Miracle-dz/UniFAR-FTUs huggingface dataset:
A n -order four variable refined theory for bending and free vibration of functionally graded plates

This paper presents a simple n-order four variable refined theory for the bending and vibration analyses of functionally graded plates. By dividing the transverse displacement into bending and shear parts, the number of unknowns and governing equations of the present theory is reduced, and hence, makes it simple to use. The present theory is variationally consistent, uses the n-order polynomial term to represent the displacement field, does not require shear correction factor, and gives rise to transverse shear stress variation such that the transverse shear stresses vary parabolically across the thickness satisfying shear stress free surface conditions. The governing equations are derived by employing the Hamilton\'s principle and the physical neutral surface concept. The accuracy of the present solutions is verified by comparing the obtained results with available published ones.
Safe and effective obtainment of access for percutaneous nephrolithotomy by urologists: the Louisiana State University experience.

BACKGROUND AND PURPOSE Access for percutaneous nephrolithotomy (PCNL) is critical to successful removal of stone burden and is often performed by a specialist other than a urologist. In many regions, however, there is limited availability of such personnel. We reviewed the complication rates that were related to PCNL access when performed at a teaching hospital to establish that access for PCNL may be safely taught to and performed by urology residents. Chief urology residents across the nation were also anonymously surveyed to better understand the current trends and dynamics regarding PCNL access in teaching institutions. PATIENTS AND METHODS A retrospective chart review was performed of all PCNLs performed at our institution from 1995 to 2009 for any complications that were related to surgery. Patients with access gained at outside institutions or not attempted at the time of surgery by residents were excluded. The complication rate was compared with those of the American College of Radiology. An eight-question survey was also sent by e-mail to all current urology chief residents regarding their experience with PCNL access during residency. RESULTS A total of 290 patients underwent PCNL with 338 separate access sites gained at the time of surgery under the supervision of nine teaching staff. Access was gained in all cases at the time of surgery. Major complications included: Transfusion in 20 (5.9%) patients, sepsis in 2 (0.6%) patients, pseudoaneurysm necessitating intervention in 2 (0.6%) patients, hydrothorax in 2 (0.6%) patients, pneuomothorax in 1 (0.3%) patient, ureteropelvic junction disruption in 1 (0.3%) patient, and one death (0.3%) after surgery. Minor complications included: Urinary tract infection in five (1.5%) patients, and collecting system injuries in 6 (1.8%) patients necessitating placement of a ureteral stent. Our survey of residents demonstrated that 53% did not routinely gain access for PCNL at their institution. The 94% who did not get instruction on PCNL access, however, thought it would be a valuable addition to their training. CONCLUSION Our results show that access for PCNL surgery can be safely and successfully obtained by genitourinary residents under the supervision of trained staff at the time of surgery. We think that access for PCNL is a valuable tool that should be in the armamentarium of all urologic surgeons on leaving an accredited urology training program.
The Flowering Repressor SVP Underlies a Novel Arabidopsis thaliana QTL Interacting with the Genetic Background

The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1). We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP). Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time.
Resveratrol and its major sulfated conjugates are substrates of organic anion transporting polypeptides (OATPs): impact on growth of ZR-75-1 breast cancer cells.

SCOPE Resveratrol is a naturally occurring polyphenolic compound with various pharmacological activities. These effects are observed despite its low bioavailability, which is particularly caused by extensive phase II metabolism. It is unknown whether resveratrol and its metabolites can accumulate to bioactive levels in organs and tissues through protein-mediated transport mechanisms. Because organic anion transporting polypeptides (OATPs) mediate the uptake of many clinically important drugs, we investigated their role in the cellular transport of resveratrol and its major glucuronides and sulfates. METHODS AND RESULTS Uptake experiments were performed with resveratrol and its glucuronides and sulfates in OATP-expressing Chinese hamster ovary (CHO) and breast cancer (ZR-75-1) cells. The uptake rates for resveratrol in OATP1B1-, OATP1B3-, and OATP2B1-transfected Chinese hamster ovary cells were four- to sixfold higher compared to wild-type cells. Resveratrol-3-O-4'-O-disulfate was transported by OATP1B1 and OATP1B3, while resveratrol-3-O-sulfate was exclusively transported by OATP1B3. However, resveratrol-4'-O-sulfate, resveratrol-3-O-glucuronide, and resveratrol-4'-O-glucuronide did not show any affinity for these OATPs. OATP-dependent uptake of resveratrol was also confirmed in ZR-75-1 cells. CONCLUSION Our data revealed that OATPs act as cellular uptake transporters for resveratrol and its major sulfates, which must be considered in humans following oral uptake of dietary resveratrol.
Globally Normalized Transition-Based Neural Networks

