Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multigene Assay Is Prognostic of Survival in Patients with Early-Stage Lung Adenocarcinoma

Purpose: Clinical staging does not adequately risk stratify patients with early stage non–small cell lung cancer. We sought to generate a real-time PCR (RT-PCR)–based prognostic model in patients with early stage lung adenocarcinoma, the dominant histology of lung cancer in the United States. Experimental Design: We studied gene expression of 61 candidate genes in 107 patients with completely surgically resected lung adenocarcinoma using RT-PCR. We used crossvalidation methods to select and validate a prognostic model based on the expression of a limited number of genes. A risk score was generated based on model coefficients, and survival of patients with high- and low-risk scores were analyzed. Results: We generated a four-gene model based on expression of WNT3a, ERBB3, LCK, and RND3. Risk score predicted mortality better than clinical stage or tumor size (adjusted hazard ratio, 6.7; 95% confidence interval, 1.6-28.9; P = 0.001). Among 70 patients with stage I disease, 5-year overall survival was 87% among patients with low-risk scores, and 38% among patients with high-risk scores (P = 0.0002). Among all patients, 5-year overall survival was 62% and 41%, respectively (P = 0.0054). Disease-free survival was also significantly different among low- and high-risk score patients. Conclusions: This multigene assay predicts overall and disease-free survival significantly better than clinical stage and tumor size in patients with early stage lung adenocarcinoma and performs especially well in patients with stage I disease. Prospective clinical trials are needed to determine whether high-risk patients with stage I disease benefit from adjuvant chemotherapy.
Interferon alpha-inducible protein 6 regulates NRASQ61K-induced melanomagenesis and growth

Mutations in the NRAS oncogene are present in up to 20% of melanoma. Here, we show that interferon alpha-inducible protein 6 (IFI6) is necessary for NRASQ61K-induced transformation and melanoma growth. IFI6 was transcriptionally upregulated by NRASQ61K, and knockdown of IFI6 resulted in DNA replication stress due to dysregulated DNA replication via E2F2. This stress consequentially inhibited cellular transformation and melanoma growth via senescence or apoptosis induction depending on the RB and p53 pathway status of the cells. NRAS-mutant melanoma were significantly more resistant to the cytotoxic effects of DNA replication stress-inducing drugs, and knockdown of IFI6 increased sensitivity to these drugs. Pharmacological inhibition of IFI6 expression by the MEK inhibitor trametinib, when combined with DNA replication stress-inducing drugs, blocked NRAS-mutant melanoma growth. Collectively, we demonstrate that IFI6, via E2F2 regulates DNA replication and melanoma development and growth, and this pathway can be pharmacologically targeted to inhibit NRAS-mutant melanoma. DOI: http://dx.doi. org/10.7554/eLife.16432. 001
Development Framework for Implementing FPGA-Based Cognitive Network Nodes

This paper identifies important features a cognitive radio framework should provide, namely a virtual architecture for hardware abstraction, an adaptive run-time system for managing cognition, and high level design tools for cognitive radio development. We evaluate a range of existing frameworks with respect to these, and propose a novel FPGA-based framework that provides all these features. By abstracting away the details of hardware reconfiguration, radio designers can implement FPGA-based cognitive nodes much as they would do for a software implementation. We apply the proposed framework to the design and implementation of a receiver node that works in two modes: discovery, where it uses spectrum sensing to find a radio transmission, and communication, in which it receives and demodulates the said transmission. We show how the whole design process does not require any hardware experience on behalf of the radio designer.
Bayesian games with contracts

The set of all Bayesian-Nash equilibrium payos that the players can achieve by signing (conditional) commitments before playing a Bayesian game coincides with the set of all feasible, incentive compat- ible and interim individually rational payos of the Bayesian game. Furthermore, the various equilibrium payos, which are achieved by means of dierent commitment devices, are also the equilibrium pay- os of a universal, deterministic commitment game.
Heteromorph ammonites from the Tata Limestone Formation (Aptian–Lower Albian), Hungary

