bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformation of the cerebellum into more ventral brainstem fates causes cerebellar agenesis in the absence of
Ptf1a
function
Authors: Millen Kathleen J. , Steshina Ekaterina Y. , Iskusnykh Igor Y. , Chizhikov Victor V. 
Published: April 2014

Significance
The contribution of cell fate misspecification to human brain disorders is poorly understood. The cerebellum, a major center of motor and sensory coordination, is frequently malformed in humans. During development it arises from dorsal hindbrain, but a long-standing question has been how the cerebellum is established along the dorsal–ventral axis of the neural tube. Here we identified the gene encoding pancreatic transcription factor PTF1A, which is inactivated in patients with cerebellar agenesis, as the first gene regulating the ventral limit of the cerebellum. We describe transformation of cerebellar neurons into more ventral extracerebellar fates as a novel mechanism of cerebellar agenesis. Our data provide some of the strongest evidence reported to date for a critical role of cell fate misspecification in a human brain developmental phenotype.
Toward a better understanding and quantification of methane emissions from shale gas development
Authors: Caulton Dana R. , Shepson Paul B. , Santoro Renee L. , Sparks Jed P. , Howarth Robert W. , Ingraffea Anthony R. , Cambaliza Maria O. L. , Sweeney Colm , Karion Anna , Davis Kenneth J. , Stirm Brian H. , Montzka Stephen A. , Miller Ben R. 
Published: April 2014

Significance
We identified a significant regional flux of methane over a large area of shale gas wells in southwestern Pennsylvania in the Marcellus formation and further identified several pads with high methane emissions. These shale gas pads were identified as in the drilling process, a preproduction stage not previously associated with high methane emissions. This work emphasizes the need for top-down identification and component level and event driven measurements of methane leaks to properly inventory the combined methane emissions of natural gas extraction and combustion to better define the impacts of our nation’s increasing reliance on natural gas to meet our energy needs.
Arthritogenic alphaviral infection perturbs osteoblast function and triggers pathologic bone loss
Authors: Chen Weiqiang , Foo Suan-Sin , Rulli Nestor E. , Taylor Adam , Sheng Kuo-Ching , Herrero Lara J. , Herring Belinda L. , Lidbury Brett A. , Li Rachel W. , Walsh Nicole C. , Sims Natalie A. , Smith Paul N. , Mahalingam Suresh 
Published: April 2014

Significance
Persistent polyarthritis, which occurs in 30–40% of alphavirus-infected patients, has been proposed to be caused by proinflammatory mediators such as IL-6. In the present study we investigated the susceptibility and response of primary human osteoblasts to Ross River virus (RRV) infection and determined whether infection could result in bone pathology. RRV infection of osteoblasts resulted in increased receptor activator of nuclear factor-kappaB ligand (RANKL) but decreased osteoprotegerin (OPG). We are the first to report that alphavirus infection results in bone loss in an established RRV murine model and that this bone loss is prevented by IL-6 inhibition. These findings reveal that RRV can disrupt bone homeostasis and that osteoblasts play an important role in alphavirus-induced arthritis by regulating IL-6 and contribute to bone loss by disrupting the RANKL/OPG balance.
Optogenetic control of chemokine receptor signal and T-cell migration
Authors: Xu Yuexin , Hyun Young-Min , Lim Kihong , Lee Hyunwook , Cummings Ryan J. , Gerber Scott A. , Bae Seyeon , Cho Thomas Yoonsang , Lord Edith M. , Kim Minsoo 
Published: April 2014

Significance
Precise regulation of chemokine signal is critical for directional migration of cells. In the study of complex cell behavior, it remains difficult to manipulate chemokine activity at precise times and places within living animals, and it is not possible to study different chemokine effects on defined cell types over a range of timescales. Furthermore, a given chemokine can activate multiple chemokine receptors and vice versa. Here we developed a photoactivatable chemokine receptor that can induce highly specific chemokine signals and guide cell migration toward the light stimulation. This work will advance our understanding of the cell migration process with a number of previously unidentified findings. Clinically, our photoactivatable chemokine receptor approach may have broad applications for adoptive cell transfer therapy.
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
Authors: Li Fay-Wei , Villarreal Juan Carlos , Kelly Steven , Rothfels Carl J. , Melkonian Michael , Frangedakis Eftychios , Ruhsam Markus , Sigel Erin M. , Der Joshua P. , Pittermann Jarmila , Burge Dylan O. , Pokorny Lisa , Larsson Anders , Chen Tao , Weststrand Stina , Thomas Philip , Carpenter Eric , Zhang Yong , Tian Zhijian , Chen Li , Yan Zhixiang , Zhu Ying , Sun Xiao , Wang Jun , Stevenson Dennis W. , Crandall-Stotler Barbara J. , Shaw A. Jonathan , Deyholos Michael K. , Soltis Douglas E. , Graham Sean W. , Windham Michael D. , Langdale Jane A. , Wong Gane Ka-Shu , Mathews Sarah , Pryer Kathleen M. 
Published: April 2014

