bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal regulatory spaces in yeast genomes
Authors: Chen Wei-Hua , Wei Wu , Lercher Martin J 
Published: June 2011

Abstract

Background
The regulatory information encoded in the DNA of promoter regions usually enforces a minimal, non-zero distance between the coding regions of neighboring genes. However, the size of this minimal regulatory space is not generally known. In particular, it is unclear if minimal promoter size differs between species and between uni- and bi-directionally acting regulatory regions.

Results
Analyzing the genomes of 11 yeasts, we show that the lower size limit on promoter-containing regions is species-specific within a relatively narrow range (80-255 bp). This size limit applies equally to regions that initiate transcription on one or both strands, indicating that bi-directional promoters and uni-directional promoters are constrained similarly. We further find that young, species-specific regions are on average much longer than older regions, suggesting either a bias towards deletions or selection for genome compactness in yeasts. While the length evolution of promoter-less intergenic regions is well described by a simplistic, purely neutral model, regions containing promoters typically show an excess of unusually long regions. Regions flanked by divergently transcribed genes have a bi-modal length distribution, with short lengths found preferentially among older regions. These old, short regions likely harbor evolutionarily conserved bi-directionally active promoters. Surprisingly, some of the evolutionarily youngest regions in two of the eleven species (S. cerevisiae and K. waltii) are shorter than the lower limit observed in older regions.

Conclusions
The minimal chromosomal space required for transcriptional regulation appears to be relatively similar across yeast species, and is the same for uni-directional and bi-directional promoters. New intergenic regions created by genome rearrangements tend to evolve towards the more narrow size distribution found among older regions.
Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize
Authors: Casati Paula , Campi Mabel , Morrow Darren J , Fernandes John F , Walbot Virginia 
Published: June 2011

Abstract

Background
Under normal solar fluence, UV-B damages macromolecules, but it also elicits physiological acclimation and developmental changes in plants. Excess UV-B decreases crop yield. Using a treatment twice solar fluence, we focus on discovering signals produced in UV-B-irradiated maize leaves that translate to systemic changes in shielded leaves and immature ears.

Results
Using transcriptome and proteomic profiling, we tracked the kinetics of transcript and protein alterations in exposed and shielded organs over 6 h. In parallel, metabolic profiling identified candidate signaling molecules based on rapid increase in irradiated leaves and increased levels in shielded organs; pathways associated with the synthesis, sequestration, or degradation of some of these potential signal molecules were UV-B-responsive. Exposure of just the top leaf substantially alters the transcriptomes of both irradiated and shielded organs, with greater changes as additional leaves are irradiated. Some phenylpropanoid pathway genes are expressed only in irradiated leaves, reflected in accumulation of pathway sunscreen molecules. Most protein changes detected occur quickly: approximately 92% of the proteins in leaves and 73% in immature ears changed after 4 h UV-B were altered by a 1 h UV-B treatment.

Conclusions
There were significant transcriptome, proteomic, and metabolomic changes under all conditions studied in both shielded and irradiated organs. A dramatic decrease in transcript diversity in irradiated and shielded leaves occurs between 0 h and 1 h, demonstrating the susceptibility of plants to short term UV-B spikes as during ozone depletion. Immature maize ears are highly responsive to canopy leaf exposure to UV-B.
An association between unrecognized gastroesophageal reflux disease and excessive daytime sleepiness in Taiwanese subjects suspected to have liver disease: a pilot study
Authors: Hu Jing-Hong , Lin Shih-Wei , Hsieh Yung-Yu , Chen Ning-Hung 
Published: June 2011

Abstract

Background
In traditional Chinese culture, liver disease is believed to underlie excessive daytime sleepiness (EDS). Consequently, Chinese patients with complaints of EDS and physicians who treat them suspect that a liver abnormality is present. If liver disease is ruled out, these patients are often discharged without treatment. Gastroesophageal reflux disease (GERD) is a common disorder also associated with EDS. This pilot study was undertaken to determine the prevalence of GERD among Taiwanese patients with complaints of EDS suspected to be related to liver disease but in whom no evidence for the latter was found.