An important new ammonite fauna was collected by Fülöp in 1953 and 1960 from basal lenses between a Tithonian hardground and the overlying Tata Limestone Formation containing many heteromorph ammonites. This assemblage of ammonites has been determined as being of Early Albian (tardefurcata Zone) age. Among the heteromorphs are species of Tonohamites and Ptychoceras, which are familiar components of Late Aptian or Early Albian ammonite faunas. The genera Ephamulina, Hamites and Protanisoceras are also recorded, the earliest species of which had previously come from sediments of late Early Albian (mammillatum Zone) age. While Hamites and Protanisoceras are common in Europe, Ephamulina had previously only been known from Madagascar. The discovery of Ephamulina, Hamites and Protanisoceras supports the view that these phylogenetically significant ammonites had radiated close to the Aptian/Albian boundary. Four new species of Hamites (H. czaszari, H. fazekasensis, H. fueloepi and H. kalvariensis) and one new species of Tonohamites (T. boldii) are described.
Association of MDM2 SNP309 Variation with Lung Cancer Risk: Evidence from 7196 Cases and 8456 Controls

Background Evidence suggests that MDM2 T309G polymorphism may be a risk factor for several cancers. Increasing investigations have been conducted on the association of MDM2 T309G polymorphisms with lung cancer risk and have yielded conflicting results. Previous meta-analyses on this issue have reported inconclusive data. The aim of the present study was to derive a more precise estimation of the relationship. Methods and Findings Updated meta-analyses examining the association between MDM2 T309G polymorphism and lung cancer risk were performed. Separate analyses on ethnicity, smoking status, histological types and gender as well as source of controls were also implemented. Eligible studies were identified for the period up to Feb 2012. Lastly, ten publications including eleven case-control studies were selected for analysis. The overall data failed to indicate a significant association between MDM2 T309G polymorphism and lung cancer risk (GG vs TT OR = 1.14; 95%CI = 0.95−1.37; dominant model: OR = 1.05; 95%CI = 0.92−1.19; recessive model: OR = 1.12; 95%CI = 0.99−1.27). In a subgroup analysis by smoking status, increased lung cancer risk was shown among never-smokers (GG vs TT: OR = 1.76; 95%CI = 1.36−2.29; dominant model: OR = 1.48; 95%CI = 1.22−1.81; recessive model: OR = 1.37; 95%CI = 1.11−1.69). In subgroup analysis by gender, elevated risk was presented among women under a recessive model (OR = 1.29; 95%CI = 1.04−1.59). In the subgroup analysis by ethnicity, histological types and source of controls, no marked associations were observed. Conclusions Compared to the previous meta-analyses, the results of this study confirmed that MDM2 T309G polymorphism might be a risk factor for lung cancer among never-smokers. However, the data failed to suggest a marked association between the G allele of MDM2 T309G and lung cancer risk among Asians. More interestingly, subgroup analysis by gender indicated that homozygous GG alleles might raise lung cancer risk among females.
Methane emission from rice fields: The effect of floodwater management

Rice fields emit methane and are important contributors to the increasing atmospheric CH4 concentration. Manipulation of rice floodwater may offer a means of mitigating methane emission from rice fields without reducing rice yields. To test methods for reducing methane emission, we applied four water management methods to rice fields planted on silty-clay soils near Beaumont, Texas. The four water treatments investigated were: normal permanent flood (46 days post planting), normal flood with mid- season drainage aeration, normal flood with multiple drainage aeration, and late flood (76 days post planting). Methane emission rates varied markedly with water regime, showing the lowest seasonal total emission (1.2 g m−2) with a multiple-aeration treatment and the highest (14.9 g m−2) with a late flood. Although the multiple- aeration water management treatment emitted 88% less methane than the normal irrigation treatment and did not reduce rice yields, the multiple-aeration treatment did require 2.7 times more water than the 202 mm required by the normal floodwater treatment. A comparison of measured methane emission and production rates obtained from incubated soil cores indicated that, depending on time of season and flood condition, from zero to over 90% of the methane produced was oxidized. The average amount of methane which was oxidized during times of high emission was 73.1 ± 13.7 percent of that produced.
Content-Based Image Retrieval: Color-selection exploited

