bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonadiabatic couplings in the collisional removal of O2(b Σ1g+,v) by O2
Authors: Dayou F. , Hernández M. I. , Campos-Martínez J. , Hernández-Lamoneda R.
Published: January 2010

The effect of nonadiabatic couplings on the collisional removal of O2(b Σ1g+,v) by O2(X Σ3g−, v=0) is investigated. Two-dimensional adiabatic and quasidiabatic potential energy surfaces for the excited dimer states and the corresponding nonadiabatic radial couplings have been computed by means of ab initio calculations. Alternately, a two-state theoretical model, based on the Landau–Zener and Rosen–Zener–Demkov assumptions, has been employed to derive analytical forms for the nonadiabatic couplings and an adiabatic-to-diabatic transformation only depending on a reduced set of adiabatic energy terms. Compared to the ab initio results, the predictions of the model are found to be highly accurate. Quantum dynamics calculations for the removal of the first ten vibrational states of O2(b Σ1g+,v) indicate a clear dominant contribution of the vibration-electronic relaxation mechanism relative to the vibration-translation energy transfer. Although the present reduced-dimensionality model precludes any quantitative comparison with experiments, it is found that the removal probabilities for v=1–3 are qualitatively consistent with the experimental observations, once the vibrational structure of the fragments is corrected with spectroscopical terms. Besides, the model served to show how the computation of the adiabatic PESs just at the crossing seam was sufficient to describe the nonadiabatic dynamics related to a given geometrical arrangement. This implies considerable savings in the calculations which will eventually allow for larger accuracy in the ab initio calculations as well as higher dimensional treatments.
Impact of noble metal nanostructures on surface trapping state of semiconductor quantum dots
Authors: Yang Zhenling , Wen Yanan , Meng Qingkun , Liu Yuqiang , Song Yunfei , He Xing , Li Aihua , Yu Guoyang , Yang Yanqiang , Wu Wenzhi
Published: January 2010

The impact of noble metal nanostructures on the surface trapping state of semiconductor quantum dots was investigated by taking nanosecond time resolved photoluminescence measurements. It was observed that nonradiative resonant energy transfer from the excitonic state of quantum dots to Au nanofilm reduced the lifetime and intensity of excitonic state emission. No nonradiative resonant energy transfer from surface trapping state to Au nanofilm was observed. It is possibly implied that noble metal nanostructures have no impact on the surface trapping state of semiconductor quantum dots.
Wilhelmy plate artifacts in elastic monolayers
Authors: Witten T. A. , Wang Jin , Pocivavsek L. , Lee K. Y. C.
Published: January 2010

A recent article [L. Pocivavsek et al., Soft Matter4, 2019 (2008)] by some of us pointed out difficulties in interpreting Wilhelmy plate measurements on elastic Langmuir monolayers that support anisotropic stress. Using a simplified geometry it showed conditions in which the Wilhelmy plate measures significantly different stress from the ambient stress. We correct a serious error in this analysis and strengthen its conclusion, showing that the Wilhelmy stress and the ambient stress can have opposite signs.
Spectroscopic measurements of SO2 line parameters in the 9.2 μm atmospheric region and theoretical determination of self-broadening coefficients
Authors: Tasinato Nicola , Charmet Andrea Pietropolli , Stoppa Paolo , Giorgianni Santi , Buffa Giovanni
Published: January 2010

Sulfur dioxide is still the subject of numerous spectroscopic studies since it plays an active role in the chemistry of Earth’s atmosphere and it is a molecule of proven astrophysical importance. In the present work we have determined the self-broadening and integrated absorption coefficients for several lines in the ν1 band spectral region around 9.2 μm. Besides the parameters of the lines belonging to the ν1 fundamental of S32O2, also those for some rovibrational lines of the ν1+ν2−ν2 hot band of the S32O2 isotopologue and the ν1 band of the S34O2 isotopic species have been determined. The measurements have been carried out at 297 K using a tunable diode laser spectrometer. The self-broadening parameters have also been theoretically determined employing a semiclassical formalism based on the Anderson–Tsao–Curnutte approximation. The study has been completed with the determination of the vibrational cross sections of the three fundamental bands measured from the spectra recorded at a resolution of 0.2 cm−1 using a Fourier transform infrared spectrometer.
Interactions of graphene sheets deduced from properties of polycyclic aromatic hydrocarbons
Authors: Podeszwa Rafał
Published: January 2010

Intermolecular interactions of coronene dimer were studied with symmetry-adapted perturbation theory based on the density functional theory description of the monomers [SAPT(DFT)]. The most stable stacked structure was found to have the interaction energy of −17.45 kcal/mol, slightly lower than the structure analogous to graphite (−17.36 kcal/mol). The latter energy was extrapolated to the interaction energy of two graphene sheets. The effects of interactions of multiple layers were also estimated leading to the exfoliation energy of graphite equal to 45.3 meV per carbon atom. The SAPT(DFT)-based decomposition into physical quantities of the interaction energies shows the dominant effect of the dispersion interactions with a weaker electrostatic contribution due to penetration effects. The extrapolated physical picture of the graphene-graphene interaction is very similar to that of smaller stacked polycyclic aromatic hydrocarbons.
Halogen and hydrogen bonding to the Br atom in complexes of FBr
Authors: McDowell Sean A. C.
Published: January 2010

