bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Human Her-2/neu Chimeric Molecule Expressed byListeria monocytogenesCan Elicit Potent HLA-A2 Restricted CD8-positive T cell Responses and Impact the Growth and Spread of Her-2/neu-positive Breast Tumors
Authors: Seavey Matthew M. , Pan Zhen-Kun , Maciag Paulo C. , Wallecha Anu , Rivera Sandra , Paterson Yvonne , Shahabi Vafa
Published: February 2009

Purpose: The aim of this study was to efficiently design a novel vaccine for human Her-2/neu-positive (hHer-2/neu) breast cancer using the live, attenuated bacterial vector Listeria monocytogenes.

Experimental Design: Three recombinant L. monocytogenes–based vaccines were generated that could express and secrete extracellular and intracellular fragments of the hHer-2/neu protein. In addition, we generated a fourth construct fusing selected portions of each individual fragment that contained most of the human leukocyte antigen (HLA) epitopes as a combination vaccine (L. monocytogenes–hHer-2/neu chimera).

Results: Each individual vaccine was able to either fully regress or slow tumor growth in a mouse model for Her-2/neu-positive tumors. All three vaccines could elicit immune responses directed toward human leukocyte antigen-A2 epitopes of hHer-2/neu. The L. monocytogenes–hHer-2/neu chimera was able to mimic responses generated by the three separate vaccines and prevent spontaneous outgrowth of tumors in an autochthonous model for Her-2/neu-positive breast cancer, induce tumor regression in transplantable models, and prevent seeding of experimental lung metastases in a murine model for metastatic breast cancer.

Conclusion: This novel L. monocytogenes–hHer-2/neu chimera vaccine proves to be just as effective as the individual vaccines but combines the strength of all three in a single vaccination. These encouraging results support future clinical trials using this chimera vaccine and may be applicable to other cancer types expressing the Her-2/neu molecule such as colorectal and pancreatic cancer.
Genetically Targeted T Cells Eradicate Established Breast Cancer in Syngeneic Mice
Authors: Wang Hao , Wei Huafeng , Zhang Ruiping , Hou Sheng , Li Bohua , Qian Weizhu , Zhang Dapeng , Kou Gen , Dai Jianxin , Guo Yajun
Published: February 2009

Purpose: The purpose of the present study was to evaluate the capacity and mechanisms of genetically modified erbB2-specific T cells to eradicate erbB2+ tumors in syngeneic mice.

Experimental Design: Primary mouse T cells were modified to target the breast tumor–associated antigen erbB2 through retroviral-mediated transfer of a chimeric antigen receptor, termed single-chain antibody (scFv)–CD28–ζ. Antitumor efficacy of scFv-CD28-ζ–modified T cells was analyzed in mice bearing D2F2/E2 breast tumors.

Results: The scFv-CD28-ζ–modified T cells were shown to specifically secrete T cytotoxic-1 cytokines and lyse erbB2+ breast tumor cells following receptor stimulation in vitro. Treatment with scFv-CD28-ζ–modified T cells was able to lead to long-term, tumor-free survival in mice bearing erbB2+ D2F2/E2 breast tumors. Importantly, the surviving mice developed a host memory response to D2F2/E2 tumor cells, and this host response was able to protect against a rechallenge with erbB2+ D2F2/E2 tumor cells and parental erbB2- D2F2 tumor cells. In addition, scFv-CD28-ζ T-cell expression of perforin and interferon-γ were essential for complete antitumor efficacy.

Conclusions: Treatment with scFv-CD28-ζ–modified T cells was able to induce a host antitumor immunity in syngeneic mice. Complete tumor elimination by scFv-CD28-ζ–modified T cells required T cell–derived interferon-γ and perforin, indicating that cytotoxicity and cytokine secretion play a role in the in vivo response.
Overcoming Cancer Immune Tolerance and Escape
Authors: Clifton Guy T. , Peoples George E.
Published: February 2009

Although HER2/neu–targeted cancer vaccines have shown initial promise in the adjuvant setting, a therapeutic vaccine remains elusive due to the tumor escape mechanisms of established cancer. As described by Seavey et al. in this issue of CCR, a Listeria-delivered vaccine may help overcome immune tolerance, leading to an effective therapeutic vaccine.
Modulation of Endothelium and Endothelial Progenitor Cell Function by Low-Density Lipoproteins: Implication for Vascular Repair, Angiogenesis and Vasculogenesis
Authors: Rodríguez Cristina , Slevin Mark , Rodríguez-Calvo Ricardo , Kumar Shant , Krupinski Jerzy , Tejerina Teresa , Martínez-González José
Published: February 2009

The endothelium regulates vascular homeostasis and is responsible for angiogenesis, a process mediated by the sprouting of endothelial cells from pre-existing vessels. Several lines of evidence indicate that endothelial progenitor cells (EPCs) also play a role in adult neovascularization as well as in the maintenance of endothelial integrity and function. Hypercholesterolemia is associated with increased cardiovascular risk by inducing a cascade of events leading to endothelial dysfunction and injury. Growing evidence indicates that low-density lipoproteins (LDLs) impair endothelial reparative processes by inducing endothelial cell apoptosis but also by reducing the number and function of EPCs. The involvement of LDLs in mechanisms associated with vascular repair and neovascularization is also suggested by data from studies using lipid-lowering drugs (statins). This review is focused on the central role of the cholesterol pathway in the biology of the endothelium and EPCs.
Changes of the Alternative Splicing Variants of Human Telomerase Reverse Transcriptase during Gastric Carcinogenesis
Authors: Xu Jin-Heng , Wang Yu-Chuan , Geng Xin , Li Yan-Yun , Zhang Wei-Ming
Published: February 2009

