bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Genetics ofAnopheles coluzziiImmune Pathways and Genes
Authors: Rottschaefer Susan M , Crawford Jacob E , Riehle Michelle M , Guelbeogo Wamdaogo M , Gneme Awa , Sagnon N’Fale , Vernick Kenneth D , Lazzaro Brian P 
Published: January 2015

AbstractNatural selection is expected to drive adaptive evolution in genes involved in host–pathogen interactions. In this study, we use molecular population genetic analyses to understand how natural selection operates on the immune system of Anopheles coluzzii (formerly A. gambiae “M form”). We analyzed patterns of intraspecific and interspecific genetic variation in 20 immune-related genes and 17 nonimmune genes from a wild population of A. coluzzii and asked if patterns of genetic variation in the immune genes are consistent with pathogen-driven selection shaping the evolution of defense. We found evidence of a balanced polymorphism in CTLMA2, which encodes a C-type lectin involved in regulation of the melanization response. The two CTLMA2 haplotypes, which are distinguished by fixed amino acid differences near the predicted peptide cleavage site, are also segregating in the sister species A. gambiae (“S form”) and A. arabiensis. Comparison of the two haplotypes between species indicates that they were not shared among the species through introgression, but rather that they arose before the species divergence and have been adaptively maintained as a balanced polymorphism in all three species. We additionally found that STAT-B, a retroduplicate of STAT-A, shows strong evidence of adaptive evolution that is consistent with neofunctionalization after duplication. In contrast to the striking patterns of adaptive evolution observed in these Anopheles-specific immune genes, we found no evidence of adaptive evolution in the Toll and Imd innate immune pathways that are orthologously conserved throughout insects. Genes encoding the Imd pathway exhibit high rates of amino acid divergence between Anopheles species but also display elevated amino acid diversity that is consistent with relaxed purifying selection. These results indicate that adaptive coevolution between A. coluzzii and its pathogens is more likely to involve novel or lineage-specific molecular mechanisms than the canonical humoral immune pathways.
hecd-1ModulatesNotchActivity inCaenorhabditis elegans
Authors: Chen Yunting , Greenwald Iva 
Published: January 2015

AbstractNotch is a receptor that mediates cell–cell interactions that specify binary cell fate decisions in development and tissue homeostasis. Inappropriate Notch signaling is associated with cancer, and mutations in Notch pathway components have been associated with developmental diseases and syndromes. In Caenorhabditis elegans, suppressors of phenotypes associated with constitutively active LIN-12/Notch have identified many conserved core components and direct or indirect modulators. Here, we molecularly identify sel(ar584), originally isolated as a suppressor of a constitutively active allele of lin-12. We show that sel(ar584) is an allele of hecd-1, the ortholog of human HECDT1, a ubiquitin ligase that has been implicated in several different mammalian developmental events. We studied interactions of hecd-1 with lin-12 in the somatic gonad and with the other C. elegans Notch gene, glp-1, in the germ line. We found that hecd-1 acts as a positive modulator of lin-12/Notch activity in a somatic gonad context—the original basis for its isolation—but acts autonomously as a negative modulator of glp-1/Notch activity in the germ line. As the yeast ortholog of HECD-1, Ufd4p, has been shown to function in quality control, and C. elegansHECD-1 has been shown to affect mitochondrial maintenance, we propose that the different genetic interactions between hecd-1 and Notch genes we observed in different cell contexts may reflect differences in quality control regulatory mechanisms or in cellular metabolism.
Condensins Exert Force on Chromatin-Nuclear Envelope Tethers to Mediate Nucleoplasmic Reticulum Formation in Drosophila melanogaster
Authors: Bozler Julianna , Nguyen Huy Q , Rogers Gregory C , Bosco Giovanni 
Published: January 2015

Abstract
Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology.
Identification of New Players in Cell Division, DNA Damage Response, and Morphogenesis Through Construction of Schizosaccharomyces pombe Deletion Strains
Authors: Chen Jun-Song , Beckley Janel R , McDonald Nathan A , Ren Liping , Mangione MariaSanta , Jang Sylvia J , Elmore Zachary C , Rachfall Nicole , Feoktistova Anna , Jones Christine M , Willet Alaina H , Guillen Rodrigo , Bitton Danny A , Bähler Jürg , Jensen Michael A , Rhind Nick , Gould Kathleen L 
Published: January 2015

