Miracle-dz/UniFAR-FTUs huggingface dataset:
ROR: An RSSI Based OMNI-Directional Routing Algorithm for GeoBroadcast in VANETs

Many broadcast protocols have been proposed in Vehicular ad-hoc Network (VANET) for safety applications and traffic efficiency. GeoBroadcast, which the sender sends information to the geographical area, has been standardized by the ETSI Technical Committee ITS. The routing protocol is a key technology satisfying communication requests of high reliability, low delay and universality for GeoBroadcast. However, there are few implementation and field test of routing protocol. This paper proposes a Received Signal Strength Indicator (RSSI) based Omni-Directional Routing (ROR) Algorithm. This protocol based on the combination of two protocols: the Greedy Forwarding (GF) that is a sender-based protocol, and the Contention-Based Forwarding (CBF) that is a receiver-based protocol. Furthermore, ROR takes RSSI, driving direction and dynamic scene into account. Meanwhile we conduct extensive field tests with more than twenty vehicles to evaluate the performance of vehicle communication in terms of Packet Loss Rate (PLR), Node Coverage Ratio (NCR) and Average End-to-End Delay (E2ED). By comparing the performance of CBF and Advanced Forwarding protocol with the ROR, ROR in real vehicle's environment has higher NCR and lower E2ED, in particular when the topology of the vehicles changes frequently in the target area.
Towards a Marketplace for the Scientific Community: Accessing Knowledge from the Computer Science Domain

As scientific output is constantly growing, it is getting more and more important to keep track not only for researchers but also for other scientific stakeholders such as funding agencies or research companies. Each stakeholder values different types of information. A funding agency, for instance, might be rather interested in the number of publications funded by their grants. However, information extraction approaches tend to be rather researcher-centric indicated, for example, by the type of named entities to be recognized. In this paper we account for additional perspectives by proposing an ontological description of one scientific domain � the computer science domain. We accordingly annotated a set of 22 computer science papers by hand and make this data set publicly available. In addition, we started to apply methods to automatically extract instances and report preliminary results. Taking various stakeholders' interests into account as well as automating the mining process represent prerequisites for our vision of a "Marketplace for the Scientific Community" where stakeholders can exchange not only information but also search concepts or annotated data.
Long-range identification of hepatocyte nuclear factor-3 (FoxA) high and low-affinity binding sites with a chimeric nuclease.

Identifying the complete set of transcription factors that bind the promoter and other regulatory regions of a gene of interest is an essential step in functional genomics. We have developed an original assay for the systematic detection of hepatocyte nuclear factor-3 (HNF-3) binding sites within cloned promoters. This assay is based on expression of a recombinant enzyme, HNF-3beta/FN, that is comprised of the rat HNF-3beta DNA-binding domain and the non-specific nuclease domain of the FokI restriction enzyme. Southern analysis of target plasmids with proven HNF-3 binding sites showed that HNF-3beta/FN was able to specifically cut both DNA strands in the vicinity of these binding sites, whereas mutagenized binding sites were no longer cleaved. Likewise, as yet undescribed HNF-3 binding sites were detected easily over a distance spanning several thousand bases. The functionality of such binding sites was confirmed by electromobility shift assay. Furthermore, the extent of cleavage by HNF-3beta/FN at a given binding site was tightly correlated with the affinity of a natural HNF-3beta molecule for this site. This novel approach can be extended to other transcription factors for long-range identification of functional transcription factor binding sites in genes.
Screens for Components of the lin-12 Notch Pathway during Vulval Development and Regulation of Anchor Cell Invasion and Uterine Cell Fates by the egl-43 Evi1 Proto-Oncogene in C. elegans

Cell invasion is a tightly controlled process occurring during development and tumor progression. The nematode Caenorhabditis elegans serves as a genetic model to study cell invasion during normal development. In the third larval stage, the anchor cell in the somatic gonad first induces and then invades the adjacent epidermal vulval precursor cells. The homolog of the Evi-1 oncogene, egl-43, is necessary for basement membrane destruction and anchor cell invasion. egl-43 is part of a regulatory network mediating cell invasion downstream of the fos-1 proto-oncogene. In addition, EGL-43 is required to specify the cell fates of ventral uterus cells downstream of or in parallel with LIN-12 NOTCH. Comparison with mammalian Evi-1 suggests a conserved pathway controlling cell invasion and cell fate specification. REGULATION OF ANCHOR CELL INVASION AND UTERINE CELL FATES BY THE EGL-43 EVI-1 PROTO-ONCOGENE IN C. ELEGANS Ivo Rimann and Alex Hajnal Institute of Zoology, University of Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland 1 Corresponding author Email: ahajnal@zool.uzh. ch Tel. +41-44-6354854, FAX +41-44-6356878
Interactions among roots, mycorrhizas and free‐living microbial communities differentially impact soil carbon processes

