Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of epidermal cell fate in Arabidopsis roots: the importance of multiple feedback loops

The specification of distinct cell types in multicellular organisms is accomplished via establishment of differential gene expression. A major question is the nature of the mechanisms that establish this differential expression in time and space. In plants, the formation of the hair and non-hair cell types in the root epidermis has been used as a model to understand regulation of cell specification. Recent findings show surprising complexity in the number and the types of regulatory interactions between the multiple transcription factor genes/proteins influencing root epidermis cell fate. Here, we describe this regulatory network and the importance of the multiple feedback loops for its establishment and maintenance.
Neuroendocrine Differentiation in the Progression of Prostate Cancer: An Update on Recent Developments

Neuroendocrine (NE) differentiation, either benign or malignant, is the hallmark of prostate cancer (PCa). Clusters of malignant NE cells are found in most prostate cancer cases. NE differentiation is among the non-mutually exclusive theories proposed to explain the progression to androgen independence of PCa. NE differentiation is usually associated with an increased aggressivity and invasiveness of prostate tumors and a poor prognosis. This review aims to present an overview of current knowledge on neuroendocrine differentiation in PCa to improve our understanding of tumour progression and androgen independence. The NE component represents an important therapeutic axis. Development of new generation of drugs that selectively target NE-like cells may lead to the development of new therapeutic modalities for advanced and hormone-refractory PCa.
The /spl mu/Jini proxy architecture for impromptu mobile services

Wireless hotspots and broadband coverage are permeating the globe giving rise to interesting spontaneous networking scenarios. The discovery and delivery of the most relevant and suitable services in a spontaneous network is a problem of paramount importance. In this paper, we propose an architecture that can support context-aware service discovery and delivery for resource-constrained mobile devices. At the heart of the architecture is the muJini proxy which mediates the discovery and delivery processes. Its delivery subsystem provides thin-client based adaptation for fat service delivery that does not fit into thin client devices. To demonstrate its effectiveness, we developed a proof-of-concept prototype, focusing first on J2ME smart-phones
Selectivity and gating of the type L potassium channel in mouse lymphocytes

Type l voltage-gated K+ channels in murine lymphocytes were studied under voltage clamp in cell-attached patches and in the whole-cell configuration. The kinetics of activation of whole-cell currents during depolarizing pulses could be fit by a single exponential after an initial delay. Deactivation upon repolarization of both macroscopic and microscopic currents was mono-exponential, except in Rb-Ringer or Cs- Ringer solution in which tail currents often displayed "hooks," wherein the current first increased or remained constant before decaying. In some cells type l currents were contaminated by a small component due to type n K+ channels, which deactivate approximately 10 times slower than type l channels. Both macroscopic and single channel currents could be dissected either kinetically or pharmacologically into these two K+ channel types. The ionic selectivity and conductance of type l channels were studied by varying the internal and external permeant ion. With 160 mM K+ in the cell, the relative permeability calculated from the reversal potential with the Goldman-Hodgkin-Katz equation was K+ (identical to 1.0) greater than Rb+ (0.76) greater than NH4+ = Cs+ (0.12) much greater than Na+ (less than 0.004). Measured 30 mV negative to the reversal potential, the relative conductance sequence was quite different: NH4+ (1.5) greater than K+ (identical to 1.0) greater than Rb+ (0.5) greater than Cs+ (0.06) much greater than Na+, Li+, TMA+ (unmeasurable). Single channel current rectification resembled that of the whole-cell instantaneous I-V relation. Anomalous mole-fraction dependence of the relative permeability PNH4/PK was observed in NH4(+)- K+ mixtures, indicating that the type l K+ channel is a multi-ion pore. Compared with other K+ channels, lymphocyte type l K+ channels are most similar to "g12" channels in myelinated nerve.
The effect of Saccharomyces cerevisiae and Aspergillus oryzae on the digestion of the cell wall fraction of a mixed diet in defaunated and refaunated sheep rumen.