SignificanceDespite being one of the oldest groups of land plants, the majority of living ferns resulted from a relatively recent diversification following the rise of angiosperms. To exploit fully the new habitats created by angiosperm-dominated ecosystems, ferns had to evolve novel adaptive strategies to cope with the low-light conditions exerted by the angiosperm canopy. Neochrome, an unconventional photoreceptor that allows ferns to “see the light” better, was likely part of the solution. Surprisingly, we discovered that fern neochrome was derived from a bryophyte lineage via horizontal gene transfer (HGT). This finding not only provides the first evidence that a plant-to-plant HGT can have a profound evolutionary impact but also has implications for the evolution of photosensory systems in plants.
Rapidly reversible redox transformation in nanophase manganese oxides at room temperature triggered by changes in hydration
Authors: Birkner Nancy , Navrotsky Alexandra 
Published: April 2014

SignificanceIn the present work, we find rapid and reversible transformations between nanoscale Mn2O3(more oxidized) and Mn3O4(more reduced) at room temperature as a function of changing hydration level. These phase transformations are controlled by a thermodynamic factor (difference in surface energy). Redox reactive Mn-oxide phases may be sensitive markers, on short time scales, of variations in water activity as well as oxygen fugacity in the local environment. Hydration-induced phase transformation has applications to geochemistry, planetary science, and technology.
MicroRNAs are critical regulators of tuberous sclerosis complex and mTORC1 activity in the size control of the
Xenopus
kidney
Authors: Romaker Daniel , Kumar Vikash , Cerqueira Débora M. , Cox Ryan M. , Wessely Oliver 
Published: April 2014

Significance
The kidney is an essential organ to remove metabolic waste products and retain essential nutrients. To successfully execute these processes, the kidney and its functional unit, the nephron, must be correctly proportioned. Surprisingly, little is known about the processes governing kidney size. Here, we use the amphibian pronephric kidney as a paradigm to study the molecular mechanisms regulating size control. We show for the first time, to our knowledge, that growth factors belonging to the Insulin growth factor family are critically important in establishing kidney size. Moreover, we demonstrate that the strength of the signal is dependent on the presence of small noncoding RNAs termed microRNAs. These provide robustness to size control and ascertain that the kidney develops properly.
Brf1 posttranscriptionally regulates pluripotency and differentiation responses downstream of Erk MAP kinase
Authors: Tan Frederick E. , Elowitz Michael B. 
Published: April 2014

Significance
Intercellular signaling pathways strongly regulate gene expression in uncommitted precursor stem cells, but the mechanisms through which these signaling pathways regulate gene targets often remain unclear. We address this question in mouse embryonic stem cells (mESCs) and highlight the importance of AU-rich element mRNA-binding proteins as regulatory intermediates of intercellular signaling. We show that the FGF/Erk MAP kinase signaling pathway strongly influences the expression of Brf1, a member of the Zfp36 protein family that is known to bind and destabilize its mRNA targets. Brf1 physically binds many pluripotency and differentiation-associated mRNAs. Moderate changes in its expression compromise self-renewal capacity and bias fate commitment, thus providing a posttranscriptional link between intercellular signaling activity and gene expression in mESCs.
Tumor microenvironment-based feed-forward regulation of NOS2 in breast cancer progression
Authors: Heinecke Julie L. , Ridnour Lisa A. , Cheng Robert Y. S. , Switzer Christopher H. , Lizardo Michael M. , Khanna Chand , Glynn Sharon A. , Hussain S. Perwez , Young Howard A. , Ambs Stefan , Wink David A. 
Published: April 2014

