bluuebunny/crossref_metadata_2025 huggingface dataset:
Coherent Region-, Species-, and Frequency-Dependent Local Climate Signals in Northern Hemisphere Tree-Ring Widths*
Authors: Wettstein Justin J. , Littell Jeremy S. , Wallace John M. , Gedalof Ze’ev
Published: May 2011

Patterns of correlation between tree rings and local temperature or precipitation are investigated using 762 International Tree-Ring Data Bank standardized ring width site chronology time series, and a gridded dataset of temperature and precipitation. Coherent regional- and, in some cases, hemispheric-scale patterns of correlation are found in the extratropical Northern Hemisphere for both the summer prior to and the summer concurrent with ring width formation across different species and over large distances.

Among those chronologies that are primarily linked to temperature, thicker ring widths are generally associated with anomalously cool prior summer temperature and anomalously warm concurrent summer temperature. Reconstructions of local summer temperature using prior, concurrent, and/or subsequent year ring widths as predictors demonstrate that useful climate–growth information generally exists in ring widths that are both concurrent with and subsequent to the summer temperature anomaly. Consistent prior summer temperature–ring width relationships have received relatively little previous attention. Among those chronologies that are primarily linked to precipitation, thicker ring widths are generally associated with high summer precipitation in both the year prior to and the year concurrent with ring formation. The magnitude and spatial consistency of temperature correlations are greater than those for precipitation, at least on the hemispheric scale. These results support and serve to generalize the conclusions of prior regionally restricted and/or species-specific studies relating ring width to energy and/or water limitations.

Regional- and hemispheric-scale patterns of ring width–temperature or ring width–precipitation correlations show up more clearly in species-specific and frequency-dependent analyses. Different species respond differently to temperature and precipitation anomalies. Consistent with the hemispheric patterns described above, most standardized ring width time series more faithfully record the high frequency component of the temperature signal than the low frequency component. The potential for enhanced coherence in regionally restricted, species-specific, and frequency-dependent analyses is independently verified by examining the correlation between ring width time series over geographical distance. This broader characterization of relationships between tree-ring widths and local climate provides an objective basis for selecting tree ring or other similarly high-resolution proxy data for regional-, hemispheric-, or global-scale paleoclimate reconstructions.
Convective Storm Structures and Ambient Conditions Associated with Severe Weather over the Northeast United States
Authors: Lombardo Kelly A. , Colle Brian A.
Published: May 2011

This study documents the convective storm structures and ambient conditions associated with severe storms (wind, hail, and tornado) over the northeastern United States for two warm seasons (May–August), including 2007 and a warm season comprising randomly selected days from 2002 to 2006. The storms were classified into three main convective organizational structures (cellular, linear, and nonlinear) as well as several subcategories. The same procedure was applied to the highly populated coastal zone of the northeastern United States, including New Jersey, Connecticut, Rhode Island, and New York. The coastal analysis included six warm seasons from 2002 to 2007. Over the Northeast, severe wind events are evenly distributed among the cellular, linear, and nonlinear structures. Cellular structures are the primary hail producers, while tornadoes develop mainly from cellular and linear structures. Over the coastal zone, primarily cellular and linear systems produce severe wind and hail, while tornadoes are equally likely from all three convective structures. Composites were generated for severe weather days over the coastal region for the three main convective structures. On average, severe cellular events develop during moderate instability [most unstable CAPE (MUCAPE) ~1200 J kg−1], with low-level warm-air advection and frontogenesis at the leading edge of a thermal ridge collocated with an Appalachian lee trough. Severe linear events develop in a similar mean environment as the cellular events, except that most linear events occur with a surface trough upstream over the Ohio River valley and half of the linear events develop just ahead of progressive midlevel troughs. Nonlinear severe events develop with relatively weak mean convective instability (MUCAPE ~460 J kg−1), but they are supported by midlevel quasigeostrophic (QG) forcing for ascent.
Varespladib Inhibits Secretory Phospholipase A2 in Bronchoalveolar Lavage of Different Types of Neonatal Lung Injury
Authors: De Luca Daniele , Minucci Angelo , Trias Joaquim , Tripodi Domenico , Conti Giorgio , Zuppi Cecilia , Capoluongo Ettore ,   On behalf of the Study Group on Secretory Phospholipase in Pediatrics
Published: May 2011

Secretory phospholipase A2 (sPLA2), which links surfactant catabolism and lung inflammation, is associated with lung stiffness, surfactant dysfunction, and degree of respiratory support in acute respiratory distress syndrome and in some forms of neonatal lung injury. Varespladib potently inhibits sPLA2 in animal models. The authors investigate varespladib ex vivo efficacy in different forms of neonatal lung injury. Bronchoalveolar lavage fluid was obtained from 40 neonates affected by hyaline membrane disease, infections, or meconium aspiration and divided in 4 aliquots added with increasing varespladib or saline. sPLA2 activity, proteins, and albumin were measured. Dilution was corrected with the urea ratio. Varespladib was also tested in vitro against pancreatic sPLA2 mixed with different albumin concentration. Varespladib was able to inhibit sPLA2 in the types of neonatal lung injury investigated. sPLA2 activity was reduced in hyaline membrane disease (P <.0001), infections (P = .003), and meconium aspiration (P = .04) using 40 μM varespladib; 10 μM was able to lower enzyme activity (P = .001), with an IC50 of 87 μM. An inverse relationship existed between protein level and activity reduction (r = 0.5; P = .029). The activity reduction/protein ratio tended to be higher in hyaline membrane disease. Varespladib efficacy was higher in vitro than in lavage fluids obtained from neonates (P <.001).
High commitment management practices re-examined: The case of Indian call centres
Authors: D’Cruz Premilla , Noronha Ernesto
Published: May 2011

