Miracle-dz/UniFAR-FTUs huggingface dataset:
A DNA structure is required for geminivirus replication origin function

The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two single-stranded circular DNAs, A and B, that replicate through a rolling-circle mechanism in nuclei of infected plant cells. The TGMV origin of replication is located in a conserved 5' intergenic region and includes at least two functional elements: the origin recognition site of the essential viral replication protein, AL1, and a sequence motif with the potential to form a hairpin or cruciform structure. To address the role of the hairpin motif during TGMV replication, we constructed a series of B-component mutants that resolved sequence changes from structural alterations of the motif. Only those mutant B DNAs that retained the capacity to form the hairpin structure replicated to wild-type levels in tobacco protoplasts when the viral replication proteins were provided in trans from a plant expression cassette. In contrast, the same B DNAs replicated to significantly lower levels in transient assays that included replicating, wild-type TGMV A DNA. These data established that the hairpin structure is essential for TGMV replication, whereas its sequence affects the efficiency of replication. We also showed that TGMV AL1 functions as a site-specific endonuclease in vitro and mapped the cleavage site to the loop of the hairpin. In vitro cleavage analysis of two TGMV B mutants with different replication phenotypes indicated that there is a correlation between the two assays for origin activity. These results suggest that the in vivo replication results may reflect structural and sequence requirements for DNA cleavage during initiation of rolling-circle replication.
A new technique to filter reduction for speech signal processing systems

In many applications, one needs to approximate a filter of very high order with that of lower order. To reduce the order of the filter, some techniques such as the balanced model reduction approach are often applied. In this paper, we introduce a new technique which is based on minimizing the H/sub 2/-norm between the filter of very high order and the reduced one. This technique shows much better performance than other existing model reduction methods and is applied to estimating the vocal tract filter for speech processing systems. A speech processing example is presented to demonstrate the design procedure and the performance of the proposed algorithm.
Node Placement and Distributed Magnetic Beamforming Optimization for Wireless Power Transfer

In multiple-input single-output (MISO) wireless power transfer (WPT) via magnetic resonant coupling, multiple transmitters are deployed to enhance the efficiency of power transfer to a single receiver by jointly adapting their source currents/voltages so as to constructively combine the induced magnetic fields at the receiver, a technique known as magnetic beamforming. In practice, since the transmitters (power chargers) are usually at fixed locations and the receiver (e.g., mobile phone) is desired to be freely located in a target region for wireless charging, its received power can fluctuate significantly over locations even with adaptive magnetic beamforming applied. To achieve uniform power coverage, the transmitters need to be optimally placed in the region such that a minimum charging power can be achieved for the receiver regardless of its location, which motivates this paper. First, we derive the optimal magnetic beamforming solution in closed form for a distributed MISO WPT system with fixed locations of the transmitters and receiver to maximize the deliverable power to the receiver subject to a given sum-power constraint at all transmitters. By applying adaptive magnetic beamforming based on this optimal solution, we then jointly optimize the locations of all transmitters to maximize the minimum power deliverable to the receiver over a given one-dimensional (1D) region. Although the formulated problem is nonconvex, we propose an iterative algorithm for solving it efficiently. Extensive simulation results are provided that show the significant performance gains by the proposed design with optimized transmitter locations and magnetic beamforming as compared to other benchmark schemes with nonadaptive and/or heuristic transmitter current allocation and node placement. Last, we extend the node placement problem to the case of 2D region, and propose efficient designs for this case.
A follow-up study of a multisite, randomized, controlled trial for children with sexual abuse-related PTSD symptoms.

OBJECTIVE To ascertain whether the differential responses that previously have been found between trauma-focused, cognitive-behavioral therapy (TF-CBT), and child-centered therapy (CCT) for treating posttraumatic stress disorder (PTSD) and related problems in children who had been sexually abused would persist following treatment and to examine potential predictors of treatment outcome. METHOD A total of 183 children 8 to 14 years old and their primary caregivers were assessed 6 and 12 months after their posttreatment evaluations. RESULTS Mixed-model repeated analyses of covariance found that children treated with TF-CBT had significantly fewer symptoms of PTSD and described less shame than the children who had been treated with CCT at both 6 and 12 months. The caregivers who had been treated with TF-CBT also continued to report less severe abuse-specific distress during the follow-up period than those who had been treated with CCT. Multiple traumas and higher levels of depression at pretreatment were positively related to the total number of PTSD symptoms at posttreatment for children assigned to the CCT condition only. CONCLUSIONS Children and caregivers assigned to TF-CBT continued to have fewer symptoms of PTSD, feelings of shame, and abuse-specific parental distress at 6- and 12-month assessments as compared to participants assigned to CCT.
Insulin‐like growth factor type I receptor gene expression and obesity in esophageal adenocarcinoma

