bluuebunny/crossref_metadata_2025 huggingface dataset:
Us and Them: The Portrayal of Malaysians and British in Malaysian History Textbooks
Authors: Rajandran Kumaran
Published: September 2012

This article conducts a linguistic analysis of the history textbook from Malaysia. It studies the way language portrays the Malaysians and British during colonization and independence. These periods are chosen because their economic and political changes resulted in social shifts which continue to influence modern Malaysia. The article analyzes the history textbook for secondary years two, three and five. Transitivity from Systemic Functional Linguistics is used as a method of analysis to explain the portrayal of the Malaysians and British during colonization and independence. The linguistic analysis of Participants (the nominal group) and Processes (the verbal group) discloses two major results. First, independence and the Malaysians are portrayed positively in the chapters about independence and identities of class and ethnicity are crucial to understand the Malaysians. Second, colonization and the British are portrayed negatively in the chapters about colonization. This posits a positive us and negative them distinction in the textbook. Hence the language of the history textbook can be interpreted as implying a nationalist version of history.
Rules of Engagement
Authors: McKillip Mary E. M. , Godfrey Kelly E. , Rawls Anita
Published: September 2012

Students who struggle in pursuit of postsecondary education tend to be Latino, Black, low-income, or first-generation college students. This article presents the case of a small public school serving students grades 6-12 from these traditionally underrepresented backgrounds in a large urban school district. Observations revealed that the school works to accomplish its primary mission of preparing students for college by merging academics with the socioemotional development of students. The relationships between and among students and staff in the school are the foundation upon which the school’s college-going culture is built. The study concludes with recommendations for ways to build a college-going culture in similar schools.
Effect of ionizing radiation on the properties of acrylonitrile butadiene rubber/clay nanocomposites
Authors: Youssef HA , Ali ZI , El-Nemr KF , Bekhit M
Published: September 2012

The effects of electron beam irradiation dose (50–150 kGy) and the concentration of montmorillonite (MMT) clay (3–10 parts per hundred part of rubber (phr)) on the properties of acrylonitrile butadiene rubber (NBR) have been investigated. The dispersion of the layered silicates was assessed by x-ray diffraction and transmission electron microscopy. The morphology of NBR nanocomposites showed exfoliated clay layers at low clay content and a combination of exfoliated and intercalated clay layers at high clay content. The mechanical properties of NBR composites such as tensile strength (TS) and tear strength were remarkably improved by the incorporation of organoclay and electron beam irradiation, while elongation at break ( Eb) was decreased. The increase in the TS of NBR nanocomposites increases with the increase in the clay content up to 10 phr, whereas the optimum gel content and TS of NBR composites were observed at 50 kGy irradiation dose. Thermogravimetric analysis studies showed that NBR/organo-MMT nanocomposites have higher decomposition temperatures in comparison with the NBR/Na+-MMT at 50 kGy irradiation dose.
Review, Revise, and Resubmit
Authors: Stellmack Mark A. , Keenan Nora K. , Sandidge Rita R. , Sippl Amy L. , Konheim-Kalkstein Yasmine L.
Published: September 2012

These experiments examined the common practice of allowing students to revise and resubmit papers after receiving feedback. Blind graders evaluated students’ first and second drafts of an introduction in American Psychological Association (APA) format. Across experiments, just over 50% of students’ scores improved across drafts when evaluated by blind graders compared to over 80% improvement for the scores assigned by the graduate student lab instructors. In examining the effects of the source of feedback on first drafts, no difference between self-critique, peer review, and feedback from the lab instructor was found in blind graders’ scores. The results suggest that high scores obtained through the review–revise–resubmit procedure do not reflect good writing in an objective sense, but rather an ability to satisfy a particular reviewer.
Divvying the Dollars
Authors: Reinagel Tyler P.
Published: September 2012

Local governments in Georgia are empowered to levy a 1 percent local option sales tax (LOST), approved by referendum at the county level and is distributed to the county and qualified municipal governments (The terms city and municipality are used interchangeably throughout this article, per OCGA 36.30.1.). Distribution shares are not based on a strict formula but rather are renegotiated at certain trigger points, including the decennial census. Using a multiple regression model, this research analyzes contextual and management factors, finding the strongest predictors of increased LOST revenue share by cities to be designation as county seat, fewer fellow municipalities, and higher reliance on LOST in the city’s total revenue stream.
Toward the Civil City Council
Authors: Vogelsang-Coombs Vera
Published: September 2012

This article examines the functions of city councils in governing the American municipality. It presents a notion of the “Civil City Council” that rests on five integrative leadership skills that incorporate particular public-regarding behaviors into municipal governance. The article argues that city councils should become the Civil City Council to govern effectively under modern conditions. To do this, the Civil City Council will empower citizens in broadly constituted interpretive communities in civil society. The article shows how the Civil City Council can sustain the political future of citizens and cities.
The Application of CT to Localize the Upper Airway Obstruction Plane in Patients with OSAHS
Authors: Tang Xu Lan , Yi Hong Liang , Luo Hui Ping , Xiong Yuan Ping , Meng Li Li , Guan Jian , Chen Bin , Yin Shan Kai
Published: September 2012

Objective

To identify a correlation in terms of airway obstruction between awake and sleep apnea using spiral computed tomography (CT).

