bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing riparian zone impacts on water and sediment movement: a new approach
Authors: Keesstra S.D. , Kondrlova E. , Czajka A. , Seeger M. , Maroulis J. 
Published: April 2015

AbstractThe state of river channels and their riparian zones in terms of geomorphology and vegetation has a significant effect on water and sediment transport in headwater catchments. High roughness in natural rivers due to vegetation and geomorphological attributes generate drag on flowing water. This drag will slow water discharge, which in turn influences the sediment dynamics of the flow. The impacts of changes in the management of rivers and their riparian zone (either by catchment managers or river restoration plans) impacts both up- as well as downstream reaches, and should be assessed holistically prior to the implementation of these plans.To assess the river's current state as well as any possible changes in geomorphology and vegetation in and around the river, effective approaches to characterise the river are needed. In this paper, we present a practical approach for making detailed surveys of relevant river attributes. This methodology has the benefit of being both detailed – describing river depth, width, channel morphology, erosive features and vegetation types – but also being practical in terms of time management. This is accomplished by identifying and describing characteristic benchmark reaches (typical sites) in detail against which the remainder of the river course can be rated. Using this method, a large river stretch can be assessed in a relatively short period while still retrieving high quality data for the total river course. In this way, models with high data requirements for assessing the condition of a river course, can be parameterised without major investments on field surveys.In a small headwater catchment (23 km2) in southwestern Poland, this field methodology was used to retrieve data to run an existing model (HEC-GeoRAS) which can assess the impact of changes in the riparian and channel vegetation and channel management on sedimentation processes and stream flow velocity. This model determines the impact of channel morphology and in-channel and riparian vegetation on stream flow and sediment transport. Using four return periods of flooding (2, 10, 20 and 100 years), two opposing channel management / morphology scenarios were run; a natural channel and a fully regulated channel. The modelling results show an increase in the effect of riparian vegetation / geomorphology with an increase in return period of the modeled peak discharge. More natural channel form and increased roughness reduces the stream flow velocity due to increasing drag from flow obstructions (vegetation and channel morphological features). The higher the flood water stage, the greater the drag due to vegetation on the floodplains of natural river reaches compared to channelised sections. Slower flow rates have an impact on sediment mobilisation and transport in the river.
Natural Disasters: The Role of the Veterinarian
Authors: Moore Roscoe M. , Kaczmarek Ronald G. , Davis Yvette M. 
Published: April 2015

AbstractNatural disasters create a multiplicity of problems and hazards ranging from outbreaks of infectious disease to animal control problems. By virtue of their unique training and clinical skills, there is considerable potential for veterinarians to fulfill major roles in disaster intervention. The potential role of the veterinarian features a number of important tasks before, during, and after a natural disaster. Some of the tasks include: 1) resolution of problems common to many natural disasters; 2) control of disease vectors; 3) control of disease transmission; 4) herd management; 5) animal health care; 6) search and rescue; 7) animal control; 8) maintenance of medical supplies; 9) information dissemination; 10) disaster assessment; and 11) pre-disaster planning.
A Virtual Reality Scenario for All Seasons:The Virtual Classroom
Authors: Rizzo Albert A. , Bowerly Todd , Buckwalter J. Galen , Klimchuk Dean , Mitura Roman , Parsons Thomas D. 
Published: April 2015

ABSTRACTTreatment and rehabilitation of the cognitive, psychological, and motor sequelae of central nervous system dysfunction often relies on assessment instruments to inform diagnosis and to track changes in clinical status. Typically, these assessments employ paper-and-pencil psychometrics, hands-on analog/computer tests, and rating of behavior within the context of real-world functional environments. Virtual reality offers the option to produce and distribute identical “standard” simulation environments in which performance can be measured and rehabilitated. Within such digital scenarios, normative data can be accumulated for performance comparisons needed for assessment/diagnosis and for treatment/rehabilitation purposes. In this manner, reusable archetypic virtual environments constructed for one purpose can also be applied for applications addressing other clinical targets. This article will provide a review of such a retooling approach using a virtual classroom simulation that was originally developed as a controlled stimulus environment in which attention processes could be systematically assessed in children with attention-deficit/hyperactivity disorder. This system is now being applied to other clinical targets including the development of tests that address other cognitive functions, eye movement under distraction conditions, social anxiety disorder, and the creation of an earthquake safety training application for children with developmental and learning disabilities.
Response of Prochlorococcus to varying CO2:O2 ratios
Authors: Bagby Sarah C , Chisholm Sallie W 
Published: April 2015