SignificanceMore than 92% of ER−breast cancer patients die with moderate to high NOS2. In this report, we show that tumor cell NOS2, through formation of a specific flux of NO, drives ER−disease to a more aggressive phenotype. Correlation between NOS2-related genes from patient cohorts, in vitro, and animal experiments show an inflammatory loop mediated by NOS2 that makes ER−breast cancer an aggressive disease.
PDGFRβ reverses EphB4 signaling in alveolar rhabdomyosarcoma
Authors: Aslam M. Imran , Abraham Jinu , Mansoor Atiya , Druker Brian J. , Tyner Jeffrey W. , Keller Charles 
Published: April 2014

Significance
Effective targeted therapies to complement already intensive chemotherapy are much needed for the childhood muscle cancer rhabdomyosarcoma, yet few targeted agents have been identified that improve long-term survival. In particular, the alveolar subtype of rhabdomyosarcoma accounts for disproportionate mortality. Herein, the receptor tyrosine kinase EphB4 is identified as a potential two-way switch for alveolar rhabdomyosarcoma. Whereas the typical EphB4 ligand, EphrinB2, drives tumor cells toward apoptosis, the interaction between EphB4 and another receptor tyrosine kinase, PDGFRβ, drives tumors to proliferate in the presence of the PDGFRβ ligand, PDGF-BB. The Food and Drug Administration-approved dual EphB4-PDGFRβ inhibitor, dasatinib, is found to have significant preclinical activity, which is clinically relevant because EphB4 and PDGFRβ are independent poor prognostic factors in this childhood disease.
Secretion of von Willebrand factor by endothelial cells links sodium to hypercoagulability and thrombosis
Authors: Dmitrieva Natalia I. , Burg Maurice B. 
Published: April 2014

Significance
Cardiovascular thrombotic events are a leading cause of mortality and morbidity worldwide. Hypercoagulability increases the risk of thrombosis. This study shows that elevated sodium concentration stimulates endothelial production of a key initiator of the clotting cascade, von Willebrand factor, leading to increased coagulation and thrombogenesis. In everyday life, increases in blood sodium often occur as the result of insufficient drinking, excessive water loss, or high salt intake. Therefore, our results indicate that water and salt intake are modifiable factors affecting coagulability and risk of thrombosis. In clinical practice, sustained elevation of plasma sodium is a part of widely used hypertonic saline therapy. Our results suggest that monitoring of coagulation during the therapy might be beneficial to prevent thrombotic complications.
Spatial and Temporal Dynamics in Brook Trout Density: Implications for Population Monitoring
Authors: Wagner Tyler , Deweber Jefferson T. , Detar Jason , Kristine David , Sweka John A. 
Published: April 2014

Abstract
Many potential stressors to aquatic environments operate over large spatial scales, prompting the need to assess and monitor both site-specific and regional dynamics of fish populations. We used hierarchical Bayesian models to evaluate the spatial and temporal variability in density and capture probability of age-1 and older Brook Trout Salvelinus fontinalis from three-pass removal data collected at 291 sites over a 37-year time period (1975–2011) in Pennsylvania streams. There was high between-year variability in density, with annual posterior means ranging from 2.1 to 10.2 fish/100 m2; however, there was no significant long-term linear trend. Brook Trout density was positively correlated with elevation and negatively correlated with percent developed land use in the network catchment. Probability of capture did not vary substantially across sites or years but was negatively correlated with mean stream width. Because of the low spatiotemporal variation in capture probability and a strong correlation between first-pass CPUE (catch/min) and three-pass removal density estimates, the use of an abundance index based on first-pass CPUE could represent a cost-effective alternative to conducting multiple-pass removal sampling for some Brook Trout monitoring and assessment objectives. Single-pass indices may be particularly relevant for monitoring objectives that do not require precise site-specific estimates, such as regional monitoring programs that are designed to detect long-term linear trends in density.
Received April 22, 2013; accepted September 18, 2013
Economic Impact of a Recreational Striped Bass Fishery
Authors: Lothrop Ryan L. , Hanson Terry R. , Sammons Steven M. , Hite Diane , Maceina Michael J. 
Published: April 2014