Considerable debate exists in the West about the effectiveness of high commitment management (HCM) practices in reducing the negative features associated with work in mass-production call centres. This debate has been glossed over the Indian context. Addressing the gap by critically examining the role of HCM practices in Indian call centres, this article highlights the crucial influence of the organizational agenda and the Indian sociocultural milieu. The findings support the crossvergence thesis while confirming that HCM practices rarely undermine the organizational imperative of control. Indeed, organizational interests prevail, being manifest via the ‘sacrificial HR strategy’. Clearly, employer organizations committed to promoting employee well-being and reducing attrition need to examine issues of job design, task demands and psychological contract obligations apart from implementing HCM practices.
Morning headache in habitual snorers: Frequency, characteristics, predictors and impacts
Authors: Chen Ping-Kun , Fuh Jong-Ling , Lane Hsien-Yuan , Chiu Pai-Yi , Tien Hui-Chi , Wang Shuu-Jiun
Published: May 2011

Objectives: Morning headache has been considered as an accompanying symptom of obstructive sleep apnoea syndrome (OSAS). However the frequency, characteristics, predictors and impacts of morning headache in habitual snorers are not well defined.

Methods: We studied consecutive patients with habitual snoring in a sleep laboratory using polysomnography. All patients were interviewed by a physician regarding the presence or absence of morning headache, migraine and insomnia. Each patient completed the Short Form-36 health survey (SF-36) and the Hospital Anxiety and Depression Scale (HADS). Morning headache was defined as headache on awakening ≥1 day/week for ≥6 months.

Results: Of the 268 participants with habitual snoring, 63 (23.5%) had morning headache and 184 (69%) had OSAS. Patients with morning headache reported lower scores in all eight domains of the SF-36 than those without (difference: 10.6 to 29.7 points, all p ≤ 0.005). The independent predictors of morning headache were migraine (adjusted odds ratio (AOR) 6.3), insomnia (AOR 4.2), psychological distress (HADS ≥ 8) (AOR 3.9) and OSAS (AOR 2.6). Morning headache in 12 patients (19%) fulfilled the criteria for migraine attacks.

Conclusions: Morning headache was common in habitual snorers and associated with a pervasive impairment of health-related quality of life. Migrainous features were not uncommon. Not only OSAS, but migraine, insomnia and psychological distress were also important predictors for morning headache, even in snoring patients.
Effects of Ethyl Loflazepate on Refractory Epilepsy in Children
Authors: Kanemura Hideaki , Sano Fumikazu , Sugita Kanji , Aihara Masao
Published: May 2011

We evaluated the safety and efficacy of ethyl loflazepate in children with epilepsy. The study group comprised 21 outpatients (4 by generalized, 17 by localization-related) aged between 9 months and 17 years. Ethyl loflazepate was administered at a dose of 0.015 mg/kg/day twice daily. The final mean dose was 1.35 mg/day. The mean number of prior antiepileptic drugs was 5.7. The entire treatment period was more than 24 months after ethyl loflazepate administration. Six children (28.6%) became seizure-free for the entire study 6 months after administration, 11 (52.4%) had a seizure reduction of more than 50% for over entire 24 months. The mean number of co-medications was 2.4. Adverse events occurred in only 1 patient. Responders, defined as reduction of ≥50% in seizure frequency, included 2/2 of patients with West syndrome and 15/17 (88.2%) with localization-related epilepsy. Ethyl loflazepate represents an important addition to the treatments available for refractory epilepsies in children.
Indigenous peoples in the accounting literature: Time for a plot change and some Canadian suggestions
Authors: Buhr Nola
Published: May 2011

There is a recent body of accounting literature that articulates a role for accounting in enabling the dispossession and devastation of Indigenous peoples in Canada, the US, Australia and New Zealand. This literature covers the events of several hundred years and informs an understanding of the transformation of Indigenous lifestyles under colonization. In so doing, the literature largely focuses on accounting “for” Indigenous peoples rather than accounting “by” Indigenous peoples. This article urges a change that emphasizes and encourages new directions for the literature. The article begins with a discussion of relevant publications and their themes, including some discussion on the genesis of this literature. From there, the article articulates the need for multiple perspectives and a more nuanced accounting history that acknowledges Indigenous peoples as subjects with agency rather than disempowered objects. Then, by way of illustration, the article provides a description of four potential research projects in the Canadian context.
A genealogical history of positivist and critical accounting research
Authors: Baker C. Richard
Published: May 2011

