bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational inference of grammars for larger-than-gene structures from annotated gene sequences
Authors: Tsafnat Guy , Schaeffer Jaron , Clayphan Andrew , Iredell Jon R. , Partridge Sally R. , Coiera Enrico
Published: January 2011

Motivation: Larger than gene structures (LGS) are DNA segments that include at least one gene and often other segments such as inverted repeats and gene promoters. Mobile genetic elements (MGE) such as integrons are LGS that play an important role in horizontal gene transfer, primarily in Gram-negative organisms. Known LGS have a profound effect on organism virulence, antibiotic resistance and other properties of the organism due to the number of genes involved. Expert-compiled grammars have been shown to be an effective computational representation of LGS, well suited to automating annotation, and supporting de novo gene discovery. However, development of LGS grammars by experts is labour intensive and restricted to known LGS.

Objectives: This study uses computational grammar inference methods to automate LGS discovery. We compare the ability of six algorithms to infer LGS grammars from DNA sequences annotated with genes and other short sequences. We compared the predictive power of learned grammars against an expert-developed grammar for gene cassette arrays found in Class 1, 2 and 3 integrons, which are modular LGS containing up to 9 of about 240 cassette types.

Results: Using a Bayesian generalization algorithm our inferred grammar was able to predict > 95% of MGE structures in a corpus of 1760 sequences obtained from Genbank (F-score 75%). Even with 100% noise added to the training and test sets, we obtained an F-score of 68%, indicating that the method is robust and has the potential to predict de novo LGS structures when the underlying gene features are known.

Availability:  http://www2.chi.unsw.edu.au/attacca.

Contact:  guyt@unsw.edu.au
Multiple effects of benzamide antibiotics on FtsZ function
Authors: Adams David W. , Wu Ling Juan , Czaplewski Lloyd G. , Errington Jeff
Published: January 2011

Cell division in almost all bacteria is orchestrated by the essential tubulin homologue FtsZ, which assembles into a ring‐like structure and acts as a scaffold for the division machinery. Division was recently validated as an important target for antibiotics by the demonstration that low‐molecular‐weight inhibitors of FtsZ, called benzamides, can cure mice infected with Staphylococcus aureus. In treated cells of Bacillus subtilis we show that FtsZ assembles into foci throughout the cell, including abnormal locations at the cell poles and over the nucleoid. These foci are not inactive aggregates because they remain dynamic, turning over almost as rapidly as untreated polymers. Remarkably, although division is completely blocked, the foci efficiently recruit division proteins that normally co‐assemble with FtsZ. However, they show no affinity for components of the Min or Nucleoid occlusion systems. In vitro, the benzamides strongly promote the polymerization of FtsZ, into hyperstable polymers, which are highly curved. Importantly, even at low concentrations, benzamides transform the structure of the Z ring, resulting in abnormal helical cell division events. We propose that benzamides act principally by promoting an FtsZ protomer conformation that is incompatible with a higher‐order level of assembly needed to make a division ring.
Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll Olea europaea L.
Authors: GRANADO‐YELA C. , GARCÍA‐VERDUGO C. , CARRILLO K. , RUBIO DE CASAS R. , KLECZKOWSKI L. A. , BALAGUER L.
Published: January 2011

Trees are modular organisms that adjust their within‐crown morphology and physiology in response to within‐crown light gradients. However, whether within‐plant variation represents a strategy for optimizing light absorption has not been formally tested. We investigated the arrangement of the photosynthetic surface throughout one day and its effects on the photosynthetic process, at the most exposed and most sheltered crown layers of a wild olive tree (Olea europaea L.). Similar measurements were made for cuttings taken from this individual and grown in a greenhouse at contrasted irradiance‐levels (100 and 20% full sunlight). Diurnal variations in light interception, carbon fixation and carbohydrate accumulation in sun leaves were negatively correlated with those in shade leaves under field conditions when light intensity was not limiting. Despite genetic identity, these complementary patterns were not found in plants grown in the greenhouse. The temporal disparity among crown positions derived from specialization of the photosynthetic behaviour at different functional and spatial scales: architectural structure (crown level) and carbon budget (leaf level). Our results suggest that the profitability of producing a new module may not only respond to construction costs or light availability, but also rely on its spatio‐temporal integration within the productive processes at the whole‐crown level.
Majocchi's granuloma in solid organ transplant recipients
Authors: Romero F.A. , Deziel P.J. , Razonable R.R.
Published: January 2011

F.A. Romero, P.J. Deziel, R.R. Razonable. Majocchi's granuloma in solid organ transplant recipients. Transpl Infect Dis 2011: 13: 424–432. All rights reserved

Abstract: Superficial fungal infections are fairly prevalent in transplant recipients and the incidence increases with more intense graft‐conserving immunosuppressive therapy. Majocchi's granuloma is a deep folliculitis caused by dermatophytes that involves deeper layers of the dermis. Only a few case reports of the condition have been documented in transplant recipients. After an extensive review of the medical literature, 21 cases were retrieved and are summarized here, together with a new case that occurred in a recent heart transplant recipient from our institution. This report aims to provide a comprehensive analysis of Majocchi's granuloma in solid organ transplant (SOT) recipients, with special focus on potential risk factors, offending pathogens, clinical presentation, therapeutic approaches, and outcome. General observations are presented emphasizing the relevance of close clinical and dermatologic follow‐up in high‐risk SOT patients with specific comments regarding treatment regimens and outcomes.
Redox changes during cold acclimation affect freezing tolerance but not the vegetative/reproductive transition of the shoot apex in wheat
Authors: Soltész A. , Tímár I. , Vashegyi I. , Tóth B. , Kellős T. , Szalai G. , Vágújfalvi A. , Kocsy G. , Galiba G.
Published: January 2011

