nils-herrmann/clean_scirepeval huggingface dataset:
Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease

Work on soils suppressive to Thielaviopsis basicola-mediated tobacco black root rot has focused on antagonistic pseudomonads to date. The role of non-Pseudomonas rhizosphere populations has been neglected, and whether they differ in black root rot-suppressive versus -conducive soils is unknown. To assess this possibility, tobacco was grown in a suppressive and a conducive soil of similar physicochemical properties, and rhizobacterial community composition was compared using a 16S rRNA taxonomic microarray. The microarray contains 1033 probes and targets 19 bacterial phyla. Among them, 398 probes were designed for Proteobacteria, Firmicutes, Actinomycetes, Cyanobacteria and Bacteroidetes genera/species known to include strains relevant for plant protection or plant growth promotion. Hierarchical clustering as well as principal component analysis of microarray data discriminated clearly between black root rot-suppressive and -conducive soils. In contrast, T. basicola inoculation had no impact on rhizobacterial community composition. In addition to fluorescent Pseudomonas, the taxa Azospirillum, Gluconacetobacter, Burkholderia, Comamonas and Sphingomonadaceae, which are known to comprise strains with plant-beneficial properties, were more prevalent in the suppressive soil. Mycobacterium, Bradyrhizobium, Rhodobacteraceae, Rhodospirillum and others were more prevalent in the conducive soil. For selected taxa, microarray results were largely corroborated by quantitative PCR and cloning/sequencing. In conclusion, this work identified novel bacterial taxa that could serve as indicators of disease suppressiveness in soil-quality assessments, and it extends the range of bacterial taxa hypothesized to participate in black root rot suppression.
Detection of Novel Network Attacks Using Data Mining

This paper introduces the Minnesota Intrusion Detection System (MINDS), which uses a suite of data mining techniques to automatically detect attacks against computer networks and systems. While the long-term objective of MINDS is to address all aspects of intrusion detection, in this paper we present two specific contributions. First, we present MINDS anomaly detection module that assigns a score to each connection that reflects how anomalous the connection is compared to the normal network traffic. Experimental results on live network traffic at the University of Minnesota show that our anomaly detection techniques have been successful in automatically detecting several novel intrusions that could not be identified using state-of-the-art signature-based tools such as SNORT. Many of these have been reported on the CERT/CC list of recent advisories and incident notes. We also present the results of comparing the MINDS anomaly detection module to SPADE (Statistical Packet Anomaly Detection Engine), which is designed to detect stealthy scans.
Collaborative conceptual design: A large software project case study

During software development, the activities of requirements analysis, functional specification, and architectural design all require a team of developers to converge on a common vision of what they are developing. There have been remarkably few studies of conceptual design during real projects. In this paper, we describe a detailed field study of a large industrial software project. We observed the development team's conceptual design activities for three months with follow-up observations and discussions over the following eight months. In this paper, we emphasize the organization of the project and how patterns of collaboration affected the team's convergence on a common vision. Three observations stand out: First, convergence on a common vision was not only painfully slow but was punctuated by several reorientations of direction; second, the design process seemed to be inherently forgetful, involving repeated resurfacing of previously discussed issues; finally, a conflict of values persisted between team members responsible for system development and those responsible for overseeing the development process. These findings have clear implications for collaborative support tools and process interventions.
Origami Programming 3.1 Introduction

3 origami (˛ orig¯  The Japanese art of making elegant designs using folds in all kinds of paper. One style of functional programming is based purely on recursive equations. Such equations are easy to explain, and adequate for any computational purpose , but hard to use well as programs get bigger and more complicated. In a sense, recursive equations are the 'assembly language' of functional programming , and direct recursion the goto. As computer scientists discovered in the 1960s with structured programming, it is better to identify common patterns of use of such too-powerful tools, and capture these patterns as new constructions and abstractions. In functional programming, in contrast to imperative programming, we can often express the new constructions as higher-order operations within the language, whereas the move from un-structured to structured programming entailed the development of new languages. There are advantages in expressing programs as instances of common patterns, rather than from first principles — the same advantages as for any kind of abstraction. Essentially, one can discover general properties of the abstraction once and for all, and infer those properties of the specific instances for free. These properties may be theorems, design idioms, implementations, optimisations, and so on. In this chapter we will look at folds and unfolds as abstractions. In a precise technical sense, folds and unfolds are the natural patterns of computation over recursive datatypes; unfolds generate data structures and folds consume them. Functional programmers are very familiar with the foldr function on lists, and its directional dual foldl; they are gradually coming to terms with the generalisation to folds on other datatypes (IFPH §3.3, §6.1.3, §6.4).
Security Limits for Compromising Emanations

