Miracle-dz/UniFAR-FTUs huggingface dataset:
Palaeo‐islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae)

Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within‐island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable ‘palaeo‐islands’ of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra‐island levels of genetic diversity larger than those between‐islands. We argue that volcanic eruptions and landslides after the merging of the palaeo‐islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo‐islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.
Cre recombinase‐mediated site‐specific modification of a cellular genome using an integrase‐defective retroviral vector

Retroviral integrase is an enzyme responsible for the integration of retroviruses. A single mutation in the integrase core domain can severely compromise its integration ability, leading to the accumulation of circular retroviral cDNA in the nuclei of infected cells. We therefore attempted to use those cDNA as substrates for Cre recombinase to perform a recombinase‐mediated cassette exchange (RMCE), thereby targeting retroviral vectors to a predetermined site. An expression unit containing a promoter, an ATG codon and marker genes (hygromycin resistance gene and red fluorescent protein gene) flanked by wild‐type and mutant loxP sites was first introduced into cellular chromosome to build founder cell lines. We then constructed another plasmid for the production of integrase‐defective retroviral vectors (IDRV), which contains an ATG‐deficient neomycin resistance gene and green fluorescent protein gene, flanked by a compatible pair of loxPs. After providing founder cells with Cre and infecting with IDRV later, effective RMCE occurred, resulting in the appearance of G418‐resistant colonies and a change in the color of fluorescence from red to green. Southern blot and PCR analyses on selected clones further confirmed site‐specific recombination. The successful substitution of the original viral integration machinery with a non‐viral mechanism could expand the application of retroviral vectors. Biotechnol. Bioeng. 2010;107:717–729. © 2010 Wiley Periodicals, Inc.
The Feasibility of Using the Spanish PHQ-9 to Screen for Depression in Primary Care in Honduras.

BACKGROUND: The Patient Health Questionnaire depression module (PHQ-9) is a brief (10 items) screening and monitoring measure designed for use in primary care settings that operationalizes most of the DSM-IV and ICD-9 diagnostic criteria for major depression. In the United States, the PHQ-9 has become the recommended depression measure in primary care settings. However, there are no published reports of its use in developing countries and no reports of the feasibility of using the Spanish version of the PHQ-9 to screen for depression. METHOD: During a medical brigade in October 2001, we tested the feasibility of using the Spanish PHQ-9 to screen for major depression in primary care clinics. A team of U.S. and Honduran physicians and medical students assessed 199 mothers of children under 10 years of age as part of a depression prevalence study in 5 rural sites. RESULTS: The PHQ-9 proved easy to administer to this population of poor, rural, young, and mostly illiterate Honduran women who had never participated in research before. Rater training required about 30 minutes of instruction for this group of physicians and medical students, plus occasional questions on the first day of use. Duration of administration of the PHQ-9 by interview ranged from 3 to 15 minutes. No items required major modification for cultural differences. The PHQ-9 identified a rate of 15% for major depression in this sample, and the PHQ-9 results showed a sensitivity of 77% and a specificity of 100% compared with the Structured Clinical Interview for DSM-IV mood disorders module. CONCLUSION: Like the English PHQ-9, the Spanish PHQ-9 is an efficient and reliable screening measure for major depression in primary care. It is useful as a research measure for estimating the prevalence of major depression and as an aid to the primary care clinician in rural Honduras.
The Importance of Wild Canids in the Epidemiology of Rabies in Northeast Brazil: A Retrospective Study

Rabies is an endemic disease in Brazil, where it is considered a serious public health problem. Although the number of human and dog‐transmitted cases has declined in recent decades, rabies in wildlife has emerged considerably. Among the sylvatic animals, wild canids have been considered important hosts of the rabies virus. We performed a retrospective study of reported cases of rabies in wild canids and human victims in Ceará state (Northeast Brazil) during 2003 to 2013. Information was provided by governmental laboratories involved in rabies detection and by the Ministry of Health. From January 2003 to December 2013, a total of 11 931 animal samples were examined for rabies. Positivity were detected in 438 samples (3.67%), of which 229 (52.28%) were domestic animals, 105 (23.97%) wild canids and 104 (23.74%) other wild animals (bats, marmosets and raccoons). Approximately 33% of wild canids surveyed (n = 317) were positive for rabies. During the studied period, a total of 1923 attacks on humans by wild canids were registered. Males (n = 1405) were more affected than females (n = 520; 72.98% versus 27.01%), and the median age of all cases was 36.5 years. Injuries to individuals up to 19 years old corresponded to approximately 30% (n = 565) of all cases. Most of the victims lived in rural areas (72.46%; n = 1395), and the majority showed bites (81.13%; n = 1677) or scratches (12.23%; n = 253). Injuries were considered profound (52.1%; n = 1003), superficial (40.91; n = 788) or multiple with severe laceration (6.98%; n = 134). Only 1300 (67.53%) victims were enrolled for the complete rabies post‐exposure prophylaxis scheme. Data from the present study confirm that wild canids are important hosts of rabies virus in northeastern Brazil and jeopardize rabies control in this area. Local authorities should focus their efforts in education of health professionals. In addition, strategies should be formulated to preserve wildlife.
Demographic history inferred from genome‐wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic

