Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Carbapenemases in Clinical Enterobacteriaceae Isolates Using the VITEK AST-N202 Card

Background The rapid and accurate detection of carbapenemase-producing Enterobacteriaceae (CPE) in clinical microbiology laboratories is essential for the treatment and control of infections caused by these microorganisms. This study was performed to evaluate the ability of the VITEK AST-N202 card to detect CPE isolates. Materials and Methods A total of 43 (Klebsiella pneumoniae, n = 37; Escherichia coli, n = 3; and Enterobacter cloacae, n = 3) CPE isolates and 79 carbapenemase-non-producing Enterobacteriaceae (CNE) isolates were included in this study. The CPE isolates harbored KPC-2 (n = 11), KPC-3 (n = 20), GES-5 (n = 5), VIM-2 (n = 2), IMP-1 (n = 1), NDM-1 (n = 2), or OXA-232 (n = 2). Of the 79 CNE isolates, eight K. pneumoniae isolates were resistant to ertapenem, imipenem, and meropenem, while the remaining 71 isolates were susceptible to the carbapenems. Antimicrobial susceptibilities were tested using the VITEK AST-N202 card, and the results were interpreted as positive when the isolates showed resistant or intermediate results. Modified-Hodge tests (MHTs) were performed using ertapenem or meropenem disks for the screening of carbapenemase production. Polymerase chain reaction (PCR) and direct sequencing were used to identify β-lactamase genes. Results Sensitivity of MHT with ertapenem and meropenem disks for the detection of carbapenemase was 81.4% (35/43) and 81.4% (35/43), respectively, and a combination with both antibiotic disks increased the sensitivity to 88.4% (38/43). Specificity of the MHT was 100% (79/79) for the CNE isolates. Sensitivity of ertapenem, imipenem, and meropenem as assessed by the VITEK AST-N202 card was 100% (43/43), 93% (40/43), and 95.3% (41/43), respectively. Specificity (89.8%, 71/79) of the test with each carbapenem was improved to 100% (71/71) when eight carbapenem-resistant CNE isolates were excluded from the testing. Conclusion The VITEK AST-N202 card showed high sensitivity for the detection of carbapenemases in Enterobacteriaceae strains. PCR and sequencing experiments for the detection of carbapenemases are recommended when clinical Enterobacteriaceae isolates show non-susceptibility to carbapenems.
Homologous over-extension: a challenge for iterative similarity searches

We have characterized a novel type of PSI-BLAST error, homologous over-extension (HOE), using embedded PFAM domain queries on searches against a reference library containing Pfam-annotated UniProt sequences and random synthetic sequences. PSI-BLAST makes two types of errors: alignments to non-homologous regions and HOE alignments that begin in a homologous region, but extend beyond the homology into neighboring sequence regions. When the neighboring sequence region contains a non-homologous domain, PSI-BLAST can incorporate the unrelated sequence into its position specific scoring matrix, which then finds non-homologous proteins with significant expectation values. HOE accounts for the largest fraction of the initial false positive (FP) errors, and the largest fraction of FPs at iteration 5. In searches against complete protein sequences, 5–9% of alignments at iteration 5 are non-homologous. HOE frequently begins in a partial protein domain; when partial domains are removed from the library, HOE errors decrease from 16 to 3% of weighted coverage (hard queries; 35–5% for sampled queries) and no-error searches increase from 2 to 58% weighed coverage (hard; 16–78% sampled). When HOE is reduced by not extending previously found sequences, PSI-BLAST specificity improves 4–8-fold, with little loss in sensitivity.
Numerical Defects of the HLL Scheme and Dissipation Matrices for the Euler Equations

The Harten--Lax--van Leer scheme is popularly used in the CFD community. However, oscillations are observed from shock tube problems for stiffened gases when the adiabatic index is greater than 3. To understand this phenomenon, the dissipation effect of the scheme is evaluated quantitatively in terms of dissipation matrices. We have proven and numerically demonstrated that lack of positive definiteness is the root of numerical defects.
Analyzing Games with Ambiguous Player Types 1 using the MINthenMAX Decision Model 2 ( work in progress )

