Miracle-dz/UniFAR-FTUs huggingface dataset:
Donor strand complementation governs intersubunit interaction of fimbriae of the alternate chaperone pathway

Fimbrial filaments assembled by distinct chaperone pathways share a common mechanism of intersubunit interaction, as elucidated for colonization factor antigen I (CFA/I), archetype of enterotoxigenic Escherichia coli (ETEC) Class 5 fimbriae. We postulated that a highly conserved β‐strand at the major subunit N‐terminus represents the donor strand, analogous to interactions within Class I pili. We show here that CFA/I fimbriae utilize donor strand complementation to promote proper folding of and interactions between CFA/I subunits. We constructed a series of genetic variants of CfaE, the CFA/I adhesin, incorporating a C‐terminal extension comprising a flexible linker and 10–19 of the N‐terminal residues of CfaB, the major subunit. Variants with a donor strand complement (dsc) of ≥ 12 residues were recoverable from periplasmic fractions. Genetic disruption of the donor β‐strand reduced CfaE recovery. A hexahistidine‐tagged variant of dsc19CfaE formed soluble monomers, folded into β‐sheet conformation, displayed adhesion characteristic of CFA/I, and elicited antibodies that inhibited mannose‐resistant haemagglutination by ETEC expressing CFA/I, CS4 and CS14 fimbriae. Immunoelectron microscopy indicated that CfaE was confined to the distal fimbrial tip. Our findings provide the basis to elucidate structure and function of this class of fimbrial adhesins and assess the feasibility of an adhesin‐based vaccine.
RT-MaG: An open-source SIMULINK toolbox for Linux-based real-time robotic applications

The new open-source Matlab/Simulink toolbox called RT-MaG presented here generates reliable standalone robotic applications running on real-time embedded Linux targets such as tiny Computers On Module (e.g., Gumstix boards). This toolbox gives direct access from Simulink to the main communication drivers classically used in robotics: network interfaces (via UDP), asynchronous and synchronous serial port interfaces (RS232, SPI), Pulse-width-modulation (PWM), general purpose input-output (GPIO) and analog-to-digital converters (ADCs). A Simulink model is automatically converted into a standalone multi-task program, which guarantees a repeatable execution time within each sampling time. The toolbox includes efficient debug modes which detect problems such as unsuitable configurations and hardware failure. The main features of the toolbox and its structure are described here. We also discuss the real-time performances and I/Os delays and show that a control loop can be implemented at frequencies of up to 1kHz. The tests performed show that RT-MaG can be used to efficiently implement all the control laws involved in stabilizing a quadrotor.
Efficient GPU-based Decompression of BTF Data Compressed using Multi-Level Vector Quantization

One of the main drawbacks of Bidirectional Texture Function (BTF), as a method of capturing realistic and accurate real-world material appearance, is the resulting size of the measured data set. Several lossy methods to compress the data were proposed over the years to cope with this problem. To efficiently use the compressed data an appropriate decompression algorithms are also needed, allowing fast random synthesis of BTF data without the need to reconstruct the whole BTF back to its original representation. One of such methods based on multi-level vector quantization and providing both good compression ratio and random access from the compressed data was proposed by Havran et al. in 2010. In this paper, we would like to share our experience with writing a GPU based implementation of the decompression part of the aforementioned method. Our goal was to evaluate the implementation difficulty, as well as the resulting performance and suitability of the algorithm for real-time use.
Evaluating Prosodic Processing for Incremental Speech Synthesis

Incremental speech synthesis (iSS) accepts input and produces output in consecutive chunks that only together result in a full utterance. Systems that use iSS thus have the ability to adapt their utterances while they are ongoing. However, starting to process with less than the full utterance available prohibits global optimization, leading to potentially suboptimal solutions. In this paper, we present a method for incrementalizing the symbolic pre-processing component of speech synthesis and assess the influence of varying “lookahead”, i. e. knowledge about the rest of the utterance, on prosodic quality. We found that high quality incremental output can be achieved even with a lookahead of less than one phrase, allowing for timely system reaction.
A Rhythmic Musical Intervention for Poor Readers: A Comparison of Efficacy With a Letter‐Based Intervention

