bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanding the role of the splicing USB1 gene from Poikiloderma with Neutropenia to acquired myeloid neoplasms
Authors: Negri Gloria , Crescenzi Barbara , Colombo Elisa Adele , Fontana Laura , Barba Gianluca , Arcioni Francesco , Gervasini Cristina , Mecucci Cristina , Larizza Lidia 
Published: August 2015

SummaryGermline mutations of the U6 biogenesis 1 (USB1) gene underlie Poikiloderma with Neutropenia (PN), a rare autosomal recessive genodermatosis conferring an increased risk of myelodysplasia. Recent evidence highlights a key role of USB1 protein in the splicing process, but nothing is known about USB1 alterations in acquired myelodysplastic syndromes, even though mutations in the spliceosome machinery represent an ubiquitous pathway in leukaemogenesis. By molecular cytogenetics and direct sequencing, we searched for USB1 deletions/duplications and point mutations in 141 bone marrow DNA samples from patients with myelodysplastic syndromes (n = 126), myelodysplastic/myeloproliferative neoplasms (n = 12) and acute myeloid leukaemia (n = 3). Three unreported variants, two in USB1 5'UTR (c.‐83G>T and c.‐66A>G), one in IVS3 (c.450‐68dupT) and one (<1%) in IVS4 (c.587+21A>G/rs200924980) were detected. The germline nature could be proved for the c.‐66A>G, but remains undefined for c.‐83G>T and c.450‐68dupT. Matched controls analysis did not reveal either 5' UTR variants in 290 chromosomes and Real‐time polymerase chain reaction showed a slight reduction in bone marrow RNA levels of the patient with c.‐66A>G. No USB1 rearrangements were detected by interphase fluorescence in situ hybridization. This pilot investigation on USB1 expanded the variations repertoire of this gene, identifying three novel sequence variants, the role of which need further investigations in myeloid malignancies.
Reducing Risk for Substance Use by Economically Disadvantaged Young Men: Positive Family Environments and Pathways to Educational Attainment
Authors: Martin Monica J. , Conger Rand D. , Sitnick Stephanie L. , Masarik April S. , Forbes Erika E. , Shaw Daniel S. 
Published: August 2015

Using prospective, longitudinal data spanning 10 years (age = 10–20) from a study of 295 economically disadvantaged males, the current investigation evaluated a developmental model that links early family environment and later educational aspirations, extracurricular activities, and educational attainment to substance use in early adulthood. The results indicate that a positive family environment during adolescence (low family conflict, high family warmth, and effective child management) predicted educational involvements during adolescence that promoted educational attainment during early adulthood. Finally, higher levels of educational attainment were associated with less substance use in early adulthood, even after controlling for adolescent substance use. These findings suggest that positive parenting promotes educational achievements that increase resilience to substance use for economically disadvantaged males.
Judging adaptive management practices of U.S. agencies
Authors: Fischman Robert L. , Ruhl J.B. 
Published: August 2015

AbstractAll U.S. federal agencies administering environmental laws purport to practice adaptive management (AM), but little is known about how they actually implement this conservation tool. A gap between the theory and practice of AM is revealed in judicial decisions reviewing agency adaptive management plans. We analyzed all U.S. federal court opinions published through 1 January 2015 to identify the agency AM practices courts found most deficient. The shortcomings included lack of clear objectives and processes, monitoring thresholds, and defined actions triggered by thresholds. This trio of agency shortcuts around critical, iterative steps characterizes what we call AM‐lite. Passive AM differs from active AM in its relative lack of management interventions through experimental strategies. In contrast, AM‐lite is a distinctive form of passive AM that fails to provide for the iterative steps necessary to learn from management. Courts have developed a sophisticated understanding of AM and often offer instructive rather than merely critical opinions. The role of the judiciary is limited by agency discretion under U.S. administrative law. But courts have overturned some agency AM‐lite practices and insisted on more rigorous analyses to ensure that the promised benefits of structured learning and fine‐tuned management have a reasonable likelihood of occurring. Nonetheless, there remains a mismatch in U.S. administrative law between the flexibility demanded by adaptive management and the legal objectives of transparency, public participation, and finality.
Toward a Metacognitive Account of Cognitive Offloading
Authors: Dunn Timothy L. , Risko Evan F. 
Published: August 2015

