Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular human immunodeficiency virus type 1 Tat protein promotes aggregation and adhesion of cerebellar neurons

Recombinant human immunodeficiency virus (HIV-1) Tat protein added to the culture medium of rat cerebellar neurons promoted aggregation and formation of spoke-like neurites in a dose-dependent manner. Tat proteins containing mutations in the Arg-Gly-Asp (RGD) cell adhesion motif or a deletion of the cysteine-rich domain had no effect on neuronal morphology. In contrast, a Tat protein that contained a deletion of the proline-rich domain promoted neuronal aggregation. Aggregation of neurons was inhibited by the addition of monoclonal antibodies directed against the RGD and basic domains of Tat, but not against the proline-rich domain. The same domains of Tat required to induce aggregation also mediated adhesion of neurons to Tat-coated substrates. The HIV-2 Tat protein, which lacks an RGD sequence but contains cysteine-rich and basic domains similar to HIV-1 Tat, induced aggregation and acted as a substrate for adhesion when added at higher concentrations than HIV-1 Tat. Vitronectin, fibronectin, and RGD- containing peptides did not induce morphological changes in neurons or act as substrates for adhesion. The ability of Tat to induce morphological changes and promote adhesion was independent of the ability of Tat to transactivate HIV gene expression. Our results suggest that extracellular Tat protein most likely alters neuronal morphology and mediates adhesion by acting in a manner similar to an extracellular matrix protein.
Information theoretic operating regimes of large wireless networks

In analyzing the point-to-point wireless channel, insights about two qualitatively different operating regimes-bandwidth- and power-limited-have proven indispensable in the design of good communication schemes. In this paper, we propose a new scaling law formulation for wireless networks that allows us to develop a theory that is analogous to the point-to-point case. We identify fundamental operating regimes of wireless networks and derive architectural guidelines for the design of optimal schemes. Our analysis shows that in a given wireless network with arbitrary size, area, power, etc., there are three parameters of importance: the short-distance SNR, the long-distance SNR, and the power path loss exponent. Depending on these parameters we identify four qualitatively different regimes. One of these regimes is especially interesting since it is fundamentally a consequence of the heterogeneous nature of links in a network and does not occur in the point-to-point case; the network capacity is both power- and bandwidth-limited. This regime has thus far remained hidden due to the limitations of the existing formulation. Existing schemes, either multihop transmission or hierarchical cooperation, fail to achieve capacity in this regime; we propose a new hybrid scheme that achieves capacity.
Support for arbitrary regions in XSL-FO

This paper proposes an extension of the XSL-FO standard which allows the specification of an unlimited number of arbitrarily shaped page regions. These extensions are built on top of XSL-FO 1.1 to enable flow content to be laid out into arbitrary shapes and allowing for page layouts currently available only to desktop publishing software. Such a proposal is expected to leverage XSL-FO towards usage as an enabling technology in the generation of content intended for personalized printing.
A distributed CSMA algorithm for throughput and utility maximization in wireless networks

In multi-hop wireless networks, designing distributed scheduling algorithms to achieve the maximal throughput is a challenging problem because of the complex interference constraints among different links. Traditional maximal-weight (MW) scheduling, although throughput-optimal, is difficult to implement in distributed networks; whereas a distributed greedy protocol similar to IEEE 802.11 does not guarantee the maximal throughput. In this paper, we introduce an adaptive CSMA scheduling algorithm that can achieve the maximal throughput distributedly under some assumptions. Major advantages of the algorithm include: (1) It applies to a very general interference model; (2) It is simple, distributed and asynchronous. Furthermore, we combine the algorithm with end-to-end flow control to achieve the optimal utility and fairness of competing flows. The effectiveness of the algorithm is verified by simulations. Finally, we consider some implementation issues in the setting of 802.11 networks.
Smoothing Spline Mixed Effects Modeling of Multifactorial Gene Expression Profiles