Methods
From July 2009 to December 2009, 121 outpatients who presented to or were referred to the Department of Gastroenterology and Hepatology of the Chiayi Gung Memorial Hospital for evaluation of a complaint of EDS thought to be due to liver disease were examined. Demographic data were collected, and physical examinations and liver function tests were performed. Forty-eight patients had liver disease and were excluded. The Chinese Epworth Sleepiness Scale questionnaire (Chinese ESS) and the Chinese Gastroesophageal Reflux Disease Questionnaire (CGERDQ) were then administered to 73 included patients.

Results
More than half (56.2%) of the included patients were found to suffer from GERD. Patients with symptoms of GERD had higher mean CGERDQ scores than patients without symptoms of the disorder (18.88 ± 5.49 and 5.56 ± 3.57, respectively; P < 0.001). Patients with symptoms of GERD also had higher mean Chinese ESS scores than patients without symptoms (8.80 ± 5.49 and 3.13 ± 3.50, respectively; P < 0.001). Chinese ESS scores indicative of EDS were observed in 48.8% of patients with symptoms of GERD and in 3.1% of those without symptoms (P < 0.001). Differences between the two groups retained their significance after controlling for potential confounders.

Conclusions
A significant percentage of Taiwanese patients who complained of EDS and were admitted to our Hepatology/Gastroenterology Department due to a suspicion of liver disease actually had symptoms of GERD. Further studies are needed to ascertain whether treatment of GERD will effectively resolve EDS in these patients.
Why is spirometry underused in the diagnosis of the breathless patient: a qualitative study
Authors: Roberts Nicola J , Smith Susan F , Partridge Martyn R 
Published: June 2011

Abstract

Background
Use of spirometry is essential for the accurate diagnosis of respiratory disease but it is underused in both primary and specialist care. In the current study, we have explored the reasons for this underuse.

Methods
Five separate focus groups were undertaken with final year medical undergraduates, junior hospital doctors, general practitioners (GPs) and specialist trainees in respiratory medicine. The participants were not told prior to the session that we were specifically interested in their views about spirometry but discussion was moderated to elicit their approaches to the diagnosis of a breathless patient, their use of investigations and their learning preferences.

Results
Undergraduates and junior doctors rarely had a systematic approach towards the breathless patient and tended, unless prompted, to focus on the emergency room situation rather than on patients with longer term causes of breathlessness. Whilst their theoretical knowledge embraced the possibility of a non-respiratory cause for breathlessness, neither undergraduates nor junior doctors spontaneously mentioned the use of spirometry in the diagnosis of respiratory disease. When prompted they cited lack of familiarity with the use and location of equipment, and lack of encouragement to use it as being major barriers to utilization. In contrast, GPs and specialist respiratory trainees were enthusiastic about its use and perceived spirometry as a core element of the diagnostic workup.

Conclusions
More explicit training is needed regarding the role of spirometry in the diagnosis and management of those with lung disease and this necessitates both practical experience and training in interpretation of the data. However, formal teaching is likely to be undermined in practice, if the concept is not strongly promoted by the senior staff who act as role models and trainers.
Reference gene selection for gene expression studies using RT-qPCR in virus-infected planthoppers
Authors: Maroniche Guillermo A , Sagadín Mónica , Mongelli Vanesa C , Truol Graciela A , del Vas Mariana 
Published: June 2011

Abstract

Background
Planthoppers not only severely affect crops by causing mechanical damage when feeding but are also vectors of several plant virus species. The analysis of gene expression in persistently infected planthoppers might unveil the molecular basis of viral transmission. Quantitative real-time RT-PCR (RT-qPCR) is currently the most accurate and sensitive method used for quantitative gene expression analysis. In order to normalize the resulting quantitative data, reference genes with constant expression during the experimental procedures are needed.

