Corrigendum: High-throughput discovery of novel developmental phenotypes.

This corrects the article DOI: 10.1038/nature19356.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.

The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.

High-throughput discovery of novel developmental phenotypes.

Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.

Estudio de la calidad de vida en cuidadores familiares de personas con discapacidad intelectual.

OBJETIVO: Explorar las experiencias y percepciones de la calidad de vida (CV) en cuidadores familiares (CF) de personas con discapacidad intelectual (PDI) en Morelos y Sinaloa, México. Material y métodos. Estudio cualitativo. Se realizaron 18 entrevistas semiestructuradas a CF de PDI que asistían a escuelas básicas públicas en Huitzilac, Morelos y Culiacán, Sinaloa, México. Se realizó análisis de contenido con apoyo del programa ATLAS.ti.8.0. RESULTADOS: Los CF experimentaron un deterioro en distintas dimensiones: bienestar emocional, físico y material, desarrollo personal, autodeterminación y relaciones interpersonales, deterioro que afecta negativamente su CV. Los lazos de empatía, acompañamiento y motivación con otros CF son beneficiosos y los libera de actividades por lapsos breves, disminuyendo así la carga del cuidado de una PDI. CONCLUSIONES: Cuidar a una PDI puede afectar negativamente la CV de las y los CF. Se sugiere el desarrollo de intervenciones para atención, apoyo y orientación integral; asimismo, crear y fortalecer grupos de ayuda mutua con otros cuidadores.

Physicochemical, Structural, Thermal and Rheological Properties of Flour and Starch Isolated from Avocado Seeds of Landrace and Hass Cultivars.

The objective of this study was to obtain and characterize flours and starches from the avocado seeds of Hass and landrace cultivars. The morphological, physical-chemical, structural, thermal and rheological characteristics were evaluated. The flour yield of the Hass and landrace cultivars was 41.56 to 46.86% (w/w), while for starch, it was 35.47 to 39.57% (w/w) (cv. Hass and landrace, respectively). Scanning electron microscopy (SEM) revealed the presence of oval starch granules and other particles in flour, in contrast to flours, starches showed lower ash, proteins and lipids content. However, the amylose content was higher in starches (42.25-48.2%). Flours showed a higher gelatinization temperature (Tp = 73.17-73.62 °C), and their starches presented greater gelatinization enthalpy (∆Hgel = 11.82-13.43 J/g). All samples showed a B-type diffraction pattern, and the crystallinity was higher in the flours. The rheological analysis (flow curves and viscoelastic tests) evidenced a pseudoplastic (n = 0.28-0.36) behavior in all samples analyzed, but the consistency index (k) was higher in starches. In general, the flours and starches from avocado seeds presented interesting proximal, thermal and functional properties for possible application in food systems, and these findings could contribute to the revaluation of this by-product.

Soft windowing application to improve analysis of high-throughput phenotyping data.

MOTIVATION: High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. RESULTS: Here we introduce 'soft windowing', a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. AVAILABILITY AND IMPLEMENTATION: The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chitosan Films Obtained from Brachystola magna (Girard) and Its Evaluation on Quality Attributes in Sausages during Storage.

High molecular weight chitosan (≈322 kDa) was obtained from chitin isolated from Brachystola magna (Girard) to produced biodegradable films. Their physicochemical, mechanical and water vapor permeability (WVP) properties were compared against commercial chitosan films with different molecular weights. Brachystola magna chitosan films (CFBM) exhibited similar physicochemical and mechanical characteristics to those of commercial chitosans. The CFBM films presented lower WVP values (10.01 × 10-11 g/m s Pa) than commercial chitosans films (from 16.06 × 10-11 to 64.30 × 10-11 g/m s Pa). Frankfurt-type sausages were covered with chitosan films and stored in refrigerated conditions (4 °C). Their quality attributes (color, weight loss, pH, moisture, texture and lipid oxidation) were evaluated at 0, 5, 10, 15 and 20 days. Sausages covered with CFMB films presented the lowest weight loss (from 1.24% to 2.38%). A higher increase in hardness (from 22.32 N to 30.63 N) was observed in sausages covered with CFMB films. Compared with other films and the control (uncovered sausages), CFMB films delay pH reduction. Moreover, this film presents the lower lipid oxidation level (0.10 malonaldehyde mg/sample kg). Thus, chitosan of B. magna could be a good alternative as packaging material for meat products with high-fat content.

