bluuebunny/crossref_metadata_2025 huggingface dataset:
Large pelagic predators could jeopardize the recovery of endangered Atlantic salmon
Authors: Lacroix Gilles L.
Published: January 2014

Long-term population viability of Bay of Fundy Atlantic salmon (Salmo salar) is threatened by high levels of marine mortality during migration. Pop-up satellite archival tags on repeat spawners provide direct evidence of extensive natural mortality of migrating salmon in coastal zones attributed to predation by large pelagic fish and no evidence of fishing mortality. Ingested tags show that salmon with a coastal migration are eaten by porbeagle shark (Lamna nasus) inside the Bay of Fundy, whereas distant migrants are consumed by Atlantic bluefin tuna (Thunnus thynnus) and other apex predators along the Scotian Shelf. Mortality is clustered in a few zones because of similar predator–prey habitat preferences and overlapping migration paths. The extent of predation in salmon populations with different migration strategies can account for observed decline rates in neighbouring populations with different life histories. The impact on endangered salmon populations that rely on multiple repeat spawners for population stability may be sufficient to hamper ongoing recovery efforts.
Changes in the proteome of the cadmium-tolerant bacteria Cupriavidus taiwanensis KKU2500-3 in response to cadmium toxicity
Authors: Siripornadulsil Surasak , Thanwisai Lalita , Siripornadulsil Wilailak
Published: January 2014

Cupriavidus taiwanensis KKU2500-3 is a cadmium (Cd)-tolerant bacterial strain that was previously isolated from rice fields contaminated with high levels of Cd. In 500 μmol/L CdCl2, the KKU2500-3 strain grew slower and with a more prolonged lag-phase than when grown in the absence of Cd. A proteomic approach was used to characterize the protein expression in the Cd-tolerant bacteria C. taiwanensis KKU2500-3 during growth under Cd stress. When compared with the untreated cells, a total of 982 differentially expressed protein spots were observed in the CdCl2-treated cells, and 59 and 10 spots exhibited >2- and >4-fold changes, respectively. The level of up- and downregulation varied from 2.01- to 11.26-fold and from 2.01- to 5.34-fold, respectively. Of the 33 differentially expressed protein spots analyzed by MALDI TOF MS/MS, 19 spots were successfully identified, many of which were involved in stress responses. The most highly upregulated protein (+7.95-fold) identified was the chaperone GroEL, which indicated that this factor likely contributed to the bacterial survival and growth in response to Cd toxicity. Detection of the downregulated protein flagellin (–3.52-fold) was consistent with the less effective ATP-mediated and flagella-driven motility. The flagella-losing cells were also observed in the Cd-treated bacteria when analyzed by scanning electron microscopy. Thus, the Cd-stressed cells may downregulate pathways involving ATP utilization in favor of other mechanisms in response to Cd toxicity. When the KKU2500-3 strain was grown in the presence of Cd, H2S was not detected, suggesting a possible role of the sulfur in precipitation with Cd. Apart from a general response, no specific process could be determined using the present proteomic approach. However, the potential role of protein folding-mediated GroEL, flagella-mediated motility and CdS biotransformation in Cd toxicity response observed in this study as well as the extent of Cd-tolerant mechanisms using other methods could facilitate the future application of this strain in addressing Cd environmental contamination.
High-order asymptotic expansion for the acoustics in viscous gases close to rigid walls
Authors: Schmidt Kersten , Thöns-Zueva Anastasia , Joly Patrick
Published: January 2014

We derive a complete asymptotic expansion for the singularly perturbed problem of acoustic wave propagation inside gases with small viscosity. This derivation is for the non-resonant case in smooth bounded domains in two dimensions. Close to rigid walls the tangential velocity exhibits a boundary layer of size [Formula: see text] where η is the dynamic viscosity. The asymptotic expansion, which is based on the technique of multiscale expansion is expressed in powers of [Formula: see text] and takes into account curvature effects. The terms of the velocity and pressure expansion are defined independently by partial differential equations, where the normal component of velocities or the normal derivative of the pressure, respectively, are prescribed on the boundary. The asymptotic expansion is rigorously justified with optimal error estimates.
FFT-based Kronecker product approximation to micromagnetic long-range interactions
Authors: Exl Lukas , Abert Claas , Mauser Norbert J. , Schrefl Thomas , Stimming Hans Peter , Suess Dieter
Published: January 2014

We derive a Kronecker product approximation for the micromagnetic long-range interactions in a collocation framework by means of separable sinc quadrature. Evaluation of this operator for structured tensors (Canonical format, Tucker format, Tensor Trains) scales below linear in the volume size. Based on efficient usage of FFT for structured tensors, we are able to accelerate computations to quasi-linear complexity in the number of collocation points used in one dimension. Quadratic convergence of the underlying collocation scheme as well as exponential convergence in the separation rank of the approximations is proved. Numerical experiments on accuracy and complexity confirm the theoretical results.
A MULTIFORMALISM MODULAR APPROACH TO ERTMS/ETCS FAILURE MODELING
Authors: FLAMMINI FRANCESCO , MARRONE STEFANO , IACONO MAURO , MAZZOCCA NICOLA , VITTORINI VALERIA
Published: January 2014

