bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear dynamic response of imperfect symmetric thin sigmoid-functionally graded material plate with metal-ceramic-metal layers on elastic foundation
Authors: Duc Nguyen Dinh , Cong Pham Hong
Published: July 2013

This paper presents a first proposal to investigate the nonlinear dynamic response of imperfect symmetric thin sigmoid-functionally graded material (S-FGM) plate resting on an elastic foundation and subjected to mechanical loads. The formulations use classical plate theory taking into account geometrical nonlinearity, initial geometrical imperfection of the S-FGM plate and stress function. The volume fractions of metal and ceramic are applied by sigmoid-law distribution (S-FGM) with metal-ceramic-metal layers. The nonlinear equations are solved by the Runge-Kutta and Bubnov-Galerkin methods using stress function. The obtained results show the effects of material, imperfection and elastic foundations on the dynamical response of S-FGM plate.
Nonlinear vibration of a two-dimensional composite laminated plate in subsonic air flow
Authors: Yao Guo , Li Feng-Ming
Published: July 2013

The nonlinear vibration of a two-dimensional composite laminated plate in subsonic air flow with simply supported boundary conditions is investigated. Based on the von Karman’s plate theory, the equation of motion of the plate is established using Hamilton’s principle. The aerodynamic pressure induced by the coupled vibration of the plate and subsonic airflow is derived from the linear potential flow theory and compared with the existing model. The variable separation method is used to transform the equation of motion of the plate into nonlinear ordinary differential equations. The influences of the flow velocity, the length-to-thickness ratio and the ply angle of the plate on the nonlinear vibration behaviors of the plate are discussed. From the analytical and numerical results it can be seen that the critical instability velocity obtained from the present aerodynamic model is the same as the existing result. The first-order expansion of the transverse displacement can reflect the dynamic characteristics of the plate. With the increase of the flow velocity and the length-to-thickness ratio, the instability interval of the nonlinear vibration can be prolonged and the nonlinear resonance frequency can be increased. The composite laminated plate with smaller ply angle exhibits more stable dynamic properties than that with larger ply angles.
Development of fuzzy controlled chopper drive for permanent magnet DC motor
Authors: Murugananth Gopal Raj , Vijayan Subramanian
Published: July 2013

In this article the fuzzy logic based closed loop chopper controlled permanent magnet DC motor drive is proposed for orthopedic surgical simulators. The proposed drive consists of an inner current control loop and an outer speed control loop. The fuzzy technique is used in the speed loop and the system is simulated using Matlab/Simulink. The steady state and transient state responses of the proposed fuzzy system are compared with conventional PI controlled system. The comparative analysis infers that the fuzzy system provides better performance.
Design and analysis of shock and random vibration isolation system for a discrete model of submerged jet impingement cooling system
Authors: Hosseinloo Ashkan Haji , Yap Fook Fah , Lim Liang Ying
Published: July 2013

High-powered embedded computing equipment using air transport rack (ATR) form-factors are playing an ever-increasing role in critical military applications in air, land and sea environments. High power and wattage of the electronics and processors require large heat dissipation, and thus more sophisticated and efficient thermal cooling systems such as loop heat pipes or jet impingement systems are demanded. However, these thermal solutions are more susceptible to harsh military environments and thus, for proper performance of thermal and electronic equipment, they need to be protected against shock and vibration inherent in harsh environments like those in military applications. In this paper, an isolated ATR chassis including two jet impingement chambers is modeled as a three-degrees-of-freedom system and its response to random vibration and shock has been studied. Both finite element and experimental modal analysis is utilized to characterize dynamics of the components of the jet impingement system. The response of the model is compared to that of the traditional single-degree-of-freedom model, and the isolation system is optimized in terms of its damping.
Parametric vibration of two shrink-fitted thin rings with time-varying interface pressure; nonlinear analysis and experimental study
Authors: Sadeghi Morteza , Hosseinzadeh Vahideh Ansari
Published: July 2013

In a shrink-fitted joint, the interface pressure plays an important role as it is the main source of the joint and it keeps the joining components together. However, time-variation of the interface pressure causes parametric instability in the system. In this paper, the effect of time-variant interface pressure on the dynamics of two shrink-fitted rings has been studied. Deriving a dynamic equation of motion of the joint of two shrink-fitted rings and substituting time-variant interface pressure in the equation, the problem extends to nonlinear vibration. The obtained equation of motion, which contains parametrically excited terms, is a general form of Mathieu’s equation. A perturbation method, to determine the instability regions of motion, is applied to obtain the transition curves. To validate the obtained stability regions, an experiment has been performed. Both the analytical and experimental results demonstrate that by increasing the value of the interface pressure, the natural frequencies of the joint increase.
An efficient method in the 2D problem on transient oscillations of the elastic half-space interacting with a rigid structure
Authors: Brigante M , Sumbatyan MA
Published: July 2013