Results
Partial sequences of the commonly used reference genes actin (ACT), α1-tubulin (TUB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1A), ribosomal protein S18 (RPS18) and polyubiquitin C (UBI) from Delphacodes kuscheli, a planthopper capable of persistently transmitting the plant fijivirus Mal de Río Cuarto virus (MRCV), were isolated for the first time. Specific RT-qPCR primers were designed and the expression stability of these genes was assayed in MRCV-infective and naïve planthoppers using geNorm, Normfinder and BestKeeper tools. The overall analysis showed that UBI, followed by 18S and ACT, are the most suitable genes as internal controls for quantitative gene expression studies in MRCV-infective planthoppers, while TUB and EF1A are the most variable ones. Moreover, EF1A was upregulated by MRCV infection.

Conclusions
A RT-qPCR platform for gene expression analysis in the MRCV-infected planthopper vector Delphacodes kuscheli was developed. Our work is the first report on reference gene selection in virus-infected insects, and might serve as a precedent for future gene expression studies on MRCV and other virus-planthopper pathosystems.
The Two-Echelon Capacitated Vehicle Routing Problem: Models and Math-Based Heuristics
Authors: Perboli Guido , Tadei Roberto , Vigo Daniele 
Published: June 2011

Multiechelon distribution systems are quite common in supply-chain and logistics. They are used by public administrations in their transportation and traffic planning strategies, as well as by companies, to model own distribution systems. In the literature, most of the studies address issues relating to the movement of flows throughout the system from their origins to their final destinations. Another recent trend is to focus on the management of the vehicle fleets required to provide transportation among different echelons. The aim of this paper is twofold. First, it introduces the family of two-echelon vehicle routing problems (VRPs), a term that broadly covers such settings, where the delivery from one or more depots to customers is managed by routing and consolidating freight through intermediate depots. Second, it considers in detail the basic version of two-echelon VRPs, the two-echelon capacitated VRP, which is an extension of the classical VRP in which the delivery is compulsorily delivered through intermediate depots, named satellites. A mathematical model for two-echelon capacitated VRP, some valid inequalities, and two math-heuristics based on the model are presented. Computational results of up to 50 customers and four satellites show the effectiveness of the methods developed.
Per l’interpretazione di Pind. Fr. 140 a S.-M. (= G 8 Ruth.)
Authors: Lucarini Carlo Martino 
Published: June 2011

Abstract
The fragment 140 a S.-M. = G 8 Ruth. is likely to deal with two different feats of Herakles. The lines b 21–b 33 seem to concern Cycnus (ξενοδαΐκτης βασιλεύς), an impious hero killed by Herakles by order of Apollo (the identifications of the ξενοδαΐκτης βασιλεύς with Laomedon or with an anonymous king of Paros are extremely unlikely). The rest of the fragment seems to concern the beginning of Herakles’ expedition against Laomedon. I think Pindarus presupposes a legend according to which Herakles spent the most part of his life in Thebes; such an interpretation might explain both the obscure expression πέραν ἰσϑμὸν διαβαίς and other details. The opinion the fragment belonged to the Paianes is in my view right.
Beyond the Word: Ink in the Islamic Manuscripts of Northern Nigeria
Authors: Biddle Michaelle L 
Published: June 2011

ABSTRACTThis paper is focused on results of a survey and study in Northern Nigeria of the inks used in Islamic manuscripts and on related information on the extant traditional technologies of ink production. Knowledge of the specific inks used in the surviving, largely undated Northern Nigerian manuscripts written in Arabic script, often referred to as Islamic manuscripts, informs us about the society that created them and embeds their production within a specific cultural context. In a place such as Africa, where the historical record and archaeological heritage are so vulnerable, we look to all vestiges of material culture in order to expand out understanding of its people, its history and their culture. These manuscripts belong to the West African tradition of Islamic culture and scholarship, of which Timbuktu was a key center. Whilst another goal of the study was to establish a watermark chronology to provide information as to the papers‘ source, when particular papers were made, when manuscripts might have been copied, and their creators‘ paper preferences, the focus of this paper is on identifying and field-testing the inks used in these manuscripts. This study of over twelve thousand folios at fourteen manuscript Northern Nigerian repositories involved 4500 km of road travel and suggested a local, interrelated tradition of dye, ink and pigment fabrication. Preliminary data led to the hypothesis that the local technology provided the basis of the indigenous manuscript production, rather than one derived from the Mediterranean and the Islamic heartlands. Finally, the diversity of these manuscripts in Arabic script reflects a culture in which not everyone was Muslim but in which Islam played a dominant role.
Health Insurance Status, Medical Debt, and Their Impact on Access to Care in Arizona
Authors: Herman Patricia M. , Rissi Jill J. , Walsh Michele E. 
Published: June 2011