European Railway Traffic Management System/European Train Control System (ERTMS/ETCS) is a recent standard aimed at improving performance, safety and inter-operability of modern railways. In order to be compliant to ERTMS/ETCS, a railway signalling system must meet strict nonfunctional requirements on system level failure modes. In this paper, a multiformalism model is employed to perform an availability analysis of an ERTMS/ETCS reference architecture at early phases of its development cycle. At this aim, a bottom-up analysis is performed from subsystem failure models (expressed by means of Generalized Stochastic Petri Nets, Fault Trees and Repairable Fault Trees) up to the overall system model. The modular approach, here used, allows to evaluate the influence of basic design parameters on the probability of system-level failure modes and demonstrates that system availability is within the bound required by the ERTMS/ETCS specification. The results show that the multiformalism modeling approach helps to cope with complexity, eases the verification of availability requirements and can be successfully applied to the analysis of complex critical systems.
MAINTENANCE CONTRACT MODEL FOR COMPLEX ASSET/EQUIPMENT
Authors: RAHMAN ANISUR
Published: January 2014

Maintenance contracts received significant attentions in the past 15 to 20 years as it has huge potential to reduce the upfront investments in maintenance infrastructure, specialized maintenance facilities, and risks to the owners through expert services provided by the original equipment manufacturers and/or specialist maintenance providers. To make maintenance contracts more effective, there is a need to develop mathematical models and understand future costs that could be built into the contract price. In this paper, a conceptual model is developed for estimating cost of outsourcing maintenance of complex and critical asset/equipment taking into account both corrective and preventive maintenance as servicing strategies and risks and penalty costs associated with such contract. The developed cost models are analyzed using illustrated numerical examples.
BOUNDARY ESTIMATION OF INSPECTION THRESHOLD FOR MULTI-COMPONENT SYSTEM
Authors: SATOW TAKASHI
Published: January 2014

Inspection threshold is one of effective methods to reduce causes of misjudgement under imperfect inspection. Based on the Bayesian theory, the threshold is defined as the boundary between inspection and noninspection execution. However, the formulation of the true threshold is difficult under a general complex system. This paper proposes approximation methods to derive the maximum and the minimum inspection thresholds for a general system. A binary reliability theory is used for the derivation of the thresholds. Structure functions, minimal path and cut sets are used for the approximation. Finally, some numerical examples are given.
A FUZZY APPROACH TO MULTIOBJECTIVE COTS PRODUCTS SELECTION OF MODULAR SOFTWARE SYSTEMS USING EXPONENTIAL MEMBERSHIP FUNCTIONS
Authors: MEHLAWAT MUKESH KUMAR
Published: January 2014

In this paper, we study a decision-making problem related to software creation using commercial-off-the-shelf (COTS) products in a modular software system. The optimal selection of COTS products is difficult due to the variations in various critical parameters such as cost, reliability, execution time, and delivery time. Further, it is difficult to estimate precisely the values of these parameters since sufficient data may not be available and also there could be measurement errors. We present a fuzzy 0–1 optimization model of the multiobjective COTS products selection problem using exponential membership functions that simultaneously minimize the total cost, size, execution time and delivery time and maximize the reliability of a modular software system subject to many realistic constraints. The fuzzy goals are defined for each selection criterion as per the preferences of the decision maker and are aggregated using product operator to obtain an equivalent optimization model for optimal COTS selection. A real-world case study is discussed to demonstrate the effectiveness of the proposed model and the solution methodology.
The Role of Innovative Communication Channels, Effective Coordination Strategy and Knowledge Management in the UK Local Government Planning System
Authors: Khilji Nasrullah K. , Roberts Stephen A.
Published: January 2014

This research is an exploratory study of innovative communication channels, effective coordination strategy and integrated knowledge management in the UK local government planning system. The UK local government planning system at present suffers delays, which slow down or prevent people building new homes, creating new facilities and bringing disused or neglected land and buildings back into productive use. This study has been carried out in the subject area to explore enhanced efficiency and effectiveness in the UK local government planning system. An integrated knowledge-based planning system is considered as an appropriate solution to achieve smart and sustainable development in the local government planning system. This research study is based primarily upon fieldwork conducted in five participating local authorities in the South East Midlands (Bedford Borough Council, Central Bedfordshire Council, Luton Borough Council, Milton Keynes Council and Northampton Borough Council) and on literature drawn from many different disciplines. A mixed methods approach is chosen for the research fieldwork. The key data collection methods applied during the fieldwork include: structured questionnaires, semi-structured interviews, online group forums, email correspondence, prearranged observations, literature review, document analysis and reviews of the local government publications and their statistical reports. The key purpose of this study is to investigate how the planning system in the UK local government can be transformed from its current "As-Is" state towards a smart and sustainable development future "To-Be" state.
Twitter Content Categorisation: A Public Library Perspective
Authors: Shiri Ali , Rathi Dinesh
Published: January 2014

