bluuebunny/crossref_metadata_2025 huggingface dataset:
Agonists binding nicotinic receptors elicit specific channel‐opening patterns at αγ and αδ sites
Authors: Stock Patrick , Ljaschenko Dmitrij , Heckmann Manfred , Dudel Josef
Published: March 2014

Key points

High‐resolution patch clamp currents evoked by epibatidine (Ebd), carbamylcholine (CCh) and acetylcholine (ACh) were compared. Ebd binds with 75‐fold higher affinity at αγ than at αδ sites, whereas CCh and ACh prefer αδ sites of nicotinic ACh receptor (nAChR) channels.

Similar short (τO1), intermediate (τO2) and long (τO3) types of opening were observed. τO2 openings were maximally prevalent at low Ebd concentrations, binding at αγ sites, whereas τO1 openings appear to be generated at αδ sites.

Short (∼0.75 ms) bursts of openings (τB1) arise from the αγ site, and long (>10 ms) bursts (τB2) arise from double liganded receptors. The duration of bursts and of openings within bursts depended on the agonist.

Limited by the temporal resolution, the closings within bursts were invariant at 3 μs.

Blocking αδ sites with α‐conotoxin M1 (CTx) eliminated both τO1 and τB2 and left only τO2 and the short τB1 bursts, as expected.

‘Embryonic’ muscle‐type nicotinic acetylcholine receptor channels (nAChRs) bind ligands at interfaces of α‐ and γ‐ or δ‐subunits. αγ and αδ sites differ in affinity, but their contributions to opening the channel have remained elusive. We compared high‐resolution patch clamp currents evoked by epibatidine (Ebd), carbamylcholine (CCh) and acetylcholine (ACh). Ebd binds with 75‐fold higher affinity at αγ than at αδ sites, whereas CCh and ACh prefer αδ sites. Similar short (τO1), intermediate (τO2) and long (τO3) types of opening were observed with all three agonists. τO2 openings were maximally prevalent at low Ebd concentrations, binding at αγ sites. By contrast, τO1 openings appear to be generated at αδ sites. In addition, two types of burst appeared: short bursts of an average of 0.75 ms (τB1) that should arise from the αγ site, and long bursts of 12–25 ms (τB2) in duration arising from double liganded receptors. Limited by the temporal resolution, the closings within bursts were invariant at 3 μs. Corrected for missed closings, in the case of ACh the openings within long bursts lasted 170 μs and those in short bursts about 30 μs. Blocking αδ sites with α‐conotoxin M1 (CTx) eliminated both τO1 and τB2 and left only τO2 and the short τB1 bursts, as expected. Furthermore we found desensitization when the receptors bound ACh only at the αγ site. When CTx was applied to ‘embryonic’ mouse endplates, monoquantal current rise times were increased, and amplitude and decay time constants were reduced, as expected. Thus the αγ and αδ sites of nAChRs elicit specific channel‐opening patterns.
Nucleus accumbens neuronal maturation differences in young rats bred for low versus high voluntary running behaviour
Authors: Roberts Michael D. , Toedebusch Ryan G. , Wells Kevin D. , Company Joseph M. , Brown Jacob D. , Cruthirds Clayton L. , Heese Alexander J. , Zhu Conan , Rottinghaus George E. , Childs Thomas E. , Booth Frank W.
Published: March 2014

Key points

Selective breeding experiments with laboratory rodents have demonstrated the heritability of voluntary exercise.

We performed RNA sequencing and bioinformatics analyses of the reward and pleasure hub in the brain – the nucleus accumbens – in rats selectively bred for low voluntary running (LVR) versus high voluntary running (HVR).

The discovery of unique genes and ‘cell cycle’‐related gene pathways between lines guided our hypothesis that neuron maturation may be lower in LVR rats.

Testing of this hypothesis revealed that the LVR line inherently possessed fewer mature medium spiny neurons and fewer immature neurons than their HVR counterparts. However, minimal running in LVR rats appeared to rescue and/or reverse these effects.

Neuron maturation in the nucleus accumbens is related to low running voluntary behaviour in our model; this allows researchers to understand the potential neural mechanisms that underlie the motivations for low physical activity behaviour.

We compared the nucleus accumbens (NAc) transcriptomes of generation 8 (G8), 34‐day‐old rats selectively bred for low (LVR) versus high voluntary running (HVR) behaviours in rats that never ran (LVRnon‐run and HVRnon‐run), as well as in rats after 6 days of voluntary wheel running (LVRrun and HVRrun). In addition, the NAc transcriptome of wild‐type Wistar rats was compared. The purpose of this transcriptomics approach was to generate testable hypotheses as to possible NAc features that may be contributing to running motivation differences between lines. Ingenuity Pathway Analysis and Gene Ontology analyses suggested that ‘cell cycle’‐related transcripts and the running‐induced plasticity of dopamine‐related transcripts were lower in LVR versus HVR rats. From these data, a hypothesis was generated that LVR rats might have less NAc neuron maturation than HVR rats. Follow‐up immunohistochemistry in G9–10 LVRnon‐run rats suggested that the LVR line inherently possessed fewer mature medium spiny (Darpp‐32‐positive) neurons (P < 0.001) and fewer immature (Dcx‐positive) neurons (P < 0.001) than their G9–10 HVR counterparts. However, voluntary running wheel access in our G9–10 LVRs uniquely increased their Darpp‐32‐positive and Dcx‐positive neuron densities. In summary, NAc cellularity differences and/or the lack of running‐induced plasticity in dopamine signalling‐related transcripts may contribute to low voluntary running motivation in LVR rats.
Light-Emitting Diodes: Exploration of Underlying Physics
Authors: Etkina Eugenia , Planinšič Gorazd
Published: March 2014

