nils-herrmann/clean_scirepeval huggingface dataset:
Metastatic colorectal cancer presenting with bone marrow metastasis: a case series and review of literature.
Venue: Journal of gastrointestinal oncology

With advances in treatment, patients with metastatic colorectal cancer (CRC) are now living longer with an apparent increase in the incidence of bone and bone marrow metastases (BMM) Common sites of metastatic disease from CRC include the liver and lungs with bone metastasis rarely occurring in the absence of visceral metastatic disease. We report a series of three patients presenting with isolated bone and BMM leading to a diagnosis of primary CRC. We have reviewed the literature regarding diagnosis, potential mechanisms leading to the development of osseous metastasis and outcome. A high level of clinical suspicion and in depth understanding of the natural history of these rare metastases may guide future management and treatment decisions.
XRay: A Function Call Tracing System

Debugging high throughput, low latency C/C+ systems in production is hard. At Google we developed XRay, a function call tracing system that allows Google engineers to get accurate function call traces with negligible overhead when off and moderate overhead when on, suitable for services deployed in production. XRay enables efficient function call entry/exit logging with high accuracy timestamps, and can be dynamically enabled and disabled. This white paper describes the XRay tracing system and its implementation. It also describes future plans with open sourcing XRay and engaging open source communities.  Call Tracing in Production At Google we run distributed systems handling massive amounts of concurrent requests that do everything from serving a webpage to storing bytes on disks. Understanding the performance of these complex systems is difficult given the abstractions involved, asynchronous programming with callbacks, and even interaction between threads synchronising amongst each other. It can be especially difficult to track down what affects performance in rare events, which can be rare because they occur at the latency tail or 1 because they are outlier requests to the service. Seeing what happens "at the tail" allows software engineers to diagnose the performance of systems in these rare events that have an impact on the overall performance of the system. The question then becomes how do you find these "needle in a haystack" events while running in production? Time based traces let developers track down these issues when standard approaches such as sampling, logging, and aggregate statistics fail. What kind of time based trace data would be useful? Ideally, we'd like to get non sampled function call traces with high precision timestamps from production servers that tell us which threads are running what code and when. However, instrumenting all functions is usually too expensive for production use. To deploy in production, we require that: The cost is acceptable when tracing and barely measurable when not tracing. Instrumentation is automatic and directed towards functions that are important for understanding the binary's execution time. Tracing is efficient in both space and time only recording what is required and what matters. In addition to the above, we also require: Tracing is configurable with thresholds for storage (how much memory to use) and accuracy (whether to log everything or only function calls taking at least some amount of time) Tracing does not require changes to the operating system nor super user privileges. Tracing can be turned on and off dynamically without having to restart the server. 1 For more on why optimising tail latency matters, refer to " The Tail at Scale " by Jeff Dean and Luiz Barroso, published to the Communications of the ACM, vol. 56 (2013) pp. 74 80.
Marine bacterial transparent exopolymer particles (TEP) and TEP precursors: Characterization and RO fouling potential

This paper investigated the characteristics and membrane fouling potential of bacterial transparent exopolymer particles (TEP)/TEP precursors released from two marine bacteria, Pseudidiomarina homiensis P. homiensis and Pseudoalteromonas atlantica P. atlantica isolated from the Red Sea. Results showed that both bacteria grew at the similar rate, but the production of TEP/TEP precursors from P. atlantica was higher than that from P. homiensis During the 168 h of incubation time, production rates of TEP/TEP precursors from P. atlantica and P. homiensis were 0.30 and 0.08 xanthan gum eq. mg/L h, respectively. Isolated bacterial TEP precursors were mainly biopolymer, and P. atlantica produced a significantly higher concentration of biopolymer than that produced by P. homiensis TEP/TEP precursors from both marine bacteria possessed protein like material and were very similar in composition to previously reported foulants isolated from a fouled reverse osmosis (RO) membrane. Bacterial TEP/TEP precursors mostly consisted of aliphatic hydrocarbon from amino acids and amide group carbon of proteins (around 55% Bacterial TEP precursors caused obvious fouling on RO membranes, which may create an ideal environment for bacteria attachment and promote to biofouling.
A gene expression programming framework for evolutionary design of metaheuristic algorithms
Venue: 2016 IEEE Congress on Evolutionary Computation (CEC)