With the rise of social media, many library and information services have begun to incorporate a wide variety of social media and social networking applications into their systems and services. Among the mainstream social networking applications, micro-blogging, in general, and Twitter, in particular, have gained increasing popularity. This paper reports the results of an exploratory study of the application of Twitter in the context of a large public library system. Specifically, this study has sampled, content analysed and categorised a select number of tweets created by a public library system in order to identify and document the ways in which Twitter can be used for various information services and knowledge management practices in public libraries. One of the main outcomes of this study is a tweet categorisation scheme that has a specific focus on the information services offered by public libraries.
Quantitative Study of Affection Generated by Knowledge Exchange in Team
Authors: Dang Yanzhong , Li Yutong , Wu Jiangning
Published: January 2014

Trust has been noted as a key component for the success of knowledge management. Recent research on affection in interpersonal trust using empirical research suggests that affection plays a critical role on team effectiveness, knowledge transfer and sharing in team. Yet, the empirical research only obtains a certain period of affection reflecting interpersonal trust; it can not observe the dynamic change of affection. The empirical data lacks universality, which is merely focused on a designated team. In this paper, we give a primitive attempt, by using an agent-based computational model, to explore interpersonal trust, especially to study the quantitative method of emotion and affection generated by knowledge exchange and factors on emotional and affective intensity. We hope that our bold attempt improves the understandings of affection generation and development, and provides agent-based modelling simulations as a supplement of the empirical research to study team effectiveness in future.
Knowledge Management and Social Media: A Case Study of Two Public Libraries in Canada
Authors: Forcier Eric , Rathi Dinesh , Given Lisa M.
Published: January 2014

It is important for all types of organisations including non-profit organisations (NPOs) to manage knowledge for effective and efficient utilisation of resources. Technology is considered as one of the key enablers of knowledge management (KM) practices but it can be costly to develop and implement in an organisation. With the advent of social media, NPOs such as public libraries have the opportunity to harness the power of technology for KM purposes as it is considered a low cost medium. A study was conducted, using an exploratory qualitative interview technique, in two contrasting public libraries: one is a large urban public library, and the other is a small rural public library. The data were analysed using a grounded theory approach informed by a social constructionist theoretical framework. This paper presents comparative findings from these case examples on their understanding of KM as a concept and their use of social media in management of knowledge. Results show that social media are valuable KM tools in public libraries, not only when directed externally for the purpose of promotion, but also to foster engagement with the public and collaborative work within the organisation.
The Use of Knowledge Management in Healthcare: The Implementation of Shared Care Plans in Electronic Medical Record Systems at One Primary Care Practice
Authors: Pascal Connie J. , McInerney Claire , Orzano John , Clark Elizabeth C. , Clemow Lynn
Published: January 2014

A transformation in the way in which primary care is delivered is underway in the US. Across the country primary care practices are grappling with how to change from the traditional physician-directed model to a more patient-centred collaborative style as part of the effort to curb the rise of chronic disease. To date, few tools or techniques exist to help the individual primary care provider make this difficult and complex transformation. One such tool that has arisen is the shared care plan (SCP). As defined in the Taking Action for Learning and Knowledge Management to improve Diabetes Mellitus (TALK/DM) study (a NIDDK funded pilot project to implement SCPs in primary care), the SCP of primary care becomes the product of collaboration between the practice and the patients. The SCP is created by combining knowledge management (KM) techniques and motivational interviewing (MI) health counselling methods to form a new knowledge object. This paper focuses on this aspect of the TALK/DM study and takes a case study approach to explore how one primary care practice is implementing the SCP as knowledge object (both a paper document and an electronic record in the EMR system) in its organisation. This study adds nuance and insight into how knowledge objects such as the SCP can serve as a tool for collaboration in primary care.
Creating Meaningful Representations
Authors: Stary Chris , Stary Edith
Published: January 2014

Demanding business environments increasingly require knowledge work. Hereby, knowledge creation needs to rely on meaningful entities and representations, in particular for organisational change processes. In this paper, we report on exploring essential benefits for stakeholders and communities when applying major principles of Maria Montessori when articulating and communicating knowledge. Experienced benefits stem from stakeholders' self-determined and individualized design experiences. We motivate the embodiment of stakeholders into physically enriched and ambient knowledge management (KM) environments and reveal insights from testing those ideas. The results of our work should guide the development of enriched KM environments.
INTEGRATION OF PRODUCT AND PROCESS PLANNING BASED ON NEURAL NETWORKS IN COOPERATIVE DESIGN METHODOLOGY
Authors: NUMTHONG C. , TICHKIEWITCH S.
Published: January 2014

Integration of product representation and process planning is necessarily to couple features of product data and machining processes. The product representation and knowledge of design and process planning should be shared and distributed between a product designer and process planner. Cooperative design and process planning works are proposed in this paper in order to integrate and exchange information between team members to obtain the efficiency of product design and process planning. In addition, this paper presents the integration of product representation and process planning of rotational parts based on neural networks technique. The neural networks technique is used to contribute in selecting suitable machining process of rotational parts. In addition, we also present CoDeMo (Cooperative Designing Modeler). It is a platform using support cooperative methodology for integrating the rotational product representation and process planning. The case study is tested with a sample part from the exemplary company.
AN EVALUATION OF ENVIRONMENTAL SUSTAINABILITY OF GRAZING LANDS USING THE ECOLOGICAL FOOTPRINT TOOL: A CASE OF CHIRUMANZU DISTRICT, ZIMBABWE
Authors: KORI EDMORE , MUSYOKI AGNES , NETHENGWE NTHADULENI S.
Published: January 2014