6 In many common interactive scenarios, participants lack information 7 about other participants, and specifically about the preferences of other 8 participants. In this work, we model an extreme case of incomplete 9 information, which we term games with type ambiguity, where a participant 10 lacks even information enabling him to form a belief on the preferences of 11 others. Under type ambiguity, one cannot analyze the scenario using the 12 commonly used Bayesian framework, and therefore he needs to model the 13 participants using a different decision model. 14 In this work, we present the MINthenMAX decision model under 15 ambiguity. This model is a refinement of Wald’s MiniMax principle, which 16 we show to be too coarse for games with type ambiguity. We characterize 17 MINthenMAX as the finest refinement of the MiniMax principle that 18 satisfies three properties we claim are necessary for games with type 19 ambiguity. This prior-less approach we present her also follows the common 20 practice in computer science of worst-case analysis. 21 Finally, we define and analyze the corresponding equilibrium concept 22 assuming all players follow MINthenMAX. We demonstrate this equi23 librium by applying it to two common economic scenarios: coordination 24 games and bilateral trade. We show that in both scenarios, an equilibrium 25 in pure strategies always exists and we analyze the equilibria. 26
A Fast Fourier Algorithm on the Rotation Group

In this paper we present an algorithm for the fast Fourier transform on the rotation group SO(3) which is based on the fast Fourier transform for nonequispaced nodes on the three-dimensional torus. This algorithm allows to evaluate the SO(3) Fourier transform of B-band-limited functions at M arbitrary input nodes in O(M +B3 logB) flops instead of O(MB3). Some numerical results will be presented establishing the algorithm’s numerical stability and time requirements.
Web Search Engines: Practice and Experience

The existence of an abundance of dynamic and heterogeneous information on the Web has offered many new opportunities for users to advance their knowledge discovery. As the amount of information on the Web has increased substantially in the past decade, it is difficult for users to find information through a simple sequential inspection of web pages or recall previously accessed URLs. Consequently, the service from a search engine becomes indispensable for users to navigate around the Web in an effective manner.
Serie Research Memoranda A Hybrid Joint Moment Ratio Test for Financial Time Series

We advocate the use of absolute moment ratio statistics in conjunction with standard variance ratio statistics in order to disentangle linear dependence, non-linear dependence, and leptokurtosis in financial time series. Both statistics are computed for multiple return horizons simultaneously, and the results are presented in a comprehensive way using a graphical device. We construct a formal joint testing procedure based on bootstrapped and block-bootstrapped uniform confidence intervals. The methodology is hybrid because it combines a formal testing procedure with volatility curve pattern recognition based on expert opinions. An application to forex data illustrates the procedure. JEL Codes: C14, F31, G14
The Case for Better Bandwidth Estimation

A Web proxy must accurately predict network performance between itself and its servers and clients in order to make good distillation decisions. In this paper, we show that the current approaches — either assuming the proxy is well-connected to all servers or using long-term observations — to make such predictions are insufficient. We propose a new prediction method, estimation with uncertainty, that will play a crucial role in web proxies as well as in other important problems.
Tough love : The behavior control justice motive facilitates forgiveness in valued relationships

When individuals in valued relationships are transgressed against, how are they able to protect the relationship while at the same time restore justice for themselves? Study 1 (N = 137) employed a recall design to demonstrate that when victims restore justice, the well-established association between relationship value and forgiveness can be explained indirectly through a motivation to control future behavior. Studies 2 (N = 122) and 3 (N = 115) replicated this finding using experimental designs, manipulating two distinct facets of valued relationships: the fact that they are continuing and close. There were no indirect effects for two alternative justice motives, just deserts and revenge. We discuss implications for relations between justice and forgiveness in the context of interpersonal relationships.
Proportional Delay Differentiation in Multi-hop Wireless Networks