We propose an efficient method to study the (two-dimensional) in-plane nonstationary (transient) problem for a rigid rectangular structure above the oscillating foundation. A massive structure is perfectly coupled with the foundation, whose oscillations are caused by an oblique plane seismic wave incoming from below to the boundary surface. The structure is assumed to be considerably more rigid than the foundation. The mathematical formulation admits application of the Laplace transform over time and Fourier transform along the horizontal coordinate. By satisfying the boundary conditions over the contact zone between the rectangle and the foundation, the problem is reduced to a system of two integral equations for normal and tangential contact stress, which contain the Laplace parameter. To solve this system, we apply a numerical method to arising Volterrà–Fredholm integral equations. Then the dynamic properties of the structure is studied for various combinations of physical and geometrical parameters.
Maternal Overreactive Sympathetic Nervous System Responses to Repeated Infant Crying Predicts Risk for Impulsive Harsh Discipline of Infants
Authors: Joosen Katharina J. , Mesman Judi , Bakermans-Kranenburg Marian J. , van IJzendoorn Marinus H.
Published: July 2013

Physiological reactivity to repeated infant crying was examined as a predictor of risk for harsh discipline use with 12-month-olds in a longitudinal study with 48 low-income mother–infant dyads. Physiological reactivity was measured while mothers listened to three blocks of infant cry sounds in a standard cry paradigm when their infants were 3 months old. Signs of harsh discipline use were observed during two tasks during a home visit when the infants were 12 months old. Mothers showing signs of harsh discipline ( n = 10) with their 12-month-olds were compared to mothers who did not ( n = 38) on their sympathetic (skin conductance levels [SCL]) and parasympathetic (respiratory sinus arrhythmia) reactivity to the cry sounds. Results showed a significant interaction effect for sympathetic reactivity only. Mean SCL of harsh-risk mothers showed a significant different response pattern from baseline to crying and onward into the recovery, suggesting that mean SCL of mothers who showed signs of harsh discipline continued to rise across the repeated bouts of cry sounds while, after an initial increase, mean SCL level of the other mothers showed a steady decline. We suggest that harsh parenting is reflected in physiological overreactivity to negative infant signals and discuss our findings from a polyvagal perspective.
Social Spending, Taxes, and Income Redistribution in Uruguay
Authors: Bucheli Marisa , Lustig Nora , Rossi Máximo , Amábile Florencia
Published: July 2013

How much redistribution does Uruguay accomplish through social spending and taxes? How progressive are revenue collection and social spending? What could be done to further increase redistribution and improve redistributional effectiveness? A standard fiscal incidence analysis shows that Uruguay achieves a nontrivial reduction in inequality and poverty when all taxes and transfers are combined. Direct taxes are progressive and indirect taxes are practically neutral. Social spending on direct transfers, contributory pensions, education, and health is quite progressive in absolute terms except for tertiary education, which is almost neutral in relative terms. Specific suggestions for improving the effectiveness are suggested.
Tax Reform for Growth, Equity, and Revenue
Authors: Gale William G. , Brown Samuel
Published: July 2013

This article examines the fiscal outlook and tax reform options in the United States. The major conclusions include the following: the United States faces a substantial fiscal shortfall in the medium- and long term; both spending cuts and tax increases should contribute to the solution; tax increases need not do significant harm to economic growth; and there are sensible ways to both reform tax structure and raise revenues, including the redesign of tax expenditures, the creation of a value-added tax or a carbon tax, or an increase in the gasoline tax.
“Parallel Societies” of the Past? Articulations of Citizenship’s Commemorative Dimension in Berlin’s Cityscape
Authors: Schwarz Anja
Published: July 2013

Historical narratives play an important role in constructing contemporary notions of citizenship. They are sites on which ideas of the nation are not only reaffirmed but also contested and reframed. In contemporary Germany, dominant narratives of the country’s modern history habitually focus on the legacy of the Third Reich and tend to marginalize the country’s rich and highly complex histories of immigration. The article addresses this commemorative void in relation to Berlin’s urban landscape. It explores how the city’s multilayered architecture provides locations for the articulation of marginal memories—and hence sites of urban citizenship—that are often denied to immigrant communities on a national scale. Through a detailed examination of a small celebration in 1965 that marked the anniversary of the founding of the modern Turkish republic, the article engages with the layers of history that coalesce around such sites in Berlin.
Vitamin D levels and risk of multiple sclerosis in patients with clinically isolated syndromes
Authors: Martinelli Vittorio , Dalla Costa Gloria , Colombo Bruno , Dalla Libera Dacia , Rubinacci Alessandro , Filippi Massimo , Furlan Roberto , Comi Giancarlo
Published: July 2013

Background:

Growing evidence suggests that vitamin D deficiency may be one of the most important environmental factors for the development of multiple sclerosis (MS).

Objectives:

The objectives of this paper are to evaluate serum 25-hydroxyvitamin D (25(OH)D) levels in patients with clinically isolated syndromes (CIS) and to examine whether they are related to MS risk.