This paper is the second in the series of LED-dedicated papers that have a goal to systematically investigate the use of LEDs in a general physics course. The first paper, published in the February 2014 issue, provided an overview of the course units where LEDs can be used and suggested three different ways of utilizing LEDs in an introductory physics course: (I) as “black boxes” that allow students to study certain properties of a system of interest, (II) as physical systems that allow students to learn a large amount of physics not usually encountered in a typical introductory course, and (III) as non-traditional devices that allow students to construct concepts that are traditionally a part of a general physics course.1 The present paper focuses on LED physics and how students can learn this physics through a guided inquiry approach (section II in the classification above). Specifically, we will: (1) introduce the Investigative Science Learning Environment (ISLE) approach,2 which we will use as a framework for student learning of the physics of the LEDs; (2) discuss the most important aspects of LED physics that students can learn in a general physics course; and (3) describe in detail classroom activities that follow the ISLE approach which will lead the students to the “discovery” of LED physics described in (2).
Blown Away
Authors: Scott Alan
Published: March 2014

On Aug. 13, 2011, at 8:45 p.m. country music fans were eagerly awaiting the band Sugarland to make its entry onto the main stage at the Indiana State Fairgrounds. Also competing for the fans' attention was an approaching storm. Sugarland never made their entrance. At 8:49 p.m. the stage rigging was hit by 59 mile/h (94 km/h) winds causing it to collapse, killing seven people and injuring 58.1 A simplified facsimile model of this collapse is presented here that can be used as a case study in applying fundamental physics concepts appropriate for an introductory class. It is a forensic physics/engineering investigation. Afterwards, key aspects of the actual investigation will be presented.
Analyzing the acoustic beat with mobile devices
Authors: Kuhn Jochen , Vogt Patrik , Hirth Michael
Published: March 2014

In this column, we have previously presented various examples of how physical relationships can be examined by analyzing acoustic signals using smartphones or tablet PCs.1–3 In this example, we will be exploring the acoustic phenomenon of small beats, which is produced by the overlapping of two tones with a low difference in frequency Δf. The resulting auditory sensation is a tone with a volume that varies periodically. Acoustic beats can be perceived repeatedly in day-to-day life and have some interesting applications. For example, string instruments are still tuned with the help of an acoustic beat, even with modern technology. If a reference tone (e.g., 440 Hz) and, for example, a slightly out-of-tune violin string produce a tone simultaneously, a beat can be perceived. The more similar the frequencies, the longer the duration of the beat. In the extreme case, when the frequencies are identical, a beat no longer arises. The string is therefore correctly tuned. Using the Oscilloscope app,4 it is possible to capture and save acoustic signals of this kind and determine the beat frequency fS of the signal, which represents the difference in frequency Δf of the two overlapping tones (for Android smartphones, the app OsciPrime Oscilloscope can be used).
Interval Training Intensity Affects Energy Intake Compensation in Obese Men
Authors: Alkahtani Shaea A. , Byrne Nuala M. , Hills Andrew P. , King Neil A.
Published: March 2014

Purpose:

Compensatory responses may attenuate the effectiveness of exercise training in weight management. The aim of this study was to compare the effect of moderate- and high-intensity interval training on eating behavior compensation.

Methods:

Using a crossover design, 10 overweight and obese men participated in 4-week moderate (MIIT) and high (HIIT) intensity interval training. MIIT consisted of 5-min cycling stages at ±20% of mechanical work at 45%VO2peak, and HIIT consisted of alternate 30-s work at 90%VO2peak and 30-s rests, for 30 to 45 min. Assessments included a constant-load exercise test at 45%VO2peak for 45 min followed by 60-min recovery. Appetite sensations were measured during the exercise test using a Visual Analog Scale. Food preferences (liking and wanting) were assessed using a computer-based paradigm, and this paradigm uses 20 photographic food stimuli varying along two dimensions, fat (high or low) and taste (sweet or nonsweet). An ad libitum test meal was provided after the constant-load exercise test.

Results:

Exerciseinduced hunger and desire to eat decreased after HIIT, and the difference between MIIT and HIIT in desire to eat approached significance (p = .07). Exercise-induced liking for high-fat nonsweet food tended to increase after MIIT and decreased after HIIT (p = .09). Fat intake decreased by 16% after HIIT, and increased by 38% after MIIT, with the difference between MIIT and HIIT approaching significance (p = .07).

