Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing the Emergence of New Caledonia: Fig Wasp Mutualism as a Case Study and a Review of Evidence

While geologists suggest that New Caledonian main island (Grande Terre) was submerged until ca 37 Ma, biologists are struck by the presence of supposedly Gondwanan groups on the island. Among these groups are the Oreosycea fig trees (Ficus, Moraceae) and their Dolichoris pollinators (Hymenoptera, Agaonidae). These partners are distributed in the Paleotropics and Australasia, suggesting that their presence on New Caledonia could result from Gondwanan vicariance. To test this hypothesis, we obtained mitochondrial and nuclear markers (5.3 kb) from 28 species of Dolichoris, used all available sequences for Oreosycea, and conducted phylogenetic and dating analyses with several calibration strategies. All our analyses ruled out a vicariance scenario suggesting instead that New Caledonian colonization by Dolichoris and Oreosycea involved dispersal across islands from Sundaland ca 45.9-32.0 Ma. Our results show that successful long-distance dispersal of obligate mutualists may happen further suggesting that presence of intimate mutualisms on isolated islands should not be used as a priori evidence for vicariance. Comparing our results to a review of all the published age estimates for New Caledonian plant and animal taxa, we showed that support for a vicariant origin of the island biota is still lacking. Finally, as demonstrating a causal relationship between geology and biology requires independent evidence, we argue that a priori assumptions about vicariance or dispersal should not be used to constrain chronograms. This circular reasoning could lead to under or overestimation of age estimates.
Effects of a yoga breath intervention alone and in combination with an exposure therapy for post‐traumatic stress disorder and depression in survivors of the 2004 South‐East Asia tsunami

Descilo T, Vedamurtachar A, Gerbarg PL, Nagaraja D, Gangadhar BN, Damodaran B, Adelson B, Braslow LH, Marcus S, Brown RP. Effects of a yoga breath intervention alone and in combination with an exposure therapy for PTSD and depression in survivors of the 2004 South‐East Asia tsunami.
Hydraulic Properties of Rice and the Response of Gas Exchange to Water Stress1

We investigated the role of xylem cavitation, plant hydraulic conductance, and root pressure in the response of rice (Oryza sativa) gas exchange to water stress. In the field (Philippines), the percentage loss of xylem conductivity (PLC) from cavitation exceeded 60% in leaves even in watered controls. The PLC versus leaf water potential relationship indicated diurnal refilling of cavitated xylem. The leaf water potential causing 50 PLC (P50) was –1.6 MPa and did not differ between upland versus lowland rice varieties. Greenhouse-grown varieties (Utah) were more resistant to cavitation with a 50 PLC of –1.9 MPa but also showed no difference between varieties. Six-day droughts caused concomitant reductions in leaf-specific photosynthetic rate, leaf diffusive conductance, and soil-leaf hydraulic conductance that were associated with cavitation-inducing water potentials and the disappearance of nightly root pressure. The return of root pressure after drought was associated with the complete recovery of leaf diffusive conductance, leaf-specific photosynthetic rate, and soil-leaf hydraulic conductance. Root pressure after the 6-d drought (61.2 ± 8.8 kPa) was stimulated 7-fold compared with well-watered plants before drought (8.5 ± 3.8 kPa). The results indicate: (a) that xylem cavitation plays a major role in the reduction of plant hydraulic conductance during drought, and (b) that rice can readily reverse cavitation, possibly aided by nocturnal root pressure.
Even More Confident Predictions with Deep Machine-Learning

Confidence measures aim at discriminating unreliable disparities inferred by a stereo vision system from reliable ones. A common and effective strategy adopted by most top-performing approaches consists in combining multiple confidence measures by means of an appropriately trained random-forest classifier. In this paper, we propose a novel approach by training an n-channel convolutional neural network on a set of feature maps, each one encoding the outcome of a single confidence measure. This strategy enables to move the confidence prediction problem from the conventional 1D feature maps domain, adopted by approaches based on random-forests, to a more distinctive 3D domain, going beyond single pixel analysis. This fact, coupled with a deep network appropriately trained on a small subset of images, enables to outperform top-performing approaches based on random-forests.
Light propagation in turbid media: Application to biological tissues

