bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coxsackievirus B transmission and possible new roles for extracellular vesicles
Authors: Inal Jameel M. , Jorfi Samireh 
Published: January 2013

Coxsackievirus B1, a member of the Picornaviridae family is a non-enveloped single-stranded RNA virus associated with human diseases including myocarditis and pancreatitis. Infection of the intestinal mucosa, lined by polarized epithelial cells, requires interaction of coxsackievirus with apically located DAF (decay-accelerating factor) before transport to the basolaterally located CAR (coxsackie and adenovirus receptor), where entry is mediated by endocytosis. As with many other non-enveloped viruses, coxsackievirus has to induce lysis of host cells in order to perpetuate infection. However, recent evidence indicates that virus spread to secondary sites is not only achieved by a lytic mechanism and a non-lytic cell–cell strategy has been suggested for coxsackievirus B3. A physical interaction between infected and non-infected cells has been shown to be an efficient mechanism for retroviral transmission and one type of extracellular vesicle, the exosome, has been implicated in HIV-1 transmission. HIV-1 also takes advantage of depolymerization of actin for spread between T-cells. Calpain-mediated depolymerization of the actin cytoskeleton, as a result of increases in intracellular calcium concentration during coxsackievirus infection, would result in a release of host cell-derived microvesicles. If so, we speculate that maybe such microvesicles, increasingly recognized as major vehicles mediating intercellular communication, could play a role in the intercellular transmission of non-enveloped viruses.
Thermococcus kodakarensis DNA replication
Authors: Li Zhuo , Kelman Lori M. , Kelman Zvi 
Published: January 2013

DNA replication plays an essential role in all life forms. Research on archaeal DNA replication began approximately 20 years ago. Progress was hindered, however, by the lack of genetic tools to supplement the biochemical and structural studies. This has changed, however, and genetic approaches are now available for several archaeal species. One of these organisms is the thermophilic euryarchaeon Thermococcus kodakarensis. In the present paper, the recent developments in the biochemical, structural and genetic studies on the replication machinery of T. kodakarensis are summarized.
G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms
Authors: Chini Bice , Parenti Marco , Poyner David R. , Wheatley Mark 
Published: January 2013

The papers resulting from the recent Biochemical Society Focused Meeting ‘G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms’ held in Prato in September 2012 are introduced in the present overview. A number of future goals for GPCR (G-protein-coupled receptor) research are considered, including the need to develop biophysical and computational methods to explore the full range of GPCR conformations and their dynamics, the need to develop methods to take this into account for drug discovery and the importance of relating observations on isolated receptors or receptors expressed in model systems to receptor function in vivo.
A dynamic perspective on language processing and development
Authors: de Bot Kees , Chan HuiPing , Lowie Wander , Plat Rika , Verspoor Marjolijn 
Published: January 2013

If language processing and development is viewed as a dynamic process in which all subsystems interact over time, then some basic assumptions behind more traditional approaches to language analysis are problematic: new methods of analysis and modeling are needed to supplement and partly replace existing paradigms. This argument is illustrated with two examples from recent studies.
After a brief history of the reasons for a paradigm shift and an explanation of the role of variability in development, the first example study presents a variability-based approach to reaction time measurements in which spectral analyses of variability found during repeated measures of the same experiment may indicate moments of behavioral change. Then the principles of dynamic modeling are explained, illustrated with vocabulary developmental data. The second recent study shows how the vocabulary development of three learners is may be dynamically modeled using a logistic model.
Evidence of Wild Juvenile Lake Trout Recruitment in Western Lake Michigan
Authors: Hanson S. Dale , Holey Mark E. , Treska Ted J. , Bronte Charles R. , Eggebraaten Ted H. 
Published: January 2013