Conclusions:

This study provides evidence that energy intake compensation differs between MIIT and HIIT.
Energy Balance, Macronutrient Intake, and Hydration Status During a 1,230 km Ultra-Endurance Bike Marathon
Authors: Geesmann Bjoern , Mester Joachim , Koehler Karsten
Published: March 2014

Athletes competing in ultra-endurance events are advised to meet energy requirements, to supply appropriate amounts of carbohydrates (CHO), and to be adequately hydrated before and during exercise. In practice, these recommendations may not be followed because of satiety, gastrointestinal discomfort, and fatigue. The purpose of the study was to assess energy balance, macronutrient intake and hydration status before and during a 1,230-km bike marathon. A group of 14 well-trained participants (VO2max: 63.2 ± 3.3 ml/kg/min) completed the marathon after 42:47 hr. Ad libitum food and fluid intake were monitored throughout the event. Energy expenditure (EE) was derived from power output and urine and blood markers were collected before the start, after 310, 618, and 921 km, after the finish, and 12 hr after the finish. Energy intake (EI; 19,749 ± 4,502 kcal) was lower than EE (25,303 ± 2,436 kcal) in 12 of 14 athletes. EI and CHO intake (average: 57.1 ± 17.7 g/hr) decreased significantly after km 618 (p < .05). Participants ingested on average 392 ± 85 ml/hr of fluid, but fluid intake decreased after km 618 (p < .05). Hydration appeared suboptimal before the start (urine specific gravity: 1.022 ± 0.010 g/ml) but did not change significantly throughout the event. The results show that participants failed to maintain in energy balance and that CHO and fluid intake dropped below recommended values during the second half of the bike marathon. Individual strategies to overcome satiety and fatigue may be necessary to improve eating and drinking behavior during prolonged ultra-endurance exercise.
Nutrition Considerations for Open-Water Swimming
Authors: Shaw Gregory , Koivisto Anu , Gerrard David , Burke Louise M.
Published: March 2014

Open-water swimming (OWS) is a rapidly developing discipline. Events of 5–25 km are featured at FINA World Championships, and the international circuit includes races of 5–88 km. The Olympic OWS event, introduced in 2008, is contested over 10 km. Differing venues present changing environmental conditions, including water and ambient temperatures, humidity, solar radiation, and unpredictable tides. Furthermore, the duration of most OWS events (1–6 hr) creates unique physiological challenges to thermoregulation, hydration status, and muscle fuel stores. Current nutrition recommendations for open-water training and competition are either an extension of recommendations from pool swimming or are extrapolated from other athletic populations with similar physiological requirements. Competition nutrition should focus on optimizing prerace hydration and glycogen stores. Although swimmers should rely on self-supplied fuel and fluid sources for shorter events, for races of 10 km or greater, fluid and fuel replacement can occur from feeding pontoons when tactically appropriate. Over the longer races, feeding pontoons should be used to achieve desirable targets of up to 90 g/hr of carbohydrates from multitransportable sources. Exposure to variable water and ambient temperatures will play a significant role in determining race nutrition strategies. For example, in extreme environments, thermoregulation may be assisted by manipulating the temperature of the ingested fluids. Swimmers are encouraged to work with nutrition experts to develop effective and efficient strategies that enhance performance through appropriate in-competition nutrition.
DrsG from Streptococcus dysgalactiae subsp. equisimilis Inhibits the Antimicrobial Peptide LL-37
Authors: Smyth Danielle , Cameron Ainslie , Davies Mark R. , McNeilly Celia , Hafner Louise , Sriprakash Kadaba S. , McMillan David J.
Published: March 2014

SIC and DRS are related proteins present in only 4 of the >200
Streptococcus pyogenes
emm types. These proteins inhibit complement-mediated lysis and/or the activity of certain antimicrobial peptides (AMPs). A gene encoding a homologue of these proteins, herein called DrsG, has been identified in the related bacterium
Streptococcus dysgalactiae
subsp.
equisimilis
. Here we show that geographically dispersed isolates representing 14 of 50 emm types examined possess variants of
drsG
. However, not all isolates within the
drsG
-positive emm types possess the gene. Sequence comparisons also revealed a high degree of conservation in different
S. dysgalactiae
subsp.
equisimilis
emm types. To examine the biological activity of DrsG, recombinant versions of two major DrsG variants, DrsGS and DrsGL, were expressed and purified. Western blot analysis using antisera raised to these proteins demonstrated both variants to be expressed and secreted into culture supernatants. Unlike SIC, but similar to DRS, DrsG does not inhibit complement-mediated lysis. However, like both SIC and DRS, DrsG is a ligand of the cathelicidin LL-37 and is inhibitory to its bactericidal activity in
in vitro
assays. Conservation of prolines in the C-terminal region also suggests that these residues are important in the biology of this family of proteins. This is the first report demonstrating the activity of an AMP-inhibitory protein in
S. dysgalactiae
subsp.
equisimilis
and suggests that inhibition of AMP activity is the primary function of this family of proteins. The acquisition of the complement-inhibitory activity of SIC may reflect its continuing evolution.
Modulation of Vacuolar pH Is Required for Replication of Edwardsiella ictaluri in Channel Catfish Macrophages
Authors: Baumgartner Wes A. , Dubytska Lidiya , Rogge Matthew L. , Mottram Peter J. , Thune Ronald L.
Published: March 2014