AbstractIndividuals frequently make use of the body and environment when engaged in a cognitive task. For example, individuals will often spontaneously physically rotate when faced with rotated objects, such as an array of words, to putatively offload the performance costs associated with stimulus rotation. We looked to further examine this idea by independently manipulating the costs associated with both word rotation and array frame rotation. Surprisingly, we found that individuals’ patterns of spontaneous physical rotations did not follow patterns of performance costs or benefits associated with being physically rotated, findings difficult to reconcile with existing theories of strategy selection involving external resources. Individuals’ subjective ratings of perceived benefits, rather, provided an excellent match to the patterns of physical rotations, suggesting that the critical variable when deciding on‐the‐fly whether to incorporate an external resource is the participant's metacognitive beliefs regarding expected performance or the effort required for each approach (i.e., internal vs. internal + external). Implications for metacognition's future in theories of cognitive offloading are discussed.
Age at stroke onset influences the clinical outcome and health‐related quality of life in pediatric ischemic stroke survivors
Authors: Ghotra Satvinder K , Johnson Jeffrey A , Qiu Weiyu , Newton Amanda , Rasmussen Carmen , Yager Jerome Y 
Published: August 2015

AimStroke in children occurs across different phases of brain development. Age at onset may affect outcome and health‐related quality of life (HRQL). We evaluated the influence of age at stroke onset on the long‐term neurological outcomes and HRQL of pediatric stroke survivors.MethodChildren with ischemic stroke were recruited into three groups according to their age at onset of stroke (presumed perinatal, neonatal, and childhood). Neurological outcomes were assessed using the Pediatric Stroke Recovery and Recurrence Questionnaire. HRQL was evaluated using proxy report versions (2–18y) of the Pediatric Quality of Life Inventory (PedsQL 4.0). A χ2/Fisher's exact test and multivariable logistic regression analysis was performed for the neurological outcomes. HRQL scores from the different age groups were compared using linear regression.ResultsNinety participants (presumed perinatal stroke, n=31; neonatal stroke, n=36; childhood stroke, n=23) were enrolled. Median age at the onset of stroke was 0.5 days and 3.7 years in neonatal and childhood participants respectively. Of the three groups, participants with presumed perinatal stroke demonstrated the worst global (p<0.002) and motor (p<0.001) outcomes and the lowest level of independence in daily activities (p<0.001). Parents reported the best global outcome and overall HRQL (p=0.007) after neonatal stroke.InterpretationThe age at stroke onset has important implications regarding long‐term clinical outcomes and HRQL for survivors. Individuals with presumed perinatal stroke should be considered at high‐risk for poor outcomes.
Human Schwann‐like cells derived from adipose‐derived mesenchymal stem cells rapidly de‐differentiate in the absence of stimulating medium
Authors: Faroni Alessandro , Smith Richard J. P. , Lu Li , Reid Adam J. 
Published: August 2015

