bluuebunny/crossref_metadata_2025 huggingface dataset:
The invariant phenylalanine of precursor proteins discloses the importance of Omp85 for protein translocation into cyanelles
Authors: Wunder Tobias , Martin Roman , Löffelhardt Wolfgang , Schleiff Enrico , Steiner Jürgen M
Published: November 2007

Background

Today it is widely accepted that plastids are of cyanobacterial origin. During their evolutionary integration into the metabolic and regulatory networks of the host cell the engulfed cyanobacteria lost their independency. This process was paralleled by a massive gene transfer from symbiont to the host nucleus challenging the development of a retrograde protein translocation system to ensure plastid functionality. Such a system includes specific targeting signals of the proteins needed for the function of the plastid and membrane-bound machineries performing the transfer of these proteins across the envelope membranes. At present, most information on protein translocation is obtained by the analysis of land plants. However, the analysis of protein import into the primitive plastids of glaucocystophyte algae, revealed distinct features placing this system as a tool to understand the evolutionary development of translocation systems. Here, bacterial outer membrane proteins of the Omp85 family have recently been discussed as evolutionary seeds for the development of translocation systems.

Results

To further explore the initial mode of protein translocation, the observed phenylalanine dependence for protein translocation into glaucophyte plastids was pursued in detail. We document that indeed the phenylalanine has an impact on both, lipid binding and binding to proteoliposomes hosting an Omp85 homologue. Comparison to established import experiments, however, unveiled a major importance of the phenylalanine for recognition by Omp85. This finding is placed into the context of the evolutionary development of the plastid translocon.

Conclusion

The phenylalanine in the N-terminal domain signs as a prerequisite for protein translocation across the outer membrane assisted by a "primitive" translocon. This amino acid appears to be optimized for specifically targeting the Omp85 protein without enforcing aggregation on the membrane surface. The phenylalanine has subsequently been lost in the transit sequence, but can be found at the C-terminal position of the translocating pore. Thereby, the current hypothesis of Omp85 being the prokaryotic contribution to the ancestral Toc translocon can be supported.
Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalis
Authors: Srivastava Jyoti , Premi Sanjay , Kumar Sudhir , Parwez Iqbal , Ali Sher
Published: November 2007

Background

Secreted modular calcium binding protein-1 (Smoc-1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. Besides its anticipated role in embryogenesis, Smoc-1 has been characterized only in a few mammalian species. We made use of the consensus sequence (5' CACCTCTCCACCTGCC 3') of 33.15 repeat loci to explore the buffalo transcriptome and uncovered the Smoc-1 transcript tagged with this repeat. The main objective of this study was to gain an insight into its structural and functional organization, and expressional status of Smoc-1 in water buffalo, Bubalus bubalis.

Results

We cloned and characterized the buffalo Smoc-1, including its copy number status, in-vitro protein expression, tissue & age specific transcription/translation, chromosomal mapping and localization to the basement membrane zone. Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family. In buffalo, this single copy gene consisted of 12 exons and was mapped onto the acrocentric chromosome 11. Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals. In silico analysis of the Smoc-1 proposed its glycoprotein nature with a calcium dependent conformation. Further, we unveiled two transcript variants of this gene, varying in their 3'UTR lengths but both coding for identical protein(s). Smoc-1 evinced highest expression of both the variants in liver and modest to negligible in other tissues. The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined. Moreover, expression of Smoc-1, though modest during the early ages, was conspicuously enhanced after 1 year and remained consistently higher during the entire life span of buffalo with gradual increment in expression of variant-02. Immunohistochemically, Smoc-1 was localized in the basement membrane zones and extracellular matrices of various tissues.

Conclusion

These data added to our understandings about the tissue, age and species specific functions of the Smoc-1. It also enabled us to demonstrate varying expression of the two transcript variants of Smoc-1 amongst different somatic tissues/gonads and ages, in spite of their identical coding frames. Pursuance of these variants for their roles in various disease phenotypes such as hepatocellular carcinoma and angiogenesis is envisaged to establish broader biological significance of this gene.
Peroxisome proliferators-activated alpha agonist treatment ameliorates hepatic damage in rats with obstructive jaundice: an experimental study
Authors: Cindoruk Mehmet , Kerem Mustafa , Karakan Tarkan , Salman Bulent , Akin Okan , Alper Murat , Erdem Ozlem , Ünal Selahattin
Published: November 2007

Background

Peroxisome proliferators-activated receptor alpha (PPARα) activation modulates cholesterol metabolism and suppresses bile acid synthesis. This study aims to evaluate the effect of short-term administration of fenofibrate, a PPARα agonist, on proinflammatory cytokines, apoptosis, and hepatocellular damage in cholestasis.

