bluuebunny/crossref_metadata_2025 huggingface dataset:
HapCol: accurate and memory-efficient haplotype assembly from long reads
Authors: Pirola Yuri , Zaccaria Simone , Dondi Riccardo , Klau Gunnar W. , Pisanti Nadia , Bonizzoni Paola
Published: August 2015

Motivation:  Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent of ‘future-generation’ sequencing technologies and their capability to produce long reads at increasing coverage. Existing methods are not able to deal with such data in a fully satisfactory way, either because accuracy or performances degrade as read length and sequencing coverage increase or because they are based on restrictive assumptions.

Results: By exploiting a feature of future-generation technologies—the uniform distribution of sequencing errors—we designed an exact algorithm, called HapCol, that is exponential in the maximum number of corrections for each single-nucleotide polymorphism position and that minimizes the overall error-correction score. We performed an experimental analysis, comparing HapCol with the current state-of-the-art combinatorial methods both on real and simulated data. On a standard benchmark of real data, we show that HapCol is competitive with state-of-the-art methods, improving the accuracy and the number of phased positions. Furthermore, experiments on realistically simulated datasets revealed that HapCol requires significantly less computing resources, especially memory. Thanks to its computational efficiency, HapCol can overcome the limits of previous approaches, allowing to phase datasets with higher coverage and without the traditional all-heterozygous assumption.

Availability and implementation: Our source code is available under the terms of the GNU General Public License at http://hapcol.algolab.eu/.

Contact:  bonizzoni@disco.unimib.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
glmgraph: an R package for variable selection and predictive modeling of structured genomic data
Authors: Chen Li , Liu Han , Kocher Jean-Pierre A. , Li Hongzhe , Chen Jun
Published: August 2015

Summary: One central theme of modern high-throughput genomic data analysis is to identify relevant genomic features as well as build up a predictive model based on selected features for various tasks such as personalized medicine. Correlating the large number of ‘omics’ features with a certain phenotype is particularly challenging due to small sample size (n) and high dimensionality (p). To address this small n, large p problem, various forms of sparse regression models have been proposed by exploiting the sparsity assumption. Among these, network-constrained sparse regression model is of particular interest due to its ability to utilize the prior graph/network structure in the omics data. Despite its potential usefulness for omics data analysis, no efficient R implementation is publicly available. Here we present an R software package ‘glmgraph’ that implements the graph-constrained regularization for both sparse linear regression and sparse logistic regression. We implement both the L1 penalty and minimax concave penalty for variable selection and Laplacian penalty for coefficient smoothing. Efficient coordinate descent algorithm is used to solve the optimization problem. We demonstrate the use of the package by applying it to a human microbiome dataset, where phylogeny structure among bacterial taxa is available.

Availability and implementation: ‘glmgraph’ is implemented in R and C++ Armadillo and publicly available under CRAN.

Contact:  chen.jun2@mayo.edu or hongzhe@upenn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CoD: inferring immune-cell quantities related to disease states
Authors: Frishberg Amit , Steuerman Yael , Gat-Viks Irit
Published: August 2015

Motivation: The immune system comprises a complex network of genes, cells and tissues, coordinated through signaling pathways and cell−cell communications. However, the orchestrated role of the multiple immunological components in disease is still poorly understood. Classifications based on gene-expression data have revealed immune-related signaling pathways in various diseases, but how such pathways describe the immune cellular physiology remains largely unknown.

Results: We identify alterations in cell quantities discriminating between disease states using ‘ Cell type of Disease’ (CoD), a classification-based approach that relies on computational immune-cell decomposition in gene-expression datasets. CoD attains significantly higher accuracy than alternative state-of-the-art methods. Our approach is shown to recapitulate and extend previous knowledge acquired with experimental cell-quantification technologies.

Conclusions: The results suggest that CoD can reveal disease-relevant cell types in an unbiased manner, potentially heralding improved diagnostics and treatment.

Availability and implementation: The software described in this article is available at http://www.csgi.tau.ac.il/CoD/.

Contact:  iritgv@post.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
A rapid assessment of trends in the multispecies small-scale fishery of Palamós (Catalonia, Spain)
Authors: Dimitriadis Caterina , Carranza Alvar , Vilela Raúl , Casadevall Margarida
Published: August 2015

Monitoring small-scale fisheries (SSFs) is challenging due to the limited information available and their underlying socioeconomic characteristics. This constitutes a serious impediment to assess the compliance level of Aichi Biodiversity Targets (ABT). The European Union has committed itself to include an Ecosystem Approach to Fisheries Management (EAFM) in its Common Fisheries Policy. EAFM depends on suites of indicators that track the pressure exercised, the state of the ecosystem, and the socio-economic consequences of management objectives. Therefore, The Living Planet Index (LPI) is proposed here for describing the performance of SSF towards the ABT. We show that the LPI can be reformulated to track trends in Fishing Effort (LPIFE), trends in Fish Populations (LPIFP), and both the state and trends related to the contribution of fisheries to broader society (LPIDEB). The implementation of the LPI in SSF applies several principles of the EAFM, including decentralization, fishers participation, and consideration of local knowledge. In this paper, we used 10-year daily data from the Cofradía at Palamós port, Catalonia - Spain. This is a multi-species SSF landing ca. 130 species, from which 10.9% are of special interest, being listed by the IUCN or in agreements by regional conventions. We observe a decreasing trend in the LPIFP, the LPIFE, and in the LPIDEB, including 36 species or groups, accounting for 90% of total landings, suggesting an overall decrease in the sustainability of this SSF. We conclude that use of the LPIFP is especially well suited to standardize the reporting of information for multispecies fisheries using a wide array of fishing strategies, and results strongly suggest the feasibility of using the LPI methodology to standardize reporting of any given agreed fisheries indicator in order enhance management towards the ABTs.
Merkel Cell Polyomavirus is Not Detected in Lung Adenocarcinomas by Immunohistochemistry
Authors: Trejo Bittar Humberto E. , Pantanowitz Liron
Published: August 2015

