bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propagule limitation and competition with nitrogen fixers limit conifer colonization during primary succession
Authors: Titus Jonathan H. , Bishop John G. 
Published: January 2014

AbstractQuestionsIs conifer colonization on primary successional sites limited by propagule availability or environmental filters? How do nitrogen‐fixing pioneer species (Lupinus lepidus and Alnus viridis) affect conifer emergence and establishment?LocationMount St. Helens, Washington State, USA.MethodsWe planted seeds of Pseudotsuga menziesii in four habitat types – barrens, young and old Lupinus patches and Alnus thickets – in a partial factorial cross with shade and soil disturbance treatments in 2002, 2003 and 2004, and monitored survival through 2006. We compared experimental results with surveys of natural establishment in 2007 and 2010.ResultsPseudotsuga menziesii emergence and survival were highest in barren and young Lupinus sites and low in old Lupinus and Alnus patches, but varied greatly among cohorts. In barrens, nearly 50% of germinated seedlings of the 2002 cohort survived year 1 and 25% through year 4, compared to 10% (year 1) and ~0% (to year 4) survival in other habitats. Survival rates were lower in subsequent cohorts. Emergence and establishment were enhanced by shade and initial soil disturbance in barren sites and young Lupinus patches. Soil moisture was higher in barren and young Lupinus habitats. Post‐experiment surveys indicated older trees were six times more abundant on sites with old Lupinus patches and Alnus thickets, consistent with earlier colonization at those sites driven by seed availability, but total tree density increased more rapidly in sites with barren and young Lupinus habitats, surpassing older sites by 2010, as predicted from experimental results.ConclusionIncreased seedling survival in barren and young Lupinus sites and under shade was attributable to decreased competition for soil moisture in those sites, possibly combined with apparent competition in old Lupinus and Alnus sites via seed and seedling predators. Overall, high emergence and survival rates in low‐density habitats suggest that P. menziesii colonization is strongly propagule limited, and that survival of seeds that successfully arrive and germinate is more strongly affected by competition in early succession than by soil N. This conclusion is supported by evidence for decreased recruitment over time in old Lupinus patches and Alnus thickets and accelerating recruitment in areas with less developed vegetation.
Teachable Moments, Learnable Moments: Medical Rounds as a Paradigm for Education
Authors: de Luise Vincent P. 
Published: January 2014

ABSTRACTThe medical profession has for almost a century employed various types of “Rounds” as pedagogical tools to engage physicians, physicians‐in‐training, and their health care teams in the clinical diagnosis and treatment of patients. More recently, this validated paradigm of medical rounds (MR) has been extended to the field of education, where it is being used as an effective strategy for administrators to better understand their own domain. There are four distinct types of MR which can be further analyzed to find commonalities and parallels with the domain of education. The four types of MR are (1) Morning Rounds, (2) Chart Rounds, (3) Grand Rounds, and (4) Ongoing Collaborations—each have unique pedagogical characteristics and serve different functions. They are, however, unified by common threads of dynamic and interpersonal interactions wherein teacher (physician) and learner (physician‐in‐training) share learning and fluidly exchange roles in the pedagogy. MR models supplant the now outmoded theory of the “empty vessel” and corroborate the concept of the teaching brain. A formal analysis of MR underscores its ongoing utility in education both for its pedagogical innovations and for the Interactive and inherently human attributes that are required between teacher and learner for its efficacy.
Evolutionary Perspectives on Mind, Brain, and Education
Authors: Howard‐Jones Paul A. 
Published: January 2014

ABSTRACTUnderstanding about human origins informs our understanding of what it means to be human. It is reasonable, therefore, to consider that an evolutionary perspective can provide insight into the nature and processes of human learning and education. This article reviews how ideas about evolution have influenced educational thinking in the past. It then considers how understanding of brain development and function is helping to inspire “new thinking” about evolution. The review converges on a range of benefits that may arise from the inclusion of evolutionary concepts within the field of mind, brain, and education. These benefits include scrutiny of evolutionary neuromyth, reconsideration of the cultural and political status of education, insight into notions of individual difference, and help with stimulating and directing research efforts aimed at improving educational outcomes.
An unusual repressor controls the expression of a crucial nicotine‐degrading gene cluster in Pseudomonas putida S16
Authors: Wang Lijuan , Tang Hongzhi , Yu Hao , Yao Yuxiang , Xu Ping 
Published: January 2014

