bluuebunny/crossref_metadata_2025 huggingface dataset:
Preliminary findings of the effect of some atmospheric parameters on Ku-band satellite link.
Authors: Ramachandran Visagaperuman , Kumar Vickal
Published: November 2018

A four-month study of the attenuation measurement on satellite TV transmission down link is reported. The time percentage distributions of the attenuation show a fairly large month-to month variation. However, such variations seem to be closely related to the variation of the rain-rate distribution. Comparison of exceedance and the cumulative rainfall during these four months with those of the ten -year data indicates a similar variation this year. Measurements on a ?cloudy? day without any rain indicate that the attenuation by cloud is small.
A fuzzy legal reasoner for university decision support
Authors: Sharma Dharmendra , Behari Saten
Published: November 2018

Deciding on university student disciplinary cases against stipulated rules and case facts an interesting problem for artificial intelligence. Reasoning with fuzzy rules and facts adds to the problem complexity. This paper discusses the various characteristics of the problem and presents a design and an implementation of a prototype that is modeled as a fuzzy expert system. Some test results are presented and the experience gained from the project is discussed. Some future work is also suggested to further strengthen the prototype to include a formal case specification and interaction language, and the possible drawing and use of relevant information from a knowledge base of previous cases.
Practical Aspects of the Information System Reengineering
Authors: Khmelevsky Youry , Ustimenko Vasyl' A.
Published: November 2018

The information system transition from the local and client-server financial and management information systems to n-tier information system is a very painful process, especially for academic and NGOs with a limited budget for computer equipment and software modernization. If such organizations area of activities are financial and project management, integrity, consistency and security become the key factors for information system development and implementation. The article presents results of the analyses, development and implementation of n-tier Oracle-based information systems for a NGO. Organizational and management problems, current technological infrastructure, financial resources availability, software platforms and developers solutions, local and headquarter offices requirements were analyzed. The systems were developed within the following requirements: financial and management information confidentiality and appropriate availability improvement and systems integration; organizational information and procedure standards development; incomplete and inconsistent information elimination from the data flow; transparency of the projects activity for public evaluation and information technology resources utilization by the non-for-profit, academic and NGOs for the project activity within Internet components. The first system prototype was presented at the European Foundations Center (EFC) Information Technology Conference in Brussels, Belgium, 24-25 June 1999. During 2000-2001, the system was migrated into Oracle Portal environment and development process was completed.
Samoa's 102 year meteorological record and a preliminary study on agricultural product and ENSO variability
Authors: Solofa Dean , Aung Than
Published: November 2018

This paper seeks to find a relationship between the El Nino/Southern Oscillation (ENSO) variability and crop production. Precipitation and mean temperature were examined first to establish an ENSO relationship while primary sector macroeconomic and crops data were analyzed to note any significant variations in output linked to ENSO impacts of significant occurrence. Institutional strengthening and improved access to markets, both local and regional, and sector development programmes however have made this assessment difficult. Subsistence agriculture (and fisheries), said to the backbone and economic mainstay of Samoa?s primary sector, ideally the best source of ENSO impacts unfortunately remains the data poor sector.
Development of strategy for competent cell preparation and high efficiency plasmid transformation using different methods
Authors: Sharma Anubhuti , Girdhar Arushi , Srivastava Nidhi
Published: November 2018

Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible. With the recent availability of complete genomic sequences of many organisms and plants, high-throughput and cost-efficient systems for gene cloning and functional analysis are in great demand. This study compares two different methods of preparation of competent cells using two strains of E. coli DH5α and HB101. From results the most efficient strain was found DH5α for cloning as it supports blue white screening utilizing galactosidase activity. The concentration of calcium chloride is another important factor; various concentrations of CaCl2 were tried. Optimum concentration was found to be 75 mM. However PEG also has great influence on transformation efficiency, use of 40% PEG gave the best transformation efficiency. A convenient and rapid method for the genetic transformation of E. coli with appropriate plasmid is proposed which can be utilised for high efficiency transformation in normal laboratory conditions.
Antimicrobial and cytotoxic activities of marine plants and invertebrates from the coast of Espirito Santo in Vanuatu
Authors: Soapi Katy , Feussner Klaus-D. , Aalbersberg William G.
Published: November 2018

Marine invertebrates and algae collected off the coast of Espirito Santo in Vanuatu were investigated for antimicrobial and cytotoxic activities. The combined crude methanol-dichloromethane extracts from 52 sponges, 5 algae, 17 soft corals (cnidaria) and 5 other samples of various marine invertebrates were screened for cytotoxicity, antibacterial and antifungal properties. The cytotoxicity of the samples was determined using a brine shrimp lethality test and, notably, 78% of the invertebrate and algae samples showed cytotoxic activity against brine shrimps with the sponge Crella spinulata displaying the strongest activity. Antimicrobial activity was determined against three resistant bacterial strains and two fungal strains. A total of 42% of the samples tested showed antimicrobial activity against at least one of the five strains. The most potent antibacterial activities were recorded for the sponges Lamellodysidea herbacea, Phyllospongia sp., a sponge in the order Halichondrida and Hippospongia metachromia. A Theonella sp. sponge displayed the strongest antifungal activity.
First screening study of metal content in soil from a mixed waste receptacle
Authors: Chandra Shaneel , Gangaiya Philomena , Togamana Culwick , Prasad Surendra
Published: November 2018