Previous
in vitro
work demonstrated that
Edwardsiella ictaluri
produces an acid-activated urease that can modulate environmental pH through the production of ammonia from urea. Additional work revealed that expression of the
E. ictaluri
type III secretion system (T3SS) is upregulated by acidic pH. Both the urease and the T3SS were previously shown to be essential to intracellular replication. In this work, fluorescence microscopy with LysoTracker Red DND-99 (LTR) indicated that
E. ictaluri
-containing vacuoles (ECV) became acidified following ingestion by head kidney-derived macrophages (HKDM).
In vivo
ratiometric imaging demonstrated a lowered ECV pH, which fell to as low as pH 4 but subsequently increased to pH 6 or greater. Inhibition of vacuolar H
+
-ATPases by use of the specific inhibitor bafilomycin A
1
abrogated both ECV acidification and intracellular replication in HKDM. Failure of an
E. ictaluri
urease knockout mutant to increase the ECV pH in the
in vivo
ratiometric assay suggests that ammonia produced by the urease reaction mediates the pH increase. Additionally, when the specific arginase inhibitor
l
-norvaline was used to treat
E. ictaluri
-infected HKDM, the ECV failed to neutralize and
E. ictaluri
was unable to replicate. This indicates that the HKDM-encoded arginase enzyme produces the urea used by the
E. ictaluri
urease enzyme. Failure of the ECV to acidify would prevent both upregulation of the T3SS and activation of the urease enzyme, either of which would prevent
E. ictaluri
from replicating in HKDM. Failure of the ECV to neutralize would result in a vacuolar pH too low to support
E. ictaluri
replication.
Fitness testing of tennis players: How valuable is it?
Authors: Fernandez-Fernandez Jaime , Ulbricht Alexander , Ferrauti Alexander
Published: March 2014

In tennis, sport-specific technical skills are predominant factors, although a complex profile of physical performance factors is also required. The fitness test batteries assist in examining tennis players’ capabilities for performance at different levels in the laboratory as well as in the field, in the junior or elite level. While laboratory tests can be, and are, used to evaluate basic performance characteristics of athletes in most individual sports, in a more specific approach, field-based methods are better suited to the demands of complex intermittent sports like tennis. A regular test battery performed at different periods of the year allows to obtain an individual's performance profile, as well as the ability to prescribe individual training interventions. Thus, the aim of the present review was to describe and evaluate the different physical tests recommended and used by practitioners, sports scientists and institutions (national tennis federations).
Neuromuscular adjustments of the knee extensors and plantar flexors following match-play tennis in the heat
Authors: Périard Julien D , Girard Olivier , Racinais Sébastien
Published: March 2014

Objectives

This study tested the hypothesis that impairments in lower limb maximal strength and voluntary activation (VA) are exacerbated following match-play tennis in hot compared with cool conditions.

Methods

Torque and VA were evaluated during brief (5 s) and sustained (20 s) maximal voluntary isometric contractions of the knee extensors (KE) and plantar flexors (PF) in 12 male tennis players before (pre) and after (post, 24 h and 48 h) ∼115 min of play in hot (∼37°C) and cool (∼22°C) conditions.

Results

Rectal temperature was higher following play in hot than in cool (∼39.2 vs ∼38.5°C; p<0.05). Torque production decreased from prematch to postmatch during the brief and sustained contractions in hot (KE: ∼22%; PF: ∼13%) and cool (KE: ∼9%, PF: ∼7%) (p<0.05). KE strength losses in hot were greater than in cool (p<0.05) and persisted for 24 h (p<0.05). Postmatch brief and sustained KE VA was lower in hot than in cool (p<0.05), in which VA was maintained. PF VA was maintained throughout the protocol. Peak twitch torque and maximum rates of torque development and relaxation in the KE and PF were equally reduced postmatch relative to prematch in hot and cool conditions (p<0.05), and were restored near baseline within 24 h.

Conclusions

Neuromuscular system integrity of the lower limbs is compromised immediately following match-play tennis in hot and cool conditions due to the development of peripheral fatigue. The larger and persistent KE strength losses observed under heat stress are associated with greater levels of central fatigue especially during sustained contractions.
Heat stress does not exacerbate tennis-induced alterations in physical performance
Authors: Girard Olivier , Christian Ryan J , Racinais Sébastien , Périard Julien D
Published: March 2014

Objectives

To assess the time course of changes in physical performance in response to match-play tennis under heat stress.

Methods

Two matches consisting of 20 min of effective playing time (2×10 min segments) were played in COOL (∼102 min; ∼22°C and 70% relative humidity (RH)) and HOT (∼119 min; ∼36°C and 35% RH) environments. Repeated-sprint ability (3×15 m, 15 s rest), 15 m sprint time with a direction change (180°), vertical jump height (squat and countermovement jumps) and leg stiffness (multirebound jumps) were assessed in 12 competitive male players prematch, midmatch and postmatch, and 24 and 48 h after match completion.

Results

During the repeated-sprint ability test, initial (+2.3% and +3.1%) and cumulated sprint (+1.5% and +2.8%) times increased from prematch to midmatch and postmatch, respectively (p<0.001), while the sprint decrement score did not change. Match-play tennis induced a slowing (average of both conditions: +1.1% and +1.3% at midmatch and postmatch time points; p=0.05) of 15 m sprint time with direction change. Compared with prematch, leg stiffness (−6.4% and −6.5%; p<0.001) and squat jump height (−1.5% and −2.4%; p=0.05), but not countermovement jump height (−0.7% and −1.3%; p>0.05), decreased midmatch and postmatch, respectively, regardless of the condition. Complete recovery in all physical performance markers occurred within 24 h.