The objective of this study was to determine the effect of two probiotics, Saccharomyces cerevisiae (SC) and Aspergillus oryzae (AO), without their culture medium, on the digestion of plant cell wall components in sheep that had been successively defaunated and refaunated. Six sheep fitted with large rumen cannulae were used to study 1) defaunated sheep with no probiotic, 2) defaunated sheep with SC or AO, 3) refaunated sheep with no probiotic, 4) refaunated sheep with SC or AO. The apparent digestibility of the plant cell walls was not altered (P > 0.05) by the probiotics in defaunated sheep but was increased (P < 0.05) with SC (+16%) in refaunated sheep. Simultaneously, SC stimulated the growth of the protozoal population in the rumen. As noted in most previous experiments, the positive effect of the presence of protozoa on plant cell wall digestion (P < 0.001) was confirmed here. The effect (P > 0.05) of SC or AO on in situ ADF digestion was either not significant or negative in defaunated rumens, whereas it became positive in refaunated rumen after a residence time of 12 h. The improvement of in situ ADF digestion due to the presence of protozoa was significant (P < 0.05 for NDF; P < 0.001 for ADF). However, we could not determine whether this was a direct effect of protozoa or an indirect effect operating via bacteria. The limits of the nylon bag technique for evaluating the microbial activity are discussed in relation to the ability of protozoa to enter and grow in the bags, and the pH regulation inside the bags. The pH values below 5.5 noted inside the bags can significantly alter the bacterial and protozoal populations and limit the validity of the technique. SC increased (P < 0.05) the specific activity of CMCase and xylanase of the solid-adherent bacteria (SAB) isolated from the rumen digesta of refaunated sheep. Stimulation of both the bacterial activity and protozoa numbers could explain the positive effect of SC on cell wall digestion in the rumen since the modelling of marker excretion in faeces showed that the ruminal mean retention time of hay measured from the model of Danhoa et al. was not modified (P > 0.05) by either refaunation or the presence of probiotics. AO increased (P < 0.05) the total retention time of the solid particles in the whole digestive tract and increased the ruminal liquid volume in the refaunated animals but it had no effect on the protozoa population or on the polysaccharidase activity of the SAB, which could explain the absence of effect of AO on the total digestibility of plant cell walls. Both probiotics decreased the liquid turnover in defaunated rumens (P < 0.05) but neither had any effect (P > 0.05) on this parameter after refaunation. The improvement of plant cell wall degradation in the whole digestive tract is probably due to a stimulation of digestion at the rumen level as indicated by the higher activity of the SAB in rumen digesta and the growth of protozoa.
A novel N440K sodium channel mutation causes myotonia with exercise-induced weakness - exclusion of CLCN1 exon deletion/duplication by MLPA

We report a 4-generation Turkish family with 10 affected members presenting with myotonia and potassium- and exerciseinduced paralytic attacks. The clinical presentation was neither typical for the chloride channel myotonias Thomsen and Becker nor for the separate sodium channel myotonia entities potassiumaggravated myotonia, paramyotonia congenita, and hyperkalemic periodic paralysis. It is best described by a combination of potassium-aggravated myotonia and hyperkalemic periodic paralysis. We excluded exonic chloride channel mutations including CLCN1 exon deletion/duplication by MLPA. Instead we identified a novel p.N440K sodium channel mutation that is located at the inner end of segment S6 of repeat I. We discuss the genotype phenotype relation.
Design and Evaluation of Dynamically Specialized Datapaths with the DySER Architecture

