Miracle-dz/UniFAR-FTUs huggingface dataset:
The agnoprotein of polyomaviruses: A multifunctional auxiliary protein

The late region of the three primate polyomaviruses (JCV, BKV, and SV40) encodes a small, highly basic protein known as agnoprotein. While much attention during the last two decades has focused on the transforming proteins encoded by the early region (small and large T‐antigens), it has become increasingly evident that agnoprotein has a critical role in the regulation of viral gene expression and replication, and in the modulation of certain important host cell functions including cell cycle progression and DNA repair. The importance of agnoprotein is underscored by its expression during lytic infection of glial cells by JCV that occurs in progressive multifocal leukoencephalopathy (PML), and also in some JCV‐associated human neural tumors particularly medulloblastoma. In this review, we will discuss the structure and function of agnoprotein in the viral life cycle during the course of lytic infection and the consequences of agnoprotein expression for the host cell. © 2004 Wiley‐Liss, Inc.
Growth, Survival and Field Performance of Bradyrhizobial Liquid Inoculant Formulations with Polymeric Additives

Liquid inoculant has become a preferred method for inoculating legumes with bradyrhizobia. Finely ground peat has been the standard of quality for inoculants for many years. Suitable peat for an inoculant carrier is difficult to find and limited in supply in many locations. We evaluated six different polymeric additives (polyvinyl pyrrolidone (PVP), polyethylene glycol (PEG), polyvinyl alcohol (PVA), gum arabic, cassava starch, and sodium alginate) for their ability to support growth and promote survival of several strains of bradyrhizobia and rhizobia during storage. Some concentrations of various additives to yeast extract mannitol (YEM) media promoted higher cell density compared to cells cultured in YEM media alone. There was a large interaction between strains of rhizobia and the additives in relation to cell survival. Shelf- life of liquid inoculant formulations depended on the strain of rhizobia and additives, when stored at room temperature. Liquid inoculants formulated with sodium alginate promoted long-term survival of all rhizobial strains, but its effect on cell survival was not as great as peat. Peat also provided the greatest protection to cells of bradyrhizobia after application to the seed surface followed by incubation at 40°C. Survival of bradyrhizobia was maintained at 10 5 cells/seed after 48 hours of incubation. Liquid inoculant formulated with gum arabic, sodium alginate, PVP, or cassava starch supported survival at only 10 4 -10 5 cells/seed, while PEG and PVA additives performed poorly and cell numbers fell to 10 3 cells/seed at 48 hours after inoculation. One-week old liquid inoculants with bradyrhizobia were tested for their ability to nodulate and fix nitrogen under field conditions. We found that liquid inoculant performance was as good as that of peat based inoculant.
Impacts of elevated nitrogen inputs on oak reproductive and seed ecology

The effects of increased anthropogenic inputs of reactive nitrogen (N) have been studied at the Harvard Forest Chronic N Experiment, where NH4NO3 has been applied experimentally since 1988 to increase atmospheric deposition rates ∼6‐ and ∼18‐fold above ambient. This paper asks whether conditions favorable to primary production also resulted in plastic increases to flower, fruit, and seedling traits, and focuses primarily on the oaks that dominate the hardwood stands of the Harvard Forest experiment. Litterfall samples collected between 1996 and 2001 revealed that flowers and fruits were significantly more abundant in N‐treated plots, and an analysis of oak tree abundance found significant variation both among and within plots. Acorn samples collected during 2003 and 2004 (a mast and a postmast year) were therefore analyzed using ancova models that included an estimate of oak tree abundance. This tree abundance estimate was the only significant driver of increased acorn production during the mast year, and in both years it was a significant factor on plots receiving the highest levels of N. In the postmast year, acorn production was increased in direct response to N‐related factors other than tree abundance. Our comparisons of control and N‐treated plots for acorn quality traits (e.g. rates of acorn damage, germination percentage, seedling growth) revealed negligible or only transient differences. Shifts in overall acorn abundance – particularly disproportionate N‐mediated increases during nonmast years – could have a wide range of ecological consequences beyond the more frequently examined impacts of N deposition on primary production and carbon sequestration.
Virtual/Real Transfer in a Large-Scale Environment: Impact of Active Navigation as a Function of the Viewpoint Displacement Effect and Recall Tasks