A computational study predicts a number of stable, unusual halogen- and hydrogen-bonded complexes involving FBr, NCH, and FH. Starting from the linear halogen-bonded FBr⋯NCH dimer, increasingly more stable complexes are obtained by the successive hydrogen bonding of one to three FH molecules to the lone pairs on the Br atom of FBr to form a trimer, tetramer, and pentamer. A hexamer is obtained from the pentamer by the bonding of FH to the F atom of FBr. The combined halogen and hydrogen bonding gives rise to a large computed zero-point corrected binding energy of 98 kJ/mol for the hexamer at the MP2/6-31++G(d,p) level of theory.
Improving proton acceleration with circularly polarized intense laser pulse by radial confinement with heavy ions
Authors: Huang L. G. , Lei A. L. , Bin J. H. , Bai Y. , Yu Wei , Yu M. Y. , Cowan T. E.
Published: January 2010

Energetic proton acceleration from interaction of intense short circularly polarized laser pulse with a sandwich target is investigated using two-dimensional particle-in-cell simulation. The sandwich target consists of a hydrogen-plasma layer surrounded by carbon-plasma layers. It is found that the transverse electric fields generated at the plasma layer interfaces efficiently confine the longitudinally accelerated protons to within the hydrogen-plasma layer such that they are collimated and have smaller energy spread compared with a pure proton layer target. The proton energy spectrum can be controlled by adjusting the target parameters, in particular the width of the hydrogen-plasma layer and the density of the carbon-plasma layer.
Distal Attribution and Distance Perception in Sensory Substitution
Authors: Siegle Joshua H , Warren William H
Published: January 2010

In sensory substitution, the user may be directly aware of distal objects, as in everyday perception, or make explicit cognitive inferences based on an awareness of the proximal stimulation. Anecdotal evidence supports the experience of distal attribution, but so far there have been few rigorous experimental tests of the claim. In this study, blindfolded participants observed a target light using a device consisting of a finger-mounted photodiode that drives tactile vibration on the back. With the blindfold off and the target removed, participants moved a reference object to match the perceived egocentric distance of the target. Participants who were instructed to attend to the distal target improved significantly during 2 h of practice, whereas those instructed to attend to proximal variables showed no improvement. Unsigned error increased with ratings of proximal attention, but decreased with ratings of target object solidity, consistent with distal attribution. Performance transferred to the non-dominant arm and to a rotated body orientation, demonstrating that learning did not depend on a joint-specific sensorimotor relationship between target distance and arm configuration. The results experimentally confirm that distal attribution can occur in sensory substitution, based on a perceptual strategy rather than an explicit cognitive strategy. Moreover, they suggest that the informational basis for distal attribution is not a joint-specific sensorimotor relation, but a more abstract spatial invariant.
Is Inattentional Blindness Related to Individual Differences in Visual Working Memory Capacity or Executive Control Functioning?
Authors: Hannon Emily M , Richards Anne
Published: January 2010

Inattentional blindness (IB) research deals with situations where, under focused attention tasks, salient stimuli that are irrelevant to that task do not reach conscious awareness. Although such research has captured popular imagination, to date very little research has been conducted on whether some are more likely to experience this phenomenon than others. Here we provide evidence that working memory capacity (WMC) contributed to this experience, with lower WMC being predictive of IB. We also investigated whether IB could be more readily explained in terms of domain-specific visual WMC. No group differences in visual WMC were found, nor any differences in the ability to perform the primary IB task. These findings suggest that differences in higher-order executive control of attention contributes to the experience of IB.
Long-range enhancers on 8q24 regulate c-Myc
Authors: Sotelo Jose , Esposito Dominic , Duhagon Maria Ana , Banfield Kelley , Mehalko Jennifer , Liao Hongling , Stephens Robert M. , Harris Timothy J. R. , Munroe David J. , Wu Xiaolin
Published: January 2010

Recent genomewide association studies have found multiple genetic variants on chromosome 8q24 that are significantly associated with an increased susceptibility to prostate, colorectal, and breast cancer. These risk loci are located in a ”gene desert,” a few hundred kilobases telomeric to the Myc gene. To date, the biological mechanism(s) underlying these associations remain unclear. It has been speculated that these 8q24 genetic variant(s) might affect Myc expression by altering its regulation or amplification status. Here, we show that multiple enhancer elements are present within this region and that they can regulate transcription of Myc. We also demonstrate that one such enhancer element physically interacts with the Myc promoter via transcription factor Tcf-4 binding and acts in an allele specific manner to regulate Myc expression.
Universal distribution of protein evolution rates as a consequence of protein folding physics
Authors: Lobkovsky Alexander E. , Wolf Yuri I. , Koonin Eugene V.
Published: January 2010

