenitor cell culture model leads to increased expression of nestin. Immunohistochemical analysis of basal-epithelial breast tumors indicates robust expression of nestin, and CK14, punctate expression of p63, and low-toundetectable levels of desmin expression. Nestin was not detected in other breast cancer sub-types, indicating selectivity for basal-epithelial breast tumors including those known to carry BRCA1 mutations. These studies coupled to the established role for p63 in the preservation of self-renewal suggest that basal breast tumors display biochemical features of mammary progenitors.
COMPARISON OF BODY AND LIVER WEIGHTS IN ALBINO RATS AFTER TREATMENT WITH TAMOXIFEN AND TAURINE

Objective: To compare the mean body weights and mean absolute and relative liver weights (in Grams) of albino rats after tamoxifen and taurine treatment. Material and Methods: This prospective experimental study was conducted in the Department of Anatomy, Khyber Medical College, Peshawar from July 2011 to December 2011. Sixty adult female albino rats were divided into four groups (A-control, B-tamoxifen-treated, C tamoxifen plus taurine-treated, and D-taurine treated). Each group was further divided into three subgroups (1, 2, 3) according to the period of treatment which was one, three and six weeks, respectively. Body weights were recorded at the commencement of the study. At the end of the respective period of treatment, the body weights were recorded again and the animals were sacrificed under deep ether anesthesia. By a midline incision, the anterior abdominal wall was opened. The livers were removed, washed with normal saline, and their weights were recorded. Results: The data show a moderately significant increase in final body weight in control groups A1 and A2 (P<0.01) and a highly significant increase (P<0.001) in final body weight in control group A3, respectively, as compared to the initial weight in these groups. There was a highly significant decrease (P<0.001) in the final body weight of groups B1, B2 and B3 when compared with the initial body weights within the group and with the control groups A1, A2 and A3 respectively. The data shows a moderately significant increase (P<0.01) in final body weights of C1 and C3 when compared with B1 and B3 respectively and a significant increase (P<0.05) in the final weights of C2 when compared with tamoxifen treated group B2. The mean absolute liver weight showed significant increase (P value < 0.05) in group B1 and B3, and a moderately significant increase (P<0.01) in group B2, when compared with corresponding control groups A1, A2 and A3. There was insignificant decrease in the mean absolute liver weight in group C1 (P>0.5), highly significant decrease (P= 0.001) in group C2 and highly significant decrease (P<0.001) in group C3 when compared with groups B1, B2 and B3 respectively. The mean relative weight was increased significantly (P value <0.05) in group B1 and B2 and highly significantly (P value <0.001) in B3, when compared to control groups A1, A2 and A3 respectively. Compared to groups B1, B2 and B3, the mean relative liver weight was decreased moderately significantly (P<0.01) in group C1, significantly (P<0.05) in C2 and highly significantly (P<0.001) in C3, respectively. Conclusion: Dietary taurine supplementation reduces the loss in mean body weight and decreases the increase in absolute and relative liver weights brought about by tamoxifen treatment in albino rats.
Effects of Whole-body Vibration with Stochastic Resonance on Balance in Persons with Balance Disability and Falls History – A Systematic Review

The aim of this systematic review was to identify and evaluate the evidence of the efficacy of stochastic resonance whole-body vibration (SR-WBV) on static, dynamic and functional balance in the elderly and in patients with neurodegenerative diseases. English and German studies were consulted in the CINAHL, Cochrane Central Register of Controlled Trials, ISI Web of Knowledge, PEDro and PubMed databases. Eight of 138 eligible studies were included, involving 381 participants. The included studies showed a low to high risk of bias. Three studies focused on long-term effects after SR-WBV. One study evaluated SR-WBV impact over three days while four studies examined its immediate effects. There is only limited evidence that SR-WBV may be effective in improving static, dynamic and functional balance among elderly individuals and patients with neurodegenerative diseases. In the future, more studies of high methodological quality are needed to improve the level of evidence.
Presence of Trypanosoma theileri in Spanish Cattle

Trypanosoma theileri (Laveran, 1902) has been diagnosed in many countries and is commonly considered as a nonpathogenic hemoparasite, although some authors have described clinical signs in cattle infected with T. theileri. In April and May, 2005, 12 blood samples were received at the Exopol Diagnostic Laboratory (Zaragoza, Spain) from a Spanish bull‐fighting farm located at Seville province. Clinical exploration of the animals revealed fever, progressive weight loss, anemia, and frequent recumbent position. Microscopic examination showed Theileria spp. in all cases (12), and in four of them, T. theileri was also observed. The clinical picture observed in the animals could be compatible with T. theileria infection. However, the contribution of T. theileri to the clinical signs seen at least in four cases is unknown. Further studies are necessary to determine the pathogenicity of T. theileri in the different animal species. To our knowledge, this is the first isolation of T. theileri in Spain.
Exploration of an Agentic Construct That Impacts Health Behaviors in General Population

th , 2012; revised July 15 th , 2012; accepted August 12 th , 2012 Hope is defined as the perceived capability to derive pathways to desired goals. The aims of the present study are to discuss hope as a self-regulation construct. Method: The study includes a convenience sample of 615 individuals from the community, 51.1% females. They fill a questionnaire that includes demographic information, disease behavior, health satisfaction, quality of life, and the Hope Scale. Results: Results suggest a statistically significant relation between hope and outcomes of good health. Conclusions: We can conclude that hope, especially agency thinking, can be an interesting variable to be considered in studies about subjective aspects of health.
Adenocarcinoma of the ethmoidal sinus complex: surgical debulking and topical fluorouracil may be the optimal treatment.