The purpose of this study was to examine the effect of navigation mode (passive versus active) on the virtual/real transfer of spatial learning, according to viewpoint displacement (ground: 1m 75 versus aerial: 4m) and as a function of the recall tasks used. We hypothesize that active navigation during learning can enhance performances when route strategy is favored by egocentric match between learning (ground-level viewpoint) and recall (egocentric frame-based tasks). Sixty-four subjects (32 men and 32 women) participated in the experiment. Spatial learning consisted of route learning in a virtual district (four conditions: passive/ground, passive/aerial, active/ground, or active/aerial), evaluated by three tasks: wayfinding, sketch-mapping, and picture-sorting. In the wayfinding task, subjects who were assigned the ground-level viewpoint in the virtual environment (VE) performed better than those with the aerial-level viewpoint, especially in combination with active navigation. In the sketch-mapping task, aerial-level learning in the VE resulted in better performance than the ground-level condition, while active navigation was only beneficial in the ground-level condition. The best performance in the picture-sorting task was obtained with the ground-level viewpoint, especially with active navigation. This study confirmed the expected results that the benefit of active navigation was linked with egocentric frame-based situations.
Clinicodemographic profile and treatment outcome in patients of ocular surface squamous neoplasia

Purpose: The aim is to study the clinicodemographic profile and treatment outcome of ocular surface squamous neoplasia (OSSN). Methods: This was a retrospective observational study of 57 eyes (56 cases) with clinically diagnosed OSSN, presenting in our center over the past year. Results: The median age of presentation was 55 years with male:female ratio being 4.5:1. Systemic predisposing conditions were xeroderma pigmentosa (1) postkidney transplant immunosuppression (1), and human immunodeficiency virus infection (1). Patients with predisposing conditions had a younger median age of onset (33 years). The majority of tumors were nodular (61.4%), gelatinous (61.4%), and had limbal involvement (96%). On ultrasound biomicroscopy (UBM), mean tumor height was 2.93 ± 1.02 mm, and intraocular extension was evident in seven eyes. OSSN with intraocular extension had a mean tumor height of 4.3 ± 1.32 mm. Nodal metastasis was seen in one case at presentation. As per American Joint Committee for Cancer Classification seventh edition staging-two cases were T1, one was T2, 46 were T3 and eight were T4. Treatment advised included conservative therapy for 39; wide local excision (4 mm margin clearance) with cryotherapy for seven; enucleation in four; and exenteration in four eyes. Overall, complete regression was achieved in 88% of cases during a mean follow-up of 13.5 ± 4.6 months. Recurrence was seen in three cases, which were treated with exenteration, radical neck dissection, and palliative chemo-radiotherapy, respectively. Conclusion: Although associated with old age, earlier onset of OSSN is seen in patients with systemic predisposing conditions. Thicker tumors in the setting of a previous surgery or immunocompromised status should be considered high-risk features for intraocular extension and should be evaluated on UBM.
Foraging optimization in swarm robotic systems based on an adaptive response threshold model

Developing an animal-like highly organized swarm system, which is capable to adapt to environmental changes as well as dynamic situations is undoubtedly complex. A good task allocation method, which can regulate and achieve an efficient labor division among the swarm agents is a crucial element for this kind of systems. In this paper, we propose an extended model of the simple Response Threshold Model using a discretized version of the Attractor Selection paradigm in order to dynamically control the threshold parameter. Simulation experiments are carried out with the purpose of studying the effects of these optimization measures on the performance of a foraging mission. Simulation experiments verified that the resultant optimized model can improve adaptation capabilities of previous systems, making a swarm of robots able to adapt more efficiently to dynamical situations, and therefore increase its survival rate. Graphical Abstract
A 12 bit analog to digital converter for VLSI applications in nuclear science

A high-density monolithic analog-to-digital converter (ADC) has been designed and tested. The ADC features small silicon area and low power consumption for use in multichannel circuits for massively parallel particle physics detectors. The tested chip contains a linear ramp, precision high-speed comparators, a pipelined counter, and double buffering storage latches fabricated in a 2- mu m, two polysilicon CMOS technology. The prototype integrated circuit successfully combines digital frequencies in excess of 70 MHz with analog signals smaller than 1 mV. Test results show 1/4096 root-mean-square errors at conversion rates above 30 kHz, with less than 4 mW/channel power dissipation. <<ETX>>
CONCEPT MAPS AS KNOWLEDGE ASSESSMENT TOOL : RESULTS OF PRACTICAL USE OF INTELLLIGENT KNOWLEDGE ASSESSMENT SYSTEM

Concept maps as a pedagogical tool have stable positions in education being used for teaching, learning and knowledge assessment. The paper gives an insight into essence of concept maps and their usage for knowledge assessment. The concept map based adaptive intelligent knowledge assessment system (IKAS) is described. The kernel of IKAS is the intelligent knowledge assessment agent which is implemented as a multiagent system consisting from the agent-expert, the communication agent, the knowledge evaluation agent and the interaction registering agent. The knowledge evaluation agent compares a teacher’s and a learner’s concept maps on the basis of graph patterns and assigns score for submitted solution. Four years long experimental use of IKAS allowed gathering student opinion about concept maps as knowledge assessment tool and the functionality of IKAS. The paper presents the summary of evaluation results of both aspects collected from students’ questionnaires.
Molecular analysis of bacterial flora associated with chronically inflamed maxillary sinuses.