Cold acclimation is necessary for winter wheat (Triticum aestivum L.) to achieve its genetically determined maximum freezing tolerance, and cold also fulfils the vernalisation requirement. Chromosome 5A is a major regulator of these traits. The aim of the present study was to discover whether changes in the half‐cell redox potential of the glutathione/glutathione disulphide (GSH/GSSG) and ascorbate/dehydroascorbate (AA/DHA) couples induced by cold acclimation are related to freezing tolerance and vernalisation requirement in a specific genetic system including chromosome 5A substitution lines. The amounts of H2O2 and AA, and the AA/DHA ratio showed a rapid and transient increase in the crown of all genotypes during the first week of acclimation, followed by a gradual increase during the subsequent 2 weeks. The amount of GSH and its ratio compared to GSSG quickly decreased during the first day, while later these parameters showed a continuous slow increase. The H2O2, AA and GSH concentrations, AA/DHA and GSH/GSSG ratios and the half‐cell reduction potential of the GSH/GSSG couple were correlated with the level of freezing tolerance after 22 days at 2 °C; hence these parameters may have an important role in the acclimation process. In contrast to H2O2 and the non‐enzymatic antioxidants, the lipid peroxide concentration and activity of the four antioxidant enzymes exhibited a transient increase during the first week, with no significant difference between genotypes. None of the parameters studied showed any relationship with the vegetative/generative transition state monitored as apex morphology and vernalisation gene expression.
Zoobenthos as an environmental quality element: the ecological significance of sampling design and functional traits
Authors: Aarnio Katri , Mattila Johanna , Törnroos Anna , Bonsdorff Erik
Published: January 2011

The EC Water Frame Directive (WFD) states that all coastal water bodies must achieve ‘good ecological status’ by the year 2015. A range of different classification methods have been developed and used to define ecological status to support the WFD. The aim of this study was to compare the effects of using two different mesh sizes of sieve (1.0 and 0.5 mm) on zoobenthic assemblages and on the ecological status of benthic macrofauna (using the Brackish water benthic index, BBI) in three ecologically distinct archipelago areas (Inner, Middle and Outer) in the Åland Islands, Northern Baltic Sea. We performed a biological trait analysis (BTA) to evaluate differences in the functional (trait) diversity of macrofauna collected using different mesh sizes and estimate the ecological relevance of mesh size. The results showed that sieve mesh size had significant effects on the recorded number of species, abundance, and total biomass of the zoobenthos. Small‐bodied species and juveniles (e.g. Macoma balthica) were not observed when using a 1.0‐mm mesh. The ecological status (sensu WFD) was only slightly affected by the mesh size, and all areas had good or high ecological status. BTA showed a difference in trait composition when using 0.5‐ or 1.0‐mm mesh, particularly in the Outer area, where the proportion of small‐sized species was high. Our results highlight how biological traits, in addition to species number and biomass, can play a key role when analyzing ecosystem structure for assessment and classification of coastal ecosystems. We show that combining traditional monitoring for the EU WFD with a functional analysis strengthens our ability to interpret environmental quality, and thus increases the precision of our advice for management purposes.
Hydrurus foetidus (Chromista, Chrysophyceae): A large freshwater chromophyte alga in laboratory culture
Authors: Klaveness Dag , Lindstrøm Eli‐Anne
Published: January 2011

The psychrophilic freshwater alga Hydrurus foetidus (Villars) Trevisan has previously resisted laboratory culturing in liquid media. We investigated the use of microbiological techniques adapted to specific requirement for low temperature and high turbulence of the alga. We found that successful culturing required cleaning steps, where pieces of the alga were dissected out and plated on agar under cold conditions. From here, unialgal colonies could be isolated and inoculated into liquid media under appropriate conditions. Turbulence, created by a laboratory shaker, is critical. Sufficient light (30–100 µmol m–2 s–1) and low temperature (here 2–3°C) are necessary. This rather common but highly under‐investigated freshwater alga has potential for basic and applied research when available as laboratory cultures.
Effects of three types of alpha‐1 adrenoceptor blocker on lower urinary tract symptoms and sexual function in males with benign prostatic hyperplasia
Authors: Yokoyama Teruhiko , Hara Ryoei , Fukumoto Kazuhiko , Fujii Tomohiro , Jo Yoshimasa , Miyaji Yoshiyuki , Nagai Atsushi , Sone Atsushi
Published: January 2011

Objectives:  The aim of the present study was to explore the effects of three different types of alpha‐1 adrenoceptor blockers (α1‐blocker) on lower urinary tract symptoms (LUTS), erectile dysfunction (ED) and ejaculatory dysfunction (EjD) in patients with benign prostatic hyperplasia.

