nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows.

Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools, MSConvert, EncyclopeDIA, and MSstats, to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible when run on either a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability of nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license; run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.

Keratinocytes: innate immune cells in atopic dermatitis.

The skin is a unique immune organ that constitutes a complex network of physical, chemical and microbiological barriers against external insults. Keratinocytes are the most abundant cell type in the epidermis. These cells form the physical skin barrier and represent the first line of the host defense system by sensing pathogens via innate immune receptors, initiating anti-microbial responses and producing various cytokines, chemokines and anti-microbial peptides, which are important events in immunity. A damaged epidermal barrier in atopic dermatitis allows the penetration of potential allergens and pathogens to activate keratinocytes. Among the dysregulation of immune responses in atopic dermatitis, activated keratinocytes play a role in several biological processes that contribute to the pathogenesis of atopic dermatitis. In this review, we summarize the current understanding of the innate immune functions of keratinocytes in the pathogenesis of atopic dermatitis, with a special emphasis on skin-derived anti-microbial peptides and atopic dermatitis-related cytokines and chemokines in keratinocytes. An improved understanding of the innate immunity mediated by keratinocytes can provide helpful insight into the pathophysiological processes of atopic dermatitis and support new therapeutic efforts.

Growth and formation mechanism of shape-selective preparation of ZnO structures: correlation of structural, vibrational and optical properties.

A shape-selective preparation method was used to obtain highly crystalline rod-, needle-, nut-, and doughnut-like ZnO morphologies with distinct particle sizes and surface areas. We study the nucleation and growth mechanism of those structures and the influence of physical-chemical parameters, such as the solvent and the pH of the solution, on the morphology, as well as the structural and optical properties. A clear correlation between the growth rate along the c-axis and surface defects was established. Our results suggest that the needle- and rod-like morphologies are formed due to the crystal growth orientation along the c-axis and the occurrence of crystalline defects, such as oxygen vacancies and interstitial Zn2+ located at the surface, whereas nuts and doughnuts are formed due to growth along all crystalline planes except those related to growth along the c-axis. Based on the experimental results, growth mechanisms for the formation of ZnO structures were proposed. We believe this synthetic route will be of guidance to prepare several materials whose shapes will depend on the desired applications.

Analytical Pipeline for Discovery and Verification of Glycoproteins from Plasma-Derived Extracellular Vesicles as Breast Cancer Biomarkers.

Glycoproteins comprise more than half of current FDA-approved protein cancer markers, but the development of new glycoproteins as disease biomarkers has been stagnant. Here we present a pipeline to develop glycoproteins from extracellular vesicles (EVs) through integrating quantitative glycoproteomics with a novel reverse phase glycoprotein array and then apply it to identify novel biomarkers for breast cancer. EV glycoproteomics show promise in circumventing the problems plaguing current serum/plasma glycoproteomics and allowed us to identify hundreds of glycoproteins that have not been identified in blood. We identified 1,453 unique glycopeptides representing 556 glycoproteins in EVs, among which 20 were verified significantly higher in individual breast cancer patients. We further applied a novel glyco-specific reverse phase protein array to quantify a subset of the candidates. Together, this study demonstrates the great potential of this integrated pipeline for biomarker discovery.

Two-dimensional antiferromagnetic nodal-line semimetal and spin Hall effect in MnC4.

Nodal-line semimetals, characterized by Dirac-like crossings along one dimensionalk-space lines, represent a unique class of topological materials. In this study, we investigate the intriguing properties of room-temperature antiferromagneticMnC4and its nodal-line features both with and without spin-orbit coupling (SOC). In the absence of SOC, we identify a doubly degenerate Dirac-nodal line, robustly protected by a combination of time-reversal, mirror, and partial-translation symmetries. Remarkably, this nodal line withstands various external perturbations, including isotropic and anisotropic strain, and torsional deformations, due to the ionic-like bonding between Mn atoms and C clusters. With the inclusion of SOC, we observe a distinctive quasi-Dirac-nodal line that emerges due to the interplay between antiferromagnetism and SOC-induced spin-rotation symmetry breaking. Finally, we observed a robust spin Hall conductivity that aligns with the energy range where the quasi-nodal line appears. This study presents a compelling example of a robust symmetry-protected Dirac-nodal line antiferromagnetic monolayer, which has potential for applications in next-generation spintronic devices.

Effect of glucose concentration on the rate of fructose consumption in native strains isolated from the fermentation of Agave duranguensis.