The hypothesis that folding robustness is the primary determinant of the evolution rate of proteins is explored using a coarse-grained off-lattice model. The simplicity of the model allows rapid computation of the folding probability of a sequence to any folded conformation. For each robust folder, the network of sequences that share its native structure is identified. The fitness of a sequence is postulated to be a simple function of the number of misfolded molecules that have to be produced to reach a characteristic protein abundance. After fixation probabilities of mutants are computed under a simple population dynamics model, a Markov chain on the fold network is constructed, and the fold-averaged evolution rate is computed. The distribution of the logarithm of the evolution rates across distinct networks exhibits a peak with a long tail on the low rate side and resembles the universal empirical distribution of the evolutionary rates more closely than either distribution resembles the log-normal distribution. The results suggest that the universal distribution of the evolutionary rates of protein-coding genes is a direct consequence of the basic physics of protein folding.
Cross-frequency coupling supports multi-item working memory in the human hippocampus
Authors: Axmacher Nikolai , Henseler Melanie M. , Jensen Ole , Weinreich Ilona , Elger Christian E. , Fell Juergen
Published: January 2010

Recent findings indicate that the hippocampus supports not only long-term memory encoding but also plays a role in working memory (WM) maintenance of multiple items; however, the neural mechanism underlying multi-item maintenance is still unclear. Theoretical work suggests that multiple items are being maintained by neural assemblies synchronized in the gamma frequency range (25–100 Hz) that are locked to consecutive phase ranges of oscillatory activity in the theta frequency range (4–8 Hz). Indeed, cross-frequency coupling of the amplitude of high-frequency activity to the phase of slower oscillations has been described both in animals and in humans, but has never been linked to a theoretical model of a cognitive process. Here we used intracranial EEG recordings in human epilepsy patients to test pivotal predictions from theoretical work. First, we show that simultaneous maintenance of multiple items in WM is accompanied by cross-frequency coupling of oscillatory activity in the hippocampus, which is recruited during multi-item WM. Second, maintenance of an increasing number of items is associated with modulation of beta/gamma amplitude with theta band activity of lower frequency, consistent with the idea that longer cycles are required for an increased number of representations by gamma cycles. This effect cannot be explained by a difference in theta or beta/gamma power. Third, we describe how the precision of cross-frequency coupling predicts individual WM performance. These data support the idea that working memory in humans depends on a neural code using phase information.
Kappa opioid receptor contributes to EGF-stimulated neurite extension in development
Authors: Tsai Nien-Pei , Tsui Yao-Chen , Pintar John E. , Loh Horace H. , Wei Li-Na
Published: January 2010

Epidermal growth factor (EGF), a mitogen, also stimulates neurite extension during development, but the underlying mechanism is elusive. This study reveals a functional role for kappa opioid receptor (KOR) in EGF-stimulated neurite extension, and the underlying mechanism. EGF and activated EGF receptor (EGFR) levels are elevated in embryonic spinal cords during late gestation stages, with concurrent rise in protein levels of KOR and axon extension markers, growth-associated protein 43 (GAP43), and transient axonal glycoprotein-1 (TAG-1). Both GAP43 and TAG-1 levels are significantly lower in KOR-null (KOR−/−) spinal cords, and EGFR inhibitors effectively reduce the levels of KOR, GAP43, and TAG-1 in wild-type embryonic spinal cords. ForKOR−/−or KOR-knockdown dorsal root ganglion (DRG) neurons, EGF can no longer effectively stimulate axon extension, which can be rescued by introducing a constitutive KOR expressing vector but not by a regulated KOR vector carrying its 5′ untranslated region, which can be bound and repressed by growth factor receptor-bound protein 7 (Grb7). Furthermore, blocking KOR activation by application of anti-dynorphin, KOR antagonist, or EGFR inhibitor effectively reduces axon extension of DRG neurons. Thus, EGF-stimulated axon extension during development is mediated, at least partially, by specific elevation of KOR protein production at posttranscriptional level, as well as activation of KOR signaling. The result also reveals an action of EGF to augment posttranscriptional regulation of certain mRNAs during developmental stages.
Keap1 is a forked-stem dimer structure with two large spheres enclosing the intervening, double glycine repeat, and C-terminal domains
Authors: Ogura Toshihiko , Tong Kit I. , Mio Kazuhiro , Maruyama Yuusuke , Kurokawa Hirofumi , Sato Chikara , Yamamoto Masayuki
Published: January 2010

Keap1 is a substrate adaptor of a Cullin 3-based E3 ubiquitin ligase complex that recognizes Nrf2, and also acts as a cellular sensor for xenobiotics and oxidative stresses. Nrf2 is a transcriptional factor regulating the expression of cytoprotective enzyme genes in response to such stresses. Under unstressed conditions Keap1 binds Nrf2 and results in rapid degradation of Nrf2 through the proteasome pathway. In contrast, upon exposure to oxidative and electrophilic stress, reactive cysteine residues in intervening region (IVR) and Broad complex, Tramtrack, and Bric-à-Brac domains of Keap1 are modified by electrophiles. This modification prevents Nrf2 from rapid degradation and induces Nrf2 activity by repression of Keap1. Here we report the structure of mouse Keap1 homodimer by single particle electron microscopy. Three-dimensional reconstruction at 24-Å resolution revealed two large spheres attached by short linker arms to the sides of a small forked-stem structure, resembling a cherry-bob. Each sphere has a tunnel corresponding to the central hole of the β-propeller domain, as determined by x-ray crystallography. The IVR domain appears to surround the core of the β-propeller domain. The unexpected proximity of IVR to the β-propeller domain suggests that any distortions generated during modification of reactive cysteine residues in the IVR domain may send a derepression signal to the β-propeller domain and thereby stabilize Nrf2. This study thus provides a structural basis for the two-site binding and hinge-latch model of stress sensing by the Nrf2-Keap1 system.
MicroRNA-19a mediates the suppressive effect of laminar flow on cyclin D1 expression in human umbilical vein endothelial cells
Authors: Qin Xiaomei , Wang Xiaohong , Wang Ying , Tang Zhihui , Cui Qinghua , Xi Jianzhong , J. Li Yi-Shuan , Chien Shu , Wang Nanping
Published: January 2010

