Miracle-dz/UniFAR-FTUs huggingface dataset:
Spillover of a biological control agent (Chrysolina quadrigemina) onto native St. Johnswort (Hypericum punctatum)

Biological control agents may have unintended effects on native biota, particularly species that are closely related to the target invader. Here, we explored how Chrysolina quadrigemina, a beetle introduced to control the invasive weed Hypericum perforatum, impacts native H. punctatum in Tompkins County, New York, USA. Using a suite of complementary field surveys and experimental manipulations, we examined beetle preference for native and exotic Hypericum species and whether beetle herbivory influences the spatial distribution of H. punctatum. We found that the introduced beetle readily consumes native H. punctatum in addition to its intended target, and that H. punctatum at our field sites generally occurs along forest edges despite higher performance of experimental plants in more open habitats. However, we found no evidence that the beetle limits H. punctatum to forest edge habitats.
Model-P: a basecalling method for resequencing microarrays of diploid samples

MOTIVATION Basecalling is a critical step of the analysis of DNA resequencing microarray data for single nucleotide polymorphism discovery and genotyping. For microarrays hybridized with DNA derived from diploid organisms, basecalling with high accuracy at high call rates is a challenging task. Current methods sometimes do not produce satisfactory results. RESULTS We explored using physical models based on the sequences of the probe and the target to predict feature intensities in resequencing microarrays. Based on these intensity-predicting models, a new basecalling method (Model-P), which takes into consideration the expected feature intensities for different potential genotypes, was developed. Model-P is shown to have better performance at high call rates compared with ABACUS, the current state-of-the-art method, on a test dataset and on relatively AT-rich regions. AVAILABILITY Model-P is available upon request.
Business Volatility , Job Destruction and Unemployment October 2007

Unemployment inflows fell from 4 percent of employment per month in the early 1980s to 2 percent or less by the mid 1990s and thereafter. U.S. data also show a secular decline in firm-level employment volatility and the job destruction rate. We interpret this decline as a decrease in the intensity of idiosyncratic labor demand shocks, a key parameter in search and matching models of frictional unemployment. According to these models, a lower intensity of idiosyncratic demand shocks produces less job destruction, fewer workers flowing through the unemployment pool and less frictional unemployment. To evaluate this theoretical mechanism, we relate industry-level unemployment flows from 1977 to 2005 to industry-level indicators for the intensity of idiosyncratic shocks. Unlike previous research, we focus on the lower frequency relationship of job destruction and business volatility to unemployment flows. We find strong evidence that declines in the intensity of idiosyncratic labor demand shocks drove large declines in the incidence of unemployment.
Directional leakage and parameter drift

A new method for eliminating parameter drift in parameter estimation problems is proposed. Existing methods for eliminating parameter drift work either on a limited time horizon, restricts the parameter estimates to a range that has to be determined a priori, or introduces bias in the parameter estimates which will degrade steady state performance. The idea of the new method is to apply leakage only in the directions in parameter space in which the exciting signal is not informative. This avoids the problem of parameter bias associated with conventional leakage. Copyright © 2005 John Wiley & Sons, Ltd.
Embedded-width: A variant of treewidth for plane graphs

We define a special case of tree decompositions for planar graphs that respect a given embedding of the graph. We study the analogous width of the resulting decomposition we call the embedded-width of a plane graph. We show both upper bounds and lower bounds for the embedded-width of a graph in terms of its treewidth and describe a fixed parameter tractable algorithm to calculate the embedded-width of a plane graph. To do so, we give novel bounds on the size of matchings in planar graphs.
Effects of nitrocompounds on uric acid-utilizing microorganisms, nitrogen retention, and microbial community in laying hen manure