Studies on hexose consumption by Saccharomyces cerevisiae show that glucose is consumed faster than fructose when both are present (9:1 fructose to glucose) in the medium during the fermentation of Agave. The objective of this work was to select strains of S. cerevisiae that consume fructose equal to or faster than glucose at high fructose concentrations by analyzing the influence of different glucose concentrations on the fructose consumption rate. The optimal growth conditions were determined by a kinetics assay using high performance liquid chromatography (HPLC) using 50 g of glucose and 50 g of fructose per liter of synthetic medium containing peptone and yeast extract. Using the same substrate concentrations, strain ITD-00185 was shown to have a higher reaction rate for fructose over glucose. At 75 g of fructose and 25 g of glucose per liter, strain ITD-00185 had a productivity of 1.02 gL(-1) h(-1) after 40 h and a fructose rate constant of 0.071 h(-1). It was observed that glucose concentration positively influences fructose consumption when present in a 3:1 ratio of fructose to glucose. Therefore, adapted strains at high fructose concentrations could be used as an alternative to traditional fermentation processes.

TNF is a potential therapeutic target to suppress prostatic inflammation and hyperplasia in autoimmune disease.

Autoimmune (AI) diseases can affect many organs; however, the prostate has not been considered to be a primary target of these systemic inflammatory processes. Here, we utilize medical record data, patient samples, and in vivo models to evaluate the impact of inflammation, as seen in AI diseases, on prostate tissue. Human and mouse tissues are used to examine whether systemic targeting of inflammation limits prostatic inflammation and hyperplasia. Evaluation of 112,152 medical records indicates that benign prostatic hyperplasia (BPH) prevalence is significantly higher among patients with AI diseases. Furthermore, treating these patients with tumor necrosis factor (TNF)-antagonists significantly decreases BPH incidence. Single-cell RNA-seq and in vitro assays suggest that macrophage-derived TNF stimulates BPH-derived fibroblast proliferation. TNF blockade significantly reduces epithelial hyperplasia, NFκB activation, and macrophage-mediated inflammation within prostate tissues. Together, these studies show that patients with AI diseases have a heightened susceptibility to BPH and that reducing inflammation with a therapeutic agent can suppress BPH.

scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data.

Single-cell RNA sequencing (scRNA-seq) is now a commonly used technique to measure the transcriptome of populations of cells. Clustering heterogeneous cells based on these transcriptomes enables identification of cell populations (Butler, Hoffman, Smibert, Papalexi, & Satija, 2018; Trapnell et al., 2014). There are multiple methods available to identify "marker" genes that differ between these populations (Butler et al., 2018; Love, Huber, & Anders, 2014; Robinson, McCarthy, & Smyth, 2009). However, there are usually too many genes in these lists to directly suggest an experimental follow-up strategy for selecting them from a bulk population (e.g. via FACS (Tung et al., 2007)). Here we present scTree, a tool that aims to provide biologists using the R programming language and scRNA-seq analysis programs a minimal set of genes that can be used in downstream experiments. The package is free, open source and available though GitHub at github.com/jspaezp/sctree.

The Nf2 tumor suppressor, merlin, functions in Rac-dependent signaling.

Mutations in the neurofibromatosis type II (NF2) tumor suppressor predispose humans and mice to tumor development. The study of Nf2+/- mice has demonstrated an additional effect of Nf2 loss on tumor metastasis. The NF2-encoded protein, merlin, belongs to the ERM (ezrin, radixin, and moesin) family of cytoskeleton:membrane linkers. However, the molecular basis for the tumor- and metastasis- suppressing activity of merlin is unknown. We have now placed merlin in a signaling pathway downstream of the small GTPase Rac. Expression of activated Rac induces phosphorylation and decreased association of merlin with the cytoskeleton. Furthermore, merlin overexpression inhibits Rac-induced signaling in a phosphorylation-dependent manner. Finally, Nf2-/- cells exhibit characteristics of cells expressing activated alleles of Rac. These studies provide insight into the normal cellular function of merlin and how Nf2 mutation contributes to tumor initiation and progression.

Cannabinoid system in neurodegeneration: new perspectives in Alzheimer's disease.

Alzheimer's disease is a chronic and progressive neurodegenerative disorder. The presence of functional cannabinoid CB2 receptors in central nervous system (CNS) has provoked that this receptor and its agonist ligands are now considered as promising pharmacological targets for neurological diseases. Herein, we review the evidences supporting the potential role of the ECS as a therapeutic target, focused on CB2 receptor and its ligands, for the treatment of Alzheimer's disease.

