cssi/SciSciGPT-SciSciNet huggingface dataset:
Temporal and structural analysis of biological networks in combination with microarray data

We introduce a graph-based relational learning approach using graph-rewriting rules for temporal and structural analysis of biological networks changing over time. The analysis of dynamic biological networks is necessary to understand life at the system-level, because biological networks continuously change their structures and properties, while an organism performs various biological activities. A dynamic graph represents dynamic properties as well as structural properties of biological networks. Microarray data can reflect dynamic properties of biological processes. Biological networks, which contain various molecules and relationships between molecules, show structural properties representing various relationships between entities. Most current graph-based data mining approaches overlook dynamic features of biological networks, because they are focused on only static graphs. Most approaches for analysis of microarray data disregard structural properties on biological systems. But our dynamic graph-based relational learning approach describes how the graphs temporally and structurally change over time in the dynamic graph representing biological networks in combination with microarray data.
Dynamic modeling of a three-way catalyst for SI engine exhaust emission control

Automotive emissions are severely regulated. Since 1980, a three-way catalyst (TWC) has been used to convert harmful emissions of hydrocarbons, carbon monoxide, and oxides of nitrogen into less harmful gases in order to meet these regulations. The TWC's efficiency of conversion of these gases is primarily dependent on the mass ratio of air to fuel (A/F) in the mixture leaving the exhaust manifold and entering the catalyst, the velocity of the exhaust mass, and the temperature of the catalyst. The goal of the paper is to develop a dynamic control-oriented model of a TWC. First, the measurement capabilities are described. Then, a simplified, dynamic catalyst model that can be determined on the basis of medium bandwidth A/F measurements and low bandwidth temperature and emission measurements is developed and validated.
Customer Efficiency, Channel Usage, and Firm Performance in Retail Banking

Innovations in technology and service design have increasingly enabled firms to incorporate self-service technology to augment or substitute for “traditional” employee-provided service channels. Although it is clear that self-service can reduce cost, less is known about how customers utilize self-service channels in a multichannel service delivery system and the resulting impact on firm performance. An important aspect of service operations is that customers are coproducers of the service. Thus, the performance of the delivery system and customers' use of service channels can be affected by customers' own efficiency or productivity in service coproduction (customer efficiency). In this paper, we utilize prior theoretical frameworks in service operations and economics to hypothesize relationships among customer characteristics (especially coproduction efficiency), channel utilization, and firm performance. We then test these hypotheses using panel data from a large retail bank. Overall, we find that higher customer efficiency in self-service channels is associated with greater profitability and has a complex relationship with customer retention and product utilization.
High-efficiency Ku-band HBT MMIC power amplifier

A Ku-band monolithic HBT power amplifier was developed using a metal-organic chemical vapor deposition (MOCVD)-grown AlGaAs/GaAs heterojunction bipolar transistor (HBT) operating in common-emitter mode. At a 7.5 V collector bias, the amplifier produced 0.5 W CW output power with 5.0 dB gain and 42% power-added efficiency in the 15-16 GHz band. When operated at a single frequency (15 GHz), 0.66 W CW output power and 5.2 dB of gain were achieved with 43% PAE. >
Ultraviolet Stand-off Raman Measurements Using a Gated Spatial Heterodyne Raman Spectrometer:

A spatial heterodyne Raman spectrometer (SHRS) is evaluated for stand-off Raman measurements in ambient light conditions using both ultraviolet (UV) and visible pulsed lasers with a gated ICCD detector. The wide acceptance angle of the SHRS simplifies optical coupling of the spectrometer to the telescope and does not require precise laser focusing or positioning of the laser on the sample. If the laser beam wanders or loses focus on the sample, as long as it is in the field of view of the SHRS, the Raman signal will still be collected. The SHRS is not overly susceptible to vibrations, and a vibration isolated optical table was not necessary for these measurements. The system performance was assessed by measuring stand-off UV and visible Raman spectra of a wide variety of materials at distances up to 18 m, using 266 nm and 532 nm pulsed lasers, with 12.4 in. and 3.8 in. aperture telescopes, respectively.
Seeing is believing, PLGA microsphere degradation revealed in PLGA microsphere/PVA hydrogel composites