Methods:  A total of 136 male LUTS patients aged 50–80 years with International Prostate Symptom Score (IPSS) ≥8 were enrolled. They were divided into three groups. Group S received silodosin at 4 mg twice a day; group T received tamsulosin at 0.2 mg once a day; and group N received naftopidil at 50 mg once a day. Assessment included IPSS, quality of life indexes (QOL), International Index of Erectile Function (IIEF‐5), an ejaculation questionnaire, Qmax and post‐void residual urine volume (PVR). These parameters were recorded at baseline, and at 1 and 3 months after treatment had ended.

Results:  Mean IPSS and Qmax significantly improved after treatment in all groups without any significant difference among them. As for the IIEF‐5 score, only group N significantly improved at 1 and 3 months. After treatment, 2.6 and 2.4% of patients complained of a de novo reduced volume of ejaculation in both groups T and N, respectively. Ten out of 41 patients (24.4%) complained of a total absence of antegrade ejaculation in group S after treatment.

Conclusions:  All three types of α1‐blockers provided an objective and subjective improvement of LUTS in the present study population. However, erectile function only improved in patients treated with naftopidil and a higher rate of EjD was observed in those receiving silodosin. Because of their variable effects, we should consider the sexual dimension when prescribing α1‐blockers for LUTS.
Incidence of osteoradionecrosis of the temporal bone
Authors: Morrissey David , Grigg Roger
Published: January 2011

Background: Osteoradionecrosis of the temporal bone is a serious, late complication of radiotherapy to the temporal bone region. The aim of this study was to determine the incidence, risk and protective factors relating to the development of osteoradionecrosis of the temporal bone.

Methods: This is a retrospective review of prospectively collected data. A single surgeon collated a database over a 10‐year period regarding patients undergoing surgery and subsequent radiotherapy for head and neck malignancies. This was reviewed, and information pertaining to demographics, nature of disease, radiation treatment regime and complications including osteoradionecrosis was extracted. Statistical analysis was then completed independently.

Results: A total of seven patients from the cohort of 82 developed osteoradionecrosis of the temporal bone within the period of the data collection. This represents an incidence of 8.5% (95% confidence interval = 3.6–13.4%). All who developed osteoradionecrosis had a metastatic parotid squamous cell carcinoma treated operatively with subsequent radiotherapy. There were no statistically significant risks or prognostic factors identified. Mean duration of follow‐up was 32 months.

Conclusion: The incidence of osteoradionecrosis of the temporal bone was 8.5% (95% confidence interval = 3.6–13.4%). Osteoradionecrosis of the temporal bone can present in excess of 10 years after treatment completion. This result may actually under ‐represent the true incidence of the complication. It has significant morbidity associated with its development and, occasionally, mortality. Those people undergoing radiotherapy to the parotid region may be at higher risk of osteoradionecrosis. A new classification system for osteoradionecrosis of the temporal bone has been proposed.
Solitary metastasis of a clear cell ovarian adenocarcinoma to the small bowel mucosa
Authors: Nakamura Miwa , Mitsuhashi Akira , Tanaka Naotake , Nagai Yuichiro , Shozu Makio
Published: January 2011

Metastasis of ovarian carcinoma to the small bowel parenchyma without peritoneal dissemination is uncommon. A 63‐year‐old woman underwent surgery for a clear cell adenocarcinoma of the ovary and received adjuvant chemotherapy. Eighteen months after the operation, she presented with recurrent occult bowel hemorrhage without evidence of an abdominal mass. Nine months later, a rapidly growing abdominal mass was detected. Laparoscopy revealed a solitary tumor of the ileum covered with an intact serosal layer. Partial ileectomy was performed for tumor resection. Histological examination revealed cells resembling the primary ovarian tumor in the mucosal surface of the small bowel along with an intact serosa. The tumor cells were positive for cytokeratin 7 and negative for cytokeratin 20, suggesting an ovarian origin. This is the first report of solitary metastasis of an ovarian carcinoma to the small bowel parenchyma without peritoneal dissemination. Metastasis to the small bowel should be considered in ovarian carcinoma patients with occult gastrointestinal hemorrhage.
Factors affecting surgical margins in nonpalpable breast tumors excised with the radioguided occult lesion localization approach
Authors: del Mar Vernet‐Tomas María , Ortega Marisa , Vidal Sergi , Corominas José M. , Carreras Ramon
Published: January 2011

Aim:  Most breast surgeons generally assume that obtaining negative margins in nonpalpable tumors is a matter of concern. The aim of this study was to examine whether it is easier to obtain negative margins in palpable tumors than in nonpalpable tumors excised with the radioguided occult lesion localization (ROLL) technique.

Methods:  A retrospective review was made of nonpalpable breast cancers excised with the ROLL technique (ROLL group, n = 83) and palpable breast cancers in which breast conservative therapy was performed (Palpable group, n = 77). The margin status and the size of the minimum margin obtained when it was negative were reviewed.

Results:  The percentage of resections with negative margins was similar in both groups: 51.9% in the Palpable group and 61.4% in the ROLL group. There was no difference between the two groups in the minimum margin obtained: mean ± SD, 5.53 ± 3.146 mm in the Palpable group and 5.96 ± 3.039 mm in the ROLL group. Risk factors for failing to obtain negative margins were analyzed in both groups and were similar. These risk factors included histological grade, extensive intraductal carcinoma and c‐erbB2 status.