High Efficiency Mercury Sorption by Dead Biomass of Lysinibacillus Sphaericus-New Insights into the Treatment of Contaminated Water.

Mercury (Hg) is a toxic metal frequently used in illegal and artisanal extraction of gold and silver which makes it a cause of environmental poisoning. Since biosorption of other heavy metals has been reported for several Lysinibacillus sphaericus strains, this study investigates Hg removal. Three L. sphaericus strains previously reported as metal tolerant (CBAM5, Ot4b31, and III(3)7) were assessed with mercury chloride (HgCl2). Bacteria were characterized by scanning electron microscopy coupled with energy dispersive spectroscopy (EDS-SEM). Sorption was evaluated in live and dead bacterial biomass by free and immobilized cells assays. Hg quantification was achieved through spectrophotometry at 508 nm by reaction of Hg supernatants with dithizone prepared in Triton X-114 and by graphite furnace atomic absorption spectroscopy (GF-AAS). Bacteria grew up to 60 ppm of HgCl2. Non-immobilized dead cell mixture of strains III(3)7 and Ot4b31 showed a maximum sorption efficiency of 28.4 µg Hg/mg bacteria during the first 5 min of contact with HgCl2, removing over 95% of Hg. This process was escalated in a semi-batch bubbling fluidized bed reactor (BFB) using rice husk as the immobilization matrix leading to a similar level of efficiency. EDS-SEM analysis showed that all strains can adsorb Hg as particles of nanometric scale that can be related to the presence of S-layer metal binding proteins as shown in previous studies. These results suggest that L. sphaericus could be used as a novel biological method of mercury removal from polluted wastewater.

ZnO-based nanofungicides: Synthesis, characterization and their effect on the coffee fungi Mycena citricolor and Colletotrichum sp.

In this work we compare the antifungal capacity of zinc oxide nanoparticles (ZnO-NPs) synthesized by a chemical route and a ZnO-based nanobiohybrid obtained by green synthesis in an extract of garlic (Allium sativum). To find out the characteristics of the materials synthesized, X-ray diffraction (XRD), IR spectroscopy and absorption in UV-Vis were used, as well as both scanning (SEM) and transmission (TEM) electron microscopy. The results showed that the samples obtained were of nanometric size (<100 nm), with a predominance of the wurtzite crystal phase of ZnO and little crystallization of the nanobiohybrids. Their antifungal capacity on two pathogenic fungi of coffee, Mycena citricolor (Berk and Curt) and Colletotrichum sp. was also evaluated. Both nanomaterials showed an efficient antifungal capacity, particularly the nanobiohybrids, with ~97% inhibition in growth of M. citricolor, and ~93% for Colletotrichum sp. The microstructural study with high resolution optical (HROM) and ultra-structural microscopy (using TEM) carried out on the fungi treated with the synthesized nanomaterials showed a strong nanofungicidal effect on the vegetative and reproductive structures and fungal cell wall, respectively. The inhibition of the growth of the fungi and micro and ultra-structural affectations were explained considering that the size of the nanomaterials allows them to pass easily through the cell membranes. This indicates that they can be absorbed easily by the fungi tested here, causing cellular dysfunction. Nanofungicide effects are also attributable to the unique properties of nanomaterials, such as the high surface-to-bulk ratio of atoms and their surface physicochemical characteristics that could directly or indirectly produce reactive oxygen species (ROS), which affect the proteins of the cell wall.

Risk factors associated with mortality of infections caused by Stenotrophomonas maltophilia: a systematic review.

The objective of this review was to assess the quality of available literature regarding risk factors associated with mortality of infections caused by S. maltophilia. PubMed and OVID were searched from March 1985 to March 2008, and eligible studies were considered to be those that related S. maltophilia infection with risk factors associated with mortality; described the characteristics of patients in detail; and provided data regarding the outcome and mortality. Thirty-eight studies were found referring to S. maltophilia (four with multivariate analysis and 10 with univariate analysis). This review has several limitations, mainly due to the heterogeneity of patients, lack of appropriate statistical analysis and lack of definition of nosocomial and community infection studies. Data reviewed suggest that infections caused by S. maltophilia have high mortality and that the risk factors associated with mortality are related to the initial clinical condition and patient type. Underlying haematological disease in cancer patients and admission to the intensive care unit are independent risk factors associated with mortality. Shock, thrombocytopenia and Acute Physiological Assessment and Chronic Health Evaluation (APACHE) score >15 are independent risk factors associated with outcome in patients with bloodstream infection and pneumonia. Organ dysfunction is the only independent risk factor associated with death from infection caused by sulfamethoxazole-resistant S. maltophilia. The impact of adequate antimicrobial therapy and removal of central venous catheter on mortality require further clinical studies.