The analysis of the propagation of light through media is fundamental for a great variety of applications, including non-guided or fiber-based guided optical communications, industrial optical cutting or welding, and biomedical optics. These applications employ sometimes heterogeneous turbid media, such as ocean water, the atmosphere or biological tissues. Turbid media present both strong absorption and scattering. As a consequence light propagation in turbid media is a complex and challenging problem. This is specially relevant in optical treatment and diagnosis of biological tissues. In this work, we describe different approaches to the calculus of light propagation in turbid media. Light-matter general interaction is first considered. Turbid media are described by means of fundamental optical properties. Special attention is paid to scattering due to its complexity. Biological tissues are classified and the most relevant morphological and optical characteristics are described. Several light propagation models are proposed, applied to the most common biological tissues, and compared. The results are essential for an adequate planning of safe optical treatments, in which no collateral damage is produced, and for obtaining high-resolution images of pathologies in order to provide an early diagnosis.
Prevalence and determinants of nonadherence to highly active antiretroviral therapy among people living with HIV/AIDS in Ibadan, Nigeria.

OBJECTIVE To determine the level of nonadherence to highly active antiretroviral therapy (HAART) and to explore the association of factors militating against adherence and nonadherence to therapy among people living with HIV/AIDS (PLWHA) at an Antiretroviral Clinic in Ibadan, Nigeria. DESIGN A cross-sectional survey was employed to determine the prevalence of nonadherence. METHODOLOGY A structured interviewer-administered questionnaire was applied to consecutive PLWHA who had been on therapy for a minimum of three months. The completed questionnaires were entered into a computer and analyzed. Multivariate logistic regression was used to determine factors associated with nonadherence. RESULTS Three hundred and eighteen people living with HIV/AIDS completed the questionnaire. Their mean age was 39.1+/-9.6 years. There were 173 (54.4%) females and 145 (45.6%) males. The median duration on HAART was 19 months (Range 3 to 28 months) and the prevalence of nonadherence was 118 (37.1%) using the less than 95% adherence profile. About a third (31.5%) of those missing therapy reportedly missed their medication because of fasting. Multiple logistic regression analysis revealed that patients who felt healthy or simply forgot to take their drugs and those not willing to disclose their HIV status were independently, significantly associated with less than 95% adherence. CONCLUSION The study showed that nonadherence to HAART is a problem in the ARV clinic and that the feeling of being healthy, forgetfulness, and unwillingness to disclose HIV status by PLWHA were significant barriers to adherence. Efforts to improve adherence in the clinic will have to address these issues among others.
Protecting Data In-Use from Firmware and Physical Attacks

Defending computers from unauthorized physical access, malicious hardware devices, or other low-level attacks has proven extremely challenging. The risks from these attacks are exacerbated in cloud-computing environments, where users lack physical control over servers executing their workloads. This paper reviews several rmware and physical attacks against x86 platforms, including bootkits, "cold booting", and malicious devices. We discuss several existing tools and technologies that can mitigate these risk such as Trusted Execution Technology (TXT) and main memory encryption. We will also discuss upcoming technologies that may help protect against rmware and physical threats.
Vorhersage des Therapieansprechens beim Mammakarzinom

