bluuebunny/crossref_metadata_2025 huggingface dataset:
Cerebrospinal fluid supports viability and proliferation of cortical cells in vitro, mirroring in vivo development
Authors: Miyan Jaleel A , Zendah Mahjiub , Mashayekhi Farhad , Owen-Lynch P Jane
Published: April 2006

Background

The central nervous system develops around a fluid filled compartment. Recently, attention has turned to the potential role of the fluid (cerebrospinal fluid, CSF) in the developmental process. In particular, the cerebral cortex develops from the germinal epithelium adjacent to the CSF with regulation of cell proliferation and differentiation provided by cells adjacent to the fluid-filled subarachnoid space.

Methods

Histological analysis of fetal rat cortical sections was used to follow the extent of in vivo cortical development. A quantitative analysis of proliferation and migration of cortical cells at E17 – E21 was obtained through immunocytochemical staining of bromodeoxyuridine (BrdU) -labelled cells. In vitro studies were performed on primary cortical cells at days E17-E20, maintained in either Neurobasal media or 100% fetal rat CSF for 72 h before analysis of proliferation.

Results

The proliferation potential of primary cortical cells varied depending on the age of extraction. E17 and E20 cells showed little proliferation while E18 and E19 cell showed the maximum. The CSF from fetuses of all ages tested, except E21, was able to maintain primary cortical cells from the developing fetus in vitro and to stimulate and support their proliferation in the absence of any additions. E17 cells showed little proliferation in any media while E19 cells showed maximum proliferation in E19 and E20 CSF.

Conclusion

CSF composition most probably changes with age, as does the proliferation potential of cells in the developing cerebral cortex. CSF alone supports viability as well as proliferation of cortical cells. CSF must therefore be regarded as an important environmental influence in brain development and can be used in vitro to maintain both the viability of cortical progenitor cells and their age-related proliferative potential.
In vitro cytotoxicity of Manville Code 100 glass fibers: Effect of fiber length on human alveolar macrophages
Authors: Zeidler-Erdely Patti C , Calhoun William J , Ameredes Bill T , Clark Melissa P , Deye Gregory J , Baron Paul , Jones William , Blake Terri , Castranova Vincent
Published: April 2006

Background

Synthetic vitreous fibers (SVFs) are inorganic noncrystalline materials widely used in residential and industrial settings for insulation, filtration, and reinforcement purposes. SVFs conventionally include three major categories: fibrous glass, rock/slag/stone (mineral) wool, and ceramic fibers. Previousin vitrostudies from our laboratory demonstrated length-dependent cytotoxic effects of glass fibers on rat alveolar macrophages which were possibly associated with incomplete phagocytosis of fibers ≥ 17 μm in length. The purpose of this study was to examine the influence of fiber length on primary human alveolar macrophages, which are larger in diameter than rat macrophages, using length-classified Manville Code 100 glass fibers (8, 10, 16, and 20 μm). It was hypothesized that complete engulfment of fibers by human alveolar macrophages could decrease fiber cytotoxicity; i.e. shorter fibers that can be completely engulfed might not be as cytotoxic as longer fibers. Human alveolar macrophages, obtained by segmental bronchoalveolar lavage of healthy, non-smoking volunteers, were treated with three different concentrations (determined by fiber number) of the sized fibersin vitro. Cytotoxicity was assessed by monitoring cytosolic lactate dehydrogenase release and loss of function as indicated by a decrease in zymosan-stimulated chemiluminescence.

Results

Microscopic analysis indicated that human alveolar macrophages completely engulfed glass fibers of the 20 μm length. All fiber length fractions tested exhibited equal cytotoxicity on a per fiber basis, i.e. increasing lactate dehydrogenase and decreasing chemiluminescence in the same concentration-dependent fashion.

Conclusion

The data suggest that due to the larger diameter of human alveolar macrophages, compared to rat alveolar macrophages, complete phagocytosis of longer fibers can occur with the human cells. Neither incomplete phagocytosis nor length-dependent toxicity was observed in fiber-exposed human macrophage cultures. In contrast, rat macrophages exhibited both incomplete phagocytosis of long fibers and length-dependent toxicity. The results of the human and rat cell studies suggest that incomplete engulfment may enhance cytotoxicity of fiber glass. However, the possibility should not be ruled out that differences between human versus rat macrophages other than cell diameter could account for differences in fiber effects.
Antimigraine Drug, Zolmitriptan, Inhibits High-Voltage Activated Calcium Currents in a Population of Acutely Dissociated Rat Trigeminal Sensory Neurons
Authors: Morikawa Tomoko , Matsuzawa Yoshiyasu , Makita Koshi , Katayama Yoshifumi
Published: April 2006

Background

Triptans, 5-HT1B/ID agonists, act on peripheral and/or central terminals of trigeminal ganglion neurons (TGNs) and inhibit the release of neurotransmitters to second-order neurons, which is considered as one of key mechanisms for pain relief by triptans as antimigraine drugs. Although high-voltage activated (HVA) Ca2+ channels contribute to the release of neurotransmitters from TGNs, electrical actions of triptans on the HVA Ca2+ channels are not yet documented.