Abstract
Many fundamental biological processes are studied using the fission yeast, Schizosaccharomyces pombe. Here we report the construction of a set of 281 haploid gene deletion strains covering many previously uncharacterized genes. This collection of strains was tested for growth under a variety of different stress conditions. We identified new genes involved in DNA metabolism, completion of the cell cycle, and morphogenesis. This subset of nonessential gene deletions will add to the toolkits available for the study of biological processes in S. pombe.
Electro-Optical Detection of Single Nanoparticles on a Nanopore-Optofluidic Chip
Authors: Liu Shuo , Zhao Yue , Stott Matthew , Parks Joshua W. , Hawkins Aaron R. , Schmidt Holger 
Published: January 2015

ABSTRACTA solid-state nanopore was integrated into an optofluidic sensor chip, liquid-core anti-resonant reflecting optical waveguide (ARROW). The solid-state nanopore worked as a smart gate, which simultaneously provided characteristic electrical signals and controlled the entry of single nanoparticles into the liquid-core channel. The subsequent fluorescence detection further identified the nanoparticles by providing optical signals within a specific wavelength range. In this work, correlated electrical and optical detection of single nanoparticles, H1N1 viruses, and λ-DNA molecules was demonstrated. Different types of particles in a mixture were successfully discriminated. Moreover, the flow velocity in the liquid-core channel was extracted with the help of combined analysis of electrical and optical signals. Enhanced electrical sensitivity using a solid-state nanopore with a thin limiting aperture sculpted by SiO2 deposition was also shown.
PbS/CdS Core/Shell Nanocrystals For Solution-Processed Colloidal Quantum Dot Solar Cells
Authors: Neo Darren C. J. , Cheng Cheng , Assender Hazel E. , Watt Andrew A. R. 
Published: January 2015

ABSTRACTAn epitaxial shell of cadmium sulphide is grown on lead sulphide quantum dots in order to reduce the concentration of surface defects. Thin solid films of these core/shell materials are found to have low carrier concentrations due to effective surface passivation which reduces the number of dangling bonds. In this paper PbS/CdS is used as a quasi-intrinsic layer in p-i-n photovoltaic devices where PbS acts as the p-layer and ZnO the n-layer. By studying different permutations of these layers and the degree of PbS p-type doping by annealing we optimise fill factor and open-circuit voltage.
Electrical Conductivity and Structural Order of p-Type Amorphous Silicon Thin Films
Authors: Shrestha K. , Whitfield D. , Lopes V. C. , Syllaios A. J. , Littler C.L. 
Published: January 2015

ABSTRACTThe dependence of dark conductivity and room temperature Raman spectra on boron and hydrogen incorporation in thin films of hydrogenated amorphous silicon (a-Si:H) prepared by plasma enhanced chemical vapor deposition was investigated. It was found that the dominant conductivity is Mott variable range hopping conduction. However, at lower temperatures, Efros-Shklosvkii hopping conduction is observed and contributes to the total conductivity. For structural characterization, transverse optical (TO) and transverse acoustic (TA) modes of the Raman spectra were studied to relate changes in short- and mid-range order to the effects of boron and hydrogen incorporation. With an increase of hydrogen incorporation and/or substrate temperature, both short and mid-range order improve, whereas the addition of boron results in the degradation of the short range order. The line width and frequency of the Raman TO Raman peak correlate with electrical measurements and suggest that this technique can be used for non-destructive characterization of a-Si:H.
Weight, Length, and Body Mass Index Growth of Children under 2 Years of Age with Cleft Lip and Palate
Authors: Miranda Gabriela Serrano , Marques Ilza Lazarini , De Barros Suely Prietto , Arena Eliane Petean , De Souza Luiz 
Published: January 2015

Objective To study the growth of length-for-age (L/A), weight-for-age (W/A), and body mass index (BMI) of children with cleft lip and palate receiving a normal diet; to establish specific growth curves for children with cleft palate with or without cleft lip (CLP/ICP) who had not undergone palatoplasty and for children with isolated cleft lip (ICL); and to assess if CLP/ICP growth differed from ICL growth and if CLP/ICP and ICL growth differed from growth for typical children. Design Prospective and cross-sectional study. Setting Hospital for Rehabilitation of Craniofacial Anomalies, Bauru, São Paulo, Brazil. Main Outcome Measures Weight and length of 381 children with cleft lip and palate and who were younger than 2 years were recorded and used to calculate W/A, L/A, and BMI growth curves. The 2006 World Health Organization growth charts were used as a reference for typical children. All children received a normal diet for age. Results Children with CLP/ICP had median W/A and BMI growth curves below growth curves for typical children but showed spontaneous recovery starting at approximately 5 months of age, even with nonoperated cleft palate. Children with ICL had growth similar to that of typical children. Children with CLP/ICP, who initially had W/A and BMI values less than those of the ICL group, had W/A and BMI equal to or higher than the ICL group after 9 months of age. Conclusion Children with CLP/ICP had impaired W/A and BMI growth with spontaneous recovery starting early in childhood. This study established specific W/A, BMI, and L/A growth curves for children with cleft lip and palate.
Multidisciplinary Aspects of 104 Patients with Pierre Robin Sequence
Authors: Filip Charles , Feragen Kristin Billaud , Lemvik Jorunn Skartveit , Lindberg Nina , Andersson Els-Marie , Rashidi Mitra , Matzen Michael , Høgevold Hans Erik 
Published: January 2015