Die Untersuchung von Mammakarzinomen auf molekularer Ebene anhand der Expression bestimmter Genmuster lässt die Unterscheidung von 4 Gruppen zu: die Subtypen Luminal A und B, den HER2-Subtyp und den basalen Subtyp. Diese 4 Gruppen unterscheiden sich in ihrer Prognose sowie in ihrem Ansprechen auf spezifische Therapiemodalitäten. Auch die Entwicklung von Genexpressionsprofilen wie dem 21-Gen-Rückfallscore (Oncotype DX®) oder dem 70-Gen-Profil (Mammaprint®) kann einen Beitrag dazu leisten, adjuvante Therapien zielgerichteter einzusetzen. Die Chemotherapie ist ein integraler Bestandteil in der Systemtherapie des frühen Mammakarzinoms. Nachdem jedoch der Grossteil der Mammakarzinome östrogenrezeptorpositiv ist und potenziell geringer auf eine Chemotherapie anspricht, ist die Identifizierung derer, die von einer solchen Therapie profitieren, von besonderer Bedeutung. Die Analyse von Genexpressionsmustern kann dazu beitragen, das traditionelle histopathologische Staging zu ergänzen.
Computing Length-Preserved Free Boundary for Quasi-Developable Mesh Segmentation

Stretch-free surface flattening has been requested by a variety of applications. At present, the most difficult problem is how to segment a given model into nearly developable atlases so that a nearly stretch-free flattening can be computed. The criterion for segmentation is needed to evaluate the possibility of flattening a given surface patch, which should be fast computed. In this paper, we present a method to compute the length-preserved free boundary (LPFB) of a mesh patch which speeds up the mesh parameterization. The distortion on parameterization can then be employed as the criterion in a trial-and-error algorithm for segmenting a given model into nearly developable atlases. The computation of LPFB is formulated as a numerical optimization problem in the angle space, where we are trying to optimize the angle excesses on the boundary while preserving the constraints derived from the closed-path theorem and the length preservation.
Graph based approach to the minimum hub problem in transportation network

In this paper we consider a hub location problem in a real multimodal public transportation network. This problem is also known as the park-and-ride problem. Hubs stations are special facilities that serve as switches in such a network. In practice the set of hubs has a strategic importance, because all of the traffic that passes through the network can be controlled by these elements. From the theoretical point of view, the minimal hub problem is NP hard. Two different approaches to this problem are presented. The first group of methods bases on the greedy algorithms. In the second group the evolutionary strategy is used. The computational results for these algorithms proved a significant efficiency, what can be clearly expressed in terms of an input data reduction and also in quality measure values for the obtained solutions of this problem.
Symbolic Model Extraction for Web Application Verification

Modern web applications use complex data models and access control rules which lead to data integrity and access control errors. One approach to find such errors is to use formal verification techniques. However, as a first step, most formal verification techniques require extraction of a formal model which is a difficult problem in itself due to dynamic features of modern languages, and it is typically done either manually, or using ad hoc techniques. In this paper, we present a technique called symbolic model extraction for extracting formal data models from web applications. The key ideas of symbolic model extraction are 1) to use the source language interpreter for model extraction, which enables us to handle dynamic features of the language, 2) to use code instrumentation so that execution of each instrumented piece of code returns the formal model that corresponds to that piece of code, 3) to instrument the code dynamically so that the models of methods that are created at runtime can also be extracted, and 4) to execute both sides of branches during instrumented execution so that all program behaviors can be covered in a single instrumented execution. We implemented the symbolic model extraction technique for the Rails framework and used it to extract data and access control models from web applications. Our experiments demonstrate that symbolic model extraction is scalable and extracts formal models that are precise enough to find bugs in real-world applications without reporting too many false positives.
The Balance between the MIR164A and CUC2 Genes Controls Leaf Margin Serration in Arabidopsis[W]

CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3 define the boundary domain around organs in the Arabidopsis thaliana meristem. CUC1 and CUC2 transcripts are targeted by a microRNA (miRNA), miR164, encoded by MIR164A, B, and C. We show that each MIR164 is transcribed to generate a large population of primary miRNAs of variable size with a locally conserved secondary structure around the pre-miRNA. We identified mutations in the MIR164A gene that deepen serration of the leaf margin. By contrast, leaves of plants overexpressing miR164 have smooth margins. Enhanced leaf serration was observed following the expression of an miR164-resistant CUC2 but not of an miR164-resistant CUC1. Furthermore, CUC2 inactivation abolished serration in mir164a mutants and the wild type, whereas CUC1 inactivation did not. Thus, CUC2 specifically controls leaf margin development. CUC2 and MIR164A are transcribed in overlapping domains at the margins of young leaf primordia, with transcription gradually restricted to the sinus, where the leaf margins become serrated. We suggest that leaf margin development is controlled by a two-step process in Arabidopsis. The pattern of serration is determined first, independently of CUC2 and miR164. The balance between coexpressed CUC2 and MIR164A then determines the extent of serration.
Cellular uptake mechanisms and potential therapeutic utility of peptidic cell delivery vectors: Progress 2001–2006