The aim of this study was to understand the polymer degradation and drug release mechanism from PLGA microspheres embedded in a PVA hydrogel. Two types of microspheres were prepared with different molecular weight PLGA polymers (approximately 25 and 7 kDa) to achieve different drug release profiles, with a 9-day lag phase and without a lag phase, respectively. The kinetics of water uptake into the microspheres coincided with the drug release profiles for both formulations. For the 25 kDa microspheres, minimal water uptake was observed in the early part of the lag phase followed by substantial water uptake at the later stages and in the drug release phase. For the 7 kDa microspheres, water uptake occurred simultaneously with drug release. Water uptake was approximately 2-3 times that of the initial microsphere weight for both formulations. The internal structure of the PLGA microspheres was evaluated using low temperature scanning electron microscopy (cryo-SEM). Burst drug release occurred followed by pore forming from the exterior to the core of both microspheres. A well-defined hydrogel/microsphere interface was observed. For the 25 kDa microspheres, internal pore formation and swelling occurred before the second drug release phase. The surface layer of the microspheres remained intact whereas swelling, and degradation of the core continued throughout the drug release period. In addition, microsphere swelling reduced glucose transport through the coatings in PBS media and this was considered to be a as a consequence of the increased thickness of the coatings. The combination of the swelling and microdialysis results provides a fresh understanding on the competing processes affecting molecular transport of bioanalytes (i.e. glucose) through these composite coatings during prolonged exposure in PBS.
Standardization of Light Scattering Measurement in Conjunction With Immunochemical Analysis.

Light scattering methods for the physical analysis of synthetic and biological polymers necessitates the use of scattering standards and absolute light scattering measurements. Standardization has not been employed when light scattering has been used to monitor immunochemical reactions using a kinetic or thermodynamic mode. The concentration of a specific protein present in a complex matrix such as urine, serum or cerebrospinal fluid, is measured by reacting the protein of interest with its specific antibody and then measuring the excess light scattering of the solution produced by the formation of antigen antibody complexes. The lack of established light scattering standards in the area of immunochemical measurements makes instrumental quality control difficult and has hindered direct comparison of data among investigators. Both solid and liquid light scattering standards would be necessary to encompass the wide range of instrumentation currently in use. Several solid standards which have been used in the past include reflecting diffusers such as vitrolite, magnesium carbonate crystals with a ground surface, magnesium oxide coatings on magnesium carbonate crystal, casein paint on vitrolite, and solid opal glass transmitting diffusers such as flashed opal glass and solid opal glass. These standards, while applicable to manual light scattering photometers, are not suitable for recently developed automated instrumentation. Liquid standards in the form of Ludox®, solutions of polystyrene, suspensions of small diameter latex spheres and even pure organic solvents could be used more easily with the continuous flow and discrete automated analyzers. The introduction of instrumental standards at this level of analysis would result in improved overall quality control and facilitate data and method comparison between laboratories.
28. Mullerian adenosarcoma: A rare endocervical polyp in a 14-year-old

Case report A 14-year-old girl presented with a 3-month history of vaginal discharge and a protruding vaginal mass. MRI revealed a cervical mass distending the upper vagina. A soft pedunculated endocervical polyp (5×3 cm) was removed piecemeal. Histologically, scattered glands lined by bland endometrioid and endocervical epithelia were surrounded by a variably cellular stroma displaying prominent periglandular cuffing, subepithelial condensation, mild stromal nuclear atypia and mitotic activity. No sarcomatous overgrowth or heterologous elements were identified. Immunostaining showed patchy reactivity for CD10, ER and PR, and negative staining for desmin and myogenin. The diagnosis of Mullerian adenosarcoma was made. Discussion Mullerian adenosarcoma arising in the cervix is much less common than those in the uterine corpus. The mean age of patients (37 years) is significantly younger than women with adenosarcoma of the corpus, the majority of whom are postmenopausal. To our knowledge, cervical adenosarcoma has been reported in 13 patients below 20 years of age. In those 5 patients in whom hysterectomy was avoided, and local conservative treatment preferred, the tumour subsequently recurred in the endometrium in four. Thus, optimal therapy for these very young patients poses a significant clinical dilemma. In our case, the decision has been for conservative management with regular watchful follow up. Clinically and histologically, adenosarcoma can be confused with other lesions and may not be correctly diagnosed until recurrence occurs. The histological features (e.g., stromal hypercellulairty, periglandular cuffing) may be subtle and patchy. Extensive sampling and attention to subtle histological changes should lead to correct diagnosis. We report a case of Mullerian adenosarcoma presented as an endocervical polyp in a 14-year-old to raise an awareness of this rare paediatric tumour.
Theory of chronopotentiometry with cylindrical electrodes: III. Successive electrochemical reactions

Abstract The theoretical transition-time equation for successive electrochemical reactions has been derived for the case of cylindrically symmetrical diffusion. Chronopotentiometric data for the successive reductions of ferric and cupric ions at a platinum wire cathode in hydrochloric acid have served to establish the validity of this relation. For the second and all subsequent reactions, the cylindricity of the diffusion field causes an increase in the transition times over and above the normal “enhancement” due to the decrease in current efficiency for these reactions. Furthermore, the cylindricity effect becomes larger and larger as the transition times increase. For the stepwise reaction of a single substance, the ratio of transition times ( i.e. , θ2/θ1) increases rapidly as the absolute magnitude of the transition times becomes larger. The deduction of n -values for stepwise reactions based on measurements of the ratio of transition times may lead to anomalous results if the cylindricity effect is neglected.
Use of Virtual Environments for the Acquisition of Spatial Knowledge: Comparison Among Different Visual Displays