Chronic maxillary sinusitis is a chronic inflammatory condition in which the role of microbial infection remains undefined. Bacteria have been isolated from chronically inflamed sinuses; however, their role in the chronicity of inflammation is unknown. The objective of this study was to determine whether bacteria are present in clinical samples from chronic maxillary sinusitis and to assess the diversity of the flora present. Washes and/or tissue samples from endoscopic sinus surgery on 11 patients with chronic maxillary sinusitis were subjected to PCR amplification of bacterial 16S rDNA using three universal primer pairs, followed by cloning and sequencing. The samples were also assessed for the presence of bacteria and fungi by conventional culture methods. Viable bacteria and/or bacterial 16S rDNA were detected from maxillary sinus samples of five of the 11 patients examined (45 %). Three sinus samples were positive by both PCR and culture methods, one was positive only by PCR, and one only by culture. Thirteen bacterial species were identified: Abiotrophia defectiva, Enterococcus avium, Eubacterium sp. , Granulicatella elegans, Neisseria sp. , Prevotella sp. , Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Stenotrophomonas maltophilia, Streptococcus gordonii, Streptococcus mitis/Streptococcus oralis and Streptococcus sp. Fungi were not detected. In one patient Streptococcus mitis/Streptococcus oralis, and in another patient Pseudomonas aeruginosa, were detected from both the sinus and the oral cavity using species-specific PCR primers. These results suggest that both aerobic and anaerobic bacteria can be detected in nearly half of chronic maxillary sinusitis cases.
Hummer : Mitigating Stragglers with Partial Clones

Small jobs typically run for interactive data analyses in datacenters, and often are delayed by long-running tasks called stragglers. Many efforts, like Blacklist, speculative execution, proactive mitigation, have been devoted to the solutions. However, they either consume too much time or waste too many resources. In this paper, we propose a new proactive method to mitigate stragglers by performing partial clones, which improves job average duration by 48% and 18% compared to LATE and Dolly.
Pediatric brachytherapy. The St. Jude children's research hospital experience

Background: The use of interstitial, intracavitary, and permanent placement of radioactive isotopes has become a common practice in adult oncology patients based on numerous reports indicating improved local control and survival when used.1–4 These same irradiation techniques and treatments have been infrequently used for children with malignant disease despite known dose localization properties that allow for highly focal irradiation delivery with rapid reduction of the dose in nearby normal tissues. The noted benefit of decreased late complications noted in the adult series is also attractive, especially when considering the treatment of children.
A zero current detector with low negative inductor current using forced freewheel switch operation in synchronous DC-DC converter

In DC-DC converter at light load, discontinuous conduction mode (DCM) and pulse frequency modulation (PFM) mode are usually used to improve efficiency instead of using low efficient continuous conduction mode (CCM) in a pulse-width modulation (PWM) control system. For these control modes in light load condition, the zero-current detector (ZCD) to prevent reverse current flowing back to the power source is essential. This paper presents a zero current detection method with enhanced time response of the freewheel switch operation. The proposed ZCD was simulated using a 0.18-μm CMOS process in a test system of PWM voltage mode type-III buck converter, with input voltage of 3.3V. The test system works in CCM at heavy load, PFM at light load, and DCM in a short transient of decision to change from CCM to PFM. The PWM switching frequency is 2MHz, and testing output voltage is 1.8V with load current from 20mA up to 300mA. Under the same test condition, the proposed ZCD shows maximum improvement of 6.9% efficiency in PFM compared to the conventional method, making the overall efficiency greater than 89.7%.
Investigation of different Compressed Sensing approaches for respiratory gating in small animal CT

Respiratory gating is necessary in cardio-thoracic small-animal imaging because of the physiological motions that are present during scanning. When applying a low-dose protocol, fewer than 180 noisy projections may be left for the reconstruction of each respiratory phase, leading to streak artifacts. The Prior Image Constrained Compressed Sensing (PICCS) algorithm enables accurate reconstruction of highly undersampled data when a prior image is available. We evaluate three CS algorithms based on the Split-Bregman approach, with different transformations of the prior penalty function: Gradient (TV-PICCS), L1-norm (L1-PICCS), and Wavelet Transform (WT-PICCS), on low-dose data acquired on a micro-CT scanner. All CS methods performed very similarly in terms of noise and resolution, greatly improving filtered back-projection (79 % noise reduction) and eliminating streaks. Wavelet domain was found to be sparser and to show a more natural texture than the commonly used gradient domain.
Avoiding bad hires: Using emotional intelligence as a selection tool