Abstract
Lake Trout Salvelinus namaycush were extirpated from Lake Michigan by the early 1950s, and as part of an effort to restore naturally reproducing populations, hatchery-reared fish have been stocked since the early 1960s. Stocked fish are marked with a fin clip to differentiate them from wild, lake-produced Lake Trout; marking error for the 2007–2010 year-classes of Lake Trout stocked by federal hatcheries averaged 3.0%. Egg deposition, emergent fry, and wild juvenile Lake Trout have previously been observed, but no sustained wild recruitment has been measured in assessment surveys or in sport and commercial fishery catches. In 2011 and 2012, we caught juvenile Lake Trout in gill-net and bottom trawl catches that were targeting Bloater Coregonus hoyi in water depths greater than 80 m. Unclipped, wild Lake Trout represented 20% of all Lake Trout caught in a southern offshore region of Lake Michigan. In northwestern Lake Michigan wild recruits represented from 10% to 27% of the 2007–2009 year-classes, and we recovered a small number of wild Lake Trout from the 2010 year-class. This is the first evidence for consecutive year-classes of naturally produced Lake Trout surviving beyond the fry stage in Lake Michigan.
Received July 13, 2012; accepted November 26, 2012
Agonist–antagonist muscle activation during drop jumps
Authors: Arai Aya , Ishikawa Masaki , Ito Akira 
Published: January 2013

AbstractPre‐programmed and stretch‐induced muscle activities of agonist muscles can play important roles during stretch‐shortening cycle exercises. It is still not clear how the antagonist muscles function when the drop and rebound intensities are varied during drop jump (DJ) exercises. The purpose of the present study was to examine the regulation of agonist–antagonist muscle activation during DJ with different drop and rebound heights. The subjects performed DJs with two drop heights (0.2 and 0.4 m) and three different efforts (maximal rebound height, 50% effort of maximal rebound height and landing without rebound). Ankle and knee joint angles, and vertical ground reaction force together with an electromyogram of the lower leg muscles (medial gastrocnemius [MG], soleus [SOL] and tibialis anterior [TA]) were measured simultaneously during DJ. Our results clearly showed that the pre‐activation of the antagonist TA was increased with increasing rebound height. Our results further showed that the coactivations of agonist and antagonist muscles during the post‐impact 30‐ms phase were increased with increasing rebound height. These results suggested that not only the pre‐programmed agonist MG muscle activation, but also the pre‐programmed antagonist TA activation and the coactivation of the post‐impact 30‐ms phase may play important roles in the control of rebound height.
AbCD: arbitrary coverage design for sequencing-based genetic studies
Authors: Kang Jian , Huang Kuan-Chieh , Xu Zheng , Wang Yunfei , Abecasis Gonçalo R. , Li Yun 
Published: January 2013

AbstractSummary: Recent advances in sequencing technologies have revolutionized genetic studies. Although high-coverage sequencing can uncover most variants present in the sequenced sample, low-coverage sequencing is appealing for its cost effectiveness. Here, we present AbCD (arbitrary coverage design) to aid the design of sequencing-based studies. AbCD is a user-friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency category, for designs with arbitrary coverage (0.5–30×) and sample size (20–10 000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans). In addition, we also present two software tools: ShotGun and DesignPlanner, which were used to generate the estimates behind AbCD. ShotGun is a flexible short-read simulator for arbitrary user-specified read length and average depth, allowing cycle-specific sequencing error rates and realistic read depth distributions. DesignPlanner is a full pipeline that uses ShotGun to generate sequence data and performs initial SNP discovery, uses our previously presented linkage disequilibrium-aware method to call genotypes, and, finally, provides minor allele frequency-specific effective sample sizes. ShotGun plus DesignPlanner can accommodate effective sample size estimate for any combination of high-depth and low-depth data (for example, whole-genome low-depth plus exonic high-depth) or combination of sequence and genotype data [for example, whole-exome sequencing plus genotyping from existing Genomewide Association Study (GWAS)].Availability and implementation: AbCD, including its downloadable terminal interface and web-based interface, and the associated tools ShotGun and DesignPlanner, including documentation, examples and executables, are available at http://www.unc.edu/∼yunmli/AbCD.html.Contact: yunli@med.unc.edu
Specific surface area and pore‐size distribution in clays and shales
Authors: Kuila Utpalendu , Prasad Manika 
Published: January 2013

