Miracle-dz/UniFAR-FTUs huggingface dataset:
SERPINB1 expression is predictive for sensitivity and outcome of cisplatin-based chemotherapy in melanoma

Despite of highly effective new therapeutic strategies, chemotherapy still is an important treatment option in metastatic melanoma. Since predictors of chemotherapy response are rare, drugs and regimens are currently chosen arbitrarily. The present study was aimed at the identification of molecular markers predicting the outcome of chemotherapy in melanoma. Tumor biopsies from metastatic lesions were collected from 203 stage IV melanoma patients prior to chemotherapy onset and used for gene expression profiling (n = 6; marker identification set), quantitative real-time PCR (n = 127; validation set 1), and immunohistochemistry on tissue microarrays (n = 70; validation set 2). The results were correlated to the tumors' in-vitro chemosensitivity and to the patients' in-vivo chemotherapy outcome. SERPINB1 was found to correlate to the in-vitro sensitivity to cisplatin-containing chemotherapy regimens (p = 0.005). High SERPINB1 gene expression was associated with favorable tumor response (p = 0.012) and prolonged survival (p = 0.081) under cisplatin-based chemotherapy. High SERPINB1 protein expression in tumor tissue from cisplatin-treated patients was associated with a favorable survival (p = 0.011), and proved as an independent predictor of survival (p = 0.008) by multivariate analysis. We conclude, that SERPINB1 expression, although not functionally involved, is predictive for the outcome of cisplatin-based chemotherapy in melanoma, and thus may be useful to personalize melanoma chemotherapy.
Discreet markers for user localization

This paper describes a localization method for wearable computer users. To realize applications of wearable computers like a navigation system, the position of a user is required for location-based services. Many localization methods in indoor environments have been proposed. One of the methods estimates user's position using IR beacons or visual markers. However, these methods have problems of power supply and/or undesirable visual effects. In order to avoid the problems, we propose a new localization method which is based on using an IR camera and discreet markers consisting of translucent retro-reflectors. In the proposed method, to extract the regions of the markers from the captured images stably, the camera captures the reflection of IR LEDs which are flashed on and off synchronously.
A Remarkable Pennsylvanian Fauna from the Mazon Creek Area, Illinois

The purpose of this note is to describe a newly discovered Middle Pennsylvanian fauna from the Francis Creek shale of the Mazon Creek area, Illinois. For convenience, the well-known terrestrial fauna is designated the Braidwood concretion fauna and the marine fauna will be referred to as the Essex concretion fauna. Most of the Essex fossils are impressions of soft-bodied forms. The fauna includes such unusual fossils as polychaete worms, jellyfish, nudibranchs, holothurians, and chitons. One abundant element is a unique wormlike fossil resembling modern bathypelagic nemerteans in general body form. The assemblage of ecologic types represented in the Essex fauna and its stratigraphic occurrence suggest a near-shore environment of deposition.
Developing Pericarp of Maize: A Model to Study Arabinoxylan Synthesis and Feruloylation

Cell walls are comprised of networks of entangled polymers that differ considerably between species, tissues and developmental stages. The cell walls of grasses, a family that encompasses major crops, contain specific polysaccharide structures such as xylans substituted with feruloylated arabinose residues. Ferulic acid is involved in the grass cell wall assembly by mediating linkages between xylan chains and between xylans and lignins. Ferulic acid contributes to the physical properties of cell walls, it is a hindrance to cell wall degradability (thus biomass conversion and silage digestibility) and may contribute to pest resistance. Many steps leading to the formation of grass xylans and their cross-linkages remain elusive. One explanation might originate from the fact that many studies were performed on lignified stem tissues. Pathways leading to lignins and feruloylated xylans share several steps, and lignin may impede the release and thus the quantification of ferulic acid. To overcome these difficulties, we used the pericarp of the maize B73 line as a model to study feruloylated xylan synthesis and crosslinking. Using Fourier-transform infra-red spectroscopy and biochemical analyses, we show that this tissue has a low lignin content and is composed of approximately 50% heteroxylans and approximately 5% ferulic acid. Our study shows that, to date, maize pericarp contains the highest level of ferulic acid reported in plant tissue. The detection of feruloylated xylans with a polyclonal antibody shows that the occurrence of these polysaccharides is developmentally regulated in maize grain. We used the genomic tools publicly available for the B73 line to study the expression of genes within families involved or suggested to be involved in the phenylpropanoid pathway, xylan formation, feruloylation and their oxidative crosslinking. Our analysis supports the hypothesis that the feruloylated moiety of xylans originated from feruloylCoA and is transferred by a member of the BAHD acyltransferase family. We propose candidate genes for functional characterization that could subsequently be targeted for grass crop breeding.
Sensitivity of the shortwave radiative budget to the parameterization of ice crystal effective radius

