Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Polyphosphate Additives on Campylobacter Survival in Processed Chicken Exudates

ABSTRACT Campylobacter spp. are responsible for a large number of the bacterial food poisoning cases worldwide. Despite being sensitive to oxygen and nutritionally fastidious, Campylobacter spp. are able to survive in food processing environments and reach consumers in sufficient numbers to cause disease. To investigate Campylobacter persistence on processed chicken, exudates from chickens produced for consumer sale were collected and sterilized. Two types of exudates from chicken products were collected: enhanced, where a marinade was added to the chickens during processing, and nonenhanced, where no additives were added during processing. Exudates from enhanced chicken products examined in this study contained a mixture of polyphosphates. Exudate samples were inoculated with Campylobacter jejuni or Campylobacter coli strains and incubated under a range of environmental conditions, and viable bacteria present in the resultant cultures were enumerated. When incubated at 42°C in a microaerobic environment, exudates from enhanced chicken products resulted in increased survival of C. jejuni and C. coli compared with that in nonenhanced exudates in the range of <1 to >4 log CFU/ml. Under more relevant food storage conditions (4°C and normal atmosphere), the exudates from enhanced chicken products also demonstrated improved Campylobacter survival compared with that in nonenhanced exudates. Polyphosphates present in the enhanced exudates were determined to be largely responsible for the improved survival observed when the two types of exudates were compared. Therefore, polyphosphates used to enhance chicken quality aid in sustaining the numbers of Campylobacter bacteria, increasing the opportunity for disease via cross-contamination or improperly cooked poultry.
Model of c-axis resistivity of high-Tc cuprates.

We propose a simple model which accounts for the major features and systematics of experiments on the {ital c}=axis resistivity, {rho}{sub {ital c}} for La{sub 2{minus}{ital x}}Sr{sub {ital x}}CuO{sub 4}, YBa{sub 2}Cu{sub 3}O{sub 6+{ital x}}, and Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8}. We argue that the {ital c}-axis resistivity can be separated into contributions from in-plane dephasing and the {ital c}-axis {open_quote}{open_quote}barrier{close_quote}{close_quote} scattering processes, with the low-temperature semiconductorlike behavior of {rho}{sub {ital c}} arising from the suppression of the in-plane density of states measured by in-plane magnetic Knight shift experiments. We report on predictions for {rho}{sub {ital c}} in impurity-doped YBa{sub 2}Cu{sub 3}O{sub 6+{ital x}} materials. {copyright} {ital 1996 The American Physical Society. }
Prognostic Value of Human Equilibrative NucleosideTransporter1 in Pancreatic Cancer Receiving Gemcitabin-Based Chemotherapy: A Meta-Analysis

Background The potential prognostic value of human equilibrative nucleoside transporter1 in pancreatic cancer receiving gemcitabine-based chemotherapy is variably reported. Objective The objective of this study was to conduct a systematic review of literature evaluating human equilibrative nucleoside transporter1 expression as a prognostic factor in pancreatic cancer receiving gemcitabine-based chemotherapy and to conduct a subsequent meta-analysis to quantify the overall prognostic effect. Methods Related studies were identified and evaluated for quality through multiple search strategies. Only studies analyzing pancreatic cancer receiving gemcitabine-based chemotherapy were eligible for inclusion. Data were collected from studies comparing overall, disease-free and progression-free survival (OS, DFS and PFS) in patients with low human equilibrative nucleoside transporter1 levels and those having high levels. The hazard ratio (HR) and its 95% confidence interval (95%CI) were used to assess the strength of associations. Hazard ratios greater than 1 reflect adverse survival associated with low human equilibrative nucleoside transporter1 levels. Results A total of 12 studies (n = 875) were involved in this meta-analysis (12 for OS, 5 for DFS, 3 for PFS). For overall and disease-free survival, the pooled HRs of human equilibrative nucleoside transporter1 were significant at 2.93 (95% confidence interval [95% CI], 2.37–3.64) and 2.67 (95% CI, 1.87–3.81), respectively. For progression-free survival, the pooled HR in higher human equilibrative nucleoside transporter1 expression in pancreatic cancer receiving gemcitabine-based chemotherapy was 2.76 (95% CI, 1.76–4.34). No evidence of significant heterogeneity or publication bias was seen in any of these studies. Conclusion These results support the case for a low human equilibrative nucleoside transporter1 level representing a significant and reproducible marker of adverse prognosis in pancreatic cancer receiving gemcitabine-based chemotherapy.
Gemcitabine Selectively Eliminates Splenic Gr-1+/CD11b+ Myeloid Suppressor Cells in Tumor-Bearing Animals and Enhances Antitumor Immune Activity

