bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses
Authors: Polavarapu Nalini , Bowen Nathan J , McDonald John F
Published: May 2012

Background

Retrotransposons, the most abundant and widespread class of eukaryotic transposable elements, are believed to play a significant role in mutation and disease and to have contributed significantly to the evolution of genome structure and function. The recent sequencing of the chimpanzee genome is providing an unprecedented opportunity to study the functional significance of these elements in two closely related primate species and to better evaluate their role in primate evolution.

Results

We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans. Molecular analysis (PCR and Southern hybridization) of CERV 2 elements demonstrates that this family is present in chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys. A survey of endogenous retroviral positional variation between chimpanzees and humans determined that approximately 7% of all chimpanzee-human INDEL variation is associated with endogenous retroviral sequences.

Conclusion

Nine families of chimpanzee endogenous retroviruses have been transpositionally active since chimpanzees and humans diverged from a common ancestor. Seven of these transpositionally active families have orthologs in humans, one of which has also been transpositionally active in humans since the human-chimpanzee divergence about six million years ago. Comparative analyses of orthologous regions of the human and chimpanzee genomes have revealed that a significant portion of INDEL variation between chimpanzees and humans is attributable to endogenous retroviruses and may be of evolutionary significance.
Constructing a fish metabolic network model
Authors: Li Shuzhao , Pozhitkov Alexander , Ryan Rachel A , Manning Charles S , Brown-Peterson Nancy , Brouwer Marius
Published: May 2012

We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types. MetaFishNet resources, including a pathway enrichment analysis tool, are accessible at http://metafishnet.appspot.com.
Quake: quality-aware detection and correction of sequencing errors
Authors: Kelley David R , Schatz Michael C , Salzberg Steven L
Published: May 2012

We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake.
Genome-wide functional analysis of human 5' untranslated region introns
Authors: Cenik Can , Derti Adnan , Mellor Joseph C , Berriz Gabriel F , Roth Frederick P
Published: May 2012

Background

Approximately 35% of human genes contain introns within the 5' untranslated region (UTR). Introns in 5'UTRs differ from those in coding regions and 3'UTRs with respect to nucleotide composition, length distribution and density. Despite their presumed impact on gene regulation, the evolution and possible functions of 5'UTR introns remain largely unexplored.

Results

We performed a genome-scale computational analysis of 5'UTR introns in humans. We discovered that the most highly expressed genes tended to have short 5'UTR introns rather than having long 5'UTR introns or lacking 5'UTR introns entirely. Although we found no correlation in 5'UTR intron presence or length with variance in expression across tissues, which might have indicated a broad role in expression-regulation, we observed an uneven distribution of 5'UTR introns amongst genes in specific functional categories. In particular, genes with regulatory roles were surprisingly enriched in having 5'UTR introns. Finally, we analyzed the evolution of 5'UTR introns in non-receptor protein tyrosine kinases (NRTK), and identified a conserved DNA motif enriched within the 5'UTR introns of human NRTKs.

Conclusions

Our results suggest that human 5'UTR introns enhance the expression of some genes in a length-dependent manner. While many 5'UTR introns are likely to be evolving neutrally, their relationship with gene expression and overrepresentation among regulatory genes, taken together, suggest that complex evolutionary forces are acting on this distinct class of introns.
Mucin5B expression by lung alveolar macrophages is increased in long-term smokers
Authors: Sepper Ruth , Prikk Kaiu , Metsis Madis , Sergejeva Svetlana , Pugatsjova Natalia , Bragina Olga , Marran Sirje , Fehniger Thomas E
Published: May 2012

Mucin5B is expressed in alveolar macrophages in long-term smokers who have developed smoking associated lung diseases.

This study investigated the expression of MUC5B by AMs in the lungs of cigarette smokers and nonsmokers. We analyzed MUC5B expression by measuring the levels of apomucin and mRNA in human BALF cells from 50 subjects (20 nonsmokers, 17 patients with CB, and 13 patients with COPD). apoMUC5B was observed in BALF mononuclear cells in 60% of all subjects, but a significantly higher frequency of apoMUC5B+ cells was found in subjects with CB (95% CI, 4.5–24.9) or COPD (95% CI, 6.2–39.6) than in nonsmokers (95% CI, 0.5-2.5). apoMUC5B+ mononuclear cells showed strong expression of CD163, confirming their identity as AMs. MUC5B mRNA expression was detected by ISH in AMs of subjects investigated, and real-time qPCR analysis confirmed MUC5B mRNA expression. In conclusion, MUC5B is expressed in a subset of lung AMs and long-term cigarette smoking may increase the level of MUC5B produced by these cells.
Differential expression of CD14-dependent and independent pathways for chemokine induction regulates neutrophil trafficking in infection
Authors: Metkar Shalaka , Kim Kwang Sik , Silver Jack , Goyert Sanna M
Published: May 2012

Harnessing the CD14-independent pathway for chemokine induction in severe infection leads to early neutrophil recruitment to the site of infection, enhanced bacterial clearance, and survival.