Nearly half a century ago, military organizations introduced “Tempest” emission-security test standards to control information leakage from unintentional electromagnetic emanations of digital electronics. The nature of these emissions has changed with evolving technology; electromechanic devices have vanished and signal frequencies increased several orders of magnitude. Recently published eavesdropping attacks on modern flat-panel displays and cryptographic coprocessors demonstrate that the risk remains acute for applications with high protection requirements. The ultra-wideband signal processing technology needed for practical attacks finds already its way into consumer electronics. Current civilian RFI limits are entirely unsuited for emission security purposes. Only an openly available set of test standards based on published criteria will help civilian vendors and users to estimate and manage emission-security risks appropriately. This paper outlines a proposal and rationale for civilian electromagnetic emission-security limits. While the presented discussion aims specifically at far-field video eavesdropping in the VHF and UHF bands, the most easy to demonstrate risk, much of the presented approach for setting test limits could be adapted equally to address other RF emanation risks.
Evaluating GPGPU Memory Performance Through the C-AMAT Model

General Purpose Graphics Processing Units (GPGPU) have become a popular platform to accelerate high performance applications. Although they provide exceptional computing power, GPGPU impose significant pressure on the off-chip memory system. Evaluating, understanding, and improving GPGPU data access delay has become an important research topic in high-performance computing. In this study, we utilize the newly proposed GPGPU/C-AMAT (Concurrent Average Memory Access Time) model to quantitatively evaluate GPGPU memory performance. Specifically, we extend the current C-AMAT model to include a GPGPU-specific modeling component and then provide its evaluation results.
Recursive autoconvolution for unsupervised learning of convolutional neural networks

In visual recognition tasks, such as image classification, unsupervised learning exploits cheap unlabeled data and can help to solve these tasks more efficiently. We show that the recursive autoconvolution operator, adopted from physics, boosts existing unsupervised methods by learning more discriminative filters. We take well established convolutional neural networks and train their filters layer-wise. In addition, based on previous works we design a network which extracts more than 600k features per sample, but with the total number of trainable parameters greatly reduced by introducing shared filters in higher layers. We evaluate our networks on the MNIST, CIFAR-10, CIFAR-100 and STL-10 image classification benchmarks and report several state of the art results among other unsupervised methods.
Censorship in the Wild: Analyzing Internet Filtering in Syria

Internet censorship is enforced by numerous governments worldwide, however, due to the lack of publicly available information, as well as the inherent risks of performing active measurements, it is often hard for the research community to investigate censorship practices in the wild. Thus, the leak of 600GB worth of logs from 7 Blue Coat SG-9000 proxies, deployed in Syria to filter Internet traffic at a country scale, represents a unique opportunity to provide a detailed snapshot of a real-world censorship ecosystem.
 This paper presents the methodology and the results of a measurement analysis of the leaked Blue Coat logs, revealing a relatively stealthy, yet quite targeted, censorship. We find that traffic is filtered in several ways: using IP addresses and domain names to block subnets or websites, and keywords or categories to target specific content. We show that keyword-based censorship produces some collateral damage as many requests are blocked even if they do not relate to sensitive content. We also discover that Instant Messaging is heavily censored, while filtering of social media is limited to specific pages. Finally, we show that Syrian users try to evade censorship by using web/socks proxies, Tor, VPNs, and BitTorrent. To the best of our knowledge, our work provides the first analytical look into Internet filtering in Syria.
A Measure of Spatial Segregation : The Generalized Neighborhood Sorting Index

The measurement of spatial segregation has often used measures such as the Neighborhood Sorting Index (NSI) or the Index of Dissimilarity (D) that do not take full account of space. We propose a Generalized Neighborhood Sorting Index (GNSI), an extension of NSI, in which each neighborhood is part of a broader community, the extent of which can be easily changed by increasing the order of contiguity or the allowable distance between neighborhood centroids. The GNSI has desirable characteristics as a valid spatial measure of segregation and significantly alleviates the checkerboard problem while NSI and similar measures are insensitive to the spatial arrangement of the geographic units in the analysis, such as census tracts. An application of GNSI to the ten largest metropolitan areas reveals that the GNSI gives a more complete account of the extent of economic segregation and the changes over time, and ranks the metropolitan areas differently in term of the level and changes in economic segregation.
Biodegradable Polymers

Learn more about our line of Polylactic Acid & Polyethylene Glycol Based Biodegradable Polymers, visit www.polysciences.com/plapeg The exploration of polyethylene glycolated (PEG) materials in biosciences and pharmaceuticals has grown rapidly. Biodegradable Polymers based on copolymers of polylactic acid (PLA) and polyethylene glycol (PEG) offer researchers and scientists new tools for controlled release formulations and drug delivery platforms.
Fundamental characteristics of electrostatic wafer chuck with insulating sealant