Endothelial cells (ECs) respond to changes in mechanical forces, leading to the modulation of signaling networks and cell function; an example is the inhibition of EC proliferation by steady laminar flow. MicroRNAs (miRs) are short noncoding 20–22 nucleotide RNAs that negatively regulate the expression of target genes at the posttranscriptional level. This study demonstrates that miRs are involved in the flow regulation of gene expression in ECs. With the use of microRNA chip array, we found that laminar shear stress (12 dyn/cm
2
, 12 h) regulated the EC expression of many miRs, including miR-19a. We further showed that stable transfection of miR-19a significantly decreased the expression of a reporter gene controlled by a conserved 3′-untranslated region of the cyclinD1 gene and also the protein level of cyclin D1, leading to an arrest of cell cycle at G1/S transition. Laminar flow suppressed cyclin D1 protein level, and this suppressive effect was diminished when the endogenous miR-19a was inhibited. In conclusion, we demonstrated that miR-19a plays an important role in the flow regulation of cyclin D1 expression. These results revealed a mechanism by which mechanical forces modulate endothelial gene expression.
Proliferative lesions and metalloproteinase activity in murine lupus nephritis mediated by type I interferons and macrophages
Authors: Triantafyllopoulou Antigoni , Franzke Claus-Werner , Seshan Surya V. , Perino Giorgio , Kalliolias George D. , Ramanujam Meera , van Rooijen Nico , Davidson Anne , Ivashkiv Lionel B.
Published: January 2010

Glomerulonephritis is a major cause of morbidity in patients with systemic lupus erythematosus. Although substantial progress has been made in the identification of pathogenic triggers that result in autoantibody production, little is known about the pathogenesis of aggressive proliferative processes that lead directly to irreversible glomerular damage and compromise of renal function. In this study, we describe a model of polyinosinic: polycytidylic acid-accelerated lupus nephritis in NZB/W mice that is characterized by severe glomerular proliferative lesions with de novo crescent formation, findings that are linked with decreased survival and adverse outcomes in lupus. Proliferative glomerulonephritis was associated with infiltrating kidney macrophages and renal expression of IFN-inducible genes, matrix metalloproteinases (MMPs), and growth factors. Crescent formation and renal MMP and growth factor expression were dependent on renal macrophages that expressed
Il10
, MMPs,
osteopontin
, and growth factors, including
Pdgfc
and
Hbegf
. Infiltrating macrophages and renal MMP expression were induced by type I IFN. These findings reveal a role for type I IFNs and alternatively activated macrophages in aggressive proliferative lesions of lupus nephritis.
Kia ora matua
Authors: Bres Julia de , Holmes Janet , Marra Meredith , Vine Bernadette
Published: January 2010

Many aspects of the use of the Maori language are highly controversial in New Zealand, and humour is one way in which the sensitivities relating to the language can be negotiated in everyday workplace contexts. This article examines the use of the Maori language by Maori and Pakeha participants during humorous episodes at staff meetings in a Maori organisation in New Zealand. The episodes analysed include humour indirectly relating to the Maori language, where the language is not the topic of discussion but its use plays an important implicit role, as well as humour directly focussed on the Maori language, where use of the language is the explicit topic of the humour. Use of the Maori language in these episodes includes Maori greetings, pronunciation of Maori words, the use of Maori lexical items, more extended stretches of Maori, Maori discursive features, and lexical items in English with Maori cultural connotations. The Maori language is used in a humorous context by both Maori and Pakeha staff members, in similar and different ways. Humorous episodes using the Maori language appear to serve a range of functions, including releasing tension (e.g. relating to sensitive issues around the Maori language), marking ingroups and outgroups (and sometimes bonding between the two), referencing Maori cultural norms, and constructing Maori identity.
Time to get up
Authors: Backhaus Peter
Published: January 2010

This paper looks at compliance-gaining interaction in a Japanese elderly care facility from a conversation analytical point of view. Focus is on the various ways compliance is sought for by the caring staff with getting the residents out of bed and starting the daily morning care procedures. Three extracts are discussed in detail. The analysis shows how the residents in all three cases display clear signs of resistance to get up, but finally have to submit to the planned course of actions pursued by the care workers. A closer look at how this is played out in interaction suggests that the residents’ compliance is enforced rather than gained.
Effective intercultural communication
Authors: Komolsevin Rosechongporn , Knutson Thomas J. , Datthuyawat Phan
Published: January 2010