Methods

Forty male Wistar rats were randomly divided into four groups: I = sham operated, II = bile duct ligation (BDL), III = BDL + vehicle (gum Arabic), IV = BDL + fenofibrate (100 mg/kg/day). All rats were sacrificed on 7th day after obtaining blood samples and liver tissue. Total bilirubin, aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP), gamma-glutamyl transferase, (GGT), tumor necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1 β), and total bile acid (TBA) in serum, and liver damage scores; portal inflammation, necrosis, bile duct number, in liver tissue were evaluated. Apoptosis in liver was also assessed by immunohistochemical staining.

Results

Fenofibrate administration significantly reduced serum total bilirubin, AST, ALT, ALP, and GGT, TNF-α, IL-1 β levels, and TBA (P < 0.01). Hepatic portal inflammation, hepatic necrosis, number of the bile ducts and apoptosis in rats with BDL were more prominent than the sham-operated animals (P < 0.01). PPARα induction improved all histopathologic parameters (P < 0.01), except for the number of the bile duct, which was markedly increased by fenofibrate therapy (P < 0.01).

Conclusion

Short-term administration of fenofibrate to the BDL rats exerts beneficial effects on hepatocellular damage and apoptosis.
Suicidal ideation and associated factors among school-going adolescents in rural Uganda
Authors: Rudatsikira Emmanuel , Muula Adamson S , Siziya Seter , Twa-Twa Jeremiahs
Published: November 2007

Background

Mental health is a neglected area of health research and practice in most of sub-Saharan African countries where the largest burden of morbidity is from infectious diseases. This even occurs despite the fact that some mental health problems may arise from infectious diseases.

Methods

We conducted secondary analysis of the Uganda Global School-Based Health Survey-2003 to obtain the prevalence of, and assess factors that may be associated with suicidal ideation among school-going adolescents in rural Uganda. Assessment of association was conducted through both bi-variate and multivariate logistic regression analysis.

Results

Altogether 21.6% of the study participants, 21.3% males and 23.5% females had seriously considered committing suicide within the past 12 months. Loneliness, worry were positively associated with suicide ideation after adjusting for age, gender, smoking, drinking, and experience of having been bullied (OR = 1.59; 95% CI [1.12, 2.26] and OR = 1.19; 95% CI [1.12, 2.25]) respectively. Males were less likely to seriously consider committing suicide than females (OR = 0.70; 95% CI [0.50, 0.98]).

Conclusion

Adolescent suicidal ideation is a major public health issue in rural Uganda. Measures aimed to prevent adolescent suicides in Uganda should incorporate our understanding of factors that are associated with suicide in rural Uganda such the gender disparity and the association observed with substance use.
The effect of priority setting decisions for new cancer drugs on medical oncologists' practice in Ontario: a qualitative study
Authors: Berry Scott R , Hubay Stacey , Soibelman Hagit , Martin Douglas K
Published: November 2007

Background

Health care policies, including drug-funding policies, influence physician practice. Funding policies are especially important in the area of cancer care since cancer is a leading cause of death that is responsible for a significant level of health care expenditures. Recognizing the rising cost of cancer therapies, Cancer Care Ontario (CCO) established a funding process to provide access to new, effective agents through a "New Drug Funding Program" (NDFP). The purpose of this study is to describe oncologists' perceptions of the impact of NDFP priority setting decisions on their practice.

Methods

This is a qualitative study involving semi-structured, in-depth interviews with 46 medical oncologists in Ontario. Oncologists were asked to describe the impact of CCO's NDFP drug funding decisions on their practice. Analysis of interview transcripts commenced with data collection.

Results

Our key finding is that many of the medical oncologists who participated in this study did not accept limits when policy decisions limit access to cancer drugs they feel would benefit their patients. Moreover, overcoming those limits had a significant impact on oncologists' practice in terms of how they spend their time and energy and their relationship with patients.

Conclusion

When priority setting decisions limit access to cancer medications, many oncologists' efforts to overcome those limits have a significant impact on their practice. Policy makers need to seriously consider the implications of their decisions on physicians, who may go to considerable effort to circumvent their policies in the name of patient advocacy.
Effect of pre-germinated brown rice intake on diabetic neuropathy in streptozotocin-induced diabetic rats
Authors: Usuki Seigo , Ito Yukihiko , Morikawa Keiko , Kise Mitsuo , Ariga Toshio , Rivner Michael , Yu Robert K
Published: November 2007

Background

To study the effects of a pre-germinated brown rice diet (PR) on diabetic neuropathy in streptozotocin (STZ)-induced diabetic rats.

Methods

The effects of a PR diet on diabetic neuropathy in STZ-induced diabetic rats were evaluated and compared with those fed brown rice (BR) or white rice (WR) diets with respect to the following parameters: blood-glucose level, motor-nerve conduction velocity (NCV), sciatic-nerve Na+/K+-ATPase activity, and serum homocysteine-thiolactonase (HTase) activity.

