bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testicular Growth and Regression Are Not Correlated With Dio2 Expression in a Wild Male Songbird, Sturnus vulgaris, Exposed to Natural Changes in Photoperiod
Authors: Bentley George E. , Tucker Shanna , Chou Heather , Hau Michaela , Perfito Nicole 
Published: March 2013

Abstract
Timing of seasonal breeding in birds and mammals is regulated by changing the day length and is dependent on the presence of thyroid hormones. A mechanism for thyroid-dependent control of seasonality has been proposed, in which exposure to long day lengths induces rapid local conversion of T4 to its bioactive form, T3, via the up-regulation of the enzyme type 2 iodothyronine deiodinase (Dio2) in the brain, and the down-regulation of Dio3 (which inactivates T3). Such changes were correlated with gonadotropin release and gonadal growth in quail. This mechanism was elucidated in a domesticated species (quail) exposed to unnatural acute changes in day length. Here we investigated the Dio2/Dio3 mechanism in a wild species, the European starling, under naturally changing day length. Although Dio2 expression varied seasonally, Dio3 did not. We found no correlation of Dio2 with photoperiod, seasonal regulation of GnRH, or testicular volume. The observed differences in data from starlings and quail could be a result of phylogeny, genetic drift from founder populations, or differences in reproductive seasonality in addition to or instead of arising from domestication or use of artificially changing photoperiods. Overall, the data indicate that in a wild species exposed to natural changes in day length, the current proposed mechanism for photoperiodic timing is less straightforward than is generally accepted and might not be as universally applicable as previously thought.
The Muscle-Bone Relationship in X-Linked Hypophosphatemic Rickets
Authors: Veilleux Louis-Nicolas , Cheung Moira S. , Glorieux Francis H. , Rauch Frank 
Published: March 2013

Context:
We recently found that patients with X-linked hypophosphatemic rickets (XLH) have a muscle function deficit in the lower extremities. As muscle force and bone mass are usually closely related, we hypothesized that patients with XLH could also have a bone mass deficit in the lower extremities.

Objective:
The study objective was to assess the muscle-bone relationship in the lower extremities of patients with XLH.

Setting:
The study was carried out in the outpatients department of a pediatric orthopedic hospital.

Patients and Other Participants:
Thirty individuals with XLH (6 to 60 y; 9 male patients) and 30 age- and gender-matched controls participated.

Main Outcome Measures:
Calf muscle size and density as well as tibia bone mass and geometry were assessed by peripheral quantitative computed tomography. Muscle function was evaluated as peak force in the multiple 2-legged hopping test.

Results:
Muscle force was significantly lower in XLH patients than in controls but muscle cross-sectional area did not differ (after adjustment for tibia length). External bone size, expressed as total bone cross-sectional area, was higher in the XLH group than in controls. The XLH cohort also had statistically significantly higher bone mineral content.

Conclusions:
Patients with XLH have increased bone mass and size at the distal tibia despite muscle function deficits.
E-cadherin–integrin crosstalk in cancer invasion and metastasis
Authors: Canel Marta , Serrels Alan , Frame Margaret C. , Brunton Valerie G. 
Published: March 2013

Summary
E-cadherin is a single-pass transmembrane protein that mediates homophilic cell–cell interactions. Tumour progression is often associated with the loss of E-cadherin function and the transition to a more motile and invasive phenotype. This requires the coordinated regulation of both E-cadherin-mediated cell–cell adhesions and integrin-mediated adhesions that contact the surrounding extracellular matrix (ECM). Regulation of both types of adhesion is dynamic as cells respond to external cues from the tumour microenvironment that regulate polarity, directional migration and invasion. Here, we review the mechanisms by which tumour cells control the cross-regulation between dynamic E-cadherin-mediated cell–cell adhesions and integrin-mediated cell–matrix contacts, which govern the invasive and metastatic potential of tumours. In particular, we will discuss the role of the adhesion-linked kinases Src, focal adhesion kinase (FAK) and integrin-linked kinase (ILK), and the Rho family of GTPases.
Mechanosensitive systems at the cadherin–F-actin interface
Authors: Huveneers Stephan , de Rooij Johan 
Published: March 2013