Results

In the present study, actions of zolmitriptan, one of triptans, were examined on the HVA Ca2+ channels in acutely dissociated rat TGNs, by using whole-cell patch recording of Ba2+ currents (IBa) passing through Ca2+ channels. Zolmitriptan (0.1–100 μM) reduced the size of IBa in a concentration-dependent manner. This zolmitriptan-induced inhibitory action was blocked by GR127935, a 5-HT1B/1D antagonist, and by overnight pretreatment with pertussis toxin (PTX). P/Q-type Ca2+ channel blockers inhibited the inhibitory action of zolmitriptan on IBa, compared to N-and L-type blockers, and R-type blocker did, compared to L-type blocker, respectively (p < 0.05). All of the present results indicated that zolmitriptan inhibited HVA P/Q- and possibly R-type channels by activating the 5-HT1B/1D receptor linked to Gi/o pathway.

Conclusion

It is concluded that this zolmitriptan inhibition of HVA Ca2+ channels may explain the reduction in the release of neurotransmitters including CGRP, possibly leading to antimigraine effects of zolmitriptan.
Comparison of P2X and TRPV1 Receptors in Ganglia or Primary Culture of Trigeminal Neurons and their Modulation by NGF or Serotonin
Authors: Simonetti Manuela , Fabbro Alessandra , D'Arco Marianna , Zweyer Marina , Nistri Andrea , Giniatullin Rashid , Fabbretti Elsa
Published: April 2006

Background

Cultured sensory neurons are a common experimental model to elucidate the molecular mechanisms of pain transduction typically involving activation of ATP-sensitive P2X or capsaicin-sensitive TRPV1 receptors. This applies also to trigeminal ganglion neurons that convey pain inputs from head tissues. Little is, however, known about the plasticity of these receptors on trigeminal neurons in culture, grown without adding the neurotrophin NGF which per se is a powerful algogen. The characteristics of such receptors after short-term culture were compared with those of ganglia. Furthermore, their modulation by chronically-applied serotonin or NGF was investigated.

Results

Rat or mouse neurons in culture mainly belonged to small and medium diameter neurons as observed in sections of trigeminal ganglia. Real time RT-PCR, Western blot analysis and immunocytochemistry showed upregulation of P2X3 and TRPV1 receptors after 1–4 days in culture (together with their more frequent co-localization), while P2X2 ones were unchanged. TRPV1 immunoreactivity was, however, lower in mouse ganglia and cultures. Intracellular Ca2+ imaging and whole-cell patch clamping showed functional P2X and TRPV1 receptors. Neurons exhibited a range of responses to the P2X agonist α, β-methylene-adenosine-5′-triphosphate indicating the presence of homomeric P2X3 receptors (selectively antagonized by A-317491) and heteromeric P2X2/3 receptors. The latter were observed in 16 % mouse neurons only. Despite upregulation of receptors in culture, neurons retained the potential for further enhancement of P2X3 receptors by 24 h NGF treatment. At this time point TRPV1 receptors had lost the facilitation observed after acute NGF application. Conversely, chronically-applied serotonin selectively upregulated TRPV1 receptors rather than P2X3 receptors.

Conclusion

Comparing ganglia and cultures offered the advantage of understanding early adaptive changes of nociception-transducing receptors of trigeminal neurons. Culturing did not prevent differential receptor upregulation by algogenic substances like NGF or serotonin, indicating that chronic application led to distinct plastic changes in the molecular mechanisms mediating pain on trigeminal nociceptors.
The developing world in The New England Journal of Medicine
Authors: Lown Bernard , Banerjee Amitava
Published: April 2006

Background

Rampant disease in poor countries impedes development and contributes to growing North-South disparities; however, leading international medical journals underreport on health research priorities for developing countries.

Methods

We examined 416 weekly issues of the New England Journal of Medicine (NEJM) over an eight-year period, January 1997 to December 2004. A total of 8857 articles were reviewed by both authors. The content of each issue was evaluated in six categories: research, review articles, editorial, correspondence, book reviews and miscellaneous. If the title or abstract concerned a topic pertinent to any health issue in the developing world, the article was reviewed.

Results

Over the eight years covered in this study, 1997–2004, in the three essential categories of original research articles, review articles and editorials, less than 3.0 percent of these addressed health issues in the developing world. Publications relevant to DC were largely concerned with HIV and communicable diseases and constituted 135 of the 202 articles of which 63 were devoted to HIV. Only 23 articles addressed non-communicable disease in the DC and only a single article – a book review – discussed heart disease.