Merkel cell polyomavirus (MCPyV) is an oncogenic DNA virus that causes Merkel cell carcinoma. Recently, MCPyV has been identified in other noncutaneous tumors including lung non–small cell carcinoma. However, the true role of this virus in lung carcinogenesis is unclear. We aimed to determine the efficacy of immunohistochemistry for detecting MCPyV in a series of lung adenocarcinomas. Nuclear expression of the MCPyV large T antigen was evaluated by immunohistochemistry (CM2B4 antibody) in formalin-fixed paraffin-embedded lung adenocarcinomas of different histologic subtypes. Of a total of 90 lung adenocarcinomas that were examined, none of the tumors (0%) were positive for MCPyV T antigen expression by immunohistochemistry. These data suggest that MCPyV immunohistochemistry alone might not be a sensitive method for detection of MCPyV in lung adenocarcinomas or that these tumors do not harbor MCPyV. Further studies are needed to correlate these data with molecular studies for MCPyV DNA integration and to similarly evaluate other types of lung carcinomas.
Heat-induced Epitope Retrieval for Immunohistochemistry at High Altitude: A Quality Assurance Study
Authors: Stevens Keith A. , Kovach Charles K. , Tompkins Michael , Ruegg Patsy , Cohen Cynthia
Published: August 2015

Introduction:

Heat-induced epitope retrieval (HIER) of formalin-fixed paraffin-embedded tissues is now a standard practice in immunohistochemistry (IHC). In this study, we aimed to test the effect of altering HIER temperature on IHC staining quality at high altitude, the hypothesis being that lower HIER temperatures would result in improved staining patterns.

Materials and Methods:

In a laboratory at high altitude (Aurora, CO), we used a platform with automated onboard epitope retrieval, and systematically tested 3 different HIER temperatures (100°C, 95°C, 90°C) with 4 IHC stains that are commonly used in routine practice: CD3, Ki67, CK20, and Melan A (n=10 for each antibody/epitope retrieval temperature combination). A scoring system was devised, the slides were scored in a blinded manner, and statistical analysis was performed. For comparison, the same study was performed in a laboratory near sea level (Atlanta, GA).

Results:

At high altitude, lower HIER temperatures resulted in improved staining patterns, as quantified by stronger staining intensity and greater area of the slides stained. The scores obtained with HIER temperatures of 95°C and 90°C were higher than those obtained with HIER of 100°C, and the difference was found to be statistically significantly for some antibody/epitope retrieval temperature combinations (P<0.05). This effect was not seen in the laboratory near sea level.

Conclusions:

We show that alternate epitope retrieval recommendations are warranted for laboratories at high altitude. Furthermore, we suggest that manufactures should consider how their instruments will perform at high altitude as they further automate the process of IHC.
Implications of simplified linkage equilibrium SNP simulation
Authors: Lee Sang Hong
Published: August 2015

In a recent paper published in PNAS (Golan et al. 2014), residual maximum likelihood (REML) seriously underestimated genetic variance explained by genomewide single nucleotide polymorphism when using a case-control design. It was concluded that Haseman–Elston regression (denoted as PCGC in their paper) should be used instead of REML. Their conclusions were based on results from simplified linkage equilibrium SNP simulation (SLES), which the authors acknowledged may be unrealistic. We found that their simulation, SLES, unrealistically inflated the correlation between the eigenvectors of the genomic relationship matrix and disease status to values that are rarely observed in real data analyses. With a more realistic simulation that the authors failed to carry out (as they noted in their paper), we showed that there was no such inflated correlation between the eigenvectors of the genomic relationship matrix and disease status. Because REML uses the eigensystem of covariance structure, the inflated correlation artefactually constrained its estimates. We compared SNP-heritabilities from SLES and a more realistic simulation, showing that there was a substantial difference between the REML estimates from the two simulation strategies. Finally, we presented that there was no difference between REML and PCGC in real data analyses. This pattern from real data results differed strikingly from the pattern in the simulation study of Golan et al. One needs to be cautious of results drawn from SLES.
The role of mentoring relationships in counseling programs
Authors: Boswell Jennifer N. , Wilson Angie D. , Stark Marcella D. , Onwuegbuzie Anthony J
Published: August 2015

Purpose

– The goals of a mentoring relationship are important to the development of mentees. The purpose of this paper is to focus on the specific needs of students and junior faculty in counseling programs.