SummaryCells integrate biochemical and mechanical information to function within multicellular tissue. Within developing and remodeling tissues, mechanical forces contain instructive information that governs important cellular processes that include stem cell maintenance, differentiation and growth. Although the principles of signal transduction (protein phosphorylation, allosteric regulation of enzymatic activity and binding sites) are the same for biochemical and mechanical-induced signaling, the first step of mechanosensing, in which protein complexes under tension transduce changes in physical force into cellular signaling, is very different, and the molecular mechanisms are only beginning to be elucidated. In this Commentary, we focus on mechanotransduction at cell–cell junctions, aiming to comprehend the molecular mechanisms involved. We describe how different junction structures are associated with the actomyosin cytoskeleton and how this relates to the magnitude and direction of forces at cell–cell junctions. We discuss which cell–cell adhesion receptors have been shown to take part in mechanotransduction. Then we outline the force-induced molecular events that might occur within a key mechanosensitive system at cell–cell junctions; the cadherin–F-actin interface, at which α-catenin and vinculin form a central module. Mechanotransduction at cell–cell junctions emerges as an important signaling mechanism, and we present examples of its potential relevance for tissue development and disease.
Principles of the mitochondrial fusion and fission cycle in neurons
Authors: Cagalinec Michal , Safiulina Dzhamilja , Liiv Mailis , Liiv Joanna , Choubey Vinay , Wareski Przemyslaw , Veksler Vladimir , Kaasik Allen 
Published: March 2013

Mitochondrial fusion-fission dynamics play a crucial role in many important cell processes. These dynamics control mitochondrial morphology, which in turn influences several important mitochondrial properties including mitochondrial bioenergetics and quality control, and it appears to be affected in several neurodegenerative diseases. However, an integrated and quantitative understanding of how fusion-fission dynamics controls mitochondrial morphology has not yet been described. Here, we took advantage of modern visualisation techniques to provide a clear explanation of how fusion and fission correlate with mitochondrial length and motility in neurons.
Our main findings demonstrate that: 1) the probability of a single mitochondrion fissing is determined by its length; 2) the probability of a single mitochondrion fusing is determined primarily by its motility; 3) the fusion and fission cycle is driven by changes in mitochondrial length and deviations from this cycle serves as a corrective mechanism to avoid extreme mitochondrial length; 4) impaired mitochondrial motility in neurons overexpressing 120Q Htt or Tau suppresses mitochondrial fusion and leads to mitochondrial shortening whereas stimulation of mitochondrial motility by overexpressing Miro-1 restores mitochondrial fusion rates and sizes.
Taken together, our results provide a novel insight into the complex crosstalk between different processes involved in mitochondrial dynamics. This knowledge will increase understanding of the dynamic mitochondrial functions in cells and in particular, the pathogenesis of mitochondrial-related neurodegenerative diseases.
The evolutionary conserved protein CG9186 is associated with lipid droplets, required for their positioning and for fat storage
Authors: Thiel Katharina , Heier Christoph , Haberl Verena , Thul Peter J. , Oberer Monika , Lass Achim , Jäckle Herbert , Beller Mathias 
Published: March 2013

Lipid droplets (LDs) represent specialized cell organelles for the storage of energy rich lipids. Although lipid storage is a conserved feature of all cells and organisms, only little is known about fundamental aspects of the cell biology of LDs, including their biogenesis, structural assembly and subcellular positioning, and the regulation of organismic energy homeostasis.We identified a novel LD-associated protein family, represented by the Drosophila protein CG9186 and its murine homolog MGI:1916082. In the absence of LDs, both proteins localize at the endoplasmic reticulum (ER). Upon lipid storage induction, they translocate to LDs using an evolutionary conserved targeting mechanism that acts via a 60 amino acids targeting motif in the center of the CG9186 protein. Overexpression of CG9186 and MGI:1916082 causes clustering of LDs in both tissue culture and salivary gland cells, whereas the RNAi knockdown results in a reduction of LDs. Organismal RNAi knock-down of CG9186 results in a reduction of the lipid storage levels of the fly. The results indicate that we identified the first members of a novel and evolutionary conserved family of lipid storage regulators, which are also required to properly position LDs within cells.
A Novel Strategy for Cell-Autonomous Gene Knockdown in Caenorhabditis elegans Defines a Cell-Specific Function for the G-Protein Subunit GOA-1
Authors: Maher Kathryn N , Swaminathan Aishwarya , Patel Parth , Chase Daniel L 
Published: March 2013