Conclusion

The medical information gap between rich and poor countries as judged by publications in the NEJM appears to be larger than the gap in the funding for research. Under-representation of developing world health issues in the medical literature is a global phenomenon. International medical journals cannot rectify global inequities, but they have an important role in educating their constituencies about the global divide.
Uneven dietary development: linking the policies and processes of globalization with the nutrition transition, obesity and diet-related chronic diseases
Authors: Hawkes Corinna
Published: April 2006

In a "nutrition transition", the consumption of foods high in fats and sweeteners is increasing throughout the developing world. The transition, implicated in the rapid rise of obesity and diet-related chronic diseases worldwide, is rooted in the processes of globalization. Globalization affects the nature of agri-food systems, thereby altering the quantity, type, cost and desirability of foods available for consumption. Understanding the links between globalization and the nutrition transition is therefore necessary to help policy makers develop policies, including food policies, for addressing the global burden of chronic disease. While the subject has been much discussed, tracing the specific pathways between globalization and dietary change remains a challenge.

To help address this challenge, this paper explores how one of the central mechanisms of globalization, the integration of the global marketplace, is affecting the specific diet patterns. Focusing on middle-income countries, it highlights the importance of three major processes of market integration: (I) production and trade of agricultural goods; (II) foreign direct investment in food processing and retailing; and (III) global food advertising and promotion.

The paper reveals how specific policies implemented to advance the globalization agenda account in part for some recent trends in the global diet. Agricultural production and trade policies have enabled more vegetable oil consumption; policies on foreign direct investment have facilitated higher consumption of highly-processed foods, as has global food marketing. These dietary outcomes also reflect the socioeconomic and cultural context in which these policies are operating.

An important finding is that the dynamic, competitive forces unleashed as a result of global market integration facilitates not only convergence in consumption habits (as is commonly assumed in the "Coca-Colonization" hypothesis), but adaptation to products targeted at different niche markets. This convergence-divergence duality raises the policy concern that globalization will exacerbate uneven dietary development between rich and poor. As high-income groups in developing countries accrue the benefits of a more dynamic marketplace, lower-income groups may well experience convergence towards poor quality obseogenic diets, as observed in western countries.

Global economic polices concerning agriculture, trade, investment and marketing affect what the world eats. They are therefore also global food and health policies. Health policy makers should pay greater attention to these policies in order to address some of the structural causes of obesity and diet-related chronic diseases worldwide, especially among the groups of low socioeconomic status.
Moment-to-moment dynamics of ADHD behaviour in South African children
Authors: Aase Heidi , Meyer Anneke , Sagvolden Terje
Published: April 2006

Background

The behaviour of children with Attention-Deficit/Hyperactivity Disorder is characterized by low predictability of responding. Low behavioural predictability is one way of operationalizing intra-individual ADHD-related variability. ADHD-related variability may be caused by inefficient behavioural selection mechanisms linked to reinforcement and extinction, as suggested by the recently published dynamic developmental theory (DDT) of ADHD. DDT argues that ADHD is a basic neurobehavioural disorder, caused by dysfunctioning dopamine systems. For establishing ADHD as a neurobehavioural disorder, findings from studies conducted in Western countries should be replicated in other cultural populations. The present study replicated the study conducted in Norway, with children from the Limpopo province in the Republic of South Africa.

Methods

Boys and girls, aged 6–9 yr, from seven ethnic groups participated. Scores by teachers on the Disruptive Behavior Disorders rating scale defined participation in either ADHD-hyperactive/impulsive (-HI), ADHD-predominantly inattentive (-PI), or ADHD-combined (-C) groups. Children below the 86th percentile were matched on gender and age and comprised the non-ADHD group. The children completed a computerized game-like task where mouse clicks on one of two squares on the screen resulted in delivery of a reinforcer according to a variable interval schedule of reinforcement. Reinforcers were cartoon pictures presented on the screen together with a sound. Predictability of response location and timing were measured in terms of explained variance.

Results

Overall, the results replicated findings from Norway. Specifically, the ADHD-C group showed significantly lower predictability of responding than the non-ADHD group, while the ADHD-HI and the ADHD-PI groups were in-between. In accordance with the previous study, response location, but not response timing, was a sensitive behavioural measure. There were no significant gender differences. Cartoon pictures were effective reinforcers as the non-ADHD group showed learning of the task. There was no relation between behavioural predictability and motor functions.

Conclusion

The present study makes a strong case for ADHD as a basic, neurobehavioural disorder, not a cultural phenomenon, by replicating findings from a wealthy Western country in a poor province of a developing country. The results were, generally, in line with predictions from the dynamic developmental theory of ADHD by indicating that reinforcers were less efficient in the ADHD group than in the non-ADHD group. Finally, the results substantiated ADHD-related variability as an etiologically important characteristic of ADHD behaviour.
Medicinal plants popularly used in the Xingó region – a semi-arid location in Northeastern Brazil
Authors: Almeida Cecília de Fátima CBR , de Amorim Elba Lúcia Cavalcanti , de Albuquerque Ulysses Paulino , Maia Maria Bernadete S
Published: April 2006

