Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular matrix assessment of infected chronic venous leg ulcers: role of metalloproteinases and inflammatory cytokines

Chronic venous ulcer (CVU) represents a dreaded complication of chronic venous disease (CVD). The onset of infection may further delay the already precarious healing process in such lesions. Some evidences have shown that matrix metalloproteinases (MMPs) are involved and play a central role in both CVUs and infectious diseases. Two groups of patients were enrolled to evaluate the expression of MMPs in infected ulcers and the levels of inflammatory cytokines as well as their prevalence. Group I comprised 63 patients (36 females and 27 males with a median age of 68·7 years) with infected CVUs, and group II (control group) comprised 66 patients (38 females and 28 males with a median age of 61·2 years) with non‐infected venous ulcers. MMP evaluation and dosage of inflammatory cytokines in plasma and wound fluid was performed by means of enzyme‐linked immunosorbent assay test; protein extraction and immunoblot analysis were performed on biopsied wounds. The first three most common agents involved in CVUs were Staphylococcus aureus (38·09%), Corynebacterium striatum (19·05%) and Pseudomonas aeruginosa (12·7%). In this study, we documented overall higher levels of MMP‐1 and MMP‐8 in patients with infected ulcers compared to those with uninfected ulcers that showed higher levels of MMP‐2 and MMP‐9. We also documented higher levels of interleukin (IL)‐1, IL‐6, IL‐8, vascular endothelial growth factor and tumour necrosis factor‐alpha in patients with infected ulcers with respect to those with uninfected ulcers, documenting a possible association between infection, MMP activation, cytokine secretions and symptoms. The present results could represent the basis for further studies on drug use that mimic the action of tissue inhibitors of metalloproteinases in order to make infected CVU more manageable.
Are the days of closed pleural biopsy over? Yes

In the modern management of pleural diseases, thoracoscopy has a clear advantage over closed pleural biopsy. By way of its high yield, both in malignant pleural disease and pleural Tuberculosis – the two commonest cause of undiagnosed pleural effusion, thoracoscopy has the added advantage of faster symptom relief and offering effective pleurodesis. This makes it an attractive diagnostic and therapeutic procedure of choice and features high in the algorithms of many international guidelines on the approach to pleural diseases.
Omnidirectional Hexapod Walking and Efficient Gaits Using Restrictedness

The “restrictedness” of a hexapod robot’s legs is the degree to which their free movement is restricted in some way. Using the restrictedness to decide when to lift the legs has previously been shown to allow omnidirectional walking using a free gait as well as a tripod gait during straight-ahead walking. In this paper, we develop the previous system to improve the range of forward walking gaits exhibited by the restrictedness controller to include a range of “wave gaits. ” A simplified robot model was used for an off-line search for the optimal restrictedness components for forward walking. Experimental results from the small hexapod “Hamlet” are presented to show the worth of the restrictedness concept and the modeling process.
Polar Active Contours for Medical Applications

The focus of this thesis is on polar active contours, i.e. a sub-class of active contours which can only describe star-shaped objects. It is suggested to solve the associated energy minimization problems in so-called Sobolev spaces which are endowed with a metric that allows the user to weight translations, scale-changes, and smooth deformations of the curve during the optimization process. The resulting polar active contours enjoy several properties which are particularly desirable for medical applications. When generalizing these ideas to surface evolutions, however, one has to solve a partial differential equation (PDE) in two or three dimensions in every iteration step. Thus, efficient numerical techniques for solving this PDE – not only for the star-shaped case – are developed and compared to the ones arising from other regularization strategies.
Coralline algae elevate pH at the site of calcification under ocean acidification

Coralline algae provide important ecosystem services but are susceptible to the impacts of ocean acidification. However, the mechanisms are uncertain, and the magnitude is species specific. Here, we assess whether species‐specific responses to ocean acidification of coralline algae are related to differences in pH at the site of calcification within the calcifying fluid/medium (pHcf) using δ11B as a proxy. Declines in δ11B for all three species are consistent with shifts in δ11B expected if B(OH)4− was incorporated during precipitation. In particular, the δ11B ratio in Amphiroa anceps was too low to allow for reasonable pHcf values if B(OH)3 rather than B(OH)4− was directly incorporated from the calcifying fluid. This points towards δ11B being a reliable proxy for pHcf for coralline algal calcite and that if B(OH)3 is present in detectable proportions, it can be attributed to secondary postincorporation transformation of B(OH)4−. We thus show that pHcf is elevated during calcification and that the extent is species specific. The net calcification of two species of coralline algae (Sporolithon durum, and Amphiroa anceps) declined under elevated CO2, as did their pHcf. Neogoniolithon sp. had the highest pHcf, and most constant calcification rates, with the decrease in pHcf being ¼ that of seawater pH in the treatments, demonstrating a control of coralline algae on carbonate chemistry at their site of calcification. The discovery that coralline algae upregulate pHcf under ocean acidification is physiologically important and should be included in future models involving calcification.
Representational Dynamics of Facial Viewpoint Encoding