Results

Compared with diabetic rats fed BR or WR diets, those fed a PR diet demonstrated significantly lower blood-glucose levels (p < 0.001), improved NCV (1.2- and 1.3-fold higher, respectively), and increased Na+/K+-ATPase activity (1.6- and 1.7-fold higher, respectively). The PR diet was also able to normalize decreased serum homocysteine levels normally seen in diabetic rats. The increased Na+/K+-ATPase activity observed in rats fed PR diets was associated with elevations in HTase activity (r = 0.913, p < 0.001). The in vitro effect of the total lipid extract from PR bran (TLp) on the Na+/K+-ATPase and HTase activity was also examined. Incubation of homocysteine thiolactone (HT) with low-density lipoprotein (LDL) in vitro resulted in generation of HT-modified LDL, which possessed high potency to inhibit Na+/K+-ATPase activity in the sciatic nerve membrane. The inhibitory effect of HT-modified LDL on Na+/K+-ATPase activity disappeared when TLp was added to the incubation mixture. Furthermore, TLp directly activated the HTase associated with high-density lipoprotein (HDL).

Conclusion

PR treatment shows efficacy for protecting diabetic deterioration and for improving physiological parameters of diabetic neuropathy in rats, as compared with a BR or WR diet. This effect may be induced by a mechanism whereby PR intake mitigates diabetic neuropathy by one or more factors in the total lipid fraction. The active lipid fraction is able to protect the Na+/K+-ATPase of the sciatic-nerve membrane from the toxicity of HT-modified LDL and to directly activate the HTase of HDL.
What is an acceptably smoothed fluence? Dosimetric and delivery considerations for dynamic sliding window IMRT
Authors: Giorgia Nicolini , Antonella Fogliata , Eugenio Vanetti , Alessandro Clivio , Filippo Ammazzalorso , Luca Cozzi
Published: November 2007

Background

The study summarised in this report aimed to investigate the interplay between fluence complexity, dose calculation algorithms, dose calculation spatial resolution and delivery characteristics (monitor units, effective field width and dose delivery against dose prediction agreement) was investigated. A sample set of complex planning cases was selected and tested using a commercial treatment planning system capable of inverse optimisation and equipped with tools to tune fluence smoothness.

Methods

A set of increasingly smoothed fluence patterns was correlated to a generalised expression of the Modulation Index (MI) concept, in nature independent from the specific planning system used that could therefore be recommended as a predictor to score fluence "quality" at a very early stage of the IMRT QA process. Fluence complexity was also correlated to delivery accuracy and characteristics in terms of number of MU, dynamic window width and agreement between calculation and measurement (expressed as percentage of field area with a γ > 1 (%FA)) when comparing calculated vs. delivered modulated dose maps. Different resolutions of the calculation grid and different photon dose algorithms (pencil beam and anisotropic analytical algorithm) were used for the investigations.

Results and Conclusion

i) MI can be used as a reliable parameter to test different approaches/algorithms to smooth fluences implemented in a TPS, and to identify the preferable default values for the smoothing parameters if appropriate tools are implemented; ii) a MI threshold set at MI < 19 could ensure that the planned beams are safely and accurately delivered within stringent quality criteria; iii) a reduction in fluence complexity is strictly correlated to a corresponding reduction in MUs, as well as to a decrease of the average sliding window width (for dynamic IMRT delivery); iv) a smoother fluence results in a reduction of dose in the healthy tissue with a potentially relevant clinical benefit; v) increasing the smoothing parameter s, MI decreases with %FA: fluence complexity has a significant impact on the accuracy of delivery and the agreement between calculation and measurements improves with the advanced algorithms.
Incorporating a New Bioinformatics Component into Genetics at a Historically Black College: Outcomes and Lessons
Authors: Holtzclaw J. David , Eisen Arri , Whitney Erika M. , Penumetcha Meera , Hoey J. Joseph , Kimbro K. Sean
Published: November 2007

Many students at minority-serving institutions are underexposed to Internet resources such as the human genome project, PubMed, NCBI databases, and other Web-based technologies because of a lack of financial resources. To change this, we designed and implemented a new bioinformatics component to supplement the undergraduate Genetics course at Clark Atlanta University. The outcomes of the Bioinformatics course were assessed. During the first week of the semester, students were assigned the Felder-Soloman's Index of Learning Styles Inventory. The overwhelming majority of students were visual (82.1%) and sequential (75.0%) learners. Furthermore, pre- and postcourse surveys were administered during the first and the last week of the course to assess learning, confidence level, and mental activity. These indicated students increased the number of hours spent using computers and doing homework. Students reported confidence in using computers to study genetics increased, enabling them to better visualize and understand genetics. Furthermore, students were more mentally engaged in a more social learning environment. Although the students appreciated the value of the bioinformatics component, they reported the additional work load was substantial enough to receive additional course credit.
Teaching Cell and Molecular Biology for Gender Equity
Authors: Sible Jill C. , Wilhelm Dayna E. , Lederman Muriel
Published: November 2007