We introduce a globally normalized transition-based neural network model that achieves state-of-the-art part-of-speech tagging, dependency parsing and sentence compression results. Our model is a simple feed-forward neural network that operates on a task-specific transition system, yet achieves comparable or better accuracies than recurrent models. We discuss the importance of global as opposed to local normalization: a key insight is that the label bias problem implies that globally normalized models can be strictly more expressive than locally normalized models.
Dependence of GABAergic Synaptic Areas on the Interneuron Type and Target Size

In the neostriatum, several types of interneuron with distinct firing patterns and expression of neuroactive substances are known to exist. We found two types of neostriatal interneurons, parvalbumin-containing fast-spiking (FS) cells and somatostatin-containing low-threshold spike (LTS) cells to both be immunoreactive for GABA at their axon terminals in immersion-fixed brain slices from rat. To reveal the differences in synaptic connections between these two types of GABAergic interneurons, the postsynaptic target and their synaptic structure were compared by three-dimensional reconstructions from electron microscopic images of intracellularly stained axon terminals. FS cells made a greater proportion of synaptic contacts onto somata than LTS cells. Although terminal boutons of FS and LTS cells were similar in volume, their synaptic junctional areas differed in size distribution and relation to the dimensions of postsynaptic dendritic shafts or spines. Whereas the synaptic junctional areas of FS cells (0.024–0.435 μm2; n = 28) sharply and linearly increased with the circumference of the postsynaptic dendrites or spines (0.939–5.146 μm), the slope for the junctional area of LTS cells (0.02–0.103 μm2; n = 29) against circumference (0.844–4.252 μm) was less steep, and a much weaker correlation was seen. In addition to the differences in firing patterns, expressed molecules, axonal arborizations, and postsynaptic targets, this variation in dependency of the synaptic area on the target size suggests functional differentiation of GABAergic interneurons.
Branch-and-price global optimization for multi-view multi-target tracking

We present a new algorithm to jointly track multiple objects in multi-view images. While this has been typically addressed separately in the past, we tackle the problem as a single global optimization. We formulate this assignment problem as a min-cost problem by defining a graph structure that captures both temporal correlations between objects as well as spatial correlations enforced by the configuration of the cameras. This leads to a complex combinatorial optimization problem that we solve using Dantzig-Wolfe decomposition and branching. Our formulation allows us to solve the problem of reconstruction and tracking in a single step by taking all available evidence into account. In several experiments on multiple people tracking and 3D human pose tracking, we show our method outperforms state-of-the-art approaches.
Inhibition of HLA-DM Mediated MHC Class II Peptide Loading by HLA-DO Promotes Self Tolerance

Major histocompatibility class II (MHCII) molecules are loaded with peptides derived from foreign and self-proteins within the endosomes and lysosomes of antigen presenting cells (APCs). This process is mediated by interaction of MHCII with the conserved, non-polymorphic MHCII like molecule HLA-DM (DM). DM activity is directly opposed by HLA-DO (DO), another conserved, non-polymorphic MHCII like molecule. DO is an MHCII substrate mimic. Binding of DO to DM prevents MHCII from binding to DM, thereby inhibiting peptide loading. Inhibition of DM function enables low stability MHC complexes to survive and populate the surface of APCs. As a consequence, DO promotes the display of a broader pool of low abundance self-peptides. Broadening the peptide repertoire theoretically reduces the likelihood of inadvertently acquiring a density of self-ligands that is sufficient to activate self-reactive T cells. One function of DO, therefore, is to promote T cell tolerance by shaping the visible image of self. Recent data also shows that DO influences the adaptive immune response by controlling B cell entry into the germinal center reaction. This review explores the data supporting these concepts.
Protein Engineering by Random Mutagenesis and Structure-Guided Consensus of Geobacillus stearothermophilus Lipase T6 for Enhanced Stability in Methanol

