nils-herrmann/clean_scirepeval huggingface dataset:
Abstract 2387: Pan cancer analysis of clonal evolution reveals the costs and adaptive benefits of genomic instability

Cancers are a mosaic of clones of varying population sizes. Any single cancer sample encodes a tumor metagenome, since it represents the aggregate genomes of diverse clones that coexist within the sample. We quantified genomic instability as the fraction of the tumor metagenome affected by copy number variations (CNVs) and leveraged two tumor mixture separation algorithms, EXPANDS and PyClone, to quantify genetic intra tumor heterogeneity (ITH) from single cancer samples. We tested the potential of measures of genomic instability and ITH as prognostic biomarkers across 1,165 exome sequenced primary tumors from 12 cancer types at TCGA. Our results suggest that a tradeoff between the costs and adaptive benefits of genomic instability governs differential radiotherapy sensitivity. Between 1 and 18 clones were estimated to coexist per tumor sample at >10% cell frequency (median 4) Clone number varied considerably within and between cancer types, with melanomas representing the most heterogeneous group. 86% all analyzed tumor samples contained at least 2 clones. Across cancer types, the presence of >2 clones was associated with worse overall survival as compared to tumors in which 75% genomic instability was shared among 75% predicted reduced risk (HR 0.15, 95% CI: 0.08 0.29) We analyzed the relation between radiotherapy intensity and overall survival among 242 individuals (21% treated with radiotherapy and found that not all individuals did benefit equally from therapy. In order to achieve the same benefit from therapy, individuals with 25 50% genomic instability required higher therapy intensity (regression slope 1.83; P 0.009) than individuals with 50 75% genomic instability (slope 2.09; P 0.005) In contrast, individuals with Radiotherapy may be particularly effective against tumors with intermediate CNV burden, by pushing them past the limit of 'tolerable' genomic instability. Our results from two independent pan cancer cohorts suggest that this limit is exceeded when >75% of a tumor9s metagenome is affected by CNVs. This upper limit of tolerable genomic instability may be responsible for the non linear association we observed between genetic ITH and survival. Leveraging a clone9s distance to the upper limit of tolerable genomic instability may represent a new strategy to optimize therapy intensity.  Noemi Andor, Trevor A. Graham, Marnix Jansen, Li C. Xia, Athena Aktipis, Claudia Petritsch, Hanlee P. Ji, Carlo C. Maley. Pan cancer analysis of clonal evolution reveals the costs and adaptive benefits of genomic instability.
The Relationship Between Marketing Mix And Customer Loyalty In Hijab Industry: The Mediating Effect Of Customer Satisfaction

In today's business market, there are so many new entrants in the same industry, selling and providing the same products and services. Therefore, business providers need to compete with one another in order to survive in the industry as there are so many competitors. Business providers need to focus on the customers' needs and preferences to maintain and retain the long term relationship. In order to make customer satisfied, business providers must know the elements in the marketing mix that they need to practice in order to attract customers especially through their buying behaviour. Thus, the objective of this study is to examine the relationship between marketing mix and customer loyalty, and the mediating effect of customer satisfaction in hijab industry. The study setting focused on female customers who are wearing and buying any hijab products at Shah Alam outlets. Questionnaires adapted from prior studies were distributed and 234 usable questionnaires were collected from this study. It is expected that findings from this study will contribute to the existing literature to both theoretical and managerial approaches in order to better understand the pattern of the marketing mix, customer satisfaction and customer loyalty, especially in hijab industry settings.
Machine Learned Machines: Adaptive co optimization of caches, cores, and On chip Network
Venue: 2016 Design, Automation Test in Europe Conference Exhibition (DATE)

Modern multicore architectures require runtime optimization techniques to address the problem of mismatches between the dynamic resource requirements of different processes and the runtime allocation. Choosing between multiple optimizations at runtime is complex due to the non additive effects, making the adaptiveness of the machine learning techniques useful. We present a novel method, Machine Learned Machines (MLM) by using Online Reinforcement Learning (RL) to perform dynamic partitioning of the last level cache (LLC) along with dynamic voltage and frequency scaling (DVFS) of the core and uncore (interconnection network and LLC) We show that the co optimization results in much lower energy delay product (EDP) than any of the techniques applied individually. The results show an average of 19.6% EDP and 2.6% execution time improvement over the baseline.
Extending System Readiness Levels to Assess and Communicate Human Readiness
Venue: Syst. Eng.

