Miracle-dz/UniFAR-FTUs huggingface dataset:
CoRisk: Credit Risk Contagion with Correlation Network Models

We propose a novel credit risk measurement model for Corporate Default Swap (CDS) spreads that combines vector autoregressive regression with correlation networks. We focus on the sovereign CDS spreads of a collection of countries that can be regarded as idiosyncratic measures of credit risk. We model CDS spreads by means of a structural vector autoregressive model, composed by a time dependent country specific component, and by a contemporaneous component that describes contagion effects among countries. To disentangle the two components, we employ correlation networks, derived from the correlation matrix between the reduced form residuals. The proposed model is applied to ten countries that are representative of the recent financial crisis: top borrowing/lending countries, and peripheral European countries. The empirical findings show that the contagion variable derived in this study can be considered as a network centrality measure. From an applied viewpoint, the results indicate that, in the last 10 years, contagion has induced a “clustering effect” between core and peripheral countries, with the two groups further diverging through, and because of, contagion propagation, thus creating a sort of diabolic loop extremely difficult to be reversed. Finally, the outcomes of the analysis confirm that core countries are importers of risk, as contagion increases their CDS spread, whereas peripheral countries are exporters of risk. Greece is an unfortunate exception, as its spreads seem to increase for both idiosyncratic factors and contagion effects.
Competitiveness and efficiency in poultry and pig production in Vietnam

Competitiveness and efficiency of local, crossbred and exotic breeds of poultry and pig production in North and South Vietnam were assessed using data from a stratified sample of 2213 farms collected in 1999. Results of policy analysis matrix show that poultry meat and egg production is generally competitive except meat and egg production with local breeds, and egg production with crossbreds in the North, and egg production with local breeds in the South, due to low productivity and high per unit cost. There are economies of scale in the North but it is not so clear in the South. Domestic prices of both outputs and inputs are higher than the world prices. If output prices fall moderately due to withdrawal of protective policies and domestic demand slows down from the current high levels, poultry breeds that are profitable under the existing situation would still remain competitive. Pig production under existing technologies and market conditions is highly competitive, especially with local and crossbreds in the North and exotic breeds in the South. Currently, producers in the South are apparently benefiting more due to market conditions and policy that make input cost higher and output price lower in the North. There are economies of scale in production, more in case of pig than in poultry. Medium farms are more cost effective, and small farms are least competitive. Several factors including feed quality and management, education of the household head, access to credit, access to government supplied inputs and services, number of extension visits, access to secondary markets significantly influenced the level of efficiency of individual farms. Policy and institutional arrangements that address these factors, especially with targeted support to small farms, will lead to improved overall efficiency. Otherwise, smallholders are likely to be pushed out of business in a more liberalised economic environment.
Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion

Microsatellite genotyping errors will be present in all but the smallest data sets and have the potential to undermine the conclusions of most downstream analyses. Despite this, little rigorous effort has been made to quantify the size of the problem and to identify the commonest sources of error. Here, we use a large data set comprising almost 2000 Antarctic fur seals Arctocephalus gazella genotyped at nine hypervariable microsatellite loci to explore error detection methods, common sources of error and the consequences of errors on paternal exclusion. We found good concordance among a range of contrasting approaches to error‐rate estimation, our range being 0.0013 to 0.0074 per single locus PCR (polymerase chain reaction). The best approach probably involves blind repeat‐genotyping, but this is also the most labour‐intensive. We show that several other approaches are also effective at detecting errors, although the most convenient alternative, namely mother–offspring comparisons, yielded the lowest estimate of the error rate. In total, we found 75 errors, emphasizing their ubiquitous presence. The most common errors involved the misinterpretation of allele banding patterns (n = 60, 80%) and of these, over a third (n = 22, 36.7%) were due to confusion between homozygote and adjacent allele heterozygote genotypes. A specific test for whether a data set contains the expected number of adjacent allele heterozygotes could provide a useful tool with which workers can assess the likely size of the problem. Error rates are also positively correlated with both locus polymorphism and product size, again indicating aspects where extra effort at error reduction should be directed. Finally, we conducted simulations to explore the potential impact of genotyping errors on paternity exclusion. Error rates as low as 0.01 per allele resulted in a rate of false paternity exclusion exceeding 20%. Errors also led to reduced estimates of male reproductive skew and increases in the numbers of pups that matched more than one candidate male. Because even modest error rates can be strongly influential, we recommend that error rates should be routinely published and that researchers make an attempt to calculate how robust their analyses are to errors.
Risk Stratification of Adult Patients Undergoing Orthotopic Liver Transplantation for Fulminant Hepatic Failure