ABSTRACT The abilities of enzymes to catalyze reactions in nonnatural environments of organic solvents have opened new opportunities for enzyme-based industrial processes. However, the main drawback of such processes is that most enzymes have a limited stability in polar organic solvents. In this study, we employed protein engineering methods to generate a lipase for enhanced stability in methanol, which is important for biodiesel production. Two protein engineering approaches, random mutagenesis (error-prone PCR) and structure-guided consensus, were applied in parallel on an unexplored lipase gene from Geobacillus stearothermophilus T6. A high-throughput colorimetric screening assay was used to evaluate lipase activity after an incubation period in high methanol concentrations. Both protein engineering approaches were successful in producing variants with elevated half-life values in 70% methanol. The best variant of the random mutagenesis library, Q185L, exhibited 23-fold-improved stability, yet its methanolysis activity was decreased by one-half compared to the wild type. The best variant from the consensus library, H86Y/A269T, exhibited 66-fold-improved stability in methanol along with elevated thermostability (+4.3°C) and a 2-fold-higher fatty acid methyl ester yield from soybean oil. Based on in silico modeling, we suggest that the Q185L substitution facilitates a closed lid conformation that limits access for both the methanol and substrate excess into the active site. The enhanced stability of H86Y/A269T was a result of formation of new hydrogen bonds. These improved characteristics make this variant a potential biocatalyst for biodiesel production.
Impact of Specific pbp5 Mutations on Expression of β-Lactam Resistance in Enterococcus faecium

ABSTRACT We tested the impact of individual PBP 5 mutations on expression of ampicillin resistance in Enterococcus faecium using a shuttle plasmid designed to facilitate expression of cloned pbp5 in ampicillin-susceptible E. faecium D344SRF. Substitutions that had been implicated in contributing to the resistance of clinical strains conferred only modest levels of resistance when they were present as single point mutations. The levels of resistance were amplified when some mutations were present in combination. In particular, a methionine-to-alanine change at position 485 (in close proximity to the active site) combined with the insertion of a serine at position 466 (located in a loop that forms the outer edge of the active site) was associated with the highest levels of resistance to all β-lactams. Affinity for penicillin generally correlated with β-lactam MICs for the mutants, but these associations were not strictly proportional.
Clostridium difficile phages: still difficult?

Phages that infect Clostridium difficile were first isolated for typing purposes in the 1980s, but their use was short lived. However, the rise of C. difficile epidemics over the last decade has triggered a resurgence of interest in using phages to combat this pathogen. Phage therapy is an attractive treatment option for C. difficile infection, however, developing suitable phages is challenging. In this review we summarize the difficulties faced by researchers in this field, and we discuss the solutions and strategies used for the development of C. difficile phages for use as novel therapeutics. Epidemiological data has highlighted the diversity and distribution of C. difficile, and shown that novel strains continue to emerge in clinical settings. In parallel with epidemiological studies, advances in molecular biology have bolstered our understanding of C. difficile biology, and our knowledge of phage–host interactions in other bacterial species. These three fields of biology have therefore paved the way for future work on C. difficile phages to progress and develop. Benefits of using C. difficile phages as therapeutic agents include the fact that they have highly specific interactions with their bacterial hosts. Studies also show that they can reduce bacterial numbers in both in vitro and in vivo systems. Genetic analysis has revealed the genomic diversity among these phages and provided an insight into their taxonomy and evolution. No strictly virulent C. difficile phages have been reported and this contributes to the difficulties with their therapeutic exploitation. Although treatment approaches using the phage-encoded endolysin protein have been explored, the benefits of using “whole-phages” are such that they remain a major research focus. Whilst we don’t envisage working with C. difficile phages will be problem-free, sufficient study should inform future strategies to facilitate their development to combat this problematic pathogen.
Biofilm dispersal cells of a cystic fibrosis Pseudomonas aeruginosa isolate exhibit variability in functional traits likely to contribute to persistent infection.

Persistent lung infection by Pseudomonas aeruginosa is typically associated with the development of biofilms, the appearance of morphotypic variants and reduction in the expression of acute virulence factors. We have characterised and compared functional traits [carbon substrate utilisation, attachment and biofilm formation, protease and elastase activity, quorum-sensing (QS)] of the biofilm dispersal populations of a representative P. aeruginosa isolate from a chronically infected cystic fibrosis individual and P. aeruginosa strain PAO1. The dispersal variants of the clinical strain exhibited significantly greater heterogeneity in all of the phenotypes tested. All morphotypic variants from the dispersal population of the clinical strain showed a significant increase in QS signal and elastase production compared to the parental strain. In contrast, isolates from planktonic cultures were phenotypically identical to the inoculum strain, suggesting that the appearance of these variants was biofilm specific. The clinical strain was shown to have a 3.4-fold higher mutation frequency than PAO1 which corroborated with the increased diversity of dispersal isolates. These data suggest that the development of a chronic infection phenotype can be reversed to recover acute infection isolates and that growth within a biofilm facilitates diversification of P. aeruginosa which is important for ecological adaptation.
NEW OPTIMIZATION METAHEURISTIC BASED ON CO-OPERATION OF BIOLOGY RELATED ALGORITHMS

