bluuebunny/crossref_metadata_2025_split huggingface dataset:
GiA Roots: software for the high throughput analysis of plant root system architecture
Authors: Galkovskyi Taras , Mileyko Yuriy , Bucksch Alexander , Moore Brad , Symonova Olga , Price Charles A , Topp Christopher N , Iyer-Pascuzzi Anjali S , Zurek Paul R , Fang Suqin , Harer John , Benfey Philip N , Weitz Joshua S 
Published: July 2012

Abstract

Background
Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.

Results
We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.

Conclusions
We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.
Stillbirths and newborn deaths in slum settlements in Mumbai, India: a prospective verbal autopsy study
Authors: Bapat Ujwala , Alcock Glyn , More Neena Shah , Das Sushmita , Joshi Wasundhara , Osrin David 
Published: July 2012

Abstract

Background
Three million babies are stillborn each year and 3.6 million die in the first month of life. In India, early neonatal deaths make up four-fifths of neonatal deaths and infant mortality three-quarters of under-five mortality. Information is scarce on cause-specific perinatal and neonatal mortality in urban settings in low-income countries. We conducted verbal autopsies for stillbirths and neonatal deaths in Mumbai slum settlements. Our objectives were to classify deaths according to international cause-specific criteria and to identify major causes of delay in seeking and receiving health care for maternal and newborn health problems.

Methods
Over two years, 2005–2007, births and newborn deaths in 48 slum areas were identified prospectively by local informants. Verbal autopsies were collected by trained field researchers, cause of death was classified by clinicians, and family narratives were analysed to investigate delays on the pathway to mortality.

Results
Of 105 stillbirths, 65 were fresh (62%) and obstetric complications dominated the cause classification. Of 116 neonatal deaths, 87 were early and the major causes were intrapartum-related (28%), prematurity (23%), and severe infection (22%). Bereavement was associated with socioeconomic quintile, previous stillbirth, and number of antenatal care visits. We identified 201 individual delays in 121/187 birth narratives (65%). Overall, delays in receiving care after arrival at a health facility dominated and were mostly the result of referral from one institution to another. Most delays in seeking care were attributed to a failure to recognise symptoms of complications or their severity.

Conclusions
In Mumbai’s slum settlements, early neonatal deaths made up 75% of neonatal deaths and intrapartum-related complications were the greatest cause of mortality. Delays were identified in two-thirds of narratives, were predominantly related to the provision of care, and were often attributable to referrals between health providers. There is a need for clear protocols for care and transfer at each level of the health system, and an emphasis on rapid identification of problems and communication between health facilities.

Trial registration
ISRCTN96256793
Application of concentrated deep sea water inhibits the development of atopic dermatitis-like skin lesions in NC/Nga mice
Authors: Bak Jong-Phil , Kim Yong-Min , Son Jeonghyun , Kim Chang-Ju , Kim Ee-Hwa 
Published: July 2012

Abstract

Background
Mineral water from deep-sea bedrock, formed over thousands of years, is rich in minerals such as Ca, Mg, Na, K, Fe and others. Our present study was to investigate the preventive effects of natural deep-sea water on developing atopic dermatitis (AD).

Methods
We elicited AD by application of DNCB (2,4-dinitro-chlorobezene) in Nc/Nga mouse dorsal skin. Deep Sea water (DSW) was filtered and concentrated by a nanofiltration process and reverse osmosis. We applied concentrated DSW (CDSW) to lesions five times per week for six weeks, followed by evaluation. 1% pimecrolimus ointment was used as positive control. The severity of skin lesions was assessed macroscopically and histologically. Levels of inflammatory mediators and cytokines in the serum were detected by Enzyme-linked immunosorbent assay (ELISA) and the levels of CD4+ and CD8+ spleen lymphocytes were determined by flow cytometry analysis.