Metaheuristic algorithms have successfully tackled many difficult and ill conditioned optimization problems. Nevertheless, performance of these methods is subjected to the complexity and fitness landscape of the problem at hand. Accordingly, designing metaheuristic algorithms that work well on a variety of optimization problems is not a trivial task. In this study, we introduce a novel framework for improving generalization capability of the metaheuristic algorithms based on the notion of gene expression programming (GEP) The proposed framework introduces a modified GEP (MGEP) in order to adaptively design search operators of a metaheuristic algorithm. During evolution process, a multi criteria procedure determines the search operators that are preferable and can obtain high accuracy results. Performance of the proposed approach is empirically evaluated on CEC 2013 test suite. The obtained results confirm that the evolved metaheuristic algorithms by this framework perform similarly to or better than the standard versions.
Constructing a linkage linkage disequilibrium map using dominant segregating markers
Venue: DNA research an international journal for rapid publication of reports on genes and genomes

The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage LD map from commonly used biallelic, single nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution.
DTMS IoT: A Dirichlet based trust management system mitigating on off attacks and dishonest recommendations for the Internet of Things
Venue: 2016 IEEE/ACS 13th International Conference of Computer Systems and Applications (AICCSA)

The Internet of Things (IoT) is based on the idea that things surrounding the human living space can be connected to the Internet, allowing smarter living environments and more comfortable life. However, adoption of the IoT might not be approved unless security issues are solved. In this paper, we propose a new Dirichlet based trust management system for the IoT called DTMS IoT. This system detects nodes malicious behaviour which permits to mitigate both on off attacks and dishonest recommendations. It also uses service levels and things capacities to reinforce security. As in many trust management systems introduced in the literature, the computation of trust in our solution is based on direct observations and recommendations. The novelty of our approach can be summed up in two aspects. The first aspect concerns recommendations that we do not consider unless direct observations are not credible. However the second aspect tries to prevent On Off attacks using the precaution factor and mitigates dishonest recommendations based on k means selection algorithm and guarantor things. The effectiveness of the proposed system is proved by simulation against on off attacks and good/bad mouthing attacks.
Generic links and paths stability model for Mobile Ad Hoc Networks
Venue: 2016 International Wireless Communications and Mobile Computing Conference (IWCMC)

A mobile ad hoc network (MANET) is a collection of autonomous mobiles nodes forming a temporary network without using any existing infrastructure or centralized administration. MANETs are characterized by a dynamic topology which makes routing a critical task. Conventional routing protocols are mainly based on shortest paths computation which could be not effective facing the mobility of nodes. Therefore, finding stable paths in MANETS is a more reliable strategy to improve routing. In this paper, we study the stability of links and paths in MANETs. At that end, we define a generic and simple model for links and paths stability in MANETs, then, we investigate, using the new defined metrics, the effect of mobility under various scenarios. Our study showed that our model is perfectly capable of predicting the behavior of links and paths and that proactive routing always constructs low stability paths even under slow moving nodes.
Behind the veil of agricultural modernization gendered dynamics of rural change in the Saiss, Morocco

The Moroccan countryside is marked by rapidly changing rural realities. The Moroccan government frames and promotes these changes as linear development towards modernity and progress for all thereby only focusing on the experiences of some audacious men 'entrepreneurs' and 'modernizing farmers' The aim of the study is to unveil Morocco's agricultural modernization plan by illustrating how agrarian processes in the agricultural plain of the Saiss are not a logical, self evident or smooth transition to a higher stage of development or modernity. They are a form of globalizing capitalist development which is messy and contradictory, and which is marked by, and re produces existing gender social hierarchies. By putting the experiences that often "fall away" from agrarian analysis at the heart of my study I am to explore how gender and social differences come to matter in process of agrarian change and are intimately linked.
BIOSAFETY ASSESSMENT OF LOCALLY DEVELOPED TRANSGENIC SUGARCANE