This research presents a new color selection interface that facilitates query-by-color in Content-Based Image Retrieval (CBIR). Existing CBIR color selection interfaces, are being judged as non-intuitive and difficult to use. Our interface copes with these problems of usability. It is based on 11 color categories, used by all people, while thinking of and perceiving color. In addition, its usability is supported by Fitts' law. The design of the color selection interface provides fast, unambiguous, intuitive, and accurate color selection.
Evaluation of Protective Coatings for the ‘In Situ’ Preservation of Historic Timber Buildings in a Harsh Antarctic Environment

The Australasian Antarctic Expedition base at Commonwealth Bay (67°S 142°E), also known as ‘Mawson's Huts’ include some of the earliest buildings in Antarctica. The prefabricated timber buildings of Oregon beams and Baltic Pine (Pinus sylvestris) claddings were erected in January 1912 and were occupied for two years: they are thus approximately contemporary with the better known Scott and Shackleton huts near McMurdo Base in the Ross Sea. The expedition was led by Dr Douglas Mawson, later Professor Sir Douglas Mawson, and its inspiration was scientific rather than a race to the South Pole. The buildings and artefacts remaining on the headland, also called Cape Denison, reflect considerable scientific achievement in geology, upper atmosphere physics, surveying, meteorology and biology and the site constitutes an important monument in the early exploration of this remote and inhospitable continent. While the huts are of recent date, the rapid rate of deterioration due to the extreme climate means there is some urgency to developing a method of preserving the building. The timbers have been seriously worn, or ‘corraded’ by snow particles carried in the katabatic winds. These winds can exceed 300km per hour, sometimes for days. The isolation of the site, accessible by sea for only three months of the year adds to the logistical difficulties. There has been considerable public debate in Australia about which method of preservation is appropriate. The author, a materials conservator and industrial chemist, visited the site in December 1985 and has been studying the problems of the site as a postgraduate student for the past year.
Possibilities and limitations of using flat operators in nested algebra expressions

In 19Y7 Makmoucb [18] proposed to generahze the relational database model by removmg the first normal form assumption Jaeschke and Schek [15] mtraduced a generallzatlon of the ordmary relational model by allowmg relations with set-valued attributes and adding two restructuring operators, the nest and the unnest operators, to manipulate such (one-level) nested relations Thomas and Fischer 1261 generalized Jaeschke and Schek’s model and allowed nested relations of arbitrary (but fixed) depth Roth, Korth and Sllberschatz [23] defined a calculus like query language for the nested relational model of Thomas and Flscher Since then numerous SQL-hhe query languages [17,20,21,22], graphical-oriented query languages [13] and datalog-hke languages [3,4,7,16] have been mtroduced for this model or slight generahzatlons of It Also, various groups [5,10,11,12,19,25] have started to implement the nested relational database model, some on top of an exlstmg database management system, others from scratch
Identification of preanalytical mistakes in the stat section of the clinical laboratory

In the era of total quality management, detection and correction of mistakes at all stages of laboratory testing is of outstanding interest, although most attention has been directed towards detecting and correcting errors in the analytical portion of the testing process (1). One of the reasons for this, in addition to the lack of focus on the problem, is the practical difficulty in reporting and measuring the number of errors (1). This situation especially applies to the stat department of the laboratory, due to the huge pressure of demands for an almost immediate response, which may influence the quality (accuracy) of test results. However, as preanalytical mistakes may account for up to 80% of overall mistakes in laboratory testing (2, 3), their detection and prevention are key strategies to improve laboratory quality, and the greatest reduction in the number of laboratory errors is likely to result from improving the quality of specimen collection (4). The University Hospital ‘‘Virgen de la Victoria’’ is a 720-bed teaching hospital with specialised care units that serves an area with a population of 300,000 served by 19 community health centres attended by general practitioners. Some 4500 blood specimens from inpatients and outpatients are processed daily in the clinical laboratory, and approximately 30% of these are referred to the stat section. As an initial step towards the identification and prevention of preanalytical mistakes in the stat section of our clinical laboratory, we retrospectively assessed the number of
Smartphone Notifications: A Study on the Sound to Soundless Tendency