Abstract
Carbon fixation has a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus—the most abundant phototroph in the oligotrophic oceans—the carbon-concentrating mechanism is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. Thus, we examined how CO2:O2 gas balance influenced growth and chlorophyll fluorescence in Prochlorococcus strain MED4. Under O2 limitation, per-cell chlorophyll fluorescence fell at all CO2 levels, but still permitted substantial growth at moderate and high CO2. Under CO2 limitation, we observed little growth at any O2 level, although per-cell chlorophyll fluorescence fell less sharply when O2 was available. We explored this pattern further by monitoring genome-wide transcription in cells shocked with acute limitation of CO2, O2 or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, both CO2 limitation conditions initially evoked a transcriptional response that resembled the pattern previously seen in high-light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen has a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.
Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris
Authors: Zhou Aifen , Hillesland Kristina L , He Zhili , Schackwitz Wendy , Tu Qichao , Zane Grant M , Ma Qiao , Qu Yuanyuan , Stahl David A , Wall Judy D , Hazen Terry C , Fields Matthew W , Arkin Adam P , Zhou Jizhong 
Published: April 2015

Abstract
To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution
Authors: Martijn Joran , Schulz Frederik , Zaremba-Niedzwiedzka Katarzyna , Viklund Johan , Stepanauskas Ramunas , Andersson Siv G E , Horn Matthias , Guy Lionel , Ettema Thijs J G 
Published: April 2015

Abstract
The bacterial family Rickettsiaceae includes a group of well-known etiological agents of many human and vertebrate diseases, including epidemic typhus-causing pathogen Rickettsia prowazekii. Owing to their medical relevance, rickettsiae have attracted a great deal of attention and their host-pathogen interactions have been thoroughly investigated. All known members display obligate intracellular lifestyles, and the best-studied genera, Rickettsia and Orientia, include species that are hosted by terrestrial arthropods. Their obligate intracellular lifestyle and host adaptation is reflected in the small size of their genomes, a general feature shared with all other families of the Rickettsiales. Yet, despite that the Rickettsiaceae and other Rickettsiales families have been extensively studied for decades, many details of the origin and evolution of their obligate host-association remain elusive. Here we report the discovery and single-cell sequencing of ‘Candidatus Arcanobacter lacustris’, a rare environmental alphaproteobacterium that was sampled from Damariscotta Lake that represents a deeply rooting sister lineage of the Rickettsiaceae. Intriguingly, phylogenomic and comparative analysis of the partial ‘Candidatus Arcanobacter lacustris’ genome revealed the presence chemotaxis genes and vertically inherited flagellar genes, a novelty in sequenced Rickettsiaceae, as well as several host-associated features. This finding suggests that the ancestor of the Rickettsiaceae might have had a facultative intracellular lifestyle. Our study underlines the efficacy of single-cell genomics for studying microbial diversity and evolution in general, and for rare microbial cells in particular.
Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis
Authors: Miao Ji , Ling Alisha V. , Manthena Praveen V. , Gearing Mary E. , Graham Mark J. , Crooke Rosanne M. , Croce Kevin J. , Esquejo Ryan M. , Clish Clary B. ,   Morbid Obesity Study Group, Torrecilla Esther , Vázquez Gumersindo Fernández , Rubio Miguel A. , Cabrerizo Lucio , Barabash Ana , Pernaute Andrés Sánchez , Torres Antonio J. , Vicent David , Biddinger Sudha B. 
Published: April 2015

AbstractDespite the well-documented association between insulin resistance and cardiovascular disease, the key targets of insulin relevant to the development of cardiovascular disease are not known. Here, using non-biased profiling methods, we identify the enzyme flavin-containing monooxygenase 3 (Fmo3) to be a target of insulin. FMO3 produces trimethylamine N-oxide (TMAO), which has recently been suggested to promote atherosclerosis in mice and humans. We show that FMO3 is suppressed by insulin in vitro, increased in obese/insulin resistant male mice and increased in obese/insulin-resistant humans. Knockdown of FMO3 in insulin-resistant mice suppresses FoxO1, a central node for metabolic control, and entirely prevents the development of hyperglycaemia, hyperlipidemia and atherosclerosis. Taken together, these data indicate that FMO3 is required for FoxO1 expression and the development of metabolic dysfunction.
Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site
Authors: Calviño Fabiola R. , Kharde Satyavati , Ori Alessandro , Hendricks Astrid , Wild Klemens , Kressler Dieter , Bange Gert , Hurt Ed , Beck Martin , Sinning Irmgard 
Published: April 2015