Efficient anchoring of nanostructured cadmium selenide on different kinds of carbon nanotubes.

We report a method for the efficient anchoring of cadmium selenide (CdSe) nanoparticles on the surface of different types of multi-walled carbon nanotubes (purified, N-doped, O-doped and exfoliated). Characterization using different types of electron microscopies (SEM, STEM, and TEM), energy dispersive spectroscopy (EDS) and x-ray diffraction showed well anchored CdSe nanoparticles (NP) on the nanotube surfaces, NP shapes and sizes varied with temperature and other synthesis conditions, and formed with good yields. The method here reported does not require previous activation of the carbon nanotube surface by chemical functionalization, nor the use of organic solvents, and the reaction proceeded in aqueous solutions, making this process simpler and more environmentally friendly than others.

Principles and application of LIMS in mouse clinics.

Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen & paper colony management, spreadsheet-based data management and manual data analysis. Hence, different Laboratory Information Management Systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.

Double layer capacitors in dye sensitized solar cells with large charge and energy storage capacity and controlled shape of output voltage signals.

The output signals in natural dyes-based solar cells (DSSC) can be either rising or decaying depending on the type of ions present in the system; these ions called added ions, are introduced by the additives: mordant and brighteners. The photon-dye interaction produces electrons, which eventually reach the electrode giving place to a superficially charged electrode in contact with an electrolyte where are the added ions. This combination produces, automatically, an electrical double-layer EDL structure which has important effects on the performance of the system: a) the added ions control, to a large extent, the initial shape of the output signal, giving rise to rising or decaying profiles; b) it is possible to store large amounts of energy and charge at high electric fields. This structure is found in many other systems that have a surface charged in contact with an electrolyte like piezoelectric materials in human body. This assertion was supported by determining important parameters such as the force between charged surfaces on both sides of the interface, the charge density, the energy density, and the capacitance. The Debye length has very small values then, many important quantities depend on this; it is possible to obtain large values for energy UDL ~ 3.6x105 Jm-3 and charge density ρDL ≈ 1.1x107 Cm-3 for double layer capacitors; these values are orders of magnitude larger than the corresponding values for electrostatic capacitors: Uelec ≈ 4.5x10-3 Jm-3 and ρelec ≈ 1.2 Cm-3. A non-linear model was also developed to fit unstable oscillations found in the output profiles produced by abrupt lighting.

Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer.

Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.

Assessing interest in cardiothoracic surgery at an osteopathic medical school: Results of an institutional survey.

Objective: Cardiothoracic surgery is a surgical subspecialty that attracts few medical students. As integrated surgical residency programs continue to grow in number, there is increased interest in what factors influence specialty selection during undergraduate medical education. Previous institutional studies have studied allopathic medical schools affiliated with academic institutions. This study aimed to assess the interest and perception of cardiothoracic surgery at an osteopathic institution. Methods: Active medical students at a US osteopathic institution were invited to complete an original online survey. Means and 95% confidence intervals were calculated and graphed for questions using Likert scale responses. Comparison of mean responses for preclinical versus clinical students was assessed by a Kruskal-Wallis nonparametric analysis of variance. Results: There were 166 surveys (22%) completed, and interest in cardiothoracic surgery was indicated by 7.8% of respondents. Work/life balance, personality of cardiothoracic surgeons, and lack of family time were negative factors associated with cardiothoracic surgery. Clinical exposure, shadowing, mentorship, and significant personal/life events before medical school were strong factors in establishing students' interest in cardiothoracic surgery. Preclinical students noted exposure to cardiothoracic surgery would further increase their interest when compared with clinical students (µ = 3.39 vs µ = 2.69, P = .008). Conclusions: All factors that established interest in cardiothoracic surgery occurred before students entered medical school. Although there are negative perceptions associated with cardiothoracic surgery, these may be ameliorated with more exposure to the field. Further research is needed to explore how early exposure in preclinical years of medical school affects students' perceptions and ultimate interest in cardiothoracic surgery.