Study Design

Case series with planned data collection.

Setting

College medical center.

Methods

Sixty‐one patients diagnosed with obstructive sleep apnea/hypopnea syndrome (OSAHS) underwent CT scans under 3 conditions: quiet breathing while awake, the end of deep inspiration during wakefulness, and apnea while asleep. The upper airway morphology under the 3 conditions was compared, and the accuracy of the obstructive planes as determined by CT scans under the 2 awake conditions was analyzed while considering the obstructive planes that occurred during apnea as a reference.

Results

The differences in the anteroposterior diameter, lateral dimension, and cross‐sectional area of the retropalatal and retroglossal regions among the 3 states were statistically significant. Obstruction of the retropalatal region occurred in 100%, whereas retroglossal obstruction occurred in 44.3% of the 61 cases during sleep apnea. The coincidence rate between the awake quiet breathing and the sleep apnea was 85.2% in the retropalatal obstruction and 52.5% in the retroglossal obstruction. The coincidence rate between the awake deep inspiration and the sleep apnea was 82.0% in the retropalatal obstruction and 54.1% in the retroglossal obstruction.

Conclusion

The main obstructive plane in patients with OSAHS was the retropalatal region. An awake upper airway CT scan can properly diagnose palatopharyngeal obstruction; however, it is not suitable for detecting retroglossal obstruction.
Prognostic Value of Olfactory Bulb Volume Measurement for Recovery in Postinfectious and Posttraumatic Olfactory Loss
Authors: Rombaux Philippe , Huart Caroline , Deggouj Naima , Duprez Thierry , Hummel Thomas
Published: September 2012

Objectives

Several prognostic factors influencing the recovery from olfactory dysfunction have been described. The aim of this study was to investigate whether olfactory bulb volume could be used as a new predictor of olfactory recovery in postinfectious and posttraumatic olfactory loss.

Study Design

Cohort study; Level of evidence, 4.

Setting

Tertiary university clinic, department of otolaryngology.

Subjects and Methods

A cohort of 60 patients with postinfectious (n = 28) and posttraumatic olfactory loss (n = 32) was investigated. Assessment of olfactory function was performed using orthonasal (Sniffin’ Sticks test) and retronasal psychophysical olfactory tests, at the time of the diagnosis (t1) and 15 months later (t2). All patients were examined on 3 tesla magnetic resonance imaging, and the olfactory bulbs volume was assessed using planimetric contouring at the time of the diagnosis (t1).

Results

Recovery rate was 25% in patients with posttraumatic olfactory loss and 36% in patients with postinfectious olfactory loss. There was a correlation between both orthonasal and retronasal olfactory testing and the initial measurement of the total olfactory bulb volume. In addition, we observed a significant correlation between changes in olfactory functions and initial measurement of the total olfactory bulb volume, with larger volumes relating to higher improvement of olfactory function. Finally, we found that none of the patients with a total olfactory bulb volume of 40 mm3 or less exhibited recovery of olfactory function.

Conclusion

Olfactory bulb volume seems to be a predictor of olfactory recovery in patients with postinfectious and posttraumatic olfactory loss.
Effect of therapist-based constraint-induced therapy at home on motor control, motor performance and daily function in children with cerebral palsy: a randomized controlled study
Authors: Chen Chia-ling , Kang Lin-ju , Hong Wei-Hsien , Chen Fei-Chuan , Chen Hsieh-Ching , Wu Ching-yi
Published: September 2012

Objective:

To determine the effect of therapist-based constraint-induced therapy at home on motor performance, daily function and reaching control for children with cerebral palsy.

Design:

A single-blinded, randomized controlled trial.

Subjects:

Forty-seven children (23 boys; 24 girls) with unilateral cerebral palsy, aged 6–12 years, were randomized to constraint-induced therapy ( n = 24) or traditional rehabilitation ( n = 23).

Interventions:

Constraint-induced therapy involved intensive functional training of the more affected arm while the less affected arm was restrained. Traditional rehabilitation involved functional unilateral and bilateral arm training. Both groups received individualized therapist-based interventions at home for 3.5–4 hours/day, two days a week for four weeks.

Main measures:

Motor performance and daily function were measured by the Peabody Developmental Motor Scale, Second Edition and the Pediatric Motor Activity Log. Reaching control was assessed by the kinematics of reaction time, movement time, movement unit and peak velocity.