Genetically modified organisms have become obligatory to adopt certain precautions to overcome the risks related to release of GMOs. Through this study, an attempt was made to evaluate bio safety concerns of transgenic sugarcane with insect resistant gene, Cry1Ac. In short term feeding trial of 120 days, 20 broiler chicks divided into four random groups were caged separately. Group I fed on commercial chicken diet; group II fed on non transgenic sugarcane diet; group III fed on transgenic diet (commercial to transgenic ratio was 1:1) while group IV was fed on high dose transgenic diet (commercial to transgenic ratio was 1:2) Body weights of chicks increased normally in all four groups during the course of study. Biochemical tests and molecular tests done on chick's blood reported no significant difference among assorted groups. At the termination of the experiment, chicks were slaughtered and dissected vital organs were used for histological studies. It was found that tissues belong to group 3 and 4 were morphologically and histological similar to group 1 and 2. Also, no mRNA expression was observed in total RNA isolated from chicken's tissues. These findings suggest that there was no deleterious or harmful effect of the GM sugarcane on the chick's health and no transgene fragment has transferred from GM crop to animal's blood neither in their vital tissues. Conclusively, it is suggested that at least in short term period feeding trial, the genetically modified sugarcane doesn't not have adverse effect on animals feeding them.
On Mandatory Labeling, With Special Reference to Genetically Modified Foods

As a result of movements for labeling food with genetically modified organisms (GMOs) Congress enacted a mandatory labeling requirement in 2016. These movements, and the legislation, raise recurring questions about mandatory product labels: whether there is a market failure, neoclassical or behavioral, that justifies them, and whether the benefits of such labels justify the costs. The first goal of this essay is to identify and to evaluate the four competing approaches that agencies now use to assess the costs and benefits of mandatory labeling in general. The second goal is to apply those approaches to the context of GM food.Assessment of the benefits of mandatory labels presents especially serious challenges. Agencies have (1) claimed that quantification is essentially impossible; (2) engaged in breakeven analysis; (3) projected various endpoints, such as health benefits or purely economic savings; and (4) relied on private willingness to pay for the relevant information. All of these approaches run into serious normative and empirical challenges. In principle, (4) is best, but in practice, (2) is sometimes both the most that can be expected and the least that can be demanded.Many people favor labeling GM food on the ground that it poses serious risks to human health and the environment, but with certain qualifications, the prevailing scientific judgment is that it does no such thing. In the face of that judgment, some people respond that even in the absence of evidence of harm, people have "a right to know" about the contents of what they are eating. But there is a serious problem with this response: there is a good argument that the benefits of such labels would be lower than the costs. Consumers would obtain no health benefits from which labels. To the extent that they would be willing to pay for them, the reason (for many though not all) is likely to be erroneous beliefs, which are not a sufficient justification for mandatory labels. Moreover, GMO labels might well lead people to think that the relevant foods are harmful and thus affirmatively mislead them.Some people contend that GMOs pose risks to the environment (including biodiversity) to intelligible moral commitments, or to nonquantifiable values. Many people think that the key issue involves the need to take precautions in the face of scientific uncertainty: Because there is a non zero risk that GM food will cause irreversible and catastrophic harm, it is appropriate to be precautionary, through labels or through more severe restrictions. The force of this response depends on the science: If there is a small or uncertain risk of serious harm, precautions may indeed be justified. If the risk is essentially zero, as many scientists have concluded, then precautions are difficult to justify. The discussion, though focused on GM foods, has implications for disclosure policies in general, which often raise difficult questions about hard to quantify benefits, the proper use of cost benefit balancing, and the appropriate role of precautionary thinking.
The Effects of Computerized Accounting System on the Performance of Banks in Nigeria

Computerization in Nigerian commercial banks has now become widely spread. However, the fact that computerization has gained acceptance in Nigerian banking sector does not mean that an improvement in bank performances has occurred over the years of adoption of computerized system. Apparently, the study aims at examining the effects of computerized accounting systems on bank performance in Nigerian banking sector. Convenience sampling method was adopted to arrive at sample size of 50 covering Guaranty Trust Bank Plc, Wema Bank Plc and First Bank Plc. The study variables consist of both dependent variable and independent variable, with Computerized Accounting System being the dependent variable and banks profitability as independent variable and customer service delivery respectively being the dependent variables. Data collected were analyzed using correlation analysis. Results show that computerized accounting system has a positive effect on bank's profitability and as well customer patronage. The study therefore recommends that computerized accounting systems should be adopted by all banks in Nigeria because it has a lot of advantages and benefits and government power supply should be replaced with inverters for the purpose of powering the computers used in their operations so as to prevent power outage which may result in data loss on the computer.  Computer accounting, Profitability, Commercial Banks, Customers Patronage
The case for academic detailing with nurse practitioners.
Venue: Journal of the American Association of Nurse Practitioners