In this paper, we propose MWTP (Multi-hop Waiting Time Priority) scheduler to guarantee proportional delay differentiation in a multi-hop wireless network with contention- based MAC protocol. The existing single-hop delay differentiation schedulers can not differentiate the contention delay suffered at multi-hop links, and whole delay differentiation accuracy is destroyed in the multi-hop wireless communications. MWTP marks packets with departing time at the upstream node to decide scheduling order at the downstream node. The marked departing time becomes a reference point of waiting time in the scheduling process. Analysis and simulation results support that MWTP guarantees more accurate delay differentiation than existing schedulers.
Brain Evoked Potentials Reflect How Emotional Faces Influence Our Decision Making

Emotion is usually not discussed as a relevant variable in rational models of decision making—but may be one. The present electroencephalographic study demonstrates the influence of emotional primes (angry, happy faces) on purchase decisions. In a within-subject design, pictures of an apartment were shown to participants who then had to make Go/NoGo decisions on whether to rent it. Their decision should be based either on its price or on its brightness. In two thirds of the trials, emotional prime pictures of happy versus unhappy faces preceded the purchase target (apartment); in one third of the trials no prime was given. Response certainty was evaluated by means of reaction times (RT) and peak amplitude of the event-related potential N200. Facial primes accelerated decisions (RT) irrespective of affective expression. Positive face primes elicited larger N200 amplitudes during purchase decision compared to negative ones. Price-based decisions were made faster and elicited larger N200 than brightnessbased decisions. These results support the cognitive-tuning model of decision making and validate the N200 as sensitive measure for the interplay of cognitive and affective aspects in decision making.
3 Single-Noun Bigrams as Components of Compound Nouns 3 . 1 Single-Noun Bigrams

In this paper, we propose a new idea of automatically recognizing domain specific terms of compound noun which is one of several definitions of collocation. Our idea is based on single-noun statistics associated with noun bigrams. More precisely, we focus basically on how many nouns adjoin the noun in question to form compound nouns. We propose several scoring methods based on this idea and experimentally evaluate them on NTCIR1 TMREC test collection. The results are very promising especially in high recall area.
Targeting of glycoprotein I (gE) of varicella-zoster virus to the trans-Golgi network by an AYRV sequence and an acidic amino acid-rich patch in the cytosolic domain of the molecule

Previous studies suggested that varicella-zoster virus (VZV) envelope glycoproteins (gps) are selectively transported to the trans-Golgi network (TGN) and that the cytosolic domain of gpI (gE) targets it to the TGN. To identify targeting signals in the gpI cytosolic domain, intracellular protein trafficking was studied in transfected cells expressing chimeric proteins in which a full-length or mutated gpI cytosolic domain was fused to the gpI transmembrane domain and interleukin-2 receptor (tac) ectodomain. Expressed protein was visualized with antibodies to tac. A targeting sequence (AYRV) and a second, acidic amino acid-rich region of the gpI cytosolic domain (putative signal patch) were each sufficient to cause expressed protein to colocalize with TGN markers. This targeting was lost when the tyrosine of the AYRV sequence was replaced with glycine or lysine, when arginine was replaced with glutamic acid, or when valine was substituted with lysine. In contrast, tyrosine could be replaced by phenylalanine and valine could be substituted with leucine. Mutation of alanine to aspartic acid or deletion of alanine abolished TGN targeting. Exposure of transfected cells to antibodies to the tac ectodomain revealed that the TCN targeting of expressed tac-gpI chimeric proteins occurred as a result of selective retrieval from the plasmalemma. These data suggest that the AYRV sequence and a second signaling patch in the cytosolic domain of gpI are responsible for its targeting to the TGN. The observations also support the hypothesis that the TGN plays a critical role in the envelopment of VZV.
The Aquatic Environment as a Reservoir of Vibrio cholerae O1 in Hydrographic Basins of the State of Pernambuco, Brazil

