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In some cases of infertility in women, human oocytes fail to mature when they reach the metaphase II (MII) stage. Mitochondria plays an important role in oocyte maturation. A large number of mitochondrial DNA (mtDNA), copied in oocytes, is essential for providing adenosine triphosphate (ATP) during oocyte maturation. The purpose of this study was to identify the relationship between transcript expression levels of the mitochondrial encoded gene (MT-CO1) and two nuclear encoded genes, nuclear respiratory factor 1 (NRF1) and mitochondrial transcription factor A (TFAM) in various stages of human oocyte maturation. Nine consenting patients, age 21-35 years old, with male factors were selected for ovarian stimulation and intracytoplasmic sperm injection (ICSI) procedures. mRNA levels of mitochondrial- related genes were performed by singlecell TaqMan® quantitative real-time polymerase chain reaction (qRT-PCR). There was no significant relationship between the relative expression levels in germinal vesicle (GV) stage oocytes (p = 0.62). On the contrary, a significant relationship was seen between the relative expression levels of TFAM and NRF1 and the MT-CO1 genes at the stages of metaphase I (MI) and MII (p = 0.03 and p = 0.002). A relationship exists between the transcript expression levels of TFAM and NRF1, and MT-CO1 genes in various stages of human oocyte maturation.

Abstract The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always possible, as this often requires access to detailed patient records. In this study we introduce GLAD, a new Semi-Supervised Learning (SSL) method for combining independent annotated datasets and unannotated datasets with the aim of identifying more robust sample classifiers. In our method, independent models are developed using subsets of genes for the annotated and unannotated datasets. These models are evaluated according to a scoring function that incorporates terms for classification accuracy on annotated data, and relative cluster separation in unannotated data. Improved models are iteratively generated using a genetic algorithm feature selection technique. Our results show that the addition of unannotated data into training, significantly improves classifier robustness.

Abstract Background The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. Results Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. Conclusions This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

Background: Genomic islands (GIs) are mobile genetic elements that integrate site-specifically into bacterial chromosomes, bearing genes that affect phenotypes such as pathogenicity and metabolism. GIs typically occur sporadically among related bacterial strains, enabling comparative genomic approaches to GI identification. For a candidate GI in a query genome, the number of reference genomes with a precise deletion of the GI serves as a support value for the GI. Our comparative software for GI identification was slowed by our original use of large reference genome databases (DBs). Here we explore smaller species-focused DBs., Results: With increasing DB size, recovery of our reliable prophage GI calls reached a plateau, while recovery of less reliable GI calls (FPs) increased rapidly as DB sizes exceeded ~500 genomes; i.e., overlarge DBs can increase FP rates. Paradoxically, relative to prophages, FPs were both more frequently supported only by genomes outside the species and more frequently supported only by genomes inside the species; this may be due to their generally lower support values. Setting a DB size limit for our SMAll Ranked Tailored (SMART) DB design speeded runtime ~65-fold. Strictly intra-species DBs would tend to lower yields of prophages for small species (with few genomes available); simulations with large species showed that this could be partially overcome by reaching outside the species to closely related taxa, without an FP burden. Employing such taxonomic outreach in DB design generated redundancy in the DB set; as few as 2984 DBs were needed to cover all 47894 prokaryotic species., Conclusions: Runtime decreased dramatically with SMART DB design, with only minor losses of prophages. We also describe potential utility in other comparative genomics projects., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Yu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Knowledge of circadian rhythm clock gene expression outside the suprachiasmatic nucleus is increasing. The purpose of this study was to determine whether expression of circadian clock genes differed within or among the bovine stress axis tissues (e.g., amygdala, hypothalamus, pituitary, adrenal cortex, and adrenal medulla). Tissues were obtained at an abattoir from eight mature nonpregnant Brahman cows that had been maintained in the same pasture and nutritional conditions. Sample tissues were stored in RNase-free sterile cryovials at -80 °C until the total RNA was extracted, quantified, assessed, and sequenced (NovaSeq 6000 system; paired-end 150 bp cycles). The trimmed reads were then mapped to a Bos taurus ( B. taurus ) reference genome (Umd3.1). Further analysis used the edgeR package. Raw gene count tables were read into RStudio, and low-expression genes were filtered out using the criteria of three minimum reads per gene in at least five samples. Normalization factors were then calculated using the trimmed mean of M values method to produce normalized gene counts within each sample tissue. The normalized gene counts important for a circadian rhythm were analyzed within and between each tissue of the stress axis using the GLM and CORR procedures of the Statistical Analysis System (SAS). The relative expression profiles of circadian clock genes differed ( p < 0.01) within each tissue, with neuronal PAS domain protein 2 ( NPAS2 ) having greater expression in the amygdala ( p < 0.01) and period circadian regulator ( PER1 ) having greater expression in all other tissues ( p < 0.01). The expression among tissues also differed ( p < 0.01) for individual circadian clock genes, with circadian locomotor output cycles protein kaput ( CLOCK ) expression being greater within the adrenal tissues and nuclear receptor subfamily 1 group D member 1 ( NR1D1 ) expression being greater within the other tissues ( p < 0.01). Overall, the results indicate that within each tissue, the various circadian clock genes were differentially expressed, in addition to being differentially expressed among the stress tissues of mature Brahman cows. Future use of these findings may assist in improving livestock husbandry and welfare by understanding interactions of the environment, stress responsiveness, and peripheral circadian rhythms.