Conclusions

In tennis, match-related fatigue is characterised by impaired repeated-sprint ability, explosive power and leg stiffness at midmatch and postmatch, with values restored to prematch baseline 24 h into recovery. In addition, physical performance responses (match and recovery kinetics) are identical when competing in cool and hot environments.
Recovery interventions and strategies for improved tennis performance
Authors: Kovacs Mark S , Baker Lindsay B
Published: March 2014

Improving the recovery capabilities of the tennis athlete is receiving more emphasis in the research communities, and also by practitioners (coaches, physical trainers, tennis performance specialists, physical therapists, etc). The purpose of this article was to review areas of recovery to limit the severity of fatigue and/or speed recovery from fatigue. This review will cover four broad recovery techniques commonly used in tennis with the belief that the interventions may improve athlete recovery and therefore improve adaptation and future performance. The four areas covered are: (1) temperature-based interventions, (2) compressive clothing, (3) electronic interventions and (4) nutritional interventions.
Hydration and thermal strain during tennis in the heat
Authors: Bergeron Michael F
Published: March 2014

Competitive tennis in the heat can prompt substantial sweat losses and extensive consequent body water and electrolyte deficits, as well as a level of thermal strain that considerably challenges a player's physiology, perception of effort, and on-court well-being and performance. Adequate hydration and optimal performance can be notably difficult to maintain when multiple same-day matches are played on successive days in hot weather. Despite the recognised effects of the heat, much more research needs to be carried out to better appreciate the broader scope and full extent of the physiological demands and hydration and thermal strain challenges facing junior and adult players in various environments, venues and competition scenarios. However, certain recommendations of best practices should be emphasised to minimise exertional heat illness risk and improve player safety, well-being and on-court performance.
Eosinophilic oesophagitis: investigations and management
Authors: Kumar Mayur , Sweis Rami , Wong Terry
Published: March 2014

Eosinophilic oesophagitis (EO) is an immune/antigen mediated, chronic, relapsing disease characterised by dysphagia, food bolus impaction and a dense oesophageal eosinophilic infiltrate. Characteristic endoscopic features include corrugated rings, linear furrows and white exudates, but none are diagnostic. Despite its increasing prevalence, EO remains underdiagnosed. There is a strong association with other atopic conditions. Symptoms, histology and endoscopic findings can overlap with gastro-oesophageal reflux disease. Currently endoscopy and oesophageal biopsies are the investigation of choice. Oesophageal physiology studies, endoscopic ultrasound, impedance planimetry and serology may have a role in the diagnosis and monitoring of response to therapy. Acid reducing medication is advocated as first line or adjuvant therapy. Dietary therapy is comprised of elimination diets or can be guided by allergen assessment. In adults, topical corticosteroids are the mainstay of therapy. Endoscopic dilatation is safe and effective for the treatment of non-responsive strictures. Other therapeutic options (immunomodulators, biological agents, leukotriene receptor antagonists) are under investigation.
Exercise training as treatment in cancer cachexia
Authors: Lira Fábio Santos , Neto José Cesar Rosa , Seelaender Marília
Published: March 2014

Cachexia is a wasting syndrome that may accompany a plethora of diseases, including cancer, chronic obstructive pulmonary disease, aids, and rheumatoid arthritis. It is associated with central and systemic increases of pro-inflammatory factors, and with decreased quality of life, response to pharmacological treatment, and survival. At the moment, there is no single therapy able to reverse cachexia many symptoms, which include disruption of intermediary metabolism, endocrine dysfunction, compromised hypothalamic appetite control, and impaired immune function, among other. Growing evidence, nevertheless, shows that chronic exercise, employed as a tool to counteract systemic inflammation, may represent a low-cost, safe alternative for the prevention/attenuation of cancer cachexia. Despite the well-documented capacity of chronic exercise to counteract sustained disease-related inflammation, few studies address the effect of exercise training in cancer cachexia. The aim of the present review was hence to discuss the results of cachexia treatment with endurance training. As opposed to resistance exercise, endurance exercise may be performed devoid of equipment, is well tolerated by patients, and an anti-inflammatory effect may be observed even at low-intensity. The decrease in inflammatory status induced by endurance protocols is paralleled by recovery of various metabolic pathways. The mechanisms underlying the response to the treatment are considered.
Spatial correlation length of normalized cone data in sand: case study in the north of Denmark
Authors: Firouzianbandpey S. , Griffiths D.V. , Ibsen L.B. , Andersen L.V.
Published: March 2014

The main topic of this study is to assess the anisotropic spatial correlation lengths of a sand layer deposit based on cone penetration testing with pore pressure measurement (CPTu) data. Spatial correlation length can be an important factor in reliability analysis of geotechnical systems, yet it is rarely estimated during routine site investigations. Results from two different sites in the north of Denmark are reported in this paper, indicating quite strong anisotropy due to the depositional process, with significantly shorter spatial correlation lengths in the vertical direction. It is observed that the normalized cone resistance is a better estimator of spatial trends than the normalized friction ratio.
Stability of dual square tunnels in cohesive-frictional soil subjected to surcharge loading
Authors: Yamamoto Kentaro , Lyamin Andrei V. , Wilson Daniel W. , Sloan Scott W. , Abbo Andrew J.
Published: March 2014