The objective of this exploratory study was to evaluate the role of the insulin‐like growth factor I receptor (IGF‐IR) in esophageal adenocarcinoma (EADC). Using quantitative PCR, we studied IGF‐IR mRNA expression in 52 well‐characterized surgically resected EADC and matched histologically normal esophageal tissues, and examined IGF‐IR expression levels in relation to clinicopathologic characteristics, body mass index (BMI), and the common IGF‐IR polymorphism (G1013A), recently proposed to modify risk of obesity for EADC. Expression levels of IGF‐IR mRNA were not significantly different between EADC and matched histologically normal esophageal epithelia. Although no significant associations were found between IGF‐IR expression and BMI, tumor differentiation, stage or survival, when stratified by genotype, patients with the polymorphic A variant had significantly higher IGF‐IR expression in EADC tissues compared with matched normal epithelia. These findings suggest that G1013A most likely modulates IGF‐IR function, possibly by influencing gene transcription or mRNA stability, and represents a plausible mechanistic link underlying the association between obesity and esophageal malignancy. © 2009 Wiley‐Liss, Inc.
Temporal query log profiling to improve web search ranking

Temporal information can be leveraged and incorporated to improve web search ranking. In this work, we propose a method to improve the ranking of search results by identifying the fundamental properties of temporal behavior of low-quality hosts and spam-prone queries in search logs and modeling those properties as quantifiable features. In particular, we introduce the concepts of host churn, a measure of changes in host visibility for user queries, and query volatility, a measure of semantic instability of query results, and propose the methods for construction of temporal profiles from search query logs that can be used for estimation of a set of features based on the introduced concepts. The utility of the proposed concepts has been experimentally demonstrated for two language-independent search tasks: the regression-based ranking of search results and a novel classification problem of detecting spam-prone queries introduced in this work.
Speech Recognition using Digital Signal Processing

Speech recognition methods can be divided into text-independent and text dependent methods. In a text independent system, speaker models capture characteristics of somebody's speech, which show up irrespective of what one is saying. In a text-dependent system, on the other hand, the recognition of the speaker's identity is based on his or her speaking one or more specific phrases, like passwords, card numbers, PIN codes, etc. This paper is based on text independent speaker recognition system and makes use of Mel frequency cepstrum coefficients to process the input signal and vector quantization approach to identify the speaker. The above task is implemented using MATLAB. Digital Signal Processing (DSP) is one of the most commonly used hardware platform that provides good development flexibility and requires relatively short application development cycle. DSP techniques have been at the heart of progress in Speech Processing during the last 25years.Simultaneously speech processing has been an important catalyst for the development of DSP theory and practice. Today DSP methods are used in speech analysis, synthesis, coding, recognition, enhancement as well as voice modification, speaker recognition, language identification. Speech recognition is generally computationally-intensive task and includes many of digital signal processing algorithms.
Association of Asthma Education with Asthma Control Evaluated by Asthma Control Test, FEV1, and Fractional Exhaled Nitric Oxide

Background. Asthma education is an important adjunct for asthma control although the way asthma education affects asthma outcomes is poorly understood. The asthma control test (ACT), forced expiratory volume in 1 s (FEV1), and fractional exhaled nitric oxide (FeNO) have all been used as markers of asthma control. However, the use of FeNO as a surrogate marker remains controversial. Objectives. (i) To examine whether asthma education is associated with asthma control; (ii) to compare absolute levels and changes of ACT, FEV1, and FeNO over a year; and (iii) to evaluate whether FeNO can be used as an additional marker of asthma control. Methods. Fifty asthmatics with poor adherence (12 mild, 21 moderate, and 17 severe) received asthma education at study entry. Medications were unchanged for the first 3 months, and ACT, FEV1, and FeNO measurements were recorded at entry, 3, 6, and 12 months. Asthma control was assessed at each visit and patients were categorized as either “stable” or “unstable” asthmatics according to the global initiative for asthma (GINA) guidelines. Results. A significant decrease in FeNO and increase in ACT score were noted in the stable asthmatic group at 3 months (p < .001), and this persisted over 12 months. Significant correlations were seen between changes (Δ) in FeNO, ACT, and FEV1 over time. However, significant correlations between the absolute levels were not maintained over 12 months. A decrease of ≥18.6% in FeNO and a ≥3-point increase in ACT score (sensitivity: 80% and 73.3% and specificity: 83.3% and 87.5%, respectively) were associated with stable asthma control although the absolute levels were not. Conclusions. Asthma education may be useful to achieve stable control. In addition, changes rather than absolute levels of FeNO and ACT may be better markers of asthma control.
CEP-28122, a Highly Potent and Selective Orally Active Inhibitor of Anaplastic Lymphoma Kinase with Antitumor Activity in Experimental Models of Human Cancers