Background: The prevalence of young patients with cardiac implantable electronic devices (CIED) is steadily increasing, accompanied by a rise in the occurrence of complications related to CIEDs. Consequently, transvenous lead extraction (TLE) has become a crucial treatment approach for such individuals., Objective: The purpose of this study was to examine the characteristics and procedural outcomes of young patients who undergo TLE, with a specific focus on identifying independent risk factors associated with adverse events., Methods: All patients in the GALLERY (GermAn Laser Lead Extraction RegistrY) were categorized into two groups based on their age at the time of enrollment: 45 years or younger, and over 45 years. A subgroup analysis was conducted specifically for the younger population. In this analysis, predictor variables for all-cause mortality, procedural complications, and procedural failure were evaluated using multivariable analyses., Results: We identified 160 patients aged 45 years or younger with a mean age of 35.3 ± 7.6 years and 42.5% ( n  = 68) female patients. Leading extraction indication was lead dysfunction in 51.3% of cases, followed by local infections in 20.6% and systemic infections in 16.9%. The most common device to be extracted were implantable cardioverter-defibrillators (ICD) with 52.5%. Mean number of leads per patient was 2.2 ± 1.0. Median age of the oldest indwelling lead was 91.5 [54.75-137.5] months. Overall complication rate was 3.8% with 1.9% minor and 1.9% major complications. Complete procedural success was achieved in 90.6% of cases. Clinical procedural success rate was 98.1%. Procedure-related mortality was 0.0%. The all-cause in-hospital mortality rate was 2.5%, with septic shock identified as the primary cause of mortality. Multivariable analysis revealed CKD (OR: 19.0; 95% CI: 1.84-194.9; p  = 0.018) and systemic infection (OR: 12.7; 95% CI: 1.14-142.8; p  = 0.039) as independent predictor for all-cause mortality. Lead age ≥ 10 years (OR: 14.58, 95% CI: 1.36-156.2; p  = 0.027) was identified as sole independent risk factor for procedural complication., Conclusion: TLE in young patients is safe and effective with a procedure-related mortality rate of 0.0%. CKD and systemic infection are predictors for all-cause mortality, whereas lead age ≥ 10 years was identified as independent risk factor for procedural complications in young patients undergoing TLE., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2023 Rexha, Chung, Burger, Ghaffari, Madej, Ziaukas, Hassan, Reichenspurner, Gessler, Willems, Butter, Pecha and Hakmi.)

Two of the big challenges in modern bioprocesses are process economics and in-depth process understanding. Getting access to online process data helps to understand process dynamics and monitor critical process parameters (CPPs). This is an important part of the quality-by- design concept that was introduced to the pharmaceutical industry in the last decade. Raman spectroscopy has proven to be a versatile tool to allow noninvasive measurements and access to a broad spectrum of analytes. This information can then be used for enhanced process control strategies. This review article will focus on the latest applications of Raman spectroscopy in established protein production bioprocesses as well as show its potential for virus, cell therapy, and mRNA processes., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2023 Sartorius Stedim Biotech GmbH. Published by Elsevier Ltd.. All rights reserved.)

Quantifying the natural inter-individual variation in DNA methylation patterns is important for identifying its contribution to phenotypic variation, but also for understanding how the environment affects variability, and for incorporation into statistical analyses. The inter-individual variation in DNA methylation patterns in female cattle and the effect that a prenatal stressor has on such variability have yet to be quantified. Thus, the objective of this study was to utilize methylation data from mature Brahman females to quantify the inter-individual variation in DNA methylation. Pregnant Brahman cows were transported for 2 h durations at days 60 ± 5; 80 ± 5; 100 ± 5; 120 ± 5; and 140 ± 5 of gestation. A non-transport group was maintained as a control. Leukocytes, amygdala, and anterior pituitary glands were harvested from eight cows born from the non-transport group (Control) and six from the transport group (PNS) at 5 years of age. The DNA harvested from the anterior pituitary contained the greatest variability in DNA methylation of cytosine-phosphate-guanine (mCpG) sites from both the PNS and Control groups, and the amygdala had the least. Numerous variable mCpG sites were associated with retrotransposable elements and highly repetitive regions of the genome. Some of the genomic features that had high variation in DNA methylation are involved in immune responses, signaling, responses to stimuli, and metabolic processes. The small overlap of highly variable CpG sites and features between tissues and leukocytes supports the role of variable DNA methylation in regulating tissue-specific gene expression. Many of the CpG sites that exhibited high variability in DNA methylation were common between the PNS and Control groups within a tissue, but there was little overlap in genomic features with high variability. The interaction between the prenatal environment and the genome could be responsible for the differences in location of the variable DNA methylation.

