bluuebunny/crossref_metadata_2025 huggingface dataset:
Mosaicism in a newEocene pufferfish highlights rapid morphological innovation near the origin of crown tetraodontiforms
Authors: Close Roger A. , Johanson Zerina , Tyler James C. , Harrington Richard C. , Friedman Matt
Published: June 2016

Tetraodontiformes (pufferfishes and kin) is a taxonomically and structurally diverse, widely‐distributed clade of acanthomorphs, whose members often serve as models for genomics and, increasingly, macroevolutionary studies. Morphologically disparatePalaeogene fossils suggest considerable early experimentation, but these flattened specimens often preserve limited information. We present a three‐dimensionally preserved beaked tetraodontiform from the earlyEocene (c. 53 Ma)LondonClayFormation,UK. Approximately coeval with the oldest crown tetraodontiforms, †Ctenoplectus williamsigen. et sp. nov. presents an unprecedented combination of characters, pairing a fused beak‐like dentition with prominent dorsal‐fin spines that insert atop transversely‐expanded pterygiophores roofing the skull.Bayesian total‐evidence tip‐dating analysis indicates that †Ctenoplectusrepresents the sister lineage ofTriodontidae and highlights considerable levels of homoplasy in early tetraodontiform evolution. According to our dataset, rates of morphological character evolution were elevated at the origin of crownTetraodontiformes, especially within gymnodonts, but declined after the principal body plans were established. Such ‘early burst’ patterns are regarded as a hallmark of adaptive radiations, but are typically associated with diversification at smaller spatiotemporal scales. However, denser sampling ofNeogene andRecent taxa is needed to confirm this pattern.
Congenital Milia En Plaque
Authors: Wang Annie R. , Bercovitch Lionel
Published: June 2016

Milia en plaque is a rare, benign, localized, entity typically seen in adults after the third decade of life. Although there have been a few cases described in children, we describe the first case in a newborn.
Time course of cardiac lesions due to Kawasaki disease in Japan: 22nd nationwide survey (2011–2012)
Authors: Goto Takahiro , Sano Takashi , Kojo Takao , Ae Ryusuke , Aoyama Yasuko , Makino Nobuko , Kotani Kazuhiko , Nakamura Yosikazu
Published: June 2016

Background

Although Kawasaki disease (KD) cardiac lesions can be treated with i.v. immunoglobulin (IVIG) and are associated with age and sex, the time course of cardiac lesions remains unclear on the large scale.

Methods

We used the data of the 22nd nationwide survey of KD in Japan (2011–2012). We divided the time course of cardiac lesions into eight groups according to the combination of timing (first visit to hospital, acute phase, and sequelae) and presence of cardiac lesions (E, existence of cardiac lesions; N, non‐existence of cardiac lesions): EEE, EEN, ENE, NEE, ENN, NEN, NNE, and NNN. For example, EEN shows that cardiac lesions existed at first visit to hospital and in the acute phase, but did not exist as sequelae. A total of 24 952 patients were analyzed.

Results

The majority (90.6%) of patients belonged to the NNN group, followed by the EEN (3.21%) and NEN (3.33%) groups. Male sex and ages ≤5 months and ≥5 years tended to be more prevalent. Non‐response to initial IVIG therapy was the most prevalent in all groups other than NNN.

Conclusions

The time course of cardiac lesions and the relationship with sex, age, and IVIG therapy have been described. KD patients who are male, aged ≤5 months or ≥5 years, and non‐responders to initial IVIG tend to have cardiac lesions at some point in the time course of KD.
Peroxyoxalate High‐Energy Intermediate is Efficiently Decomposed by the Catalyst Imidazole
Authors: Boaro Andreia , Bartoloni Fernando Heering
Published: June 2016

The peroxyoxalate reaction is a highly efficient chemiluminescence system, its chemiexcitation process involving the intermolecular interaction between an activator (ACT) and the high‐energy intermediate (HEI) of the reaction. Typically, the HEI is generated through the reaction of an oxalate ester with H2O2, in the presence of a basic/nucleophilic catalyst, such as imidazole (IMI‐H). IMI‐H, besides catalyzing the formation of the HEI, is also known to decompose this peroxidic intermediate. Despite that, up to now, no rate constant value has been determined for such significant interaction. Through kinetic measurements, we have observed that IMI‐H is roughly four times more efficient than 9,10‐diphenylanthracene (DPA), a classic ACT, in catalyzing the decomposition of the HEI by a bimolecular electron transfer reaction through a Chemically Initiated Electron Exchange Luminescence‐like process. For instance, when IMI‐H and DPA are at the same concentration, 78% of the generated HEI is actually consumed by the nonemissive bimolecular interaction with IMI‐H. We have obtained an average singlet excited state formation quantum yield, at infinite ACT concentration, of (5.5 ± 0.5) × 10−2 E mol−1, determined at five different IMI‐H concentrations. This ultimately suggests that the yield of formation of HEI actually does not depend on the IMI‐H concentration.
Effects of selenium on biological and physiological properties of the duckweed Landoltia punctata
Authors: Zhong Y. , Cheng J. J.
Published: June 2016

Duckweed can be used for bioremediation of selenium (Se) polluted water because of its capability of absorbing minerals from growing media. However, the presence of Se in the media may affect the growth of the duckweed. Landoltia punctata 7449 has been studied for its changes in chemical and biological properties with the presence of Se in the media.