Previous studies have shown that CD14−/− mice are resistant to peritoneal infection with some clinical isolates of Escherichia coli and that this resistance is accompanied by an enhanced ability to clear the bacteria; in contrast, normal mice expressing CD14 fail to clear the bacteria, causing severe sepsis and death. The enhanced clearance in CD14−/− mice is dependent on early neutrophil recruitment to the local foci of infection in the PC. The studies described show that neutrophil recruitment in CD14−/− mice occurs as a result of the local induction of the CXCL1 and CXCL2 chemokines, KC and MIP-2. Although local induction of these chemokines also occurs in normal mice, their effects on neutrophil recruitment to the PC appear to be counterbalanced by very high levels of these chemokines in the blood of normal, but not CD14−/−, mice. Neutrophil recruitment to the PC is also inhibited in normal mice in response to LPS, which also induces high chemokine levels in the blood of normal, but not CD14−/−, mice. However, MPLA, a monophosphorylated derivative of LPS, is able to induce early neutrophil recruitment in normal mice; this is because MPLA, unlike LPS or E. coli, induces MIP-2 and KC in the PC but not in the blood of normal mice. The pretreatment of normal mice with MPLA is able to protect them from a lethal E. coli infection. Thus, stimulation of a local CD14-independent chemokine induction pathway without triggering a systemic CD14-dependent chemokine pathway can protect against severe E. coli infections.
Deterministic inversion of seismic data in the depth domain
Authors: Singh Yeshpal
Published: May 2012

Deterministic seismic inversion in the time domain has been used for four decades to derive acoustic impedance from seismic data. This study introduces deterministic inversion of seismic data in the depth domain. PSDM volumes are increasingly common in exploration seismology. However, attempts to tie wells to PSDM volumes are notoriously fraught with problems. Therefore, standard practice converts PSDM output into the time domain for seismic-synthetic correlation, inversion, and reservoir property prediction. It is then necessary to convert reservoir properties back to the depth domain for the development of reservoir models. If the seismic-synthetic match and seismic inversion in the depth domain exploits depth-domain output directly for quantitative analysis, the depth-to-time conversion and time-to-depth conversion steps can be avoided without compromising quality.
In Vivo Changes in Central and Peripheral Insulin Sensitivity in a Large Animal Model of Obesity
Authors: Adam Clare L. , Findlay Patricia A. , Aitken Raymond P. , Milne John S. , Wallace Jacqueline M.
Published: May 2012

Obesity disrupts homeostatic energy balance circuits leading to insulin resistance. Here we examined in vivo peripheral and central insulin sensitivity, and whether central insensitivity in terms of the voluntary food intake (VFI) response occurs within the hypothalamus or at blood-brain transfer level, during obesity and after subsequent weight loss. Sheep with intracerebroventricular (icv) cannulae were fed complete diet for 40 wk ad libitum (obese group) or at control level (controls). Thereafter, obese sheep were food restricted (slimmers) and controls fed ad libitum (fatteners) for 16 wk. Dual-energy x-ray absorptiometry (DEXA) measured total body fat, insulin analyses in blood and cerebrospinal fluid (CSF) assessed blood-brain transfer, iv glucose tolerance test (GTT) and insulin tolerance test (ITT) measured peripheral insulin sensitivity, and VFI responses to icv insulin assessed intrahypothalamic sensitivity. Insulinemia was higher in obese than controls; plasma insulin correlated with DEXA body fat and CSF insulin. Insulinemia was higher in fatteners than slimmers but ratio of CSF to plasma insulin correlated only in fatteners. Plasma glucose baseline and area under the curve were higher during GTT and ITT in obese than controls and during ITT in fatteners than slimmers. GTT and ITT glucose area under the curve correlated with DEXA body fat. VFI decreased after icv insulin, with response magnitude correlating negatively with DEXA body fat. Overall, insulin resistance developed first in the periphery and then within the brain, thereafter correlating with adiposity; central resistance in terms of VFI response resulted from intrahypothalamic insensitivity rather than impaired blood-brain transfer; modest weight loss improved peripheral but not central insulin sensitivity and induced central hypoinsulinemia.
On the Importance of Affirmative Action: Labor Liberals and the Recasting of “Contract Unionism”
Authors: Deslippe Dennis
Published: May 2012