Results
DNCB-treated mice showed atopic dermatitis-like skin lesions. Treatment of mice with CDSW reduced the severity of symptoms in the skin lesions, including edema, erythema, dryness, itching, and transepidermal water loss (TEWL). Histological analyses demonstrated that epidermal thickness and infiltration of inflammatory cells were decreased after CDSW treatment. Given these interesting observations, we further evaluated the effect of CDSW on immune responses in this AD model. Treatment AD mice with CDSW inhibited up-regulation of IgE, histamine, and pro-inflammatory cytokines in the serum. Also, the CD4+/CD8+ ratio in spleen lymphocyte was down-regulated after treatment with CDSW. Finally, cytokines, especially IL-4 and IL-10 which are important for Th2 cell development, were reduced.

Conclusions
Our data suggests that topical application of CDSW could be useful in preventing the development of atopic dermatitis.
Increased risks of malaria due to limited residual life of insecticide and outdoor biting versus protection by combined use of nets and indoor residual spraying on Bioko Island, Equatorial Guinea
Authors: Bradley John , Matias Abrahan , Schwabe Christopher , Vargas Daniel , Monti Feliciano , Nseng Gloria , Kleinschmidt Immo 
Published: July 2012

Abstract

Background
Malaria is endemic on Bioko Island, Equatorial Guinea, with year-round transmission. In 2004 an intensive malaria control strategy primarily based on indoor residual spraying (IRS) was launched. The limited residual life of IRS poses particular challenges in a setting with year-round transmission, such as Bioko. Recent reports of outdoor biting by Anopheles gambiae are an additional cause for concern. In this study, the effect of the short residual life of bendiocarb insecticide and of children spending time outdoors at night, on malaria infection prevalence was examined.

Methods
Data from the 2011 annual malaria indicator survey and from standard WHO cone bioassays were used to examine the relationship between time since IRS, mosquito mortality and prevalence of infection in children. How often children spend time outside at night and the association of this behaviour with malaria infection were also examined.

Results
Prevalence of malaria infection in two to 14 year-olds in 2011 was 18.4%, 21.0% and 28.1% in communities with median time since IRS of three, four and five months respectively. After adjusting for confounders, each extra month since IRS corresponded to an odds ratio (OR) of 1.44 (95% CI 1.15–1.81) for infection prevalence in two to 14 year-olds. Mosquito mortality was 100%, 96%, 81% and 78%, at month 2, 3, 4 and 5 respectively after spraying. Only 4.1% of children spent time outside the night before the survey between the hours of 22.00 and 06.00 and those who did were not at a higher risk of infection (OR 0.87, 95% CI 0.50–1.54). Sleeping under a mosquito net provided additive protection (OR 0.68, 95% CI 0.54–0.86).

Conclusions
The results demonstrate the epidemiological impact of reduced mosquito mortality with time since IRS. The study underscores that in settings of year-round transmission there is a compelling need for longer-lasting IRS insecticides, but that in the interim, high coverage of long-lasting insecticidal nets (LLINs) may ameliorate the loss of effect of current shorter-lasting IRS insecticides. Moreover, continued use of IRS and LLINs for indoor-oriented vector control is warranted given that there is no evidence that spending time outdoors at night increases infection prevalence in children.
What is the role and authority of gatekeepers in cluster randomized trials in health research?
Authors: Gallo Antonio , Weijer Charles , White Angela , Grimshaw Jeremy M , Boruch Robert , Brehaut Jamie C , Donner Allan , Eccles Martin P , McRae Andrew D , Saginur Raphael , Zwarenstein Merrick , Taljaard Monica 
Published: July 2012