Results:

There were larger effects in favour of constraint-induced therapy on motor performance, daily function, and some aspects of reaching control compared with traditional rehabilitation. Children receiving constraint-induced therapy demonstrated higher scores for Peabody Developmental Motor Scale, Second Edition – Grasping (pretest mean ± SD, 39.9 ± 3.1; posttest, 44.1 ± 2.8; P < 0.001), Pediatric Motor Activity Log (pretest, 1.8 ± 0.3; posttest, 2.5 ± 0.3; P < 0.001) and shorter reaction time, normalized movement time ( P < 0.001) and higher peak velocity ( P = 0.004) of reaching movement.

Conclusions:

Constraint-induced therapy induced better grasping performance, daily function, and temporal and spatiotemporal control of reaching in children with unilateral cerebral palsy than traditional rehabilitation.
Feasibility of assessing the needs of stroke patients after six months using the GM-SAT
Authors: Rothwell Katy , Boaden Ruth , Bamford David , Tyrrell Pippa J
Published: September 2012

Objective:

To investigate the feasibility of administering the Greater Manchester Stroke Assessment Tool (GM-SAT), a structured evidence-based needs assessment tool, in a community setting and its acceptability to stroke patients and their carers.

Setting:

Community stroke services.

Subjects:

One hundred and thirty-seven stroke patients at six months post hospital discharge with no communication or cognitive difficulties residing in their own homes.

Intervention:

Patients’ needs were assessed by information, advice and support (IAS) coordinators from the UK Stroke Association using the GM-SAT.

Main measures:

Number and nature of unmet needs identified and actions required to address these; patient/carer feedback; and IAS coordinator feedback.

Results:

The mean number of unmet needs identified was 3 (min 0, max 14; SD 2.5). The most frequently identified unmet needs related to fatigue (34.3%), memory, concentration and attention (25.5%), secondary prevention non-lifestyle (21.9%) and depression (19.0%). It was found that 50.4% of unmet needs could be addressed through the provision of information and advice. Patients/carers found the assessment process valuable and IAS coordinators found the GM-SAT easy to use.

Conclusions:

Results demonstrate that the GM-SAT is feasible to administer in the community using IAS coordinators and is acceptable to patients and their carers, as well as staff undertaking the assessments. Further research is needed to determine whether the application of the GM-SAT at six months improves outcomes for patients.
Racial-Ethnic Identity and Adjustment in Canadian Indigenous Adolescents
Authors: Gfellner Barbara M. , Armstrong Helen D.
Published: September 2012

This study supported associations between three theoretically driven conceptualizations of racial and ethnic identity (REI; Multigroup Ethnic Identity Measure; Multidimensional Racial Identity Measure; Bicultural Identity Measure) and with adaptive functioning among Canadian indigenous adolescents in middle school to high school. Age differences were found across the ethnic identity statuses but not for the continuous REI measures. Overall, adolescents placed predominantly at the traditional (identified with indigenous culture) and marginal (neither identified with indigenous nor mainstream culture) ethnic identity statuses with fewer marginal and more bicultural (identified with both indigenous and mainstream cultures) categorized adolescents across the age-range. Traditional students followed by those classified as bicultural evidenced greater REI and adaptive functioning in comparison with marginal and mainstream students. Predicted relationships between REI and adjustment among Canadian First Nation adolescents were supported; findings suggest potential benefits of First Nation communities for REI development.
Arnold Gehlen
Authors: Magerski Christine
Published: September 2012

Arnold Gehlen is one of the most controversial figures of German intellectual history. Gehlen’s commitment to National Socialism (a commitment he never disavowed) is mostly seen in close connection with his theoretical focus on institutions. According to Gehlen, what mankind requires above all is order and thus the protection of institutions. And yet, by reducing Gehlen’s sociology to the necessity of order one misses the analytical scope of his writings. As this article aims to show, the strength of Gehlen’s sociology lies less in its theory of institutionalization than in its attempt to comprehend change, i.e. the conceptual clarification of the interplay between radical innovation and institutionalization. In order to apprehend Gehlen’s understanding of change we have to look at his sociology of art as it is art which works as ‘a small symbol of society’. To approach Gehlen from this perspective is not to rehabilitate the controversial thinker. Instead, I am trying to show that Gehlen’s theoretical framework is as complex as modern culture itself and should therefore not prematurely be declared a reactionary testimony of the past.
Crisis and contingency
Authors: Makropoulos Michael
Published: September 2012

The text reconstructs central theoretical positions in the discourse of modernity in the Weimar Republic in the double semantic context of crisis and contingency. On the one hand, these categories ground the dialectic of destruction and construction, which provides hegemonial evidence for the political and aesthetic concepts of totality in classical modernity. On the other hand, these categories also ground the openness of a thinking in possibilities, which remained marginal in the Weimar Republic but has become dominant in the postmodern critique of modernity.
Value as a Self-Sustaining Mechanism
Authors: Knutsen Wenjue Lu
Published: September 2012