Factors associated with mortality in patients with bloodstream infection and pneumonia due to Stenotrophomonas maltophilia.

Severe infections caused by Stenotrophomonas maltophilia are associated with high mortality, and strategies to improve the clinical outcome for infected patients are needed. A retrospective cohort study of patients with bloodstream infection (BSIs) and pneumonia caused by S. maltophilia was conducted. Multivariate analysis was performed to access factors associated with 14-day mortality. A total of 60 infections were identified. Among these, eight (13%) were pneumonias and 52 were BSIs; 33.3% were primary, 13% were central venous catheter (CVC)-related and 40% were secondary BSIs. Fifty-seven (85%) patients had received previous antimicrobial therapy; 88% had CVC, 57% mechanical ventilation and 75% were in the intensive care unit at the onset of infection. Malignancy (45%) was the most frequent underlying disease. The mean of the Acute Physiology and Chronic Health Evaluation II (APACHE II) scores was 17 and for the Sepsis-related Organ Failure Assessment (SOFA) score, it was 7 points. The overall and 14-day mortality were, respectively, 75% and 48%. Forty-seven (78%) patients were treated and, of these, 74% received trimethoprim-sulfamethoxazole. Independent risk factors associated with mortality were SOFA index >6 points (0.005) and septic shock (0.03). The Kaplan-Meier estimations curves showed that patients with APACHE II score >20 and SOFA score >10 had a survival chance of, respectively, less than 8% and less than 10% (P

Influence of the suture in the propagation of tears in calf pericardium employed in the construction of cardiac bioprostheses.

The tearing of the fibers of biomaterials employed in implants or bioprostheses leads to early the failure of these devices. The purpose of this study was to determine the force necessary to propagate a tear in a biological tissue, calf pericardium, when sutured. We analyzed the outcome of 230 trials. There was a loss of resistance to tearing in samples sutured edge-to-edge as compared to unsutured control samples. This loss was not observed when the suture was preceded by an intact or protective zone. The values corresponding to the tearing force for an overlapping suture, especially when sewn with Gore-Tex(R), were higher than those obtained in controls. This study confirms the deleterious effect of the edge-to-edge suture, which can be minimized by protecting the suture, and the excellent behavior of the overlapping suture.

Relationship between children’s motor development and the physical activity level of their parents / Relación entre desarrollo motriz de niños y nivel actividad física de padres

The objective of this study is to determine the relationship between children’s motor development and the physical activity level of their parents. A total of 154 subjects, 77 boys and girls and 77 parents, from two school institutions participated. The ages of the children range from 6.6 to 10.5 years with a mean of 8.74 (± 1.23). The study is of a correlational, non-experimental, cross-sectional type. The Test of Gross Motor Development (TGMD-2) was used to identify the motor development level and the International Physical Activity Questionnaire (IPAQ) was employed to identify the physical activity level of the parents. For the correlational analysis, Fisher's exact test was applied, checking the statistical significance with a confidence level of 95% (p <0.05). The results indicate that there is no relationship between the physical activity level of the parents and the motor development of their children (AU)

Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain.

BACKGROUND: Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory constraints on kinase activity, can promote malignant transformation, and appear to be a major determinant of response to kinase inhibitor therapy. Missense mutations in the EGFR kinase domain, for example, have recently been identified in patients who showed clinical responses to EGFR kinase inhibitor therapy. METHODS AND FINDINGS: Encouraged by the promising clinical activity of epidermal growth factor receptor (EGFR) kinase inhibitors in treating glioblastoma in humans, we have sequenced the complete EGFR coding sequence in glioma tumor samples and cell lines. We identified novel missense mutations in the extracellular domain of EGFR in 13.6% (18/132) of glioblastomas and 12.5% (1/8) of glioblastoma cell lines. These EGFR mutations were associated with increased EGFR gene dosage and conferred anchorage-independent growth and tumorigenicity to NIH-3T3 cells. Cells transformed by expression of these EGFR mutants were sensitive to small-molecule EGFR kinase inhibitors. CONCLUSIONS: Our results suggest extracellular missense mutations as a novel mechanism for oncogenic EGFR activation and may help identify patients who can benefit from EGFR kinase inhibitors for treatment of glioblastoma.