We report the first screening study for the metals copper, zinc, lead, nickel and cadmium in the Lami municipal disposal facility, in Suva, Fiji where virtually uncontrolled dumping has been carried out for over fifty years. Soil from three parts of the facility having had different degrees of usage was analysed for a range of heavy metals, and evaluated according to international guidelines. The results show copper (100–220 mg kg–1), lead (200–500 mg kg–1) and zinc (220–350 mg kg–1) concentrations exceeded commonly used eco-toxicity threshold values (copper, 160 mg kg–1; lead, 210 mg kg–1; and zinc, 220 mg kg–1). Moreover, there were indications that considerable leaching may have been occurring for long periods of time at the site. Overall, this study shows that even in areas with little industrialization, lack of adequate waste management controls can result in unusually high levels of contamination. The results raise concerns about the wellbeing of the communities living adjacent to the facility that depend on the adjacent marine environment for subsistence.
Predicting wildfire vulnerability using logistic regression and artificial neural networks: a case study in Brazil's Federal District
Authors: de Bem Pablo Pozzobon , de Carvalho Júnior Osmar Abílio , Matricardi Eraldo Aparecido Trondoli , Guimarães Renato Fontes , Gomes Roberto Arnaldo Trancoso
Published: November 2018

Predicting the spatial distribution of wildfires is an important step towards proper wildfire management. In this work, we applied two data-mining models commonly used to predict fire occurrence – logistic regression (LR) and an artificial neural network (ANN) – to Brazil’s Federal District, located inside the Brazilian Cerrado. We used Landsat-based burned area products to generate the dependent variable, and nine different anthropogenic and environmental factors as explanatory variables. The models were optimised via feature selection for best area under receiver operating characteristic curve (AUC) and then validated with real burn area data. The models had similar performance, but the ANN model showed better AUC (0.77) and accuracy values when evaluating exclusively non-burned areas (73.39%), whereas it had worse accuracy overall (66.55%) when classifying burned areas, in which LR performed better (65.24%). Moreover, we compared the contribution of each variable to the models, adding some insight into the main causes of wildfires in the region. The main driving aspects of the burned area distribution were land-use type and elevation. The results showed good performance for both models tested. These studies are still scarce despite the importance of the Brazilian savanna.
GUV-AP: multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles
Authors: Sych Taras , Schubert Thomas , Vauchelles Romain , Madl Josef , Omidvar Ramin , Thuenauer Roland , Richert Ludovic , Mély Yves , Römer Winfried
Published: November 2018

Motivation

Giant Unilamellar Vesicles (GUVs) are widely used synthetic membrane systems that mimic native membranes and cellular processes. Various fluorescence imaging techniques can be employed for their characterization. In order to guarantee a fast and unbiased analysis of imaging data, the development of automated recognition and processing steps is required.

Results

We developed a fast and versatile Fiji-based macro for the analysis of digital microscopy images of GUVs. This macro was designed to investigate membrane dye incorporation and protein binding to membranes. Moreover, we propose a fluorescence intensity-based method to quantitatively assess protein binding.

Availability and implementation

The ImageJ distribution package FIJI is freely available online: https://imagej.net/Fiji. The macro file GUV-AP.ijm is available at https://github.com/AG-Roemer/GUV-AP.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Effect of Onset Age of Visual Deprivation on Visual Cortex Surface Area Across-Species
Authors: Andelin Adrian K , Olavarria Jaime F , Fine Ione , Taber Erin N , Schwartz Daniel , Kroenke Christopher D , Stevens Alexander A
Published: November 2018

Blindness early in life induces permanent alterations in brain anatomy, including reduced surface area of primary visual cortex (V1). Bilateral enucleation early in development causes greater reductions in primary visual cortex surface area than at later times. However, the time at which cortical surface area expansion is no longer sensitive to enucleation is not clearly established, despite being an important milestone for cortical development. Using histological and MRI techniques, we investigated how reductions in the surface area of V1 depends on the timing of blindness onset in rats, ferrets and humans. To compare data across species, we translated ages of all species to a common neuro-developmental event-time (ET) scale. Consistently, blindness during early cortical expansion induced large (~40%) reductions in V1 surface area, in rats and ferrets, while blindness occurring later had diminishing effects. Longitudinal measurements on ferrets confirmed that early enucleation disrupted cortical expansion, rather than inducing enhanced pruning. We modeled the ET associated with the conclusion of the effect of blindness on surface area at maturity (ETc), relative to the normal conclusion of visual cortex surface area expansion, (ETdev). A final analysis combining our data with extant published data confirmed that ETc occurred well before ETdev.
Multi-hop assortativities for network classification
Authors: Gutiérrez-Gómez Leonardo , Delvenne Jean-Charles
Published: November 2018

