X-ray Crystallographic Study of Preferred Spacing by the NF-κB p50 Homodimer on κB DNA.

Though originally characterized as an inactive or transcriptionally repressive factor, the NF-κB p50 homodimer has become appreciated as a physiologically relevant driver of specific target gene expression. By virtue of its low affinity for cytoplasmic IκB protein inhibitors, p50 accumulates in the nucleus of resting cells, where it is a binding target for the transcriptional co-activator IκBζ. In this study, we employed X-ray crystallography to analyze the structure of the p50 homodimer on κB DNA from the promoters of human interleukin-6 (IL-6) and neutrophil-gelatinase-associated lipocalin (NGAL) genes, both of which respond to IκBζ. The NF-κB p50 homodimer binds 11-bp on IL-6 κB DNA, while, on NGAL κB DNA, the spacing is 12-bp. This begs the question: what DNA binding mode is preferred by NF-κB p50 homodimer? To address this, we engineered a "Test" κB-like DNA containing the core sequence 5'-GGGGAATTCCCC-3' and determined its X-ray crystal structure in complex with p50. This revealed that, when presented with multiple options, NF-κB p50 homodimer prefers to bind 11-bp, which necessarily imposes asymmetry on the complex despite the symmetry inherent in both the protein and its target DNA, and that the p50 dimerization domain can contact DNA via distinct modes.

Capturing in-field root system dynamics with RootTracker.

Optimizing root system architecture offers a promising approach to developing stress tolerant cultivars in the face of climate change, as root systems are critical for water and nutrient uptake as well as mechanical stability. However, breeding for optimal root system architecture has been hindered by the difficulty in measuring root growth in the field. Here, we describe the RootTracker, a technology that employs impedance touch sensors to monitor in-field root growth over time. Configured in a cylindrical, window shutter-like fashion around a planted seed, 264 electrodes are individually charged multiple times over the course of an experiment. Signature changes in the measured capacitance and resistance readings indicate when a root has touched or grown close to an electrode. Using the RootTracker, we have measured root system dynamics of commercial maize (Zea mays) hybrids growing in both typical Midwest field conditions and under different irrigation regimes. We observed rapid responses of root growth to water deficits and found evidence for a "priming response" in which an early water deficit causes more and deeper roots to grow at later time periods. Genotypic variation among hybrid maize lines in their root growth in response to drought indicated a potential to breed for root systems adapted for different environments. Thus, the RootTracker is able to capture changes in root growth over time in response to environmental perturbations.

Finite frequency range iterative learning fault-tolerant control for discrete time-delay uncertain systems with actuator faults.

The subject area considered is discrete linear time delay systems operating repetitively on a finite time interval with actuator faults, where the system resets at the end of each operation. Regulation of the dynamics is by iterative learning control and performance goals imposed over finite frequency intervals for the case of uncertainty in the dynamic model. To derive the results, the generalized Kalman-Yakubovich-Popov lemma is used. A simulation based case study is also given to demonstrate the applicability of the new results.

Physiological mechanisms contributing to the QTL qDTY3.2 effects on improved performance of rice Moroberekan x Swarna BC2F3:4 lines under drought.

BACKGROUND: Traditional rice (Oryza sativa) varieties are valuable resources for the improvement of drought resistance. qDTY3.2 is a drought-yield quantitative trait locus that was identified in a population derived from the traditional variety Moroberekan and the drought-susceptible variety Swarna. In this study, our aim was to characterize the physiological mechanisms associated with qDTY3.2. Our approach was to phenotype fifteen BC2F3:4 lines for shoot and root drought resistance-related traits as compared to Swarna in the field under well-watered and drought stress conditions. Four BC2F3:4 lines contrasting for yield under drought were selected for detailed characterization of shoot morphology, water use related traits, flowering time and root system architecture in the field as well as in controlled environments (lysimeters in a greenhouse, and gel imaging platform in a growth chamber). RESULTS: Across five field experiments, grain yield correlated significantly with root growth along the soil profile, flowering time, and canopy temperature under drought conditions. The four selected BC2F3:4 lines showed earlier flowering time, reduced distribution of root growth to shallow soil layers which resulted in lower water uptake (between 0 and 30 cm) and drought-induced increased distribution of root growth to deep soil layers (between 30 and 60 cm) as compared to Swarna in the field. Root system architecture phenotypes were confirmed in whole root systems in lysimeters, and corresponded to higher numbers of root tips in a gel imaging platform, highlighting the potential stability of some root traits across different growth stages and systems. CONCLUSIONS: We conclude that earlier flowering time, reduced shallow root growth, and drought-induced increased deep root growth are associated with the presence of qDTY3.2 since these phenotypes were consistently observed in the selected QTL lines with full introgression of qDTY3.2. We hypothesize that the qDTY3.2 associated RSA phenotypes led to better use of water and metabolic resources which, combined with earlier flowering time, improved yield under drought.

