Miracle-dz/UniFAR-FTUs huggingface dataset:
CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects

MOTIVATION Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computational part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other whole genome sequences. Most importantly, it allows annotation of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds to the sequence of the ORF with 500 additional bases before the ORF and 200 bases after. For annotation, additional information like Blast results can be added or linked to the IPFs as well as automatic and/or manual annotations. When a new assembly is performed, CAAT-Box creates new IPFs according to the old IPF panel. CAAT-Box recognizes the modified IPFs which are the only ones used for a new automatic analysis after each assembly. Using this strategy, the user works with a group of IPFs independently of the closure phase progression. The IPFs are accessible by a web server and can therefore be modified and commented by different groups. RESULT CAAT-Box was used to obtain and to annotate several complete genomes like Listeria monocytogenes or Streptococcus agalactiae. AVAILABILITY The program may be obtained from the authors and is freely available to non-profit organisations.
Towards MCTS for Creative Domains

Monte Carlo Tree Search (MCTS) has recently demonstrated considerable success for computer Go and other difficult AI problems. We present a general MCTS model that extends its application from searching for optimal actions in games and combinatorial optimisation tasks to the search for optimal sequences and embedded subtrees. The primary application of this extended MCTS model will be for creative domains, as it maps naturally to a range of procedural content generation tasks for which Markovian or evolutionary approaches would typically be used.
Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles

MOTIVATION Capillary electrophoresis (CE) is a powerful approach for structural analysis of nucleic acids, with recent high-throughput variants enabling three-dimensional RNA modeling and the discovery of new rules for RNA structure design. Among the steps composing CE analysis, the process of finding each band in an electrophoretic trace and mapping it to a position in the nucleic acid sequence has required significant manual inspection and remains the most time-consuming and error-prone step. The few available tools seeking to automate this band annotation have achieved limited accuracy and have not taken advantage of information across dozens of profiles routinely acquired in high-throughput measurements. RESULTS We present a dynamic-programming-based approach to automate band annotation for high-throughput capillary electrophoresis. The approach is uniquely able to define and optimize a robust target function that takes into account multiple CE profiles (sequencing ladders, different chemical probes, different mutants) collected for the RNA. Over a large benchmark of multi-profile datasets for biological RNAs and designed RNAs from the EteRNA project, the method outperforms prior tools (QuSHAPE and FAST) significantly in terms of accuracy compared with gold-standard manual annotations. The amount of computation required is reasonable at a few seconds per dataset. We also introduce an 'E-score' metric to automatically assess the reliability of the band annotation and show it to be practically useful in flagging uncertainties in band annotation for further inspection. AVAILABILITY AND IMPLEMENTATION The implementation of the proposed algorithm is included in the HiTRACE software, freely available as an online server and for download at http://hitrace.stanford.edu. CONTACT sryoon@snu.ac. kr or rhiju@stanford.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Interactions of Opioids and HIV Infection in the Pathogenesis of Chronic Pain

Over 50% of HIV-1/AIDS patients suffer chronic pain. Currently, opioids are the cornerstone medications for treating severe pain in these patients. Ironically, emerging clinical data indicates that repeated use of opiate pain medicines might in fact heighten the chronic pain states in HIV patients. Both laboratory-based and clinical studies strongly suggest that opioids exacerbate the detrimental effects of HIV-1 infection on the nervous system, both on neurons and glia. The combination of opioids and HIV-1infection may promote the damage of neurons, including those in the pain sensory and transmission pathway, by activating both caspase-dependent and caspase-independent pro-apoptotic pathways. In addition, the opiate-HIV-1 interaction may also cause widespread disturbance of glial function and elicit glial-derived pro-inflammatory responses that dysregulate neuronal function. The deregulation of neuron-glia cross-talk that occurs with the combination of HIV-1 and opioids appears to play an important role in the development of the pathological pain state. In this article, we wish to provide an overview of the potential molecular and cellular mechanisms by which opioids may interact with HIV-1 to cause neurological problems, especially in the context of HIV-associated pathological pain. Elucidating the underlying mechanisms will help researchers and clinicians to understand how chronic use of opioids for analgesia enhances HIV-associated pain. It will also assist in optimizing therapeutic approaches to prevent or minimize this significant side effect of opiate analgesics in pain management for HIV patients.
Neural Correlates of Delusions in Patients with Alzheimerâ s Disease