This issue's Up For Debate features Dennis Deslippe's revisionist argument about labor's response to affirmative action. Contrary both to those scholars who have fixed the unions as a primary obstacle to affirmative action plans pushed by civil rights organizations and public officials and to those who have identified affirmative action as an unalterable stumbling block for collective (as opposed to individual) rights on the job, Deslippe suggests a middle path of accommodation to the letter and spirit of the equal-opportunity cause on the part of an identifiable “labor liberal” sector of unions and their leaders, who opted for a progressively modified version of traditional “contract unionism.” Though such accommodation to the demands of minorities and women proved easier in relation to hiring than layoffs (where nearly all unions took a stand against the abridgment of the seniority principle), Deslippe finds that the labor movement as a whole was not the benighted monolith turning its back to the future that it appears to be in some accounts of the 1970s. Moreover, rather than an inevitable clash between union “solidarity” versus the “rights claims” of the new social movements, Deslippe suggests that the most successful unions of the period were precisely those that embraced the spirit and constituencies associated with the civil rights and women's movements. The respondents give Deslippe mixed marks. For Paul Moreno, the only good union seems to be a weak union, for to him any union preference or job protection is an economically inefficient “privilege” inevitably blocking minority access to authentic “freedom of contract.” Ava Baron welcomes Deslippe's attempt to identify a historical move among unionists to overcome divisions of race and gender, but she fears that he underestimates the basic contradictions of a labor law based on collective bargaining (and never constitutionally anchored) and employment law rooted in a deeper-sanctioned civil rights agenda. While welcoming Deslippe's challenge to the either/or view of unionism versus new social movement dichotomy of the 1960s and 1970s, both Joseph McCartin and William Jones insist on a more sector-specific (and, for McCartin, more time-sensitive) approach to the unions' evolving affirmative action policies. The large nonwhite and female memberships of the unions that chose the “egalitarian” policy path, suggests Jones, are perhaps both telling and limiting qualifiers to the expanded reach of contract unionism. Deslippe, of course, enjoys the last word.
Analysis of incidental focal hypermetabolic uptake in the breast as detected by 18F-FDG PET/CT: clinical significance and differential diagnosis
Authors: Chae Eun Young , Cha Joo Hee , Kim Hak Hee , Shin Hee Jung , Kim Hyun Ji , Oh Ha Yeun , Koh Young Hwan , Moon Dae Hyuk
Published: May 2012

Background

With the widespread use of PET/CT, incidental hypermetabolic foci unrelated to the known malignancy have been described with increasing frequency.

Purpose

To determine the frequency and clinical significance of incidental focal hypermetabolic uptake in the breast as detected by 18F-FDG PET/CT, and to explore factors differentiating benign and malignant breast uptake.

Material and Methods

From January 2005 to June 2010, a total of 51,971 whole-body FDG PET/CT examinations were performed in our clinic. After excluding 7254 sets of PET/CT data from patients known to have breast cancer, we retrospectively identified patients showing incidental focal hypermetabolic activity in the breast. Of 44,717 PET/CT examinations conducted on 32,988 patients, we identified 131 patients with no previous known or suspected benign and malignant breast disease. The etiology, mean SUVmax, and diameter of breast lesions were assessed. We also compared the presentation of the lesions on CT, mammography, and ultrasonography.

Results

Of the 131 patients, 60 were histologically diagnosed with breast lesions, including 32 with malignant and 28 with benign lesions. An additional 11 patients were followed-up for more than 2 years and were clinically considered to have benign lesions. The remaining 60 patients who had neither histologic confirmation nor followed-up for more than 2 years were excluded. Therefore, 71 patients were finally included. The mean SUVmax of 39 benign lesions and 32 malignant lesions were 2.02 ± 1.52 and 3.71 ± 3.83, respectively ( P = 0.0001). At a cut-off value of 2.3, the rate of malignancy and specificity of the mean SUVmax for differentiating benign and malignant breast lesions were 61.3%, 76.3, respectively. The CT data from PET/CT revealed that the mean diameters of benign and malignant lesions were 1.19 ± 0.97 cm and 2.26 ± 1.96 cm, respectively ( P = 0.0009).

Conclusion

Incidental focal 18F-FDG uptake in the breast as detected by PET/CT was indicative of malignancy in 45% of patients. Both mean SUVmax and diameter were greater for malignant than benign lesions.
Obesity, type 2 diabetes, and cancer: the insulin and IGF connection
Authors: Cohen Dara Hope , LeRoith Derek
Published: May 2012

Epidemiological studies suggest a positive association between obesity and type 2 diabetes mellitus (T2D) with the risk of cancer and cancer-related mortality. Insulin resistance, hyperinsulinemia, increased levels of IGF, elevated levels of steroid and peptide hormones, and inflammatory markers appear to play a role in the connection between these different diseases. Medications, such as metformin and exogenous insulin, used to treat T2D may affect the risk of cancer and cancer-related mortality. Newer therapies targeting the insulin and IGF1 systems are being developed for use in cancer therapy.
Charge Carrier TransportMechanism of ð-Conjugated Organic Materials
Authors: Kim Seong Hyun , Yang Yong Suk , Lee Jung Hun , Lim Sang Chul , Zyung Taehyoung
Published: May 2012

The complex dielectric constants of several π-conjugated materials were measured, and generalized Langevin equation was used to analyze the dielectric behavior in the frequency domain. From the results of the fitting the experimental data using the generalized Langevin equation, we suggest that the charge carriers are electrically screened by the neighboring charges through the structural relaxation, and the carriers are not interact each other. We confirmed that the generalized Langevin equation offers a very good approach to analyze and understand the transport properties of charge carriers in π-conjugated materials.
Load transfer behaviour of a tapered rigid pile
Authors: LIU J. , HE J. , WU Y.-P. , YANG Q.-G.
Published: May 2012