Accounting history has tended to ignore the accounting research enterprise, focusing instead on particular episodes or periods, such as histories of standards-setting or histories of the accounting profession. In effect, methodological and theoretical differences within the accounting research discipline have so profoundly divided the discipline that researchers working in one area are relatively unable or unwilling to understand the key issues in other areas. This paper seeks to shed some light on what is perhaps the greatest divide in accounting research, that is the divide between positive and critical accounting research. It is the argument of this paper that both positive and critical accounting research can trace their origins to certain key figures who were doctoral students at the University of Chicago in the late 1960s and early 1970s. The paper employs Foucault’s concept of genealogy to examine the origins of the positivist and critical paradigms in accounting research.
The cultural politics of justice: Bakhtin, stand-up comedy and post-9/11 securitization
Authors: Campbell Elaine
Published: May 2011

For Rabelais,‘folk humour’ and its boundless forms are not frivolous, inconsequential aspects of the human condition but, rather, are central to modes of critique and the formation of discourses which seek radical cultural transformation by evading, exposing, resisting, scandalizing and mocking ‘official culture’. Taking its cue from Bakhtin’s exposition of the grotesque realism of the Rabelaisian novel, this article explores the abstract notion of ‘justice’ through the lens of ‘folk humour’—specifically, stand-up comedy which references securitization in the post-9/11 period. In so doing, it calls into question Habermasian discourse ethics, proposing instead a model of ‘doing justice’ predicated on Bakhtinian dialogism.
Pedophile crime films as popular criminology: A problem of justice?
Authors: Kohm Steven A. , Greenhill Pauline
Published: May 2011

This article responds to Nicole Rafter’s recent call to develop a popular criminology using cultural representations of crime and criminal justice to supplement and extend mainstream criminological knowledge. Using representations of child sexual abuse in film, we begin to build a popular criminology of the pedophile. In cinema, this figure opens up a cultural space to interrogate key criminological dilemmas about the nature and shape of justice. Pedophile crime films work through concepts by making emotion central to understanding and by using child sexual abuse as a moral context for otherwise abstract dilemmas. Because of their form as well as their content, recent examples of the subgenre hold the potential to challenge popular conceptions of justice in ways that mainstream academic discourse cannot.
Revascularization of complete and incomplete distal finger amputations in children below 2 years of age: a report of three cases
Authors: Sakamoto Akio , Yoshida Tatsuya , Matsumoto Yoshihiro , Kozuma Masakazu , Iwamoto Yukihide
Published: May 2011

Three cases of fingertip amputation at the level between the distal phalanx and the nail base in children below 2 years of age were treated by replantation or revascularization. The injury was complete in two, and incomplete in one. All three fingerstips survived with artery anastomosis without the need for a blood transfusion. In two venous anastomosis failed and venous drainage was achieved by 3-hourly pinprick. Survival of an amputated finger can be expected in cases where venous reconstruction is not possible, provided that there is adequate venous drainage.
Abrogation of donor T-cell IL-21 signaling leads to tissue-specific modulation of immunity and separation of GVHD from GVL
Authors: Hanash Alan M. , Kappel Lucy W. , Yim Nury L. , Nejat Rebecca A. , Goldberg Gabrielle L. , Smith Odette M. , Rao Uttam K. , Dykstra Lindsay , Na Il-Kang , Holland Amanda M. , Dudakov Jarrod A. , Liu Chen , Murphy George F. , Leonard Warren J. , Heller Glenn , van den Brink Marcel R. M.
Published: May 2011

IL-21 is a proinflammatory cytokine produced by Th17 cells. Abrogation of IL-21 signaling has recently been shown to reduce GVHD while retaining graft-versus-leukemia/lymphoma (GVL) responses. However, the mechanisms by which IL-21 may lead to a separation of GVHD and GVL remain incompletely understood. In a murine MHC-mismatched BM transplantation model, we observed that IL-21 receptor knockout (IL-21R KO) donor T cells mediate decreased systemic and gastrointestinal GVHD in recipients of a transplant. This reduction in GVHD was associated with expansion of transplanted donor regulatory T cells and with tissue-specific modulation of Th-cell function. IL-21R KO and wild-type donor T cells showed equivalent alloactivation, but IL-21R KO T cells showed decreased infiltration and inflammatory cytokine production within the mesenteric lymph nodes. However, Th-cell cytokine production was maintained peripherally, and IL-21R KO T cells mediated equivalent immunity against A20 and P815 hematopoietic tumors. In summary, abrogation of IL-21 signaling in donor T cells leads to tissue-specific modulation of immunity, such that gastrointestinal GVHD is reduced, but peripheral T-cell function and GVL capacity are retained. IL-21 is thus an exciting target for therapeutic intervention and improvement of clinical transplantation outcomes.
Sumoylation of CCAAT/enhancer–binding protein α promotes the biased primitive hematopoiesis of zebrafish
Authors: Yuan Hao , Zhou Jun , Deng Min , Zhang Yong , Chen Yi , Jin Yi , Zhu Jiang , Chen Sai Juan , de The Hugues , Chen Zhu , Liu Ting Xi , Zhu Jun
Published: May 2011