Objective: We attempted to reveal the changes of the human telomerase reverse transcriptase (hTERT) alternative splicing pattern in gastric carcinogenesis. Methods: Three alternative splicing sites (α, β, γ) were selected and designed PCR primer. The expression of 8 hTERT alternative splicing variants (ASVs) in normal gastric mucosa, precancerous lesions and gastric cancer were detected by seminested RT-PCR. The expression of β-site remaining ASV (β+ ASV) in specimens of precancerous lesions and specimens of gastric cancer was detected by SYBER Green real-time PCR. Results: The positive rate of α+β+γ+ ASV was significantly higher in gastric cancer than in precancerous lesions and normal mucosa (94.7 vs. 40.0% and 0%, p < 0.05). The positive rates of other ASVs were not different among the 3 groups (p > 0.05). The positive rates of β+ ASVs (including α+β+γ+ ASV, α-deletion ASV, γ-deletion ASV, αγ-deletion ASV) were 11.1% in normal mucosa, 40.0% in precancerous lesions and 94.7% in gastric cancer (p < 0.05). SYBR Green real-time RT-PCR showed that the expression level of β+ ASV was 6.99 times higher in gastric cancer than in precancerous lesions. Conclusion: hTERT alternative splicing pattern is different during gastric carcinogenesis. β+ ASV was widely expressed in gastric carcinogenesis and may provide some information for diagnosis of gastric cancer or precancerous lesions.
Immunohistochemical Analysis of Neuroendocrine Differentiation in Prostate Cancer
Authors: Ishida Eiwa , Nakamura Mitsutoshi , Shimada Keiji , Tasaki Masato , Konishi Noboru
Published: February 2009

Objective: To clarify the significance of neuroendocrine differentiation in prostate cancer. Methods: We immunohistochemically examined 96 samples of prostatic cancers obtained from radical prostatectomies using a specific neuroendocrine marker and various neuropeptides, as well as markers for cell proliferation, angiogenesis and androgen-receptor expression. Results: We frequently found neuroendocrine cells in atrophic glands with or without chronic inflammation in nontumorous tissues. Neuroendocrine cells were detected in 36.5% of prostate cancer samples overall, but had no significant correlation to angiogenesis, cell proliferation or biochemical recurrence. However, patients with a high frequency of neuroendocrine cells (9.4%) tended to undergo preoperative hormonal therapy (p = 0.060), which led to their cancers being atrophic with inflammation. The neuroendocrine cells in these patients contained calcitonin-positive cells (p ≤ 0.0001), and calcitonin positivity showed significant association with high Gleason score (p = 0.045) in the group without preoperative therapy. In the group undergoing preoperative therapy, a high prostate-specific antigen titer at first admission correlated to significant biochemical recurrence (p = 0.003). Conclusions: Neuroendocrine cells may be induced under conditions of atrophy with or without chronic inflammation in both noncancerous glands and in cancers, including calcitonin-positive cells. Neither positive neuroendocrine nor positive androgen-receptor status appears predictive for biochemical recurrence.
COX-2 Expression Does Not Correlate with Microvessel Density in Breast Cancer
Authors: Thorat Mangesh A. , Mehrotra Sanjana , Morimiya Akira , Badve Sunil
Published: February 2009

Background:Cyclooxygenase-2 (COX-2), implicated in carcinogenesis and tumour progression in many cancers including breast cancer, is hypothesised to cause progression by promoting angiogenesis. The exact mechanism of such action is not known and the clinical evidence of such interaction is weak. We studied COX-2 expression and microvessel density (MVD) in malignant breast tissues. Methods:COX-2 expression was analysed by immunohistochemistry in 89 breast cancer cases. MVD was assessed by CD31 immunohistochemistry using the Chalkey count method. COX-2 expression and MVD data were correlated with each other and with other prognostic factors. Results: COX-2 expression, observed in 70 (79%) cases, correlated positively with tumour type (p = 0.037) and tumour grade (p = 0.045), but negatively with oestrogen receptor (p = 0.013). It did not correlate with tumour size, axillary lymph node status, progesterone receptor and HER-2 status. MVD varied from 2.09 to 40.38, correlated positively with tumour grade (p = 0.050) and tumour size (p = 0.044), but negatively with progesterone receptor (p = 0.040). MVD did not correlate with tumour type, axillary lymph node status, oestrogen receptor and HER-2. There was no correlation between COX-2 expression and MVD (p = 0.702). Conclusions: COX-2 expression does not correlate with angiogenesis in breast cancer. Angiogenesis in breast cancer may be dependent on multiple genes, rather than on COX-2 alone.
Determinants of Interleukin-6 and C-Reactive Protein Vary in Polycystic Ovary Syndrome, as Do Effects of Short- and Long-Term Metformin Therapy
Authors: Tsilchorozidou Tasoula , Mohamed-Ali Vidya , Conway Gerard S.
Published: February 2009