Faces provide a wealth of information, including the identity of the seen person and social cues, such as the direction of gaze. Crucially, different aspects of face processing require distinct forms of information encoding. Another person's attentional focus can be derived based on a view-dependent code. In contrast, identification benefits from invariance across all viewpoints. Different cortical areas have been suggested to subserve these distinct functions. However, little is known about the temporal aspects of differential viewpoint encoding in the human brain. Here, we combine EEG with multivariate data analyses to resolve the dynamics of face processing with high temporal resolution. This revealed a distinct sequence of viewpoint encoding. Head orientations were encoded first, starting after around 60 msec of processing. Shortly afterward, peaking around 115 msec after stimulus onset, a different encoding scheme emerged. At this latency, mirror-symmetric viewing angles elicited highly similar cortical responses. Finally, about 280 msec after visual onset, EEG response patterns demonstrated a considerable degree of viewpoint invariance across all viewpoints tested, with the noteworthy exception of the front-facing view. Taken together, our results indicate that the processing of facial viewpoints follows a temporal sequence of encoding schemes, potentially mirroring different levels of computational complexity.
Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

In the early days of HIV treatment, drug resistance occurred rapidly and predictably in all patients, but under modern treatments, resistance arises slowly, if at all. The probability of resistance should be controlled by the rate of generation of resistance mutations. If many adaptive mutations arise simultaneously, then adaptation proceeds by soft selective sweeps in which multiple adaptive mutations spread concomitantly, but if adaptive mutations occur rarely in the population, then a single adaptive mutation should spread alone in a hard selective sweep. Here, we use 6717 HIV-1 consensus sequences from patients treated with first-line therapies between 1989 and 2013 to confirm that the transition from fast to slow evolution of drug resistance was indeed accompanied with the expected transition from soft to hard selective sweeps. This suggests more generally that evolution proceeds via hard sweeps if resistance is unlikely and via soft sweeps if it is likely. DOI: 10.7554/eLife.10670. 00
Using Test Oracles Generated from Program Documentation

The paper illustrates how software can be described precisely using LD-relations, how these descriptions can be presented in a readable manner using tabular notations, and one way such descriptions can be used to test programs. The authors describe an algorithm that can be used to generate a test oracle from program documentation, and present the results of using a tool based on it to help test part of a commercial network management application. The results demonstrate that these methods can be effective at detecting errors and greatly increase the speed and accuracy of test evaluation when compared with manual evaluation. Such oracles can be used for unit testing, in situ testing, constructing self-checking software, and ensuring consistency between code and documentation.
Efficient specification-assisted error localization

We present a new error localization tool, Archie, that accepts a specification of key data structure consistency constraints, then generates an algorithm that checks if the data structures satisfy the constraints. We also present a set of specification analyses and optimizations that (for our benchmark software system) significantly improve the performance of the generated checking algorithm, enabling Archie to efficiently support interactive debugging. We evaluate Archie’s effectiveness by observing the actions of two developer populations (one using Archie, the other using standard error localization techniques) as they attempted to localize and correct three data structure corruption errors in a benchmark software system. With Archie, the developers were able to localize each error in less than 10 minutes and correct each error in (usually much) less than 20 minutes. Without Archie, the developers were, with one exception, unable to locate each error after more than an hour of effort.
Poly-N-acetyl glucosamine fibers are synergistic with vacuum-assisted closure in augmenting the healing response of diabetic mice.

BACKGROUND Vacuum-assisted closure (VAC) has become the preferred modality to treat many complex wounds but could be further improved by methods that minimize bleeding and facilitate wound epithelialization. Short fiber poly-N-acetyl glucosamine nanofibers (sNAG) are effective hemostatic agents that activate platelets and facilitate wound epithelialization. We hypothesized that sNAG used in combination with the VAC device could be synergistic in promoting wound healing while minimizing the risk of bleeding. METHODS Membranes consisting entirely of sNAG nanofibers were applied immediately to dorsal excisional wounds of db/db mice followed by application of the VAC device. Wound healing kinetics, angiogenesis, and wound-related growth factor expression were measured. RESULTS The application of sNAG membranes to wounds 24 hours before application of the VAC device was associated with a significant activation of wounds (expression of PDGF, TGFβ, EGF), superior granulation tissue formation rich in Collagen I as well as superior wound epithelialization (8.6% ± 0.3% vs. 1.8% ± 1.1% of initial wound size) and wound contraction. CONCLUSIONS The application of sNAG fiber-containing membranes before the application of the polyurethane foam interface of VAC devices leads to superior healing in db/db mice and represents a promising wound healing adjunct that can also reduce the risk of bleeding complications.
Streaming in a connected world: querying and tracking distributed data streams