Design/methodology/approach

– The authors used a psychological phenomenological research approach to understand the role and significance of a mentor and the mentoring relationship. In this qualitative research study, pre-tenured faculty, doctoral- and master’s-level students in counselor education programs in the USA were interviewed (n=30), to explore the mentorship needs.

Findings

– In the study, the authors identified 28 codes that emerged from the participants’ lived experiences, which then were organized into seven meta-codes. The seven meta-codes were: relationship between mentor and mentee; communication style or patterns; preferred gender of mentor; introduction to the relationship; mentee needs; mentee benefits; and experiences as a mentee.

Originality/value

– In the paper, the authors sought to explore the mentoring needs of students and junior faculty in counselor education programs and how these needs can begin to be addressed effectively.
STEM mentoring and the use of the principles of Adult Mentoring Inventory
Authors: Feldhaus Charles , Bentrem Kristin
Published: August 2015

Purpose

– The purpose of this convergent parallel mixed methods paper is to explore the mentoring experience within the context of a science, technology, engineering and math (STEM) specific mentoring program for urban, at risk, high school youth, using the Principles of Adult Mentoring Inventory (PAMI) as an instrument that modeled effective mentoring behavior. The study took place at a large, urban, Midwestern university in the USA.

Design/methodology/approach

– A research design was developed and both quantitative and qualitative data were collected in parallel, analyzed separately and then merged to determine results. The PAMI instrument that measures six constructs of mentor effectiveness was administered to STEM mentors as a pre/post-test and enabled researchers to collect quantitative data. Researchers used focus groups to collect qualitative data in the form of transcribed interviews. This study sought to inform STEM mentoring program development by collecting both qualitative and quantitative data independently and simultaneously in order to confirm findings. Researchers used a convergent parallel mixed methods design to first, reinforce and corroborate the findings given the small sample size (n=8); second, minimize alternative interpretations from data gathering and analysis, third, make clear various factors contributing to the effectiveness of STEM mentoring.

Findings

– Throughout the mentoring experience, mentor perceptions of their mentoring abilities increased to be in the “more highly effective” range within PAMI. In five of the six constructs the results indicated mentors scored lower on the pre-test than they did on the post-test of the PAMI, meaning mentor perceptions of mentoring abilities improved overall during the course and the mentoring experience. Common themes from both quantitative and qualitative results were developed, are discussed using the PAMI constructs as organizers, and include communication, information, and gender differences.

Originality/value

– This study added to the dearth of literature and investigations surrounding STEM mentoring. Many studies have concentrated primarily on mentoring but few have investigated the concept of STEM mentoring program best practices. The results of this study provided a multidimensional look at STEM mentoring programs that impact urban, at risk, high school youth.
Healthcare succession management: are we ready?
Authors: VanVactor Jerry D.
Published: August 2015

Purpose

– The purpose of this paper is to present practicing management professionals with a model related to succession management and planning.

Design/methodology/approach

– Using a review of existent literature, this work examines and expounds upon the impact of succession management and planning as a potential genesis of, and an opportunity to mitigate, organizational problems related to senior executive turnover.

Findings

– This manuscript presents a succession management and planning model for practicing professionals that is based on three key tenets: first, a plan (of some sort) is necessary for corporate resilience and sustainability; second, an organization has in inherent responsibility and need to plan for replacements and prioritize allocation of resources; and third, succession management planning aids in the establishment of organizational resilience and stability amid contingencies.

Practical implications

– This work examines how, ultimately, succession management and planning is a means to risk/crisis management aimed at reducing gaps and associated problems related to changes among human capital distribution.

Social implications

– While this work is written with emphasis placed upon managing transition among healthcare organizations and personnel, the information is equally relevant and applicable to a broader audience. In an applied sense, this model provides management professionals with concepts related to orchestrating change at both the individual and organizational levels.

Originality/value

– While there is a dearth of literature examining succession management in a variety of industries, little information is directed specifically toward healthcare. This manuscript provides concepts related to effective risk mitigation via defined succession management and planning.
Evaluation of dimensional accuracy and material properties of the MakerBot 3D desktop printer
Authors: Melenka Garrett W. , Schofield Jonathon S. , Dawson Michael R. , Carey Jason P.
Published: August 2015

Purpose

– This paper aims to evaluate the material properties and dimensional accuracy of a MakerBot Replicator 2 desktop 3D printer.

Design/methodology/approach

– A design of experiments (DOE) test protocol was applied to determine the effect of the following variables on the material properties of 3D printed part: layer height, per cent infill and print orientation using a MakerBot Replicator 2 printer. Classical laminate plate theory was used to compare results from the DOE experiments with theoretically predicted elastic moduli for the tensile samples. Dimensional accuracy of test samples was also investigated.

Findings

– DOE results suggest that per cent infill has a significant effect on the longitudinal elastic modulus and ultimate strength of the test specimens, whereas print orientation and layer thickness fail to achieve significance. Dimensional analysis of test specimens shows that the test specimen varied significantly (p
<
0.05) from the nominal print dimensions.