Objective, Design and Methods: Circulating levels of interleukin-6 (IL-6) and C-reactive protein (CRP) were determined in 59 women with polycystic ovary syndrome, of whom 37 were retested after receiving metformin for 6 weeks and 6 months, to ascertain the response of these inflammatory markers to weight loss and insulin sensitization. Results: IL-6 levels correlated significantly with body mass index (BMI; r = 0.55), homoeostasis model insulin resistance index (HOMA-R; r = 0.47) and CRP (r = 0.59). On multiple regression analysis, adiposity rather than IL-6 accounted for most of the variability of CRP independently of insulin resistance, while IL-6 remained closely with adiposity. After 6 weeks of metformin therapy (n = 37) there was a significant reduction in BMI (p < 0.001), waist (p < 0.001) and CRP (p < 0.01), while at 6 months there was not only a significant reduction in BMI and waist but also in HOMA-R (p = 0.01) and IL-6 levels (p < 0.01) with no further reduction of CRP. Conclusions: In polycystic ovary syndrome, obesity rather than IL-6 or insulin resistance is the main determinant of CRP. While short-term metformin therapy facilitates weight loss with a concomitant reduction in CRP, long-term therapy results in a reduction of IL-6 and insulin resistance. Metformin-associated reduction of CRP levels prior to any significant changes in insulin resistance or IL-6 perhaps involves different mechanisms of action.
Prevalence of Thyroid Dysfunction in Obese Children and Adolescents before and after Weight Reduction and Its Relation to Other Metabolic Parameters
Authors: Shalitin S. , Yackobovitch-Gavan M. , Phillip M.
Published: February 2009

Aim: To establish the prevalence of elevated thyroid-stimulating hormone (TSH) levels in obese children and adolescents, and identify the relationship between changes in TSH levels and other metabolic and hormonal variables before and after weight reduction. Methods: 207 obese participants aged 5–18 years were evaluated for anthropometric, biochemical, metabolic and hormonal variables before and after a weight reduction. Results: At baseline, 46 participants (22.2%) had hyperthyrotropinemia (≥4.0 mIU/l). Free T4 levels were normal in all cases. Triglyceride levels were significantly higher in participants with hyperthyrotropinemia than in those with normal thyroid function (p = 0.011). Baseline TSH was significantly correlated with triglyceride levels (r = 0.261, p < 0.001), but not with age, anthropometric, or laboratory variables. Of the 142 participants who completed the intervention, 27 (19 %) had hyperthyrotropinemia. There was no significant relationship between changes in TSH level and changes in body mass index-standard deviation score. A significant correlation was found between the final TSH level and triglyceride level (r = 0.167, p = 0.045), and between the decrease in TSH level and the decrease in waist circumference (r = 0.291, p = 0.013). Conclusions: In obese children, hyperthyrotropinemia with normal free T4 levels appears to be frequent. The correlation of hyperthyrotropinemia with waist circumference and higher triglyceride levels raises the question of the necessity to treat the elevated TSH levels.
Analysis of Craniofacial and Extremity Growth in Patients with Growth Hormone Deficiency during Growth Hormone Therapy
Authors: de Faria Maria Estela Justamante , Carvalho Luciani R. , Rossetto Shirley M. , Amaral Terezinha Sampaio , Berger Karina , Arnhold Ivo Jorge Prado , Mendonca Berenice Bilharinho
Published: February 2009

Background/Aims: There are many controversies regarding side effects on craniofacial and extremity growth due to growth hormone (GH) treatment. Our aim was to estimate GH action on craniofacial development and extremity growth in GH-deficient patients. Methods: Twenty patients with GH deficiency with a chronological age ranging from 4.6 to 24.3 years (bone age from 1.5 to 13 years) were divided in 2 groups: group 1 (n = 6), naive to GH treatment, and group 2 (n = 14), ongoing GH treatment for 2–11 years. GH doses (0.1–0.15 U/kg/day) were adjusted to maintain insulin-like growth factor 1 and insulin-like growth factor binding protein 3 levels within the normal range. Anthropometric measurements, cephalometric analyses and facial photographs to verify profile and harmony were performed annually for at least 3 years. Results: Two patients with a disharmonious profile due to mandibular growth attained harmony, and none of them developed facial disharmony. Increased hand or foot size (>P97) was observed in 2 female patients and in 4 patients (1 female), respectively, both not correlated with GH treatment duration and increased levels of insulin-like growth factor 1. Conclusions: GH treatment with standard doses in GH-deficient patients can improve the facial profile in retrognathic patients and does not lead to facial disharmony although extremity growth, mainly involving the feet, can occur.
Familial Tumoral Calcinosis Caused by a Novel FGF23 Mutation: Response to Induction of Tubular Renal Acidosis with Acetazolamide and the Non-Calcium Phosphate Binder Sevelamer
Authors: Lammoglia Juan Javier , Mericq Veronica
Published: February 2009