AbstractFinding a viable cell‐based therapy to address peripheral nerve injury holds promise for enhancing the currently suboptimal microsurgical approaches to peripheral nerve repair. Autologous nerve grafting is the current gold standard for surgical repair of nerve gaps; however, this causes donor nerve morbidity in the patient, and the results remain unsatisfactory. Transplanting autologous Schwann cells (SCs) results in similar morbidity, as well as limited cell numbers and restricted potential for expansion in vitro. Adipose‐derived stem cells (ASCs), ‘differentiated’ towards an SC‐like phenotype in vitro (dASCs), have been presented as an alternative to SC therapies. The differentiation protocol stimulates ASCs to mimic the SC phenotype; however, the efficacy of dASCs in nerve repair is not yet convincing, and the practicality of the SC‐like phenotype is unproven. Here, we examined the stability of dASCs by withdrawing differentiation medium for 72 h after the full 18‐day differentiation protocol, and measuring changes in morphology, gene expression, and protein levels. Withdrawal of differentiation medium from dASCs resulted in a rapid reversion to stem cell‐like characteristics. Quantitative real‐time polymerase chain reaction and enzyme‐linked immunosorbent assay analyses demonstrated a significant reduction in gene and protein expression of growth factors that were expressed at high levels following ‘differentiation’. Therefore, we question the relevance of differentiation to an SC‐like phenotype, as withdrawal of differentiation medium, a model of transplantation into an injured nerve, results in rapid reversion of the dASC phenotype to stem cell‐like characteristics. Further investigation into the differentiation process and the response of dASCs to an injured environment must be undertaken prior to the use of dASCs in peripheral nerve repair therapies.
Terrestrial origin of bacterial communities in complex boreal freshwater networks
Authors: Ruiz‐González Clara , Niño‐García Juan Pablo , del Giorgio Paul A. 
Published: August 2015

AbstractBacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal aquatic network by determining the taxonomic composition of bacterial communities along the entire terrestrial/aquatic continuum, including soil and soilwaters, headwater streams, large rivers and lakes. We show that the network metacommunity has a directional spatial structure driven by a common terrestrial origin of aquatic communities, which are numerically dominated by taxa recruited from soils. Local community assembly is driven by variations along the hydrological continuum in the balance between mass effects and species sorting of terrestrial taxa, and seems further influenced by priority effects related to the spatial sequence of entry of soil bacteria into the network.
Climate change‐associated tree mortality increases without decreasing water availability
Authors: Luo Yong , Chen Han Y. H. 
Published: August 2015

AbstractTemporal increases of tree mortality have been observed in regions where global warming has decreased long‐term water availability and/or induced droughts. However, temporal decreases in water availability are not a global phenomenon. Understanding how water deficit‐free forests respond to the recent effects of climate change is paramount towards a full appreciation of the impacts of climate change on global forests. Here, we reveal temporally increasing tree mortality across all study species over the last three decades in the central boreal forests of Canada, where long‐term water availability has increased without apparent climate change‐associated drought. In addition, we find that the effects of conspecific tree‐to‐tree competition have intensified temporally as a mechanism for the increased mortality of shade‐intolerant tree species. Our results suggest that the consequences of climate change on tree mortality are more profound than previously thought.
Gene flow and natural selection shape spatial patterns of genes in tree populations: implications for evolutionary processes and applications
Authors: Sork Victoria L. 
Published: August 2015

AbstractA central question in evolutionary biology is how gene flow and natural selection shape geographic patterns of genotypic and phenotypic variation. My overall research program has pursued this question in tree populations through complementary lines of inquiry. First, through studies of contemporary pollen and seed movement, I have studied how limited gene movement creates fine‐scale genetic structure, while long‐distance gene flow promotes connectivity. My collaborators and I have provided new tools to study these processes at a landscape scale as well as statistical tests to determine whether changes in landscape conditions or dispersal vectors affect gene movement. Second, my research on spatial patterns of genetic variation has investigated the interacting impacts of geography and climate on gene flow and selection. Third, using next‐generation genomic tools, I am now studying genetic variation on the landscape to find initial evidence of climate‐associated local adaptation and epigenetic variation to explore its role in plant response to the climate. By integrating these separate lines of inquiry, this research provides specific insight into real‐world mechanisms shaping evolution in tree populations and potential impacts of landscape transformation and climate change on these populations, with the prospective goal of contributing to their management and conservation.
Real‐time analysis of conformational control in electron transfer reactions of human cytochrome P450 reductase with cytochrome c
Authors: Hedison Tobias M. , Hay Sam , Scrutton Nigel S. 
Published: August 2015