Practical implications

– Although desktop 3D printers are an attractive manufacturing option to quickly produce functional components, this study suggests that users must be aware of this manufacturing process’ inherent limitations, especially for components requiring high geometric tolerance or specific material properties. Therefore, higher quality 3D printers and more detailed investigation into the MakerBot MakerWare printing settings are recommended if consistent material properties or geometries are required.

Originality/value

– Three-dimensional (3D) printing is a rapidly expanding manufacturing method. Initially, 3D printing was used for prototyping, but now this method is being used to create functional final products. In recent years, desktop 3D printers have become commercially available to academics and hobbyists as a means of rapid component manufacturing. Although these desktop printers are able to facilitate reduced manufacturing times, material costs and labor costs, relatively little literature exists to quantify the physical properties of the printed material as well as the dimensional consistency of the printing processes.
+TUO project: low cost 3D printers as helpful tool for small communities with rheumatic diseases
Authors: Ostuzzi Francesca , Rognoli Valentina , Saldien Jelle , Levi Marinella
Published: August 2015

Purpose

– This paper aims to present a pilot study’s aims to identify opportunities and limits deriving from the use of low-cost 3D printing (3DP), fused deposition modelling (FDM), open-source technologies in co-design and co-production processes involving persons with rheumatic diseases (RDs).

Design/methodology/approach

– In the paper, the authors outline why the use of low-cost, entry-level FDM can be meaningful for this scenario, implying a complete sharing of the design and the production phases of small assistive devices. The +TUO process is composed of several stages, among which the generative session represents the core.

Findings

– This study highlights as the introduction of this low-cost technology in co-generative processes with people with RDs is a real challenge that can lead to new products and solutions, and that can sustain a social and local manufacturing approach for people facing a specific disablement.

Research limitations/implications

– This research is a first step of a broader research, new researches are going to explore further details related with the technology and of the adopted method.

Practical implications

– Involving actively, the end user during the creation process can bring advantages such as meeting more precisely their needs and create innovative products, as shown in the text.

Social implications

– For people living with RDs, an occupation is important to sustain a process of empowerment. Adopting assistive devices supports daily activities and facilitates the occupation.

Originality/value

– +TUO is a pilot study that explore a topic already discussed in the scientific arena, without focusing on the specific use of low-cost 3DP technologies.
An assessment of implementation of entry-level 3D printers from the perspective of small businesses
Authors: Conner Brett P. , Manogharan Guha P. , Meyers Kerry L.
Published: August 2015

Purpose

– The purpose of this paper is to examine the implementation of entry-level printers in small businesses and education to identify corresponding benefits, implications and challenges.

Design/methodology/approach

– Data were collected from four small businesses in northeast Ohio through survey- and interview-based feedback to develop an understanding of their use of entry-level 3D printing. Three businesses are representative of typical manufacturing-related small companies (final part fabrication-, tooling- and system-level suppliers) and the fourth company provides manufacturing-related educational tools. Corresponding learning from implementation and outcomes are assessed.

Findings

– Adoption of 3D printing technology was enabled through hands-on experience with entry-level 3D printers, even with their shortcomings. Entry-level 3D printing provided a workforce development opportunity to prepare small businesses to eventually work with production grade systems.

Originality/value

– This paper details industry-based findings on venturing into commercializing 3D printing through first-hand experiences enabled by entry-level 3D printing.
Entanglements of Periphery and Informality in Mexico City
Authors: Gilbert Liette , De Jong Feike
Published: August 2015

Mexico City is a well‐known case of urban expansion. Most of the growth has been in its peripheries, occurring during two phases of housing privatization: a predominantly self‐built urbanization by residents establishing irregular settlements (starting in the 1930s); and a relatively recent surge of mass‐produced small‐scale single‐family housing built by state‐sponsored development companies (underway since the year 2000). Informality, we argue, should not be understood as a mode of housing production setting in opposition self‐build practices against industry‐led and/or state‐sponsored processes, but rather as a dialectical urbanization logic shaped by the entanglements of in/formal processes in governance practices, land privatization and regularization, and urban infrastructure and services deficits. We are particularly interested in a dominant narrative whereby the embeddedness of informality is constantly underplayed and irregular settlements are cast as a residual category, a problem to tolerate or in need of intervention, or the inevitable combination of demographic growth and housing shortage, rather than the direct outcome of urban policies and development processes. Conversely, recent housing policy in Mexico is officially narrated as an economic stimulus, a means to control and order (irregular) urban expansion, and an impulse to democratize homeownership. Our discussion of the entanglements of informality in Mexico City is based on an extended literature review of academic articles and official reports (predominantly in English), supplemented by a series of street and neighborhood explorations (in the summers of 2012 and 2013) across the metropolis.
Motor development in children prenatally exposed to selective serotonin reuptake inhibitors: a large population‐based pregnancy cohort study
Authors: Handal M , Skurtveit S , Furu K , Hernandez‐Diaz S , Skovlund E , Nystad W , Selmer R
Published: August 2015

Objectives

To estimate the association between prenatal exposure to selective serotonin reuptake inhibitors (SSRIs) and motor development in children considering the effect of maternal symptoms of anxiety and depression before, during and after pregnancy.

