bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating the Metapopulation and Habitat Paradigms for Understanding Broad‐Scale Declines of Species
Authors: ARMSTRONG DOUG P.
Published: September 2005

Abstract: Caughley (1994)argued that researchers working on threatened populations tended to follow the “small population paradigm” or the “declining population paradigm,” and that greater integration of these paradigms was needed. Here I suggest that two related paradigms exist at the broader spatial scale, namely the metapopulation paradigm and habitat paradigm, and that these two paradigms also need to be integrated if we are to provide sound management advice. This integration is not trivial, and I outline five problems that need to be addressed: (1) habitat variables may not measure habitat quality, so site‐specific data on vital rates are needed to resolve the effects of habitat quality and metapopulation dynamics; (2) measurements of vital rates may be confounded by movements; (3) vital rates may be density dependent; (4) vital rates may be affected by genotype; and (5) vital rates cannot be measured in unoccupied patches. I reviewed papers published inConservation Biologyfrom 1994 to 2003 and found 41 studies that analyzed data from 10 or more sites to understand the factors limiting species' distributions. Five of the analyses presented were purely within the metapopulation paradigm, 14 were purely within the habitat paradigm, 17 involved elements of both paradigms, and 7 were theoretically ambiguous (2 papers presented 2 distinct analyses and were counted twice). This suggests that many researchers appreciate the need to integrate the paradigms. Only one study, however, used data on vital rates to resolve the effects of habitat quality and metapopulation dynamics (problem 1), and this study did not address problems 2–5. I conclude that more intensive research incorporating site‐specific data on vital rates and movement is needed to complement the numerous analyses of distributional data being produced.
Bush Tucker, Bush Pets, and Bush Threats: Cooperative Management of Feral Animals in Australia's Kakadu National Park
Authors: ROBINSON CATHERINE J. , SMYTH DERMOT , WHITEHEAD PETER J.
Published: September 2005

Abstract:  Although feral animal management is often based on the proposition that introduced species threaten ecological and conservation values, that view is not necessarily shared by all stakeholders, including those indigenous people who own and co‐manage Kakadu National Park with Australia's federal government. Drawing on field‐based interviews with the Jawoyn people, we found that these indigenous people categorize water buffalo ( Bubalus bubalis) as an important food source (tucker), view horses ( Equus caballus) as bush pets, and consider pigs ( Sus scrofa) a threat to their lands. As a result, Jawoyn people want more water buffalo in the park, have high tolerance of environmental damage caused by horses, and are open to the idea that pig population densities should be reduced. Jawoyn also advocate an adaptive and participatory approach to feral animal control so that the consequences of any management actions can be properly understood before irrevocable change occurs. These findings highlight one example of how indigenous people's ecological knowledge has adapted in response to changing landscapes and community aspirations. Co‐management strategies that aim to incorporate the dynamics of indigenous people's views need to start with issues on which there is agreement between different groups and take a cautious approach to joint exploration of more contentious issues. That approach should include ongoing and on‐site monitoring so that the consequences of management actions can be properly understood and comprehensively negotiated by all parties.
Habitat Suitability Models and the Shortfall in Conservation Planning for African Vertebrates
Authors: RONDININI CARLO , STUART SIMON , BOITANI LUIGI
Published: September 2005

Abstract:  Ongoing loss of biodiversity requires identifying large‐scale conservation priorities, but the detailed information on the distribution of species required for this purpose is often missing. We present a systematic reserve selection for 1223 African mammals and amphibians in which habitat suitability models are used as estimates of the area occupied by species. In the framework of the World Conservation Union (IUCN) Global Amphibian Assessment and IUCN Global Mammal Assessment, we collected the geographic range (extent of occurrence) and habitat preferences for each species. We used the latter to build species‐specific habitat suitability models inside geographic ranges, and for 181 species we verified the models by comparing suitability levels to presence‐absence data collected in the field. We then used the suitable areas as estimators of the area of occupancy and compared the results of systematic reserve selection based on geographic ranges to those based on estimated areas of occupancy. Our results showed that the reserve system would need a 30‐100% expansion to achieve minimal conservation targets, concentrated in the tropics, where species richness reaches a maximum. Comparative analyses revealed that using geographic ranges, which overestimate the area occupied by species, underestimates the total amount of area that needs to be conserved. The area selected for conservation doubled when we used the estimated area of occupancy in place of the geographic ranges. This happened because the suitable areas potentially occupied by each species overlapped less than their geographic ranges. As a result, any given protected area contained fewer species than predicted by the analysis of ranges. Because species are more specialized than our estimates of distribution based on extent of occurrence suggest, we propose that this is a general effect in systematic conservation planning.
The Predictive Value of Abbreviated Migraine Diagnostic Criteria
Authors: Martin Vincent T. , Penzien Donald B. , Houle Timothy T. , Andrew Michael E. , Lofland Kenneth R.
Published: September 2005

Objective.—To determine the operating characteristics and predictive value of abbreviated criteria for the diagnosis of migraine headache.

Background.—The International Headache Society (IHS) diagnostic criteria for migraine have been adopted in limited fashion in clinical practice. Primary care physicians in particular deal with innumerable conditions and diagnostic algorithms. Unless the IHS criteria are simplified the recognition of migraine headache in primary care settings will not be apt to improve.