Methods:

This is a retrospective study of 100 CIS patients hospitalized from 2000 to 2009 at San Raffaele Hospital, Milan, Italy. We evaluated baseline 25(OH)D level as well as clinical, brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) data.

Results:

A total of 52% of CIS patients had vitamin D deficiency (25(OH)D < 50 nmol/l). During follow-up (median: 7.17 years), 55 patients developed clinically definite MS (CDMS). Patients with very low (< 10th percentile) and low (< 25th percentile) 25(OH)D levels were particularly at risk of CDMS (HRs (95% CIs): 2.12 (0.91–4.96) and 1.61 (0.85–3.03), respectively), while no further reduction in the HRs of disease was observed at high levels of 25(OH)D. This association was even stronger after adjustment for additional risk factors for CDMS development (HRs (95% CIs) for 25(OH)D levels < 10th and 25th percentiles: 3.34 (1.32–8.45) and 2.04 (0.96–4.36), respectively).

Conclusion:

Low serum vitamin D is associated with increased MS risk in patients with CIS.
Hypoperfusion and T1-hypointense lesions in white matter in multiple sclerosis
Authors: Narayana Ponnada A , Zhou Yuxiang , Hasan Khader M , Datta Sushmita , Sun Xiaojun , Wolinsky Jerry S
Published: July 2013

Background:

Longitudinal magnetic resonance imaging (MRI) studies show that a fraction of the multiple sclerosis (MS) T2-lesions contain T1-hypointense components that may persist to represent severe, irreversible tissue damage. It is not known why certain lesions convert to persistent T1-hypointense lesions.

Objective:

We hypothesized that the T1-hypointense lesions disproportionately distribute in the more hypoperfused areas of the brain. Here we investigated the association between hypoperfusion and T1-hypointense lesion distributions.

Methods:

MRI and cerebral blood flow (CBF) data were acquired on 45 multiple sclerosis (MS) patients and 20 healthy controls. CBF maps were generated using pseudo-continuous arterial spin labeling technique. The lesion probability distribution maps were superimposed on the CBF maps.

Results:

Two distinct CBF clusters were observed in the white matter (WM) both in healthy controls and MS patients. An overall reduction in CBF was observed in MS patients compared to healthy controls. The majority of the T1-hypointense lesions were concentrated almost exclusively in the WM regions with lower CBF. The T2-hyperintense lesions were more generally distributed in both higher and lower perfused WM.

Conclusion:

This study suggests an association between hypoperfusion and T1-hypointense lesions.
Is it time to regulate microfinance?
Authors: Ahmed Fakhruddin , Brown Brad , Williams Susan Perry
Published: July 2013

In this article we suggest a new future for microfinance institutions (MFIs). In order to better serve the needs of the poor, we propose government regulation, improved organizational governance and business models for MFIs. With a strict definition of ‘microfinance’, true microfinance can be properly distinguished from other forms of financial activities. With adequate regulation and supervision, MFIs can take deposits from the poor thus providing a valuable service while obtaining money to lend. We propose that MFIs meet a strict definition and then be regulated and monitored to protect borrowers, which will also help to legitimize the microfinance industry.
Book Review: From recipients to donors: Emerging powers and the changing development landscape
Authors: Said Maurice
Published: July 2013

Mawdsley, E. 2012: From recipients to donors: Emerging powers and the changing development landscape. London and New York: Zed Books. x + 270 pp. £18.99 paperback. ISBN: 9781848139466
Daylight exposure has a positive carryover effect on nighttime performance and subjective sleepiness
Authors: Figueiro MG , Nonaka S , Rea MS
Published: July 2013

Two studies were designed to investigate the carryover effects of daylight on performance and self-reports of sleepiness. The effects of daylight and of darkness were compared independent of the effects of simultaneous periodic, 1-hour exposures to narrow-band blue and red lights over the course of 26-hour sessions. Nighttime performance on a 54-minute tracking task, but not subjective sleepiness, was significantly better following exposure to daylight. There was no differential effect on performance or sleepiness from exposure to the blue or red lights. Eight of the participants returned to experience a completely dark session and a replication of the daylight and intermittent blue light session. Nighttime performance and subjective sleepiness were significantly worse for the dark session than for daylight-plus-blue sessions in both studies.
Micromechanical analysis of loop-formed fiber-reinforced soil composite
Authors: Hejazi Seyed Mahdi , Abtahi Seyed Mahdi , Sheikhzadeh Mohammad , Mostashfi Amir
Published: July 2013

In this research, loop-formed fiber is introduced as a novel reinforcement method of soil composites instead of using ordinary fibers. In order to investigate the materials' mechanical properties, the shear behavior of both fiber and looped-fiber-reinforced soil composites was analyzed by micromechanical method (finite element method) and a set of direct shear tests. The results indicate that the looped-fiber soil composite exhibits greater failure strain energy compared with fiber-reinforced soil composite at the same fiber orientation in the substrate. Furthermore, the proposed model demonstrated two major reinforcing components: “the fiber effect” and “the loop effect.” The latter effect is the key benefit and the main advantage of using looped fibers over ordinary fibers in soil reinforcement. Altogether, there is a close agreement between finite element method outputs and experimental results, suggestive of a novel technical textile material that could potentially be used in geotechnical engineering.
Institutional Effectiveness
Authors: Murphy Joel
Published: July 2013