Based on Mohr–Coulomb theory and the load transfer method, a new method of analysing the load–settlement relation and the axial force distribution model in a tapered pile is suggested. The method proposed in the paper considers the influence of the pile–soil radial interaction on the bearing capacity and settlement behaviour. The calculation results show that the pile–soil radial interaction is strengthened and the bearing capacity of a single pile is increased when the taper angle of a rigid pile is increased. The reliability was verified by two model tests. Calculated results obtained by the proposed method were compared with the test data. The close agreement between the calculated and measured values confirmed that the method is reasonably accurate for analysing the behaviour of tapered rigid piles.
Ecosystem assembly rules: the interplay of green and brown webs during salt marsh succession
Authors: Schrama Maarten , Berg Matty P. , Olff Han
Published: May 2012

Current theories about vegetation succession and food web assembly are poorly compatible, as food webs are generally viewed to be static, and succession is usually analyzed without the inclusion of higher trophic levels. In this study we present results from a detailed analysis of ecosystem assembly rules over a chronosequence of 100 years of salt marsh succession. First, using 13 yearlong observations on vegetation and soil parameters in different successional stages, we show that the space‐for‐time substitution is valid for this chronosequence. We then quantify biomass changes for all dominant invertebrate and vertebrate species across all main trophic groups of plants and animals. All invertebrate and vertebrate species were assigned to a trophic group according to feeding preference, and changes in trophic group abundance were quantified for seven different successional stages of the ecosystem. We found changes from a marine‐fueled, decomposer‐based (brown) food web in early stages to a more terrestrial, plant‐based, herbivore‐driven (green) food web in intermediate succession stages, and finally to a decomposer‐based, terrestrial‐driven food web in the latest stages. These changes were accompanied not only by an increase in live plant biomass and a leveling toward late succession but also by a constant increase in the amount of dead plant biomass over succession. Our results show that the structure and dynamics of salt marsh food webs cannot be understood except in light of vegetation succession, and vice versa.
A multi‐isotope (δ13C, δ15N, δ2H) feather isoscape to assign Afrotropical migrant birds to origins
Authors: Hobson K. A. , Van Wilgenburg S. L. , Wassenaar L. I. , Powell R. L. , Still C. J. , Craine J. M.
Published: May 2012

A universal challenge in methodology used to study the ecology, conservation and evolutionary biology of migratory species is the quantification of connectivity among breeding, wintering and stopover sites. For the avian Eurasian‐Afrotropical migratory system, knowledge of geographical wintering areas used by migrants that breed in Europe remains deficient, despite the advent of satellite transmitters and geolocators. Here we explored the use of theoretical plant δ13C and δ15N landscape distributions coupled with δ2H hydrologic models to construct multi‐isotopic avian foodweb clusters for Africa. The cluster analysis identified four distinct regions of Africa based on all three isotopes (13C, 2H, 15N), and five regions based only on 13C and 15N. We applied known isotopic diet‐tissue discrimination factors to map equivalent feather isotopic clusters for Africa. The validity of these feather isotopic clusters was tested by examining how well known‐ and unknown‐origin species were placed in regions of Africa using previously published feather isotope data. The success of this multi‐isotopic cluster model depended upon the species of interest and additionally on how well potential winter molt origins in Africa were constrained by prior information. Ground‐truthing data suggested this approach will be useful for first‐order approximation of overwintering regions for Afrotropical migrants and will be improved as our understanding of the nature of isoscapes for Africa is refined.
Community Health Worker Encounter Forms: A Tool to Guide and Document Patient Visits and Worker Performance
Authors: Lemay Celeste A. , Ferguson Warren J. , Hargraves J. Lee
Published: May 2012

Objectives. We explored the benefits of using community health worker (CHW) encounter forms to collect data on patient interactions and assessed the effectiveness of these forms in guiding and directing interactions.

Methods. A 1-page standardized encounter form was developed to document topics discussed during visits with diabetes patients. A portion of the form was designed to be used as a script to guide the interaction and assist patients in setting appropriate self-management goals. Data were also collected via CHW work logs and interviews with CHWs and their supervisors to validate findings.

Results. Data were collected for 1198 interactions with 540 patients at 6 community health centers. Self-management goals were set during 62% of encounters. With respect to the most recent self-management goal set, patients who had set a challenging goal were more likely to be in the action stage of change than in other stages. Work logs revealed that CHWs engaged in a number of activities not involving direct patient interactions and thus not captured on encounter forms.

Conclusions. Evaluating and monitoring CHWs’ daily activities has been challenging. Encounter forms have great potential for documenting the work of CHWs with patients.
Lessons Learned From a Community–Academic Initiative: The Development of a Core Competency–Based Training for Community–Academic Initiative Community Health Workers
Authors: Ruiz Yumary , Matos Sergio , Kapadia Smiti , Islam Nadia , Cusack Arthur , Kwong Sylvia , Trinh-Shevrin Chau
Published: May 2012

Objectives. Despite the importance of community health workers (CHWs) in strategies to reduce health disparities and the call to enhance their roles in research, little information exists on how to prepare CHWs involved in community–academic initiatives (CAIs). Therefore, the New York University Prevention Research Center piloted a CAI–CHW training program.