Bioenergetics of acquired cisplatin resistant H1299 non-small cell lung cancer and P31 mesothelioma cells.

Acquired cisplatin resistance is a common feature of tumours following cancer treatment with cisplatin and also of non-small cell lung cancer (H1299) and mesothelioma (P31) cell lines exposed to cisplatin. To elucidate the cellular basis of acquired cisplatin resistance, a comprehensive bioenergetic analysis was undertaken. We demonstrate that cellular oxygen consumption was significantly decreased in cisplatin resistant cells and that the reduction was primarily due to reduced mitochondrial activity as a result of reduced mitochondrial abundance. The differential mitochondrial abundance was supported by data showing reduced sirtuin 1 (SIRT1), peroxisome-proliferator activator receptor-γ co-activator 1-alpha (PGC1α), sirtuin 3 (SIRT3) and mitochondrial transcription factor A (TFAM) protein expression in resistant cells. Consistent with these data we observed increased reactive oxygen species (ROS) production and increased hypoxia inducible factor 1-alpha (HIF1α) stabilization in cisplatin resistant cells when compared to cisplatin sensitive controls. We also observed an increase in AMP kinase subunit α2 (AMPKα2) transcripts and protein expression in resistant H1299 cells. mRNA expression was also reduced for cisplatin resistant H1299 cells in these genes, however the pattern was not consistent in resistant P31 cells. There was very little change in DNA methylation of these genes, suggesting that the cells are not stably reprogrammed epigenetically. Taken together, our data demonstrate reduced oxidative metabolism, reduced mitochondrial abundance, potential for increased glycolytic flux and increased ROS production in acquired cisplatin resistant cells. This suggests that the metabolic changes are a result of reduced SIRT3 expression and increased HIF-1α stabilization.

X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture.

Root system architecture (RSA) impacts plant fitness and crop yield by facilitating efficient nutrient and water uptake from the soil. A better understanding of the effects of soil on RSA could improve crop productivity by matching roots to their soil environment. We used x-ray computed tomography to perform a detailed three-dimensional quantification of changes in rice (Oryza sativa) RSA in response to the physical properties of a granular substrate. We characterized the RSA of eight rice cultivars in five different growth substrates and determined that RSA is the result of interactions between genotype and growth environment. We identified cultivar-specific changes in RSA in response to changing growth substrate texture. The cultivar Azucena exhibited low RSA plasticity in all growth substrates, whereas cultivar Bala root depth was a function of soil hardness. Our imaging techniques provide a framework to study RSA in different growth environments, the results of which can be used to improve root traits with agronomic potential.

Cross-Disciplinary Consultancy to Enhance Predictions of Asthma Exacerbation Risk in Boston.

This paper continues an initiative conducted by the International Society for Disease Surveillance with funding from the Defense Threat Reduction Agency to connect near-term analytical needs of public health practice with technical expertise from the global research community. The goal is to enhance investigation capabilities of day-to-day population health monitors. A prior paper described the formation of consultancies for requirements analysis and dialogue regarding costs and benefits of sustainable analytic tools. Each funded consultancy targets a use case of near-term concern to practitioners. The consultancy featured here focused on improving predictions of asthma exacerbation risk in demographic and geographic subdivisions of the city of Boston, Massachusetts, USA based on the combination of known risk factors for which evidence is routinely available. A cross-disciplinary group of 28 stakeholders attended the consultancy on March 30-31, 2016 at the Boston Public Health Commission. Known asthma exacerbation risk factors are upper respiratory virus transmission, particularly in school-age children, harsh or extreme weather conditions, and poor air quality. Meteorological subject matter experts described availability and usage of data sources representing these risk factors. Modelers presented multiple analytic approaches including mechanistic models, machine learning approaches, simulation techniques, and hybrids. Health department staff and local partners discussed surveillance operations, constraints, and operational system requirements. Attendees valued the direct exchange of information among public health practitioners, system designers, and modelers. Discussion finalized design of an 8-year de-identified dataset of Boston ED patient records for modeling partners who sign a standard data use agreement.