The literature describes various approaches that community colleges use to achieve institutional effectiveness; however there is no information about how Hispanic Serving Institutions (HSIs) go about this process. The purpose of this article is to review some principles and processes of accountability and to describe the strategic review and planning process undertaken by one HSI. The article concludes with “lessons learned” that may be helpful to other HSIs as they undertake strategic review and planning.
Trust, Punishment, and Cooperation Across 18 Societies
Authors: Balliet Daniel , Van Lange Paul A. M.
Published: July 2013

Punishment promotes contributions to public goods, but recent evidence suggests that its effectiveness varies across societies. Prior theorizing suggests that cross-societal differences in trust play a key role in determining the effectiveness of punishment, as a form of social norm enforcement, to promote cooperation. One line of reasoning is that punishment promotes cooperation in low-trust societies, primarily because people in such societies expect their fellow members to contribute only if there are strong incentives to do so. Yet another line of reasoning is that high trust makes punishment work, presumably because in high-trust societies people may count on each other to make contributions to public goods and also enforce norm violations by punishing free riders. This poses a puzzle of punishment: Is punishment more effective in promoting cooperation in high- or low-trust societies? In the present article, we examine this puzzle of punishment in a quantitative review of 83 studies involving 7,361 participants across 18 societies that examine the impact of punishment on cooperation in a public goods dilemma. The findings provide a clear answer: Punishment more strongly promotes cooperation in societies with high trust rather than low trust.
How “Paternalistic” Is Spatial Perception? Why Wearing a Heavy Backpack Doesn’t—and Couldn’t—Make Hills Look Steeper
Authors: Firestone Chaz
Published: July 2013

A chief goal of perception is to help us navigate our environment. According to a rich and ambitious theory of spatial perception, the visual system achieves this goal not by aiming to accurately depict the external world, but instead by actively distorting the environment’s perceived spatial layout to bias action selection toward favorable outcomes. Scores of experimental results have supported this view—including, famously, a report that wearing a heavy backpack makes hills look steeper. This perspective portrays the visual system as unapologetically paternalistic: Backpacks make hills harder to climb, so vision steepens them to discourage ascent. The “paternalistic” theory of spatial perception has, understandably, attracted controversy; if true, it would radically revise our understanding of how and why we see. Here, this view is subjected to a kind and degree of scrutiny it has yet to face. After characterizing and motivating the case for paternalistic vision, I expose several unexplored defects in its theoretical framework, arguing that extant accounts of how and why spatial perception is ability-sensitive are deeply problematic and that perceptual phenomenology belies the view’s claims. The paternalistic account of spatial perception not only isn’t true—it couldn’t be true, even if its empirical findings were accepted at face value.
Perceiving Minds and Gods
Authors: Gervais Will M.
Published: July 2013

Most people believe in the existence of empirically unverifiable gods. Despite apparent heterogeneity, people’s conceptions of their gods center on predictable themes. Gods are overwhelmingly represented as intentional agents with (more or less) humanlike mental lives. This article reviews converging evidence suggesting that this regularity in god concepts exists in part because the ability to represent gods emerges as a cognitive by-product of the human capability to perceive minds. Basic human mind-perception abilities both facilitate and constrain belief in gods, with profound implications for individual differences in religious beliefs, implicit representations of supernatural agents, and the varieties of nonreligious experience. Furthermore, people react similarly to both reminders of gods and cues of social surveillance (e.g., audiences or video cameras), leading to interesting consequences in the domains of prosocial behavior, socially desirable responding, and self-awareness. Converging evidence indicates that mind perception is both cause and consequence of many religious beliefs.
An Embodied Approach to Perception
Authors: Proffitt Dennis R.
Published: July 2013

When humans perceive the environment, angular units of visual information must be transformed into units appropriate for the specification of such parameters of surface layout as extent, size, and orientation. Our embodied approach to perception proposes that these scaling units derive from the body. For example, hand size is relevant for scaling the size of a strawberry, whereas an extent across a meadow is scaled by the amount of walking required to traverse it. In his article, Firestone (2013, this issue) argued that our approach is wrong; in fact, he argued that it must be wrong. This reply to Firestone’s critique is organized into three parts, which address the following questions: (a) What is the fundamental question motivating our approach? (b) How does our approach answer this question? (c) How can we address Firestone’s arguments against our approach? A point-by-point critique of Firestone’s arguments is presented. Three conclusions are drawn: (a) Most of Firestone’s arguments reflect a misunderstanding of our approach, (b) none of his arguments are the fatal flaws in our approach that he believes them to be, and (c) there are good reasons to believe that perception—just like any other biological function—is a phenotypic expression.
Beyond the encyclopedia: Collective memories in Wikipedia
Authors: Ferron Michela , Massa Paolo
Published: July 2013

