Founder reconstruction enables scalable and seamless pangenomic analysis.

MOTIVATION: Variant calling workflows that utilize a single reference sequence are the de facto standard elementary genomic analysis routine for resequencing projects. Various ways to enhance the reference with pangenomic information have been proposed, but scalability combined with seamless integration to existing workflows remains a challenge. RESULTS: We present PanVC with founder sequences, a scalable and accurate variant calling workflow based on a multiple alignment of reference sequences. Scalability is achieved by removing duplicate parts up to a limit into a founder multiple alignment, that is then indexed using a hybrid scheme that exploits general purpose read aligners. Our implemented workflow uses GATK or BCFtools for variant calling, but the various steps of our workflow (e.g. vcf2multialign tool, founder reconstruction) can be of independent interest as a basis for creating novel pangenome analysis workflows beyond variant calling. AVAILABILITY AND IMPLEMENTATION: Our open access tools and instructions how to reproduce our experiments are available at the following address: https://github.com/algbio/panvc-founders. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An Extremely Low-Frequency Vortex Magnetic Field Modifies Protein Expression, Rearranges the Cytoskeleton, and Induces Apoptosis of a Human Neuroblastoma Cell Line.

Homogeneous extremely low-frequency electromagnetic fields (ELF-EMFs) alter biological phenomena, including the cell phenotype and proliferation rate. Heterogenous vortex magnetic fields (VMFs), a new approach of exposure to magnetic fields, induce systematic movements on charged biomolecules from target cells; however, the effect of VMFs on living systems remains uncertain. Here, we designed, constructed, and characterized an ELF-VMF-modified Rodin's coil to expose SH-SY5Y cells. Samples were analyzed by performing 2D-differential-gel electrophoresis, identified by MALDI-TOF/TOF, validated by western blotting, and characterized by confocal microscopy. A total of 106 protein spots were differentially expressed; 40 spots were downregulated and 66 were upregulated in the exposed cell proteome, compared to the control cell proteome. The identified spots are associated with cytoskeleton and cell viability proteins, and according to the protein-protein interaction network, a significant interaction among them was found. Our data revealed a decrease in cell survival associated with apoptotic cells without effects on the cell cycle, as well as evident changes in the cytoskeleton. We demonstrated that ELF-VMFs, at a specific frequency and exposure time, alter the cell proteome and structurally affect the target cells. This is the first report showing that VMF application might be a versatile system for testing different hypotheses in living systems, using appropriate exposure parameters.© 2022 Bioelectromagnetics Society.

Effect of parota (Enterolobium cyclocarpum) pod protein supplement on feed intake and digestibility and calf ruminal characteristics.

The objective of this study was to evaluate feed intake and digestibility and ruminal characteristics of development-stage calves fed mulatto II (Brachiaria sp.) grass hay (MGH) and a protein supplement (PS) consisting of increasing levels of the parota (Enterolobium cyclocarpum) pod (PP). We used eight Swiss-zebu calves in growth stage with an average age of 11 months and initial average weight of 157.6 ± 8.5 kg. They were distributed in a repeated 4 × 4 Latin square design with 4 treatments (period 30 days): 0% (PP0), 25% (PP25), 50% (PP50), and 75% (PP75) of the PP. Calves in the PP0 and PP25 treatments had higher intake of PS and MGH as dry matter (DM) than those in the PP50 and PP75 treatments (p < 0.05). Organic matter intake (OMI) of the PP75 calves was lower than that of PP0 and PP25 calves. Crude protein intakes (CPI) of PP0 and PP25 calves were higher than those of PP50 and PP75 calves (p < 0.05). Apparent digestibility of crude protein was higher in the PP0, PP25, and PP50 treatments compared with that in treatment PP75 (p < 0.05). The treatments did not affect total bacterial count, cellulolytic bacterial count, cellulase enzymatic activity, volatile fatty acids, or the acetate/propionate ratio (p > 0.05). Rumen pH in the PP0 calves was higher than that of the PP25 calves, whereas the protozoa count and ammonia content were higher in PP0 calves than in PP75 (p < 0.05). In conclusion, the inclusion of 25% PP in the PS for forage-fed calves is a feeding alternative.

