Miracle-dz/UniFAR-FTUs huggingface dataset:
Chloramphenicol Resistance in Clostridium difficile Is Encoded on Tn4453 Transposons That Are Closely Related to Tn4451 from Clostridium perfringens

ABSTRACT The chloramphenicol resistance gene catD fromClostridium difficile was shown to be encoded on the transposons Tn4453a and Tn4453b, which were structurally and functionally related to Tn4451 fromClostridium perfringens. Tn4453a and Tn4453b excised precisely from recombinant plasmids, generating a circular form, as is the case for Tn4451. Evidence that this process is mediated by Tn4453-encodedtnpX genes was obtained from experiments which showed that in trans these genes complemented a Tn4451tnpXΔ1 mutation for excision. Nucleotide sequencing showed that the joint of the circular form generated by the excision of Tn4453a and Tn4453b was similar to that from Tn4451. These results suggest that the Tn4453-encoded TnpX proteins bind to similar DNA target sequences and function in a manner comparable to that of TnpX from Tn4451. Furthermore, it has been shown that Tn4453a and Tn4453b can be transferred to suitable recipient cells by RP4 and therefore are mobilizable transposons. It is concluded that, like Tn4451, they must encode a functional tnpZ gene and a targetoriT or RSA site. The finding that related transposable elements are present in C. difficile andC. perfringens has implications for the evolution and dissemination of antibiotic resistance genes and the mobile elements on which they are found within the clostridia.
INTERAÇÃO ENTRE OS MECANISMOS CROMÁTICO E ACROMÁTICO NA CROMOESTEREOPSIA.

In order to know if the mechanisms that process luminance are independent of those that process colour, or, conversely, if there is an interaction between them, we have executed two experiments. In the first, we studied how the changes in the perception of depth elicited by chromostereopsis with couples of isoluminants and anisochromatic patches inserted in a uniform background, which varied in luminance from trial to trial. In a second experiment, we used a square-wave grating background, in which every strip changes the luminance of the colour. The different background could be, on the one hand, isoluminant/anisoluminant, or, on the other hand, isochromatic/anisochromatic. The results showed: 1) that perceived depth varied as a function of the luminance variation. That is, reversing the depth when the sign of the difference in luminance between figure and background changes; 2) that it is possible to elicit chromoesteropsis at isoluminance; 3) a weak interaction between the variation of chromatic contrast and achromatic contrast; 4) that interactions between the two mechanisms should occur at pre-retinal levels; and 5) the responses of the two mechanisms are separable.
Larynx Trauma and Hyoid Bone Fracture after Bite Injury in Dog: Case Report

An 8-year-old male Jack Russell crossbreed dog was admitted to our hospital with dyspnea and shock following a dog-bite injury on the ventral neck. Radiographs revealed subcutaneous emphysema and bilateral thyrohyoid bone fractures. Intraoperatively, rupture of both sternohyoid muscles, both hyoepiglotticus muscles, both thyrohyoid muscles, and a partial cranial rupture of the superficial sphincter colli muscle were detected. Part of the epiglottis was detached from the thyroid cartilage. The patient’s severed muscles and torn epiglottis were reattached using a simple interrupted suture pattern. Hyoepiglotticus muscles could not be identified. The bilateral thyrohyoid bone fractures were repaired with intraosseous wire suture. A temporary tracheostomy tube and an esophageal feeding tube were placed postoperatively. The dog was discharged after 8 days, re-examined at 2 and 6 months and laryngeal and pharyngeal function were evaluated as normal. To the authors’ knowledge, this is the first report of a dog that presented with laryngeal trauma with hyoid bone fracture and acute dyspnea that underwent surgical treatment resulting in an acceptable outcome.
Energy-optimal scheduling with dynamic channel acquisition in wireless downlinks

We consider a wireless base station serving L users through L time-varying channels. It is well known that opportunistic scheduling algorithms with full channel state information (CSI) can stabilize the system and achieve the full capacity region. However, opportunistic scheduling algorithms with full CSI may not be energy efficient when the cost of channel acquisition is high and traffic rates are low. In particular, under the low traffic rate regime, it may be sufficient and more energy-efficient to transmit data with no CSI, i.e., to transmit data blindly, since no power for channel acquisition is consumed. In general, we show that purely channel-aware or purely channel-blind strategies are not necessarily optimal, and we must consider mixed strategies. We derive a unified scheduling algorithm that dynamically chooses to transmit data with full or no CSI based on queue backlog and channel statistics. Through Lyapunov analysis, we show that the unified algorithm can stabilize the downlink with optimal power consumption.
In Pursuit of the Optimal Fed‐Batch Process for Monoclonal Antibody Production