The analysis of time-course microarray data is challenging because of the wide range of gene expression patterns, multiple sources of variation, and dependency of the measurements. The performance of smoothing spline mixed effects models to describe time-dependent gene expression trajectories, technical and experimental sources of variation were studied. The comparison of spline, polynomial ANCOVA and ANOVA models allowed us to characterize the balance between model simplicity and adequacy to describe microarray element expression trajectories. Gene expression measurements at honey bee behavioral maturation time points with, with deviations from the overall pattern across honey bee races and host colonies were analyzed. Complementary criteria were used to compare model adequacy including, visual comparison of expression trajectories, number of microarray elements with significant time-dependent terms and consistent time-dependent trends across models. Spline models were favored for the vast majority of the microarray elements when model fit and model simplicity criteria were considered.
Decentralized prognosis of failures in discrete event systems

We study the prognosis of failures, i.e., their prediction prior to their occurrence, in discrete event systems in a decentralized setting where multiple prognosers use their local observations to issue local prognosis decisions. We define the notion of correctness of a decentralized set of prognosers in terms of ldquono missed detectionsrdquo (each failure is prognosed prior to its occurrence) and ldquono false alarmsrdquo (an incorrect prognostic decision is never issued), and introduce the notion of coprognosability as an existence condition. When specialized to the centralized case (i.e., the case of a single prognoser), this condition turns out to be weaker than the one introduced in (S. Gene and Sl Lafortune, 2006) since a uniform bound on the number of steps within which a failure will occur is not required. For comparison we also introduce the stronger notion of ldquouniformly bounded coprognosabilityrdquo and identify the subclass of decentralized prognosers for which it serves as an existence condition. We show that the two notions coincide when the underlying system and its nonfailure specification possess finite-state representations, and present a verification algorithm. We also introduce the notion of reaction bound for coprognosis as the earliest time beyond a prognostic decision when a failure can occur, and present an algorithm for computing it. An algorithm is also presented for an online prognosis of failures. We show that the notions of coprognosability and its uniformly bounded version are in general incomparable with the notion of codiagnosability (that guarantees a uniformly bounded delay detection of a failure by a local diagnoser). When the system cannot execute an unbounded sequence of unobservable events, uniformly bounded coprognosability implies codiagnosability, whereas coprognosability and codiagnosability remain incomparable.
Genome-Wide Screen for Salmonella Genes Required for Long-Term Systemic Infection of the Mouse

A microarray-based negative selection screen was performed to identify Salmonella enterica serovar Typhimurium (serovar Typhimurium) genes that contribute to long-term systemic infection in 129X1/SvJ (Nramp1r) mice. A high-complexity transposon-mutagenized library was used to infect mice intraperitoneally, and the selective disappearance of mutants was monitored after 7, 14, 21, and 28 d postinfection. One hundred and eighteen genes were identified to contribute to serovar Typhimurium infection of the spleens of mice by 28 d postinfection. The negatively selected mutants represent many known aspects of Salmonella physiology and pathogenesis, although the majority of the identified genes are of putative or unknown function. Approximately 30% of the negatively selected genes correspond to horizontally acquired regions such as those within Salmonella pathogenicity islands (SPI 1–5), prophages (Gifsy-1 and −2 and remnant), and the pSLT virulence plasmid. In addition, mutations in genes responsible for outer membrane structure and remodeling, such as LPS- and PhoP-regulated and fimbrial genes, were also selected against. Competitive index experiments demonstrated that the secreted SPI2 effectors SseK2 and SseJ as well as the SPI4 locus are attenuated relative to wild-type bacteria during systemic infection. Interestingly, several SPI1-encoded type III secretion system effectors/translocases are required by serovar Typhimurium to establish and, unexpectedly, to persist systemically, challenging the present description of Salmonella pathogenesis. Moreover, we observed a progressive selection against serovar Typhimurium mutants based upon the duration of the infection, suggesting that different classes of genes may be required at distinct stages of infection. Overall, these data indicate that Salmonella long-term systemic infection in the mouse requires a diverse repertoire of virulence factors. This diversity of genes presumably reflects the fact that bacteria sequentially encounter a variety of host environments and that Salmonella has evolved to respond to these selective forces in a way that permits both the bacteria and the host to survive.
Decentralized quadratically approximated alternating direction method of multipliers