Protein domain dynamics and electron transfer chemistry are often associated, but real‐time analysis of domain motion in enzyme‐catalysed reactions and the elucidation of mechanistic schemes that relate these motions to the reaction chemistry are major challenges for biological catalysis research. Previously we suggested that reduction of human cytochrome P450 reductase with the reducing coenzyme NADPH is accompanied by major structural re‐orientation of the FMN‐ and FAD‐binding domains through an inferred dynamic cycle of ‘open’ and ‘closed’ conformations of the enzyme (PLoS Biol, 2011, e1001222). However, these studies were restricted to stopped‐flow/FRET analysis of the reductive half‐reaction, and were compromised by fluorescence quenching of the acceptor by the flavin cofactors. Here we have improved the design of the FRET system, by using dye pairs with near‐IR fluorescence, and extended studies on human cytochrome P450 reductase to the oxidative half‐reaction using a double‐mixing stopped‐flow assay, thereby analysing in real‐time conformational dynamics throughout the complete catalytic cycle. We correlate redox changes accompanying the reaction chemistry with protein dynamic changes observed by FRET, and show that redox chemistry drives a major re‐orientation of the protein domains in both the reductive and oxidative half‐reactions. Our studies using the tractable (soluble) surrogate electron acceptor cytochrome c provide a framework for analysing mechanisms of electron transfer in the endoplasmic reticulum between cytochrome P450 reductase and cognate P450 enzymes. More generally, our work emphasizes the importance of protein dynamics in intra‐ and inter‐protein electron transfer, and establishes methodology for real‐time analysis of structural changes throughout the catalytic cycle of complex redox proteins.
Northerly shift of warm‐water copepods in the western subarctic North Pacific: Continuous Plankton Recorder samples (2001–2013)
Authors: Yoshiki Tomoko M. , Chiba Sanae , Sasaki Yuka , Sugisaki Hiroya , Ichikawa Tadafumi , Batten Sonia 
Published: August 2015

AbstractSpatial and temporal variation in copepod community structure, abundance, distribution and biodiversity were examined in the western subarctic North Pacific (40–53°N, 144–173°E) during 2001–2013. Continuous Plankton Recorder (CPR) observational data during the summer season (June and July) were analyzed. The latitudinal distribution of warm‐water species in June shifted northward after 2011 while no apparent latitudinal shift of cold‐water and other species was observed. Species number and the Shannon–Wiener biodiversity index (H′) in June tended to increase in the northern area after 2011. The warm‐water species abundance and center latitude of warm‐water distribution were positively correlated with sea surface temperature (SST) across sampling locations, whereas no significant correlations with SST were observed for cold‐water species or other species. Warm SSTs in June after 2011 appeared to cause the northward shift of warm‐water species distribution, which in turn contributed to the higher biodiversity in the northern area. This study demonstrated the rapid response of warm‐water species to warm SST variation, whereas cold‐water and other species did not exhibit such clear responses. These findings indicate that the response of copepods to environmental changes differs among copepod species, highlighting the importance of investigating lower trophic levels to the species level to evaluate individual species’ responses to climate change.
Sequential molecularly targeted drug therapy including axitinib for a patient with end‐stage renal failure and metastatic renal cell carcinoma
Authors: Nishida Hayato , Fukuhara Hiroki , Yamagishi Atsushi , Sakurai Toshihiko , Shibasaki Tomohiro , Kawazoe Hisashi , Kato Tomoyuki , Tomita Yoshihiko 
Published: August 2015

AbstractA 62‐year‐old male patient with end‐stage renal disease and metastatic renal cell carcinoma (RCC) was referred to our hospital. Sequential targeted therapy consisting of sorafenib, sunitinib, and everolimus was administered, but the patient's disease gradually progressed. Axitinib was subsequently administered at a decreased dose of 6 mg/day for 2 weeks, after which the dose was escalated to 10 mg/day. Axitinib therapy was maintained for a total of 6 months without severe adverse effects. Sequential molecularly targeted drug therapy including axitinib, with careful monitoring, is one possible treatment option for patients with metastatic RCC with renal impairment.
One-year case fatality rate following stroke in the Mashhad Stroke Incidence Study: a population-based study of stroke in Iran
Authors: Shoeibi Ali , Salehi Maryam , Thrift Amanda G. , Kapral Moira K. , Farzadfard Mohammad Taghi , Azarpazhooh Amir , Layegh Parvaneh , Hashemi Peyman , Amiri Amin , Mokhber Naghmeh , Hassankhani Bahare , Azarpazhooh Mahmoud Reza 
Published: August 2015