The 1992 United Nations World Commission on Environment and Development Summit underscored the need to conduct environmental sustainability evaluations. Such evaluations are important as they communicate the relationship between natural resources extraction and environmental regenerative capacity. We use the Ecological Footprint tool to evaluate the environmental sustainability of grazing landuse for Chirumanzu District of Zimbabwe. Empirical evidence presented here relates to livestock data obtained from the Veterinary Department and a sample household survey. Results revealed the presence of a large ecological reserve, depicting sustainable utilization of environmental resources. Further unravelling of the results, however, revealed under utilisation of the available biocapacity. Livestock-limited environmentally sustainable is the concept used to describe this scenario. Further interpretation of the large ecological reserve indicates insecure land tenure system, low livestock ownership and difficult economic hardships faced by resettled farmers. The paper recommends that the government adopts policies that encourage the development of a sustainable livestock sector.
Probabilistic Forecasting
Authors: Gneiting Tilmann , Katzfuss Matthias
Published: January 2014

A probabilistic forecast takes the form of a predictive probability distribution over future quantities or events of interest. Probabilistic forecasting aims to maximize the sharpness of the predictive distributions, subject to calibration, on the basis of the available information set. We formalize and study notions of calibration in a prediction space setting. In practice, probabilistic calibration can be checked by examining probability integral transform (PIT) histograms. Proper scoring rules such as the logarithmic score and the continuous ranked probability score serve to assess calibration and sharpness simultaneously. As a special case, consistent scoring functions provide decision-theoretically coherent tools for evaluating point forecasts. We emphasize methodological links to parametric and nonparametric distributional regression techniques, which attempt to model and to estimate conditional distribution functions; we use the context of statistically postprocessed ensemble forecasts in numerical weather prediction as an example. Throughout, we illustrate concepts and methodologies in data examples.
ALCAM/CD166 Is a TGF-β–Responsive Marker and Functional Regulator of Prostate Cancer Metastasis to Bone
Authors: Hansen Amanda G. , Arnold Shanna A. , Jiang Ming , Palmer Trenis D. , Ketova Tatiana , Merkel Alyssa , Pickup Michael , Samaras Susan , Shyr Yu , Moses Harold L. , Hayward Simon W. , Sterling Julie A. , Zijlstra Andries
Published: January 2014

The dissemination of prostate cancer to bone is a common, incurable aspect of advanced disease. Prevention and treatment of this terminal phase of prostate cancer requires improved molecular understanding of the process as well as markers indicative of molecular progression. Through biochemical analyses and loss-of-function in vivo studies, we demonstrate that the cell adhesion molecule, activated leukocyte cell adhesion molecule (ALCAM), is actively shed from metastatic prostate cancer cells by the sheddase ADAM17 in response to TGF-β. Not only is this posttranslational modification of ALCAM a marker of prostate cancer progression, the molecule is also required for effective metastasis to bone. Biochemical analysis of prostate cancer cell lines reveals that ALCAM expression and shedding is elevated in response to TGF-β signaling. Both in vitro and in vivo shedding is mediated by ADAM17. Longitudinal analysis of circulating ALCAM in tumor-bearing mice revealed that shedding of tumor, but not host-derived ALCAM is elevated during growth of the cancer. Gene-specific knockdown of ALCAM in bone-metastatic PC3 cells greatly diminished both skeletal dissemination and tumor growth in bone. The reduced growth of ALCAM knockdown cells corresponded to an increase in apoptosis (caspase-3) and decreased proliferation (Ki67). Together, these data demonstrate that the ALCAM is both a functional regulator as well as marker of prostate cancer progression. Cancer Res; 74(5); 1404–15. ©2014 AACR.
Epigenetic Potentiation of NY-ESO-1 Vaccine Therapy in Human Ovarian Cancer
Authors: Odunsi Kunle , Matsuzaki Junko , James Smitha R. , Mhawech-Fauceglia Paulette , Tsuji Takemasa , Miller Austin , Zhang Wa , Akers Stacey N. , Griffiths Elizabeth A. , Miliotto Anthony , Beck Amy , Batt Carl A. , Ritter Gerd , Lele Shashikant , Gnjatic Sacha , Karpf Adam R.
Published: January 2014