In the age of increasing time demands on nurse practitioners (NPs) and rapidly evolving changes to the evidence base underpinning clinical practice, there is a clear need to provide clinicians with continuing professional development in an effective and time efficient manner. Academic detailing (also called educational outreach) combines the communication and marketing skills of industry with the intellectual rigor of academe to construct and deliver medical education programs. Trained facilitators visit healthcare practitioners one on one in their place of work to deliver key clinical messages on a defined topic of interest and relevance to the provider. The key messages are often phrased as succinct action statements to help support behavior change. The sessions between facilitator and provider are highly interactive and seek to elicit the specific needs of the individual provider, as well as discussing the key messages of the topic. The overall goal of academic detailing programs is to facilitate good clinical decision making by providing clinicians and patients with evidence based, practical, clinically relevant, and independent/unbiased information that takes a biopsychosocial approach. An extensive review of the biomedical literature and writing of de novo clinical reviews help to elicit the key messages and support each educational topic. An important aspect of successful academic detailing programs is to establish how outcomes from clinical trials should influence real life clinical practice. In particular, this has involved determining the comparative effectiveness of active therapies in relation to clinical outcomes rather than surrogate markers. We have been providing academic detailing programs to physicians in the United States and Australia for more than 15 years, and more recently to NPs, particularly in their role as prescribers. The programs are universally well received, uptake is high, and retention rates approach 100% A number of themes that clinicians value in the programs consistently emerge in their feedback: (a) the independent noncommercial nature of the information provided; (b) the clinical relevance of the key messages framed as action statements; (c) a focus on comparative effectiveness of active therapies, not just therapy versus placebo; (d) a willingness to discuss individual clinical needs; (e) a translation of how clinical trial results should influence clinical practice; and (f) the individualized oneon one visit in their workplace. Rationale for academic detailing
General Systems Theory

to look at the systems idea not as an ephemeral fashion or recent technique, but in the context of the history of ideas. (For an introduction and a survey of the field see  with an extensive bibliography and Suggestions for Further Reading in the various topics of general systems theory. In a certain sense it can be said that the notion of system is as old as European philosophy. If we try to define the central motif in the birth of philosophical scientific thinking with the Ionian pre Socratics of the sixth century B.C. one way to spell it out would be as follows. Man in early culture, and even primitives of today, experience themselves as being "thrown" into a hostile world, governed by chaotic and incomprehensible demonic forces which, at best, may be propitiated or influenced by way of magical practices. Philosophy and its descendant, science, was born when the early Greeks learned to consider or find, in the experienced world, an order or kosmos which was intelligible and, hence, controllable by thought and rational action. One formulation of this cosmic order was the Aristotelian world view with its holistic and telelogical notions. Aristotle's statement, "The whole is more than the sum of its parts," is a definition of the basic system problem which is still valid. Aristotelian teleology was eliminated in the later development of Western science, but the problems contained in it, such as the order and goal directedness of living systems, were negated and by passed rather than solved. Hence, the basic system is still not obsolete. A more detailed investigation would enumerate a long array of thinkers who, in one way or another, contributed notions to what nowadays we call systems theory. If we speak of hierarchic order, we use a term introduced
In Search of General Systems Theory

The search for a General Systems Theory (GST) formally became a scientific enterprise with the founding of the Society for the Advancement of General Systems Theory (living on today as the International Society for the Systems Sciences) in 1954. Many scientific advances have been made towards a GST, but GST is still incomplete and there is a rich ongoing debate about the nature, structure and value of GST. In this paper we argue that the general theory of a discipline has a generic structure, which can be inferred by attending to the process by which disciplines build up their knowledge base. We develop a model of this generic structure and then use it to envision the structure and scope of GST. This provides a principled baseline for assessing the developmental status of GST, planning work towards its completion, and defending the potential value of GST.