The neural correlates of delusions in Alzheimer’s disease (AD) remain unclear. This thesis examined the neuropathological, structural volumetric, and resting-state functional connectivity (rs-fc) correlates associated with delusions in AD. We hypothesized that delusional AD patients will have greater disease severity characterized by higher AD pathology load and increased atrophy, as well as altered rs-fc compared to non-delusional patients. We found that delusions were associated with Lewy body pathology, vascular pathology, and vascular risk factors, but were not correlated with increased AD pathology. Patients who developed delusions showed increased atrophy of regions within the default mode network (DMN) following the onset of delusions, while the cohort that did not develop delusions did not exhibit significant atrophy in the DMN over a similar time frame. We found that decreased connectivity within the DMN, in particular disintegration of the inferior parietal lobule with the overall network, may be associated with delusions in AD.
Usability of Social Ubiquitous Computing

Software design is ideally directed by the discipline of usability engineering. Unfortunately, current usability theories and practices are focused on single user scenarios while the increasingly crucial social aspects of computing are weakly addressed. Ubiquitous computing complicates things further by enabling an almost limitless variation of new social contexts to computing. This paper reviews different approaches to addressing the various social issues that concern the design of usable ubiquitous multi-user systems.
Subtype-Specific Regulation of Inositol 1,4,5-Trisphosphate Receptors

A rise in intracellular calcium ([Ca2+]i) in response to binding of inositol 1,4,5 trisphosphate (InsP3) to its receptors is a ubiquitous signaling system, which is implicated in the control of a myriad of cellular functions (Berridge 1993). Three distinct InsP3 receptors are expressed to varying degrees in individual cell types (Wojcikiewicz 1995). Activation of these receptors results in [Ca2+]i signals that display impressive fidelity, frequently manifested through a complex array of temporal and spatial characteristics. [Ca2+]i signals in nonexcitable cells are initiated in defined regions (Kasai and Augustine 1990; Rooney et al. 1990); can be spatially limited to a portion of a cell (Kasai et al. 1993) or alternatively spread as repetitive, global, oscillatory waves throughout an entire cell (Lechleiter et al. 1991; Straub et al. 2000). In addition, the periodicity of these spatial events is tightly regulated and has been proposed to provide effectors with a digitally encoded signal.
Changes in Striatal Signaling Induce Remodeling of RGS Complexes Containing Gβ5 and R7BP Subunits

ABSTRACT Neurotransmitter signaling via G protein coupled receptors is crucially controlled by regulators of G protein signaling (RGS) proteins that shape the duration and extent of the cellular response. In the striatum, members of the R7 family of RGS proteins modulate signaling via D2 dopamine and μ-opioid receptors controlling reward processing and locomotor coordination. Recent findings have established that R7 RGS proteins function as macromolecular complexes with two subunits: type 5 G protein β (Gβ5) and R7 binding protein (R7BP). In this study, we report that the subunit compositions of these complexes in striatum undergo remodeling upon changes in neuronal activity. We found that under normal conditions two equally abundant striatal R7 RGS proteins, RGS9-2 and RGS7, are unequally coupled to the R7BP subunit, which is present in complex predominantly with RGS9-2 rather than with RGS7. Changes in the neuronal excitability or oxygenation status resulting in extracellular calcium entry, uncouples RGS9-2 from R7BP, triggering its selective degradation. Concurrently, released R7BP binds to mainly intracellular RGS7 and recruits it to the plasma membrane and the postsynaptic density. These observations introduce activity-dependent remodeling of R7 RGS complexes as a new molecular plasticity mechanism in striatal neurons and suggest a general model for achieving rapid posttranslational subunit rearrangement in multisubunit complexes.
Block assembly for global registration of building scans

We propose a framework for global registration of building scans. The first contribution of our work is to detect and use portals (e.g., doors and windows) to improve the local registration between two scans. Our second contribution is an optimization based on a linear integer programming formulation. We abstract each scan as a block and model the blocks registration as an optimization problem that aims at maximizing the overall matching score of the entire scene. We propose an efficient solution to this optimization problem by iteratively detecting and adding local constraints. We demonstrate the effectiveness of the proposed method on buildings of various styles and that our approach is superior to the current state of the art.
Destination Personality: An Application of Brand Personality to Tourism Destinations

As tourism destinations become more substitutable due to increasing competition in global tourism markets, destination personality is seen as a viable metaphor for building destination brands and crafting a unique identity for tourism places. At the conceptual level, although the importance of destination personality has been acknowledged, to the best of our knowledge, no empirical research has yet identified its dimensions. Adopting Aaker’s brand personality scale, this study aimed to identify whether tourists ascribed personality traits to tourism destinations. The findings of the study indicate that perception of destination personality is 3-dimensional: sincerity, excitement, and conviviality. The study also found that destination personality has positive impact on perceived destination image and intention to recommend. In particular, the conviviality dimension moderated the impact of cognitive image on tourists’ intention to recommend.
Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase

Abstract Detailed understanding of the action of biological molecular machines must overcome the challenge of gaining a clear knowledge of the corresponding free-energy landscape. An example for this is the elucidation of the nature of converting chemical energy to torque and work in the rotary molecular motor of F1-ATPase. A major part of the challenge involves understanding the rotary–chemical coupling from a non-phenomenological structure/energy description. Here we focused on using a coarse-grained model of F1-ATPase to generate a structure-based free-energy landscape of the rotary–chemical process of the whole system. In particular, we concentrated on exploring the possible impact of the position of the catalytic dwell on the efficiency and torque generation of the molecular machine. It was found that the experimentally observed torque can be reproduced with landscapes that have different positions for the catalytic dwell on the rotary–chemical surface. Thus, although the catalysis is undeniably required for torque generation, the experimentally observed position of the catalytic dwell at 80° might not have a clear advantage for the force generation by F1-ATPase. This further implies that the rotary–chemical couplings in these biological motors are quite robust and their efficiencies do not depend explicitly on the position of the catalytic dwells. Rather, the specific positioning of the dwells with respect to the rotational angle is a characteristic arising due to the structural construct of the molecular machine and might not bear any clear connection to the thermodynamic efficiency for the system.
COSTUME: a method for building quality models for composite COTS-based software systems

The use of quality models during the selection of commercial, off-the-shelf (COTS) products provides a framework for the description of the domains which the COTS products belong to. Descriptions of COTS products and user quality requirements may be translated into the quality concepts defined in the model, making selection more efficient and reliable. We propose a method for the construction of quality models for composite COTS-based software systems (CCSS), defined as systems that are composed by several interconnected COTS products. Selection processes carried out when procuring a CCSS require not a single COTS product to be selected but a set of them. As a consequence, instead of a classical quality model, we need a more elaborated one, defined as the composition of those models that belong to the domains of the COTS products that form the CCSS.
Robots for social training of autistic children

We apply a participatory co-creation process to empower health researchers/practitioners with robot assistants or mediators in behavioral therapies for children with autism. This process combines (a) a user centered design of a platform to support therapists to create and share behavioral training scenarios with robots and (b) acquisition of domain specific knowledge from the therapists in order to design robot-child interaction scenarios that accomplish specific learning goals. These two aspects of the process are mutually dependant and therefore require an iterative design of a technological platform that will make gradual steps towards creating optimal affordances for therapists to create robot-mediated scenarios to the best of the technical capabilities of the robot, i.e. through co-creation. For this purpose an end-user programming environment augmented with learning by demonstration tool and textual commands is being developed. The initial tests showed that this tool can be used by the therapists to create own training scenarios with existing behavioral components. We conclude that this platform comply with the needs of the contemporary practices that focus on personalization of the training programs for every child. In addition, the proposed framework makes possible to include extensions to the platform for future developments.
Pressure jump interface law for the Stokes–Darcy coupling: confirmation by direct numerical simulations

Abstract It is generally accepted that the effective velocity of a viscous flow over a porous bed satisfies the Beavers–Joseph slip law. To the contrary, the interface law for the effective stress has been a subject of controversy. Recently, a pressure jump interface law has been rigourously derived by Marciniak-Czochra and Mikelić. In this paper, we provide a confirmation of the analytical result using direct numerical simulation of the flow at the microscopic level. To the best of the authors’ knowledge, this is the first numerical confirmation of the pressure interface law in the literature.
FoAM - A Framework for Application-Oriented O/R Mapping

This paper enumerates the typical O/R mapping problems, analyses the most critical ones and shows a way to overcome them by using the mapping framework FoAM. FoAM supports aplication oriented mapping of classes to database tables and has succesfully been used in real world Java/J2EE and C# projects together with Oracle and Microsoft SQL-Server databases. In one project it has been used to replace TopLink[1] which increased the performance of the productive system by a factor of 2.5.
Diabetes regulates fructose absorption through thioredoxin-interacting protein

Metabolic studies suggest that the absorptive capacity of the small intestine for fructose is limited, though the molecular mechanisms controlling this process remain unknown. Here we demonstrate that thioredoxin-interacting protein (Txnip), which regulates glucose homeostasis in mammals, binds to fructose transporters and promotes fructose absorption by the small intestine. Deletion of Txnip in mice reduced fructose transport into the peripheral bloodstream and liver, as well as the severity of adverse metabolic outcomes resulting from long-term fructose consumption. We also demonstrate that fructose consumption induces expression of Txnip in the small intestine. Diabetic mice had increased expression of Txnip in the small intestine as well as enhanced fructose uptake and transport into the hepatic portal circulation. The deletion of Txnip in mice abolished the diabetes-induced increase in fructose absorption. Our results indicate that Txnip is a critical regulator of fructose metabolism and suggest that a diabetic state can promote fructose uptake. DOI: http://dx.doi. org/10.7554/eLife.18313. 001
The negative cognitive bias of self-schema in worriers

