Miracle-dz/UniFAR-FTUs huggingface dataset:
Immortalization and altered differentiation of human keratinocytes in vitro by the E6 and E7 open reading frames of human papillomavirus type 18

The E6-E7 region of human papillomavirus types 16 and 18 is selectively retained and expressed in cervical carcinoma cells. In cultured human keratinocytes, expression of the E6 and E7 open reading frames of human papillomavirus type 18, under the control of its homologous promoter, resulted in high-frequency immortalization. Furthermore, by using a system that allows for stratification of keratinocytes in vitro (raft system), we observed that the morphological differentiation of these E6-E7 immortalized cells was altered such that parabasal cells extended throughout most of the epithelium, with abnormal nuclei present in the upper regions. Examination of E6-E7-expressing cell lines in the raft system at a later passage revealed that complete loss of morphological differentiation had occurred. E7 alone was a much less effective immortalizing agent than E6 and E7 together and acted only minimally to alter morphological differentiation in vitro. No such activities were found for E6 alone. High-frequency transformation of human epithelial cells thus appears to require expression of both E6 and E7 gene products.
Effect of Human Burn Wound Exudate on Pseudomonas aeruginosa Virulence

Microbial infection of severe burn wounds is currently a major medical challenge. Of the infections by bacteria able to colonize such injuries, those by Pseudomonas aeruginosa are among the most severe, causing major delays in burn patient recovery or leading to fatal issues. In this study, we investigated the growth properties of several burn wound pathogens in biological fluids secreted from human burn wounds. We found that P. aeruginosa strains were able to proliferate but not those of the other pathogens tested. In addition, burn wound exudates (BWEs) stimulate the expression of virulence factors in P. aeruginosa. The chemical composition analysis of BWEs enabled us to determine the major components of these fluids. These data are essential for the development of an artificial medium mimicking the burn wound environment and for in vitro analysis of the initial step in the development of burn wound infections. ABSTRACT Burn wound sepsis is currently the main cause of morbidity and mortality after burn trauma. Infections by notorious pathogens such as Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii impair patient recovery and can even lead to fatality. In this study, we investigated the effect of burn wound exudates (BWEs) on the virulence of those pathogens. BWEs were collected within 7 days after burn trauma from 5 burn patients. We first monitored their effect on pathogen growth. In contrast to A. baumannii and S. aureus, P. aeruginosa was the only pathogen able to grow within these human fluids. Expression of typical virulence factors such as pyocyanin and pyoverdine was even enhanced compared the levels seen with standard laboratory medium. A detailed chemical composition analysis of BWE was performed, which enabled us to determine the major components of BWE and underline the metabolic modifications induced by burn trauma. These data are essential for the development of an artificial medium mimicking the burn wound environment and the establishment of an in vitro system to analyze the initial steps of burn wound infections. IMPORTANCE Microbial infection of severe burn wounds is currently a major medical challenge. Of the infections by bacteria able to colonize such injuries, those by Pseudomonas aeruginosa are among the most severe, causing major delays in burn patient recovery or leading to fatal issues. In this study, we investigated the growth properties of several burn wound pathogens in biological fluids secreted from human burn wounds. We found that P. aeruginosa strains were able to proliferate but not those of the other pathogens tested. In addition, burn wound exudates (BWEs) stimulate the expression of virulence factors in P. aeruginosa. The chemical composition analysis of BWEs enabled us to determine the major components of these fluids. These data are essential for the development of an artificial medium mimicking the burn wound environment and for in vitro analysis of the initial step in the development of burn wound infections.
Drifting grating stimulation reveals particular activation properties of visual neurons in the caudate nucleus