A study was conducted to evaluate effects of nitrocompounds on growth of uric acid-utilizing microorganisms, nitrogen retention, and microbial community in laying hen manure. There were three treatments: control, 100 mM nitropropanol (NPL), and 100 mM nitropropionic acid (NPC). The mixed laying hen manure was divided into 3 groups and incubated at 23°C for 7 days. On Days 0, 3, and 7, samples were collected to measure the quantity of uric acid-utilizing microorganisms, total nitrogen retention, and microbial community changes. Both nitrocompounds significantly reduced growth of the uric acid-utilizing microorganisms on Day 3 (P < 0.05). Inhibitory effects of both nitrocompounds remained until Day 7 when the experiment was terminated. NPL treatment retained significantly more manure nitrogen compared to the control on both Days 3 and 7. Manure nitrogen levels of NPC treatment were also significantly higher than the control on Day 7. We further investigated the effects of NPL and NPC on microbial community changes during a 7-day incubation. NPC treatment and control on Day 7 exhibited 94% community similarity. NPC on Day 3 and NPL on Day 7 also showed high community similarity (approximately 94%). Control on Day 0 and Day 7 yielded less than 80% community similarity. Control and NPL treatment groups on Day 3 gave the lowest community similarity (approximately 64%) compared to the other groups. This result indicated that incubation time and treatment moderately influenced microbial community changes. In summary, these results indicate that both nitrocompounds increased manure nitrogen retention by inhibiting the growth of uric acid-utilizing microorganisms, and that NPL and NPC could be used as manure treatments in order to reduce ammonia volatilization and nitrogen retention in poultry manure. Moreover, nitrocompounds may have potential as feed additives to reduce ammonia volatilization.
Inference over the web

The World Wide Web contains vast amounts of text written about nearly any topic imaginable. Recent work in Information Extraction has sought to recover the information stated in this text, aggregating it into massive bodies of knowledge. These knowledge bases have the potential to significantly improve future Web search engines and Web-based Question-Answering systems, allowing them to answer more complex queries. However, despite its size there are still a large number of facts that are never explicitly mentioned on the Web. Much of the knowledge available on the Web is implicit, and must be inferred from other facts, possibly stated on separate pages. A system wishing to access this implicit knowledge must not only determine what inferences should be made, but also it must do so in a way that handles the noise, scale, and diversity of knowledge on the Web. This dissertation demonstrates that it is possible for systems to discover the implicit knowledge that exists within large knowledge bases extracted from the Web. It describes SHERLOCK-HOLMES, an unsupervised system that learns first-order Horn-clauses from facts extracted from the Web. Experiments show that the rules it learns can infer many facts not explicitly stated in the corpus, and furthermore that the long-tailed nature of facts on the Web allows the system to learn and use the rules in a scalable way.
Hitting the Wall

We examine the experience of boredom and its relationship to troublemaking and drug use among rural youth in southwestern New Mexico. We draw on qualitative research with area youth to describe what they think about drug use and how they situate it within their social circumstances. We then locate youth drug use within globalized processes affecting this setting, including a local economic environment with limited educational and employment opportunities for youth. Drug use emerges as a common social practice that enables youth to ameliorate boredom, yet only some youth become known as troublemakers. Study findings offer insight into how dominant social institutions—schools and juvenile justice authorities—shape the construction of trouble from the perspectives of youth. We contend that boredom and troublemaking among rural youth are not simply age-appropriate forms of self-expression but instead represent manifestations of social position, political economic realities, and assessments of possible futures.
Visual saliency based bag of phrases for image retrival

This paper presents a saliency based bag-of-phrases (Saliency-BoP for short) method for image retrieval. It combines saliency detection with visual phrase construction to extract bag-of-phrase features. To achieve this, the method first detects salient regions in images. Then, it constructs visual phrases using the word pairs which are from the same salient regions. Finally, it extracts the bag of visual phrases from the first K salient regions to describe images. Experimental results on Corel 1K and Microsoft Research Cambridge image database demonstrated that the Saliency-BoP method outperforms related methods such as Bag-of-Words (BoW) or Saliency-BoW.
Enhancing Democracy Through Legislative Redistricting

We demonstrate the surprising benefits of legislative redistricting (including partisan gerrymandering) for American representative democracy. In so doing, our analysis resolves two long-standing controversies in American politics. First, whereas some scholars believe that redistricting reduces electoral responsiveness by protecting incumbents, others, that the relationship is spurious, we demonstrate that both sides are wrong: redistricting increases responsiveness. Second, while some researchers believe that gerrymandering dramatically increases partisan bias and others deny this effect, we show both sides are in a sense correct. Gerrymandering biases electoral systems in favor of the party that controls the redistricting as compared to what would have happened if the other party controlled it, but any type of redistricting reduces partisan bias as compared to an electoral system without redistricting. Incorrect conclusions in both literatures resulted from misjudging the enormous uncertainties present during redistricting periods, making simplified assumptions about the redistricters' goals, and using inferior statistical methods.
iPAK: An In-Situ Pairwise Key Bootstrapping Scheme for Wireless Sensor Networks