The duckweed was cultivated over a 12‐day period at different initial concentrations of selenite (Na2SeO3) from 0 to 80 μmol·l−1. The growth rate, the organic and total Se contents, the activity of antioxidant enzymes, the photosynthetic pigment contents, the chlorophyll a fluorescence OJIP transient, and the ultrastructure of the duckweed were monitored during the experiment.

The results have shown that Se at low concentrations of ≤20 μmol·l−1 promoted the growth of the L. punctata and inhibited lipid peroxidation. Substantial increases in duckweed growth rate and organic Se content in the duckweed were observed at low Se concentrations. The anti‐oxidative effect occurred likely with the increases in guaiacol peroxidase, catalase and superoxide dismutase activities as well as the amount of photosynthetic pigments. However, negative impact to the duckweed was observed when the L. punctata was exposed to high Se concentrations (≥40 μmol·l−1), in which the duckweed growth was inhibited by the selenium.

The results indicate that L. punctata 7449 can be used for bioremediation of selenium (Se) polluted water when the Se concentration is ≤20 μmol·l−1.
Characterization of the novel HLA‐C*02:106 allele in a hematopoietic stem cell volunteer donor
Authors: Testi M. , Battarra M. , Catalano M. , Troiano M. , Andreani M.
Published: June 2016

HLA‐C*02:106 allele differs from C*02:02:02:01 by a C to T substitution in exon 4.
Contrastive focus in Ghanaian English discourse
Authors: LOMOTEY CHARLOTTE FOFO
Published: June 2016

Research on Englishes outside the Inner Circle points to the fact that it is not always that speakers select prominence to communicate their intended meaning. This study examined the selection of prominence in marking contrastive focus in Ghanaian English and how this might affect information packaging. Data obtained from 200 university students representing the major languages of Ghana were analyzed both auditorily and acoustically. Results suggest that similar to other Outer Circle varieties of English, Ghanaians do not always assign prominence to the ‘target’ word and this also affects how they mark contrastive focus.
Toll‐like receptors 2 and 4 exert opposite effects on the contractile response induced by serotonin in mouse colon: role of serotonin receptors
Authors: Forcén R. , Latorre E. , Pardo J. , Alcalde A. I. , Murillo M. D. , Grasa L.
Published: June 2016

New Findings

What is the central question of this study?

The action of Toll‐like receptors (TLRs) 2 and 4 on the motor response to serotonin in mouse colon has not previously been reported.

What is the main finding and its importance?

Toll‐like receptors 2 and 4 modulate the serotonin‐induced contractile response in mouse colon by modifying the expression of serotonin (5‐HT) receptors. Alterations in 5‐HT2A and 5‐HT2C receptors explain the increase of the response to serotonin in TLR2−/− mice. Alterations in 5‐HT2C and 5‐HT4 receptors explain the suppression of the response to serotonin in TLR4−/− mice.

The microbiota, through Toll‐like receptors (TLRs), may regulate gastrointestinal motility by activating neuroendocrine mechanisms. We evaluated the influence of TLR2 and TLR4 in spontaneous contractions and in the serotonin (5‐HT)‐induced motor response in mouse colon, and assessed the 5‐HT receptors involved. Muscle contractility studies to evaluate the intestinal spontaneous motility and the response to 5‐HT were performed in the colon from wild‐type (WT), TLR2−/−, TLR4−/− and TLR2/4 double knockout (DKO) mice. The 5‐HT receptor mRNA expression was determined by real‐time PCR. The amplitude and frequency of the spontaneous contractions of the colon were smaller in TLR4−/− and TLR2/4 DKO mice with respect to WT mice. In WT, TLR2−/− and TLR2/4 DKO mice, 100 μm 5‐HT evoked a contractile response. The contractile response induced by 5‐HT was significantly higher in TLR2−/− than in WT mice. In TLR4−/− mice, 5‐HT did not evoke any contractile response. The mRNA expression of 5‐HT2A was increased in TLR2−/− and TLR2/4 DKO mice. The 5‐HT2C and 5‐HT4 mRNA expressions were increased in TLR4−/− and TLR2/4 DKO mice. The 5‐HT2C mRNA expression was diminished in TLR2−/− mice. The 5‐HT3 mRNA expression was increased in TLR2−/−, TLR4−/− and TLR2/4 DKO mice. The 5‐HT7 mRNA expression was diminished in TLR2/4 DKO mice. In WT, TLR2−/− and TLR2/4 DKO mice, 5‐HT2, 5‐HT3, 5‐HT4 and 5‐HT7 receptor antagonists reduced or blocked the contractile response evoked by 5‐HT. We postulate that TLR2 and TLR4 modulate the serotonin contractile motor response in mouse colon in an opposing manner by modifying the expression of several serotonin receptors.
Optimization of a Mobile Platform for a Wheeled Manipulator
Authors: Song Tao , Xi Fengfeng (Jeff) , Guo Shuai , Lin Yu
Published: June 2016