How to avoid bad hiring decisions persists as a human resource challenge. The use of a role-customized interview panel designed to probe the subjective factor of behavior fi t of managerial-level job candidates is a potential tool for addressing this challenge. This panel model is based on the integration of competency-based interviewing, behavior event interviewing, and the four dimensions of emotional intelligence. Details of the panel process, as piloted in fi ve organizations, are presented, along with positive indications and cautions regarding the potential utility of such a hiring tool. Preliminary outcome fi ndings collected between 2004 and 2006 suggest this may be a useful recruitment tool. Future areas for research are also identifi ed.
Immunofluorescence Confocal Microscopy

Cytoskeletal proteins are known to sculpt the structural architecture of cells. However, their role as bridges linking the functional crosstalk of different ion channels is unknown. Here, we demonstrate that a small conductance Ca -activated K channels (SK2 channel), present in a variety of cells, where they integrate changes in intracellular Ca concentration [Ca i] with changes in K conductance and membrane potential, associate with L-type Ca channels; Cav1.3 and Cav1.2 through a physical bridge, -actinin2 in cardiac myocytes. SK2 channels do not physically interact with L-type Ca channels, instead, the 2 channels colocalize via their interaction with -actinin2 cytoskeletal protein. The association of SK2 channel with -actinin2 localizes the channel to the entry of external Ca source, which regulate the channel function. Furthermore, we demonstrated that the functions of SK2 channels in atrial myocytes are critically dependent on the normal expression of Cav1.3 Ca 2 channels. Null deletion of Cav1.3 channel results in abnormal function of SK2 channel and prolongation of repolarization and atrial arrhythmias. Our study provides insight into the molecular mechanisms of the coupling of SK2 channel with voltage-gated Ca channel, and represents the first report linking the coupling of 2 different types of ion channels via cytoskeletal proteins. (Circ Res. 2007;100:112-120.)
Coccoid Helicobacter pylori Can Directly Adhere and Invade in Agminated Formation to Human Gastric Epithelial Cells

Helicobacter pylori (H. pylori) can infect into the epithelial cell to cause benign or malignant disorders. Under stressful environment, a spiral form of H. pylori is transformed into a coccoid form. The infectivity of the coccoid form is still controversial. Since spiral forms are transformed into two types of coccoid forms via different mechanisms, the infectivity of the two types of coccoid forms into human gastric epithelial cell was examined. A laboratory and a clinical strain of H. pyloriv were cultured in liquid medium under different conditions to produce the two types of coccoid forms. These coccoid H. pylorisv were then co-cultured with human derived gastric epithelial cell, MKN-28. Adhesion and penetration of bacteria into MKN-28 cells were monitored by scanning-, standard transmission- and immunotransmission-electron microscopy (SEM, TEM and ITEM). We observed that both coccoid forms were able to adhere onto the surface of MKN-28 cells in agminated formation and also penetrated into the gastric epithelial cells besides the spiral form of H. pyloriv. Coccoid H. pylori is not a passive entity but can actively infect the human gastric epithelial cell.
Regulation and Function of T1/ST2 Expression on CD4+ T Cells: Induction of Type 2 Cytokine Production by T1/ST2 Cross-Linking1

The orphan receptor T1/ST2, a member of the IL-1R family, is preferentially expressed on the surface of murine Th2 cells. In this study, we analyzed the kinetics and function of T1/ST2 expression on Th2 cells in vitro. Whereas naive CD4+ cells did not express T1/ST2, most CD4+ cells became T1/ST2+ upon repeated antigenic stimulation under Th2-polarizing conditions. Flow cytometric analyses revealed that the kinetics of T1/ST2 expression on Th2 cells was delayed compared with the kinetics of type 2 cytokine production. Exogenous IL-6, IL-5, IL-1, and TNF-α enhanced the expression of T1/ST2 on Th2 cells, and IL-6 was by far most effective in this regard. However, the expression of T1/ST2 did not depend on the presence of IL-6 and was also detected in IL-6-deficient mice. Most important, cross-linking of T1/ST2 provided a costimulatory signal for Th2 but not Th1 cells and directly induced proliferation and type 2 cytokine production. Thus, T1/ST2 is not only a Th2 cell marker but also plays an important role in the activation of Th2 cells.
Cascading Failures in a New Multi-coupling-links Three-dimensional Coupled Networks Based on Coupled Map Lattices Model

The paper presented a new multi-coupling-links scale-free coupled networks model based on the existing scale-free network model. More precisely, we investigated the cascading failures of multi-coupling-links three-dimensional coupled networks based on coupled map lattices model. And through Matlab simulation, this paper detailedly studied the cascading failure under different attack strategies, different coupling strength and different network’s scale. The results indicate that the deliberate attack has a faster transmission speed than the random attack under the same perturbation amplitude; the greater coupling strength of the network, the more likely to occur global failure; the coupled networks performs more robust to resist cascading failures if each sub-network possess a larger average scale; and under the deliberate attack, the network in a isolated state is more vulnerable than in a coupled state.