Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic resources for the conservation and management of the harpy eagle (Harpia harpyja, Falconiformes, Accipitridae)

Abstract We report the characterization and optimization of 45 heterologous microsatellite loci, and the development of a newsetofmolecularsexmarkersfortheconservationandmanagementoftheNeotropicalharpyeagle(HarpiaharpyjaL.1758). Of the 45 microsatellites tested, 24 were polymorphic, six monomorphic, 10 uncharacterizable due to multiplebandsandfivedidnotamplify.TheobservedgenediversityoftheanalyzedsampleofH. harpyjawaslowandsimilarto that of other threatened Falconiformes. While a high proportion of the microsatellite markers were highly variable,individuals of H. harpyjacould be differentiated by a joint analysis of just three (p = 2.79 x 10 -4 ) or four markers(p=2.89x10 -5 ). Paternity could be rejected with 95.23% and 97.83% probabilities using the same three and fourmarkers, respectively. The sex determination markers easily and consistently differentiated males from femalesevenwithhighlydegradedDNAextractedfromnaturallyshedfeathers.Themarkersreportedinthisstudypotentiallyprovide an excellent set of molecular tools for the conservation and management of wild and captive H. harpyjaandthey may also prove useful for the enigmatic Neotropical crested eagle (Morphnus guianensisDaudin 1800).
Unreliable Accounts: How Regulators Fabricate Conceptual Narratives to Diffuse Criticism

Abstract In 2010, the U.S. accounting rulemaker (FASB) updated its longstanding constitution to eliminate “reliability” as a fundamental accounting property. FASB argued that “reliability” was misunderstood in practice and that this amendment clarified its original intent. Drawing on primary archival resources and field interviews with regulators, I provide evidence that the change also sought to legitimize the rise of fair-value accounting. By eliminating the need for accounting to be “reliable,” the change attempted to neutralize concerns about the subjectivity in fair-value estimates. Such subjectivity can facilitate accounting manipulation, and some fair-value rules can be attributed to lobbying by managers who stand to benefit. The change illustrates “conceptual veiling,” wherein regulators, seeking to diffuse criticism, including suspicions of capture, manufacture costly conceptual narratives for justifying their actions.
Measuring Farmer Risk Preferences in Europe: A Systematic Review

We present a systematic review of the extensive body of research on farmer risk preference measurement across Europe. We capture the methodological developments over time and discuss remaining challenges and potential areas for further research. Given the constantly evolving policy environment in Europe, and increasing climate‐change related risks and uncertainties, there is large value to be gained from enhancing our understanding of this fundamental aspect of farmers’ decision‐making processes and consequent actions.
The brain effects of occupational strength 50 Hz magnetic field

Human cognitive behavioural and neurophysiological effects during exposure to extremely low frequency (ELF) 50 Hz magnetic field (MF) of 28.4 /spl mu/T were measured triple-blinded. Forty subjects were exposed to MF and sham in two visits in counterbalanced orders. The visits were scheduled after two training sessions and one baseline session. Two of the 29 parameters assessed were inter-peak latencies of visual evoked response (VER) and auditory evoked response (AER). The other 27 variables were measures of the brain performance, reaction time (RT), learning, memory (spatial, short-term, long-term, working and secondary), storage and retrieval of information (numerical, verbal and pictorial), accuracy, errors, attention, alertness and vigilance. The conclusion was a small decline in the human brain performance and in particular statistically significant deterioration in choice reaction time accuracy (p=0.03), word recognition accuracy (p=0.03) and numerical working memory (p=0.05). This study found no effect in grouped measures of alertness. No adjustment for multiple comparisons has been made, and as such, with 29 outcome variables, the authors acknowledge that any statistically significant result at a 5% level may be due solely to chance.
Structure and evolution of the Phasianidae mitochondrial DNA control region

Abstract The mitochondrial DNA control region is an area of the mitochondrial genome which is non-coding DNA. To infer the structural and evolutionary characteristics of Phasianidae mitochondrial DNA control region, the entire control region sequences of 34 species were analyzed. The length of the control region sequences ranged from 1144 bp (Phasianus colchicus) to 1555 bp (Coturnix japonica) and can be separated into three domains. The average genetic distances among the species within the genera varied from 1.96% (Chrysolophus) to 12.05% (Coturnix). The average genetic distances showed significantly negative correlation with ts/tv. In most genera (except Coturnix), domain I is the most variable among the three domains. However, the first 150 nucleotides apparently evolved at unusually low rates. Four conserved sequence boxes in the domain II of Phasianidae sequences were identified. The alignment of the Phasianidae four boxes and CSB-1 sequences showed considerable sequence variation.
Modification of plasmid DNA topology by 'histone-mimetic' gold nanoparticles.