Due to limits in technology scaling, energy efficiency of logic devices is decreasing in successive generations. To provide continued performance improvements without increasing power, regardless of the sequential or parallel nature of the application, microarchitectural energy efficiency must improve. We propose Dynamically Specialized Execution to improve the energy efficiency of general purpose programmable processors. The key insights of this work are the following. First, applications execute in phases and these phases can be determined by creating a path-tree of basic-blocks rooted at the inner-most loop. Second, specialized datapaths corresponding to these path-trees can be constructed by interconnecting a set of heterogeneous computation units with a circuit-switched network, which we refer to as DySER blocks. These blocks can be easily integrated with a conventional processor. A synthesized RTL implementation using an industry 55nm technology library shows a 64-functional-unit DySER block occupies approximately the same area as a 64 KB single-ported SRAM and can execute at 2 GHz. Using the GCC compiler, we identify path-trees and evaluate the PARSEC, SPEC and Parboil benchmarks suites, using our extensions for mapping code to DySER. Our results show that in most cases two DySER blocks can achieve the same performance (within 5%) as having a specialized block for each path-tree. A 64-FU DySER block can cover 12% to 100% of the dynamically executed instruction stream. When integrated with a dual-issue out-of-order processor, two DySER blocks provide geometric mean speedup of 2.1X (1.15X to 10X), and geometric mean energy reduction of 40% (up to 70%), and 60% energy reduction if no performance improvement is required.
Survival analysis of critically ill dogs with hypotension with or without hyperlactatemia: 67 cases (2006-2011).

OBJECTIVE To determine whether critically ill hypotensive dogs without hyperlactatemia have the same prognosis as critically ill hypotensive dogs with hyperlactatemia. DESIGN Retrospective case series. ANIMALS 67 critically ill dogs with hypotension. PROCEDURES Medical records were searched from January 2006 through December 2011 for dogs that were hospitalized in the intensive care unit and that had hypotension and measurement of blood lactate concentration. Blood lactate concentration, systolic blood pressure, and survival rate were compared between hypotensive dogs with and without hyperlactatemia. RESULTS 19 of 67 (28%) dogs survived and were discharged from the hospital. Hypotensive dogs without hyperlactatemia had a significantly higher systolic blood pressure and were 3.23 (95% confidence interval, 1.04 to 9.43) times as likely to survive, compared with hypotensive dogs with hyperlactatemia. Age, weight, severity of clinical illness, and duration of hospitalization did not differ significantly between hypotensive dogs with and without hyperlactatemia. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that hypotensive dogs without hyperlactatemia had a better prognosis and chance of surviving to hospital discharge than did hypotensive dogs with hyperlactatemia. Because blood lactate concentration was negatively associated with systolic blood pressure and survival probability, it may be a useful metric for determining the prognosis of hypotensive dogs.
Tool integration, collaboration and user interaction issues in component-based software architectures

Component based software architectures are becoming increasingly popular solutions for use in a wide range of software applications. Particular areas in which these architectures may provide improved software development support include tool integration, distribution and collaborative work support, and human interaction and end user configuration. However, a number of open research issues exist to do with the deployment of component based solutions in these areas. We review our recent research experiences in deploying component based solutions in these problem domains, and overview potential research directions.
Design of Serially Concatenated Systems Depending on the Block Length

We study the convergence behavior of iterative decoding for a number of serially concatenated systems, such as a serially concatenated code, coded data transmission over a n inter-symbol interference channel, bit-interleaved cod ed modulation, or trellis-coded modulation. We rederive an ex isting analysis technique called EXIT chart, simplify its construction, and construct simple irregular codes to impr ove the convergence of iterative decoding. An efficient and optimal optimization algorithm yields systems, which appr oach information theoretic limits very closely. However, these systems exhibit their performance only for very long b lock lengths. To overcome this problem, we optimize the decoding convergence after a fixed, finite amount of iteratio ns yielding systems, which perform very well for short block lengths, too. As an example, optimal system configurat ions for communication over an additive white Gaussian noise channel are presented.
Automated Pharmacophore Identification for Large Chemical Data Sets1

The identification of three-dimensional pharmacophores from large, heterogeneous data sets is still an unsolved problem. We developed a novel program, SCAMPI (statistical classification of activities of molecules for pharmacophore identification), for this purpose by combining a fast conformation search with recursive partitioning, a data-mining technique, which can easily handle large data sets. The pharmacophore identification process is designed to run recursively, and the conformation spaces are resampled under the constraints of the evolving pharmacophore model. This program is capable of deriving pharmacophores from a data set of 1000-2000 compounds, with thousands of conformations generated for each compound and in less than 1 day of computational time. For two test data sets, the identified pharmacophores are consistent with the known results from the literature.
Murine Coronavirus Cell Type Dependent Interaction with the Type I Interferon Response

