bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Ability of Tiger Muskellunge to Eradicate Brook Trout in Idaho Alpine Lakes
Authors: Koenig Martin K. , Meyer Kevin A. , Kozfkay Joseph R. , DuPont Joseph M. , Schriever Edward B. 
Published: July 2015

Abstract
In western North America, nonnative Brook Trout Salvelinus fontinalis in alpine lakes threaten the persistence of native trout and often offer limited sport fishing opportunity as they are prone to stunting. Stocking tiger muskellunge (Northern Pike Esox lucius × Muskellunge E. masquinongy), which are reproductively sterile, may be an option to eradicate Brook Trout in some alpine lakes. We used floating gill nets to survey 17 alpine lake Brook Trout populations, then stocked 13 lakes with tiger muskellunge, with four additional lakes serving as controls. Tiger muskellunge were stocked at a mean TL of 317 mm and a density of 40 fish/ha. Brook Trout were resampled for 4 or 5 years after stocking to evaluate changes in Brook Trout TL and CPUE (fish/net-night). Declines in CPUE were substantial for both treatment and control lakes but were significantly greater in treatment lakes. Mean Brook Trout CPUE in treatment lakes declined from 23.1 fish/net-night to 2.3 fish/net-night 5 years after stocking tiger muskellunge, whereas in control lakes, CPUE declined from 25.5 fish/net-night to 7.8 fish/net-night 5 years later. Complete eradication appeared to occur in two lakes within 2 years, and in two more lakes by year 5. In lakes where tiger muskellunge were stocked, the proportion of Brook Trout ≥250 mm TL in the catch increased significantly in years 1, 2, and 4 after stocking (compared with prestocking data), whereas no increase occurred in control lakes. Tiger muskellunge were most successful in reducing Brook Trout CPUE in lakes with no inlets or outlets, while elevation and lake area may also have played a role. Our results suggest tiger muskellunge can improve the size structure and potentially eradicate Brook Trout populations from some alpine lakes. However, we recommend combining any tiger muskellunge stocking with other conventional removal methods to increase the likelihood of successful eradication.
Received October 27, 2014; accepted March 22, 2015
Climate Change Adaptation and Restoration of Western Trout Streams: Opportunities and Strategies
Authors: Williams Jack E. , Neville Helen M. , Haak Amy L. , Colyer Warren T. , Wenger Seth J. , Bradshaw Stan 
Published: July 2015

Abstract
Climate change is contributing to the severity and rate of stream degradation by changing the timing of peak flows, altering flow regimes, creating more frequent and intense disturbances, and increasing stream temperatures. Herein we describe three case studies of trout stream adaptation that address existing and climate-driven causes of degradation through habitat restoration. The case studies vary in geography and complexity, but all include restoration efforts intended to address multiple causes of stream degradation and improve the resilience of these streams to floods, droughts, and wildfires. Four elements of successful climate adaptation projects emerge: (1) habitat assessments that help drive project location and design, (2) projects that directly address climate change impacts and increase habitat resilience, (3) projects that combine to achieve watershed-scale impacts, and (4) projects that include sufficient monitoring to determine their effectiveness. We describe solutions to common challenges in conducting climate change adaptation, including how to balance scientific assessments with opportunities when choosing projects, how smaller projects can be aggregated to achieve watershed-scale benefits, and how citizen science efforts can augment monitoring programs.
El cambio climático está contribuyendo a incrementar la severidad y la tasa de degradación de los ríos a través de la alteración en la estacionalidad del flujo máximo, modificación del régimen de flujos, generación de perturbaciones más frecuentes e intensas e incremento de la temperatura de los ríos. Aquí se describen tres casos de estudio de la adaptación de ríos en donde habita la trucha, en los que se abordan las causas de la degradación que son provocadas por el cambio climático, mediante la restauración del hábitat. Los casos de estudio varían en cuanto a ubicación geográfica y complejidad, pero en todos se contemplan esfuerzos de restauración enfocados a abordar múltiples causas de degradación de ríos y mejoramiento de la resiliencia de éstos ante inundaciones, sequías e incendios naturales. Se consideraron cuatro elementos para lograr una adaptación exitosa al cambio climático: 1) evaluaciones del hábitat que ayuden a diseñar y establecer dónde llevar a cabo los proyectos; 2) proyectos que aborden directamente los impactos del cambio climático y el incremento en la resiliencia del hábitat; 3) proyectos que, al combinarse, logren resultados a nivel de cuenca hidrológica; y 4) proyectos que incluyan un monitoreo suficiente como para que se pueda determinar su efectividad. También se describen soluciones a los clásicos retos que implica la adaptación al cambio climático, incluyendo cómo encontrar un balance entre evaluaciones científicas y elección de proyectos, cómo se pueden integrar varios proyectos pequeños para conseguir beneficios a escala de cuenca y cómo se puede incrementar el monitoreo mediante esfuerzos ciudadanos.
Application of a ℤ₃-orbifold construction to the lattice vertex operator algebras associated to Niemeier lattices
Authors: Sagaki Daisuke , Shimakura Hiroki 
Published: July 2015