Several social, medical, engineering and biological challenges rely on discovering the functionality of networks from their structure and node metadata, when it is available. For example, in chemoinformatics one might want to detect whether a molecule is toxic based on structure and atomic types, or discover the research field of a scientific collaboration network. Existing techniques rely on counting or measuring structural patterns that are known to show large variations from network to network, such as the number of triangles, or the assortativity of node metadata. We introduce the concept of multi-hop assortativity, that captures the similarity of the nodes situated at the extremities of a randomly selected path of a given length. We show that multi-hop assortativity unifies various existing concepts and offers a versatile family of ‘fingerprints’ to characterize networks. These fingerprints allow in turn to recover the functionalities of a network, with the help of the machine learning toolbox. Our method is evaluated empirically on established social and chemoinformatic network benchmarks. Results reveal that our assortativity based features are competitive providing highly accurate results often outperforming state of the art methods for the network classification task.
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
Authors: Calus Szymon T , Ijaz Umer Z , Pinto Ameet J
Published: November 2018

Background

Amplicon sequencing on Illumina sequencing platforms leverages their deep sequencing and multiplexing capacity but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences sequencing platforms overcome this limitation, their application has been limited due to higher error rates or lower data output.

Results

In this study, we introduce an amplicon sequencing workflow, i.e., NanoAmpli-Seq, that builds on the intramolecular-ligated nanopore consensus sequencing (INC-Seq) approach and demonstrate its application for full-length 16S rRNA gene sequencing. NanoAmpli-Seq includes vital improvements to the INC-Seq protocol that reduces sample processing time while significantly improving sequence accuracy. The developed protocol includes chopSeq software for fragmentation and read orientation correction of INC-Seq consensus reads while nanoClust algorithm was designed for read partitioning-based de novo clustering and within cluster consensus calling to obtain accurate full-length 16S rRNA gene sequences.

Conclusions

NanoAmpli-Seq accurately estimates the diversity of tested mock communities with average consensus sequence accuracy of 99.5% for 2D and 1D2 sequencing on the nanopore sequencing platform. Nearly all residual errors in NanoAmpli-Seq sequences originate from deletions in homopolymer regions, indicating that homopolymer aware base calling or error correction may allow for sequencing accuracy comparable to short-read sequencing platforms.
Sodium bicarbonate catheter lock solution reduces hemodialysis catheter loss due to catheter-related thrombosis and blood stream infection: an open-label clinical trial
Authors: El-Hennawy Adel S , Frolova Elena , Romney Wesley A
Published: November 2018

Background

There is no ideal lock solution that prevents hemodialysis (HD) catheter loss due to catheter-related thrombosis (CRT) and catheter-related bloodstream infection (CRBSI). Catheter loss is associated with increased hospitalization and high inpatient costs. Sodium bicarbonate (NaHCO3) demonstrates anti-infective and anticoagulation properties with a good safety profile, making it an ideal lock solution development target.

The objective of this study was to determine the safety and efficacy of using sodium bicarbonate catheter lock solution (SBCLS) as a means of preventing HD catheter loss due to CRT and CRBSI.

Methods

The study took place in a community hospital in Brooklyn, NY, USA. All admitted patients ≥18 years of age who needed HD treatment through CVC were included in the study. 451 patients included in the study were provided SBCLS or NSCLS post-dialysis. Catheter loss due to CRT or CRBSI was evaluated over a period of 546 days.

Results

A total of 452 patients met the criteria; 1 outlier was excluded, 226 were in the NSCLS group and 225 were in the SBCLS group. There were no significant differences between groups in comorbidities at the outset. The NSCLS group had CRT and CRBSI rates of 4.1 and 2.6/1000 catheter days (CD), respectively, compared with 0.17/1000 CD for both outcomes in the SBCLS group. SBCLS patients had a significantly reduced catheter loss rate due to CRT (P < 0.0001) and CRBSI (P = 0.0004). NSCLS patients had higher odds of losing their catheter due to CRT {odds ratio [OR] 26.6 [95% confidence interval (CI) 3.57–198.52]} and CRBSI [OR 15.9 (95% CI 2.09–121.61)] during the study period.

Conclusion

The novel approach of using SBCLS was found to be safe and was statistically superior to normal saline in preventing HD catheter loss due to CRT and CRBSI. NaHCO3 solution is inexpensive, readily available in various settings and holds the potential to decrease hospitalization, length of stay and dialysis-related costs.

Trial registration

Maimonides Medical Center Investigational Review Board, Study IRB 2015-06-25-CIH. ClinicalTrials.gov identifier: NCT03627884.
TFound: A Software to Map Cis-Regulatory Elements in Yeast
Authors: Gomes-Silva Adriano , Silva-Rocha Rafael
Published: November 2018