This experiment investigated the effects of three visual display systems differing in immersiveness: A wide field of view (FOV) 3-D helmet-mounted display (HMD); a 3-D HMD with a narrow FOV; and a ...
High-Efficiency Tandem Absorbers for Economical Solar Hydrogen Production

In this talk I will present an overview of our research strategy to develop a semiconductor-based device capable of over 20% solar-to-hydrogen efficiency with several thousand hours of stability under operating conditions. Our goal is to improve solar-to-hydrogen (STH) efficiency from 12.4% to over 20% by developing novel tandem semiconductor materials and configurations. Our approach focuses on classes of materials that have either demonstrated exceptionally high efficiency or theoretically can produce highly efficient materials. The four tandem material sets in our research portfolio are III-Vs on GaAs, InGaN on Si, III-V-N on Si, and dual photoelectrode pairings. We are evaluating catalytic nitride, oxide, and sulfide-based semiconductor surface modifications to extend durability from a few hundred hours to nearly 1000 hours, with a stretch target of 3500 hours. Cost reductions in the synthesis of high-efficiency III-V photoelectrochemical devices could be realized from emerging epitaxial synthesis technologies such as spalling, epitaxial lift-off, close-space vapor transport, or hydride vapor phase epitaxy to yield economical hydrogen production. Our group addresses synthesis cost, in a limited capacity, by investigating novel material configurations. Within the next few years, we plan to demonstrate a prototype photoreactor that produces 3 L of standard hydrogen within an 8-hour period under moderate solar concentration (10x), which can be accomplished using only 6 cm2 of a 20% STH material.
Autobiography and Memory

(1998). Autobiography and Memory. a/b: Auto/Biography Studies: Vol. 13, Autobiography & Neuroscience, pp. 61-70.
Hypolipidemic and Antihyperlipidemic Drugs

Hyperlipidemia is a metabolic (mainly inherited) disorder characterized by elevated lipid and/or lipoprotein levels in the blood and is an important risk factor in development of atherosclerosis and heart disease.
Bayesian characterization of buildings using seismic interferometry on ambient vibrations

Abstract Continuous monitoring of engineering structures provides a crucial alternative to assess its health condition as well as evaluate its safety throughout the whole service life. To link the field measurements to the characteristics of a building, one option is to characterize and update a model, against the measured data, so that it can best describe the behavior and performance of the structure. In this paper, we present a novel computational strategy for Bayesian probabilistic updating of building models with response functions extracted from ambient noise measurements using seismic interferometry. The intrinsic building impulse response functions (IRFs) can be extracted from ambient excitation by deconvolving the motion recorded at different floors with respect to the measured ambient ground motion. The IRF represents the representative building response to an input delta function at the ground floor. The measurements are firstly divided into multiple windows for deconvolution and the IRFs for each window are then averaged to represent the overall building IRFs. A hierarchical Bayesian framework with Laplace priors is proposed for updating the finite element model. A Markov chain Monte Carlo technique with adaptive random-walk steps is employed to sample the model parameters for uncertainty quantification. An illustrative example is studied to validate the effectiveness of the proposed algorithm for temporal monitoring and probabilistic model updating of buildings. The structure considered in this paper is a 21-storey concrete building instrumented with 36 accelerometers at the MIT campus. The methodology described here allows for continuous temporal health monitoring, robust model updating as well as post-earthquake damage detection of buildings.
Six-month-old infants expect agents to minimize the cost of their actions

Substantial evidence indicates that infants expect agents to move directly to their goals when no obstacles block their paths, but the representations that articulate this expectation and its robustness have not been characterized. Across three experiments (total N=60), 6-month-old infants responded to a novel, curvilinear action trajectory on the basis of its efficiency, in accord with the expectation that an agent will move to its goal on the least costly path that the environment affords. Infants expected minimally costly action when presented with a novel constraint, and extended this expectation to agents who had previously acted inefficiently. Infants' understanding of goal-directed action cannot be explained alone by sensitivity to specific features of agent's actions (e.g. agents tend to move on straight paths, along supporting surfaces, when facing their goals directly) or extrapolations of agents' past actions to their future ones (e.g. if an agent took the shortest path to an object in the past, it will continue to do so in the future). Instead, infants' reasoning about efficiency accords with the overhypothesis that agents minimize the cost of their actions.
Effects of a brief ED-based alcohol and violence intervention on depressive symptoms