Collective memory processes have been studied from many different perspectives. For example, while psychology has investigated collaborative recall in small groups, other research traditions have focused on flashbulb memories or on the cultural processes involved in the formation of collective memories of entire nations. In this article, considering the online encyclopedia Wikipedia as a global memory place, we analyze online commemoration patterns of traumatic events. We extracted 88 articles and talk pages related to traumatic events, and using logistic regression, we analyzed their edit activity comparing it with more than 370,000 other Wikipedia pages. Results show that the relative amount of edits during anniversaries can significantly distinguish between pages related to traumatic events and other pages. The logistic regression results, together with the transcription of a group of messages exchanged by the users during the anniversaries of the September 11 attacks and the Virginia Tech massacre, suggest that commemoration activities take place in Wikipedia, opening the way to the quantitative study of online collective memory building processes on a large scale.
Focal portal vein stenosis in an adolescent potentially related to complicated umbilical catheter insertion in the neonatal period
Authors: Maleux Geert , Hoffman Ilse , Heye Sam , Cassiman David
Published: July 2013

A 14-year-old girl, with no medical history except for a preterm birth at 7 months, presented with clinical and laboratory signs of pancytopenia. Radiological investigation, including abdominal ultrasound and magnetic resonance imaging revealed a focal irregular main portal vein wall and splenomegaly. Endoscopy showed major esophageal and gastric varices. Definitive diagnosis was made by direct, transhepatic portography revealing a focal stenosis associated with a dissection of the main portal vein. Percutaneous treatment including balloon angioplasty and stent placement resulted in complete re-expansion of the portal vein main branch. Clinical and radiological follow-up over 5 years showed complete disappearance of all clinical signs and normalization of laboratory data and splenic volume.
Genetic interaction between Kit and Scl
Authors: Lacombe Julie , Krosl Gorazd , Tremblay Mathieu , Gerby Bastien , Martin Richard , Aplan Peter D. , Lemieux Sebastien , Hoang Trang
Published: July 2013

Key Points

Scl operates both downstream of Kit to control the survival of Kit+ multipotent and erythroid progenitors and upstream of Kit to determine Kit expression levels. Scl and Kit establish a positive feedback loop in hematopoietic progenitors.
Detection of MRD may predict the outcome of patients with Philadelphia chromosome–positive ALL treated with tyrosine kinase inhibitors plus chemotherapy
Authors: Ravandi Farhad , Jorgensen Jeffrey L. , Thomas Deborah A. , O’Brien Susan , Garris Rebecca , Faderl Stefan , Huang Xuelin , Wen Sijin , Burger Jan A. , Ferrajoli Alessandra , Kebriaei Partow , Champlin Richard E. , Estrov Zeev , Challagundla Pramoda , Wang Sa A. , Luthra Rajyalakshmi , Cortes Jorge E. , Kantarjian Hagop M.
Published: July 2013

From 2001 to 2011, 122 patients with newly diagnosed Philadelphia chromosome–positive acute lymphoblastic leukemia were treated with chemotherapy + imatinib (n = 54) or + dasatinib (n = 68). One hundred fifteen (94%) achieved complete remission (CR) including 101 patients who achieved it with only 1 induction course and had at least 1 minimal residual disease (MRD) assessment; 25 patients underwent an allogeneic stem cell transplant in first CR and were excluded, leaving 76 patients as the subject of this report. MRD monitoring by multiparameter flow cytometry (MFC) and real-time quantitative polymerase chain reaction (PCR) was performed at the end of induction and at ∼3-month intervals thereafter. Median age was 54 years (range, 21-84 years). There was no difference in survival by achievement of at least a major molecular response (MMR; BCR-ABL/ABL < 0.1%) at CR (P = .22). Patients achieving MMR at 3, 6, 9, and 12 months had a better survival (P = .02, .04, .05, and .01, respectively). Negative MFC at CR did not predict for improved survival (P = .2). At 3 and 12 months, negative MRD by MFC was associated with improved survival (P = .04 and .001). MRD monitoring by PCR and MFC identifies patients who benefit from treatment intensification in first CR.
CD30 targeting with brentuximab vedotin: a novel therapeutic approach to primary effusion lymphoma
Authors: Bhatt Shruti , Ashlock Brittany M. , Natkunam Yasodha , Sujoy Victoria , Chapman Jennifer Rose , Ramos Juan Carlos , Mesri Enrique A. , Lossos Izidore S.
Published: July 2013

Key Points

Brentuximab vedotin serves as an effective therapy for PEL. Brentuximab vedotin led to cytotoxic effects in PEL cell lines and extended survival of xenograft mice.
Proplatelet generation in the mouse requires PKCε-dependent RhoA inhibition
Authors: Gobbi Giuliana , Mirandola Prisco , Carubbi Cecilia , Masselli Elena , Sykes Stephen M. , Ferraro Francesca , Nouvenne Antonio , Thon Jonathan N. , Italiano Joseph E. , Vitale Marco
Published: July 2013

Key Points

PKCε, regulating RhoA activity, is a critical mediator of proplatelet formation. PKCε shut down results in RhoA expression levels that are incompatible with normal platelet generation.
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling
Authors: Ahmed Zeeshan , Zeeshan Saman , Huber Claudia , Hensel Michael , Schomburg Dietmar , Münch Richard , Eisenreich Wolfgang , Dandekar Thomas
Published: July 2013

Background

The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution.