There is growing evidence that children with reading difficulties show impaired auditory rhythm perception and impairments in musical beat perception tasks. Rhythmic musical interventions with poorer readers may thus improve rhythmic entrainment and consequently improve reading and phonological skills. Here we compare the effects of a musical intervention for poor readers with a software intervention of known efficacy based on rhyme training and phoneme-grapheme learning. The research question was whether the musical intervention would produce gains of comparable effect sizes to the phoneme-grapheme intervention for children who were falling behind in reading development. Broadly, the two interventions had similar benefits for literacy, with large effect sizes.
UvA-DARE ( Digital Academic Repository ) Learning to categorize verbs and nouns : studies on Dutch

Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva. nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.
Identifying Communities and Key Vertices by Reconstructing Networks from Samples

Sampling techniques such as Respondent-Driven Sampling (RDS) are widely used in epidemiology to sample “hidden” populations, such that properties of the network can be deduced from the sample. We consider how similar techniques can be designed that allow the discovery of the structure, especially the community structure, of networks. Our method involves collecting samples of a network by random walks and reconstructing the network by probabilistically coalescing vertices, using vertex attributes to determine the probabilities. Even though our method can only approximately reconstruct a part of the original network, it can recover its community structure relatively well. Moreover, it can find the key vertices which, when immunized, can effectively reduce the spread of an infection through the original network.
Varenicline-Induced Mania in a Bipolar Patient

Objective:Varenicline is a novel antismoking agent that reduces cravings and blocks pleasure of nicotine by serving as a partial agonist to the nicotinic receptor. Varencicline was initially described as easily tolerated and without any special psychiatric precautions, but it was studied exclusively in normal populations. We report on a bipolar patient who developed a manic episode after treatment with varenicline. Methods:The patient was interviewed and examined, and additional information was obtained from the medical record. The Naranjo adverse drug reaction scale was applied. Relevant literature was reviewed. Conclusion:Postmarketing reports of neuropsychiatric problems have recently led to a general warning to monitor for such symptoms. The bipolar patient described here became manic shortly after treatment with varenicline. We suggest close observation of patients with bipolar disorder on varenicline and further study varenicline-induced neuropsychiatric symptoms among mentally ill patients.
Family of prokaryote cyclic nucleotide-modulated ion channels

Significance We describe a previously unidentified family of prokaryote cyclic nucleotide-modulated ion channels. In eukaryotes, CNG channels play important roles in signal transduction as they mediate the passage of ions across the cell membrane in response to cAMP or cGMP. In this study, we demonstrate that two prokaryote homologs, AmaK and SthK, can be expressed and purified from Escherichia coli membranes. We reveal that SthK has functional properties that closely resemble eukaryote HCN or CNG channels. SthK is gated by cyclic AMP, but not cyclic GMP, and selects K+ over Na+ ions in a weakly voltage-dependent manner. Our results contribute to understanding the evolutionary origin of cyclic nucleotide-modulated ion channels and pave the way for future structural and functional studies. Cyclic nucleotide-modulated ion channels are molecular pores that mediate the passage of ions across the cell membrane in response to cAMP or GMP. Structural insight into this class of ion channels currently comes from a related homolog, MloK1, that contains six transmembrane domains and a cytoplasmic cyclic nucleotide binding domain. However, unlike eukaryote hyperpolarization-activated cyclic nucleotide-modulated (HCN) and cyclic nucleotide-gated (CNG) channels, MloK1 lacks a C-linker region, which critically contributes to the molecular coupling between ligand binding and channel opening. In this study, we report the identification and characterization of five previously unidentified prokaryote homologs with high sequence similarity (24–32%) to eukaryote HCN and CNG channels and that contain a C-linker region. Biochemical characterization shows that two homologs, termed AmaK and SthK, can be expressed and purified as detergent-solubilized protein from Escherichia coli membranes. Expression of SthK channels in Xenopus laevis oocytes and functional characterization using the patch-clamp technique revealed that the channels are gated by cAMP, but not cGMP, are highly selective for K+ ions over Na+ ions, generate a large unitary conductance, and are only weakly voltage dependent. These properties resemble essential properties of various eukaryote HCN or CNG channels. Our results contribute to an understanding of the evolutionary origin of cyclic nucleotide-modulated ion channels and pave the way for future structural and functional studies.
Why Did You Do That? An Economic Examination of the Effect of Extrinsic Compensation on Intrinsic Motivation and Performance

