bluuebunny/crossref_metadata_2025 huggingface dataset:
Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Authors: Basu Swaraj , Müller Ferenc , Sanges Remo
Published: December 2019

Background

Long non-coding RNAs (lncRNA) are a major class of non-coding RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and DNA methylation. Through these mechanisms they are reported to play a role in cellular differentiation and development. They show an enriched expression in the brain where they are implicated in maintaining cellular identity, homeostasis, stress responses and plasticity. Low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncRNAs in other vertebrates. A computational evaluation of the lncRNAs through systematic conservation analyses of both sequences as well as their genomic architecture is required.

Results

Our results show that a subset of mouse candidate lncRNAs could be distinguished from random sequences based on their alignment with zebrafish phastCons elements. Using ROC analyses we were able to define a measure to select significantly conserved lncRNAs. Indeed, starting from ~2,800 mouse lncRNAs we could predict that between 4 and 11% present conserved sequence fragments in fish genomes. Gene ontology (GO) enrichment analyses of protein coding genes, proximal to the region of conservation, in both organisms highlighted similar GO classes like regulation of transcription and central nervous system development. The proximal coding genes in both the species show enrichment of their expression in brain. In summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncRNA, overlap with ESTs and proximity to genes involved in nervous system development.

Conclusions

Conservation at the sequence level can identify a subset of putative lncRNA orthologs. The similar protein-coding neighborhood and transcriptional information about the conserved candidates provide support to the hypothesis that they share functional homology. The pipeline herein presented represents a proof of principle showing that a portion between 4 and 11% of lncRNAs retains region of conservation between mammals and fishes. We believe this study will result useful as a reference to analyze the conservation of lncRNAs in newly sequenced genomes and transcriptomes.
A LDA-based approach to promoting ranking diversity for genomics information retrieval
Authors: Chen Yan , Yin Xiaoshi , Li Zhoujun , Hu Xiaohua , Huang Jimmy Xiangji
Published: December 2019

Background

In the biomedical domain, there are immense data and tremendous increase of genomics and biomedical relevant publications. The wealth of information has led to an increasing amount of interest in and need for applying information retrieval techniques to access the scientific literature in genomics and related biomedical disciplines. In many cases, the desired information of a query asked by biologists is a list of a certain type of entities covering different aspects that are related to the question, such as cells, genes, diseases, proteins, mutations, etc. Hence, it is important of a biomedical IR system to be able to provide relevant and diverse answers to fulfill biologists' information needs. However traditional IR model only concerns with the relevance between retrieved documents and user query, but does not take redundancy between retrieved documents into account. This will lead to high redundancy and low diversity in the retrieval ranked lists.

Results

In this paper, we propose an approach which employs a topic generative model called Latent Dirichlet Allocation (LDA) to promoting ranking diversity for biomedical information retrieval. Different from other approaches or models which consider aspects on word level, our approach assumes that aspects should be identified by the topics of retrieved documents. We present LDA model to discover topic distribution of retrieval passages and word distribution of each topic dimension, and then re-rank retrieval results with topic distribution similarity between passages based on N-size slide window. We perform our approach on TREC 2007 Genomics collection and two distinctive IR baseline runs, which can achieve 8% improvement over the highest Aspect MAP reported in TREC 2007 Genomics track.

Conclusions

The proposed method is the first study of adopting topic model to genomics information retrieval, and demonstrates its effectiveness in promoting ranking diversity as well as in improving relevance of ranked lists of genomics search. Moreover, we proposes a distance measure to quantify how much a passage can increase topical diversity by considering both topical importance and topical coefficient by LDA, and the distance measure is a modified Euclidean distance.
A UML profile for the OBO relation ontology
Authors: Guardia Gabriela DA , Vêncio Ricardo ZN , de Farias Cléver RG
Published: December 2019

Background

Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain.

Results

We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO).