Methods.—This study was a retrospective analysis of four discrete research databases: headache clinic patients (N = 390), private practice neurology patients (N = 290), college students (N = 99), and community‐based patients (N = 784). Physicians and psychologists expert in the diagnostic criteria for migraine headache syndromes conducted a standardized diagnostic interview in all patients (N = 1524). Each was later assigned an IHS headache diagnosis by a previously validated computer‐based algorithm. The sensitivity, specificity, positive and negative predictive values, and accuracy were calculated for single‐ and multiple‐variable models of migraine predictors. Optimal models were defined as those with positive likelihood ratios (+LRs) of >4.5 and negative likelihood ratios (−LRs) of <0.25 for the combined population.

Results.—The only optimal single‐variable model was nausea, which had an overall +LR of 4.8 and −LR of 0.23. None of the two‐variable models met criteria for an optimal model. The best of the optimal three‐variable models were nausea/photophobia/pulsating (+LR 6.7, −LR 0.23) and nausea/photophobia/worsening with physical activity (+LR 5.9, −LR 0.21). These three models maintained positive predictive values >0.80 in all 4 patient populations and negative predictive values >0.70 in the majority of populations.

Conclusion.—The single‐variable model of nausea and the three‐variable models of nausea/photophobia/worse with exertion and nausea/phonophobia/pulsating can effectively predict migraine in diverse clinical settings. These models however, should only be applied after a careful exclusion of secondary headache disorders.
A Self‐Administered Behavioral Intervention Using Tailored Messages for Migraine
Authors: Nicholson Robert , Nash Justin , Andrasik Frank
Published: September 2005

Objective.—The objective of this study was to evaluate the effectiveness of a Self‐Administered Behavioral Intervention using Tailored messages (SEABIT) for migraine. The primary measures were headache days, headache‐related disability, behavioral/emotional factors, and headache‐related beliefs.

Background.—Behavioral and cognitive‐behavioral interventions for migraine treatment are well established and possess “Grade‐A” evidence based on the U.S. Headache Consortium evidence‐based guidelines. To increase the accessibility of behavioral interventions in primary and other settings, treatment can be delivered in self‐administered formats. Incorporating tailored health communication strategies (via tailored messages) into a self‐administered format can help maintain a level of personalization without requiring regular visits to a behavioral specialist. Tailored messages are created using individual‐level assessment data to educate and motivate the patient to develop behavioral skills and strategies for migraine prevention and management.

Methods.—Twenty‐five individuals (95% female, 90% Caucasian, mean headache years = 21.0) began and 84% (21/25) completed all phases of the 8‐week SEABIT developed for migraine prevention (preceded by a 1‐month baseline phase and followed by a 1‐month postintervention phase).

Results.—Overall, 62% (13/21) reported at least a 50% reduction in headache frequency, and mean headache frequency for the group was also significantly reduced from baseline to postintervention (16.9 vs. 10.7, P < .001; η2= .61). Headache‐related disability, behavioral/emotional factors, and headache‐management self‐efficacy also showed significant improvement.

Conclusion.—The findings suggest that the SEABIT for migraine prevention is an effective behavioral intervention that potentially could be accessed and distributed in a variety of settings including primary care.
Defining the Relationship Between Ovarian Hormones and Migraine Headache
Authors: Martin Vincent T. , Wernke Suzanne , Mandell Karen , Ramadan Nabih , Kao Lily , Bean Judy , Liu James , Zoma Willie , Rebar Robert
Published: September 2005

Objective.—(1) To determine whether the attack characteristics of migraine differ between different intervals of the menstrual cycle; (2) To ascertain whether the “rate of change,”“magnitude of change,” or “total burden” of urinary hormone metabolites correlates with headaches outcome measures during different intervals of the menstrual cycle.

Background.—The mechanisms through which migraines are influenced by ovarian hormones remain unclear. No previous studies until now have identified “hormonally defined” time intervals within the female menstrual cycle and compared headache outcome measures among these intervals in female migraineurs.

Methods.—Daily headache diary data were obtained from 21 female migraineurs during three native menstrual cycles. Daily urine samples were collected and later assayed for estrogen and progesterone metabolites. Seven 3‐day time intervals were identified within each menstrual cycle based on urine hormone measurements. Primary (headache index) and secondary (disability index, headache severity, and headache frequency) outcome measures were compared between intervals using the mixed model approach. “Rates of change,”“magnitude of change,” and the “total burden” of ovarian hormones were estimated from urine hormone metabolites and correlated with headache outcome measures.

Results.—The headache index was significantly different across different intervals of the menstrual cycle (P values <.001) and was higher during menstrual intervals (first 6 days of the menstrual cycle) than during mid‐cycle and mid‐luteal intervals (P < .002). Similarly, secondary outcome measures were highest during the menstrual intervals. “Higher burdens” of urinary progesterone metabolites were positively correlated with headache outcome measures during the luteal intervals of the menstrual cycle. “Rates of change” and the “magnitude of change” of urinary hormone metabolites did not correlate with headache outcome measures.

Conclusions.—Migraine headache is more severe, disabling, and frequent during the menstrual intervals of the female reproductive cycle than during mid‐luteal or mid‐cycle intervals. Progesterone metabolites may play a role in modulating migraine headaches during luteal intervals of the menstrual cycle.
Prevalence of HFE (Hemochromatosis) Gene Mutations in Patients With Cluster Headache
Authors: Rainero Innocenzo , Rivoiro Chiara , Rubino Elisa , Milli Valentina , Valfrè Walter , De Martino Paola , Lo Giudice Rossana , Angilella Giuseppina , Savi Lidia , Gallone Salvatore , Pinessi Lorenzo
Published: September 2005

Objective.—To evaluate whether polymorphisms of the HFE gene would modify the occurrence and the clinical features of cluster headache (CH).