The Malvinas/Falkland Islands (MFI) constitute the largest archipelago in the southern Atlantic, and harbour endemic lineages that presumably evolved after sea‐level rise, associated with glacial periods, isolated ancestral populations. We investigate the role of the MFI in isolating populations from continental counterparts of two highly vagile species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps.
The use of Taqman genotyping assays for rapid confirmation of β‐thalassaemia mutations in the Malays: accurate diagnosis with low DNA concentrations

In Malaysia, β‐thalassaemia is a common inherited blood disorder in haemoglobin synthesis with a carrier rate of 4.5%. Currently, PCR‐incorporating techniques such as amplification refractory mutation system (ARMS) or reverse dot blot hybridization (RDBH) are used in β‐thalassaemia mutation detection. ARMS allows single‐mutation identification using two reactions, one for wild type and another for mutant alleles. RDBH requires probe immobilization and optimization of hybridization and washing temperatures which is time consuming. The aim of our study was to investigate whether β‐thalassaemia mutations can be identified in samples with low DNA concentrations.
Relaxation and physical aging in network glasses: a review

Recent progress in the description of glassy relaxation and aging are reviewed for the wide class of network-forming materials such as GeO2, GexSe1−x, silicates (SiO2–Na2O) or borates (B2O3–Li2O), all of which have an important usefulness in domestic, geological or optoelectronic applications. A brief introduction of the glass transition phenomenology is given, together with the salient features that are revealed both from theory and experiments. Standard experimental methods used for the characterization of the slowing down of the dynamics are reviewed. We then discuss the important role played by aspects of network topology and rigidity for the understanding of the relaxation of the glass transition, while also permitting analytical predictions of glass properties from simple and insightful models based on the network structure. We also emphasize the great utility of computer simulations which probe the dynamics at the molecular level, and permit the calculation of various structure-related functions in connection with glassy relaxation and the physics of aging which reveal the non-equilibrium nature of glasses. We discuss the notion of spatial variations of structure which leads to the concept of ‘dynamic heterogeneities’, and recent results in relation to this important topic for network glasses are also reviewed.
Home Monitoring in Asthma Self-Management

Peak flow monitoring of asthma came into vogue with the advent of asthma self-management programs. Because it offered an objective way to gauge asthma severity, it promised improvement in the accuracy of asthma monitoring over that attainable by symptom monitoring. This promise has not been fulfilled. The ensuing years have witnessed a debate concerning the relative merits of symptom and peak flow monitoring. The debate has focused both on the degree to which peak flow and symptom scores are related to one another and on the relative effectiveness of symptom and peak flow monitoring for asthma control. We review research relating to these topics. The work shows that the strength of the relationship between peak flow and symptoms is low to moderate and varies between individuals and that benefits of peak flow monitoring in asthma self-management provide, at best, no more than a small increment in effectiveness beyond that afforded by symptom monitoring.
Sexual Dimorphism of Pancreatic Gene Expression in Normal Mice

A differential pancreatic behavior observed between male and female mice in diabetes and pancreatitis led us to study the gene and protein expressions of endocrine and exocrine pancreatic proteins in normal mice. We compared the levels of expression of six pancreatic genes and of four of the corresponding proteins in male and female mice OF1. Amylase gene expression was found to be significantly higher in females than in males, whereas trypsinogen and lipase gene expression were significantly lower. For chymotrypsinogen, reg, and insulin the differences were not significant. This sexual dimorphism did not exist in rat pancreas, where no gender difference was observed. After characterization of mice enzymes by sodium dodecylsulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and antibodies directed to the closely related human pancreatic enzymes, we have compared the levels of these proteins in mice pancreatic homogenates. No significant difference was observed between males and females at the level of protein expression. These data suggest a hormonal sexual difference in the regulation of pancreatic protein synthesis at the pre-and posttranscriptional levels in normal mice, which may play a role in the development of mice pancreatic diseases.
Intermittent high-volume hemofiltration promotes remission in steroid-resistant idiopathic nephrotic syndrome

