bluuebunny/crossref_metadata_2025_split huggingface dataset:
Summer Habitat Use of Large Adult Striped Bass and Habitat Availability in Lake Martin, Alabama
Authors: Sammons Steven M. , Glover David C. 
Published: July 2013

Abstract
To identify the summer habitat use by Gulf strain Striped Bass Morone saxatilis in Lake Martin, Alabama, 36 fish greater than 4 kg were tracked weekly from June through September in 2009 and 2010. Temperature and dissolved oxygen profiles were collected biweekly from July to October each year and were incorporated into a hypsographic curve to estimate summertime volumes of Striped Bass habitat. Striped Bass moved downstream in the reservoir and deeper in the water column as the summer progressed in both years. Across all temperatures and dissolved oxygen concentrations (DOCs) measured, fish generally selected cooler temperatures when DOCs were greater than 3.1 mg/L, but below that level, fish selected warmer temperatures. By early July each year, quality Striped Bass habitat (≤21.0°C and ≥3.2 mg/L DOC) comprised 40–50% of the total habitat available in Lake Martin. However, in 2009 all quality habitat was gone from the reservoir by August 1, and total habitat (≤25.0°C and ≥1.6 mg/L DOC) rapidly decreased until there was no suitable habitat found in Lake Martin by mid-September. The quantity of quality and total habitat declined more rapidly in 2009 than in 2010; although quality habitat was eliminated from the reservoir by the end of August 2010, total habitat persisted throughout the summer. In both years, habitat availability increased when reservoir destratification began. Analysis of historical data indicated that quality habitat was found in the lower portion of the reservoir during the latter half of August in only 6 of 15 years; total Striped Bass habitat was available in all but 1 year. The amount of water flowing through the system during the spring and summer was a key determinant of Striped Bass habitat availability by late summer.
Received September 26, 2012; accepted May 15, 2013
Overcoming Patient Barriers to Discussing Physician Hand Hygiene: Do Patients Prefer Electronic Reminders to Other Methods?
Authors: Michaelsen Kaarin , Sanders Jason L. , Zimmer Shanta M. , Bump Gregory M. 
Published: July 2013

Background.Despite agreement that handwashing decreases hospital-acquired infections (HAIs), physician hand hygiene remains suboptimal. Interventions to empower patients to discuss handwashing have had variable success.Objective.To understand patient perceived barriers to discussing physician hand hygiene and to determine whether patients prefer electronic alerts over printed information as an intervention to discuss physician handwashing.Design.Cross-sectional study of 250 medical/surgical patients at an academic medical center.Results.Ninety-six percent of patients had heard of HAIs. Ninety-six percent of patients thought it was important for physicians to clean their hands before touching anything in a patient's room. The majority of patients (78%) believed patients should remind physicians to clean their hands. Thirty-two percent of patients observed physician hand hygiene noncompliance. In multivariate analysis, predictors of not speaking up regarding physician hand hygiene included never having worked in health care (odds ratio [OR], 2.8 [95% confidence interval (CI), 1.5-5.1]), not observing a physician clean hands before touching the patient (OR, 2.4 [95% CI, 1.3-4.4]), and not thinking patients should have to remind physicians to clean hands (OR, 5.5 [95% CI, 2.4-12.7]). Ninety-three percent of patients favored electronic device reminders over printed information as an intervention to encourage patients to discuss hand hygiene with their doctors.Conclusions.The strongest predictor of not challenging a doctor to clean their hands was not believing it was the patient's role to do so. Patients prefer electronic device reminders to printed information as an aid in overcoming barriers to discussing hand hygiene with physicians.
GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks
Authors: Camilo Esther , Bovolenta Luiz A. , Acencio Marcio L. , Rybarczyk-Filho José L. , Castro Mauro A.A. , Moreira José C.F. , Lemke Ney 
Published: July 2013