Science, technology, engineering, and math (STEM) fields, including cell biology, are characterized by the “leaky pipeline” syndrome in which, over time, women leave the discipline. The pipeline itself and the pond into which it empties may not be neutral. Explicating invisible norms, attitudes, and practices by integrating social studies of science into science education may be the necessary first step in helping female students persist in STEM disciplines. In 2003 and 2004, a sophomore Cell and Molecular Biology course at Virginia Tech (Blacksburg, VA) was taught integrating social studies of science with standard material. The course was successfully implemented, teaching students factual content while increasing awareness of the cultures of science and their self-confidence in engaging with the subject. Course evaluation data indicated that females in particular perceived greater gains in logical thinking and problem-solving abilities than females in a traditional cell biology course. Consistent with K–12 studies, males in this class were likely to view scientists as male only, whereas females viewed scientists as male and female. This pilot project demonstrates that social studies can be integrated successfully in a cell biology course. Longitudinal studies of this cohort of students will indicate whether this approach contributes to the retention of women in the field.
A Simple and Effective Protein Folding Activity Suitable for Large Lectures
Authors: White Brian
Published: November 2007

This article describes a simple and inexpensive hands-on simulation of protein folding suitable for use in large lecture classes. This activity uses a minimum of parts, tools, and skill to simulate some of the fundamental principles of protein folding. The major concepts targeted are that proteins begin as linear polypeptides and fold to three-dimensional structures, noncovalent interactions drive this folding process, and the final folded shape of a protein depends on its amino acid sequence. At the start of the activity, students are given pieces of insulated wire from which they each construct and fold their own polypeptide. This activity was evaluated in three ways. A random sample of student-generated polypeptides collected after the activity shows that most students were able to create an appropriate structure. After this activity, students (n = 154) completed an open-ended survey. Their responses showed that more than three-quarters of the students learned one or more of the core concepts being demonstrated. Finally, a follow-up survey was conducted seven weeks after the activity; responses to this survey (n = 63) showed that a similar fraction of students still retained these key concepts. This activity should be useful in large introductory-level college biology or biochemistry lectures.
A Simple Classroom Teaching Technique To Help Students Understand Michaelis-Menten Kinetics
Authors: Runge Steven W. , Hill Brent J.F. , Moran William M.
Published: November 2007

A new, simple classroom technique helps cell biology students understand principles of Michaelis-Menten enzyme kinetics. A student mimics the enzyme and the student's hand represents the enzyme's active site. The catalytic event is the transfer of marbles (substrate molecules) by hand from one plastic container to another. As predicted, increases in marble concentration increase the number of marbles transferred per unit time (initial rate, V0) until the turnover number becomes rate limiting and V0 approaches the maximum velocity (Vmax), as described by the Michaelis-Menten equation. With this demonstration, students visualize an important concept: the turnover number is constant and independent of marble concentration. A student assessment of this exercise showed that it helped students visualize the turnover number and Vmax but not Km, the marble concentration at which V0 is one-half Vmax. To address the concept of Km, we use supplemental laboratory and lecture exercises. This exercise with plastic containers and marbles is equally suited to demonstrate the kinetics of carrier-mediated membrane transport. We conclude that this exercise helps students visualize the turnover number and Vmax and gives students important insights into the kinetic parameters used to characterize the catalytic activity of enzymes and membrane transporters.
Assessment of the Effects of Student Response Systems on Student Learning and Attitudes over a Broad Range of Biology Courses
Authors: Preszler Ralph W. , Dawe Angus , Shuster Charles B. , Shuster Michèle
Published: November 2007

With the advent of wireless technology, new tools are available that are intended to enhance students' learning and attitudes. To assess the effectiveness of wireless student response systems in the biology curriculum at New Mexico State University, a combined study of student attitudes and performance was undertaken. A survey of students in six biology courses showed that strong majorities of students had favorable overall impressions of the use of student response systems and also thought that the technology improved their interest in the course, attendance, and understanding of course content. Students in lower-division courses had more strongly positive overall impressions than did students in upper-division courses. To assess the effects of the response systems on student learning, the number of in-class questions was varied within each course throughout the semester. Students' performance was compared on exam questions derived from lectures with low, medium, or high numbers of in-class questions. Increased use of the response systems in lecture had a positive influence on students' performance on exam questions across all six biology courses. Students not only have favorable opinions about the use of student response systems, increased use of these systems increases student learning.
Clickers in the Large Classroom: Current Research and Best-Practice Tips
Authors: Caldwell Jane E.
Published: November 2007