ABSTRACTOne of the biggest challenges in estimating the elastic, transport and storage properties of shales has been a lack of understanding of their complete pore structure. The shale matrix is predominantly composed of micropores (pores less than 2 nm diameter) and mesopores (pores with 2–50 nm diameter). These small pores in the shale matrix are mainly associated with clay minerals and organic matter and comprehending the controls of these clays and organic matter on the pore‐size distribution is critical to understand the shale pore network. Historically, mercury intrusion techniques are used for pore‐size analysis of conventional reservoirs. However, for unconventional shale reservoirs, very high pressures (> 414 MPa (60 000 psi)) would be required for mercury to access the full pore structure, which has potential pitfalls. Current instrumental limitations do not allow reliable measurement of significant portions of the total pore volume in shales. Nitrogen gas‐adsorption techniques can be used to characterize materials dominated by micro‐ and mesopores (2–50 nm). A limitation of this technique is that it fails to measure large pores (diameter >200 nm). We use a nitrogen gas‐adsorption technique to study the micro‐ and mesopores in shales and clays and compare the results from conventional mercury porosimetry techniques.Our results on pure clay minerals and natural shales show that (i) they have a multiscale pore structure at different dimensions (ii) fine mesopores, with a characteristic 3 nm pore size obtained with N2 gas‐adsorption are associated with an illite‐smectite group of clays but not with kaolinite; (iii) compaction results in a decrease of pore volume and a reduction of pore size in the ‘inter‐aggregate’ macropores of the illite‐smectite clays while the fine ‘intra‐tachoid’ mesopores are shielded from compaction; (iv) for natural shales, mineralogy controls the pore‐size distributions for shales and the presence of micropores and fine mesopores in natural shales can be correlated with the dominance of the illite‐smectite type of clays in the rock. Our assessment of incompressible 3 nm sized pores associated with illite‐smectite clays provides an important building block for their mineral modulus.
Static and dynamic behaviour of compacted sand and clay: Comparison between measurements in Triaxial and Oedometric test systems
Authors: Bhuiyan M. H. , Holt R. M. , Larsen I. , Stenebråten J.F. 
Published: January 2013

ABSTRACTIn rock mechanics and rock physics, like in many other branches of research, it is important to compare results obtained in different kinds of apparatus that are meant to measure the same properties. Differences may in general be due to differences in samples, or in test procedures. Here we compare uniaxial compaction experiments in oedometric and triaxial tests systems, using brine‐saturated samples made from pure kaolinite or from Ottawa sand. Small differences in sample manufacturing or in initial loading of the specimens were found to cause significant differences in static behaviour and in ultrasonic velocities during the tests. The influence of differences in sample geometry (wide and thin samples in the oedometer versus long and slim samples in the triaxial set‐up) and the influence of different boundary conditions caused by the confining medium (steel in the oedometer, thin soft sleeve in the triaxial system) were studied, amongst others with the use of discrete particle modelling. Although the boundary conditions may have an influence, the most significant sources of discrepancy in our experiments were associated with the manufacturing and preparation of the samples to be tested. The test data show that the drained static compaction modulus for sand is close to its dynamic counterpart, while for kaolinite, the dynamic modulus is significantly larger than the static one.
Sensitivity of flow and elastic properties to fabric heterogeneity in carbonates
Authors: Sharma Ravi , Prasad Manika , Batzle Mike , Vega Sandra 
Published: January 2013