Objective To describe Pierre Robin sequence patients with a cleft palate from a multidisciplinary perspective. Patients A total of 104 individuals with Pierre Robin sequence and cleft palate, born between 1980 and 2010. Method Data were collected retrospectively and compared with large control groups. Results Of 104 patients, 19 (18.3%) were treated with a nasopharyngeal or oropharyngeal tube, continuous positive airway pressure, and/or a tracheotomy. The mean weight percentile for newborns with Pierre Robin sequence was 30.9. It decreased to 29.9 at the time of cleft palate repair (mean age, 13.7 months) ( P = .78). Of 87 patients, 30 (34.5%) developed normal speech after cleft palate repair. Of 93 nonsyndromic Pierre Robin sequence patients, 31 (33.3%) had or are having surgery for velopharyngeal insufficiency, a rate that is significantly higher when compared with a control group of cleft palate–only patients (19.4%; P = .004). Of 31 patients, 25 (80.6%) developed normal resonance after surgery for velopharyngeal insufficiency. There was no significant difference in the rate of syndromes between the Pierre Robin sequence patients and a control group of cleft palate patients without Pierre Robin sequence ( P = .25). Seven of 39 boys (17.9%) with Pierre Robin sequence had a diagnosis of autism spectrum disorder. Conclusion Even though the mean weight percentile for newborns with Pierre Robin sequence was low, the patients did not show a growth spurt during the first year of life. The high rate of velopharyngeal insufficiency after cleft palate repair in patients with Pierre Robin sequence needs further investigation. Also, the high rate of autism spectrum disorder among boys with Pierre Robin sequence prompts further investigation.
A Novel Water-Injectivity Model and Experimental Validation With CT-Scanned Corefloods
Authors: Yerramilli Ramesh Chandra , Zitha P.L.J.. L.J. , Yerramilli Sanjay Surya , Bedrikovetsky Pavel 
Published: January 2015

Summary
Injectivity decline is an issue during produced-water reinjection (PWRI) for water disposal in aquifers, waterflooding, chemical enhanced oil recovery, and geothermal-energy exploitation. A novel model for injectivity decline under flow conditions reminiscent of PWRI was developed taking into account deep-bed filtration and buildup of external filter cake. A distinct feature of the model is that it describes particle-retention kinetics responsible for internal filtration by an exponential decaying function of the retained-particle concentration. The corresponding nonlinear governing partial-differential equations were solved numerically and coupled with a known analytical model for external filtration with the concept of transition time. Coreflood experiments consisting of the injection of brine containing suspended hematite particles (volume fractions in the range of 2 to 6 ppm) were also performed. Computed-tomography (CT) scans of the core were taken to obtain deposition profiles along the core at different times. In addition, effect of various parameters (particle concentration and number of grids) on injectivity was investigated. From CT-scan and optical-microscope analyses, it was found that surface deposition in the porous medium and face plugging at the injection face of the core were responsible for decline in injectivity. The transition time from pure internal to external filtration was accurately determined from the CT-scan and pressure data. The newly proposed model and experiments were found to be in excellent agreement, indicating that the adopted retention function is a good heuristic description of particle retention.
Understanding Shale Gas Flow Behavior Using Numerical Simulation
Authors: Sun Hao , Chawathé Adwait , Hoteit Hussein , Shi Xundan , Li Lin 
Published: January 2015