Notifications are the mechanism that mobile applications utilize to let users know that a new message, email, call or similar has been received. Notifications may make a sound, a vibration or modify the app icon in some way. They may make us stop what we are doing, thus interrupting us and having a negative effect on our work. Before defining a cause-effect relation between notifications and their impact on the users' current tasks, first we have to study how users manage notifications. This paper describes the results of a survey on how users react when they receive a notification. The results of this descriptive research show how people are moving from sound to visual notifications, which reflects the ability of people to adapt to new technologies.
Center-surround or spreading inhibition: which mechanism caused the negative effect from repeated masked semantic primes?

In the paradigm of repeated masked semantic priming (Wentura & Frings. 2005), prime and mask are repeatedly and rapidly interchanged. Using this technique in a semantic priming task with category labels as primes and category exemplars as targets (related, e.g. BIRD - swan --> BIRD - finch; unrelated, e.g., BIRD - lily --> FRUIT - finch), Wentura and Frings found a negatively signed priming effect. Here we used the repeated masking technique with category exemplars as targets and primes (i.e., identity priming) for analyzing, whether this effect reflects center-surround or spreading inhibition. If the repeated masked technique reflects spreading inhibition, a negative effect should also appear for identity priming. In contrast, a center-surround approach would predict a positive effect. In accordance with the latter hypothesis, we found a significant positive effect in identity priming (Experiment 1a) and significant difference to the negatively signed semantic priming effect when primes were category labels (Experiment 1b). This is indicative of the repeated masked semantic priming effect being a negatively signed semantic priming effect due to a center-surround mechanism.
Effect of water level and climatic factors on the radial growth of black alder

Effect of water level and climatic factors on the radial growth of black alder Black alder (Alnus glutinosa (L.) Gaertn. ) is a widespread tree species in Europe and the western part of the temperate climate zone. The area of forest in Latvia dominated by this tree species has substantially decreased due to wide-spread forest drainage. To predict future changes due to environmental change, it is extremely important to understand the function of ecosystems with black alder and their dynamics. Tree rings can be used as a proxy of past environmental factors. The aim of the study was to determine the effects of meteorological and hydrological factors on radial growth of black alder at two study sites (Dursupe and Raķupe) in Latvia. The response of black alder trees to the influence of climatic and hydrological factors was found to depend on site conditions, i.e. a climatic effect was observed in conditions when the water level was low. Spatial variation in the strength of the relationship of black alder growth to temperature, precipitation, and river level suggests that alder growth is more susceptible to drought stress on higher river banks, where the water table is deeper. Black alder trees growing on low river banks can potentially be used to reconstruct past water-levels. Ūdens līmeņa un klimatisko faktoru ietekme uz melnalkšņa radiālo augšanu Melnalksnis (Alnus glutinosa (L.) Gaertn. ) ir plaši izplatīta koku suga Eiropā un mērenās klimata zonas rietumu daļā. Latvijā melnalkšņu mežu daudzums ir ievērojami krities sakarā ar mežu nosusināšanu. Lai prognozētu nākotnes izmaiņas saistībā ar vides izmaiņām, ir ļoti svarīgi saprast ekosistēmu ar melnalksni funkcionēšanu un dinamiku. Koku gadskārtas var izmantot kā informācijas avotu par pagātnes vides faktoriem. Šī pētījuma mērķis bija noskaidrot meteorologisko un hidrologisko faktoru ietekmi uz melnalkšņa radiālo augšanu divās teritorijās Latvijā (Dursupe un Raķupe). Tika noskaidrots, ka melnalkšņa atbilde uz klimatisko un hidrologisko faktoru ietekmi ir atkarīga no vietas apstākļiem, tas ir, klimata ietekmes efekts novērojams apstākļos, kad ūdens līmenis bija zems. Sakarības starp melnalkšņa augšanu un temperatūru, nokrišņiem un ūdens līmeni telpiskā variācija norāda, ka melnalkšņa augšana ir vairāk pakļauta sausuma ietekmei uz augstākiem upju krastiem, kur ūdens līmenis ir zemāks. Melnalkšņi, kas auga uz zemiem upju krastiem, potenciāli var būt izmantojami ūdens līmeņu rekonstrukcijai par senākiem laika periodiem.
Towards the Separation of Rigid and Non-rigid Motions for Facial Expression Analysis