The cancer–testis/cancer germline antigen, NY-ESO-1, is a vaccine target in epithelial ovarian cancer (EOC), but its limited expression is a barrier to vaccine efficacy. As NY-ESO-1 is regulated by DNA methylation, we hypothesized that DNA methyltransferase inhibitors may augment NY-ESO-1 vaccine therapy. In agreement, global DNA hypomethylation in EOC was associated with the presence of circulating antibodies to NY-ESO-1. Preclinical studies using EOC cell lines showed that decitabine treatment enhanced both NY-ESO-1 expression and NY-ESO-1–specific CTL-mediated responses. On the basis of these observations, we performed a phase I dose-escalation trial of decitabine, as an addition to NY-ESO-1 vaccine and doxorubicin liposome chemotherapy, in 12 patients with relapsed EOC. The regimen was safe, with limited and clinically manageable toxicities. Both global and promoter-specific DNA hypomethylation occurred in blood and circulating DNAs, the latter of which may reflect tumor cell responses. Increased NY-ESO-1 serum antibodies and T-cell responses were observed in the majority of patients, and antibody spreading to additional tumor antigens was also observed. Finally, disease stabilization or partial clinical response occurred in six of ten evaluable patients. On the basis of these encouraging results, evaluation of similar combinatorial chemo-immunotherapy regimens in EOC and other tumor types is warranted. Cancer Immunol Res; 2(1); 37–49. ©2014 AACR.
Eosinophils and Cancer
Authors: Davis Benjamin P. , Rothenberg Marc E.
Published: January 2014

Eosinophils have long been known to infiltrate tumors, and in most cases, this is associated with an improved prognosis. However, the reasons behind this infiltration and the mechanism of action of the eosinophil have remained elusive. In this article, we explore the biology of eosinophils and examine their function in homeostasis and disease states, specifically focusing on what is currently known about the association of the eosinophil with cancer. Cancer Immunol Res; 2(1); 1–8. ©2014 AACR.
Detection of Atrial Fibrillation After Ischemic Stroke or Transient Ischemic Attack
Authors: Kishore Amit , Vail Andy , Majid Arshad , Dawson Jesse , Lees Kennedy R. , Tyrrell Pippa J. , Smith Craig J.
Published: January 2014

Background and Purpose—

Atrial fibrillation (AF) confers a high risk of recurrent stroke, although detection methods and definitions of paroxysmal AF during screening vary. We therefore undertook a systematic review and meta-analysis to determine the frequency of newly detected AF using noninvasive or invasive cardiac monitoring after ischemic stroke or transient ischemic attack.

Methods—

Prospective observational studies or randomized controlled trials of patients with ischemic stroke, transient ischemic attack, or both, who underwent any cardiac monitoring for a minimum of 12 hours, were included after electronic searches of multiple databases. The primary outcome was detection of any new AF during the monitoring period. We prespecified subgroup analysis of selected (prescreened or cryptogenic) versus unselected patients and according to duration of monitoring.

Results—

A total of 32 studies were analyzed. The overall detection rate of any AF was 11.5% (95% confidence interval, 8.9%–14.3%), although the timing, duration, method of monitoring, and reporting of diagnostic criteria used for paroxysmal AF varied. Detection rates were higher in selected (13.4%; 95% confidence interval, 9.0%–18.4%) than in unselected patients (6.2%; 95% confidence interval, 4.4%–8.3%). There was substantial heterogeneity even within specified subgroups.

Conclusions—

Detection of AF was highly variable, and the review was limited by small sample sizes and marked heterogeneity. Further studies are required to inform patient selection, optimal timing, methods, and duration of monitoring for detection of AF/paroxysmal AF.
A new species of Hohenbergia (Bromeliaceae) from Bahia, Brazil
Authors: Maciel Jefferson Rodrigues , Louzada Rafael Batista
Published: January 2014

In this paper a new species of Hohenbergia from Bahia, Brazil, H. lativaginata, is described. Compared with 4 other related species and illustrated.
A new species of spiny-tailed iguanid lizard (Iguania: Stenocercus) from northwestern Peru
Authors: VENEGAS PABLO J. , ECHEVARRIA LOURDES Y. , ALVAREZ SILVANA C.
Published: January 2014

We describe a new species of Stenocercus from the interandean valley of Río Chotano on the Amazonian slope of the northern portion of the Cordillera Occidental of Peru (Cajamarca Region), at elevations of between 1997 and 2318 m. Stenocercus arndti sp. nov. differs from other Stenocercus, except from S. bolivarensis, S. carrioni, S. chlorostictus, S. crassicaudatus, S. empetrus, S. eunetopsis, S. simonsii, and S. torquatus, in having granular scales on the posterior surface of the thighs, two caudal whorls per autotomic segment, mucronate caudal scales, and distinct longitudinal row of enlarged vertebral scales. However, Stenocercus arndti sp. nov. is easily distinguished from these species in having a bold black transversal band at midbody that extends ventrolaterally in adult males.
Diurnal Cycles of Cumulus, Cumulonimbus, Stratus, Stratocumulus, and Fog from Surface Observations over Land and Ocean
Authors: Eastman Ryan , Warren Stephen G.
Published: January 2014

A worldwide climatology of the diurnal cycles of low clouds is obtained from surface observations made eight or four times daily at 3- or 6-h intervals from weather stations and ships. Harmonic fits to the daily cycle are made for 5388 weather stations with long periods of record, and for gridded data on a 5° × 5° or 10° × 10° latitude–longitude grid over land and ocean areas separately.