The aim of this study was to identify plant species among the diverse flora of the caatinga ecosystem that are used therapeutically. Research was undertaken in the municipalities of Piranhas and Delmiro Gouveia, in the Xingó region (state of Alagoas, NE Brazil). In order to identify the medicinal plants used in this region, semi-structured questionnaires were applied. The species cited were collected and sent to the Xingó Herbarium for taxonomic analysis. The relative importance (RI) of each species cited was calculated to verify their cultural importance. The therapeutic indications attributed to the species were classified under 16 body systems. A total of 187 medicinal species were cited, from 64 families and 128 genera. The main indications for medicinal plant use were against common colds, bronchitis, cardiovascular problems, kidney problems, inflammations in general, and as tranquilizers. Approximately 16% (30 plant species) were versatile in relation to their use, with an Relative Importance value over 1, having been indicated for up to nine body systems. The body systems that stood out the most were: the respiratory system, the gastrointestinal system, and infectious diseases. Most cited plant parts used for medicinal purposes were flowers, leaves, and inner stem bark.
The milk of human kindness: the story of the Mothers Milk Bank at Austin
Authors: Wilson-Clay Barbara
Published: April 2006

Increased scientific study of human milk and awareness of the special nutritional needs of the premature infant have stimulated interest in human donor milk banking. Yet only three donor human milk banks existed in the United States in 1998. Having observed better outcomes in human milk-fed neonatal intensive care patients, two neonatologists in Austin, Texas, founded The Mothers Milk Bank at Austin (MMBA). Since opening in 1999, the MMBA has expanded rapidly as the result of careful planning, innovative procedures, fiscal stability, and widespread community support. The non-profit organizational structure, diversity and progressive vision of the board of directors and staff, and creative on-going public relations efforts have contributed to the success of the project. The MMBA demonstrates a model for 21st century milk banking.
First-Person Neuroscience: A new methodological approach for linking mental and neuronal states
Authors: Northoff Georg , Heinzel Alexander
Published: April 2006

Though the brain and its neuronal states have been investigated extensively, the neural correlates of mental states remain to be determined. Since mental states are experienced in first-person perspective and neuronal states are observed in third-person perspective, a special method must be developed for linking both states and their respective perspectives. We suggest that such method is provided by First-Person Neuroscience. What is First-Person Neuroscience? We define First-Person Neuroscience as investigation of neuronal states under guidance of and on orientation to mental states. An empirical example of such methodological approach is demonstrated by an fMRI study on emotions. It is shown that third- and first-person analysis of data yield different results. First-person analysis reveals neural activity in cortical midline structures during subjective emotional experience. Based on these and other results neural processing in cortical midline structures is hypothesized to be crucially involved in generating mental states. Such direct linkage between first- and third-person approaches to analysis of neural data allows insight into the "point of view from within the brain", that is what we call the First-Brain Perspective. In conclusion, First-Person Neuroscience and First-Brain Perspective provide valuable methodological tools for revealing the neuronal correlate of mental states.
Is translational research compatible with preclinical publication strategies?
Authors: Linder Stig , Shoshan Maria C
Published: April 2006

The term "translational research" is used to describe the transfer of basic biological knowledge into practical medicine, a process necessary for motivation of public spending. In the area of cancer therapeutics, it is becoming increasingly evident that results obtained in vitro and in animal models are difficult to translate into clinical medicine. We here argue that a number of factors contribute to making the translation process inefficient. These factors include the use of sensitive cell lines and fast growing experimental tumors as targets for novel therapies, and the use of unrealistic drug concentrations and radiation doses. We also argue that aggressive interpretation of data, successful in hypothesis-building biological research, does not form a solid base for development of clinically useful treatment modalities. We question whether "clean" results obtained in simplified models, expected for publication in high-impact journals, represent solid foundations for improved treatment of patients. Open-access journals such as Radiation Oncology have a large mission to fulfill by publishing relevant data to be used for making actual progress in translational cancer research.
TGF β-induced cartilage repair is maintained but fibrosis is blocked in the presence of Smad7
Authors: Blaney Davidson Esmeralda N , Vitters Elly L , van den Berg Wim B , van der Kraan Peter M
Published: April 2006

