Miracle-dz/UniFAR-FTUs huggingface dataset:
How hazardous is the Sahara Desert crossing for migratory birds? Indications from satellite tracking of raptors

We investigated the risk associated with crossing the Sahara Desert for migrating birds by evaluating more than 90 journeys across this desert by four species of raptors (osprey Pandion haliaetus, honey buzzard Pernis apivorus, marsh harrier Circus aeruginosus and Eurasian hobby Falco subbuteo) recorded by satellite telemetry. Forty per cent of the crossings included events of aberrant behaviours, such as abrupt course changes, slow travel speeds, interruptions, aborted crossings followed by retreats from the desert and failed crossings due to death, indicating difficulties for the migrants. The mortality during the Sahara crossing was 31 per cent per crossing attempt for juveniles (first autumn migration), compared with only 2 per cent for adults (autumn and spring combined). Mortality associated with the Sahara passage made up a substantial fraction (up to about half for juveniles) of the total annual mortality, demonstrating that this passage has a profound influence on survival and fitness of migrants. Aberrant behaviours resulted in late arrival at the breeding grounds and an increased probability of breeding failure (carry-over effects). This study also demonstrates that satellite tracking can be a powerful method to reveal when and where birds are exposed to enhanced risk and mortality during their annual cycles.
Transdermal Buprenorphine for Central Neuropathic Pain: Clinical Reports

Transdermal buprenorphine is an effective analgesic for a variety of pain conditions. Traditionally, neuropathic pain is treated with medications such as tricyclic antidepressants or anticonvulsants, with opioid medications as second or third‐line agents. We present two different painful conditions of presumed neuropathic origin, with complex etiopathogenesis, which were successfully treated with buprenorphine. The results of treatment of these neuropathic pain syndromes with buprenorphine are encouraging, suggesting that it might represent a valid alternative to standard approaches for central neuropathic pain.
EPIDEMIOLOGICAL STUDIES ON RESPIRATORY INFECTIONS OF THE RABBIT

1. Four general types of spontaneous pneumonia, associated with strains of Bact. lepisepticum similar in biology and virulence, are described: (1) an acute, diffuse form, with subpleural and perivascular orientation of the exudate, (2) lobar, (3) pleuro-, and (4) abscess pneumonia. 2. The acute, diffuse, lobar, and pleuro pneumonias may be induced experimentally by intranasal instillation of a virulent strain of Bact. lepisepticum. 3. These same types occur when the organisms are inoculated intravenously, intratesticularly, and subcutaneously. 4. Intrabronchial insufflation of the organisms brings about infection in less than half of the animals. When effective, a sharply circumscribed, peribronchial lesion is found at the base of the lung, which spreads peripherally by direct extension, and generally by invasion of the blood stream. 5. It is concluded that differences in the types of pneumonia following infection with similar strains of Bact. lepisepticum depend upon the resistance of the animal, and that the usual portal of entry of this organism into the lungs, in cases of acute and lobar pneumonia, is by way of the blood stream.
An EM-like algorithm for color-histogram-based object tracking

The iterative procedure called 'mean-shift' is a simple robust method for finding the position of a local mode (local maximum) of a kernel-based estimate of a density function. A new robust algorithm is given here that presents a natural extension of the 'mean-shift' procedure. The new algorithm simultaneously estimates the position of the local mode and the covariance matrix that describes the approximate shape of the local mode. We apply the new method to develop a new 5-degrees of freedom (DOF) color histogram based non-rigid object tracking algorithm.
Usability processes in open source projects

We explore how some open source projects address issues of usability. We describe the mechanisms, techniques and technology used by open source communities to design and refine the interfaces to their programs. In particular we consider how these developers cope with their distributed community, lack of domain expertise, limited resources and separation from their users. We also discuss how bug reporting and discussion systems can be improved to better support bug reporters and open source developers. Copyright © 2006 John Wiley & Sons, Ltd.
An official American Thoracic Society statement: continuous positive airway pressure adherence tracking systems. The optimal monitoring strategies and outcome measures in adults.

BACKGROUND Continuous positive airway pressure (CPAP) is considered the treatment of choice for obstructive sleep apnea (OSA), and studies have shown that there is a correlation between patient adherence and treatment outcomes. Newer CPAP machines can track adherence, hours of use, mask leak, and residual apnea-hypopnea index (AHI). Such data provide a strong platform to examine OSA outcomes in a chronic disease management model. However, there are no standards for capturing CPAP adherence data, scoring flow signals, or measuring mask leak, or for how clinicians should use these data. METHODS American Thoracic Society (ATS) committee members were invited, based on their expertise in OSA and CPAP monitoring. Their conclusions were based on both empirical evidence identified by a comprehensive literature review and clinical experience. RESULTS CPAP usage can be reliably determined from CPAP tracking systems, but the residual events (apnea/hypopnea) and leak data are not as easy to interpret as CPAP usage and the definitions of these parameters differ among CPAP manufacturers. Nonetheless, ends of the spectrum (very high or low values for residual events or mask leak) appear to be clinically meaningful. CONCLUSIONS Providers need to understand how to interpret CPAP adherence tracking data. CPAP tracking systems are able to reliably track CPAP adherence. Nomenclature on the CPAP adherence tracking reports needs to be standardized between manufacturers and AHIFlow should be used to describe residual events. Studies should be performed examining the usefulness of the CPAP tracking systems and how these systems affect OSA outcomes.
A performance model for wormhole-switched interconnection networks under self-similar traffic

