Miracle-dz/UniFAR-FTUs huggingface dataset:
Seed-associated subspecies of the genus Clavibacter are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis.

The genus Clavibacter contains one recognized species, Clavibacter michiganensis. Clavibacter michiganensis is subdivided into subspecies based on host specificity and bacteriological characteristics, with Clavibacter michiganensis subsp. michiganensis causing bacterial canker of tomato. Clavibacter michiganensis subsp. michiganensis is often spread through contaminated seed leading to outbreaks of bacterial canker in tomato production areas worldwide. The frequent occurrence of non-pathogenic Clavibacter michiganensis subsp. michiganensis-like bacteria (CMB) is a concern for seed producers because Clavibacter michiganensis subsp. michiganensis is a quarantine organism and detection of a non-pathogenic variant may result in destruction of an otherwise healthy seed lot. A thorough biological and genetic characterization of these seed-associated CMB strains was performed using standard biochemical tests, cell wall analyses, metabolic profiling using Biolog, and single-gene and multilocus sequence analyses. Combined, these tests revealed two distinct populations of seed-associated members of the genus Clavibacter that differed from each other, as well as from all other described subspecies of Clavibacter michiganensis. DNA-DNA hybridization values are 70 % or higher, justifying placement into the single recognized species, C. michiganensis, but other analyses justify separate subspecies designations. Additionally, strains belonging to the genus Clavibacter isolated from pepper also represent a distinct population and warrant separate subspecies designation. On the basis of these data we propose subspecies designations for separate non-pathogenic subpopulations of Clavibacter michiganensis: Clavibacter michiganensis subsp. californiensis subsp. nov. and Clavibacter michiganensis subsp. chilensis subsp. nov. for seed-associated strains represented by C55(T) ( = ATCC BAA-2691(T) = CFBP 8216(T)) and ZUM3936(T) ( = ATCC BAA-2690(T) = CFBP 8217(T)), respectively. Recognition of separate subspecies is essential for improved international seed testing operations.
An Open Set Protocol for Improving Malware Classification in Intrusion Detection

Confidently distinguishing a malicious intrusion over a network is an important challenge. Most intrusion detection system evaluations have been performed in a closed set protocol in which only classes seen during training are considered during classification. Thus far, there has been no realistic application in which novel types of behaviors unseen at training – unknown classes as it were – must be recognized for manual categorization. This paper comparatively evaluates malware classification using both closed set and open set protocols for intrusion recognition on the KDD’99 dataset. In contrast to much of the previous work, we employ a fine-grained recognition protocol, in which the dataset is loosely open set – i.e., recognizing individual intrusion types – e.g., “sendmail”, “snmp guess”, . , etc., rather than more general attack categories (e.g., “DoS”,“Probe”,“R2L”,“U2R”,“Normal”). We also employ two different classifier types – Gaussian RBF kernel SVMs, which are not theoretically guaranteed to bound open space risk, and W-SVMs, which are theoretically guaranteed to bound open space risk. We find that the W-SVM offers superior performance under the open set regime, particularly as the cost of misclassifying unknown classes at test (i.e., classes not present in the training set) increases. Results of performance tradeoff with respect to cost of unknown as well as discussion of the ramifications of these findings in an operational setting are presented.
Formal Assurance for Cognitive Architecture Based Autonomous Agent

Autonomous systems are designed and deployed in diﬀerent modeling paradigms. These environments focus on speciﬁc concepts in designing the system. We focus our eﬀort in the use of cognitive architectures to design autonomous agents to collaborate with humans to accomplish tasks in a mission. Our research focuses on introducing formal assurance methods to verify the behavior of agents designed in Soar, by translating the agent to the formal veriﬁcation environment Uppaal.
Versican V0 and V1 Guide Migratory Neural Crest Cells*

