Miracle-dz/UniFAR-FTUs huggingface dataset:
Envelope-Function-Based Transport Simulation of a Graphene Ribbon With an Antidot Lattice

We have performed numerical simulations to study the effect of a regular lattice of antidots on the conductance, and in particular on the gap, of an armchair graphene ribbon. We have used an envelope-function approach, with a nonzero mass term mimicking the presence of the antidots. With a very efficient simulation procedure, consisting in a reciprocal space solution of the envelope-function equation in the transverse direction followed by a recursive scattering matrix calculation in the transport direction, we have been able to analyze the impact of the different geometrical parameters characterizing the structure. We have observed that the conductance of the device rapidly reaches an asymptotic value when the length of the region containing the antidot lattice is increased. The dependence of the energy gap on the geometrical features of the antidot lattice is quite similar to that observed in unconfined graphene, excluding the cases of very small or distant antidots, for which the energy gap of the pristine graphene ribbons is recovered. The tilt angle of the lattice with respect to the transport direction has a negligible influence on the gap, which is also quite robust with respect to the introduction of disorder in the antidot lattice.
Preoperative risk factors for the development of acute renal failure in cardiac surgery.

OBJECTIVE To evaluate clinical risk factors for the development of Acute Renal Failure (ARF) in patients who undergo cardiac surgery. METHOD Over a period of 21 consecutive months, one hundred and fifty patients who underwent cardiac surgery were studied. There was a slight prevalence of men (57%) and the average age was 56 +/- 14.8 years. Sixty-six percent presented with coronary artery disease as the main diagnosis and 34% valvular heart disease. The median preoperative serum creatinine was 1.1 mg/dL. ARF was defined as a 30% increase in serum creatinine above baseline. The protocol of clinical variables initiated 48 hours before the surgical procedure and finished 48 hours after it and included cardiological and non-cardiological variables and laboratory data. RESULTS ARF was present in 34% of the cases. After multivariate analysis, being a man and the presence of peripheral vascular disease were identified as the preoperative factors. CONCLUSION The results obtained in this study identified some risk factors for the development of ARF in cardiac surgery, suggesting simple clinical procedures that may prevent renal dysfunction in these situations and, consequently, reduce the mortality rate. In the present study, the sample size has possibly impeded the identification of other significant risk factors.
Association between cerebral palsy and microscopically verified placental infarction in extremely preterm infants

Previously, cerebral palsy has been associated with placental infarctions diagnosed macroscopically by midwifes. However, the risk of misclassification of infarctionsis is high without a histological verification. Therefore, the objective of this study was to study placental histopathology in relation to developmental outcome at 2.5 years corrected age in a population born extremely preterm.
Predicted Structure and Domain Organization of Rotavirus Capping Enzyme and Innate Immune Antagonist VP3