Plant roots, their associated microbial community and free‐living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant–microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free‐living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are present in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free‐living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil in situ in a temperate mixed deciduous forest. We added 13C‐labelled substrate to trace metabolized carbon in respiration and measured carbon‐degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13C‐labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free‐living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady‐state model simulations suggested that root presence increased mineral‐associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral‐associated organic carbon pools. Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root–mycorrhizal–microbial interactions. Using our experimental data in a decomposition simulation model, we show that root–mycorrhizal–microbial interactions may have longer‐term legacy effects on soil carbon sequestration. Overall, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.
Dynamical evolution of North Atlantic ridges and poleward Jet Stream displacements

The development of a particular wintertime atmospheric circulation regime over the North Atlantic, comprising a northward shift of the North Atlantic eddy-driven jet stream and an associated strong and persistent ridge in the subtropics, is investigated. Several different methods of analysis are combined to describe the temporal evolution of the events and relate it to shifts in the phase of the North Atlantic Oscillation and East Atlantic pattern. First, the authors identify a close relationship between northward shifts of the eddydriven jet, the establishment and maintenance of strong and persistent ridges in the subtropics, and the occurrence of upper-tropospheric anticyclonic Rossby wave breaking over Iberia. Clear tropospheric precursors are evident prior to the development of the regime, suggesting a preconditioning of the Atlantic jet stream and an upstream influence via a large-scale Rossby wave train from the North Pacific. Transient (2–6 days) eddy forcing plays a dual role, contributing to both the initiation and then the maintenance of the circulation anomalies. During the regime there is enhanced occurrence of anticyclonic Rossby wave breaking, which may be described as low-latitude blocking-like events over the southeastern North Atlantic. A strong ridge is already established at the time of wave-breaking onset, suggesting that the role of wave-breaking events is to amplify the circulation anomalies rather than to initiate them. Wave breaking also seems to enhance the persistence, since it is unlikely that a persistent ridge event occurs without being also accompanied by wave breaking.
General and unique partitioning of molecular electronic properties into atomic contributions.

We demonstrate that any first-order property can be uniquely partitioned into atomic contributions. The atomic contribution is given as a trace of the respective generalized atomic polar tensor and can be evaluated without invoking numerical integration. Partitionings of the potential energy in a model one-electron problem and of the electric charge in some molecules containing lithium atoms are used to illustrate the new formalism.
DISRUPTION OF BACTERIAL SPORES BY SUPERHEATING-A METHOD FOR FAST DNA RELEASE

Bacterial spores are forms of bacteria that are cap able of surviving in harsh conditions. We have inve stigated thermal lysis of the spores and subsequently release of their DNA . We were able to heat water-based samples at ambie nt pr ssure to temperatures far above 100 °C without boiling, known a s superheating process. It resulted in the breaking of spores in a matter of seconds. Successful release of DNA from spores of t he genus Bacillus was confirmed by real-time PCR (polymerase chain reaction). This process can be used for release DNA from Anthrax spores, allowing its presence to be d etected.
Soluble T Cell Immunoglobulin Mucin Domain 3 Is Shed from CD8+ T Cells by the Sheddase ADAM10, Is Increased in Plasma during Untreated HIV Infection, and Correlates with HIV Disease Progression

ABSTRACT Chronic HIV infection results in a loss of HIV-specific CD8+ T cell effector function, termed “exhaustion,” which is mediated, in part, by the membrane coinhibitory receptor T cell immunoglobulin mucin domain-3 (Tim-3). Like many other receptors, a soluble form of this protein has been described in human blood plasma. However, soluble Tim-3 (sTim-3) is poorly characterized, and its role in HIV disease is unknown. Here, we show that Tim-3 is shed from the surface of responding CD8+ T cells by the matrix metalloproteinase ADAM10, producing a soluble form of the coinhibitory receptor. Despite previous reports in the mouse model, no alternatively spliced, soluble form of Tim-3 was observed in humans. Shed sTim-3 was found in human plasma and was significantly elevated during early and chronic untreated HIV infection, but it was not found differentially modulated in highly active antiretroviral therapy (HAART)-treated HIV-infected subjects or in elite controllers compared to HIV-uninfected subjects. Plasma sTim-3 levels were positively correlated with HIV load and negatively correlated with CD4 counts. Thus, plasma sTim-3 shedding correlated with HIV disease progression. Despite these correlations, we found that shedding Tim-3 did not improve the function of CD8+ T cells in terms of gamma interferon production or prevent their apoptosis through galectin-9. Further characterization studies of sTim-3 function are needed to understand the contribution of sTim-3 in HIV disease pathogenesis, with implications for novel therapeutic interventions. IMPORTANCE Despite the overall success of HAART in slowing the progression to AIDS in HIV-infected subjects, chronic immune activation and T cell exhaustion contribute to the eventual deterioration of the immune system. Understanding these processes will aid in the development of interventions and therapeutics to be used in combination with HAART to slow or reverse this deterioration. Here, we show that a soluble form of T cell exhaustion associated coinhibitory molecule 3, sTim-3, is shed from the surface of T cells. Furthermore, sTim-3 is elevated in the plasma of treatment-naive subjects with acute or chronic HIV infection and is associated with markers of disease progression. This is the first study to characterize sTim-3 in human plasma, its source, and mechanism of production. While it is still unclear whether sTim-3 contributes to HIV pathogenesis, sTim-3 may represent a new correlate of HIV disease progression.
The relationship of ABH(O) blood group antigen expression in intraepithelial dysplastic lesions to clinicopathologic properties of associated transitional cell carcinoma of the bladder