Conclusion:  It is concluded that excision of nonpalpable breast tumors with the ROLL approach obtains similar results for margins as conservative surgery performed for palpable tumors.
Assisted reproductive technologies in Thailand: 2001–2007 results generated from the ART Registry, Royal Thai College of Obstetricians and Gynaecologists
Authors: Vutyavanich Teraporn , Piromlertamorn Waraporn , Ellis Jason ,   On Behalf of the Reproductive Medicine Subcommittee, The Royal Thai College of Obstetricians and Gynaecologists
Published: January 2011

Aim:  To present the results of assisted reproductive technology (ART) performed in Thailand during 2001–2007.

Methods:  All licensed ART centers are obliged to submit annual reports on the number of patients, cycles, ART techniques and treatment outcomes to the Reproductive Medicine Subcommittee of the Royal Thai College of Obstetricians and Gynaecologists. Data from all centers were aggregated and analyzed retrospectively.

Results:  Cycles were categorized into fresh and frozen/thawed embryo transfer (FET) cycles. Initiated cycles in the first category for 2001 to 2007 were 2183, 2112, 2780, 2717, 3458, 3579 and 4288, respectively. FET cycles during the same period were 467, 558, 733, 768, 1136, 1210 and 1473, respectively. The average pregnancy rate for in vitro fertilization (IVF) was 28.9% per retrieval (range, 26–32.3%) or 33.8% per transfer (range, 30.7–38.6%). Multiple pregnancies (of which 89.3% were twins) from all treatment procedures during this period were 11.4% (range, 9.2–14.5%). A congenital abnormality was reported in 0.56% of live births. The number of embryos per transfer in IVF decreased from 4.1 to 2.9, with no drop in pregnancy rates. Oocyte insemination by intracytoplasmic sperm injection (ICSI) was utilized more often than standard IVF, while gamete intrafallopian transfer and zygote intrafallopian transfer were almost completely replaced by IVF/ICSI. There was a significant difference in pregnancy rates (P < 0.01) when clinics were classified by cycle volumes (<100, 100–400 and >400 cycles/year).

Conclusions:  Despite many limitations, the data provided in this report will help patients, clinicians and policy makers understand the current situation of ART practice in Thailand.
Arranged Marriages as Support for Intra‐ethnic Matchmaking? A Case Study on Muslim Migrants in Germany
Authors: Hense Andrea , Schorch Marén
Published: January 2011

This article discusses the behavioural and institutional mechanisms that guide the matchmaking process of arranged marriages1 amongst Muslim migrants in Germany and clarifies how this practice may influence ethnic homogamy. The focus is on general characteristics of arranged marriages rather than differences between diverse ethnic groups. The methodology is qualitative due to the sensitive and complex topic and the current state of research. Typically, the whole family is deeply involved in the process of arrangement, which consists of three stages (pre‐engagement, engagement, marriage). Thereby, the extension of parental scope of action by means of institutionalized admission procedures turns out to be vitally important. In consideration of the fact that mate selection takes place at the pre‐engagement stage, it is the most crucial. Furthermore, differences to other partner‐choosing processes are at their most distinct at this point, being responsible for the identification and labelling of this model as an arranged marriage. Selection criteria are mainly determined by the reputation of the marriage candidate and her/his family along with cultural features (such as belonging to a particular religious group, ethnicity or nationality). In our study, preferences for a cultural homogenous match were the most dominant ones. This inclination may cause the tendency towards transnational marriages when there are no suitable marriage candidates to be found in Germany.
Financial Frictions, Bank Efficiency and Risk: Evidence from the Eurozone
Authors: Chortareas Georgios E. , Girardone Claudia , Ventouri Alexia
Published: January 2011

Abstract:  This paper employs a simultaneous equations approach to investigate the dynamics between financial frictions, efficiency and risk for eurozone's commercial banks. We consider two related channels through which financial frictions may arise: informational and market structure imperfections, and allow for a possible reverse causation from efficiency to banks’ asset quality. The findings validate the presence of both channels of financial frictions and are consistent with the efficiency‐lending quality hypothesis that low efficiency signals poor asset quality loans. Finally, our findings suggest that policies aimed at constraining banks’ degree of openness may ultimately direct management choices towards riskier investments.
Mate guarding and parental influence on mate choice
Authors: BUUNK ABRAHAM P. , SOLANO ALEJANDRO CASTRO
Published: January 2011

The hypothesis that the degree to which parents control the mate choice of their children may explain differences in mate guarding across and within cultures was tested. Study 1, in a sample of 80 students from 30 different countries studying in The Netherlands, showed that the perceived level of parental influence on mate choice in a culture was associated with more mate guarding reported by individuals from that culture. Study 2, in a sample of 242 Argentinean individuals, showed that individuals who were more in favor of parental influence on mate choice did report more mate guarding. The effects remained intact when controlling for potentially confounding variables.
Ectopic Cilia in a 14‐Year‐Old Boy
Authors: BAGHESTANI SHAHRAM , BANIHASHEMI SEYYED ALI
Published: January 2011