Abstract
This article is part of a series of papers examining ethical issues in cluster randomized trials (CRTs) in health research. In the introductory paper in this series, we set out six areas of inquiry that must be addressed if the CRT is to be set on a firm ethical foundation. This paper addresses the sixth of the questions posed, namely, what is the role and authority of gatekeepers in CRTs in health research? ‘Gatekeepers’ are individuals or bodies that represent the interests of cluster members, clusters, or organizations. The need for gatekeepers arose in response to the difficulties in obtaining informed consent because of cluster randomization, cluster-level interventions, and cluster size. In this paper, we call for a more restrictive understanding of the role and authority of gatekeepers.
Previous papers in this series have provided solutions to the challenges posed by informed consent in CRTs without the need to invoke gatekeepers. We considered that consent to randomization is not required when cluster members are approached for consent at the earliest opportunity and before any study interventions or data-collection procedures have started. Further, when cluster-level interventions or cluster size means that obtaining informed consent is not possible, a waiver of consent may be appropriate. In this paper, we suggest that the role of gatekeepers in protecting individual interests in CRTs should be limited. Generally, gatekeepers do not have the authority to provide proxy consent for cluster members. When a municipality or other community has a legitimate political authority that is empowered to make such decisions, cluster permission may be appropriate; however, gatekeepers may usefully protect cluster interests in other ways. Cluster consultation may ensure that the CRT addresses local health needs, and is conducted in accord with local values and customs. Gatekeepers may also play an important role in protecting the interests of organizations, such as hospitals, nursing homes, general practices, and schools. In these settings, permission to access the organization relies on resource implications and adherence to institutional policies.
Small incision lenticule extraction (SMILE) versus laser in-situ keratomileusis (LASIK): study protocol for a randomized, non-inferiority trial
Authors: Ang Marcus , Tan Donald , Mehta Jodhbir S 
Published: July 2012

Abstract

Background
Small incision lenticule extraction or SMILE is a novel form of ‘flapless’ corneal refractive surgery that was adapted from refractive lenticule extraction (ReLEx). SMILE uses only one femtosecond laser to complete the refractive surgery, potentially reducing surgical time, side effects, and cost. If successful, SMILE could potentially replace the current, widely practiced laser in-situ keratomileusis or LASIK. The aim of this study is to evaluate whether SMILE is non-inferior to LASIK in terms of refractive outcomes at 3 months post-operatively.

Methods/Design
Single tertiary center, parallel group, single-masked, paired-eye design, non-inferiority, randomized controlled trial. Participants who are eligible for LASIK will be enrolled for study after informed consent. Each participant will be randomized to receive SMILE and LASIK in each eye. Our primary hypothesis (stated as null) in this non-inferiority trial would be that SMILE differs from LASIK in adults (>21 years old) with myopia (> −3.00 diopter (D)) at a tertiary eye center in terms of refractive predictability at 3 months post-operatively. Our secondary hypothesis (stated as null) in this non-inferiority trial would be that SMILE differs from LASIK in adults (>21 years old) with myopia (> −3.00 D) at a tertiary eye center in terms of other refractive outcomes (efficacy, safety, higher-order aberrations) at 3 months post-operatively. Our primary outcome is refractive predictability, which is one of several standard refractive outcomes, defined as the proportion of eyes achieving a postoperative spherical equivalent (SE) within ±0.50 D of the intended target. Randomization will be performed using random allocation sequence generated by a computer with no blocks or restrictions, and implemented by concealing the number-coded surgery within sealed envelopes until just before the procedure. In this single-masked trial, subjects and their caregivers will be masked to the assigned treatment in each eye.

Discussion
This novel trial will provide information on whether SMILE has comparable, if not superior, refractive outcomes compared to the established LASIK for myopia, thus providing evidence for translation into clinical practice.

Trial registration
Clinicaltrials.gov NCT01216475.
Omentin as a novel biomarker of metabolic risk factors
Authors: Shibata Rei , Ouchi Noriyuki , Takahashi Ryotaro , Terakura Yuya , Ohashi Koji , Ikeda Nobuo , Higuchi Akiko , Terasaki Hiroko , Kihara Shinji , Murohara Toyoaki 
Published: July 2012

Abstract

Background
Omentin is an adipocytokine that is abundantly expressed in visceral fat tissue. We investigated the association of omentin with the number of metabolic risk factors.