AIMS Our aim is to explore whether gold nanoparticles (AuNPs) functionalized with a carboxylated polyethylene glycol (PEG) and protamine (AuNP@PEG@Prot) can modulate - enhance or restrain - DNA condensation, altering DNA conformation and inducing structural changes. Understanding how these nanoconjugates modulate DNA structure, size and shape of DNA condensates, and enable control over the resulting 3D structures is of major biological and therapeutic importance. MATERIALS & METHODS Citrate-AuNPs were covered with a dense layer of a hetero-functional octa(ethylene glycol) (SH-EG(8)-COOH). Conjugation of protamine to the AuNP@PEG was achieved by taking advantage of the carboxylated surface previously generated on the surface of the NP and the remaining amino groups from the protamine, using carbodiimide and N-hydroxysulfosuccinimide coupling reactions. RESULTS & CONCLUSION AuNP@PEG@Prot modulates the structure and topology of DNA, not only for condensation, but also for decondensation, via formation of higher quantities of dimers and multimers, when compared with AuNP@PEG and free protamine.
Novel High-Throughput Screening Method for Identification of Fungal Dimorphism Blockers

Invasive mycoses have been increasing worldwide, with Candida spp. being the most prevalent fungal pathogen causing high morbidity and mortality in immunocompromised individuals. Only few antimycotics exist, often with severe side effects. Therefore, new antifungal drugs are urgently needed. Because the identification of antifungal compounds depends on fast and reliable assays, we present a new approach based on high-throughput image analysis to define cell morphology. Candida albicans and other fungi of the Candida clade switch between different growth morphologies, from budding yeast to filamentous hyphae. Yeasts are considered proliferative, whereas hyphae are required for invasion and dissemination. Thus, morphotype switching in many Candida spp. is connected to virulence and pathogenesis. It is, consequently, reasonable to presume that morphotype blockers interfere with the virulence, thereby preventing hazardous colonization. Our method efficiently differentiates yeast from hyphal cells using a combination of automated microscopy and image analysis. We selected the parameters length/width ratio and mean object shape to quantitatively discriminate yeasts and hyphae. Notably, Z′ factor calculations for these parameters confirmed the suitability of our method for high-throughput screening. As a second stage, we determined cell viability to discriminate morphotype-switching inhibitors from those that are fungicidal. Thus, our method serves as a basis for the identification of candidates for next-generation antimycotics.
Hepatic Insulin Resistance Following Chronic Activation of the CREB Coactivator CRTC2*

Background: Loss of CRTC2 improves insulin sensitivity, but it is unknown if chronic CRTC2 activity causes hepatic insulin resistance. Results: Liver expression of constitutively active CRTC2 increased hepatic glucose production, despite compensatory increases in FOXO1 phosphorylation. Conclusion: Persistent increases in CRTC2 activation promote hepatic insulin resistance. Significance: Disrupting CREB signaling in liver could provide therapeutic benefit against insulin resistance. Under fasting conditions, increases in circulating concentrations of glucagon maintain glucose homeostasis via the induction of hepatic gluconeogenesis. Triggering of the cAMP pathway in hepatocytes stimulates the gluconeogenic program via the PKA-mediated phosphorylation of CREB and dephosphorylation of the cAMP-regulated CREB coactivators CRTC2 and CRTC3. In parallel, decreases in circulating insulin also increase gluconeogenic gene expression via the de-phosphorylation and activation of the forkhead transcription factor FOXO1. Hepatic gluconeogenesis is increased in insulin resistance where it contributes to the attendant hyperglycemia. Whether selective activation of the hepatic CREB/CRTC pathway is sufficient to trigger metabolic changes in other tissues is unclear, however. Modest hepatic expression of a phosphorylation-defective and therefore constitutively active CRTC2S171,275A protein increased gluconeogenic gene expression under fasting as well as feeding conditions. Circulating glucose concentrations were constitutively elevated in CRTC2S171,275A-expressing mice, leading to compensatory increases in circulating insulin concentrations that enhance FOXO1 phosphorylation. Despite accompanying decreases in FOXO1 activity, hepatic gluconeogenic gene expression remained elevated in CRTC2S171,275A mice, demonstrating that chronic increases in CRTC2 activity in the liver are indeed sufficient to promote hepatic insulin resistance and to disrupt glucose homeostasis.
Magnetic Immuno-PCR Assay with Inhibitor Removal for Direct Detection of Helicobacter pylori in Human Feces

ABSTRACT A PCR protocol was developed to detect Helicobacter pylori in human stool specimens. This protocol was based on the association of a magnetic immuno-PCR assay with a technique to remove inhibitors (agarose-embedded DNA preparation). Of the 47 H. pylori-positive and 57 H. pylori-negative patients included in this study, 38 were positive and 66 were negative by this new protocol. The sensitivity, specificity, and predictive values for a positive or a negative result were 80.9% (95% confidence interval [CI], 66.3 to 90.4), 100% (95% CI, 92.1 to 100), 100% (95% CI, 88.6 to 100), and 86.4% (95% CI, 75.2 to 93.2), respectively.
Interplay between IFN-γ and IL-6 signaling governs neutrophil trafficking and apoptosis during acute inflammation