Transcription factors (TFs) are responsible for regulating the rate of transcription of genes in all organisms. These factors can be represented computationally by position weight matrices (PWM). TFound was developed to allow the detailed visualization of predicted binding sites of transcription factors in multiple sequences based on the PWMs, by using the graphic user interface (GUI). The tool was loaded with the genome of Saccharomyces cerevisiae and PWMs from the YeTFaSCo database (http://yetfasco.ccbr.utoronto.ca/), also allowing the insertion of new sequences and PWMs. Thus, the user is allowed to load custom PWMs and genomes to perform easily mining and visualization of binding site motifs of cis-regulatory elements of interest, permitting an efficient way to inspect DNA assembly projects for complex synthetic circuits. This work describes the functionality of the current version of the tool, which is coded in Python and is freely available at the repository https://github.com/adri4nogomes/TFound.
Incremental BLAST: incremental addition of new sequence databases through e-value correction
Authors: Dash Sajal , Rahman Sarthok , Hines Heather M. , Feng Wu-chun
Published: November 2018

Motivation

Search results from local alignment search tools use statistical parameters sensitive to the size of the database. NCBI BLAST, for example, reports important matches using similarity scores and expect or e-values calculated against database size. Over the course of an investigation, the database grows and the best matches may change. To update the results of a sequence similarity search to find the most optimal hits, bioinformaticians must rerun the BLAST search against the entire database; this translates into irredeemable spent time, money, and computational resources.

Results

We develop an efficient way to redeem spent BLAST search effort by introducing the Incremental BLAST. This tool makes use of the previous BLAST search results as it conducts new searches on only the incremental part of the database, recomputes statistical metrics such as e-values and combines these two sets of results to produce updated results. We develop statistics for correcting e-values of any BLAST result against any arbitrary sequence database. The experimental results and accuracy analysis demonstrate that Incremental BLAST can provide search results identical to NCBI BLAST at a significantly reduced computational cost. We apply three case studies to showcase different use cases where Incremental BLAST can make biological discovery more efficiently at a reduced cost. This tool can be used to update sequence blasts during the course of genomic and transcriptomic projects, such as in re-annotation projects, and to conduct incremental addition of taxon-specific sequences to a BLAST database. Incremental BLAST performs (1 + δ)/δ times faster than NCBI BLAST for δ fraction of database growth.

Availability

Incremental BLAST is available at https://bitbucket.org/sajal000/incremental-blast.

Contact

sajal@vt.edu

Supplementary information

Supplementary data are available at https://bitbucket.org/sajal000/incremental-blast
Malaria-induced remodelling of the bone marrow microenvironment mediates loss of haematopoietic stem cell function
Authors: Haltalli Myriam L.R. , Watcham Samuel , Wilson Nicola K. , Eilers Kira , Lipien Alexander , Vainieri Maria L. , Ruivo Nicola , Ang Heather , Sinden Robert E. , Duffy Ken R. , Göttgens Berthold , Blagborough Andrew M. , Celso Cristina Lo
Published: November 2018

Severe infections are a major source of stress on haematopoiesis, where consequences for haematopoietic stem cells (HSCs) have only recently started to emerge. HSC function critically depends on the integrity of complex bone marrow niches, which have been shown to be altered during ageing and haematopoietic malignancies. Whether the bone marrow (BM) microenvironment plays a role in mediating the effects of infection on HSCs remains an open question. Here we used an murine model of malaria coupled with intravital microscopy, single cell RNA-Seq, mathematical modelling and transplantation assays to obtain a quantitative understanding of the proliferation dynamics of haematopoietic stem and progenitor cells (HSPCs) duringPlasmodiuminfection. We uncovered that duringPlasmodiuminfection the HSC compartment turns over significantly faster than in steady state, and that a global interferon response and loss of functional HSCs are linked to alterations in BM endothelium function and osteoblasts number. Interventions that targeted osteoblasts uncoupled HSC proliferation and function, thus opening up new avenues for therapeutic interventions that may improve the health of survivors of severe infections.
DeepCapTail: A Deep Learning Framework to Predict Capsid and Tail Proteins of Phage Genomes
Authors: Abid Dhoha , Zhang Liqing
Published: November 2018

The capsid and tail proteins are considered the main structural proteins for phages and also their footprint since they exist only in phage genomes. These proteins are known to lack sequence conservation, making them extremely diverse and thus posing a major challenge to identify and annotate them in genomic sequences. In this study, we aim to overcome this challenge and predict these proteins by using deep neural networks with composition-based features. We develop two models trained with k-mer features to predict capsid and tail proteins respectively. Evaluating the models on two different testing sets shows that they outperform state-of-the-art methods with improved F-1 scores.
High-order finite volume approximation for population density model based on quadratic integrate-and-fire neuron
Authors: Singh Paramjeet , Kumar Santosh , Koksal Mehmet Emir
Published: November 2018

Purpose

The purpose of this paper is to develop and apply a high-order numerical method based on finite volume approximation for quadratic integrate-and-fire (QIF) neuron model with the help of population density approach.

Design/methodology/approach

The authors apply the population density approach for the QIF neuron model to derive the governing equation. The resulting mathematical model cannot be solved with existing analytical or numerical techniques owing to the presence of delay and advance. The numerical scheme is based along the lines of approximation: spatial discretization is performed by weighted essentially non-oscillatory (WENO) finite volume approximation (FVM) and temporal discretization are performed by strong stability-preserving explicit Runge–Kutta (SSPERK) method. Compared with existing schemes of orders 2 and 3 from the literature, the proposed scheme is found to be more efficient and it produces accurate solutions with few grid cells. In addition to this, discontinuity is added in the application of the model equation to illustrate the high performance of the proposed scheme.