For all cloud types, the diurnal cycle has larger amplitude over land than over ocean, on average by a factor of 2. Diurnal cycles of cloud amount appear to be proprietary to each low cloud type, showing the same cycle regardless of whether that type dominates the diurnal cycle of cloud cover. Stratiform cloud amounts tend to peak near sunrise, while cumuliform amounts peak in the afternoon; however, cumulonimbus amounts peak in the early morning over the ocean. Small latitudinal and seasonal variation is apparent in the phase and amplitude of the diurnal cycles of each type. Land areas show more seasonality compared to ocean areas with respect to which type dominates the diurnal cycle.

Multidecadal trends in low cloud cover are small and agree between day and night regardless of the local climate.

Diurnal cycles of base height are much larger over land than over the ocean. For most cloud types, the bases are highest in the midafternoon or early evening.
Urbanization Effect on Trends of Extreme Temperature Indices of National Stations over Mainland China, 1961–2008
Authors: Ren Guoyu , Zhou Yaqing
Published: January 2014

Understanding the long-term change of extreme temperature events is important to the detection and attribution of climate change. It is unclear, however, how much effect urbanization has had on trends of the extreme temperature indices series constructed based on the commonly used datasets on a subcontinental scale. Applying a homogenized daily temperature dataset of the national reference climate stations and basic meteorological stations, and a rural station network previously developed, urbanization effects on trends of extreme temperature indices in mainland China for the time period 1961–2008 are evaluated. It is found that 1) the country-averaged annual- and seasonal-mean extreme temperature indices series generally experience statistically significant trends; 2) annual-mean urbanization effects in the country as a whole are statistically significant for daily minimum temperature (Tmin), maximum temperature (Tmax), and mean temperature of Tmin and Tmax (Tavg), reaching 0.070°, 0.023°, and 0.047°C (10 yr)−1, respectively, with the largest values for annual-mean Tmin occurring in north China; 3) annual- and seasonal-mean urbanization effects for the declining diurnal temperature range (DTR) are highly significant, and the largest seasonal-mean DTR decline because of urbanization occurs in winter and spring; 4) annual-mean urbanization effects for the lowest Tmin, summer days, tropical nights, and frost days series are significant, but an insignificant urbanization effect is detected for icing days series; 5) urbanization has led to a highly significant decline of annual cold nights at a rate of −1.485 days (10 yr)−1 and a highly significant increase of annual warm nights at a rate of 2.264 days (10 yr)−1. Although urbanization effects are also significant for cold days and warm days, they are relatively smaller, and 6) the smallest absolute values of annual-mean urbanization effects for most of the indices series are found to dominantly appear during 1966–76, a well-known deurbanization period resulting from the Cultural Revolution.
An Atmospheric–Hydrologic Forecasting Scheme for the Indus River Basin
Authors: Shrestha Kristofer Y. , Webster Peter J. , Toma Violeta E.
Published: January 2014

South Asia is vulnerable to extreme weather events, and the Indus River basin (IRB) is subject to flood risk. Flooding occurred in Pakistan during the monsoon seasons from 2010 to 2012, causing major economic damage and significant loss of life. The nature of slow-rise discharge on the Indus and overtopping of riverbanks in the IRB indicates the need for extended warning time (1–10 days). Daily mean streamflow at Tarbela Dam, a major control structure on the Indus River, is reproduced by using numerical weather prediction initialization data from the ECMWF to drive the Variable Infiltration Capacity macroscale hydrologic model. A one-dimensional routing model conducts base flow and surface runoff from each grid cell through a stream network. Comparisons of reconstructions with inflow data at Tarbela Dam over a 3-yr period yield an R2 correlation of 0.93 and RMSE of 692 m3 s−1. From 2010 to 2012, 276 daily ensemble hindcasts are generated. In comparing the ensemble mean of 10-day hindcasts to reconstructed inflow, the R2 correlation was >0.85 for 2010, >0.70 for 2011, and >0.70 for 2012. The RMSE was <24% of mean streamflow for 2010, <28% for 2011, and <34% for 2012. A method to translate this type of probabilistic streamflow forecast data into communicable information is described. A two-dimensional model is described to simulate movement of overflow water into the floodplain.
Stochastic Rainfall Downscaling of Climate Models
Authors: D’Onofrio D. , Palazzi E. , von Hardenberg J. , Provenzale A. , Calmanti S.
Published: January 2014

Precipitation extremes and small-scale variability are essential drivers in many climate change impact studies. However, the spatial resolution currently achieved by global climate models (GCMs) and regional climate models (RCMs) is still insufficient to correctly identify the fine structure of precipitation intensity fields. In the absence of a proper physically based representation, this scale gap can be at least temporarily bridged by adopting a stochastic rainfall downscaling technique. In this work, a precipitation downscaling chain is introduced where the global 40-yr ECMWF Re-Analysis (ERA-40) (at about 120-km resolution) is dynamically downscaled using the Protheus RCM at 30-km resolution. The RCM precipitation is then further downscaled using a stochastic downscaling technique, the Rainfall Filtered Autoregressive Model (RainFARM), which has been extended for application to long climate simulations. The application of the stochastic downscaling technique directly to the larger-scale reanalysis field at about 120-km resolution is also discussed. To assess the ability of this approach in reproducing the main statistical properties of precipitation, the downscaled model results are compared with the precipitation data provided by a dense network of 122 rain gauges in northwestern Italy, in the time period from 1958 to 2001. The high-resolution precipitation fields obtained by stochastically downscaling the RCM outputs reproduce well the seasonality and amplitude distribution of the observed precipitation during most of the year, including extreme events and variance. In addition, the RainFARM outputs compare more favorably to observations when the procedure is applied to the RCM output rather than to the global reanalyses, highlighting the added value of reaching high enough resolution with a dynamical model.
The Bene Israel of India and the Politics of Jewish Identity
Authors: Kuikman Jacoba
Published: January 2014