Conclusions

The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.
Efficient calculation of steady state probability distribution for stochastic biochemical reaction network
Authors: Karim Shahriar , Buzzard Gregery T , Umulis David M
Published: December 2019

The Steady State (SS) probability distribution is an important quantity needed to characterize the steady state behavior of many stochastic biochemical networks. In this paper, we propose an efficient and accurate approach to calculating an approximate SS probability distribution from solution of the Chemical Master Equation (CME) under the assumption of the existence of a unique deterministic SS of the system. To find the approximate solution to the CME, a truncated state-space representation is used to reduce the state-space of the system and translate it to a finite dimension. The subsequent ill-posed eigenvalue problem of a linear system for the finite state-space can be converted to a well-posed system of linear equations and solved. The proposed strategy yields efficient and accurate estimation of noise in stochastic biochemical systems. To demonstrate the approach, we applied the method to characterize the noise behavior of a set of biochemical networks of ligand-receptor interactions for Bone Morphogenetic Protein (BMP) signaling. We found that recruitment of type II receptors during the receptor oligomerization by itself doesn't not tend to lower noise in receptor signaling, but regulation by a secreted co-factor may provide a substantial improvement in signaling relative to noise. The steady state probability approximation method shortened the time necessary to calculate the probability distributions compared to earlier approaches, such as Gillespie's Stochastic Simulation Algorithm (SSA) while maintaining high accuracy.
Species-level classification of the vaginal microbiome
Authors: Fettweis Jennifer M , Serrano Myrna G , Sheth Nihar U , Mayer Carly M , Glascock Abigail L , Brooks J Paul , Jefferson Kimberly K ,   Vaginal Microbiome Consortium (additional members), Buck Gregory A
Published: December 2019

Background

The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies.

Results

We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment.

Conclusions

This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.
Accelerating read mapping with FastHASH
Authors: Xin Hongyi , Lee Donghyuk , Hormozdiari Farhad , Yedkar Samihan , Mutlu Onur , Alkan Can
Published: December 2019

With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on the existence of computational techniques that can process and analyze the enormous amount of sequence data quickly and accurately. Unfortunately, the current read mapping algorithms have difficulties in coping with the massive amounts of data generated by NGS.

We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while maintaining the high sensitivity and comprehensiveness of such methods. FastHASH is a generic algorithm compatible with all seed-and-extend class read mapping algorithms. It introduces two main techniques, namely Adjacency Filtering, and Cheap K-mer Selection.

We implemented FastHASH and merged it into the codebase of the popular read mapping program, mrFAST. Depending on the edit distance cutoffs, we observed up to 19-fold speedup while still maintaining 100% sensitivity and high comprehensiveness.
Immunogenicity and cross-reactivity against Mycobacterium tuberculosis of proteoliposomes derived from Mycobacterium bovis BCG
Authors: Reyes Fátima , Tirado Yanely , Puig Alina , Borrero Reinier , Reyes Giselle , Fernández Sonsire , Pérez José Luis , Kadir Ramlah , Zayas Caridad , Norazmi Mohd Nor , Sarmiento María E , Acosta Armando
Published: December 2019

The only currently available vaccine against tuberculosis (TB) is Mycobacterium bovis Bacille Calmette-Guerin (BCG), which has inconsistent efficacy to protect against the disease in adults. M. tuberculosis (MTB) cell wall components have been implicated in the pathogenicity of TB and therefore have been a prime target for the identification and characterization of cell wall proteins with potential application in vaccine development. In this regard, proteoliposomes (PLs) derived from mycobacteria containing lipids and cell wall proteins could be potential vaccine candidates against TB. In the present study PLs derived from BCG were prepared. These homogeneous population of spherical microparticles was then immunized into Balb/c mice. Sera of immunized animals showed high IgG response and strong cross-reactivity against different MTB antigens.These results showed that BCG PLs could be potential vaccine candidates against TB.
Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA
Authors: Almagro-Moreno Salvador , Napolitano Michael G , Boyd E Fidelma
Published: December 2019

Background

Vibrio Pathogenicity Island-2 (VPI-2) is a 57 kb region present in choleragenic V. cholerae isolates that is required for growth on sialic acid as a sole carbon source. V. cholerae non-O1/O139 pathogenic strains also contain VPI-2, which in addition to sialic acid catabolism genes also encodes a type 3 secretion system in these strains. VPI-2 integrates into chromosome 1 at a tRNA-serine site and encodes an integrase intV2 (VC1758) that belongs to the tyrosine recombinase family. IntV2 is required for VPI-2 excision from chromosome 1, which occurs at very low levels, and formation of a non-replicative circular intermediate.