Abstract
Summary: Network-level visualization of functional data is a key aspect of both analysis and understanding of biological systems. In a continuing effort to create clear and integrated visualizations that facilitate the gathering of novel biological insights despite the overwhelming complexity of data, we present here the GrAph LANdscape VisualizaTion (GALANT), a Cytoscape plugin that builds functional landscapes onto biological networks. By using GALANT, it is possible to project any type of numerical data onto a network to create a smoothed data map resembling the network layout. As a Cytoscape plugin, GALANT is further improved by the functionalities of Cytoscape, the popular bioinformatics package for biological network visualization and data integration.
Availability: http://www.lbbc.ibb.unesp.br/galant.
Contact: esther@ibb.unesp.br
Supplementary Information: Supplementary data are available at Bioinformatics online.
Designing and Evaluating Culturally Specific Smoking Cessation Interventions for American Indian Communities
Authors: Fu Steven S. , Rhodes Kristine L. , Robert Christina , Widome Rachel , Forster Jean L. , Joseph Anne M. 
Published: July 2013

Abstract

Introduction:
American Indians have the highest smoking rates in the United States, yet few randomized controlled trials of culturally specific interventions exist. This study assessed American Indians’ opinions about evidence-based treatment and attitudes toward participating in clinical trials.

Methods:
Six focus groups were conducted based on smoking status (current/former smoker), sex, and elder status (55 years and older or younger). Meetings were held at local American Indian community organizations. This project was accomplished in partnership with the American Indian Community Tobacco Projects, a community–academic research partnership at the University of Minnesota. Thematic qualitative data analyses were conducted.

Results:
Participants desired the following: (a) programs led by trained American Indian community members, (b) the opportunity to connect with other American Indian smokers interested in quitting, and (c) programs promoting healthy lifestyles. Strategies desired for treatment included (a) free pharmacotherapy, including nicotine replacement therapy (NRT); (b) nominal incentives, e.g., gift cards for groceries; and (c) culturally specific program components such as American Indian images, education on traditional tobacco use, and quit-smoking messages that target the value of family and include narratives or story telling in recruitment and program materials. Biochemical verification of smoking abstinence, such as salivary cotinine or carbon monoxide breathalyzers, is likely acceptable. Standard treatment or delayed treatment control groups were viewed as potentially acceptable for randomized study designs.

Conclusions:
Rigorously conducted randomized controlled trials of culturally specific smoking cessation interventions are sorely needed but will only be accomplished with the commitment of funders, researchers, and collaborative trusting relationships with the community.
Avoidance of Wrong-level Thoracic Spine Surgery Using Sterile Spinal Needles
Authors: Chin Kingsley R. , Seale Jason , Cumming Vanessa 
Published: July 2013

Study Design:
A technical report.

Objective:
The aim of the present study was to present an improvement on localization techniques employed for use in the thoracic spine using sterile spinal needles docked on the transverse process of each vertebra, which can be performed in both percutaneous and open spinal procedures.

Summary of Background Data:
Wrong-level surgery may have momentous clinical and emotional implications for a patient and surgeon. It is reported that one in every 2 spine surgeons will operate on the wrong level during his or her career. Correctly localizing the specific thoracic level remains a significant challenge during spine surgery.

Methods:
Fluoroscopic anteroposterior and lateral views were obtained starting in the lower lumbar spine, and an 18-G spinal needle was placed in the transverse process of L3 counting up from the sacrum and also at T12. The fluoroscopy was then moved cephalad and counting from the spinal needle at T12, the other spinal needles were placed at the targeted operating thoracic vertebrae. Once this was done, we were able to accurately determine the thoracic levels for surgical intervention.

Results:
Using this technique, the markers were kept in place even after the incisions were made. This prevented us from losing our location in the thoracic spine. Correctly placed instrumentation was made evident with postoperative imaging.