Background. Orthotopic liver transplantation (OLT) is an effective treatment for fulminant hepatic failure (FHF), but postOLT mortality is higher for patients with FHF than for patients with other indications for OLT. In the current study, a large cohort of patients who underwent OLT for FHF was evaluated to develop and validate a system useful for estimating postOLT patient survival. Methods. The 1,457 patients who underwent OLT for FHF in the United States between 1988 and 2003 were enrolled through the UNOS database. This group was divided into a modeling group (n=972) and a crossvalidation group (n=486). With a multivariate regression analysis, the modeling group was used to identify clinical parameters that had a significant association with postOLT survival. This regression analysis was used to create a scoring system that was subsequently assessed in the crossvalidation group. Results. Four risk factors were identified with the multivariate analysis: 1) body mass index ≥30 kg/m2; 2) serum creatinine >2.0 mg/dL; 3) recipient age >50 years old; and 4) history of life support. By assigning points based on the number of risk factors present, the scoring system was able to differentiate between low-risk patients (5-year survival, 81%) and high-risk patients (5-year survival, 42%). The relative risk of postOLT mortality increased by approximately 150% for each additional point. Conclusion. The scoring system risk-stratified the crossvalidation group and accurately predicted postOLT survival. A scoring system utilizing clinical and demographic information readily available prior to OLT may help predict the probability of survival after OLT for FHF.
Characterization of potassium binding with human telomeres

Human telomeres are G‐rich tandem repeats that assume G‐quadruplex structures at the ends of chromosomes. Stabilization of telomeric G‐quadruplex represents a significant drug target for inhibiting the telomerase activity that is required in about 85% of cancers. Metal ions have been revealed as important stabilizers to DNA G‐quadruplexes, but their binding process with human telomeric G‐quadruplex remains unclear. In this report, we show that K+ traverses into the G‐tetrads centre of two G‐tetrad layers through the half‐capped top pathway constructed by the two edge‐wise loop bases. The binding is mediated by the electrostatic interactions between K+ and the nearby bases of G‐tetrads. However, direct traverse of K+ into the interior of G‐quadruplex is negatively regulated by the steric hindrance of water molecules. Once K+ enters the G‐quadruplex, stabilization of the in‐plane or sandwiched conformation of the telomeric G‐quadruplex‒K+ complex is maintained by surrounding water molecules. These findings provide insights into the atomic interactions between K+ and telomere G‐tetrads for targeted drug design.
Analysis of Oxidative Damage by Gene‐Specific Quantitative PCR

This unit describes the gene‐specific quantitative PCR‐based (QPCR) assay, which is used to measure DNA integrity of both nuclear and mitochondrial genomes based on amplification of long DNA targets. QPCR can be used to quantify the formation of DNA damage and the kinetics of DNA repair by following restoration of amplification of the target DNA over time after removal of the damaging agent. A detailed protocol to set up QPCR in any laboratory, highlighting critical parameters for successful establishment of the assay and interpretation of the results, is provided here. Advantages (e.g., the use of nanogram amounts of DNA) and limitations (e.g., the inability to define the specific type of lesion present on the DNA) of using QPCR to assay DNA damage in human cells are also described. Curr. Protoc. Hum. Genet. 62:19.1. 1‐19.1. 13. © 2009 by John Wiley & Sons, Inc.
Mechanisms of potassium transfer across the dually perfused rat placenta.