Results

We determined the conditions and the factors that affect excision of VPI-2 in V. cholerae N16961. We demonstrate that excision from chromosome 1 is induced at low temperature and after sublethal UV-light irradiation treatment. In addition, after UV-light irradiation compared to untreated cells, cells showed increased expression of three genes, intV2 (VC1758) , and two putative recombination directionality factors (RDFs), vefA (VC1785) and vefB (VC1809) encoded within VPI-2. We demonstrate that along with IntV2, the RDF VefA is essential for excision. We constructed a knockout mutant of vefA in V. cholerae N16961, and found that no excision of VPI-2 occurred, indicating that a functional vefA gene is required for excision. Deletion of the second RDF encoded by vefB did not result in a loss of excision. Among Vibrio species in the genome database, we identified 27 putative RDFs within regions that also encoded IntV2 homologues. Within each species the RDFs and their cognate IntV2 proteins were associated with different island regions suggesting that this pairing is widespread.

Conclusions

We demonstrate that excision of VPI-2 is induced under some environmental stress conditions and we show for the first time that an RDF encoded within a pathogenicity island in V. cholerae is required for excision of the region.
CSF from Parkinson disease Patients Differentially Affects Cultured Microglia and Astrocytes
Authors: Schiess Mya C , Barnes Jennifer L , Ellmore Timothy M , Poindexter Brian J , Dinh Kha , Bick Roger J
Published: December 2019

Background

Excessive and abnormal accumulation of alpha-synuclein (α-synuclein) is a factor contributing to pathogenic cell death in Parkinson's disease. The purpose of this study, based on earlier observations of Parkinson's disease cerebrospinal fluid (PD-CSF) initiated cell death, was to determine the effects of CSF from PD patients on the functionally different microglia and astrocyte glial cell lines. Microglia cells from human glioblastoma and astrocytes from fetal brain tissue were cultured, grown to confluence, treated with fixed concentrations of PD-CSF, non-PD disease control CSF, or control no-CSF medium, then photographed and fluorescently probed for α-synuclein content by deconvolution fluorescence microscopy. Outcome measures included manually counted cell growth patterns from day 1-8; α-synuclein density and distribution by antibody tagged 3D model stacked deconvoluted fluorescent imaging.

Results

After PD-CSF treatment, microglia growth was reduced extensively, and a non-confluent pattern with morphological changes developed, that was not evident in disease control CSF and no-CSF treated cultures. Astrocyte growth rates were similarly reduced by exposure to PD-CSF, but morphological changes were not consistently noted. PD-CSF treated microglia showed a significant increase in α-synuclein content by day 4 compared to other treatments (p ≤ 0.02). In microglia only, α-synuclein aggregated and redistributed to peri-nuclear locations.

Conclusions

Cultured microglia and astrocytes are differentially affected by PD-CSF exposure compared to non-PD-CSF controls. PD-CSF dramatically impacts microglia cell growth, morphology, and α-synuclein deposition compared to astrocytes, supporting the hypothesis of cell specific susceptibility to PD-CSF toxicity.
Comparing CenteringPregnancy® to standard prenatal care plus prenatal education
Authors: Benediktsson Ingunn , McDonald Sheila W , Vekved Monica , McNeil Deborah A , Dolan Siobhan M , Tough Suzanne C
Published: December 2019

Background

There is significant evidence to support the importance of prenatal care in preventing adverse outcomes such as preterm birth and low infant birth weight. Previous studies have indicated that the benefits of prenatal care are not evenly distributed throughout the social strata. In addition, emerging evidence suggests that among particular populations, rates of preterm birth are unchanged or increasing. This suggests that an alternate care model is necessary, one that seeks to addresses some of the myriad of social factors that also contribute to adverse birth outcomes. In previous studies, the group prenatal care model CenteringPregnancy® had been shown to reduce adverse birth outcomes, but to date, no comparison had been made with a model that included prenatal education. This study sought to investigate whether any significant difference remained within the comparison groups when both models accounted for social factors.

Methods

This analysis was based on survey data collected from a prospective cohort of pregnant women through the All Our Babies Study in Calgary, Alberta.

