Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining Sex of Magellanic Penguins Using Molecular Procedures and Discriminant Functions

Abstract Magellanic Penguins (Spheniscus magellanicus) show little sexual dimorphism, and although males are usually larger than females, sexing by direct observation may be difficult, especially in the case of chicks. In this paper we evaluate the utility of four different PCR-based sex determination techniques using genomic DNA for sexing Magellanic Penguins. We found that the primer set designed for sex determination in Collared Flycatcher (Ficedula albicollis) also provided a reliable, simple and convenient sexing procedure for Magellanic Penguins. Additionally, we obtained discriminant functions for sexing adults and chicks, sampled at six colonies differing in size and other ecological characteristics. Discriminant function for adults used two variables, bill length and bill depth that correctly classified 97% of the birds. Discriminant function for chicks included bill length and flipper length and correctly classified 78% of the individuals. Although molecular and biometric approaches could be useful for sexing adult Magellanic Penguins, only molecular procedures proved appropriate for accurately sexing chicks.
What Happened, and Why: Toward an Understanding of Human Error Based on Automated Analyses of Incident Reports. Volume 1

The objective of the Aviation System Monitoring and Modeling (ASMM) project of NASA s Aviation Safety and Security Program was to develop technologies that will enable proactive management of safety risk, which entails identifying the precursor events and conditions that foreshadow most accidents. This presents a particular challenge in the aviation system where people are key components and human error is frequently cited as a major contributing factor or cause of incidents and accidents. In the aviation "world", information about what happened can be extracted from quantitative data sources, but the experiential account of the incident reporter is the best available source of information about why an incident happened. This report describes a conceptual model and an approach to automated analyses of textual data sources for the subjective perspective of the reporter of the incident to aid in understanding why an incident occurred. It explores a first-generation process for routinely searching large databases of textual reports of aviation incident or accidents, and reliably analyzing them for causal factors of human behavior (the why of an incident). We have defined a generic structure of information that is postulated to be a sound basis for defining similarities between aviation incidents. Based on this structure, we have introduced the simplifying structure, which we call the Scenario as a pragmatic guide for identifying similarities of what happened based on the objective parameters that define the Context and the Outcome of a Scenario. We believe that it will be possible to design an automated analysis process guided by the structure of the Scenario that will aid aviation-safety experts to understand the systemic issues that are conducive to human error.
Reinforcement versus Fluidization in Cytoskeletal

Every adherent eukaryotic cell exerts appreciable traction forces upon its substrate. Moreover, every resident cell within the heart, great vessels, bladder, gut or lung routinely experiences large periodic stretches. As an acute response to such stretches the cytoskeleton can stiffen, increase traction forces and reinforce, as reported by some, or can soften and fluidize, as reported more recently by our laboratory, but in any given circumstance it remains unknown which response might prevail or why. Using a novel nanotechnology, we show here that in loading conditions expected in most physiological circumstances the localized reinforcement response fails to scale up to the level of homogeneous cell stretch; fluidization trumps reinforcement. Whereas the reinforcement response is known to be mediated by upstream mechanosensing and downstream signaling, results presented here show the fluidization response to be altogether novel: it is a direct physical effect of mechanical force acting upon a structural lattice that is soft and fragile. Cytoskeletal softness and fragility, we argue, is consistent with early evolutionary adaptations of the eukaryotic cell to material properties of a soft inert microenvironment. Citation: Krishnan R, Park CY, Lin Y-C, Mead J, Jaspers RT, et al. (2009) Reinforcement versus Fluidization in Cytoskeletal Mechanoresponsiveness. PLoS ONE 4(5): e5486. doi:10.1371/journal.pone. 0005486 Editor: Rainer Heintzmann, Kings College London, United Kingdom Received January 22, 2009; Accepted April 2, 2009; Published May 8, 2009 Copyright: 2009 Krishnan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: NIH RO1 HL 084224 (Fredberg); NIH RO1 HL65960 (Fredberg). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: jfredber@hsph.harvard. edu
Sialylation may be dispensable for reciprocal modulation of helper T cells by intravenous immunoglobulin

