Miracle-dz/UniFAR-FTUs huggingface dataset:
Life History Trade-Offs Assemble Ecological Guilds

Ecological theory predicts that competition for a limiting resource will lead to the exclusion of species unless the within-species effects outweigh the between-species effects. Understanding how multiple competitors might coexist on a single resource has focused on the prescriptive formalism of a necessary niche width and limiting similarity. Here, we show how continuously varying life histories and trade-offs in these characteristics can allow multiple competitors to coexist, and we reveal how limiting similarity emerges and is shaped by the ecological and evolutionary characteristics of competitors. In this way, we illustrate how the interplay of ecological and evolutionary processes acts to shape ecological communities in a unique way. This leads us to argue that evolutionary processes (life-history trait trade-offs) are fundamental to the understanding of the structure of ecological communities.
Prognostic value of cyclin E expression in patients with ovarian cancer: a Meta-analysis.

PURPOSE Cell cycle is mainly mediated by cyclins, cyclin- dependent kinases (CDK), and CDK inhibitors. Cyclin E is the main regulator for transition from G1 to S phase, and is involved in cancer pathogenesis, progression and metastasis. Nevertheless, there is still a controversy of the prognostic value of cyclin E overexpression in ovarian cancer patients. This meta-analysis is the first study aimed at analyzing the effect of cyclin E overexpression on the prognosis of ovarian cancer. METHODS By systematically searching the PUBMED, EMBASE and MEDLINE databases for relevant articles with publication dates up to January 2016 and selection following inclusion and exclusion criteria, 8 studies with 1470 patients were enrolled in our meta-analysis. The overall survival (OS) of patients with cyclin E overexpression was calculated using hazard ratio (HR) with 95% confidence intervals (CIs). The studies were categorized according to the author and year, demographic data in each study, ovarian cancer related information, and cyclin E cut-off value. RESULTS Cyclin E overexpression in ovarian cancer was a poor prognostic factor with statistical significance for OS (HR=1.48, 95%CI: 1.12,1.85). Using confunnel, we found no publication bias in our analysis. CONCLUSION Cyclin E might be considered as a prognostic factor for ovarian cancer, as supported by our meta-analysis. However, more high-quality studies should be conducted to find better clinical use of cyclin E in ovarian cancer.
Magnetic field measurements near a compact kiosk type substation

The last decades the concern of the public, regarding the possible affects from the exposure to magnetic and electric fields, has grown considerably. This is because the generation, transmission and distribution of electric power are accompanied with the presence of the above mentioned fields. This paper attempts to illustrate the values of the resultant magnetic field in the low frequency range, near a compact kiosk type substation 630KVA, 20–0.4 kV. The measurements were performed in a park, in the city center of Chania, Greece, during summer time. All measured magnetic field values were lower in comparison to the value of 100µT introduced by ICNIRP.
Variation in Intensity and Costs of Care by Payer and Race for Patients Dying of Cancer in Texas: An Analysis of Registry-linked Medicaid, Medicare, and Dually Eligible Claims Data

Purpose:To investigate end-of-life care for Medicaid, Medicare, and dually eligible beneficiaries dying of cancer in Texas. Methods:We analyzed the Texas Cancer Registry (TCR)-Medicaid and TCR-Medicare linked databases’ claims data for 69,572 patients dying of cancer in Texas from 2000 to 2008. We conducted regression models in adjusted analyses of cancer-directed and acute care and total costs of care (in 2014 dollars) in the last 30 days of life. Results:Medicaid patients were more likely to receive chemotherapy and radiation therapy. Medicaid patients were more likely to have >1 emergency room (ER) [odds ratio (OR)=5.27; 95% confidence interval (CI), 4.76–5.84], and were less likely to enroll in hospice (OR=0.59; 95% CI, 0.55–0.63) than Medicare patients. Dual eligibles were more likely to have >1 ER visit than Medicare-only beneficiaries (OR=1.19; 95% CI, 1.07–1.33). Black and Hispanic patients were more likely to experience >1 ER visit and >1 hospitalization than whites. Costs were higher for nonwhite Medicare, Medicaid, and dually eligible patients compared with white Medicare enrollees. Conclusions:Variation in acute care utilization and costs by race and payer suggest efforts are needed to address palliative care coordination at the end of life for Medicaid and dually eligible beneficiaries and minority patients dying of cancer.
Ranking Distributions with Generalized Lorenz Curves