Abstract Objective Depressive symptoms frequently co-exist in adolescents with alcohol use and peer violence. This paper's purpose was to examine the secondary effects of a brief alcohol-and-violence-focused ED intervention on depressive symptoms. Method Adolescents (ages 14–18) presenting to an ED for any reason, reporting past year alcohol use and aggression, were enrolled in a randomized control trial (control, therapist-delivered brief intervention [TBI], or computer-delivered brief intervention [CBI]). Depressive symptoms were measured at baseline, 3, 6, and 12months using a modified 10-item Center for Epidemiological Studies Depression Scale (CESD-10). Poisson regression was used (adjusting for baseline age, gender, and depressive symptoms) to compare depressive symptoms at follow-up. Results Among 659 participants, higher baseline depressive symptoms, female gender, and age≥16 were associated with higher depressive symptoms over time. At 3months, CBI and TBI groups had significantly lower CESD-10 scores than the control group; at 6months, intervention and control groups did not differ; at 12months, only CBI had a significantly lower CESD-10 score than control. Conclusions A single-session brief ED-based intervention focused on alcohol use and violence also reduces depressive symptoms among at-risk youth. Findings also point to the potential efficacy of using technology in future depression interventions.
HIV Risk Behaviors and Utilization of Prevention Services, Urban and Rural Men Who Have Sex with Men in the United States: Results from a National Online Survey.

Rural men who have sex with men (MSM) are heavily affected by HIV, and many lack culturally competent HIV prevention resources. Rural MSM may find sexual partners on the internet, which may also be a way to deliver prevention services to them. To understand the differences between rural and urban MSM with respect to HIV risk factors and behaviors and the utilization of online HIV prevention services, we used data from the 2012 Web-Based HIV Behavioral Survey (WHBS). Using WHBS data collected between June and August 2012, we compared the characteristics of MSM with positive or unknown HIV infection status who had sex with a male in the past 12 months, from rural vs urban areas using Chi square tests and median tests. We used logistic regression and calculated adjusted prevalence ratios (aPR) and 95% confidence intervals (CI) to compare self-reported HIV risk behaviors, HIV/STI testing behaviors, use of prevention services, and perceived discrimination. Of the 8166 MSM included in our analysis, 3583 (44%) were from rural areas, and 4583 (56%) were from urban areas. Compared to urban MSM, rural MSM were less likely to ever test for HIV (aPR = 0.94, CI 0.92–0.95), to be tested for HIV in the last year (aPR = 0.83, CI 0.79–0.87), or to receive free condoms (aPR = 0.83, CI 0.79–0.86) or individual prevention counseling in the past year (aPR = 0.86, CI 0.78–0.95). Rural MSM were less likely to have been tested in the last year for syphilis, gonorrhea, or chlamydia (aPR = 0.70, CI 0.62–0.78; aPR = 0.72, CI 0.64–0.81; aPR = 0.75, CI 0.67–0.85, respectively). Rural MSM also reported perceiving less tolerance of gays and bisexuals within their community (aPR = 0.80, CI 0.77–0.84). HIV prevalence is lower among MSM in rural areas compared to MSM in urban areas, but rural MSM report that they are more likely to face intolerance and are less likely to use basic HIV prevention services compared to urban MSM. Therefore, this hard-to-reach population could benefit from prevention services offered through the internet.
Fungal Pre-mRNA 3′-End Processing

3′ end processing of messenger RNAs (mRNAs) is not only an essential step in eukaryotic gene expression, but it also impacts many other aspects of mRNA maturation and decay. A large portion of eukaryotic genes produce multiple mRNAs with different 3′ ends through alternative cleavage/polyadenylation (APA). mRNA 3′ processing and especially APA has been increasingly recognized as an important mechanism for gene regulation. Much of what we currently know about eukaryotic mRNA 3′ processing came from studies using the genetically tractable yeast systems. Here we review the fungal mRNA 3′ processing system by describing both the evolutionarily conserved mechanisms as well as the fungus-specific features.
Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes.

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei . Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae . The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae , E . hormaechei subsp. steigerwaltii , and E. xiangfangensis , and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E . hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI’s RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei : E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.
Regulation of Sirtuins by Systemic NAD+ Biosynthesis

Abstract In recent years, nicotinamide adenine dinucleotide (NAD + ) biology has been increasingly drawing significant attention within the scientific community and providing its vast implication for various age-associated pathophysiologies and disease conditions. Particularly, the role of NAD + in the regulation of sirtuins, an evolutionary conserved family of NAD + -dependent deacetylases/deacylases, has been extensively studied. Systemic NAD + biosynthesis mediated by intra- and extracellular nicotinamide phosphoribosyltransferase and sirtuins cooperate to regulate many fundamental biological processes in different tissues and organs and promote physiological resilience in response to nutritional and environmental perturbations. Accumulating lines of evidence suggest that systemic decline in NAD + availability is a critical trigger for age-associated functional decline and disease conditions through the reduction in sirtuin activities in different subcellular compartments. In this chapter, we will discuss the current understanding of the intimate connection between systemic NAD + biosynthesis and sirtuin functions and its implications in aging and longevity control.
A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems

The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.
Theory of cool loops and the dividing line

Static models for coronal loops have been widely used to interpret observations of the coronae of cool stars. Although these models have been successful in explaining several features of the observations; they have been unsuccessful in accounting for two key features: (a) in dwarf stars they do not agree with the observed form of the differential emission measure at low temperatures, T 105 K (the so-called dividing line). It appears that in high gravity stars there is more cool material than the standard models of the transition region predict; whereas in low gravity stars there is less hot material than the loop models predict.
The X-ray emission of E and S0 Galaxies

It is well known by now that E and S0 galaxies are associated with hot, X- ray emitting gaseous halos, subject to central cooling flows, but otherwise homogeneous, which can be used to trace the galaxy potential and thus measure the total gravitational mass. Recent ASCA observations suggest that these halos have a surprisingly low metal abundance.
Sensory processing disorders.

Most people are able to effectively process and respond to the sensory stimuli of daily life. But people who have sensory processing disorders struggle to form meaningful responses to sensory stimuli. As a result these individuals often exhibit problems with coordination, sensory-seeking or sensory-avoiding behaviors, and sensory modulation. The concept of sensory processing disorders stems from the work of occupational therapist Jean Ayres, Ph.D. Her work has launched a sensory-based treatment approach, primarily practiced by occupational therapists. This article outlines the theories supporting the notion of sensory processing disorders, options for assessment and treatment, and research on the efficacy of treatment.
Inflammation, adiposity, and progression of arterial stiffness in adolescents with type 1 diabetes: The SEARCH CVD Study

Abstract Aims We examined the association between inflammation and progression of arterial stiffness in a population of youth with type 1 diabetes (T1D). Methods A total of 287 youth with T1D (median age 13 years) from SEARCH CVD, an ancillary study to the SEARCH for Diabetes in Youth, were included. Markers of inflammation (CRP, IL-6, fibrinogen, leptin, and adiponectin) and measures of pulse wave velocity (PWV) of the arm (PWV-R), trunk (PWV-T), and lower extremity (PWV-LE) were measured at baseline. Measures of PWV were repeated approximately five years later. Results PWV-R (0.50 m/s), PWV-T (0.65 m/s), and PWV-LE (1.0 m/s) significantly increased over the follow-up (p Conclusions Improved understanding of adiposity, inflammation, and functional changes in the vascular system in patients with T1D is crucial.
Clinical characteristics and prognosis of 50 patients with a myeloproliferative syndrome and deletion of part of the long arm of chromosome 5

Of 50 consecutive patients (30 female and 20 male; median age, 70 years) with a myeloproliferative disorder and a 5q- chromosome, 12 (24%) had refractory anemia, 16 (32%) had refractory anemia with excess blasts, 13 (26%) had acute nonlymphocytic leukemia, six (12%) had the 5q- syndrome, and three (6%) had an unclassifiable myeloproliferative disease. Twenty-five patients had only a 5q- anomaly (group 1), and 25 had a 5q- plus additional chromosome abnormalities (group 2). Four types of 5q- anomalies were recognized: a del(5)(q13q33) occurred in 39 patients, a del(5)(q31q35) in nine, a del(5)(q22q33) in one, and a del(5)(q13q35) in one. The survival distribution for patients in group 1 was significantly better (P = .012) than for those in group 2. Cox-model analyses indicated that having a 5q- chromosome and other abnormalities is significantly (P less than .01) associated with poor survival even after adjustment for the effects of other important factors such as type of disease, age, and sex. The two groups had similar distributions of most variables, including age, sex, and disease types. However, patients in group 1 had a significantly higher platelet count and mean corpuscular volume than those in group 2. Only two patients in group 1 had had prior chemotherapy, but nine in group 2 had had either prior chemotherapy or radiation or both, and one patient in group 2 had had heavy exposure to pesticides.
Distance optimal formation control on graphs with a tight convergence time guarantee

For the task of moving a set of indistinguishable agents on a connected graph with unit edge distance to an arbitrary set of goal vertices, free of collisions, we propose a fast distance optimal control algorithm that guides the agents into the desired formation. Moreover, we show that the algorithm also provides a tight convergence time guarantee (time optimality and distance optimality cannot be simultaneously satisfied). Our generic graph formulation allows the algorithm to be applied to scenarios such as grids with holes (modeling obstacles) in arbitrary dimensions. Simulations, available online1, confirm our theoretical developments.
Transcriptional elongation machinery controls vulnerability of breast cancer cells to PRC2 inhibitors

CTR9 is the scaffold subunit in Paf1c, a multifunctional complex regulating multiple steps of RNA Pol II-mediated transcription. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the expression of a subset of KDMs, including KDM6A and Jarid2, is strictly controlled by CTR9. Global analyses of histone modifications revealed a significant increase of H3K27me3 upon loss of CTR9. Loss of CTR9 results in a decrease of H3K4me3 and H3K36me3 in gene bodies, and elevated levels and genome-wide expansion of H3K27me3. Mechanistically, CTR9 depletion triggers a PRC2 subtype switching from PRC2.2 to PRC2.1. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution, provide a unique mechanism of transition from transcriptionally active to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.
Biomass energy: green or dirty?