This paper considers an optimization problem that components of the objective function are available at different nodes of a network and nodes are allowed to only exchange information with their neighbors. The decentralized alternating method of multipliers (DADMM) is a well-established iterative method for solving this category of problems; however, implementation of DADMM requires solving an optimization subproblem at each iteration for each node. This procedure is often computationally costly for the nodes. We introduce a decentralized quadratic approximation of ADMM (DQM) that reduces computational complexity of DADMM by minimizing a quadratic approximation of the objective function. Notwithstanding that DQM successively minimizes approximations of the cost, it converges to the optimal arguments at a linear rate which is identical to the convergence rate of DADMM. Further, we show that as time passes the coefficient of linear convergence for DQM approaches the one for DADMM. Numerical results demonstrate the effectiveness of DQM.
Safety in numbers: Learning categories from few examples with multi model knowledge transfer

Learning object categories from small samples is a challenging problem, where machine learning tools can in general provide very few guarantees. Exploiting prior knowledge may be useful to reproduce the human capability of recognizing objects even from only one single view. This paper presents an SVM-based model adaptation algorithm able to select and weight appropriately prior knowledge coming from different categories. The method relies on the solution of a convex optimization problem which ensures to have the minimal leave-one-out error on the training set. Experiments on a subset of the Caltech-256 database show that the proposed method produces better results than both choosing one single prior model, and transferring from all previous experience in a flat uninformative way.
Fat-soluble vitamin deficiency in children with intestinal failure receiving home parenteral nutrition.

T o the Editor: Ubesie et al (1) reported a high prevalence of vitamin D deficiency (39.8%) in children with intestinal failure (IF). We routinely monitored vitamin A, E, and D levels every 6 months for children who were receiving home parenteral nutrition for IF, following European Society for Pediatric Gastroenterology, Hepatology, and Nutrition guidelines (2). In 2013, we completed a cross-sectional assessment of 32 home parenteral nutrition patients who had fat-soluble vitamin levels measured for 1 year. Twenty children with nonsurgical IF (dysmotility and malabsorption) (group A) and 12 with surgical IF (short bowel syndrome) (group B) were included in the study. All of the patients received daily parenteral nutrition with a standard pediatric multivitamin formulation containing vitamin A, 3500 IU; vitamin D, 250 IU; and vitamin E, 11.20 IU. Vitamin levels were low in groups A and B, respectively, as follows: vitamin A in 5 (25%) and 4 (30%), vitamin D in 9 (45%) and 4 (30%), and vitamin E in 2 (10%) and 0. Overall, 15 patients in group A (75%) and 6 patients in group B (50%) showed low levels of fat-soluble vitamins. The likelihood of low fat-soluble vitamin levels was significantly greater in nonsurgical IF than in patients with short bowel syndrome (odds ratio 6, 95% confidence interval 1.5–24.5). Thus, we agree that routine surveillance of fat-soluble vitamins and consideration of enteral or parenteral supplementation, including periodic intramuscular injection, may be useful in children with IF.
Whole Liver Versus Split Liver Versus Living Donor in the Adult Recipient—An Analysis of Outcomes by Graft Type

