Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Assembly of the Outer Core of the Lipopolysaccharide from Escherichia coli K-12 and Salmonella typhimurium

There are five distinct core structures in the lipopolysaccharides of Escherichia coli and at least two in Salmonella isolates, which vary principally in the outer core oligosaccharide. Six outer core glycosyltransferases, E. coli K-12 WaaG, WaaB, and WaaO and Salmonella typhimurium WaaI, WaaJ, and WaaK, were cloned, overexpressed, and purified. A novel substrate for WaaG was isolated from ΔwaaG E. coli overexpressing the lipid A phosphatase lpxE and the lipid A late acyltransferase lpxM. The action of lpxE and lpxM in the ΔwaaG background yielded heptose2-1-dephospho Kdo2-lipid A, a 1-dephosphorylated hexa-acylated lipid A with the inner core sugars that is easily isolated by organic extraction. Using this structurally defined acceptor and commercially available sugar nucleotides, each outer core glycosyltransferases was assayed in vitro. We show that WaaG and WaaB add a glucose and galactose sequentially to heptose2-1-dephospho Kdo2-lipid A. E. coli K-12 WaaO and S. typhimurium WaaI add a galactose to the WaaG/WaaB product but can also add a galactose to the WaaG product directly without the branched core sugar added by WaaB. Both WaaI and WaaO require divalent metal ions for optimal activity; however, WaaO, unlike WaaI, can add several glucose residues to its lipid acceptor. Using the product of WaaG, WaaB, and WaaI, we show that S. typhimurium WaaJ and WaaK transfer a glucose and N-acetylglucosamine, respectively, to yield the full outer core. This is the first demonstration of the in vitro assembly of the outer core of the lipopolysaccharide using defined lipid A-oligosaccharide acceptors and sugar donors.
Use of an automated DNA analysis system (DARAS) for sequence-specific recognition of Neisseria meningitidis DNA.

OBJECTIVES To combine use of the polymerase chain reaction (PCR) for rapid diagnosis of meningococcal meningitis with a novel automated detection system for sequence-specific recognition of PCR products. METHODS DNA was extracted from cerebrospinal fluid (CSF) by a quick boil-lysis method, followed by PCR with primers specific for Neisseria meningitidis. Sequence-specific recognition of N. meningitidis DNA was performed with an automated DNA analysis system (DARAS) and the data were compared with results following agarose gel electrophoresis or conventional microbiological culture. RESULTS The DARAS system had a sensitive detection limit of 102 meningococci/mL with spiked samples, compared with a detection limit of 104 meningococci/mL following agarose gel electrophoresis. When the system was used to examine 74 CSF samples, the 19 CSF samples positive for N. meningitidis by conventional microbiological methods were also all positive in the DARAS system and the 55 samples negative by DARAS for meningococci were also negative by conventional microbiological methods. CONCLUSION The sensitivity and specificity of the DARAS system makes it a useful tool for the diagnosis of meningococcal meningitis. The system is user-friendly, requires minimal hands-on time and generates data in an informative numerical format.
Calcium-Dependent Synthesis of Prostacyclin in ATP-Stimulated Venous Endothelial Cells

Prostacyclin is a powerful vasodilator that is released from vascular endothelial cells. Previous studies in our laboratory have indicated that arachidonic acid metabolites from venous endothelium play an important role in the dilation of adjacent arterioles during muscle stimulation. Furthermore, recent studies have suggested that ATP released from red blood cells during hypoxia stimulates dilation of arterioles. We tested the hypothesis that an ATP-induced increase in intracellular Ca2+ in venous endothelium promotes prostacyclin synthesis. Small branches of femoral veins were isolated from male golden hamsters, placed in a 1 mL bath, and cannulated for perfusion with 3-(N-morpholino) propanesulfonic acid (MOPS)-buffered physiological salt solution at 37°C. Prostacyclin synthesis was determined by enzyme immunoassay of bath solution. Perfusion of veins with ATP increased prostacyclin synthesis from 50±5 to 627±46 pg/mL (n=49). ATP-induced prostacyclin synthesis was inhibited by removal of extracellular Ca2+, chelation of intracellular Ca2+ with 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA) (10 &mgr;mol/L for 10 minutes), and preincubation with cytosolic phospholipase A2 (PLA2) inhibitors, AACOCF3, and bromoenol lactone. Changes in intracellular Ca2+ in cultured human venous endothelial cells were assessed by fura-2 spectrofluorometry. ATP induced a transient Ca2+ peak within seconds, and the subsequent Ca2+ plateau was abolished by removal of extracellular Ca2+. An increase in prostacyclin synthesis was detected in these cells 2 minutes after application of ATP. These findings suggest that the ATP-induced increase in intracellular Ca2+ stimulates prostacyclin synthesis in venous endothelial cells.
Different representations and strategies in mental rotation