Today, a majority of data is fundamentally distributed in nature. Data for almost any task is collected over a broad area, and streams in at a much greater rate than ever before. In particular, advances in sensor technology and miniaturization have led to the concept of the sensor network: a (typically wireless) collection of sensing devices collecting detailed data about their surroundings. A fundamental question arises: how to query and monitor this rich new source of data? A similar scenario emerges within more traditional, wired networks: if data is collected over remote sites, either about observed external conditions or about the network itself (e.g. in IP network monitoring), how to process this data in order to answer certain queries? Additionally, other emerging models of distributed computation, such as peer-to-peer (P2P) networks and grid-based computing face the same problems of managing and interrogating data streams observed by distributed participants. The prevailing paradigm in database systems has been understanding management of centralized data: how to organize, index, access, and query data that is held centrally on a single machine or a small number of closely linked machines. In these distributed scenarios, the axiom is overturned: now, data typically streams into remote sites at high rates. Here, it is not feasible to collect the data in one place: the volume of data collection is too high, and the capacity for data communication relatively low. For example, in battery-powered wireless sensor networks, the main drain on battery life is communication, which is orders of magnitude more expensive than computation or sensing. This establishes a fundamental concept for distributed stream monitoring: if we can perform more computational work within the network to reduce the communication needed, then we can significantly improve the value of our network, by increasing its useful
A novel object-oriented stereo matching on multi-scale superpixels for low-resolution depth mapping

This paper presents a novel object-oriented stereo matching on multi-scale superpixels to generate a low-resolution depth map. It overcomes the classic downsampling methods' disadvantages, such as boundary blurring, outlier enlargement and foreground objects merging to background, etc. The approach we exploited is to segment the image in three scales' superpixels from dense to sparse ones according to downsampling scale first, then compute disparity directly on superpixel's stereo matching. The post-processing of region constraint and local refinement uses hierarchical multi-scale superpixels as well. The proposed approach is validated on Middle-bury test-bed, and the experimental results outperform the current state-of-the-art stereo matching methods in low resolutions.
Ranking Candidate Networks of relations to improve keyword search over relational databases

Relational keyword search (R-KwS) systems based on schema graphs take the keywords from the input query, find the tuples and tables where these keywords occur and look for ways to “connect” these keywords using information on referential integrity constraints, i.e., key/foreign key pairs. The result is a number of expressions, called Candidate Networks (CNs), which join relations where keywords occur in a meaningful way. These CNs are then evaluated, resulting in a number of join networks of tuples (JNTs) that are presented to the user as ranked answers to the query. As the number of CNs is potentially very high, handling them is very demanding, both in terms of time and resources, so that, for certain queries, current systems may take too long to produce answers, and for others they may even fail to return results (e.g., by exhausting memory). Moreover, the quality of the CN evaluation may be compromised when a large number of CNs is processed. Based on observations made by other researchers and in our own findings on representative workloads, we argue that, although the number of possible Candidate Networks can be very high, only very few of them produce answers relevant to the user and are indeed worth processing. Thus, R-KwS systems can greatly benefit from methods for accessing the relevance of Candidate Networks, so that only those deemed relevant might be evaluated. We propose in this paper an approach for ranking CNs, based on their probability of producing relevant answers to the user. This relevance is estimated based on the current state of the underlying database using a probabilistic Bayesian model we have developed. Experiments that we performed indicate that this model is able to assign the relevant CNs among the top-4 in the ranking produced. In these experiments we also observed that processing only a few relevant CNs has a considerable positive impact, not only on the performance of processing keyword queries, but also on the quality of the results obtained.
Pollination context alters female advantage in gynodioecious Silene vulgaris

Gynodioecy, the co‐occurrence of females and hermaphrodites, is arguably the most common angiosperm gender polymorphism in many florae. Females’ ability to invade and persist among hermaphrodites depends, in part, on pollinators providing adequate pollination to females. We directly measured diurnal and nocturnal pollinators’ contributions to female and hermaphrodite seed production in artificial populations of gynodioecious Silene vulgaris by experimentally restricting pollinator access. We found that female relative seed production in this system depended strongly on pollination context: females produced more than twice as many seeds as hermaphrodites in the context of abundant, nectar‐collecting moths. Conversely, females showed no seed production advantage in the context of pollen‐collecting syrphid flies and bees due to acutely hermaphrodite‐biased visitation. We infer that variation in pollinator type, behaviour and abundance may be important for achieving the female relative fitness thresholds necessary for the maintenance of gynodioecy. Generally, our study illustrates how pollinator‐mediated mechanisms may influence the evolution of breeding systems and associated suites of floral traits. Segments of a pollinator community may facilitate gynodioecy by selecting for plant characteristics that increase the attractiveness of both sexes to pollinators, such as nectar rewards. Conversely, discriminating visitors in search of pollen may restrict gynodioecy in associated plant lineages by reducing male steriles’ fitness below threshold levels.
Effect of rifampicin and erythromycin on the initiation of galactose induced cataract in rats