Program managers need to understand the maturity of all aspects of their system to make intelligent investment decisions during product development. Technology Readiness Levels TRL are regularly applied to classify and communicate the state of technology development and to guide investment during technology and system development. This concept has recently been extended to include integration readiness to understand the maturity of the interfaces between technology components in a system. However, these methods do not consider whether human interfaces to the system have been fully matured. The current research extends the TRL and Integration Readiness Level IRL concepts to include the human elements of the system. The method proposes two concepts: the Human Capability Level and the Human IRL. The Human Capability Level refers to the capability of a system to reliably provide well equipped personnel with sufficient skills and the ability to perform successfully with the system. The Human Integration Readiness Level refers to the demonstration of effective human integration with system technologies. Each of these concepts are then combined with previous work to demonstrate the development of a System Readiness Level, which includes technology and human elements. We show that these Human Capability and Integration Level concepts can be used in conjunction with the existing TRL and IRL concepts to compare the relative maturity of components of the system for supporting each class of human users as well as performing its technical functions.
FIRST REPORT OF 'CANDIDATUS PHYTOPLASMA SOLANI' IN PEPPER AND CELERY IN BOSNIA AND HERZEGOVINA

In August 2015, in Bijeljina (Semberija province of Bosnia and Herzegovina) pepper and celery plants were surveyed for phytoplasma infections. During the survey pepper plants (Capsicum annuum of cvs Fortesa, Niska Sipka and Amanda showing stunting and leaf yellowing were observed, while celery plants (Apium graveolens L. variety 'Giant Prague' expressed leaf whitening and stunting; the percentages of symptomatic plants ranged from 20 to 30% respectively. Leaf samples from symptomatic and asymptomatic plants were tested to verify phytoplasma presence using nested PCR/RFLP analyses. Results of 16S rDNA RFLP analyses with Tru1I and tuf typing using HpaII (Langer and Maixner, 2004) indicated the presence of a 'Candidatus Phytoplasma solani' related strain in all the symptomatic samples tested. There was no variability in the tuf gene and only tuf type b was detected. Four symptomatic pepper and two celery samples were selected for further characterization amplifying vmp1 and stamp genes (Fialova et al. 2009; Fabre et al. 2011) The nucleotide sequences of the obtained amplicons were submitted to GenBank (accession Nos. KU340846 51 and KU295501 06 for vmp1 and stamp sequences, respectively) Homology with 'Ca. P. solani' sequences from database was 96 100% for the vmp1 and 99 100% for the stamp gene. Combined RFLP analyses using Tru1I and Hpy188I on stamp and RsaI on vmp1 genes distinguished four 'Ca. P. solani' lineages indicating the presence of genetic variability among the phytoplasmas studied. This is the first report of 'Ca. P. solani' presence in symptomatic pepper and celery in Bosnia and Herzegovina.
Role of Hotels and Resorts to Promote Ancient Ayurveda through Health Tourism: A Special Reference to Odisha

Health Tourism is one of the emerging segments of travel and has gained remarkable fame to India for attracting tourists to cater their health as well as relaxation needs. Even though a new phenomenon; it is almost surely to be a major source of income for the country. Ayurveda has been the USP of health tourism to offer a complete package of travel experiences with psychological, physical and spiritual wellbeing. Presently alternative therapy and herbal treatment is widely popular globally and makes India a major tourist attraction. Hopefully, within few years India will be the most preferred destination for best of the health services with holistic healing therapies. Thus, endorsing Ayurveda through health tourism provides a new dimension to the hospitality and tourism in India itself. The main purpose of the paper is to focus on recent developmental trends in health tourism in India for promoting holistic therapy Ayurveda in global context. The study highlights the implementation of ancient therapies in various hotels and resorts of Odisha as an ancillary service to provide the guest utmost satisfaction. The scope of the study only focuses on promoting Ayurvedic remedies as a significant element of health tourism in hotels and resorts of Odisha. Based on the data collected through secondary sources, this paper makes an assessment of the extent of social awareness, innovativeness and responsiveness of tourism sector for marketing Ayurveda. In the concluding section, limitations of the study have been discussed and recommendations provided for undertaking more detailed investigations in the area.
An integrated modelling framework from cells to organism based on a cohort of digital embryos
Venue: Scientific reports

We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi level probabilistic model that reproduced embryo level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage. Our resulting artificial prototype was embedded in 3D space by biomechanical agent based modelling and simulation, which allowed a systematic exploration and optimisation of free parameters to fit the experimental data and test biological hypotheses. The spherical monolayered blastula and the spatial arrangement of its different cell types appeared tightly constrained by cell stiffness, cell adhesion parameters and blastocoel turgor pressure.
Electrospun cellulose acetate/poly(vinylidene fluoride) nanofibrous membrane for polymer lithium ion batteries
Venue: Journal of Solid State Electrochemistry