The purpose of this study was to directly investigate the mechanisms of K+ transfer across the rat placenta, which was isolated and perfused through both its maternal and fetal circulations. Unidirectional maternofetal (Kmf) and fetomaternal (Kfm) clearances for 42K, 51Cr-labeled EDTA (used as a diffusion-limited paracellular marker), and 3H2O (used as a flow-limited marker) were respectively 232 +/- 36, 12 +/- 4, and 1,020 +/- 260 (mf) and 96 +/- 26, 18 +/- 6, and 737 +/- 176 (fm) microliters.min-1 x g placenta-1. Calculated K+ fluxes were asymmetric, being 0.75 +/- 0.12 and 0.41 +/- 0.12 mumol.min-1 x g placenta-1 for maternofetal and fetomaternal, respectively (mean +/- SE, n = 6; P < 0.01, paired t test). Although Kmf for 3H2O was 28% higher than Kfm, this could not completely account for the asymmetry in K+ fluxes. Kmf for 42K was 12-70 times higher than that for 51Cr-EDTA (presumed to be a paracellular marker), although its diffusion coefficient is only 2.5 times higher. An apparent Michaelis constant (Km) of 11.0 +/- 2.4 mM and maximum velocity (Vmax) of 3.8 +/- 0.33 mumol.min-1 x g placenta-1 was calculated by Michaelis-Menten analysis of the transcellular component of maternofetal flux (Jmf) for K+. Ouabain or barium (1 mM in maternal and fetal perfusate) reduced Kmf for 42K from 250 +/- 38 to 76 +/- 13 microliters.min-1 x g placenta-1 (n = 4; P < 0.01) and from 358 +/- 31 to 106 +/- 18 microliters.min-1 x g placenta-1 (n = 5; P < 0.001). Neither drug had any effect on Kmf for 51Cr-EDTA or 3H2O. (ABSTRACT TRUNCATED AT 250 WORDS)
A novel pattern and frequency reconfigurable antenna

A simple septagon slotted, frequency and radiation pattern reconfigurable microstrip patch antenna is proposed in this paper. The antenna operates in the C band and is capable of switching between two different frequencies 3.9 GHz and 5.9 GHz. The radiation pattern can be reconfigured between boresight pattern and conical pattern. Beam Lead PIN diodes (MA4AGBLP912) are used as switching element for reconfiguring the frequency and radiation pattern. Two parasitic elements are used; a circular ring for frequency reconfiguration and shorting posts for radiation pattern reconfiguration.
Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation.

PREMISE OF THE STUDY Qat (Catha edulis, Celastraceae) is a woody plant species cultivated for its stimulant alkaloids. Qat is important to the economy and culture in large regions of Ethiopia, Kenya, and Yemen. Despite the importance of this species, the wild origins and dispersal of cultivars have only been described in often contradictory historical documents. We examined the wild origins, human-mediated dispersal, and genetic divergence of cultivated qat compared to wild qat. METHODS We sampled 17 SSR markers and 1561 wild and cultivated individuals across the historical areas of qat cultivation. KEY RESULTS On the basis of genetic structure inferred using Bayesian and nonparametric methods, two centers of origin in Kenya and one in Ethiopia were found for cultivated qat. The centers of origin in Ethiopia and northeast of Mt. Kenya are the primary sources of cultivated qat genotypes. Qat cultivated in Yemen is derived from Ethiopian genotypes rather than Yemeni wild populations. Cultivated qat with a wild Kenyan origin has not spread to Ethiopia or Yemen, whereas a small minority of qat cultivated in Kenya originated in Ethiopia. Hybrid genotypes with both Ethiopian and Kenyan parentage are present in northern Kenya. CONCLUSIONS Ethiopian cultivars have diverged from their wild relatives, whereas Kenyan qat has diverged less. This pattern of divergence could be caused by the extinction of the wild-source qat populations in Ethiopia due to deforestation, undersampling, and/or artificial selection for agronomically important traits.
14q32 Translocations discriminate IgM multiple myeloma from Waldenstrom's macroglobulinemia.

Even though the diagnosis of Waldenstrom's macroglobulinemia WM is usually clear, the differential diagnosis with IgM multiple myeloma (MM) might be possible. IgM MM is usually characterized by the accumulation of small mature plasma cells within the bone marrow, and the detection of a monoclonal IgM in the serum. However, in contrast with classical MM, IgM MM is rarely associated with these patients' extensive osteolytic lesions. We analyzed eight cases of IgM MM. None presented with extensive bone lesions. All cases were characterized by the presence of small mature plasma cells within the bone marrow. Molecular cytogenetic analysis revealed a t(11;14) in seven of the eight cases. In contrast, a similar analysis in 17 WM cases failed to detect any t(11;14) cases. We performed further fluorescence in situ hybridization (FISH) experiments, focused on the 14q32 region, and especially on the IgH gene. In contrast to MM (in which illegitimate IgH rearrangements are common), we did not detect any abnormality in the WM cases. In conclusion, even though the cells of origin in WM and MM are mature heavily mutated cells, they differ by the IgH gene rearrangements. Especially in IgM MM, the search for t(11;14) might be useful in difficult cases to discriminate with WM.
A Spatial Focusing Model for G Protein Signals