A method for optimizing a mobile platform to form a wheeled manipulator is presented. For a given manipulator, this mobile platform is optimized to have maximum tip-over stability against the reaction forces and moments caused by the movement of the manipulator. This optimization is formulated as a max–min problem, i.e., to maximize a stable region ratio (SRR) over the manipulator's workspace while minimizing a tip-over moment (TOM). For a practical solution, this max–min problem is converted to two subproblems. The first one is the worst-case analysis to determine the maximum positive value of TOM through searching over the manipulator's workspace. A positive value of TOM indicates tip-over instability. The three parameters used for this search are pertaining to the mobile platform itself, i.e., the number of support wheels, the size, and mass of the mobile platform. The second subproblem is to optimize the placement of the manipulator and accessory on the mobile platform against the identified worst case so that the entire manipulator's workspace is stable. The effectiveness of the proposed method is demonstrated by applying it to optimize a mobile drilling and riveting robot.
Rail Integrity Experience on the Washington Metro System
Authors: Frison Benjamin , Jeong David Y.
Published: June 2016

The Washington Metropolitan Area Transit Authority (WMATA) provides passenger rail service to the nation’s capital. Although the rail system carries only passenger trains, the rail integrity issues that WMATA must manage are similar to those that freight railroads also face. These issues include occurrences of broken rail from internal rail head defects, detection of such defects, and repair of the rail to restore service. Another example is the development of damage on the running surface of the rail, called rolling contact fatigue (RCF). Such surface damage is known to adversely affect the detection of internal rail head defects beneath RCF conditions. While WMATA’s rail integrity issues may be similar to those that freight railroads also encounter, the management of such issues are different, which are also discussed in this paper.

This paper describes the recent experience of broken rails on the WMATA rail system. In addition, results from engineering fracture mechanics analyses are presented to help understand how operational, environmental, design, and maintenance factors influence rail failure.
On Railroad Tank Car Puncture Performance: Part II — Estimating Metrics
Authors: Jeong David Y. , Carolan Michael E. , Perlman Benjamin
Published: June 2016

This paper is the second in a two-part series on the puncture performance of railroad tank cars carrying hazardous materials in the event of an accident. Various metrics are often mentioned in the open literature to characterize the structural performance of tank cars under accident loading conditions. One of the consequences in terms of structural damage to the tank during accidents is puncture. This two-part series of papers focuses on four metrics to quantify the performance of tank cars against the threat of puncture: (1) speed, (2) force, (3) energy, and (4) conditional probability of release.

In Part I, generalized tank car impact scenarios were illustrated. Particular focus is given to the generalized shell impact scenario because performance-based requirements for shell puncture resistance are being considered by the regulatory agencies in United States and Canada. Definitions for the four performance metrics were given. Physical and mathematical relationships among these metrics were outlined. Strengths and limitations of these performance metrics were discussed.

In this paper (Part II), the multi-disciplinary approach to develop engineering tools to estimate the performance metrics is described. The complementary connection between testing and modeling is emphasized. Puncture performance metrics, which were estimated from other sources, are compared for different tank car designs. These comparisons are presented to interpret the metrics from a probabilistic point of view. In addition, sensitivity of the metrics to the operational and design factors is examined qualitatively.
NYCT Solid State Interlocking (SSI) Safety Certification
Authors: Georgiadis Sofia K. , Parrella William , Hacken George
Published: June 2016

The New York City Transit (NYCT) Signal Modernization Program has been ongoing since the mid-1990s. The current phase of modernization involves the procurement of Solid State Interlocking (SSI) systems that are designed to replace relay-based interlockings. SSI procurement has necessitated significant adjustments to NYCT’s system deployment processes, most notably in the areas of design, implementation, test, maintenance, and safety certification. NYCT has successfully met the challenge of applying the updated deployment processes to multiple, concurrent system procurements.

The most fundamental change to the NYCT procurement approach required a shift from the traditional design-build model of acquisition for relay-based systems to a software-based development lifecycle for SSIs. The relay-based Interlocking systems’ design-build model has traditionally involved the realization of complex relay logic with well-known hardware components such as relays, trip-stops, signals and switch machines. The SSI systems’ software model however requires additional consideration of software and hardware development phases, such as designated in the V-lifecycle.