Purpose: Myeloid suppressor (Gr-1+/CD11b+) cells accumulate in the spleens of tumor-bearing mice where they contribute to immunosuppression by inhibiting the function of CD8+ T cells and by promoting tumor angiogenesis. Elimination of these myeloid suppressor cells may thus significantly improve antitumor responses and enhance effects of cancer immunotherapy, although to date few practical options exist. Experimental Design: The effect of the chemotherapy drug gemcitabine on the number of (Gr-1+/CD11b+) cells in the spleens of animals bearing large tumors derived from five cancer lines grown in both C57Bl/6 and BALB/c mice was analyzed. Suppressive activity of splenocytes from gemcitabine-treated and control animals was measured in natural killer (NK) cell lysis and Winn assays. The impact of myeloid suppressor cell activity was determined in an immunogene therapy model using an adenovirus expressing IFN-β. Results: This study shows that the chemotherapeutic drug gemcitabine, given at a dose similar to the equivalent dose used in patients, was able to dramatically and specifically reduce the number of myeloid suppressor cells found in the spleens of animals bearing large tumors with no significant reductions in CD4+ T cells, CD8+ T cells, NK cells, macrophages, or B cells. The loss of myeloid suppressor cells was accompanied by an increase in the antitumor activity of CD8+ T cells and activated NK cells. Combining gemcitabine with cytokine immunogene therapy using IFN-β markedly enhanced antitumor efficacy. Conclusions: These results suggest that gemcitabine may be a practical strategy for the reduction of myeloid suppressor cells and should be evaluated in conjunction with a variety of immunotherapy approaches.
On hierarchical content-based image retrieval by dynamic indexing and guided search

This paper presents a new approach to content-based image retrieval by using dynamic indexing and guided search in a hierarchical structure, and extending date mining and data warehousing techniques. The proposed algorithms include: a wavelet-based scheme for multiple image feature extraction, the extension of a conventional data warehouse and an image database to an image data warehouse for dynamic image indexing, an image data schema for hierarchical image representation and dynamic image indexing, a statistically based feature selection scheme to achieve flexible similarity measures, and a feature component code to facilitate query processing and guide the search for the best matching. A series of case studies are reported, which include a wavelet-based image color hierarchy, classification of satellite images, tropical cyclone pattern recognition, and personal identification using multi-level palmprint and face features.
Linear MMSE Multi-User MIMO Downlink Precoding for Users with Multiple Antennas

In this paper, the multi-user MIMO downlink channel is considered, where a single transmitter (base station) sends data to several users within the same resource unit. Assuming perfect channel state information (CSI) at the transmitter, different linear precoding schemes are studied, aiming at mean square error minimizing transmission to all users. The exact MMSE solution can be obtained by exploiting uplink/downlink duality. A suboptimal solution based on necessary conditions for MMSE optimality may also be computed directly in the downlink domain. Our results indicate that the performance difference between the direct and duality-based method that is visible in uncoded BER curves vanishes when channel coding is introduced to the system. We also compare the MMSE-optimal approaches to other existing linear precoding schemes (BD, S-MMSE)
Cystatin C– and Creatinine-Based Estimated Glomerular Filtration Rate, Vascular Disease, and Mortality in Persons With Diabetes in the U.S.

OBJECTIVE Serum cystatin C is an alternative to serum creatinine for estimating glomerular filtration rate (GFR), since cystatin C is less influenced by age and muscle mass. Among persons with diabetes, we compared the performance of GFR estimated using cystatin C (eGFRcys) with that using creatinine (eGFRcr) for the identification of reduced kidney function and its association with diabetes complications. RESEARCH DESIGN AND METHODS We analyzed data from adult participants from the 1999–2002 National Health and Nutrition Examination Survey with available cystatin C (N = 4,457). Kidney function was dichotomized as preserved (eGFR ≥60 mL/min/1.73 m2) or reduced (eGFR <60 mL/min/1.73 m2) using the 2012 Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) cystatin C and the 2009 CKD-EPI creatinine equations. RESULTS Among 778 persons with diabetes, the prevalence of reduced kidney function was 16.5% using eGFRcr and 22.0% using eGFRcys. More persons with diabetes were reclassified from preserved kidney function by eGFRcr to reduced kidney function by eGFRcys than persons without diabetes (odds ratio 3.1 [95% CI 1.9–4.9], P < 0.001). The associations between lower eGFR and higher prevalence of albuminuria, retinopathy, peripheral arterial disease, and coronary artery disease were robust regardless of filtration marker. Similarly, the risk of all-cause mortality increased with lower eGFRcr and eGFRcys. Only lower eGFRcys was significantly associated with cardiovascular mortality. CONCLUSIONS More persons with diabetes had reduced kidney function by eGFRcys than by eGFRcr, and lower eGFRcys was strongly associated with diabetes complications. Whether eGFRcys is superior to eGFRcr in approximating true kidney function in a diabetic population requires additional study.
Decentralized resilient grid resource management overlay networks