Background.—Recent studies suggested that iron metabolism may be involved in the pathophysiology of primary headaches. The HFE gene encodes for a protein that modulates iron absorption. Mutations in this gene are responsible for toxic iron overload in several body organs.

Methods.—Genomic DNA was extracted from 109 CH patients and 211 age and sex‐matched healthy controls and genotyped for the C282Y and H63D mutations of the HFE gene. Allele and genotype frequencies of the HFE gene were compared between cases and controls. The clinical characteristics of the disease were compared according to the different HFE gene genotypes.

Results.—No C282Y mutation was found in both cases and controls. The prevalence of the H63D mutation was nearly identical in cases and controls. The four patients carrying the HFE D63D genotype showed a significantly (P < .001) later age at onset of the disease in comparison with both H63H and H63D patients. The remaining clinical characteristics of the disease did not significantly differ in the presence or absence of the H63D mutation.

Conclusion.—Our data do not support the hypothesis that genetic variations within the HFE gene are associated with CH. However, the HFE gene may influence the disease phenotype and may be regarded as a disease modifier gene.
Familial Hemiplegic Migraine Presenting as Recurrent Encephalopathy in a Native Indian Family
Authors: Spacey Sian D. , Vanmolkot Kaate R. J. , Murphy Colleen , Van Den Maagdenberg Arn M. J. M. , Hsiung Robin G. Y.
Published: September 2005

Background.—Familial hemiplegic migraine (FHM) is an autosomal dominant disorder, which can result from mutations in the CACNA1A (FHM1) and ATP1A2 (FHM2) genes. Typically, FHM presents with an aura of hemiplegia accompanied by a moderate‐to‐severe headache. FHM can be associated with other neurological findings including coma and seizures.

Methods.—We describe the clinical and genetic features of a two‐generation, seven‐member Native Indian family with recurrent encephalopathy and FHM.

Results.—Two of the three affected family members presented initially with encephalopathy, the third family member presented with classic episodes of migraine and hemiparesis. The CACNA1A gene locus was excluded in this family by haplotype analysis and no mutations were identified in the coding region of the ATP1A2 gene by direct sequencing.

Conclusions.—This emphasizes the genetic and clinical heterogeneity in familial hemiplagic migraine FHM and highlights the need to consider the diagnosis of FHM in cases of recurrent encephalopathy.
Potential for Alcohol and Prescription Drug Interactions in Older People
Authors: Pringle Kristine E. , Ahern Frank M. , Heller Debra A. , Gold Carol H. , Brown Theresa V.
Published: September 2005

Objectives: To examine the patterns and prevalence of concomitant alcohol and alcohol‐interactive (AI) drug use in older people.

Design: Cross‐sectional analysis of survey and prescription claims data.

Setting: The Pennsylvania Pharmaceutical Assistance Contract for the Elderly (PA‐PACE) program, a state‐funded program providing prescription benefits to older people with low to moderate incomes.

Participants: A total of 83,321 PA‐PACE cardholders (age range 65–106) who were using any prescription medications at the time of survey completion.

Measurements: All AI drugs were identified using a database of medication warning labels obtained from First DataBank. Prescription drug claims were used to characterize AI drug exposure according to therapeutic class of prescription drug use. A mail survey of PA‐PACE cardholders was used to examine alcohol use, as well as sociodemographic and health factors associated with concomitant use of alcohol and AI drugs.

Results: Seventy‐seven percent of all prescription drug users were exposed to AI medications, with significant variation in exposure and concomitant alcohol use according to therapeutic class. Overall, 19% of AI drug users reported concomitant alcohol use, compared with 26% of non‐AI drug users (P<.001). Multinomial logistic regression analyses showed that certain groups of older people, including younger older people, men, and those with higher educational levels, were at greater risk for concomitant exposure to alcohol and AI drugs.

Conclusion: Many older people use alcohol in combination with AI prescription drugs. Clinicians should warn every patient who is prescribed an AI drug about alcohol–drug interactions, especially those at high risk for concomitant exposure.
The Measurement of Residual Strains Within Thermal Barrier Coatings Using High‐Energy X‐Ray Diffraction
Authors: Thornton J. , Slater S. , Almer J.
Published: September 2005

The residual strains through the entire thickness of the zirconia layer of pristine and heat‐treated thermal barrier coatings (TBCs) were mapped to help elucidate the failure mechanisms of TBCs. The strains were measured using 80.72 keV synchrotron radiation and a transmission geometry. The heat‐treated TBC showed that a compressive strain formed in the zirconia layer of the TBC on cooling but this strain was diluted and reversed by the oxidation‐driven expansion of the underlying metals. It also showed large (0.0024) out‐of‐plane tensile strains in the zirconia layer just above its interface with a thick underlying oxide layer.
Evaluation of Hot Pressing and Hot Isostastic Pressing Parameters on the Optical Properties of Spinel
Authors: Gilde Gary , Patel Parimal , Patterson Philip , Blodgett David , Duncan Donald , Hahn Daniel
Published: September 2005