Hematopoiesis is evolutionarily conserved from zebrafish to mammals, and this includes both primitive and definitive waves during embryogenesis. Primitive hematopoiesis is dominated by erythropoiesis with limited myelopoiesis. Protein sumoylation, a ubiquitination-like posttranslational protein modification, is implicated in a variety of biochemical processes, most notably in transcriptional repression. We show here that the loss of 6 small ubiquitin-related modifier (SUMO) paralogs triggers a sharp up-regulation of the myeloid-specific marker mpo and down-regulation of the erythroid-specific marker gata1 in myelo-erythroid progenitor cells (MPCs) in the intermediate cell mass (ICM) during primitive hematopoiesis. Accordingly, in transgenic zebrafish lines, hyposumoylation expands myelopoiesis at the expense of erythropoiesis. A SUMO–CCAAT/enhancer–binding protein α (SUMO-C/ebpα) fusion restores the normal myelopoiesis/erythropoiesis balance, suggesting that sumoylation status of C/ebpα contributes to myelo-erythroid lineage determination. Our results therefore implicate sumoylation in early lineage determination and reveal the possible molecular mechanism underlying the puzzling biased primitive hematopoiesis in vertebrates.
Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non-repetitive tomato gene
Authors: González Rodrigo M , Ricardi Martiniano M , Iusem Norberto D
Published: May 2011

Background

Eukaryotic DNA methylation is one of the most studied epigenetic processes, as it results in a direct and heritable covalent modification triggered by external stimuli. In contrast to mammals, plant DNA methylation, which is stimulated by external cues exemplified by various abiotic types of stress, is often found not only at CG sites but also at CNG (N denoting A, C or T) and CNN (asymmetric) sites. A genome-wide analysis of DNA methylation in Arabidopsis has shown that CNN methylation is preferentially concentrated in transposon genes and non-coding repetitive elements. We are particularly interested in investigating the epigenetics of plant species with larger and more complex genomes than Arabidopsis, particularly with regards to the associated alterations elicited by abiotic stress.

Results

We describe the existence of CNN-methylated epialleles that span Asr1, a non-transposon, protein-coding gene from tomato plants that lacks an orthologous counterpart in Arabidopsis. In addition, to test the hypothesis of a link between epigenetics modifications and the adaptation of crop plants to abiotic stress, we exhaustively explored the cytosine methylation status in leaf Asr1 DNA, a model gene in our system, resulting from water-deficit stress conditions imposed on tomato plants. We found that drought conditions brought about removal of methyl marks at approximately 75 of the 110 asymmetric (CNN) sites analysed, concomitantly with a decrease of the repressive H3K27me3 epigenetic mark and a large induction of expression at the RNA level. When pinpointing those sites, we observed that demethylation occurred mostly in the intronic region.

Conclusions

These results demonstrate a novel genomic distribution of CNN methylation, namely in the transcribed region of a protein-coding, non-repetitive gene, and the changes in those epigenetic marks that are caused by water stress. These findings may represent a general mechanism for the acquisition of new epialleles in somatic cells, which are pivotal for regulating gene expression in plants.
Small invasive colon cancer with systemic metastasis: A case report
Authors: Matsumoto Minori , Nakajima Takeshi , Kato Ken , Kouno Tsutomu , Sakamoto Taku , Matsuda Takahisa , Kushima Ryoji , Saito Yutaka
Published: May 2011

Background

Recently, especially in Japan, several researchers have suggested that colorectal cancer can develop not only through an adenoma-carcinoma sequence but also from normal mucosa via a de novo pathway, and that these de novo cancers have more aggressive malignant potential. We report a case of aggressive colon cancer resulting in systemic metastasis despite small tumour size.

Case Presentation

A 35-year-old woman presented at the referring hospital with swelling of the left cervical lymph node. Biopsy of the lymph node revealed metastatic adenocarcinoma; however, CT scan and mammography were unable to identify the site of the primary lesion. She was diagnosed with unknown primary cancer and referred to our hospital for further examination. Immunohistochemical reevaluation showed the cervical lymph node biopsy specimen to be positive for CDX2 and CK20 and negative for CK7 expression, leading us to suspect the presence of a primary colorectal cancer. We performed a total colonoscopy, and detected a small protruding lesion in the transverse colon. The tumour was only 12 mm in diameter, with a central depressed component and a severely thickened stalk, which suggested direct cancer invasion of the deep submucosa. We concluded that this lesion was the site of origin of the metastasis despite the small tumour size, and performed diagnostic endoscopic mucosal resection. The lesion was found to have an intramucosal cancer component, demonstrating that this lesion represented primary colon cancer. The patient was referred to the gastrointestinal oncology division for systemic chemotherapy.

Conclusions

In this case, immunohistochemical findings strongly suggested the existence of a colorectal cancer. The non-polypoid gross appearance of the tumour suggested that it can originate de novo , thus providing a valuable case in support of the aggressive malignant potential of a de novo colorectal cancer pathway.
Understanding, comprehensibility and acceptance of an evidence-based consumer information brochure on fall prevention in old age: a focus group study
Authors: Lins Sabine , Icks Andrea , Meyer Gabriele
Published: May 2011

Background

Evidence-based patient and consumer information (EBPI) is an indispensable component of the patients' decision making process in health care. Prevention of accidental falls in the elderly has gained a lot of public interest during preceding years. Several consumer information brochures on fall prevention have been published; however, none fulfilled the criteria of an EBPI. Little is known about the reception of EBPI by seniors. Therefore we aimed to evaluate a recently developed EBPI brochure on fall prevention with regard to seniors' acceptance and comprehensibility in focus groups and to explore whether the participants' judgements differed depending on the educational background of the study participants.