Building Interest in Cardiothoracic Surgery at an Osteopathic Medical School: Results of an Institutional Study and a Guide for Medical Schools.

Objective A previous study at this institution revealed a connection between interest group involvement and specialty interest while identifying the negative perceptions of cardiothoracic (CT) surgery. This study aimed to build interest and ameliorate the negative perceptions of CT surgery by exposing pre-clinical students to the field through engaging events. Methods Students at a US osteopathic institution who attended CT surgery committee events were invited to complete an online survey after each event. Associations between the number of events attended and ranked responses to survey questions were assessed by two-tailed Spearman correlations. Statistical comparisons in ranked responses between the events attended and the survey questions were assessed by a two-way analysis of variance (ANOVA). Pre-clinical students actively enrolled at the institution during the 2022-2023 academic year were eligible for inclusion. Results There were 83 surveys completed over seven events. There was a significant association between the number of events a student attended and their perception of CT surgeon's work/life balance with a correlation coefficient of .258 (P=0.019) and whether CT surgeons have time for their families with a correlation coefficient of .235 (P=0.035). Residents and medical student events as well as wet lab events increased interest the most and helped students feel equipped to apply for CT surgery. Conclusions While negative perceptions associated with CT surgery exist, these may be ameliorated with more exposure to the field. Unique events that expose pre-clinical students to multiple facets of CT surgery, including physicians and trainees in the field, as well as offering hands-on activities, may increase interest in the field and further pursuit of the field during clinical years.

HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) is a quiescent B-cell malignancy that depends on transcriptional dysregulation for survival. The histone deacetylases are transcriptional regulators whose role within the regulatory chromatin and consequence on the CLL transcriptome is poorly characterized. Here, we profiled and integrated the genome-wide occupancy of HDAC1, BRD4, H3K27Ac, and H3K9Ac signals with chromatin accessibility, Pol2 occupancy, and target expression signatures in CLL cells. We identified that when HDAC1 was recruited within super-enhancers (SEs) marked by acetylated H3K27 and BRD4, it functioned as a transcriptional activator that drove the de novo expression of select genes to facilitate survival and progression in CLL. Targeting HDACs reduced BRD4 and Pol2 engagement to downregulate the transcript and proteins levels of specific oncogenic driver genes in CLL such as BLK, a key mediator of the B-cell receptor pathway, core transcription factors such as PAX5 and IKZF3, and the antiapoptotic gene, BCL2. Concurrently, HDAC1, when recruited in the absence of SEs, repressed target gene expression. HDAC inhibition reversed silencing of a defined set of protein-coding and noncoding RNA genes. We focused on a specific set of microRNA genes and showed that their upregulation was inversely correlated with the expression of CLL-specific survival, transcription factor, and signaling genes. Our findings identify that the transcriptional activator and repressor functions of HDACs cooperate within the same tumor to establish the transcriptional dependencies essential for survival in CLL.

The Involvement of Krüppel-like Factors in Cardiovascular Diseases.