Hyperphosphatemic familial tumoral calcinosis (HFTC) is an uncommon disease characterized by periarticular calcifications produced by the deposition of amorphous extraosseous calcifications of hydroxyapatite. It is associated with hyperphosphatemia due to increased tubular phosphate reabsorption, despite normal renal function and normal plasma PTH levels. The disease can be caused by inactivating mutations in either the fibroblast growth factor 23 (FGF23) gene, the UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene or in human KLOTHO (KL) gene. Herein, we describe a Caucasian 3-year-old girl with tumoral calcinosis who presented with elevated serum phosphorus levels and a large calcified mass at her left elbow which led to ulceration of the skin. Treatment with the phosphate binder sevelamer and the carbonic anhydrase inhibitor acetazolamide successfully reduced the serum phosphate levels and led to a reduction of the calcified mass. This medical management has not been described previously. Her 7-month-old sister also had elevated serum phosphate levels, but did not have ectopic calcifications. Sequencing analysis revealed a novel homozygous FGF23 missense mutation (c.367G>T, p.Gly123Trp) in both siblings while the parents were carriers of the mutation.
Antimicrobial Susceptibility Pattern of Bacterial Pathogens Causing Urinary Tract Infections in a Saudi Arabian Hospital
Authors: Al-Tawfiq Jaffar A. , Anani Adnan A.
Published: February 2009

The study describes the pathogens causing urinary tract infections (UTI) and the antimicrobial susceptibility pattern of health care-associated (HCA) and community-acquired (CA) isolates. Of the total of 3,989 nonrepetitive urinary cultures, 4.7% (n = 188) were HCA and 95.3% (n = 3,801) were CA isolates. Gram-negative organisms totaled 3,607 (90.4%) vs. 9.6% Gram-positive organisms. In CA-UTI, Escherichia coli, Klebsiella pneumoniae and Enterococcus faecalis constituted 66, 11.4, and 5.4%, respectively. HCA-UTI episodes were caused by E. coli (37.8%), K. pneumoniae (14.4%) and Pseudomonas aeruginosa (6.4%). The susceptibility rates of E. coli to ciprofloxacin, trimethoprim-sulfamethoxazole (TMP-SMX), nitrofurantoin and ceftriaxone in HCA and CA isolates were 53.3 and 74.1%, 42.2 and 62.7%, 32.5 and 97.0%, and 62.3 and 92.7%, respectively. Extended-spectrum β-lactamase production was detected in 8.1 and 7.4% isolates, respectively, of CA and HCA isolates of E. coli. CA isolates of K. pneumoniae were more susceptible to TMP-SMX (89.2 vs. 60.4%), ciprofloxacin (92.6 vs. 67.9%) and cefuroxime (93.8 vs. 24.5%) than HCA isolates. The susceptibility of HCA and CA isolates of E. faecalis to penicillin G and nitrofurantoin were 34.8 and 80%, and 78.3 and 93.6%, respectively (p < 0.001). In conclusion, antimicrobial resistance is high to commonly used oral agents, rendering them inappropriate for empirical use.
Activity of Nilotinib (AMN-107) Alone in Advanced Gastrointestinal Stromal Tumors Progressing on Imatinib and Sunitinib
Authors: Sevinc Alper
Published: February 2009

Nilotinib is a novel tyrosine kinase inhibitor targeting KIT (CD117), PDGFR and BCR-ABL and inhibiting the proliferation of both imatinib-sensitive and imatinib-resistant cells in vitro. Nilotinib, alone or in combination with imatinib, has promising activity in imatinib-resistant patients with advanced gastrointestinal stromal tumors (GISTs), including those who progressed on sunitinib and other tyrosine kinase inhibitors. We describe the beneficial effect of nilotinib 400 mg b.i.d. orally in a 53-year-old patient with metastatic GISTs who had radiologically confirmed disease progression on both imatinib (800 mg/day) and sunitinib (50 mg/day). A positron emission tomography-computerized tomography evaluation showed marked decreases in 18F-fluorodeoxyglucose uptake in the liver and mesentery region after 3 months of therapy with nilotinib. Nilotinib is an option for patients with advanced GISTs progressing on both imatinib and sunitinib.
A Literature Review of International Implementation of Opioid Substitution Treatment in Prisons: Equivalence of Care?
Authors: Larney Sarah , Dolan Kate
Published: February 2009

Background/Aims: Opioid substitution treatment (OST) is an effective treatment for heroin dependence. The World Health Organization has recommended that OST be implemented in prisons because of its role in reducing drug injection and associated problems such as HIV transmission. The aim of this paper was to examine the extent to which OST has been implemented in prisons internationally. Methods: Literature review. Results: As of January 2008, OST had been implemented in prisons in at least 29 countries or territories. For 20 of those countries, the proportion of all prisoners in OST could be calculated, with results ranging from less than 1% to over 14%. At least 37 countries offer OST in community settings, but not prisons. Conclusion: This study has identified an increase in the international implementation of OST in prisons. However, there remain large numbers of prisoners who are unable to access OST, even in countries that provide such programs. This raises issues of equivalence of care for prisoners and HIV prevention in prisons.
Prevention of Atrial Fibrillation
Authors: Benjamin Emelia J. , Chen Peng-Sheng , Bild Diane E. , Mascette Alice M. , Albert Christine M. , Alonso Alvaro , Calkins Hugh , Connolly Stuart J. , Curtis Anne B. , Darbar Dawood , Ellinor Patrick T. , Go Alan S. , Goldschlager Nora F. , Heckbert Susan R. , Jalife José , Kerr Charles R. , Levy Daniel , Lloyd-Jones Donald M. , Massie Barry M. , Nattel Stanley , Olgin Jeffrey E. , Packer Douglas L. , Po Sunny S. , Tsang Teresa S.M. , Van Wagoner David R. , Waldo Albert L. , Wyse D. George
Published: February 2009