Findings

The developed scheme works nicely for the simulation of the resulting model equation. The authors discussed the role of inhibitory and excitatory parts in variation of neuronal firing. The validation of the designed scheme is measured by its comparison with existing schemes in the literature. The efficiency of the designed scheme is demonstrated via numerical simulations.

Practical implications

It is expected that the present study will be a useful tool to tackle the complex neuron model and related studies.

Originality/value

The novel aspect of this paper is the application of the numerical methods to study the modified version of leaky integrate-and-fire neuron based on a QIF neuron. The model of the current study is inspired from the base model given in Stein (1965) and modified version in Kadalbajoo and Sharma (2005) and Wang and Zhang (2014). The applicability was confirmed by taking some numerical examples.
Role of internal service quality in enhancing patient centricity and internal customer satisfaction
Authors: Prakash Gyan , Srivastava Shefali
Published: November 2018

Purpose

The purpose of this paper is to identify the antecedents and outcomes of internal service quality (ISQ) in a health-care environment. The relationships among the heterogeneous health-care environment, coordinated care, perceived organisational support (POS), ISQ, internal customer satisfaction and patient-centred care were explored.

Design/methodology/approach

Based on a review of the literature, a structural model was developed. A 37-item questionnaire was circulated among service providers in the health-care system, including doctors, nurses and system staff, all over India. The random sampling method was adopted to collect data. A total of 238 valid responses were received. The data were analysed using structural equation modelling.

Findings

The results show that the heterogeneous environment, coordinated care and POS act as antecedents of ISQ, which drives internal customer satisfaction and patient centricity in health care.

Research limitations/implications

The paper contributes to the health-care literature by identifying the antecedents and consequences of ISQ and developing a structural relationship among ISQ, the heterogeneous health-care environment, coordinated care, POS, internal customer satisfaction and patient-centred care.

Practical implications

Hospital administrators may use various constructs of POS, ISQ and coordinated care to measure process and employee performance, which may aid the design of appropriate processes and improve employee selection. The constructs of patient centricity and internal customer satisfaction may be used as benchmarking tools to facilitate the formulation of immediate corrective actions and policies for future courses of action.

Social implications

This paper highlights how patient centricity may be achieved by focussing on ISQ, coordinated care processes and a facilitative internal environment. This understanding may aid the design of processes that in turn deliver health as a social good in an effective manner.

Originality/value

This paper extends past research on ISQ by showing that ISQ affects internal customer satisfaction and, in turn, the quality of service delivery in the system. In the health-care context, heterogeneity in patient needs, coordinated care and organisational support play crucial roles in determining ISQ, which in turn influences the level of patient-centred care.
Effect of thermal radiation on engine oil nanofluid flow over a permeable wedge under convective heating
Authors: Kotha Gangadhar , Kukkamalla Keziya , Ibrahim S.M.
Published: November 2018

Purpose

The purpose of this paper is to examine the magneto hydrodynamic flow and heat transfer of nanofluids over a permeable wedge based on engine oil which is under the effects of thermal radiation and convective heating.

Design/methodology/approach

The equations governing the flow are transformed into differential equations by applying similarity transformations. Keller box method is used to bring out the numerical solution.

Findings

The discovery interprets that temperature as well as the velocity of Ag-engine oil nanofluids are more noticeable than Cu-engine oil nanofluids. Thermal boundary layer increases for radiation parameter as well as Biot number. Fluctuations of co-efficient of drag skin friction as well heat transfer rate at the wall are also tested.

Originality/value

Till now, no numerical studies are reported on the heat transfer enhancement of the permeable wedge under thermal radiation on engine oil nanofluid flow by considering convective heating.
Differential clustering of fecal and mucosa‐associated microbiota in ‘healthy’ individuals
Authors: Carstens Adam , Roos Annika , Andreasson Anna , Magnuson Anders , Agréus Lars , Halfvarson Jonas , Engstrand Lars
Published: November 2018

Objective

Fecal samples are often used to characterize gut microbiota. However, whether or not fecal microbiota differs from mucosa‐associated microbiota remains largely unknown. This may be specifically relevant in conditions that are characterized by complex mucosal microbe–host interactions, such as Crohn’s disease. We aimed to determine the degree of agreement between fecal and mucosal microbiota profiles in ‘healthy’ individuals, using two commonly used collection procedures.

Methods

The gut microbiota composition of fecal samples (sent at ambient temperature before storage at −70°C) and of colonic biopsies (obtained at endoscopy and immediately stored at −70°C) was determined by sequencing the 16S rRNA gene. Altogether 31 randomly selected ‘healthy’ individuals from the population‐based colonoscopy (Popcol) study were included.