Empirical observations increasingly evidence that nonprofit organizations are becoming a less distinctive form of organization due to commercialization and the adoption of government practices. This fact challenges nonprofit theory development, which lags behind the development of practices in the field. This study examines one representative service nonprofit and asks how and why it is similar to and, simultaneously, different from private and public organizations. The purpose is to contribute to the debate on the assumption of nonprofit theory—should we study nonprofits as a distinct form of organization or perhaps as hybrids? The case study reveals that the case organization’s self-sustaining mechanism is based on value that generates many kinds of assistance at no cost. This mechanism, paired with a community base and a not-for-profit identity, formulates a distinct nonprofit model. However, due to the inadequacy of the value-based self-sustaining mechanism, the organization has to adopt business and government practices.
‘I do not need a flu shot because I lead a healthy lifestyle’: Compensatory health beliefs make vaccination less likely
Authors: Ernsting Anna , Schwarzer Ralf , Lippke Sonia , Schneider Michael
Published: September 2012

Compensatory health beliefs, a self-defence strategy, were examined in a theory-guided intervention promoting influenza vaccination at the workplace. In total, 851 employees were randomised to one group aimed at enhancing intention formation (standard group) or to another one assisting self-regulation (intervention group). Assessments took place after the intervention and 5 months later, investigating whether the intervention would interfere with compensatory health beliefs. The intervention generated an indirect effect via planning on vaccination. Compensatory health beliefs mediated between intention and behaviour. An interaction between intervention group and compensatory health beliefs on behaviour transpired. At low compensatory health belief levels, the intervention group resulted in more vaccinations than the standard group.
Effects of Transcranial Electrical Stimulation on Cognition
Authors: Kuo Min-Fang , Nitsche Michael A.
Published: September 2012

Alterations of cortical excitability, oscillatory as well as non-oscillatory, are physiological derivates of cognitive processes, such as perception, working memory, learning, and long-term memory formation. Since noninvasive electrical brain stimulation is capable of inducing alterations in the human brain, these stimulation approaches might be attractive tools to modulate cognition. Transcranial direct current stimulation (tDCS) alters spontaneous cortical activity, while transcranial alternating current stimulation (tACS) and transcranial random noise stimulation (tRNS) are presumed to induce or interfere with oscillations of cortical networks. Via these mechanisms, the respective stimulation techniques have indeed been shown to modulate cognitive processes in a multitude of studies conducted during the last years. In this review, we will gather knowledge about the potential of noninvasive electrical brain stimulation to study and modify cognitive processes in healthy humans and discuss directions of future research.
Functional Neuroimaging and Transcranial Electrical Stimulation
Authors: Turi Zsolt , Paulus Walter , Antal Andrea
Published: September 2012

Transcranial electrical stimulation (tES) is a noninvasive tool for inducing local and widespread neuroplastic changes in brain networks. The combination of tES with various neuroimaging techniques provides whole brain data on the working mechanisms of tES, in particular on the development of large-scale activation patterns of interconnected neuronal regions induced by tES. This review focuses on the combined usage of a noninvasive application of transcranial direct current stimulation and functional magnetic resonance imaging and on magnetic resonance spectroscopy.
Travel Medicine
Authors: Sleet David A. , Balaban Victor
Published: September 2012

Injuries to children while traveling is an important topic in travel medicine. Traffic injuries and drowning are the first and second leading causes of death in children who travel, and are a far greater risk than infectious and chronic diseases. Effective prevention strategies are available, particularly for travelers who find themselves in unfamiliar environments and who may be unaware of the potential risks to their family. Despite greater understanding and increased research efforts in this field, data on the magnitude and severity of injuries are still incomplete or unreliable in many countries, but some general advice to parents, children, and adolescents can help keep them safe while traveling.
Stromal SPARC contributes to the detrimental fibrotic changes associated with myeloproliferation whereas its deficiency favors myeloid cell expansion
Authors: Tripodo Claudio , Sangaletti Sabina , Guarnotta Carla , Piccaluga Pier P. , Cacciatore Matilde , Giuliano Michela , Franco Giovanni , Chiodoni Claudia , Sciandra Marika , Miotti Silvia , Calvaruso Giuseppe , Carè Alessandra , Florena Ada M. , Scotlandi Katia , Orazi Attilio , Pileri Stefano A. , Colombo Mario P.
Published: September 2012

In myeloid malignancies, the neoplastic clone outgrows normal hematopoietic cells toward BM failure. This event is also sustained by detrimental stromal changes, such as BM fibrosis and osteosclerosis, whose occurrence is harbinger of a dismal prognosis. We show that the matricellular protein SPARC contributes to the BM stromal response to myeloproliferation. The degree of SPARC expression in BM stromal elements, including CD146+ mesenchymal stromal cells, correlates with the degree of stromal changes, and the severity of BM failure characterizing the prototypical myeloproliferative neoplasm primary myelofibrosis. Using Sparc−/− mice and BM chimeras, we demonstrate that SPARC contributes to the development of significant stromal fibrosis in a model of thrombopoietin-induced myelofibrosis. We found that SPARC deficiency in the radioresistant BM stroma compartment impairs myelofibrosis but, at the same time, associates with an enhanced reactive myeloproliferative response to thrombopoietin. The link betwen SPARC stromal deficiency and enhanced myeloid cell expansion under a myeloproliferative spur is also supported by the myeloproliferative phenotype resulting from the transplantation of defective Apcmin mutant hematopoietic cells into Sparc−/− but not WT recipient BM stroma. Our results highlight a complex influence of SPARC over the stromal and hematopoietic BM response in myeloproliferative conditions.
The population genetics of cooperative gene regulation
Authors: Stewart Alexander J , Seymour Robert M , Pomiankowski Andrew , Plotkin Joshua B
Published: September 2012