Many recent studies have convincingly demonstrated that network traffic exhibits a noticeable self-similar nature, which has a considerable impact on queuing performance. However, the networks used in current multicomputers have been primarily designed and analyzed under the assumption of the traditional Poisson arrival process, which is inherently unable to capture traffic self-similarity. Consequently, it is crucial to reexamine the performance properties of multicomputer networks in the context of more realistic traffic models before practical implementations show their potential faults. In an effort toward this end, we propose the first analytical model for wormhole-switched k-ary n-cubes in the presence of self-similar traffic. Simulation experiments demonstrate that the proposed model exhibits a good degree of accuracy for various system sizes and under different operating conditions. The analytical model is then used to investigate the implications of traffic self-similarity on network performance. We reveal that the network suffers considerable performance degradation when subjected to self-similar traffic, stressing the great need for improving network performance to ensure efficient support for this type of traffic.
Gap Junction Remodeling and Spironolactone-Dependent Reverse Remodeling in the Hypertrophied Heart

Pressure overload is a common pathological insult to the heart and the resulting hypertrophy is an independent risk factor for sudden cardiac death. Gap junction remodeling (GJR) has been described in hypertrophied hearts; however, a detailed understanding of the remodeling process and its effects on impulse propagation is lacking. Moreover, there has been little progress developing therapeutic strategies to diminish GJR. Accordingly, transverse aortic banding (TAC) was performed in mice to determine the effects of progressive pathological hypertrophy on connexin (Cx)43 expression, posttranslational phosphorylation, gap junction assembly, and impulse propagation. Within 2 weeks after TAC, total and phospho-Cx43 abundance was reduced and incorporation of Cx43 into gap junctional plaques was markedly diminished. These molecular changes were associated with progressive slowing of impulse propagation, as determined by optical mapping with voltage-sensitive dyes. Treatment with the aldosterone receptor antagonist spironolactone, which has been shown to diminish sudden arrhythmic death in clinical trials, was examined for its effects on GJR. We found that spironolactone blunted the development of GJR and also potently reversed established GJR, both at the molecular and functional levels, without diminishing the extent of hypertrophy. These data suggest a potential mechanism for some of the salutary electrophysiological and clinical effects of mineralocorticoid antagonists in myopathic hearts.
Diverging Prices of Novel Goods

It is well-established that the costs of consumer search lead many markets to exhibit price dispersion in equilibrium. However, relatively little attention is paid to how dispersion changes over time. The presiding assumption is that prices out of equilibrium should converge. We develop a model in which shifts in demand combined with menu costs lead dispersion to naturally rise soon after release for some novel goods. We examine an online market for collectible cards and find that price dispersion increases over time for more than half of the goods in the market.
Selecting Appropriate Management Strategies for Chronic Hepatitis B: Who to Treat

BACKGROUND: Hepatitis B virus (HBV) infection is a significant problem. In the United States estimates indicate that 0.3% of the population (1.25 million individuals) have chronic hepatitis B infection.METHODS: Review of published practice guidelines and literature on management of hepatitis B to determine: 1) Which persons in Western populations are at the highest risk for HBV infection and should be screened for HBV seromarkers to identify those who are chronically infected and those who need to be protected with hepatitis B vaccine; 2) The importance of regular monitoring in persons with chronic hepatitis B, the frequency of monitoring, and which tests should be performed; 3) How to identify the patients who are appropriate candidates for antiviral therapy.RESULTS: Recommendations for screening, diagnosis, monitoring, and treatment of chronic HBV infection are reviewed. Important differences are discussed between the Practice Guidelines for chronic hepatitis B developed by the American Association for the Study of Liver Diseases (AASLD), the European Association for the Study of the Liver (EASL), and the Asian Pacific Association for the Study of the Liver (APASL). In addition, this article reviews which patients who are no covered by these Guidelines might be candidates for antiviral therapy.DISCUSSION: Established practice guidelines provide direction to providers for the diagnosis and management of chronic HBV infection to reduce the risk of serious sequelae. However, not all patients with chronic hepatitis B are identified, and many of those who are diagnosed do not receive adequate management and follow-up.
Private Heat for Public Warmth: How Huddling Shapes Individual Thermogenic Responses of Rabbit Pups

