Miracle-dz/UniFAR-FTUs huggingface dataset:
Cable-Piliated Burkholderia cepaciaBinds to Cytokeratin 13 of Epithelial Cells

ABSTRACT Although the Burkholderia cepacia complex consists of several genomovars, one highly transmissible strain of B. cepacia has been isolated from the sputa of cystic fibrosis (CF) patients throughout the United Kingdom and Canada. This strain expresses surface cable (Cbl) pili and is thought to be the major strain associated with the fatal “cepacia syndrome. ” In the present report we characterize the specific 55-kDa buccal epithelial cell (BEC) protein that binds cable pilus-positive B. cepacia. N-terminal sequences of CNBr-generated internal peptides identified the protein as cytokeratin 13 (CK13). Western blots of BEC extracts probed with a specific monoclonal antibody to CK13 confirmed the identification. Mixed epidermal cytokeratins (which contain CK13), cytokeratin extract from BEC (which consists essentially of CK13 and CK4), and a polyclonal antibody to mixed cytokeratins inhibitedB. cepacia binding to CK13 blots and to normal human bronchial epithelial (NHBE) cells. Preabsorption of the antikeratin antibody with the BEC cytokeratin fraction reversed the inhibitory effect of the antibody. A cytokeratin mixture lacking CK13 was ineffective as an inhibitor of binding. Colocalization of CK13 andB. cepacia by confocal microscopy demonstrated that intact nonpermeabilized NHBE cells express small amounts of surface CK13 and bind Cbl-positive B. cepacia in the same location. Binding to intact NHBE cells was dependent on bacterial concentration and was saturable, whereas a Cbl-negative isolate exhibited negligible binding. These findings raise the possibility that surface-accessible CK13 in respiratory epithelia may be a biologically relevant target for the binding of cable piliated B. cepacia.
Posterior Sparsity in Unsupervised Dependency Parsing

A strong inductive bias is essential in unsupervised grammar induction. In this paper, we explore a particular sparsity bias in dependency grammars that encourages a small number of unique dependency types. We use part-of-speech (POS) tags to group dependencies by parent-child types and investigate sparsity-inducing penalties on the posterior distributions of parent-child POS tag pairs in the posterior regularization (PR) framework of Graca et al. (2007). In experiments with 12 different languages, we achieve significant gains in directed attachment accuracy over the standard expectation maximization (EM) baseline, with an average accuracy improvement of 6.5%, outperforming EM by at least 1% for 9 out of 12 languages. Furthermore, the new method outperforms models based on standard Bayesian sparsity-inducing parameter priors with an average improvement of 5% and positive gains of at least 1% for 9 out of 12 languages. On English text in particular, we show that our approach improves performance over other state-of-the-art techniques.
Meltdown

The output of a differential scanning fluorimetry (DSF) assay is a series of melt curves, which need to be interpreted to get value from the assay. An application that translates raw thermal melt curve data into more easily assimilated knowledge is described. This program, called “Meltdown,” conducts four main activities—control checks, curve normalization, outlier rejection, and melt temperature (Tm) estimation—and performs optimally in the presence of triplicate (or higher) sample data. The final output is a report that summarizes the results of a DSF experiment. The goal of Meltdown is not to replace human analysis of the raw fluorescence data but to provide a meaningful and comprehensive interpretation of the data to make this useful experimental technique accessible to inexperienced users, as well as providing a starting point for detailed analyses by more experienced users.
The thioredoxin system—From science to clinic

The thioredoxin system—formed by thioredoxin reductase and its characteristic substrate thioredoxin—is an important constituent of the intracellular redox milieu. Interactions with many different metabolic pathways such as DNA‐synthesis, selenium metabolism, and the antioxidative network as well as significant species differences render this system an attractive target for chemotherapeutic approaches in many fields of medicine—ranging from infectious diseases to cancer therapy. In this review we will present and evaluate the preclinical and clinical results available today. Current trends in drug development are emphasized. © 2003 Wiley Periodicals, Inc. Med Res Rev, 24, No. 1, 40–89, 2004
SPFD-based wire removal in standard-cell and network-of-PLA circuits