Methods

Seven focus groups were conducted with 40 seniors, aged 60 years or older living independently in a community. Participants were recruited by two gatekeepers. A discussion guide was used and seniors were asked to judge the EBPI brochure on fall prevention using a Likert scale 1-6. The focus group discussions were tape recorded, transcribed verbatim, and analysed using content analysis.

Results

The participants generally accepted the EBPI brochure on fall prevention. Several participants expressed a need for more practical advice. The comprehensibility of the brochure was influenced positively by brief chapter summaries. Participants dismissed the statistical illustrations such as confidence intervals or a Fagan nomogram and only half of them agreed with the meta-information presented in the first chapter. The detailed information about fall prevalence was criticised by some seniors. The use of a case story was well tolerated by the majority of participants.

Conclusion

Our findings indicate that the recently developed EBPI brochure on fall prevention in old age was generally well accepted by seniors, but some statistical descriptions were difficult for them to understand. The brochure has to be updated. However, not all issues raised by the participants will be taken into account since some of them are contrary to the principles of EBPI.
Monosodium Iodoacetate-Induced Joint Pain is Associated with Increased Phosphorylation of Mitogen Activated Protein Kinases in the Rat Spinal Cord
Authors: Lee Younglim , Pai Madhavi , Brederson Jill-Desiree , Wilcox Denise , Hsieh Gin , Jarvis Michael F , Bitner Robert S
Published: May 2011

Background:

Intra-articular injection of monosodium iodoacetate (MIA) in the knee joint of rats disrupts chondrocyte metabolism resulting in cartilage degeneration and subsequent nociceptive behavior that has been described as a model of osteoarthritis (OA) pain. Central sensitization through activation of mitogen activated protein kinases (MAPKs) is recognized as a pathogenic mechanism in chronic pain. In the present studies, induction of central sensitization as indicated by spinal dorsal horn MAPK activation, specifically ERK and p38 phosphorylation, was assessed in the MIA-OA model.

Results:

Behaviorally, MIA-injected rats displayed reduced hind limb grip force 1, 2, and 3 weeks post-MIA treatment. In the same animals, activation of phospho ERK1/2 was gradually increased, reaching a significant level at post injection week 3. Conversely, phosphorylation of p38 MAPK was enhanced maximally at post injection week 1 and decreased, but remained elevated, thereafter. Double labeling from 3-wk MIA rats demonstrated spinal pERK1/2 expression in neurons, but not glia. In contrast, p-p38 was expressed by microglia and a subpopulation of neurons, but not astrocytes. Additionally, there was increased ipsilateral expression of microglia, but not astrocytes, in 3-wk MIA-OA rats. Consistent with increased MAPK immunoreactivity in the contralateral dorsal horn, mechanical allodynia to the contralateral hind-limb was observed 3-wk following MIA. Finally, intrathecal injection of the MEK1 inhibitor PD98059 blocked both reduced hind-limb grip force and pERK1/2 induction in MIA-OA rats.

Conclusion:

Results of these studies support the role of MAPK activation in the progression and maintenance of central sensitization in the MIA-OA experimental pain model.
Association of the rs3743205 variant of DYX1C1 with dyslexia in Chinese children
Authors: Lim Cadmon K P , Ho Connie S H , Chou Crystal H N , Waye Mary M Y
Published: May 2011

Background

Dyslexia is a learning disability that is characterized by difficulties in the acquisition of reading and spelling skills independent of intelligence, motivation or schooling. Studies of western populations have suggested that DYX1C1 is a candidate gene for dyslexia. In view of the different languages used in Caucasian and Chinese populations, it is therefore worthwhile to investigate whether there is an association of DYX1C1 in Chinese children with dyslexia.

Method and Results

Eight single nucleotide polymorphisms (SNPs) were genotyped from three hundred and ninety three individuals from 131 Chinese families with two which have been reported in the literature and six tag SNPs at DYX1C1. Analysis for allelic and haplotypic associations was performed with the UNPHASED program and multiple testing was corrected using false discovery rates. We replicated the previously reported association of rs3743205 in Chinese children with dyslexia (p

corrected
= 0.0072). This SNP was also associated with rapid naming, phonological memory and orthographic skills in quantitative trait analysis.

Conclusion

Our findings suggest that DYX1C1 is associated with dyslexia in people of Chinese ethnicity in Hong Kong.
ConReg-R: Extrapolative recalibration of the empirical distribution of p-values to improve false discovery rate estimates
Authors: Li Juntao , Paramita Puteri , Choi Kwok Pui , Karuturi R Krishna Murthy
Published: May 2011

Background

False discovery rate (FDR) control is commonly accepted as the most appropriate error control in multiple hypothesis testing problems. The accuracy of FDR estimation depends on the accuracy of the estimation of p-values from each test and validity of the underlying assumptions of the distribution. However, in many practical testing problems such as in genomics, the p-values could be under-estimated or over-estimated for many known or unknown reasons. Consequently, FDR estimation would then be influenced and lose its veracity.