According to empirical evidence, extrinsic incentives often crowd out intrinsic motivation, thus reducing the effort choices of workers. This article presents a principal-agent model that incorporates insights from cognitive evaluation theory in order to show how the introduction of explicit incentives causes a discontinuous reduction in worker effort and why motivation crowding out occurs. Motivation crowding out is shown to be a rational response of the agent to the introduction of incentives when rewards are perceived as controlling, since controlled behavior does not provide intrinsic satisfaction. Extrinsic rewards could be perceived as controlling under two conditions. The first is when the object of an agent's intrinsic motivation is also the source of the agent's extrinsic compensation. The second is when the incentives offered to the agent are too large.
Incidence, Risk Factors and Causes of Severe Neonatal Hyperbilirubinemia in the South of Iran (Fars Province)

Background Today, Severe hyperbilirubinemia is the most common cause of neonatal readmissions. Identification of the cause of neonatal hyperbilirubinemia is useful in determining whether therapeutic interventions can prevent severe hyperbilirubinemia. Objectives We conducted this study to estimate the incidence of severe hyperbilirubinemia in Fars province and to determine the underlying causes and risk factors, which would be of value in identifying and implementing strategies to prevent morbidity from this condition. Patients and Methods All infants less than 28 days referred due to severe indirect hyperbilirubinemia were included. Complete history, physical examination and lab work up were performed. This is a longitudinal prospective study in 2009-2010. Results More common causes of severe indirect hyperbilirubinemia were blood group incompatibility, G6PD deficiency, sepsis and unknown. Risk factors of severe hyperbilirubinemia were Male sex, previous siblings with severe hyperbilirubinemia, early discharge, NVD, Breast feeding and cultural background of mothers. Conclusions Our study showed severe neonate indirect hyperbilirubinemia is still prevalence in Fars province and ethnic and cultural background of the mothers was more effective than school education in preventing hyperbilirubinemia complication.
Transitive closure and recursive Datalog implemented on clusters

Implementing recursive algorithms on computing clusters presents a number of new challenges. In particular, we consider the endgame problem: later rounds of a recursion often transfer only small amounts of data, causing high overhead for interprocessor communication. One way to deal with the endgame problem is to use an algorithm that reduces the number of rounds of the recursion. Especially, in an application like transitive closure ("TC") there are several recursive-doubling algorithms that use a logarithmic, rather than linear, number of rounds. Unfortunately, recursive-doubling algorithms can deduce many more facts than the linear TC algorithms, which could negate the cost savings from the elimination of the overhead due to the proliferation of small files. We are thus led to consider TC algorithms that, like the linear algorithms, have the unique decomposition property that assures paths are discovered only once. We find that many such algorithms exist, and we show that they are incomparable, in that any of them could prove best on some data --- even lower in cost than the linear algorithms in some cases. The recursive-doubling approach to TC extends to other recursions as well. However, it is not acceptable to reduce the number of rounds at the expense of a major increase in the number of facts that are deduced. In this paper, we prove it is possible to implement any Datalog program of right-linear chain rules with a logarithmic number of rounds and no order-of-magnitude increase in the number of facts deduced. On the other hand, there are linear recursions for which the two goals of reducing the number of rounds and maintaining the total number of deduced facts cannot be met simultaneously. We show that the reachability problem cannot be solved in logarithmic rounds without using a binary predicate, thus squaring the number of potential facts to be deduced. We also show that the samegeneration recursion cannot be solved in logarithmic rounds without using a predicate of arity three.
Epileptic Electroencephalogram Signal Classification Based on Shearlet and Contourlet Transforms