Fed‐batch culture currently represents the most attractive choice for large scale production of monoclonal antibodies (MAbs), due to its operational simplicity, reliability, and flexibility for implementation in multipurpose facilities. Development of highly productive cell lines, maximization of cell culture longevity, and maintenance of high specific antibody secretion rates through genetic engineering techniques, nutrient supplementation, waste product minimization, and control of environmental conditions are important for the design of high‐yield fed‐batch processes. Initially simple supplementation protocols have evolved into sophisticated serum‐free multi‐nutrient feeds that result in MAb titers on the order of 1–2 g/L. Limited research has been published to date on the effects of various culture parameters on potentially important quality issues, such as MAb glycosylation and stability. Although most fed‐batch protocols to date have relied on relatively simple control schemes, increasingly sophisiticated algorithms must be applied in order to take full advantage of the potentially additive effects of manipulating nutrient and environmental parameters to maximize fed‐batch process productivity.
Slow Spatial Recruitment of Neocortex during Secondarily Generalized Seizures and Its Relation to Surgical Outcome

Understanding the spatiotemporal dynamics of brain activity is crucial for inferring the underlying synaptic and nonsynaptic mechanisms of brain dysfunction. Focal seizures with secondary generalization are traditionally considered to begin in a limited spatial region and spread to connected areas, which can include both pathological and normal brain tissue. The mechanisms underlying this spread are important to our understanding of seizures and to improve therapies for surgical intervention. Here we study the properties of seizure recruitment—how electrical brain activity transitions to large voltage fluctuations characteristic of spike-and-wave seizures. We do so using invasive subdural electrode arrays from a population of 16 patients with pharmacoresistant epilepsy. We find an average delay of ∼30 s for a broad area of cortex (8 × 8 cm) to be recruited into the seizure, at an estimated speed of ∼4 mm/s. The spatiotemporal characteristics of recruitment reveal two categories of patients: one in which seizure recruitment of neighboring cortical regions follows a spatially organized pattern consistent from seizure to seizure, and a second group without consistent spatial organization of activity during recruitment. The consistent, organized recruitment correlates with a more regular, compared with small-world, connectivity pattern in simulation and successful surgical treatment of epilepsy. We propose that an improved understanding of how the seizure recruits brain regions into large amplitude voltage fluctuations provides novel information to improve surgical treatment of epilepsy and highlights the slow spread of massive local activity across a vast extent of cortex during seizure.
Relationships among cognition, emotion, and motivation: implications for intervention and neuroplasticity in psychopathology

Emotion-cognition and motivation-cognition relationships and related brain mechanisms are receiving increasing attention in the clinical research literature as a means of understanding diverse types of psychopathology and improving biological and psychological treatments. This paper reviews and integrates some of the growing evidence for cognitive biases and deficits in depression and anxiety, how these disruptions interact with emotional and motivational processes, and what brain mechanisms appear to be involved. This integration sets the stage for understanding the role of neuroplasticity in implementing change in cognitive, emotional, and motivational processes in psychopathology as a function of intervention.
Seismic shear wave reflectivity structure of the mantle beneath northeast China and the northwest Pacific

Using multiple ScS reverberations, we examine the mantle reflectivity structure beneath northeast China and the northwest Pacific. We find several upper mantle discontinuities, including a melt layer with a mean thickness of 64 km atop the 410 km discontinuity, present on both sides of the subducting slab near the Nankai trench. The transition zone contains a split 520 km discontinuity in several paths, and tomographic images show stagnant slabs at this depth. We believe that this may be slab related based on experimental work. A negative reflector is found in one path beneath the northeast China craton at a depth of 598 km. Mid‐mantle reflectors are found in all of our paths and are present throughout a wide depth range (~750–1600 km).
ACAT2 Is Localized to Hepatocytes and Is the Major Cholesterol-Esterifying Enzyme in Human Liver

Background—Two acyl-coenzyme A:cholesterol acyltransferase (ACAT) genes, ACAT1 and ACAT2, have been identified that encode 2 proteins responsible for intracellular cholesterol esterification. Methods and Results—In this study, immunohistology was used to establish their cellular localization in human liver biopsies. ACAT2 protein expression was confined to hepatocytes, whereas ACAT1 protein was found in Kupffer cells only. Studies with a highly specific ACAT2 inhibitor, pyripyropene A, in microsomal activity assays demonstrated that ACAT2 activity was highly variable among individual human liver samples, whereas ACAT1 activity was more similar in all specimens. ACAT2 provided the major cholesterol-esterifying activity in 3 of 4 human liver samples examined. Conclusions—The data suggest that in diseases in which dysregulation of cholesterol metabolism occurs, such as hypercholesterolemia and atherosclerosis, ACAT2 should be considered a target for prevention and treatment.
Dynamic modeling of inter-instruction effects for execution time estimation