In the semiconductor industry, many manufacturing processes, such as CVD or dry etching, are performed in vacuum condition. The electrostatic wafer chuck is the most preferable handling method under such circumstances. It enables retention of a wafer flat and enhanced heat transfer through the whole surface area because the wafer can firmly contact with the chuck. We have investigated the fundamental study of an electrostatic chuck with comb type electrodes and a thin dielectric film. In order to remove the air gap between them, silicone oil is used as a filler to prevent breakdown. The experimental results proved the potential to use the electrostatic chuck for silicon wafer handling. There, however, is a problem which comes from using silicone oil as an insulating filler. The thin dielectric film is easily deformed by tension when the object starts moving. In this report experimental results of the electrostatic wafer chuck are shown when insulating sealant, instead of silicone oil, is used. The electrostatic force acting on the 4 inch silicon wafer is examined with several types of sealant and dielectric films. The electrostatic force increased with the square of the applied voltage for lower voltage and gradually saturated at higher voltage, and the maximum force obtained was approximately 30 N.
Optimal Least-Squares Design of Sparse FIR Filters for Big-Data Signal Processing

Since amount of big data is extremely huge, low-delay and low-complexity signal processing devices are strongly required in big data signal processing. Digital filters are the key device for digital signal processing. Digital filters with sparse coefficients (0 coefficients) are beneficial to reduce the computational complexity. This paper proposes a design method for low-delay FIR filters with sparse coefficients. We consider the optimization of combination of selection for sparse coefficients. If the sparse coefficients are selected, the real coefficients can be computed based on the Lagrange multiplier method. We employ the branch and bound method incorporated with the Lagrange multiplier method. Also, we propose a selection method of the initial cost for high-speed search. The feature of this method is as follows: (a) The number of 0 coefficients can explicitly specify. (b) The optimality is guaranteed in the least squares sense. We present a design example in order to demonstrate the effectiveness of our method.
Chemical Genetics of Acetyl-CoA Carboxylases

Chemical genetic studies on acetyl-CoA carboxylases (ACCs), rate-limiting enzymes in long chain fatty acid biosynthesis, have greatly advanced the understanding of their biochemistry and molecular biology and promoted the use of ACCs as targets for herbicides in agriculture and for development of drugs for diabetes, obesity and cancers. In mammals, ACCs have both biotin carboxylase (BC) and carboxyltransferase (CT) activity, catalyzing carboxylation of acetyl-CoA to malonyl-CoA. Several classes of small chemicals modulate ACC activity, including cellular metabolites, natural compounds, and chemically synthesized products. This article reviews chemical genetic studies of ACCs and the use of ACCs for targeted therapy of cancers.
INEQUALITY AND VIOLENT CRIME

In this article we take an empirical cross-country perspective to investigate the robustness and causality of the link between income inequality and crime rates. First, we study the correlation between the Gini index and, respectively, homicide and robbery rates along different dimensions of the data (within and between countries). Second, we examine the inequality-crime link when other potential crime determinants are controlled for. Third, we control for the likely joint endogeneity of income inequality in order to isolate its exogenous impact on homicide and robbery rates. Fourth, we control for the measurement error in crime rates by modelling it as both unobserved country-specific effects and random noise. Lastly, we examine the robustness of the inequality-crime link to alternative measures of inequality. The sample for estimation consists of panels of non-overlapping 5-year averages for 39 countries over 1965-95 in the case of homicides, and 37 countries over 1970-1994 in the case of robberies. We use a variety of statistical techniques, from simple correlations to regression analysis and from static OLS to dynamic GMM estimation. We find that crime rates and inequality are positively correlated (within each country and, particularly, between countries), and it appears that this correlation reflects causation from inequality to crime rates, even controlling for other crime determinants.  We are grateful for comments and suggestions from Francois Bourguignon, Dante Contreras, Francisco Ferreira, Edward Glaeser, Sam Peltzman, Debraj Ray, Luis Servén, and an anonymous referee. N. Loayza worked at the research group of the Central Bank of Chile during the preparation of the paper. This study was sponsored by the Latin American Regional Studies Program, The World Bank. The opinions and conclusions expressed here are those of the authors and do not necessarily represent the views of the institutions to which they are affiliated.
A Low-Flicker-Noise 30-GHz Class-F23 Oscillator in 28-nm CMOS Using Implicit Resonance and Explicit Common-Mode Return Path