Inside minds, beneath diseases: social cognition in amyotrophic lateral sclerosis-frontotemporal spectrum disorder.

OBJECTIVE: To compare social cognition performance between patients with amyotrophic lateral sclerosis (ALS) and those patients with behavioural variant frontotemporal dementia (bvFTD). METHODS: We included 21 participants with ALS, 20 with bvFTD and 21 healthy controls who underwent a comprehensive cognitive battery, including the short version of the Social Cognition and Emotional Assessment (Mini-SEA), which comprises the faux pas test and Facial Emotion Recognition Test (FERT); Mini-Mental State Examination; Frontal Assessment Battery; lexical fluency (F-A-S), category fluency (animals/minute), digit span (direct and backwards) tests and the Hayling test. A post hoc analysis was conducted with the patients with ALS divided into two subgroups: patients without cognitive impairment (ALScn; n=13) and patients with cognitive impairment (ALSci; n=8). RESULTS: No significant difference was noted between participant groups in terms of the age, sex and education. ALS-total group and patients with bvFTD had similar disease durations. Patients with ALSci performed poorly when compared with controls with regard to the FERT (p<0.001), the faux pas (p<0.004) and the Mini-SEA (p<0.002) total scores. Moreover, patients with bvFTD performed poorly in comparison with controls in executive and social cognition tests. The performance of patients with ALSci was similar to that of patients with bvFTD, while the performance of patients with ALScn was similar to that of controls. DISCUSSION: Our findings support a cognitive continuum between ALS and bvFTD and shed light on the cognitive heterogeneity of ALS, expanding its possible neuropsychological profiles.

Novel Regulatory Mechanisms for the SoxC Transcriptional Network Required for Visual Pathway Development.

What pathways specify retinal ganglion cell (RGC) fate in the developing retina? Here we report on mechanisms by which a molecular pathway involving Sox4/Sox11 is required for RGC differentiation and for optic nerve formation in mice in vivo, and is sufficient to differentiate human induced pluripotent stem cells into electrophysiologically active RGCs. These data place Sox4 downstream of RE1 silencing transcription factor in regulating RGC fate, and further describe a newly identified, Sox4-regulated site for post-translational modification with small ubiquitin-related modifier (SUMOylation) in Sox11, which suppresses Sox11's nuclear localization and its ability to promote RGC differentiation, providing a mechanism for the SoxC familial compensation observed here and elsewhere in the nervous system. These data define novel regulatory mechanisms for this SoxC molecular network, and suggest pro-RGC molecular approaches for cell replacement-based therapies for glaucoma and other optic neuropathies.SIGNIFICANCE STATEMENT Glaucoma is the most common cause of blindness worldwide and, along with other optic neuropathies, is characterized by loss of retinal ganglion cells (RGCs). Unfortunately, vision and RGC loss are irreversible, and lead to bilateral blindness in ∼14% of all diagnosed patients. Differentiated and transplanted RGC-like cells derived from stem cells have the potential to replace neurons that have already been lost and thereby to restore visual function. These data uncover new mechanisms of retinal progenitor cell (RPC)-to-RGC and human stem cell-to-RGC fate specification, and take a significant step toward understanding neuronal and retinal development and ultimately cell-transplant therapy.

Towards pan-genome read alignment to improve variation calling.

BACKGROUND: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation. RESULTS: We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation - a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC . CONCLUSIONS: Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.

Recombination-aware alignment of diploid individuals.