[1] A new effective particle size (R eff ) parameterization for ice clouds has been formulated based on depth into cloud relative to cloud top. This parameterization has been developed based on an extensive data set of lidar and radar ice cloud retrievals. Using this parameterization within the stand-alone radiation code from the European Centre for Medium Range Weather Forecasting (cy23r4), the performance of the new parameterization is compared with the more commonly used parameterizations based on temperature and/or ice water content. An evaluation is performed on the basis of observed shortwave fluxes for 13 days with persistent ice cloud decks, with no liquid clouds beneath, over the Cabauw Experimental Site for Atmospheric Research in the Netherlands. For each of these clouds the shortwave flux is calculated after which the distribution of the differences between the observed and modeled shortwave fluxes from the combined 13 days are compared with each other. The new parameterization shows a median absolute difference of 0.7 W m -2 relative to the observations. The control parameterization based on temperature shows a median absolute difference of 15 W m -2 . Within the framework of the KNMI regional climate model (RACMO2), the new parameterization yields an effective particle size versus temperature distribution very similar to the observed distributions from lidar and radar retrievals. Results from a 1-year integration indicate that the domain averaged monthly mean planetary albedo and transmissivity change by a maximum of 2.6 and 2.4%, respectively, using the new parameterization compared to the temperature-based parameterization.
S‐P conversion from the transition zone beneath Tonga and the nature of the 670 km discontinuity

SUMMARY Using more than 300 recordings of deep Tonga earthquakes from the Warramunga Seismic Array (central Australia), we have searched for short-period S-P conversions from the 670 km discontinuity arriving in the P-wave codas. The array seismograms were stacked and plotted in sections to optimize observation of S670P yielding the following results: For the northern part of Tonga (17.3°–18.4°S), S670P-phases are observed with apparent conversion depths between about 660 and 680 km. For the central part (20.2°–22.3°S), S670P is not clearly observed. For the southern part (23.1°–25.7°S), S670P is observed for conversion depths between about 660 and 700 km. Intermittent occurrence of S-P conversion may result from different characteristic source radiation patterns among the three sections. Overall uncertainties in conversion depths (resulting from unmodelled lateral velocity variations and hypocentral location errors) are perhaps a few tens of kilometres. The S-P rays must travel either within or very close to the subducted slab because of the source/receiver/slab-dip geometry, so we conclude that large (>50 km) deformations of the 670 km discontinuity do not occur beneath Tonga. Our observations appear to be inconsistent with a chemical discontinuity at 670 km, but are easily explained if the 670 km discontinuity is a strongly pressure-dependent and, perhaps, moderately endothermic phase change in both the slab and surrounding mantle.
Constructing Semantic Networks of Development Activities from Weekly Reports

In the development departments of some manufacturing companies, there are weekly reports describing the status of events, but they are poorly structured plain texts. In this report, we propose a method for constructing semantic networks of development activities from weekly reports. Our ontology-based method extracts things such as the events, statuses and agents from the reports, constructs the relations between them, and creates Semantic MediaWiki pages from the semantic networks to visualize development activities. We show a use case in which the method is applied to the actual weekly reports and internal documents of a development department.
New dinosaur and crocodylomorph material from the Middle Jurassic (Bathonian) Kilmaluag Formation, Skye, Scotland

Synopsis Archosaur specimens collected from the Kilmaluag Formation (Great Estuarine Group) of Cladach a’Ghlinne, Skye are described. These comprise crocodylomorph material; a pubis and group of osteoderms with an associated tooth; a theropod tooth; and a dinosaur limb bone. The material is regionally important as the Skye assemblage is dominated by aquatic amphibians and amphibious reptiles with terrestrial taxa being comparatively rare. The crocodylomorph pubis is referable to an indeterminate mesoeucrocodylian; the osteoderms and associated tooth to an indeterminate neosuchian. The Kilmaluag Formation has now yielded the only associated and articulated terrestrial/freshwater Middle Jurassic crocodylomorphs from the UK thus far. The theropod tooth is referable to an indeterminate theropod, and provides the first body fossil evidence of a small theropod taxon from the Bathonian of the Hebridean Basin. The dinosaur limb bone is regarded conservatively as an indeterminate dinosaur although it does possess possible theropod affinities.
Sineoamphisbaena hexatabularis, an amphisbaenian (Diapsida: Squamata) from the Upper Cretaceous redbeds at Bayan Mandahu (Inner Mongolia, People's Republic of China), and comments on the phylogenetic relationships of the Amphisbaenia