It is still debated whether holistic or piecemeal transformation is applied to carry out mental rotation (MR) as an aspect of visual imagery. It has been recently argued that various mental representations could be flexibly generated to perform MR tasks. To test the hypothesis that imagery ability and types of stimuli interact to affect the format of representation and the choice of strategy in performing MR task, participants, grouped as good or poor imagers, were assessed using four MR tasks, comprising two sets of ‘Standard’ cube figures and two sets of ‘non-Standard’ ones, designed by withdrawing cubes from the Standard ones. Both good and poor imagers performed similarly under the two Standard conditions. Under non-Standard conditions, good imagers performed much faster in non-Standard objects than Standard ones, whereas poor imagers performed much slower in non-Standard objects than Standard ones. These results suggested that (1) individuals did not differ in processing the integrated Standard object, whereas (2) in processing the non-Standard objects, various visual representations and strategies could be applied in MR by diverse individuals: Good imagers were more flexible in generating different visual representations, whereas poor imagers applied different strategies under different task demands.
Research on Network Security Situation Assessment and Prediction

The overall objective of the network security situation assessment is to establish security situation assessment system. This system can unify the large-scale network. First, it provides a security policy unified the whole network. It also provides the techniques for wide-area situation assessment. At the same time this system provides situational awareness and decision support tools for the implementation of network security command. Firstly, the information model of security situation was studied based on XML. Then the security situation value of system including three levels: service, host and network was analyzed and calculated. The-support vector regression machine was chosen for predicting the network security situation and determined the parameter values. Finally, the effectiveness of the method was verified through experimental analysis.
The KIT Lecture Corpus for Speech Translation

Academic lectures offer valuable content, but often do not reach their full potential audience due to the language barrier. Human translations of lectures are too expensive to be widely used. Speech translation technology can be an affordable alternative in this case. State-of-the-art speech translation systems utilize statistical models that need to be trained on large amounts of in-domain data. In order to support the KIT lecture translation project in its effort to introduce speech translation technology in KIT's lecture halls, we have collected a corpus of German lectures at KIT. In this paper we describe how we recorded the lectures and how we annotated them. We further give detailed statistics on the types of lectures in the corpus and its size. We collected the corpus with the purpose in mind that it should not just be suited for training a spoken language translation system the traditional way, but should also enable us to research techniques that enable the translation system to automatically and autonomously adapt itself to the varying topics and speakers of lectures
General gate array routing using a k-terminal net routing algorithm with failure prediction

A general approach to gate array routing based on an abstract routing space model is presented. An efficient k-terminal net maze runner is described. It does not partition nets into two-terminal net routing problems, but solves the problem by simultaneously growing k search waves. It is shown that the explored routing space diminishes when compared to bidirectional routing schemes. Experimental data show a reduction of CPU time up to 55% and a decrease of total net length up to 6% compared to a bidirectional maze router. For k-terminal nets it is shown that net length decreases with increasing k. Additional routing space restriction is attained by use of variable search space restriction and by the introduction of a dynamic routing space partitioning method based on the concept of regions. This concept allows for determination of nonroutable nets or parts of nets in an efficient way. The new partitioning method may be implemented in any maze runner without increasing the complexity of the maze runner algorithm. Results show an additional decrease of CPU time up to 35%. >
Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells

We constructed a series of recombinant genomes which directed expression of the enzyme chloramphenicol acetyltransferase (CAT) in mammalian cells. The prototype recombinant in this series, pSV2-cat, consisted of the beta-lactamase gene and origin of replication from pBR322 coupled to a simian virus 40 (SV40) early transcription region into which CAT coding sequences were inserted. Readily measured levels of CAT accumulated within 48 h after the introduction of pSV2-cat DNA into African green monkey kidney CV-1 cells. Because endogenous CAT activity is not present in CV-1 or other mammalian cells, and because rapid, sensitive assays for CAT activity are available, these recombinants provided a uniquely convenient system for monitoring the expression of foreign DNAs in tissue culture cells. To demonstrate the usefulness of this system, we constructed derivatives of pSV2-cat from which part or all of the SV40 promoter region was removed. Deletion of one copy of the 72-base-pair repeat sequence in the SV40 promoter caused no significant decrease in CAT synthesis in monkey kidney CV-1 cells; however, an additional deletion of 50 base pairs from the second copy of the repeats reduced CAT synthesis to 11% of its level in the wild type. We also constructed a recombinant, pSV0-cat, in which the entire SV40 promoter region was removed and a unique HindIII site was substituted for the insertion of other promoter sequences.
Discrete wavelet transform on consumer-level graphics processing unit

The discrete wavelet transform (DWT) has been extensively studied and developed in various scientific and engineering fields. The multiresolution and local nature of the DWT facilitates applications requiring progressiveness and the capture of high-frequency details. However, the intensive computation of DWT caused by multilevel filtering/down-sampling will become a significant bottleneck in real-time applications when the data size is large. This paper presents a SIMD-based parallel processing framework as a commodity solution to this problem, that is based on the consumer-level programmable graphic processing unit (GPU) on personal computers. Simulation tests show that, in contrast to those CPU-based solutions for DWT, this GPU-based parallel processing framework can bring a significant performance gain on a normal PC without extra cost.
Safety and Efficacy of Treatment of Pediatric Cholesteryl Ester Storage Disease with Lovastatin

The aim of this study was to prospectively assess the safety and efficacy of lovastatin in the treatment of cholesteryl ester storage disease in siblings who were ages 11.6 and 5 y at the beginning of treatment. Mean total and LDL cholesterol in the male proband, 7.40 and 5.68 mmol/L, respectively, on diet alone, fell 30% to 5.2 (p ≤ 0.001) and 31% to 3.9 mmol/L (p ≤ 0.001) on lovastatin 40 mg/d over 3.3 y, with simultaneous resolution of hepatosplenomegaly. In his sister, on lovastatin 20 mg/d for 1.5 y, total and LDL cholesterol fell, but not significantly; her hepatosplenomegaly was also reduced on treatment. Lovastatin was well tolerated without overt side effects or complications and without adverse changes in liver function tests or creatine phosphokinase. Normal and expected accretion of height and weight occurred during the treatment period for both children. Lovastatin appears to be a safe and effective treatment for pediatric cholesteryl ester storage disease.
Order estimation of Japanese paragraphs by supervised machine learning

In this paper, we propose a method to estimate the order of paragraphs by supervised machine learning. We use a support vector machine (SVM) for supervised machine learning. The estimation of paragraph order is useful for sentence generation and sentence correction. The proposed method obtained a high accuracy (0.86) in the order estimation experiments of the first two paragraphs of an article and achieved the same accuracy as manual estimation. In addition, it obtained a higher accuracy than the baseline methods in the experiments using two paragraphs of an article. We performed feature analysis and we found that adnominals, conjunctions, and dates were effective for the order estimation of the first two paragraphs, and the ratio of new words and the similarity between the preceding paragraphs and an estimated paragraph were effective for the order estimation of all pairs of paragraphs. Moreover, we compared the order estimation of sentences and paragraphs and clarified differences. For the order estimation of the first two paragraphs, paragraph order estimation would be easier than sentence order estimation because paragraphs have more information than sentences. For the order estimation of all pairs of paragraphs, paragraph order estimation would be more difficult than sentence order estimation because a story may conclude in a paragraph.
Testing in Service-Oriented Environments