Results

We propose a new extrapolative method called Constrained Regression Recalibration (ConReg-R) to recalibrate the empirical p-values by modeling their distribution to improve the FDR estimates. Our ConReg-R method is based on the observation that accurately estimated p-values from true null hypotheses follow uniform distribution and the observed distribution of p-values is indeed a mixture of distributions of p-values from true null hypotheses and true alternative hypotheses. Hence, ConReg-R recalibrates the observed p-values so that they exhibit the properties of an ideal empirical p-value distribution. The proportion of true null hypotheses (π
0) and FDR are estimated after the recalibration.

Conclusions

ConReg-R provides an efficient way to improve the FDR estimates. It only requires the p-values from the tests and avoids permutation of the original test data. We demonstrate that the proposed method significantly improves FDR estimation on several gene expression datasets obtained from microarray and RNA-seq experiments.

Reviewers

The manuscript was reviewed by Prof. Vladimir Kuznetsov, Prof. Philippe Broet, and Prof. Hongfang Liu (nominated by Prof. Yuriy Gusev).
Agrobacterium-mediated transformation of safflower and the efficient recovery of transgenic plants via grafting
Authors: Belide Srinivas , Hac Luch , Singh Surinder P , Green Allan G , Wood Craig C
Published: May 2011

Background

Safflower (Carthamus tinctorius L.) is a difficult crop to genetically transform being susceptible to hyperhydration and poor in vitro root formation. In addition to traditional uses safflower has recently emerged as a broadacre platform for the production of transgenic products including modified oils and pharmaceutically active proteins. Despite commercial activities based on the genetic modification of safflower, there is no method available in the public domain describing the transformation of safflower that generates transformed T1 progeny.

Results

An efficient and reproducible protocol has been developed with a transformation efficiency of 4.8% and 3.1% for S-317 (high oleic acid content) and WT (high linoleic acid content) genotypes respectively. An improved safflower transformation T-DNA vector was developed, including a secreted GFP to allow non-destructive assessment of transgenic shoots. Hyperhydration and necrosis of Agrobacterium-infected cotyledons was effectively controlled by using iota-carrageenan, L-cysteine and ascorbic acid. To overcome poor in vitro root formation for the first time a grafting method was developed for safflower in which ~50% of transgenic shoots develop into mature plants bearing viable transgenic T1 seed. The integration and expression of secreted GFP and hygromycin genes were confirmed by PCR, Southern and Western blot analysis. Southern blot analysis in nine independent lines indicated that 1-7 transgenes were inserted per line and T1 progeny displayed Mendelian inheritance.

Conclusions

This protocol demonstrates significant improvements in both the efficiency and ease of use over existing safflower transformation protocols. This is the first complete method of genetic transformation of safflower that generates stably-transformed plants and progeny, allowing this crop to benefit from modern molecular applications.
Clinical outcomes of chemoradiotherapy for locally recurrent rectal cancer
Authors: Lee Joo Ho , Kim Dae Yong , Kim Sun Young , Park Ji Won , Choi Hyo Seong , Oh Jae Hwan , Chang Hee Jin , Kim Tae Hyun , Park Suk Won
Published: May 2011

Background

To assess the clinical outcome of chemoradiotherapy with or without surgery for locally recurrent rectal cancer (LRRC) and to find useful and significant prognostic factors for a clinical situation.

Methods

Between January 2001 and February 2009, 67 LRRC patients, who entered into concurrent chemoradiotherapy with or without surgery, were reviewed retrospectively. Of the 67 patients, 45 were treated with chemoradiotherapy plus surgery, and the remaining 22 were treated with chemoradiotherapy alone. The mean radiation doses (biologically equivalent dose in 2-Gy fractions) were 54.6 Gy and 66.5 Gy for the chemoradiotherapy with and without surgery groups, respectively.

Results

The median survival duration of all patients was 59 months. Five-year overall (OS), relapse-free (RFS), locoregional relapse-free (LRFS), and distant metastasis-free survival (DMFS) were 48.9%, 31.6%, 66.4%, and 40.6%, respectively. A multivariate analysis demonstrated that the presence of symptoms was an independent prognostic factor influencing OS, RFS, LRFS, and DMFS. No statistically significant difference was found in OS (p = 0.181), RFS (p = 0.113), LRFS (p = 0.379), or DMFS (p = 0.335) when comparing clinical outcomes between the chemoradiotherapy with and without surgery groups.

Conclusions

Chemoradiotherapy with or without surgery could be a potential option for an LRRC cure, and the symptoms related to LRRC were a significant prognostic factor predicting poor clinical outcome. The chemoradiotherapy scheme for LRRC patients should be adjusted to the possibility of resectability and risk of local failure to focus on local control.
Quantitative interpretation of pulsed neutron capture logs: Part 1 — Fast numerical simulation
Authors: Mimoun Jordan G. , Torres-Verdín Carlos , Preeg William E.
Published: May 2011