Background In developing countries, there are few comprehensive studies of mortality following stroke. Aims and/or hypothesis We aimed to determine the one-year case fatality rate following stroke and to identify factors associated with death in a population-based stroke incidence study in Iran. Methods Six hundred eighty-four patients who had suffered a stroke between November 21, 2006, and November 20, 2007, and were recruited to the Mashhad Stroke Incidence Study were followed up at one-year. Most patients were seen in an outpatient visit. When patients had died, a verbal autopsy was conducted by telephone with the next of kin. Results A total of 226 (34.3%) patients died during the first year following stroke. The cumulative one-year case fatality rate was 30.6% following ischemic stroke and 53.0% following hemorrhagic stroke (55.8% after intracerebral hemorrhage and 35.7% after subarachnoid hemorrhage). The majority of these deaths occurred in the first 28 days after stroke (17.7% with ischemic and 43.0% with hemorrhagic stroke). Factors associated with greater mortality at one-year (excluding those who died during the first week) were hemorrhagic stroke [hazard ratio (HR) 3.99; 95% confidence interval 1.90-8.37], age (HR 1.05; 95% confidence interval 1.03-1.08), previous transient ischemic attack (HR 2.45; 95% confidence interval 1.00-5.99), and National Institutes of Health Stroke Scale on admission (HR 1.14; 95% confidence interval 1.10-1.17). Conclusion Despite the younger age of stroke occurrence in Iran, the one-year case fatality rate following stroke is similar to that reported in developed countries.
Water Diplomacy: A Negotiated Approach to Manage Complex Water Problems
Authors: Islam Shafiqul , Repella Amanda C. 
Published: August 2015

AbstractMany water management decisions have evolved from addressing simple problems, such as accessing water near its source, to complex problems of managing and allocating water in the face of multiple and competing demands in the natural, societal and political domains. The Water Diplomacy Framework (WDF) is emerging as an alternative to traditional techno‐ or values‐focused approaches to water management. The WDF is an approach that diagnoses water problems, identifies intervention points, and proposes sustainable resolutions that incorporate diverse viewpoints and uncertainty as well as changing and competing demands. As such, WDF rests upon diverse forms of contextual inquiry of and intervention in complex water problems, with negotiation functioning as the fulcrum of diagnosis and intervention. Several case studies from this volume are used to highlight the utility of this framework for understanding and managing complexity, uncertainty and contingency when addressing complex water problems. We invite the reflective water community to identify and analyze water case studies ‐ from different places, settings, and scales ‐ that will contribute to our collective effort of developing actionable approaches to manage complex water problems in our AquaPedia database.
Bringing the Elephant into the Room: Integrating Risk into Interdisciplinary Water Programs
Authors: Read Laura , Kuhl Laura 
Published: August 2015

AbstractProblems that require risk management are usually cross‐disciplinary in nature, which makes it difficult to educate students and professionals on common language, skills, and strategies. Recognition of the interdisciplinary nature of many water challenges in terms of quality, allocation, future supply, infrastructure, damages, etc. has led to the establishment of interdisciplinary graduate water programs. Motivated by experience in an interdisciplinary water program at Tufts University, this paper argues that explicit coverage of the subject of risk is an important component of an interdisciplinary water training program, and that understanding risk should be a core competency of a water professional. The literature on water education is reviewed, particularly regarding the core competencies of an interdisciplinary water professional. Existing interdisciplinary water graduate programs are also surveyed to identify if, and how, risk features in their program descriptions or curriculums. Our analysis found that risk was not mentioned as a core competency or key issue in any of the literature on interdisciplinary water education or training, and featured in only a few program descriptions or curriculums. Based on this analysis, we conclude that there is a significant need to address risk more centrally and explicitly in interdisciplinary water programs.