In this paper we describe and investigate a new self-tuning metaheuristic approach called Co-Operation of Biology Related Algorithms (COBRA) based on five well-known nature-inspired optimization methods such as Particle Swarm Optimization, Wolf Pack Search, Firefly Algorithm, Bat Algorithm and Cuckoo Search Algorithm. Besides, two modifications of COBRA are introduced. Also new metaheuristic was used for adjustment of neural network’s weight coefficients for solving different classification problems.
Treatment of patients with aortic disease during pregnancy and after delivery

Objective This study aimed to review treatment of patients with aortic disease during pregnancy and after delivery in Beijing Anzhen Hospital. Methods A retrospective study was conducted using data from 12 patients with aortic disease during pregnancy and after delivery in our institution from May 2005 to December 2014. Patients were provided different treatments based on the type of aortic disease and clinical characteristics. Results The mean age was 29.83 ± 4.17 years, mean height was 171.7 ± 8.22 cm, mean weight was 68.55 ± 10.62 kg, and mean body mass index was 23.18 ± 2.93 kg/m2. Two patients with Stanford type A aortic dissection died of renal failure after surgery. All of the other patients were discharged. Six foetuses survived. One patient continued her pregnancy after an aortic operation. The gestational age of the remaining five patients was less than 28 weeks at the time of the operation and all foetuses of these five patients died. Conclusions A suitable treatment strategy for aortic disease during pregnancy and after delivery should be chosen based on an individual’s comprehensive clinical condition. Foetal management should be chosen based on gestational age and severity of aortic disease.
Ant search strategies after interrupted tandem runs

SUMMARY Tandem runs are a form of recruitment in ants. During a tandem run, a single leader teaches one follower the route to important resources such as sources of food or better nest sites. In the present study, we investigate what tandem leaders and followers do, in the context of nest emigration, if their partner goes missing. Our experiments involved removing either leaders or followers at set points during tandem runs. Former leaders first stand still and wait for their missing follower but then most often proceed alone to the new nest site. By contrast, former followers often first engage in a Brownian search, for almost exactly the time that their former leader should have waited for them, and then former followers switch to a superdiffusive search. In this way, former followers first search their immediate neighbourhood for their lost leader before becoming ever more wide ranging so that in the absence of their former leader they can often find the new nest, re-encounter the old one or meet a new leader. We also show that followers gain useful information even from incomplete tandem runs. These observations point to the important principle that sophisticated communication behaviours may have evolved as anytime algorithms, i.e. procedures that are beneficial even if they do not run to completion.
Traveling Agents: Political Change and Bureaucratic Turnover in India

Abstract We develop a framework to empirically examine how politicians with electoral pressures control bureaucrats with career concerns and the consequent implications for bureaucrats' career investments. Unique microlevel data on Indian bureaucrats support our key predictions. Politicians use frequent reassignments (transfers) across posts of varying importance to control bureaucrats. High-skilled bureaucrats face less frequent political transfers and lower variability in the importance of their posts. We find evidence of two alternative paths to career success: officers of higher initial ability are more likely to invest in skill, but caste affinity to the politician's party base also helps secure important positions.
Nonrandom Dimerization of Murine Leukemia Virus Genomic RNAs

ABSTRACT Retroviral genomes consist of two unspliced RNAs linked noncovalently in a dimer. Although these two RNAs are generally identical, two different RNAs can be copackaged when virions are produced by coinfected cells. It has been assumed, but not tested, that copackaging results from random RNA associations in the cytoplasm to yield encapsidated RNA homodimers and heterodimers in Hardy-Weinberg proportions. Here, virion RNA homo- and heterodimerization were examined for Moloney murine leukemia virus (MLV) using nondenaturing Northern blotting and a novel RNA dimer capture assay. The results demonstrated that coexpressed MLV RNAs preferentially self-associated, even when RNAs were identical in known packaging and dimerization sequences or when they differed overall by less than 0.1%. In contrast, HIV-1 RNAs formed homo- and heterodimers in random proportions. We speculate that these species-specific differences in RNA dimer partner selection may at least partially explain the higher frequency of genetic recombination observed for human immunodeficiency virus type 1 than for MLV.