Background

Changes in gene regulatory networks drive the evolution of phenotypic diversity both within and between species. Rewiring of transcriptional networks is achieved either by changes to transcription factor binding sites or by changes to the physical interactions among transcription factor proteins. It has been suggested that the evolution of cooperative binding among factors can facilitate the adaptive rewiring of a regulatory network.

Results

We use a population-genetic model to explore when cooperative binding of transcription factors is favored by evolution, and what effects cooperativity then has on the adaptive re-writing of regulatory networks. We consider a pair of transcription factors that regulate multiple targets and overlap in the sets of target genes they regulate. We show that, under stabilising selection, cooperative binding between the transcription factors is favoured provided the amount of overlap between their target genes exceeds a threshold. The value of this threshold depends on several population-genetic factors: strength of selection on binding sites, cost of pleiotropy associated with protein-protein interactions, rates of mutation and population size. Once it is established, we find that cooperative binding of transcription factors significantly accelerates the adaptive rewiring of transcriptional networks under positive selection. We compare our qualitative predictions to systematic data on Saccharomyces cerevisiae transcription factors, their binding sites, and their protein-protein interactions.

Conclusions

Our study reveals a rich set of evolutionary dynamics driven by a tradeoff between the beneficial effects of cooperative binding at targets shared by a pair of factors, and the detrimental effects of cooperative binding for non-shared targets. We find that cooperative regulation will evolve when transcription factors share a sufficient proportion of their target genes. These findings help to explain empirical pattens in datasets of transcription factors in Saccharomyces cerevisiae and, they suggest that changes to physical interactions between transcription factors can play a critical role in the evolution of gene regulatory networks.
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
Authors: Suzuki Hitoshi , MacDonald Jacqueline , Syed Khajamohiddin , Salamov Asaf , Hori Chiaki , Aerts Andrea , Henrissat Bernard , Wiebenga Ad , vanKuyk Patricia A , Barry Kerrie , Lindquist Erika , LaButti Kurt , Lapidus Alla , Lucas Susan , Coutinho Pedro , Gong Yunchen , Samejima Masahiro , Mahadevan Radhakrishnan , Abou-Zaid Mamdouh , de Vries Ronald P , Igarashi Kiyohiko , Yadav Jagjit S , Grigoriev Igor V , Master Emma R
Published: September 2012

Background

Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.

Results

P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.

Conclusions

The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.
Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains
Authors: Gazi Anastasia D , Sarris Panagiotis F , Fadouloglou Vasiliki E , Charova Spyridoula N , Mathioudakis Nikolaos , Panopoulos Nicholas J , Kokkinidis Michael
Published: September 2012

Background

The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. SomePseudomonas syringaestrains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterizedHrc1T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. The aim of this study is to perform anin silicoanalysis of T3SS-2, and to compare it with other known T3SSs.

Results

Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of theP. syringaepv. phaseolicola strain is grouped with a second T3SS found in the pNGR234b plasmid ofRhizobiumsp. These additional T3SS gene clusters define a subgroup within theRhizobiumT3SS family. Although, T3SS-2 is not distributed as widely as theHrc1T3SS inP. syringaestrains, it was found to be constitutively expressed inP. syringaepv phaseolicola through RT-PCR experiments.

Conclusions

The relatedness of theP. syringaeT3SS-2 to a second T3SS from the pNGR234b plasmid ofRhizobiumsp., member of subgroup II of the rhizobial T3SS family, indicates common ancestry and/or possible horizontal transfer events between these species. Functional analysis and genome sequencing of more rhizobia andP. syringaepathovars may shed light into why these bacteria maintain a second T3SS gene cluster in their genome.
Prevalence of Vitamin D insufficiency and low bone mineral density in elderly Thai nursing home residents
Authors: Kruavit Anuk , Chailurkit La-or , Thakkinstian Ammarin , Sriphrapradang Chutintorn , Rajatanavin Rajata
Published: September 2012

Background

Numerous emerging data from research on osteoporosis among Asians found differences from Caucasians. Therefore, the aim of this study was to determine the prevalence of vitamin D insufficiency and osteoporosis in elderly participants from two nursing homes in Thailand, a country located near the equator.

Methods

The subjects of this cross-sectional study comprised 93 elderly Thai women who were living in institutional long-term nursing homes for the aged. Demographic data, daily food and calcium intake, physical activity, and sunlight exposure were measured. Lumbar spine and femoral neck bone mineral density (BMD) and biochemical levels including serum 25 hydroxyvitamin D [25(OH)D] and bone turnover markers were assessed. Vitamin D insufficiency was defined as 25(OH)D level < 70 nmol/l.