The conversion to biomass energy has played a key role in reducing our dependence on fossil fuels. But is this renewable energy source really as green as we first thought? Kate Ravilious investigates
Multi-contact 3C data reveal that the human genome is largely unentangled

The genome is organized into chromosome territories that are themselves spatially segregated in A and B compartments. The extent to which interacting compartment domains and chromosomes are topologically entangled is not known. We show that detection of series of co-occurring chromatin interactions using multi-contact 3C (MC-3C) reveals insights into the topological entanglement of compartment domains and territories. We find that series of co-occurring interactions and their order represent interaction percolation paths through nuclear space in single cells where fragment 1 interacts with fragment 2, which in turn interacts with fragment 3 and so on. Analysis of paths that cross two chromosome territories revealed very little mixing of chromatin from the two chromosomes. Similarly, paths that cross compartment domains show that loci from interacting domains do not mix. Polymer simulations show that such paths are consistent with chromosomes and compartment domains behaving as topologically closed polymers that are not catenated with one another. Simulations show that even low levels of random strand passage, e.g. through topoisomerase II activity, would result in entanglements and mixing of loci of different chromosomes and compartment domains with concomitant changes in interaction paths inconsistent with MC-3C data. Our results show that cells maintain a largely unentangled state of chromosomes and compartment domains.
Heparinized chitosan stabilizes the bioactivity of BMP-2 and potentiates the osteogenic efficacy of demineralized bone matrix.

Demineralized bone matrix (DBM), an allograft bone processed to better expose osteoinductive factors such as bone morphogenetic proteins (BMPs), is increasingly used for clinical bone repair. However, more extensive use of DBM is limited by its unpredictable osteoinductivity and low bone formation capacity. Commercial DBM products often employ polymeric carriers to enhance handling properties but such carriers generally do not possess bioactive functions. Heparin is a highly sulfated polysaccharide and is shown to form a stable complex with growth factors to enhance their bioactivities. In this study, a new heparinized synthetic carrier for DBM is developed based on photocrosslinking of methacrylated glycol chitosan and heparin conjugation. Heparinized chitosan exerts protective effects on BMP bioactivity against physiological stressors related to bone fracture healing. It also enhances the potency of BMPs by inhibiting the activity of BMP antagonist, noggin. Moreover, heparinized chitosan is effective to deliver bone marrow stromal cells and DBM for enhanced osteogenesis by sequestering and localizing the cell-produced or DBM-released BMPs. This research suggests an essential approach of developing a new hydrogel carrier to stabilize the bioactivity of BMPs and improve the clinical efficacy of current bone graft therapeutics for accelerated bone repair.
Solving Critical Point Conditions for the Hamming and Taxicab Distances to Solution Sets of Polynomial Equations

Minimizing the Euclidean distance (l2 -norm) from a given point to the solution set of a given system of polynomial equations can be accomplished via critical point techniques. This article extends critical point techniques to minimization with respect to Hamming distance (l0-"norm") and taxicab distance (l1 -norm). Numerical algebraic geometric techniques are derived for computing a finite set of real points satisfying the polynomial equations which contains a global minimizer. Several examples are used to demonstrate the new techniques.
Thinking outside the box: problem-solving in free-living lizards