We previously showed the selective expression of the chondroitin sulfate proteoglycans versican V0 and V1 in barrier tissues that impede the migration of neural crest cells during embryonic trunk development (Landolt, R. M., Vaughan, L., Winterhalter, K. H., and Zimmermann, D. R. (1995) Development 212, 2303-2312). To test for an active involvement of these isoforms in the guidance process, we have now established protocols to isolate intact versican V0 and V1 in quantities sufficient for functional experiments. Using stripe choice assays, we demonstrate that pure preparations of either a mixture of versican V0/V1 or V1 alone strongly inhibit the migration of multipotent Sox10/p75NTR double-positive early neural crest stem cells on fibronectin by interfering with cell-substrate adhesion. We show that this inhibition is largely core glycoprotein-dependent, as the complete removal of the glycosaminoglycan chains has only a minor effect on the inhibitory capacity. Our findings support the notion that versican variants V0 and V1 act, possibly in concert with other inhibitory molecules such as aggrecan and ephrins, in directing the migratory streams of neural crest cells to their appropriate target tissues.
Miniature pH sensor based on thin-core fiber Mach-Zehnder interferometer

A miniature pH sensor by using a tapered thin-core optical fiber based Mach-Zehnder interferometer coated with a pH sensitive film is demonstrated. Polyvinyl alcohol (PVA) and polyacrylic acid (PAA) were used to form a membrane structure on the taper by laminating self-assembly technique. By measuring wavelength change of the interference pattern or optical intensity, we achieved high sensitivity pH value measurement up to 2.06 nm/pH unit. The proposed sensor has small size, simple structure, good stability and a relatively short response time less than 52 s.
Review of optical flow technique for moving object detection

Object detection in a video is a challenging task in the field of image processing. Some applications of the domain are Human Machine Interaction (HMI), Security and Surveillance, Supplemented Authenticity, Traffic Monitoring on Roads, Medicinal Imaging etc. There happens to be a number of methods available for object detection. Each of the method has some constraints on the kind of application it has been used for. This paper presents one of such method which is termed as Optical Flow technique. This technique is found to be more robust and efficient for moving object detection and the same has been shown by an experiment in the paper. Applying optical flow to an image gives flow vectors of the points corresponding to the moving objects. Next part of marking the required moving object of interest counts to the post processing. Post processing is the legitimate contribution of the paper for moving object detection problem. This here is discussed as Blob Analysis. It is tested on datasets available online, real time videos and also on videos recorded manually. The results show that the moving objects are successfully detected using optical flow technique and the required post processing.
Further evidence for a type 2 diabetes susceptibility locus on chromosome 11q

Grant sponsor: American Diabetes Association; Grant sponsor: National Institutes of Health; Grant numbers: R01 DK42273, R01 DK47482, R01 DK53889, MH59490. Correspondence to: Dr. Ravindranath Duggirala, Ph.D., Department of Genetics, Southwest Foundation for Biomedical Research, P.O. Box 760549, 7620 NW Loop 410, San Antonio, TX 78254-0549. E-mail: ravid@darwin.sfbr. org Received for publication 24 May 2002; Revision accepted 11 December 2002 Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/gepi.10233
Microwave Differential Circuit Design [Book Review]

84 October 2006 Differential circuits are the basis for much of analog and digital integrated circuit design. However, microwave circuit design has had a difficult time with differential circuits largely because test equipment and characterization methods are single-ended. The book Microwave Differential Circuit Design Using MixedMode S-Parameters describes both the mathematics and the testing methods for differential circuits. Microwave Differential Circuit Design is not just a mathematical treatise, but really a practical guide to designing and testing microwave differential circuits. This book is centered around a mixedmode S-parameter matrix which converts a single-ended four-port matrix to a matrix with two differential ports, two common-mode ports, and crossconversion terms. Larger matrices can also be handled by the transformation technique. Older circuit designers will think of evenand odd-mode circuit designs and such landmark papers as Reed and Wheeler’s “A Method of Analysis of Symmetric Coupler FourPort Networks. ” While there is enough math to describe converting regular Sparameters to mixed-mode parameters in Chapters 2 and 6, the text is mostly application oriented. Several of the chapters focus on differential low noise amplifier design, amplifier distortion, coupler designs, balun designs on multilayer substrates, filters, and isolator designs. The chapter on the time domain concentrates more on convolution and time domain reflectometry than mixedmode implications. Chapter 2 also includes the schematic of a differential mode S-parameter test set. Chapter 1 has a very nice overview of differential mode applications and benefits. Each chapter has a short list of references. Another practical aspect of this book is the inclusion of a CD-ROM with a library of 180 nm SiGe BiCMOS process elements developed by Jazz Semiconductor for the Agilent ADS program. Most every book has its grungy bits: Figure 1.6 has voltage sources without polarity indicators, Figure 3.7 has an “8” where an “S” is probably supposed to be, and the jitter equation on page 6 claims to be based in time but inexplicably has
CONFOUNDING, HOMOGENEITY AND COLLAPSIBILITY FOR CAUSAL EFFECTS IN EPIDEMIOLOGIC STUDIES