Finding
The study population comprised 201 Japanese men who underwent annual health checkups. Plasma omentin levels were determined by enzyme-linked immunosorbent assay. We divided the subjects into 4 groups according to omentin levels. A reduction of plasma omentin levels significantly correlated with an increase in the mean number of metabolic risk factors such as increased waist circumference, dyslipidemia, high blood pressure and glucose intolerance.

Conclusions
Circulating omentin levels negatively correlated with the multiplicity of metabolic risk factors, suggesting that omentin acts as a biomarker of metabolic disorders.
Healing rates following venous surgery for chronic venous leg ulcers in an independent specialist vein unit
Authors: Thomas C A , Holdstock J M , Harrison C C , Price B A , Whiteley M S 
Published: July 2012

Objectives This is a retrospective study over 12 years reporting the healing rates of leg ulcers at a specialist vein unit. All patients presented with active chronic venous leg ulcers (clinical, aetiological, anatomical and pathological elements [CEAP]: C6) and had previously been advised elsewhere that their ulcers were amenable to conservative measures only. Method Seventy-two patients (84 limbs) were treated between March 1999 and June 2011. Patients were contacted in August 2011 by questionnaire and telephone. Of 72 patients, two were deceased and two had moved location at follow-up, so were not contactable. Fifty patients replied and 18 did not (response rate 74%), representing a mean follow-up time of 3.1 years. Results Ulcer healing occurred in 85% (44 of 52 limbs) of which 52% (27) limbs were no longer confined to compression. Clinical improvement was achieved in 98% of limbs. Conclusions This study shows that a significant proportion of ulcers currently managed conservatively can be healed by surgical intervention.
Denosumab, a RANK Ligand Inhibitor, for Postmenopausal Women with Osteoporosis
Authors: Sutton Emily E , Riche Daniel M 
Published: July 2012

OBJECTIVE: To review the evidence for use of denosumab for the treatment of postmenopausal osteoporosis. DATA SOURCES: A search of MEDLINE and EMBASE databases was conducted during January 2012, using the terms denosumab and osteoporosis, with index dates of 2000 to 2011. Additional information was gathered from Amgen and references cited in articles retrieved. STUDY SELECTION AND DATA EXTRACTION: English-language articles including clinical trials involving denosumab for treatment of osteoporosis and review articles were reviewed. Articles using denosumab in males or as treatment for conditions other than osteoporosis or osteopenia were excluded. DATA SYNTHESIS: Many clinical trials have supported the safety and efficacy of denosumab in postmenopausal women with bone loss. It has been shown to improve bone mineral density, decrease markers of bone turnover, and prevent new vertebral fractures. It shows improvement over placebo in studies and has at least similar efficacy to alendronate in measurements of bone mineral density, with less risk for osteonecrosis of the jaw and atypical fracture, but with an increased risk of infections and neoplasms. European cost-effectiveness studies have also demonstrated that denosumab is a cost-effective choice compared to risedronate and no treatment for fracture prevention for postmenopausal women with osteoporosis. CONCLUSIONS: Denosumab has demonstrated efficacy and safety as a first-line treatment for postmenopausal osteoporosis in multiple clinical trials over at least 6 years. It may be most cost-effective for women who are unable or refuse to take bisphosphonate drugs.
End anchorage and bond stress in prestressed concrete
Authors: Marshall G. 
Published: July 2012

Summary: Research into the properties and problems of prestressed concrete has been pursued for some ten years in the Civil Engineering Laboratories of Leeds University and this paper deals with the results of tests on prestressed concrete columns to find the transmission lengths required to ensure complete bond between the wires and the concrete. It is seen that the initial transmission length for 0·2 inch diameter wires stressed to 70 tons per sq. in. is about 125 diameters (25 in.) and for 0·08 inch diameter wires stressed to 100 tons per sq. in. about 60 diameter (5 in.). These values apply only if the concrete is of good quality. It is seen that bad placing can cause these transmission lengtlrs to be greatly increased. A transmission length of approximately 400 diameters was measured in badly placed concrete. It is recommended that som~ form of mechanical locking device should be used when structures of short length are to be prestressed by 0·2 in. diameter wires. The use of 0·08 in. wires eliminates any uncertainity with regard to the end anchorage.
The measurement of vibrations in freshly placed concrete
Authors: Whiffin A. C. , Morris S. A. H. , Smith R. T. 
Published: July 2012