This paper summarizes several studies conducted over the past fifteen years investigating Thai communication behavior. Thai cultural values emphasize social harmony, a trait strongly influencing intercultural communication effectiveness (ICE). Various studies are reported identifying those communication behaviors associated with ICE. The paper presents critical commentary about the methods and means of the research program and suggests ways in which Thai communication behavior contribute to ICE. The paper concludes with recommendations for future research.
Predictors of Substance Abuse Treatment Entry among Rural Illicit Stimulant Users in Ohio, Arkansas, and Kentucky
Authors: Carlson Robert G. , Sexton Rocky , Wang Jichuan , Falck Russel , Leukefeld Carl G. , Booth Brenda M.
Published: January 2010

Illicit drug use in the rural United States is increasingly common, yet little is known about drug users’ treatment-seeking behaviors. This study identifies predictors of substance abuse treatment entry over 24 months among 710 illicit stimulant users in rural areas of Ohio, Arkansas, and Kentucky. Active users of powdered cocaine, crack cocaine, and/or methamphetamine (MA) were recruited using respondent-driven sampling. Participants completed structured interviews at baseline and follow-up questionnaires every 6 months for 24 months. Data were analyzed using the Cox proportional hazards model. The paper is informed by the Anderson-Newman Model. Overall, 18.7% of the sample entered treatment. Ohio or Kentucky residence, perceived need for substance abuse treatment, higher Addiction Severity Index (ASI) legal problem composite scores, prior substance abuse treatment, and tranquilizer use were positively associated with treatment entry. Nondaily crack cocaine users and marijuana users were less likely to enter treatment. The findings can help inform rural substance abuse treatment program development and outreach.
Institutional Denial or Minimization: Substance Abuse Training in Social Work Education
Authors: Quinn Gregorio
Published: January 2010

Substance abuse in the United States has reached catastrophic proportions. 23.6 million people needed treatment for an illicit drug or alcohol use problem ( 1 ). According to the National Association of Social Workers, 60% of all mental health services are carried out by social workers ( 3 ). Therefore, social workers are in a critical and unique position to address substance abuse. This study examined the education and training new social workers receive at 216 graduate programs accredited or in-candidacy for accreditation by the Council of Social Work Education. An overwhelming number did not have substance abuse courses as a requirement for all students, and a significant number did not have one course dedicated to substance abuse. These astounding deficiencies can only be described as an institutional denial or minimization.
Two-Year Trajectory of Stimulant Use in 18- to 21-Year-Old Rural African Americans
Authors: Kramer Teresa L. , Booth Brenda M. , Han Xiaotong
Published: January 2010

Little is known about stimulant use trajectories of rural African American youth. The purpose of the present study is to explore substance use over 24 months in 98 African Americans, ages 18 to 21, who used cocaine or methamphetamine 30 days prior to baseline. The majority was male, unemployed, and had not graduated from high school. At baseline, almost half of the participants met criteria for abuse/dependence of cocaine—the primary stimulant used—which decreased to 25% by the final follow-up. Similar decreases were noted in rates of alcohol and marijuana abuse/dependence, although monthly use remained high. Participants reported minimal utilization of mental health or substance abuse services, but demonstrated significant improvements on physical and mental health measures. In summary, cocaine use declined, but other substances were used at high rates, suggesting a significant need for intervention services that address multisubstance use in rural areas.
Willingness of Facial Injury Patients to Change Causal Substance Using Behaviors
Authors: Murphy Debra A. , Shetty Vivek , Zigler Corwin , Resell Judith , Yamashita Dennis-Duke
Published: January 2010

Many injuries due to interpersonal violence among patients presenting to urban trauma centers for treatment are preventable, with alcohol and illicit drug use presenting as common antecedent risk factors. However, many patients with such problems do not seek treatment. Substance use patients were surveyed to determine how many recognized they had a problem and whether they had previously received treatment for substance use problems. Almost 60% of the patients treated for a facial injury screened for problem alcohol use, and slightly more than 25% screened for problem drug use. Only approximately one third of patients indicated any movement towards dealing with these problems and of these, only 20% had actually sought treatment. Employment had an effect on treatment seeking, with fewer employed patients seeking help. Utilizing the critical window of opportunity for emergency department (ED) personnel to make referrals may have an impact on treatment seeking for problem level substance use.
The Relationship of Social Support to Treatment Entry and Engagement: The Community Assessment Inventory
Authors: Kelly Sharon M. , O'Grady Kevin E. , Schwartz Robert P. , Peterson James A. , Wilson Monique E. , Brown Barry S.
Published: January 2010

This study was conducted to determine the psychometric properties of a measure of social support, the Community Assessment Inventory (CAI), and to examine the role of social support in recovery. The CAI and the Addiction Severity Index (ASI) were administered to 196 opioid-dependent adults in ( n = 135) or out of ( n = 61) methadone treatment in Baltimore, Maryland, between 2004 and 2006. Baseline CAI scale scores indicated a generally high level of internal consistency (α scores). Pearson correlations showed that the scales were stable and had good discriminant validity with the ASI composite scores. One-way analysis of variance indicated that in-treatment participants reported significantly more support at baseline than out-of-treatment participants. This study's findings indicate the CAI may be a useful measure of social support and that such support is an important factor in treatment entry.
Psychotropic Medications and Substances of Abuse Interactions in Youth
Authors: Kaminer Yifrah , Goldberg Pablo , Connor Daniel F.
Published: January 2010