V-model phases include requirement, design, implementation, and test. For SSI systems, NYCT adopted a “double” V-Life cycle approach, one V for the supplier’s SSI hardware and software (executive) platform, and one V for the SSI application (site-specific field) logic. At NYCT, the first V is dedicated to the suppliers’ executive platform. Hardware and software comprising the supplier platform are verified to meet safety and performance requirements. Safety analyses such as Fault Tree Analysis, Failure Modes and Effects Analysis, Timing Analysis, and Hazard Analysis are generated by SSI suppliers. System Safety Concepts, e.g., Numerical Assurance, Checked Redundancy, Intrinsic Fail-Safety are also assessed. NYCT’s second V is dedicated to the application software, i.e., the site-specific relay-based logic, which is implemented as Boolean logic within the SSI. For the Booleans, the process of traditional circuit checking is supplemented by Model Checking, wherein NYCT General Safety Properties are used to verify the site-specific logic. Model Checking provides assurance that safety properties are met throughout the entire interlocking design, for every system state, and does not rely on a manual review process. This paper will focus on the benefits NYCT has realized as a result of adopting Model Checking as a requirement for safety certification, along with an overview of the NYCT SSI safety certification process.
Multi-Tiered Cognitive Radio Network for Positive Train Control Operations
Authors: Bandara K. R. Damindra S. , Melaragno Anthony P. , Wijesekara Duminda , Costa Paulo
Published: June 2016

Positive Train Controller (PTC) is a communication based system designed to enforce PTC safety objectives for trains such as train-to-train collisions, train derailments, and ensure railroad worker safety. Existing PTC designs consider risks due to operational environment such as location of other trains, switches, and speed limits.

We propose to enhance PTC by using a multi-tiered cognitive radio network that considers multiple risks such as those due to bandwidth congestion, packet length limitations, propagation losses, detectable exploitation of Software Defined Radio vulnerabilities, and protocol vulnerabilities. Radios operating at PTC nodes (such as train, WIU and Base station) is equipped with a cognitive layer, which communicates with other nodes to create a cognitive radio network. The proposed network as a whole strives to provide spectrum management and security for the radio communication system, which can enhance the PTC functionality.

Each cognitive radio in our proposed network consists of multiple tiers. The upper tier consists of a master cognitive engine that holistically evaluates the operational risks of the network and acts to mitigate them using the lower tiers. The lower tier (immediate slave tier to the master) consists of sub cognitive engines for cryptographic operations and spectrum management. The traditional PTC protocol is implemented at a lower tier module that interface with the master Cognitive Engine (CE). The master-slave communications within one radio is implemented using middleware.

The proposed cognitive radio network can be modeled as a cyber-physical system by incorporating train movement dynamics, radio transmission characteristics and cryptographical computations, thereby constituting a distributed system of communicating hybrid automatons. This design enables us to verify safety and the security of the system using formal methods, which constitutes our ongoing work. We also discuss potential issues such as FRA mandated safety cases that needs to be addressed if the proposed features are to be added to the PTC systems.
Tank Car Top Fittings Protection: Evaluation of Derailment Failure Risks — A Conceptual Study
Authors: Di Bacco Barbara , Kirney Christopher , Prabhakaran Anand , Booth Graydon F. , Gantoi Florentina M. , Wen Rou
Published: June 2016

Top fittings devices on tank cars are subject to damage and failure under derailment conditions, potentially leading to the release of hazardous lading. This paper describes the conceptual development of an objective methodology for evaluating the risk of fittings protection failure and the potential reduction in that risk when mitigating strategies such as improved fittings protective structure are deployed. The methodology captures several key elements that affect fittings survival, including: the speed of derailment initiation, the impact velocity/force spectrum experienced by the fittings protective structure during the event, the strength/structural capacity of the protective structure, and the rigidity of the ground surface.

Detailed finite element modeling efforts were employed to capture derailment dynamics and corresponding impact velocity spectra, as well as the strength of multiple protective designs. Future work, including validation, is planned to extend the concept into a detailed methodology.
Finite Element Model of High Strength Reduced Modulus High Performance Concrete
Authors: Ortiz Albert R. , Caicedo Juan M. , Rizos Dimitris
Published: June 2016

High Performance Concrete (HPC) with early strength development is the material of choice in the fabrication of prestressed concrete railroad ties. The higher strength of HPC results in significantly higher values of the Elastic Modulus and increases the brittleness and the rigidity of the material, leading to premature cracking and the deterioration of the railroad ties. A High-Strength Reduced-Modulus High Performance Concrete (HSRM-HPC) material has been developed by the authors and used in the fabrication of prototype concrete ties. Detailed models based on the Finite Element Method of the HSRM-HPC have been developed to simulate the ASTM-C469 tests for elastic modulus. The HSRM-HPC constituent materials, i.e. aggregates and cement mortar, have been explicitly modeled and assigned properties determined experimentally. Aggregates size and distribution is modeled using a combination of probabilistic distributions consistent with the results of an experimental sieve analysis. Details of the development of each model are discussed. The models are verified with experimental data. Assessment studies have been performed in order to optimize the models with respect to efficiency, the quality of the results and computational times.
Sources of Transportation Accident Information
Authors: Schlesinger Dave
Published: June 2016

Accident investigation reports and related documents provide a wealth of information for rail professionals, even across different modes of transportation. This information can be used to improve operations, maintenance, safety, training, and emergency response. It can also guide the procurement and design of new equipment and infrastructure. At the same time, the historical nature of the information as well as the volume available and variety of sources can be a barrier to effective use. This paper will provide an introduction to some of the sources of transportation accident data and reports, including the variety of topic-specific information and special reports that are available. The discussion will include less-considered sources of accident information including foreign transportation safety boards as well as specialized federal and state agencies. Accidents that were investigated and reported on by more than one organization are also discussed.
Online 3D EPID‐based dose verification: Proof of concept
Authors: Spreeuw Hanno , Rozendaal Roel , Olaciregui‐Ruiz Igor , González Patrick , Mans Anton , Mijnheer Ben , van Herk Marcel
Published: June 2016