Anaplastic lymphoma kinase (ALK) is constitutively activated in a number of human cancer types due to chromosomal translocations, point mutations, and gene amplification and has emerged as an excellent molecular target for cancer therapy. Here we report the identification and preclinical characterization of CEP-28122, a highly potent and selective orally active ALK inhibitor. CEP-28122 is a potent inhibitor of recombinant ALK activity and cellular ALK tyrosine phosphorylation. It induced concentration-dependent growth inhibition/cytotoxicity of ALK-positive anaplastic large-cell lymphoma (ALCL), non-small cell lung cancer (NSCLC), and neuroblastoma cells, and displayed dose-dependent inhibition of ALK tyrosine phosphorylation in tumor xenografts in mice, with substantial target inhibition (>90%) for more than 12 hours following single oral dosing at 30 mg/kg. Dose-dependent antitumor activity was observed in ALK-positive ALCL, NSCLC, and neuroblastoma tumor xenografts in mice administered CEP-28122 orally, with complete/near complete tumor regressions observed following treatment at doses of 30 mg/kg twice daily or higher. Treatment of mice bearing Sup-M2 tumor xenografts for 4 weeks and primary human ALCL tumor grafts for 2 weeks at 55 or 100 mg/kg twice daily led to sustained tumor regression in all mice, with no tumor reemergence for more than 60 days postcessation of treatment. Conversely, CEP-28122 displayed marginal antitumor activity against ALK-negative human tumor xenografts under the same dosing regimens. Administration of CEP-28122 was well tolerated in mice and rats. In summary, CEP-28122 is a highly potent and selective orally active ALK inhibitor with a favorable pharmaceutical and pharmacokinetic profile and robust and selective pharmacologic efficacy against ALK-positive human cancer cells and tumor xenograft models in mice. Mol Cancer Ther; 11(3); 670–9. ©2011 AACR.
The role of phosphodiesterase inhibitors in the management of pulmonary vascular diseases

Phosphodiesterase inhibitors (PDE) can be used as therapeutic agents for various diseases such as dementia, depression, schizophrenia and erectile dysfunction in men, as well as congestive heart failure, chronic obstructive pulmonary disease, rheumatoid arthritis, other inflammatory diseases, diabetes and various other conditions. In this review we will concentrate on one type of PDE, mainly PDE5 and its role in pulmonary vascular diseases.
A randomized study of three interventions for aspiration of thin liquids in patients with dementia or Parkinson's disease.

PURPOSE This study was designed to identify which of 3 treatments for aspiration on thin liquids-chin-down posture, nectar-thickened liquids, or honey-thickened liquids-results in the most successful immediate elimination of aspiration on thin liquids during the videofluorographic swallow study in patients with dementia and/or Parkinson's disease. METHOD This randomized clinical trial included 711 patients ages 50 to 95 years who aspirated on thin liquids as assessed videofluorographically. All patients received all 3 interventions in a randomly assigned order during the videofluorographic swallow study. RESULTS Immediate elimination of aspiration on thin liquids occurred most often with honey-thickened liquids for patients in each diagnostic category, followed by nectar-thickened liquids and chin-down posture. Patients with most severe dementia exhibited least effectiveness on all interventions. Patient preference was best for chin-down posture followed closely by nectar-thickened liquids. CONCLUSION To identify best short-term intervention to prevent aspiration of thin liquid in patients with dementia and/or Parkinson's disease, a videofluorographic swallow assessment is needed. Evidence-based practice requires taking patient preference into account when designing a dysphagic patient's management plan. The longer-term impact of short-term prevention of aspiration requires further study.
Constitutive activation of alternative nuclear factor kappa B pathway in canine diffuse large B-cell lymphoma contributes to tumor cell survival and is a target of new adjuvant therapies

Abstract Activation of the classical nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway is a common molecular event observed in both human and canine diffuse large B-cell lymphoma (DLBCL). Although the oncogenic potential of the alternative NFκB pathway (ANFκBP) has also been recently identified in DLBCL, its precise role in tumor pathogenesis and potential as a treatment target is understudied. We hypothesized that up-regulation of the ANFκBP plays an important role in the proliferation and survival of canine DLBCL cells, and we demonstrate that the ANFκBP is constitutively active in primary canine DLBCL samples and a cell line (CLBL1). We further demonstrate that a small interfering RNA inhibits the activation of the NFκB pathway and induces apoptosis in canine DLBCL cells. In conclusion, the ANFκBP facilitates survival of canine DLBCL cells, and thus, dogs with spontaneous DLBCL can provide a useful large animal model to study therapies targeting the ANFκBP.
An open system framework for component-based CNC machines