Abstract:  Ectopic cilia is a very rare condition in human beings, usually presented as a tuft of densely grouped hair on the lateral quadrant of the upper eyelid or conjunctival surface of the eyelid. The embryologic origin of this anomaly is unknown, and few cases have been recorded in literature. In most cases, it causes no apparent medical morbidity but is treated by surgical excision because of its cosmetic aspect. We report a 14‐year‐old boy with ectopic cilia with approximately 20 hairs occurring as single and grouped hairs pattern emerging from anterior surface of eyelid. Positive history of the same anomaly in his paternal grandfather demonstrates evidence of an inherited genetic disorder.
Poroid Hidradenoma in a Child: An Unusual Presentation
Authors: LÓPEZ VERÓNICA , SANTONJA NURIA , CALDUCH‐RODRÍGUEZ LUIS , JORDÁ ESPERANZA
Published: January 2011

Abstract:  Poroid neoplasm is a benign sweat gland neoplasm that accounts for 10% of sudoriferous tumors. Poroid hidradenoma is an uncommon variant that usually affects adults, with a peak of incidence in the seventh decade. It is rare in children. We report the first case of poroid hidradenoma presenting in a 13‐year‐old boy.
Evaluation of algorithms for the diagnostic assessment and the reentry of blood donors who tested reactive for antibodies against hepatitis B core antigen
Authors: Juhl David , Luhm Jürgen , Görg Siegfried , Ziemann Malte , Hennig Holger
Published: January 2011

BACKGROUND: Screening of blood donations for antibodies against hepatitis B core antigen (anti‐HBc) is an accepted method to prevent some transfusion‐transmitted hepatitis B virus (HBV) infections. However, anti‐HBc testing may result in donor loss due to unspecific results in the currently available anti‐HBc tests. Algorithms to distinguish true‐positive from false‐positive results and for reentry of those donors who tested false anti‐HBc positive were evaluated retrospectively.

STUDY DESIGN AND METHODS: Samples that tested reactive for anti‐HBc by chemiluminescent microparticle immunoassay (CMIA) were investigated for anti‐HBc by microparticle immunoassay, for anti‐HBs and hepatitis B surface antigen (HBsAg) by CMIA, and for HBV DNA by individual‐donor nucleic acid testing. Results were classified true positive, indeterminate, and false positive for anti‐HBc. Donors who tested indeterminate and false positive were admitted for reentry if follow‐up testing for anti‐HBc became negative and no further evidence for an HBV infection was apparent.

RESULTS: A total of 554 of 148,000 samples, taken from 30,000 individuals within 3 years tested reactive for anti‐HBc by CMIA. Of those, 553 could be further classified: 142 (26%) true positive, 76 (14%) indeterminate, and 335 (60%) false positive. A total of 214 of 411 (52%) samples termed indeterminate or false positive were admitted for reentry and able to provide further donations. In one donor, anti‐HBc–positive/HBsAg‐ and HBV DNA–negative HBV DNA was detectable during follow‐up.

CONCLUSION: According to our proposed algorithm, 26% of anti‐HBc–reactive results tested by CMIA were true positive. Many donors tested indeterminate or false positive can provide future donations if our proposed algorithm for reentry is applied. One donor at risk for transmitting HBV was identified solely by anti‐HBc testing.
Qualification of a new and precise automatic tool for the assessment of hair diameters in phototrichograms
Authors: Scheede Stefan , Herpens Andreas , Burmeister Frank , Oltrogge Bernhard , Saenger K. , Schmidt‐Rose Thomas , Schreiner Volker , Wenck Horst , Knieps Torsten , Berlage Thomas
Published: January 2011

Background/purpose: To automatically assess hair growth during cosmetic trials, incorporating parameters such as anagen‐to‐telogen rate, growth rate, and especially hair diameter.

Methods: We designed and qualified a new and automatic phototrichogram system based on a high‐resolution DSLR camera system (theoretical resolution of 2.557 μm/pixel) and modular macrolens system with fixed focus, combined with a trainable pattern recognition software for automated analysis.

Results: We improved the standard routine for dermatological phototrichogram technique to overcome inaccuracy in thickness measurements due to hair swelling by using an alternative immersion fluid, and increased the effective resolution for hair size and thickness measurement to <4 μm. After having qualified manual measurements as gold standard for the determination of hair diameters, we established a new trainable automatic picture analysis software able to locate and measure individual hairs in length and thickness even in picture series taken from the same skin area at different time points. Comparisons between manual and automatic measurements of the same hairs showed a >90% correlation, and by comparing the automatic results with manual measurements of the same images without individual hair annotation, we could find a correlation of at least 80%.

Conclusion: According to the results and findings generated in this qualification study, we have a reliable tool now that enables us to test cosmetic products for hair treatment in a highly automated way with a sufficient degree of precision and accuracy to detect even small changes in hair diameter during cosmetic trials.
An indicator framework for the climatic adaptive capacity of natural ecosystems
Authors: Czúcz Bálint , Csecserits Anikó , Botta‐Dukát Zoltán , Kröel‐Dulay György , Szabó Rebeka , Horváth Ferenc , Molnár Zsolt
Published: January 2011

Questions: Can the climatic adaptive capacity of natural ecosystems be estimated with using landscape indicators based on vegetation or land‐cover data? Can species distribution model (SDM) outputs be enhanced using such indicators? What are the data requirements and optimal parameter values of potential indicators?

Location: Indicator framework: unspecified. Case study: Kiskunság, Hungary.

Methods: (1) We define a general framework for handling adaptation in ecological climate change impact assessments based on IPCC definitions. (2) As a part of this general framework, we propose an indicator framework consisting of two specific indicators (landscape connectivity and landscape diversity index) to estimate adaptive capacity of ecosystems to climate change. (3) Using old‐field regeneration as a proxy process, we test the proposed indicators, perform sensitivity analysis to optimize them and detect limits of their applicability.