Pulsed neutron capture (PNC) logs are commonly used for formation evaluation behind casing and to assess time-lapse variations of hydrocarbon pore volume. Because conventional interpretation methods for Σ logs assume homogeneous formations, errors may arise, especially in thinly bedded formations, when appraising petrophysical properties of hydrocarbon-bearing beds. There exist no quantitative interpretation methods to account for shoulder-bed effects on Σ logs acquired in sand-shale laminated reservoirs. Because of diffusion effects between dissimilar beds, Σ logs acquired in such formations do not obey mixing laws between the Σ responses of pure-sand and pure-shale end members of the sedimentary sequence. We have developed a new numerical method to simulate PNC rapidly and accurately logs. The method makes use of late-time, thermal-neutron flux sensitivity functions (FSFs) to describe the contribution of multilayer formations toward the measured capture cross section. It includes a correction procedure based on 1D neutron diffusion theory that adapts the transport-equation-derived, base-case FSF of a homogeneous formation to simulate the response of vertically heterogeneous formations. Benchmarking exercises indicate that our simulation method yields average differences smaller than two capture units within seconds of computer central processing unit time with respect to PNC logs simulated with rigorous Monte Carlo methods for a wide range of geometrical, petrophysical, and fluid properties.
Geophysics Master’s Theses
Authors: Akerberg Peeter
Published: May 2011

Geophysics publishes titles of relevant master’s theses in print and online. URL links to full theses also will be published if provided. To submit a title for consideration, complete the appropriate submission form at http://seg.org/dissertationabstracts and e-mail it to dissertationabstracts@seg.org.
Disentangling the Threads of Civil-Military Relations in Turkey: Promises and Perils
Authors: Cizre Umit
Published: May 2011

When one takes stock of Turkey's capacities and limitations not in terms of geopolitics, Islamism, or the Kurdish question but from a sociological and political perspective focused on internal challenges and prospects, perhaps the most critical concern turns out to be the civil—military imbalance. There is a need for a better understanding of the possibilities and challenges for establishing new game rules and a more democratic redefinition of civil—military equation in Turkey, where a politically “autonomous” and “religiously secular” military bloc is pitted against a popularly elected “Islam-friendly” government in the context of an electoral democracy dominated by suspicion, conflict, and open confrontation between the sides. This essay examines the critical impact of the victory of the “yes” votes in the historic referendum of 12 September 2010 and the Ergenekon incident as catalysts for change and reform in Turkey's civil—military balance.
The (Paper)Work of Medicine: Understanding International Medical Costs
Authors: Cutler David M , Ly Dan P
Published: May 2011

This paper draws on international evidence on medical spending to examine what the United States can learn about making its healthcare system more efficient. We focus primarily on understanding contemporaneous differences in the level of spending, generally from the 2000s. Medical spending differs across countries either because the price of services differs (for example, a coronary bypass surgery operation may cost more in the United States than in other countries) or because people receive more services in some countries than in others (for example, more bypass surgery operations). Within the price category, there are two further issues: whether factors earn different returns across countries and whether more clinical or administrative personnel are required to deliver the same care in different countries. We first present the results of a decomposition of healthcare spending along these lines in the United States and in Canada. We then delve into each component in more detail—administrative costs, factor prices, and the provision of care received—bringing in a broader range of international evidence when possible. Finally, we touch upon the organization of primary and chronic disease care and discuss possible gains in that area.
Lymphoscintigraphic findings: delayed oedema after great saphenous vein harvesting
Authors: Belczak C E Q , de Godoy J M P , Cruz A F , Tyszca A L , Neto H J G , Caffaro R A
Published: May 2011

Objective

The aim of this study was to identify lymphoscintigraphic changes associated with lower-extremity oedema after the harvesting of the saphenous vein using a series of short Q2 incisions for coronary bypass.

Method

Forty-four patients (32 males and 12 females) with a mean age of 62.7 ± 7.8 (47–75 years old) were evaluated in a retrospective, quantitative, cross-sectional study from June 2007 to January 2008, three to 188 months (mean: 46 months) after the surgical procedure. Assessment was by water displacement volumetry and lymphoscintigraphy of the lower limbs. Results expressed as means with standard deviations were compared employing the Student's t-test and the chi-square or Fisher's exact tests were used to compare data expressed as frequencies. An alpha error of 5% was considered acceptable ( P ≤ 0.05).

Results

The presence of dermal backflow, as identified by lymphoscintigraphy with an accumulation of radiotracer in the thoracic duct and popliteal lymph nodes was significantly greater on the operated side.

Conclusion

There was a significant association between dermal backflow and delayed oedema.
Managerial Perspectives on Key Aspects of Training Management in the Turkish National Police
Authors: Zengin Cevdet , Clements Phil , Kul Mehmet
Published: May 2011

A number of studies have been undertaken into the training structures, processes and practices in the Turkish National Police (TNP) in the last decade. The predominant thrust of this literature is in relation to evaluation of training provision and delivery. The literature represents an increased focus in Turkey on the development and improvement of the training function to deliver a more effective police service through enhanced police performance. These professional and academic studies have provided an opportunity for training portfolio-holders at all levels to identify areas of improvement in police training. This paper builds on a previous literature review that was conducted to examine the in-service training provision and delivery in the TNP. The review revealed seven themes which represented areas for possible improvement: policymaking and planning, employment and deployment, training needs analysis, design, delivery, evaluation, and training audit. A questionnaire was designed, based on the themes, to measure the perspectives of the training portfolio-holders including senior, business and line managers across the training function. The resultant survey data suggest that, in order to make training provision in the TNP more effective, there is a need for a comprehensive revision in a number of areas including policy-making, strategic management of training, tenure and competencies of the training staff, robust curriculum development, outcome-based evaluation and value-added inspection.
Youth, Race, and Serious Crime: Examining Trends and Critiquing Policy
Authors: Benekos Peter J. , Merlo Alida V. , Puzzanchera Charles M.
Published: May 2011