SummaryTranscriptional factors that contain helix–turn–helix (HTH) DNA‐binding domains are widespread in bacteria for regulating gene expression on demand, and function as homodimers that bind a palindromic DNA segment. Here, we show that an HTH‐containing transcriptional regulator, NicR2, in Pseudomonas putida S16 plays a critical role in controlling the expression of a crucial gene cluster (nic2) in nicotine degradation, and NicR2 binds DNA in a manner different from most other DNA‐binding proteins that use HTHs for recognition. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting indicate that NicR2 directly interacts with a 28 bp inverted repeat (IR) in the nic2 promoter region. Using EMSA with synthetic DNA fragments, we found that both NicR2 dimer and tetramer can bind to the half‐site of the IR. This is confirmed independently by biolayer interferometry and cross‐linking experiments. Our results indicate that two NicR2 dimers bind to the IR cooperatively through protein–protein interactions, with each dimer binding the half‐site of the IR. Thus, NicR2 appears to be an unusual regulator, which uses HTH for recognition and displays the binding characteristics of some regulators that use β‐sheets. The transcriptional regulation of nicotine degradation in Pseudomonas highlights a new level of complexity in prokaryotic transcriptional regulation.
Efficacy of deep brain stimulation in an adolescent patient with DYT11 myoclonus‐dystonia
Authors: Kimura Yasuyoshi , Mihara Masahito , Kawarai Toshitaka , Kishima Haruhiko , Sakai Norio , Takahashi Masanori P. , Mochizuki Hideki 
Published: January 2014

AbstractMyoclonus‐dystonia is a movement disorder characterized by myoclonic jerks and dystonia. We herein report the case of an 18‐year‐old Japanese male patient with DYT11 myoclonus‐dystonia who developed myoclonic jerks at 2 years‐of‐age. He harbored a novel heterozygous mutation in the major responsible gene, ε‐sarcoglycan. As medication was ineffective and the myoclonus had become disabling, deep brain stimulation of the bilateral globus pallidus internus was carried out. After surgery, his symptoms showed overt improvement. Although reports of deep brain stimulation treatment in children or adolescents with myoclonus‐dystonia are scarce, the treatment should be considered when symptoms, particularly myoclonus, become refractory, sustained and disabling.
Drought stress provokes the down‐regulation of methionine and ethylene biosynthesis pathways in Medicago truncatula roots and nodules
Authors: LARRAINZAR ESTÍBALIZ , MOLENAAR JOHANNA A. , WIENKOOP STEFANIE , GIL‐QUINTANA ERENA , ALIBERT BÉNÉDICTE , LIMAMI ANIS M. , ARRESE‐IGOR CESAR , GONZÁLEZ ESTHER M. 
Published: January 2014

AbstractSymbiotic nitrogen fixation is one of the first physiological processes inhibited in legume plants under water‐deficit conditions. Despite the progress made in the last decades, the molecular mechanisms behind this regulation are not fully understood yet. Recent proteomic work carried out in the model legume Medicago truncatula provided the first indications of a possible involvement of nodule methionine (Met) biosynthesis and related pathways in response to water‐deficit conditions. To better understand this involvement, the drought‐induced changes in expression and content of enzymes involved in the biosynthesis of Met, S‐adenosyl‐L‐methionine (SAM) and ethylene in M. truncatula root and nodules were analyzed using targeted approaches. Nitrogen‐fixing plants were subjected to a progressive water deficit and a subsequent recovery period. Besides the physiological characterization of the plants, the content of total sulphur, sulphate and main S‐containing metabolites was measured. Results presented here show that S availability is not a limiting factor in the drought‐induced decline of nitrogen fixation rates in M. truncatula plants and provide evidences for a down‐regulation of the Met and ethylene biosynthesis pathways in roots and nodules in response to water‐deficit conditions.
Herbivore‐induced volatile emission in black poplar: regulation and role in attracting herbivore enemies
Authors: CLAVIJO MCCORMICK ANDREA , IRMISCH SANDRA , REINECKE ANDREAS , BOECKLER G. ANDREAS , VEIT DANIEL , REICHELT MICHAEL , HANSSON BILL S. , GERSHENZON JONATHAN , KÖLLNER TOBIAS G. , UNSICKER SYBILLE B. 
Published: January 2014