Regulated recruitment and clearance of neutrophils (PMN) is the hallmark of competent host defense and resolution of inflammation. We now report that IFN-gamma controls PMN infiltration and modulates IL-6 signaling through its soluble receptor (sIL-6R) to promote their apoptosis and clearance. Induction of peritoneal inflammation in IFN-gamma-deficient (IFN-gamma-/-) mice emphasized that the initial rate of PMN recruitment was impaired. This defect in PMN recruitment was also associated with the suppressed intraperitoneal expression of IL-1beta and IL-6. Reconstitution of IFN-gamma signaling restored the rate of PMN infiltration and IL-6 levels and was accompanied by normalization of PMN-activating CXC chemokine expression. To test whether local IL-6 signaling modulated PMN recruitment, inflammation was induced in IFN-gamma-/- and IL-6-/- mice and cytokine signaling adapted by intraperitoneal sIL-6R-IL-6 fusion protein (HYPER-IL-6) or IFN-gamma. Although HYPER-IL-6 attenuated PMN influx in IFN-gamma-/- mice, IFN-gamma had no effect on PMN infiltration in IL-6-/- mice. Examination of the leukocyte infiltrate from IFN-gamma-/-, IL-6-/-, and wild-type mice showed that apoptosis was aberrant in the absence of IFN-gamma and IL-6 as a result of impaired sIL-6R signaling. These data emphasize a pivotal role for IFN-gamma in regulating innate immunity through control of both the recruitment and clearance phases of PMN trafficking.
Mixed analog-digital fuzzy logic controller with continuous-amplitude fuzzy inferences and defuzzification

A fuzzy logic controller has been realized using mixed analog-digital CMOS very large scale integration (VLSI) circuits for application in cases where the input and output variables are in analog form. It employs a new architecture where time sweeping of variables allows continuous-amplitude evaluation of fuzzy inferences and defuzzification during each evaluation cycle without having to discretize input and output variables. Direct processing of the analog input signal is used to obtain the corresponding crisp value; the digital portion is used only for programmability. No A/D and D/A converters are needed. The controller can handle three inputs, one output, and 25 programmable fuzzy rules. The test IC chips were fabricated using 0.7-/spl mu/m CMOS technology. A control problem of stabilizing a ping-pong ball in a tube with a controllable air flow has been successfully demonstrated.
Standardized Patient Encounters: Periodic Versus Postencounter Evaluation of Nontechnical Clinical Performance

Introduction Standardized patients are a beneficial component of modern healthcare education and training, but few studies have explored cognitive factors potentially impacting clinical skills assessment during standardized patient encounters. This study examined the impact of a periodic (vs. traditional postencounter) evaluation approach and the appearance of critical verbal and nonverbal behaviors throughout a standardized patient encounter on scoring accuracy in a video-based scenario. Methods Forty-nine standardized patients scored either periodically or at only 1 point in time (postencounter) a healthcare provider’s verbal and nonverbal clinical performance during a videotaped standardized patient encounter. The healthcare provider portrayed in this study was actually a standardized patient delivering carefully scripted verbal and nonverbal behaviors in their portrayal of an actual physician. The encounter itself was subdivided into 3 distinct segments for the purpose of supporting periodic evaluation, with the expectation that both verbal and nonverbal cues occurring in the middle segment would be more challenging to accurately report for participants in the postscenario evaluation group as a result of working memory decay. Results Periodic evaluators correctly identified a significantly greater number of critical verbal cues midscenario than postencounter evaluators (P < 0.01) and correctly identified a significantly greater number of critical nonverbal cues than their postscenario counterparts across all 3 scenario segments (P < 0.001). Further, postscenario evaluations exhibited a performance decrement in terms of midscenario correct identifications that periodic evaluators did not (P < 0.01). Also, periodic evaluators exhibited fewer verbal cue false-positives during the first segment of the scenario than postscenario evaluators (P < 0.001), but this effect did not extend to other segments regardless of the cue type (ie, verbal or nonverbal). Discussion Pausing lengthier standardized patient encounters periodically to allow for more frequent scoring may result in better reporting accuracy for certain clinical behavioral cues. This could enable educators to provide more specific formative feedback to individual learners at the session’s conclusion. The most effective encounter design will ultimately depend on the specific goals and training objectives of the exercise itself.
A Methodology for Deriving Tissue Residue Benchmarks for Aquatic Biota: A Case Study for Fish Exposed to 2,3,7,8-Tetrachlorodibenzo- p-Dioxin and Equivalents