Results

The mean age of subjects was 75.2 ± 6.0 (SD) years. Dietary calcium intake was low (322 ± 158 mg/day) The mean 25(OH)D level was 64.3 ± 14.9 nmol/L and the prevalence of vitamin D insufficiency was 38.7% (95% CI: 28.8%, 49.4%). There was no correlation between serum 25(OH)D concentrations and age (r = −.11, p = 0.3). The mean BMD of lumbar spine and femoral neck were 0.92 ± 0.19 and 0.65 ± 0.10 g/cm2, respectively. Nearly a half of the subjects had osteopenia (44.1%, 95% CI: 33.8%, 54.8%) and osteoporosis (47.3%, 95% CI: 36.9%, 57.9%). Circulating C-terminal telopeptide of type I collagen (CTx) level correlated significantly with both lumbar spine (r = −0.26, p = 0.01) and femoral neck BMD (r = −0.25, p = 0.02).

Conclusions

More than one-third of Thai elderly women residing in nursing homes had vitamin D insufficiency. Almost all nursing home residents had osteoporosis and/or osteopenia.
Appraising the performance of genotyping tools in the prediction of coreceptor tropism in HIV-1 subtype C viruses
Authors: Crous Saleema , Shrestha Ram Krishna , Travers Simon A
Published: September 2012

Background

In human immunodeficiency virus type 1 (HIV-1) infection, transmitted viruses generally use the CCR5 chemokine receptor as a coreceptor for host cell entry. In more than 50% of subtype B infections, a switch in coreceptor tropism from CCR5- to CXCR4-use occurs during disease progression. Phenotypic or genotypic approaches can be used to test for the presence of CXCR4-using viral variants in an individual’s viral population that would result in resistance to treatment with CCR5-antagonists. While genotyping approaches for coreceptor-tropism prediction in subtype B are well established and verified, they are less so for subtype C.

Methods

Here, using a dataset comprising V3 loop sequences from 349 CCR5-using and 56 CXCR4-using HIV-1 subtype C viruses we perform a comparative analysis of the predictive ability of 11 genotypic algorithms in their prediction of coreceptor tropism in subtype C. We calculate the sensitivity and specificity of each of the approaches as well as determining their overall accuracy. By separating the CXCR4-using viruses into CXCR4-exclusive (25 sequences) and dual-tropic (31 sequences) we evaluate the effect of the possible conflicting signal from dual-tropic viruses on the ability of a of the approaches to correctly predict coreceptor phenotype.

Results

We determined that geno2pheno with a false positive rate of 5% is the best approach for predicting CXCR4-usage in subtype C sequences with an accuracy of 94% (89% sensitivity and 99% specificity). Contrary to what has been reported for subtype B, the optimal approaches for prediction of CXCR4-usage in sequence from viruses that use CXCR4 exclusively, also perform best at predicting CXCR4-use in dual-tropic viral variants.

Conclusions

The accuracy of genotyping approaches at correctly predicting the coreceptor usage of V3 sequences from subtype C viruses is very high. We suggest that genotyping approaches can be used to test for coreceptor tropism in HIV-1 group M subtype C with a high degree of confidence that they will identify CXCR4-usage in both CXCR4-exclusive and dual tropic variants.
The injury mortality burden in Guinea
Authors: Mamady Keita , Yao Hongyan , Zhang Xujun , Xiang Huiyun , Tan Hongzhuan , Hu Guoqing
Published: September 2012

Background

The injury mortality burden of Guinea has been rarely addressed. The paper aimed to report patterns of injury mortality burden in Guinea.

Methods

We retrieved the mortality data from the Guinean Annual Health Statistics Report 2007. The information about underlying cause of deaths was collected based on Guinean hospital discharge data, Hospital Mortuary and City Council Mortuary data. The causes of death are coded in the 9th International Classification of Diseases (ICD-9). Multivariate Poisson regression was used to test the impacts of sex and age on mortality rates. The statistical analyses were performed using Statatm 10.0.

Results

In 2007, 7066 persons were reported dying of injuries in Guinea (mortality: 72.8 per 100,000 population). Transportation, fire/burn, falls, homicide and drowning were the five leading causes of fatal injuries for the whole population, accounting for 37%, 22%, 12%, 10% and 6% of total deaths, respectively. In general, age-specific injury causes displayed similar patterns of the whole population except that poisoning replaced falls as a leading cause among children under five years old. Males were at 30-50% more risk of dying from six commonest causes than females and old age groups had higher injury mortality rates than younger age groups.