Recently, grid and peer-to-peer overlays have attracted attention from research communities as well as industry. However, the overwhelming majority of industrial, commercial and academic activities are geared around applications, servers, and middleware. There have been some efforts in the management of the underlying networks (the connectivity for the overlays), but far from enough. This paper proposes a resilient, fault-adaptive, overlay resource management framework, with lightweight state management infrastructure, taken from some ongoing work by the authors in this area. This research aims to solve the problems of: (a) managing distributed network resources in a decentralized way; (b) providing resilient QoS for highly dynamic networks.
Efficient linear combination of partial Monte Carlo estimators

In many practical scenarios, including those dealing with large data sets, calculating global estimators of unknown variables of interest becomes unfeasible. A common solution is obtaining partial estimators and combining them to approximate the global one. In this paper, we focus on minimum mean squared error (MMSE) estimators, introducing two efficient linear schemes for the fusion of partial estimators. The proposed approaches are valid for any type of partial estimators, although in the simulated scenarios we concentrate on the combination of Monte Carlo estimators due to the nature of the problem addressed. Numerical results show the good performance of the novel fusion methods with only a fraction of the cost of the asymptotically optimal solution.
Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-Sequence Retaining Transcripts in Mouse and Rat Neurons

Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the neuronal CIRT KCNMA1i16 contributes to the firing properties of hippocampal neurons. Intronic sub-sequence retention within IL1-β mRNA in anucleate platelets has been implicated in activity-dependent splicing and translation. In a recent study, we showed CIRTs harbor functional SINE ID elements which are hypothesized to mediate dendritic localization in neurons. Based on these studies and others, we hypothesized that CIRTs may be present in a broad set of transcripts and comprise novel signals for post-transcriptional regulation. We carried out a transcriptome-wide survey of CIRTs by sequencing micro-dissected subcellular RNA fractions. We sequenced two batches of 150-300 individually dissected dendrites from primary cultures of hippocampal neurons in rat and three batches from mouse hippocampal neurons. After statistical processing to minimize artifacts, we found a broad prevalence of CIRTs in the neurons in both species (44-60% of the expressed transcripts). The sequence patterns, including stereotypical length, biased inclusion of specific introns, and intron-intron junctions, suggested CIRT-specific nuclear processing. Our analysis also suggested that these cytoplasmic intron-sequence retaining transcripts may serve as a primary transcript for ncRNAs. Our results show that retaining intronic sequences is not isolated to a few loci but may be a genome-wide phenomenon for embedding functional signals within certain mRNA. The results hypothesize a novel source of cis-sequences for post-transcriptional regulation. Our results hypothesize two potentially novel splicing pathways: one, within the nucleus for CIRT biogenesis; and another, within the cytoplasm for removing CIRT sequences before translation. We also speculate that release of CIRT sequences prior to translation may form RNA-based signals within the cell potentially comprising a novel class of signaling pathways.
Effect of Vehicle Mobility on Connectivity of Vehicular Ad Hoc Networks

Connectivity is a fundamental requirement in the planning, design and evaluation of vehicular ad hoc networks (VANET). In this paper, we propose a new equivalent speed parameter and develop an analytical model to explain the effect of vehicle mobility on the connectivity of highway segments in a VANET. We prove that the equivalent speed is different from the average vehicle speed and it decreases as the standard deviation of the vehicle speed increases. Using the equivalent speed we derive a novel analytical expression for the average number of vehicles on a highway segment, which allows us to accurately predict the network 1 connectivity. We verify the correctness of our analytical approach by comparing the numerical results with simulations. The results show that increasing the average vehicle speed increases the equivalent speed, which leads to a decrease in the average number of vehicles on a highway segment and consequently degrades connectivity. On the other hand increasing the standard deviation of the vehicle speed decreases the equivalent speed, which leads to an increase in the average number of vehicles on a highway segment and consequently improves connectivity. The results also show that vehicles in a VANET can adaptively choose their transmission range to ensure network connectivity in highway segments while minimising power consumption.
Displacement Mapping on the GPU — State of the Art