Abstract Tissue residue-based toxicity benchmarks (TRBs) have typically been developed using the results of individual studies selected from the literature. In the past, TRBs have been developed using a point estimate (e.g., LC50 value) reported in a study on a single species deemed to be most closely related to the receptor of interest. Despite attempts to maximize the protectiveness and relevance of TRBs, their relationship to specific receptors remains uncertain, and their general applicability for use in broader ecological risk assessment contexts is limited. This article proposes a novel framework that establishes benchmarks as distributions rather than single-point estimates. Benchmark distributions allow the user to select a tissue concentration that is associated with the protection of a specific percentage of organisms, rather than linked to a specific receptor. A methodology is proposed for searching, reviewing, and analyzing linked, tissue residue effect data to derive benchmark distributions. The approach is demonstrated for contaminants having a dioxin-like mechanism of toxic action and is based on residue effects data for 2,3,7,8-tetrachlorodibenzo- p-dioxin (2,3,7,8-TCDD) and equivalents in early life stage fish. The calculated tissue residue benchmarks for 2,3,7,8-TCDD toxic equivalency (TEQ) derived from the resulting distribution could range from 0.057- to 0.699-ng TCDD/g lipid depending on the level of protection needed; the lower estimate is protective of 99% of fish species whereas the higher end is protective of 90% of fish species.
Role of PCR in Diagnosis and Prognosis of Visceral Leishmaniasis in Patients Coinfected with Human Immunodeficiency Virus Type 1

ABSTRACT A group of 76 consecutive human immunodeficiency virus (HIV)-positive patients with fever of unknown origin (n = 52) or fever associated with pulmonary diseases was evaluated in order to assess the usefulness of PCR with peripheral blood in the diagnosis and follow-up of visceral leishmaniasis. We identified 10 cases of visceral leishmaniasis among the 52 patients with fever of unknown origin. At the time of diagnosis, all were parasitemic by PCR with peripheral blood. During follow-up, a progressive decline in parasitemia was observed under therapy, and all patients became PCR negative after a median of 5 weeks (range, 6 to 21 weeks). However, in eight of nine patients monitored for a median period of 88 weeks (range, 33 to 110 weeks), visceral leishmaniasis relapsed, with positive results by PCR with peripheral blood reappearing 1 to 2 weeks before the clinical onset of disease. Eight Leishmania infantum and two Leishmania donovani infections were identified by PCR-restriction fragment length polymorphism analysis. PCR with peripheral blood is a reliable method for diagnosis of visceral leishmaniasis in HIV-infected patients. During follow-up, it substantially reduces the need for traditional invasive tests to assess parasitological response, while a positive PCR result is predictive of clinical relapse.
Proteomic Characterization of Phagosomal Membrane Microdomains During Phagolysosome Biogenesis and Evolution*

After their formation at the cell surface, phagosomes become fully functional through a complex maturation process involving sequential interactions with various intracellular organelles. In the last decade, series of data indicated that some of the phagosome functional properties occur in specialized membrane microdomains. The molecules associated with membrane microdomains, as well as the organization of these structures during phagolysosome biogenesis are largely unknown. In this study, we combined proteomics and bioinformatics analyses to characterize the dynamic association of proteins to maturing phagosomes. Our data indicate that groups of proteins shuffle from detergent-soluble to detergent-resistant membrane microdomains during maturation, supporting a model in which the modulation of the phagosome functional properties involves an important reorganization of the phagosome proteome by the coordinated spatial segregation of proteins.
The global economic costs of substituting dietary protein from fish with meat, grains and legumes, and dairy

This paper estimates the costs to replace fish by protein from meat, from grains and legumes, or from dairy products. We apply the World Trade Model, an input–output model of the interactions among major world regions based on comparative advantage, to analyze alternative scenarios about protein content and sources in global diets. We find that the substitution of fish by meat or dairy entails several trillion U.S. dollars of additional costs annually, corresponding to increased use of pastureland, cropland, water, and other factors of production. The price of animal products increases steeply as higher‐cost producers need to come online, yielding rents to owners of scarce resources. By contrast, the global economy adjusts at significantly lower costs to the substitution of fish by grains and legumes, but this dietary shift involves substantial modification in the mix of agricultural output and its geographic distribution. There have been few analytic studies able to associate costs and prices directly with specific combinations of dietary options. We provide a flexible economic framework for analyzing alternative scenarios about the present and future production of food. The focus on the provision of protein for the human diet, allowing for substitutions between land‐based and aquatic sources, lays the groundwork for subsequent closer examinations of the potential future contribution of aquaculture and, in a yet broader framework, the impact of the coming generation of large dams on fish habitat and freshwater ecosystems more generally.