The National Heart, Lung, and Blood Institute convened an expert panel April 28 to 29, 2008, to identify gaps and recommend research strategies to prevent atrial fibrillation (AF). The panel reviewed the existing basic scientific, epidemiological, and clinical literature about AF and identified opportunities to advance AF prevention research. After discussion, the panel proposed the following recommendations: (1) enhance understanding of the epidemiology of AF in the population by systematically and longitudinally investigating symptomatic and asymptomatic AF in cohort studies; (2) improve detection of AF by evaluating the ability of existing and emerging methods and technologies to detect AF; (3) improve noninvasive modalities for identifying key components of cardiovascular remodeling that promote AF, including genetic, fibrotic, autonomic, structural, and electrical remodeling markers; (4) develop additional animal models reflective of the pathophysiology of human AF; (5) conduct secondary analyses of already-completed clinical trials to enhance knowledge of potentially effective methods to prevent AF and routinely include AF as an outcome in ongoing and future cardiovascular studies; and (6) conduct clinical studies focused on secondary prevention of AF recurrence, which would inform future primary prevention investigations.
Global Links and Environmental Flows: Oil Disputes in Ecuador
Authors: Widener Patricia
Published: February 2009

Employing the works of Spaargaren and Mol, the intersections of “environmental flows,” including both material flows (the extraction, transportation and exportation of oil) as well as non-material flows (community and environmental campaigns), are examined along an oil supply chain. Four communities in Ecuador are studied in order to reveal how a community's spatial and social dimensions influence its response to the construction of an oil pipeline as well as its establishment of advocacy networks. By holding constant the point of contention, these cases reveal that grassroots and professional organizations in communities most integrated in petroleum's commodity chain are least coupled with transnational campaigns. In contrast, environmental groups in areas least experienced in the environmental and health burdens associated with residing near oil facilities establish denser international ties. From these findings, this article calls for the insertion of community deliberation and community monitoring as necessary links in the flow of oil.
Conceptualizing Climate Governance Beyond the International Regime
Authors: Okereke Chukwumerije , Bulkeley Harriet , Schroeder Heike
Published: February 2009

The governance of climate change has traditionally been conceived as an issue of international co-operation and considered through the lens of regime analysis. Increasingly, scholars of global governance have highlighted the multiple parallel initiatives involving a range of actors at different levels of governance through which this issue is being addressed. In this paper, we argue that this phenomenon warrants a re-engagement with some of the conceptual cornerstones of international studies. We highlight the conceptual challenges posed by the increasing involvement of non-nation-state actors (NNSAs) in the governance of climate change and explore the potential for drawing from alternative theoretical traditions to address these challenges. Specifically, the paper combines insights from neo-Gramscian and governmentality perspectives as a means of providing the critical space required to generate deeper understanding of: (a) the nature of power in global governance; (b) the relationship between public and private authority; (c) the dynamics between structure and agency; and (d) the rationalities and practices of governance.
Beyond Betrayal: Beijing, Moscow, and the Paris Negotiations, 1971–1973
Authors: Lüthi Lorenz M.
Published: February 2009

Contrary to later Vietnamese allegations, China did not “sell out” the Democratic Republic of Vietnam (DRV) during the last two years of the Paris negotiations (1971–1973). North Vietnamese, Chinese, Soviet, East European, and American sources show that Hanoi could have gotten from Washington an agreement similar to the final Paris Agreement (January 1973) as early as the spring of 1971. Sino-American rapprochement did not help the United States in the negotiations, as claimed by the North Vietnamese, because the Chinese side made no concessions at all on Vietnam. In fact, China increased military aid to the DRV. Similarly, U.S.-Soviet detente did not damage the North Vietnamese effort, although Moscow unsuccessfully tried to mediate between Hanoi and Washington. In the end, U.S. success in rebuffing the DRV's Easter Offensive and Hanoi's miscalculations about U.S. domestic developments in 1972 prolonged the Vietnam War unnecessarily.
Intragroup behavioral variation in white-fronted capuchin monkeys (Cebus albifrons): mixed evidence for social learning inferred from new and established analytical methods
Authors: Matthews Luke
Published: February 2009