Results

At baseline, there were significant differences between the comparison groups in their psychosocial health, with the women in the CenteringPregnancy® group scoring higher levels of depressive symptoms, stress and anxiety. At four months postpartum, the differences between the groups were no longer significant. Conclusions: These results suggest that CenteringPregnancy® can recruit and retain a demographically vulnerable group of women with a constellation of risk factors for poor pregnancy and birth outcomes, including poverty, language barriers and poor mental health. Post program, the rates of stress, anxiety and depression were similar to other women with more social and financial advantage. These findings suggest that CenteringPregnancy® may be a community based care strategy that contributes to improved mental health, knowledge, and behaviours to optimize outcomes for mothers and children.
Efficient protein structure search using indexing methods
Authors: Kim Sungchul , Sael Lee , Yu Hwanjo
Published: December 2019

Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.
Single cell oils of the cold-adapted oleaginous yeast Rhodotorula glacialis DBVPG 4785
Authors: Amaretti Alberto , Raimondi Stefano , Sala Maurizio , Roncaglia Lucia , De Lucia Marzia , Leonardi Alan , Rossi Maddalena
Published: December 2019

Background

The production of microbial lipids has attracted considerable interest during the past decade since they can be successfully used to produce biodiesel by catalyzed transesterification with short chain alcohols. Certain yeast species, including several psychrophilic isolates, are oleaginous and accumulate lipids from 20 to 70% of biomass under appropriate cultivation conditions. Among them, Rhodotorula glacialis is a psychrophilic basidiomycetous species capable to accumulate intracellular lipids.

Results

Rhodotorula glacialis DBVPG 4785 is an oleaginous psychrophilic yeast isolated from a glacial environment. Despite its origin, the strain abundantly grew and accumulated lipids between -3 to 20°C. The temperature did not influence the yield coefficients of both biomass and lipids production, but had positive effect on the growth rate and thus on volumetric productivity of lipid. In glucose-based media, cellular multiplication occurred first, while the lipogenic phase followed whenever the culture was limited by a nutrient other than glucose. The extent of the carbon excess had positive effects on triacylglycerols production, that was maximum with 120 g L-1 glucose, in terms of lipid concentration (19 g L-1), lipid/biomass (68%) and lipid/glucose yields (16%). Both glucose concentration and growth temperature influenced the composition of fatty acids, whose unsaturation degree decreased when the temperature or glucose excess increased.

Conclusions

This study is the first proposed biotechnological application for Rhodotorula glacialis species, whose oleaginous biomass accumulates high amounts of lipids within a wide range of temperatures through appropriate cultivation C:N ratio. Although R. glacialis DBVPG 4785 is a cold adapted yeast, lipid production occurs over a broad range of temperatures and it can be considered an interesting microorganism for the production of single cell oils.
Malaria on isolated Melanesian islands prior to the initiation of malaria elimination activities
Authors:   The Pacific Malaria Initiative Survey Group (PMISG) on behalf of the Ministries of Health of Vanuatu and Solomon Islands
Published: December 2019

Background

The Australian Government's Pacific Malaria Initiative (PacMI) is supporting the National Malaria Program in both Solomon Islands and Vanuatu, complementing assistance from the Global Fund for AIDS, Tuberculosis and Malaria (GFATM). Two remote island groups - Tafea Province, Vanuatu and Temotu Province, Solomon Islands have been selected by the governments of both countries as possible malaria elimination areas. To provide information on the prevalence and distribution of the disease within these island groups, malariometric surveys were conducted during the wet seasons of 2008.

Methods

In Tafea Province, a school-based survey was conducted which included the 2-12 y age group, while in Temotu a village based all-ages survey was conducted. An effort was made to sample villages or schools from a wide an area as possible on all islands. Diagnosis was initially based on Giemsa stained blood slides followed by molecular analysis using polymerase chain reaction (PCR).

Results

In Tafea Province, 73% (5238/7150) of children (2-12 y) were surveyed and in Temotu Province, in the all-ages survey, 50.2% (8742/17410) of the provincial population participated in the survey. In both Vanuatu and Solomon Islands malariometric surveys of their southern-most islands in 2008 showed relatively low over-all malaria parasite prevalence (2 to 3%). Other features of malaria in these island groups were low parasitaemia, low gametocyte carriage rates, low spleen rates, low malaria associated morbidity, a high incidence of asymptomatic infections, and a predominance of Plasmodium vivax over Plasmodium falciparum.