BACKGROUND: Traditionally biological similarity search has been studied under the abstraction of a single string to represent each genome. The more realistic representation of diploid genomes, with two strings defining the genome, has so far been largely omitted in this context. With the development of sequencing techniques and better phasing routines through haplotype assembly algorithms, we are not far from the situation when individual diploid genomes could be represented in their full complexity with a pair-wise alignment defining the genome. RESULTS: We propose a generalization of global alignment that is designed to measure similarity between phased predictions of individual diploid genomes. This generalization takes into account that individual diploid genomes evolve through a mutation and recombination process, and that predictions may be erroneous in both dimensions. Even though our model is generic, we focus on the case where one wants to measure only the similarity of genome content allowing free recombination. This results into efficient algorithms for direct application in (i) evaluation of variation calling predictions and (ii) progressive multiple alignments based on labeled directed acyclic graphs (DAGs) to represent profiles. The latter may be of more general interest, in connection to covering alignment of DAGs. Extensions of our model and algorithms can be foreseen to have applications in evaluating phasing algorithms, as well as more fundamental role in phasing child genome based on parent genomes.

[Overlapping features of frontotemporal dementia and amyotrophic lateral sclerosis]. / Manifestaciones neuropsiquiátricas y cognitivas en demencia frontotemporal y esclerosis lateral amiotrófica: dos polos de una entidad común.

Recent genetic and neuropathologic advances support the concept that frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are overlapping multisystem disorders. While 10-15% of ALS patients fulfil criteria for FTD, features of motor neuron disease appear in approximately 15% of FTD patients, during the evolution of the disease. This overlap has been reinforced by the discovery of Transactive Response DNA Binding Protein 43 kDa (TDP43) inclusions as the main neuropathologic finding in the majority of ALS cases and almost a half of FTD cases. Also, an expansion in the intron of C9ORF72 (chromosome 9p21) has been identified in families affected by ALS, ALS-FTD and FTD. This review provides an update on the recent genetic and neuropathologic findings of ALS and FTD and a characterization of their clinical presentation forms, based on the current diagnostic criteria. Finally it underscores the importance of having a national registry of patients with ALS and FTD, to provide an earlier diagnosis and a multidisciplinary care.

Incidence of amyotrophic lateral sclerosis in Chile.

OBJECTIVE: This study aimed to estimate amyotrophic lateral sclerosis (ALS) incidence and survival rates in the Metropolitan region of Chile. METHODS: We conducted a cohort study of ALS cases in the Metropolitan Region from 2016 to 2019. A total of 219 ALS patients were recruited from Corporación ELA-Chile registry, in collaboration with neurologists from Sociedad de Neurología, Psiquiatría y Neurocirugía de Chile. We calculated incidence rates by sex and age and determined median survival from onset and diagnosis. Survival analysis used the Kaplan-Meier statistic, estimating hazard ratios for age, sex, time from symptom onset and from diagnosis using a Weibull regression model. All analyses were done using R 4.1.0. RESULTS: Overall, ALS diagnosis incidence was 0.97 cases per 100,000 inhabitants, peaking in the 70-79 age group and declining thereafter. The male-to-female ratio was 1.23. The median time to death from diagnosis was 2.3 years (95% confidence interval [CI]: 1.9-2.5), and from the first symptom, it was 3.1 years (95% CI: 2.8-3.5). CONCLUSIONS: This is the first population-based study reporting ALS incidence and survival rates in Chile's Metropolitan region. Incidence resembled other Latin American studies. Median survival from diagnosis and from the first symptom were in line with previous findings. Our results corroborated lower ALS rates in Latin America, consistent with prior research.

The Latin American Epidemiology Network for ALS (Laenals).