The majority of youth with substance use disorders (SUDs) manifest one or more co-occurring psychiatric disorders. Consequently, many of these youths are being prescribed with psychotropic medications. As prescribing rates continue to increase for early-onset psychiatric disorders, potential risk for substance of abuse–psychiatric medication interactions may be enhanced. Because this type of drug-drug interaction has received little attention in the scientific literature, the authors conducted a systematic literature search examining the potential interactive adverse effects between psychotropic medications and substances of abuse in youth. Regardless of the scarcity of psychotropic medications–substance of abuse interactions found, it is important to stay vigilant due to the continued introduction of new classes of medications as well as the ever-changing map of street drugs.
How is Substance Use Linked to Psychosis? A Study of the Course and Patterns of Substance Dependence in Psychosis
Authors: Saddichha Sahoo , Sur Shravani , Sinha Baxi Neeraj Prasad , Khess Christoday Raja Jayant
Published: January 2010

Substance use in mentally ill patients is now a major problem that influences the course and outcome of psychosis. With prevalence ranging up to 60%, several theories were postulated to explain the link. It would be interesting to know if substances have different effects in persons with psychosis than in those without. This study aimed to explore patterns of symptomatology of dependence and comorbid psychiatric illness by comparing and contrasting it with a group suffering from pure substance dependence. Consecutively admitted patients who were matched for age, sex, and tobacco use were divided into 3 groups. These were substance dependence without any comorbid psychiatric disorder (SD; n = 32), schizophrenia with substance dependence (SC; n = 31), and bipolar disorder with substance dependence (BD; n = 31). Patients were administered the Schedules for Clinical Assessment in Neuropsychiatry (SCAN) and Mini International Neuropsychiatric Inventory (MINI) to evaluate the chronology of criterion of International Classificiation of Diseases (ICD)-10 dependence. Results showed that cannabis was the most common substance used by both the SC (100%) and BD (80%) groups. This was followed by alcohol as the most common substance used, with prevalence of 87% in SC and 77% in BD groups. There was a significant difference in the pattern of use of cannabis in patients with psychosis, who developed tolerance much faster ( P = .018) and had longer durations of cannabis use ( P = .001) than the SD group. The presence of “loss of control” over drug use criterion seems to be a specific marker predicting development of dependence and psychosis. Cannabis use is more strongly associated with development of psychosis than any other substance.
Constructive Empiricism and Deflationary Truth
Authors: Asay Jamin
Published: January 2010

Constructive empiricists claim to offer a reconstruction of the aim and practice of science without adopting all the metaphysical commitments of scientific realism. Deflationists about truth boast of the ability to offer a full account of the nature of truth without adopting the metaphysical commitments accompanying substantive accounts. Though the two views would form an attractive package, I argue that the pairing is not possible: constructive empiricism requires a substantive account of truth. I articulate what sort of account of truth and empirical adequacy the constructive empiricist must offer and then show why deflationists cannot uphold such an account.
Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach
Authors: Wicker Jörg , Fenner Kathrin , Ellis Lynda , Wackett Larry , Kramer Stefan
Published: January 2010

Motivation: Current methods for the prediction of biodegradation products and pathways of organic environmental pollutants either do not take into account domain knowledge or do not provide probability estimates. In this article, we propose a hybrid knowledge- and machine learning-based approach to overcome these limitations in the context of the University of Minnesota Pathway Prediction System (UM-PPS). The proposed solution performs relative reasoning in a machine learning framework, and obtains one probability estimate for each biotransformation rule of the system. As the application of a rule then depends on a threshold for the probability estimate, the trade-off between recall (sensitivity) and precision (selectivity) can be addressed and leveraged in practice.

Results: Results from leave-one-out cross-validation show that a recall and precision of ∼0.8 can be achieved for a subset of 13 transformation rules. Therefore, it is possible to optimize precision without compromising recall. We are currently integrating the results into an experimental version of the UM-PPS server.

Availability: The program is freely available on the web at http://wwwkramer.in.tum.de/research/applications/biodegradation/data.

Contact:  kramer@in.tum.de
iMotifs: an integrated sequence motif visualization and analysis environment
Authors: Piipari Matias , Down Thomas A. , Saini Harpreet , Enright Anton , Hubbard Tim J.P.
Published: January 2010

Motivation: Short sequence motifs are an important class of models in molecular biology, used most commonly for describing transcription factor binding site specificity patterns. High-throughput methods have been recently developed for detecting regulatory factor binding sites in vivo and in vitro and consequently high-quality binding site motif data are becoming available for increasing number of organisms and regulatory factors. Development of intuitive tools for the study of sequence motifs is therefore important.

iMotifs is a graphical motif analysis environment that allows visualization of annotated sequence motifs and scored motif hits in sequences. It also offers motif inference with the sensitive NestedMICA algorithm, as well as overrepresentation and pairwise motif matching capabilities. All of the analysis functionality is provided without the need to convert between file formats or learn different command line interfaces.