Conclusion

For various reasons malaria rates are declining in these provinces providing a favourable situation for local malaria elimination. This will be advanced using mass distribution of bed nets and selective indoor residual spraying, the introduction of rapid diagnostic tests and artemisinin combination therapy, and intensive case detection and surveillance. It is as yet uncertain whether malaria parasites can themselves be sustainably eliminated from entire Melanesian islands, where they have previously been endemic. Key issues on the road to malaria elimination will be continued community involvement, improved field diagnostic methods and elimination of residual P. vivax parasites from the liver of asymptomatic persons.
Proteomic analysis of small acid soluble proteins in the spore core of Bacillus subtilis ΔprpE and 168 strains with predictions of peptides liquid chromatography retention times as an additional tool in protein identification
Authors: Macur Katarzyna , Temporini Caterina , Massolini Gabriella , Grzenkowicz-Wydra Jolanta , Obuchowski Michał , Bączek Tomasz
Published: December 2019

Background

Sporulation, characteristic for some bacteria such as Bacillus subtilis, has not been entirely defined yet. Protein phosphatase E (PrpE) and small, acid soluble spore proteins (SASPs) influence this process. Nevertheless, direct result of PrpE interaction on SASPs content in spore coat of B. subtilis has not been evidenced so far. As proteomic approach enables global analysis of occurring proteins, therefore it was chosen in this experiment to compare SASPs occurrence in two strains of B. subtilis, standard 168 and ΔprpE, lacking PrpE phosphatase. Proteomic analysis is still a challenge, and despite of big approach in mass spectrometry (MS) field, the identification reliability remains unsatisfactory. Therefore there is a rising interest in new methods, particularly bioinformatic tools that would harden protein identification. Most of currently applied algorithms are based on MS-data. Information from separation steps is not still in routine usage, even though they also provide valuable facts about analyzed structures. The aim of this research was to apply a model for peptides retention times prediction, based on quantitative structure-retention relationships (QSRR) in SASPs analysis, obtained from two strains of B. subtilis proteome digests after separation and identification of the peptides by LC-ESI-MS/MS. The QSRR approach was applied as the additional constraint in proteomic research verifying results of MS/MS ion search and confirming the correctness of the peptides identifications along with the indication of the potential false positives and false negatives.

Results

In both strains of B. subtilis, peptides characteristic for SASPs were found, however their identification confidence varied. According to the MS identity parameter Xcorr and difference between predicted and experimental retention times (ΔtR) four groups could be distinguished: correctly and incorrectly identified, potential false positives and false negatives. The ΔprpE strain was characterized by much higher amount of SASPs peptides than standard 168 and their identification confidence was, mostly for alpha- and beta-type SASP, satisfactory.

Conclusions

The QSRR-based model for predicting retention times of the peptides, was a useful additional to MS tool, enhancing protein identification. Higher content of SASPs in strain lacking PrpE phosphatase suggests that this enzyme may influence their occurrence in the spores, lowering levels of these proteins.
Black silicon with self-cleaning surface prepared by wetting processes
Authors: Zhang Ting , Zhang Peng , Li Shibin , Li Wei , Wu Zhiming , Jiang Yadong
Published: December 2019

This paper reports on a simple method to prepare a hydrophobic surface on black silicon, which is fabricated by metal-assisted wet etching. To increase the reaction rate, the reaction device was placed in a heat collection-constant temperature type magnetic stirrer and set at room temperature. It was demonstrated that the micro- and nanoscale spikes on the black silicon made the surface become hydrophobic. As the reaction rate increases, the surface hydrophobicity becomes more outstanding and presents self-cleaning until the very end. The reflectance of the black silicon is drastically suppressed over a broad spectral range due to the unique geometry, which is effective for the enhancement of absorption.
Meditation acutely improves psychomotor vigilance, and may decrease sleep need
Authors: Kaul Prashant , Passafiume Jason , Sargent R Craig , O'Hara Bruce F
Published: December 2019

Background

A number of benefits from meditation have been claimed by those who practice various traditions, but few have been well tested in scientifically controlled studies. Among these claims are improved performance and decreased sleep need. Therefore, in these studies we assess whether meditation leads to an immediate performance improvement on a well validated psychomotor vigilance task (PVT), and second, whether longer bouts of meditation may alter sleep need.