Objectives. We examined the impact of health insurance status on medical debt among Arizona residents and the impact of both of these factors on access to care. Methods. We estimated logistic regression models for medical debt (problems paying and currently paying medical bills) and access to care (medical care and medications delayed or missed because of cost or lack of insurance). Results. Insured status did not predict medical debt after control for health status, income, age, and household characteristics. Insured status (adjusted odds ratio [AOR] = 0.32), problems paying medical bills (AOR = 4.96), and currently paying off medical bills (AOR = 3.04) were all independent predictors of delayed medical care, but only problems paying (AOR = 6.16) and currently paying (AOR = 3.68) medical bills predicted delayed medications. Inconsistent coverage, however, was a strong predictor of problems paying bills, and both of these factors led to delays in medical care and medications. Conclusions. At least in Arizona, health insurance does not protect individuals from medical debt, and medical debt and lack of insurance coverage both predict reduced access to care. These results may represent a troubling message for US health care in general.
Mental Health Promotion in Public Health: Perspectives and Strategies From Positive Psychology
Authors: Kobau Rosemarie , Seligman Martin E.P. , Peterson Christopher , Diener Ed , Zack Matthew M. , Chapman Daniel , Thompson William 
Published: June 2011

Positive psychology is the study of what is “right” about people—their positive attributes, psychological assets, and strengths. Its aim is to understand and foster the factors that allow individuals, communities, and societies to thrive. Cross-sectional, experimental, and longitudinal research demonstrates that positive emotions are associated with numerous benefits related to health, work, family, and economic status. Growing biomedical research supports the view that positive emotions are not merely the opposite of negative emotions but may be independent dimensions of mental affect. The asset-based paradigms of positive psychology offer new approaches for bolstering psychological resilience and promoting mental health. Ultimately, greater synergy between positive psychology and public health might help promote mental health in innovative ways.
Fortification of Corn Masa Flour With Folic Acid in the United States
Authors: Fleischman Alan R. , Oinuma Motoko 
Published: June 2011

Food fortification is an effective public health tool for addressing micronutrient deficiencies. The mandatory fortification of enriched cereal grains (e.g., wheat flour) with folic acid, which began in the United States in 1998, is an example of a successful intervention that significantly reduced the rate of neural tube defects (NTDs). However, despite the drop in NTD rates across all racial/ethnic groups after fortification, Hispanics continue to have the highest rates of this condition. One possible way to reduce this disparity is to fortify corn masa flour to increase the overall intake of folic acid in Hispanic women. We present the available evidence in favor of this approach, address possible safety issues, and outline next steps in the fortification of corn masa flour with folic acid in the United States.
The Prevention of Global Chronic Disease: Academic Public Health's New Frontier
Authors: Greenberg Henry , Raymond Susan U. , Leeder Stephen R. 
Published: June 2011