Sineoamphisbaena hexatabularis Wu et al., 1993 is the earliest known amphisbaenian represented by well-preserved cranial and postcranial material. It reveals a mosaic of generalized lizard-like features and amphisbaenian characters. Most distinctive of the latter are features of cranial consolidation adaptive for a fossorial way of life. Phylogenetic analyses strongly confirm the monophyly of the Amphisbaenia inclusive of S. hexatabularis. The Amphisbaenia is diagnosed by a suite of apomorphic characters. The available evidence suggests a probable Amphisbaenia-Macrocephalosauridae relationship within the Scincomorpha. This is supported primarily by the unique modifications of the palate and temporal region of the skull. It is argued here that the Amphisbaenia evolved in Central Asia during the Cretaceous, in response to the transition from a perennial lacustrine environment to a dry, semiarid eolian environment. The relatively primitive morphology indicates that S. hexatabularis was not permanently subterranean. The further derived modifications of later forms are associated with tunneling in an environment of more compact soils.
Cloud feedback in atmospheric general circulation models: An update

Six years ago, we compared the climate sensitivity of 19 atmospheric general circulation models and found a roughly threefold variation among the models; most of this variation was attributed to differences in the models' depictions of cloud feedback. In an update of this comparison, current models showed considerably smaller differences in net cloud feedback, with most producing modest values. There are, however, substantial differences in the feedback components, indicating that the models still have physical disagreements.
Powering indoor sensing with airflows: a trinity of energy harvesting, synchronous duty-cycling, and sensing

Whereas a lot of efforts have been put on energy conservation in wireless sensor networks, the limited lifetime of these systems still hampers their practical deployments. This situation is further exacerbated indoors, as conventional energy harvesting (e.g., solar) ceases to work. To enable long-lived indoor sensing, we report in this paper a self-sustaining sensing system that draws energy from indoor environments, adapts its duty-cycle to the harvested energy, and pays back the environment by enhancing the awareness of the indoor microclimate through an "energy-free" sensing. First of all, given the pervasive operation of heating, ventilation and air conditioning (HVAC) systems indoors, our system harvests energy from airflow introduced by the HVAC systems to power each sensor node. Secondly, as the harvested power is tiny (only of hundreds of μW), an extremely low but synchronous duty-cycle has to be applied whereas the system gets no energy surplus to support existing synchronization schemes. So we design two complementary synchronization schemes that cost virtually no energy. Finally, we exploit the feature of our harvester to sense the airflow speed (which can be used to infer the indoor microclimate) in an energy-free manner. To our knowledge, this is the first indoor wireless sensing system that encapsulates energy harvesting, network operating, and sensing all together.
FAST DB: a website resource for the study of the expression regulation of human gene products

Human genes use various mechanisms to generate different transcripts having different exon content, which in turn generate multiple protein isoforms having differential and even opposite biological activities. To understand the biological consequences of gene transcriptional activity modulation, it is necessary to integrate the capability of genes to generate distinct functional products, particularly because transcriptional stimuli also affect the exon content of their target gene products. For this purpose, we have developed a bioinformatics suite, FAST DB, which defines easily and accurately the exon content of all known transcripts produced by human genes. In addition, several tools have been developed, including a graphical presentation of all gene products, a sequence multi-alignment of all gene transcripts and an in silico PCR computer program. The FAST DB interface also offers extensive links to website resources for promoter analysis and transcription factor binding site prediction, splicing regulatory sequence prediction, as well as 5′- and 3′-untranslated region analysis. FAST DB has been designed to facilitate studies that integrate transcriptional and post-transcriptional events to investigate the expression regulation of human gene products.
Event-based temperature control system in a penning-type ion source

The ion sources are the first step in particle accelerators, which are important instruments in today's scientific advance, with multiple applications. The design and construction of those machines involves complex technical challenges. One of the keys in the correct operation of an Ion Source is the control system. In this work, an event-based control of the temperature in the transport line and cesium boilers is presented, necessary elements in a Penning-type ion source. The main objective of the controller is to maintain a constant temperature in the transport line and the boiler, providing an adequate concentration of cesium in the plasma chamber. The event-based nature of the controller reduces the control rate and, hence, the activity of the actuators. Therefore, the lifetime of the devices is increased, improving system reliability.
Stein block thresholding for wavelet-based image deconvolution

In this paper, we propose a fast image deconvolution algorithm that combines adaptive block thresholding and Vaguelet-Wavelet Decomposition. The approach consists in first denoising the observed image using a wavelet-domain Stein block thresholding, and then inverting the convolution operator in the Fourier domain. Our main theoretical result investigates the minimax rates over Besov smoothness spaces, and shows that our block estimator can achieve the optimal minimax rate, or is at least nearlyminimax in the least favorable situation. The resulting algorithm is simple to implement and fast. Its computational complexity is dominated by that of the FFT in the Fourier-domain inversion step. We report a simulation study to support our theoretical findings. The practical performance of our block vaguelet-wavelet deconvolution compares very favorably to existing competitors on a large set of test images.
Snow-cover characteristics using Hyperion data for the Himalayan region