Abstract
Striped Bass Morone saxatilis are stocked in numerous southeastern U.S. reservoirs to enhance angling opportunities. Many of these reservoirs are near rural communities, where expenditures by anglers provide economic benefits. This study estimated the value of the recreational Striped Bass fishery at Lewis Smith Lake, Alabama, to the local counties surrounding the lake and the state of Alabama using surveys that collected information on angler expenditures; further, we calculated generated tax revenues and estimated the demand and consumer surplus for the fishery. Annual Striped Bass angler effort represented 23% of the total effort with 53,000 h (SE, 3,800 h) or approximately 10,200 trips. Catch and harvest effort for Striped Bass anglers was 0.40 fish/h and 0.18 fish/h, respectively. Annual aggregated expenditures by Striped Bass anglers were US$0.7 million, with 84% of expenditures occurring within the local counties. A cost-benefit analysis determined that for every $1 spent in stocking costs, $2 were generated in taxes for local county road maintenance, education, and general funds and $7 were generated for statewide tax-funded programs; thus, Striped Bass stocking costs were justified through the increase in resulting angler expenditures. A count model using a negative binomial distribution was used to estimate demand. Demand estimation showed that an increase in travel cost to the site and an increase in party size decreased the number of visits an angler would make to fish for Striped Bass at Lewis Smith Lake. Consumer surplus was estimated to be $0.6 million for the Striped Bass fishery and $77 per angler visit. In conclusion, this work has shown that the economic impact assessment for a fishery should be taken into account when total fishery management plans are being evaluated.
Received January 26, 2013; accepted November 4, 2013
Application of the Genetic Mark–Recapture Technique for Run Size Estimation of Yukon River Chinook Salmon
Authors: Hamazaki Toshihide , DeCovich Nick 
Published: April 2014

Abstract
We present an application of the genetic mark–recapture technique to estimate salmon run size in a large river. Application of this technique requires modifications to estimation methodology. Under a typical Lincoln–Petersen mark–recapture estimation of salmon run size (N = M/p), individual fish are captured and marked (M) in the lower river and are recaptured (m) at escapement (E: the number of fish reached spawning ground) monitoring sites selected upriver where the proportion of marked individuals (p = m/E) is estimated. In this genetic mark–recapture technique, the marked individuals are not captured and recaptured, but rather the naturally distinctive genetic (marked) population is captured and recaptured. Genetically, the lower river population is a mixture of multiple genetic stocks, whereas the upriver escapement population consists of a single genetic stock. Hence, the mark–recapture experiment (N = M/pm) is reversed. The proportion of “marked” genetic stock (pm) is estimated in the lower river, and size of the “marked” stock in the lower river (M) is estimated by summing its upriver escapement (Em) and harvest (Cm) between the lower and upper portions of river (M = Em+Cm). The harvest is calculated as a product of total upriver harvest (C) and the proportion of the “marked” stock (pcm) in the harvest (Cm = C·pcm). Further, when the proportion of multiple genetic stocks (pk) is identified, stock-specific run size (Nk = N·pk), escapement (Ek = Nk−Ck, where Ck = C ·pck), and exploitation rate (Exk = Ck /Nk) can also be estimated, which provides substantially more information than does the conventional approach. We illustrate an application of this technique for estimating run size of Chinook Salmon Oncorhynchus tshawytscha in the Yukon River, Alaska.
Received June 6, 2013; accepted November 20, 2013
Evaluating the Effectiveness of the Pickering Nuclear Generating Station Fish Diversion System Barrier Net
Authors: Patrick Paul H. , Mason Elaine , Powell Jennifer , Milne Scott , Poulton J. S. 
Published: April 2014

Abstract
Barrier nets can be an effective alternative for reducing impingement mortality of fish at power plant intakes. In 2010, a paired, split-beam hydroacoustic method was used as the primary assessment tool for comparing relative fish density between the lake (“outside”) and station (“inside”) side of the Pickering Nuclear Generating Station fish diversion system (FDS) barrier net while it was in place. Behavioral information was also collected using a DIDSON acoustic camera and underwater video camera to determine fish responses to the FDS. Verification monitoring was completed using conventional gill netting. The DIDSON provided useful and valuable information on relative fish densities, relative school sizes, and behavior of fish as individuals, small groups, or schools on both the outside and inside of the FDS, as well as general behavior of fish approaching the FDS. There was no evidence of passage through the net based on DIDSON evaluation; however, fish passage occurred when the FDS net was considered to be in a degraded condition (from biofouling or storm events, or both) and passage occurred over the net, not through it. Analysis of the hydroacoustic data based on the weighted average biomass indicated that FDS effectiveness was 75, 98, and 100% for the spring, summer, and fall periods, respectively, and 98% for the three seasons combined. The summer and fall estimates were based on net performance under optimal net-deployment conditions and if the net degrades, effectiveness is reduced significantly as observed in the spring data. Our study results were supported by impingement monitoring at the station whereby impingement biomass was reduced by greater than 80% for each of the first 3 years after installation compared with before installation of the barrier net. Overall, the FDS was demonstrated to offer significant fish protection from potential impingement at the Pickering Nuclear Generating Station.
Received July 21, 2013; accepted December 6, 2013
Influence of Age-1 Conspecifics, Sediment Type, Dissolved Oxygen, and the Deepwater Horizon Oil Spill on Recruitment of Age-0 Red Snapper in the Northeast Gulf of Mexico during 2010 and 2011
Authors: Szedlmayer Stephen T. , Mudrak Peter A. 
Published: April 2014