Abstract Inflammation is a key part in the etiology and progression of idiopathic nephrotic syndrome (INS), we hypothesize that removing pro-inflammatory cytokines with intermittent high-volume hemofiltration (IHVHF) could improve the outcome in INS patients. The purpose of the current study is to examine whether IHVHF promotes remission in steroid-resistant INS. Fifty-one steroid-resistant INS patients were followed up on an open-label basis with prospective evaluations. Thirty-five patients received mycophenolate mofetil (SRD group) and 16 patients received drugs and IHVHF due to volume overload despite of diuretics (SRDF group). The rate of complete remission (CR) was analyzed. We also recruited 30 healthy individuals and 36 steroid-sensitive (SS) INS patients as controls to investigate the correlation of interleukin (IL)-8, IL-10, IL-6 and IL-17 with INS activity. Compared with the patients in the SRD group, the 6-month CR rate was higher (44% vs. 9%, p < 0.001) and time to first CR was significantly shorter (7.3 ± 3.6 vs. 11.1 ± 5.3 months, p = 0.02) in the SRDF group. Serum IL-8 was highest in the SRDF group and reduced by IHVHF clearance. Serum IL-8 was lower during remission than at onset or recurrence of INS, whereas no significant difference was seen in the other cytokines. Receiver operating characteristic curve analysis demonstrated that serum IL-8 predicted steroid sensitivity with moderate accuracy (area under the curve = 0.79, 95% CI: 0.69–0.87). IHVHF promotes remission in patients with steroid-resistant INS and it may be partly due to serum IL-8 clearance.
Experience in the use of clobazam in the treatment of Lennox–Gastaut syndrome

Clobazam is a 1,5-benzodiazepine used successfully worldwide since the 1970s as an anxiolytic and antiepileptic drug. Since its recent Food and Drug Administration (FDA) approval in the United States in 2011 as adjunctive treatment for Lennox–Gastaut syndrome, it has continued to show sustained efficacy and a better safety and tolerability profile compared with other benzodiazepines. The two randomized, controlled studies that led to the US FDA approval, as well as the follow-up multicenter, open-label study of clobazam, showed ≥50% seizure reduction for more than 50% of Lennox–Gastaut syndrome patients, while none of the other FDA-approved treatments for LGS have demonstrated efficacy rates better than 50%. Clobazam appears to have a safe profile and sustained effectiveness over the first 3 years of use in LGS and other epilepsy syndromes with intractable seizures, which makes it a viable long-term treatment option.
On the use of convex optimization for electromagnetic near-field shaping

Near-field shaping at microwave or millimeter wave frequencies is an emerging field of study, able to accelerate a variety of technologies. Applications from sensing to medical imaging will benefit from accurate near-field shaping methods. In this communication, the use of convex optimization to shape the near field of a flat radiating aperture is investigated. The proposed approach, that is known to provide optimal solutions, is compared to existing near-field shaping methods.
A spatio-temporal reconstruction algorithm for diffuse optical tomography based on a hemodynamic response function model

Diffuse optical tomography (DOT) can reconstruct localized changes in oxy- and deoxygenated hemoglobin concentrations in tissue, and is an effective technique for functional brain imaging. To recover the spatial distribution and temporal variation of changes evoked by brain activation, an inverse solution for a joint spatio-temporal reconstruction is proposed, in contrast to traditional methods which treat the problem independently at each time instant. We use a hemodynamic response function model patterned after fMRI. The DOT setting is more complicated than fMRI however, and we describe required extensions of this model. Simulation results show improvement in spatial resolution and contrast-to-noise ratio over traditional frame-by-frame reconstruction even after posterior fitting with same temporal prior
Detecting Contrastive Sentences for Sentiment Analysis

Contradiction Analysis is a relatively new multidisciplinary and complex area with the main goal of identifying contradictory pieces of text. It can be addressed from the perspectives of different research areas such as Natural Language Processing, Opinion Mining, Information Retrieval, and Information Extraction. This work focuses on the problem of detecting sentiment-based contradictions which occur in the sentences of a given review text. Unlike other types of contradictions, the detection of sentiment-based contradictions can be tackled as a post-processing step in the traditional sentiment analysis task. In this context, we make two main contributions. The first is an exploratory study of the classification task, in which we identify and use different tools and resources. Our second contribution is adapting and extending an existing contradiction analysis framework by filtering its results to remove the reviews that are erroneously labeled as contradictory. The filtering method is based on two simple term similarity algorithms. An experimental evaluation on real product reviews has shown proportional improvements of up to 30% in classification accuracy and 26% in the precision of contradiction detection.
Effects of mean airway pressure and tidal volume on lung and chest wall mechanics in the dog.