Results

The fecal samples were characterized by a reduced degree of richness (P < 0.0001) and diversity (P = 0.016), and also differences in several phyla, including a lower relative abundance of Proteobacteria (P < 0.0001) and Verrucomicrobia (P = 0.008) than in biopsies. Only three of 30 individuals had a similar fecal and mucosal microbiota profile, based on weighted UniFrac analysis. A difference in Crohn’s disease dysbiosis‐associated bacteria was observed, including a lower relative abundance of Faecalibacterium (P = 0.004) and a higher relative abundance of Ruminococcus (P = 0.001) in feces than in biopsies.

Conclusions

The observed differences between fecal samples, transported at ambient temperature, and the colonic mucosa‐associated microbiota have implications for the interpretation of the previous literature, and may be specifically relevant to studies on Crohn’s disease.
Diverse roles of the E2/E3 hybrid enzyme UBE2O in the regulation of protein ubiquitination, cellular functions, and disease onset
Authors: Ullah Kifayat , Zubia Emmanuel , Narayan Mahesh , Yang Jing , Xu Guoqiang
Published: November 2018

The ubiquitin‐proteasome system is an important regulatory machinery involved in proteostasis and cellular signaling. Proteins are ubiquitinated via the concerted action of E1 ubiquitin‐activating enzymes, E2 ubiquitin‐conjugating enzymes, and E3 ubiquitin ligases. Although most of the studies to date focus on the significance of E3 ubiquitin ligases in disease development and therapeutic treatment, recent discoveries suggest that E2 ubiquitin‐conjugating enzymes might also be potential drug targets. The ubiquitin‐conjugating enzyme E2 O (UBE2O), an E3‐independent E2 (i.e. an E2/E3 hybrid enzyme), can directly mediate the ubiquitination of many substrates. These include 5′‐AMP‐activated protein kinase catalytic subunit α2 (AMPKα2), tumor suppressor ubiquitin carboxyl‐terminal hydrolase BAP1, mixed‐lineage leukemia (MLL) protein, SMAD family member 6 (SMAD6), transcription factor c‐Maf and aryl hydrocarbon receptor nuclear translocator‐like protein 1 (ARNTL or BMAL1), and free ribosomal proteins, which are ubiquitinated in distinct ways, thereby associating UBE2O with a variety of biological functions. Furthermore, UBE2O is frequently amplified or mutated in multiple cancers, and its high expression is associated with low survival rate of gastric, lung, breast, and prostate cancer patients. However, the molecular mechanisms by which UBE2O contributes to tumor initiation and progression are not fully elucidated. This review focuses on emerging insights from genetics, biochemistry, and cell biology to explore the biological functions of UBE2O and its therapeutic potential.
Effect of silica on the ZnS nanoparticles for stable and sustainable antibacterial application
Authors: Kumar Sunil , Jain Anita , Panwar Sanjay , Sharma Indu , Jeon Hee Chang , Kang Tae Won , Choubey Ravi Kant
Published: November 2018

Silica‐capped Zinc Sulfide (ZnS) nanoparticles were synthesized for the use as stable and long‐term antibacterial agents because silica is a very important component in food packaging applications for moisture absorption in tune with its property of biocompatibility and water solubility. The variation in morphological and optical properties of core‐shell nanostructures was studied by changing the concentration of silica in a core‐shell combination. The structural and morphological properties of silica‐capped ZnS have been observed by powder X‐ray diffraction (PXRD) and transmission electron microscopic (TEM) studies, respectively. Uncapped ZnS nanoparticles with particle size of 2‐4 nm in a highly agglomerated state have been observed from TEM, which shows that they can be used only for short‐term antibacterial action despite its excellent zone of inhibition (antibiotic sensitivity). However, ZnS/SiO2 core‐shell nanostructures are highly monodisperse in nature and the particle size increases up to 5‐8 nm with increase in silica concentration. Fourier‐transform infrared spectroscopy (FTIR) analysis confirms the formation of silica capping on the ZnS surface. The inhibition of defect‐related emission by silica capping in energy‐resolved photoluminescence studies also shows the formation of very stable ZnS nanoparticles. To study the antibacterial properties of the pure and silica‐capped ZnS nanostructure the agar‐well diffusion method was employed against both gram‐positive and gram‐negative bacteria. The obtained results indicate that pure ZnS shows excellent antibacterial action but it can last only for few days.
Carboxytherapy: Controls the inflammation and enhances the production of fibronectin on wound healing under venous insufficiency
Authors: Brochado Themis M. M. , de Carvalho Schweich Laynna , Di Pietro Simões Naudimar , Oliveira Rodrigo J. , Antoniolli‐Silva Andréia C. M. B.
Published: November 2018

To examine the influence of carboxytherapy on wound healing under venous insufficiency, full‐thickness excisional wounds were created on Wistar rats. We used three groups with 32 rats each: Group (I): daily cleaning with 0.9% saline solution; Group Sulfadiazine (II): 1% silver sulfadiazine; and Carboxytherapy (III): subcutaneous application of 0.3 mL of carbon dioxide. The predetermined periods of analysis were the 3rd, 7th, 14th, and 30th day. The slides were stained with haematoxylin and eosin and Picrosirius red and submitted for immunohistochemistry. Groups II and III presented a statistically significant decrease in relation to the presence of neutrophilic and lymphocytic infiltrates. The presence of collagen significant increased in groups II and III. However, group III presented better organisation. Only group I maintained the neovascularisation until the 30th day. The new epithelium statistically significantly increased in groups II and III. On immunohistochemistry, regarding fibronectin expression, only group III demonstrated a statistically significant increase since the beginning of the healing process. Thus, the use of carboxytherapy promotes the formation of a tissue better structured and that may be an important resource for the treatment of wounds under venous insufficiency, especially those of recurrent re‐openings.
Characteristics of extruded cereal snacks enriched by an addition of freeze‐dried red and purple potatoes
Authors: Gumul Dorota , Ziobro Rafał , Korus Jarosław , Kruczek Marek , Árvay Július
Published: November 2018