AbstractDuring 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1–RpL5-N–RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1–RpL5–RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP.
The effects of Rho-associated kinase inhibitor Y-27632 on primary human corneal endothelial cells propagated using a dual media approach
Authors: Peh Gary S. L. , Adnan Khadijah , George Benjamin L. , Ang Heng-Pei , Seah Xin-Yi , Tan Donald T. , Mehta Jodhbir S. 
Published: April 2015

AbstractThe global shortage of donor corneas has garnered extensive interest in the development of graft alternatives suitable for endothelial keratoplasty using cultivated primary human corneal endothelial cells (CECs). We have recently described a dual media approach for the propagation of human CECs. In this work, we characterize the effects of a Rho-kinase inhibitor Y-27632 on the cultivation of CECs propagated using the dual media culture system. Seventy donor corneas deemed unsuitable for transplantation were procured for this study. We assessed the use of Y-27632 for its effect at each stage of the cell culture process, specifically for cell attachment, cell proliferation and during both regular passaging and cryopreservation. Lastly, comparison of donor-matched CEC-cultures expanded with or without Y-27632 was also performed. Our results showed that Y-27632 significantly improved the attachment and proliferation of primary CECs. A non-significant pro-survival effect was detected during regular cellular passage when CECs were pre-treated with Y-27632, an effect that became more evident during cryopreservation. Our study showed that the inclusion of Y-27632 was beneficial for the propagation of primary CECs expanded via the dual media approach and was able to increase overall cell yield by between 1.96 to 3.36 fold.
Allergic fetal priming leads to developmental, behavioral and neurobiological changes in mice
Authors: Schwartzer J J , Careaga M , Chang C , Onore C E , Ashwood P 
Published: April 2015

AbstractThe state of the mother’s immune system during pregnancy has an important role in fetal development and disruptions in the balance of this system are associated with a range of neurologic, neuropsychiatric and neurodevelopmental disorders. Epidemiological and clinical reports reveal various clues that suggest a possible association between developmental neuropsychiatric disorders and family history of immune system dysfunction. Over the past three decades, analogous increases have been reported in both the incidence of neurodevelopmental disorders and immune-related disorders, particularly allergy and asthma, raising the question of whether allergic asthma and characteristics of various neurodevelopmental disorders share common causal links. We used a mouse model of maternal allergic asthma to test this novel hypothesis that early fetal priming with an allergenic exposure during gestation produces behavioral deficits in offspring. Mothers were primed with an exposure to ovalbumin (OVA) before pregnancy, then exposed to either aerosolized OVA or vehicle during gestation. Both male and female mice born to mothers exposed to aerosolized OVA during gestation exhibited altered developmental trajectories in weight and length, decreased sociability and increased marble-burying behavior. Moreover, offspring of OVA-exposed mothers were observed to have increased serotonin transporter protein levels in the cortex. These data demonstrate that behavioral and neurobiological effects can be elicited following early fetal priming with maternal allergic asthma and provide support that maternal allergic asthma may, in some cases, be a contributing factor to neurodevelopmental disorders.
In vivo characterization of chronic traumatic encephalopathy using [F-18]FDDNP PET brain imaging
Authors: Barrio Jorge R. , Small Gary W. , Wong Koon-Pong , Huang Sung-Cheng , Liu Jie , Merrill David A. , Giza Christopher C. , Fitzsimmons Robert P. , Omalu Bennet , Bailes Julian , Kepe Vladimir 
Published: April 2015

Significance
Mild traumatic brain injuries are frequent events in the general population and are associated with a severe neurodegenerative disease, chronic traumatic encephalopathy (CTE). This disease is characterized by abnormal accumulation of protein aggregates, primarily tau proteins, which accumulate in brain areas responsible for mood, fear, stress, and cognition. There is no definitive clinical diagnosis of CTE at the present time, and this new work shows how a tau-sensitive brain imaging agent, [F-18]FDDNP, may be able to detect the disease in living people with varying degrees of symptoms. Early detection would facilitate the most effective management strategies and provide a baseline to measure the effectiveness of treatments.
Structural basis for substrate specificity of an amino acid ABC transporter
Authors: Yu Jie , Ge Jingpeng , Heuveling Johanna , Schneider Erwin , Yang Maojun 
Published: April 2015