Background Within their litter, young altricial mammals compete for energy (constraining growth and survival) but cooperate for warmth. The aim of this study was to examine the mechanisms by which huddling in altricial infants influences individual heat production and loss, while providing public warmth. Although considered as a textbook example, it is surprising to note that physiological mechanisms underlying huddling are still not fully characterised. Methodology/Principal Findings The brown adipose tissue (BAT) contribution to energy output was assessed as a function of the ability of rabbit (Oryctolagus cuniculus) pups to huddle (placed in groups of 6 and 2, or isolated) and of their thermoregulatory capacities (non-insulated before 5 days old and insulated at ca. 10 days old). BAT contribution of pups exposed to cold was examined by combining techniques of infrared thermography (surface temperature), indirect calorimetry (total energy expenditure, TEE) and telemetry (body temperature). Through local heating, the huddle provided each pup whatever their age with an ambient “public warmth” in the cold, which particularly benefited non-insulated pups. Huddling allowed pups facing a progressive cold challenge to buffer the decreasing ambient temperature by delaying the activation of their thermogenic response, especially when fur-insulated. In this way, huddling permitted pups to effectively shift from a non-insulated to a pseudo-insulated thermal state while continuously allocating energy to growth. The high correlation between TEE and the difference in surface temperatures between BAT and back areas of the body reveals that energy loss for non-shivering thermogenesis is the major factor constraining the amount of energy allocated to growth in non-insulated altricial pups. Conclusions/Significance By providing public warmth with minimal individual costs at a stage of life when pups are the most vulnerable, huddling buffers cold challenges and ensures a constant allocation of energy to growth by reducing BAT activation.
Hidden Semi-Markov Models for Single-Molecule Conformational Dynamics

The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable. However, the evolution of the conformational states of proteins mostly shows non-Markovian behavior, recognizable by non-monoexponential state dwell time histograms. The application of a Hidden Markov Model technique to a cyclic system demonstrating semi-Markovian dynamics is presented in this paper and the required extension of the model design is discussed. As standard ranking criteria of models cannot deal with these systems properly, a new approach is proposed considering the shape of the dwell time histograms. We observed the rotational kinetics of a single F1-ATPase alpha3beta3gamma sub-complex over six orders of magnitude of different ATP to ADP and Pi concentration ratios, and established a general model describing the kinetics for the entire range of concentrations. The HMM extension described here is applicable in general to the accurate analysis of protein dynamics.
A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3

The yeast IMD2 gene encodes an enzyme involved in GTP synthesis. Its expression is controlled by guanine nucleotides through a set of alternate start sites and an intervening transcriptional terminator. In the off state, transcription results in a short non-coding RNA that starts upstream of the gene. Transcription terminates via the Nrd1-Nab3-Sen1 complex and is degraded by the nuclear exosome. Using a sensitive terminator read-through assay, we identified trans-acting Terminator Override (TOV) genes that operate this terminator. Four genes were identified: the RNA polymerase II phosphatase SSU72, the RNA polymerase II binding protein PCF11, the TRAMP subunit TRF4 and the hnRNP-like, NAB3. The TOV phenotype can be explained by the loss of function of these gene products as described in models in which termination and RNA degradation are coupled to the phosphorylation state of RNA polymerase II's repeat domain. The most interesting mutations were those found in NAB3, which led to the finding that the removal of merely three carboxy-terminal amino acids compromised Nab3's function. This region of previously unknown function is distant from the protein's well-known RNA binding and Nrd1 binding domains. Structural homology modeling suggests this Nab3 ‘tail’ forms an α-helical multimerization domain that helps assemble it onto an RNA substrate.
Modified neighbor embedding-based face hallucination using coupled mappings of partial least squares

Neighbor embedding based face hallucination usually assumes that the two manifolds formed by the small patches in the low-resolution (LR) and corresponding high-resolution (HR) images share the same local geometric structure. However, since there are generally multiple HR images that can be reduced to the same LR image, the assumption does not hold always. Therefore, face hallucination directly based on the assumption may result in blurring and artifacts. To enhance the consistency relationship in face hallucination, we employ partial least squares (PLS) to learn coupled mappings simultaneously and to map the original HR and LR image patches onto a unified feature space, where the distinction between LR and HR image patches pairs is minimized. Then, the k nearest neighbors searching and the computation of optimal reconstruction weights is performed in the unified feature space. Experimental results show that the proposed method outperforms some latest image hallucination algorithms.
Effect of Adding Seeds During Maceration on Quality of Wine From Vitis Vinifera CV. Cabernet Sauvignon