Cartilage damage in osteoarthritis (OA) is considered an imbalance between catabolic and anabolic factors, favoring the catabolic side. We assessed whether adenoviral overexpression of transforming growth factor-β (TGFβ) enhanced cartilage repair and whether TGFβ-induced fibrosis was blocked by local expression of the intracellular TGFβ inhibitor Smad7. We inflicted cartilage damage by injection of interleukin-1 (IL-1) into murine knee joints. After 2 days, we injected an adenovirus encoding TGFβ. On day 4, we measured proteoglycan (PG) synthesis and content. To examine whether we could block TGFβ-induced fibrosis and stimulate cartilage repair simultaneously, we injected Ad-TGFβ and Ad-Smad7. This was performed both after IL-1-induced damage and in a model of primary OA. In addition to PG in cartilage, synovial fibrosis was measured by determining the synovial width and the number of procollagen I-expressing cells. Adenoviral overexpression of TGFβ restored the IL-1-induced reduction in PG content and increased PG synthesis. TGFβ-induced an elevation in PG content in cartilage of the OA model. TGFβ-induced synovial fibrosis was strongly diminished by simultaneous synovial overexpression of Smad7 in the synovial lining. Of great interest, overexpression of Smad7 did not reduce the repair-stimulating effect of TGFβ on cartilage. Adenoviral overexpression of TGFβ stimulated repair of IL-1- and OA-damaged cartilage. TGFβ-induced synovial fibrosis was blocked by locally inhibiting TGFβ signaling in the synovial lining by simultaneously transfecting it with an adenovirus overexpressing Smad7.
Reduction in bone relapse and improved survival with oral clodronate for adjuvant treatment of operable breast cancer [ISRCTN83688026]
Authors: Powles Trevor , Paterson Alexander , McCloskey Eugene , Schein Phil , Scheffler Bobbi , Tidy Alwynne , Ashley Sue , Smith Ian , Ottestad Lars , Kanis John
Published: April 2006

Introduction

Experimental and clinical data show that the oral bisphosphonate clodronate (Bonefos®) can inhibit tumor-induced osteoclastic bone resorption. This randomized, double-blind, placebo-controlled, multicenter trial was designed to determine if the addition of oral clodronate to standard treatment for primary operable breast cancer could reduce the subsequent occurrence of bone metastases and thereby improve overall survival.

Methods

1,069 patients with primary operable stage I-III breast cancer were randomized to receive oral clodronate (1,600 mg/day) or placebo for 2 years, in conjunction with standard treatment for primary breast cancer including surgery, radiotherapy, adjuvant chemotherapy, and/or tamoxifen. All patients were assessed for bone metastases at two and five years and additionally when clinically indicated. Survival status was determined as of the close of the study on 30 June 2000 with a median follow up of 5.6 years. The treatment arms were compared using the unstratified log-rank test. Hazard ratios (HRs) with 95% confidence intervals were calculated.

Results

Oral clodronate significantly reduced the risk of bone metastases in all patients over the 5 year study period (51 patients versus 73 patients with placebo; HR = 0.692, P = 0.043); the difference was also statistically significant over the 2 year medication period (19 patients versus 35 patients with placebo; HR = 0.546, P = 0.031). These differences were most pronounced in patients with stage II/III disease (39 patients versus 64 patients with placebo, HR = 0.592, P = 0.009 over 5 years; 16 patients versus 32 patients with placebo, HR= 0.496, P = 0.020 over 2 years). Survival data also favoured the clodronate arm (HR for all patients = 0.768, P = 0.048; HR for stage II/III disease = 0.743, P = 0.041), although this was not significant due to multiple analyses. Oral clodronate was well tolerated, with mild-to-moderate diarrhoea being the most frequently reported adverse event.

Conclusion

These results confirm that oral clodronate will significantly improve the 5 year bone relapse free survival when used as a supplementary adjuvant treatment for patients receiving standard treatment for primary operable breast cancer.
One year ago not business as usual: Wound management, infection and psychoemotional control during tertiary medical care following the 2004 Tsunami disaster in southeast Asia
Authors: Maegele Marc , Gregor Sven , Yuecel Nedim , Simanski Christian , Paffrath Thomas , Rixen Dieter , Heiss Markus M , Rudroff Claudia , Saad Stefan , Perbix Walter , Wappler Frank , Harzheim Andreas , Schwarz Rosemarie , Bouillon Bertil
Published: April 2006

Introduction

Following the 2004 tsunami disaster in southeast Asia severely injured tourists were repatriated via airlift to Germany. One cohort was triaged to the Cologne-Merheim Medical Center (Germany) for further medical care. We report on the tertiary medical care provided to this cohort of patients.

Methods

This study is an observational report on complex wound management, infection and psychoemotional control associated with the 2004 Tsunami disaster. The setting was an adult intensive care unit (ICU) of a level I trauma center and subjects included severely injured tsunami victims repatriated from the disaster area (19 to 68 years old; 10 females and 7 males with unknown co-morbidities).

Results

Multiple large flap lacerations (2 × 3 to 60 × 60 cm) at various body sites were characteristic. Lower extremities were mostly affected (88%), followed by upper extremities (29%), and head (18%). Two-thirds of patients presented with combined injuries to the thorax or fractures. Near-drowning involved the aspiration of immersion fluids, marine and soil debris into the respiratory tract and all patients displayed signs of pneumonitis and pneumonia upon arrival. Three patients presented with severe sinusitis. Microbiology identified a variety of common but also uncommon isolates that were often multi-resistant. Wound management included aggressive debridement together with vacuum-assisted closure in the interim between initial wound surgery and secondary closure. All patients received empiric anti-infective therapy using quinolones and clindamycin, later adapted to incoming results from microbiology and resistance patterns. This approach was effective in all but one patient who died due to severe fungal sepsis. All patients displayed severe signs of post-traumatic stress response.

