Miracle-dz/UniFAR-FTUs huggingface dataset:
Aspects and Applications of Pulse Sequence Design for Solution-State Nuclear Magnetic Resonance Spectroscopy

NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of C,N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.
A Faster Iterative Scaling Algorithm for Conditional Exponential Model

Conditional exponential model has been one of the widely used conditional models in machine learning field and improved iterative scaling (IIS) has been one of the major algorithms for finding the optimal parameters for the conditional exponential model. In this paper, we proposed a faster iterative algorithm named FIS that is able to find the optimal parameters faster than the IIS algorithm. The theoretical analysis shows that the proposed algorithm yields a tighter bound than the traditional IIS algorithm. Empirical studies on the text classification over three different datasets showed that the new iterative scaling algorithm converges substantially faster than both the IIS algorithm and the conjugate gradient algorithm (CG). Furthermore, we examine the quality of the optimal parameters found by each learning algorithm in the case of incomplete training. Experiments have shown that, when only a limited amount of computation is allowed (e.g. no convergence is achieved), the new algorithm FIS is able to obtain lower testing errors than both the IIS method and the CG method.
NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results

UNLABELLED NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. AVAILABILITY A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Oiahcr: online isolated arabic handwritten character recognition using neural network

In this paper, an online isolated Arabic handwritten character recognition system is introduced. The system can be adapted to achieve the demands of hand$held and dig ital tablet applications. To achieve this goal, despite of single neural networks, four neural networks are used, one for each cluster of characters. Feed forward back propagation neural networks are used in classification process. This approach is employed as classifiers due to the low computation overhead during training and recall process. The system recognizes on$line isolated Arabic character and achieves an a ccuracy rate 9٥. 7% from untrained writers and 99.1% for trained writers.
Risk Uncertainty and Supply Chain Decisions: A Real Options Perspective

Supply chain risk uncertainty can create severe repercussions, thus it is not surprising that research interest in supply chain risk has been growing. While extant inquiry is informative, there is a lack of investigations that center on supply chain investment decisions when facing high levels of risk uncertainty. Given the potential dollar value involved in these decisions, an understanding of how these supply chain decisions are made is of significant theoretical and practical importance. Real options theory, with its focus on decision making under conditions of uncertainty, is an appealing theoretical lens for this endeavor. In essence, real options theory asserts that managerial decisions center on creating and then exercising or not exercising certain opportunities. To date, theorizing about and investigations of real options have used firms as their focus. Not yet examined are real options within supply chains that cross firm boundaries and drive much of the competitive activity in the modern economy. Accordingly, we extend real options theory to the supply chain context by examining how different types of options are approached relative to supply chain project investments. Specifically, we theorize how the options will be related to perceived value under conditions of high supply chain risk uncertainty. Overall, our investigation builds knowledge by extending real options theory to the supply chain context and by providing evidence suggesting some options operate differently in supply chains than they do in firms.
The RopGEF Gene Family and Their Potential Roles in Responses to Abiotic Stress in Brassica rapa

Guanine nucleotide-exchange factors (GEFs) genes play key roles in plant root and pollen tube growth, phytohormone responses, and abiotic stress responses. RopGEF genes in Brassica rapa have not yet been explored. Here, GEF genes were found to be distributed across eight chromosomes in B. rapa and were classified into three subfamilies. Promoter sequence analysis of BrRopGEFs revealed the presence of cis-elements characteristic of BrRopGEF promoters, and these cis-elements play a role in regulating abiotic stress tolerance and stress-related hormone responses. Organ-specific expression profiling demonstrated that BrRopGEFs were ubiquitously expressed in all organs, especially the roots, suggesting that they play a role in diverse biological processes. Gene expression analysis revealed that the expression of BrRopGEF13 was significantly up-regulated under osmotic stress and salt stress. RT-qPCR analysis revealed that the expression of BrRopGEF13 was significantly down-regulated under various types of abiotic stress. Protein–protein interaction (PPI) network analysis revealed interactions between RopGEF11, the homolog of BrRopGEF9, and the VPS34 protein in Arabidopsis thaliana, as well as interactions between AtRopGEF1, the homolog of BrRopGEF13 in Arabidopsis, and the ABI1, HAB1, PP2CA, and CPK4 proteins. VPS34, ABI1, HAB1, PP2CA, and CPK4 have previously been shown to confer resistance to unfavorable environments. Overall, our findings suggest that BrRopGEF9 and BrRopGEF13 play significant roles in regulating abiotic stress tolerance. These findings will aid future studies aimed at clarifying the functional characteristics of BrRopGEFs.
Assessment of Social Cognition in Non-human Primates Using a Network of Computerized Automated Learning Device (ALDM) Test Systems