Conclusions:
We have described the successful use of a new technique using spinal needles docked against transverse processes to correctly and reliably identify thoracic levels before instrumentation. The technique was reproducible in both open surgeries and for a percutaneous procedure. This technique maintains the correct spinal level during an open procedure. We posit that wrong-level thoracic spine surgery may be preventable.
Evidence that acidification‐induced declines in plant diversity and productivity are mediated by changes in below‐ground communities and soil properties in a semi‐arid steppe
Authors: Chen Dima , Lan Zhichun , Bai Xue , Grace James B. , Bai Yongfei 
Published: July 2013

SummaryAnthropogenic acid deposition–induced soil acidification is one of the major threats to biodiversity, ecosystem functioning and services. Few studies, however, have explored in detail how above‐ground changes in plant species richness and productivity resulting from soil acidification are mediated by effects on below‐ground biota and soil properties.To increase our understanding of this linkage, we collected data on below‐ and above‐ground communities and soil properties in a 3‐year field experiment with seven levels of acid addition rate to build‐up broad intensities of soil acidification in the semi‐aridInnerMongolian grassland.Acid addition directly elevated concentrations of soil Al3+ions, decreased the base cations Ca2+, Mg2+and Na+, and increased soil moisture and available phosphorus. Acid addition also appears to have altered the soil microbial community via changes in H+and Al3+ions and altered the nematode community via changes in H+ions and soil moisture.The observed changes in soilNavailability (i.e. netNmineralization,‐N and‐N) could be explained by mediating changes in the H+and Al3+ions, microbial community (i.e. community structure, bacteria and fungi/bacteria as indicated by phospholipid fatty acids analysis) and the nematode community (i.e. total abundance, taxa richness and maturity index).Declines in plant species richness and productivity were greater at high intensities of soil acidification in the second sampling year than in the first sampling year.The changes in plant community observed were mostly explained by soil nutrient pathways (e.g. N availability or base mineral cations), which were in turn regulated by the soil microbial or nematode communities as well as by the direct effects of the increase in H+or Al3+ions.Synthesis. Our results suggest that the below‐ground microbial and nematode communities are more sensitive to soil acidification than the plant communities are, and further that soil acidification–induced changes in plants are mediated by changes in below‐ground communities and soil nutrients. These findings improve our understanding of the links between below‐ and above‐ground communities in theInnerMongolia grassland, especially in the context of anthropogenic acid enrichment.
Climate Change and the Management of Fire‐Prone Vegetation in Southwest and Southeast Australia
Authors: ENRIGHT NEAL J. , FONTAINE JOSEPH B. 
Published: July 2013

AbstractMediterranean regions worldwide, and southwest (SW) Australia in particular, are characterised by their high plant biodiversity, fire‐prone vegetation, and substantial conservation challenges in relation to human land use, expanding populations and changing climate. Recent climate change is evident in SW Australia, with markedly decreasing rainfall and increasing temperatures since the 1970s. Fire management in SW Australia, historically focused in the southern forests, but now also engaged with a rapidly expanding wildland‐urban interface, is faced with the formidable challenge of increased fire likelihoods due to increased fire danger weather under a warming climate, and more human‐caused ignitions as population growth proceeds. Here, we review key components of the fire–environment relationship, the use of fuel reduction burning as a wildfire mitigation strategy, and the potential impacts of changing climate on fire regimes and fire management in the SW, including ecological impacts. We draw comparisons between SW and southeastern (SE) Australia, contrasting the recent history of fire in these two regions, how they differ, and how this helps us to understand the circumstances under which planned fire may be an effective approach to fire hazard mitigation in SW Australia. Evidence suggests that fuel reduction burning in wildlands produces little benefit for wildfire control. While wildfire sizes differ between regions, a concentration of resources and fire management near human infrastructure and not in wildlands seems warranted with increasing emphasis on fire suppression and fuels management.
Excavating the Pilbara: A Polanyian Exploration
Authors: PECK JAMIE 
Published: July 2013

AbstractTaking its cues from the ‘substantivist’ economics of Karl Polanyi, the paper retraces a socio‐economic history of the Pilbara from the pastoral capitalism of the region's initially tenuous colonial settlement to the contemporary regime of extractive capitalism. Spatial fixes have been etched deeply into the landscape of this heterogeneously ‘productive’ region, but crises of social reproduction have remained endemic. Since the nineteenth century, disequilibrium has been the reigning principle, as successive failures of commodification and marketisation have marked a long and non‐linear history of double movements.
Autologous serum eye drops diluted with sodium hyaluronate: clinical and experimental comparative study
Authors: López‐García José S. , García‐Lozano Isabel , Rivas Luis , Ramírez Nuria , Raposo Rafaela , Méndez Maria T. 
Published: July 2013