Conclusion

Transportation, fire/burn, falls, homicide, and drowning accounted for the majority of total injury mortality burden in Guinea. Males and old adults were high-risk population of fatal injuries and should be targeted by injury prevention. Lots of work is needed to improve weak capacities for injury control in order to reduce the injury mortality burden.
Vectorial secretion of CTGF as a cell-type specific response to LPA and TGF-β in human tubular epithelial cells
Authors: Zuehlke Jonathan , Ebenau Astrid , Krueger Bettina , Goppelt-Struebe Margarete
Published: September 2012

Background

Increased expression of the pro-fibrotic protein connective tissue growth factor (CTGF) has been detected in injured kidneys and elevated urinary levels of CTGF are discussed as prognostic marker of chronic kidney disease. There is evidence that epithelial cells lining the renal tubular system contribute to uptake and secretion of CTGF. However, the role of different types of tubular epithelial cells in these processes so far has not been addressed in primary cultures of human cells.

Results

Tubular epithelial cells of proximal and distal origin were isolated from human kidneys and cultured as polarized cells in insert wells. The pro-fibrotic stimuli lysophosphatidic acid (LPA) and transforming growth factor β (TGF-β) were used to induce CTGF secretion.

LPA activated CTGF secretion in proximal tubular cells when applied from either the apical or the basolateral side as shown by immunocytochemistry. CTGF was secreted exclusively to the apical side. Signaling pathways activated by LPA included MAP kinase and Rho kinase signaling. TGF-β applied from either side also stimulated CTGF secretion primarily to the apical side with little basolateral release.

Interestingly, TGF-β activation induced different signaling pathways depending on the side of TGF-β application. Smad signaling was almost exclusively activated from the basolateral side most prominently in cells of distal origin. Only part of these cells also synthesized CTGF indicating that Smad activation alone was not sufficient for CTGF induction. MAP kinases were involved in apical TGF-β-mediated activation of CTGF synthesis in proximal cells and a subset of epithelial cells of distal origin. This subpopulation of distal tubular cells was also able to internalize recombinant apical CTGF, in addition to proximal cells which were the main cells to take up exogenous CTGF.

Conclusions

Analysis of polarized human primary renal epithelial cells in a transwell system shows that vectorial secretion of the pro-fibrotic protein CTGF depends on the cell type, the stimulus and the signaling pathway activated. In all conditions, CTGF was secreted mainly to the apical side upon TGF-β and LPA treatment and therefore, likely contributes to increased urinary CTGF levels in vivo. Moreover, CTGF secreted basolaterally may be active as paracrine pro-fibrotic mediator.
Characterization of hybrid cobalt-porous silicon systems: protective effect of the Matrix in the metal oxidation
Authors: Muñoz-Noval Álvaro , Gallach Darío , García Miguel Ángel , Ferro-Llanos Vicente , Herrero Pilar , Fukami Kazuhiro , Ogata Yukio H , Torres-Costa Vicente , Martín-Palma Raúl J , Ciment-Font Aurelio , Manso-Silván Miguel
Published: September 2012

In the present work, the characterization of cobalt-porous silicon (Co-PSi) hybrid systems is performed by a combination of magnetic, spectroscopic, and structural techniques. The Co-PSi structures are composed by a columnar matrix of PSi with Co nanoparticles embedded inside, as determined by Transmission Electron Microscopy (TEM). The oxidation state, crystalline structure, and magnetic behavior are determined by X-Ray Absorption Spectroscopy (XAS) and Alternating Gradient Field Magnetometry (AGFM). Additionally, the Co concentration profile inside the matrix has been studied by Rutherford Backscattering Spectroscopy (RBS). It is concluded that the PSi matrix can be tailored to provide the Co nanoparticles with extra protection against oxidation.
Structural variations of Si1−xC
x
and their light absorption controllability
Authors: Moon Jihyun , Baik Seung Jae , O Byungsung , Lee Jeong Chul
Published: September 2012

The emergence of third-generation photovoltaics based on Si relies on tunable bandgap materials with embedded nanocrystalline Si. One of the most promising approaches is based on the mixed-phase Si1 − x
C
x
. We have investigated the light absorption controllability of nanocrystalline Si-embedded Si1 − x
C
x
produced by thermal annealing of the Si-rich Si1 − x
C
x
and composition-modulated superlattice structure. In addition, stoichiometric SiC was also investigated to comparatively analyze the characteristic differences. As a result, it was found that stoichiometric changes of the matrix material and incorporation of oxygen play key roles in light absorption controllability. Based on the results of this work and literature, a design strategy of nanocrystalline Si-embedded absorber materials for third-generation photovoltaics is discussed.
Development and validation of a method for purification of mallein for the diagnosis of glanders in equines
Authors: de Carvalho Filho Maurício Baltazar , Ramos Rodrigo Mauro , Fonseca Antônio Augusto , de Lima Orzil Lívia , Sales Mariana Lázaro , de Assis Santana Vania Lucia , de Souza Marcilia Maria Alves , dos Reis Machado Evandro , Filho Paulo Rodrigues Lopes , Leite Rômulo Cerqueira , dos Reis Jenner Karlisson Pimenta
Published: September 2012

Background

The allergic test of mallein is one of the most frequently used tests, together with the Complement Fixation Test (CFT), for the diagnosis of glanders in endemic areas. Mallein, a purified protein derivative (PPD), is produced similarly to PPD tuberculin and the end product is a primarily proteic antigen, which is only poorly purified. The immuno-allergic activity of mallein is believed to be due to a high molecular weight group of proteins present in the antigen. To improve the quality of the antigen, in terms of sensitivity and specificity, a new method of mallein production was developed, in which purification was accomplished by ultrafiltration in a Tangential Flow Filtration system (TFF).