Results

The open-source software “Least Square Mass Isotopomer Analyzer” (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman’s least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed.

Conclusions

The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.
Caspase-9, caspase-3 and caspase-7 have distinct roles during intrinsic apoptosis
Authors: Brentnall Matthew , Rodriguez-Menocal Luis , De Guevara Rebeka Ladron , Cepero Enrique , Boise Lawrence H
Published: July 2013

Background

Apoptosis is a form of programmed cell death that is regulated by the Bcl-2 family and caspase family of proteins. The caspase cascade responsible for executing cell death following cytochromecrelease is well described; however the distinct roles of caspases-9, -3 and -7 during this process are not completely defined.

Results

Here we demonstrate several unique functions for each of these caspases during cell death. Specific inhibition of caspase-9 allows for efficient release of cytochromec, but blocks changes in mitochondrial morphology and ROS production. We show that caspase-9 can cleave Bid into tBid at amino acid 59 and that this cleavage of Bid is required for ROS production following serum withdrawal. We also demonstrate that caspase-3-deficient MEFs are less sensitive to intrinsic cell death stimulation, yet have higher ROS production. In contrast, caspase-7-deficient MEFs are not resistance to intrinsic cell death, but remain attached to the ECM.

Conclusions

Taken together, these data suggest that caspase-9 is required for mitochondrial morphological changes and ROS production by cleaving and activating Bid into tBid. After activation by caspase-9, caspase-3 inhibits ROS production and is required for efficient execution of apoptosis, while effector caspase-7 is required for apoptotic cell detachment.
A high-resolution cucumber cytogenetic map integrated with the genome assembly
Authors: Sun Jianying , Zhang Zhonghua , Zong Xu , Huang Sanwen , Li Zongyun , Han Yonghua
Published: July 2013

Background

High-resolution cytogenetic map can provide not only important biological information on genome organization but also solid foundation for genetic and genomic research. The progress in the molecular and cytogenetic studies has created the basis for developing the cytogenetic map in cucumber (Cucumis sativus L.).

Results

Here, the cytogenetic maps of four cucumber chromosomes (chromosomes 1, 3–5) were constructed by fluorescence in situ hybridization (FISH) analysis on cucumber pachytene chromosomes. Together with our previously constructed cytogenetic maps of three cucumber chromosomes (chromosomes 2, 6–7), cucumber has a complete cytogenetic map with 76 anchoring points between the genetic, the cytogenetic and the draft genome assembly maps. To compare our pachytene FISH map directly to the genetic linkage and draft genome assembly maps, we used a standardized map unit—relative map position (RMP) to produce the comparative map alignments. The alignments allowed a global view of the relationship of genetic and physical distances along each cucumber chromosome, and accuracy and coverage of the draft genome assembly map.

Conclusions

We demonstrated a good correlation between positions of the markers in the linkage and physical maps, and essentially complete coverage of chromosome arms by the draft genome assembly. Our study not only provides essential information for the improvement of sequence assembly but also offers molecular tools for cucumber genomics research, comparative genomics and evolutionary study.
RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapaand their use for genome-wide linkage mapping and specific-region fine mapping
Authors: Paritosh Kumar , Yadava Satish K , Gupta Vibha , Panjabi-Massand Priya , Sodhi Yashpal S , Pradhan Akshay K , Pental Deepak
Published: July 2013

Background

Brassica rapa (AA) contains very diverse forms which include oleiferous types and many vegetable types. Genome sequence of B. rapa line Chiifu (ssp. pekinensis), a leafy vegetable type, was published in 2011. Using this knowledge, it is important to develop genomic resources for the oleiferous types of B. rapa. This will allow more involved molecular mapping, in-depth study of molecular mechanisms underlying important agronomic traits and introgression of traits from B. rapa to major oilseed crops - B. juncea (AABB) and B. napus (AACC). The study explores the availability of SNPs in RNA-seq generated contigs of three oleiferous lines of B. rapa - Candle (ssp. oleifera, turnip rape), YSPB-24 and Tetra (ssp. trilocularis, Yellow sarson) and their use in genome-wide linkage mapping and specific-region fine mapping using a RIL population between Chiifu and Tetra.