Recently Shorrocks [29] and Kakwani [18] have extended Atkinson's [1] theorem on Lorenz dominance and social welfare to allow social welfare evaluations of income distributions with unequal mean incomes. ' Shorrocks and Kakwani independently develop the "generalized" Lorenz curve as a device for simultaneously taking account of differences in mean incomes and the degree of income inequality. The generalized Lorenz curve is ". constructed by scaling up the Lorenz curve by the mean of the distribution" [29, 6]. Thus, the height of the generalized Lorenz curve reflects the level of incomes, while the convexity of the generalized Lorenz curve reflects degree of income inequality. Shorrocks and Kakwani both show that, regardless of mean incomes, generalized Lorenz dominance is equivalent to preference by all increasing, S-concave social welfare functions.2
Rice Inositol Polyphosphate Kinase (OsIPK2) Directly Interacts with OsIAA11 to Regulate Lateral Root Formation

The plant hormone auxin controls many aspects of plant growth and development by promoting the degradation of Auxin/Indole-3-acetic acid (Aux/IAA) proteins. The domain II (DII) of Aux/IAA proteins is sufficient for eliciting the degradation by directly interacting with the auxin receptor F-box protein TIR1 to form a TIR1/AFBs-Aux/IAA complex in an auxin-dependent manner. However, the underlying mechanisms of fine-tuning Aux/IAA degradation by auxin stimuli remain to be elucidated. Here, we show that OsIPK2, a rice (Oryza sativa) inositol polyphosphate kinase, directly interacts with an Aux/IAA protein OsIAA11 to repress its degradation. In a rice protoplast transient expression system, the auxin-induced degradation of Myc-OsIAA11 fusion was delayed by co-expressed GFP-OsIPK2 proteins. Furthermore, expressing additional OsIPK2 or its N-terminal amino acid sequence enhanced the accumulation of OsIAA11 proteins in transgenic plants, which in turn caused defects in lateral root formation and auxin response. Taken together, we identify a novel co-factor of Aux/IAA in auxin signaling and demonstrate its role in regulating lateral root development.
Conserved two‐component Hik34‐Rre1 module directly activates heat‐stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942

Bacteria and other organisms, including cyanobacteria, employ two‐component signal transducing modules comprising histidine kinases and response regulators to acclimate to changing environments. While the number and composition of these modules differ among cyanobacteria, two response regulators that contain DNA binding domains, RpaB and Rre1, are conserved in all sequenced cyanobacterial genomes and are essential for viability. Although RpaB negatively or positively regulates high light and other stress‐responsive gene expression, little is known about the function of Rre1. Here, they investigated the direct regulatory targets of Rre1 in the cyanobacterium Synechococcus elongatus PCC 7942. Chromatin immunoprecipitation and high‐density tiling array analysis were used to map Rre1 binding sites. The sites included promoter regions for chaperone genes such as dnaK2, groESL‐1, groEL‐2, hspA and htpG, as well as the group 2 sigma factor gene rpoD2. In vivo and in vitro analyses revealed that Rre1 phosphorylation level, DNA binding activity and adjacent gene transcription increased in response to heat stress. These responses were much diminished in a knock‐out mutant of Hik34, a previously identified heat shock regulator. Based on our results, we propose Hik34‐Rre1 is the heat shock‐responsive signaling module that positively regulates major chaperone and other genes in cyanobacteria.
Analyzing the Synchronization between the Financial and Business Cycles in Turkey