OBJECTIVES To report our experience with the management of adenocarcinoma of the ethmoidal sinuses using a regimen of surgical debulking and topical chemotherapy, to report long-term survival, and to compare our results with recently published series of patients undergoing craniofacial resection. DESIGN Review of prospectively collected data. SETTING Tertiary cancer center. PATIENTS Seventy consecutive patients with ethmoidal adenocarcinoma referred to the Department of Head and Neck Surgery, University Hospital of Rotterdam, Rotterdam, the Netherlands, between January 1976 and December 1997. Sixty-two patients were eligible for primary treatment. INTERVENTIONS Surgical debulking via an extended anterior maxillary antrostomy followed by a combination of repeated topical chemotherapy (fluorouracil) and necrotomy. Additionally 8 patients (13%) required radiotherapy for local recurrence; 1 patient required surgery for regional lymph node metastases. MAIN OUTCOME MEASURES Survival measured by the Kaplan-Meier method. Clinical complications related to the therapy. RESULTS There were no perioperative deaths. Complications did occur, such as temporary periorbital swelling (25 patients [40%]) and temporary cerebrospinal fluid leakage (5 patients [8%]). One patient (1.6%) developed meningitis. Adjusted disease-free survival at 2, 5, and 10 years is 96%, 87%, and 74%, respectively. CONCLUSION Our 23-year experience with a combination of surgical debulking and repeated topical chemotherapy for patients with adenocarcinoma of the ethmoidal sinuses leads us to believe that it represents the current treatment of choice for these patients for long-term disease-free survival.
Studies of the Regulation of Basal Adenylate Cyclase Activity by Membrane Polyunsaturated Fatty Acids in Cultured Neuroblastoma

The role of membrane polyunsaturated fatty acids (PUFAs) in the regulation of basal adenylate cyclase activity was examined in intact N1E‐115 neuroblastoma cells. Addition of linoleic acid (50 μM) to the culture medium for 48 h resulted in a significant increase in phospholipid PUFA content and in a two‐ to fivefold increase in basal accumulation of cyclic AMP (cAMP). Both phenomena were reversed on removal of linoleate from the medium. PUFA enrichment stimulated cell proliferation by —20% without altering the relative proportion of cellular protein. The supplemented cells synthesized significantly larger amounts of prostaglandin (PG) E and D than did the controls; however, blockade of PG synthesis by indomethacin or ibuprofen did not alter cAMP formation. Supplemented cells contained higher levels of malondialdehyde (MDA) than did controls, and MDA formation was reduced by coculture with α‐tocopherol; however, its inclusion in the medium did not affect cAMP accumulation. Linoleate‐supplemented cells responded to cyclase‐activating agonists to the same extent as did control cells. Responses to inhibitory agonists (e.g., isoproterenol and carbamylcholine) were altered, but not to a sufficient extent to account for the PUFA‐dependent increases in basal adenylate cyclase activity.
Area-Efficient SOT-MRAM With a Schottky Diode

This letter presents a spin-orbit torque magnetic random access memory (SOT-MRAM) for high-density, reliable, and energy-efficient on-chip memory application. Unlike the conventional SOT-MRAM requiring two access transistors, the proposed MRAM uses only one access transistor along with a Schottky diode in order to achieve high integration density while maintaining the advantages of SOT-MRAM, such as low write energy and enhanced reliability of magnetic tunnel junction. The Schottky diode is forward-biased during read, whereas it is reverse-biased during write to prevent sneak current paths. Our simulation results show that the proposed MRAM can achieve 30% and 50% reduction in bit-cell area in comparison to conventional spin-transfer torque MRAM (STT-MRAM) and SOT-MRAM, respectively, and ~2.5× improvement in write power compared with the STT-MRAM.
Cocaine-induced Psychosis and Brain-derived Neurothrophic Factor in Patients with Cocaine Dependence: Report of Two Cases

Brain-derived neurotrophic factor (BDNF) is linked to numerous brain functions. In addition, BDNF alterations contribute to neurological, mental, and addictive disorders. Cocaine dependence has received much attention recently due to its prevalence and psychological effects. Symptoms of psychosis are one of the most serious adverse events precipitated by cocaine use. It is particularly important to identify patients at risk of developing cocaine-induced psychosis (CIP). We described two cases of patients with cocaine dependence who presented with CIP and had changes in their BDNF levels during the psychotic episode. BDNF levels were initially low in both patients, and then decreased by more than 50% in association with CIP. The relationship between BDNF and psychosis is described in the literature. These cases revealed that BDNF levels decreased during a CIP episode and, thus, it is necessary to investigate BDNF and its relationship with CIP further.