By applying Miyamoto’s

Z

3

\mathbb {Z}_{3}

-orbifold construction to the lattice vertex operator algebras associated to Niemeier lattices and their automorphisms of order

3
3

, we construct holomorphic vertex operator algebras of central charge

24
24

whose Lie algebras of the weight one spaces are of types

A

2
,
3

6

A_{2,3}^6

,

E

6
,
3

G

2
,
1

3

E_{6,3}G_{2,1}^{3}

, and

A

5
,
3

D

4
,
3

A

1
,
1

3

A_{5,3}D_{4,3}A_{1,1}^{3}

, which correspond to No. 6, No. 17, and No. 32 on Schellekens’ list, respectively.
ProFET: Feature engineering captures high-level protein functions
Authors: Ofer Dan , Linial Michal 
Published: July 2015

Abstract
Motivation: The amount of sequenced genomes and proteins is growing at an unprecedented pace. Unfortunately, manual curation and functional knowledge lag behind. Homologous inference often fails at labeling proteins with diverse functions and broad classes. Thus, identifying high-level protein functionality remains challenging. We hypothesize that a universal feature engineering approach can yield classification of high-level functions and unified properties when combined with machine learning approaches, without requiring external databases or alignment.
Results: In this study, we present a novel bioinformatics toolkit called ProFET (Protein Feature Engineering Toolkit). ProFET extracts hundreds of features covering the elementary biophysical and sequence derived attributes. Most features capture statistically informative patterns. In addition, different representations of sequences and the amino acids alphabet provide a compact, compressed set of features. The results from ProFET were incorporated in data analysis pipelines, implemented in python and adapted for multi-genome scale analysis. ProFET was applied on 17 established and novel protein benchmark datasets involving classification for a variety of binary and multi-class tasks. The results show state of the art performance. The extracted features’ show excellent biological interpretability. The success of ProFET applies to a wide range of high-level functions such as subcellular localization, structural classes and proteins with unique functional properties (e.g. neuropeptide precursors, thermophilic and nucleic acid binding). ProFET allows easy, universal discovery of new target proteins, as well as understanding the features underlying different high-level protein functions.
Availability and implementation: ProFET source code and the datasets used are freely available at https://github.com/ddofer/ProFET.
Contact: michall@cc.huji.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Depletion of enteroantigen-activated CD4+ T cells: effects on proliferation and pathogenicity
Authors: Belmaáti Mohammed-Samir , Claesson Mogens H. 
Published: July 2015

Abstract
Naive CD4+ T cells depleted of natural Treg (CD25+) cells proliferate extensively when exposed to a fecal extract [enteroantigen (eAg)] pulsed on antigen-presenting cells (APC). When transplanted into SCID recipient mice, the CD25-depleted T cells induce a chronic colitis with a lethal course. We observed here that if T cells, pre-activated for 48h by eAg from BALB/c or SCID mice, are removed and then reexposed to either of the two sources of antigen, these T cells have completely lost their anti-eAg proliferative capacity in vitro. This observation indicates that eAgs derived from Balb/c and SCID mice are recognized by similar subsets of T cells. However, when transferred into SCID mice, eAg-activation-depleted T cells are still capable of inducing a severe colitis fully comparable with the disease induced by naive CD4+ T cells
Radial distributions of arm–gas offsets as an observational test of spiral theories
Authors: Baba Junichi , Morokuma-Matsui Kana , Egusa Fumi 
Published: July 2015