Aims: The GermAn Laser Lead Extraction RegistrY: GALLERY is a retrospective, national multicentre registry, investigating the safety and efficacy of laser lead extraction procedures in Germany., Methods and Results: Twenty-four German centres that are performing laser lead extraction have participated in the registry. All patients, treated with a laser lead extraction procedure between January 2013 and March 2017, were consecutively enrolled. Safety and efficacy of laser lead extraction were investigated. A total number of 2524 consecutive patients with 6117 leads were included into the registry. 5499 leads with a median lead dwell time of 96 (62-141) months were treated. The mean number of treated leads per patient was 2.18 ± 1.02. The clinical procedural success rate was 97.86% and the complete lead removal was observed in 94.85%. Additional extraction tools were used in 6.65% of cases. The rate of procedural failure was 2.14% with lead age  ≥10 years being its only predictor. The overall complication rate was 4.32%, including 2.06% major and 2.26% minor complications. Procedure-related mortality was 0.55%. Female sex and the presence of abandoned leads were predictors for procedure-related complications. The all-cause in-hospital mortality was 3.56% with systemic infection being the strongest predictor, followed by age ≥75 years and chronic kidney disease., Conclusion: In the GALLERY, a high success- and low procedure-related complication rates have been demonstrated. In multivariate analysis, female sex and the presence of abandoned leads were predictors for procedure-related complications, while the presence of systemic infection, age ≥75 years, and chronic kidney disease were independent predictors for all-cause mortality., Competing Interests: Conflict of interest: S.P. reports grants and personal fees from Philips/Spectranetics, Medtronic, and AtriCure. H.B. reports grants and personal fees from Philips/Spectranetics, Cook Medical, Zoll Medical, Braun Medical, Abbott, Sorin Group/LivaNova, Impulse Dynamics, Biotronik, and Medtronic. B.O. reports grants and personal fees from Philips/Spectranetics and Medtronic. H.E. reports personal fees from Philips/Spectranetics. N.G. reports grants and personal fees from Boston Scientific, Medtronic, and Bayer Vital. M.K. reports grants and personal fees from Philips/Spectranetics, Zoll Medical, Sorin Group/LivaNova, Medtronic, Boston Scientific, and CVRx. H.R. reports personal fees from Medtronic. S.W. reports grants and personal fees from Abbott, Boston Scientific, Medtronic, Boehringer Ingelheim, Bristol Myers Squibb, Bayer Vital, Acutus, and Daiichi Sankyo. S.H. reports grants and personal fees from Boston Scientific, Edwards Lifesciences, Medtronic, Meril, Philips/Spectranetics, and Zoll Medical. All other authors have no conflicts of interest., (© The Author(s) 2022. Published by Oxford University Press on behalf of the European Society of Cardiology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Prenatal stress can alter postnatal performance and temperament of cattle. These phenotypic effects may result from changes in gene expression caused by stress-induced epigenetic alterations. Specifically, shifts in gene expression caused by DNA methylation within the brain's amygdala can result in altered behavior because it regulates fear, stress response and aggression in mammals Thus, the objective of this experiment was to identify DNA methylation and gene expression differences in the amygdala tissue of 5-year-old prenatally stressed (PNS) Brahman cows compared to control cows. Pregnant Brahman cows ( n = 48) were transported for 2-h periods at 60 ± 5, 80 ± 5, 100 ± 5, 120 ± 5, and 140 ± 5 days of gestation. A non-transported group ( n = 48) were controls (Control). Amygdala tissue was harvested from 6 PNS and 8 Control cows at 5 years of age. Overall methylation of gene body regions, promoter regions, and cytosine-phosphate-guanine (CpG) islands were compared between the two groups. In total, 202 genes, 134 promoter regions, and 133 CpG islands exhibited differential methylation (FDR ≤ 0.15). Following comparison of gene expression in the amygdala between the PNS and Control cows, 2 differentially expressed genes were identified (FDR ≤ 0.15). The minimal differences observed could be the result of natural changes of DNA methylation and gene expression as an animal ages, or because this degree of transportation stress was not severe enough to cause lasting effects on the offspring. A younger age may be a more appropriate time to assess methylation and gene expression differences produced by prenatal stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Baker, Earnhardt, Cilkiz, Collins, Littlejohn, Cardoso, Ghaffari, Long, Riggs, Randel, Welsh and Riley.)

Flaxseed is a plant that grows and is cultivated in more than 50 countries; the main flax producer countries are Canada, China, the United States, and India. The purpose of the present study was to overview the source, chemical compounds, and mechanisms of the therapeutic effects of this valuable plant. For writing this manuscript, we made a list of relevant keywords and phrases, and then we started searching for studies in PubMed, Scopus, and Web of Science databases. The main constituents of flaxseed include lipids, proteins, lignans, fibers, and minerals. Flaxseed is full of antioxidants such as tocopherols, betacarotene, cysteine, and methionine which result in a decrease in blood pressure, heart disease, hepatic and neurological disorders, and increased insulin sensitivity. Flaxseed is commonly used for its antidiabetic and anticancer activities and also it is beneficial for cardiovascular, gastrointestinal, hepatic, urological, and reproductive disorders, and because of these beneficial effects, it is recognized as a medical plant.