Note from the Editor

Use of the audience response devices known as “clickers” is growing, particularly in large science courses at the university level, as evidence for the pedagogical value of this technology continues to accumulate, and competition between manufacturers drives technical improvements, increasing user-friendliness and decreasing prices. For those who have not yet tried teaching with clickers and may have heard unsettling stories about technical problems with earlier models, the decision to use them and the choice of an appropriate brand may be difficult. Moreover, like any classroom technology, clickers will not automatically improve teaching or enhance student learning. Clickers can be detrimental if poorly used, but highly beneficial if good practices are followed, as documented in a growing body of educational literature. In this Special Feature, we present two reviews that should assist instructors and teachers at all levels in taking the step toward clicker use and choosing an appropriate model. In the first, Barber and Njus compare the features, advantages, and disadvantages of the six leading brands of radio-frequency clicker systems. In the second, Caldwell reviews the pedagogical literature on clickers and summarizes some of the best practices for clicker use that have emerged from educational research. In a related article elsewhere in this issue, Prezsler et al. present the results of a study showing that clicker use can improve student learning and attitudes in both introductory and more advanced university biology courses.
Clicker Evolution: Seeking Intelligent Design
Authors: Barber Maryfran , Njus David
Published: November 2007

Note from the Editor

Use of the audience response devices known as “clickers” is growing, particularly in large science courses at the university level, as evidence for the pedagogical value of this technology continues to accumulate, and competition between manufacturers drives technical improvements, increasing user-friendliness and decreasing prices. For those who have not yet tried teaching with clickers and may have heard unsettling stories about technical problems with earlier models, the decision to use them and the choice of an appropriate brand may be difficult. Moreover, like any classroom technology, clickers will not automatically improve teaching or enhance student learning. Clickers can be detrimental if poorly used, but highly beneficial if good practices are followed, as documented in a growing body of educational literature. In this Special Feature, we present two reviews that should assist instructors and teachers at all levels in taking the step toward clicker use and choosing an appropriate model. In the first, Barber and Njus compare the features, advantages, and disadvantages of the six leading brands of radio-frequency clicker systems. In the second, Caldwell reviews the pedagogical literature on clickers and summarizes some of the best practices for clicker use that have emerged from educational research. In a related article elsewhere in this issue, Prezsler et al. present the results of a study showing that clicker use can improve student learning and attitudes in both introductory and more advanced university biology courses.
An Alcohol Oxidase Dipstick Rapidly Detects Methanol in the Serum of Mice
Authors: Hack Jason B. , Early Jacqueline , Brewer Kori L.
Published: November 2007

Background Patients presenting with ingestions of methanol and ethylene glycol pose a significant challenge to emergency physicians. The decision to initiate antidotal therapy must be made quickly and is currently based on the presence of indirect signs, symptoms, and laboratory tests, because no real‐time diagnostic test exists to measure these substances.

Objectives To determine whether a commercially available ethanol‐in‐saliva detecting dipstick (ALCO‐Screen) would be a reliable and rapid indicator of toxic alcohol presence in the serum of an animal model.

Methods Fifty mice randomly received intraperitoneal doses of methanol, ethylene glycol, or ethanol to induce serum concentrations of approximately 5–400 mg/dL. Thirty minutes after injection, serum was obtained. Serum was both applied to the dipstick and frozen for definitive concentration determination by gas chromatography. After 2 minutes, dipsticks were evaluated for color change by a blinded observer and photographed to be evaluated by other blinded observers at a later time.

Results All concentrations of methanol ≥5 mg/dL consistently caused a color change on the ALCO‐Screen. Ethylene glycol reliably caused a color change at ≥300 mg/dL. There was significant agreement among multiple observers whether or not color change had occurred using the ALCO‐Screen.

Conclusions A commercially available dipstick that uses an alcohol oxidase colorimetric reaction reliably and rapidly detects very low serum concentrations of methanol but not ethylene glycol in this animal model. This color change is easily detected by most observers.
International Emergency Medicine: A Review of the Literature from 2006
Authors: Levine Adam C. , Goel Ashish , Keay C. Ryan , Lay Cappi , Melnick Edward R. , Nielson Jeffrey A. , Becker Joseph , Khaleghi Murdoc , Chicharoen Nina , Johar Sandeep , Lippert Suzanne , Tebb Zachary D. , Rosborough Stephanie , Arnold Kris
Published: November 2007

The field of international emergency medicine (IEM) has grown rapidly over the past several decades, with a rise in the number of IEM fellowship positions, sustained growth in the international sections of major emergency medicine organizations, and an increase in the range of topics included under its rubric. One of the greatest obstacles to the continued growth of IEM remains the lack of a high‐quality, consolidated, and easily accessible evidence base of literature. In response to this perceived need, members of the Emergency Medicine Residents' Association IEM Committee, in conjunction with members of the Society for Academic Emergency Medicine International Health Interest Group, embarked on the task of creating a recurring review of IEM literature. This article reviews 25 IEM research articles published in 2006. Research articles were selected for the review according to explicit, predetermined criteria that included both methodological quality and perceived impact of the research. It is the authors' hope that this annual review will act as a forum for disseminating best practices while also stimulating further research in the field of IEM.
Toward a Connectionist Model of Recursion in Human Linguistic Performance
Authors: Christiansen Morten H , Chater Nick
Published: November 2007