Abstract
Theories of stellar spiral arms in disk galaxies can be grouped into two classes based on the longevity of a spiral arm. Although the quasi-stationary density wave theory supposes that spirals are rigidly rotating, long-lived patterns, the dynamic spiral theory predicts that spirals are differentially rotating, transient, recurrent patterns. In order to distinguish between the two spiral models from observations, we performed hydrodynamic simulations with steady and dynamic spiral models. Hydrodynamic simulations in steady spiral models demonstrated that the dust lane locations relative to the stellar spiral arms (hereafter, arm–gas offsets) depend on radius, regardless of the strength and pitch angle of the spiral and the model of the interstellar medium. In contrast, we found that the dynamic spiral models show no systematic radial dependence of the arm–gas offsets. The arm–gas offset radial profile method, together with the other test methods, will help us to distinguish between the two spiral models in observed spiral galaxies.
Antioxidants Protect Calsequestrin-1 Knockout Mice from Halothane- and Heat-induced Sudden Death
Authors: Michelucci Antonio , Paolini Cecilia , Canato Marta , Wei-Lapierre Lan , Pietrangelo Laura , De Marco Alessandro , Reggiani Carlo , Dirksen Robert T. , Protasi Feliciano 
Published: July 2015

AbstractAbstract
Antioxidant pretreatment with N-acetylcysteine and Trolox protected calsequestrin-1-null mice from otherwise lethal episodes triggered by exposure to either halothane or heat stress. The results support evidence for a potential role of oxidative stress in life-threatening events of malignant hyperthermia and heat stress.

Background:
Mice lacking calsequestrin-1 (CASQ1-null), a Ca2+-binding protein that modulates the activity of Ca2+ release in the skeletal muscle, exhibit lethal hypermetabolic episodes that resemble malignant hyperthermia in humans when exposed to halothane or heat stress.

Methods:
Because oxidative species may play a critical role in malignant hyperthermia crises, we treated CASQ1-null mice with two antioxidants, N-acetylcysteine (NAC, Sigma-Aldrich, Italy; provided ad libitum in drinking water) and (±)-6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid (Trolox, Sigma-Aldrich; administered by intraperitoneal injection), before exposure to halothane (2%, 1 h) or heat (41°C, 1 h).

Results:
NAC and Trolox significantly protected CASQ1-null mice from lethal episodes, with mortality being 79% (n = 14), 25% (n = 16), and 20% (n = 5) during halothane exposure and 86% (n = 21), 29% (n = 21), and 33% (n = 6) during heat stress in untreated, NAC-treated, and Trolox-treated mice, respectively. During heat challenge, an increase in core temperature in CASQ1-null mice (42.3° ± 0.1°C, n=10) was significantly reduced by both NAC and Trolox (40.6° ± 0.3°C, n = 6 and 40.5° ± 0.2°C, n = 6). NAC treatment of CASQ1-null muscles/mice normalized caffeine sensitivity during in vitro contracture tests, Ca2+ transients in single fibers, and significantly reduced the percentage of fibers undergoing rhabdomyolysis (37.6 ± 2.5%, 38/101 fibers in 3 mice; 11.6 ± 1.1%, 21/186 fibers in 5 mice). The protective effect of antioxidant treatment likely resulted from mitigation of oxidative stress, because NAC reduced mitochondrial superoxide production, superoxide dismutase type-1 expression, and 3-nitrotyrosine expression, and increased both reduced glutathione and reduced glutathione/oxidized glutathione ratio.