Detection of confounding and confounders is important for observational studies, and especially so for epidemiologic studies. Miettinen and Cook (1981) derived two criteria for detecting confounders. Using a model, Wickramaratne and Holford (1987) proved that the two criteria are necessary but not sufficient conditions for confounders. We take uniform nonconfounding to mean there is no confounding at a coarse-subpopulation-level obtained by pooling any number of subpopulations. We discuss the necessity and sufficiency of the two criteria for uniform nonconfounding. The concepts of homogeneity and collapsibility for causal effects are also defined, and the relation among confounding, homogeneity and collapsibility is discussed. We show that the common causal effect over all fine subpopulations is just the causal effect of the whole population. The presence of confounding in an epidemiologic study hinders the estimation of causal effects. Miettinen and Cook (1981) derived two criteria of a confounder: (a) it must be predictive of risk in the unexposed population; and (b) it must have different distributions between the exposed and unexposed pop- ulations. Greenland and Robins (1986) discussed a logical connection among identifia- bility, exchangeability and confounding. Using a model, Wickramaratne and Holford (1987) showed that the above criteria are necessary but not sufficient conditions for confounding. Based on the counterfactual model (Rubin (1974) and Holland (1986)), Holland (1989) discussed causal effects and confounding in epidemiologic studies. Holland and Rubin (1988) defined causal effects for three different levels: unit-level, subpopulation-level and population-level. The population-level causal effect is measured by comparing the proportion of dis- eased in the exposed population with the proportion of diseased in the same
Pivotal role of β-intercalated cells in maintaining body fluid and electrolyte balance

Inactivation of the B1 proton pump subunit (ATP6V1B1) in intercalated cells (ICs) leads to type I distal renal tubular acidosis (dRTA), a disease associated with saltand potassium-losing nephropathy. Here we show that mice deficient in ATP6V1B1 (Atp6v1b1-/mice) displayed renal loss of NaCl, K+, and water, causing hypovolemia, hypokalemia, and polyuria. We demonstrated that NaCl loss originated from the cortical collecting duct, where activity of both the epithelial sodium channel (ENaC) and the pendrin/Na+-driven chloride/bicarbonate exchanger (pendrin/NDCBE) transport system was impaired. ENaC was appropriately increased in the medullary collecting duct, suggesting a localized inhibition in the cortex. We detected high urinary prostaglandin E2 (PGE2) and ATP levels in Atp6v1b1/mice. Inhibition of PGE2 synthesis in vivo restored ENaC protein levels specifically in the cortex. It also normalized protein levels of the large conductance calcium-activated potassium channel and the water channel aquaporin 2, and improved polyuria and hypokalemia in mutant mice. Furthermore, pharmacological inactivation of the proton pump in -ICs induced release of PGE2 through activation of calcium-coupled purinergic receptors. In the present study, we identified ATP-triggered PGE2 paracrine signaling originating from -ICs as a mechanism in the development of the hydroelectrolytic imbalance associated with dRTA. Our data indicate that in addition to principal cells, ICs are also critical in maintaining sodium balance and, hence, normal vascular volume and blood pressure. DOI: https://doi.org/10.1172/JCI63492 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-81970 Journal Article Accepted Version Originally published at: Gueutin, Victor; Vallet, Marion; Jayat, Maximilien; Peti-Peterdi, Janos; Cornière, Nicolas; Leviel, Françoise; Sohet, Fabien; Wagner, Carsten A; Eladari, Dominique; Chambrey, Régine (2013). Renal -intercalated cells maintain body fluid and electrolyte balance. Journal of Clinical Investigation, 123(10):4219-4231. DOI: https://doi.org/10.1172/JCI63492
RELOOP: A Python-Embedded Declarative Language for Relational Optimization