Fagot & Paleressompoulle1 and Fagot & Bonte2 have published an automated learning device (ALDM) for the study of cognitive abilities of monkeys maintained in semi-free ranging conditions. Data accumulated during the last five years have consistently demonstrated the efficiency of this protocol to investigate individual/physical cognition in monkeys, and have further shown that this procedure reduces stress level during animal testing3. This paper demonstrates that networks of ALDM can also be used to investigate different facets of social cognition and in-group expressed behaviors in monkeys, and describes three illustrative protocols developed for that purpose. The first study demonstrates how ethological assessments of social behavior and computerized assessments of cognitive performance could be integrated to investigate the effects of socially exhibited moods on the cognitive performance of individuals. The second study shows that batteries of ALDM running in parallel can provide unique information on the influence of the presence of others on task performance. Finally, the last study shows that networks of ALDM test units can also be used to study issues related to social transmission and cultural evolution. Combined together, these three studies demonstrate clearly that ALDM testing is a highly promising experimental tool for bridging the gap in the animal literature between research on individual cognition and research on social cognition.
SkyStitch: A Cooperative Multi-UAV-based Real-time Video Surveillance System with Stitching

Recent advances in unmanned aerial vehicle (UAV) technologies have made it possible to deploy an aerial video surveillance system to provide an unprecedented aerial perspective for ground monitoring in real time. Multiple UAVs would be required to cover a large target area, and it is difficult for users to visualize the overall situation if they were to receive multiple disjoint video streams. To address this problem, we designed and implemented SkyStitch, a multiple-UAV video surveillance system that provides a single and panoramic video stream to its users by stitching together multiple aerial video streams. SkyStitch addresses two key design challenges: (i) the high computational cost of stitching and (ii) the difficulty of ensuring good stitching quality under dynamic conditions. To improve the speed and quality of video stitching, we incorporate several practical techniques like distributed feature extraction to reduce workload at the ground station, the use of hints from the flight controller to improve stitching efficiency and a Kalman filter-based state estimation model to mitigate jerkiness. Our results show that SkyStitch can achieve a stitching rate that is 4 times faster than existing state-of-the-art methods and also improve perceptual stitching quality. We also show that SkyStitch can be easily implemented using commercial off-the-shelf hardware.
Stereo Camera Setup for 360° Digital Image Correlation to Reveal Smart Structures of Hakea Fruits

About forty years after its first application, digital image correlation (DIC) has become an established method for measuring surface displacements and deformations of objects under stress. To date, DIC has been used in a variety of in vitro and in vivo studies to biomechanically characterise biological samples in order to reveal biomimetic principles. However, when surfaces of samples strongly deform or twist, they cannot be thoroughly traced. To overcome this challenge, different DIC setups have been developed to provide additional sensor perspectives and, thus, capture larger parts of an object’s surface. Herein, we discuss current solutions for this multi-perspective DIC, and we present our own approach to a 360° DIC system based on a single stereo-camera setup. Using this setup, we are able to characterise the desiccation-driven opening mechanism of two woody Hakea fruits over their entire surfaces. Both the breaking mechanism and the actuation of the two valves in predominantly dead plant material are models for smart materials. Based on these results, an evaluation of the setup for 360° DIC regarding its use in deducing biomimetic principles is given. Furthermore, we propose a way to improve and apply the method for future measurements.
Alteration in Dissolution Characteristics of Gelatin-Containing Formulations A Review of the Problem, Test Methods, and Solutions

The autors review the literature about the problem of the alteration in dissolution characteristics of gelatin-based formulations. This article also includes a brief introduction to gelatin as a pharmaceutical ingredient and describes examples of the altered dissolution profile ; the established cause, mechanisms, influencing factors, and stress methods for study of the behavior ; methods for determining the nature and extent of the change, and the reported solutions to the problem.
Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