Naturally occurring speech contains only a limited amount of complex recursive structure, and this is reflected in the empirically documented difficulties that people experience when processing such structures. We present a connectionist model of human performance in processing recursive language structures. The model is trained on simple artificial languages. We find that the qualitative performance profile of the model matches human behavior, both on the relative difficulty of center‐embedding and cross‐dependency, and between the processing of these complex recursive structures and right‐branching recursive constructions. We analyze how these differences in performance are reflected in the internal representations of the model by performing discriminant analyses on these representations both before and after training. Furthermore, we show how a network trained to process recursive structures can also generate such structures in a probabilistic fashion. This work suggests a novel explanation of people's limited recursive performance, without assuming the existence of a mentally represented competence grammar allowing unbounded recursion.
Strategies in Syllogistic Reasoning
Authors: Bucciarelli Monica , Johnson‐Laird P.N.
Published: November 2007

This paper is about syllogistic reasoning, i.e., reasoning from such pairs of premises as, All the chefs are musicians; some of the musicians are painters. We present a computer model that implements the latest account of syllogisms, which is based on the theory of mental models. We also report four experiments that were designed to test this account. Experiments 1 and 2 examined the strategies revealed by the participants' use of paper and pencil as aids to reasoning. Experiment 3 used a new technique to externalize thinking. The participants had to refute, if possible, putative conclusions by constructing external models that were examples of the premises but counterexamples of the conclusions. Experiment 4 used the same techniques to examine the participants' strategies as they drew their own conclusions from syllogistic premises. The results of the experiments showed that individuals not trained in logic can construct counterexamples, that they use similar operations to those implemented in the computer model, but that they rely on a much greater variety of interpretations of premises and of search strategies than the computer model does. We re‐evaluates current theories of syllogistic reasoning in the light of these results.
A Probabilistic Constraints Approach to Language Acquisition and Processing
Authors: Seidenberg Mark S. , MacDonald Maryellen C.
Published: November 2007

This article provides an overview of a probabilistic constraints framework for thinking about language acquisition and processing. The generative approach attempts to characterize knowledge of language (i.e., competence grammar) and then asks how this knowledge is acquired and used. Our approach is performance oriented: the goal is to explain how people comprehend and produce utterances and how children acquire this skill. Use of language involves exploiting multiple probabilistic constraints over various types of linguistic and nonlinguistic information. Acquisition is the process of accumulating this information, which begins in infancy. The constraint satisfaction processes that are central to language use are the same as the bootstrapping processes that provide entry to language for the child. Framing questions about acquisition in terms of models of adult performance unifies the two topics under a set of common principles and has important consequences for arguments concerning language learnability.
Neural cell adhesion molecule regulates the cellular response to fibroblast growth factor
Authors: Francavilla Chiara , Loeffler Sébastien , Piccini Daniele , Kren Angelika , Christofori Gerhard , Cavallaro Ugo
Published: November 2007

Neural cell adhesion molecule (NCAM) mediates cell-cell adhesion and signaling in the nervous system, yet NCAM is also expressed in non-neural tissues, in which its function has in most parts remained elusive. We have previously reported that NCAM stimulates cell-matrix adhesion and neurite outgrowth by activating fibroblast growth factor receptor (FGFR) signaling. Here, we investigated whether the interplay between NCAM and FGFR has any impact on the response of FGFR to its classical ligands, FGFs. To this end, we employed two fibroblast cell lines, NCAM-negative L cells and NCAM-positive NIH-3T3 cells, in which the expression of NCAM was manipulated by means of transfection or RNAi technologies, respectively. The results demonstrate that NCAM expression reduces FGF-stimulated ERK1/2 activation, cell proliferation and cell-matrix adhesion, in both L and NIH-3T3 cells. Furthermore, our data show that NCAM inhibits the binding of FGF to its high-affinity receptor in a competitive manner, providing the mechanisms for the NCAM-mediated suppression of FGF function. In this context, a small peptide that mimics the binding of NCAM to FGFR was sufficient to block FGF-dependent cell proliferation. These findings point to NCAM as being a major regulator of FGF-FGFR interaction, thus introducing a novel type of control mechanism for FGFR activity and opening new therapeutic perspectives for those diseases characterized by aberrant FGFR function.
A 2000-Year Global Temperature Reconstruction Based on Non-Treering Proxies
Authors: Loehle Craig
Published: November 2007