Regulators of G protein signaling (RGS) are GTPase-accelerating proteins (GAPs), which can inhibit heterotrimeric G protein pathways. In this study, we provide experimental and theoretical evidence that high concentrations of receptors (as at a synapse) can lead to saturation of GDP-GTP exchange making GTP hydrolysis rate-limiting. This results in local depletion of inactive heterotrimeric G-GDP, which is reversed by RGS GAP activity. Thus, RGS enhances receptor-mediated G protein activation even as it deactivates the G protein. Evidence supporting this model includes a GTP-dependent enhancement of guanosine 5′-3-O-(thio)triphosphate (GTPγS) binding to Gi by RGS. The RGS domain of RGS4 is sufficient for this, not requiring the NH2- or COOH-terminal extensions. Furthermore, a kinetic model including only the GAP activity of RGS replicates the GTP-dependent enhancement of GTPγS binding observed experimentally. Finally in a Monte Carlo model, this mechanism results in a dramatic “spatial focusing” of active G protein. Near the receptor, G protein activity is maintained even with RGS due to the ability of RGS to reduce depletion of local Gα-GDP levels permitting rapid recoupling to receptor and maintained G protein activation near the receptor. In contrast, distant signals are suppressed by the RGS, since Gα-GDP is not depleted there. Thus, a novel RGS-mediated “kinetic scaffolding” mechanism is proposed which narrows the spatial range of active G protein around a cluster of receptors limiting the spill-over of G protein signals to more distant effector molecules, thus enhancing the specificity of Gi protein signals.
Evening vs morning isradipine sustained release in essential hypertension: a double-blind study with 24 h ambulatory monitoring.

A randomized, double-blind, placebo controlled study evaluated the effects on 24 h ambulatory blood pressure (ABP) of isradipine sustained release (I-SRO) administered once daily, in the morning (AM) or in the evening (PM). Eighteen uncomplicated essential hypertensives (10 men, mean age 55 +/- 6 years) with casual sitting DBP 96-110 mm Hg received, according to a triple-way crossover design, I-SRO 5 mg AM, or 5 mg PM, or placebo for 4 weeks. A 24 h ABP monitoring (Spacelabs 90207) was carried out at the end of each treatment. Twenty-four hour BP was 145.3/89.8 mm Hg after randomized placebo. AM and PM I-SRO significantly reduced 24 h BP, by 13.7/8.7 and 12.9/8.2 mm Hg respectively. Daytime (07.00 h-23.00 h) BP significantly decreased by 15.0/9.7 mm Hg with AM and 13.2/8.7 mm Hg with PM regimen; night-time BP (23.00 h-07.00 h) significantly decreased by 11.6/7.1 and 12.3/7.4 mm Hg, respectively. Nocturnal nadir BP values were 132.6/78.1 after randomized placebo, 120.9/71.4 after AM I-SRO and 121.0/72.4 mm Hg after PM I-SRO. Morning peak BP values were 154.6/96.9, 139.5/87.6 and 137.5/85.5 mm Hg, respectively. Mean BP values in the early morning hours (i.e. between 03.00 h and 08.00 h) were significantly decreased by 12.1/7.3 mm Hg after AM and 14.3/7.9 mm Hg after PM intake. No significant differences were detected in the BP lowering effect of the two I-SRO regimens. (ABSTRACT TRUNCATED AT 250 WORDS)
GABAA and glycine receptor‐mediated transmission in rat lamina II neurones: relevance to the analgesic actions of neuroactive steroids