Methods. We applied a core competency framework to an existing CHW curriculum and bolstered the curriculum to include research-specific sessions. We employed diverse training methods, guided by adult learning principles and popular education philosophy. Evaluation instruments assessed changes related to confidence, intention to use learned skills, usefulness of sessions, and satisfaction with the training.

Results. Results demonstrated that a core competency–based training can successfully affect CHWs’ perceived confidence and intentions to apply learned content, and can provide a larger social justice context of their role and work.

Conclusions. This program demonstrates that a core competency–based framework coupled with CAI-research–specific skill sessions (1) provides skills that CAI–CHWs intend to use, (2) builds confidence, and (3) provides participants with a more contextualized view of client needs and CHW roles.
Social Patterning of Cumulative Biological Risk by Education and Income Among African Americans
Authors: Hickson DeMarc A. , Diez Roux Ana V. , Gebreab Samson Y. , Wyatt Sharon B. , Dubbert Patricia M. , Sarpong Daniel F. , Sims Mario , Taylor Herman A.
Published: May 2012

Objectives. We examined the social patterning of cumulative dysregulation of multiple systems, or allostatic load, among African Americans adults.

Methods. We examined the cross-sectional associations of socioeconomic status (SES) with summary indices of allostatic load and neuroendocrine, metabolic, autonomic, and immune function components in 4048 Jackson Heart Study participants.

Results. Lower education and income were associated with higher allostatic load scores in African American adults. Patterns were most consistent for the metabolic and immune dimensions, less consistent for the autonomic dimension, and absent for the neuroendocrine dimension among African American women. Associations of SES with the global allostatic load score and the metabolic and immune domains persisted after adjustment for behavioral factors and were stronger for income than for education. There was some evidence that the neuroendocrine dimension was inversely associated with SES after behavioral adjustment in men, but the immune and autonomic components did not show clear dose–response trends, and we observed no associations for the metabolic component.

Conclusions. Findings support our hypothesis that allostatic load is socially patterned in African American women, but this pattern is less consistent in African American men.
Racial Residential Segregation and Rates of Gonorrhea in the United States, 2003–2007
Authors: Biello Katie B , Kershaw Trace , Nelson Robert , Hogben Matthew , Ickovics Jeannette , Niccolai Linda
Published: May 2012

Objectives. In the United States, Black persons are disproportionately affected by sexually transmitted infections (STIs), including gonorrhea. Individual behaviors do not fully explain these racial disparities. We explored the association of racial residential segregation with gonorrhea rates among Black persons and hypothesized that specific dimensions of segregation would be associated with gonorrhea rates.

Methods. We used 2003 to 2007 national STI surveillance data and 2000 US Census Bureau data to examine associations of 5 dimensions of racial residential segregation and a composite measure of hypersegregation with gonorrhea rates among Black persons in 257 metropolitan statistical areas, overall and by sex and age. We calculated adjusted rate ratios with generalized estimating equations.

Results. Isolation and unevenness were significantly associated with gonorrhea rates. Centralization was marginally associated with gonorrhea. Isolation was more strongly associated with gonorrhea among the younger age groups. Concentration, clustering, and hypersegregation were not associated with gonorrhea.

Conclusions. Certain dimensions of segregation are important in understanding STI risk among US Black persons. Interventions to reduce sexual risk may need to account for racial residential segregation to maximize effectiveness and reduce existent racial disparities.
A Call for Further Research on the Impact of State-Level Immigration Policies on Public Health
Authors: Hardy Lisa J. , Getrich Christina M. , Quezada Julio C. , Guay Amanda , Michalowski Raymond J. , Henley Eric
Published: May 2012

Arizona’s Support Our Law Enforcement and Safe Neighborhoods Act, signed into law in April 2010, is already adversely affecting public health in the state.

Our findings from a study on childhood obesity in Flagstaff suggest that the law changed health-seeking behaviors of residents of a predominantly Latino neighborhood by increasing fear, limiting residents’ mobility, and diminishing trust of officials. These changes could exacerbate barriers to healthy living, limit access to care, and affect the overall safety of the neighborhood.

Documentation of the on-the-ground impact of Arizona's law and similar state-level immigration policies is urgently needed. To inform effective policymaking, such research must be community engaged and include safety measures beyond the usual protocols.
The Bittersweet Truth About Sugar Labeling Regulations: They Are Achievable and Overdue
Authors: Pomeranz Jennifer L.
Published: May 2012

The recent Institute of Medicine recommendation to the Food and Drug Administration to include added sugar in a new front-of-package system provides new justification for reviewing outdated regulations pertinent to sugar and analyzing whether the government’s previous resistance to sugar labeling remains valid given new and robust science.

I have provided an overview of US sugar consumption, its public health implications, and the science related to added sugar detection. I reviewed US and international sugar intake recommendations and suggested revised regulations to better inform and protect consumers.