This paper presents a millimeter-wave (mmW) frequency generation stage aimed at minimizing phase noise (PN) via waveform shaping and harmonic extraction while suppressing flicker noise upconversion via proper harmonic terminations. A 2nd-harmonic resonance is assisted by a proposed embedded decoupling capacitor inside a transformer for explicit common-mode current return path. Class-F operation with 3rd-harmonic boosting and extraction techniques allow maintaining high quality factor of a 10-GHz tank at the 30-GHz frequency generation. We further propose a comprehensive quantitative analysis method of flicker noise upconversion mechanism exploiting latest insights into the flicker noise mechanisms in nanoscale short-channel transistors, and it is numerically verified against foundry models. The proposed 27.3- to 31.2-GHz oscillator is implemented in TSMC 28-nm CMOS. It achieves PN of −106 dBc/Hz at 1-MHz offset and figure-of-merit (FoM) of −184 dBc/Hz at 27.3 GHz. Its flicker phase-noise ( $1/f^{3}$ ) corner of 120 kHz is an order-of-magnitude better than currently achievable at mmW.
A Crowdsourced Alternative to Eye-tracking for Visualization Understanding

In this study we investigate the utility of using mouse clicks as an alternative for eye fixations in the context of understanding data visualizations. We developed a crowdsourced study online in which participants were presented with a series of images containing graphs and diagrams and asked to describe them. Each image was blurred so that the participant needed to click to reveal bubbles - small, circular areas of the image at normal resolution. This is similar to having a confined area of focus like the human eye fovea. We compared the bubble click data with the fixation data from a complementary eye-tracking experiment by calculating the similarity between the resulting heatmaps. A high similarity score suggests that our methodology may be a viable crowdsourced alternative to eye-tracking experiments, especially when little to no eye-tracking data is available. This methodology can also be used to complement eye-tracking studies with an additional behavioral measurement, since it is specifically designed to measure which information people consciously choose to examine for understanding visualizations.
Initial combination therapy with metformin, pioglitazone and exenatide is more effective than sequential add-on therapy in subjects with new-onset diabetes. Results from the Efficacy and Durability of Initial Combination Therapy for Type 2 Diabetes (EDICT): a randomized trial.

To test our hypothesis that initiating therapy with a combination of agents known to improve insulin secretion and insulin sensitivity in subjects with new-onset diabetes would produce greater, more durable reduction in glycated haemoglobin (HbA1c) levels, while avoiding hypoglycaemia and weight gain, compared with sequential addition of agents that lower plasma glucose but do not correct established pathophysiological abnormalities.



Drug-naïve, recently diagnosed subjects with type 2 diabetes mellitus (T2DM) were randomized in an open-fashion design in a single-centre study to metformin/pioglitazone/exenatide (triple therapy; n = 106) or an escalating dose of metformin followed by sequential addition of sulfonylurea and glargine insulin (conventional therapy; n = 115) to maintain HbA1c levels at <6.5% for 2 years.



Participants receiving triple therapy experienced a significantly greater reduction in HbA1c level than those receiving conventional therapy (5.95 vs. 6.50%; p < 0.001). Despite lower HbA1c values, participants receiving triple therapy experienced a 7.5-fold lower rate of hypoglycaemia compared with participants receiving conventional therapy. Participants receiving triple therapy experienced a mean weight loss of 1.2 kg versus a mean weight gain of 4.1 kg (p < 0.01) in those receiving conventional therapy.



The results of this exploratory study show that combination therapy with metformin/pioglitazone/exenatide in patients with newly diagnosed T2DM is more effective and results in fewer hypoglycaemic events than sequential add-on therapy with metformin, sulfonylurea and then basal insulin.
Statins in abdominal surgery: a systematic review.

l l Statins (3-hydroxy-3-methylglutaryl coenzyme A [HMGCoA] or HMG-CoA reductase inhibitors) are the most commonly prescribed class of lipid-lowering drugs. In addiion to their established role in the medical management of ardiovascular disease, benefits have also been demontrated in cardiac and vascular surgery, where they have een shown to decrease cardiovascular complications nd reduce perioperative mortality. These cardioprotective effects also extend to the wider surgical population, with similar benefits seen in noncardiovascular surgical settings. Interestingly, some cardiovascular benefits of statins precede any substantial reduction in cholesterol levels or preexisting atheroma. Thishasbeenattributed to theadditional ffects of statins that extend beyond cholesterol-lowering, includng anti-inflammatory, antioxidant, immunomodulatory, and ibrinolytic properties. The mechanism behind these holesterol-independent or pleiotropic effects of statins is ecoming increasingly recognized. Through inhibition of he HMG-CoA reductase enzyme, statins inhibit the conersion of HMG-CoA to mevalonate and important downtream isoprenoids, such as farnesyl pyrophosphate and eranyl-geranyl pyrophosphate. In addition to reducing holesterol synthesis, inhibition of these intermediate molcules decreases isoprenylation of important signaling molcules, such as RhO and Ras, which leads to modulation of arious cellular activities . These effects on ellular function are considered the basis for the observed holesterol-independent effects of statins (Table 1). Along with their cardioprotective effects, these pleiotroic properties are relevant to the general surgical populaion and there is growing evidence that statins can offer articular benefits in abdominal surgery. Laboratory tudies have demonstrated the relevance of these pleiotroic effects to abdominal surgery, with statins improving