ABSTRACT Rotaviruses and orbiviruses are nonturreted Reoviridae members. The rotavirus VP3 protein is a multifunctional capping enzyme and antagonist of the interferon-induced cellular oligoadenylate synthetase-RNase L pathway. Despite mediating important processes, VP3 is the sole protein component of the rotavirus virion whose structure remains unknown. In the current study, we used sequence alignment and homology modeling to identify features common to nonturreted Reoviridae capping enzymes and to predict the domain organization, structure, and active sites of rotavirus VP3. Our results suggest that orbivirus and rotavirus capping enzymes share a domain arrangement similar to that of the bluetongue virus capping enzyme. Sequence alignments revealed conserved motifs and suggested that rotavirus and orbivirus capping enzymes contain a variable N-terminal domain, a central guanine-N7-methyltransferase domain that contains an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5′-triphosphatase domain. Sequence conservation and homology modeling suggested that the insertion in the guanine-N7-methyltransferase domain is a ribose-2′-O-methyltransferase domain for most rotavirus species. Our analyses permitted putative identification of rotavirus VP3 active-site residues, including those that form the ribose-2′-O-methyltransferase catalytic tetrad, interact with S-adenosyl-l-methionine, and contribute to autoguanylation. Previous reports have indicated that group A rotavirus VP3 contains a C-terminal 2H-phosphodiesterase domain that can cleave 2′-5′ oligoadenylates, thereby preventing RNase L activation. Our results suggest that a C-terminal phosphodiesterase domain is present in the capping enzymes from two additional rotavirus species. Together, these findings provide insight into a poorly understood area of rotavirus biology and are a springboard for future biochemical and structural studies of VP3. IMPORTANCE Rotaviruses are an important cause of severe diarrheal disease. The rotavirus VP3 protein caps viral mRNAs and helps combat cellular innate antiviral defenses, but little is known about its structure or enzymatic mechanisms. In this study, we used sequence- and structure-based alignments with related proteins to predict the structure of VP3 and identify enzymatic domains and active sites therein. This work provides insight into the mechanisms of rotavirus transcription and evasion of host innate immune defenses. An improved understanding of these processes may aid our ability to develop rotavirus vaccines and therapeutics.
An improved resource allocation algorithm for testability

A weighted compatibility graph-based resource allocation algorithm (WCGRAA) is proposed in this paper and a weight formula concerning testability and interconnection cost is given. An improved weighted clique partition algorithm is used to handle weighted compatibility graph, thereby achieving the goal to give consideration both to circuit testability and interconnection cost. Experimental results show that the resource allocation algorithm proposed in this paper can improve circuit testability and interconnection cost.1.
Boundary stabilization and matched disturbance rejection of hyperbolic PDE systems: A sliding-mode approach

This paper deals with the robust boundary stabilization problem of hyperbolic partial differential equations (PDEs) subject to boundary uncertainties. These systems include a second-order undamped wave equation and a first-order delay system. By taking the integral transformation, we obtain a nominal PDE with asymptotic stability in the new coordinates when an appropriate boundary control input is applied. The associated Lyapunov function can then be used for designing an infinite-dimensional sliding surface, on which the system exhibits exponential stability, invariant of the bounded matched disturbance. A continuous sliding-mode boundary control law satisfied with reaching condition is employed to ensure the system's will reach the proposed sliding surface within finite time. Simulation results of a second-order wave equation are provided to demonstrate and compare with the other control schemes.
What should be done in an operating room when an insulinoma cannot be found?

Insulinoma is the most common (functioning) islet cell tumour of the pancreas and is highly curable with accurate localization and precise extirpation of the often benign, solitary lesion. Although previous reports describe high success rates without pre‐operative localization, more recent recognition of the overlap among causes of endogenous hyperinsulinism, coupled with the deleterious long‐term effects of blind distal pancreatectomy and re‐operation, mandate the need for precise pre‐operative localization or regionalization of the tumour(s). If these criteria have not been met and the surgeon finds him/herself in the operating room without a localized or regionalized tumour, the operation should be concluded without resection, the diagnosis reconfirmed, and a calcium stimulation test performed. At experienced centres, this can be often carried out within 24–48 h and the patient returned to the operating room for a gradient‐guided resection. Intraoperative venous sampling for insulin might be an option in the future but its accuracy has not been validated in sufficient numbers of patients to date.
Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples

ABSTRACT Little is known about bacterial communities that colonize mucosal surfaces in the human gastrointestinal tract, but they are believed to play an important role in host physiology. The objectives of this study were to investigate the compositions of these populations in the distal small bowel and colon. Healthy mucosal tissue from either the terminal ileum (n = 6) or ascending (n = 8), transverse (n = 8), or descending colon (n = 4) of 26 patients (age, 68.5 ± 1.2 years [mean ± standard deviation]) undergoing emergency resection of the large bowel was used to study these communities. Mucosa-associated eubacteria were characterized by using PCR-denaturing gradient gel electrophoresis (DGGE), while real-time PCR was employed for quantitative analysis. Mucosal communities were also visualized in situ using confocal laser scanning microscopy. DGGE banding profiles from all the gut regions exhibited at least 45% homology, with five descending colon profiles clustering at ca. 75% concordance. Real-time PCR showed that mucosal bacterial population densities were highest in the terminal ileum and that there were no significant differences in overall bacterial numbers in different parts of the colon. Bifidobacterial numbers were significantly higher in the large bowel than in the terminal ileum (P = 0.006), whereas lactobacilli were more prominent in the distal large intestine (P = 0.019). Eubacterium rectale (P = 0.0004) and Faecalibacterium prausnitzii (P = 0.001) were dominant in the ascending and descending colon. Site-specific colonization in the gastrointestinal tract may be contributory in the etiology of some diseases of the large intestine.
Query Expansion with Enriched User Profiles for Personalized Search Utilizing Folksonomy Data

Query expansion has been widely adopted in Web search as a way of tackling the ambiguity of queries. Personalized search utilizing folksonomy data has demonstrated an extreme vocabulary mismatch problem that requires even more effective query expansion methods. Co-occurrence statistics, tag-tag relationships, and semantic matching approaches are among those favored by previous research. However, user profiles which only contain a user's past annotation information may not be enough to support the selection of expansion terms, especially for users with limited previous activity with the system. We propose a novel model to construct enriched user profiles with the help of an external corpus for personalized query expansion. Our model integrates the current state-of-the-art text representation learning framework, known as word embeddings, with topic models in two groups of pseudo-aligned documents. Based on user profiles, we build two novel query expansion techniques. These two techniques are based on topical weights-enhanced word embeddings, and the topical relevance between the query and the terms inside a user profile, respectively. The results of an in-depth experimental evaluation, performed on two real-world datasets using different external corpora, show that our approach outperforms traditional techniques, including existing non-personalized and personalized query expansion methods.
LONO1 Encoding a Nucleoporin Is Required for Embryogenesis and Seed Viability in Arabidopsis1[C][W][OA]

Early embryogenesis in Arabidopsis (Arabidopsis thaliana) is distinguished by a predictable pattern of cell divisions and is a good system for investigating mechanisms of developmental pattern formation. Here, we identified a gene called LONO1 (LNO1) in Arabidopsis in which mutations can abolish the first asymmetrical cell division of the zygote, alter planes and number of cell divisions in early embryogenesis, and eventually arrest embryo development. LNO1 is highly expressed in anthers of flower buds, stigma papilla of open flowers, and embryo and endosperm during early embryogenesis, which is correlated with its functions in reproductive development. The homozygous lno1-1 seed is not viable. LNO1, a homolog of the nucleoporin NUP214 in human (Homo sapiens) and Nup159 in yeast (Saccharomyces cerevisiae), encodes a nucleoporin protein containing phenylalanine-glycine repeats in Arabidopsis. We demonstrate that LNO1 can functionally complement the defect in the yeast temperature-sensitive nucleoporin mutant nup159. We show that LNO1 specifically interacts with the Arabidopsis DEAD-box helicase/ATPase LOS4 in the yeast two-hybrid assay. Furthermore, mutations in AtGLE1, an Arabidopsis homolog of the yeast Gle1 involved in the same poly(A) mRNA export pathway as Nup159, also result in seed abortion. Our results suggest that LNO1 is a component of the nuclear pore complex required for mature mRNA export from the nucleus to the cytoplasm, which makes LNO1 essential for embryogenesis and seed viability in Arabidopsis.
Is Dolphin Morbillivirus Virulent for White-Beaked Dolphins (Lagenorhynchus albirostris)?