Dependencies of the dynamic mechanical properties of the respiratory system on mean airway pressure (Paw) and the effects of tidal volume (VT) are not completely clear. We measured resistance and dynamic elastance of the total respiratory system (Rrs and Ers), lungs (RL and EL), and chest wall (Rcw and Ecw) in six healthy anesthetized paralyzed dogs during sinusoidal volume oscillations at the trachea (50-300 ml; 0.4 Hz) delivered at mean Paw from -9 to +23 cmH2O. Changes in end-expiratory lung volume, estimated with inductance plethysmographic belts, showed a typical sigmoidal relationship to mean Paw. Each dog showed the same dependencies of mechanical properties on mean Paw and VT. All elastances and resistances were minimal between 5 and 10 cmH2O mean Paw. All elastances, Rrs, and RL increased greatly with decreasing Paw below 5 cmH2O. Ers and EL increased above 10 cmH2O. Ecw, Ers, Rcw, and Rrs decreased slightly with increasing VT, but RL and EL were independent of VT. We conclude that 1) respiratory system impedance is minimal at the normal mean lung volume of supine anesthetized paralyzed dogs; 2) the dependency of RL on lung volume above functional residual capacity is dependent on VT and respiratory frequency; and 3) chest wall, but not lung, mechanical behavior is nonlinear (i.e., VT dependent) at any given lung volume.
ℋ︁‐matrix preconditioners for symmetric saddle‐point systems from meshfree discretization

Meshfree methods are suitable for solving problems on irregular domains, avoiding the use of a mesh. To deal with the boundary conditions, we can use Lagrange multipliers and obtain a sparse, symmetric and indefinite system of saddle‐point type. Many methods have been developed to solve the indefinite system. Previously, we presented an algebraic method to construct an LU‐based preconditioner for the saddle‐point system obtained by meshfree methods, which combines the multilevel clustering method with the ℋ︁‐matrix arithmetic. The corresponding preconditioner has both ℋ︁‐matrix and sparse matrix subblocks. In this paper we refine the above method and propose a way to construct a pure ℋ︁‐matrix preconditioner. We compare the new method with the old method, JOR and smoothed algebraic multigrid methods. The numerical results show that the new preconditioner outperforms the preconditioners based on the other methods. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis and Design of a 195.6 dBc/Hz Peak FoM P-N Class-B Oscillator With Transformer-Based Tail Filtering

A complementary p-n class-B oscillator with two magnetically coupled second harmonic tail resonators is presented and compared to an N-only reference one. An in depth analysis of phase noise, based on direct derivation of the Impulse Sensitivity Function (ISF), provides design insights on the optimization of the tail resonators. In principle the complementary p-n oscillator has the same optimum Figure of Merit (FoM) of the N-only at half the voltage swing. At a supply voltage of 1.5 V, the maximum allowed oscillation amplitude of the N-only is constrained, by reliability considerations, to be smaller than the value that corresponds to the optimum FoM even when 1.8 V thick oxide transistors are used. For an oscillation amplitude that ensures reliable operation and the same tank, the p-n oscillator achieves a FoM 2 to 3 dB better than the N, only depending on the safety margin taken in the design. After frequency division by 2, the p-n oscillator has a measured phase noise that ranges from -150.8 to -151.5 dBc/Hz at 10 MHz offset from the carrier when the frequency of oscillation is varied from 7.35 to 8.4 GHz. With a power consumption of 6.3 mW, a peak FoM of 195.6 dBc/Hz is achieved.
A Limited Group of Class I Histone Deacetylases Acts To Repress Human Immunodeficiency Virus Type 1 Expression

ABSTRACT Silencing of the integrated human immunodeficiency virus type 1 (HIV-1) genome in resting CD4+ T cells is a significant contributor to the persistence of infection, allowing the virus to evade both immune detection and pharmaceutical attack. Nonselective histone deacetylase (HDAC) inhibitors are capable of inducing expression of quiescent HIV-1 in latently infected cells. However, potent global HDAC inhibition can induce host toxicity. To determine the specific HDACs that regulate HIV-1 transcription, we evaluated HDAC1 to HDAC11 RNA expression and protein expression and compartmentalization in the resting CD4+ T cells of HIV-1-positive, aviremic patients. HDAC1, -3, and -7 had the highest mRNA expression levels in these cells. Although all HDACs were detected in resting CD4+ T cells by Western blot analysis, HDAC5, -8, and -11 were primarily sequestered in the cytoplasm. Using chromatin immunoprecipitation assays, we detected HDAC1, -2, and -3 at the HIV-1 promoter in Jurkat J89GFP cells. Targeted inhibition of HDACs by small interfering RNA demonstrated that HDAC2 and HDAC3 contribute to repression of HIV-1 long terminal repeat expression in the HeLa P4/R5 cell line model of latency. Together, these results suggest that HDAC inhibitors specific for a limited number of class I HDACs may offer a targeted approach to the disruption of persistent HIV-1 infection.