ABSTRACTCarbonate rocks are heterogeneous at various levels from deposition to diagenesis. Any existing depositional heterogeneity becomes more complex when carbonate rocks are in contact with polar fluids. Our experiments on carbonate rocks show that change in textural heterogeneity leads to heterogeneity in the distribution of storage and flow properties that may govern changes in saturation patterns. This would be akin to any carbonate reservoir with a mix of heterogeneous and homogeneous facies within a formation and their control on saturation distribution in response to a standard imbibition process. Associated with the saturation pattern heterogeneities, the resultant elastic property distributions also change. We quantify this heterogeneity and its effects on flow and seismic properties based on a few textural extremes of fabric heterogeneity in samples that can exist in any typical carbonate reservoir system. Our measurements show that textural heterogeneity can lead to anisotropy in permeability and in acoustic velocities. Permeability anisotropy measurements varied between 40% and 100% while acoustic velocity anisotropy measurements varied between 8% and 30% with lower values for homogeneous samples respectively. Under similar conditions of the saturation experiment (spontaneous imbibition at the benchtop and undrained pressure imbibition at 1000 psi), the imbibing brine replaced 97% of the pore volume in a homogeneous sample (porosity 20% and permeability 2.6 mD) compared to 80% pore volume in a heterogeneous sample (porosity 29% and permeability 23.4 mD). Furthermore, after pressure saturation, a change of +79% in the bulk modulus and ‐11% in the shear modulus is observed for homogeneous samples in comparison to +34% in the bulk modulus and −1% in the shear modulus for heterogeneous samples, with respect to the dry state moduli values of the samples. We also examined the uncertainties associated with Gassmann models of elastic properties due to variations in fluid saturations.Our results provide significant information on the saturation and, with it, modulus variations that are often ignored during fluid substitution modelling in time‐lapse seismic studies in carbonate reservoirs. We show that the bulk modulus could vary by 45% and the shear modulus by 10% between homogeneous and heterogeneous patches of a reservoir after a water flooding sequence for secondary recovery. Our findings demonstrate the need to incorporate and couple such fabric‐controlled saturation heterogeneities in reservoir simulation and in seismic fluid substitution models.
New species of Simulium (Nevermannia) from Korea, with reference to its allied species in the S. vernum species group (Diptera: Simuliidae) in Korea and Japan
Authors: Kim Sam‐Kyu 
Published: January 2013

AbstractThe larvae and pupae of a new species, Simulium (Nevermannia) immaculatum sp. nov., are described from Korea. Descriptions are supplemented with photographs of larvae and pupae and habitat information. The new species can be distinguished from other Asian members of the S. vernum group by the cephalic plate and thorax of the pupa devoid of tubercles, 4 pupal gill filaments lying close together, larva with postgenal cleft shorter than postgenal bridge, spot under ocellus absent, and rectal papillae with three simple lobes with single digit‐like small secondary lobule basally.
Circadian Misalignment, Reward‐Related Brain Function, and Adolescent Alcohol Involvement
Authors: Hasler Brant P. , Clark Duncan B. 
Published: January 2013

BackgroundDevelopmental changes in sleep and circadian rhythms that occur during adolescence may contribute to reward‐related brain dysfunction, and consequently increase the risk of alcohol use disorders (AUDs).MethodsThis review (i) describes marked changes in circadian rhythms, reward‐related behavior and brain function, and alcohol involvement that occur during adolescence, (ii) offers evidence that these parallel developmental changes are associated, and (iii) posits a conceptual model by which misalignment between sleep–wake timing and endogenous circadian timing may increase the risk of adolescent AUDs by altering reward‐related brain function.ResultsThe timing of sleep shifts later throughout adolescence, in part due to developmental changes in endogenous circadian rhythms, which tend to become more delayed. This tendency for delayed sleep and circadian rhythms is at odds with early school start times during secondary education, leading to misalignment between many adolescents' sleep–wake schedules and their internal circadian timing. Circadian misalignment is associated with increased alcohol use and other risk‐taking behaviors, as well as sleep loss and sleep disturbance. Growing evidence indicates that circadian rhythms modulate the reward system, suggesting that circadian misalignment may impact adolescent alcohol involvement by altering reward‐related brain function. Neurocognitive function is also subject to sleep and circadian influence, and thus circadian misalignment may also impair inhibitory control and other cognitive processes relevant to alcohol use. Specifically, circadian misalignment may further exacerbate the cortical–subcortical imbalance within the reward circuit, an imbalance thought to explain increased risk‐taking and sensation‐seeking during adolescence. Adolescent alcohol use is highly contextualized, however, and thus studies testing this model will also need to consider factors that may influence both circadian misalignment and alcohol use.ConclusionsThis review highlights growing evidence supporting a path by which circadian misalignment may disrupt reward mechanisms, which may in turn accelerate the transition from alcohol use to AUDs in vulnerable adolescents.
The impact of Broussonetia papyrifera (L.) vent. on community characteristics in the forest and forest–savannah transition ecosystems of Ghana
Authors: Bosu Paul P. , Apetorgbor Mary M. , Nkrumah Elvis E. , Bandoh Kwabena P. 
Published: January 2013