The primary purpose of this study was to investigate the relationships between the financial and business cycles in Turkey. A quarterly dataset was used for the analysis that covers the period from 1998Q1 to 2014Q4. The cycles were obtained with a Hodrick-Prescott (HP) filter design. The concordance index values, cross-correlation values and Dynamic Conditional Correlation (DCC) model were used to identify the characteristics of the relationships between the financial and business cycles. The empirical results revealed that the financial and business cycles are highly synchronized in Turkey. The results also indicate that while the credit volume cycle is the leading factor of the GDP cycle, the GDP cycle leads from the BIST 100 cycle in Turkey. The last significant conclusion is that the positive and high dynamic conditional correlations between the financial and business cycles experienced a break during the 2008 global crisis.
Genetic counseling for familial conditions during pregnancy: an analysis of patient characteristics

Reproductive genetic counseling for a familial genetic risk factor preferably takes place before conception. However, of the women with a family history of genetic conditions who attend our department of clinical genetics, about 10–20% attend for the first time during a pregnancy. The current study aims to explore patient‐related factors that may affect this late timing of reproductive genetic counseling. Consecutive pregnant (n = 100) and non‐pregnant (n = 84) women visiting the department of clinical genetics for a genetic risk factor which was not age related completed a questionnaire immediately prior to the consultation. The questionnaire asked for (a) background characteristics, i.e. socio‐demographic, obstetric, and disease characteristics (b) cognitive factors, i.e. initiative of referral, knowledge of the risk factor involved, risk perception, worry, child wish, attitudes toward abortion, and preferred participation in decision making, and (c) reasons for the timing of the consultation and for seeking genetic counseling. Pregnant women appeared to be higher educated, considered their children more often as healthy and were less often affected themselves, as compared to non‐pregnant women. They also estimated their chance of having an affected child as lower, and they worried less. Furthermore, the initiative for referral was taken less often by the pregnant woman herself and more often by a medical worker. There were no major differences between the two study groups in knowledge, perceived severity of the risk factor, child wish, attitudes toward abortion, desired participation in decision making, and reasons to seek genetic counseling. Women indicated no specific reasons for their timing of referral for reproductive genetic counseling, e.g. during vs before pregnancy. Our data suggest that this timing of referral is not influenced predominantly by the women's level of knowledge. Rather, women's estimation of genetic risks and their degree of worry, which may be in accordance with the actual risk figures, seem to play a role in seeking genetic counseling. Although further studies are required, a more active role of health care providers seems warranted if we want to prevent genetic counseling for familial genetic conditions during pregnancy as much as possible.
The surgical treatment of sleep-related upper airway obstruction.

BACKGROUND Obstructive sleep apnea (OSA) is a very common disorder among adults: the prevalence of mild OSA is 20%, and that of moderate or severe OSA is 6% to 7%. Simple snoring is even more common. Conservative treatments such as nocturnal ventilation therapy and oral appliances are successful as long as the patient actually uses them, but they do not eliminate the underlying obstruction of the upper airway. METHOD The relevant literature up to 2008 on the surgical treatment of OSA was selectively reviewed. RESULTS Five types of surgical treatment for OSA are available, each for its own indications: optimization of the nasal airway to support nasal ventilation therapy, (adeno-)tonsillectomy as first-line treatment for OSA in children, minimally invasive surgery for simple snoring and mild OSA, invasive surgery as first- and second-line treatment for mild OSA, and invasive multilevel surgery as second-line treatment of moderate to severe OSA that remains refractory to ventilation therapy. CONCLUSION Surgical treatment for OSA is appropriate for specific indications as a complement to the established conservative treatment methods.
Cloning of a double-stranded cDNA that codes for a portion of chicken preproalbumin. A general method for isolating a specific DNA sequence from partially purified mRNA.