We present RELOOP, a domain-speciﬁc language for relational optimization embedded in Python. It allows the user to express relational optimization problems in a natural syntax that follows logic and linear algebra, rather than in the restrictive standard form required by solvers, and can automatically compile the model to a lower-order but equivalent model. Moreover, RELOOP makes it easy to combine relational optimization with high-level features of Python such as loops, parallelism and interfaces to relational databases. RELOOP is available at http://www-ai.cs. uni-dortmund.de/weblab/ static/RLP/html/ along with documentation and examples.
Maternal Child-Rearing Attitudes, IQ, and Socioeconomic Status as Related to Cognitive Abilities of Five-Year-Old Children

The effects of maternal child-rearing attitudes, as measured by the Child Rearing Practices Report, on 5-yr. -old children's Verbal IQ and Performance IQ were investigated in a Scandinavian sample of 108 boys and 126 girls. The maternal child-rearing attitude of Restrictiveness, as defined by scores on the Report, showed negative relations to the cognitive measures. However, the significant negative relation between Restrictiveness and Verbal IQ, obtained for both sexes, disappeared when the effects of maternal IQ and socioeconomic status were controlled. The maternal child-rearing attitude of Nurturance, as defined by scores on the Report, was significantly related to Verbal IQ and Performance IQ for boys only. Significant relationships between scores on Nurturance and cognitive abilities of boys remained when the effects of maternal IQ and socioeconomic status were controlled.
Chemical Odorant of Colonial Seabird Repels Mosquitoes

Abstract The crested auklet, Aethia cristatella, emits a class of aldehydes shown to be potent invertebrate repellents when used by heteropterans against their predators. Our aim was to determine the efficacy of these aldehydes against mosquitoes in the laboratory. Synthetic analogues of the auklet odorant were strongly repellent to mosquitoes in controlled laboratory trials. Furthermore, the efficacy was similar to previous reports for commercial mosquito repellents. These results, in combination with a previously published study, show that constituents of the aldehyde odorant are broad spectrum in efficacy against ectoparasitic arthropods of birds. Our report is the first empirical evidence for an endogenous mosquito repellent in birds.
Occurrence of anti‐HPA‐5b alloantibodies during intravenous immunoglobulin treatment in an HPA‐15b alloimmunised woman: a case report

Dear Sir, Since the platelet-specific alloantigen named the Gova/b system was first described in 1990 (Kelton et al., 1990), few cases of foetal and neonatal alloimmune thrombocytopenia (FNAIT) due to HPA-15 alloantibodies have been reported. Their clinical influence has been characterised as severe (Bordin et al., 1997; Berry et al., 2000; Ghevaert et al., 2007). Furthermore, the intravenous immunoglobulin (IVIG) treatment given alone to alloimmunised pregnant women seems not to be effective in 50% of foetuses with severe FNAIT (Vinograd & Bussel, 2010). This paper reports the case of an HPA-15b alloimmunised woman whose first child had suffered from severe FNAIT due to HPA-15b antibodies (Moncharmont et al., 2007). She was treated successfully by IVIG during her second pregnancy. In 2006, a 22-year-old mother, gravida1/para0, gave birth to a male infant suffering from a severe FNAIT induced by her HPA15b alloimmunisation. A few hours after birth, the newborn developed purpura with extensive haematomas but without any visceral or intracranial haemorrhage; his platelet count was 3 × 109 L−1 on day 0. He received two platelet transfusions and his clinical development evolved satisfactorily. In 2010, the mother became pregnant again, gravida2/para1. Because of the previous history of FNAIT, and that the father had platelet genotype HPA-15b/b and in order to prevent a second FNAIT, IVIG treatment was started. The treatment was given from week 17 of gestation until delivery by infusion (1 g kg−1 week−1); it was well tolerated without side effects. The 26-year-old mother gave birth to a male infant by elective caesarean section at 36 weeks of gestation. At birth, the paediatrician noted the absence of bleeding, hepatomegaly or splenomegaly. The APGAR score was 10, 10 and 10 at 1, 5 and 10 min. The platelet count of the infant was 174 × 109 L−1 and reached 210 and 220 ×109 L−1 on day 2 and 5, respectively. The clinical development and final outcome for the infant were fine. Screening for platelet-specific antibodies was performed with the direct and indirect Monoclonal Antibody-specific Immobilization of Platelet Antigen (MAIPA) assays (Kiefel et al., 1987). Three major platelet glycoproteins (GP) were evaluated: GPIaIIa, GPIIbIIIa and GPIbIX. The three main platelet antigen
[The percutaneous CT-guided treatment of osteoid osteomas: a combined procedure with a biopsy drill and subsequent ethanol injection].