Wireless sensor networks (WSNs) are characterized by resource constraints and large scalability. Many applications of WSNs require secure communication, a crucial component especially in hostile environments. However, the low computational capability and small storage budget within sensors render many popular public-key-based cryptographic systems impractical. Symmetric key cryptography, on the other hand, is attractive due to its efficiency. Nevertheless, establishing a shared key for communicating parties is a challenging problem. In this paper, we propose and analyze an in situ PAirwise Key bootstrapping scheme (iPAK) for large-scale WSNs. Our theoretical analysis and simulation study demonstrate that iPAK can achieve a high key-sharing probability between neighboring sensors and a strong resilience against node-capture attacks at the cost of low storage overhead.
Mining Developer Behavior Across GitHub and StackOverflow

Nowadays, software developers are increasingly involved in GitHub and StackOverflow, creating a lot of valuable data in the two communities. Researchers mine the information in these software communities to understand developer behaviors, while previous work mainly focuses on mining data within a single community. In this paper, we propose a novel approach to mining developer behaviors across GitHub and StackOverflow. This approach links the accounts from two communities using a CART decision tree, leveraging the features from usernames, user behaviors and writing styles. Then, it explores cross-site developer behaviors through T-graph analysis, LDA-based topics clustering and cross-site tagging. We conducted several experiments to evaluate this approach. The results show that the precision and F-Score of our identity linkage method are higher than previous methods in software communities. Especially, we discovered that (1) active issue committers are also active question askers; (2) for most developers, the topics of their contents in GitHub are similar to that of their questions and answers in StackOverflow; (3) developers’ concerns in StackOverflow shift over the time of their current participating projects in GitHub; (4) developers’ concerns in GitHub are more relevant to their answers than questions and comments in StackOverflow.
Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype–phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes.
High-density lipoprotein mass, cholesteryl ester transport protein, and macrophage reverse cholesterol transport: from the bedside back to the bench.

In December 2006, the ILLUMINATE study was unexpectedly terminated because of excess mortality in the treatment group. In this study, which enrolled more than 15 000 patients, the leading cholesteryl ester transport protein (CETP) inhibitor Torcetrapib, plus Atorvastatin, was compared with Atorvastatin plus placebo in a high cardiovascular risk population. An impressive response with a 72.1% increase in high-density lipoprotein (HDL)–cholesterol accompanied by a 24.9% decrease in low-density lipoprotein (LDL)–cholesterol was demonstrated. However, a 25% increased rate of cardiovascular events and a 40% increase in cardiovascular death occurred, and mortality due to noncardiovascular events was doubled.1 Other trials failed to show any benefit of Torcetrapib in the postponement of atherosclerosis in the common carotid2 and coronary arteries.3 Off-target effects of CETP inhibition were demonstrated and thorough discussions of cholesterol metabolism followed.4,5 In effect, the ILLUMINATE study brought a dramatic end to three decades of enthusiasm about the ‘Gordian knot’ between the unlimited protection of high HDL mass, measured by its cholesterol content, against cardiovascular events. Also, the traditional assumption that HDL elevation, such as in the case of CETP inhibition, will lead to the same protective effect was seriously challenged. Reverse cholesterol transport (RCT) refers to the process that returns cholesterol from extra-hepatic peripheral tissues to the liver for excretion. The anti-atherogenic capacity of HDL relies on its ability … Corresponding author. Tel: +972 4 854 2263; fax: +972 4 854 3286. E-mail address : ys_levy{at}rambam.health. gov.il
Changes at peptide residues buried in the major histocompatibility complex (MHC) class I binding cleft influence T cell recognition: a possible role for indirect conformational alterations in the MHC class I or bound peptide in determining T cell recognition

Recent crystallographic studies on two peptide complexes with the mouse Kb molecule have shown that peptide binding appears to alter the conformation of the class I alpha-helical regions that flank the antigen binding cleft. Given that this study also showed that much of the foreign peptide is buried within the class I binding cleft with only a small portion accessible for direct interaction with the components of the T cell receptor, this finding suggests that at least some component of T cell specificity may arise as a consequence of peptide-induced conformational changes in the class I structure. To assess this possibility, we have made systematic substitutions at residues within the Kb-restricted determinant from ovalbumin (OVA257- 264) that are thought to be buried on binding to the class I molecule. We have found that changes in this determinant at the completely buried second residue (P2) can influence T cell recognition without affecting binding to Kb, suggesting that the substitutions may indirectly determine T cell recognition by altering the conformation of the class I molecule or the bound peptide.
Automatic Protocol Blocker for Privacy-Preserving Public Auditing in Cloud Computing