Cell delivery vectors (CDVs) are short amphipathic and cationic peptides and peptide derivatives, usually containing multiple lysine and arginine residues. They possess inherent membrane activity and can be conjugated or complexed with large impermeable macromolecules and even microscopic particles to facilitate cell entry. Various mechanisms have been proposed but it is now becoming clear that the main port of entry into cells of such CDV constructs involves adsorptive‐mediated endocytosis rather than direct penetration of the plasma membrane. It is still unclear, however, how and to what extent CDV constructs are capable of exiting endosomal compartments and reaching their intended cellular site of action, usually the cytosol or the nucleus. Furthermore, although many CDVs can mediate cellular uptake of their cargo and appear comparatively non‐toxic to cells in tissue culture, the utility of CDVs for in vivo applications remains poorly understood. Whatever the mechanisms of cell entry and disposition, the overriding question as far as potential pharmacological application of CDV conjugates is concerned is whether or not a therapeutic margin can be achieved by their administration. Such a margin will only result if the intracellular concentration in the target tissues necessary to elicit the biological effect of the CDV cargo can be achieved at systemic CDV exposure levels that are non‐toxic to both target and bystander cells. It is proposed that the focus of CDV research now be shifted from mechanistic in vitro studies with labeled but otherwise unconjugated CDVs to in vivo pharmacological and toxicological studies using CDV‐derivatized and other cationized forms of inherently non‐permeable macromolecules of true therapeutic interest. © 2006 Wiley Periodicals, Inc. Med Res Rev, 27, No. 6, 755–795, 2007
Intravitreal triamcinolone acetonide as an additional tool in pars plana vitrectomy for proliferative diabetic retinopathy.

PURPOSE To evaluate the safety and efficacy of intravitreal injections of crystalline triamcinolone acetonide as an adjunctive procedure in pars plana vitrectomy for proliferative diabetic retinopathy. METHODS This nonrandomized comparative study included 30 patients (32 eyes) who underwent standardized pars plana vitrectomy for treatment of proliferative diabetic retinopathy and who received an intravitreal injection of 25 mg triamcinolone acetonide at the end of surgery. Mean follow-up time was 5.60 5.14 months. The study group was compared with a control group (32 eyes) matched with the study group for preoperative and intraoperative parameters and who underwent pars plana vitrectomy for proliferative diabetic retinopathy without intravitreal injection of triamcinolone acetonide. RESULTS The study group and the control group did not vary significantly in frequency of postoperative retinal detachment, re-pars plana vitrectomy, or postoperative enucleation or phthisis bulbi, or in best postoperative visual acuity, visual acuity at end of the study, or gain in visual acuity. CONCLUSIONS In this pilot study, the study group with pars plana vitrectomy and intravitreal triamcinolone acetonide injection compared with the nonrandomized control group without intravitreal triamcinolone acetonide injection did not show a higher than usual rate of postoperative complications. As a corollary, however, the data do not suggest the adjunct use of 25 mg intravitreal triamcinolone acetonide combined with pars plana vitrectomy as treatment of proliferative diabetic retinopathy. (Eur J Ophthalmol 2003; 13: 468-73).
An alternative approach to estimate age‐related mortality of kidney transplant recipients compared to the general population: results in favor of old‐to‐old transplantations