The role of the caudate nucleus (CN) in motor control has been widely studied. Less attention has been paid to the dynamics of visual feedback in motor actions, which is a relevant function of the basal ganglia during the control of eye and body movements. We therefore set out to analyse the visual information processing of neurons in the feline CN. Extracellular single‐unit recordings were performed in the CN, where the neuronal responses to drifting gratings of various spatial and temporal frequencies were recorded. The responses of the CN neurons were modulated by the temporal frequency of the grating. The CN units responded optimally to gratings of low spatial frequencies and exhibited low spatial resolution and fine spatial frequency tuning. By contrast, the CN neurons preferred high temporal frequencies, and exhibited high temporal resolution and fine temporal frequency tuning. The spatial and temporal visual properties of the CN neurons enable them to act as spatiotemporal filters. These properties are similar to those observed in certain feline extrageniculate visual structures, i.e. in the superior colliculus, the suprageniculate nucleus and the anterior ectosylvian cortex, but differ strongly from those of the primary visual cortex and the lateral geniculate nucleus. Accordingly, our results suggest a functional relationship of the CN to the extrageniculate tecto‐thalamo‐cortical system. This system of the mammalian brain may be involved in motion detection, especially in velocity analysis of moving objects, facilitating the detection of changes during the animal's movement.
Hierarchical self-organization of cytoskeletal active networks

The structural reorganization of the actin cytoskeleton is facilitated through the action of motor proteins that crosslink the actin filaments and transport them relative to each other. Here, we present a combined experimental-computational study that probes the dynamic evolution of mixtures of actin filaments and clusters of myosin motors. While on small spatial and temporal scales the system behaves in a very noisy manner, on larger scales it evolves into several well distinct patterns such as bundles, asters and networks. These patterns are characterized by junctions with high connectivity, whose formation is possible due to the organization of the motors in ‘oligoclusters’ (intermediate-size aggregates). The simulations reveal that the self-organization process proceeds through a series of hierarchical steps, starting from local microscopic moves and ranging up to the macroscopic large scales where the steady-state structures are formed. Our results shed light on the mechanisms involved in processes such as cytokinesis and cellular contractility, where myosin motors organized in clusters operate cooperatively to induce the structural organization of cytoskeletal networks.
Obesity Elicits Interleukin 1-Mediated Deficits in Hippocampal Synaptic Plasticity

Adipose tissue is a known source of proinflammatory cytokines in obese humans and animal models, including the db/db mouse, in which obesity arises as a result of leptin receptor insensitivity. Inflammatory cytokines induce cognitive deficits across numerous conditions, but no studies have determined whether obesity-induced inflammation mediates synaptic dysfunction. To address this question, we used a treadmill training paradigm in which mice were exposed to daily training sessions or an immobile belt, with motivation achieved by delivery of compressed air on noncompliance. Treadmill training prevented hippocampal microgliosis, abolished expression of microglial activation markers, and also blocked the functional sensitization observed in isolated cells after ex vivo exposure to lipopolysaccharide. Reduced microglial reactivity with exercise was associated with reinstatement of hippocampus-dependent memory, reversal of deficits in long-term potentiation, and normalization of hippocampal dendritic spine density. Because treadmill training evokes broad responses not limited to the immune system, we next assessed whether directly manipulating adiposity through lipectomy and fat transplantation influences inflammation, cognition, and synaptic plasticity. Lipectomy prevents and fat transplantation promotes systemic and central inflammation, with associated alterations in cognitive and synaptic function. Levels of interleukin 1β (IL1β) emerged as a correlate of adiposity and cognitive impairment across both the treadmill and lipectomy studies, so we manipulated hippocampal IL1 signaling using intrahippocampal delivery of IL1 receptor antagonist (IL1ra). Intrahippocampal IL1ra prevented synaptic dysfunction, proinflammatory priming, and cognitive impairment. This pattern supports a central role for IL1-mediated neuroinflammation as a mechanism for cognitive deficits in obesity and diabetes.
Achieving High Reliability via Expediting the Repair of Critical Blocks in Replicated Storage Systems