Krüppel-like factors (KLFs) are a set of DNA-binding proteins belonging to a family of zinc-finger transcription factors, which have been associated with many biological processes related to the activation or repression of genes, inducing cell growth, differentiation, and death, and the development and maintenance of tissues. In response to metabolic alterations caused by disease and stress, the heart will undergo cardiac remodeling, leading to cardiovascular diseases (CVDs). KLFs are among the transcriptional factors that take control of many physiological and, in this case, pathophysiological processes of CVD. KLFs seem to be associated with congenital heart disease-linked syndromes, malformations because of autosomal diseases, mutations that relate to protein instability, and/or loss of functions such as atheroprotective activities. Ischemic damage also relates to KLF dysregulation because of the differentiation of cardiac myofibroblasts or a modified fatty acid oxidation related to the formation of a dilated cardiomyopathy, myocardial infarctions, left ventricular hypertrophy, and diabetic cardiomyopathies. In this review, we describe the importance of KLFs in cardiovascular diseases such as atherosclerosis, myocardial infarction, left ventricle hypertrophy, stroke, diabetic cardiomyopathy, and congenital heart diseases. We further discuss microRNAs that have been involved in certain regulatory loops of KLFs as they may act as critical in CVDs.

Application of C5.0 Algorithm for the Assessment of Perceived Stress in Healthcare Professionals Attending COVID-19.

Coronavirus disease (COVID-19) represents one of the greatest challenges to public health in modern history. As the disease continues to spread globally, medical and allied healthcare professionals have become one of the most affected sectors. Stress and anxiety are indirect effects of the COVID-19 pandemic. Therefore, it is paramount to understand and categorize their perceived levels of stress, as it can be a detonating factor leading to mental illness. Here, we propose a computer-based method to better understand stress in healthcare workers facing COVID-19 at the beginning of the pandemic. We based our study on a representative sample of healthcare professionals attending to COVID-19 patients in the northeast region of Mexico, at the beginning of the pandemic. We used a machine learning classification algorithm to obtain a visualization model to analyze perceived stress. The C5.0 decision tree algorithm was used to study datasets. We carried out an initial preprocessing statistical analysis for a group of 101 participants. We performed chi-square tests for all questions, individually, in order to validate stress level calculation (p < 0.05) and a calculated Cronbach's alpha of 0.94 and McDonald's omega of 0.95, demonstrating good internal consistency in the dataset. The obtained model failed to classify only 6 out of the 101, missing two cases for mild, three for moderate and one for severe (accuracy of 94.1%). We performed statistical correlation analysis to ensure integrity of the method. In addition, based on the decision tree model, we concluded that severe stress cases can be related mostly to high levels of xenophobia and compulsive stress. Thus, showing that applied machine learning algorithms represent valuable tools in the assessment of perceived stress, which can potentially be adapted to other areas of the medical field.

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes.

BACKGROUND: Dysregulation of imprinted genes, which are expressed in a parent-of-origin-specific manner, plays an important role in various human diseases, such as cancer and behavioral disorder. To date, however, fewer than 100 imprinted genes have been identified in the human genome. The recent availability of high-throughput technology makes it possible to have large-scale prediction of imprinted genes. Here we propose a Bayesian model (dsPIG) to predict imprinted genes on the basis of allelic expression observed in mRNA-Seq data of independent human tissues. RESULTS: Our model (dsPIG) was capable of identifying imprinted genes with high sensitivity and specificity and a low false discovery rate when the number of sequenced tissue samples was fairly large, according to simulations. By applying dsPIG to the mRNA-Seq data, we predicted 94 imprinted genes in 20 cerebellum samples and 57 imprinted genes in 9 diverse tissue samples with expected low false discovery rates. We also assessed dsPIG using previously validated imprinted and non-imprinted genes. With simulations, we further analyzed how imbalanced allelic expression of non-imprinted genes or different minor allele frequencies affected the predictions of dsPIG. Interestingly, we found that, among biallelically expressed genes, at least 18 genes expressed significantly more transcripts from one allele than the other among different individuals and tissues. CONCLUSION: With the prevalence of the mRNA-Seq technology, dsPIG has become a useful tool for analysis of allelic expression and large-scale prediction of imprinted genes. For ease of use, we have set up a web service and also provided an R package for dsPIG at http://www.shoudanliang.com/dsPIG/.