Background: Asthma is a chronic inflammatory respiratory disorder. Nutritional conditions affect allergic diseases such as asthma. The aim of this study was to review the serum zinc level in children with asthma., Methods: This is a review article found in databases such as Google, PubMed, SID, Irandoc, Scopus and up-to-date. Key words for search included zinc, asthma, children and pediatric. There was no time limitation for the search. These articles on zinc levels in asthmatic children were meta-analyzed., Results: Out of the 40 articles, 19 articles were excluded and 21 articles were included in this analysis. 15 articles evaluated serum zinc levels, 4 articles on hair zinc levels, one article evaluated nail zinc levels and another on zinc level in erythrocyte cells in children with asthma. Only 3 articles evaluated effects of zinc supplement treatment in children with asthma. Meta-analysis of studies showed that there was no significant difference between the standard mean differences of zinc level in asthmatic patients compared to the control group. We cannot analyze the association between zinc levels in hair and nail in children with asthma. All clinical trial studies show that zinc supplement improves clinical manifestations of asthma and patient's pulmonary function test., Conclusion: We found that the mean serum zinc level difference is not significant in children with asthma than healthy control group and it seems that there is no relation between mean serum zinc level and severity of asthma in children., (Copyright © 2020, Babol University of Medical Sciences.)

Ticks from the genus Rhipicephalus have enormous global economic impact as ectoparasites of cattle. Rhipicephalus microplus and Rhipicephalus annulatus are known to harbor infectious pathogens such as Babesia bovis, Babesia bigemina , and Anaplasma marginale . Having reference quality genomes of these ticks would advance research to identify druggable targets for chemical entities with acaricidal activity and refine anti-tick vaccine approaches. We sequenced and assembled the genomes of R. microplus and R. annulatus , using Pacific Biosciences and HiSeq 4000 technologies on very high molecular weight genomic DNA. We used 22 and 29 SMRT cells on the Pacific Biosciences Sequel for R. microplus and R. annulatus , respectively, and 3 lanes of the Illumina HiSeq 4000 platform for each tick. The PacBio sequence yields for R. microplus and R. annulatus were 21.0 and 27.9 million subreads, respectively, which were assembled with Canu v. 1.7. The final Canu assemblies consisted of 92,167 and 57,796 contigs with an average contig length of 39,249 and 69,055 bp for R. microplus and R. annulatus , respectively. Annotated genome quality was assessed by BUSCO analysis to provide quantitative measures for each assembled genome. Over 82% and 92% of the 1066 member BUSCO gene set was found in the assembled genomes of R. microplus and R. annulatus , respectively. For R. microplus , only 189 of the 1066 BUSCO genes were missing and only 140 were present in a fragmented condition. For R. annulatus , only 75 of the BUSCO genes were missing and only 109 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information., Competing Interests: This work was funded in parts by the USDA-ARS CRIS Project No. 3094-32000-036-00D, a USDA-ARS Cooperative Agreement No. 58-3094-6-017 with the Department of Entomology, Texas A&M AgriLife Research, College Station, TX, USA, and by Texas A&M AgriLife Research through an Insect Vector Diseases Competitive Grant and High Consequence Genomics Research Project on Vector-borne Diseases to the Department of Entomology. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562. Specifically, it used the Bridges system, which is supported by NSF award number ACI-1445606, at the Pittsburgh Supercomputing Center (PSC).

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) in December 2019 form Wuhan, China leads to coronavirus disease 2019 (COVID-19) pandemic. While the common cold symptoms are observed in mild cases, COVID-19 is accompanied by multiorgan failure in severe patients. The involvement of different organs in severe patients results in lengthening the hospitalization duration and increasing the mortality rate. In this review, we aimed to investigate the involvement of different organs in COVID-19 patients, particularly in severe cases. Also, we tried to define the potential underlying mechanisms of SARS-CoV2 induced multiorgan failure. The multi-organ dysfunction is characterized by acute lung failure, acute liver failure, acute kidney injury, cardiovascular disease, and as well as a wide spectrum of hematological abnormalities and neurological disorders. The most important mechanisms are related to the direct and indirect pathogenic features of SARS-CoV2. Although the presence of angiotensin-converting enzyme 2, a receptor of SARS-CoV2 in the lung, heart, kidney, testis, liver, lymphocytes, and nervous system was confirmed, there are controversial findings to about the observation of SARS-CoV2 RNA in these organs. Moreover, the organ failure may be induced by the cytokine storm, a result of increased levels of inflammatory mediators, endothelial dysfunction, coagulation abnormalities, and infiltration of inflammatory cells into the organs. Therefore, further investigations are needed to detect the exact mechanisms of pathogenesis. Since the involvement of several organs in COVID-19 patients is important for clinicians, increasing their knowledge may help to improve the outcomes and decrease the rate of mortality and morbidity.