Coronaviruses infect many species of animal including humans, causing acute and chronic diseases of many organ systems. Murine coronavirus, mouse hepatitis virus (MHV) infection of the mouse, provides animal models for the study of central nervous system disease, including encephalitis and demyelinating diseases such as Multiple Sclerosis and for hepatitis. While there are many studies of the adaptive immune response to MHV, there has until recently been scant information on the type I interferon (IFN) response to MHV. The relationship between MHV and the IFN-α/β response is paradoxical. While the type I IFN response is a crucial aspect of host defense against MHV in its natural host, there is little if any induction of IFN following infection of mouse fibroblast cell lines in vitro. Furthermore, MHV is relatively resistant to the antiviral effects of IFN-α/β in mouse fibroblast cell lines and in human 293T cells. MHV can, under some circumstances, compromise the antiviral effects of IFN signaling. The nucleocapsid protein as well as the nsp1 and nsp3 proteins of MHV has been reported to have IFN antagonist activity. However, in primary cell types such as plasmacytoid dendritic cells (pDC) and macrophages, IFN is induced by MHV infection and an antiviral state is established. Other primary cell types such as neurons, astrocytes and hepatocytes fail to produce IFN following infection and, in vivo, likely depend on IFN produced by pDCs and macrophages for protection from MHV. Thus MHV induction of IFN-α/β and the ability to induce an antiviral state in response to interferon is extremely cell type dependent. IFN induced protection from MHV pathogenesis likely requires the orchestrated activities of several cell types, however, the cell types involved in limiting MHV replication may be different in the liver and in the immune privileged CNS.
Interaction Relation Ontology Learning

Ontology is widely used in semantic computing and reasoning, and various biomedicine ontologies have become institutionalized to make the heterogeneous knowledge computationally amenable. Relation words, especially verbs, play an important role when describing the interaction between biological entities in molecular function, biological process, and cellular component; however, comprehensive research and analysis are still lacking. In this article, we propose an automatic method to build interaction relation ontology by investigating relation verbs, analyzing the syntactic relation of PubMed abstracts to perform relation vocabulary expansion, and integrating WordNet into our method to construct the hierarchy of relation vocabulary. Five attributes are populated automatically for each word in interaction relation ontology. As a result, the interaction relation ontology is constructed; it contains a total of 963 words and covers the most relation words used in existing methods of proteins interaction relation.
Design of Schottky Contacts for Optimum Performance of Thin-Film Silicon Solar Cells

A full-scale model combining TCAD simulations with circuit modeling of p-type window layers in thin-film silicon solar cells is validated by experiment. The results demonstrate that Schottky contacts with a barrier height greater than 0.5 eV cause a kink in the simulated J-V characteristics that represents a considerable reduction of the open-circuit voltage when thermionic emission is the dominant transport mechanism. An optimum cell can be designed by facilitating tunneling mechanism through the Schottky barrier via an adjustment of the doping concentration of the semiconductor or by introducing thin μc-Si:H(p) in order to lower the barrier height between ZnO and a-Si:H(p). In such a case, however, the narrower bandgap of μc-Si:H compared with that of a-Si:H, and the misalignment of the energy bands between μc-Si:H(p) and a-Si:H(i), also compromise the short-circuit current and open-circuit voltage of the cell, respectively. Optimum interfaces for our 15-nm window layer are found when a combined μc-Si:H(p)/a-Si:H(p) with a 4/11-nm thickness ratio is used. A general circuit model for solar cells that accounts for the effects of nonohmic contacts is demonstrated. The ideality factor “n2 ” of the Schottky junction of the contact indicates the transport mechanism at the interface with values less than 0.5 eV having no impact on the cell performance.
The Misperception of Inflation by Irish Consumers