Red wines were made from Vitis vinifera cv. Cabernet Sauvignon in China at different methods of maceration. The effects of adding seeds during maceration on the quality characteristics, in terms of colour, aroma profile and sensory characteristics, of the wines before bottling were evaluated, and made a comparison with the effects of adding skins. Seed contact treatments raised wine colour intensity, proanthocyanidins, tannins, and polyphenols content in comparison to the control wines. However, as indicated in the sensory evolution, the significant increase in astringency intensity was found in the wines with seed contact. Besides, the bitterness of the red wine also increased in the wines with seed contact, but it was not significantly
Preterm Birth Analysis Using Nonlinear Methods (a preliminary study)

In this report we review modern nonlinearity methods that can be used in the preterm birth analysis. The nonlinear analysis of uterine contraction signals can provide information regarding physiological changes during the menstrual cycle and pregnancy. This information can be used both for the preterm birth prediction and the preterm labor control. Keywords: preterm birth, complex data analysis, nonlinear methods
Group selection and kin selection: Two concepts but one process

In a recent paper, Traulsen and Nowak use a multilevel selection model to show that cooperation can be favored by group selection in finite populations [Traulsen A, Nowak M (2006) Proc Natl Acad Sci USA 103:10952–10955]. The authors challenge the view that kin selection may be an appropriate interpretation of their results and state that group selection is a distinctive process “that permeates evolutionary processes from the emergence of the first cells to eusociality and the economics of nations. ” In this paper, we start by addressing Traulsen and Nowak's challenge and demonstrate that all their results can be obtained by an application of kin selection theory. We then extend Traulsen and Nowak's model to life history conditions that have been previously studied. This allows us to highlight the differences and similarities between Traulsen and Nowak's model and typical kin selection models and also to broaden the scope of their results. Our retrospective analyses of Traulsen and Nowak's model illustrate that it is possible to convert group selection models to kin selection models without disturbing the mathematics describing the net effect of selection on cooperation.
THE NASA-UC ETA-EARTH PROGRAM. I. A SUPER-EARTH ORBITING HD 7924

We report the discovery of the first low-mass planet to emerge from the NASA-UC Eta-Earth Program, a super-Earth orbiting the K0 dwarf HD 7924. Keplerian modeling of precise Doppler radial velocities reveals a planet with minimum mass MPsin i = 9.26 M⊕ in a P = 5.398 d orbit. Based on Keck-HIRES measurements from 2001 to 2008, the planet is robustly detected with an estimated false alarm probability of less than 0.001. Photometric observations using the Automated Photometric Telescopes at Fairborn Observatory show that HD 7924 is photometrically constant over the radial velocity period to 0.19 mmag, supporting the existence of the planetary companion. No transits were detected down to a photometric limit of ∼0.5 mmag, eliminating transiting planets with a variety of compositions. HD 7924b is one of only eight planets detected by the radial velocity technique with MPsin i < 10 M⊕ and as such is a member of an emerging family of low-mass planets that together constrain theories of planet formation.
Irregular Rhythm Adversely Influences Calcium Handling in Ventricular Myocardium: Implications for the Interaction Between Heart Failure and Atrial Fibrillation

Background—Despite adequate rate control, the combination of atrial fibrillation with heart failure (HF) has been shown, in a number of studies, to hasten HF progression. In this context, we aimed to test the hypothesis that an irregular ventricular rhythm causes an alteration in ventricular cardiomyocyte excitation–contraction coupling which contributes to the progression of HF. Methods and Results—We investigated the effects of electrical field stimulation (average frequency 2 Hz) in an irregular versus regular drive train pattern on the expression of calcium-handling genes and proteins in rat ventricular myocytes. The effect of rhythm on intracellular calcium transients was examined using Fura-2AM fluorescence spectroscopy. In conjunction, calcium-handling protein expression was examined in left ventricular samples obtained from end-stage HF patients, in patients with either persistent atrial fibrillation or sinus rhythm. Compared with regularly paced ventricular cardiomyocytes, in cells paced irregularly for 24 hours, there was a significant reduction in the expression of sarcoplasmic reticulum calcium (Ca2+) ATPase together with reduced serine-16 phosphorylation of phospholamban. These findings were accompanied by a 59% reduction (P<0.01) in the peak Ca2+ transient in irregulary paced myocytes compared with those with regular pacing. Consistent with these observations, we observed a 54% (P<0.05) decrease in sarcoplasmic reticulum Ca2+ATPase protein expression and an 85% (P<0.01) reduction in the extent of phosphorylation of phospholamban in the left ventricular myocardium of HF patients in atrial fibrillation compared with those in sinus rhythm. Conclusions—Together, these data demonstrate that ventricular rhythmicity contributes significantly to excitation–contraction coupling by altering the expression and activity of key calcium-handling proteins. These data suggest that control of rhythm may be of benefit in patients with HF.