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

The longhorned tick, Haemaphysalis longicornis , feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand. A New Zealand-USA consortium was established to sequence, assemble, and annotate the genome of this tick, using ticks obtained from New Zealand's North Island. In New Zealand, the tick is considered exclusively parthenogenetic and this trait was deemed useful for genome assembly. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq4000 and the long-read Pac Bio Sequel platforms. Twenty-eight SMRT cells produced a total of 21.3 million reads which were assembled with Canu on a reserved supercomputer node with access to 12 TB of RAM, running continuously for over 24 days. The final assembly dataset consisted of 34,211 contigs with an average contig length of 215,205 bp. The quality of the annotated genome was assessed by BUSCO analysis, an approach that provides quantitative measures for the quality of an assembled genome. Over 95% of the BUSCO gene set was found in the assembled genome. Only 48 of the 1066 BUSCO genes were missing and only 9 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information., (© 2019 The Author(s).)

The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes. Consistent with the various biological functions under clock control, rhythmic gene expression is tissue-specific despite an identical clockwork mechanism in every cell. Here we show that BMAL1 DNA binding is largely tissue-specific, likely because of differences in chromatin accessibility between tissues and cobinding of tissue-specific transcription factors. Our results also indicate that BMAL1 ability to drive tissue-specific rhythmic transcription is associated with not only the activity of BMAL1-bound enhancers but also the activity of neighboring enhancers. Characterization of physical interactions between BMAL1 enhancers and other cis -regulatory regions by RNA polymerase II chromatin interaction analysis by paired-end tag (ChIA-PET) reveals that rhythmic BMAL1 target gene expression correlates with rhythmic chromatin interactions. These data thus support that much of BMAL1 target gene transcription depends on BMAL1 capacity to rhythmically regulate a network of enhancers., (© 2019 Beytebiere et al.; Published by Cold Spring Harbor Laboratory Press.)

Fungal agents account for the clinical manifestation of allergic disorders. The aim of the present study was to review the prevalence of hypersensitivity reactions to fungal aeroallergens in patients with allergic disorders, including allergic rhinitis, asthma, urticaria, and eczema, in Iran. The initial literature search resulted in the identification of 50 records, 26 cases of which met the inclusion criteria. Regarding the methods adopted for the detection of fungal allergens, serum-specific IgE and skin prick tests were used in 6 and 20 studies, respectively. Aspergillus fumigatus and Alternaria alternata sensitization was the most common allergic sensitization among the patients with allergic disorders. According to the reviewed studies, despite the humid climate of the north of Iran, fungal sensitization has a prevalence range of 5-70% in this region. In other regions, such as central and southern Iran, which have a dry and warm climate, fungal sensitization reportedly has a prevalence range of 5-65%. The prevalence of fungal sensitizations varies in different allergic disorders due to the factors related to geographic and genetic issues, gender, sample size, test operator, and assessment method., Competing Interests: Authors declare that there is no conflict of interest.

Background: The information content of genomes plays a crucial role in the existence and proper development of living organisms. Thus, tremendous effort has been dedicated to developing DNA sequencing technologies that provide a better understanding of the underlying mechanisms of cellular processes. Advances in the development of sequencing technology have made it possible to sequence genomes in a relatively fast and inexpensive way. However, as with any measurement technology, there is noise involved and this needs to be addressed to reach conclusions based on the resulting data. In addition, there are multiple intermediate steps and degrees of freedom when constructing genome assemblies that lead to ambiguous and inconsistent results among assemblers., Methods: Here we introduce HiMMe, an HMM-based tool that relies on genetic patterns to score genome assemblies. Through a Markov chain, the model is able to detect characteristic genetic patterns, while, by introducing emission probabilities, the noise involved in the process is taken into account. Prior knowledge can be used by training the model to fit a given organism or sequencing technology., Results: Our results show that the method presented is able to recognize patterns even with relatively small k-mer size choices and limited computational resources., Conclusions: Our methodology provides an individual quality metric per contig in addition to an overall genome assembly score, with a time complexity well below that of an aligner. Ultimately, HiMMe provides meaningful statistical insights that can be leveraged by researchers to better select contigs and genome assemblies for downstream analysis.

Objectives: The aim of this study was to evaluate and compare the retentive strength of orthodontic bands cemented with amorphous calcium phosphate (ACP)-containing and conventional glass ionomer cements (GICs)., Materials and Methods: One-hundred-and-twenty mandibular third molars were embedded in acrylic resin blocks with the buccal surface of crowns perpendicular to the base of the mold. The teeth were randomly divided into four groups containing 30 teeth each. Groups 1 and 3 were cemented using conventional GIC and groups 2 and 4 were cemented using ACP-containing orthodontic cement. Groups 1 and 2 without thermocycling, and groups 3 and 4 after thermocycling (5000 cycles, 5° to 55°C) were tested for retentive strength using a universal testing machine (crosshead speed of 1mm/minute). Two-way ANOVA was performed to compare the retentive strength of the groups., Results: The highest retentive strength belonged to group 1, and it was significantly higher than that of group 2 (P<0.001) and group 3 (P=0.02). The mean strength for group 2 was significantly lower than that of group 1 (P<0.001) and group 4 (P=0.04)., Conclusions: Although retentive strength decreased when ACP was added to GIC, the retentive strength of the samples cemented by ACP-containing GIC was remarkably high after thermocycling. It seems that in the oral cavity, ACP-containing GIC provides sufficient strength to endure forces applied on posterior teeth.