The stability of dual square tunnels in cohesive-frictional soils subjected to surcharge loading has been investigated theoretically and numerically assuming plane strain conditions. From the viewpoint of the efficient utilization of underground space for human activities, noncircular openings and tunnels should be preferred in the design stage. Despite the importance of this issue, previous research on the subject is very limited. At present, no generally accepted design or analysis method is available to evaluate the stability of multiple tunnels–openings in cohesive-frictional soils. In the design stage, it is important to consider the interaction effects of dual tunnels. Unlike the case of a single tunnel, the centre-to-centre distance appears as a new parameter that must be considered and plays a key role in tunnel stability. In this study, continuous loading is applied to the ground surface and a smooth interface condition is modelled. For a series of tunnel size-to-depth ratios and material properties, rigorous lower- and upper-bound solutions for the ultimate surcharge loading are obtained by applying finite element limit analysis techniques. For practical suitability, the results are presented in the form of dimensionless stability charts and a table with the actual tunnel stability numbers closely bracketed from above and below. As an additional verification of the solutions, upper-bound rigid-block mechanisms have been developed, and the predicted collapse loads from these mechanisms are compared with those from finite element limit analysis. Finally, a discussion is presented regarding the location of the critical tunnel spacing between dual square tunnels where interaction no longer occurs.
Patterns of host and flea communities along an elevational gradient in Colorado
Authors: Maher S.P. , Timm R.M.
Published: March 2014

Patterns in community composition across a landscape are the result of mechanistic responses and species interactions. Interactions between hosts and parasites have additional complexity because of the contingency of host presence and interactions among parasites. To assess the role of environmental changes within host and parasite communities, we surveyed small mammals and their fleas over a dynamic elevational gradient in the Front Range in Colorado, USA. Communities were characterized using several richness and diversity metrics and these were compared using a suite of frequentist and randomization approaches. We found that flea species richness was related to the number of host species based upon rarefaction, but no patterns in richness with elevation were evident. Values of diversity measures increased with elevation, representing that small-mammal and flea communities were more even upslope, yet turnover in composition was not related to examined variables. The results suggest there are strong local effects that drive these small-mammal and flea communities, although the breadth of flea species is tied to host availability.
Quantified "Shock-Sensitivity" Above the Maxwell Load
Authors: Thompson J. M. T. , van der Heijden G. H. M.
Published: March 2014

Using the static-dynamic analogy, work at Bath and Bristol has uncovered the vital organizing role of the Maxwell "energy criterion" load in the advanced post-buckling of long-thin structures which exhibit severe shell-like imperfection sensitivity. It has become clear that above the Maxwell load, PM, there are localized solutions offering an order-of-magnitude increase in sensitivity to lateral side-loads, whether static or dynamic. We propose to call this "shock-sensitivity", and notice that so far only the seminal paper by Horak et al. in 2006 has quantified this in terms of an E(P) energy-barrier versus load graph. In this paper, we present three graphs of this nature for archetypal problems: the free twisted rod, the cylindrically constrained rod, and the strut on a softening elastic foundation. We find in all cases that the energy barrier of the localizing solution above PM is quite close to the energy of a single periodic wave. Now a single such wave is not kinematically admissible, and the corresponding periodic barrier must be for all the waves in the long structure, N, say. So in practice N will be large, and does indeed tend to infinity with the length of the structure. Thus the sensitivity increases by a factor of a large N as the Maxwell load is exceeded. This is important in its own right, and we do not seek to explain or fit curves to the scattered experimental buckling loads of shell structures.
Stochastic Multiresonance in an Electronic Chaotic Circuit
Authors: Stemler Thomas , Werner Johannes P. , Benner Hartmut
Published: March 2014

Methods to estimate the amplification by stochastic resonance are tested in an electronic circuit experiment showing chaotic dynamics. We demonstrate that the linear response ansatz used for the estimation in stochastic systems can be also applied to chaotic systems showing crisis induced intermittency. In addition, the applied method explains the mechanism leading to stochastic multiresonance.
Bifurcation of a Duffing Oscillator Having Nonlinear Fractional Derivative Feedback
Authors: Leung A. Y. T. , Yang H. X. , Zhu P.
Published: March 2014

Active feedback control is commonly used to attenuate undesired vibrations in vibrating machineries and structures, such as bridges, highways and aircrafts. In this paper, we investigate the primary resonance and 1/3 subharmonic resonance of a harmonically forced Duffing oscillator under fractional nonlinear feedback control. By means of the first order averaging method, slow flow equations governing the modulations of amplitude and phase of the oscillator are obtained. An approximate solution for the steady state periodic response is derived and its stability is determined by the Routh–Hurwitz criterion. We demonstrate that appropriate choices on the control strategies and feedback gains can delay or eliminate the undesired bifurcations and reduce the amplitude peak both of the primary and subharmonic resonances. Analytical results are verified by comparisons with the numerical integration results.
Microwave-Photonic Sensor for Remote Water-Level Monitoring Based on Chaotic Laser
Authors: Ji Yongning , Zhang Mingjiang , Wang Yuncai , Wang Peng , Wang Anbang , Wu Yuan , Xu Hang , Zhang Yongning
Published: March 2014