AbstractAfter herbivory, plants release volatile organic compounds from damaged foliage as well as from nearby undamaged leaves that attract herbivore enemies. Little is known about what controls the volatile emission differences between damaged and undamaged tissues and how these affect the orientation of herbivore enemies. We investigated volatile emission from damaged and adjacent undamaged foliage of black poplar (Populus nigra) after herbivory by gypsy moth (Lymantria dispar) caterpillars and determined the compounds mediating the attraction of the gypsy moth parasitoid Glyptapanteles liparidis (Braconidae). Female parasitoids were more attracted to gypsy moth‐damaged leaves than to adjacent non‐damaged leaves. The most characteristic volatiles of damaged versus neighbouring undamaged leaves included terpenes, green leaf volatiles and nitrogen‐containing compounds, such as aldoximes and nitriles. Electrophysiological recordings and olfactometer bioassays demonstrated the importance of nitrogenous volatiles. Under field conditions, parasitic Hymenoptera were more attracted to traps baited with these substances than most other compounds. The differences in volatile emission profiles between damaged and undamaged foliage appear to be regulated by jasmonate signalling and the local activation of volatile biosynthesis. We conclude that characteristic volatiles from damaged black poplar foliage are essential cues enabling parasitoids to find their hosts.
Diaporthe sclerotioides exhibits no host specificity among cucurbit species
Authors: Shishido M. , Ohashi T. , Momma N. 
Published: January 2014

Plant–fungal specificity between cucurbitaceous crops and Diaporthe sclerotioides, the causal agent of black root rot, was studied using cucumbers (Cucumis sativa), melons (Cucumis melo), pumpkins (Cucurbita maxima), watermelons (Citrullus lanatus) and bottlegourd (Lagenaria siceraria var. gourda). Twelve D. sclerotioides isolates from these cucurbit species were cross‐inoculated. The virulence of the isolates was evaluated as the area under the disease progress curve (AUDPC). All cucurbit species were susceptible to each isolate, but AUDPCs were significantly different among the hosts, with the order of greatest to least being melon, cucumber, watermelon, bottlegourd and finally, pumpkin. The infectiveness of isolates was assessed as the quantity of D. sclerotioides DNA detected in the hypocotyls of seedlings 2 weeks after inoculation using a real‐time PCR protocol. The fungal DNA quantities varied among the species in the same order as the AUDPCs. Whilst there were statistically significant correlations between the virulence and infectiveness of D. sclerotioides isolates in cucumbers, melons and bottlegourds, their coefficients of determination were not high (r2 < 0·6). Orthogonal contrasts indicated no specificity in either the fungal virulence or infectiveness between D. sclerotioides isolates and the cucurbit hosts from which these isolates originated. Thus, although the degree of host susceptibility to D. sclerotioides varies among cucurbit species, the absence of specificity to the host species in either virulence or infectiveness suggests the pathogen may spread via various cucurbit crops, irrespective of their original host species.
High prevalence of malignancy in HIV‐positive patients with mediastinal lymphadenopathy: A study in the era of antiretroviral therapy
Authors: Alçada Joana , Taylor Magali N. , Shaw Penny J. , Janes Sam M. , Navani Neal , Miller Robert F. 
Published: January 2014

AbstractBackground and objectiveMediastinal lymphadenopathy (MLN) in human immunodeficiency virus (HIV) infection has a wide spectrum of aetiologies with different prognoses and treatments. The decision to pursue a histopathological diagnosis represents a clinical challenge as patients present with non‐specific symptoms. This study aimed to determine the aetiology and predictive factors of MLN in a cohort of HIV‐infected patients in the combination antiretroviral therapy (cART) era.MethodsSingle‐centre retrospective cohort study of 217 consecutive HIV‐infected patients who underwent computed tomography (CT) of the chest between January 2004 and December 2009. Fifty‐two patients were identified to have MLN (>10 mm in short axis). CT images were re‐reviewed by an independent radiologist blinded to the clinical information. Final diagnoses of MLN were obtained from clinical records. Multivariate analysis was performed to identify predictors of aetiology of MLN.ResultsSeventeen patients (33%) had a diagnosis of malignancy. Consolidation on CT was associated with a reduced likelihood of malignancy odds ratio (OR) 0.03 (95% confidence interval 0.002–0.422), and larger lymph nodes were associated with an increase in the odds of malignancy (OR 2.89; 95% confidence interval 1.24–6.71). CD4 count was found not to be a predictor of aetiology of MLN.ConclusionsIn the era of combination cART, opportunistic infections and malignancy remain to be the frequent causes of MLN in HIV‐positive patients, but the prevalence of non‐HIV related malignancy has increased compared with previous studies. Although certain findings are predictors of non‐malignant disease, pathological diagnosis of MLN in HIV‐positive patients should be pursued whenever possible.
Unravelling the influence of water depth and wave energy on the facies diversity of shelf carbonates
Authors: Purkis Sam J. , Rowlands Gwilym P. , Kerr Jeremy M. 
Published: January 2014