This paper focuses on the Bene Israel community in Mumbai, a remnant of a once thriving Jewish population decimated in part because of emigration to Israel. I argue that the Bene Israel, who have been maligned because of their dark skin colour and borrowed customs, primarily from Hinduism, constitute a way of being Jewish that consciously rejects authoritarian and rabbinic hegemony. They constitute a ‘third,’ hybrid kind of space signifying that the borders of Jewish identity are permeable and flexible. They are therefore a prime example of the possibilities within Judaism not limited to a prescribed, and circumscribed system of belief and practice but a living testament to cultural and religious multiplicity.
Australian border policing: regional ‘solutions’ and neocolonialism
Authors: Grewcock Michael
Published: January 2014

Australia’s punitive border policing regime, aimed at deterring asylum seekers attempting unauthorised entry into the country, was ratcheted up even further in 2013 by the former Labor-led government and its successor (as of September 2013), the Liberal National Party Coalition. In effect, under the guise of combating ‘people-smuggling’, and a pledge to ‘Stop the Boats’, policies such as the mandatory detention of unauthorised arrivals and the use of off-shore detention facilities have been made even more draconian. Now the aim is to block entirely any right to resettlement or residence for refugees in Australia itself, using the weaker and poorer states of Nauru and Papua New Guinea, historically under Australia’s control, to act – to their own long-standing detriment – as detention and resettlement centres, for increasing numbers of migrants.
Profilin 1 is essential for retention and metabolism of mouse hematopoietic stem cells in bone marrow
Authors: Zheng Junke , Lu Zhigang , Kocabas Fatih , Böttcher Ralph T. , Costell Mercedes , Kang Xunlei , Liu Xiaoye , DeBerardinis Ralph J. , Wang Qianming , Chen Guo-Qiang , Sadek Hesham , Zhang Cheng Cheng
Published: January 2014

Key Points

The deletion of pfn1 led to bone marrow failure, loss of quiescence, increased apoptosis and mobilization, and a metabolic switch of HSCs. Pfn1 partially acts through the axis of pfn1/Gα13/EGR1 to regulate stem cell retention and metabolism in the bone marrow.
ITEP: An integrated toolkit for exploration of microbial pan-genomes
Authors: Benedict Matthew N , Henriksen James R , Metcalf William W , Whitaker Rachel J , Price Nathan D
Published: January 2014

Background

Comparative genomics is a powerful approach for studying variation in physiological traits as well as the evolution and ecology of microorganisms. Recent technological advances have enabled sequencing large numbers of related genomes in a single project, requiring computational tools for their integrated analysis. In particular, accurate annotations and identification of gene presence and absence are critical for understanding and modeling the cellular physiology of newly sequenced genomes. Although many tools are available to compare the gene contents of related genomes, new tools are necessary to enable close examination and curation of protein families from large numbers of closely related organisms, to integrate curation with the analysis of gain and loss, and to generate metabolic networks linking the annotations to observed phenotypes.

Results

We have developed ITEP, an Integrated Toolkit for Exploration of microbial Pan-genomes, to curate protein families, compute similarities to externally-defined domains, analyze gene gain and loss, and generate draft metabolic networks from one or more curated reference network reconstructions in groups of related microbial species among which the combination of core and variable genes constitute the their "pan-genomes". The ITEP toolkit consists of: (1) a series of modular command-line scripts for identification, comparison, curation, and analysis of protein families and their distribution across many genomes; (2) a set of Python libraries for programmatic access to the same data; and (3) pre-packaged scripts to perform common analysis workflows on a collection of genomes. ITEP’s capabilities include de novo protein family prediction, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, annotation curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.

Conclusions

ITEP is a powerful, flexible toolkit for generation and curation of protein families. ITEP's modular design allows for straightforward extension as analysis methods and tools evolve. By integrating comparative genomics with the development of draft metabolic networks, ITEP harnesses the power of comparative genomics to build confidence in links between genotype and phenotype and helps disambiguate gene annotations when they are evaluated in both evolutionary and metabolic network contexts.
Vertical blockade of the IGFR- PI3K/Akt/mTOR pathway for the treatment of hepatocellular carcinoma: the role of survivin
Authors: Ou Da-Liang , Lee Bin-Shyun , Lin Liang-In , Liou Jun-Yang , Liao Sheng-Chieh , Hsu Chiun , Cheng Ann-Lii
Published: January 2014

Background

To explore whether combining inhibitors that target the insulin-like growth factor receptor (IGFR)/PI3K/Akt/mTOR signaling pathway (vertical blockade) can improve treatment efficacy for hepatocellular carcinoma (HCC).