Methods

The primary study assessed PVT reaction times before and after 40 minute periods of mediation, nap, or a control activity using a within subject cross-over design.

This study utilized novice meditators who were current university students (n = 10). Novice meditators completed 40 minutes of meditation, nap, or control activities on six different days (two separate days for each condition), plus one night of total sleep deprivation on a different night, followed by 40 minutes of meditation.

A second study examined sleep times in long term experienced meditators (n = 7) vs. non-meditators (n = 23). Experienced meditators and controls were age and sex matched and living in the Delhi region of India at the time of the study. Both groups continued their normal activities while monitoring their sleep and meditation times.

Results

Novice meditators were tested on the PVT before each activity, 10 minutes after each activity and one hour later. All ten novice meditators improved their PVT reaction times immediately following periods of meditation, and all but one got worse immediately following naps. Sleep deprivation produced a slower baseline reaction time (RT) on the PVT that still improved significantly following a period of meditation. In experiments with long-term experienced meditators, sleep duration was measured using both sleep journals and actigraphy. Sleep duration in these subjects was lower than control non-meditators and general population norms, with no apparent decrements in PVT scores.

Conclusions

These results suggest that meditation provides at least a short-term performance improvement even in novice meditators. In long term meditators, multiple hours spent in meditation are associated with a significant decrease in total sleep time when compared with age and sex matched controls who did not meditate. Whether meditation can actually replace a portion of sleep or pay-off sleep debt is under further investigation.
Adrenocortical carcinosarcoma: a case report and review of the literature
Authors: Sasaki Kotaro , Desimone Marisa , Rao Harsha R , Huang George J , Seethala Raja R
Published: December 2019

Adrenocortical carcinosarcoma is an extremely rare and aggressive variant of adrenocortical carcinoma characterized by the presence of both carcinomatous and sarcomatous components, with the latter often showing heterologous differentiation. Due to the rarity and unusual histology, it may pose a diagnostic challenge. In order to increase awareness and identify potential diagnostic pitfalls, we report the ninth case of non-functioning adrenocortical carcinosarcoma in a 45-year-old man who presented with worsening epigastric pain and a left large retroperitoneal mass in close proximity to the body/tail of pancreas and third portion of the duodenum with displacement of the kidney without parenchymal invasion and multiple liver nodules detected by computed tomographic scan. On en bloc resection, the tumor grossly did not involve the pancreas, kidney or colon. Histologically, the tumor was composed of two distinct components - an epithelioid component with granular cytoplasm that stained for synaptophysin, Melan-A, calretinin, and vimentin compatible with adrenocortical differentiation, and a pleomorphic to spindled component that was positive for desmin and myogenin, compatible with rhabdomyosarcomatous differentiation. A wedge biopsy of a liver nodule showed morphologic features similar to the epithelial component of the primary tumor. The patient died three months after surgery due to locoregional and distant recurrence. Adrenocortical carcinosarcoma is a rare malignancy that adds to the differential diagnostic considerations for a retroperitoneal epithelioid malignancy. Awareness of this as a possibility will help in distinguishing this tumor from other carcinomas, melanomas, and true sarcomas.
Gene set analysis exploiting the topology of a pathway
Authors: Massa Maria Sofia , Chiogna Monica , Romualdi Chiara
Published: December 2019

Background

Recently, a great effort in microarray data analysis is directed towards the study of the so-called gene sets. A gene set is defined by genes that are, somehow, functionally related. For example, genes appearing in a known biological pathway naturally define a gene set. The gene sets are usually identified from a priori biological knowledge. Nowadays, many bioinformatics resources store such kind of knowledge (see, for example, the Kyoto Encyclopedia of Genes and Genomes, among others). Although pathways maps carry important information about the structure of correlation among genes that should not be neglected, the currently available multivariate methods for gene set analysis do not fully exploit it.

Results

We propose a novel gene set analysis specifically designed for gene sets defined by pathways. Such analysis, based on graphical models, explicitly incorporates the dependence structure among genes highlighted by the topology of pathways. The analysis is designed to be used for overall surveillance of changes in a pathway in different experimental conditions. In fact, under different circumstances, not only the expression of the genes in a pathway, but also the strength of their relations may change. The methods resulting from the proposal allow both to test for variations in the strength of the links, and to properly account for heteroschedasticity in the usual tests for differential expression.