It is inferred that platelet aggregation inducing activity of FRB extracts is a limiting factor for its utilization despite having proven therapeutic potential. Thus, detailed and more intensive studies are warranted in order to elucidate the mechanism of platelet aggregatory action of Ficus extracts. The study also warrants isolation and characterization of the specific compound(s) responsible for the platelet aggregatory activity of the Ficus extracts for its optimum utilization as a therapeutic agent.
The b 3-Integrin Binding Protein b 3-Endonexin Is a Novel Negative Regulator of Hypoxia-Inducible Factor-1

Aims: Integrins are multifunctional heterodimeric adhesion receptors that mediate the attachment between a cell and the extracellular matrix or other surrounding cells. In endothelial cells, integrins can modulate cell migration and motility. In particular, b3-integrin is expressed in angiogenic vessels. Signal transduction by b3integrins requires the recruitment of intracellular signaling molecules. b3-endonexin is a highly spliced molecule that has been identified as a b3-integrin binding protein. b3-endonexin isoforms are expressed in endothelial cells and have been suggested to act as shuttle proteins between the membrane and the nucleus. However, their functional role in angiogenesis is unclear. In this study, we investigated whether b3-endonexin isoforms are involved in endothelial angiogenic processes under hypoxia. Results: The overexpression of b3endonexin isoforms decreased endothelial proliferation and tube formation under hypoxia, while the depletion of b3-endonexin by RNAi promoted angiogenic responses in vitro and in vivo. In hypoxia, b3-endonexin accumulated in the nucleus, and prevention of this response by depletion of b3-endonexin increased hypoxic activation and induction of the hypoxia-inducible factor (HIF)-1 and its target genes VEGF and PAI-1. b3endonexin diminished nuclear factor kappa B (NFkB) activation and decreased NFkB binding to the HIF-1a promoter under hypoxia, subsequently diminishing NFkB-dependent transcription of HIF-1a under hypoxia. Innovation: Our results indicate for the first time that the overexpression of b3-endonexin can decrease hypoxic induction and activation of HIF-1a and can prevent hypoxic endothelial proliferation and angiogenic responses. Conclusion: b3-endonexin can act as a novel anti-angiogenic factor specifically in the response to hypoxia due to its negative impact on the activation of HIF-1. Antioxid. Redox Signal. 20, 1964–1976.
QoS in distributed wireless 802.11-based multi-hop networks

Wireless Local Area Networks (WLAN)s are today common for access to Internet; well-known and used is IEEE 802.11 standardized technology. Some drawbacks of the standardized distributed medium access scheme, Distributed Coordination Function (DCF) has resulted in considerations made to extend the DCF from single-hop communications to multi-hop. Multihopping has the potential to reduce energy consumption and increase throughput and coverage. The drawback is lack of Quality-of-Service (QoS) support, which already with single-hop communication was bad, but extending a communication between two peers to multi-hop significantly reduces the possibility to offer reliable transmissions. The contention-based medium access performed at each hop with the DCF results in large uncertainties as to when a packet arrives to its end-destination. There are two general approaches for extending the DCF with QoS functionality: 1. Allocate resources for a flow and 2. Assign a flow higher priority than other flows. My hypothesis is that for strict QoS guarantees, a reservation-based approach is the better one. This has been my motivation to design a new medium access protocol; based on the DCF, periodic time slots for QoS-demanding real-time applications are reserved. The Distributed Allocation of time slots for Real-time traffic (DARE) is unique as it totally distributed sets up an end-to-end reservation before the transmission of data begins, repairs broken reservations, support many periods and time slot sizes and distribute piggy-backed information even to a two-hop radius from a receiver. This thesis describes the DARE protocol and also presents results from comparisons of DARE, DCF and the IEEE 802.11 E standardized priority-based QoS medium access protocol Enhanced Distributed Channel Access (EDCA). Using simulations, this thesis shows that DARE offers constant end-to-end packet delay for a flow, very low average packet delay in the whole system and constant throughput. EDCA and DCF depend strongly on the total network load; average packet delay for a real-time flow increases rapidly with the surrounding load. DARE outperforms both DCF and EDCA when many flows are present, even in networks with frequent topology changes where reservations must be repaired. Thus, the reservation-based DARE protocol is the most suitable approach for extending DCF with QoS.