Compared to dialysis, kidney transplantation appears to be the best treatment for chronic kidney failure, even for older aged patients. Nevertheless, the individual benefit of transplanting elderly patients has to be balanced against the corresponding increase in the number of patients awaiting grafts. We analyzed the excess mortality related to kidney transplant recipients by taking into account the expected mortality of the general population (additive regression model for relative survival). We applied this method to a cohort of patients who received a first deceased‐donor kidney transplant between 1998 and 2009 in France (DIVAT, n = 3641). Overall 10‐year mortality was 13%. As expected, recipient age was the main risk factor associated with overall mortality. In contrast, recipient age was no longer significantly associated with the excess of mortality related to kidney transplant status by subtracting the expected mortality of the general population. Delayed graft function (DGF), pretransplantation immunization, and past history of diabetes appeared as the main risk factors of this higher mortality rate. Our results constitute a strong argument in favor of kidney transplantation, regardless of the patient's age. Preventing DGF may be more effective for decreasing the risk of death specifically attributable to the disease.
A Smartphone-Based Intervention With Diaries and Therapist-Feedback to Reduce Catastrophizing and Increase Functioning in Women With Chronic Widespread Pain: Randomized Controlled Trial

Background Internet-based interventions using cognitive behavioral approaches can be effective in promoting self-management of chronic pain conditions. Web-based programs delivered via smartphones are increasingly used to support the self-management of various health disorders, but research on smartphone interventions for persons with chronic pain is limited. Objective The aim of this trial was to study the efficacy of a 4-week smartphone-delivered intervention with written diaries and therapist feedback following an inpatient chronic pain rehabilitation program. Methods A total of 140 women with chronic widespread pain who participated in a 4-week inpatient rehabilitation program were randomized into 2 groups: with or without a smartphone intervention after the rehabilitation. The smartphone intervention consisted of 1 face-to-face session and 4 weeks of written communication via a smartphone. Participants received 3 smartphone diary entries daily to support their awareness of and reflection on pain-related thoughts, feelings, and activities. The registered diaries were immediately available to a therapist who submitted personalized written feedback daily based on cognitive behavioral principles. Both groups were given access to a noninteractive website after discharge to promote constructive self-management. Outcomes were measured with self-reported questionnaires. The primary outcome measure of catastrophizing was determined using the pain catastrophizing scale (score range 0-52). Secondary outcomes included acceptance of pain, emotional distress, functioning, and symptom levels. Results Of the 140 participants, 112 completed the study: 48 in the intervention group and 64 in the control group. Immediately after the intervention period, the intervention group reported less catastrophizing (mean 9.20, SD 5.85) than the control group (mean 15.71, SD 9.11, P<.001), yielding a large effect size (Cohen’s d=0.87) for study completers. At 5-month follow-up, the between-group effect sizes remained moderate for catastrophizing (Cohen’s d=0.74, P=.003), acceptance of pain (Cohen’s d=0.54, P=.02), and functioning and symptom levels (Cohen’s d=0.75, P=.001). Conclusions The results suggest that a smartphone-delivered intervention with diaries and personalized feedback can reduce catastrophizing and prevent increases in functional impairment and symptom levels in women with chronic widespread pain following inpatient rehabilitation. Trial Registration Clinicaltrials.gov NCT01236209; http://www.clinicaltrials. gov/ct2/show/NCT01236209 (Archived by WebCite at http://www.webcitation.org/6DUejLpPY)
SHDF - A Scalable Hierarchical Distributed Framework for Data Centre Management

A promising approach to increase the efficiency of infrastructure usage is to adapt the assignment of resources to workloads. This can be used, for example, to consolidate existing workloads so that the new capability can be used to serve new requests, or alternatively unused resources may be turned off to reduce energy consumption. Many architectural solutions have been presented for data centre management, however these tend to be centralised and may suffer in their ability to scale and support data centres with tens of thousands of nodes. Distributed approaches solve the scalability problem, however these do not have a global view of resources across the data centre. To address this, we propose a novel hybrid distributed hierarchical framework that is effective at providing the information needed for decision making at scale. We evaluate the performance of our approach by simulation, and demonstrate that a hybrid approach is a viable solution for managing large data centres, through rapid information dissemination and ability to make decisions using a global view.