Methods

HCC cell lines (including Hep3B, Huh7, and PLC5) and HUVECs (human umbilical venous endothelial cells) were tested. The molecular targeting therapy agents tested included NVP-AEW541 (IGFR kinase inhibitor), MK2206 (Akt inhibitor), BEZ235 (PI3K/mTOR inhibitor), and RAD001 (mTOR inhibitor). Potential synergistic antitumor effects were tested by median dose-effect analysis in vitro and by xenograft HCC models. Apoptosis was analyzed by flow cytometry (sub-G1 fraction analysis) and Western blotting. The activities of pertinent signaling pathways and expression of apoptosis-related proteins were measured by Western blotting.

Results

Vertical blockade induced a more sustained inhibition of PI3K/Akt/mTOR signaling activities in all the HCC cells and HUVEC tested. Synergistic apoptosis-inducing effects, however, varied among different cell lines and drug combinations and were most prominent when NVP-AEW541 was combined with MK2206. Using an apoptosis array, we identified survivin as a potential downstream mediator. Over-expression of survivin in HCC cells abolished the anti-tumor synergy between NVP-AEW541 and MK2206, whereas knockdown of survivin improved the anti-tumor effects of all drug combinations tested. In vivo by xenograft studies confirmed the anti-tumor synergy between NVP-AEW541 and MK2206 and exhibited acceptable toxicity profiles.

Conclusions

Vertical blockade of the IGFR/PI3K/Akt/mTOR pathway has promising anti-tumor activity for HCC. Survivin expression may serve as a biomarker to predict treatment efficacy.
Atypical behavior of NFATc1 in cultured intercostal myofibers
Authors: Robison Patrick , Hernández-Ochoa Erick O , Schneider Martin F
Published: January 2014

Background

The NFATc transcription factor family is responsible for coupling cytoplasmic calcium signals to transcription programs in a wide variety of cell types. In skeletal muscle, these transcription factors control the fiber type in response to muscle activity. This excitation-transcription (E-T) coupling permits functional adaptation of muscle according to use. The activity dependence of these transcription programs is sensitive to the firing patterns of the muscle, not merely the period of activity, enabling a nuanced adaptation to various functional tasks.

Methods

Isolated skeletal muscle fibers expressing exogenous fluorescent NFATc1 were studied by confocal microscopy under stimulation both with and without pharmacological inhibitors. Western blots of whole muscle lysates were also used.

Results

This study investigates the activity dependent response of NFATc1 skeletal muscle fibers cultured from mice, comparing fibers of respiratory origin to muscles responsible for limb locomotion. Using patterns of stimulation known to strongly activate NFATc1 in the commonly cultured flexor digitorum brevis and soleus muscles, we have observed significant deactivation of NFATc1 in cultured intercostal muscle fibers. This effect is at least partially dependent on the action of JNK and CaMKII in intercostal fibers.

Conclusions

Our findings highlight the role of lineage in the NFAT pathway, showing that the respiratory intercostal muscle fibers decode similar E-T coupling signals into NFAT transcriptional programs in a different manner from the more commonly studied locomotor muscles of the limbs.
Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study
Authors: Mishra Sudhanshu , Singh Sujeet Kumar , Munjal Ashok Kumar , Aspi Jouni , Goyal Surendra Prakash
Published: January 2014

In India, six landscapes and source populations that are important for long-term conservation of Bengal tigers (Panthera tigris tigris) have been identified. Except for a few studies, nothing is known regarding the genetic structure and extent of gene flow among most of the tiger populations across India as the majority of them are small, fragmented and isolated. Thus, individual-based relationships are required to understand the species ecology and biology for planning effective conservation and genetics-based individual identification has been widely used. But this needs screening and describing characteristics of microsatellite loci from DNA from good-quality sources so that the required number of loci can be selected and the genotyping error rate minimized. In the studies so far conducted on the Bengal tiger, a very small number of loci (n = 35) have been tested with high-quality source of DNA, and information on locus-specific characteristics is lacking. The use of such characteristics has been strongly recommended in the literature to minimize the error rate and by the International Society for Forensic Genetics (ISFG) for forensic purposes. Therefore, we describe for the first time locus-specific genetic and genotyping profile characteristics, crucial for population genetic studies, using high-quality source of DNA of the Bengal tiger. We screened 39 heterologous microsatellite loci (Sumatran tiger, domestic cat, Asiatic lion and snow leopard) in captive individuals (n = 8), of which 21 loci are being reported for the first time in the Bengal tiger, providing an additional choice for selection. The mean relatedness coefficient (R = −0.143) indicates that the selected tigers were unrelated. Thirty-four loci were polymorphic, with the number of alleles ranging from 2 to 7 per locus, and the remaining five loci were monomorphic. Based on the PIC values (> 0.500), and other characteristics, we suggest that 16 loci (3 to 7 alleles) be used for genetic and forensic study purposes. The probabilities of matching genotypes of unrelated individuals (3.692 × 10-19) and siblings (4.003 × 10-6) are within the values needed for undertaking studies in population genetics, relatedness, sociobiology and forensics.