Wire removal is a technique by which the total number of wires between individual circuit nodes is reduced, either by removing wires or replacing them with other new wires. The wire removal techniques we describe in this paper are based on both binary and multivalued sets of pairs of functions to be distinguished (SPFDs). Recently, it was shown that a design style based on a multilevel network of approximately equal-sized programmable logic arrays (PLAs) results in a dense, fast, and crosstalk-resistant layout. This paper describes the application of SPFD-based wire removal techniques for circuit implementations utilizing networks of PLAs as well as standard-cells. In our first set of wire removal experiments (which utilize binary SPFD-based wire removal), we demonstrate that the benefit of SPFD-based wire removal is insignificant when the circuit is mapped using standard cells. We demonstrate that this technique is very effective in the context of a network of PLAs. In the next set of wire removal experiments, we focus only on circuits implemented using a network of PLAs. Three separate wire removal experiments are performed. Wire removal is invoked before clustering the original netlist into a network of PLAs, or after clustering, or both before and after clustering. For wire removal before clustering, binary SPFD-based wire removal is used. For wire removal after clustering, multivalued SPFD-based wire removal is used since the multioutput PLAs can be viewed as multivalued single output nodes. We demonstrate that these techniques are effective. The most effective approach is to perform wire removal both before and after clustering. Using these techniques, we obtain a reduction in placed and routed circuit area of about 11%. This reduction is significantly higher (about 20%) for the larger circuits we used in our experiments.
Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6–7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.
Expurgated Random-Coding Ensembles: Exponents, Refinements, and Connections

This paper studies expurgated random-coding bounds and exponents for channel coding with a given (possibly suboptimal) decoding rule. Variations of Gallager's analysis are presented, yielding several asymptotic and nonasymptotic bounds on the error probability for an arbitrary codeword distribution. A simple nonasymptotic bound is shown to attain an exponent of Csiszár and Körner under constant-composition coding. Using Lagrange duality, this exponent is expressed in several forms, one of which is shown to permit a direct derivation via cost-constrained coding that extends to infinite and continuous alphabets. The method of type class enumeration is studied, and it is shown that this approach can yield improved exponents and better tightness guarantees for some codeword distributions. A generalization of this approach is shown to provide a multiletter exponent that extends immediately to channels with memory.
Nanoparticles isolated from blood: a reflection of vesiculability of blood cells during the isolation process

Background Shedding of nanoparticles from the cell membrane is a common process in all cells. These nanoparticles are present in body fluids and can be harvested by isolation. To collect circulating nanoparticles from blood, a standard procedure consisting of repeated centrifugation and washing is applied to the blood samples. Nanoparticles can also be shed from blood cells during the isolation process, so it is unclear whether nanoparticles found in the isolated material are present in blood at sampling or if are they created from the blood cells during the isolation process. We addressed this question by determination of the morphology and identity of nanoparticles harvested from blood. Methods The isolates were visualized by scanning electron microscopy, analyzed by flow cytometry, and nanoparticle shapes were determined theoretically. Results The average size of nanoparticles was about 300 nm, and numerous residual blood cells were found in the isolates. The shapes of nanoparticles corresponded to the theoretical shapes obtained by minimization of the membrane free energy, indicating that these nanoparticles can be identified as vesicles. The concentration and size of nanoparticles in blood isolates was sensitive to the temperature during isolation. We demonstrated that at lower temperatures, the nanoparticle concentration was higher, while the nanoparticles were on average smaller. Conclusion These results indicate that a large pool of nanoparticles is produced after blood sampling. The shapes of deformed blood cells found in the isolates indicate how fragmentation of blood cells may take place. The results show that the contents of isolates reflect the properties of blood cells and their interaction with the surrounding solution (rather than representing only nanoparticles present in blood at sampling) which differ in different diseases and may therefore present a relevant clinical parameter.
An Algorithmic Approach to the Extensibility of Association Schemes

An association scheme which is associated to a height t presuperscheme is said to be extensible to height t. Smith (1994, 2007) showed that an association scheme X=(Q,\Gamma) of order d:=|Q| is Schurian iff X is extensible to height (d-2). In this work, we formalize the maximal height t_max(X) of an association scheme X as the largest positive integer such that X is extensible to height t (we also include the possibility t_max(X)=\infty, which is equivalent to t_max(X)\ge (d-2)). Intuitively, the maximal height provides a natural measure of how close an association scheme is to being Schurian. For the purpose of computing the maximal height, we introduce the association scheme extension algorithm. On input an association scheme X=(Q,\Gamma) of order d:=|Q| and an integer t such that 1\le t\le (d-2), the association scheme extension algorithm decides in time d^(O(t)) if the scheme X is extensible to height t. In particular, if t is a fixed constant, then the running time of the association scheme extension algorithm is polynomial in the order of X. The association scheme extension algorithm is used to show that all non-Schurian association schemes up to order 26 are completely inextensible, i.e. they are not extensible to a positive height. Via the tensor product of association schemes, the latter result gives rise to a multitude of examples of infinite families of completely inextensible association schemes.
Ezh2 regulates anteroposterior axis specification and proximodistal axis elongation in the developing limb