Paraffin‐embedded, giant‐step sections of 13 bladders with transitional cell carcinomas were stained with monoclonal anti‐A or anti‐B antibodies to investigate whether intraepithelial dysplastic lesions are related to obvious tumors. Normal and/or hyperplastic lesions were retained in only eight bladders; severe dysplasia and/or carcinoma in situ were found in all bladders except two. AB‐antigen expression was retained in intraepithelial lesions of bladders with invasive carcinoma. Most intraepithelial lesions were AB‐antigen negative in bladders with frequently recurrent tumors. In bladders with initially multiple tumors, AB‐antigen expression was negative in almost one half of the intraepithelial lesions. Therefore, it appears likely that most multiple or recurrent bladder carcinomas arise from dysplastic cells in intraepithelial lesions which have acquired malignant potential; initially invasive tumors quickly develop from a limited lesion acquiring a high malignant potential without changes of cell phenotype in most intraepithelial lesions.
Immunochemical detection of sodium channel in human tissue and cell lines

Mouse monoclonal antibodies have been raised to the C–terminal region of rat type II voltage–dependent sodium channel. One of these, designated 13A4–G4, recognizes a 260 Kd putative sodium channel protein in human fetal brain, heart and skeletal muscle, at 14–18 weeks of gestation. Faint immunoreactivity is also present in human fetal kidney but none has been detected in human fetal liver, lung or spleen. The antibody reacts in both western blots and immunocytochemical preparations with the human neuroblastoma cell lines SK–N–SH and SK–N–MC, the rhabdomyoblastoma cell line TE671, Y79 retinoblastoma cells and IPSB–18 astrocytoma cells. No 13A4–G4 immunoreactivity has been detected in several human cell lines derived from tissues that do not normally express sodium channels.
STOCHASTIC ORDERS AND COMPARISON OF EXPERIMENTS

Exploring criteria for majorization, exact and approximate, univariate and multivariate, we relate them to criteria for information orderings of statistical experiments. After providing some basic criteria for comparison pf experiments, we observe their straightforward generalizations to general families of measures. Thus LeCam's randomization criterion extends to a criterion for comparing families of measures. Reversing the randomizations, we obtain dilation like kernels mapping densities, exactly or approximately, into densities. Using this, we derive criteria for comparison of measures in terms of integrals of given functions. In particular we obtain well-known criteria for one measure being a dilation of another measure and for stochastic orderings of distributions on partially ordered sets. Experiments having two point parameters sets, i.e. dichotomies, enjoy a variety of striking properties which are not shared by experiments in general. Dichotomies may be studied in terms of their Neyman-Pearson functions, which are functions describing the relationships between the probabilities of errors of the two kinds for most powerful tests. These functions are the inverses of the Lorenz functions of econometrics. Observing this, we readily obtain various criteria for one distribution being approximately Lorenz majorized by another.
A new method for determining the heat capacity change for protein folding.

In order to use results from calorimetry or thermal unfolding curves to estimate the free energy change for protein unfolding at 25 degrees C, it is necessary to know the change in heat capacity for unfolding, delta Cp. We describe a new method for measuring delta Cp which is based on results from urea and thermal unfolding curves but does not require a calorimeter. We find that delta Cp = 1650 +/- 200 cal/(deg.mol) for the unfolding of ribonuclease T1 and that delta Cp = 2200 +/- 300 cal/(deg.mol) for the unfolding of ribonuclease A.
Epidemiology and Prevention of Transfusion‐Associated Human Immunodeficiency Virus Transmission in Sub‐Saharan Africa