Cloud Computing is the long dreamed vision of computing as a utility, where users can remotely store their data into the cloud so as to enjoy the on-demand high quality applications and services from a shared pool of configurable computing resources. By data outsourcing, users can be relieved from the burden of local data storage and maintenance. However, the fact that users no longer have physical possession of the possibly large size of outsourced data makes the data integrity protection in Cloud Computing a very challenging and potentially formidable task, especially for users with constrained computing resources and capabilities. Thus, enabling public auditability for cloud data storage security is of critical importance so that users can resort to an external audit party to check the integrity of outsourced data when needed. To securely introduce an effective Third Party Auditor (TPA), the following two fundamental requirements have to be met: 1) TPA should be able to efficiently audit the cloud data storage without demanding the local copy of data, and introduce no additional on-line burden to the cloud user; 2) The Third Party Auditing process should bring in no new vulnerabilities towards user data privacy. In this paper we are extending the previous system by using automatic blocker for privacy preserving public auditing for data storage security in cloud computing. we utilize the public key based homomorphic authenticator and uniquely integrate it with random mask technique and automatic blocker. to achieve a privacy-preserving public auditing system for cloud data storage security while keeping all above requirements in mind. Extensive security and performance analysis shows the proposed schemes are provably secure and highly efficient.
Progress Report on the Chronus System: ATIS Benchmark Results

The speech understanding system we propose in this paper is based on the stochastic modeling of a sentence as a sequence of elemental units that represent its meaning. According to this paradigm, the original meaning of a sentence, can be decoded using a dynamic programming algorithm, although the small amount of training data currently available suggested the integration of the decoder with a more traditional technique. However, the advantage of this method consists in the development of a framework in which a closed training loop reduces the amount of human supervision in the design phase of the understanding component. The results reported here for the February 1992 DARPA ATIS test are extremely promising, considering the small amount of hand tuning the system required.
Non-invariant two-loop counterterms for the three-gauge-boson vertices

Some practical applications of algebraic renormalization are discussed. In particular we consider the two-loop QCD corrections to the three-gauge-boson vertices involving photons, Z and W bosons. For this purpose also the corresponding two-point functions have to be discussed. A recently developed procedure is used to analyze the breaking terms of the functional identities and explicit formulae for the universal counterterms are provided. Special attention is devoted to the treatment of infrared divergences.
Confidence measure driven scalable two-pass recognition strategy for large list grammars

In this article we will discuss recognition performance on large list grammars, a class of tasks often encountered in telephony applications. In these tasks, the user makes a selection from a large list of choices (e.g. stock quotes, yellow pages, etc). Though the redundancy of the complete utterance is often high enough to achieve high recognition accuracy, large search space presents a challenge for the recognizer, in particular, when real-time, low latency performance is required. We propose a conﬁdence measure driven two-pass search strategy, exploiting the high mutual information between grammar states to improve pruning efﬁciency while minimizing the need for memory.
Quantitative and Qualitative Urine Protein Excretion in Dogs with Severe Inf lammatory Response Syndrome

Background: Proteinuria is an established characteristic of renal disease in dogs, providing diagnostic and prognostic information. Little is known about the occurrence and severity of proteinuria in dogs with severe inflammatory response syndrome (SIRS). Hypothesis: The quantitative and qualitative urinary protein (UP) excretion is altered in dogs with SIRS. Animals: Thirty-nine dogs with SIRS and 15 healthy control dogs at admission. Methods: A case control study was performed. Diagnosis of SIRS was based on clinical and clinicopathological findings. Urinary protein (UP) was measured by a colorimetric assay. Urinary albumin (UAlb) and urinary retinol-binding protein (URBP) were measured by ELISA and quantified in relation to urinary creatinine (UC). Sodium dodecyl sulfate polyacrylamid-gel electrophoresis was conducted to identify the qualitative pattern of proteinuria. Mann–Whitney U-test was used to assess differences in UP/UC, UAlb/UC and URBP/UC between the groups. P-values < . 05 were considered significant. Results: Dogs with SIRS had higher ratios of UP/UC, UAlb/UC and URBP/UC (all P < .001) in comparison to healthy control dogs. Dogs with SIRS had a total of 11 protein bands compared to 3 bands in healthy controls. In dogs with SIRS, 58% of the total counted bands were in the low molecular weight range (<60 kDa) whereas 42% were in the middle (60–80 kDa)/high molecular weight range (>80 kDa). Conclusions and Clinical Importance: SIRS alters UP excretion in dogs. Further studies should evaluate whether or not the magnitude of proteinuria is predictive of the severity and outcome of dogs with SIRS.