Effect of Packaging and Salt Content and Type on Antioxidant and ACE-Inhibitory Activities in Requeson Cheese.

Requeson cheese is obtained from whey proteins. The production of this cheese is the most economical way to recover and concentrate whey proteins, which is why it is frequently made in some Latin American countries. Four requeson cheese treatments were prepared with different concentrations and combinations of salts (sodium chloride and/or potassium chloride) and were conventionally or vacuum packed. Proteolysis, peptide concentration, angiotensin-converting enzyme (ACE) inhibitory and antioxidant (DPPH and ABTS) activities were evaluated over time (one, seven and fourteen days). Requeson cheese presented antioxidant and ACE inhibitory activities, however, these values vary depending on salt addition, type of packaging and time of storage. The highest values of antioxidant activity (ABTS) were found in cheese added with 1.5% NaCl and 1.5% (NaCl/KCl, 1:1). Cheese without added salt and vacuum packed presented the highest ACE inhibition percentage at day seven. Therefore, it can be concluded that requeson cheese elaborated exclusively of sweet whey, presents antioxidant and ACE inhibition activity. However, for a cheese with ACE inhibitory capacity, it is recommended not to add salts or add at 1% (NaCl) and vacuum pack it. Additionally, for a cheese with antioxidant activity, it is recommended to add salt at 1.5% either NaCl or (1:1) NaCl/KCl and pack it either in a polyethylene bag or vacuum. In conclusion, requeson cheese elaborate with 100% sweet whey is a dairy product with antioxidant and ACE inhibition activity, being low in salt and fat.

Antioxidant and Antimicrobial Activity of Rosemary (Rosmarinus officinalis) and Garlic (Allium sativum) Essential Oils and Chipotle Pepper Oleoresin (Capsicum annum) on Beef Hamburgers.

The inclusion of natural ingredients to preserve meat and meat products has increased in recent years. This study evaluated rosemary (REO) and garlic essential oils (GEO) as well as chipotle pepper oleoresin (CPO), alone or in combination, as preservatives on beef hamburgers (BH). Six treatments were evaluated: T1 (control, without additives), T2 (GEO 1%), T3 (REO 1%), T4 (CPO 0.5%), T5 (GEO 1% + CPO 0.5%) and T6 (REO 1% + CPO 0.5%). The microbiological quality, physicochemical characteristics, sensory evaluation, and lipid oxidation of hamburgers were evaluated. REO, GEO and CPO limited the growth of aerobic microorganisms, S. aureus, Salmonella spp., B. thermosphacta, moulds and yeasts, lactic acid bacteria and coliforms (p < 0.05); however, this effect depended on time. Furthermore, lipid oxidation decreased significantly (p < 0.5) in all treatments, except for T5 (GEO 1% + CPO 0.5%). Regarding sensory acceptance, consumers preferred BH with GEO in terms of colour, odour, flavour and overall appearance (p < 0.05). It is concluded that REO, GEO and CPO, alone or in combination, improve microbiological quality and inhibit the lipid oxidation of BH.

Cancer Stem Cells in Tumor Microenvironment of Adenocarcinoma of the Stomach, Colon, and Rectum.

Gastrointestinal adenocarcinomas are one of the world's deadliest cancers. Cancer stem cells and the tissue microenvironment are highly regulated by cell and molecular mechanisms. Cancer stem cells are essential for maintenance and progression and are associated with resistance to conventional treatments. This article reviews the current knowledge of the role of the microenvironment during the primary establishment of gastrointestinal adenocarcinomas in the stomach, colon, and rectum and its relationship with cancer stem cells. We also describe novel developments in cancer therapeutics, such as targeted therapy, and discuss the advantages and disadvantages of different treatments for improving gastrointestinal cancer prognosis.