The present study demonstrates the potential of hyperspectral imaging Hyperion data for the mapping of snow grain size and snow mixed objects in the Himalayan region. The spectral signatures collected using a field spectroradiometer for different types of snow grain size and vegetation-/soil-mixed snow were used for the identification/comparison of collected image spectra. Snow grain size was estimated using the spectral angle mapper (SAM) method and compared/validated with the grain sizes obtained from grain index and asymptotic radiative transfer (ART) theory methods. The overall matching area was 81% among different snow grain size classes using SAM and grain index methods. A good match was observed between the class-wise (i.e. fine, medium, and coarse) grain sizes and quantitatively obtained grain sizes using the ART theory; however, the grain diameters obtained from the ART method were small, which may be due to the difference between equivalent grain and effective optical grain size. The obtained grain size was also supported by the field snow conditions of the region. The spectra of mixed snow cover were collected from Hyperion images and compared with the spectra collected from snow mixed objects during field experiments. The vegetation-mixed and contamination/patchy (soil-mixed) snow-cover areas were identified in Hyperion scenes and the results supported using high-resolution images and snow conditions of the region. This study is of importance in the mapping of snow-cover characteristics, which can provide valuable input for climatology, hydrology, and mountain hazard applications.
Software Health Management with Bayesian Networks

Most modern aircraft as well as other complex machinery is equipped with diagnostics systems for its major subsystems. During operation, sensors provide important information about the subsystem (e.g., the engine) and that information is used to detect and diagnose faults. Typically, FDDR (fault detection, diagnosis, and recovery) or IVHM (Integrated Vehicle Health Management) systems are used for this purpose. Most of these systems focus on the monitoring of a mechanical, hydraulic, or electromechanical subsystem of the vehicle or machinery. Only recently, health management systems that monitor software have been developed (for an overview see, e.g., [1]). In this paper, we will discuss our approach of using Bayesian networks for Software Health Management (SWHM) [2], [3], [4]. The field of system health management for hardware is quite mature; many industrial systems use diagnostics/IVHM systems (e.g., automotive or aerospace industry). However, the health management of software has to adhere to substantially different requirements. The most striking difference is that faults in a software system usually occur instantaneously, whereas faults in hardware systems tend to develop over time (e.g., an oil leak). 1 Furthermore, many software problems are caused by problematic software-hardware interactions, which means that both the software and the hardware must be monitored. At the same time, software has features that might make system health monitoring easier and more promising in some ways. First, software redundancy does not increase the weight of a system, while hardware redundancy clearly does. Second, software can be debugged and fixed remotely, without need for human presence at the location where the system (say, a robotic vehicle on Mars) is deployed.
Probing Virtual Boundaries and the Perception of Delayed Stiffness

During interaction with robotic manipulanda, the human brain constructs internal representations of the environment imposed by the robotic device. These representations (i) provide cognitive interpretation of the interfaced environment and (ii) generate motor commands for future interaction with the imposed environment. Interestingly, cognitive and motor representations are not always mutually consistent. We consider a simple environment consisting of a spring-like surface, where either the delay between force and position or the location of the boundary is experimentally altered. We explored the cognitive representation of rigidity by asking subjects which of two surfaces is stiffer. We also considered the motor representation by investigating adaptation to the same virtual environments. We asked subject to reach a target inside virtual surface, and observed adaptation and its after effects in catch trials. In the cognitive study, we constructed psychometric curves based on the verbal reports of the subjects. In the motor study, we constructed analogous curves, which we name 'motormetric curves', describing the implicit motor expectation of rigidity, as expressed not verbally but by the errors in catch trials, where the delay was unexpectedly removed. We simulated motormetric curves from a simplified mechanical model of the arm and neural controller. We found that the cognitive reports reflected our measure of the motor behavior in the case of delayed stiffness, but not in the case of shifted boundary.
A Comparative Study of Process Mediator Components That Support Behavioral Incompatibility

Most businesses these days use the web services technology as a medium to allow interaction between a service provider and a service requestor. However, both the service provider and the requestor would be unable to achieve their business goals when there are miscommunications between their processes. This research focuses on the process incompatibility between the web services and the way to automatically resolve them by using a process mediator. This paper presents an overview of the behavioral incompatibility between web services and the overview of process mediation in order to resolve the complications faced due to the incompatibility. Several state-of the-art approaches have been selected and analyzed to understand the existing process mediation components. This paper aims to provide a valuable gap analysis that identifies the important research areas in process mediation that have yet to be fully explored.
Validation of power system models

Since models form the basis for most power system studies, power system model validation is an essential procedure for maintaining system security and reliability. The procedure may be viewed as a “top-down” approach to model verification; comparisons with measured data indicate the quality of the overall model. Analysis of the differences demonstrates which subsystem component models need to be revalidated. Numerous examples are presented to illustrate the use and importance of system model validation.