Purpose:

Delivery errors during radiotherapy may lead to medical harm and reduced life expectancy for patients. Such serious incidents can be avoided by performing dose verification online, i.e., while the patient is being irradiated, creating the possibility of halting the linac in case of a large overdosage or underdosage. The offline EPID‐based 3D in vivo dosimetry system clinically employed at our institute is in principle suited for online treatment verification, provided the system is able to complete 3D dose reconstruction and verification within 420 ms, the present acquisition time of a single EPID frame. It is the aim of this study to show that our EPID‐based dosimetry system can be made fast enough to achieve online 3D in vivo dose verification.

Methods:

The current dose verification system was sped up in two ways. First, a new software package was developed to perform all computations that are not dependent on portal image acquisition separately, thus removing the need for doing these calculations in real time. Second, the 3D dose reconstruction algorithm was sped up via a new, multithreaded implementation. Dose verification was implemented by comparing planned with reconstructed 3D dose distributions delivered to two regions in a patient: the target volume and the nontarget volume receiving at least 10 cGy. In both volumes, the mean dose is compared, while in the nontarget volume, the near‐maximum dose (D2) is compared as well. The real‐time dosimetry system was tested by irradiating an anthropomorphic phantom with three VMAT plans: a 6 MV head‐and‐neck treatment plan, a 10 MV rectum treatment plan, and a 10 MV prostate treatment plan. In all plans, two types of serious delivery errors were introduced. The functionality of automatically halting the linac was also implemented and tested.

Results:

The precomputation time per treatment was ∼180 s/treatment arc, depending on gantry angle resolution. The complete processing of a single portal frame, including dose verification, took 266 ± 11 ms on a dual octocore Intel Xeon E5‐2630 CPU running at 2.40 GHz. The introduced delivery errors were detected after 5–10 s irradiation time.

Conclusions:

A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for two different kinds of gross delivery errors. Thus, online 3D dose verification has been technologically achieved.
Fifty-four-month survival in a 3-year-old child presenting with an aggressive metastatic dedifferentiated clival chordoma
Authors: Kearns Ciléin , Kearns Cónail
Published: June 2016

Dedifferentiated chordoma is a rare, aggressive, chemoresistant and radioresistant malignancy arising from notochord remnants that can occur anywhere along the spine. Incidence in patients under 20 years of age is 1 per 250 million. We report a case of dedifferentiated clival chordoma presenting in a 3-year-old boy with pulmonary metastasis, which responded unusually well to chemotherapy, achieving complete metastatic clearance and debulking of the primary tumour. Proton beam therapy achieved further tumour control, with excellent quality of life for multiple years. On disease relapse, an atypical lateral transcondylar surgical approach achieved complete macroscopic clearance but there was cutaneous seeding. This, and continued primary site activity, failed to be controlled with targeted therapy, traditional chemotherapy and photon radiation, resulting in gradual neurological decline and death. Intensive management resulted in above-average survival despite diagnosis late in the disease course, which may be of value directing investigation into optimal management.
The arithmetic of reducing relative and absolute inequalities in health: a theoretical analysis illustrated with European mortality data
Authors: Mackenbach Johan P , Martikainen Pekka , Menvielle Gwenn , de Gelder Rianne
Published: June 2016

Background

Reducing inequalities in health is a great challenge for public health, but how relative and absolute inequalities in mortality respond to changes in mortality by socioeconomic group is not well understood.

Methods

We derived arithmetically what combinations of changes and starting levels of mortality by socioeconomic group produce narrowing, and what combinations produce widening of relative and absolute inequalities in mortality. We then determined empirically how often these scenarios actually occur with data on inequalities in cause-specific mortality in five European countries spanning four decades (1970–2010).

Results

Changes in the rate ratio depend exclusively on the ratio of relative mortality change between socioeconomic groups, whereas changes in the rate difference depend on whether the ratio of relative mortality change between socioeconomic groups is larger or smaller than the rate ratio. This implies that, in case of declining mortality and faster relative mortality decline in higher socioeconomic groups, the rate difference will increase until the rate ratio becomes equal to the ratio of relative mortality decline, but will then start to decline. In the most common scenario in our data set (starting rate ratio above 1.00 and faster relative mortality decline in higher than lower socioeconomic groups), the rate ratio indeed always goes up but the rate difference goes down in about half of all cases, sometimes after a period of growth.