Background: Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A "Mixed Effects" Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of a mutant strain impaired in the establishment of biotrophy, allowing detailed dissection of events occurring specifically during penetration, and during early versus late biotrophy., Results: More than 2000 fungal genes were differentially transcribed during appressorial maturation, penetration, and colonization. Secreted proteins, secondary metabolism genes, and membrane receptors were over-represented among the differentially expressed genes, suggesting that the fungus engages in an intimate and dynamic conversation with the host, beginning prior to penetration. This communication process probably involves reception of plant signals triggering subsequent developmental progress in the fungus, as well as production of signals that induce responses in the host. Later phases of biotrophy were more similar to necrotrophy, with increased production of secreted proteases, inducers of plant cell death, hydrolases, and membrane bound transporters for the uptake and egress of potential toxins, signals, and nutrients., Conclusions: This approach revealed, in unprecedented detail, fungal genes specifically expressed during critical phases of host penetration and biotrophic establishment. Many encoded secreted proteins, secondary metabolism enzymes, and receptors that may play roles in host-pathogen communication necessary to promote susceptibility, and thus may provide targets for chemical or biological controls to manage this important disease. The differentially expressed genes could be used as 'landmarks' to more accurately identify developmental progress in compatible versus incompatible interactions involving genetic variants of both host and pathogen.

We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this assembly and the affiliated targeted homology searches greatly enrich the curated transcripts currently available in public databases for this species. Comparison with the model arthropod Daphnia allows some insights into defining characteristics of decapod crustaceans. This large-scale gene discovery gives the broadest depth yet to the annotated transcriptome of this important species and should be of value to ongoing genomics and immunogenetic resistance studies in this shrimp of paramount global economic importance.

A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was whether preservation of the pleura during internal mammary artery (IMA) harvesting improved clinical outcomes after coronary artery bypass graft surgery. More than 210 papers were found using the reported search, of which 18 presented the best evidence to answer the clinical question. The author, journal, date and country of publication, patient group studies, relevant outcomes, results and study weakness of these papers are tabulated. Most studies dealt with investigating the radiographic changes, pulmonary function tests, ventilation time and also clinical consequences, such as bleeding, the need for blood transfusion, pain scores and the length of hospital stay. There is still no meta-analysis and systematic review regarding this surgical problem. Eighteen articles were found, of which 6 were prospective randomized, controlled trials and 12 were cohort studies. In these studies, some beneficial clinical outcomes were reported including: pleural effusion (15 studies), atelectasis (11 studies), pulmonary function tests (9 studies), arterial blood gases (5 studies), postoperative pain (6 studies), tamponade (2 studies), ventilation time (12 studies with), blood loss (9 studies), transfusion (4 studies), intensive care unit stay (5 studies) and hospital stay (12 studies). Based on our findings, preservation of pleural integrity seems to contribute to decreased pulmonary complications and improved clinical outcomes, such as bleeding, pain and length of hospital stay., (© The Author 2014. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

Background: Although using light-cured composites for bonding orthodontic brackets has become increasingly popular, curing light cannot penetrate the metallic bulk of brackets and polymerization of composites is limited to the edges. Limited access and poor direct sight may be a problem in the posterior teeth. Meanwhile, effectiveness of the trans-illumination technique is questionable due to increased bucco-lingual thickness of the posterior teeth. Light-emitting diode (LED) light-curing units cause less temperature rise and lower risk to the pulpal tissue. The purpose of this study was to evaluate the clinical effectiveness of trans-illumination technique in bonding metallic brackets to premolars, using different light intensities and curing times of an LED light-curing unit., Methods: Sixty premolars were randomly divided into six groups. Bonding of brackets was done with 40- and 80-s light curing from the buccal or lingual aspect with different intensities. Shear bond strengths of brackets were measured using a universal testing machine. Data were analyzed by one-way analysis of variance test and Duncan's post hoc test., Results: The highest shear bond belonged to group 2 (high intensity, 40 s, buccal) and the lowest belonged to group 3 (low intensity, 40 s, lingual). Bond strength means in control groups were significantly higher than those in experimental groups., Conclusions: In all experimental groups except group 6 (80 s, high intensity, lingual), shear bond strength was below the clinically accepted values. In clinical limitations where light curing from the same side of the bracket is not possible, doubling the curing time and increasing the light intensity during trans-illumination are recommended for achieving acceptable bond strengths.