Abstract : This report makes recommendations for testing service-oriented architecture (SOA) implementations consisting of infrastructure, services, and end-to-end processes. Testing implementations of SOA infrastructure, services, and end-to-end processing in support of business processes is complex. SOA infrastructure is often composed of multiple, independently constructed commercial products-often from different vendors-that must be carefully configured to interact in an appropriate manner. Services are loosely coupled components which are intended to make minimal assumptions about where, why, and under what environmental conditions they are invoked. Business processes link together multiple services and other systems in support of specific tasks. These services and systems may operate on remote platforms controlled by different organizations and with different SOA infrastructures. Such complications make it difficult to establish appropriate environments for tests, to ensure specific qualities of service, and to keep testing up-to-date with changing configurations of platforms, infrastructure, services, and other components.
On sparse subgraphs preserving connectivity properties

From a theorem of W. Mader [“Uber minimal n-fach zusammenhangende unendliche Graphen und ein Extremal problem,” Arch. Mat. , Vol. 23 (1972), pp. 553–560] it follows that a k-connected (k-edge-connected) graph G = (V,E) always contains a k-connected (k-edge-connected) subgraph G′ = (V,E′) with O(k|V|) edges. T. Nishizeki and S. Poljak “K-Connectivity and Decomposition of Graphs into Forests,” Discrete Applied Mathematics, submitted) showed how G′ can be constructed as the union of k forests. H. Nagamochi and T. Ibaraki [A Linear Time Algorithm for Finding a Sparse k-Connected Spanning Subgraph of a k-Connected Graph, Algorithmica, Vol. 7 (1992), pp. 583–596] constructed such a subgraph Gk in linear time and showed for any pair x,y of nodes that Gk contains k openly disjoint (edge-disjoint) paths connecting x and y if G contains k openly disjoint (edge-disjoint) paths connecting x and y (even if G is not k-connected (k-edge-connected)). In this article we provide a much shorter proof of a common generalization of the edge- and node-connectivity versions showing that the subgraph Gk has a certain mixed connectivity property. © 1993 John Wiley & Sons, Inc.
Relaxation of Dense , Reacting Two-Temperature-Plasmas

The driver energy in many dense plasma experiments is almost exclusively coupled into one species and, thus, a two-temperature plasma is created after a short relaxation. Beam particles or field ionization can also create a nonequilibrium charge state distribution. Although ionization kinetics and temperature equilibration usually occur on separated time scales (for solid density ≈ 100 fs and ≈ 10 ps, respectively), they do influence each other. This coupled relaxation is investigated here for nonideal plasmas. In contrast to Ref. [1], where kinetic equations are used, we directly start from the well-known internal energy density for weakly nonideal systems
The Role of Anchoring Discussion in Mediating Effective Online Interaction for Collaborative Knowledge Construction

This paper reports a quasi-experimental study carried out with two social technologies in order to support and enhance collaborative knowledge construction among doctoral students discussing research papers. We conducted a fine-grained investigation of discourse in both systems by using three coherent theories of collaborative learning to guide three different methods of analysis. We started our investigation by analyzing the content of discussions in search for active meaning making. Then, we examined the interaction processes to identify new cognitions emerged from interacting individuals. We completed our investigation by evaluating the positive interdependence of distributed competencies in each group. Results indicate that the anchored discussion system seems to be particularly suited for theory-oriented collaborative processing of research papers.
Connections between science teachers' professional development preferences and their teaching practices and beliefs