Results: Landscape metrics could provide significant information on regeneration success of old‐fields. A combination of large‐scale connectivity and local diversity had the highest explanatory power, with connectivity being clearly superior. The tested indicator framework can be applied on the basis of commonly available land‐cover data sets. Ecological factors (like dispersal distances) are more important determinants of indicator performance than technical parameters or data resolution, provided minimum data quality is given. The dispersal distance of characteristic species of the Kiskunság forest–steppe region was ∼1 to 8 km during the last one to four decades.

Conclusions: The results convincingly show that relatively simple and tractable metrics can effectively indicate the landscape‐specific capacity of ecosystems to adjust to climatic changes. We argue that the use of adaptive capacity indicator frameworks consisting of simple but ecologically meaningful indicators should accompany every policy‐oriented SDM study.
Quantomo: Validation of a Computer-Assisted Methodology for the Volumetric Analysis of Intracerebral Haemorrhage
Authors: Kosior Jayme C. , Idris Sherif , Dowlatshahi Dar , Alzawahmah Mohamed , Eesa Muneer , Sharma Pranshu , Tymchuk Sarah , Hill Michael D. , Aviv Richard I. , Frayne Richard , Demchuk Andrew M. ,   for the PREDICT/Sunnybrook CTA ICH study investigators
Published: January 2011

Background

Volume measurements of intracerebral haemorrhage are prognostically important and are increasingly used in clinical trials to measure the effects of potential interventions. The purpose of this work is to establish the reliability of haematoma volume measurements obtained using a computer-assisted method called Quantomo (for quantitative tomography) and the ABC/2 method.

Hypothesis

Quantomo reliably detects smaller changes in intracerebral haemorrhage volume as compared with the ABC/2 method because computer-assisted volume measurements are tailored to measure the geometry of individual haematoma volumes whereas the ABC/2 method approximates all haematoma volumes as ellipsoids.

Methods

Thirty randomly selected computed tomography scans with intracerebral haemorrhage were measured by four raters a total of four times each (two sessions using Quantomo and two using the ABC/2 method). Interrater and intrarater reliability for both techniques were calculated simultaneously using a two-way random-effects analysis of variance model. The precision of intracerebral haemorrhage volume measurement was quantified as the minimum detectable difference with 95% confidence intervals.

Results

The median (first quartile and third quartile) intracerebral haemorrhage volume measurements of all rater and sessions for Quantomo were 32·7 ml (6·2 and 54·4 ml) and for ABC/2 40·7 ml (8·6 and 76·0 ml). Quantomo intracerebral haemorrhage volume measurements were more precise, having an inter- and intrarater minimum detectable difference of 8·1 and 5·3 ml, while the inter- and intrarater minimum detectable difference for ABC/2 were 37·0 and 15·7 ml.

Conclusions

Quantomo is a computer-assisted methodology that is more reliable for quantifying intracerebral haemorrhage volume as compared with the ABC/2 method.
The role of STAT5 in the development, function, and transformation of B and T lymphocytes
Authors: Heltemes‐Harris Lynn M. , Willette Mark J. L. , Vang Kieng B. , Farrar Michael A.
Published: January 2011

The transcription factor signal transducer and activator of transcription 5 (STAT5) is activated by a number of cytokine and growth hormone receptors and plays a key role in the development and function of many organ systems. In this review, we focus on recent discoveries about the role of STAT5 in the development and function of B and T lymphocytes. Of particular interest is the growing appreciation for the function of STAT5 as a transcriptional repressor. Finally, we discuss recent discoveries about the role of STAT5 in transformation of B and T lymphocytes.
The Impact of Ice Formation on Wind Turbine Performance and Aerodynamics
Authors: Barber S. , Wang Y. , Jafari S. , Chokani N. , Abhari R. S.
Published: January 2011

Wind energy is the world’s fastest growing source of electricity production; if this trend is to continue, sites that are plentiful in terms of wind velocity must be efficiently utilized. Many such sites are located in cold, wet regions such as the Swiss Alps, the Scandinavian coastline, and many areas of China and North America, where the predicted power curves can be of low accuracy, and the performance often deviates significantly from the expected performance. There are often prolonged shutdown and inefficient heating cycles, both of which may be unnecessary. Thus, further understanding of the effects of ice formation on wind turbine blades is required. Experimental and computational studies are undertaken to examine the effects of ice formation on wind turbine performance. The experiments are conducted on a dynamically scaled model in the wind turbine test facility at ETH Zurich. The central element of the facility is a water towing tank that enables full-scale nondimensional parameters to be more closely matched on a subscale model than in a wind tunnel. A novel technique is developed to yield accurate measurements of wind turbine performance, incorporating the use of a torquemeter with a series of systematic measurements. These measurements are complemented by predictions obtained using a commercial Reynolds-Averaged Navier–Stokes computational fluid dynamics code. The measured and predicted results show that icing typical of that found at the Guetsch Alpine Test Site (2330 m altitude) can reduce the power coefficient by up to 22% and the annual energy production (AEP) by up to 2%. Icing in the blade tip region, 95–100% blade span, has the most pronounced effect on the wind turbine’s performance. For wind turbines in more extreme icing conditions typical of those in Bern Jura, for example, icing can result in up to 17% losses in AEP. Icing at high altitude sites does not cause significant AEP losses, whereas icing at lower altitude sites can have a significant impact on AEP. Thus, the classification of icing is a key to the further development of prediction tools. It would be advantageous to tailor blade heating for prevention of ice buildup on the blade’s tip region. An “extreme” icing predictive tool for the project development of wind farms in regions that are highly susceptible to icing would be beneficial to wind energy developers.
The AQUASOL System: Solar Collector Field Efficiency and Solar-Only Mode Performance
Authors: Blanco Julián , Alarcón Diego , Guillén Elena , Gernjak Wolfgang
Published: January 2011