The aim of the study was to analyze polyphenolic compounds and carotenoids present in maize extrudates with different share (5; 15 and 25%) of freeze‐dried red and purple potatoes of varieties—Magenta Love (red variety) and Blue Star (purple variety), and to determine their antioxidant capacity, and indicate which of the above varieties would be more favorable for enrichment of maize snacks with health‐promoting compounds. Moreover, the analysis of basic nutrients and physical properties of extrudates with the share of freeze‐dried red/purple potatoes was done. High level of bioactive polyphenols in freeze‐dried red and purple potatoes allowed the production of innovative maize snacks with elevated antioxidant potential. The best results were obtained with 25% levels of freeze‐dried Magenta Love potatoes in the extrudates. Such addition also allowed maintenance of physical properties of extrudates and improvement of nutritional value and pro‐health value.

Practical applications

Extrusion is a continuous, comprehensive and efficient industrial technology. The process is increasingly being used in food technology, as it gives the opportunity to obtain products of the profiled nutritional and dietary quality. Red and purple potatoes are rich in bioactive compounds from the group of polyphenols, which could improve quality and pro‐health value of extruded products. It seems that their use for the manufacture of extruded maize snacks could enrich these products in bioactive components, and on the other hand extend the portfolio of gluten‐free products available for patients with celiac disease.
Molecular processes in iron and zinc homeostasis and their modulation for biofortification in rice
Authors: Kawakami Yuta , Bhullar Navreet K.
Published: November 2018

More than a billion people suffer from iron or zinc deficiencies globally. Rice (Oryza sativa L.) iron and zinc biofortification; i.e., intrinsic iron and zinc enrichment of rice grains, is considered the most effective way to tackle these deficiencies. However, rice iron biofortification, by means of conventional breeding, proves difficult due to lack of sufficient genetic variation. Meanwhile, genetic engineering has led to a significant increase in the iron concentration along with zinc concentration in rice grains. The design of impactful genetic engineering biofortification strategies relies upon vast scientific knowledge of precise functions of different genes involved in iron and zinc uptake, translocation and storage. In this review, we present an overview of molecular processes controlling iron and zinc homeostasis in rice. Further, the genetic engineering approaches adopted so far to increase the iron and zinc concentrations in polished rice grains are discussed in detail, highlighting the limitations and/or success of individual strategies. Recent insight suggests that a few genetic engineering strategies are commonly utilized for elevating iron and zinc concentrations in different genetic backgrounds, and thus, it is of great importance to accumulate scientific evidence for diverse genetic engineering strategies to expand the pool of options for biofortifying farmer‐preferred cultivars.
Femoral Neuropathy Following Transfemoral Neuroendovascular Procedures. An Analysis of a Prospective Registry
Authors: Qureshi Adnan I. , Babar Sehar , Kherani Danish , Saleem Muhammad A. , Qi Laura , Wallery Shawn S. , Raja Faisal M.
Published: November 2018

BACKGROUND AND PURPOSE

Although femoral neuropathy is recognized as an adverse consequence following transfemoral neuroendovascular procedures, no reliable estimates are available. We analyzed data from a prospective registry to ascertain the frequency and characteristics of femoral neuropathy following transfemoral neuroendovascular procedures.

METHODS

Consecutive patients who underwent neuroendovascular procedures through the transfemoral route were included. Detailed assessment was performed if any patient reported occurrence of sensory or motor symptoms in the femoral or lower extremity region including neurological examination (sensory/motor deficits) and femoral region ultrasound.

RESULTS

Femoral neuropathy was diagnosed following 4 of 270 neurovascular procedures with an occurrence rate of 1.5% (95% confidence intervals = .4‐3.7%). The symptoms were exclusively sensory without any motor involvement. The femoral neuropathy appeared to involve anterior femoral cutaneous nerves in all and medial cutaneous branches in 2 patients, and more than one nerve distribution in 1 patient in whom lateral cutaneous nerve appeared to be involved. All patients reported resolution of symptoms within a period ranging from 1 week to 2 months. No local hematoma or arterial pseudoaneurysm was identified at femoral region ultrasound.

CONCLUSIONS

Femoral neuropathy is a rare occurrence following transfemoral neuroendovascular procedures and it usually occurs with pure sensory manifestations with complete resolution.
Ultrasound, Clinical, and Electrophysiological Findings in Persistent Carpal Tunnel Syndrome
Authors: Kerasnoudis Antonios , Barmpalios Georgios , Ntasiou Panagiota , Lakkos Thomas , Venouziou Aaron
Published: November 2018

BACKGROUND AND PURPOSE

We present the clinical, electrophysiological, and nerve ultrasound findings in cases of persistent carpal tunnel syndrome (PCTS).