The membranes for gel polymer electrolyte (GPE) for lithium ion batteries were prepared by electrospinning a blend of poly(vinylidene fluoride) (PVdF) with cellulose acetate (CA) The performances of the prepared membranes and the resulted GPEs were investigated, including scanning electron microscopy (SEM) Fourier transform infrared spectroscopy (FT IR) differential scanning calorimetry (DSC) X ray diffraction (XRD) porosity, hydrophilicity, electrolyte uptake, mechanical property, thermal stability, AC impedance measurements, linear sweep voltammetry, and charge discharge cycle tests. The effect of the ratio of CA to PVdF on the performance of the prepared membranes was considered. It is found that the GPE based on the blended polymer with CA:PVdF =2:8 (in weight) has an outstanding combination property strength (11.1 MPa) electrolyte uptake (768.2 thermal stability (no shrinkage under 80 degC without tension) and ionic conductivity (2.61 x 10 3 S cm 1) The Li/GPE/LiCoO2 battery using this GPE exhibits superior cyclic stability and storage performance at room temperature. Its specific capacity reaches up to 204.15 mAh g 1, with embedded lithium capacity utilization rate of 74.94 which is higher than the other lithium ion batteries with the same cathode material LiCoO2 (about 50
Review of snow water equivalent microwave remote sensing
Venue: Science China Earth Sciences

Accurate quantitative global scale snow water equivalent information is crucial for meteorology, hydrology, water cycle and global change studies, and is of great importance for snow melt runoff forecast, water resources management and flood control. With land surface process model and snow process model, the snow water equivalent can be simulated with certain accuracy, with the forcing data as input. However, the snow water equivalent simulated using the snow process models has large uncertainties spatially and temporally, and it may be far from the needs of practical applications. Thus, the large scale snow water equivalent information is mainly from remote sensing. Beginning with the launch of Nimbus 7 satellite, the research on microwave snow water equivalent remote sensing has developed for more than 30 years, researchers have made progress in many aspects, including the electromagnetic scattering and emission modeling, ground and airborne experiments, and inversion algorithms for future global high resolution snow water equivalent remote sensing program. In this paper, the research and progress in the aspects of electromagnetic scattering/emission modeling over snow covered terrain and snow water equivalent inversion algorithm will be summarized.
Scattering and emission models for microwave remote sensing of snow using numerical solutions of maxwell equations
Venue: 2016 IEEE International Geoscience and Remote Sensing Symposium (IGARSS)

Snowpack consists of ice grains that are densely packed in the wavelength scale at microwave frequencies so that the coherent microwave interactions among the ice grains are important in microwave signatures. We have used Numerical Maxwell Model of 3D simulations (NMM3D) of random media discrete scatterer to study such interactions. In the partial coherent model of Dense Media Radiative Transfer (DMRT) we use NMM3D to calculate the effective propagation constants, the extinction coefficients and the phase matrices. These are then used in radiative transfer equations to calculate the emission and backscattering signatures. In the fully coherent model, we use NMM3D to calculate the bistatic scattering and emissivity for a layer of snow pack over the ground. Using the fully coherent approach, we calculate the complex scattering amplitudes from the snowpack, including both magnitude and phase. In microstructure characterization of snow, we have used 2 models a) densely packed scatters of sticky particles or multiple sizes, and b) computer generated bicontinuous media. Both models can be characterized by correlation functions. In this paper, we also describe the recent simulated results for tomography and co polarization phase differences of anisotropic dense media.
Mining Process Models from Natural Language Text A State ofthe Art Analysis

Workflow projects are time consuming processes. They include the knowledge extraction and the creation of process models. The necessary information is often available as textual resources. Therefore, process model mining from natural language text has been a research area of growing interest. This paper gives an overview of the current state of the art in text to model mining. For this purpose, different approaches focusing on business process models are presented, analyzed and compared against each other on a theoretical and technical level. The resulting overview covers both advantages and disadvantages of current techniques. This should establish a sturdy basis on which further research can be conducted.
Shades of wickedness Attempting to advance the conceptualization and operationalization of wicked problems