Regulation of plant root system architecture: implications for crop advancement.

Root system architecture (RSA) plays a major role in plant fitness, crop performance, and grain yield yet only recently has this role been appreciated. RSA describes the spatial arrangement of root tissue within the soil and is therefore crucial to nutrient and water uptake. Recent studies have identified many of the genetic and environmental factors influencing root growth that contribute to RSA. Some of the identified genes have the potential to limit crop loss caused by environmental extremes and are currently being used to confer drought tolerance. It is hypothesized that manipulating these and other genes that influence RSA will be pivotal for future crop advancements worldwide.

The application of precisely controlled functional electrical stimulation to the shoulder, elbow and wrist for upper limb stroke rehabilitation: a feasibility study.

BACKGROUND: Functional electrical stimulation (FES) during repetitive practice of everyday tasks can facilitate recovery of upper limb function following stroke. Reduction in impairment is strongly associated with how closely FES assists performance, with advanced iterative learning control (ILC) technology providing precise upper-limb assistance. The aim of this study is to investigate the feasibility of extending ILC technology to control FES of three muscle groups in the upper limb to facilitate functional motor recovery post-stroke. METHODS: Five stroke participants with established hemiplegia undertook eighteen intervention sessions, each of one hour duration. During each session FES was applied to the anterior deltoid, triceps, and wrist/finger extensors to assist performance of functional tasks with real-objects, including closing a drawer and pressing a light switch. Advanced model-based ILC controllers used kinematic data from previous attempts at each task to update the FES applied to each muscle on the subsequent trial. This produced stimulation profiles that facilitated accurate completion of each task while encouraging voluntary effort by the participant. Kinematic data were collected using a Microsoft Kinect, and mechanical arm support was provided by a SaeboMAS. Participants completed Fugl-Meyer and Action Research Arm Test clinical assessments pre- and post-intervention, as well as FES-unassisted tasks during each intervention session. RESULTS: Fugl-Meyer and Action Research Arm Test scores both significantly improved from pre- to post-intervention by 4.4 points. Improvements were also found in FES-unassisted performance, and the amount of arm support required to successfully perform the tasks was reduced. CONCLUSIONS: This feasibility study indicates that technology comprising low-cost hardware fused with advanced FES controllers accurately assists upper limb movement and may reduce upper limb impairments following stroke.

Electrical stimulation and iterative learning control for functional recovery in the upper limb post-stroke.

Therapies using functional electrical stimulation (FES) in conjunction with practice of everyday tasks have proven effective in facilitating recovery of upper limb function following stroke. The aim of the current study is to develop a multi-channel electrical stimulation system that precisely controls the assistance provided in goal-orientated tasks through use of advanced model-based 'iterative learning control' (ILC) algorithms to facilitate functional motor recovery of the upper limb post-stroke. FES was applied to three muscle groups in the upper limb (the anterior deltoid, triceps and wrist extensors) to assist hemiparetic, chronic stroke participants to perform a series of functional tasks with real objects, including closing a drawer, turning on a light switch and repositioning an object. Position data from the participants' impaired upper limb was collected using a Microsoft Kinect® and was compared to an ideal reference. ILC used data from previous attempts at the task to moderate the FES signals applied to each muscle group on a trial by trial basis to reduce performance error whilst supporting voluntary effort by the participant. The clinical trial is on-going. Preliminary results show improvements in performance accuracy for each muscle group, as well as improvements in clinical outcome measures pre and post 18 training sessions. Thus, the feasibility of applying precisely controlled FES to three muscle groups in the upper limb to facilitate functional reach and grasp movements post stroke has been demonstrated.

Functional electrical stimulation mediated by iterative learning control and 3D robotics reduces motor impairment in chronic stroke.