Water scarcity is a global problem that will be of capital importance during the first half of this century, when seawater desalination will often be the only way to achieve sustainable development. Despite significant energy efficiency improvements during recent years, seawater desalination is still an intensive energy consumer; therefore, in the current instability of oil prices and environmental requirements, the sustainability of this technological solution inevitably passes through continued improvement of energy efficiency of the physical processes involved, as well as the use of renewable energy resources such as solar energy. In 2006, the “Enhanced Zero Discharge Seawater Desalination Using Hybrid Solar Technology” Project (AQUASOL) concluded with the erection of a complete solar desalination facility at the Plataforma Solar de Almeria (Spain) for the main purpose of developing an improved-cost, energy-efficient multi-effect distillation (MED) solar desalination technology. The system was designed to make the following three desalination operating modes feasible: (a) solar-only: the energy to the first distillation effect comes exclusively from thermal energy from the solar collector field, (b) fossil-only: a double-effect absorption heat pump powered by gas supplies all of the heat required by the distillation plant, and (c) hybrid: the energy comes from both the heat pump and the solar field. In this paper, solar-only mode system performance is presented and discussed. Optimum working conditions achieved in the solar-only mode were in the range of 64–67°C of MED first cell inlet temperature, which implies specific thermal energy consumption from around 58 kW hth/m3 to 62 kW hth/m3 and a performance ratio of 11.1–10.4, respectively.
High rate deep Si etching for through-silicon via applications
Authors: Sakai Itsuko , Sakurai Noriko , Ohiwa Tokuhisa
Published: January 2011

High rate deep Si etching for through-silicon via (TSV) applications is reported. The requirements for the Si etch process is discussed from the viewpoint of TSV size and productivity, and the effective processes are described. For “small” TSV a few microns in diameter and up to 10 μm deep, profile control is the most important requirement, For “large” TSV with diameters of more than 50 μm and depths up to 100 μm and more, an ultrahigh Si etch rate is indispensable. The “medium” TSV with diameters and depths several tens of microns requires both high etch rate and profile control. Capacitively coupled plasma MERIE at high pressure is shown to be effective, by using HBr gas chemistry for small TSV, and by using SF6 gas chemistry and high rf frequency for large and medium TSV where an extremely high etch rate can be obtained.
Inductively coupled plasma etching of high aspect ratio two-dimensional photonic crystals in Al-rich AlGaAs and AlGaAsSb
Authors: Larrue A. , Belharet D. , Dubreuil P. , Bonnefont S. , Gauthier-Lafaye O. , Monmayrant A. , Lozes-Dupuy F. , Moumdji S.
Published: January 2011

Planar two-dimensional photonic crystals are key tools for the development of advanced optoelectronic devices. However, their practical realization often requires deep etching of air holes with high aspect ratio. In this article, the authors report on a time-multiplexed inductively coupled plasma reactive ion etching technique, allowing deep etching of AlGaAs and AlGaAsSb heterostructures. Air holes of 130 nm wide and 1.85 μm deep have been realized in AlGaAs heterostructures with up to 60% Al.
Microtubule Stabilization Reduces Scarring and Causes Axon Regeneration After Spinal Cord Injury
Authors: Hellal Farida , Hurtado Andres , Ruschel Jörg , Flynn Kevin C. , Laskowski Claudia J. , Umlauf Martina , Kapitein Lukas C. , Strikis Dinara , Lemmon Vance , Bixby John , Hoogenraad Casper C. , Bradke Frank
Published: January 2011

Taxol stimulates the capacity of axons to grow after spinal cord injury.
Role of a child death review team in a small rural county in California: Figure 1
Authors: Keleher Nancy , Arledge Dawn N
Published: January 2011

Humboldt County is one of California's most rural counties. Located in far Northern California, it is 6–7 h by car from the nearest major urban areas of San Francisco and Sacramento. In landmass it is one of the largest of the California counties, about the size of Rhode Island. In 1991, the Humboldt County Public Health Branch began a Fetal Infant Mortality Review programme. Because of the county's small size, the Fetal Infant Mortality Review process was combined with the review of child deaths through age 17. Responding to a high proportion of cases of child deaths due to unintentional injury, the team developed a workgroup to explore injury prevention strategies. Funding was identified to hire a coordinator who formed a Childhood Injury Prevention Program and developed a strategic plan. The plan prioritised both motor vehicle/traffic safety related injuries and general childhood injury. Funding was obtained for child passenger safety and youth safe driving programmes. The Childhood Injury Prevention Program also collaboratively addressed other injury prevention areas, including water safety. As a small, rural county in California, committed safety advocates from multiple agencies were able to utilise the child death review process to guide injury prevention efforts. Case reviews provided the motivation and quantitative and qualitative data to design programmes and implement interventions that addressed specific unintentional injuries causing child deaths and injuries in Humboldt County.
Assessment of caregiver responsibility in unintentional child injury deaths: challenges for injury prevention
Authors: Schnitzer Patricia G , Covington Theresa M , Kruse Robin L
Published: January 2011