I concluded by noting new directions in the area of sugar research for future public health policy.
National Institutes of Health Approaches to Dissemination and Implementation Science: Current and Future Directions
Authors: Glasgow Russell E. , Vinson Cynthia , Chambers David , Khoury Muin J. , Kaplan Robert M. , Hunter Christine
Published: May 2012

To address the vast gap between current knowledge and practice in the area of dissemination and implementation research, we address terminology, provide examples of successful applications of this research, discuss key sources of support, and highlight directions and opportunities for future advances. There is a need for research testing approaches to scaling up and sustaining effective interventions, and we propose that further advances in the field will be achieved by focusing dissemination and implementation research on 5 core values: rigor and relevance, efficiency, collaboration, improved capacity, and cumulative knowledge.
Global Health in Conflict Understanding Opposition to Vitamin A Supplementation in India
Authors: Wallace Sarah K.
Published: May 2012

Vitamin A supplementation is a public health intervention that clinical trials have suggested can significantly improve child survival in the developing world. Yet, prominent scientists in India have questioned its scientific validity, opposed its implementation, and accused its advocates of corruption and greed. It is ironic that these opponents were among the pioneers of populationwide vitamin A supplementation for ocular health. Historically, complex interests have shaped vitamin A supplementation resistance in India. Local social and nutritional revolutions and shifting international paradigms of global health have played a role. Other resistance movements in Indian history, such as those in response to campaigns for bacillus Calmette-Guérin and novel vaccines, have been structured around similar themes. Public health resistance is shaped by the cultural and political context in which it develops. Armed with knowledge of the history of a region and patterns of past resistance, public health practitioners can better understand how to negotiate global health conflicts.
Vortex-Shedding Forces and the Fatigue Analysis of Offshore Structures
Authors: Walker S. , Brazier S. G.
Published: May 2012

This paper describes a method of incorporating vortex-shedding effects into a finite element model of a steel jacket. Recent experimental evidence has indicated fatigue rates are greater than predicted by conventional fatigue studies only incorporating direct wave loading.

The forces due to vortex shedding have been considered with reference to a large steel structure in 300 feet of water in the North Sea. These vortex shedding forces have been found to be important because they are generated with frequencies much higher than the frequency of the wave producing them. This produces effective forcing at frequencies where the dynamic natural natural response of the structure is appreciable.
Data Assimilation with Soil Water Content Sensors and Pedotransfer Functions in Soil Water Flow Modeling
Authors: Pan Feng , Pachepsky Yakov , Jacques Diederik , Guber Andrey , Hill Robert L.
Published: May 2012

Soil water flow models are based on simplified assumptions about the mechanisms, processes, and parameters of water retention and flow. That causes errors in soil water flow model predictions. Data assimilation (DA) with the ensemble Kalman filter (EnKF) corrects modeling results based on measured state variables, information on uncertainty in measurement results and uncertainty in modeling results. The objectives of this work were (i) to evaluate pedotransfer functions (PTFs) as a source of data to generate an ensemble of Richards′ equation‐based models for the EnKF application to the assimilation of soil water content data and (ii) to research how effective assimilation of soil moisture sensor data can be in correcting simulated soil water content profiles in field soil. Data from a field experiment were used in which 60 two‐rod time domain reflectometry (TDR) probes were installed in a loamy soil at five depths to monitor the soil water content. The ensemble of models was developed with six PTFs for water retention and four PTFs for the saturated hydraulic conductivity (Ksat). Measurements at all five depths and at one or two depths were assimilated. Accounting for the temporal stability of water contents substantially decreased the estimated noise in data. Applicability of the Richards′ equation was confirmed by the satisfactory calibration results. In absence of calibration and data assimilation, simulations developed a strong bias caused by the overestimation of Ksat from PTFs. Assimilating measurements from a single depth of 15 cm or of 35 cm provided substantial improvements at all other observation depths. An increase in data assimilation frequency improved model performance between the assimilation times. Overall, bringing together developments in pedotransfer functions, temporal stability of soil water patterns, and soil water content sensors can create a new source of data to improve modeling results in soil hydrology and related fields.
Carbon Flow from Plant Detritus and Soil Organic Matter to Microbes—Linking Carbon and Nitrogen Cycling in Semiarid Soils
Authors: Hooker Toby D. , Stark John M.
Published: May 2012