The effect of different hot pressing and hot isostatic pressing (HIP) temperatures and pressures on the optical properties of spinel was studied. Extinction coefficients of spinel samples were estimated by comparing the measured transmittance with the theoretical transmittance as calculated via a Sellmeier model. Results showed that the relative size of the scattering sites was large compared with the wavelengths of light (0.35–5.5 μm). Overall, increasing HIP temperature and pressure resulted in decreasing the optical extinction. The lower of two hot pressing temperatures (1620° vs 1650°C) prior to HIPing resulted in lower scatter coefficients after HIPing; this effect was most significant in the infrared.
Carrier Generation in Wide‐Gap Conductor, Zinc Antimonate
Authors: Kikuchi Naoto , Hosono Hideo , Kawazoe Hiroshi , Tanegashima Osamu , Ota Isao , Kimura Yutaka
Published: September 2005

Mechanisms for carrier generation in zinc antimonate (ZnSb2O6) with a wide band gap were examined in relation to its crystallinity. ZnSb2O6 prepared by the reaction of Sb2O5 sol and 3ZnCO3·4Zn(OH)2 was sintered at 893, 1173, and 1393 K, and characterized by X‐ray diffraction (XRD), electrical conductivity and diffuse reflectance measurements. A higher conductivity was found for ZnSb2O6 sintered at lower temperatures. Rietveld analysis of XRD patterns showed that the cations in conductive ZnSb2O6 occupied irregular sites, similar to the random rutile structure. Electron carriers were also considered to be generated by oxygen vacancies in ZnSb2O6 samples which have a structure similar to the random rutile structure.
Thermal Conductivity of 2/1‐Mullite Single Crystals
Authors: Hildmann Bernd , Schneider Hartmut
Published: September 2005

The thermal diffusivities Dth of mullite single crystals with about 2/1‐composition parallel to the crystallographic a, b, and c axes (i.e., parallel to [100], [010], and [001]) and of monophase, dense mullite ceramics were measured between room temperature and 1200°C using the laser flash method. The semi‐transparent mullite disks were covered by thin layers of argon‐sputtered platinum and sprayed colloidal graphite in order to minimize heat radiation transfer effects. The phonon‐produced thermal conductivity of mullite was calculated according to K=DthCpρ using experimentally measured values for thermal diffusivity, Dth(T), and specific heat, Cp(T), and thermal expansion coefficients, αi, for the determination of temperature‐dependent density ρ(T) and sample thickness d(T). The anisotropy of thermal diffusivity and conductivity is evident with highest values parallel to the crystallographic c axis (i.e., [001]; e.g., at T=100°C K[001]=6.862 W/mK), corresponding to the direction of strongest bonds and highest elastic stiffness in the mullite crystal structure. Perpendicular to the c axis, thermal diffusivities and conductivities are smaller, with the values parallel to the a axis (i.e., [100]) being slightly higher than parallel to b (i.e., [010]; e.g., at T=100°C K[100]=4.563 W/mK and K[010]=4.400 W/mK), indicating lower bond strength and elastic stiffness in these crystallographic directions. Conductivity anisotropy factors are around 1.33 for K[001]/Kaverage, 0.90 for K[100]/Kaverage, and 0.85 for K[010]/Kaverage with little variation between room temperature and 1200°C. The thermal diffusivity and conductivity of dense, monophase mullite ceramics display similar values as the averaged single crystal data, thus providing a master curve for the temperature‐dependent thermal conductivity.
Relationships between trauma and psychosis: an exploration of cognitive and dissociative factors
Authors: Kilcommons A. M. , Morrison A. P.
Published: September 2005

Objective:  There is a growing awareness of the relationship between trauma and psychosis. Studies have found associations between traumatic life experiences and the development of psychosis.

Method:  This study examined the prevalence of trauma exposure and post‐traumatic stress disorder (PTSD) in 32 people with psychotic diagnoses and investigated associations between specific traumas and psychotic symptoms. The role of dissociation and cognitive factors was also explored.

Results:  The prevalence of lifetime trauma was high (94% of the sample reported at least one traumatic event). The prevalence of current PTSD was 53%. Severity of trauma was associated with severity of PTSD and psychotic experiences. Physical abuse was associated with positive psychotic symptoms and sexual abuse was specifically related to hallucinations. Dissociative processes and negative beliefs formed as a result of trauma were associated with psychotic experiences (particularly hallucinations).

Conclusion:  These findings are consistent with the suggestion that psychosis may be trauma‐induced, and other implications are considered.
Neuropsychological test profiles in schizophrenia and non‐psychotic depression
Authors: Rund B. R. , Sundet K. , Asbjørnsen A. , Egeland J. , Landrø N. I. , Lund A. , Roness A. , Stordal K. I. , Hugdahl K.
Published: September 2005

Objective:  The study examined to what degree schizophrenia is characterized by a neuropsychological (NP) test profile specific in shape and level compared with depression and normal functioning.

Method:  Fifty‐three patients with schizophrenia, 45 with non‐psychotic depression, and 50 normals were assessed with a comprehensive NP test battery and clinical instruments. NP test scores were factor analyzed into seven composite scores.

Results:  Schizophrenia patients performed significantly below normals across all seven composite scores, whereas depression patients were impaired in two. Verbal memory was most impaired. Sixty‐two percent of schizophrenia patients were moderately or severely impaired, the corresponding figure for depression was 28%. Impairment was moderately associated with IQ level and clinical symptom load in schizophrenia, but not in depression.