Conclusion

Individuals evacuated to our facility sustained traumatic injuries to head, chest, and limbs that were often contaminated with highly resistant bacteria. Transferred patients from disaster areas should be isolated until their microbial flora is identified as they may introduce new pathogens into an ICU. Successful wound management, including aggressive debridement combined with vacuum-assisted closure was effective. Initial anti-infective therapy using quinolones combined with clindamycin was a good first-line choice. Psychoemotional intervention alleviated severe post-traumatic stress response. For optimum treatment and care a multidisciplinary approach is mandatory.
Reference based annotation with GeneMapper
Authors: Chatterji Sourav , Pachter Lior
Published: April 2006

We introduce GeneMapper, a program for transferring annotations from a well annotated genome to other genomes. Drawing on high quality curated annotations, GeneMapper enables rapid and accurate annotation of newly sequenced genomes and is suitable for both finished and draft genomes. GeneMapper uses a profile based approach for mapping genes into multiple species, improving upon the standard pairwise approach. GeneMapper is freely available for academic use.
Mediterranean ecosystems: problems and tools for conservation
Authors: Vogiatzakis I. N. , Mannion A. M. , Griffiths G. H.
Published: April 2006

Mediterranean ecosystems rival tropical ecosystems in terms of plant biodiversity. The Mediterranean Basin (MB) itself hosts 25 000 plant species, half of which are endemic. This rich biodiversity and the complex biogeographical and political issues make conservation a difficult task in the region. Species, habitat, ecosystem and landscape approaches have been used to identify conservation targets at various scales: ie, European, national, regional and local. Conservation decisions require adequate information at the species, community and habitat level. Nevertheless and despite recent improvements/efforts, this information is still incomplete, fragmented and varies from one country to another. This paper reviews the biogeographic data, the problems arising from current conservation efforts and methods for the conservation assessment and prioritization using GIS. GIS has an important role to play for managing spatial and attribute information on the ecosystems of the MB and to facilitate interactions with existing databases. Where limited information is available it can be used for prediction when directly or indirectly linked to externally built models. As well as being a predictive tool today GIS incorporate spatial techniques which can improve the level of information such as fuzzy logic, geostatistics, or provide insight about landscape changes such as 3D visualization. Where there are limited resources it can assist with identifying sites of conservation priority or the resolution of environmental conflicts (scenario building). Although not a panacea, GIS is an invaluable tool for improving the understanding of Mediterranean ecosystems and their dynamics and for practical management in a region that is under increasing pressure from human impact.
The progress and perspectives of landscape ecology in China
Authors: Fu Bo-jie , Lu Yi-he
Published: April 2006

After 20 years of research and application, landscape ecology in China has gained many achievements and established a concrete foundation for further development. The major progress of landscape ecology in China was in the fields of land-use structure and ecological processes, landscape pattern and dynamics analysis, theoretical and methodological development, and landscape ecological applications. Past researches emphasized particularly the theories and applications, while the methodological study accounted for a comparatively small part; urban and suburban landscapes, regional and catchment scale landscapes, cold and arid zone landscapes, forest landscapes, agricultural landscapes and wetland landscapes were the main research subjects. Major problems with past researches include the following. 1) There was unbalanced attention on conceptual/theoretical analysis, monitoring, methodological development and applications. 2) Landscape metrics were widely used, whereas the ecological implications were not fully addressed. 3) The researches on the relationship between landscape pattern and ecological processes and scaling were largely preliminary. 4) The risk, uncertainty and accuracy of the data processing were seldom mentioned. 5) The original methodological innovation was scant. To solve these problems effectively and promote landscape ecology in China to full development at a whole new stage of the twenty-first century, the following four closely interrelated and complementary tasks should be addressed: 1) establishing appropriate strategies for the development of landscape ecology; 2) enhancing experiment-based and long-term research; 3) improving landscape planning, design, conservation and management; 4) initiating and advancing the development of unified landscape ecology with Chinese characteristics.
The 1906 San Francisco Earthquake and Fire—Enduring Lessons for Fire Protection and Water Supply
Authors: Scawthorn C. , O'Rourke T. D. , Blackburn F. T.
Published: April 2006

Prior to 18 April 1906 the San Francisco Fire Department and knowledgeable persons in the insurance industry regarded a conflagration in San Francisco as inevitable. The 1906 San Francisco earthquake and ensuing fire is the greatest single fire loss in U.S. history, with 492 city blocks destroyed and life loss now estimated at more than 3,000. This paper describes fire protection practices in the United States prior to 1906; the conditions in San Francisco on the eve of the disaster; ignitions, spread, and convergence of fires that generated the 1906 conflagration; and damage to the water supply system in 1906 that gave impetus to construction of the largest high-pressure water distribution network ever built—San Francisco's Auxiliary Water Supply System (AWSS). In the 1980s hydraulic network and fire simulation modeling identified weaknesses in the fire protection of San Francisco—problems mitigated by an innovative Portable Water Supply System (PWSS), which transports water long distances and helped extinguish the Marina fire during the 1989 Loma Prieta earthquake. The AWSS and PWSS concepts have been extended to other communities and provide many lessons, paramount of which is that communities need to develop an integrated disaster preparedness and response capability and be constantly vigilant in maintaining that capability. This lesson is especially relevant to highly seismic regions with large wood building inventories such as the western United States and Japan, which are at great risk of conflagration following an earthquake.
When the Big One Strikes Again—Estimated Losses due to a Repeat of the 1906 San Francisco Earthquake
Authors: Kircher Charles A. , Seligson Hope A. , Bouabid Jawhar , Morrow Guy C.
Published: April 2006