Conclusions

The use of graphical models allows a deeper look at the components of the pathway that can be tested separately and compared marginally. In this way it is possible to test single components of the pathway and highlight only those involved in its deregulation.
A randomised controlled trial of the efficacy of the ABCD Parenting Young Adolescents Program: rationale and methodology
Authors: Burke Kylie , Brennan Leah , Roney Sarah
Published: December 2019

Background

The transition to adolescence is a time of increased vulnerability for risk taking and poor health, social and academic outcomes. Parents have an important role in protecting their children from these potential harms. While the effectiveness of parenting programs in reducing problem behavior has been demonstrated, it is not known if parenting programs that target families prior to the onset of significant behavioral difficulties in early adolescence (9-14 years) improve the wellbeing of adolescents and their parents. This paper describes the rationale and methodology of a randomised controlled trial testing the efficacy of a parenting program for the promotion of factors known to be associated with positive adolescent outcomes, such as positive parenting practices, parent-adolescent relationships and adolescent behavior.

Methods/Design

One hundred and eighty parents were randomly allocated to an intervention or wait list control group. Parents in the intervention group participated in the ABCD Parenting Young Adolescents Program, a 6-session behavioral family intervention program which also incorporates acceptance-based strategies. Participants in the Wait List control group did not receive the intervention during a six month waiting period. The study was designed to comply with recommendations of the CONSORT statement. The primary outcome measures were reduction in parent-adolescent conflict and improvements in parent-adolescent relationships. Secondary outcomes included improvements in parent psychosocial wellbeing, parenting self-efficacy and perceived effectiveness, parent-adolescent communication and adolescent behavior.

Conclusions

Despite the effectiveness of parenting programs in reducing child behavioral difficulties, very few parenting programs for preventing problems in adolescents have been described in the peer reviewed literature. This study will provide data which can be used to examine the efficacy of a universal parenting interventions for the promotion of protective factors associated with adolescent wellbeing and will add to the literature regarding the relationships between parent, parenting and adolescent factors.

Trial Registration

Australian New Zealand Clinical Trials Registry ACTRN12609000194268.
Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production
Authors: Shi Shuobo , Valle-Rodríguez Juan Octavio , Khoomrung Sakda , Siewers Verena , Nielsen Jens
Published: December 2019

Background

Wax ester synthases (WSs) can synthesize wax esters from alcohols and fatty acyl coenzyme A thioesters. The knowledge of the preferred substrates for each WS allows the use of yeast cells for the production of wax esters that are high-value materials and can be used in a variety of industrial applications. The products of WSs include fatty acid ethyl esters, which can be directly used as biodiesel.

Results

Here, heterologous WSs derived from five different organisms were successfully expressed and evaluated for their substrate preference in Saccharomyces cerevisiae. We investigated the potential of the different WSs for biodiesel (that is, fatty acid ethyl esters) production in S. cerevisiae. All investigated WSs, from Acinetobacter baylyi ADP1, Marinobacter hydrocarbonoclasticus DSM 8798, Rhodococcus opacus PD630, Mus musculus C57BL/6 and Psychrobacter arcticus 273-4, have different substrate specificities, but they can all lead to the formation of biodiesel. The best biodiesel producing strain was found to be the one expressing WS from M. hydrocarbonoclasticus DSM 8798 that resulted in a biodiesel titer of 6.3 mg/L. To further enhance biodiesel production, acetyl coenzyme A carboxylase was up-regulated, which resulted in a 30% increase in biodiesel production.

Conclusions

Five WSs from different species were functionally expressed and their substrate preference characterized in S. cerevisiae, thus constructing cell factories for the production of specific kinds of wax ester. WS from M. hydrocarbonoclasticus showed the highest preference for ethanol compared to the other WSs, and could permit the engineered S. cerevisiae to produce biodiesel.
The multifaceted role of pirfenidone and its novel targets
Authors: Macías-Barragán José , Sandoval-Rodríguez Ana , Navarro-Partida Jose , Armendáriz-Borunda Juan
Published: December 2019

Background

Pirfenidone (PFD) is a molecule that exhibits antifibrotic properties in a variety of in vitro and animal models of lung, liver and renal fibrosis. These pathologies share many fibrogenic pathways with an abnormal fibrous wound-healing process; consequently, tissue repair and tissue regeneration-regulating mechanisms are altered.