In intelligent environments, computer systems not solely serve as passive input devices waiting for user interaction but actively analyze their environment and adapt their behaviour according to changes in environmental parameters. One essential ability to achieve this goal is to analyze the mood, emotions and dispositions a user experiences while interacting with such intelligent systems. Features allowing to infer such parameters can be extracted from auditive, as well as visual sensory input streams. For the visual feature domain, in particular facial expressions are known to contain rich information about a user's emotional state and can be detected by using either static and/or dynamic image features. During interaction facial expressions are rarely performed in isolation, but most of the time co-occur with movements of the head. Thus, optical flow based facial features are often compromised by additional motions. Parts of the optical flow may be caused by rigid head motions, while other parts reflect deformations resulting from facial expressivity (non-rigid motions). In this work, we propose the first steps towards an optical flow based separation of rigid head motions from non-rigid motions caused by facial expressions. We suggest that after their separation, both, head movements and facial expressions can be used as a basis for the recognition of a user's emotions and dispositions and thus allow a technical system to effectively adapt to the user's state.
Pen + touch = new tools

We describe techniques for direct pen+touch input. We observe people's manual behaviors with physical paper and notebooks. These serve as the foundation for a prototype Microsoft Surface application, centered on note-taking and scrapbooking of materials. Based on our explorations we advocate a division of labor between pen and touch: the pen writes, touch manipulates, and the combination of pen + touch yields new tools. This articulates how our system interprets unimodal pen, unimodal touch, and multimodal pen+touch inputs, respectively. For example, the user can hold a photo and drag off with the pen to create and place a copy; hold a photo and cross it in a freeform path with the pen to slice it in two; or hold selected photos and tap one with the pen to staple them all together. Touch thus unifies object selection with mode switching of the pen, while the muscular tension of holding touch serves as the "glue" that phrases together all the inputs into a unitary multimodal gesture. This helps the UI designer to avoid encumbrances such as physical buttons, persistent modes, or widgets that detract from the user's focus on the workspace.
Microfilament‐dependent movement of the β3 integrin subunit within focal contacts of endothelial cells

To gain insight into the dynamic properties of focal contacts, we induced expression of green fluorescent protein‐tagged β3 integrin (GFP‐β3) and actinin‐1 (GFP‐actinin‐1) in endothelial cells. Both tagged proteins localize with αvβ3 integrin in focal contacts distributed towards the periphery of transfected cells. Labeled focal contacts migrate at about 0.1 μm/min in stationary live endothelial cells. We compared β3 integrin and actinin‐1 dynamics in focal contacts by using fluorescence recovery after photobleaching. Recovery of signal in bleached focal contacts that have incorporated actinin‐1 is rapid and occurs within less than 4 min. This recovery is energy‐dependent. In contrast, recovery of bleached focal contacts that contain GFP‐β3 integrin takes longer than 30 min. Yet, when a narrow stripe of fluorescence is bleached across a β3 integrinlabeled focal contact, recovery is complete within 16 min. The latter recovery is energy‐dependent and is blocked not only by actin‐filament disrupting drugs but also by a myosin light chain kinase inhibitor. Thus, integrins are not immobile when incorporated into focal contacts, as some have suggested. We propose that integrins are mobile within the confines of focal contacts and that this mobility is supported by an actin‐associated molecular motor.