This paper presents interim results of an ongoing study of building damage and losses likely to occur due to a repeat of the 1906 San Francisco earthquake, using the HAZUS technology. Recent work by Boatwright et. al. (2006) provides MMI-based ShakeMap estimates of spectral response accelerations derived from observations of intensities in the 1906 San Francisco earthquake. This paper calculates damage and loss estimates using those estimated ground motions, then compares the resulting estimates with those calculated using a method parallel with that of current seismic provisions of building codes for a magnitude M7.9 event on the San Andreas Fault, and contrasts differences in damage and loss patterns for these two scenarios. The study region of interest comprises 19 counties of the greater San Francisco Bay Area and adjacent areas of Northern California, covering 24,000 square miles, with a population of more than ten million people and about $1.5 trillion of building and contents exposure. The majority of this property and population is within 40 km (25 miles) of the San Andreas Fault. The current population of this Northern California region is about ten times what it was in 1906, and the replacement value of buildings is about 500 times greater. Despite improvements in building codes and construction practices, the growth of the region over the past 100 years causes the range of estimated fatalities, approximately 800–3,400 depending on time of day and other variables, to be comparable to what it was in 1906. The forecast property loss to buildings for a repeat of the 1906 earthquake is in the range of approximately $90–120 billion; 7,000–10,000 commercial buildings in the region are estimated to be closed due to serious damage; and about 160,000–250,000 households calculated to be displaced from damaged residences. Losses due to fire following earthquake, as well as losses to utility and transportation systems, would be in addition to these estimates.
The Conformal Motive in Birdsong, Music, and Language: An Introduction
Authors: MERKER BJORN
Published: April 2006

Abstract:Human song and music are part of what may be called a ritual stratum of human culture. As such, they involve special behaviors and neural mechanisms with an uneven but interesting distribution in nature. This may be turned to account not only for shedding light on the biological background of human song and music, but also for elucidating the nature of the cultural traditions within which these arts are practiced and elaborated. The purpose of this chapter is accordingly threefold: (1) to highlight the uniqueness of human culture compared to that of other primates by defining and contrasting two very different types of traditions that coexist within it: those of instrumental culture and those of ritual culture; (2) to outline the crucial role of the mechanism of vocal learning as an enabling device for ritual culture, specifically, by way of the well‐studied behavioral biology of birdsong; and (3) to introduce theconformal motiveas a so‐far neglected, but essential, aspect of the neural mechanisms required for vocal learning. Taken together, these considerations will then be used to sketch some of the roles this postulated conformal motive appears to play in human culture, stratified into instrumental, ritual, and language traditions. Some of the implications of this perspective for our understanding of a number of issues related to the human facility for imitation, expressive mimesis, and deliberate teaching are also briefly touched upon.
The Relationship of Music to the Melody of Speech and to Syntactic Processing Disorders in Aphasia
Authors: PATEL ANIRUDDH D.
Published: April 2006

Abstract:Two new empirical studies address the relationship between music and language. The first focuses on melody and uses research in phonetics to investigate the long‐held notion that instrumental music reflects speech patterns in a composer's native language. The second focuses on syntax and addresses the relationship between musical and linguistic syntactic processing via the study of aphasia, an approach that has been explored very little. The results of these two studies add to a growing body of evidence linking music and language with regard to structural patterns and brain processing.
Implicit Investigations of Tonal Knowledge in Nonmusician Listeners
Authors: TILLMANN BARBARA
Published: April 2006

Abstract: By mere exposure to musical pieces in everyday life, Western listeners acquire sensitivity to the regularities of the tonal system and to the context dependency of musical sounds. This implicitly acquired tonal knowledge allows nonmusician listeners to perceive relationships among musical events and to develop expectations for future events that then influence the processing of these events. The musical priming paradigm is one method of the indirect investigation of listeners' tonal knowledge. It investigates the influence of a preceding context (with its musical structures and relationships) on the processing of a musical target event, without asking participants for direct evaluations. Behavioral priming data have provided evidence for facilitated processing of musically related events in comparison to unrelated and less‐related events. The sensitivity of implicit investigations is further shown by I.R., a patient with severe amusia, showing spared implicit knowledge of music. Finally, the priming paradigm allows us to investigate the neural correlates of musical structure processing. Two fMRI studies reported the implication of inferior frontal regions in musical priming, contrasting related and unrelated events, as well as finer structural manipulations contrasting in‐key events.
Brain Networks That Track Musical Structure
Authors: JANATA PETR
Published: April 2006