Several mechanisms account for the beneficial effect of intravenous immunoglobulin (IVIg) in autoimmune and inflammatory diseases. These mechanisms include effects on the cellular compartment and on the humoral compartment. Thus, IVIg impacts on dendritic cells, macrophages, neutrophils, basophils, NK cells, and B and T lymphocytes. Several studies have emphasized that the antiinflammatory effect of IVIg is dependent on α2,6‐sialylation of the N‐linked glycan on asparagine‐297 of the Fc portion of IgG. However, recent reports have questioned the necessity of sialylated Fc and the role of FcγRIIB in IVIg‐mediated antiinflammatory effects. In view of the critical role played by Th17 cells in several autoimmune pathologies and the increasing use of IVIg in several of these conditions, by using neuraminidase‐treated, desialylated IVIg, we addressed whether the α2,6‐sialylation of IgG is essential for the beneficial effect of IVIg in experimental autoimmune encephalomyelitis (EAE), a Th17‐driven condition, and for the reciprocal modulation of helper T‐cell subsets. We observed no difference in the ability of IVIg to ameliorate EAE irrespective of its sialylation. Our findings thus show that sialylation of IVIg is not necessary for IVIg‐mediated amelioration of EAE or for downregulation of Th17 cells and upregulation of regulatory T cells.
Nodulation and nitrogen fixation of field grown common bean (Phaseolus vulgaris) as influenced by fungicide seed treatment

A field experiment was conducted at Bel Air station, in Dakar using 15N isotope dilution technique and the non nodulating soybean (Glycine max) variety m129 as reference plant to test the compatibility of Dichlorofenthion-thiram (DCT) fungicide to the inoculation of common bean (Phaseolus vulgaris) Paulista variety with both Rhizobium etli ISRA 353 and R. tropici strain ISRA 554. Nodulation was not induced with R. etli ISRA 353 and nitrogen fixation did not occur. With R. tropici ISRA 554, a decrease in nodulation was observed, but nitrogen fixation was not significantly different compared to that of the non DCT-treated common bean. (African Journal of Biotechnology: 2003 2(7): 198-201)
Role of the Intronic Enhancer in Tumor Necrosis Factor-mediated Induction of Manganous Superoxide Dismutase*

Manganous superoxide dismutase (Mn-SOD), a tumor necrosis factor (TNF)-inducible gene product, plays an important role in removing superoxide anions produced inside mitochondria. Two regulatory regions, the proximal promoter region (PPR), which is upstream from the transcription initiation site, and the TNF-responsive element (TNFRE), which is inside intron 2, are responsible for Mn-SOD expression. To understand how each of these regions contributes to the transcription of Mn-SOD, quantitative reverse transcription-PCR, chromatin immunoprecipitations, and in vivo nuclease sensitivity assays were performed on the murine Mn-SOD gene. These assays demonstrate that Sp1 and nuclear factor (NF)-κB p65 are required for Mn-SOD induction by TNF. Sp1 bound the PPR constitutively, whereas NF-κB p65 and C/EBP-β bound the TNFRE only after TNF treatment. Binding of C/EBP-β to the TNFRE was dependent on the presence of NF-κB p65. The chromatin structure within the TNFRE became more accessible to nuclease digestion after TNF treatment. This accessibility required Sp1 and NF-κB p65. Treatment of cells with an inhibitor of histone deacetylation, or transient transfection with coactivator-expressing plasmids, enhanced the expression of Mn-SOD. NF-κB p65 binding was required for acetylation of histones H3 and H4 at the PPR and the TNFRE. Together, these data suggest communication between the PPR and the TNFRE which involves chromatin remodeling and histone acetylation during the induction process of Mn-SOD in response to TNF.
The Impact of Incremental Strategic Information Systems Planning in an Uncertain Environment