Background. We studied patient and graft survival rates in adult liver transplant recipients, analyzing outcomes based on donor source (deceased donor [DD] vs. living donor [LD]) and graft type (whole liver vs. partial liver). Methods. A retrospective database analysis of all adult liver transpants performed at our center over a 7-year period of time. Results. Between 1999 and 2005, 384 liver transplants were performed in adult recipients, either as a whole liver from a deceased donor (DD-WL, n=284), split liver from a DD (DD-SL, n=31), or a partial transplant from a living donor (LD, n=69). DD-SL transplants were performed with a full right or left lobe graft, while LD transplants used the right lobe. Demographic differences in the three groups were most noticeable for lower model for end-stage liver disease scores in LD recipients (P<0.001) and younger donor age in DD-SL recipients (P<0.001). Superior graft survival results were seen in LD recipients versus either DD-WL recipients or DD-SL recipients (P=0.02 and P=0.05, respectively). Multivariate analysis showed hepatitis C (HR=1.53, P=0.05) and hepatocellular carcinoma (HR=1.74, P=0.03) to be significant risk factors for patient survival. Hepatitis C (HR=1.61, P=0.03) and donor age more than 50 (HR=1.64, P=0.04) were significant risk factors for graft survival. However, neither graft type nor donor source were significant independent risk factors for patient or graft survival. Conclusions. Our data suggests that the status of the recipient is probably a more important determinant of outcome than graft type or donor source.
Subcarrier-Pair Based Resource Allocation for Cooperative AF Multi-Relay OFDM Systems

In this paper, we study the joint allocation of three types of resources, namely, power, subcarriers and relay nodes, in multi-relay assisted dual-hop cooperative OFDM systems. All the relays adopt the amplify-and-forward protocol and assist the transmission from the source to destination simultaneously but on orthogonal subcarriers. The objective is to maximize the system transmission rate subject to individual power constraints on each node or a total network power constraint. We formulate such a problem as a subcarrier-pair based resource allocation that seeks the joint optimization of subcarrier pairing, subcarrier-pair-to-relay assignment, and power allocation. Using a dual approach, we solve this problem efficiently in an asymptotically optimal manner. Specifically, for the optimization problem with individual power constraints, the computational complexity is polynomial in the number of subcarriers and relay nodes, whereas the complexity of the problem with a total power constraint is polynomial in the number of subcarriers.We further propose two suboptimal algorithms for the former to trade off performance for complexity. Simulation studies are conducted to evaluate the average transmission rate and outage probability of the proposed algorithms. The impact of relay location is also discussed.
Impact of oxidative and osmotic stresses on Candida albicans biofilm formation

Abstract Candida albicans possesses an ability to grow under different host-driven stress conditions by developing robust protective mechanisms. In this investigation the focus was on the impact of osmotic (2M NaCl) and oxidative (5 mM H2O2) stress conditions during C. albicans biofilm formation. Oxidative stress enhanced extracellular DNA secretion into the biofilm matrix, increased the chitin level, and reduced virulence factors, namely phospholipase and proteinase activity, while osmotic stress mainly increased extracellular proteinase and decreased phospholipase activity. Fourier transform infrared and nuclear magnetic resonance spectroscopy analysis of mannan isolated from the C. albicans biofilm cell wall revealed a decrease in mannan content and reduced β-linked mannose moieties under stress conditions. The results demonstrate that C. albicans adapts to oxidative and osmotic stress conditions by inducing biofilm formation with a rich exopolymeric matrix, modulating virulence factors as well as the cell wall composition for its survival in different host niches.
Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum

Resolving the physiological mechanisms by which rhizobacteria enhance plant growth is difficult, since many such bacteria contain multiple plant growth-promoting properties. To understand further how the 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCd)-containing rhizobacterium Variovorax paradoxus 5C-2 affects plant growth, the flows and partitioning of mineral nutrients and abscisic acid (ABA) and ABA metabolism were studied in pea (Pisum sativum) plants following rhizosphere bacterial inoculation. Although root architecture was not affected, inoculation increased root and shoot biomass, and stomatal conductance, by 20, 15, and 24%, respectively, and increased N, P, K, Ca, and Mg uptake by 16, 81, 50, 46, and 58%, respectively. P deposition in inoculated plant roots was 4.9 times higher than that in uninoculated controls. Rhizobacterial inoculation increased root to shoot xylem flows and shoot to root phloem flows of K by 1.8- and 2.1-fold, respectively. In control plants, major sinks for K deposition were the roots and upper shoot (43% and 49% of total uptake, respectively), while rhizobacterial inoculation increased K distribution to the lower shoot at the expense of other compartments (xylem, phloem, and upper shoot). Despite being unable to metabolize ABA in vitro, V. paradoxus 5C-2 decreased root ABA concentrations and accumulation by 40–60%. Although inoculation decreased xylem ABA flows, phloem ABA flows increased. Whether bacterial ACCd attenuates root to shoot ABA signalling requires further investigation, since ABA is critical to maintain growth of droughted plants, and ACCd-containing organisms have been advocated as a means of minimizing growth inhibition of plants in drying soil.
Controlling murine and rat chronic pain through A3 adenosine receptor activation