Conclusions

A narrowing of absolute inequalities occurs under a wider range of conditions than a narrowing of relative inequalities in mortality.
The effects of oxygen depletion due to upwelling groundwater on the posthatch fitness of Atlantic salmon (Salmo salar)
Authors: Bloomer Jack , Sear David , Dutey-Magni Peter , Kemp Paul
Published: June 2016

The conditions experienced by incubating Atlantic salmon (Salmo salar) eggs are strongly influenced by hyporheic exchange. In some rivers, periods of intense groundwater upwelling can reduce oxygen levels in the incubation zone to 0% saturation. The present study investigated the effect of oxygen sags on the posthatch fitness of Atlantic salmon. A laboratory experiment allowed fine-scale control of oxygen concentrations to replicate those induced by low oxygen groundwater in rivers. Extreme oxygen sags in the earlier stages of embryo development resulted in a developmental lag with alevin hatching later and at an underdeveloped state. At the latest stages of development, oxygen sags caused premature hatching of severely underdeveloped alevin. These findings combined with a review of the literature suggest posthatch survival of embryos exposed to groundwater-induced hypoxia will be lower because of predation and poor competitiveness.
Effect of green manure crops, termination method, stubble crops, and fallow on soil water, available N, and exchangeable P
Authors: Mooleki S.P. , Gan Y. , Lemke R.L. , Zentner R.P. , Hamel C.
Published: June 2016

Green manure crops may have a role to play in the development of sustainable agricultural systems in the semiarid northern Great Plains of North America. This study determined the benefits of different green manure crops, seeding dates, and termination methods on soil nitrogen, phosphorus, and moisture, as well as the performance of durum wheat following green manures the following year. Field experiments were conducted at Swift Current, Saskatchewan, from 2006 to 2009. Three green manure crops [forage pea (Pisum sativum L.), chickling vetch (Lathyrus sativus L.), and black lentil (Lens culinaris Medik.)] were seeded in May, June, and July, and terminated at full bloom using glyphosate, rototilling or by frost. Other treatments included summerfallow and stubble of selected crops harvested for grain or silage. Different green manure crops, seeding dates or termination methods had similar effects on soil moisture, available N, and exchangeable P at termination or the following spring. These effects of green manure management on soil residual characteristics were comparable to those observed under summerfallow, but higher than those on grain or silage stubble. Therefore, green manure is a viable alternative to summerfallowing and could be seeded any time during the growing season. If seeded late, green manure could be terminated by frost, thus saving on costs.
N-soliton-like and double Casoratian solutions of a nonisospectral Ablowitz–Ladik equation
Authors: Chen Shou-Ting , Li Qi , Chen Deng-Yuan , Cheng Jun-Wei
Published: June 2016

A bilinear form of a nonisospectral differential-difference equation related to the Ablowitz–Ladik (AL) spectral problem is derived by a transformation of dependent variables. Exact solutions to the resulting bilinear equation are found. The [Formula: see text]-soliton-like solutions and the double Casoratian solutions are derived by means of Hirota’s direct method and the double Casoratian technique, respectively. Moreover, the connection between those two classes of solutions is explored.
Almost Engel finite and profinite groups
Authors: Khukhro E. I. , Shumyatsky P.
Published: June 2016

Let [Formula: see text] be an element of a group [Formula: see text]. For a positive integer [Formula: see text], let [Formula: see text] be the subgroup generated by all commutators [Formula: see text] over [Formula: see text], where [Formula: see text] is repeated [Formula: see text] times. We prove that if [Formula: see text] is a profinite group such that for every [Formula: see text] there is [Formula: see text] such that [Formula: see text] is finite, then [Formula: see text] has a finite normal subgroup [Formula: see text] such that [Formula: see text] is locally nilpotent. The proof uses the Wilson–Zelmanov theorem saying that Engel profinite groups are locally nilpotent. In the case of a finite group [Formula: see text], we prove that if, for some [Formula: see text], [Formula: see text] for all [Formula: see text], then the order of the nilpotent residual [Formula: see text] is bounded in terms of [Formula: see text].
On principles between ∑1- and ∑2-induction, and monotone enumerations
Authors: Kreuzer Alexander P. , Yokoyama Keita
Published: June 2016

We show that many principles of first-order arithmetic, previously only known to lie strictly between [Formula: see text]-induction and [Formula: see text]-induction, are equivalent to the well-foundedness of [Formula: see text]. Among these principles are the iteration of partial functions ([Formula: see text]) of Hájek and Paris, the bounded monotone enumerations principle (non-iterated, [Formula: see text]) by Chong, Slaman, and Yang, the relativized Paris–Harrington principle for pairs, and the totality of the relativized Ackermann–Péter function. With this we show that the well-foundedness of [Formula: see text] is a far more widespread than usually suspected. Further, we investigate the [Formula: see text]-iterated version of the bounded monotone iterations principle ([Formula: see text]), and show that it is equivalent to the well-foundedness of the ([Formula: see text])-height [Formula: see text]-tower [Formula: see text].
SHOULDER AND ELBOW JOINT ANGLE ESTIMATION FOR UPPER LIMB REHABILITATION TASKS USING LOW-COST INERTIAL AND OPTICAL SENSORS
Authors: ALIZADEGAN ALIREZA , BEHZADIPOUR SAEED
Published: June 2016