Design

Population‐based prospective pregnancy cohort study.

Setting

The Norwegian Mother and Child Cohort study (MoBa) (1999–2008).

Population

A total of 51 404 singleton pregnancies.

Methods

Self‐reported use of SSRIs was collected for the 6 months before pregnancy and prospectively during pregnancy. We used ordinal logistic regression as the statistical analysis.

Main outcome measures

Motor development was assessed by maternal reports of fine and gross motor development at child age 3 years by items from the Ages and Stages Questionnaire (ASQ). The maternal ASQ scores were compared with data from a MoBa sub‐study where clinicians assessed motor development with the Gross and Fine Motor Mullen scales of early learning.

Results

In all 381 women (0.7%) reported use of SSRIs during pregnancy, of these 159 reported on at least two questionnaires (prolonged use). Prolonged SSRI exposure was associated with a delay in fine motor development, odds ratio 1.42 (95% CI 1.07–1.87) compared with no SSRI exposure, after adjusting for symptoms of anxiety and depression before and during pregnancy. Severity of maternal depression seemed to explain the association only partially. Stratifying on depression after pregnancy had no impact on the estimated effect of SSRIs.

Conclusions

Prolonged prenatal exposure to SSRIs was weakly associated with a delayed motor development at age 3 years, but not to the extent that the delay was of clinical importance.

Tweetable abstract

Long‐term prenatal SSRI exposure is weakly associated with delayed motor development independent of depression.
Assessing the damage control resuscitation: Development, drivers and direction
Authors: Quinn David , Frith Daniel
Published: August 2015

Damage control resuscitation (DCR) has become a more widely adopted acute management strategy over the past decade. A cornerstone of this strategy is the performance of an initial limited surgical intervention for the control of active bleeding and contamination. This technique is indicated where significant physiological compromise exists and immediate surgical intervention is required. This damage control surgery itself is completed judiciously to allow a period of resuscitative stabilisation before later definitive surgical solutions. This discussion describes the three further principles of DCR and then explores the rationale and drivers behind the development of this approach.
Review article: Quality of follow‐up care for anaphylaxis in the emergency department
Authors: Burnell Fiona J , Keijzers Gerben , Smith Pete
Published: August 2015

The prevalence of allergic disorders is rising, with a corresponding increase in patients presenting to an ED with anaphylaxis. Appropriate follow up is required for patients with anaphylaxis. We reviewed two potential performance indicators for the quality of post‐discharge care: (i) the rate of self‐injectable adrenaline prescription; and (ii) the referral rate for follow‐up care with allergy specialists. A search of Cochrane Library, PubMed and Google Scholar was performed using the following initial search string: anaphylaxis and ‘emergency department’. We considered any (interventional or observational design) study assessing post‐discharge care in anaphylaxis, measured by either adrenaline self‐injection prescription or allergist referral. Subjects were patients with (suspected) anaphylaxis or severe allergic reaction, with no age limit. This review summarises findings from 16 relevant papers, all retrospective analyses of post‐discharge care for anaphylaxis. Weighted arithmetic means were calculated for rates of prescription of adrenaline auto‐injector and referral to an allergist following admission to an ED in patients with (suspected) anaphylaxis or severe allergic reaction. Prescription rates for self‐injected adrenaline at the time of discharge following anaphylaxis varied from 0% to 68%, with a mean of 44%. Allergist referral rates ranged from 0% to 84%, with a mean of 33%. This review demonstrates that there is room for improvement in post‐discharge care for patients who present to the ED with an anaphylactic reaction.
Probiotic Bacillus spp. in Soy‐Curd: Nutritional, Rheological, Sensory, and Antioxidant Properties
Authors: Shobharani P. , Prakash Maya , Halami Prakash M.
Published: August 2015

The focus of this study was to coculture probiotic Bacillus spp. with dairy starter cultures namely, Streptococcus thermophilus and Lactobacillus bulgaricus for enhanced nutritional properties of soy‐curd. Subsequently, rheological, sensory, and antioxidant properties of soy‐curd along with mineral as well as fatty acid composition were analyzed. Data revealed an increase in the cell viability of probiotic Bacillus spp. on coculturing rather than as mono‐culture. Proximate analysis showed higher nutritional value along with increased trace elements. UFA/SFA ratio, rheology, and sensory properties of probiotic soy‐curd were in the acceptable range. Probiotic soy‐curd showed higher antioxidant activity as measured by the ability to scavenge free radicals. No significant difference in the overall quality within the probiotic products was observed. However, B. flexus MCC2427 cocultured product displayed slightly better attributes than other samples. In general, the results suggest that soy‐curd can be a suitable carrier for probiotic Bacillus spp. and the enhanced nutritional and antioxidant properties could be of additional advantage to combat malnutrition problem.
Surgical and medical treatment in patients with acute severe ulcerative colitis
Authors: Fornaro Rosario , Caratto Michela , Barbruni Ginevra , Fornaro Francesco , Salerno Alexander , Giovinazzo Davide , Sticchi Camilla , Caratto Elisa
Published: August 2015