Abstract
We developed a novel knockdown strategy to examine cell-specific gene function in Caenorhabditis elegans. In this strategy a null mutation in any gene is replaced with a genetically stable transgene that contains a wild-type copy of the gene fused to a 3′ tag that targets the mRNA transcript for degradation by the host nonsense-mediated decay (NMD) machinery. In NMD-defective animals, tagged transgene mRNA is expressed at levels similar to the endogenous gene it replaced and is translated into wild-type protein that fully rescues gene function. Cell-specific activation of NMD cell autonomously knocks down transgene expression in specific cell types without affecting its expression or function in other cells of the organism. To demonstrate the utility of this system, we replaced the goa-1 gene, encoding the pan-neuronally expressed G-protein subunit GOA-1, with a degradation-tagged transgene. We then knocked down expression of the transgene from only two neurons, the hermaphrodite-specific neurons (HSNs), and showed that GOA-1 acts cell autonomously in the HSNs to inhibit egg-laying behavior.
A Review of Total Job Times for Repair and Maintenance Jobs for Well Servicing Activities in the Permian Basin
Authors: Conine Lynn W. , Burke Phil 
Published: March 2013

Abstract
The well servicing function is one of the last frontiers in the exploration and production industry to utilize modern instrumentation coupled with continuous improvement techniques to improve the safety, quality and efficiency of this particular industry segment. In 1999 Newman, et al, described a device for recording critical rig parameters while operating a well service unit. In a later paper (2002) he described several examples of how to utilize the data to gain insight into the operation of the service unit. This current paper analyzes job time data for 4,532 Repair and Maintenance jobs in the Permian Basin performed during 2009-2012. All jobs utilized in the analysis include rod and tubing activities but do not include traditional workover activities such as cementing, logging, perforating, swabbing or acidizing. The data encompasses twenty one counties in the heart of the Permian Basin from a variety of operators, although no individual operators are named. Several standard metrics such as total job time and job time versus depth will be included. The job times will also be subdivided into various groups of activities (categories) such as mobilization, tripping activities, BOP/TAC/PKR activities, transition activities, well control activities, crew break time, safety time, wait time and miscellaneous activities. In addition, ranges of expected performance times will be shown for both total job times and activity groups (categories) based on Statistical Process Control calculations. It is anticipated that by establishing quantitative benchmarks for service rig activities, producers will be able to identify areas for operational improvement, thereby resulting in an increase in the well service rig productivity. The basic data for this study has been obtained from the Key Energy Services Database. The authors are not aware of any previous papers which have presented this type of detailed well servicing time based information.
Enhanced Plunger Lift Performance Utilizing Reservoir Modeling
Authors: Parsa E. , Ozkan E. , Lowery B. , Cathcart D. , Lohmann M. 
Published: March 2013

Abstract
Liquid loading is an important determinant for the performance of tight, unconventional gas wells. Although plunger lift is one of the best solutions when applicable, marginal economics of unconventional gas production does not tolerate un-optimized plunger lift performance. In this paper a reservoir-performance based algorithm proposed by Ozkan et al. (2003) is applied to optimize the gas production and shut-in periods of plunger lift operation. The objective of the optimization is to maximize gas production with the condition that the liquid loaded during production can be lifted to the surface by the pressure that builds up during the following shut-in period. Unlike the current plunger lifts that work in time mode (like timer clock), this algorithm is based on pressure (pressure mode). The optimization algorithm combines the conventional plunger-lift theory with an analytical description of the reservoir performance. The conventional plunger lift theory provides the pressure required for lifting the plunger with a liquid column on top of it, and the analytical reservoir model is used to optimize the sequence of production and shut-in times. The optimization algorithm presented in this paper improves the economics of unconventional gas production not only by increasing gas production but also automating the process by which optimization is achieved. Another advantage of the proposed method is the ability to automatically adjust to changes in the line pressure. A case study is presented to demonstrate that the proposed automated model can achieve the same optimization performance as that implemented by expert technicians.
The Flow Behavior of Friction Reducer in Microchannels during Slickwater Fracturing
Authors: Sun Yongpeng , Wu Qihua , Bai Baojun , Ma Yinfa 
Published: March 2013