This paper describes a framework for open, component-based, manufacturing controllers. The framework is based on the analysis of computer numerically controlled (CNC) machines. The framework includes a control class hierarchy, plug-and-play modules aggregated from the class hierarchy, and a model of collaboration. The framework can be used to build applications that range from a single-axis device to a multi-arm robot.
Dynamic Properties of Human Eyes

This paper presents novel details on the dynamic behavior of human eyes. A high speed camera is used to capture the movement of the eye surface, which is excited by an air jet. For one group of subjects the dynamic response of the eyes ends shortly after the air jet stops. For another group of subjects a distinct offset in the displacement remains, which takes a significantly longer time to vanish. The two distinct phases in the eye movement are the result of the dynamic response of the cornea and the total eye, respectively. A deeper understanding of the eye dynamics is important for obtaining a higher reliability of diagnostic tools for glaucoma
Global self-esteem and attitudes toward the high achiever for Australian and Japanese students

This study compared two samples of Australian and Japanese University students in regard to global self-esteem and their attitudes toward high achievers, or tall poppies'. It was predicted that the Japanese students would show lower levels of global self-esteem than the Australian students and would be more in favor of seeing high achievers fall. This prediction was based on the assumption that construals of self tend to be more interdependent and less independent in the Japanese culture than in the Australian culture. Results supported this prediction and also indicated a negative correlation between global self-esteem and the favor fall' variable in the Australian sample, which was consistent with theoretical expectation and with previous findings
Both morph‐ and species‐dependent asymmetries affect reproductive barriers between heterostylous species

Abstract The interaction between floral traits and reproductive isolation is crucial to explaining the extraordinary diversity of angiosperms. Heterostyly, a complex floral polymorphism that optimizes outcrossing, evolved repeatedly and has been shown to accelerate diversification in primroses, yet its potential influence on isolating mechanisms remains unexplored. Furthermore, the relative contribution of pre‐ versus postmating barriers to reproductive isolation is still debated. No experimental study has yet evaluated the possible effects of heterostyly on pre‐ and postmating reproductive mechanisms. We quantify multiple reproductive barriers between the heterostylous Primula elatior (oxlip) and P. vulgaris (primrose), which readily hybridize when co‐occurring, and test whether traits of heterostyly contribute to reproductive barriers in unique ways. We find that premating isolation is key for both species, while postmating isolation is considerable only for P. vulgaris; ecogeographic isolation is crucial for both species, while phenological, seed developmental, and hybrid sterility barriers are also important in P. vulgaris, implicating sympatrically higher gene flow into P. elatior. We document for the first time that, in addition to the aforementioned species‐dependent asymmetries, morph‐dependent asymmetries affect reproductive barriers between heterostylous species. Indeed, the interspecific decrease of reciprocity between high sexual organs of complementary floral morphs limits interspecific pollen transfer from anthers of short‐styled flowers to stigmas of long‐styled flowers, while higher reciprocity between low sexual organs favors introgression over isolation from anthers of long‐styled flowers to stigmas of short‐styled flowers. Finally, intramorph incompatibility persists across species boundaries, but is weakened in long‐styled flowers of P. elatior, opening a possible backdoor to gene flow through intramorph pollen transfer between species. Therefore, patterns of gene flow across species boundaries are likely affected by floral morph composition of adjacent populations. To summarize, our study highlights the general importance of premating isolation and newly illustrates that both morph‐ and species‐dependent asymmetries shape boundaries between heterostylous species.
Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”

ABSTRACT The genus of Marinobacter is one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content of Marinobacter aquaeolei VT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many “opportunitrophic” genetic characteristics and strategies that M. aquaeolei has adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential of M. aquaeolei and its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles.
A Gbyte / s Parallel Fiber-Optic Network Interface for Multimedia Applications

We explore parallel fiber-optics and single-chip CMOS interface solutions to support broadband multimedia applications in a small workgroup environment. Initial implementation of a network interface card used in our testbed of Intel Pentium-based PCs is described. Feasibility of a CMOS bridge to parallel optics is demonstrated using an adapter chip implemented in 0.5 μm CMOS technology for a point-to-point configuration and providing a measured peak bandwidth of 4.8 Gbit/s on independent transmit and receive directions. In addition, we describe the design of a Gbyte/s parallel fiber-optic network interface for a slotted ring network currently being developed. We present a medium access control to be implemented on a single CMOS chip. The proposed network is a potentially cost-effective solution for small workgroup clusters.