Summary: Descriptions are given of the electronic apparatus and techniques developed at the Road Research Laboratory for measuring vibrations. The equipment had been used, in the first instance, for measuring the movements produced in freshly placed concrete by an experimental vibrator operating on the surface. Details are given of the circuits, the calibration arrangements, and the type of information obtainable.
A method, of design for shell concrete roofs using prestressed edge beams
Authors: Silvera V. M. 
Published: July 2012

Summary: In a beam provided with prestressing cables which follow a continuous curve between supports, the prestressing force resolves itself into two components: firstly, a horizontal compressive force, which remains very nearly constant throughout the span and secondly, a vertical distributed load, acting upwards and balanced by two downward reactions at the anchorages over the supports. By selecting a suitable curve for the cables, this vertical distributed load can be made uniform throughout the span: it can also be made to equal in value the uniformly distributed permanant loads acting on the beam, thereby cancelling all deflections caused by such loads. Prestressing forces are usually designed to counteract tensile stresses, the effect of such forces on the deflection being purely incidental. In the case however of thin concrete shells, the vertical prestressing forces provide an effective means of cancelling the edge disturbances caused by deflections in edge beams, thereby enabling the thin shells to be regarded as membranes wirhout any appreciable bending stresses. In the following article, an attempt is made to analyse the efreCI on thin shell structures of the prestressing forces resulting from suitable arrangement of cables. Some reference is also made 10 polygonal shell structures. Incidentally, it may be noted that the provision of curved cables inducing upward vertical loads may lead 10 reasonably economical design in other types of structure not mentioned in this article, such as continuous girders or large span rectangular slabs.
Analysis of new N-category on prognosis of oesophageal cancer with positive lymph nodes in a Chinese population
Authors: Xu Yaping , Jiang Youhua , Yu Xinmin , Chen Qixun , Zhou Xinming , Mao Weimin 
Published: July 2012

Abstract
Background. The 7th edition of the new TNM classification system for oesophageal cancer (EC) has been published. N-category is now divided into N0, N1, N2 and N3. In this study, we aimed to validate the prognostic ability of the new N classification system in EC with positive lymph nodes in a Chinese population, and evaluate whether the new N classification system can help the decision-making for postoperative adjuvant therapy.
Patients and methods. From 2002 to 2008, thoracic EC who underwent oesophagectomy were retrospectively analysed. Patients pathological stage 6th edition of the American Joint Committee on Cancer / Union International Against Cancer (AJCC/UICC) TNM classification were switched to pathological stage 7th edition for this analysis. Patients with pathological stage T1-4N1-3M0 EC were selected. Kaplan-Meier method and Cox regression analysis were employed to compare overall survival (OS).
Results. A total of 545 patients met the inclusion criteria: 346 (63.5%) received oesophagectomy alone, 199 (36.5%) received oesophagectomy and adjuvant radiotherapy, and 36.1% (197/545) received oesophagectomy and adjuvant chemotherapy. Univariate analysis and multivariate analysis revealed significant difference in OS among patients at different postoperative pN-category (p<0.001). This was also present in patients receiving postoperative radiotherapy (p<0.001) and those undergoing postoperative chemotherapy (p<0.001). There was no marked difference in OS between patients receiving postoperative adjuvant therapy and surgery alone at the same postoperative pN-category, except that postoperative radiotherapy marginally improved OS in patients with pN2 and pN3 disease.
Conclusions. Our results validated the prognostic ability of new N classification system. The N-category is an independent prognostic factor in patients with resectable thoracic EC who were positive for lymph nodes in a Chinese population. Further studies are required to clarify the role of new N classification system in the decision-making for postoperative adjuvant therapy.