Conclusion:  Schizophrenia is characterized by deficits across a wide range of NP functions. Thirty‐eight percent of the patients are within normal limits. A mild and limited NP disturbance is apparent in depression.
Positive symptoms and duration of illness predict functional laterality and attention modulation in schizophrenia
Authors: Løberg E.‐M. , Jørgensen H. A. , Green M. F. , Rund B. R. , Lund A. , Diseth Å. , Øie M. , Hugdahl K.
Published: September 2005

Objective:  Dichotic listening (DL) performance in schizophrenia, reflecting hemispheric asymmetry and the functional integrity of the left temporal lobe, can vary with clinical characteristics. Previous studies have not taken the co‐linearity of clinical variables into account. The aim of the present study was to evaluate the roles of positive symptoms and duration of illness in DL through Structural Equation Modeling (SEM), thus allowing for complex relationships between the variables.

Method:  We pooled patients from four previous DL studies to create a heterogeneous group of 129 schizophrenic patients, all tested with a consonant‐vowel syllables DL procedure that included attentional instructions.

Results:  A model where positive symptoms predicted a laterality component and duration of illness predicted an attention component in DL was confirmed.

Conclusion:  Positive symptoms predicted reduced functional laterality, suggesting involvement of left temporal lobe language processing. Duration of illness predicted impaired attention modulation, possibly reflecting the involvement of frontotemporal networks.
Why do idiopathic scoliosis patients participate more in gymnastics?
Authors: Meyer C. , Cammarata E. , Haumont T. , Deviterne D. , Gauchard G. C. , Leheup B. , Lascombes P. , Perrin Ph. P.
Published: September 2005

The influence of physical and sporting activities (PSA) on idiopathic scoliosis (IS) is still obscure. The aim of this study was to investigate whether such an influence exists and if so, to determine its characteristics. Two hundred and one teenagers with IS and a control group of 192 adolescents completed an epidemiological questionnaire. Those practising gymnastics were more numerous in the IS group than in the control group. Moreover, the practice of gymnastics was chosen before IS was diagnosed. As gymnastic activities are considered neither as a therapy nor as a precursor of IS, the distribution observed could be linked to a common factor that both increases the likelihood of IS and favors the practice of gymnastics. Joint laxity (JL) may be such a common factor, and was therefore tested (wrist and middle finger) on 42 girls with IS and 21 girls of a control group. IS patients, practising gymnastics or not, showed a higher JL than the control group practising gymnastics or not. Furthermore, the groups practising gymnastic activities did not show higher JL levels than the other groups. Children with a high JL could be drawn toward gymnastics because of their ability to adapt to the constraints of this sport. Girls with a high JL may therefore be prone to developing IS. The fact that most teenagers with IS practise gymnastics could be related to a higher JL.
As You Like It: Senior Federal Judges and the Political Economy of Judicial Tenure
Authors: Yoon Albert
Published: September 2005

One interesting feature of the federal judiciary is that Article III judges enjoy lifetime tenure, a unique privilege not shared by members of the federal executive or legislative branches. In addition, judges who serve the requisite years can retire at full salary, guaranteed for life. Yet, the overwhelming majority of judges elect to remain on the bench for, effectively, their entire lives, first as active judges, then as senior judges. Despite the steady increase of both active and senior judges over the past century, little is known about the factors that motivate individuals to become and remain federal judges, even in the absence of financial incentives. Drawing from statistical data provided by the Federal Judicial Center and responses from a fall 2003 survey sent to all senior circuit and district federal court judges, this article describes how institutional and political developments, as well as the onset of aging, influence the capacity in which judges preside on, but not their commitment to, the federal bench. These findings provide insight into the political economy of the federal judiciary, as well as how individuals generally contribute to their respective professions as they grow older.
Time-Series Forecasting
Authors: Chatfield Chris
Published: September 2005

As we go through life, everyone makes forecasts all the time, often without realising it. Sadly these forecasts are often (very) inaccurate. Chris Chatfield looks at the chequered history of forecasting and asks how we might do it better using time-series data, and what statistical techniques and models might help us.
Galton Misrepresented
Authors: Gilchrist Warren
Published: September 2005

Sir Francis Galton is often referred to in the statistical literature as the originator of many of the ideas and tools of the modern statistician. But even a casual look at the historical literature shows that many of his ideas were altered by later, more mathematical statisticians, losing some valuable insights in the process. Warren Gilchrist explores three of these ideas.
Accuracy in Computing Acceleration of Free Fall in the Air
Authors: Benacka Jan , Stubna Igor
Published: September 2005

Acceleration of free fall is commonly measured in high school and college physics. One method is based on a free fall of the body from a known height while the duration of its falling is measured by an electronic stopwatch. Acceleration g is calculated using the formula for free fall in a vacuum. In this paper we show the error resulting from the use of this formula if the free fall occurs in the air and present the necessary conditions for using this formula.
Ubiquitous Drawing Errors for the Simple Pendulum
Authors: Santos-Benito Julio V. , Gras-Marti Albert
Published: September 2005