AbstractCarbonate sequence stratigraphy is founded on the principle that changes in relative sea‐level are recorded in the rock record by the accumulation of sediment with relative water depth‐dependent attributes. While at the scale of a shelf to basin transect, facies clearly arrange by water depth, the relation blurs for depths <40 m, the most vigorous zone of carbonate production. The reason for this change in behaviour is two‐fold. Firstly, in shallow water, the intrinsic processes of storm and wave reworking influence the seabed through submarine erosion and sediment redistribution. Secondly, facies diversity tends to be greater in shallow water than deep water because of a greater diversity in grain producers. Remote sensing imagery, field observations and hydrodynamic models for two reef‐rimmed shore‐attached carbonate platforms in the Red Sea show neither water depth nor energy regime to be reliable indicators of facies type when considered in isolation. Considered together, however, the predictive power of the two variables rises significantly. The results demonstrate it to be an oversimplification to assume a direct link between palaeo‐water depth and depositional diversity of subtidal lithofacies, while highlighting the importance of hydrodynamics in directing the accumulation of carbonate sediments in the shallow photic zone. While the size distributions of facies extents in the two focus areas follow power laws, no direct relation between the lateral continuity of the facies belts and water depth or wave height is reported. The work is relevant for the interpretation of metre‐scale subtidal carbonate cycles throughout the geological record by demonstrating how caution must be applied when inferring palaeo‐water depths from depositional facies.
Including the Tukey Mean‐Difference (Bland–Altman) Plot in a Statistics Course
Authors: Kozak Marcin , Wnuk Agnieszka 
Published: January 2014

SummaryThe Tukey mean‐difference plot, also called the Bland–Altman plot, is a recognized graphical tool in the exploration of biometrical data. We show that this technique deserves a place on an introductory statistics course by encouraging students to think about the kind of graph they wish to create, rather than just creating the default graph for the variables types they have. This graphical technique is described, and two examples are presented: one dealing with official agricultural data of Poland and the other one with an experiment on anorexia. Our opinion is that the plot is so easy and yet efficient in visualizing paired data that it should be included in statistics courses to support understanding and interpretation of data and their analysis. © 2014 The Authors. Teaching Statistics © 2014 Teaching Statistics Trust
Reduction in red blood cell transfusion associated with engagement of the ordering physician
Authors: Tavares Maria M. , Diquattro Pamela J. , Sweeney Joseph D. 
Published: January 2014

BackgroundData on red blood cell (RBC) transfusion in the United States show variation in practice and overprescribing or overdosing is considered to be prevalent. Education or restrictive interventions could modify practice.Study Design and MethodsRBC transfusion and mortality rates were recorded in a single institution over a 15‐year period. The first 3 years were used as a baseline. Education measures were used to influence practice for 3 years followed by a 9‐year period when questionable RBC orders in nonbleeding inpatients resulted in prospective physician notification for potential modification. Physician notification was done by blood bank technologists with transfusion medicine physician support, if needed. Pretransfusion hemoglobin levels of more than 9 g/dL were recommended for cancellation and levels between 8 and 9 g/dL advised for a single unit, if 2 or more units were requested. RBC transfusion rates were described as inpatient units per 1000 discharges to allow for interyear comparison.ResultsA downward trend in RBC transfusion was noted for the intervention period. Comparison of the baseline period with the past 3 years of the intervention period showed an approximate 33% decrease, which was highly significant (508 ± 66 vs. 341 ± 32, p < 0.01). Inpatient mortality rates declined over this period.ConclusionPhysician education in appropriate transfusion practice is desirable but may not greatly impact RBC use. Engagement of physicians who prescribe RBCs that appear inappropriate for indication or dose was associated with a significant decline in RBC use without evidence of a change in mortality.
A Wearable Gait Monitor and Terrain Prediction System
Authors: Sullivan Christopher , DeBartolo Elizabeth , Lamkin-Kennard Kathleen 
Published: January 2014