BACKGROUND: Novel stroke rehabilitation techniques that employ electrical stimulation (ES) and robotic technologies are effective in reducing upper limb impairments. ES is most effective when it is applied to support the patients' voluntary effort; however, current systems fail to fully exploit this connection. This study builds on previous work using advanced ES controllers, and aims to investigate the feasibility of Stimulation Assistance through Iterative Learning (SAIL), a novel upper limb stroke rehabilitation system which utilises robotic support, ES, and voluntary effort. METHODS: Five hemiparetic, chronic stroke participants with impaired upper limb function attended 18, 1 hour intervention sessions. Participants completed virtual reality tracking tasks whereby they moved their impaired arm to follow a slowly moving sphere along a specified trajectory. To do this, the participants' arm was supported by a robot. ES, mediated by advanced iterative learning control (ILC) algorithms, was applied to the triceps and anterior deltoid muscles. Each movement was repeated 6 times and ILC adjusted the amount of stimulation applied on each trial to improve accuracy and maximise voluntary effort. Participants completed clinical assessments (Fugl-Meyer, Action Research Arm Test) at baseline and post-intervention, as well as unassisted tracking tasks at the beginning and end of each intervention session. Data were analysed using t-tests and linear regression. RESULTS: From baseline to post-intervention, Fugl-Meyer scores improved, assisted and unassisted tracking performance improved, and the amount of ES required to assist tracking reduced. CONCLUSIONS: The concept of minimising support from ES using ILC algorithms was demonstrated. The positive results are promising with respect to reducing upper limb impairments following stroke, however, a larger study is required to confirm this.

Localizing transcriptional regulatory elements at the mouse Dlk1 locus.

Much effort has focused recently on determining the mechanisms that control the allele-specific expression of genes subject to genomic imprinting, yet imprinting regulation is only one aspect of configuring appropriate expression of these genes. Imprinting control mechanisms must interact with those regulating the tissue-specific expression pattern of each imprinted gene in a cluster. Proper expression of the imprinted Delta-like 1 (Dlk1)-Maternally expressed gene 3 (Meg3) gene pair is required for normal fetal development in mammals, yet the mechanisms that control tissue-specific expression of these genes are unknown. We have used a combination of in vivo and in vitro expression assays to localize cis-regulatory elements that may regulate Dlk1 expression in the mouse embryo. A bacterial artificial chromosome transgene encompassing the Dlk1 gene and 77 kb of flanking sequence conferred expression in most endogenous Dlk1-expressing tissues. In combination with previous transgenic data, these experiments localize the majority of Dlk1 cis-regulatory elements to a 41 kb region upstream of the gene. Cross-species sequence conservation was used to further define potential regulatory elements, several of which functioned as enhancers in a luciferase expression assay. Two of these elements were able to drive expression of a lacZ reporter transgene in Dlk1-expressing tissues in the mouse embryo. The sequence proximal to Dlk1 therefore contains at least two discrete regions that may regulate tissue-specificity of Dlk1 expression.

Cell type-specific transcriptional profiling: implications for metabolite profiling.

Plant development and survival is centered on complex regulatory networks composed of genes, proteins, hormone pathways, metabolites and signaling pathways. The recent advancements in whole genome biology have furthered our understanding of the interactions between these networks. As a result, numerous cell type-specific transcriptome profiles have been generated that have elucidated complex gene regulatory networks occurring at the cellular level, many of which were masked during whole-organ analysis. Modern technologies have also allowed researchers to generate multiple whole-organ metabolite profiles; however, only a limited number have been generated at the level of individual cells. Recent advancements in the isolation of individual cell populations have made cell type-specific metabolite profiles possible, enabling the enhanced detection and quantification of metabolites that were formerly unavailable when considering the whole organ. The comparison of metabolite and transcriptome profiles from the same cells has been a valuable resource to generate predictions regarding specific metabolite activity and function. In this review, we focus on recent studies that demonstrate the value of cell type-specific transcriptional profiles and their comparison with profiles generated from whole organs. Advancements in the isolation of single-cell populations will be highlighted, and the potential application towards generating detailed metabolic profiles will be discussed.

Synthesis and biological evaluation of 2',4'- and 3',4'-bridged nucleoside analogues.