Specification and determination (commitment) of positional identities precedes overt pattern formation during development. In the limb bud, it is clear that the anteroposterior axis is specified at a very early stage and is prepatterned by the mutually antagonistic interaction between Gli3 and Hand2. There is also evidence that the proximodistal axis is specified early and determined progressively. Little is known about upstream regulators of these processes or how epigenetic modifiers influence axis formation. Using conditional mutagenesis at different time points, we show that the histone methyltransferase Ezh2 is an upstream regulator of anteroposterior prepattern at an early stage. Mutants exhibit posteriorised limb bud identity. During later limb bud stages, Ezh2 is essential for cell survival and proximodistal segment elongation. Ezh2 maintains the late phase of Hox gene expression and cell transposition experiments suggest that it regulates the plasticity with which cells respond to instructive positional cues.
The telomeric transcriptome of Schizosaccharomyces pombe

Eukaryotic telomeres are transcribed into telomeric repeat-containing RNA (TERRA). Telomeric transcription has been documented in mammals, birds, zebra fish, plants and budding yeast. Here we show that the chromosome ends of Schizosaccharomyces pombe produce distinct RNA species. As with budding yeast and mammals, S. pombe contains G-rich TERRA molecules and subtelomeric RNA species transcribed in the opposite direction of TERRA (ARRET). Moreover, fission yeast chromosome ends produce two novel RNA species: C-rich telomeric repeat-containing transcripts (ARIA) and subtelomeric transcripts complementary to ARRET (αARRET). RNA polymerase II (RNAPII) associates with pombe chromosome ends in vivo and the telomeric factor Rap1 negatively regulates this association, as well as the cellular accumulation of RNA emanating from chromosome ends. We also show that the RNAPII subunit Rpb7 and the non-canonical poly(A) polymerases Cid12 and Cid14 are involved in the regulation of TERRA, ARIA, ARRET and αARRET transcripts. We confirm the evolutionary conservation of telomere transcription, and reveal intriguing similarities and differences in the composition and regulation of telomeric transcripts among model organisms.
Ropivacaine-Induced Contraction Is Attenuated by Both Endothelial Nitric Oxide and Voltage-Dependent Potassium Channels in Isolated Rat Aortae

This study investigated endothelium-derived vasodilators and potassium channels involved in the modulation of ropivacaine-induced contraction. In endothelium-intact rat aortae, ropivacaine concentration-response curves were generated in the presence or absence of the following inhibitors: the nonspecific nitric oxide synthase (NOS) inhibitor N ω-nitro-L-arginine methyl ester (L-NAME), the neuronal NOS inhibitor N ω-propyl-L-arginine hydrochloride, the inducible NOS inhibitor 1400W dihydrochloride, the nitric oxide-sensitive guanylyl cyclase (GC) inhibitor ODQ, the NOS and GC inhibitor methylene blue, the phosphoinositide-3 kinase inhibitor wortmannin, the cytochrome p450 epoxygenase inhibitor fluconazole, the voltage-dependent potassium channel inhibitor 4-aminopyridine (4-AP), the calcium-activated potassium channel inhibitor tetraethylammonium (TEA), the inward-rectifying potassium channel inhibitor barium chloride, and the ATP-sensitive potassium channel inhibitor glibenclamide. The effect of ropivacaine on endothelial nitric oxide synthase (eNOS) phosphorylation in human umbilical vein endothelial cells was examined by western blotting. Ropivacaine-induced contraction was weaker in endothelium-intact aortae than in endothelium-denuded aortae. L-NAME, ODQ, and methylene blue enhanced ropivacaine-induced contraction, whereas wortmannin, N ω-propyl-L-arginine hydrochloride, 1400W dihydrochloride, and fluconazole had no effect. 4-AP and TEA enhanced ropivacaine-induced contraction; however, barium chloride and glibenclamide had no effect. eNOS phosphorylation was induced by ropivacaine. These results suggest that ropivacaine-induced contraction is attenuated primarily by both endothelial nitric oxide and voltage-dependent potassium channels.
Communication logics for networked control systems