A confluence of stimuli is propelling academic public health to embrace the prevention of chronic disease in developing countries as its new frontier. These stimuli are a growing recognition of the epidemic, academia's call to reestablish public health as a mover of societal tectonics rather than a handmaiden to medicine's focus on the individual, and the turmoil in the US health system that makes change permissible. To enable graduating professionals to participate in the assault on chronic diseases, schools of public health must allocate budgets and other resources to this effort. The barriers to chronic disease prevention and risk factor modulation are cultural and political; confronting them will require public health to work with a wide variety of disciplines. Chronic disease will likely become the dominant global public health issue soon. In addressing this issue, academia needs to lead, not follow.
Effect of Computer-Generated Tailored Feedback on Glycemic Control in People With Diabetes in the Community
Authors: Sherifali Diana , Greb Janet L. , Amirthavasar Gaya , Hunt Dereck , Haynes R. Brian , Harper William , Holbrook Anne , Capes Sarah , Goeree Ron , O’Reilly Daria , Pullenayegum Eleanor , Gerstein Hertzel C. 
Published: June 2011

OBJECTIVE
It is unknown whether computer-generated, patient-tailored feedback leads to improvements in glycemic control in people with type 2 diabetes.

RESEARCH DESIGN AND METHODS
We recruited people with type 2 diabetes aged ≥40 years with a glycated hemoglobin (A1C) ≥7%, living in Hamilton, Canada, who were enrolled in a community-based program (Diabetes Hamilton) that provided regular evidence-based information and listings of community resources designed to facilitate diabetes self-management. After completing a questionnaire, participants were randomly allocated to either receive or not receive periodic computer-generated, evidence-based feedback on the basis of their questionnaire responses and designed to facilitate improved glycemic control and diabetes self-management. The primary outcome was a change in A1C after 1 year.

RESULTS
A total of 465 participants (50% women, mean age 62 years, and mean A1C 7.83%) were randomly assigned, and 12-month A1C values were available in 96% of all participants, at which time the A1C level had decreased by an absolute amount of 0.24 and 0.15% in the intervention and control groups, respectively. The difference in A1C reduction for the intervention versus control group was 0.09% (95% CI −0.08 to 0.26; P = 0.3). No between-group differences in measures of quality of life, diabetes self-management behaviors, or clinical outcomes were observed.

CONCLUSIONS
Providing computer-generated tailored feedback to registrants of a generic, community-based program that supports diabetes self-management does not lead to lower A1C levels or a better quality of life than participation in the community-based program (augmented by periodic A1C testing) alone.
Increased Risk of Myocardial Infarction in Depressed Patients With Type 2 Diabetes
Authors: Scherrer Jeffrey F. , Garfield Lauren D. , Chrusciel Timothy , Hauptman Paul J. , Carney Robert M. , Freedland Kenneth E. , Owen Richard , True William R. , Lustman Patrick J. 
Published: June 2011

OBJECTIVE
To investigate major depressive disorder (MDD), which complicates the course of type 2 diabetes and is associated with an increased risk of cardiovascular disease and death. This risk may be due to a greater susceptibility for myocardial infarction (MI) in depressed patients with type 2 diabetes compared with nondepressed patients with type 2 diabetes.

RESEARCH DESIGN AND METHODS
Veterans Administration electronic medical records were analyzed to identify a cohort free of cardiovascular disease in fiscal years 1999 and 2000, aged 25 to 80 years. ICD-9-CM codes were used to create a four-level risk group indicating 1) neither diabetes nor MDD (n = 214,749), 2) MDD alone (n = 77,568), 3) type 2 diabetes alone (n = 40,953), and 4) comorbid MDD and type 2 diabetes (n = 12,679). Age-adjusted Cox proportional hazards models were computed before and after adjusting for baseline sociodemographic and time-dependent covariates.

RESULTS
After adjusting for covariates, patients with type 2 diabetes alone and patients with MDD alone were at ∼30% increased risk for MI, and patients with type 2 diabetes and MDD were at 82% increased risk for MI (hazard ratio 1.82 [95% CI 1.69–1.97]) compared with patients without either condition.

CONCLUSIONS
Compared with patients with only diabetes or only MDD, individuals with type 2 diabetes and MDD are at increased risk for new-onset MI. Monitoring cardiovascular health in depressed patients with type 2 diabetes may reduce the risk of MI in this especially high-risk group.