The virulence of morbilliviruses for toothed whales (odontocetes) appears to differ according to host species. In 4 species of odontocetes, morbilliviruses are highly virulent, causing large-scale epizootics with high mortality. In 8 other species of odontocetes, including white-beaked dolphins (Lagenorhynchus albirostris), morbilliviruses have been found as an incidental infection. In these species, the virulence of morbilliviruses is not clear. Therefore, the admission of 2 white-beaked dolphins with morbillivirus infection into a rehabilitation center provided a unique opportunity to investigate the virulence of morbillivirus in this species. By phylogenetic analysis, the morbilliviruses in both animals were identified as a dolphin morbillivirus (DMV) most closely related to that detected in a white-beaked dolphin in Germany in 2007. Both animals were examined clinically and pathologically. Case No. 1 had a chronic neural DMV infection, characterized by polioencephalitis in the cerebrum and morbillivirus antigen expression limited to neurons and glial cells. Surprisingly, no nervous signs were observed in this animal during the 6 months before death. Case No. 2 had a subacute systemic DMV infection, characterized by interstitial pneumonia, leucopenia, lymphoid depletion, and DMV antigen expression in mononuclear cells and syncytia in the lung and in mononuclear cells in multiple lymphoid organs. Cause of death was not attributed to DMV infection in either animal. DMV was not detected in 2 contemporaneously stranded white-beaked dolphins. Stranding rate did not increase in the region. These results suggest that DMV is not highly virulent for white-beaked dolphins.
Knowledge and Perceptions of Agricultural Communications Pilot Curriculum in Arkansas Secondary Agricultural Classrooms

The purpose of this mixed-method study was to assess the effectiveness of agricultural communications curriculum developed and incorporated into a semester-long agricultural leadership and communications course for secondary agricultural education programs in Arkansas. Students (N = 297) participated in newly developed instructional modules addressing four categories of agriculture-themed curricula predetermined by a committee of agricultural education and communications faculty at the University of Arkansas (careers, writing, design, and multimedia). Student agricultural communications knowledge change was assessed using preand post-test instruments in each module of study. Additionally, content analysis of participating teachers’ journals was used to identify emergent themes related to teachers’ experiences teaching the curriculum throughout the semester. Overall, the findings from this study indicated students’ knowledge increased after instruction for each curriculum module: careers (16.2%), writing (23.1%), design (35.7%), and multimedia (31.3%). Lack of time, limited technology, teacher training, and curriculum content were the most common emergent themes among teachers. Based on findings from this study, it was concluded future efforts should be made to provide technology for agricultural education instructors to improve agricultural communications program effectiveness and reach.
Curiosity-based topological reinforcement learning

Recent works involved in enhancing the learning convergence of reinforcement learning (RL) in mobile robot navigation have investigated methods to obtain knowledge from efficiently exploring the robot's environment. In RL, this knowledge is highly desirable to reduce the high number of interactions required for updating the value function and to eventually find an optimal or suboptimal policy for the agent. In this work, we propose a curiosity-based topological RL (CBT-RL) algorithm that makes use of the topological relationships among the observed states of the environment in which the agent acts. This algorithm builds an incremental topological map of the environment using Instantaneous Topological Map (ITM) model, which we use for facilitating value function updates as well as providing a guided exploration. We evaluate our algorithm against the original Q-Learning and Influence Zone algorithms in static and dynamic environments.
Critical incident analysis – a reflection

Abstract The ability to reflect upon an event allows the individual to consider their actions and consequences. The use of a model of reflection can help guide the individual through a structured process of contemplation. Difficult decisions and dilemmas are something that the veterinary profession deal with on a daily basis. The ability to reflect is a skill that can be implemented throughout the individual’s professional life. Professional practice, legal implications and ethical considerations were evaluated and considered concerning a critical incident.
A Resource-Centered Runtime Software Coordination Model and Its Implementation

Coordination among components is an important problem for software system, especially for building large scale software systems. In this paper, we present a resource-centered runtime software coordination model, which divides software system into three parts: computation entities, coordinators and coordination space. Computation entity is consisted of role, actors and services. Coordinator is used to achieve coordination among computation entities. Coordinator includes three types: communication coordinator, resource coordinator and service coordinator. Coordination space contains description information of the system as the basis of runtime coordination. We define coordination relation for shared resources, and give resource-centered runtime software coordination algorithms, including initialization of resource object, request of resource and release of resource.
Site-directed mutagenesis of putative active-site amino acid residues of 3,2-trans-enoyl-CoA isomerase, conserved within the low-homology isomerase/hydratase enzyme family.