The study of socially learned traditions in field settings has been complicated by the need to rule out alternative hypothesized causes of behavioral variation, including underlying genetic variation, and asocial reinforcement learning that shapes behavior in response to microecological variations. Intragroup associations of spatial proximity and behavioral similarity support the tradition hypothesis when the associations are predicted specifically by social learning and not by alternative hypotheses. This paper attempts to test for socially learned traditions by combining variations in multiple foraging techniques into pairwise behavioral similarity matrices. This method thereby avoids loss of power from conducting multiple statistical tests. These matrices are then compared through correlation and cluster analysis to a proximity association matrix. Cluster analysis enables very specific predictions to be made from the social learning hypothesis, predictions that are not particularly likely under alternative hypotheses that do not invoke social learning or traditions. The results are mixed, with binary behavioral variations being consistent with a traditional influence of social learning, and with variations in the frequency of technique use being inconsistent with traditions.
Conspicuousness and vestigial escape behaviour by two dendrobatid frogs, Dendrobates auratus and Oophaga pumilio
Authors: Caldwell Janalee , Vitt Laurie , Cooper William
Published: February 2009

Aposematic prey are thought to move slowly and openly near predators, but exhibit reduced escape behaviour. We studied conspicuousness and escape by aposematic poison frogs (Dendrobates auratus and Oophaga pumilio). In circles of leaf litter, observers detected poison frogs quickly. Flight initiation distance (FID, predator-prey distance when escape begins) increases with approach speed in non-cryptic palatable prey, but not for frogs in clearings, which permitted close approach. On trails frogs moved slowly into forest and FID in D. auratus increased with approach speed. Distance from cover and handling exposing predators to distastefulness may account for greater reliance on aposematism in clearings. We observed responses to a simulated predator (stick with painted face) in three conditions: not approached, approached, and touched. Latency to hop and time to exit circles decreased and exit from circles was directed further away from the approach path in the order not approached, approached, touched. Oophaga pumilio changed directions less when approached than not; many exhibited no escape behaviour. Aposematic dendrobatids move slowly near predators, but retain risk-assessment mechanisms due to occasional predation. Differences in escape between dendrobatids and palatable Craugastor frogs suggest that dendrobatid defensive behavior may have been molded to maximize the effectiveness of aposematism.
Decision-making in group departures of female domestic geese
Authors: Ramseyer Amandine , Petit Odile , Thierry Bernard
Published: February 2009

Group-living animals have to make trade-offs to reach consensus and travel together. We investigated the recruitment processes underpinning decision-making at departure in a group of 20 female domestic geese (Anser domesticus) kept in semi-free-range conditions. Two observers continuously videotaped the behaviours of the birds. Data were analyzed using multiple regression analyses. We found that decision-making was a continuous and distributed process. Departure was preceded by an increase in the arousal state of group members and their initial orientation influenced recruitment. Patterns of group movement could be predicted from the behaviours of individuals before departure. Individuals' locations, moves and signals could act as passive or communicative cues. A higher number of vocalisations and arousal behaviours led to a larger number of individuals recruited. Some individuals were more efficient than others in recruiting followers but any geese could initiate a movement. First movers recruited a higher number of mates when they had a greater number of neighbours. Not only the first mover but also the behaviours of the second and third movers prompted further individuals to follow. There was no evidence that geese were able to intentionally recruit others, rather they synchronized and adjusted each other's motives until reaching a consensus.
Energy Balance Partitioning and Net Radiation Controls on Soil Moisture–Precipitation Feedbacks
Authors: Jones Aubrey R. , Brunsell Nathaniel A.
Published: February 2009

A series of model runs using the University of Oklahoma’s Advanced Regional Prediction System (ARPS) were conducted to investigate the relative impacts of energy balance partitioning and net radiation on soil moisture–precipitation feedbacks in the U.S. central plains and to examine how the dominant physical processes are affected by changes in mean soil moisture and spatial resolution. Soil temperature and Bowen ratio are influenced nonlinearly by soil moisture, and by varying the mean soil moisture in the model it was possible to examine the relationship between soil moisture and the scaling characteristics of these fields using the statistical moments. Information theory metrics were used to provide an indication of the uncertainty associated with varying model resolutions. It was determined that energy balance partitioning plays a dominant role in the occurrence of soil moisture–precipitation feedback, while net radiation was not impacted by mean soil moisture. A strong relationship was seen between soil moisture and the scaling properties of Bowen ratio, while soil moisture did not appear to influence the scaling characteristics of soil temperature. Spatial resolution had a large effect on the representation of boundary layer turbulence, with coarser resolutions unable to capture turbulent motions, which are necessary for convective processes. The ability of the model to capture boundary layer turbulence will alter the dynamics of soil moisture–precipitation feedback as the horizontal transport of moisture by turbulent motions will affect the spatial and temporal scales over which feedback occurs. Higher-resolution runs are generally associated with a higher information content. This may provide a methodology for monitoring land–atmosphere feedbacks via remotely sensed soil moisture and vegetation fields through statistical knowledge of the dependency of the resulting precipitation signal on soil moisture and vegetation fields at the resolution they were observed.
An Indirect Data Assimilation Scheme for Deep Soil Temperature in the Pleim–Xiu Land Surface Model
Authors: Pleim Jonathan E. , Gilliam Robert
Published: February 2009