Abstract
Tight formations with extremely low matrix permeabilities, such as gas shale, can produce at economical rates is due to inborn fissures and fractures introduced during hydraulic stimulation. Hydraulic fracturing in gas shale can connect/generate these microfractures, causing them to become much more complex fracture networks. During a fracturing treatment, a pair of main fractures firstly is generated perpendicular to the wellbore direction. As the fluids continue to pump, more micro-sized fractures are generated near the main fractures. These microfractures have much more contact area with the matrix and therefore hold the majority of the productivity potential of gas shale. Slickwater fracturing has been proved to be an effective method by which to increase the recovery of shale gas reservoirs.
Friction reducer is the primary component of this fluid. It can decrease the flowing friction in macro tubing. Lab tests and field applications have addressed this issue thoroughly. However, the flow characteristics of this solution in microfractures are not clear.
The present study attempts to represent how this solution flows in microfractures by considering how it flows in microchannels. A commercial friction reducer was prepared with deionized water. The size of the particles in the FR first was analyzed from the macro to the nano scale. Then, the FR solution fluxed the microchannels with various velocities. Different solution concentrations, microchannel size effects and Reynolds number (Re) were investigated in detail. The Microchannels wettabilities, fluid shear rates and residual resistance factors also were studied. Finally, the experimental results were compared with field data, and its impact on the gas shale matrix was analyzed.
Pipe Diameter Effect on Liquid Loading in Vertical Gas Wells
Authors: Skopich A. , Pereyra E. , Sarica C. , Kelkar M. 
Published: March 2013

Abstract
The effect of pipe diameter on liquid loading initiation has been experimentally investigated using 2-in and 4-in pipe diameters. Two-phase flow parameters such as pressure gradient and liquid holdup were measured. Flow characteristics were determined by visual observation using a high speed video camera. Critical gas flow rate for liquid loading initiation has been identified and comparison between the two pipe diameters is presented. The critical superficial gas velocity corresponding to the minimum pressure gradient is larger for the smallest diameter. When the comparison is carried out in terms of mass flow rates, critical flow rate for liquid loading in 2-in pipe is smaller than that in 4-in. pipe. This supports the use of velocity strings to extend the production life of the gas well. Additionally, comparison of the data with available mechanistic models prediction shows significant discrepancies. Possible reasons for these discrepancies are presented.
Solutions for Difficult Reservoirs Direct NMR Fluid Type and Permeability
Authors: Smith Charles H. , Ramakrishna Sandeep , Hamilton Layne 
Published: March 2013

Abstract
Conventional reservoir calculations using resistivity and density/neutron porosity have been the industry standard for defining reservoir characteristics. The calculation of water saturation from these measurements is used in every reservoir situation. Many reservoirs are not easily analyzed; therefore, various and complicated analysis techniques have been developed.
In some cases, years were spent in characterization before these log measurements could be applied with confidence. This time and expenditure of resources drained capital from exploration to research processes and produced many inefficient completion attempts in reservoirs that were incorrectly characterized as productive.
The great hope with the introduction of NMR tools to the industry was that reservoir parameters could be established and applied in an uncomplicated manner. Advances in technology of NMR responses have produced the ability to capture polarization time and relaxation time in a single pass through the reservoir. Nuclear magnetic polarization time has been demonstrated to have a relationship to the fluid type in the reservoir. The relaxation time (T2) has been used to characterize permeability with an excellent relationship to production. The Bray-Smith permeability equation was developed from this observation. This equation incorporates relaxation time and calculates permeability. No alterations to the equation for rock type or texture changes were needed.
This paper presents examples of logs in three different and difficult-to-evaluate reservoirs. A reservoir with lenticular sand, another with a thinly-bedded sand and shale sequence, and a conglomerate/mudstone reservoir are each evaluated for fluid type and permeability. Effective porosity, fluid type, and permeability are all resolved accurately by the NMR. Comparisons to production results are presented.
Reactions of Simple Organic Acids and Chelating Agents with Dolomite
Authors: Adenuga Olusegun Olatunbosun , Nasr-El-Din Hisham A. , Sayed Mohammed Ali Ibrahim 
Published: March 2013