The market for embedded applications is facing a growing interest in power consumption issues. The work presented is intended to provide a new model to estimate software-level power consumption of 32-bit microprocessors. This model extends previous ones by considering dynamic inter-instruction effects that take place during code execution, providing a static means to characterize their energy consumption. The model is formally sound; it is conceived for a generic architecture and it has been preliminarily validated on the Intel486/sup TM/ architecture.
Attributed Graph Models: Towards the Sharing of Relational Network Data

The growth of the internet has created large scale collections of relational data. In these cases, datasets contain relationships between the items or individuals that are being modeled – e.g, hyperlinks connect webpages on the internet, while friendships (Facebook), followers (Twitter) or messages (Email) form between individuals in social networks. Individuals connected through these relationships exhibit relational correlation, or a statistical dependence of their attributes [2]. Modeling these relationships can give better predictions about users, or a better understanding of the underlying social processes. The field of Statistical Relational Learning (SRL) utilizes these relational connections to collectively predict the unknown labels in the network, with resulting methods able to largely outperform traditional independent learning methods (for a summary of SRL see [3]). The developed methods can undertake tasks such as identifying fraudulent securities traders or inferring gene interactions, as well as predict user traits or personalize content. Similarly, Social Network Mining (SNM) mines information of the individuals given their attributes and relational structure, focusing on tasks such as predicting future links or on identifying communities within a network (for an introduction see [1]). In these domains, large scale data is necessary to drive further research towards developing accurate and scalable algorithms that continuously push the state of the art forwards. However, attributed data in relational domains is particularly sensitive in comparison to other domains. Datasets such as the UCI collection exist for moderate testing and comparison of traditional machine learning algorithms, while large scale unattributed network repositories exist such as SNAP or the UF Sparse Matrix Collection. In contrast, attributed relational datasets are typically the product of collections of social interactions, such as Facebook, Twitter, LinkedIn, LivingSocial, Email, and more. A large collec-
Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

The analysis of the Arabidopsis genome revealed evidence of three ancient polyploidy events in the evolution of the Brassicaceae, but the exact phylogenetic placement of these events is still not resolved. The most recent event is called the At-α (alpha) or 3R, the intermediate event is referred to as the At-β (beta) or 2R, and the oldest is the At-γ (gamma) or 1R. It has recently been established that At-γ is shared with other Rosids, including papaya (Carica), poplar (Populus), and grape (Vitis), whereas data to date suggest that At-α is Brassicaceae specific. To address more precisely when the At-α and At-β events occurred and which plant lineages share these paleopolyploidizations, we sequenced and analyzed over 4,700 normalized expressed sequence tag sequences from the Cleomaceae, the sister family to the Brassicaceae. Analysis of these Cleome data with homologous sequences from other Rosid genomes (Arabidopsis, Carica, Gossypium, Populus, and Vitis) yielded three major findings: 1) confirmation of a Cleome-specific paleopolyploidization (Cs-α) that is independent of the Brassicaceae At-α paleopolyploidization; 2) Cleome and Arabidopsis share the At-β duplication, which is lacking from papaya within the Brassicales; and 3) rates of molecular evolution are faster for the herbaceous annual taxa Arabidopsis and Cleome than the other predominantly woody perennial Rosid lineages. These findings contribute to our understanding of the dynamics of genome duplication and evolution within one of the most comprehensively surveyed clades of plants, the Rosids, and clarify the complex history of the At-α, At-β, and At-γ duplications of Arabidopsis.
Click&draw selection

In interactive shape modeling, surface selection is one of the basic, cornerstone interaction: this task may be performed hundreds of times by the user for the modification of a single shape. Despite the numerous automatic selection methods introduced in the literature, this remains a cumbersome operation in a number of scenarios, where the user is ultimately asked to paint over everything she wants to select. Without imposing a full visual grammar, we observe that a more effective selection process can be designed around a simple classification of the user interaction: point click, open and close strokes. Our basic idea is to relate this simple classification to a specific set of selection algorithms, targeting the three main classes of surface selections: connected components, parts and patches. We also address the problem of repetitive similar selections by providing an automatic expansion process which captures regions which are detected as similar to the selected one.
A Quick Guide to Organizing Computational Biology Projects