Worry represents a repetitive form of negative thinking, during which a cognitive attempt is made to anticipate and to prepare for possible damaging outcomes in the future. Research has demonstrated that self-schema is derived from past experience, which guides the processing of self-related unknowns and helps to make predictions. It remains unclear whether the repetitive negative anticipation during worry is based on the maladaptive self-schema. Previous studies have found that self-schema is closely related to the processing of self-related information. Therefore, we shall explore the distinctions of self-schema between high-level worriers and a control group with regard to self-related activities. We hypothesized that the negative cognitive bias of self-schema in worriers would be manifested through abnormally self-related activities and linguistic features. The participants were screened into two categories: the unit consisting of worriers and the control group. In Experiment 1, individuals with different levels of worry were tested for their self-related processing and their relationship with solely neutral stimuli. Experiment 2 was performed by combining the Sentence Completion Test to the first experiment to investigate the linguistic features common to worriers. Meanwhile, participants were asked to complete the Remote Association Test (RAT) to control their associative ability during tasks. The results of Experiment 1 indicated that: (i) compared to the control group, the worriers made more self-related judgments and displayed delayed reactions. (ii) The worriers demonstrated more negative relationships with the neutral stimuli and made automatic responses. The results obtained from Experiment 2 established that: (i) there were pronouncedly more negative sentences iterated by the set of worriers than by the control group. (ii) Compared to the control group, the worriers uttered more self-related words. Notably, no significant distinctions were found in the RAT between two groups, suggesting that there was no meaningful difference in the associative abilities of the two categories of participants. The research initiative confirmed that worriers tend to make more negative self-related judgments with regard to neutral prompts and that they are more likely to project negative concepts about themselves. The results revealed the negative self-schema in worriers and illustrated the psychology mechanism of those who are anxiety prone. The investigation also explained why worriers extensively anticipated negative outcomes about the unknown. This study would be beneficial to practitioners in the treatment of affective disorders in which worry is the primary characteristic.
Use of Carnosine for Oxidative Stress Reduction in Different Pathologies

The main properties and biological effects of the antioxidant carnosine, the natural dipeptide β-alanyl-L-histidine, are considered. Data on the effective use of carnosine in different pathologies are presented. Special attention is paid to issues of use of carnosine in neurologic and mental diseases, in alcoholism as well as in physiological states accompanied by activation of free-radical processes and formation of oxidative stress.
Towards radix-4, parallel interleaver design to support high-throughput turbo decoding for re-configurability

Parallel, radix-4 turbo decoding is used to enhance the throughput and at the same time reduce the overall memory cost. The bottleneck is the higher complexity associated with radix-4 parallel interleaver implementation. This paper addresses the implementation issues of radix-4, parallel interleaver and also proposes necessary modifications in the interleaver algorithms for parallel address generation. It presents a re-configurable architecture which enables the use of same turbo decoding core to be used for multiple standards. The proposed interleaver architecture is capable of handling the memory conflicts on-the-fly. It consumes 12.5K gates and can run at a frequency of 285MHz, thus supporting a throughput of 173.3Mpbs, which can cover most of the emerging communication standards.
Effects of elaboration delays on the polling time of IEEE 802.11 networks for industrial applications

The performance evaluation of wireless networks for industrial applications represents a relevant issue for the scientific community. One of the most important aspects of these activities is concerned with the validation of the theoretical models derived from accurate analysis of the protocols employed by the networks. In this paper we focus on a typical industrial application of the IEEE 802.11 wireless LAN. Particularly, we consider a master-slave protocol and provide an exhaustive analysis of the polling time of a slave station aimed at understanding the effects of the internal delays of the components employed along with their influence on the overall behavior of the networks.
Digital image authentication and encryption using digital signature

In this paper, a methodology for digital image authentication using digital signature is proposed. The hash of the original image is taken and is encrypted by RSA. The digital signature obtained is concealed in the image. Digital signature is sent along with the encrypted image which decreases the probability of meticulous attack by the intruder. The encrypted image is shuffled using Chaotic Logistic Map to get the final shuffled encrypted image. The use of Logistic Map improves the randomness in the image. For the authentication, a comparator is employed which evaluates correctness of the hash extracted. The simulations have been carried out to examine the proposed authentication and encryption technique.