According to the World Health Organization (2023), epilepsy is a chronic brain disorder that affects around 50 million people of all ages worldwide, mainly (approximately 80%) those living in low- and middle-income regions. The most common method used to diagnose epilepsy is Electroencephalography (EEG), which involves monitoring brain activity. However, an-alyzing EEG recordings to detect epileptic seizures can be a tiresome and time-consuming task, even for experts. In addition, different physicians may have varying levels of experience, leading to differing diagnostic opinions. As the main contribution of this work, we propose and evaluate a novel method that combines time-frequency transforms and 1D convolutional neural networks to extract and process EEG features. Experiments performed on a widely used public data set show that our approach is competitive when compared to other EEG signal classification methods.
Base station identification for FH-OFDMA systems

A base station (BS) identification scheme for frequency-hopping (FH) orthogonal frequency division multiple access (OFDMA) is proposed. This scheme is based on the use of periodically inserted pilot tones carrying binary information. The identification process consists of two steps. First, locations of pilot tones are detected and second, the binary sequence associated with the pilots are identified. Modified maximum likelihood (ML) rules for the two steps are derived. Computer simulation results demonstrate that the proposed scheme can outperform the existing method that utilizes the slope of pilot tone hopping sequences, yet it is considerably simpler to implement.
NR2 subunit‐dependence of NMDA receptor channel block by external Mg2+

The vital roles played by NMDA receptors in CNS physiology depend critically on powerful voltage‐dependent channel block by external Mg2+ (Mg2+o). NMDA receptor channel block by Mg2+o depends on receptor subunit composition: NR1/2A receptors (receptors composed of NR1 and NR2A subunits) and NR1/2B receptors are more strongly inhibited by Mg2+o than are NR1/2C or NR1/2D receptors. We investigated the effects of Mg2+o on single‐channel and whole‐cell currents recorded from recombinant NR1/2D and NR1/2A receptors expressed in HEK293 and 293T cells. The main conclusions are as follows: (1) Voltage‐dependent inhibition by Mg2+o of whole‐cell NR1/2D receptor responses was at least 4‐fold weaker than inhibition of NR1/2A receptor responses at all voltages tested. (2) Channel block by Mg2+o reduced the duration of NR1/2D receptor single‐channel openings; this reduction was used to estimate the apparent blocking rate of Mg2+o (k+,app). The k+,app for NR1/2D receptors was similar to but moderately slower than the k+,app obtained from cortical NMDA receptors composed of NR1, NR2A and NR2B subunits at all voltages tested. (3) Mg2+o blocking events induced an additional component in the closed‐duration distribution; this component was used to estimate the apparent unblocking rate of Mg2+o (k−,app). The k−,app for NR1/2D receptors was much faster than the k−,app for cortical receptors at all voltages tested. The voltage‐dependence of the k−,app of NR1/2D and cortical receptors differed in a manner that suggested that Mg2+o may permeate NR1/2D receptors more easily than cortical receptors. (4) Mg2+o inhibits NR1/2D receptors less effectively than cortical receptors chiefly because Mg2+o unbinds much more rapidly from NR1/2D receptors.
Constructing the meaning of being at-risk: the experiences of individuals living in families at risk for arrhythmogenic right ventricular cardiomyopathy in the province of Newfoundland and Labrador