Abstract
The Deepwater Horizon oil spill was one of the largest oil spills in U.S. history. The timing of this spill coincided with peaks in spawning and recruitment of Red Snapper Lutjanus campechanus and may have led to reduced recruitment or to year-class failure. Artificial recruitment reefs were deployed in 2010 (n = 30) and 2011 (n = 30) to measure Red Snapper recruitment off the coast of Alabama at four sites (three inshore sites, 13 km south: west, center, and east sites, each 30 km apart; and one offshore site, 25 km south). Substantial age-0 Red Snapper recruitment (density range = 0–34.5 fish/m3) occurred in 2010, with higher densities on inshore reefs than on offshore reefs. Age-0 Red Snapper recruitment was again observed in 2011 (density range = 0–108.5 fish/m3) along with age-1 Red Snapper (density range = 0–78.9 fish/m3) from the 2010 year-class. There was a negative correlation between the densities of age-0 and age-1 Red Snapper, indicating that older Red Snapper excluded younger fish from the reefs. Higher fractions of silt in the substrate at the west site compared with the center and east sites were associated with higher densities of age-0 Red Snapper, but the effects of sediment type were less important than exposure to hypoxic conditions at the west site in late August 2011 (dissolved oxygen fell to concentrations as low as 0.4 mg/L), which caused an almost complete loss of fish. The abundances of age-0 and age-1 Red Snapper in 2010 and 2011 provide evidence that the oil spill did not result in a year-class failure and that the most important variables affecting age-0 Red Snapper abundances were age-1 Red Snapper presence and dissolved oxygen concentration.
Received August 23, 2013; accepted December 19, 2013
Stabilization of Moloney murine leukemia virus reverse transcriptase by site-directed mutagenesis of surface residue Val433
Authors: Konishi Atsushi , Ma Xiaochen , Yasukawa Kiyoshi 
Published: April 2014

Abstract
After thermal incubation at 48 °C for 10 min, single variants of Moloney murine leukemia virus reverse transcriptase, V433R and V433K in which a surface hydrophobic residue, Val433, was mutated, retained 55% of initial reverse transcription activity, while the wild-type enzyme retained 17%. After thermal incubation at 50 °C for 10 min, multiple variants D108R/E286R/V433R and D108R/E286R/V433R/D524A, in which Val433→Arg was combined with stabilizing mutations we identified previously, Asp108→Arg and Glu286→Arg, and RNase H activity-eliminating mutation Asp524→Ala, retained 70% of initial activity, exhibiting higher stability than V433R or V433K.
A Simple Cultivation Method for Chesapeake Bay Ulva intestinalis for Algal Seed Stock
Authors: Li Ji , Kangas Patrick , Terlizzi Daniel E 
Published: April 2014

Abstract
Ulva spp. are valuable economically as edible green algae, and they also have environmental value in biofiltration. Cultivation of Ulva spp., in fact macroalgal cultivation generally, is limited in the USA. As part of a larger effort to develop macroalgal cultivation in the Chesapeake Bay for nutrient remediation, we developed a “seeding” method for Chesapeake Bay isolates of U. intestinalis. Ulva intestinalis thalli were induced to produce and release free-swimming zoospores by desiccation and rehydration. The zoospores then were induced to settle on the nylon nets by dark incubation. Rhizoids from the zoospores formed on the nets, and the nets became covered with green filaments which developed tubular thalli. Nets with thalli can be incubated in indoors or deployed in natural water to generate production-scale cultivation of U. intestinalis in the Chesapeake Bay. Such cultivation can be integrated with the growing oyster aquaculture industry in the Chesapeake Bay area, U. intestinalis serving as biofilters to remove oyster wastes and increase economic benefit through water quality enhancement and nutrient credits, and as an aquaculture product in their own right.