Ulcerative colitis (UC) is a chronic inflammatory disease of the mucosa of the colorectum. The treatment of UC depends on the severity of symptoms and the extent of the disease. Acute severe colitis (ASC) occurs in 12–25% of patients with UC. Patients with ASC must be managed by a multidisciplinary team. Medically or surgically aggressive treatment is carried out with the final aim of reducing mortality. Intravenous administration of corticosteroids is the mainstay of the therapy. Medical rescue therapy based on cyclosporine or infliximab should be considered if there is no response to corticosteroids for 3 days. If there has been no response to medical rescue therapy after 4–7 days, the patient must undergo colectomy in emergency surgery. Prolonged observation is counterproductive, as over time it increases the risk of toxic megacolon and perforation, with a very high mortality rate. The best potential treatment is subtotal colectomy with ileostomy and preservation of the rectum. Emergency surgery in UC should not be seen as a last chance, but can be considered as a life‐saving procedure. Colectomies in emergency setting are characterized by high morbidity rates but the mortality is low.
Clinical outcomes of esophageal stents in patients with malignant esophageal obstruction according to palliative additional treatment
Authors: Kim Ji Yeon , Kim Sang Gyun , Lim Joo Hyun , Im Jong Pil , Kim Joo Sung , Jung Hyun Chae
Published: August 2015

Objective

To evaluate the efficacy and feasibility of esophageal self‐expanding metal stents (SEMS) insertion for malignant esophageal obstruction (MEO) in patients with or without additional palliative treatment.

Methods

We retrospectively reviewed the medical records of the patients with SEMS for MEO. Baseline characteristics, changes in Mellow–Pinkas dysphagia score, and adverse events were collected and compared according to the presence and absence of additional palliative treatment.

Results

Altogether 192 patients underwent 236 SEMS insertion procedures. Esophageal, gastric cardiac and lung cancers were seen in 46.4%, 33.3% and 15.1% of the patients, respectively. Their Mellow–Pinkas score significantly decreased within one week and one month after the SEMS insertion (1.66 ± 0.79 and 1.71  ±  0.87 vs 3.09  ±  0.79, respectively, P =  0.000). Complications occurred in 54 (22.9%) of 236 SEMS insertion; there were 28 (11.9%) stent obstruction, 5 (2.1%) perforation (2.1%), 10 (4.2%) stent migration, 5 (2.1%) tracheoesophageal fistula, but no procedure‐related death. Most complications were managed by inserting additional SEMS. The risk of stent obstruction was significantly higher in uncovered stents than in covered SEMS (OR 3.56, 95% CI 1.39–9.12, P = 0.006). Mean duration to the development of complications was 74.8 ± 111.1 days. Overall survival (169.0 ± 127.8 days vs 96.4 ± 90.6 days, P = 0.000) and stent patency (143.3 ± 123.9 days vs 67.6 ± 71.3 days, P = 0.000) were significantly favorable in patients with SEMS and additional palliative treatments compared with those with SEMS alone.

Conclusion

SEMS insertion is effective and safe for treating MEO, and additional palliative treatment might lengthen stent patency by prolonging the patient's survival.
Vitamin D deficiency in patients with intestinal malabsorption syndromes – think in and outside the gut
Authors: Margulies Samantha L , Kurian Divya , Elliott Mark S , Han Zhiyong
Published: August 2015

There is a very high prevalence of vitamin D deficiency, which is defined by a serum level of 25‐hydroxyvitamin D [25(OH)D] of lower than 20 ng/mL, in all populations of the world. Unfortunately, the prevalence of vitamin D deficiency in patients with intestinal malabsorption syndromes, including cystic fibrosis (CF), celiac disease (CD), short bowel syndrome and inflammatory bowel disease (IBD), is higher than that in the general population, indicating the presence of disease‐specific causative factors. In this review, we aimed to present clinical findings to highlight the roles of insufficient exposure to sunlight and inflammation in the development of vitamin D deficiency in patients with intestinal malabsorption syndromes. Furthermore, we aimed to present experimental evidence that supported a role of vitamin D deficiency in the pathogenesis of IBD. Finally, we reviewed clinical intervention strategies aiming to normalize vitamin D status in and even to improve the conditions of patients and to discuss certain issues that needed to be addressed in future research.
Geochemical Characteristics of Volcanic Rocks from ODP Site 794, Yamato Basin: Implications for Deep Mantle Processes of the Japan Sea
Authors: Shuangshuang CHEN , Jiaqi LIU , Zhengfu GUO , Shengsheng CHEN , Chunqing SUN
Published: August 2015