A scheme is presented for cloning a double-stranded cDNA molecule that codes for a portion of chicken preproalbumin. This method, which does not require pure mRNA or cDNA, has widespread applicability. Chicken preproalbumin was identified as a Mr = 72,000 polypeptide by immunoprecipitation of proteins synehesized in a wheat germ cell-free translation system from total, guanidine.HCl-extracted, rooster liver RNA. After removal of the bulk of the ribosomal RNA by poly(U)-Sephadex G-10 chromatography, albumin mRNA was enriched approximately 2-fold by centrifugation through low salt, isokinetic sucrose gradients, until it represented about 30% of the mRNA sequences present. Double-stranded cDNA prepared from this mRNA was then inserted into the Pst 1 site of the plasmid PBR322 by the "G-C tailing" technique and the recombinant DNA was used to transform Echerichia coli stran X1776. Transformants containing putative albumin DNA sequences were identified by colony hybridization with a cDNA probe that was highly enriched for albumin cDNA sequences. This probe was isolated by hybridizing the partially purified RNA preparation to its cDNA, under conditions of RNA excess, to a R0t value such that only the most abundant cDNA sequences had hybridized. Unhybridized, less abundant, sequences were destroyed by subsequent S1 nuclease digestion. The identity of clones that hybridized to this abundant class cDNA was established by DNA-mRNA hybrid-arrested cell-free translation. Hybridization of nick-translated, albumin-containing, plasmid DNA to total liver poly(A)+ RNA, that had been separated on methyl mercury agarose gels and transferred to diazobenzyloxymethyl paper, established that avian albumin mRNA has a molecular weight of 850,000. This molecular weight corresponds to approximately 2,600 nucleotides, or 600 nucleotides longer than the size required to code for the preproalbumin polypeptide.
An Export-Specific Reporter Designed for Gram-Positive Bacteria: Application to Lactococcus lactis

ABSTRACT The identification of exported proteins by fusion studies, while well developed for gram-negative bacteria, is limited for gram-positive bacteria, in part due to drawbacks of available export reporters. In this work, we demonstrate the export specificity and use of theStaphylococcus aureus secreted nuclease (Nuc) as a reporter for gram-positive bacteria. Nuc devoid of its export signal (called ΔSPNuc) was used to create two fusions whose locations could be differentiated. Nuclease activity was shown to require an extracellular location in Lactococcus lactis, thus demonstrating the suitability of ΔSPNuc to report protein export. The shuttle vector pFUN was designed to construct ΔSPNuc translational fusions whose expression signals are provided by inserted DNA. The capacity of ΔSPNuc to reveal and identify exported proteins was tested by generating anL. lactis genomic library in pFUN and by screening for Nuc activity directly in L. lactis. All ΔSPNuc fusions displaying a strong Nuc+ phenotype contained a classical or a lipoprotein-type signal peptide or single or multiple transmembrane stretches. The function of some of the predicted signals was confirmed by cell fractionation studies. The fusions analyzed included long (up to 455-amino-acid) segments of the exported proteins, all previously unknown in L. lactis. Homology searches indicate that several of them may be implicated in different cell surface functions, such as nutrient uptake, peptidoglycan assembly, environmental sensing, and protein folding. Our results with L. lactis show that ΔSPNuc is well suited to report both protein export and membrane protein topology.
Single high dose atorvastatin does not ameliorate endothelial function and large arterial stiffness in dyslipidemic patients without atherosclerosis.

BACKGROUND Many studies show that statins have beneficial effects on atherosclerotic risk factors and markers such as flow mediated dilatation (FMD). However, studies on early effects of statins on endothelial function of non atherosclerotic humans are limited. AIM The purpose of this study was to determine whether a single high dose of atorvastatin could improve endothelial function and large arterial stiffness in statin naive dyslipidemic non-atherosclerotic patients. MATERIALS AND METHODS Thirty statin naïve dyslipidemic non-atherosclerotic patients from Cardiology Outpatient Clinic were enrolled. Arterial stiffness and endothelial function of patients were evaluated by assessing the finger photoplethysmography and the flow-mediated dilatation (FMD) of the brachial artery before and 24 hour after oral administration of 80 mg atorvastatin. RESULTS Stiffness indices and FMD 24 hours after administration of 80mg atorvastatin did not differ from baseline measurements (6.89 +/- 1.90 vs. 7.06 +/- 2.37 p : NS and 9.13 +/- 6.07 vs. 9.80 +/- 6.34 p : NS). CONCLUSIONS Although it is widely accepted that statins improve endothelial function, evidences of early effect might largely be associated with endothelial injury. Our study suggests that beneficial early effects of statins might not be applicable to patients without atherosclerosis.
Improvements to the LIUM French ASR system based on CMU sphinx: what helps to significantly reduce the word error rate?