Nearly one million people in 2009 were discharged from the hospital with stroke as the primary diagnosis [1]. One of the many lasting side effects of a stroke can be foot drop, or an inability to dorsiflex the foot. In order to remedy this, many people wear an ankle-foot orthotic (AFO) post-stroke. Interviews with AFO users revealed that they frequently have difficulty walking on stairs and ramps, because the AFO limits the plantarflexion that is natural in navigating those ground types. An active AFO that adapts to changing ground terrain would provide a more natural gait pattern for these individuals, if it could be designed to respond appropriately to upcoming terrain. In order to respond to terrain, the device must first identify the terrain.
This paper outlines a system [2] that simultaneously predicts the type of terrain a user is approaching as they walk, and captures information about that user’s walking activity. Such a system can be used as the control system for an active orthotic or prosthetic device. Additionally, this system can be used as a stand-alone gait and terrain monitor to aid in rehabilitation monitoring in between patient visits with a clinician.
A Hemi Fontan Operation Performed by an Engineer: Considerations on Virtual Surgery
Authors: Biglino Giovanni , Kung Ethan , Dorfman Adam , Taylor Andrew M. , Bove Edward , Marsden Alison , Hsia Tain-Yen , Schievano Silvia 
Published: January 2014

Single ventricle circulation, characterized at birth by a rudimentary or absent left or right ventricle, presents a challenging and life-threatening physiological scenario. Surgical palliation aims to restore the balance between systemic and pulmonary blood flow and is staged, each of the three stages presenting the surgeon with different options:
- Stage 1 (Norwood procedure) involves different types of shunting to source pulmonary blood flow, or recently a hybrid approach [1];
- Stage 2 can involve a superior cavopulmonary connection (Glenn operation) or patching between the right atrium and the pulmonary arteries (Hemi Fontan operation [2]);
- Stage 3 involves a total cavopulmonary connection with extracardiac conduit or lateral tunnel, or with novel alternatives such as the Y-graft [3].
CRISPR-Cas Functional Module Exchange in Escherichia coli
Authors: Almendros Cristóbal , Mojica Francisco J. M. , Díez-Villaseñor César , Guzmán Noemí M. , García-Martínez Jesús 
Published: January 2014

ABSTRACT

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (
cas
) genes constitute the CRISPR-Cas systems found in the
Bacteria
and
Archaea
domains. At least in some strains they provide an efficient barrier against transmissible genetic elements such as plasmids and viruses. Two CRISPR-Cas systems have been identified in
Escherichia coli
, pertaining to subtypes I-E (
cas
-E genes) and I-F (
cas
-F genes), respectively. In order to unveil the evolutionary dynamics of such systems, we analyzed the sequence variations in the CRISPR-Cas loci of a collection of 131
E. coli
strains. Our results show that the strain grouping inferred from these CRISPR data slightly differs from the phylogeny of the species, suggesting the occurrence of recombinational events between CRISPR arrays. Moreover, we determined that the primary
cas
-E genes of
E. coli
were altogether replaced with a substantially different variant in a minor group of strains that include K-12. Insertion elements play an important role in this variability. This result underlines the interchange capacity of CRISPR-Cas constituents and hints that at least some functional aspects documented for the K-12 system may not apply to the vast majority of
E. coli
strains.

IMPORTANCE
Escherichia coli
is a model microorganism for the study of diverse aspects such as microbial evolution and is a component of the human gut flora that may have a direct impact in everyday life. This work was undertaken with the purpose of elucidating the evolutionary pathways that have led to the present situation of its significantly different CRISPR-Cas subtypes (I-E and I-F) in several strains of
E. coli
. In doing so, this information offers a novel and wider understanding of the variety and relevance of these regions within the species. Therefore, this knowledge may provide clues helping researchers better understand these systems for typing purposes and make predictions of their behavior in strains that, depending on their particular genetic dotation, would result in different levels of immunity to foreign genetic elements.