Deep mantle processes and the dynamic mechanism of magmatism in the Japan Sea Basin are important processes that have not been studied in detail. In this paper, systematic evaluation of basalt samples from the ocean drilling program Site 794 in the Japan Sea was performed, which included petrography, whole‐rock major‐ and trace‐element analysis, Sr‐Nd‐Pb isotopic composition, and electron microprobe analysis of plagioclase and clinopyroxene. These basalts belong to the tholeiitic series with porphyritic texture and massive Ca‐rich plagioclase, clinopyroxene, and minor olivine phenocrysts. The basalts are characterized as flat rare earth elements and high‐field‐strength elements with remarkably low ratios of (La/Yb)N (0.75–2.51), significant positive anomalies of Ba, Sr, and Rb and no Eu anomaly (δEu = 0.99–1.36). The samples showed relatively high 87Sr/86Sr (0.70425–0.70522), 207Pb/204Pb (15.511–15.610), and 208Pb/204Pb (38.064–38.557) values and a low 143Nd/144Nd ratio (0.51271–0.51295). The basalts from Site 794 can be divided into upper, middle, and lower volcanic rocks (UVR, MVR, and LVR) on the basis of their stratigraphic level. The MVR was geochemically derived from the depleted mantle, whereas the UVR and LVR originated from a nondepleted and relatively enriched mantle source with contributions from subducted Pacific plate fluid and sediments. Use of geothermobarometers indicates that the crystallization pressure for the UVR and LVR (6.25–11.19 kbar) was significantly higher than that of the MVR (3.48–5.84 kbar). The UVR and LVR may have been derived from the low‐degree (5%–10%) partial melting of spinel lherzolite, while the MVR originated from a shallower mantle source with a high degree (10%–20%) of partial melting. In addition, the geochemical characteristics of the samples are consistent with a younger age (13–17 Ma) and the depleted composition of the MVR and an older age (17–23 Ma) and slightly enriched composition of the UVR and LVR. Therefore, temporal changes in the mantle source from old and enriched to young and depleted and subsequently to old and nondepleted may have been associated with progressive lithospheric extension and thinning, as well as at least two episodes of diverse asthenospheric upwelling and pull‐apart tectonic motion in the Yamato Basin.
Major and Trace Elements of Magnetite from the Qimantag Metallogenic Belt: Insights into Evolution of Ore–forming Fluids
Authors: Liwen YI , Xiangping GU , Anhuai LU , Jianping LIU , Hao LEI , Zhiling WANG , Yu CUI , Hongyan ZUO , Can SHEN
Published: August 2015

Magnetite, as a genetic indicator of ores, has been studied in various deposits in the world. In this paper, we present textural and compositional data of magnetite from the Qimantag metallogenic belt of the Kunlun Orogenic Belt in China, to provide a better understanding of the formation mechanism and genesis of the metallogenic belt and to shed light on analytical protocols for the in situ chemical analysis of magnetite. Magnetite samples from various occurrences, including the ore‐related granitoid pluton, mineralised endoskarn and vein–type iron ores hosted in marine carbonate intruded by the pluton, were examined using scanning electron microscopy and analysed for major and trace elements using electron microprobe and laser ablation–inductively coupled plasma–mass spectrometry. The field and microscope observation reveals that early–stage magnetite from the Hutouya and Kendekeke deposits occurs as massive or banded assemblages, whereas late–stage magnetite is disseminated or scattered in the ores. Early–stage magnetite contains high contents of Ti, V, Ga, Al and low in Mg and Mn. In contrast, late–stage magnetite is high in Mg, Mn and low in Ti, V, Ga, Al. Most magnetite grains from the Qimantag metallogenic belt deposits except the Kendekeke deposit plot in the “Skarn” field in the Ca+Al+Mn vs Ti+V diagram, far from typical magmatic Fe deposits such as the Damiao and Panzhihua deposits. According to the (MgO+MnO)–TiO2‐Al2O3 diagram, magnetite grains from the Kaerqueka and Galingge deposits and the No.7 ore body of the Hutouya deposit show typical characteristics of skarn magnetite, whereas magnetite grains from the Kendekeke deposit and the No.2 ore body of the Hutouya deposit show continuous elemental variation from magmatic type to skarn type. This compositional contrast indicates that chemical composition of magnetite is largely controlled by the compositions of magmatic fluids and host rocks of the ores that have reacted with the fluids. Moreover, a combination of petrography and magnetite geochemistry indicates that the formation of those ore deposits in the Qimantag metallogenic belt involved a magmatic–hydrothermal process.
Ultrasound‐guided catheterisation of the subclavian vein: freehand vs needle‐guided technique
Authors: Maecken T. , Heite L. , Wolf B. , Zahn P. K. , Litz R. J.
Published: August 2015

The objective of this prospective, randomised study was to examine the impact of a multi‐angle needle guide for ultrasound‐guided, in‐plane, central venous catheter placement in the subclavian vein. One hundred and sixty patients were randomly allocated to two groups, freehand or needle‐guided, and then 159 catheterisations were analysed. Cannulation of the first examined access site was successful in 96.9% of cases with no significant difference between groups. There were three arterial punctures and no other severe injuries. Catheter misplacements did not differ between the groups. Higher success rates within the first and second attempts in the needle‐guided group were observed (p = 0.041 and p = 0.019, respectively). Use of the needle guide reduced the access time from a median (IQR [range]) of 30 (18–76 [6–1409]) s to 16 (10–30 [4–295]) s; p = 0.0001, and increased needle visibility from 31.8% (9.7%–52.2% [0–96.67]) to 86.2% (62.5%–100% [0–100]); p < 0.0001. A multi‐angle needle guide significantly improved aligning the needle and ultrasound plane compared with the freehand technique when cannulating the subclavian vein. Use of the guide resulted in faster access times and increased success at the first and second attempts.
Advantages of collecting multiple urinary iodine concentrations when assessing iodine status of a population
Authors: Samidurai AJ , Ware RS , Davies PSW
Published: August 2015

Aim

To evaluate the effect of collecting multiple (four) urine samples on the extensive variance often observed within a cohort when determining iodine status via urinary iodine concentration (UIC).