A microwave-photonic sensor for remote water-level monitoring based on chaotic laser is proposed and demonstrated. The probe chaotic signal with bandwidth of 18 GHz is generated in the central office and then transmitted at the remote antenna unit after a 24 km single-mode fiber transmission. And the monitoring data from the remote antenna unit is sent back to the central office over fiber. The water-level measuring is accomplished by cross-correlation between reference signal and probe signal at the central office. So the remote water-level monitoring system with a high spatial resolution of 2 cm is achieved and the height of water surface can be displayed in real time.
Three-Dimensional Hopf Bifurcation for a Class of Cubic Kolmogorov Model
Authors: Du Chaoxiong , Wang Qinlong , Huang Wentao
Published: March 2014

We study the Hopf bifurcation for a class of three-dimensional cubic Kolmogorov model by making use of our method (i.e. singular values method). We show that the positive singular point (1, 1, 1) of an investigated model can become a fine focus of 5 order, and moreover, it can bifurcate five small limit cycles under certain coefficients with disturbed condition. In terms of three-dimensional cubic Kolmogorov model, published references can hardly be seen, and our results are new. At the same time, it is worth pointing out that our method is valid to study the Hopf bifurcation problem for other three-dimensional polynomial differential systems.
Designing modular reaction-diffusion programs for complex pattern formation
Authors: Scalise Dominic , Schulman Rebecca
Published: March 2014

Cells use sophisticated, multiscale spatial patterns of chemical instructions to control cell fate and tissue growth. While some types of synthetic pattern formation have been well studied1-6, it remains unclear how to design chemical processes that can reproducibly create similar spatial patterns. Here we describe a scalable approach for the design of processes that generate such patterns, which can be implemented using synthetic DNA reaction-diffusion networks7,8. In our method, black-box modules are connected together into integrated programs for arbitrarily complex pattern formation. These programs can respond to input stimuli, process information, and ultimately produce stable output patterns that differ in size and concentration from their inputs. To build these programs, we break a target pattern into a set of patterning subtasks, design modules to perform these subtasks independently, and combine the modules into networks. We demonstrate in simulation how programs designed with our methodology can generate complex patterns, including a French flag and a stick figure.
A novel ultrathin collagen nanolayer assembly for 3-D microtissue engineering: Layer-by-layer collagen deposition for long-term stable microfluidic hepatocyte culture
Authors: McCarty William J. , Usta O. Berk , Luitje Martha , Bale Shyam Sundhar , Bhushan Abhinav , Hegde Manjunath , Golberg Inna , Jindal Rohit , Yarmush Martin L.
Published: March 2014

The creation of stable hepatocyte cultures using cell-matrix interactions has proven difficult in microdevices due to dimensional constraints limiting the utility of classic tissue culture techniques that involve the use of hydrogels such as the collagen "double gel" or "overlay". To translate the collagen overlay technique into microdevices, we modified collagen using succinylation and methylation reactions to create polyanionic and polycationic collagen solutions, and deposited them layer-by-layer to create ultrathin collagen nanolayers on hepatocytes. These ultrathin collagen layers covered hepatocytes in microdevices and 1) maintained cell morphology, viability, and polarity, 2) induced bile canalicular formation and actin reorganization, and 3) maintained albumin and urea secretions and CYP activity similar to those observed in hepatocytes in collagen double gel hepatocytes in plate cultures. Beyond the immediate applications of this technique to create stable, in vitro microfluidic hepatocyte cultures for drug toxicity testing, this technique is generally applicable as a thin biomaterial for other 3D microtissues.
4D Wheeler diagrams: concept and applications
Authors: Qayyum Farrukh , De Groot Paul , Hemstra Nanne , Catuneanu Octavian
Published: March 2014

The conventional Wheeler diagram aids the construction of a spatiotemporal framework of strata. The diagrams are created manually by studying outcrops, wells, or seismic data. For the latter case, automated methods now exist, which support the construction of 2D, as well as 3D Wheeler diagrams. Seismic data contains information in three dimensions,
X
,
Y
and
Z
, where ‘
Z
’ is either two-way time or depth. Seismic horizons are correlated surfaces that often follow geological time lines. In this case, a set of interpreted seismic horizons contains information in four dimensions (
X
,
Y
,
Z
, and Geological Time). In the mapping from the structural domain to Wheeler space, information about
Z
(thickness) is lost. This means that one dimension is missing in the conventional Wheeler diagram. This paper describes a method to add information from the
Z
dimension to the Wheeler domain. It is done by computing stratigraphic thicknesses per sequence stratigraphic unit and displaying these as colour-coded overlays in the Wheeler domain. Thus displayed, thickness variations help in understanding changes in accommodation, sedimentation rate, and depositional trends. 3D Wheeler displays with colour-coded thickness information are referred to as 4D Wheeler diagrams. In this article, the method is described and applied to a case study from the southern North Sea.
Tomahawk
Authors: Arnold Oliver , Matus Emil , Noethen Benedikt , Winter Markus , Limberg Torsten , Fettweis Gerhard
Published: March 2014