Results

The TFF methodology efficiently separated the high and low molecular weight protein groups of mallein. The five TFF-purified malleins, produced from Burkholderia mallei strains isolated from clinical cases of glanders in Brazil, proved to be more potent than standard mallein in the induction of an allergic reaction in sensitized animals. Regarding specificity, two of the purified malleins were equivalent to the standard and three were less specific.

Conclusion

Some of the TFF-purified malleins showed considerable potential to be used as an auxiliary test in the diagnosis of glanders.
Targeted next-generation sequencing identifies a homozygous nonsense mutation in ABHD12, the gene underlying PHARC, in a family clinically diagnosed with Usher syndrome type 3
Authors: Eisenberger Tobias , Slim Rima , Mansour Ahmad , Nauck Markus , Nürnberg Gudrun , Nürnberg Peter , Decker Christian , Dafinger Claudia , Ebermann Inga , Bergmann Carsten , Bolz Hanno Jörn
Published: September 2012

Background

Usher syndrome (USH) is an autosomal recessive genetically heterogeneous disorder with congenital sensorineural hearing impairment and retinitis pigmentosa (RP). We have identified a consanguineous Lebanese family with two affected members displaying progressive hearing loss, RP and cataracts, therefore clinically diagnosed as USH type 3 (USH3). Our study was aimed at the identification of the causative mutation in this USH3-like family.

Methods

Candidate loci were identified using genomewide SNP-array-based homozygosity mapping followed by targeted enrichment and next-generation sequencing.

Results

Using a capture array targeting the three identified homozygosity-by-descent regions on chromosomes 1q43-q44, 20p13-p12.2 and 20p11.23-q12, we identified a homozygous nonsense mutation, p.Arg65X, in ABHD12 segregating with the phenotype.

Conclusion

Mutations of ABHD12, an enzyme hydrolyzing an endocannabinoid lipid transmitter, cause PHARC (p olyneuropathy, h earing loss, a taxia, r etinitis pigmentosa, and early-onset c ataract). After the identification of the ABHD12 mutation in this family, one patient underwent neurological examination which revealed ataxia, but no polyneuropathy. ABHD12 is not known to be related to the USH protein interactome. The phenotype of our patient represents a variant of PHARC, an entity that should be taken into account as differential diagnosis for USH3. Our study demonstrates the potential of comprehensive genetic analysis for improving the clinical diagnosis.
An integer optimization algorithm for robust identification of non-linear gene regulatory networks
Authors: Chemmangattuvalappil Nishanth , Task Keith , Banerjee Ipsita
Published: September 2012

Background

Reverse engineering gene networks and identifying regulatory interactions are integral to understanding cellular decision making processes. Advancement in high throughput experimental techniques has initiated innovative data driven analysis of gene regulatory networks. However, inherent noise associated with biological systems requires numerous experimental replicates for reliable conclusions. Furthermore, evidence of robust algorithms directly exploiting basic biological traits are few. Such algorithms are expected to be efficient in their performance and robust in their prediction.

Results

We have developed a network identification algorithm to accurately infer both the topology and strength of regulatory interactions from time series gene expression data in the presence of significant experimental noise and non-linear behavior. In this novel formulism, we have addressed data variability in biological systems by integrating network identification with the bootstrap resampling technique, hence predicting robust interactions from limited experimental replicates subjected to noise. Furthermore, we have incorporated non-linearity in gene dynamics using the S-system formulation. The basic network identification formulation exploits the trait of sparsity of biological interactions. Towards that, the identification algorithm is formulated as an integer-programming problem by introducing binary variables for each network component. The objective function is targeted to minimize the network connections subjected to the constraint of maximal agreement between the experimental and predicted gene dynamics. The developed algorithm is validated using both in silico and experimental data-sets. These studies show that the algorithm can accurately predict the topology and connection strength of the in silico networks, as quantified by high precision and recall, and small discrepancy between the actual and predicted kinetic parameters. Furthermore, in both the in silico and experimental case studies, the predicted gene expression profiles are in very close agreement with the dynamics of the input data.

Conclusions

Our integer programming algorithm effectively utilizes bootstrapping to identify robust gene regulatory networks from noisy, non-linear time-series gene expression data. With significant noise and non-linearities being inherent to biological systems, the present formulism, with the incorporation of network sparsity, is extremely relevant to gene regulatory networks, and while the formulation has been validated against in silico and E. Coli data, it can be applied to any biological system.