Conclusion:
These studies provide a deeper understanding of the mechanisms that underlie hyperthermic crises in CASQ1-deficient muscle and demonstrate that antioxidant pretreatment may prevent them.
Achieving Kaiser Permanente quality
Authors: McHugh Matthew D. , Aiken Linda H. , Eckenhoff Myra E. , Burns Lawton R. 
Published: July 2015

Background:
The Kaiser Permanente model of integrated health delivery is highly regarded for high-quality and efficient health care. Efforts to reproduce Kaiser’s success have mostly failed. One factor that has received little attention and that could explain Kaiser’s advantage is its commitment to and investment in nursing as a key component of organizational culture and patient-centered care.

Purpose:
The aim of this study was to investigate the role of Kaiser’s nursing organization in promoting quality of care.

Methodology:
This was a cross-sectional analysis of linked secondary data from multiple sources, including a detailed survey of nurses, for 564 adult, general acute care hospitals from California, Florida, Pennsylvania, and New Jersey in 2006–2007. We used logistic regression models to examine whether patient (mortality and failure-to-rescue) and nurse (burnout, job satisfaction, and intent-to-leave) outcomes in Kaiser hospitals were better than in non-Kaiser hospitals. We then assessed whether differences in nursing explained outcomes differences between Kaiser and other hospitals. Finally, we examined whether Kaiser hospitals compared favorably with hospitals known for having excellent nurse work environments—Magnet hospitals.

Findings:
Patient and nurse outcomes in Kaiser hospitals were significantly better compared with non-Magnet hospitals. Kaiser hospitals had significantly better nurse work environments, staffing levels, and more nurses with bachelor’s degrees. Differences in nursing explained a significant proportion of the Kaiser outcomes advantage. Kaiser hospital outcomes were comparable with Magnet hospitals, where better outcomes have been largely explained by differences in nursing.

Implications:
An important element in Kaiser’s success is its investment in professional nursing, which may not be evident to systems seeking to achieve Kaiser’s advantage. Our results suggest that a possible strategy for achieving outcomes like Kaiser may be for hospitals to consider Magnet designation, a proven and cost-effective strategy to improve process of care through investments in nursing.
Distributed leadership in health care teams
Authors: Chreim Samia , MacNaughton Kate 
Published: July 2015

Background and Purpose:
Recent literature has been critical of research that adopts a narrow focus on single leaders and on leadership attributes and has called for attention to leadership that is distributed among individuals and to practices in which leaders engage. We conducted a study of health care teams where we attended to role distribution among leadership constellation members and to loose or tight coupling practices between leaders and the remainder of the team. This focus provides insights into how leadership can be practiced and structured to enhance team functioning.

Methodology:
A qualitative, multicase study of four teams was conducted. Data collection involved 44 interviews with almost all the members of the teams and 18 team meeting observations. Thematic analysis was conducted by the two authors.

Findings:
Leadership constellations can give rise to leadership role overlaps and gaps that may create ambiguity within teams, ambiguity is diminished if the leaders can agree on which leader assumes ultimate authority in an area, the presence of more leaders does not necessarily entail more comprehensive fulfillment of team needs, and teams’ needs for tight or loose leadership practices are influenced by contextual factors that we elaborate.

Practice Implications:
(a) It is important to recognize areas of overlap and gaps in leadership roles and to provide clarity about role boundaries to avoid ambiguity. Role mapping exercises and open discussions should be considered. (b) Attempting to spread formal leadership responsibilities informally among individuals is not always a workable strategy for addressing team needs. (c) Organizations need to examine critically the allocation of resources to leadership activities.
The influence of organization tenure on nurses’ perceptions of multiple work process improvement initiatives
Authors: Edwardson Nicholas , Gregory Sean , Gamm Larry 
Published: July 2015

Background:
A nurse’s optimism or skepticism toward an organization-mandated change initiative largely depends on their experience with similar change initiatives and their unit’s and organization’s track record with previous change efforts. Thus, depending on the context, organization tenure can work in favor or against any particular change initiative. However, few studies have examined the impact of organization tenure on perceptions toward change initiatives. The few studies that have been conducted have yielded mixed results and have only targeted single or similar work initiatives.

Purpose:
The aim of this study was to examine how organization tenure impacts nurses’ perceptions toward a diverse array of work process improvement initiatives.