Background: A key goal of systems biology and translational genomics is to utilize high-throughput measurements of cellular states to develop expression-based classifiers for discriminating among different phenotypes. Recent developments of Next Generation Sequencing (NGS) technologies can facilitate classifier design by providing expression measurements for tens of thousands of genes simultaneously via the abundance of their mRNA transcripts. Because NGS technologies result in a nonlinear transformation of the actual expression distributions, their application can result in data that are less discriminative than would be the actual expression levels themselves, were they directly observable., Results: Using state-of-the-art distributional modeling for the NGS processing pipeline, this paper studies how that pipeline, via the resulting nonlinear transformation, affects classification and feature selection. The effects of different factors are considered and NGS-based classification is compared to SAGE-based classification and classification directly on the raw expression data, which is represented by a very high-dimensional model previously developed for gene expression. As expected, the nonlinear transformation resulting from NGS processing diminishes classification accuracy; however, owing to a larger number of reads, NGS-based classification outperforms SAGE-based classification., Conclusions: Having high numbers of reads can mitigate the degradation in classification performance resulting from the effects of NGS technologies. Hence, when performing a RNA-Seq analysis, using the highest possible coverage of the genome is recommended for the purposes of classification.

Background: RNA-Seq is the recently developed high-throughput sequencing technology for profiling the entire transcriptome in any organism. It has several major advantages over current hybridization-based approach such as microarrays. However, the cost per sample by RNA-Seq is still prohibitive for most laboratories. With continued improvement in sequence output, it would be cost-effective if multiple samples are multiplexed and sequenced in a single lane with sufficient transcriptome coverage. The objective of this analysis is to evaluate what sequencing depth might be sufficient to interrogate gene expression profiling in the chicken by RNA-Seq., Results: Two cDNA libraries from chicken lungs were sequenced initially, and 4.9 million (M) and 1.6 M (60 bp) reads were generated, respectively. With significant improvements in sequencing technology, two technical replicate cDNA libraries were re-sequenced. Totals of 29.6 M and 28.7 M (75 bp) reads were obtained with the two samples. More than 90% of annotated genes were detected in the data sets with 28.7-29.6 M reads, while only 68% of genes were detected in the data set with 1.6 M reads. The correlation coefficients of gene expression between technical replicates within the same sample were 0.9458 and 0.8442. To evaluate the appropriate depth needed for mRNA profiling, a random sampling method was used to generate different number of reads from each sample. There was a significant increase in correlation coefficients from a sequencing depth of 1.6 M to 10 M for all genes except highly abundant genes. No significant improvement was observed from the depth of 10 M to 20 M (75 bp) reads., Conclusion: The analysis from the current study demonstrated that 30 M (75 bp) reads is sufficient to detect all annotated genes in chicken lungs. Ten million (75 bp) reads could detect about 80% of annotated chicken genes, and RNA-Seq at this depth can serve as a replacement of microarray technology. Furthermore, the depth of sequencing had a significant impact on measuring gene expression of low abundant genes. Finally, the combination of experimental and simulation approaches is a powerful approach to address the relationship between the depth of sequencing and transcriptome coverage.

Background: One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of stationary control policies. In large networks, it becomes computationally burdensome to derive an optimal control policy. To overcome this problem, greedy intervention approaches based on the concept of the Mean First Passage Time or the steady-state probability mass of the network states were previously proposed. Another possible approach is to use reduction mappings to compress the network and develop control policies on its reduced version. However, such mappings lead to loss of information and require an induction step when designing the control policy for the original network., Results: In this paper, we propose a novel solution, CoD-CP, for designing intervention policies for large Boolean networks. The new method utilizes the Coefficient of Determination (CoD) and the Steady-State Distribution (SSD) of the model. The main advantage of CoD-CP in comparison with the previously proposed methods is that it does not require any compression of the original model, and thus can be directly designed on large networks. The simulation studies on small synthetic networks shows that CoD-CP performs comparable to previously proposed greedy policies that were induced from the compressed versions of the networks. Furthermore, on a large 17-gene gastrointestinal cancer network, CoD-CP outperforms other two available greedy techniques, which is precisely the kind of case for which CoD-CP has been developed. Finally, our experiments show that CoD-CP is robust with respect to the attractor structure of the model., Conclusions: The newly proposed CoD-CP provides an attractive alternative for intervening large networks where other available greedy methods require size reduction on the network and an extra induction step before designing a control policy.

Background: Statins have been shown to inhibit conduit vessel constrictor responses via the endothelial nitric oxide (NO) pathway. Clinical studies have implicated an effect in microvascular resistance vessels; however, direct effects of therapeutically relevant statin concentrations have not been examined. We examined the effect of acute pravastatin pretreatment on vasoconstrictor responsiveness of isolated rat mesenteric small vessels., Methods and Results: Pravastatin (112 nmol/L) pretreatment for 60 min reduced both the potency and maximal constrictor responses to phenylephrine, thromboxane (U46619) and serotonin in small vessels. This effect was abolished by endothelial denudation, NO synthase (NOS) inhibition with N-ω-nitro-L-arginine methyl ester (L-NAME 300 µmol/L) and Akt inhibition (Akt1/2 kinase inhibitor 500 nmol/L), confirming an endothelium-dependent mechanism and implicating a NO-mediated effect via the Akt pathway. Maximal superoxide scavenging with polyethylene glycol-superoxide dismutase (PEG-SOD), 150 U/ml did not influence phenylephrine constrictor responses but potentiated pravastatin's effect, suggesting that the statin did not increase NO bioavailability merely via an antioxidant mechanism. In contrast, pravastatin did not affect endothelin-1 (ET-1) constrictor responses. However, after pre-incubation with a selective endothelin-B (ET(B)) receptor antagonist (BQ788 3 µmol/L) pravastatin inhibited ET-1 constriction, suggesting that its effect is via the same mechanistic pathway as the ET(B) receptor., Conclusions: In small vessels, pravastatin inhibits constrictor responses by increasing endothelial NO bioavailability via the Akt pathway. Furthermore, ET(B) receptor blockade unmasks this effect in ET-1 constrictor responses.