Abstract.Purpose:  To assess the efficacy of sodium hyaluronate as vehicle for diluting autologous serum.Methods:  The concentration and temporal stability of EGF, TGF‐β, PDGF‐AB and albumin in fresh and frozen samples of autologous serum diluted with sodium hyaluronate and saline solution, as well as the pH, osmolarity and density was studied. In parallel, the clinic effects of autologous serum diluted to 20% with sodium hyaluronate were compared with another solution of autologous serum diluted to 20% with saline in a prospective, comparative, randomized and double‐blind study in 26 patients (52 eyes) with Sjögren syndrome. Patients underwent a complete ophthalmic assessment including tear film evaluation and corneal and conjunctival impression cytology at the beginning of the study and 2 months later.Results:  The growth factor (GF) concentration remained stable during 1 month at 4°C both in fresh and defrosted samples without any differences being found between both preparations. No differences were found related to osmolarity, pH and density between these preparations before and after frosting. Autologous serum diluted with sodium hyaluronate caused a significant improvement of the tear film stability, fluorescein and rose Bengal stain, break‐up time, corneal and conjunctival squamous metaplasia as well as in the patient subjective perception.Conclusions:  Sodium hyaluronate is an excellent vehicle for diluting autologous serum due to the gradual release of GF and increasing their duration and effect on the ocular surface. Preparations diluted with sodium hyaluronate are better tolerated by patients and require a lower number of drops administrations.
Changes in aqueous cytokines after intravitreal triamcinolone versus bevacizumab for macular oedema in branch retinal vein occlusion
Authors: Sohn Hee Jin , Han Dae Heon , Lee Dae Yeong , Nam Dong Heun 
Published: July 2013

Abstract.Purpose:  To investigate the changes in the aqueous levels of various cytokines after intravitreal triamcinolone or bevacizumab for branch retinal vein occlusion (BRVO).Methods:  Twenty‐four eyes with macular oedema associated with BRVO and six eyes of six patients undergoing cataract surgery participated in this study. Each patient with BRVO randomly received an intravitreal injection of either 4 mg triamcinolone or 1.25 mg bevacizumab. Aqueous samples were obtained before and 4 weeks after the intravitreal injection in the BRVO group and before surgery in the control group. Aqueous concentrations of 16 cytokines were measured via multiplex bead assay.Results:  Prior to the administration of the drugs, aqueous levels of interleukin (IL)‐6, IL‐8, IL‐17 and vascular endothelial growth factor (VEGF) were significantly higher in the BRVO group than in the control group (p = 0.044, p = 0.013, p < 0.001, and p = 0.008, respectively). Between the control group and the BRVO group, no significant differences were noted between pre‐ and postinjection best‐corrected visual acuity (p = 0.60, p = 0.54) and central foveal thickness (p = 0.47, p = 0.82). In the triamcinolone group, levels of IL‐6, IL‐17, IP‐10, platelet‐derived growth factor (PDGF)‐AA and VEGF were reduced significantly (p = 0.012, p < 0.001, p < 0.001, p = 0.015, and p < 0.001, respectively). But in bevacizumab group, only VEGF was significantly reduced (p < 0.001). Between the IVTA group and the IVBe group, no significant differences in the changes in VEGF levels were noted (p = 0.06).Conclusion:  Triamcinolone injection reduces plural inflammatory cytokines in BRVO, while bevacizumab has no influence on other cytokines as selective anti‐VEGF therapy. No differences in the therapeutic effect were noted between an inhibition of plural inflammatory cytokines and an inhibition of VEGF only.
An Optimal Test with Maximum Average Power While Controlling FDR with Application to RNA‐Seq Data
Authors: Si Yaqing , Liu Peng 
Published: July 2013