Despite evidence that organisms are more likely to exhibit their full range of cognitive abilities under conditions found in nature, studies evaluating cognition under such conditions remain rare, particularly in vertebrate species. Here, we conducted an experiment to evaluate problem-solving and motor self-regulation in free-living arboreal lizards, Anolis sagrei, under natural conditions. We presented lizards with a novel detour problem which challenged individuals to circumvent a transparent barrier in order to obtain a food reward. Individuals varied in their ability to solve the detour problem. Furthermore, those that solved the problem were able to improve their performance across trials by modifying the natural response of attempting to strike the reward through the transparent barrier, providing evidence of motor self-regulation. Solving the problem required individuals to modify their typical foraging behavior, as approaching the prey in a single burst of movement that culminated with an attack was an unsuccessful strategy. Contrary to expectations, our findings provide evidence of motor self-regulation in a visually oriented, sit-and-wait predator under natural conditions, suggesting motor self-regulation is not limited by foraging strategy. Our results also underscore the need to evaluate the cognitive abilities of free-living organisms in the wild, particularly for taxa that perform poorly under laboratory conditions. Studies of animal cognition have a long history in animal behavior, which, in vertebrate species, has been dominated by experiments conducted under controlled laboratory conditions. Here, we showed that experiments can be taken “outside the box,” from the laboratory into natural conditions, and by doing so overcome some of the obstacles that have hindered our ability to study cognition in species unlikely to remain motivated when removed from the wild. We implemented a modified version of the cylinder task, which provided the stimuli needed for a visually oriented, sit-and-wait foraging lizard to participate in the experiments. Individuals of Anolis sagrei learned to solve the task by modifying what was previously described as a stereotyped prey capture behavior. In addition, individuals decreased the number of times they attempted to strike the prey through the transparent barrier. These findings provide further evidence of behavioral flexibility in anoles and new evidence of motor self-regulation. The latter demonstrates the need to extend our current understanding of potential forces favoring the evolution of cognition beyond those that have been proposed in birds and mammals. More generally, our findings demonstrate the importance of using experimental paradigms that are rooted in an understanding of the natural history of the species of interest.
Simulation-based evaluation of an energy oriented production planning system

Abstract Energy intensive companies are trying to adopt their production to volatility of the energy market in Germany because of the increasing amount of renewable energies. Therefore, established production planning processes must be changed to adapt their energy consumption according to the volatility of energy prices using energy flexibility potentials. The energy oriented production planning system supports the company by scheduling their production system cost efficient. The attainable benefit depends on the planned time period which is optimized and the uncertainties during the operation mode. Therefore this paper introduces a method to evaluate an energy oriented production planning system focusing on the optimization parameters and the optimized planning period.
Enhancing Adaptable Topological Wave Bandwidth in Piezoelectric Metamaterials via Circuitry and Lattice Symmetry Control

Recently, an electromechanical metamaterial with integrated resonant circuit elements was developed that enables on-demand tailoring of the operating frequency and interface routes for topological wave transmission. However, limitations to the operating frequency region still exist, and a full exploration of the adaptive characteristics of the topological electromechanical metamaterial has yet to be undertaken. To advance the state of the art, this study investigates the ability to enhance the range of operating frequencies for topological wave transmission in a piezoelectric metamaterial by the reconfiguration of lattice symmetries and connection of negative capacitance circuitry. In addition, the capability to modify the interface mode localization is analyzed. The plane wave expansion method is utilized to define a working frequency region for protected topological wave transmission by evaluating a local topological charge. Numerical simulations verify the existence of topologically protected interface modes and illuminate how the localization and shape of these modes can be altered via external circuit parameters. Results show that the reconfiguration of the lattice structure and connection to negative capacitance circuity enhances the operating frequency bandwidth and interface mode localization control, greatly expanding the adaptive metamaterial capabilities.
Religiously Metaphysical Arguments Against Agrifood Biotechnology

Metaphysical claims assert categories and categorical systems for the broadest and most general characterizations of reality and experience. The chapter discusses the nature of metaphysical claims and the role of religious or theological doctrines in lending support to them. Early debates over gene technology emphasized metaphysical and religious topics and questioned whether established doctrines in mainstream religious traditions were compatible with applications of genetic engineering. The chapter surveys those debates, with emphasis to their significance for agrifood biotechnologies, and situates them within the context of other technologies that have been alleged to pose religious or metaphysical challenges. Those who write in favor of gene technology from a religious perspective have not based their arguments on metaphysical claims. Hence, religiously metaphysical arguments tend to take a critical stance toward gene technology. However, metaphysical arguments appear to have decreased in frequency and significance since earlier editions of this book.
Violence risk assessment for young adults receiving treatment for early psychosis.

Abstract Aim Although the absolute risk of violence is small for individuals with mental illnesses, a specific subgroup of individuals who appear to be at increased risk for violence includes young people experiencing emerging or early psychosis. Prior research has identified risk factors for violence in this population, though no prior studies using a formal risk assessment tool have been identified. This study used the Historical Clinical Risk Management-20, version 3 (HCR-20) to identify risk of future violence among a sample of young adults with early psychosis and relevant predictors of risk unique to this population. Methods The HCR-20 was administered to a sample of young adults with early psychosis (N = 53) enrolled at one OnTrackNY site, part of a statewide program providing early intervention services to young adults presenting with a first episode of non-affective psychosis. A Confirmatory Factor Analysis (CFA) was conducted to explore the relative importance of the HCR-20 items for this population. Results The average age of participants was 21.9 years (SD 3.6 years) and most were male (69.8%, n = 37). Most patients were assessed to be at low risk for future violence based on the Case Prioritization summary risk rating (67.9%, n = 36). The CFA identified 4 items that were not of relative predictive value in identifying the risk of violence in this sample: history of substance use (item H5), history of major mental disorder (item H6), living situation (item R2), and personal support (item R3). Conclusion This study presents a formal approach to assessing violence risk in a population at elevated risk of violence, demonstrates the feasibility of using a standardized risk assessment tool in early intervention services, and identifies factors of particular importance associated with predicting violence in this population. Future research should implement violence risk assessment with a structured tool such as the HCR-20 and assess its accuracy in predicting future violent behavior in this setting.
Quantitative Tracking of Protein Trafficking to the Nucleus Using Cytosolic Protein Delivery by Nanoparticle-Stabilized Nanocapsules