The application includes a bundled and graphically integrated version of the NestedMICA motif inference suite that has no outside dependencies. Problems associated with local deployment of software are therefore avoided.

Availability: iMotifs is licensed with the GNU Lesser General Public License v2.0 (LGPL 2.0). The software and its source is available at http://wiki.github.com/mz2/imotifs and can be run on Mac OS X Leopard (Intel/PowerPC). We also provide a cross-platform (Linux, OS X, Windows) LGPL 2.0 licensed library libxms for the Perl, Ruby, R and Objective-C programming languages for input and output of XMS formatted annotated sequence motif set files.

Contact:  matias.piipari@gmail.com; imotifs@googlegroups.com
invertFREGENE: software for simulating inversions in population genetic data
Authors: O'Reilly Paul F. , Coin Lachlan J. M. , Hoggart Clive J.
Published: January 2010

Summary: Inversions are a common form of structural variation, which may have a marked effect on the genome and methods to infer quantities of interest such as those relating to population structure and natural selection. However, due to the challenge in detecting inversions, little is presently known about their impact. Software to simulate inversions could be used to provide a better understanding of how to detect and account for them; but while there are several software packages for simulating population genetic data, none incorporate inversion polymorphisms. Here, we describe a software package, modified from the forward-in-time simulator FREGENE, which simulates the evolution of an inversion polymorphism, of specified length, location, frequency and age, in a population of sequences. We describe previously unreported signatures of inversions in SNP data observed in invertFREGENE results and a known inversion in humans.

Availability: C++ source code and user manual are available for download from http://www.ebi.ac.uk/projects/BARGEN/ under the GPL licence.

Contact:  l.coin@ic.ac.uk; c.hoggart@ic.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
XDIA: improving on the label-free data-independent analysis
Authors: Carvalho Paulo C. , Han Xuemei , Xu Tao , Cociorva Daniel , Carvalho Maria da Gloria , Barbosa Valmir C. , Yates John R.
Published: January 2010

Summary: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (∼250%) and unique peptides (∼30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively.

Availability: The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA

Contact:  paulo@pcarvalho.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Acupuncture to Treat Primary Dysmenorrhea in Women: A Randomized Controlled Trial
Authors: Smith Caroline A. , Crowther Caroline A. , Petrucco Oswald , Beilby Justin , Dent Hannah
Published: January 2010

We examined the effectiveness of acupuncture to reduce the severity and intensity of primary dysmenorrhea. A randomized controlled trial compared acupuncture with control acupuncture using a placebo needle. Eligible women were aged 14–25 years with a diagnosis of primary dysmenorrhea. Women received nine sessions of the study treatment over 3 months. The primary outcomes were menstrual pain intensity and duration, overall improvement in dysmenorrhea symptoms and reduced need for additional analgesia, measured at 3, 6 and 12 months from trial entry. A total of 92 women were randomly assigned to the intervention (acupuncture n = 46 and control n = 46). At 3 months although pain outcomes were lower for women in the acupuncture group compared with the control group, there was no significant difference between groups. Women receiving acupuncture reported a small reduction in mood changes compared with the control group, relative risk (RR) 0.72, 95% confidence interval (CI) 0.53–1.00, P = .05. Follow‐up at 6 months found a significant reduction in the duration of menstrual pain in the acupuncture group compared with the control group, mean difference –9.6, 95% CI –18.9 to –0.3, P = .04, and the need for additional analgesia was significantly lower in the acupuncture group compared with the control group, RR 0.69, 95% CI 0.49–0.96, P = .03, but the follow‐up at 12 months found lack of treatment effect. To conclude, although acupuncture improved menstrual mood symptoms in women with primary dysmenorrhea during the treatment phase, the trend in the improvement of symptoms during the active phase of treatment, and at 6 and 12 months was non‐significant, indicating that a small treatment effect from acupuncture on dysmenorrhea may exist. In the study, acupuncture was acceptable and safe, but further appropriately powered trials are needed before recommendations for clinical practice can be made.
Relaxed predation risk reduces but does not eliminate sociality in birds
Authors: Beauchamp Guy
Published: January 2010

Disentangling the relative contribution of predation avoidance and increased foraging efficiency in the evolution of sociality in animals has proven difficult given that the two types of benefits often operate concurrently. I identified different types of refuges from predation in birds related to morphological and ecological traits, providing an opportunity to examine concomitant changes in sociality over evolutionary times. Results of a matched-species comparative analysis indicated a reduction in the size of foraging or non-foraging groups but not complete disappearance under negligible predation risk. The results suggest that while predation avoidance is an important component in the evolution of sociality in birds, it is most probably not acting alone but rather in conjunction with other benefits such as increased foraging efficiency.
Avian magnetite-based magnetoreception: a physiologist's perspective
Authors: Cadiou Hervé , McNaughton Peter A.
Published: January 2010