High reliability is critical to large data centers consisting of hundreds to thousands of storage nodes where node failures are not rare. Data replication is a typical technique deployed to achieve high reliability. When a node failure is detected, blocks with lost replicas are identified and recovered. Long timeouts are usually used for node failure detection. For blocks with one lost replica, the long timeouts can significantly reduce network traffic induced by data recovery. However, for blocks with two or more lost replicas, which can be caused by concurrent node failures that are not rare in large data centers, the long timeouts will result in a high risk of loss of these blocks. In this paper, we propose MFR to separate the identification of the blocks with two or more lost replicas from that of the blocks with one lost replica in a way that the identification of the blocks with two or more replicas can be accelerated while that of the blocks with one lost replica stays the same. Consequently, MFR can significantly improve data reliability while keeping the network traffic induced by data recovery stable. The results from our simulation and prototype implementation show that MFR improves the reliability of storage systems by a factor of up to 4.0 in terms of mean time to data loss. As blocks with two or more lost replicas are far fewer than blocks with one lost replica, the extra network traffic caused by MFR is less than 0.54% of total network traffic for data recovery.
Xenogeneic endothelial cells activate human prothrombin.

BACKGROUND Delayed xenograft rejection is characterized by platelet activation and fibrin deposition and is thought to occur independently of complement activation. We have therefore investigated the potential for xenogeneic endothelial cells (EC) to regulate the conversion of prothrombin to thrombin, a central component of the final common pathway of coagulation and an important platelet agonist. METHODS AND RESULTS Quiescent porcine aortic EC (PAEC) were found to convert high levels of human prothrombin to thrombin (0.234+/-0.019 IU/ml) when compared with human aortic EC (0.017+/-0 IU/ml, 30-min time point, chromogenic assay; P<0.001). PAEC activation by human complement resulted in comparable levels of thrombin generation. Prothrombin conversion by PAEC as determined by generation of F1+2 (1.909+/-0.119 nmol/L) and formation of thrombin-antithrombin III complexes (125.611+/-6.373 microg/L) was significantly greater than the matched human aortic EC values (F1+2: 1.539+/-0.03 nmol/L, P<0.001; thrombin-antithrombin III: 1.833+/-0.104 microg/L, P<0.001). Sequential analysis of prothrombin activation by PAEC indicated generation of the intermediate meizothrombin followed by autolytically accelerated thrombin formation. Subsequent experiments established important cross-species' incompatibilities with respect to porcine thrombomodulin interaction with human thrombin and protein C in that PAEC had a reduced capacity to generate activated human protein C in vitro. CONCLUSION These observations indicate a potentially important molecular barrier involving blood coagulation that may impact on the planned clinical application of porcine transgenic organs.
Re: “Polymorphisms of three genes (ACE, AGT and CYP11B2) in the renin–angiotensin–aldosterone system are not associated with blood pressure salt sensitivity: a systematic meta-analysis”

We read with interest the article recently published in Blood Pressure by J. Sun and colleagues. [1] The authors conducted a meta-analysis of the literature investigating genetic variations in ACE (I/D), AGT (M235T) and CYP11B2 (C344T) with salt-sensitive hypertension. According to the title and conclusions of the paper, the authors conclude that these genetic variants are not associated with salt-sensitive hypertension. However, notable limitations in the design of their study preclude making this conclusion. The main limitation is that the authors did not consider other studies that examined genetic variants that are in strong linkage disequilibrium (LD) with the 3 markers of interest and they did not identify this as a limitation in their discussion. For example, ACE I/D is in complete LD with ACE rs4343 and studies that report either of these two variants are examining essentially the same variant. [2–4] Other examples include AGT (M235T) which is in strong LD with AGT A(-6)G [5] and CYP11B2 (C344T), which is in complete LD with CYP11B2 at rs28491316 [6]. Because of this oversight, the authors failed to identify several studies. One study that was omitted was completed by Iwai et al., which found an association between the C344T variant in CYP11B2, which is in complete LD with CYP11B2 rs28491316 and salt-sensitive hypertension. [6,7] To ensure that all biologically relevant studies are included in the meta-analysis, the search terms should have included SNPs that are in complete or strong (>80%) LD with the three variants of interest in order to assess all relevant literature to appropriately and adequately address the research question. Furthermore, there was no discussion detailing the reason for excluding randomized controlled trials (RCTs), or how the exclusion of such studies may have impacted the conclusion. As RCTs did not meet the inclusion criteria, several robust studies were disregarded including a randomized, double-blinded, placebocontrolled Latin-square trial, which found a significant link between salt-sensitive hypertension and the AGT gene at M235T. [8] An additional limitation is that only one study that did not meet the inclusion criteria was cited and discussed. That study also found no significant association between the three variants of interest and blood pressure salt sensitivity. [2] However, the authors failed to discuss other opposing studies, which did find that the variants of interest affected blood pressure salt sensitivity. [8] Given the main limitation of omitting highly relevant studies, which could alter the conclusions drawn, the authors should consider updating their methods and analysis to include all relevant studies.
On two-pair two-way relay channel with an intermittently available relay