Heterogeneity and parallelism in MPSoCs for 4G (and beyond) communications signal processing are inevitable in order to meet stringent power constraints and performance requirements. The question arises on how to cope with the problem of system programmability and runtime management incurred by the statically or even dynamically varying number and type of processing elements. This work addresses this challenge by proposing the concept of a heterogeneous many-core platform called Tomahawk. Apart from the definition of the system architecture, in this approach a unified framework including a model of computation, a programming interface and a dedicated runtime management unit called CoreManager is proposed. The increase of system complexity in terms of application parallelism and number of resources may lead to a dramatic increase of the management costs, hence causing performance degradation. For this reason, the efficient implementation of the CoreManager becomes a major issue in system design. This work compares the performance and capabilities of various CoreManager HW/SW solutions, based on ASIC, RISC and ASIP paradigms. The results demonstrate that the proposed ASIP-based solution approaches the performance of the ASIC realization, while preserving the full flexibility of the software (RISC-based) implementation.
NoC contention analysis using a branch-and-prune algorithm
Authors: Dasari Dakshina , Nikoli'c Borislav , N'elis Vincent , Petters Stefan M.
Published: March 2014

“Many-core” systems based on a Network-on-Chip (NoC) architecture offer various opportunities in terms of performance and computing capabilities, but at the same time they pose many challenges for the deployment of real-time systems, which must fulfill specific timing requirements at runtime. It is therefore essential to identify, at design time, the parameters that have an impact on the execution time of the tasks deployed on these systems and the upper bounds on the other key parameters. The focus of this work is to determine an upper bound on the
traversal time
of a packet when it is transmitted over the NoC infrastructure. Towards this aim, we first identify and explore some limitations in the existing recursive-calculus-based approaches to compute the Worst-Case Traversal Time (WCTT) of a packet. Then, we extend the existing model by integrating the characteristics of the tasks that generate the packets. For this extended model, we propose an algorithm called “Branch and Prune” (BP). Our proposed method provides tighter and safe estimates than the existing recursive-calculus-based approaches. Finally, we introduce a more general approach, namely “Branch, Prune and Collapse” (BPC) which offers a configurable parameter that provides a flexible trade-off between the computational complexity and the tightness of the computed estimate. The recursive-calculus methods and BP present two special cases of BPC when a trade-off parameter is 1 or ∞, respectively. Through simulations, we analyze this trade-off, reason about the implications of certain choices, and also provide some case studies to observe the impact of task parameters on the WCTT estimates.
HARP
Authors: Lashgar Ahmad , Khonsari Ahmad , Baniasadi Amirali
Published: March 2014

SIMT accelerators are equipped with thousands of computational resources. Conventional accelerators, however, fail to fully utilize available resources due to branch and memory divergences. This underutilization is manifested in two underlying inefficiencies: pipeline width underutilization and pipeline depth underutilization. Width underutilization occurs when SIMD execution units are not entirely utilized due to branch divergences. This affects lane activity and results in SIMD inefficiency. Depth underutilization takes place when the pipeline runs out of active threads and is forced to leave pipeline stages idle. This work addresses both inefficiencies by harnessing inactive threads available to the pipeline. We introduce Harnessing inActive thReads in many-core Processors (or simply HARP) to improve width and depth utilization in accelerators. We show how using inactive yet ready threads can enhance performance. Moreover, we investigate implementation details and study microarchitectural changes needed to build a HARP-enhanced accelerator. Furthermore, we evaluate HARP under a variety of microarchitectural design points. We measure the area overhead associated with HARP and compare to conventional alternatives. Under Fermi-like GPUs, we show that HARP provides 10% speedup on average (maximum of 1.6X) at the cost of 3.5% area overhead. Our analysis shows that HARP performs better under narrower SIMD and shorter pipelines.
NoC-based fault-tolerant cache design in chip multiprocessors
Authors: Banaiyanmofrad Abbas , Girão Gustavo , Dutt Nikil
Published: March 2014

Advances in technology scaling increasingly make emerging Chip MultiProcessor (CMP) platforms more susceptible to failures that cause various reliability challenges. In such platforms, error-prone on-chip memories (caches) continue to dominate the chip area. Also, Network-on-Chip (NoC) fabrics are increasingly used to manage the scalability of these architectures. We present a novel solution for efficient implementation of fault-tolerant design of Last-Level Cache (LLC) in CMP architectures. The proposed approach leverages the interconnection network fabric to protect the LLC cache banks against permanent faults in an efficient and scalable way. During an LLC access to a faulty block, the network detects and corrects the faults, returning the fault-free data to the requesting core. Leveraging the NoC interconnection fabric, designers can implement any cache fault-tolerant scheme in an efficient, modular, and scalable manner for emerging multicore/manycore platforms. We propose four different policies for implementing a remapping-based fault-tolerant scheme leveraging the NoC fabric in different settings. The proposed policies enable design trade-offs between NoC traffic (packets sent through the network) and the intrinsic parallelism of these communication mechanisms, allowing designers to tune the system based on design constraints. We perform an extensive design space exploration on NoC benchmarks to demonstrate the usability and efficacy of our approach. In addition, we perform sensitivity analysis to observe the behavior of various policies in reaction to improvements in the NoC architecture. The overheads of leveraging the NoC fabric are minimal: on an 8-core, 16-cache-bank CMP we demonstrate reliable access to LLCs with additional overheads of less than 3% in area and less than 7% in power.