In this study, the authors examine trends in juvenile violent offending over a 20-year period and focus specifically on the race of the offender. Although aggregate data indicate the disproportionate representation of Black youth in the juvenile justice system, it is difficult to determine the role that race plays in specific violent offences. By focusing on murder, aggravated assault and robbery, the authors contend that a more complete picture of youthful offending and system responses emerges. The trend data clearly demonstrate continuing disproportionate handling of Black juvenile offenders. Some policy implications are reviewed and future directions are explored.
The Athlete Biological Passport
Authors: Sottas Pierre-Edouard , Robinson Neil , Rabin Olivier , Saugy Martial
Published: May 2011

BACKGROUND

In elite sports, the growing availability of doping substances identical to those naturally produced by the human body seriously limits the ability of drug-testing regimes to ensure fairness and protection of health.

CONTENT

The Athlete Biological Passport (ABP), the new paradigm in testing based on the personalized monitoring of biomarkers of doping, offers the enormous advantage of being independent of this endless pharmaceutical race. Doping triggers physiological changes that provide physiological enhancements. In the same way that disease-related biomarkers are invaluable tools that assist physicians in the diagnosis of pathology, specifically selected biomarkers can be used to detect doping.

The ABP is a new testing paradigm with immense potential value in the current climate of rapid advancement in biomarker discovery. In addition to its original aim of providing proof of a doping offense, the ABP can also serve as a platform for a Rule of Sport, with the presentation before competition of the ABP to objectively demonstrate that the athlete will participate in a healthy physiological condition that is unaltered by performance-enhancing drugs. Finally, the decision-support system used today for the biological monitoring of world top-level athletes can also be advantageously transferred to other areas of clinical practice to reach the goal of personalized medicine.
Acidic oxidation of kraft lignin into aromatic monomers catalyzed by transition metal salts
Authors: Werhan Holger , Mir Joan Mora , Voitl Tobias , Rudolf von Rohr Philipp
Published: May 2011

As one of the three main components in woody biomass, lignin is an abundant but underused renewable raw material and carbon source. Owing to its aromatic structure and large availability as a by-product of pulping, its conversion into chemicals is highly attractive. In the present work, the oxidation of a softwood kraft lignin in acidic media was investigated in the presence of a homogeneous catalyst. The objective was to find a cheap but efficient catalyst for the depolymerization of kraft lignin into aromatic monomers. Different transition metal salts were screened and compared to phosphomolybdic acid, which was investigated in previous studies, and to experiments in sulfuric acid without additional catalyst. Vanillin and methyl vanillate were the main monomeric products detected by gas chromatography/mass spectrometry but their formation was only slightly increased by using transition metal salts (up to 6.28 wt% yield). However, the presence of iron or copper chloride resulted in fast formation kinetics and significant amounts of other monomeric products. In addition, an efficient fragmentation of the lignin molecule from a weight-average molecular weight of 3500 g mol-1down to 500 g mol-1was observed by size-exclusion chromatography. The enhanced incorporation of oxygen into the reaction products in the presence of those catalysts was proven by Fourier transform infrared spectroscopy and the influence of the catalyst concentration was studied.
Fungal pretreatment of pine wood to reduce the emission of volatile organic compounds
Authors: Stratev Daniel , Gradinger Cornelia , Ters Thomas , Fackler Karin , Kuncinger Thomas , Srebotnik Ewald
Published: May 2011

Sterilized pine wood strands were treated with the ascomycete Ophiostoma piliferum (Cartapip 97™) in an attempt to reduce aldehyde emissions through degradation of aldehyde-forming precursors. Wooden boards were then produced from the treated strands by means of a laboratory press. VOC emissions of these boards were characterized and the concentrations of seven major substances were followed for a period of 28 days in Markes μ-CTE micro-chambers employing Tenax-TDAS/GC/MS analytics. Boards made from treated strands showed a highly significant (P<0.001) reduction in aldehyde emissions by 70% compared to the control boards, while differences in the monoterpene emissions were not significant (P>0.05). Wood extractives from treated and untreated strands were also analyzed by GC/MS after milling and acetone/water extraction. A marked decrease of C18 unsaturated fatty acids was detected in agreement with the reduction of aldehyde emissions, and the monosaccharides as indicators of fungal growth were depleted and stilbenes and lignans were partially degraded.
A conceptual critique of parenting research in Hong Kong
Authors: Fok Hung-Kit , Shek Daniel T.L.
Published: May 2011

Parenting processes have been investigated for over 30 years in Hong Kong. Three conceptual limitations are identified, based on 90 studies selected from the PsycINFO database: lack of investigation of indigenous parenting concepts; lack of investigation of causes, concomitants and consequences of the parenting process; and lack of alternative explanations for results. Suggestions for improvement are also made in each area. Limitations of the present study are discussed.