Here we review recent advances in understanding the regulation of mRNA synthesis in Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been conserved in all eukaryotes, and budding yeast has been at the forefront in the discovery and dissection of these conserved mechanisms. Topics covered include upstream activation sequence and promoter structure, transcription factor classification, and examples of regulated transcription factor activity. We also examine advances in understanding the RNA polymerase II transcription machinery, conserved coactivator complexes, transcription activation domains, and the cooperation of these factors in gene regulatory mechanisms.
Swapping Evaluation : A Memory-Scalable Solution for Answer-On-Demand Tabling

One of the differences among the various approaches to suspension-based tabled evaluation is the scheduling strategy. The two most popular strategies are local and batched evaluation. The former collects all the solutions to a tabled predicate before making any one of them available outside the tabled computation. The latter returns answers one by one before computing them all, which in principle is better if only one answer (or a subset of the answers) is desired. Batched evaluation is closer to SLD evaluation in that it computes solutions lazily as they are demanded, but it may need arbitrarily more memory than local evaluation, which is able to reclaim memory sooner. Some programs which in practice can be executed under the local strategy quickly run out of memory under batched evaluation. This has led to the general adoption of local evaluation at the expense of the more depth-first batched strategy. In this paper we study the reasons for the high memory consumption of batched evaluation and propose a new scheduling strategy which we have termed swapping evaluation. Swapping evaluation also returns answers one by one before completing a tabled call, but its memory usage can be orders of magnitude less than batched evaluation. An experimental implementation in the XSB system shows that swapping evaluation is a feasible memory-scalable strategy that need not compromise execution speed.
Distributed Mobility Management for Target Tracking in Mobile Sensor Networks

Mobility management is a major challenge in mobile ad hoc networks (MANETs) due in part to the dynamically changing network topologies. For mobile sensor networks that are deployed for surveillance applications, it is important to use a mobility management scheme that can empower nodes to make better decisions regarding their positions such that strategic tasks such as target tracking can benefit from node movement. In this paper, we describe a distributed mobility management scheme for mobile sensor networks. The proposed scheme considers node movement decisions as part of a distributed optimization problem which integrates mobility-enhanced improvement in the quality of target tracking data with the associated negative consequences of increased energy consumption due to locomotion, potential loss of network connectivity, and loss of sensing coverage.
Low-cost Attitude and Heading Reference System: Filter design and experimental evaluation

This paper presents the design and performance evaluation of a low-cost Attitude and Heading Reference System (AHRS) for autonomous vehicles. A single sensor pack, an Inertial Measurement Unit (IMU), provides all the data required to feed the attitude filter. The design is sensor-driven and departs from traditional solutions as no explicit representations of the attitude, e.g., Euler angles, quaternions, or rotation matrices, are considered in the filter design. Moreover, the proposed solution includes the estimation of rate gyros biases, systematic tuning procedures, and also allows for the inclusion of frequency weights to model colored noise on the different sensor channels. Due to its inherent structure, the filter is complementary, allows for temporary loss of sensor measurements, and also copes well with slowly time-varying rate gyros biases. The performance of the proposed algorithm is experimentally evaluated with a low-cost IMU and resorting to a high precision calibration table, which provides ground truth signals for comparison with the resulting filter estimates.
Polyglutamine-Modulated Striatal Calpain Activity in YAC Transgenic Huntington Disease Mouse Model: Impact on NMDA Receptor Function and Toxicity

Huntington disease (HD), caused by CAG expansion in the ubiquitously expressed huntingtin gene, is characterized by early dysfunction and death of striatal medium-sized spiny neurons (MSNs). Previous work has shown MSN-specific alterations in NMDA receptor (NMDAR) expression and cell death signaling. Furthermore, studies in HD human brain tissue and a knock-in mouse model demonstrate increases in calpain activity, which can be stimulated by NMDARs and contribute to excitotoxicity. Here, we report increased calpain activity in MSNs from the yeast artificial chromosome (YAC) transgenic mouse model of HD, expressing human full-length huntingtin with 128 polyglutamine repeats (YAC128), compared with wild type. Moreover, the calpain-cleaved product of NMDAR subunit NR2B is increased early, and NR2B expression levels are reduced, in YAC128 striatum. Although steady-state NMDAR surface expression is similar in wild-type and YAC128 MSNs, the rate of loss of NR2B-containing surface receptors is enhanced in YAC128 MSNs, suggesting that NMDAR forward trafficking to the surface is also faster, as previously reported for YAC72 MSNs. Calpain inhibitor-1 treatment normalized the loss rate of surface NMDARs in YAC128 MSNs to that of wild type, and significantly increased surface NMDAR expression in YAC128, but not in wild type or YAC72. With acute NMDAR overstimulation, the increase in calpain activity correlated with polyglutamine length, and calpain inhibitor treatment reduced NMDA-induced apoptosis in YAC72 and YAC128 MSNs to wild-type levels. Thus, the cumulative effect of increasing huntingtin polyglutamine length is to enhance MSN sensitivity to excitotoxicity at least in part by calpain-mediated cell death signaling.
Lobularia maritima as a nutrient-rich floral food source for two parasitoid wasps of Tuta absoluta

: Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is one of the main pests threatening tomato production worldwide. Since its detection in the Mediterranean basin, it has been the target of research aiming to reduce damage in tomato crops. Current conservation biological control approaches focus on the polyphagous predators Macrolophus pyg-maeus (Rambur) and Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), which are very effective predators of the pest’s eggs but have little effect on T. absoluta larvae. Surveys conducted in northeast of Spain have concluded that the eulophid Necremnus tutae Ribes & Bernardo and the braconid Dolichogenidea gelechiidivoris (Marsh) are the most abundant larval parasitoids. It is well known that adding floral resources near crops can provide high-quality food for natural enemies and thus enhance biological control. Previous studies showed that Lobularia maritima L. (Brassicaceae) flowers are a reliable food source for N. tutae . The present study examines whether the availability of L. maritima flowers positively influences the fitness of D. gelechiidivoris and the biological control of T. absoluta by parasitoids. To study this aspect, the perfor - mance of both wasps was evaluated in a simple and complex arena at high and low densities of T. absoluta , respectively. Our results demonstrate that the nectar of L. maritima is a nutrient-rich food source for both N. tutae and D. gelechiidivoris with profound implications on the biological control of T. absoluta in tomatoes.
Metabotropic Glutamate Receptors Trigger Homosynaptic Protein Synthesis to Prolong Long-Term Potentiation

We investigated the mechanisms by which previous “priming” activation of group I metabotropic glutamate receptors (mGluRs) facilitates the persistence of long-term potentiation (LTP) in area CA1 of rat hippocampal slices. Priming of LTP was elicited by either pharmacological or synaptic activation of mGluRs before a weak tetanic stimulus that normally produced only a rapidly decaying phase of LTP that did not involve protein synthesis or mGluRs. Pharmacological priming of LTP persistence by a selective group I mGluR agonist was blocked by an inhibitor of group I mGluRs and by inhibitors of translation, but not by a transcriptional inhibitor. The same mGluR agonist increased 35S-methionine incorporation into slice proteins. LTP could also be facilitated using a synaptic stimulation priming protocol, and this effect was similarly blocked by group I mGluR and protein synthesis inhibitors. Furthermore, using a two-pathway protocol, the synaptic priming of LTP was found to be input-specific. To test for the contribution of group I mGluRs and protein synthesis to LTP in nonprimed slices, a longer duration control tetanization protocol was used to elicit a more slowly decaying form of LTP than did the weak tetanus used in the previous experiments. The persistence of the LTP induced by this stronger tetanus was dependent on mGluR activation and protein synthesis but not on transcription. Together, these results suggest that mGluRs couple to nearby protein synthesis machinery to homosynaptically regulate an intermediate phase of LTP dependent on new proteins made from pre-existing mRNA.
Articulatory model for the study of speech production.

Study of midsagittal x‐ray tracings reveals that the vocal‐tract outline can be accurately represented by means of variables specifying the positions of the jaw, tongue body, tongue tip, lips, velum, and hyoid. As the articulators move, they modify the vocal‐tract cross‐sectional area and the vocal‐tract transfer function computed thereform. The speech signal may be synthesized by concatenating the responses to repeated excitation of the quasistatic vocal tract. Vowels are specified in terms of variables denoting the positions of the jaw, tongue body, lips, and velum. Consonants are implemented as transformations on the underlying vowel‐derived articulatory states that satisfy given constraints on the position of an articulator relative to the fixed structures. The set of states which satisfy the given constraint corresponds to the allowed productions of the consonant. Coarticulation effects control the selection of the underlying state and thus determine the particular consonant produced. Vowel‐consonant.