We describe a method for quantitative monitoring of subcellular protein trafficking using nanoparticle-stabilized nanocapsules for protein delivery. This method provides rapid delivery of the protein into the cytosol, eliminating complications from protein homeostasis processes found with cellularly expressed proteins. After delivery, nuclear protein trafficking was followed by real time microscopic imaging. Quantitative analyses of the accumulation percentage and the import dynamics of the nuclear protein trafficking, demonstrate the utility of this method for studying intracellular trafficking systems.
Vagal afferent nerves with nociceptive properties in guinea-pig oesophagus

Some vagal afferent nerves are thought to mediate autonomic responses evoked by noxious oesophageal stimuli and participate in the perception of pain originating in the oesophagus. However, the vagal nociceptive nerve phenotypes implicated in this function have yet to be identified. In this study, nociceptive fibres were defined by the capacity to discriminate noxious mechanical stimuli (wide range of oesophageal distension with pressure up to 100 mmHg) and detect noxious chemical stimuli (the activators of capsaicin receptor TRPV1). Using immunohistochemical techniques with retrogradely labelled oesophagus-specific neurones and performing extracellular recordings from the isolated vagally innervated oesophagus, we show that in the guinea-pig, the vagus nerves supply the oesophagus with a large population of nociceptive-like afferent nerve fibres. Vagal nociceptive-like fibres in the guinea-pig oesophagus are derived from two embryonically distinct sources: neurones situated in the nodose vagal ganglia and neurones situated in the jugular vagal ganglia. Nodose (placode-derived) nociceptive-like fibres are exclusively C-fibres sensitive to a P2X receptors agonist and rarely express the neuropeptide substance P. In contrast, jugular (neural crest-derived) nociceptive-like fibres include both A-fibres and C-fibres, are insensitive to P2X receptors agonist and mostly express substance P. The non-nociceptive vagal tension mechanoreceptors are distinguished from nociceptors by their saturable response to oesophageal distension and by the lack of TRPV1. These tension mechanoreceptors are exclusively A-fibres arising from the nodose ganglion. We conclude that the vagus nerves supply the guinea-pig oesophagus with nociceptors in addition to tension mechanoreceptors. The vagal nociceptive-like fibres in the oesophagus comprise two distinct subtypes dictated by the ganglionic location of their cell bodies.
Past Life on Mars

Letters from: [ Frank von Hippel and Ted von Hippel ][1] [ Harold J. Morowitz ][1] [ Louis J. DeTolla ][1] [ David S. McKay, et al. ][1] Richard A. Kerr's News article about possible traces of life found on a Martian meteorite ([16 Aug., p. 864][2]) focuses primarily on the validity of the
Coeliac disease: the great imitator

Coeliac disease (CD) is caused by a complex immunological response provoked by grain protein in susceptible people. The majority of people with CD are symptom-free adults; the remainder are prone to a bewildering variety of signs and symptoms, ranging from infertility to type 1 diabetes. Many patients with undiagnosed CD spend years seeking help for complaints such as chronic tiredness or mild abdominal symptoms. In primary care, an appropriate target group to test for CD is people with anaemia (especially women), chronic tiredness, non-specific abdominal symptoms (including so-called "irritable bowel syndrome"), or a family history of CD. The response to an appropriate gluten-free diet is often life-transforming for symptomatic patients. Positive serological tests for CD require confirmation by duodenal biopsy and, if confirmed, referral to a dietitian and a coeliac society, followed by a life-long gluten-free diet.
F-Continuous Graphs

For a nontrivial connected graph F, the F-degree of a vertex υ in a graph G is the number of copies of F in G containing υ. A graph G is F-continuous (or F-degree continuous) if the F-degrees of every two adjacent vertices of G differ by at most 1. All P3-continuous graphs are determined. It is observed that if G is a nontrivial connected graph that is F-continuous for all nontrivial connected graphs F, then either G is regular or G is a path. In the case of a 2-connected graph F, however, there always exists a regular graph that is not F-continuous. It is also shown that for every graph H and every 2-connected graph F, there exists an F-continuous graph G containing H as an induced subgraph.