The so-called simple pendulum is found in all introductory physics textbooks, and one or more figures are usually devoted to its study. However, some textbook authors seem to exercise insufficient care in drawing the force diagrams for the motion, and mistakes in these drawings may confound the reader. In particular, there exists considerable confusion about the correct relative magnitude of the forces acting on the pendulum mass. This paper points out some of the common errors.
Ultrahigh Strength in Nanocrystalline Materials Under Shock Loading
Authors: Bringa Eduardo M. , Caro Alfredo , Wang Yinmin , Victoria Maximo , McNaney James M. , Remington Bruce A. , Smith Raymond F. , Torralva Ben R. , Van Swygenhoven Helena
Published: September 2005

Molecular dynamics simulations of nanocrystalline copper under shock loading show an unexpected ultrahigh strength behind the shock front, with values up to twice those at low pressure. Partial and perfect dislocations, twinning, and debris from dislocation interactions are found behind the shock front. Results are interpreted in terms of the pressure dependence of both deformation mechanisms active at these grain sizes, namely dislocation-based plasticity and grain boundary sliding. These simulations, together with new shock experiments on nanocrystalline nickel, raise the possibility of achieving ultrahard materials during and after shock loading.
High-Level β-Lactam Resistance and Cell Wall Synthesis Catalyzed by the
mecA
Homologue of
Staphylococcus sciuri
Introduced into
Staphylococcus aureus
Authors: Severin Anatoly , Wu Shang Wei , Tabei Keiko , Tomasz Alexander
Published: September 2005

A close homologue of
mecA
, the determinant of broad-spectrum β-lactam resistance in
Staphylococcus aureus
was recently identified as a native gene in the animal commensal species
Staphylococcus sciuri
. Introduction of the
mecA
homologue from a methicillin-resistant strain of
S. sciuri
into a susceptible strain of
S. aureus
caused an increase in drug resistance and allowed continued growth and cell wall synthesis of the bacteria in the presence of high concentrations of antibiotic. We determined the muropeptide composition of the
S. sciuri
cell wall by using a combination of high-performance liquid chromatography, mass spectrometric analysis, and Edman degradation. Several major differences between the cell walls of
S. aureus
and
S. sciuri
were noted. The pentapeptide branches in
S. sciuri
were composed of one alanine and four glycine residues in contrast to the pentaglycine units in
S. aureus
. The
S. sciuri
wall but not the wall of
S. aureus
contained tri- and tetrapeptide units, suggesting the presence of
dd
- and
ld
-carboxypeptidase activity. Most interestingly,
S. aureus
carrying the
S. sciuri mecA
and growing in methicillin-containing medium produced a cell wall typical of
S. aureus
and not
S. sciuri
, in spite of the fact that wall synthesis under these conditions had an absolute dependence on the heterologous
S. sciuri
gene product. The protein product of the
S. sciuri mecA
can efficiently participate in cell wall biosynthesis and build a cell wall using the cell wall precursors characteristic of the
S. aureus
host.
Signal Transduction Protein P
II
Phosphatase PphA Is Required for Light-Dependent Control of Nitrate Utilization in
Synechocystis
sp. Strain PCC 6803
Authors: Kloft Nicole , Forchhammer Karl
Published: September 2005

Signal transduction protein P
II
is dephosphorylated in
Synechocystis
sp. strain PCC 6803 by protein phosphatase PphA. To determine the impact of PphA-mediated P
II
dephosphorylation on physiology, the phenotype of a PphA-deficient mutant was analyzed. Mutants lacking either PphA or P
II
were impaired in efficient utilization of nitrate as the nitrogen source. Under conditions of limiting photosystem I (PSI)-reduced ferredoxin, excess reduction of nitrate along with impaired reduction of nitrite occurred in P
II
signaling mutants, resulting in excretion of nitrite to the medium. This effect could be reversed by increasing the level of PSI-reduced ferredoxin. We present evidence that nonphosphorylated P
II
controls the utilization of nitrate in response to low light intensity by tuning down nitrate uptake to meet the actual reduction capacity. This control mechanism can be bypassed by exposing cells to excess levels of nitrate. Uncontrolled nitrate uptake leads to light-dependent nitrite excretion even in wild-type cells, confirming that nitrate uptake controls nitrate utilization in response to limiting photon flux densities.
Cyclic AMP Receptor Protein and RhaR Synergistically Activate Transcription from the
l
-Rhamnose-Responsive
rhaSR
Promoter in
Escherichia coli
Authors: Wickstrum Jason R. , Santangelo Thomas J. , Egan Susan M.
Published: September 2005

The
Escherichia coli rhaSR
operon encodes two AraC family transcription activator proteins, RhaS and RhaR, which regulate expression of the
l
-rhamnose catabolic regulon in response to
l
-rhamnose availability. RhaR positively regulates
rhaSR
in response to
l
-rhamnose, and RhaR activation can be enhanced by the cyclic AMP (cAMP) receptor protein (CRP) protein. CRP is a well-studied global transcription regulator that binds to DNA as a dimer and activates transcription in the presence of cAMP. We investigated the mechanism of CRP activation at
rhaSR
both alone and in combination with RhaR in vivo and in vitro. Base pair substitutions at potential CRP binding sites in the
rhaSR-rhaBAD
intergenic region demonstrate that CRP site 3, centered at position −111.5 relative to the
rhaSR
transcription start site, is required for the majority of the CRP-dependent activation of
rhaSR
. DNase I footprinting confirms that CRP binds to site 3; CRP binding to the other potential CRP sites at
rhaSR
was not detected. We show that, at least in vitro, CRP is capable of both RhaR-dependent and RhaR-independent activation of
rhaSR
from a total of three transcription start sites. In vitro transcription assays indicate that the carboxy-terminal domain of the alpha subunit (α-CTD) of RNA polymerase is at least partially dispensable for RhaR-dependent activation but that the α-CTD is required for CRP activation of
rhaSR
. Although CRP requires the presence of RhaR for efficient in vivo activation of
rhaSR
, DNase I footprinting assays indicated that cooperative binding between RhaR and CRP does not make a significant contribution to the mechanism of CRP activation at
rhaSR
. It therefore appears that CRP activates transcription from
rhaSR
as it would at simple class I promoters, albeit from a relatively distant position.
Identification of theBacillus anthracisγ Phage Receptor
Authors: Davison Sophie , Couture-Tosi Evelyne , Candela Thomas , Mock Michèle , Fouet Agnès
Published: September 2005