After the worldwide cholera epidemic in 1993, permanent environmental monitoring of hydrographic basins was established in Pernambuco, Brazil, where cholera is endemic. After a quiescent period, 4 rfbN (serogroup O1) positive water samples that were culture negative were detected by multiplex single-tube nested PCR (MSTNPCR); 2 of these were also ctxA (cholera toxin) positive. From May to June 2012, 30 V. cholerae O1 isolates were obtained by culturing samples. These isolates were analyzed for the presence of virulence genes by PCR, intergenic spacer region 16S-23S PCR (ISR-PCR), and pulsed field gel electrophoresis (PFGE). The isolates were positive for the rfbN gene and negative for the assessed pathogenic genes and were classified into 2 groups by ISR and the same profile by PFGE. Close genetic similarity was observed between them (2012) and environmental strains from 2004 to 2005, indicating the permanence of endemic V. cholerae O1 in the region.
Nobody likes Mondays: foreground detection and behavioral patterns analysis in complex urban scenes

Streams of images from large numbers of surveillance webcams are available via the web. The continuous monitoring of activities at different locations provides a great opportunity for research on the use of vision systems for detecting actors, objects, and events, and for understanding patterns of activity and anomaly in real-world settings. In this work we show how images available on the web from surveillance webcams can be used as sensors in urban scenarios for monitoring and interpreting states of interest such as traffic intensity. We highlight the power of the cyclical aspect of the lives of people and of cities. We extract from long-term streams of images typical patterns of behavior and anomalous events and situations, based on considerations of day of the week and time of day. The analysis of typia and atypia required a robust method for background subtraction. For this purpose, we present a method based on sparse coding which outperforms state-of-the-art works on complex and crowded scenes.
A Physically Transient Form of Silicon Electronics

Reversible Implants Silicon electronics are generally designed to be stable and robust—it would be counterproductive if the key parts of your computer or cell phone slowly dissolved away while you were using it. In order to develop transient electronics for use as medical implants, Hwang et al. (p. 1640, see the cover) produced a complete set of tools and materials that would be needed to make standard devices. Devices were designed to have a specific lifetime, after which the component materials, such as porous silicon and silk, would be resorbed by the body. A platform of materials and fabrication methods furnishes resorbable electronic devices for in vivo use. A remarkable feature of modern silicon electronics is its ability to remain physically invariant, almost indefinitely for practical purposes. Although this characteristic is a hallmark of applications of integrated circuits that exist today, there might be opportunities for systems that offer the opposite behavior, such as implantable devices that function for medically useful time frames but then completely disappear via resorption by the body. We report a set of materials, manufacturing schemes, device components, and theoretical design tools for a silicon-based complementary metal oxide semiconductor (CMOS) technology that has this type of transient behavior, together with integrated sensors, actuators, power supply systems, and wireless control strategies. An implantable transient device that acts as a programmable nonantibiotic bacteriocide provides a system-level example.
Action-angle representation of waves and instabilities in flowing plasmas

Action-angle representation of linear fluctuation in plasma is formally performed by taking the Lagrange-Hamilton theory as the basis and invoking the recent spectral technique [Hirota and Fukumoto, J. Math. Phys. 49 083101 (2008)], which is shown to be applicable equally to the magnetohydrodynamic (MHD) system and the Vlasov-Maxwell system. This formalism leads to a natural definition of the wave energy (as well as the wave action) for each eigenmode and continuum mode. Negative energy mode is generally responsible for onsets of various instabilities in flowing plasmas. It is shown that the canonical form of the linearized system, formulated by Hamilton’s principle of least action, facilitates the consideration of the action-angle representation, and the spectral technique becomes more sophisticated than the previous work that based on the noncanonical form.
Making things happen : the role of affect for proactive behaviours at work