The external environment plays a major role in the success or failure of many organizations. Researchers have suggested that more incremental strategic information systems planning (SISP) in an uncertain environment produces greater planning success. The purpose of this study was to test the effect of incremental SISP on planning success in environments of varying dynamism, heterogeneity, and hostility. Using five-point Likert-scales, a questionnaire operationalized SISP in terms of the characteristics of incremental planning; environmental uncertainty in terms of dynamism, heterogeneity, and hostility dimensions; and planning success as composed of alignment, analysis, cooperation, and capabilities factors. Five IS executives pilot tested the instrument. A postal survey then collected data from 161 IS executives. The constructs were extensively validated. In general, greater incrementalism in planning predicted less planning success, but dynamism moderated the impact of incremental SISP on SISP success whereas heterogeneity and hostility did not. These findings suggest that planners are more successful when shifting toward greater incrementalism in a more dynamic environment.
Molecular hybridization used to characterize the RNA synthesized by isolated bovine thymus nuclei.

In vitro synthesis of RNA by nuclei isolated from various tissues has been observed in many laboratories (1-3). Several investigators have realized the usefulness of isolated nuclei for studying the regulation of RNA synthesis. The effects of nuclear proteins (4) and various hormones, (5-7) for example, on the incorporation of various precursors into RNA have been analyzed recently. However, if the full potential of isolated nuclei as an assay system for studying the regulation of RNA synthesis is to be realized, then it is necessary that the characterization of the synthesized RNA be more complete. In the present studies, we have used the technique of DNA-RNA hybridization in an attempt to characterize the RNA synthesized in vitro by thymus nuclei. We have shown that the isolated thymus nucleus is capable of synthesizing a population of RNA molecules that is specific to thymus. The intracellular distribution of RNA species was also investigated and differences were found between nuclear RNA and cytoplasmic RNA. The isolated nucleus was shown to synthesize RNA similar to that found in the nucleus and in the cytoplasm.
THE EVOLUTION OF POSTREPRODUCTIVE LIFE SPAN AS AN INSURANCE AGAINST INDETERMINACY

Postreproductive life span remains a puzzle for evolutionary biologists. The explanation of increased inclusive fitness through parental care after reproduction that applies for humans is unrealistic for many species. We propose a new selective mechanism, independent of parental care, which relies on the hypothesis that postreproductive life span can evolve as an insurance against indeterminacy: longer life expectancy reduces the risk of dying by chance before the cessation of reproductive activity. We demonstrate numerically that the duration of evolved postreproductive life span is indeed expected to increase with variability in life span duration. An unprecedented assay of 11 strains of the collembola Folsomia candida shows the existence of (1) postreproductive life span in the absence of parental care; (2) genetic variability in mean postreproductive life span and postreproductive life span variability itself; (3) strong genetic correlation between latter traits. This new explanation brings along the novel idea that loose canalization of a trait (here, somatic life span) can itself act as a selective pressure on other traits.
Endovascular treatment of aortic pseudoaneurysm after liver transplantation