How people perceive and forecast inflation has the potential to impact on a range of economic outcomes. We reveal large, systematic overestimation of inflation by Irish consumers, which varies by social group. In contrast to previous work in this area, our models suggest the upward bias and the variation by social group should be considered substantially separate phenomena. We also offer evidence that inflation misperceptions are linked to attitudes and intentions with respect to consumption and saving and, hence, are likely to affect household decision-making. The findings therefore raise issues regarding the relationship between financial literacy and consumer behaviour.
Screening for Methicillin Resistant Staphylococcus aureus (MRSA) colonization in health care workers, working in critical care areas at a tertiary care hospital, Karnataka, India

Introduction: Rise of MRSA infection in hospitals is a matter of concern. MRSA infection in hospitals is acquired either by MRSA colonizers i.e. health care worker or fomites which are heavily contaminated with MRSA. It is necessary to detect MRSA carriers among health care workers in order to cut down the increasing rate of MRSA infection in hospitalized patients, especially in intensive care units. Aims & objectives: To find the MRSA carriage rate among health care workers in intensive care units. To find out the antibiotic susceptibility pattern in these MRSA isolates. Materials & methods: Hand & nasal swabs were collected from the health care workers of critical care units. The isolation of MRSA & their antimicrobial susceptibility were carried out by standard bacteriological procedures. Result: MRSA carriage rate was 6.35% by nasal swab method whereas it was 4.76% by hand swab method. MRSA isolates were resistant to most of the antibiotics. Conclusion: Strict adherence to infection control practices is the single most important factor in preventing MRSA infection. Simple preventive measures like hand washing before & after patient examination, the use of sterile aprons & masks can reduce the disease transmission rate considerably.
Cardiac and renal protective effects of urate-lowering therapy

Patients with gout often have co-morbidities such as cardiovascular disease, renal failure and metabolic syndrome components. Some studies, but not all, have suggested that hyperuricaemia and gout are associated with increased risk of myocardial infarction, renal failure and death primarily because of increased risk of cardiovascular events. Therefore, knowledge of the effects of urate-lowering therapy (ULT) on co-morbidities, in particular cardiovascular events and chronic kidney disease, is crucial. Randomized controlled trials (RCTs) have suggested that allopurinol, a xanthine oxidase inhibitor, could improve exercise capacity in patients with chronic stable angina and could decrease blood pressure in adolescents. In contrast, a well-designed RCT found no effect of allopurinol in patients with heart failure. The impact of ULT in patients with chronic kidney disease is unclear. Some RCTs found that allopurinol could slow the decline in kidney function, whereas a recent controlled trial found no benefit of febuxostat. Large randomized placebo-controlled trials are warranted to confirm or not the benefit of ULT on co-morbidities.
Mathematical control theory [Book Review]

Important topics and new insights in mathematical control theory associated with the work of Roger W. Brockett are surveyed in nine articles by 13 distinguished researchers who have been associated with him. The occasion was the celebration of his 60th birthday. Other items include a Foreword by Sanjoy Mitter, a Preface by the editors, and Brockett’s Curriculum Vitae, all of which give some idea of how many control theorists and practitioners have profited from his generosity with good ideas. The chapters of Mathematical Control Theory are independent surveys; five of them share the concerns and notation of mechanical systems and the geometric approach to control systems. They introduce currently significant research areas to readers who have had some graduate study in control theory or related areas, such as mechanics, mathematics, or robotics, and are good guides to the literature. They comprise the following: 1) Path Integrals and Stabilityby Jan Willems; 2) The Estimation Algebra of Nonlinear Filtering Systems by Wing S. Wong and Stephen S. T. Yau; 3) Feedback Linearizationby Arthur J. Krener; 4) On the Global Analysis of Linear Systems by Christopher I. Byrnes; 5) Geometry and Optimal Control by Hector J. Sussmann; 6) Languages, Behaviors, Hybrid Architectures, and Motion Control by Vikram Manikonda, P. S. Krishnaprasad, and James Hendler; 7) Optimal Control, Geometry, and Mechanics by Velimir Jurdjevic; 8) Optimal Control, Optimization, and Analytical Mechanics by Anthony M. Bloch and Peter E. Crouch; 9) The Geometry of Controlled Mechanical Systems by John Baillieul.