Significance
Here we report the crystal structures of an amino acid ATP-binding cassette (ABC) importer either in its apo form or in complex with substrates (Arg, His) and/or ATPs. Interestingly, each transmembrane domain has a negatively charged pocket, allowing amino acids carrying positively charged groups to pass through. Functional analyses of the transporter in proteoliposomes indicate its capability to undergo substrate-dependent conformational changes resulting in stimulated ATPase activity. Taken together, we identified a previously undefined substrate binding mode of ABC transporters and shed light on the mechanism underlying how ABC transporters select and translocate their substrates.
Female peers in small work groups enhance women's motivation, verbal participation, and career aspirations in engineering
Authors: Dasgupta Nilanjana , Scircle Melissa McManus , Hunsinger Matthew 
Published: April 2015

Significance
Advances in science, technology, engineering, and mathematics are critical to the American economy and require a robust workforce. The scarcity of women in this workforce is a well-recognized problem, but data-driven solutions to this problem are less common. We provide experimental evidence showing that gender composition of small groups in engineering has a substantial impact on undergraduate women’s persistence. Women participate more actively in engineering groups when members are mostly female vs. mostly male or in equal gender proportions. Women feel less anxious in female-majority groups vs. minority groups, especially as first-year students. Gender-parity groups are less effective than female-majority groups in promoting verbal participation. Female peers protect women’s confidence and engineering career aspirations despite masculine stereotypes about engineering.
fMRI of the rod scotoma elucidates cortical rod pathways and implications for lesion measurements
Authors: Barton Brian , Brewer Alyssa A. 
Published: April 2015

Significance
We use functional MRI to investigate the cortical effects on V1, V2, V3, hV4, and VO-1 when humans’ eyes have adapted to low-light vision. We show that populations of neurons with receptive fields interacting with the central rod scotoma are silenced because of lack of stimulation, shift their locations ectopically, and/or scale their sizes in some maps because of partial stimulation when the receptive fields overlap with the rod scotoma. These same effects have been cited as hallmarks of long-term reorganization, but our results show that these effects can be the result of the normal short-term adaptation of the visual system. In contrast, we observe no cortical differences between general rod and cone input other than rod scotoma effects.
Asphyxia-activated corticocardiac signaling accelerates onset of cardiac arrest
Authors: Li Duan , Mabrouk Omar S. , Liu Tiecheng , Tian Fangyun , Xu Gang , Rengifo Santiago , Choi Sarah J. , Mathur Abhay , Crooks Charles P. , Kennedy Robert T. , Wang Michael M. , Ghanbari Hamid , Borjigin Jimo 
Published: April 2015

Significance
How does the heart of a healthy individual cease to function within just a few minutes in the absence of oxygen? We addressed this issue by simultaneously examining the heart and the brain in animal models during asphyxiation and found that asphyxia markedly stimulates neurophysiological and neurochemical activities of the brain. Furthermore, previously unidentified corticocardiac coupling showed increased intensity as the heart deteriorated. Blocking efferent input to the heart markedly increased survival time of both the heart and the brain. The results show that targeting the brain’s outflow may be an effective strategy to delay the death of the heart and the brain from asphyxia.
Effect of kumquat (Fortunella crassifolia) pericarp on natural killer cell activity in vitro and in vivo
Authors: Nagahama Kiyoko , Eto Nozomu , Shimojo Tomofumi , Kondoh Tomomi , Nakahara Keiko , Sakakibara Yoichi , Fukui Keiichi , Suiko Masahito 
Published: April 2015

Abstract
Natural killer (NK) cells play a key role in innate immune defense against infectious disease and cancer. A reduction of NK activity is likely to be associated with increased risk of these types of disease. In this study, we investigate the activation potential of kumquat pericarp acetone fraction (KP-AF) on NK cells. It is shown to significantly increase IFN-γ production and NK cytotoxic activity in human KHYG-1 NK cells. Moreover, oral administration of KP-AF significantly improves both suppressed plasma IFN-γ levels and NK cytotoxic activity per splenocyte in restraint-stressed mice. These results indicate that raw kumquat pericarp activates NK cells in vitro and in vivo. To identify the active constituents, we also examined IFN-γ production on KHYG-1 cells by the predicted active components. Only β-cryptoxanthin increased IFN-γ production, suggesting that NK cell activation effects of KP-AF may be caused by carotenoids such as β-cryptoxanthin.