Methods

Fifty‐one children aged two to three years and thirty children aged 8–10 years participated in the study in South East Queensland, Australia. Each child's four urine samples were analysed using ammonium persulphate digestion before a Sandell–Kolthoff reaction method. Analysis of variance techniques were used to assess the effect of using multiple urine samples.

Results

The median UICs were 223.3 and 141 μg/L for two‐ to three‐year‐olds and eight‐ to 10‐year‐olds, respectively. The coefficient of variance (CV) of UIC for children aged two to three years was reduced by 35.6%, 36.5% and 39.7% when two, three and four samples were included in the adjustment, respectively. Similarly, the CV of UIC for children aged 8–10 years was reduced by 24.7%, 30.7% and 34.7%, respectively.

Conclusion

Although the practicality and cost of collecting multiple UICs need to be considered, collecting multiple UIC samples from each participant provides a more accurate reflection of a cohort iodine status.
Plasma levels of growth‐related oncogene (CXCL1‐3) associated with fibrosis and platelet counts in HCV‐infected patients
Authors: Johansson S. , Talloen W. , Tuefferd M. , Darling J. M. , Scholliers A. , Fanning G. , Fried M. W. , Aerssens J.
Published: August 2015

Background

Fibrosis progression in hepatitis C virus (HCV)‐infected patients varies greatly between individuals. Chemokines recruit immune cells to the infected liver and may thus play a role in the fibrosis process.

Aim

To investigate plasma levels of a diverse chemokine panel in relation to liver fibrosis.

Methods

African‐American and Caucasian HCV genotype 1 infected patients were treated with peginterferon (pegIFN) and ribavirin (RBV) for 48 weeks (VIRAHEP‐C cohort). Plasma levels of 13 cytokines were studied at baseline (n = 386). Subsequently, GROα levels were assessed in a sub cohort (n = 99) at baseline, and at 4 and 12 weeks after start of pegIFN/RBV treatment.

Results

Increased severity of fibrosis (Ishak fibrosis score 0–2 vs. 3–6) was associated with increased plasma IP‐10 (CXCL10) and IL‐8 (CXCL8) levels, and decreased plasma levels of the chemokine growth‐related oncogene (GRO, CXCL1‐3). Plasma GRO levels were also positively correlated with platelet counts, and were higher in African‐American as compared to Caucasian patients. In response to pegIFN/RBV treatment, GROα levels increased in Caucasian but not African‐American patients from week 4 onwards.

Conclusions

The association with severity of fibrosis and platelet count positions plasma GRO as a potential biomarker for liver fibrosis in HCV‐infected patients. The secretion of GRO by platelets may explain the correlation between GRO plasma level and platelet count. The ethnic difference in GRO levels both pre‐treatment and in response to pegIFN/RBV might be driven by a genetic polymorphism in GROα associated with higher plasma levels and more common in the African‐American population.
A Discussion on the Emergence and Development of Ancient Chinese Artificial Barium Copper Silicate Pigments from Simulation Experiments
Authors: Qin Y. , Wang Y.‐H. , Chen X. , Li H.‐M. , Li X.‐L.
Published: August 2015

The ancient Chinese barium copper silicate minerals mainly comprise Chinese purple (BaCuSi2O6) and Chinese blue (BaCuSi4O10), which were widely used from the late Warring States Period to the late Eastern Han Dynasty. In order to clarify the raw material of the pigment, a series of simulation experiments was conducted to produce Chinese purple pigment under varying mineral conditions. The minerals that we applied in the experiment were quartz as the source of silicon, malachite and copper oxide as the sources of copper, barite and witherite as the sources of barium and lead oxide as the source of lead. Simulation experiments showed that the barium copper silicate minerals and the purple pigment can be produced easily when witherite is used as the barium‐containing raw material. From the perspective of mineral resources, the birth of the ancient Chinese pigment associated with a unique barium mineral resource. The Chinese copper‐based pigments are assumed to have been developed independently and are presumably an outcome of historical developments in glazing techniques.
Repair of sacral fractures using pins and polymethylmethacrylate (six cases)
Authors: Wilson L
Published: August 2015

Case reports

Sacral fracture repair was accomplished in a cat and five dogs using a composite technique consisting of pins and polymethylmethacrylate (PMMA). In three of the cases, planned traditional iliosacral lag screw fixation was either abandoned or considered inadequate and in the other three, fracture configuration demanded an alternate repair method. All six cases healed uneventfully with no surgery‐associated complications. To the author's knowledge, the use of a composite technique has been previously described for vertebral fracture repair, but not in the stabilisation of sacral fractures. Indications for the composite technique include failed iliosacral lag screw repairs, augmentation of a tenuous repair and any sacral fracture configuration not amenable to lag screw fixation.

Conclusion

Composite repair is a versatile primary, ancillary or revision technique for sacral fracture fixation.