This paper proposes a new method to improve accuracy and real-time performance of inertial joint angle estimation for upper limb rehabilitation applications by modeling body acceleration and adding low-cost markerless optical position sensors. A method based on a combination of the 3D rigid body kinematic equations and Denavit-Hartenberg (DH) convention is used to model body acceleration. Using this model, body acceleration measurements of the accelerometer are utilized to increase linearization order and compensate for body acceleration perturbations. To correct for the sensor-to-segment misalignment of the inertial sensors, position measurements of a low-cost markerless position sensor are used. Joint angles are estimated by Extended Kalman Filter (EKF) and compared with Unscented Kalman Filter (UKF) in terms of performance. Simulations are performed to quantify the existing error and potential improvements achievable by the proposed method. Experiments on a human test subject performing an upper limb rehabilitation task is used to validate the simulation results in realistic conditions.
Asymmetric latent semantic indexing for gene expression experiments visualization
Authors: González Javier , Muñoz Alberto , Martos Gabriel
Published: June 2016

We propose a new method to visualize gene expression experiments inspired by the latent semantic indexing technique originally proposed in the textual analysis context. By using the correspondence word-gene document-experiment, we define an asymmetric similarity measure of association for genes that accounts for potential hierarchies in the data, the key to obtain meaningful gene mappings. We use the polar decomposition to obtain the sources of asymmetry of the similarity matrix, which are later combined with previous knowledge. Genetic classes of genes are identified by means of a mixture model applied in the genes latent space. We describe the steps of the procedure and we show its utility in the Human Cancer dataset.
Analytical approximation of heat and mass transfer in MHD non-Newtonian nanofluid flow over a stretching sheet with convective surface boundary conditions
Authors: Freidoonimehr Navid , Rashidi Mohammad Mehdi , Momenpour Mohammad Hossein , Rashidi Saman
Published: June 2016

The paper provides an analytical investigation, homotopy analysis method (HAM), of the heat and mass transfer for magnetohydrodynamic Oldroyd-B nanofluid flow over a stretching sheet in the presence of convective boundary condition. The PDE governing equations, which consist of equations of continuity, momentum, energy and nanoparticles, are converted to ordinary differential equations using similarity transformations. The current HAM solution demonstrates very good correlation with those of the previously published studies in the special cases. The influences of different flow physical parameters such as the Deborah numbers in terms of relaxation and retardation times ([Formula: see text], [Formula: see text]), magnetic parameter (M), Prandtl number (Pr), Brownian motion parameter (Nb), thermophoresis parameter (Nt), Lewis number (Le), and Biot number (Bi) on the fluid velocity component [Formula: see text], temperature distribution [Formula: see text] and concentration [Formula: see text] as well as the local Nusselt number [Formula: see text] and the local Sherwood number [Formula: see text] are discussed in detail.
Controlling Large-Scale Self-Organized Networks with Lightweight Cost for Fast Adaptation to Changing Environments
Authors: Kuze Naomi , Kominami Daichi , Kashima Kenji , Hashimoto Tomoaki , Murata Masayuki
Published: June 2016

Self-organization has potential for high scalability, adaptability, flexibility, and robustness, which are vital features for realizing future networks. Convergence of self-organizing control, however, is slow in some practical applications compared to control with conventional deterministic systems using global information. It is therefore important to facilitate convergence of self-organizing controls. In controlled self-organization, which introduces an external controller into self-organizing systems, the network is controlled to guide systems to a desired state. Although existing controlled self-organization schemes could achieve this feature, convergence speed for reaching an optimal or semioptimal solution is still a challenging task. We perform potential-based self-organizing routing and propose an optimal feedback method using a reduced-order model for faster convergence at low cost. Simulation results show that the proposed mechanism improves the convergence speed of potential-field construction (i.e., route construction) by at most 22.6 times with low computational and communication cost.
Baymax
Authors: Chen Quan , Yang Hailong , Mars Jason , Tang Lingjia
Published: June 2016

Modern warehouse-scale computers (WSCs) are being outfitted with accelerators to provide the significant compute required by emerging intelligent personal assistant (IPA) workloads such as voice recognition, image classification, and natural language processing. It is well known that the diurnal user access pattern of user-facing services provides a strong incentive to co-locate applications for better accelerator utilization and efficiency, and prior work has focused on enabling co-location on multicore processors. However, interference when co-locating applications on non-preemptive accelerators is fundamentally different than contention on multi-core CPUs and introduces a new set of challenges to reduce QoS violation. To address this open problem, we first identify the underlying causes for QoS violation in accelerator-outfitted servers. Our experiments show that queuing delay for the compute resources and PCI-e bandwidth contention for data transfer are the main two factors that contribute to the long tails of user-facing applications. We then present Baymax, a runtime system that orchestrates the execution of compute tasks from different applications and mitigates PCI-e bandwidth contention to deliver the required QoS for user-facing applications and increase the accelerator utilization. Using DjiNN, a deep neural network service, Sirius, an end-to-end IPA workload, and traditional applications on a Nvidia K40 GPU, our evaluation shows that Baymax improves the accelerator utilization by 91.3% while achieving the desired 99%-ile latency target for for user-facing applications. In fact, Baymax reduces the 99%-ile latency of user-facing applications by up to 195x over default execution.
CSR
Authors: Shalev Noam , Harpaz Eran , Porat Hagar , Keidar Idit , Weinsberg Yaron
Published: June 2016

One of the adverse effects of shrinking transistor sizes is that processors have become increasingly prone to hardware faults. At the same time, the number of cores per die rises. Consequently, core failures can no longer be ruled out, and future operating systems for many-core machines will have to incorporate fault tolerance mechanisms.