We used in situ 13C‐labeling of an annual grass to examine the decomposition rate and fate of detrital C over 17 mo in a sagebrush ecosystem. We coupled these measurements with 15N pool dilution and tracer measurements to examine seasonal changes in gross N cycling rates in bulk soil and organic matter density fractions. Annual grass fine roots decomposed rapidly (0.23 mo−1) over the 17 mo, substantially faster than rates typically reported for other semiarid ecosystems using litterbags. Despite a long summer dry period, recent detrital C was rapidly respired and incorporated into microbial biomass and nonmicrobial fractions between summer and autumn. Decomposition of recent detritus accounted for 13% of mineralized C and 9% of microbial C produced during the summer following plant labeling. These proportions declined by 50% in autumn, indicating that microbes relied more heavily on recent detritus for C and energy during the dry summer than during the following moist autumn months. In spite of this, decomposition rates of recent plant detritus were faster during autumn than summer due to higher rates of microbial activity. Nitrogen immobilization into soil organic matter (SOM) fractions increased from summer to autumn and was fastest in spring. Rates of N immobilization into the supposedly recalcitrant heavy‐fraction (HF) SOM were faster than into the light fraction; however, rates in light and heavy fractions were similar when expressed per unit organic C. Rates of N immobilization were positively correlated with the 13C content of density fractions, suggesting that inputs of new plant C were an important driver of N immobilization. While addition of NH4+ stimulated nitrification rates in both summer and autumn, NH4+ addition only stimulated rates of N immobilization during spring, indicating that heterotrophic microbial growth was N limited during spring but C limited during summer and autumn when plants were not actively growing. Our results indicate that root decomposition in semiarid soils is more rapid than previously thought, and is not likely to be N limited. Moreover, HF SOM is not as recalcitrant as is frequently assumed, but instead, it is a strong sink for recent plant C inputs and a driver of N immobilization in soil.
Generalized Coupled Source–Sink Model for Evaluating Transient Water Uptake in Trickle Irrigation: II. Irrigation Scheduling Scenarios
Authors: Communar Gregory , Friedman Shmulik P.
Published: May 2012

The previously derived coupled source–sink modeling approach for vertically heterogeneous cylindrical domains was extended to conditions prevailing when water uptake is controlled by diurnally time‐varying, transpiration‐driven plant resistance and by cyclic water applications, both leading to unsteady flow regimes in the rooting zone. Examples include simulations of diurnal variations in water uptake rates by plant roots (sinks) in homogeneous and vertically heterogeneous soils of various texture, under conditions of steady, continuous and unsteady water application, representative of various irrigation scheduling practices: pulsed, daily, and every few days. In coarse‐textured, fast‐responding soil, it is possible to meet the diurnal transpiration demand, but water losses through deep percolation are high. In soils of finer texture, daily short applications in the morning result in uptake patterns skewed toward morning, whereas all‐day‐long irrigation pushes the temporal uptake pattern toward the afternoon. In fine‐textured soils irrigated every few days, similar water uptake volumes result from either prolonged, all‐day, or short, morning applications, but the through‐cycle uptake rates are more even with all‐day applications.
A New Method for Developing Equations Applied to the Water Retention Curve
Authors: Gould Scott , Rajeev Pathmanathan , Kodikara Jayantha , Zhao Xiao-Ling , Burn Stewart , Marlow David
Published: May 2012

The soil water retention curve (WRC) represents the relationship between soil suction and water content. Previous equations for representing the WRC do not include a direct relationship between features of the curve and equation fitting parameters. We present a new method for developing equations for representing empirical data that ensures that features of the curve are directly related to fitting parameters in the equation. The method also ensures that the equation has a simple derivative and is readily integrated, an important property if the equation is to be used as part of a numerical model. This method has been applied to the WRC, producing a new equation that is able to accurately represent the entire WRC using a single equation. The direct relationship between the main features of the curve and fitting parameters ensures that the fitting parameters have clear theoretical meaning. Additionally, this direct relationship allows fitting parameters, such as the air‐entry value, to be calculated using pedotransfer functions. The equation has been fitted to a wide range of experimental data and has been demonstrated to achieve an excellent fit for sand, silt, and clay soils across the entire suction range from the minimum measured suction value to 106 kPa.
Soil Microbial Community Recovery in Reclaimed Soils on a Surface Coal Mine Site
Authors: Dangi Sadikshya R. , Stahl Peter D. , Wick Abbey F. , Ingram Lachlan J. , Buyer Jeffrey S.
Published: May 2012

Recovery of belowground microbial community structure is important for reclamation success. In this study, the recovery of soil microbial community structure in cool‐season grass dominated and sagebrush dominated reclaimed sites were examined using chronosequences ranging in time following reclamation from <1 to 26 yr. Phospholipid fatty acid (PLFA) analysis was used to characterize changes in microbial community structure with time. Initial effects of surface mining resulted in reductions of total microbial biomass and diversity, with the greatest influence on saprophytic fungi and arbuscular mycorrhizal fungi relative to undisturbed soils. The total concentration of PLFA biomarkers increased after 14 yr in soils established under cool‐season grass communities and 5 yr in soils colonized by sagebrush communities. Canonical multivariate analysis of variance indicated that soil microbial communities under reestablished sagebrush were more similar to one another than those under cool‐season grasses. In general, microbial biomarkers of reclaimed soils recovered to predisturbance levels within 5 to 14 yr, which indicated that the most important phase of microbial community recovery occurs between 5 and 14 yr after reclamation.
Prediction of Soil Nitrogen Supply in Corn Production using Soil Chemical and Biological Indices
Authors: Nyiraneza Judith , Ziadi Noura , Zebarth Bernie J. , Sharifi Mehdi , Burton David L. , Drury Craig F. , Bittman Shabtai , Grant Cynthia A.
Published: May 2012