Bacillus anthracis, a gram-positive, spore-forming bacterium, is the etiological agent of anthrax. It belongs to theBacillus cereusgroup, which also containsBacillus cereusandBacillus thuringiensis. MostB. anthracisstrains are sensitive to phage γ, but mostB. cereusandB. thuringiensisstrains are resistant to the lytic action of phage γ. Here, we report the identification of a protein involved in the bacterial receptor for the γ phage, which we term GamR (Gamma phagereceptor). It is an LPXTG protein (BA3367, BAS3121) and is anchored by the sortase A. AB. anthracissortase A mutant is not as sensitive as the parental strain nor as the sortase B and sortase C mutants, whereas the GamR mutant is resistant to the lytic action of the phage. Electron microscopy reveals the binding of the phage to the surface of the parental strain and its absence from the GamR mutant. SpontaneousB. anthracismutants resistant to the phage harbor mutations in the gene encoding the GamR protein. AB. cereusstrain that is sensitive to the phage possesses a protein similar (89% identity) to GamR.B. thuringiensis97-27, a strain which, by sequence analysis, is predicted to harbor a GamR-like protein, is resistant to the phage but nevertheless displays phage binding.
Lactate Racemization as a Rescue Pathway for Supplying
d
-Lactate to the Cell Wall Biosynthesis Machinery in
Lactobacillus plantarum
Authors: Goffin Philippe , Deghorain Marie , Mainardi Jean-Luc , Tytgat Isabelle , Champomier-Vergès Marie-Christine , Kleerebezem Michiel , Hols Pascal
Published: September 2005

Lactobacillus plantarum
is a lactic acid bacterium that produces
d
- and
l
-lactate using stereospecific NAD-dependent lactate dehydrogenases (LdhD and LdhL, respectively). However, reduction of glycolytic pyruvate by LdhD is not the only pathway for
d
-lactate production since a mutant defective in this activity still produces both lactate isomers (T. Ferain, J. N. Hobbs, Jr., J. Richardson, N. Bernard, D. Garmyn, P. Hols, N. E. Allen, and J. Delcour, J. Bacteriol. 178:5431-5437, 1996). Production of
d
-lactate in this species has been shown to be connected to cell wall biosynthesis through its incorporation as the last residue of the muramoyl-pentadepsipeptide peptidoglycan precursor. This particular feature leads to natural resistance to high concentrations of vancomycin. In the present study, we show that
L. plantarum
possesses two pathways for
d
-lactate production: the LdhD enzyme and a lactate racemase, whose expression requires
l
-lactate. We report the cloning of a six-gene operon, which is involved in lactate racemization activity and is positively regulated by
l
-lactate. Deletion of this operon in an
L. plantarum
strain that is devoid of LdhD activity leads to the exclusive production of
l
-lactate. As a consequence, peptidoglycan biosynthesis is affected, and growth of this mutant is
d
-lactate dependent. We also show that the growth defect can be partially restored by expression of the
d
-alanyl-
d
-alanine-forming Ddl ligase from
Lactococcus lactis
, or by supplementation with various
d
-2-hydroxy acids but not
d
-2-amino acids, leading to variable vancomycin resistance levels. This suggests that
L. plantarum
is unable to efficiently synthesize peptidoglycan precursors ending in
d
-alanine and that the cell wall biosynthesis machinery in this species is specifically dedicated to the production of peptidoglycan precursors ending in
d
-lactate. In this context, the lactate racemase could thus provide the bacterium with a rescue pathway for
d
-lactate production upon inactivation or inhibition of the LdhD enzyme.
A Periplasmic Drug-Binding Site of the AcrB Multidrug Efflux Pump: a Crystallographic and Site-Directed Mutagenesis Study
Authors: Yu Edward W. , Aires Julio R. , McDermott Gerry , Nikaido Hiroshi
Published: September 2005