Background: There is evolving evidence of non-uniform distribution of ALS worldwide, with apparently lower incident and prevalent rates outside populations of European origin. However, the phenotype, survival and environmental risk in populations of mixed ancestral origin have not been well established. Large scale population based studies of incidence, prevalence, phenotype and risk factors in admixed populations are necessary to determine the true demography of ALS, and to test the hypothesis of differential risk and phenotype in populations of mixed ancestry. Methods: The Latin American Epidemiological Network of ALS (LAENALS) has been established to perform a comparative analysis of ALS epidemiology between three different Latin American populations (Cuba, Uruguay and Chile), and to test the hypothesis that the demographics, phenotype and outcome of ALS are influenced by ancestral origin, and that environmental and occupational risk factors differ across different ethnicities due to subtle differences in gene- environmental interactions. Recognition and interrogation of these differences is an important step toward novel therapeutic approaches and personalized medicine for all ALS both in the US, and worldwide. Discussion: This work will enable direct and detailed comparative studies between different ancestral populations with varying degrees of admixture, with facility for comparison with a large European reference dataset for ALS, and will provide a unique and rich dataset of admixed populations for later comparative genomic studies.

Acute macular neuroretinopathy following Pfizer-BioNTech COVID-19 vaccination.

PURPOSE: To describe a case of acute macular neuroretinopathy (AMN) in a patient immediately following administration of the Pfizer-BioNTech COVID-19 vaccine. OBSERVATIONS: The patient complained of paracentral scotoma supported by paracentral visual field loss on multiple Humphrey visual fields that corresponded to outer retinal pathology on optical coherence tomography. The patient's symptoms resolved without treatment. CONCLUSIONS AND IMPORTANCE: We conclude that the clinical testing demonstrated findings consistent with AMN. AMN may be an exceedingly rare adverse ocular effect of a novel vaccine and likely only in the setting of multiple other risk factors. Despite this, we strongly recommend vaccination against COVID-19.

Distributed hybrid-indexing of compressed pan-genomes for scalable and fast sequence alignment.

Computational pan-genomics utilizes information from multiple individual genomes in large-scale comparative analysis. Genetic variation between case-controls, ethnic groups, or species can be discovered thoroughly using pan-genomes of such subpopulations. Whole-genome sequencing (WGS) data volumes are growing rapidly, making genomic data compression and indexing methods very important. Despite current space-efficient repetitive sequence compression and indexing methods, the deployed compression methods are often sequential, computationally time-consuming, and do not provide efficient sequence alignment performance on vast collections of genomes such as pan-genomes. For performing rapid analytics with the ever-growing genomics data, data compression and indexing methods have to exploit distributed and parallel computing more efficiently. Instead of strict genome data compression methods, we will focus on the efficient construction of a compressed index for pan-genomes. Compressed hybrid-index enables fast sequence alignments to several genomes at once while shrinking the index size significantly compared to traditional indexes. We propose a scalable distributed compressed hybrid-indexing method for large genomic data sets enabling pan-genome-based sequence search and read alignment capabilities. We show the scalability of our tool, DHPGIndex, by executing experiments in a distributed Apache Spark-based computing cluster comprising 448 cores distributed over 26 nodes. The experiments have been performed both with human and bacterial genomes. DHPGIndex built a BLAST index for n = 250 human pan-genome with an 870:1 compression ratio (CR) in 342 minutes and a Bowtie2 index with 157:1 CR in 397 minutes. For n = 1,000 human pan-genome, the BLAST index was built in 1520 minutes with 532:1 CR and the Bowtie2 index in 1938 minutes with 76:1 CR. Bowtie2 aligned 14.6 GB of paired-end reads to the compressed (n = 1,000) index in 31.7 minutes on a single node. Compressing n = 13,375,031 (488 GB) GenBank database to BLAST index resulted in CR of 62:1 in 575 minutes. BLASTing 189,864 Crispr-Cas9 gRNA target sequences (23 MB in total) to the compressed index of human pan-genome (n = 1,000) finished in 45 minutes on a single node. 30 MB mixed bacterial sequences were (n = 599) were blasted to the compressed index of 488 GB GenBank database (n = 13,375,031) in 26 minutes on 25 nodes. 78 MB mixed sequences (n = 4,167) were blasted to the compressed index of 18 GB E. coli sequence database (n = 745,409) in 5.4 minutes on a single node.