Background and objectives: Compared to industrialised nations, countries in sub‐Saharan Africa experience a greater amount of transfusion‐associated HIV transmission due to high rates of transfusion in some groups of patients, a higher incidence and prevalence of HIV infection in donor populations, a lack of HIV antibody screening in some areas, and a higher residual risk of contamination in blood supplies despite antibody screening. Materials and methods: Epidemiologic review. Results: Epidemiologic evidence supports the effectiveness of three relatively inexpensive strategies to prevent transfusion‐associated HIV transmission in sub‐Saharan Africa: HIV antibody screening, avoidance of unnecessary use of blood products, and exclusion of donors at high risk of infection. Such prevention strategies have not been universally implemented. Conclusions: International aid to establish and maintain HIV antibody screening programmes, implementation of sound criteria for transfusion, and the search for HIV risk factors to use as donor exclusion criteria must be expanded in the region.
Characterization of responses of T2-T4 spinal cord neurons to esophageal distension in the rat.

1. Three hundred fifty neurons in the T2-T4 spinal segments of 38 intact, pentobarbital sodium-anesthetized, pancuronium-paralyzed male rats were examined for somatic receptive fields and responses to midthoracic esophageal distension (ED). Recordings were made at a depth of 0.1-1.45 mm from the dorsal spinal cord surface and from the midline to approximately 1.0 mm lateral. 2. Fifty-six of the 350 total neurons (16%) responded to ED, produced by air inflation of a latex balloon (0.5-1.5 ml). Most of these 56 neurons (84%) were excited by ED, and all except one were excited at a short latency (< 2 s) to stimulus onset. The response to ED in about one-half of all excited neurons terminated abruptly with termination of the stimulus; the other neurons exhibited an afterdischarge of 5 to > 80 s. Repeated ED at a constant intensity (1.25 ml, 30 s every 6 min) produced stable and reproducible responses of neurons excited by ED. Twenty-one percent of neurons that responded to ED were antidromically invaded from the spinomedullary junction. 3. Graded ED (0.5-1.5 ml, 30 s every 6 min) produced linear and accelerating stimulus-response functions in the 29 neurons tested. The mean threshold for distension, determined with a least-squares regression analysis, was extrapolated to near 0.5 ml of distending volume, and no difference in response threshold was found between neuronal groups with or without after-discharge. 4. The spontaneous activity of 7 of the 56 neurons (12.5%) that responded to ED was inhibited by the stimulus. Stimulus-response functions for four neurons inhibited by ED were intensity dependent. The spontaneous activity of these neurons was inhibited to a mean of 24.5% of the prestimulus control by 1.25 ml ED. 5. Two neurons of the total sample of 56 (3.5%) responded to ED (1.50 ml) in a biphasic excitatory-inhibitory manner. The excitatory component of excitatory-inhibitory neurons encoded the intensity of ED; the inhibitory component during the second half of ED was apparent only at greater distending volumes (1.25-1.5 ml). 6. Somatic receptive fields were found for 303/350 neurons, and 98% were located on the thorax and proximal forearm (all ipsilateral). Five neurons in T2-T4 spinal segments had their cutaneous receptive fields located on caudal parts of the body (tail, hindleg, scrotum). (ABSTRACT TRUNCATED AT 400 WORDS)
Error modeling for surrogates of dynamical systems using machine learning

A machine learning–based framework for modeling the error introduced by surrogate models of parameterized dynamical systems is proposed. The framework entails the use of high‐dimensional regression techniques (eg, random forests, and LASSO) to map a large set of inexpensively computed “error indicators” (ie, features) produced by the surrogate model at a given time instance to a prediction of the surrogate‐model error in a quantity of interest (QoI). This eliminates the need for the user to hand‐select a small number of informative features. The methodology requires a training set of parameter instances at which the time‐dependent surrogate‐model error is computed by simulating both the high‐fidelity and surrogate models. Using these training data, the method first determines regression‐model locality (via classification or clustering) and subsequently constructs a “local” regression model to predict the time‐instantaneous error within each identified region of feature space. We consider 2 uses for the resulting error model: (1) as a correction to the surrogate‐model QoI prediction at each time instance and (2) as a way to statistically model arbitrary functions of the time‐dependent surrogate‐model error (eg, time‐integrated errors). We apply the proposed framework to model errors in reduced‐order models of nonlinear oil‐water subsurface flow simulations, with time‐varying well‐control (bottom‐hole pressure) parameters. The reduced‐order models used in this work entail application of trajectory piecewise linearization in conjunction with proper orthogonal decomposition. When the first use of the method is considered, numerical experiments demonstrate consistent improvement in accuracy in the time‐instantaneous QoI prediction relative to the original surrogate model, across a large number of test cases. When the second use is considered, results show that the proposed method provides accurate statistical predictions of the time‐ and well‐averaged errors.