AbstractFollowing its introduction in the late 1960s, Broussonetia papyrifera L. Vent. Moraceae (paper mulberry) has emerged as a major exotic invasive species in Ghana's forest ecosystems. This study was carried out to assess the effects of B. papyrifera invasion on community composition in forest and forest–savannah transition ecosystems. Comparative and removal experiments were conducted in paired B. papyrifera invaded versus uninvaded plots. In the comparative assessment, species composition was found to be similar in both invaded and uninvaded plots. However, relative per cent cover of resident species and guilds including Chromolaena odorata, indigenous broadleaves and indigenous grasses were significantly lower in invaded plots. Seven months after B. papyrifera was experimentally removed from invaded stands, cover by indigenous broadleaves increased by 35%, as against only 5% in control plots at the forest site. However, at the transition site, the increase in per cent cover of indigenous broadleaves (18%) was not significantly different from control (2.5%) plots. We conclude that B. papyrifera has the capacity to reduce the abundance of indigenous broadleaf species, although its removal is more likely to favour regeneration in a forest than a forest–savannah transition ecosystem.
PACCRETA: Clinical situations at high risk of Placenta ACCRETA/Percreta: impact of diagnostic methods and management on maternal morbidity
Authors: Kayem Gilles , Deneux‐Tharaux Catherine , Sentilhes Loic ,   The PACCRETA group
Published: January 2013

AbstractBackgroundNo population‐based study has assessed the prevalence of placenta accreta, the predictive value of prenatal diagnostic examinations, the maternal morbidity associated with its management, or its psychological effects. Moreover, the technical resources necessary for the safest delivery of women at risk have not been clearly identified.ObjectivesThe primary objectives are to identify individual risk factors, as well as factors associated with types of management and with the healthcare facilities for postpartum hemorrhage. Secondary objectives are to (i) determine the prevalence of placenta accreta among women at risk; (ii) assess the predictive value of ultrasound and MRI for the diagnosis of placenta accreta in this population; (iii) evaluate psychological impact and physical complications; and (iv) report maternal physical complications during the year after delivery.DesignPopulation‐based prospective observational study of pregnant women with a placenta inserted at a uterine scar.SettingA total of 182 centers in eight French regions, with 270 000 deliveries annually.MethodsWe expect to include 620 women at risk of placenta accreta in two years, of whom approximately 120 (20%) will have placenta accreta.Main outcome measuresThe primary outcome measure is severe maternal hemorrhage; secondary outcome measures are maternal morbidity and deaths, predictive value of ultrasound and MRI, and psychological evaluations at 6 and 12 months.ConclusionThis study will be the first prospective population‐based study to include women at risk of placenta accreta and to investigate incidence, prenatal detection, type of management, morbidity and maternal psychological consequences.
Electrohysterographic evaluation of preterm contractions in a patient with a unicornuate uterus
Authors: van 't Hooft Janneke , Rabotti Chiara , Oei S.Guid 
Published: January 2013

AbstractWomen with Müllerian anomalies are at increased risk of preterm labor. The analysis of parameters derived by the electrohysterogram such as its conduction velocity are promising for preterm delivery prediction. However, an electrohysterogram has never been measured in Müllerian anomalies. A multiparous woman with a unicornuate uterus presented at 28 weeks of gestation with preterm contractions. Three electrohysterogram recordings were performed between 28 and 30 weeks of gestation, 4 weeks before delivery. The conduction velocity values were in line with previous literature and differed significantly (p < 0.001) showing an increase between the first and last two recordings. The parameters derived from the electrohysterogram such as conduction velocity and power density spectrum peak frequency are promising ones to follow the evolution of pregnancy towards labor, and to distinguish between productive and unproductive uterine contractions, in the case of a unicornuate uterus as well as one that is normally developed.