An Unusual Granular Ulcer Secondary Oral Tuberculosis of Vestibule Mandibular Mucosa.

Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis. In the oral cavity, clinical manifestations are considered atypical lesions. The aim of this study was to report an unusual granular ulcer secondary oral TB that does not heal, chronic, had irregular appearance with deep depression of 2 cm in diameter, and was located in buccal mucosa of the premolar area-the left mandibular arch, of a 42-year-old woman. The patient was subjected to surgical excision of ulcer in its entirety and accordingly a periodontal plastic surgery in the area of the lesion was performed positioning an autograft subepithelial connective tissue. We obtained optimal results in improving oral health, function, and patient's comfort, in postoperative controls at 15, 30, and 60 days, respectively.

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics.

Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence analysis. In this paper, we show that the computational complexity will change for natural extensions of alignments to pan-genome representations and to diploid genomes. More broadly, our approach can also be seen as a minimal extension of sequence alignment to labelled directed acyclic graphs (labeled DAGs). Namely, we show that finding a covering alignment of two labeled DAGs is NP-hard even on binary alphabets. A covering alignment asks for two paths R1 (red) and G1 (green) in DAG D1 and two paths R2 (red) and G2 (green) in DAG D2 that cover the nodes of the graphs and maximize the sum of the global alignment scores: as(sp(R1),sp(R2))+as(sp(G1),sp(G2)), where sp(P) is the concatenation of labels on the path P. Pair-wise alignment of haplotype sequences forming a diploid chromosome can be converted to a two-path coverable labelled DAG, and then the covering alignment models the similarity of two diploids over arbitrary recombinations. We also give a reduction to the other direction, to show that such a recombination-oblivious diploid alignment is NP-hard on alphabets of size 3.

Surface roughness implant-retained mandibular bar and ball joint overdentures and adherence of microorganisms.

OBJECTIVE: The aim of this study is to assess the surface roughness of the implant-retained mandibular bar overdenture (BOD) and the implant-retained mandibular ball joint overdenture (BJOD) in jaw and its relation with the adhesion of molds and yeasts and mesophyll aerobe, in time 30 and 180 days in mouth. MATERIALS AND METHODS: Five-systems titanium bar CARES® and synOcta® Straumann® Dental Implant System, Holding AG Inc., Basel, Switzerland (BOD), and five-systems joint ball Klockner® Implant System; Soadco Inc., Escaldes-Engordany; Andorra (BJOD), were used in two parallel groups of five participants, in an essay to simple blind person. To 30 and 180 days, the overdentures were withdrawn and evaluated the Ra: um. SJ-301® Mitutoyo Corporation Inc., Kanagawa, Japan, and the adhesion of microorganisms (colony-forming unit/ml). RESULTS: The results were as follows: the R a: Um (30th and 180th): BOD, 0.965-1.351; BJOD, 1.325-2.384. Adhesion: Molds and yeasts, BOD, 2.6 × 102 and 4.6 × 103; BJOD, 3.0 × 102 and 5.3 × 104. Adhesion: Mesophyll aerobe, BOD, 3.8 × 106 and 5.8 × 106; BJOD, 4.3 × 106 and 7.1 × 107. CONCLUSIONS: At 30 days (P = 0.489), there were no differences in BOD and BJOD for adhesion of molds and yeasts and mesophyll aerobe between both overdentures. At 180 days (P = 0.723), there were differences in the adhesion of mold and yeast and mesophyll aerobe, being greater in BJOD.