Most nucleosides in solution typically exist in equilibrium between two major sugar pucker forms, N-type and S-type, but bridged nucleosides can be locked into one of these conformations depending on their specific structure. While many groups have researched these bridged nucleosides for the purpose of determining their binding affinity for antisense applications, we opted to look into the potential for biological activity within these conformationally-locked structures. A small library of 2',4'- and 3',4'-bridged nucleoside analogues was synthesized, including a novel 3',4'-carbocyclic bridged system. The synthesized compounds were tested for antibacterial, antitumor, and antiviral activities, leading to the identification of nucleosides possessing such biological activities. To the best of our knowledge, these biologically active compounds represent the first example of 2',4'-bridged nucleosides to demonstrate such properties. The most potent compound, nucleoside 33, exhibited significant antiviral activity against pseudoviruses SF162 (IC(50)=7.0 µM) and HxB2 (IC(50)=2.4 µM). These findings render bridged nucleosides as credible leads for drug discovery in the anti-HIV area of research.

VcR-CVAD induction chemotherapy followed by maintenance rituximab in mantle cell lymphoma: a Wisconsin Oncology Network study.

Intensive chemotherapy regimens are not feasible in many adults with mantle cell lymphoma (MCL). We sought to build upon our previous experience with a non-intensive regimen, modified R-hyperCVAD chemotherapy (rituximab, cyclophosphamide, vincristine, doxorubicin, dexamethasone) with maintenance rituximab (MR), by the incorporation of bortezomib (VcR-CVAD) and the extension of MR beyond 2 years. Patients with previously untreated MCL received VcR-CVAD chemotherapy every 21 d for six cycles. Patients achieving at least a partial response to induction chemotherapy received rituximab consolidation (375 mg/m(2) × 4 weekly doses) and MR (375 mg/m(2) every 12 weeks × 20 doses). The primary end points were overall and complete response (CR), and secondary endpoints were progression-free (PFS) and overall survival (OS). Thirty patients were enrolled, with a median age of 61 years. All patients had advanced stage disease, and 60% had medium/high MCL International Prognostic Index risk factors. A CR or unconfirmed CR was achieved in 77% of patients. After a median follow-up of 42 months, the 3-year PFS and OS were 63% and 86%, respectively. The observed 3-year PFS and OS with VcR-CVAD in MCL were comparable to reported outcomes with more intensive regimens. A cooperative group trial (E1405) is attempting to replicate these promising results.

Stroke participants' perceptions of robotic and electrical stimulation therapy: a new approach.

PURPOSE: User perceptions are critical, yet often ignored factors in the design and development of rehabilitation technologies. In this article, measures for collection of patient perceptions are developed and applied to a novel upper limb workstation that combines robotic therapy and electrical stimulation (ES). METHOD: Five participants with chronic upper limb hemiplegia post-stroke used a robotic workstation to undertake supported tracking tasks augmented by precisely controlled ES to their triceps muscle. Following a 6 week trial, a purpose designed set of questions was developed and individual interviews were conducted by an independent health psychologist. RESULTS: The simple, quick to administer question set showed that participants had a positive response to the system, and contributed valuable feedback with regard to its usability and effectiveness. Participants want a home-based system targeting their whole arm. CONCLUSION: This article demonstrates the value in assessing user perceptions of a rehabilitation system via a simple question set. While the results of this study have implications for a wider audience, our recommendations are for a qualitative study to develop a generic evaluation tool which could be used across the growing number of devices to provide feedback to enhance future development of any new technology for rehabilitation.

Upper limb stroke rehabilitation: the effectiveness of Stimulation Assistance through Iterative Learning (SAIL).

A novel system has been developed which combines robotic therapy with electrical stimulation (ES) for upper limb stroke rehabilitation. This technology, termed SAIL: Stimulation Assistance through Iterative Learning, employs advanced model-based iterative learning control (ILC) algorithms to precisely assist participant's completion of 3D tracking tasks with their impaired arm. Data is reported from a preliminary study with unimpaired participants, and also from a single hemiparetic stroke participant with reduced upper limb function who has used the system in a clinical trial. All participants completed tasks which involved moving their (impaired) arm to follow an image of a slowing moving sphere along a trajectory. The participants' arm was supported by a robot and ES was applied to the triceps brachii and anterior deltoid muscles. During each task, the same tracking trajectory was repeated 6 times and ILC was used to compute the stimulation signals to be applied on the next iteration. Unimpaired participants took part in a single, one hour training session and the stroke participant undertook 18, 1 hour treatment sessions composed of tracking tasks varying in length, orientation and speed. The results reported describe changes in tracking ability and demonstrate feasibility of the SAIL system for upper limb rehabilitation.