The
Escherichia coli
AcrB multidrug efflux pump is a membrane protein that recognizes many structurally dissimilar toxic compounds. We previously reported the X-ray structures of four AcrB-ligand complexes in which the ligands were bound to the wall of the extremely large central cavity in the transmembrane domain of the pump. Genetic studies, however, suggested that discrimination between the substrates occurs mainly in the periplasmic domain rather than the transmembrane domain of the pump. We here describe the crystal structures of the AcrB mutant in which Asn109 was replaced by Ala, with five structurally diverse ligands, ethidium, rhodamine 6G, ciprofloxacin, nafcillin, and Phe-Arg-β-naphthylamide. The ligands bind not only to the wall of central cavity but also to a new periplasmic site within the deep external depression formed by the C-terminal periplasmic loop. This depression also includes residues identified earlier as being important in the specificity. We show here that conversion into alanine of the Phe664, Phe666, or Glu673 residue in the periplasmic binding site produced significant decreases in the MIC of most agents in the N109A background. Furthermore, decreased MICs were also observed when these residues were mutated in the wild-type AcrB background, although the effects were more modest. The MIC data were also confirmed by assays of ethidium influx rates in intact cells, and our results suggest that the periplasmic binding site plays a role in the physiological process of drug efflux.
Mutator Phenotype Resulting from DNA Polymerase IV Overproduction in
Escherichia coli
: Preferential Mutagenesis on the Lagging Strand
Authors: Kuban Wojciech , Banach-Orlowska Magdalena , Bialoskorska Malgorzata , Lipowska Aleksandra , Schaaper Roel M. , Jonczyk Piotr , Fijalkowska Iwona J.
Published: September 2005

We investigated the mutator effect resulting from overproduction of
Escherichia coli
DNA polymerase IV. Using
lac
mutational targets in the two possible orientations on the chromosome, we observed preferential mutagenesis during lagging strand synthesis. The mutator activity likely results from extension of mismatches produced by polymerase III holoenzyme.
THE NUMBER OF PURE CONVOLUTIONS ARISING FROM CONDITIONALLY FREE CONVOLUTION
Authors: ORAVECZ FERENC
Published: September 2005

We show that there are eight special cases of the conditionally free convolution of Bożejko, Leinert and Speicher with the property that in the corresponding moment-cumulant formula no nontrivial weights appear. All the eight convolutions are given. These include the free, the boolean and the Fermi convolutions, another special case of the bold t-free convolution and four more convolution laws that were not treated before.
HILBERT SPACE OF ANALYTIC FUNCTIONS ASSOCIATED WITH THE MODIFIED BESSEL FUNCTION AND RELATED ORTHOGONAL POLYNOMIALS
Authors: ASAI NOBUHIRO
Published: September 2005

Let μ be a probability measure on I ⊂ ℝ with finite moment of all orders and γα, c1, 2 be a probability measure on ℂ which is expressed by the modified Bessel function. In this paper, we shall first consider operators B-, B+, B° and express them in terms of bosonic creation and annihilation operators. Secondly, we shall construct the Hilbert space of analytic L2 functions with respect to γα, c1, 2, [Formula: see text]. It will be seen that the Sμ-transform under certain conditions is a unitary operator from L2 (I, μ) onto [Formula: see text]. Moreover, we shall give explicit examples including Laguerre, Meixner and Meixner–Pollaczek polynomials and explain how the Hilbert space [Formula: see text] and B-, B+, B° are related from the probabilistic point of view. It will also be given the relationship between the heat kernel on ℂ and γα, c1, 2 (subordination property).
Switching Characterization and Failure Analysis of In2Se3 Based Phase Change Memory
Authors: Lee Heon , Kang Dae-Hwan
Published: September 2005

Stoichiometric In2Se3 films were deposited at room temperature. X-ray diffractometry (XRD) and field-emission scanning electron microscopy (FE-SEM) showed that the as-deposited films were amorphous and had very smooth surface morphology while the films annealed at 250°C or higher temperatures were crystalline and had a rough surface. A cross-point-type phase change memory device with a Mo/In2Se3/Mo layered structure was fabricated. Static mode (or DC mode) and pulsed mode switching tests were successfully carried out on these cross-point-type devices. In the DC mode test, the as-grown amorphous In2Se3 resistor showed very high resistance in the low-voltage region. However, when it reached the threshold voltage, the electrical resistance of the device was markedly reduced due to the formation of an electrically conducting path (or a crystallized path). Pulsed mode switching performed on a phase change memory device with 0.7-µm-diameter contact hole showed that the resetting (amorphization) and setting (crystallization) of the device were achieved with a 70 ns pulse and a 1 µs pulse, respectively. After repeated switching, most of devices were stuck in the set state and could no longer be switched to the reset state. Cross-sectional SEM of these failed devices showed agglomerated voids near the interface between the In2Se3 resistor and Mo electrode, which may be responsible for the stuck-set failure of the devices.
Study on Light and Temperature Properties of AlN pH-Ion-Sensitive Field-Effect Transistor Devices
Authors: Chiang Jung-Lung , Chou Jung-Chuan , Chen Ying-Chung
Published: September 2005

Aluminum nitride (AlN) thin films were deposited by rf sputtering in an investigation on surface potential properties and hydrogen ion sensing characteristics. The pH sensitivity and surface potential of the produced AlN thin films were analyzed. AlN pH-ion-sensitive field-effect transistor (ISFET) devices have a high pH sensitivity (∼53 mV/pH) at pHs of 1–11. However, light exposure and temperature effects are very critical for ISFET applications. In this study, the light effect and temperature characteristics for the pH response based on AlN/SiO2 sensing gate ISFET are emphasized. The influence of light and temperature on AlN pH-ISFET behavior under various light intensities (0–4000 lx) and ambient temperatures (5–65°C) is examined. The results show that incident light results in an increased leakage current and a decreased pH sensitivity interference. The pH response of the AlN pH-ISFET was in the 48–57 mV/pH range that was also influenced by the ambient temperature.