We report herein a case of a 59-year-old Caucasian female who experienced noninfected pseudoaneurysm, of the aorto-hepatic anastomosis of the jump graft, after third liver transplantation, that was successfully treated by endovascular aortic repair (EVAR). Three months after the third transplant characterized by arterial revascularization using the interposition of a cadaveric aorto-hepatic jump, with normal graft function, the patient complained of abdominal discomfort and tenderness; at laboratory exams only slight anemia was evident (Hb 1⁄4 9 g/dl). A spiral computed tomography (CT)-scan of the abdomen revealed the presence of a huge (8.5 cm of diameter) pseudoaneurysm of the aorto-hepatic jump at the level of the aortic anastomosis with the iliac cadaveric graft. The arterial jump was cranially thrombosed and no arterial blood flow to the liver could be detected at 3D CT-scan reconstruction. No local or systemic signs of infection were present. We treated the problem by a minimally invasive endovascular approach. The right femoral artery was surgically prepared and a 22 French introducer was inserted inside the arterial lumen. The controlateral femoral artery was cannulated by a five French catheter. An angiogram confirmed the presence of a huge pseudoaneurysm of the aortic wall at the level of the aorto-hepatic jump anastomosis (Fig. 1a). A 16 · 55 mm AneuRx stent-graft (Medtronic AVE, Santa Rosa, CA, USA) was inserted over an Amplatz super stiff guide wire (Boston Scientific Corporation, MA, USA). The stent-graft was released over the aortic wall defect after a control angiogram taken through the left femoral access. The stentgraft was dilated up to 25 mm by a percutaneous transluminal angioplasty (PTA) balloon (Cordis, J & J, FL, USA). The angiogram taken after the procedure (Fig. 1b) revealed a complete exclusion of the pseudoaneurismatic sac. The renal arteries were not involved in stent-graft positioning. The patient tolerated the procedure well; no
Isoflurane alters proximal tubular cell susceptibility to toxic and hypoxic forms of attack.

BACKGROUND Fluorinated anesthetics can profoundly alter plasma membrane structure and function, potentially impacting cell injury responses. Because major surgery often precipitates acute renal failure, this study assessed whether the most commonly used fluorinated anesthetic, isoflurane, alters tubular cell responses to toxic and hypoxic attack. METHODS Mouse proximal tubule segments were incubated under control conditions or with a clinically relevant isoflurane dose. Cell viability (lactate dehydrogenase release), deacylation (fatty acid, such as C20:4 levels), and adenosine triphosphate (ATP) concentrations were assessed under one or more of the following conditions: (a) exogenous phospholipase A2 (PLA2) or C20:4 addition, (b) Ca2+ overload (A23187 ionophore), (c) increased metabolic work (Na ionophore), and (d) hypoxia- or antimycin A-induced attack. Isoflurane's effect on NBD phosphatidylserine uptake (an index of plasma membrane aminophospholipid translocase activity) was also assessed. RESULTS Isoflurane alone caused trivial deacylation and no lactate dehydrogenase release. However, it strikingly sensitized to both PLA2- and A23187-induced deacylation and cell death. Isoflurane also exacerbated C20:4's direct membrane lytic effect. Under conditions of mild ATP depletion (Na ionophore-induced increased ATP consumption; PLA2-induced mitochondrial suppression), isoflurane provoked moderate/severe ATP reductions and cell death. Conversely, under conditions of maximal ATP depletion (hypoxia, antimycin), isoflurane conferred a modest cytoprotective effect. Isoflurane blocked aminophospholipid translocase activity, which normally maintains plasma membrane lipid asymmetry (that is, preventing its "flip flop"). CONCLUSIONS Isoflurane profoundly and differentially affects tubular cell responses to toxic and hypoxic attack. Direct drug-induced alterations in lipid trafficking/plasma membrane orientation and in cell energy production are likely involved. Although the in vivo relevance of these findings remains unknown, they have potential implications for intraoperative renal tubular cell structure/function and how cells may respond to superimposed attack.
Occurrence and Features of Childhood Myocarditis: A Nationwide Study in Finland