Abstract:As the functional neuroimaging literature grows, it becomes increasingly apparent that music and musical activities engage diverse regions of the brain. In this paper I discuss two studies to illustrate that exactly which brain areas are observed to be responsive to musical stimuli and tasks depends on the tasks and the methods used to describe the tasks and the stimuli. In one study, subjects listened to polyphonic music and were asked to either orient their attention selectively to individual instruments or in a divided or holistic manner across multiple instruments. The network of brain areas that was recruited changed subtly with changes in the task instructions. The focus of the second study was to identify brain regions that follow the pattern of movement of a continuous melody through the tonal space defined by the major and minor keys of Western tonal music. Such an area was identified in the rostral medial prefrontal cortex. This observation is discussed in the context of other neuroimaging studies that implicate this region in inwardly directed mental states involving decisions about the self, autobiographical memory, the cognitive regulation of emotion, affective responses to musical stimuli, and familiarity judgments about musical stimuli. Together with observations that these regions are among the last to atrophy in Alzheimer disease, and that these patients appear to remain responsive to autobiographically salient musical stimuli, very early evidence is emerging from the literature for the hypothesis that the rostral medial prefrontal cortex is a node that is important for binding music with memories within a broader music‐responsive network.
Neural Encoding and Retrieval of Sound Sequences
Authors: RAUSCHECKER JOSEF P.
Published: April 2006

Abstract: Although considerable progress has been made recently in our understanding of the coding of complex sounds in the cerebral cortex, the processing and storage of tone sequences is still poorly understood. We have used functional magnetic resonance imaging to identify brain mechanisms involved in the encoding and retrieval of melodies by studying the anticipation of familiar music. The results suggest a specific role for each of the following brain structures: the anterior part of the right superior temporal cortex, the right inferior frontal cortex and anterior insula, the left anterior prefrontal cortex, the lateral cerebellum, and the anterior cingulate. In a separate study, we investigated single‐neuron responses in the auditory cortex of awake behaving monkeys to alternating tone sequences that in humans evoke the perception of “streaming.” Depending on the frequency separation between the tones, an initial single stream may segregate into two streams after a build‐up period of several seconds. The neural responses in the monkeys' primary auditory cortex (A1) mirror the psychophysical time course extremely well, suggesting that habituation within A1 may be one reason for stream segregation. However, the higher auditory and prefrontal areas found to be activated by musical melodies are expected to interact with primary areas in both bottom‐up and top‐down fashion to bring about the perceptual organization of sound sequences.
Neurophysiology and Neuroanatomy of Pitch Perception: Auditory Cortex
Authors: TRAMO MARK JUDE , CARIANI PETER A. , KOH CHRISTINE K. , MAKRIS NIKOS , BRAIDA LOUIS D.
Published: April 2006

Abstract:We present original results and review literature from the past fifty years that address the role of primate auditory cortex in the following perceptual capacities: (1) the ability to perceive small differences between the pitches of two successive tones; (2) the ability to perceive the sign (i.e., direction) of the pitch difference [higher (+) vs. lower (−)]; and (3) the ability to abstract pitch constancy across changes in stimulus acoustics. Cortical mechanisms mediating pitch perception are discussed with respect to (1) gross and microanatomical distribution; and (2) candidate neural coding schemes. Observations by us and others suggest that (1) frequency‐selective neurons in primary auditory cortex (A1) and surrounding fields play a critical role in fine‐grained pitch discrimination at the perceptual level; (2) cortical mechanisms that detect pitch differences are neuroanatomically dissociable from those mediating pitch direction discrimination; (3) cortical mechanisms mediating perception of the “missing fundamental frequency (F0)” are neuroanatomically dissociable from those mediating pitch perception when F0 is present; (4) frequency‐selective neurons in both right and left A1 contribute to pitch change detection and pitch direction discrimination; (5) frequency‐selective neurons in right A1 are necessary for normal pitch direction discrimination; (6) simple codes for pitch that are based on single‐ and multiunit firing rates of frequency‐selective neurons face both a “hyperacuity problem” and a “pitch constancy problem”—that is, frequency discrimination thresholds for pitch change direction and pitch direction discrimination are much smaller than neural tuning curves predict, and firing rate patterns change dramatically under conditions in which pitch percepts remain invariant; (7) cochleotopic organization of frequency‐selective neurons bears little if any relevance to perceptual acuity and pitch constancy; and (8) simple temporal codes for pitch capable of accounting for pitches higher than a few hundred hertz have not been found in the auditory cortex. The cortical code for pitch is therefore not likely to be a function of simple rate profiles or synchronous temporal patterns. Studies motivated by interest in the neurophysiology and neuroanatomy of music perception have helped correct longstanding misconceptions about the functional role of auditory cortex in frequency discrimination and pitch perception. Advancing knowledge about the neural coding of pitch is of fundamental importance to the future design of neurobionic therapies for hearing loss.