Most unintentional injury deaths among young children result from inadequate supervision or failure by caregivers to protect the child from potential hazards. Determining whether inadequate supervision or failure to protect could be classified as child neglect is a component of child death review (CDR) in most states. However, establishing that an unintentional injury death was neglect related can be challenging as differing definitions, lack of standards regarding supervision, and changing norms make consensus difficult. The purpose of this study was to assess CDR team members' categorisation of the extent to which unintentional injury deaths were neglect related. CDR team members were surveyed and asked to classify 20 vignettes—presented in 10 pairs—that described the circumstances of unintentional injury deaths among children. Vignette pairs differed by an attribute that might affect classification, such as poverty or intent. Categories for classifying vignettes were: (1) caregiver not responsible/not neglect related; (2) some caregiver responsibility/somewhat neglect related; (3) caregiver responsible /definitely neglect related. CDR team members from five states (287) completed surveys. Respondents assigned the child's caregiver at least some responsibility for the death in 18 vignettes (90%). A majority of respondents classified the caregiver as definitely responsible for the child's death in eight vignettes (40%). This study documents attributes that influence CDR team members' decisions when assessing caregiver responsibility in unintentional injury deaths, including supervision, intent, failure to use safety devices, and a pattern of previous neglectful behaviour. The findings offer insight for incorporating injury prevention into CDR more effectively.
Cc2d1a, a C2 domain containing protein linked to nonsyndromic mental retardation, controls functional maturation of central synapses
Authors: Zhao Meng , Raingo Jesica , Chen Zhijian “James” , Kavalali Ege T.
Published: January 2011

Cc2d1a is an evolutionarily conserved protein composed of NH2-terminal Drosophila melanogaster 14 domain (DM14) domains and a COOH-terminal C2 domain. Human patients with homozygotic mutation in the gene suffer from nonsyndromic mental retardation, implying that Cc2d1a functions in the central nervous system. To examine the physiological role of the Cc2d1a, we generated and analyzed Cc2d1a knockout (KO) mice. Cc2d1a KO mice die soon after birth, apparently because of their inability to breathe. Histological analysis of Cc2d1a KO animals did not identify any structural defects in the peripheral respiratory apparatus. However, functional analysis of synapses formed between Cc2d1a-deficient cortical neurons revealed a robust increase in the pace of maturation of evoked synaptic responses as well as synaptic vesicle trafficking. This synaptic anomaly was rescued by reintroducing full-length Cc2d1a but not C2-domain-deletion mutant, underscoring the functional importance of C2 domain. Our data suggest that Cc2d1a is required for mouse survival and performs essential function in controlling functional maturation of synapses.
VaR: Exchange Rate Risk and Jump Risk
Authors: Chen Fen-Ying
Published: January 2011

Incorporating the Poisson jumps and exchange rate risk, this paper provides an analytical VaR to manage market risk of international portfolios over the subprime mortgage crisis. There are some properties in the model. First, different from past studies in portfolios valued only in one currency, this model considers portfolios not only with jumps but also with exchange rate risk, that is vital for investors in highly integrated global financial markets. Second, in general, the analytical VaR solution is more accurate than historical simulations in terms of backtesting and Christoffersen′s independence test (1998) for small portfolios and large portfolios. In other words, the proposed model is reliable not only for a portfolio on specific stocks but also for a large portfolio. Third, the model can be regarded as the extension of that of Kupiec (1999) and Chen and Liao (2009).
Platelet-Derived Growth Factors in Non-GIST Soft-Tissue Sarcomas Identify a Subgroup of Patients with Wide Resection Margins and Poor Disease-Specific Survival
Authors: Kilvaer Thomas Karsten , Valkov Andrej , Sorbye Sveinung W. , Donnem Tom , Smeland Eivind , Bremnes Roy Martin , Busund Lill-Tove
Published: January 2011

Background. Optimal treatment of nongastrointestinal stromal tumor soft-tissue sarcomas (non-GIST STSs) is resection with wide margins. This study investigates the prognostic impact of the angiogenesis-associated platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) in non-GIST STS patients with wide and nonwide resection margins.Method. Tumor samples and clinical data from 249 patients with non-GIST STS were obtained, and tissue microarrays were constructed for each specimen. Immunohistochemistry was used to evaluate the expression of PDGF-A, -B, -C, and -D and PDGFR-αand -β.Results. In the multivariate analysis of patients with wide resection margins, high expression of PDGF-B (, HR = 2.954, and 95% CI = 1.255–6.956) and the coexpression of PDGF-B and PDGFR-α(overall; , high-low/low-high; , HR = 2.678, 95% CI = 0.996–7.200, high/high; , HR = 3.930, 95% CI = 1.542–10.015) were independent negative prognostic markers for disease-specific survival.Conclusion.PDGF-B and the coexpression of PDGF-B and PDGFR-αare strong and independent prognostic factors in non-GIST STSs with wide resection margins.