Results

RNA-seq was carried out on the RNA isolated from young inflorescences containing unopened floral buds, floral axis and small leaves, using Illumina paired-end sequencing technology. Sequence assembly was carried out using the Velvet de-novo programme and the assembled contigs were organised against Chiifu gene models, available in the BRAD-CDS database. RNA-seq confirmed the presence of more than 17,000 single-copy gene models described in the BRAD database. The assembled contigs and the BRAD gene models were analyzed for the presence of SSRs and SNPs. While the number of SSRs was limited, more than 0.2 million SNPs were observed between Chiifu and the three oleiferous lines. Assays for SNPs were designed using KASPar technology and tested on a F7-RIL population derived from a Chiifu x Tetra cross. The design of the SNP assays were based on three considerations - the 50 bp flanking region of the SNPs should be strictly similar, the SNP should have a read-depth of ≥7 and no exon/intron junction should be present within the 101 bp target region. Using these criteria, a total of 640 markers (580 for genome-wide mapping and 60 for specific-region mapping) marking as many genes were tested for mapping. Out of 640 markers that were tested, 594 markers could be mapped unambiguously which included 542 markers for genome-wide mapping and 42 markers for fine mapping of the tet-o locus that is involved with the trait tetralocular ovary in the line Tetra.

Conclusion

A large number of SNPs and PSVs are present in the transcriptome of B. rapa lines for genome-wide linkage mapping and specific-region fine mapping. Criteria used for SNP identification delivered markers, more than 93% of which could be successfully mapped to the F7–RIL population of Chiifu x Tetra cross.
Etiological analysis and predictive diagnostic model building of community-acquired pneumonia in adult outpatients in Beijing, China
Authors: Liu Ya-Fen , Gao Yan , Chen Mei-Fang , Cao Bin , Yang Xiao-Hua , Wei Lai
Published: July 2013

Background

Etiological epidemiology and diagnosis are important issues in adult community-acquired pneumonia (CAP), and identifying pathogens based on patient clinical features is especially a challenge. CAP-associated main pathogens in adults include viruses as well as bacteria. However, large-scale epidemiological investigations of adult viral CAP in China are still lacking. In this study, we analyzed the etiology of adult CAP in Beijing, China and constructed diagnostic models based on combinations of patient clinical factors.

Methods

A multicenter cohort was established with 500 adult CAP outpatients enrolled in Beijing between November 2010 to October 2011. Multiplex and quantitative real-time fluorescence PCR were used to detect 15 respiratory viruses and mycoplasma pneumoniae, respectively. Bacteria were detected with culture and enzyme immunoassay of the Streptococcus pneumoniae urinary antigen. Univariate analysis, multivariate analysis, discriminatory analysis and Receiver Operating Characteristic (ROC) curves were used to build predictive models for etiological diagnosis of adult CAP.

Results

Pathogens were detected in 54.2% (271/500) of study patients. Viruses accounted for 36.4% (182/500), mycoplasma pneumoniae for 18.0% (90/500) and bacteria for 14.4% (72/500) of the cases. In 182 of the patients with viruses, 219 virus strains were detected, including 166 single and 53 mixed viral infections. Influenza A virus represented the greatest proportion with 42.0% (92/219) and 9.1% (20/219) in single and mixed viral infections, respectively. Factors selected for the predictive etiological diagnostic model of viral CAP included cough, dyspnea, absence of chest pain and white blood cell count (4.0-10.0) × 109/L, and those of mycoplasma pneumoniae CAP were being younger than 45 years old and the absence of a coexisting disease. However, these models showed low accuracy levels for etiological diagnosis (areas under ROC curve for virus and mycoplasma pneumoniae were both 0.61, P < 0.05).

Conclusions

Greater consideration should be given to viral and mycoplasma pneumoniae infections in adult CAP outpatients. While predictive etiological diagnostic models of viral and mycoplasma pneumoniae based on combinations of demographic and clinical factors may provide indications of etiology, diagnostic confirmation of CAP remains dependent on laboratory pathogen test results.
Effect of treatment on urinary kidney injury molecule-1 in IgA nephropathy
Authors: Seo Mi Seon , Park Moo Yong , Choi Soo Jeong , Jeon Jin Seok , Noh Hyunjin , Kim Jin Kuk , Han Dong Cheol , Hwang Seung Duk , Jin So Young , Kwon Soon Hyo
Published: July 2013

Background

Kidney injury molecule-1 (KIM-1) is a biomarker useful for detecting early tubular damage and has been recently reported as a useful marker for evaluating kidney injury in IgA nephropathy (IgAN). We therefore investigated whether treatment decreases urinary KIM-1 excretion in IgAN.

Methods

We prospectively enrolled 37 patients with biopsy-proven IgAN. Urinary KIM-1 was assessed before and after treatment, which included low salt diet, blood pressure control, pharmacotherapy with angiotensin receptor blockers and/or angiotensin converting enzyme inhibitors, and immunosuppressive agents as necessary. The median treatment duration was 24 months.