In this thesis, I investigate how affective experience influences proactivity at work. Proactivity is a special type of goal-directed behaviour in which individuals actively take charge of situations to bring about change in a future-focused way for themselves or their organisation. Firstly, I draw on self-regulation research to conceptualise and empirically validate a model of proactive goal regulation that comprises employees' efforts in setting a proactive goal (envisioning), preparing to implement their proactive goal (planning), implementing their proactive goal (enacting) and engaging in learning processes concerning the outcomes of their proactive goal (reflecting). Secondly, I draw on affect research to argue that different types of work-related moods and emotions have an impact on the elements of proactive goal regulation in important ways. I investigate the relationship between affective experience and proactive goal regulation in three empirical studies: In Study 1, I use a cross-sectional survey design to investigate the role of moods for work-related proactive goal regulation in a study of call centre employees (N=227). In Study 2, I replicate and extend findings from Study 1 in the context of career-relatedp roactive goal regulation.S pecifically, I draw on longitudinal surveys of undergraduatem edical students( N=250) over four time pointsa crosst he academicy ear in order to test how moodsa ndc areer-relatedp roactive goal regulation are related over time. In Study 3, I employ a qualitative interview approach in a sample of call centre employees (N=39) to explore the role of emotions in employees' accounts of past proactive goal regulation. The findings of this thesis provide initial empirical support for the model of proactive goal regulation. Results also indicate that work-related moods and emotions are significant predictors of proactive goal regulation and that the role of affective experience for proactivity at work is more nuanced than previously assumed.
The Second Language Problem in User Support 1

Interaction between humans and computers is seldom perfect. Interactive software often includes aspects of user support to reduce the uncertainty and propensity to error experienced by many users. The present paper briefly reviews some of the common strategies for helping users and characterises the ‘second-language problem’ as a special case for support. Since most software packages are written for an English-speaking audience and presuppose reasonable proficiency in English comprehension non-native speakers of English face the daunting task of interacting via a second-language. One can reasonably expect greater confusion and interactive difficulties in this class of users. Software implementors have gone some way toward addressing this problem with occasional provision of font and native language support (localisation). Some of these attempts are outlined here. The paper concludes by advocating a strategy of selective native language support based upon reasonable expectations of troublespots in interaction.
A base-station oriented anomaly detection for wireless sensor networks

In this paper, an anomalous intrusion detection system is developed to detect malicious nodes in sensor networks. The proposed system has more reliability in comparison of its analogues and consumes the resources more efficiently. Here the base-station was known to be a trusted source and this helps the system can moderate the network more efficiently. In addition a node doesnpsilat block a compromised node when detects it and only send an alert to the base-station. Then the base-station will check transmission buffer of that node and if the base-station concludes that the node is compromised, the rest of the network will be informed, and the appropriate actions will be taken. This mechanism reduces the false positive rate.
Morphological approach for detection of protein spots from 2D-gel image

The present paper on detection of Protein spots from 2D gel image used several morphological operators. Protein spots are associated mostly with those regions whose intensity is least in 2D gel images. As maximum protein spots are in round shape, a disk shape structuring element is used for identification. More number of protein spots is presents in complex region of 2D gel image. For detecting more number of protein spots from 2D gel image, radius of structuring elements are taken care up in this paper.
Assisting concept assignment using probabilistic classification and cognitive mapping

The problem of concept assignment, that is, the problem of mapping human oriented concepts to elements in the code base of a system under study, and approaches which facilitate concept assignment can be considered as central to assisting software engineers in comprehending the unfamiliar systems they encounter. This paper presents a technique called cognitive assignment that attempts to capture what expert engineers know about the systems they work with and uses that information to generate classifiers that are used to implement a ranked search over a set of software ele-
Creating Multilingual Translation Lexicons with Regional Variations Using Web Corpora

The purpose of this paper is to automatically create multilingual translation lexicons with regional variations. We propose a transitive translation approach to determine translation variations across languages that have insufficient corpora for translation via the mining of bilingual search-result pages and clues of geographic information obtained from Web search engines. The experimental results have shown the feasibility of the proposed approach in efficiently generating translation equivalents of various terms not covered by general translation dictionaries. It also revealed that the created translation lexicons can reflect different cultural aspects across regions such as Taiwan, Hong Kong and mainland China.