PURPOSE The purpose of this study was the clinical evaluation of a percutaneous treatment modality in patients with an osteoidosteoma. PATIENTS AND METHODS 6 patients with an osteoidosteoma of the upper (n = 1) and lower (n = 5) extremity which were confirmed on plain film radiographs and computed tomography underwent CT controlled drill biopsy of the nidus with subsequent injection of 96% ethanol into the biopsy channel to sclerose probably remaining remnants of the nidus. The procedure was started under local anaesthesia, but drilling of the nidus was carried out under a short general anaesthesia using ketamine. RESULTS The intervention was successful in all patients. No postinterventional infection occurred and no recurrence was observed in any of the patients in a follow-up time between 0.5 and 2 years. CONCLUSION Although only 6 patients were treated until now, we conclude that this combined procedure using a bone biopsy system and the subsequent injection of alcohol is a safe and successful procedure for percutaneous treatment of osteoidosteoma.
Aligning sequences to general graphs in O(V + mE) time

Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction, and variant calling with respect to a variation graph. Given the wide range of applications of this basic problem, it is surprising that algorithms with optimal runtime are, to the best of our knowledge, yet unknown. In particular, aligning sequences to cyclic graphs currently represents a challenge both in theory and practice. Here, we introduce an algorithm to compute the minimum edit distance of a sequence of length m to any path in a node-labeled directed graph (V, E) in O(|V |+m|E|) time and O(|V |) space. The corresponding alignment can be obtained in the same runtime using space. The time complexity depends only on the length of the sequence and the size of the graph. In particular, it does not depend on the cyclicity of the graph, or any other topological features.
Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)

Lectin receptor kinases (LRKs) play a critical role in plants during development and stress conditions, but a comprehensive analysis at genome level is still not carried out in Triticum aestivum. Herein, we performed the genome wide identification, characterization and expression analysis of these genes in T. aestivum (TaLRK). In-total 263 TaLRK genes were identified, which were further classified into three groups based on the nature of lectin domain. We identified, two TaLRKs consisted of calcium-dependent lectin (C-LRK), while 84 legume-lectin (L-LRK) and 177 bulb-lectin (B-LRK) domains. The L-LRK and B-LRK genes were distributed throughout the genome of T. aestivum. Most of the TaLRKs were clustered as homologs, which were distributed either in proximity on same chromosome or on homoeologous chromosomes of A, B and D sub-genomes. A total of 9 and 58 duplication events were also predicted in L-LRK and B-LRK, respectively. Phylogenetic analysis indicated conserved evolutionary relationship of homologous and orthologous genes from multiple plant species. Gene ontology analysis indicated TaLRKs role in binding, signaling and receptor activities. Most of the TaLRKs consisted of a trans-membrane domain and predicted to be localized in the plasma-membrane. A diverse expression pattern of TaLRK genes was found in various developmental stages and stress conditions. Some TaLRKs were found to be highly affected during a particular stress, which indicated a specialized role of each LRK gene in a specific stress condition. These results described various characteristic feature and expression pattern of TaLRK genes, which will pave the way for functional characterization in wheat.