We present CSR, a strategy for recovery from unexpected permanent processor faults in commodity operating systems. Our approach overcomes surprise removal of faulty cores, and also tolerates cascading core failures. When a core fails in user mode, CSR terminates the process executing on that core and migrates the remaining processes in its run-queue to other cores. We further show how hardware transactional memory may be used to overcome failures in critical kernel code. Our solution is scalable, incurs low overhead, and is designed to integrate into modern operating systems. We have implemented it in the Linux kernel, using Haswell's Transactional Synchronization Extension, and tested it on a real system.
M3
Authors: Asmussen Nils , Völp Marcus , Nöthen Benedikt , Härtig Hermann , Fettweis Gerhard
Published: June 2016

In the last decade, the number of available cores increased and heterogeneity grew. In this work, we ask the question whether the design of the current operating systems (OSes) is still appropriate if these trends continue and lead to abundantly available but heterogeneous cores, or whether it forces a fundamental rethinking of how systems are designed. We argue that: 1. hiding heterogeneity behind a common hardware interface unifies, to a large extent, the control and coordination of cores and accelerators in the OS, 2. isolating at the network-on-chip rather than with processor features (like privileged mode, memory management unit, ...), allows running untrusted code on arbitrary cores, and 3. providing OS services via protocols over the network-on-chip, instead of via system calls, makes them accessible to arbitrary types of cores as well.

In summary, this turns accelerators into first-class citizens and enables a single and convenient programming environment for all cores without the need to trust any application.

In this paper, we introduce network-on-chip-level isolation, present the design of our microkernel-based OS, M3, and the common hardware interface, and evaluate the performance of our prototype in comparison to Linux. A bit surprising, without using accelerators, M3 outperforms Linux in some application-level benchmarks by more than a factor of five.
TaxDC
Authors: Leesatapornwongsa Tanakorn , Lukman Jeffrey F. , Lu Shan , Gunawi Haryadi S.
Published: June 2016

We present TaxDC, the largest and most comprehensive taxonomy of non-deterministic concurrency bugs in distributed systems. We study 104 distributed concurrency (DC) bugs from four widely-deployed cloud-scale datacenter distributed systems, Cassandra, Hadoop MapReduce, HBase and ZooKeeper. We study DC-bug characteristics along several axes of analysis such as the triggering timing condition and input preconditions, error and failure symptoms, and fix strategies, collectively stored as 2,083 classification labels in TaxDC database. We discuss how our study can open up many new research directions in combating DC bugs.
Paravirtual Remote I/O
Authors: Kuperman Yossi , Moscovici Eyal , Nider Joel , Ladelsky Razya , Gordon Abel , Tsafrir Dan
Published: June 2016

The traditional "trap and emulate" I/O paravirtualization model conveniently allows for I/O interposition, yet it inherently incurs costly guest-host context switches. The newer "sidecore" model eliminates this overhead by dedicating host (side)cores to poll the relevant guest memory regions and react accordingly without context switching. But the dedication of sidecores on each host might be wasteful when I/O activity is low, or it might not provide enough computational power when I/O activity is high. We propose to alleviate this problem at rack scale by consolidating the dedicated sidecores spread across several hosts onto one server. The hypervisor is then effectively split into two parts: the local hypervisor that hosts the VMs, and the remote hypervisor that processes their paravirtual I/O. We call this model vRIO---paraVirtual Remote I/O. We find that by increasing the latency somewhat, it provides comparable throughput with fewer sidecores and superior throughput with the same number of sidecores as compared to the state of the art. vRIO additionally constitutes a new, cost-effective way to consolidate I/O devices (on the remote hypervisor) while supporting efficient programmable I/O interposition.
Lifting Assembly to Intermediate Representation
Authors: Hasabnis Niranjan , Sekar R.
Published: June 2016

Translating low-level machine instructions into higher-level intermediate language (IL) is one of the central steps in many binary analysis and instrumentation systems. Existing systems build such translators manually. As a result, it takes a great deal of effort to support new architectures. Even for widely deployed architectures, full instruction sets may not be modeled, e.g., mature systems such as Valgrind still lack support for AVX, FMA4 and SSE4.1 for x86 processors. To overcome these difficulties, we propose a novel approach that leverages knowledge about instruction set semantics that is already embedded into modern compilers such as GCC. In particular, we present a learning-based approach for automating the translation of assembly instructions to a compiler's architecture-neutral IL. We present an experimental evaluation that demonstrates the ability of our approach to easily support many architectures (x86, ARM and AVR), including their advanced instruction sets. Our implementation is available as open-source software.