During beta-oxidation of unsaturated fatty acids, mitochondrial 3,2-trans-enoyl-CoA isomerase (mECI) converts 3-cis- or 3-trans-enoyl-CoA intermediates into their 2-trans isomers. The cDNA-derived amino acid sequence of mECI shows weak but significant homologies to the peroxisomal trifunctional enzyme (pTFE), the alpha-subunit of the fatty acid degradation complex from Escherichia coli (FadB), the mitochondrial 2-enoyl-CoA hydratase (mECH), the naphthoate synthase encoded by the menB gene from Bacillus subtilis (MenB), and the 4-chlorobenzoyl-CoA dehalogenase from Pseudomonas sp. (CBDH). These proteins from the isomerase/hydratase enzyme family. Tyr-150, Arg-151, and Asp-211 of the mECI are the only amino acids with protic side chains conserved within the enzymes with isomerase activity (pTFE and FadB). These amino acids are exchanged in the remaining enzymes of the isomerase/hydratase family. Glu-165 is conserved in all enzymes with isomerase and/or hydratase activity (pTFE, FadB, and mECH). We argue that these amino acids are possibly involved in the proton transfer at the active site of mECI. To test this hypothesis, mECI was functionally expressed in E. coli. The recombinant enzyme (rmECI) exhibits the same specific activity as the enzyme from rat liver. Exchange of the candidate active-site amino acids by site-directed mutagenesis revealed that Tyr-150 is not involved in isomerase catalysis. The exchange of Arg-151 and Asp-211 leads to a reduced expression of the recombinant enzyme accompanied by a reduced specific activity. The replacement of Glu-165 by Gln leads to a strongly reduced enzymatic activity. (ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of nanoscale transformations in polyelectrolyte multilayers fabricated from plasmid DNA using laser scanning confocal microscopy in combination with atomic force microscopy

Laser scanning confocal microscopy (LSCM) and atomic force microscopy (AFM) were used to characterize changes in nanoscale structure that occur when ultrathin polyelectrolyte multilayers (PEMs) are incubated in aqueous media. The PEMs investigated here were fabricated by the deposition of alternating layers of plasmid DNA and a hydrolytically degradable polyamine onto a precursor film composed of alternating layers of linear poly(ethylene imine) (LPEI) and sodium poly(styrene sulfonate) (SPS). Past studies of these materials in the context of gene delivery revealed transformations from a morphology that is smooth and uniform to one characterized by the formation of nanometer‐scale particulate structures. We demonstrate that in‐plane registration of LSCM and AFM images acquired from the same locations of films fabricated using fluorescently labeled polyelectrolytes allows the spatial distribution of individual polyelectrolyte species to be determined relative to the locations of topographic features that form during this transformation. Our results suggest that this physical transformation leads to a morphology consisting of a relatively less disturbed portion of film composed of polyamine and DNA juxtaposed over an array of particulate structures composed predominantly of LPEI and SPS. Characterization by scanning electron microscopy and energy‐dispersive X‐ray microanalysis provides additional support for this interpretation. The combination of these different microscopy techniques provides insight into the structures and dynamics of these multicomponent thin films that cannot be achieved using any one method alone, and could prove useful for the further development of these assemblies as platforms for the surface‐mediated delivery of DNA. Microsc. Res. Tech. 73:834–844, 2010. © 2010 Wiley‐Liss, Inc.