Clinical management of chronic neuropathic pain is limited by marginal effectiveness and unacceptable side effects of current drugs. We demonstrate A3 adenosine receptor (A3AR) agonism as a new target‐based therapeutic strategy. The development of mechanoallodynia in a well‐characterized mouse model of neuropathic pain following chronic constriction injury of the sciatic nerve was rapidly and dose‐depend‐ently reversed by the A3AR agonists: IB‐MECA, its 2‐chlorinated analog (Cl‐IB‐MECA), and the structurally distinct MRS1898. These effects were naloxone insensitive and thus are not opioid receptor mediated. IB‐MECA was ≥1.6‐fold more efficacious than morphine and >5‐fold more potent. In addition, IB‐MECA was equally efficacious as gabapentin (Neurontin) or amitriptyline, but respectively >350‐ and >75‐fold more potent. Besides its potent standalone ability to reverse established mechanoallodynia, IB‐MECA significantly increased the antiallodynic effects of all 3 analgesics. Moreover, neuropathic pain development in rats caused by widely used chemotherapeutics in the taxane (paclitaxel), platinum‐complex (oxaliplatin), and proteasome‐inhibitor (bortezomib) classes was blocked by IB‐MECA without antagonizing their antitumor effect. A3AR agonist effects were blocked with A3AR antagonist MRS1523, but not with A1AR (DPCPX) or A2AAR (SCH‐442416) antagonists. Our findings provide the scientific rationale and pharmacological basis for therapeutic development of A3AR agonists for chronic pain. —Chen, Z. , Janes, K. , Chen, C. , Doyle, T. , Bryant, L. , Tosh, D.K. , Jacobson, K.A. , Salvemini, D. Controlling murine and rat chronic pain through A3 adenosine receptor activation. FASEB J. 26, 1855‐1865 (2012). www.fasebj. org
Experimental assessment of CT-based thermometry during laser ablation of porcine pancreas

Laser interstitial thermotherapy (LITT) is employed to destroy tumors in organs, and its outcome strongly depends on the temperature distribution inside the treated tissue. The recent introduction of computed tomography (CT) scan thermometry, based on the CT number dependence of the tissue with temperature, overcomes the invasiveness of other techniques used to monitor temperature during LITT. The averaged CT number (ROI = 0.02 cm2) of an ex vivo swine pancreas is monitored during LITT (Nd:YAG laser power of 3 W, treatment time: 120 s) at different distances from the applicator (from 4 to 30 mm). The averaged CT number shows a clear decrease during treatment: it is highest at 4 mm from the applicator (mean variation in the whole treatment of −0.256 HU s−1) and negligible at 30 mm, since the highest temperature increase is present close to the applicator (i.e., 45 °C at 4 mm and 25 °C at 6 mm). To obtain the relationship between CT numbers and pancreas temperature, the reference temperature was measured by 12 fiber Bragg grating sensors. The CT number decreases as a function of temperature, showing a nonlinear trend with a mean thermal sensitivity of −0.50 HU °C−1. Results here reported are the first assessment of pancreatic CT number dependence on temperature, at the best of our knowledge. Findings can be useful to further investigate CT scan thermometry during LITT on the pancreas.