Results

Urinary KIM-1/creatinine (Cr) was significantly decreased in patients with IgAN after treatment compared to baseline (P < 0.0001, 1.16 [0.51-1.83] vs 0.26 [0.12-0.65] ng/mg). There was a decrease in the amount of proteinuria after treatment, but it was not statistically significant (P = 0.052, 748.1 [405-1569.7] vs 569.2 [252.2-1114] g/d). Estimated glomerular filtration rate (eGFR) did not change with treatment (P = 0.599, 79.28 ± 30.56 vs 80.98 ± 32.37 ml/min/1.73 m2). Urinary KIM-1 was not correlated with proteinuria baseline or follow up (pre-: R = - 0.100, P = 0.577, post-: R = 0.001, P = 0.993). In patients with higher baseline urinary KIM-1, both urinary KIM-1 level and proteinuria were significantly decreased following treatment.

Conclusions

Treatment decreases urinary KIM-1/Cr in patients with IgAN. It also reduces proteinuria in patients with higher baseline urinary KIM-1. These results suggest a potential role for urinary KIM-1 as a biomarker for predicting treatment response in IgAN, however, further study is needed to verify this.
Standardised exhaled breath collection for the measurement of exhaled volatile organic compounds by proton transfer reaction mass spectrometry
Authors: Bikov Andras , Paschalaki Koralia , Logan-Sinclair Ron , Horváth Ildiko , Kharitonov Sergei A , Barnes Peter J , Usmani Omar S , Paredi Paolo
Published: July 2013

Background

Exhaled breath volatile organic compound (VOC) analysis for airway disease monitoring is promising. However, contrary to nitric oxide the method for exhaled breath collection has not yet been standardized and the effects of expiratory flow and breath-hold have not been sufficiently studied. These manoeuvres may also reveal the origin of exhaled compounds.

Methods

15 healthy volunteers (34 ± 7 years) participated in the study. Subjects inhaled through their nose and exhaled immediately at two different flows (5 L/min and 10 L/min) into methylated polyethylene bags. In addition, the effect of a 20 s breath-hold following inhalation to total lung capacity was studied. The samples were analyzed for ethanol and acetone levels immediately using proton-transfer-reaction mass-spectrometer (PTR-MS, Logan Research, UK).

Results

Ethanol levels were negatively affected by expiratory flow rate (232.70 ± 33.50 ppb vs. 202.30 ± 27.28 ppb at 5 L/min and 10 L/min, respectively, p < 0.05), but remained unchanged following the breath hold (242.50 ± 34.53 vs. 237.90 ± 35.86 ppb, without and with breath hold, respectively, p = 0.11). On the contrary, acetone levels were increased following breath hold (1.50 ± 0.18 ppm) compared to the baseline levels (1.38 ± 0.15 ppm), but were not affected by expiratory flow (1.40 ± 0.14 ppm vs. 1.49 ± 0.14 ppm, 5 L/min vs. 10 L/min, respectively, p = 0.14). The diet had no significant effects on the gasses levels which showed good inter and intra session reproducibility.

Conclusions

Exhalation parameters such as expiratory flow and breath-hold may affect VOC levels significantly; therefore standardisation of exhaled VOC measurements is mandatory. Our preliminary results suggest a different origin in the respiratory tract for these two gasses.
Factors influencing specialist care referral of multidrug- and extensively drug-resistant tuberculosis patients in Gauteng/South Africa: a descriptive questionnaire-based study
Authors: Nkosi Deliwe , Janssen Saskia , Padanilam Xavier , Louw Rianna , Menezes Colin N , Grobusch Martin P
Published: July 2013

Background

Sizwe Tropical Diseases Hospital is the only specialized Hospital for the management of multidrug-resistant (MDR)-TB and extensively drug-resistant (XDR)-TB cases in Gauteng Province. In South Africa, there is a mismatch between numbers of individuals with a laboratory diagnosis of drug-resistant tuberculosis (TB) and those being referred for the initiation of specialist treatment. We determined reasons for non-referral of MDR-TB and XDR-TB cases.

Methods

We conducted a descriptive questionnaire-based study amongst provincial primary health care facilities (PHC) and hospitals providing routine care for (drug-susceptible) TB, regarding specialist care referral of patients whose TB culture and susceptibility testing confirmed MDR-TB or XDR-TB diagnoses in the first half of 2008.

Results

In total 148 cases were analyzed; 144/148 (97%) had MDR-TB and 4/148 (3%) had XDR-TB. The main reason for non-referral to specialist care was loss to follow up, for patients diagnosed in-hospital (74/97; 76%) as well as in PHCs (11/21; 52%). Nineteen per cent (18/97) of patients diagnosed in hospital versus 33% (7/21) of patients diagnosed in PHCs deceased before referral.

Conclusions

A significant problem in the fight to control DR-TB is follow-up after diagnosis with a delay in patient tracing. TB Focal Points in hospital need to be strengthened in order to improve on patient follow-up and care, and tracer teams should assist with community follow up.