Summary
Shale gas has changed the energy equation around the world, and its impact has been especially profound in the United States. It is now generally agreed that the fabric of shale systems comprises primarily organic matter, inorganic material, and natural fractures. However, the underlying flow mechanisms through these multiporosity and multipermeability systems are poorly understood. For instance, debate still exists about the predominant transport mechanism (diffusion, convection, and desorption), as well as the flow interactions between organic matter, inorganic matter, and fractures. Furthermore, balancing the computational burden of precisely modeling the gas transport through the pores vs. running full reservoir scale simulation is also contested. To that end, commercial reservoir simulators are developing new shale gas options, but some, for expediency, rely on simplification of existing data structures and/or flow mechanisms.
We present here the development of a comprehensive multimechanistic (desorption, diffusion, and convection), multiporosity (organic materials, inorganic materials, and fractures), and multipermeability model that uses experimentally determined shale organic and inorganic material properties to predict shale gas reservoir performance. Our multimechanistic model takes into account gas transport caused by both pressure driven convection and concentration driven diffusion. The model accounts for all the important processes occurring in shale systems, including desorption of multicomponent gas from the organics' surface, multimechanistic organic/inorganic material mass transfer, multimechanistic inorganic material/fracture network mass transfer, and production from a hydraulically fractured wellbore.
Our results show that a dual porosity, dual permeability (DPDP) model with Knudsen diffusion is generally adequate to model shale gas reservoir production. Adsorption can make significant contributions to original gas in place, but is not important to gas production because of adsorption equilibrium. By comparing triple porosity, dual permeability; DPDP; and single porosity, single permeability formulations under similar conditions, we show that Knudsen diffusion is a key mechanism and should not be ignored under low matrix pressure (Pematrix) cases, whereas molecular diffusion is negligible in shale dry gas production. We also guide the design of fractures by analyzing flow rate limiting steps. This work provides a basis for long term shale gas production analysis and also helps define value adding laboratory measurements.
The First Visualization of Acid Treatments on Carbonates With 3D Nuclear-Magnetic-Resonance Imaging
Authors: Krebs M.. , Lungwitz B.. , Souza A.. , Pépin A.. , Montoya S.. , Schlicht P.. , Boyd A.. , Vidoto E.. , Polli R.. , Bonagamba T.. 
Published: January 2015

Summary
Carbonate reservoirs often show great heterogeneity in their inner rock structure, and stimulation treatments are often necessary to maintain or establish fluid production. Therefore, core-flow tests are usually conducted to test and model stimulation treatments within a laboratory scale to predict their performance. The visualization of wormholes that were created within core-flow tests requires novel technologies for evaluation and pathway-prediction purposes. Unfortunately, past visualization techniques were always associated with the destruction of the core sample, creating a demand for nondestructive methods.
Nuclear-magnetic-resonance imaging (NMRI) is such a method that fulfills the approach of being nondestructive. The technology is widely known by medical applications, and this study developed a procedure on how to use the NMRI technology to visualize wormholes with NMRI in 3D.
The study was started by initially choosing and obtaining various core samples that have different contents of calcite and dolomite. These core samples were imaged with the NMRI and microfocus-computed-tomography (µCT) technology in their unchanged state, and basic petrophysical experiments were conducted for initial experiments. The μCT technology was used as a reference visualization technique, because it provides a very high resolution with a corresponding high level of detail. Afterward, core-flow tests were conducted on the core samples with various acid systems and wormholes generated. Finally, the core samples with wormholes were imaged again with the NMRI and μCT technology, whereby the NMRI acquisition technique was improved toward imaging of rock samples, and the results were compared with the μCT results. The NMRI results showed moderate imaging achievements for the unchanged rock samples and high-quality imaging achievements for the extracted wormholes.
Dynamic Modeling of Channel Formation During Fluid Injection Into Unconsolidated Formations
Authors: Ameen S.. , Taleghani A. Dahi 
Published: January 2015

SummaryInjectivity loss is a common problem in unconsolidated-sand formations. Injection of water into a poorly cemented granular medium may lead to internal erosion, and consequently formation of preferential flow paths within the medium because of channelization. Channelization in the porous medium might occur when fluid-induced stresses become locally larger than a critical threshold and small grains are dislodged and carried away; hence, porosity and permeability of the medium will evolve along the induced flow paths. Vice versa, flowback during shut-in might carry particles back to the well and cause sand accumulation inside the well, and subsequently loss of injectivity. In most cases, to maintain the injection rate, operators will increase injection pressure and pumping power. The increased injection pressure results in stress changes and possibly further changes in channel patterns around the wellbore. Experimental laboratory studies have confirmed the presence of the transition from uniform Darcy flow to a fingered-pattern flow. To predict these phenomena, a model is needed to fill this gap by predicting the formation of preferential flow paths and their evolution. A model based on the multiphase-volume-fraction concept is used to decompose porosity into mobile and immobile porosities where phases may change spatially, evolve over time, and lead to development of erosional channels depending on injection rates, viscosity, and rock properties. This model will account for both particle release and suspension deposition. By use of this model, a methodology is proposed to derive model parameters from routine injection tests by inverse analysis. The proposed model presents the characteristic behavior of unconsolidated formation during fluid injection and the possible effect of injection parameters on downhole-permeability evolution.