Background Epidemiology of myocarditis in childhood is largely unknown. Men are known to have a higher incidence of myocarditis than women in adults aged <50 years, but whether this is true by sex in pediatric age groups is unknown. We set out to study the occurrence and potential sex differences of myocarditis in a general pediatric population. Methods and Results Data of all hospital admissions with myocarditis in Finland occurring in patients aged ≤15 years from 2004 to 2014 were collected from a mandatory nationwide registry. All patients with myocarditis as a primary, secondary, or tertiary cause of admission were included. Total and age‐ and sex‐specific incidence rates were calculated using corresponding population data. There were 213 admissions with myocarditis in pediatric patients. Myocarditis was the primary cause of admission in 86%. The overall incidence rate of myocarditis was 1.95/100 000 person‐years. Of all patients, 77% were boys, but sex differences in incidence rates were age‐dependent. In children aged 0 to 5 years, there was no sex difference in the occurrence of myocarditis. Boys aged 6 to 10 years had a higher incidence rate compared with girls (72% boys; incidence rate ratio: 2.46; 95% confidence interval, 1.03–5.89; P=0.04). Sex difference further increased in children aged 11 to 15 years (80% boys; incidence rate ratio: 3.5; 95% confidence interval, 2.68–5.67; P<0.0001). Conclusions Myocarditis leading to hospital admission is relatively uncommon in children, but occurrence of myocarditis increases with age. There is no sex difference in the risk of myocarditis during the first 6 years of life, but boys have a significantly higher risk at ages 6 to 15 years.
Otitic Meningitis, Superior Semicircular Canal Dehiscence, and Encephalocele: A Case Series

Background Otitic meningitis in the postantibiotic era is still a serious condition, requiring intensive treatment and prolonged rehabilitation. In view of the significant morbidity and mortality rate, conditions that may increase the likelihood of otitic meningitis developing should be treated promptly. The incidence of meningitis after asymptomatic encephaloceles of the middle cranial fossa varies greatly, and the management differs between elective surgical repair and expectant careful observation. Superior semicircular canal dehiscences (SSCDs) are postulated to have a congenital origin and are associated with a thin or dehiscent tegmen. Several cases of simultaneous SCCD and tegmen defects have been reported, but the findings of otitic meningitis, SCCD, and encephaloceles has, to the best of our knowledge, not been previously explored in the literature. Methods We reviewed a series of 4 patients who all presented with a combination of otitic meningitis, encephaloceles, and SSCD. Results All the 4 patients we reviewed had meningitis secondary to otitis media with computed tomographic scans confirming the presence of SCCD with ipsilateral tegmen tympani defects and associated cephaloceles. All patients were treated with intravenous antibiotics and underwent surgery that ranged from myringotomy and ventilation tube insertions, mastoidectomy, and burr hole drainage for temporal lobe abscess. They were all associated with intensive care unit admission, significant morbidity, and prolonged hospital stays. There were no mortalities. Conclusion We propose that in all SSCD patients, a careful computed tomographic examination of the cranial base should be undertaken to exclude other associated tegmen tympani defects. In cases of SSCD requiring surgery, we support the view that elective surgical repair be recommended where asymptomatic ipsilateral encephaloceles are found, to reduce the risk of otitic meningitis.
Review of Previous Studies on Energy Utilization and Adaptation in Uganda

The level of development of a society can be measured not only in terms of quantity of goods and services but also from the energy consumed. The importance of energy security derives from the critical role that it plays in all aspects of livelihoods of any society. The Government of Uganda is committed to well-planned urbanization and effective management of urban growth. This brings issues of low income settlements to the forefront of the national development agenda under one umbrella, but the provision of energy services to meet demand in low income settlements remains a critical challenge. Low income settlements in the four urban areas in Uganda were identified and a survey of energy demand patterns was conducted. This paper adopts ordered logistic regression modelling integrated with factor analysis (principal components analysis) to explore: 1) the relative importance of variable factors in determining household energy utilization, and 2) how they shape adaptation to energy insecurity within and across low-income settlements in selected urban centres in Uganda. Results indicate that, although charcoal use is uniform across all households, a large percentage of the slum population is heavily dependent for its energy services on multiple energy sources. Furthermore, households are burdened with relatively high retail prices for energy, electricity instabilities and wood shortages and wasteful/inefficient energy use. The logistic model indicates that household size, the share of adults in the household and gender in combination explain the utilization of firewood and electricity. Furthermore, adaptation strategies to energy insecurity coalesce around self-generation and use of improved energy technologies, adjustments in cooking practices and energy substitutions, and adjustments in sleeping schedules. Urban areas in Uganda are the residences of the future and efforts aimed at building energy security are very important.