Objective

To investigate the usefulness of PFD as an antifibrotic agent in clinical and experimental models of fibrotic disease.

Conclusions

There is a growing understanding of the molecular effects of PFD on the wound healing mechanism, leading to novel approaches for the management of fibrosis in lung, liver and renal tissues. Although the optimum treatment for fibrosis remains undefined, it is possible that combined therapeutic regimens that include this wide-application molecule, pirfenidone, could offer a useful treatment for fibrotic disease.
Integrated lipidomics and transcriptomic analysis of peripheral blood reveals significantly enriched pathways in type 2 diabetes mellitus
Authors: Zhao Chen , Mao Jinghe , Ai Junmei , Shenwu Ming , Shi Tieliu , Zhang Daqing , Wang Xiaonan , Wang Yunliang , Deng Youping
Published: December 2019

Background

Insulin resistance is a key element in the pathogenesis of type 2 diabetes mellitus. Plasma free fatty acids were assumed to mediate the insulin resistance, while the relationship between lipid and glucose disposal remains to be demonstrated across liver, skeletal muscle and blood.

Methods

We profiled both lipidomics and gene expression of 144 total peripheral blood samples, 84 from patients with T2D and 60 from healthy controls. Then, factor and partial least squares models were used to perform a combined analysis of lipidomics and gene expression profiles to uncover the bioprocesses that are associated with lipidomic profiles in type 2 diabetes.

Results

According to factor analysis of the lipidomic profile, several species of lipids were found to be correlated with different phenotypes, including diabetes-related C23:2CE, C23:3CE, C23:4CE, ePE36:4, ePE36:5, ePE36:6; race-related (African-American) PI36:1; and sex-related PE34:1 and LPC18:2. The major variance of gene expression profile was not caused by known factors and no significant difference can be directly derived from differential gene expression profile. However, the combination of lipidomic and gene expression analyses allows us to reveal the correlation between the altered lipid profile with significantly enriched pathways, such as one carbon pool by folate, arachidonic acid metabolism, insulin signaling pathway, amino sugar and nucleotide sugar metabolism, propanoate metabolism, and starch and sucrose metabolism. The genes in these pathways showed a good capability to classify diabetes samples.

Conclusion

Combined analysis of gene expression and lipidomic profiling reveals type 2 diabetes-associated lipid species and enriched biological pathways in peripheral blood, while gene expression profile does not show direct correlation. Our findings provide a new clue to better understand the mechanism of disordered lipid metabolism in association with type 2 diabetes.
Predictive factors of non-deterioration of glucose tolerance following a 2-year behavioral intervention
Authors: Almeida-Pititto Bianca , Hirai Amélia T , Sartorelli Daniela S , Harima Helena A , Gimeno Suely GA , Ferreira Sandra RG ,   the Japanese-Brazilian Diabetes Study Group
Published: December 2019

Aim

To identify predictive factors associated with non-deterioration of glucose metabolism following a 2-year behavioral intervention in Japanese-Brazilians.

Methods

295 adults (59.7% women) without diabetes completed 2-year intervention program. Characteristics of those who maintained/improved glucose tolerance status (non-progressors) were compared with those who worsened (progressors) after the intervention. In logistic regression analysis, the condition of non-progressor was used as dependent variable.

Results

Baseline characteristics of non-progressors (71.7%) and progressors were similar, except for the former being younger and having higher frequency of disturbed glucose tolerance and lower C-reactive protein (CRP). In logistic regression, non-deterioration of glucose metabolism was associated with disturbed glucose tolerance - impaired fasting glucose or impaired glucose tolerance - (p < 0.001) and CRP levels ≤ 0.04 mg/dL (p = 0.01), adjusted for age and anthropometric variables. Changes in anthropometry and physical activity and achievement of weight and dietary goals after intervention were similar in subsets that worsened or not the glucose tolerance status.

Conclusion

The whole sample presented a homogeneous behavior during the intervention. Lower CRP levels and diagnosis of glucose intolerance at baseline were predictors of non-deterioration of the glucose metabolism after a relatively simple intervention, independent of body adiposity.