The Pleim–Xiu land surface model (PX LSM) has been improved by the addition of a second indirect data assimilation scheme. The first, which was described previously, is a technique in which soil moisture is nudged according to the biases in 2-m air temperature and relative humidity between the model- and observation-based analyses. The new technique involves nudging the deep soil temperature in the soil temperature force–restore (FR) model according to model bias in 2-m air temperature only during nighttime. While the FR technique is computationally efficient and very accurate for the special conditions for which it was derived, it is very dependent on the deep soil temperature that drives the restoration term of the surface soil temperature equation. Thus, adjustment of the deep soil temperature to optimize the 2-m air temperature during the night, when surface forcing is minimal, provides significant advantages over other methods of deep soil moisture initialization. Simulations of the Weather Research and Forecasting Model (WRF) using the PX LSM with and without the new deep soil temperature nudging scheme demonstrate substantial benefits of the new scheme for reducing error and bias of the 2-m air temperature. The effects of the new nudging scheme are most pronounced in the winter (January 2006) during which the model’s cold bias is greatly reduced. Air temperature error and bias are also reduced in a summer simulation (August 2006) with the greatest benefits in less vegetated and more arid regions. Thus, the deep temperature nudging scheme complements the soil moisture nudging scheme because it is most effective for conditions in which the soil moisture scheme is least effective, that is, when evapotranspiration is not important (winter and arid climates).
The Role of Monthly Updated Climate Forecasts in Improving Intraseasonal Water Allocation
Authors: Sankarasubramanian A. , Lall Upmanu , Devineni Naresh , Espinueva Susan
Published: February 2009

Seasonal streamflow forecasts contingent on climate information are essential for short-term planning (e.g., water allocation) and for setting up contingency measures during extreme years. However, the water allocated based on the climate forecasts issued at the beginning of the season needs to be revised using the updated climate forecasts throughout the season. In this study, reservoir inflow forecasts downscaled from monthly updated precipitation forecasts from ECHAM4.5 forced with “persisted” SSTs were used to improve both seasonal and intraseasonal water allocation during the October–February season for the Angat reservoir, a multipurpose system, in the Philippines. Monthly updated reservoir inflow forecasts are ingested into a reservoir simulation model to allocate water for multiple uses by ensuring a high probability of meeting the end-of-season target storage that is required to meet the summer (March–May) demand. The forecast-based allocation is combined with the observed inflows during the season to estimate storages, spill, and generated hydropower from the system. The performance of the reservoir is compared under three scenarios: forecasts issued at the beginning of the season, monthly updated forecasts during the season, and use of climatological values. Retrospective reservoir analysis shows that the operation of a reservoir by using monthly updated inflow forecasts reduces the spill considerably by increasing the allocation for hydropower during above-normal-inflow years. During below-normal-inflow years, monthly updated streamflow forecasts could be effectively used for ensuring enough water for the summer season by meeting the end-of-season target storage. These analyses suggest the importance of performing experimental reservoir analyses to understand the potential challenges and opportunities in improving seasonal and intraseasonal water allocation by using real-time climate forecasts.
Wave-Induced Wind in the Marine Boundary Layer
Authors: Semedo Alvaro , Saetra Øyvind , Rutgersson Anna , Kahma Kimmo K. , Pettersson Heidi
Published: February 2009

Recent field observations and large-eddy simulations have shown that the impact of fast swell on the marine atmospheric boundary layer (MABL) might be stronger than previously assumed. For low to moderate winds blowing in the same direction as the waves, swell propagates faster than the mean wind. The momentum flux above the sea surface will then have two major components: the turbulent shear stress, directed downward, and the swell-induced stress, directed upward. For sufficiently high wave age values, the wave-induced component becomes increasingly dominant, and the total momentum flux will be directed into the atmosphere. Recent field measurements have shown that this upward momentum transfer from the ocean into the atmosphere has a considerable impact on the surface layer flow dynamics and on the turbulence structure of the overall MABL. The vertical wind profile will no longer exhibit a logarithmic shape because an acceleration of the airflow near the surface will take place, generating a low-level wave-driven wind maximum (a wind jet). As waves propagate away from their generation area as swell, some of the wave momentum will be returned to the atmosphere in the form of wave-driven winds.

A model that qualitatively reproduces the wave-following atmospheric flow and the wave-generated wind maximum, as seen from measurements, is proposed. The model assumes a stationary momentum and turbulent kinetic energy balance and uses the dampening of the waves at the surface to describe the momentum flux from the waves to the atmosphere. In this study, simultaneous observations of wind profiles, turbulent fluxes, and wave spectra during swell events are presented and compared with the model. In the absence of an established model for the linear damping ratio during swell conditions, the model is combined with observations to estimate the wave damping. For the cases in which the observations showed a pronounced swell signal and almost no wind waves, the agreement between observed and modeled wind profiles is remarkably good. The resulting attenuation length is found to be relatively short, which suggests that the estimated damping ratios are too large. The authors attribute this, at least partly, to processes not accounted for by the model, such as the existence of an atmospheric background wind. In the model, this extra momentum must be supplied by the waves in terms of a larger damping ratio.
Nonlinear Wave Statistics in a Focal Zone
Authors: Janssen T. T. , Herbers T. H. C.
Published: February 2009