The concept of wicked problem (WP) has recently gained increasing prominence in public policy (Ferlie et al. 2011, Head 2008, Head and Alford 2013) and in the social sciences at large (Camillus 2008, Meckenstock et al 2015, Burns et al. 2013) Initially, Rittel and Webber (1973) used 10 characteristics to define WPs, but they remain silent about their possible combinations and intensities. Furthermore, these characteristics are quite abstract and difficult to use in empirical analysis. Consequently, they are rarely used as analytical categories and scholars often revert to wickedness as a binary concept (tame wicked) Head (2008) intends to increase the analytical depth of the concept and suggests conceptualizing a WP as a combination of the dimensions "complexity" "uncertainty" and "value divergence" of stakeholders involved. In his view, WPs are those problems that are characterized by simultaneously showing high levels of two or three of these dimensions. The paper, however, does not explain in more detail what these three dimensions exactly are, how they could be measured and how combinations of different levels will lead to different shades of wickedness. This academic exercise becomes highly relevant, if we manage to connect different types of interventions to different shades of wickedness in order to cope with WPs. Our paper tries to make progress in that direction by first developing a more detailed operationalization of the three wickedness dimensions. Second, based on the results of step 1, we will report the results of a field experiment in which respondents were invited to categorize different WPs according to (combinations of the three dimensions) to see how people perceive possible variations. Third, we will discuss to what extent such a more detailed conceptualization can be used on different levels of analysis (e.g. global, sectoral, organizational or team level)
Novelty, conditioning and attentional bias to sexual rewards
Venue: Journal of psychiatric research

The Internet provides a large source of novel and rewarding stimuli, particularly with respect to sexually explicit materials. Novelty seeking and cue conditioning are fundamental processes underlying preference and approach behaviors implicated in disorders of addiction. Here we examine these processes in individuals with compulsive sexual behaviors (CSB) hypothesizing a greater preference for sexual novelty and stimuli conditioned to sexual rewards relative to healthy volunteers. Twenty two CSB males and forty age matched male volunteers were tested in two separate behavioral tasks focusing on preferences for novelty and conditioned stimuli. Twenty subjects from each group were also assessed in a third conditioning and extinction task using functional magnetic resonance imaging. CSB was associated with enhanced novelty preference for sexual, as compared to control images, and a generalized preference for cues conditioned to sexual and monetary versus neutral outcomes compared to healthy volunteers. CSB individuals also had greater dorsal cingulate habituation to repeated sexual versus monetary images with the degree of habituation correlating with enhanced preference for sexual novelty. Approach behaviors to sexually conditioned cues dissociable from novelty preference were associated with an early attentional bias to sexual images. This study shows that CSB individuals have a dysfunctional enhanced preference for sexual novelty possibly mediated by greater cingulate habituation along with a generalized enhancement of conditioning to rewards. We further emphasize a dissociable role for cue conditioning and novelty preference on the early attentional bias for sexual cues. These findings have wider relevance as the Internet provides a broad range of novel and potentially rewarding stimuli.
Ancient gene flow from early modern humans into Eastern Neanderthals
Venue: Nature

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000 65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Post traumatic stress, anxiety and depression following miscarriage or ectopic pregnancy: a prospective cohort study
Venue: BMJ Open

This is a pilot study to investigate the type and severity of emotional distress in women after early pregnancy loss (EPL) compared with a control group with ongoing pregnancies. The secondary aim was to assess whether miscarriage or ectopic pregnancy impacted differently on the type and severity of psychological morbidity.  This was a prospective survey study. Consecutive women were recruited between January 2012 and July 2013. We emailed women a link to a survey 1, 3 and 9 months after a diagnosis of EPL, and 1 month after the diagnosis of a viable ongoing pregnancy.  The Early Pregnancy Assessment Unit (EPAU) of a central London teaching hospital.  We recruited 186 women. 128 had a diagnosis of EPL, and 58 of ongoing pregnancies. 11 withdrew consent, and 11 provided an illegible or invalid email address.  Post traumatic stress disorder (PTSD) was measured using the Post traumatic Diagnostic Scale (PDS) and anxiety and depression using the Hospital Anxiety and Depression Scale (HADS) Results Response rates were 69/114 at 1 month and 44/68 at 3 months in the EPL group, and 20/50 in controls. Psychological morbidity was higher in the EPL group with 28% meeting the criteria for probable PTSD, 32% for anxiety and 16% for depression at 1 month and 38% 20% and 5% respectively, at 3 months. In the control group, no women met criteria for PTSD and 10% met criteria for anxiety and depression. There was little difference in type or severity of distress following ectopic pregnancy or miscarriage.  We have shown a large number of women having experienced a miscarriage or ectopic pregnancy fulfil the diagnostic criteria for probable PTSD. Many suffer from moderate to severe anxiety, and a lesser number depression. Psychological morbidity, and in particular PTSD symptoms, persists at least 3 months following pregnancy loss.