Historical data provide a baseline for judging how anomalous recent temperature changes are and for assessing the degree to which organisms are likely to be adversely affected by current or future warming. Climate histories are commonly reconstructed from a variety of sources, including ice cores, tree rings, and sediment. Tree-ring data, being the most abundant for recent centuries, tend to dominate reconstructions. There are reasons to believe that tree ring data may not properly capture long-term climate changes. In this study, eighteen 2000-year-long series were obtained that were not based on tree ring data. Data in each series were smoothed with a 30-year running mean. All data were then converted to anomalies by subtracting the mean of each series from that series. The overall mean series was then computed by simple averaging. The mean time series shows quite coherent structure. The mean series shows the Medieval Warm Period (MWP) and Little Ice Age (LIA) quite clearly, with the MWP being approximately 0.3°C warmer than 20th century values at these eighteen sites.
Temporal Variability in Local Air Temperature Series Shows Negative Feedback
Authors: Kärner Olavi
Published: November 2007

Long daily surface air temperature series from 24 European and Asian stations are analyzed, among them the Central England temperature dataset (1772 – 2005). The mean seasonal cycle in each series is removed and correlations between the consecutive increments of various increment intervals for the anomaly series are calculated. The sample correlations appear to behave similarly for all series. A positive coefficient between the short-term (daily etc) increments rapidly changes to the negative side while the increment interval increases. The value of the coefficient saturates at the level −0.5 and stays at that level for long range of intervals from 20 to 2000 days. The feature is a testimony to the regulating role of (cumulative) negative feedback in the climate system during the last two centuries.
The Fraud Allegation against Some Climatic Research of Wei-Chyung Wang
Authors: Keenan Douglas J.
Published: November 2007

Wei-Chyung Wang has been a respected researcher in global warming studies for decades. I have formally alleged that he committed fraud in some of his research, including research cited by the Fourth Assessment Report of the IPCC (2007) on “urban heat islands” (a critical issue). Herein, the allegation is reviewed, and some of its implications are explicated.
Chemical basis of glycine riboswitch cooperativity
Authors: Kwon Miyun , Strobel Scott A.
Published: November 2007

The glycine binding riboswitch forms a unique tandem aptamer structure that binds glycine cooperatively. We employed nucleotide analog interference mapping (NAIM) and mutagenesis to explore the chemical basis of glycine riboswitch cooperativity. Based on the interference pattern, at least two sites appear to facilitate cooperative tertiary interactions, namely, the minor groove of the P1 helix from aptamer 1 and the major groove of the P3a helix from both aptamers. Mutation of these residues altered both the cooperativity and binding affinity of the riboswitch. The data support a model in which the P1 helix of the first aptamer participates in a tertiary interaction important for cooperativity, while nucleotides in the P1 helix of the second aptamer interface with the expression platform. These data have direct analogy to well-characterized mutations in hemoglobin, which provides a framework for considering cooperativity in this RNA-based system.
Micrographics: A Quarter-Century Perspective
Authors: Ach William K.
Published: November 2007

Micrographics once served the world of banking, finance and government. Microfilm was the medium. Since then, the micropublishing world has turned its attention to higher education and has devised a variety of formats: microcards, microprint, 16 and 35 millimeter microfilm, microfiche and ultrafiche to capture that market during a quarter-century period. Micrographics has responded to the information explosion that triggered the technology revolution which drives much of the world's economy. Developments in electrical engineering and the electronics industry gave contemporary society the semiconductor which revolutionized the storage, retrieval and dissemination of information, an issue of vital importance to the library profession. Developments in communication technology brought about by fiber optics and speedier microprocessors followed.
Preservation Issues in Digital Imaging Technology
Authors: Lossau Norbert , Liebetruth Martin
Published: November 2007

“Conservation” and “Digitization” represent key terms from two different worlds. Conservation has overtones of longstanding tradition, carefully applied to holdings of honorable institutions like museums, libraries or galleries to ensure the longevity of their treasures. Digitization has the flavor of new technology, and although it is becoming a more widely accepted strategy for improving access to a lot of different resources, it still comes with imponderabilities in terms of digital asset lifespan, authenticity, etc.
From Source to Database
Authors: Townsend Sean , Chappell Cressida , Strujvé Oscar
Published: November 2007

It hardly needs saying that the act of creating a digital historical database involves the process of converting information from one format (paper) to another (digital). This conversion process is ultimately the essence of creating the resource, and those embarking on the endeavor need to think very hard about exactly what it is they are about to do. Talking to others who have gone through similar processes in related disciplines, reading appropriate literature, and evaluating and using a range of database technologies are possible initial starting points. The much-used maxim ‘Garbage In – Garbage Out’ is, unsurprisingly, appropriate here as the decisions taken and methodology employed in this critical stage of the resource's development, define the future value and usefulness of the resource. Bad judgements and fudged decisions at the design stage are almost always amplified in the final product which, at best, can make the database extremely problematic to use and, at worst, completely worthless.
Guides to Quality in Visual Resource Imaging
Authors: Rhodes Erin
Published: November 2007