When multiple users share the same resource for physical layer cooperation such as relay terminals in their vicinities, this shared resource may not be always available for every user, and it is critical for transmitting terminals to know whether other users have access to that common resource in order to better utilize it. Failing to learn this critical piece of information may cause severe issues in the design of such cooperative systems. In this paper, we address this problem by investigating a two-pair two-way relay channel with an intermittently available relay. In the model, each pair of users need to exchange their messages within their own pair via the shared relay. The shared relay, however, is only intermittently available for the users to access. The accessing activities of different pairs of users are governed by independent Bernoulli random processes. Our main contribution is the characterization of the capacity region to within a bounded gap in a symmetric setting, for both delayed and instantaneous state information at transmitters. An interesting observation is that the bottleneck for information flow is the quality of state information (delayed or instantaneous) available at the relay, not those at the end users. To the best of our knowledge, our work is the first result regarding how the shared intermittent relay should cooperate with multiple pairs of users in such a two-way cooperative network.
Vector quantized phase shift analog beamformers for millimeter-wave systems

Millimeter-wave (MMW) is a probable technology for the future cellular systems. Its main challenge is achieving sufficient operating link margin, and directional beamforming with large antenna arrays may be a viable approach. With bandwidths on the order of gigahertz, high-resolution analog-to-digital converters are a power consumption bottleneck. One solution is to employ an hybrid implementation, digital at baseband and analog at radio frequencies. In this paper we develop two iterative hybrid beamforming design algorithms for the MMW channel, using vector quantization of the analog beamformers. The proposed algorithms accounts for the RF precoding constraints and assumes the channel matrix is known but not the ray phase vector responses. We compare the proposed algorithms with the state-of-art hybrid schemes and the simulation results show that performance of the proposed algorithms can approximate that of the maximum-ratio-beamforming upper bound even if computational complexity may be higher for systems with small number of antennas.
Ontology Based Semantic Measures in Document Similarity Ranking

Recent work has shown that ontologies are useful to improve the performance of retrieval. In this paper, we present a new distance measure using ontologies. Ontology based correlation analysis is implemented to find the relations between the terms. Combining the ontology based correlation analysis and the traditional vector space model, the document similarity is calculated. Our results show that ontology based distance measure makes better relevance measure. The proposed method has been evaluated on USGS Science directory collection. Preliminary experiments results show that our method may generate relevant document in the top rank.
Aqueous Angiopoietin-Like 4 Levels Correlate With Nonperfusion Area and Macular Edema in Branch Retinal Vein Occlusion.