This paper describes the new ASR system developed by the LIUM and analyzes the various origins of the signiﬁcant drop of the word error rate observed in comparison to the previous LIUM ASR system. This study was made on the test data of the latest evaluation campaign of ASR systems on French broadcast news, called ESTER2 and organized in December 2008. For the same computation time, the new system yields a word error rate about 38% lower than what the previous system (which reached the second position during the ESTER1 evaluation campaign) did. This paper evaluates the gain provided by various changes to the system: implementation of new search and training algorithms, new training data, vocabulary size, etc. The LIUM ASR system was the best open-source ASR system of the ESTER2 campaign.
Infant Iron Deficiency, Child Affect, and Maternal Unresponsiveness: Testing the Long-Term Effects of Functional Isolation

Children who are iron deficient (ID) or iron-deficient anemic (IDA) have been shown to seek and receive less stimulation from their caregivers, contributing to functional isolation. Over time, the reduced interactions between child and caregiver are thought to interfere with the acquisition of normative social competencies and adversely affect the child’s development. The current study examined functional isolation in children who were ID or IDA in infancy in relation to social difficulties in middle childhood and problem behaviors in adolescence. Using a sample of 873 Chilean children, 45% of whom were ID or IDA in infancy, structural equation modeling results indicated that infant IDA was associated with children’s dull affect and social reticence at age 5, which were related to mothers’ unresponsiveness and understimulation. Mothers’ limited responsiveness and stimulation were, in turn, related to children’s peer rejection at age 10, which further linked to problem behaviors and associating with deviant peers at adolescence. Findings support the functional isolation hypothesis and suggest that early limited caregiver responsiveness and stimulation contribute to long-term social difficulties in adolescents who were iron-deficient anemic in infancy.
Research of asynchronous algorithm for molecular dynamics task on the PDCS “Buran” models

Molecular dynamics (MD) task scales poorly due to the global barriers used to maintain neighbour lists. The paper presents the asynchronous algorithm for MD task simulation free from this drawback. The experiments with MD on various models of parallel dataflow computing system (PDCS) “Buran ” also presented. Synchronization in this algorithm relies solely on the local interactions between the cores responsible for nearby areas. The paper describes a series of experiments with MD task on cycle-accurate and behaviour block-register models as well as on PDCS emulator (on cluster) which allow to re-assessing capabilities of the created computing system. Scalability for the tasks with equal size on PDCS will be by one-two orders higher than on the traditional systems. Furthermore, the research has shown the possibility to create the simple version of basic algorithm, from which can be derived the more efficient completely asynchronous algorithm based on counting of the transmitted particles.
Manipulation planning: building paths on constrained manifolds

Constrained motion planning and Manipulation planning, for generic non-linear constraints, highly rely on the ability of solving non-linear equations. The Newton-Raphson method, often used in this context, is discontinuous with respect to its input and point wise path projection can lead to discontinuous constrained paths. The discontinuities come from the pseudo-inverse involved at each iteration of the Newton-Raphson algorithm. An interval of continuity for one iteration is derived from an upper bound of the norm of the Hessian of the constraints. Such a bound is easy to compute for constraints involving joint positions and orientations. We introduce two heuristical path projection algorithms and empirically show that they generate continuous constrained paths. The algorithms are integrated into a motion planning algorithm to empirically assert the continuity of the solution.