A transforming MET mutation discovered in non-small cell lung cancer using microarray-based resequencing.

We have designed resequencing microarrays to test the performance of this platform when interrogating a large number of exons (164 total) from genes associated with cancer. To evaluate false positive and negative rates, dideoxy sequencing was done for 335,420 bases interrogated by the arrays. From the array data, calls could be made for approximately 97.5% of the bases, and false positive rates were very low with only a single mutation reported from the array dataset for which the corresponding dideoxy trace had a clean wildtype sequence. For the nucleotide positions where array calls were made, false negative rates were 1.41% for heterozygous mutations. All the homozygous mutations were detected, but 8.11% were erroneously reported as heterozygous changes from the reference sequence by the array analysis software. In addition, 20 non-small cell lung cancer (NSCLC) samples were analyzed using the arrays, and both somatic and germline mutations were found. The most interesting findings were two MET mutations that have recently been implemented in NSCLC. Large scale MALDI-TOF genotyping indicated that one of these mutations (T1010I) might represent a true cancer-causing genotype, whereas the other (N375S) appears to be a common germline polymorphism.

Durability of a cardiac valve leaflet made of calf pericardium: fatigue and energy consumption.

We studied the mechanical behavior of membranes of calf pericardium, similar to those employed in prosthetic valve leaflets, when subjected to tensile fatigue. The objective was to assess its durability, as a fundamental property of cardiac bioprosthesis, and analyze the energy consumption. For this purpose, the authors built a hydraulic simulator to subject a spherical valve leaflet made of calf pericardium to cyclic stress mimicking cardiac function. A total of 522 assays were performed in 40 samples, subjected to cyclic pressures greater than 6 atm, and 482 subjected to pressures ranging between 2 and 6 atm. The mathematical expression that establishes the relationship between the pressure exerted and the frequency was obtained. If we assume that the function is continuous, this equation provides the range of fatigue tolerated for a given number of cycles. Using the optimal values (the five highest values per series), the expression was found to be y = 9.95x(-0 1214) (R(2) = 0.955), where x represents the frequency in cycles per second and y the pressure in atmospheres. In addition, we established the mathematical relationship between the energy consumed and the frequency, which was a function of the pressure exerted, regardless of the region or zone from which the samples had been obtained. The methods of manual and morphology-based selection employed produced widely dispersed results. When a mechanical criterion was included, the similarity in the energy consumed during fatigue testing markedly improved the correlation, with a coefficient of determination between paired samples of R(2) = 0.7477. A mechanical criterion, such as energy consumption, can help to improve sample selection and produce more consistent results. Finally, we obtained the mathematical expression that relates the energy consumed to the pressure exerted and the number of cycles per second to which the valve leaflet was subjected. This procedure enables us to establish the limit to the energy that a biomaterial can consume over a period of time during which it is subjected to a working pressure and, thus, calculate more precisely its durability.

Biochemical and mechanical behavior of ostrich pericardium as a new biomaterial.

We have performed a comparative analysis of glutaraldehyde-preserved ostrich pericardium, as a novel biomaterial, with bovine pericardium. The biochemical characteristics (histology, water content, amino acid composition, and collagen and elastin contents), mechanical properties, and in vivo calcification in a subcutaneous rat model were examined. Ostrich pericardium is slightly thinner and shows a higher water content (70+/-2% vs. 62+/-2%) than bovine pericardium. Additionally, ostrich pericardium presents 1.6-fold lower elastin content and a lower percentage of collagen in reference to the total protein content (68+/-2% vs. 76+/-2%). However, ostrich pericardium shows better mechanical properties, with higher tensile stress at rupture (32.4+/-7.5 vs. 11.5+/-4.6) than calf pericardium. In vivo calcification studies in a rat subcutaneous model show that ostrich pericardium is significantly less calcified than bovine pericardium (23.95+/-13.30 vs. 100.10+/-37.36 mg/g tissue) after 60 days of implantation. In conclusion, glutaraldehyde-stabilized ostrich pericardium tissue shows better mechanical properties than calf tissue. However, calcium accumulation in implanted ostrich tissue is still too high to consider it a much better alternative to bovine pericardium, and anticalcification treatments should be considered.