Most bioinformatics coursework focuses on algorithms, with perhaps some components devoted to learning programming skills and learning how to use existing bioinformatics software. Unfortunately, for students who are preparing for a research career, this type of curriculum fails to address many of the day-to-day organizational challenges associated with performing computational experiments. In practice, the principles behind organizing and documenting computational experiments are often learned on the fly, and this learning is strongly influenced by personal predilections as well as by chance interactions with collaborators or colleagues. The purpose of this article is to describe one good strategy for carrying out computational experiments. I will not describe profound issues such as how to formulate hypotheses, design experiments, or draw conclusions. Rather, I will focus on relatively mundane issues such as organizing files and directories and documenting progress. These issues are important because poor organizational choices can lead to significantly slower research progress. I do not claim that the strategies I outline here are optimal. These are simply the principles and practices that I have developed over 12 years of bioinformatics research, augmented with various suggestions from other researchers with whom I have discussed these issues.
Coding theoretic study of secure network coding and quantum secret sharing

The common goal of (classical) secure network coding and quantum secret sharing is to encode secret so that an adversary has as little information of the secret as possible. Both can be described by a nested pair of classical linear codes, while the strategies available to the adversary are different. The security properties of both schemes are closely related to combinatorial properties of the underlying linear codes. We survey connections among them.
Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA

PCNA ubiquitination in response to DNA damage leads to the recruitment of specialized translesion polymerases to the damage locus. This constitutes one of the initial steps in translesion synthesis (TLS)—a critical pathway for cell survival and for maintenance of genome stability. The recent crystal structure of ubiquitinated PCNA (Ub–PCNA) sheds light on the mode of association between the two proteins but also revealed that paradoxically, the ubiquitin surface engaged in PCNA interactions was the same as the surface implicated in translesion polymerase binding. This finding implied a degree of flexibility inherent in the Ub–PCNA complex that would allow it to transition into a conformation competent to bind the TLS polymerase. To address the issue of segmental flexibility, we combined multiscale computational modeling and small angle X-ray scattering. This combined strategy revealed alternative positions for ubiquitin to reside on the surface of the PCNA homotrimer, distinct from the position identified in the crystal structure. Two mutations originally identified in genetic screens and known to interfere with TLS are positioned directly beneath the bound ubiquitin in the alternative models. These computationally derived positions, in an ensemble with the crystallographic and flexible positions, provided the best fit to the solution scattering, indicating that ubiquitin dynamically associated with PCNA and is capable of transitioning between a few discrete sites on the PCNA surface. The finding of new docking sites and the positional equilibrium of PCNA–Ub occurring in solution provide unexpected insight into previously unexplained biological observations.
The program-size complexity of self-assembled squares (extended abstract)

Molecular self-assembly gives rise to a great diversity of complex forms, from crystals and DNA helices to microtubules and holoenzymes. We study a formal model of pseudocrystalline self-assembly, called the Tile Assembly Model, in which a tile may be added to the growing object when the total interaction strength with its neighbors exceeds a parameter Τ. This model has been shown to be Turing-universal. Thus, self-assembled objects can be studied from the point of view of computational complexity. Here, we define the program size complexity of an NxN square to be the minimum number of distinct tiles required to self-assemble the square and no other objects. We study this complexity under the Tile Assembly Model and find a dramatic decrease in complexity, from N^2 tiles to O(log N) tiles, as Τ is increased from 1 (where bonding is noncooperative) to 2 (allowing cooperative bonding). Further, we find that the size of the largest square uniquely produced by a set of n tiles grows faster than any computable function.
Inhibition of marine biofouling by bacterial quorum sensing inhibitors

Seventy eight natural products from chemical libraries containing compounds from marine organisms (sponges, algae, fungi, tunicates and cyanobacteria) and terrestrial plants, were screened for the inhibition of bacterial quorum sensing (QS) using a reporter strain Chromobacterium violaceum CV017. About half of the natural products did not show any QS inhibition. Twenty four percent of the tested compounds inhibited QS of the reporter without causing toxicity. The QS inhibitory activities of the most potent and abundant compounds were further investigated using the LuxR-based reporter E. coli pSB401 and the LasR-based reporter E. coli pSB1075. Midpacamide and tenuazonic acid were toxic to the tested reporters. QS-dependent luminescence of the LasR-based reporter, which is normally induced by N-3-oxo-dodecanoyl-L-homoserine lactone, was reduced by demethoxy encecalin and hymenialdisin at concentrations >6.6 μM and 15 μM, respectively. Hymenialdisin, demethoxy encecalin, microcolins A and B and kojic acid inhibited responses of the LuxR-based reporter induced by N-3-oxo-hexanoyl-L-homoserine lactone at concentrations >0.2 μM, 2.2 μM, 1.5 μM, 15 μM and 36 μM, respectively. The ability to prevent microfouling by one of the compounds screened in this study (kojic acid; final concentrations 330 μM and 1 mM) was tested in a controlled mesocosm experiment. Kojic acid inhibited formation of microbial communities on glass slides, decreasing the densities of bacteria and diatoms in comparison with the control lacking kojic acid. The study suggests that natural products with QS inhibitory properties can be used for controlling biofouling communities.