The effect of professional development preference, in relation to its effect on teacher practices and beliefs, has not been well studied. In order to better understand this dynamic, a nationwide online survey was developed and sent to secondary science teachers. The findings of this survey indicate a relationship does exist, but only within specific practices. During analysis, teachers were grouped by preference of professional development type including collaboration, reflection, conducting research, and professional development (such as conferences and workshops). Significant differences emerged from each group and implications for effective professional development practices will be addressed. CONNECTIONS BETWEEN PREFERENCES AND PRACTICES 1
Effects of Dredging and Lanthanum-Modified Clay on Water Quality Variables in an Enclosure Study in a Hypertrophic Pond

An enclosure experiment was conducted between July and September 2009 to compare the effectiveness of a phosphate fixative, the lanthanum-modified bentonite clay Phoslock® (LMB), dredging, and their combination in controlling eutrophication in a hypertrophic urban pond in Heesch, The Netherlands. In total, 25 water quality variables were monitored. Multivariate analysis revealed that the combination LMB-treated and dredged enclosures deviated most from the pond (reference) and the controls, and showed the strongest eutrophication reduction. Overall, dredging significantly increased transparency, lowered turbidity, and improved the oxygen conditions in the enclosures compared to non-dredged ones. Nonetheless, one dredged enclosure deviated dramatically from the others, which might reflect methodological issues with dredging. The LMB treatment appeared to be less effective at mitigating eutrophication than dredging, and phosphate concentrations even increased during the experiment in the LMB-treated enclosures. Chemical equilibrium modeling suggested that humic substances could have formed complexes with lanthanum (La) from the LMB, rendering it unavailable for intercepting P over the course of the enclosure experiment. Residual lanthanum concentrations in combination dredging and LMB treatments exceeded the Dutch standard 10-fold. Total zooplankton abundance, and particularly Cladocera, increased in all enclosures over the course of the experiment. The limited effect of LMB in the enclosure experiment and the violation of the Dutch La standard when combined with dredging disqualify LMB as an intervention agent in the restoration of the pond.
A Distributed Population Mechanism for the 3-D Oculomotor Reference Frame Transformation. Running Head: Neural Network Model for 3-D saccades

Human saccades require a non-linear, eye orientation-dependent reference frame transformation in order to transform visual codes to the motor commands for eye muscles. Primate neurophysiology suggests that this transformation is performed between the superior colliculus and brainstem burst neurons, but provides little clues as to how this is done. To understand how the brain might accomplish this, we trained a 3-layer neural net to generate accurate commands for kinematically correct 3-D saccades. The inputs to the network were a 2-D, eye centered, topographic map of Guassian visual receptive fields and an efference copy of eye position in sixdimensional, push-pull “neural integrator” coordinates. The output was an eye orientation displacement command in similar coordinates appropriate to drive brainstem burst neurons. The network learned to generate accurate, kinematically correct saccades, including the eye orientation-dependent tilts in saccade motor error commands required to match saccade trajectories to their visual input. Our analysis showed that the hidden units developed complex, eye-centered visual receptive fields, widely distributed fixed-vector motor commands, and “gainfield”-like eye position sensitivities. The latter evoked subtle adjustments in the relative motor contributions of each hidden unit, thereby rotating the population motor vector into the correct correspondence with the visual target input for each eye orientation: a distributed population mechanism for the visuomotor reference frame transformation. These findings were robust; there was little variation across networks with between 9-49 hidden units. Since essentially the same observations have been reported in the visuomotor transformations of the real oculomotor system, as well as other visuomotor systems (though interpreted elsewhere in terms of other models) we suggest that the mechanism for visuomotor reference frame transformations identified here is the same solution used in the real brain.
ERIC: a generic rule-based framework for an affective embodied commentary agent

We present ERIC, an affective embodied agent for realtime commentary in many domains. The underlying architecture is rule-based, generic, and lightweight - based on Java/Jess modules. Apart from reasoning about dynamically changing events, the system can produce coherent natural language and non-verbal behaviour, based on a layered model of affect (personality, mood, emotion). We show how reasoning, template-based natural language generation and affective appraisal can be implemented within the same rule-based paradigm. To make the system domain independent we worked on two different domains, a virtual horse race and a multi-player tank battle game. We empirically evaluated the genericness of the system by measuring the effort it takes to change the domain, and discuss the results.