This paper reviews the latest developments of displacement mapping algorithms implemented on the vertex, geometry, and fragment shaders of graphics cards. Displacement mapping algorithms are classified as per-vertex and per-pixel methods. Per-pixel approaches are further categorized as safe algorithms that aim at correct solutions in all cases, to unsafe techniques that may fail in extreme cases but are usually much faster than safe algorithms, and to combined methods that exploit the robustness of safe and the speed of unsafe techniques. We discuss the possible roles of vertex, geometry, and fragment shaders to implement these algorithms. Then the particular GPU based bump, parallax, relief, sphere, horizon mapping, cone stepping, local ray tracing, pyramidal and view-dependent displacement mapping methods, as well as their numerous variations are reviewed providing also implementation details of the shader programs. We present these methods using uniform notations and also point out when different authors called similar concepts differently. In addition to basic displacement mapping, self-shadowing and silhouette processing are also reviewed. Based on our experiences gained having re-implemented these methods, their performance and quality are compared, and the advantages and disadvantages are fairly presented.
Adversarial Planning Through Strategy Simulation

Adversarial planning in highly complex decision domains, such as modern video games, has not yet received much attention from AI researchers. In this paper, we present a planning framework that uses strategy simulation in conjunction with Nash-equilibrium strategy approximation. We apply this framework to an army deployment problem in a real-time strategy game setting and present experimental results that indicate a performance gain over the scripted strategies that the system is built on. This technique provides an automated way of increasing the decision quality of scripted AI systems and is therefore ideally suited for video games and combat simulators
Excitatory Multimodal Interaction on Mobile Devices

Shoogle is a novel, intuitive interface for sensing data within a mobile device, such as presence and properties of text messages or remaining resources. It is based around active exploration: devices are shaken, revealing the contents rattling around “inside”. Vibrotactile display and realistic impact sonification create a compelling system. Inertial sensing is used for completely eyes-free, single-handed interaction that is entirely natural. Prototypes are described running both on a PDA and on a mobile phone with a wireless sensor pack. Scenarios of use are explored where active sensing is more appropriate than the dominant alert paradigm.
Fractional power-law behavior and its origin in iron-chalcogenide and ruthenate superconductors: Insights from first-principles calculations

We perform realistic first-principles calculations of iron chalcogenides and ruthenate based materials to identify experimental signatures of Hund's coupling induced correlations in these systems. We find that FeTe and K$_x$Fe$_{2-y}$Se$_2$ display unusual orbital dependent fractional powerlaw behavior in their quasiparticle self energy and optical conductivity, a phenomena first identified in SrRuO$_3$. Strong incoherence in the paramagnetic state of these materials results in electronic states hidden to angle-resolved photoemission spectroscopy which reemerge at low temperatures. We identify the effective low energy Hamiltonian describing these systems and show that these anomalies are not controlled by the proximity to a quantum critical point but result from coexistence of fast quantum mechanical orbital fluctuations and slow spin fluctuations.
A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda)

Abstract Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be monophyletic; a deep systematic reorganization of the order is thus needed and the present subfamilial system should be abandoned. The main characters on which the classical systematics of the group has been built, such as scolex morphology or relative position of genital organs in relation to the longitudinal musculature, are of limited value, as demonstrated by the very weak support for morphologically-defined subfamilies. However, new characters, such as the pattern of uterus development, relative ovary size, and egg structure have been identified, which may be useful in defining phylogenetically well-supported subgroups. A strongly supported lineage infecting various snakes from a wide geographical distribution was found. Although several improvements over previous works regarding phylogenetic resolution and taxon coverage were achieved in this study, the major polytomy in our tree, composed largely of siluriform parasites from the Neotropics, remained unresolved and possibly reflects a rapid radiation. The genus Spasskyellina Freze, 1965 is resurrected for three species of Monticellia bearing spinitriches on the margins of their suckers.
Pedestal Studies at ASDEX Upgrade

The ASDEX Upgrade suite of edge pedestal diagnostics has been significantly improved. A new edge ion temperature and toroidal velocity diagnostic as well as a novel diagnostic for radial electric fields (Er) have been added. The application of integrated data analysis in a probabilistic framework contributes substantially to the quality of Er and electron density profiles. The equilibrium reconstruction, taking into account scrape off layer (SOL) tile currents, renders equilibria on a 1 ms time base, which are used for mapping edge profile data synchronized to edge localised modes (ELMs). An example is shown, where the width of the pedestal pressure increases with NBI heating power, which can be assigned to ion and electron temperature profiles. The analysis of profiles over an ELM cycle shows that conclusions regarding the convective or conductive nature of an ELM can only be drawn with an accurate knowledge of the plasma position.