PURPOSE To investigate whether macular edema (ME) due to branch retinal vein occlusion (BRVO) associates with retinal overexpression of angiopoietin-like 4 (ANGPTL4). The aqueous ANGPTL4 and vascular endothelial growth factor (VEGF) levels in patients with ME due to BRVO were measured, and the relationships between ANGPTL4 levels and the degree of retinal ischemia and edema were determined. METHODS The study and control groups consisted of all consecutive patients who were scheduled to undergo intravitreal bevacizumab injection for treatment-naïve BRVO with ME and senile cataract surgery, respectively. The study group was divided into the major BRVO and macular BRVO subgroups on the basis of the involved retinal area. The aqueous ANGPTL4 and VEGF levels were measured by enzyme-linked immunosorbent assay. In the patients with BRVO, capillary nonperfusion area by fluorescein angiography and central subfield macular thickness (CSMT) and total macular volume (TMV) by spectral-domain optical coherence tomography were determined. RESULTS Patients with ME due to BRVO (50 eyes) had higher aqueous ANGPTL4 and VEGF levels than the controls (61 eyes) (both P < 0.001). The major BRVO had higher ANGPTL4 and VEGF levels than the macular BRVO (both P < 0.001). The aqueous ANGPTL4 levels of all BRVO patients correlated positively with nonperfusion area (r = 0.901, P < 0.001), CSMT (r = 0.574, P < 0.001), and TMV (r = 0.453, P = 0.001), even after adjustment for VEGF levels. CONCLUSIONS The aqueous ANGPTL4 levels correlated significantly with phenotypes of BRVO with ME. This suggests that ANGPTL4 may be a candidate biomarker and treatment target in ischemia-induced retinopathies, including BRVO.
Toward Studying Music Cognition with Information Retrieval Techniques: Lessons Learned from the OpenMIIR Initiative

As an emerging sub-field of music information retrieval (MIR), music imagery information retrieval (MIIR) aims to retrieve information from brain activity recorded during music cognition–such as listening to or imagining music pieces. This is a highly inter-disciplinary endeavor that requires expertise in MIR as well as cognitive neuroscience and psychology. The OpenMIIR initiative strives to foster collaborations between these fields to advance the state of the art in MIIR. As a first step, electroencephalography (EEG) recordings of music perception and imagination have been made publicly available, enabling MIR researchers to easily test and adapt their existing approaches for music analysis like fingerprinting, beat tracking or tempo estimation on this new kind of data. This paper reports on first results of MIIR experiments using these OpenMIIR datasets and points out how these findings could drive new research in cognitive neuroscience.
SASeS: A Framework for the Development of Service-based Self-adaptive Applications

Self-adaptive Systems (SaS) enable the structural or behavioral adaptation at runtime in response to context changes or user's new needs without interruption in their execution. In service-based SaS, the adaptation activity can be considered as a complex activity, since such systems need to modify or replace a service (e.g., due to an unforeseen situation or failure) at runtime without perception of their stakeholders (i.e., client of these services). Based on this scenario, a framework called SASeS (Self-Adaptive Service-based System) was design. In short, this framework was developed based on web services standards and design patterns that support common tasks in the development of such systems. Moreover, SASeS provides a mechanism for the management of the control loop (or feedback loop), which enables constantly self-evaluating (i.e., monitor, analyze, plan, and execute) the adaptation activity. In order to show the applicability of our framework, two case studies are reported in this paper.
Adaptive Robust Control of Servo Mechanisms With Compensation for Nonlinearly Parameterized Dynamic Friction

In this brief, an adaptive robust control (ARC) scheme with compensation for nonlinearly parameterized dynamic friction is proposed. Both parametric uncertainties and external disturbances are considered in this method. Our method takes advantage of a Lipschitzian property with respect to the parameters of nonlinearly parameterized model in the ARC design. The outcome is that the number of parameters to be updated in the ARC is equal to the number of unknown parameters in the plant, and thus the resulting control algorithm is convenient to be implemented. We have proved theoretically that the proposed method can not only guarantee desired transient performance for the system, but also make the magnitude of steady-state tracking error to be arbitrarily small in the presence of parametric uncertainties only. Experimental results are given to demonstrate the effectiveness of the proposed ARC scheme.