Abstract
Regular HCl has been used as the main acidizing fluid. At high temperatures, rapid spending of the acid with carbonates prevents deeper penetration of the acid into the formations. Alternatives such as acetic and formic acid have lent themselves to retarded reaction rates, low corrosivity and reduced tendency to form acid/oil sludge in asphaltene-rich crudes. The same problem of high reaction rate is still observed with organic acids at very high temperatures.
Complex thermodynamics equilibrium and reaction kinetics have been cited as issues apparent in selecting suitable organic acid as a stimulation fluid for specific acidizing treatment. Chelating agents, with the added advantage of complexing with carbonate to form a water-soluble product, have been introduced as stimulation fluids. Glutamic acid diacetic acid (GLDA), is a polycarboxylic acid with this property.
To predict the spending of GLDA relative to the organic acids, the kinetics of dolomite dissolution in organic acids and GLDA solution was investigated. The rotating disk apparatus was used to compare the reactivity of these solutions by varying the disk rotational speed from 100 to 1500 rpm and for 0.886N solutions at 120°C. Samples of the reacted acids, from the reactor, were collected and analyzed with Inductively Coupled Plasma.
Experimental results indicated that dolomite dissolution rates increased in all the acid solutions as the disk rotational speed increased at 120°C. At disk rotational speed of 1000 rpm and higher; the dissolution rate of dolomite in formic acid remained the same. Hence, the prevailing reaction regime in the acid solutions were mass transfer limited processes until the process shifted to reaction kinetics controlled at 1000 rpm in formic acid. Compared to the organic acids, GLDA demonstrated the lowest reactivity with dolomite at the same acid molarity and reaction conditions.
Analytical Determination of Interwell Connectivity Based on Flow Rate Fluctuations in Waterflood Reservoirs
Authors: Dinh Anh V. , Tiab Djebbar 
Published: March 2013

Abstract
Interwell connectivity, an important element in reservoir characterization, especially for secondary recovery such as waterflooding, is essential when making decisions on well patterns, infill wells, and injection rates for oil recovery optimization. An existing technique uses multivariate linear regression analysis of flow rates in a waterflood to infer interwell connectivity. Advantages of this technique include a simplified one-step calculation and the availability of production data. A capacitance model was introduced as an extension of the technique to account for shut-in periods and changes in bottomhole pressures in the producers; however, this approach is based on trial and error and requires subjective judgment.
This paper presents an alternative analytical approach based on analytic concepts, providing an in-depth understanding of the technique and relationships between interwell connectivity coefficients and other reservoir parameters. The analytical approach uses a mathematical model for bottomhole pressure responses of injectors and producers in a waterflood system. The model is based on a solution for fully penetrating vertical wells in a closed rectangular reservoir with an assumption of steady-state flow. This model is then used to calculate relative interwell permeabilities, which represent the connectivity levels of signal response well pairs.
Different synthetic reservoir models were analyzed, including homogeneous, anisotropic reservoirs, and reservoirs with high-permeability channels and transmissibility barriers. Comparisons with results obtained from previous studies of production data and bottomhole pressure data are presented.
The main findings of this study are: (a) the mathematical model performs well with interwell connectivity coefficients calculated from flow rate data to quantify reservoir parameters; (b) the proposed approach provides a better understanding of interwell connectivity determination from flow rate data;and (c) the results for relative interwell permeability from flow rate data are similar to those obtained from previous studies of bottomhole pressure data.