Methodology:
The data are derived from a survey of 421 medical-surgical nurses representing 41 units across four hospitals. The survey was designed to capture nurses’ perceptions toward three change initiatives—AIDET (Acknowledge, Introduce, Duration, Explanation, and Thank You), hourly rounding, and discharge phone calls—and their impact across two subscales—patient care and individual work change.

Findings:
Organization tenure is significantly and negatively associated with change receptivity for the non-patient safety-oriented initiative (AIDET). This negative relationship dissipates as we evaluate more patient safety-oriented work process initiatives (hourly rounding and discharge phone calls).

Practice Implications:
Significant differences in nurses’ perceptions toward change do exist depending on how long they have worked for their employer. For non-patient safety-oriented change initiatives, veteran-to-the-organization nurses may exhibit more recalcitrance than their new-to-the-organization counterparts. However, our findings also suggest the presence of a patient safety exception rule where veteran-to-the-organization nurses do not exhibit differences in opinion than their new-to-the-organization counterparts for patient safety-oriented change initiatives.
Experiences of Young Adults With Pacemakers and/or Implantable Cardioverter Defibrillators
Authors: Larimer Karen , Durmus Julie , Florez Elizabeth 
Published: July 2015

Background:
The number of implanted devices (pacemakers [PMs] and implantable cardioverter defibrillators [ICDs]) is increasing. Because of technological advances, these devices are used in greater numbers in children and adolescents. Challenges of having these devices have been well studied in adults, but little is known about the lived experiences from the perspective of young adults.

Objective:
This study explored the lived experiences, coping behaviors, and challenges of young adults who had cardiac devices implanted during childhood.

Methods:
A descriptive qualitative study design was used. Purposive sampling was used to identify young adults aged 18 to 29 years, living with a PM and/or ICD. Participants were interviewed about their experiences and challenges related to living with a PM or ICD, with common themes identified and analyzed.

Results:
A total of 6 participants were interviewed for this study. The challenges of living with a PM and/or ICD included insecurity about physical appearance, device compliance, physical sensations of the device, future uncertainty, and limited support. The identified coping behaviors utilized by the participants were confrontation, acceptance, educating others, spreading awareness, avoidance, and humor. The overall lived experiences described were appreciation for device benefits, fear of device malfunction, and attracting attention.

Conclusions:
The lived experiences of young recipients often mirror that of older adults; however, it is clear that there are challenges and coping behaviors unique to young adults living with a PM and/or ICD. It is important to educate healthcare providers about the unique challenges that young adults may face so they can provide the appropriate support to this population.
Credibility, peer review, and
Nature
, 1945–1990
Authors: Baldwin Melinda 
Published: July 2015

This paper examines the refereeing procedures at the scientific weekly
Nature
during and after World War II. In 1939 former editorial assistants L. J. F. Brimble and A. J. V. Gale assumed a joint editorship of
Nature
. The Brimble–Gale era is now most famous for the editors' unsystematic approach to external refereeing. Although Brimble and Gale did sometimes consult external referees, papers submitted or recommended by scientists whom the pair trusted were often not sent out for further review. Their successor, John Maddox, would also print papers he admired without external refereeing. It was not until 1973 that editor David Davies made external peer review a requirement for publication in
Nature. Nature
's example shows that as late as the 1960s a journal could be considered scientifically respectable even if its editors were known to eschew systematic external peer review.
Thermal motion of DNA in an MspA pore
Authors: Lu Bo , Fleming Stephen , Szalay Tamas , Golovchenko Jene 
Published: July 2015

ABSTRACTWe report on an experiment and calculations that determine the thermal motion of a voltage-clamped ssDNA-NeutrAvidin complex in an MspA nanopore. The electric force and diffusion constant of DNA inside an MspA pore have been determined in order to evaluate DNA’s thermal position fluctuations. We show that an out-of-equilibrium state returns to equilibrium so quickly that experiments usually measure a weighted average over the equilibrium position distribution. Averaging over the equilibrium position distribution is consistent with results of state-of-the-art nanopore sequencing experiments. It is shown that a reduction in thermal averaging can be achieved by increasing the electrophoretic force used in nanopore sequencing devices.