Motivation: A key goal of studying biological systems is to design therapeutic intervention strategies. Probabilistic Boolean networks (PBNs) constitute a mathematical model which enables modeling, predicting and intervening in their long-run behavior using Markov chain theory. The long-run dynamics of a PBN, as represented by its steady-state distribution (SSD), can guide the design of effective intervention strategies for the modeled systems. A major obstacle for its application is the large state space of the underlying Markov chain, which poses a serious computational challenge. Hence, it is critical to reduce the model complexity of PBNs for practical applications., Results: We propose a strategy to reduce the state space of the underlying Markov chain of a PBN based on a criterion that the reduction least distorts the proportional change of stationary masses for critical states, for instance, the network attractors. In comparison to previous reduction methods, we reduce the state space directly, without deleting genes. We then derive stationary control policies on the reduced network that can be naturally induced back to the original network. Computational experiments study the effects of the reduction on model complexity and the performance of designed control policies which is measured by the shift of stationary mass away from undesirable states, those associated with undesirable phenotypes. We consider randomly generated networks as well as a 17-gene gastrointestinal cancer network, which, if not reduced, has a 2(17) × 2(17) transition probability matrix. Such a dimension is too large for direct application of many previously proposed PBN intervention strategies.

Motivation: Gene regulatory networks serve as models from which to derive therapeutic intervention strategies, in particular, stationary control policies over time that shift the probability mass of the steady state distribution (SSD) away from states associated with undesirable phenotypes. Derivation of control policies is hindered by the high-dimensional state spaces associated with gene regulatory networks. Hence, network reduction is a fundamental issue for intervention., Results: The network model that has been most used for the study of intervention in gene regulatory networks is the probabilistic Boolean network (PBN), which is a collection of constituent Boolean networks (BNs) with perturbation. In this article, we propose an algorithm that reduces a BN with perturbation, designs a control policy on the reduced network and then induces that policy to the original network. The coefficient of determination (CoD) is used to choose a gene for deletion, and a reduction mapping is used to rewire the remaining genes. This CoD-reduction procedure is used to construct a reduced network, then either the previously proposed mean first-passage time (MFPT) or SSD stationary control policy is designed on the reduced network, and these policies are induced to the original network. The efficacy of the overall algorithm is demonstrated on networks of 10 genes or less, where it is possible to compare the steady state shifts of the induced and original policies (because the latter can be derived), and by applying it to a 17-gene gastrointestinal network where it is shown that there is substantial beneficial steady state shift., Availability: The code for the algorithms is available at: http://gsp.tamu.edu/Publications/supplementary/ghaffari10a/ Please Contact Noushin Ghaffari at nghaffari@tamu.edu for further questions., Supplementary Information: Supplementary data are available at Bioinformatics online.

Background: A salient purpose for studying gene regulatory networks is to derive intervention strategies, the goals being to identify potential drug targets and design gene-based therapeutic intervention. Optimal stochastic control based on the transition probability matrix of the underlying Markov chain has been studied extensively for probabilistic Boolean networks. Optimization is based on minimization of a cost function and a key goal of control is to reduce the steady-state probability mass of undesirable network states. Owing to computational complexity, it is difficult to apply optimal control for large networks., Results: In this paper, we propose three new greedy stationary control policies by directly investigating the effects on the network long-run behavior. Similar to the recently proposed mean-first-passage-time (MFPT) control policy, these policies do not depend on minimization of a cost function and avoid the computational burden of dynamic programming. They can be used to design stationary control policies that avoid the need for a user-defined cost function because they are based directly on long-run network behavior; they can be used as an alternative to dynamic programming algorithms when the latter are computationally prohibitive; and they can be used to predict the best control gene with reduced computational complexity, even when one is employing dynamic programming to derive the final control policy. We compare the performance of these three greedy control policies and the MFPT policy using randomly generated probabilistic Boolean networks and give a preliminary example for intervening in a mammalian cell cycle network., Conclusion: The newly proposed control policies have better performance in general than the MFPT policy and, as indicated by the results on the mammalian cell cycle network, they can potentially serve as future gene therapeutic intervention strategies.

The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always possible, as this often requires access to detailed patient records. In this study we introduce GLAD, a new Semi-Supervised Learning (SSL) method for combining independent annotated datasets and unannotated datasets with the aim of identifying more robust sample classifiers. In our method, independent models are developed using subsets of genes for the annotated and unannotated datasets. These models are evaluated according to a scoring function that incorporates terms for classification accuracy on annotated data, and relative cluster separation in unannotated data. Improved models are iteratively generated using a genetic algorithm feature selection technique. Our results show that the addition of unannotated data into training, significantly improves classifier robustness.