It is now well established that animals use the Earth's magnetic field to perform long-distance migration and other navigational tasks. However, the transduction mechanisms that allow the conversion of magnetic field variations into an electric signal by specialized sensory cells remain largely unknown. Among the species that have been shown to sense Earth-strength magnetic fields, birds have been a model of choice since behavioural tests show that their direction-finding abilities are strongly influenced by magnetic fields. Magnetite, a ferromagnetic mineral, has been found in a wide range of organisms, from bacteria to vertebrates. In birds, both superparamagnetic (SPM) and single-domain magnetite have been found to be associated with the trigeminal nerve. Electrophysiological recordings from cells in the trigeminal ganglion have shown an increase in action potential firing in response to magnetic field changes. More recently, histological evidence has demonstrated the presence of SPM magnetite in the subcutis of the pigeon's upper beak. The aims of the present review are to review the evidence for a magnetite-based mechanism in birds and to introduce physiological concepts in order to refine the proposed models.
An exceptionally preserved myodocopid ostracod from the Silurian of Herefordshire, UK
Authors: Siveter David J. , Briggs Derek E. G. , Siveter Derek J. , Sutton Mark D.
Published: January 2010

An exceptionally preserved new ostracod crustacean from the Silurian of Herefordshire, UK, represents only the third fully documented Palaeozoic ostracod with soft-part preservation. Appendages, gills, gut system, lateral compound eyes and even a medial eye with a Bellonci organ are preserved, allowing assignment of the fossil to a new genus and species of cylindroleberidid myodocope (Myodocopida, Cylindroleberididae). The Bellonci organ is recorded for the first time in fossil ostracods. The find also represents a rare occurrence of gills in fossil ostracods and confirms the earliest direct evidence of a respiratory-cum-circulatory system in the group. The species demonstrates remarkably conserved morphology within myodocopes over a period of 425 Myr. Its shell morphology more closely resembles several families of myodocopes other than the Cylindroleberididae, especially the Cypridinidae and Sarsiellidae, thus questioning the utility of the carapace alone in establishing the affinity of fossil ostracods.
Cell Wall-Degrading Enzymes Enlarge the Pore Size of Intervessel Pit Membranes in Healthy andXylella fastidiosa-Infected Grapevines
Authors: Pérez-Donoso Alonso G. , Sun Qiang , Roper M. Caroline , Greve L. Carl , Kirkpatrick Bruce , Labavitch John M.
Published: January 2010

The pit membrane (PM) is a primary cell wall barrier that separates adjacent xylem water conduits, limiting the spread of xylem-localized pathogens and air embolisms from one conduit to the next. This paper provides a characterization of the size of the pores in the PMs of grapevine (Vitis vinifera). The PM porosity (PMP) of stems infected with the bacterium Xylella fastidiosa was compared with the PMP of healthy stems. Stems were infused with pressurized water and flow rates were determined; gold particles of known size were introduced with the water to assist in determining the size of PM pores. The effect of introducing trans-1,2-diaminocyclohexane-N,N,N′,N′-tetraacetic acid (CDTA), oligogalacturonides, and polygalacturonic acid into stems on water flux via the xylem was also measured. The possibility that cell wall-degrading enzymes could alter the pore sizes, thus facilitating the ability of X. fastidiosa to cross the PMs, was tested. Two cell wall-degrading enzymes likely to be produced by X. fastidiosa (polygalactuoronase and endo-1,4- β -glucanase) were infused into stems, and particle passage tests were performed to check for changes in PMP. Scanning electron microscopy of control and enzyme-infused stem segments revealed that the combination of enzymes opened holes in PMs, probably explaining enzyme impacts on PMP and how a small X. fastidiosa population, introduced into grapevines by insect vectors, can multiply and spread throughout the vine and cause Pierce's disease.
Analysis of Arabidopsis with Highly Reduced Levels of Malate and Fumarate Sheds Light on the Role of These Organic Acids as Storage Carbon Molecules
Authors: Zell Martina B. , Fahnenstich Holger , Maier Alexandra , Saigo Mariana , Voznesenskaya Elena V. , Edwards Gerald E. , Andreo Carlos , Schleifenbaum Frank , Zell Christiane , Drincovich María F. , Maurino Verónica G.
Published: January 2010

While malate and fumarate participate in a multiplicity of pathways in plant metabolism, the function of these organic acids as carbon stores in C3 plants has not been deeply addressed. Here, Arabidopsis (Arabidopsis thaliana) plants overexpressing a maize (Zea mays) plastidic NADP-malic enzyme (MEm plants) were used to analyze the consequences of sustained low malate and fumarate levels on the physiology of this C3 plant. When grown in short days (sd), MEm plants developed a pale-green phenotype with decreased biomass and increased specific leaf area, with thin leaves having lower photosynthetic performance. These features were absent in plants growing in long days. The analysis of metabolite levels of rosettes from transgenic plants indicated similar disturbances in both sd and long days, with very low levels of malate and fumarate. Determinations of the respiratory quotient by the end of the night indicated a shift from carbohydrates to organic acids as the main substrates for respiration in the wild type, while MEm plants use more reduced compounds, like fatty acids and proteins, to fuel respiration. It is concluded that the alterations observed in sd MEm plants are a consequence of impairment in the supply of carbon skeletons during a long dark period. This carbon starvation phenotype observed at the end of the night demonstrates a physiological role of the C4 acids, which may be a constitutive function in plants.