Analgesic neurosteroids such as 5α‐pregnan‐3α‐ol‐20‐one (5α3α) are potent selective endogenous modulators of the GABAA receptor (GABAAR) while certain synthetic derivatives (i.e. minaxolone) additionally enhance the function of recombinant glycine receptors (GlyR). Inhibitory transmission within the superficial dorsal horn has been implicated in mediating the analgesic actions of neurosteroids. However, the relative contribution played by synaptic and extrasynaptic receptors is unknown. In this study, we have compared the actions of 5α3α and minaxolone upon inhibitory transmission mediated by both GABAA and strychnine‐sensitive GlyRs in lamina II neurones of juvenile (P15–21) rats. At the near physiological temperature of 35°C and at a holding potential of −60 mV we recorded three kinetically distinct populations of miniature IPSCs (mIPSCs): GlyR‐mediated, GABAAR‐mediated and mixed GABAAR‐GlyR mIPSCs, arising from the corelease of both inhibitory neurotransmitters. In addition, sequential application of strychnine and bicuculline revealed a small (5.2 ± 1.0 pA) GlyR‐ but not a GABAAR‐mediated tonic conductance. 5α3α (1–10 μm) prolonged GABAAR and mixed mIPSCs in a concentration‐dependent manner but was without effect upon GlyR mIPSCs. In contrast, minaxolone (1–10 μm) prolonged the decay of GlyR mIPSCs and, additionally, was ∼10‐fold more potent than 5α3α upon GABAAR mIPSCs. However, 5α3α and minaxolone (1 μm) evoked a similar bicuculline‐sensitive inhibitory conductance, indicating that the extrasynaptic GABAARs do not discriminate between these two steroids. Furthermore, ∼92% of the effect of 1 μm 5α3α upon GABAergic inhibition could be accounted for by its action upon the extrasynaptic conductance. These findings are relevant to modulation of inhibitory circuits within spinally mediated pain pathways and suggest that extrasynaptic GABAARs may represent a relevant molecular target for the analgesic actions of neurosteroids.
Interleukin‐6 and interleukin‐6 receptor expression, localization, and involvement in pain‐sensing neuron activation in a mouse intervertebral disc injury model

The pathological mechanism of intractable low back pain is unclear. However, intervertebral disc (IVD) degeneration is a primary cause of low back pain, and pain‐related mediators, such as interleukin‐6 (IL‐6), have been correlated with discogenic pain. The objective of this study is to elucidate the mechanism of local IL‐6 and IL‐6 receptor (IL‐6R) expression after IVD injury as well as determine the involvement of IL‐6/IL‐6 signaling in discogenic pain. To do this, quantitative and immunohistological analyses in a mouse model of IVD injury were performed. Firstly, we measured the local expression levels of IL‐6 and IL‐6R in IVDs by enzyme‐linked immunosorbent assay (ELISA). Secondly, we immunohistochemically confirmed their localization in injured IVDs. Lastly, we evaluated the effects of intradiscal injection of an IL‐6 inhibitor by evaluating pain‐related protein, calcitonin gene‐related peptide (CGRP), expression in dorsal root ganglia (DRG) neurons that innervate IVDs. Injured IVDs showed increased production of IL‐6 and IL‐6R. IL‐6 and IL‐6R expression in the injured IVD were predominantly localized in the annulus fibrosus and endplate, and intradiscal injection of the IL‐6 inhibitor suppressed CGRP expression in the DRG neurons. These results show that IL‐6 and IL‐6R expression levels are responsive to IVD injury and that inhibition of IL‐6/IL‐6R signaling may be a promising analgesic treatment for degenerative disc diseases. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:1508–1514, 2015.
Perceived barriers to exercise in Hispanic adults by level of activity.

BACKGROUND National data show that Hispanics report low levels of physical activity. Limited information on barriers to exercise in this population exists in the literature. METHODS Surveys were administered to 398 Hispanic participants from two colonias in South Texas to investigate self-reported levels of and perceived barriers to exercise. One-way ANOVA by level of activity and t tests by gender were conducted. Exploratory factor analysis was used to examine patterns by level of activity. RESULTS Results show that 67.6% of respondents did not meet physical activity recommendations of at least 150 minutes per week, as compared with 55.6% nationally. Overall, the most frequently reported barriers included "lack of time," "very tired," and "lack of self-discipline" to exercise. An exploratory factor analysis of the barriers reported by participants not meeting physical activity recommendations resulted in a 3-factor structure. A unidimensional scale was found for participants meeting recommendations. CONCLUSIONS Findings suggest that future interventions should be specific to gender and exercise level to address the high prevalence of inactivity in this population.