Imprinting analysis in the Acrodysplasia region of mouse chromosome 12.

The insertional mouse mutation Adp (Acrodysplasia) confers a parent-of-origin developmental phenotype, with animals inheriting the mutation from their father showing skeletal abnormalities, whereas those inheriting the mutation from their mother are normal. This parental-specific phenotype, along with mapping of the insertion to a region of chromosome 12 proposed to contain imprinted genes, suggested that disruption of genomic imprinting might underlie the Adp phenotype. Genomic imprinting is the process by which autosomal genes are epigenetically silenced on one of the two parental alleles; imprinting mutation phenotypes manifest after inheritance from one parent but not the other. Imprinted genes typically occur in dense clusters that contain few non-imprinted genes and therefore representative genes from the Adp critical region could be assayed to identify any imprinted domains. None of the genes analysed were found to be imprinted, however, suggesting that other explanations for the Adp phenotype must be considered.

Follicular lymphoma in the United States: first report of the national LymphoCare study.

PURPOSE: Optimal therapy of follicular lymphoma (FL) is not defined. We analyzed a large prospective cohort study to identify current demographics and patterns of care of FL in the United States. PATIENTS AND METHODS: The National LymphoCare Study is a multicenter, longitudinal, observational study designed to collect information on treatment regimens and outcomes for patients with newly diagnosed FL in the United States. Patients were enrolled between 2004 and 2007. There is no study-specific prescribed treatment regimen or intervention. RESULTS: Two thousand seven hundred twenty-eight subjects were enrolled at 265 sites, including the 80% of patients enrolled from nonacademic sites. Using the Follicular Lymphoma International Prognostic Index (FLIPI), three distinct groups independent of histologic grade could be defined. Initial therapeutic strategy was: observation, 17.7%; rituximab monotherapy, 13.9%; clinical trial 6.1%; radiation therapy, 5.6%; chemotherapy only, 3.2%; chemotherapy plus rituximab, 51.9%. Chemotherapy plus rituximab regimens were: rituximab plus cyclophosphamide, doxorubicin, vincristine, prednisone, 55.0%; rituximab plus cyclophosphamide, vincristine, and prednisone, 23.1%; rituximab plus fludarabine based, 15.5%; other, 6.4%. The choice to initiate therapy rather than observe was associated with age, FLIPI, stage, and grade (P < .01). Significant differences in treatment (P < .01) across regions of the United States were noted. Contrary to practice guidelines, treatment of stage I FL frequently omits radiation therapy. CONCLUSION: Widely disparate therapeutic approaches are utilized for FL. Initial therapy is deferred in a small subset of patients. There is no single standard of care for the treatment of de novo FL, although antibody use is ubiquitous when therapy is initiated. These disparate approaches to the initial care of patients with FL render a heterogeneous group of patients at relapse.

A model of the upper extremity using FES for stroke rehabilitation.

A model of the upper extremity is developed in which the forearm is constrained to lie in a horizontal plane and electrical stimulation is applied to the triceps muscle. Identification procedures are described to estimate the unknown parameters using tests that can be performed in a short period of time. Examples of identified parameters obtained experimentally are presented for both stroke patients and unimpaired subjects. A discussion concerning the identification's repeatability, together with results confirming the accuracy of the overall representation, is given. The model has been used during clinical trials in which electrical stimulation is applied to the triceps muscle of a number of stroke patients for the purpose of improving both their performance at reaching tasks and their level of voluntary control over their impaired arm. Its purpose in this context is threefold: Firstly, changes occurring in the levels of stiffness and spasticity in each subject's arm can be monitored by comparing frictional components of models identified at different times during treatment. Secondly, the model is used to calculate the moments applied during tracking tasks that are due to a patient's voluntary effort, and it therefore constitutes a useful tool with which to analyze their performance. Thirdly, the model is used to derive the advanced controllers that govern the level of stimulation applied to subjects over the course of the treatment. Details are provided to show how the model is applied in each case, and sample results are shown.