Assessment of the soil N supply capacity is essential to optimize N fertilizer use. The soil N supply capacity of 102 soil samples (0–15 cm) from 25 sites collected from 2004 to 2007 across four Canadian provinces was evaluated by comparing a group of chemical N availability indices with soil mineralizable N pools and a field‐based measure of soil N supply. Soil N supply was estimated by corn (Zea mays L.) N uptake corrected for starter fertilizer N. Two subgroups were created based on the soil texture and were compared to the whole data set. Grouping soils provided limited benefits in predicting soil potentially mineralizable nitrogen (N0), but improved the prediction of soil N supply. The N0 was weakly related to soil N supply for the whole data set (r = 0.09) and in fine‐textured soils (r = 0.37) but the relationship was improved (r = 0.68) in medium‐ to coarse‐textured soils. The N0 was not necessarily a good predictor of soil N supply under field conditions which emphasizes the need to also consider environmental conditions. The UV absorbance of a 0.01 M NaHCO3 extract at 205 nm (NaHCO3–205), the hot KCl extractable NH4–N (HotKCl–N) and Pool I (a labile mineralizable N pool) plus NO3–N were the most promising N availability indices because they are easy to perform and they were positively and significantly related to soil N supply in the whole data set as well as the soil texture subgroups (0.28 ≤ r ≤ 0.62). This study demonstrated that grouping soils based on texture can increase the proportion of variation in soil N supply explained by N availability indices when data from contrasting environmental conditions, soil types, and years are used.
Tall Fescue Management in the Piedmont: Sequestration of Soil Organic Carbon and Total Nitrogen
Authors: Franzluebbers A. J. , Endale D. M. , Buyer J. S. , Stuedemann J. A.
Published: May 2012

High‐quality surface‐soil characteristics are important for developing environmentally sustainable agroecosystems. We evaluated the factorial combination of fertilization regime (inorganic and broiler litter) and tall fescue [Lolium arundinaceum (Schreb.) Darbysh.]–endophyte association (free, novel, and wild) with cattle grazing (plus a control treatment of inorganic fertilizer + novel endophyte with haying) on surface soil compaction and soil organic C and total N sequestration during 8 yr of management on a previously degraded Typic Kanhapludult in Georgia. Soil organic C and total N were sequestered with time at all depth intervals to 20 cm (0–3, 3–6, 6–12, and 12–20 cm). At a depth of 0 to 6 cm (surface zone most responsive to management), soil organic C sequestration was (i) greater with grazed than with hayed management (1.36 vs. 0.69 Mg C ha−1 yr−1, respectively), (ii) similar between broiler litter and inorganic fertilization, (iii) similar among endophyte associations, and (iv) similar among zones within a grazed pasture. At a depth of 0 to 20 cm, soil organic C and total N sequestration were not significantly affected by treatment variables, but high mean sequestration rates of 1.51 Mg C ha−1 yr−1 and 0.126 Mg N ha−1 yr−1 during managed grazing of tall fescue in addition to the previous decade of unmanaged herbaceous fallow (implied sequestration rates of 0.76 Mg C ha−1 yr−1 and 0.062 Mg N ha−1 yr−1) suggests that improved grazing management systems can have an enormous benefit to surface soil fertility restoration of degraded soils in the southeastern United States.
Prediction of Soil Nitrogen Supply in Potato Fields using Soil Temperature and Water Content Information
Authors: Dessureault-Rompré Jacynthe , Zebarth Bernie J. , Burton David L. , Georgallas Alex , Sharifi Mehdi , Porter Gregory A. , Moreau Gilles , Leclerc Yves , Arsenault Walter J. , Chow T. Lien , Grant Cynthia A.
Published: May 2012

This study evaluated different strategies for use of a simple first‐order kinetic model (Nmin = N0[1– e−kt] where N0 is potentially mineralizable nitrogen and k is the mineralization rate constant) to predict growing season soil nitrogen supply (SNS) in potato (Solanum tuberosum L.) fields under cool humid climatic conditions. All strategies considered spring soil mineral nitrogen (SMN) and the labile mineralizable N pool (Pool I), and correction of the value of k was evaluated based on temperature (T) only, or based on both T and water content (θ). The strategies examined: (i) the depth of the soil used; (ii) the choice of k value used for Pool I; and (iii) the replenishment of the mineralizable N pools. Predicted SNS was compared with a field‐based estimate of plant available soil nitrogen supply (PASNS) measured as plant (vine plus tuber) N uptake plus residual nitrate at harvest in unfertilized plots. When k was corrected using T only, the strategies generally overestimated the PASNS. When k was corrected using both T and θ, predicted SNS was not significantly different from PASNS in most cases. The most promising strategy used a depth of 0 to 20 cm, the common depth for tillage, rather than 0 to 15 cm, which represents the actual depth used for soil sampling. This study demonstrated that SNS can be adequately predicted using a simple kinetic model, and that consideration of soil water content was important in predicting SNS even in humid soil moisture regimes.