In this paper, the combined effects of refraction and nonlinearity on the evolution of ocean surface wave statistics are considered and possible implications for the likelihood of extreme waves, also known as freak or rogue waves, are examined. A frequency-angular spectrum model is derived that accounts for cubic nonlinear dynamics and weak lateral homogeneity of the medium. Through Monte Carlo simulations, the evolution of wave statistics in freely developing waves, waves over an opposing shearing current, and waves refracted over an isolated topographical feature is modeled. The simulations show that freely developing, directionally spread wave fields generally maintain near-Gaussian statistics, which was also found in earlier model studies. However, the enhanced nonlinearity caused by the refractive focusing of narrowband wave fields can result locally in strongly non-Gaussian statistics and an associated increased likelihood of extreme wave events.
CALIPSO Lidar Description and Performance Assessment
Authors: Hunt William H. , Winker David M. , Vaughan Mark A. , Powell Kathleen A. , Lucker Patricia L. , Weimer Carl
Published: February 2009

This paper provides background material for a collection of Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) algorithm papers that are to be published in the Journal of Atmospheric and Oceanic Technology. It provides a brief description of the design and performance of CALIOP, a three-channel elastic backscatter lidar on the Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellite. After more than 2 yr of on-orbit operation, CALIOP performance continues to be excellent in the key areas of laser energy, signal-to-noise ratio, polarization sensitivity, and overall long-term stability, and the instrument continues to produce high-quality data products. There are, however, some areas where performance has been less than ideal. These include short-term changes in the calibration coefficients at both wavelengths as the satellite passes between dark and sunlight, some radiation-induced effects on both the detectors and the laser when passing through the South Atlantic Anomaly, and slow transient recovery on the 532-nm channels. Although these issues require some special treatment in data analysis, they do not seriously detract from the overall quality of the level 2 data products.
Automation: A Step toward Improving the Quality of Daily Temperature Data Produced by Climate Observing Networks*
Authors: Fiebrich Christopher A. , Crawford Kenneth C.
Published: February 2009

The research documented in this manuscript demonstrates that undeniable differences exist between values of daily temperature recorded by the National Weather Service Cooperative Observer Program network and data recorded by the Oklahoma Mesonet. Because of this fact, a transition to automated observations would have the effect of changing the climate record for Oklahoma. However, the change to automated observations would produce an improvement in overall data quality.

A sampling of daily data from the two networks was compared for closely spaced station pairs for the period 1 January 2003 through 31 December 2005. As a result, a host of observer errors were discovered (including transcription errors, incorrectly resetting the manual sensors, and delaying the observation time). These errors created large daily differences that sometimes exceeded 5°C between the two datasets. More than 55% of the paired observations were found to differ by more than 1°C.
Numerical Study of the Rainfall Event due to the Interaction of Typhoon Babs (1998) and the Northeasterly Monsoon
Authors: Wu Chun-Chieh , Cheung Kevin K. W. , Lo Ya-Yin
Published: February 2009

A heavy rainfall event in the Taiwan area associated with the interaction between Typhoon Babs (1998) and the East Asia winter monsoon is studied. Typhoon Babs is a case in point demonstrating the often-observed phenomenon that heavy rainfall can be induced in the eastern and/or northeastern region of Taiwan. Such heavy rainfall was caused by the joint convergent flow associated with the outer circulation of typhoons and the strengthening northeasterly monsoon in late typhoon season, even though Babs remained distant from Taiwan when it moved through the island of Luzon in the Philippines and stayed over the South China Sea. This heavy rainfall event is simulated in this study using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) with three nested domains and a highest horizontal resolution of 6.67 km. The control experiments with Kain–Fritsch cumulus parameterization perform well in terms of both simulated track and intensity. The 20-km resolution simulation reproduces the correct rainfall distribution during the three days studied, and the fine domain with 6.67-km resolution further improves the maximum simulated rainfall to very close to the observations. A series of sensitivity experiments that include model physics, terrain effect, typhoon vortex structure, and monsoon strength is performed, aiming at investigating the predictability of this typhoon–monsoon–terrain system when some of its components are perturbed. The rainfall event is analyzed based on two rainfall modes of different dominant mechanisms: monsoon mode during 0000 UTC 24–25 October and topographic mode during 0000 UTC 25–26 October. Removal of the Taiwan terrain in one of the sensitivity experiments results in completely different rainfall distribution due to the lack of the convection by orographic lifting, and the terrain is also found to play a key role in changing the low-level convergence pattern between the typhoon circulation and monsoonal northeasterlies. When the radius of the bogus vortex is reduced, the cold front to the north migrates southward in a faster pace than in the control simulation, and rain rate at the front also increases such that total accumulated rainfall at northern Taiwan is comparable with that in the control simulation but with shifted maximum position. In the extreme case in which no bogus vortex is implanted at all, rainfall is mainly associated with evolution of the cold front (pure frontal mode). In addition, a technique is developed to modify the monsoon strength over China. It is found that low-level (1000–700 hPa) reduction in monsoon strength weakens interaction with the typhoon, and rain distribution remains the same as in the control simulation. However, the simulated typhoon track is considerably sensitive to the deep-layer (1000–300 hPa) monsoon strength.