METHODS

Eighteen PCTS patients underwent evaluation with the Boston Carpal Tunnel Syndrome Questionnaire (BCTSQ), electrophysiology, and nerve ultrasound with a mean of 3.5 months (SD ± 1.4) after open surgery.

RESULTS

PCTS patients showed a mean symptom severity scale score of 3.1 (SD ± 1.1) and functional severity scale score of 3.2 (SD ± 0.9) in BCTSQ. Nerve conduction studies revealed axonal affection of the median nerve in 13/18 patients, ultrasound showed disturbed echogenicity in all patients, a pathological wrist to forearm ratio in 16/18 patients, and cross‐sectional area enlargement of the median nerve at the distal wrist crease in 12/18 patients. Ultrasound documented scar tissue formation (in 12/18 patients), incomplete release of retinaculum flexorum (in 4/18 patients), and neuroma of the median nerve (in 2/18 patients) as PCTS cause.

CONCLUSION

Our data show significant functional disability, axonal nerve damage, and scar tissue formation as common PCTS causes.
Clustering Multiple Time Series with Structural Breaks
Authors: Wang Yongning , Tsay Ruey S.
Published: November 2018

Time series clustering pattern could change over time. In this article we develop a new Bayesian approach to handle clustering analysis of multiple time series with structural breaks. The number of breaks is treated as a random variable, with group membership and group‐specific parameters allowed to change on these breaks. Group‐specific parameters in each regime can be integrated analytically, so we only have a small number of parameters to be handled by posterior simulation. We further discuss prediction, identification, clustering, and detection of the number of groups. Using Monte Carlo simulation, we document the performance of the proposed approach in statistical efficiency, forecasting, and detection of the structural breaks. An application on quarterly industrial production growth rates of 21 countries links regimes to historical business cycles. Prediction performance and economic gains are illustrated based on the proposed method.
The Erosion of FAPE for Students with LD
Authors: Calhoon Mary Beth , Berkeley Sheri , Scanlon David
Published: November 2018

How schoolsfulfill Free and Appropriate Public Education (FAPE) requirements has evolved. Decades of general and special education reforms have led to dramatic increases in expectations for students in special education to be included in the general education classroom and curriculum and to achieve to the same high standards as their general education peers. Students with learning disabilities (LD) in particular are impacted by these reforms. The notion of their individually‐appropriate education has been slowly eroded as limitations in special education practices and the goals of education reform have been responded to. As special education intentions and practices advance, stakeholders have a responsibility to protect the FAPE of students with LD, to ensure meeting these students’ individualized learning needs.
Comparison of space‐plant versus sward plot selection in thickspike wheatgrass (Elymus lanceolatus)
Authors: Robins Joseph G. , Jensen Kevin B.
Published: November 2018

Thickspike wheatgrass (Elymus lanceolatus [Scribn. & J.G. Sm.] Gould) is an important native perennial grass species used for rangeland revegetation in North America. Plant breeding efforts relying on space‐plant evaluations have resulted in limited improvement in this species. The purpose of this study was to characterize the performance of thickspike wheatgrass half‐sib families under space‐plant and sward plot evaluations, estimate the correlation between measured traits in both evaluation settings, and determine the validity of selecting thickspike wheatgrass for rangeland revegetation in the nontarget environment space‐plant plots. The study included 50 thickspike wheatgrass half‐sib families and five commercial cultivars and experimental populations which were evaluated over 3 years in space‐plant and sward plot evaluations at a field site in Box Elder County, Utah, USA. Collected data included stand percentage, flag leaf height, and herbage dry mass. Narrow‐sense heritability estimates were low to moderate (h2 < 0.60) and Spearman and genetic correlation estimates among traits were also generally low to moderate. Overall, there was little evidence to suggest the use space‐plant evaluations in thickspike wheatgrass improvement programmes.
Living libraries: Nurse integration in interprofessional homeless health care team
Authors: Mariano Melanie A. , Harmon Monica J.
Published: November 2018

Background

Despite an increase in national health care service utilization, entry into the health care system remains inequitable. This disparity in health care access disproportionately affects those experiencing homelessness. Because the homeless population faces significant financial and nonfinancial barriers, health care system engagement with these individuals must be reconsidered.

Objective

This article will describe the piloting of an interprofessional model within an urban library to address barriers to health care access that homeless individuals face.

Design

The library's unique status as a community hub presents an opportunity for partnership in addressing this population's health care access issues. This community‐based model is the first recorded to utilize three distinct professions—nursing, social work, and library science—in a public library.

Results and Conclusions

The implementation of this pilot project resulted in a high retention rate of referrals to community health services for those unstably housed and facilitated a system of warm transfers. Although opportunities to improve generalizability exist, this initiative sets the stage for discussion around co‐location of health and social services in a nontraditional community‐based setting to achieve equitable access to health care.