The past decade has seen a proliferation of available predictive genetic tests. These are the result of one of the most significant scientific advances of the 21st century: the Human Genome Project. Social scientists have examined how the availability of genetic testing shapes the lived experience of at-risk people as well as subsequent health decision-making. Little attention has been paid to how the embodiment of risk is (re)shaped in light of changing genetic technologies or how experience of risk may in turn shape the development of genetics. A grounded theory approach was used to gain a fuller understanding of how 29 individuals living in a family at risk for Arrhythmogenic Right Ventricular Cardiomyopathy, in the province of Newfoundland and Labrador, construct the meaning of being at-risk prior to, during, and following genetic testing in relation to the various stages of gene discovery and test availability. Three phases of constructing meaning were identified: (1) Awakening to a New Meaning of Being At-Risk, (2) Deciphering the Meaning of Being At-Risk, and (3) Embodying a New Meaning of Being At-Risk. This study found that at-risk individuals' understandings of the meaning of being at-risk both shapes and is shaped by the "lived experience" of the genetic testing process and also impacts (and is impacted by) health care decisions. The meaning assigned to being at-risk is pragmatic, transient, and fluid. It is pragmatic in that the participants juxtapose three types of contextual dimensions (scientific knowledge, experiential knowledge, and phase of the genetic testing process) against the existing conditions, or specific factors that influence risk perception, as they assign meaning to being at-risk and make decisions, a process that is ongoing throughout the genetic testing process. The meaning assigned to risk is transient, in that as one's risk perception fluctuates so do the contextual dimensions and conditions that influence participants' choices. It is fluid, in that the meaning of being at-risk is shaped and reshaped (and the decisions change), with each new experience and coincident with the particular stage of gene discovery. These findings lead to recommendations for genetic service providers, health policy makers, and genetic scientists on best practices for health care in the context of novel gene discovery.
Phytochemical variation in echinacea from roots and flowerheads of wild and cultivated populations.

Quantitative phytochemical variation was determined from roots and inflorescences of native plant populations in the genus Echinacea. Specimens were collected in situ throughout the natural range of each putative taxon and transplanted to greenhouse cultivation. Ethanolic extracts from individual plants were separated by reversed-phase HPLC to quantify the alkamides, polyenes/ynes, and phenolics, and then grouped by age and taxonomically, according to a recent morphometric taxonomic revision of the genus. Canonical discriminant analysis revealed that cichoric acid, the diene alkamides 1-3 and 7, and ketoalkene 24 were the best taxonomic markers. Mean content for each of 26 phytochemicals revealed useful agronomic information, such as those varieties and organs with the highest accumulations, as well as the optimal age and growth conditions for each variety. The highest amounts of cichoric acid were measured from the older, wild inflorescences of E. pallida var.sanguinea, whereas the highest quantities of the alkamides 1-3 and 7 were present in roots of wild and transplanted E. purpurea. Baseline phytochemical data and chromatographic profiles for all types of wild Echinacea may be used for protection of wild stands, germplasm identification, and crop improvement.
Beden Eğitimi Derslerinde Kullanılan Farklı Öğretim Yöntemlerinin Akademik Öğrenme Zamanına Etkisi

This study aims at seeing the effects of different teaching styles on student behaviours and course content activities and academic learning time in physical education scores. The participants are 30 grade four students at Abant Izzet Baysal University, Department of Teaching Physical Education during 2010–2011 academic year. Forty minute lessons of 30 pre-service teachers using command style (n=10), practice style (n=10) and reciprocal style (n=10) were videotaped and recordings were examined using the “observation form of academic learning time in physical education”. The results of the analysis revealed that significant differences among academic learning time and three different teaching styles were utilized by pre-service teachers in physical education and sport classes. As a result of this study, academic learning time has been concluded in lessons using practice style at most, then the reciprocal style, at least the command style.
In situ ruminal protein degradation of switchgrass and smooth bromegrass

(.) Two experiments were conducted to assess ruminal espace protein using an in situ rumen technique for switch-grass (Panicum virgatum L.) and smooth bromegrass (Bromus inermis Leyss.). Whole-plant, leaf, and stem samples were harvested at specific stages of maturity in 1987. Duplicate samples of each grass were incubated for 12 h in situ. Escape protein values were expressed as concentration [grams escape protein per kilogram dry matter (DM) adjusted for acid detergent insoluble nitrogen (ADIN)] and as a percentage of total plant protein concentration (grams protein per kilogram DM adjusted for ADIN) to characterize protein composition (.)