Over the past several years, a number of publications listing best practices and guidelines for scanning have emerged from institutions engaged in digital imaging projects. Many of these guidelines are well written and have contributed significantly to understanding the imaging process; however, they are by nature institution-specific and often reflect local needs and decisions. Fortunately, we now have a series of guides that address issues of quality in a broad context. The
Handbook for Digital Projects: A Management Tool for Preservation and Access
Authors: Long Andrew Stawowczyk
Published: November 2007

The growing number of digital conversion professionals will be very pleased with the release of a new book:
E-books and the Challenge of Preservation
Authors: Romano Frank
Published: November 2007

The concept of electronic publishing was first articulated by Vannevar Bush of MIT in the seminal 1945 article ‘As We May Think.’ In 1991, Apple Computer introduced Jurassic Park as an electronic book for their Powerbook 100 laptop using the Adobe Acrobat portable document format (PDF). In 1998, the Rocket E-book was introduced, and in 1999, Simon & Schuster and Stephen King published an electronic novella that could be read on any Internet browser on virtually any computer, or downloaded to certain e-book devices. For the foreseeable future, most e-publishing will involve scientific, technical, professional and academic information as well as some original fiction work. Librarians and others involved in digital asset management will have to preserve at least some of this material for future reference, since it is expected that original works will be created and many of these may only exist in electronic form. E-books are not an historical artifact/anomaly, but a new form of content conveyance – important for certain constituencies and also important from the perspective of maintaining a record, especially since many works will be in e-book format only. Growth, while steady, may be slow due to competing technical standards, digital rights management, definitional issues and re-structuring within traditional publishing as creators, existing publishing houses and software companies position and re-position themselves in a changing market. A critical and perhaps underestimated set of issues concerns user acceptance.
Primary Source Publishers in a Googling World
Authors: van Dijk Arjan
Published: November 2007

In December 2004, Google Inc. announced its plans to digitize millions of books from prestigious libraries such as Harvard, Stanford, and the New York Public Library. Most of the books are in the public domain and will be available for free on the Internet. The Google initiative is one among many, including the American Memory Project of the Library of Congress, the San Francisco-based Internet Archive, and Gallica, the digital library of the Bibliothèque nationale de France. All of these programs offer free access to good-quality digital materials. Another common feature is that they are heavily funded.
Human Cortical Activity during Streaming without Spectral Cues Suggests a General Neural Substrate for Auditory Stream Segregation
Authors: Gutschalk Alexander , Oxenham Andrew J. , Micheyl Christophe , Wilson E. Courtenay , Melcher Jennifer R.
Published: November 2007

The brain continuously disentangles competing sounds, such as two people speaking, and assigns them to distinct streams. Neural mechanisms have been proposed for streaming based on gross spectral differences between sounds, but not for streaming based on other nonspectral features. Here, human listeners were presented with sequences of harmonic complex tones that had identical spectral envelopes, and unresolved spectral fine structure, but one of two fundamental frequencies (f0) and pitches. As thef0difference between tones increased, listeners perceived the tones as being segregated into two streams (one stream for eachf0) and cortical activity measured with functional magnetic resonance imaging and magnetoencephalography increased. This trend was seen in primary cortex of Heschl's gyrus and in surrounding nonprimary areas. The results strongly resemble those for pure tones. Both the present and pure tone results may reflect neuronal forward suppression that diminishes as one or more features of successive sounds become increasingly different. We hypothesize that feature-specific forward suppression subserves streaming based on diverse perceptual cues and results in explicit neural representations for auditory streams within auditory cortex.
Is the Prefrontal Cortex Necessary for Establishing Cognitive Sets?
Authors: Rowe James B. , Sakai Katsuyuki , Lund Torben E. , Ramsøy Thomas , Christensen Mark Schram , Baare William F. C. , Paulson Olaf B. , Passingham Richard E.
Published: November 2007

There is evidence from neuroimaging that the prefrontal cortex may be involved in establishing task set activity in advance of presentation of the task itself. To find out whether it plays an essential role, we examined patients with unilateral lesions of the rostral prefrontal cortex. They were first instructed as to whether to perform a spatial or a verbal working memory task and then given spatial and verbal items after a delay of 4–12 s. The patients showed an increase in switch costs, making more errors by repeating what they had done on the previous trial. They were able to establish regional task set activity during the instruction delay, as evidenced by sustained changes in the blood oxygenation level-dependent signal in caudal frontal regions. However, in contrast to healthy controls, they were less able to maintain functional connectivity among the surviving task-related brain regions, as evidenced by reduced correlations between them during instruction delays. The results suggest that the left rostral prefrontal cortex is indeed required for establishing a cognitive set but that the essential function is to support the functional connectivity among the task-related regions.