SummaryThe recent RNA‐seq technology is an attractive method to study gene expression. One of the most important goals in RNA‐seq data analysis is to detect genes differentially expressed across treatments. Although several statistical methods have been published, there are no theoretical justifications for whether these methods are optimal or how to search for the optimal test. Furthermore, most proposed tests are designed for testing whether the mean expression levels are exactly the same or not across treatments, whereas sometimes, biologists are interested in detecting genes with expression changes larger than a certain threshold. Another issue with current methods is that the false discovery rate (FDR) control is not well studied. In this manuscript, we propose a test to address all the above issues. Under model assumptions, we derive an optimal test that achieves the maximum of average power among those that control FDR at the same level. We also provide an approximated version, the approximated most average powerful (AMAP) test, for practical implementation. The proposed method allows for testing null hypotheses that are much more general than the ones most previous studies have considered, and it leads to a natural way of controlling the FDR. Through simulation studies, we show that our test has a higher power than other methods, including the widely‐used edgeR, DESeq, and baySeq methods, as well as better FDR control than two other FDR control procedures commonly used in practice. For demonstration, we also apply the proposed method to a real RNA‐seq dataset obtained from maize.
Does the presence of a high grade internal rectal prolapse affect the outcome of pelvic floor retraining in patients with faecal incontinence or obstructed defaecation?
Authors: Adusumilli S. , Gosselink M. P. , Fourie S. , Curran K. , Jones O. M. , Cunningham C. , Lindsey I. 
Published: July 2013

AbstractAimPelvic floor retraining is considered first‐line treatment for patients with faecal incontinence or obstructed defaecation. There are at present no data on the effect of a high grade internal rectal prolapse on outcomes of pelvic floor retraining. The current study aimed to assess this influence.MethodIn all, 120 consecutive patients were offered pelvic floor retraining. The predominant symptom was faecal incontinence in 56 patients (47%) and obstructed defaecation in 64 patients (53%). Patients were assessed before and after therapy using the Fecal Incontinence Severity Index (FISI), the Patient Assessment of Constipation Symptoms (PAC‐SYM) score and the Gastrointestinal Quality of Life Index (GIQLI). Defaecography and anorectal manometry were performed in all patients before pelvic floor retraining.ResultsA high grade internal rectal prolapse was observed in 42 patients (35%). In patients with faecal incontinence without a high grade internal rectal prolapse, the FISI score decreased from 36 to 27 (P < 0.01). The FISI score did not change (32 vs 32; P = 0.93) in patients with a high grade internal rectal prolapse. The PAC‐SYM score improved significantly (24 vs 19; P = 0.01) in patients with obstructed defaecation without a high grade rectal prolapse compared with no significant change (26 vs 25; P = 0.21) in patients with a high grade rectal prolapse. Quality of life (GIQLI) improved only in patients without a high grade internal rectal prolapse.ConclusionPelvic floor retraining may be useful in patients with defaecation disorders not associated with a high grade internal rectal prolapse. Patients with a high grade internal rectal prolapse may be considered for surgery from the outset.
Histopathology of acneiform eruptions in patients treated with epidermal growth factor receptor inhibitors
Authors: Brodell Lindsey A. , Hepper Donna , Lind Anne , Gru Alejandro A. , Anadkat Milan J. 
Published: July 2013

BackgroundEpidermal growth factor receptor inhibitors (EGFRIs) are anticancer agents that have been approved for use in a variety of solid tumors. EGFR‐inhibiting agents produce a variety of cutaneous adverse events: most commonly a follicular papulopustular (acneiform) eruption on the face, scalp, chest and upper back.ObjectiveThe goal of this manuscript is to elucidate the histopathologic findings associated with this most common adverse event.MethodsThe histopathological findings of 10 patients with papulopustular eruptions induced by EGFRIs are described and compared to the four prior published case series of acneiform rashes attributed to EGFRIs.ResultsAll 10 patients in our case series showed a superficial, predominantly neutrophilic suppurative folliculitis with ectatic follicular infundibula and rupture of the epithelial lining. Similar pathology was found in the four other case series discussing this phenomenon.ConclusionWhile the characteristic clinical appearance of this rash precludes the need for a biopsy in most cases, this knowledge promotes our understanding of the pathophysiologic process. As the use of EGFRIs expands, dermatopathologists will see these reactions more commonly and will need to recognize this pattern.