Perfil de pacientes adultos hospitalizados por COVID-19 antes y después de la introducción de las vacunas contra SARS-CoV-2 / Profile of adult patients hospitalized with COVID-19 before and after the introduction of vaccines against SARS-CoV-2

INTRODUCCIÓN: La introducción progresiva de vacunas contra SARS-CoV-2 a partir de 2021, priorizando grupos de mayor edad, podría implicar un cambio en el perfil de pacientes hospitalizados por COVID-19 en el tiempo. OBJETIVO: Comparar las características y evolución de pacientes adultos hospitalizados por COVID-19 en un período anterior en 2020 (PER1) y otro posterior al inicio de la vacunación masiva contra SARS-CoV-2 (PER2). PACIENTES Y MÉTODOS: Se registró edad, género, comorbilidades, complicaciones y evolución de los pacientes hospitalizados por COVID-19 en una clínica privada, en Santiago, Chile. Se calculó el puntaje de gravedad y riesgo nutricional. RESULTADOS: En PER2, los pacientes fueron de menor edad, pero con comorbilidades similares al PER1, excepto por mayor malnutrición por exceso. Los pacientes del PER2 no vacunados requirieron más ventilación mecánica (38,9 vs. 14,3%, p = 0,03) y evolucionaron más gravemente (puntaje 6) que aquellos adecuadamente inmunizados (puntaje 5, p = 0,048). Las variables que más predijeron mortalidad fueron edad > 60 años (OR 28.995) y presencia de riesgo nutricional (OR 5.246). DISCUSIÓN: El cambio en el perfil y evolución de los pacientes hospitalizados con COVID-19 está asociado con la secuencia de priorización de vacunas contra SARS-CoV-2, cuyo efecto redujo las hospitalizaciones y gravedad de COVID-19 en adultos mayores.

BACKGROUND: During the COVID-19 pandemic, the early prioritization of SARS-CoV-2 vaccines for older adults may have affected the characteristics of hospitalized COVID-19 patients over time. AIM: To compare the clinical characteristics and outcomes of adult patients admitted for COVID-19 before (PER1) and after (PER2) the initiation of mass vaccination for SARS-CoV-2. METHODS: Data on age, gender, comorbidities, complications, and outcomes of adult patients hospitalized for COVID-19 in a private clinic of Santiago, Chile, were collected. Scores for COVID-19 severity and nutritional risk were calculated. RESULTS: In PER2, patients were younger but had similar comorbidities, except for a higher prevalence of overweight and obesity compared to PER1. Unvaccinated COVID-19 patients in PER2 required more invasive ventilatory support (38.9% vs. 14.3%, p = 0.03) and had a higher severity score (six) than vaccinated patients (five, p = 0.048). The variables that best predicted mortality were age > 60 years (OR 28,995) and the presence of nutritional risk (OR 5,246). DISCUSSION: Changes in the profile and outcomes of hospitalized patients during the COVID-19 pandemic are associated with the prioritization of SARS-CoV-2 vaccines and their protective effect in reducing hospitalizations and disease severity in older adults.

A Pigmented Iris Lesion.

A patient in their mid-60s presented with a left iris pigmented lesion that had been present for decades and remained stable in size. What would you do next?

Amyotrophic lateral sclerosis mortality rates in Chile: A population based study (1994-2010).

Our objective was to describe amyotrophic lateral sclerosis (ALS) mortality rates in the Chilean population over a 17-year period. Chilean death records (1994-2010) were reviewed for the ICD-10 diagnosis G.12.2 (including motor neuron disease and similar conditions), and weighted with population data. Crude and standardized mortality rates by ALS were calculated at the nationwide level and by geographic zone. A risk analysis was performed in successive cohorts from 1910-1919 to 1960-1969, comparing mortality slopes. One thousand six hundred and seventy-one deaths were recorded during 1994-2010, with an average of 1.13 per 100,000, a 1.2:1 male/female ratio, and a statistically significant increase in mortality rate. According to geographical distribution, the Austral area, with a larger population of European origin, showed higher mortality rates compared to the national average. The cohort analysis showed an increasing risk of dying from ALS for all cohorts, and highest above 64 years of age, becoming a competitive cause of death in older ages. In conclusion, as expected, the mortality rate in Chile by ALS is higher than that reported previously in our country, and similar to other Latin American countries. ALS mortality rate has increased over time probably due to the aging of the population and decline in rates for competing causes of death.