This paper addresses the control of spatially distributed processes. We utilize a distributed architecture in which multiple local controllers coordinate their efforts through a data network that allows information exchange. We focus our work on linear time invariant processes disturbed by Gaussian white noise and propose several logics to determine when the local controllers should communicate. We provide conditions under which these logics guarantee boundedness and investigate the trade-off between the amount of information exchanged and the performance achieved. The resulting closed-loop systems evolve according to stochastic differential equations with resets triggered by stochastic counters. This type of stochastic hybrid system seems to be interesting on its own. The theoretical results are validated through Monte Carlo simulations.
Experimental and Automated Analysis Techniques for High-resolution Electrical Mapping of Small Intestine Slow Wave Activity

Background/Aims Small intestine motility is governed by an electrical slow wave activity, and abnormal slow wave events have been associated with intestinal dysmotility. High-resolution (HR) techniques are necessary to analyze slow wave propagation, but progress has been limited by few available electrode options and laborious manual analysis. This study presents novel methods for in vivo HR mapping of small intestine slow wave activity. Methods Recordings were obtained from along the porcine small intestine using flexible printed circuit board arrays (256 electrodes; 4 mm spacing). Filtering options were compared, and analysis was automated through adaptations of the falling-edge variable-threshold (FEVT) algorithm and graphical visualization tools. Results A Savitzky-Golay filter was chosen with polynomial-order 9 and window size 1.7 seconds, which maintained 94% of slow wave amplitude, 57% of gradient and achieved a noise correction ratio of 0.083. Optimized FEVT parameters achieved 87% sensitivity and 90% positive-predictive value. Automated activation mapping and animation successfully revealed slow wave propagation patterns, and frequency, velocity, and amplitude were calculated and compared at 5 locations along the intestine (16.4 ± 0.3 cpm, 13.4 ± 1.7 mm/sec, and 43 ± 6 µV, respectively, in the proximal jejunum). Conclusions The methods developed and validated here will greatly assist small intestine HR mapping, and will enable experimental and translational work to evaluate small intestine motility in health and disease.
Wearable Soft Robotic Device Supports the Failing Heart in vivo

Soft robots fabricated from low modulus, compliant materials hold significant potential for medical device applications that warrant safe, synergistic interaction with humans. We have recently applied this technology to develop ventricular assistive devices (VADs) that can externally massage the failing heart [1][2]. In heart failure (HF), the heart cannot provide sufficient pumping support to meet the metabolic needs of the body. For patients in end-stage HF, impeller-based VADs can be implanted to supplement heart function. However, these devices are associated with complications including bleeding and thromboembolism as a result of blood clots that form on the non-biologic surfaces of the device. Direct cardiac compression devices are an alternative form of VAD which use an inflatable cuff positioned around the ventricles to apply compressive forces during systole. This allows augmentation of cardiac pumping function without the need to contact the blood directly [3]. Based on this principle, we developed a soft robotic sleeve that fits around the heart and emulates the native cardiac muscle motion in order to restore function to the failing heart [1]. Subsequently, we developed a wearable soft robotic device which could be mechanically coupled to the ventricles [2]. This work demonstrated that actuator synchronization and mechanical coupling to the heart are significant factors for augmenting cardiac output. Here, we report the use of this wearable soft robotic device [2] with additional in vivo data to demonstrate repeatable performance.
Neurodevelopmental Outcomes of Infants Born Prematurely

ABSTRACT. Long-term follow-up of infants born prematurely is necessary to determine neurodevelopmental outcomes, particularly with the expansion of interest from major disabilities to high prevalence/low severity dysfunctions. Models of pathogenesis include changes due to developmental disruptions and to injury, the magnitude and type of change influenced by the infant's age, and central nervous system recovery and reorganization. Alterations in neurogenesis, migration, myelination, cell death, and synaptogenesis occur even in the absence of insult. Despite increased knowledge regarding these processes, the functional significance of brain abnormalities is unclear. Because of methodologic problems in follow-up studies, it is difficult to characterize outcome definitively. Nonetheless, an acceptable degree of agreement across studies is found with regard to specific neurodevelopmental outcomes: motor/neurologic function, visuomotor integrative skills, IQ, academic achievement, language, executive function, and attention-deficit hyperactivity disorder/behavioral issues. In general, children born prematurely have more problems in these areas than do their normal birth weight counterparts. Suggestions for improved analyses and clarification of outcomes include use of cluster analysis, structural equation modeling, growth curve analysis, developmental epidemiologic approaches, and better control of background variables using risk indexes and factor scores. Better assessment techniques measuring functions documented to be at higher risk of problems are discussed.