Speech's syllabic rhythm and articulatory features produced under different auditory feedback conditions identify Parkinsonism.

Diagnostic tests for Parkinsonism based on speech samples have shown promising results. Although abnormal auditory feedback integration during speech production and impaired rhythmic organization of speech are known in Parkinsonism, these aspects have not been incorporated into diagnostic tests. This study aimed to identify Parkinsonism using a novel speech behavioral test that involved rhythmically repeating syllables under different auditory feedback conditions. The study included 30 individuals with Parkinson's disease (PD) and 30 healthy subjects. Participants were asked to rhythmically repeat the PA-TA-KA syllable sequence, both whispering and speaking aloud under various listening conditions. The results showed that individuals with PD had difficulties in whispering and articulating under altered auditory feedback conditions, exhibited delayed speech onset, and demonstrated inconsistent rhythmic structure across trials compared to controls. These parameters were then fed into a supervised machine-learning algorithm to differentiate between the two groups. The algorithm achieved an accuracy of 85.4%, a sensitivity of 86.5%, and a specificity of 84.3%. This pilot study highlights the potential of the proposed behavioral paradigm as an objective and accessible (both in cost and time) test for identifying individuals with Parkinson's disease.

Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation.

The expressed Ab repertoire is a critical determinant of immune-related phenotypes. Ab-encoding transcripts are distinct from other expressed genes because they are transcribed from somatically rearranged gene segments. Human Abs are composed of two identical H and L chain polypeptides derived from genes in IGH locus and one of two L chain loci. The combinatorial diversity that results from Ab gene rearrangement and the pairing of different H and L chains contributes to the immense diversity of the baseline Ab repertoire. During rearrangement, Ab gene selection is mediated by factors that influence chromatin architecture, promoter/enhancer activity, and V(D)J recombination. Interindividual variation in the composition of the Ab repertoire associates with germline variation in IGH, implicating polymorphism in Ab gene regulation. Determining how IGH variants directly mediate gene regulation will require integration of these variants with other functional genomic datasets. In this study, we argue that standard approaches using short reads have limited utility for characterizing regulatory regions in IGH at haplotype resolution. Using simulated and chromatin immunoprecipitation sequencing reads, we define features of IGH that limit use of short reads and a single reference genome, namely 1) the highly duplicated nature of the DNA sequence in IGH and 2) structural polymorphisms that are frequent in the population. We demonstrate that personalized diploid references enhance performance of short-read data for characterizing mappable portions of the locus, while also showing that long-read profiling tools will ultimately be needed to fully resolve functional impacts of IGH germline variation on expressed Ab repertoires.

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry.

Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of the IG loci has hindered use of standard high-throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we use long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n = 36), representing the first comprehensive description of IGK haplotype variation. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and novel structural variants harboring functional IGKV genes. Among 47 functional IGKV genes, we identify 145 alleles, 67 of which were not previously curated. We report inter-population differences in allele frequencies for 10 IGKV genes, including alleles unique to specific populations within this dataset. We identify haplotypes carrying signatures of gene conversion that associate with SNV enrichment in the IGK distal region, and a haplotype with an inversion spanning the proximal and distal regions. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.

Suppressor tRNAs at the interface of genetic code expansion and medicine.

Suppressor transfer RNAs (sup-tRNAs) are receiving renewed attention for their promising therapeutic properties in treating genetic diseases caused by nonsense mutations. Traditionally, sup-tRNAs have been created by replacing the anticodon sequence of native tRNAs with a suppressor sequence. However, due to their complex interactome, considering other structural and functional tRNA features for design and engineering can yield more effective sup-tRNA therapies. For over 2 decades, the field of genetic code expansion (GCE) has created a wealth of knowledge, resources, and tools to engineer sup-tRNAs. In this Mini Review, we aim to shed light on how existing knowledge and strategies to develop sup-tRNAs for GCE can be adopted to accelerate the discovery of efficient and specific sup-tRNAs for medical treatment options. We highlight methods and milestones and discuss how these approaches may enlighten the research and development of tRNA medicines.

Acute presentation of Wunderlich syndrome in a pregnant woman treated with supra-selective cannulation of renal segmental arteries and nephrectomy: A case report.

Wunderlich syndrome is characterized by the presence of abdominal pain, hematuria, and hypovolemic shock. We report a rare case of a 25-year-old pregnant woman, who came to the emergency department due to the sudden onset of low back pain and diaphoresis. The patient, during medical evaluation, experienced an altered state of consciousness. Diagnosed with hypovolemic shock, she was admitted to the operating room, where examination of the abdominal cavity revealed a left retroperitoneal hematoma. Damage control surgery was performed, but given the postoperative clinical deterioration, computerized tomography angiography of the abdomen was performed, showing a mass-like lesion arising from the upper pole of the left kidney, consistent with Wunderlich syndrome. Left nephrectomy was the definitive treatment for the 10-cm renal angiomyolipoma. Since Wunderlich syndrome is a potentially lethal entity, CT is usually the preferred diagnostic approach, and supra-selective vascular embolization is the first-line treatment.

Vaccination induces broadly neutralizing antibody precursors to HIV gp41.

A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.

Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates.

Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to HIV and other pathogens. However, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. In this work, immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in eight of eight rhesus macaques to substantial frequencies and with diverse lineages in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo-electron microscopy. Our results demonstrate proof of principle for HCDR3-dominant bnAb-precursor priming in outbred animals and suggest that N332-GT5 holds promise for the induction of similar responses in humans.

Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins.

Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA-ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins' active sites. Overall, our work demonstrates the feasibility of creating functional mRNA-rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.

Occupational Balance and Emotional Regulation in People With and Without Serious Mental Illness.

Background. Serious mental illness affects daily functioning, including occupational balance. Purpose. This study aims to compare occupational balance and emotional regulation between people with serious mental illness and the healthy population and to examine the relationship between occupational balance and emotional regulation. Method. A cross-sectional study was performed. Occupational balance and emotional regulation were measured using the Occupational Balance Questionnaire and the Emotional Regulation Questionnaire, respectively. A multivariate analysis (analysis of covariance) was conducted. Findings. The sample consisted of 112 individuals, divided into two groups: the serious mental illness group (n = 55); and the healthy group (n = 57). People with serious mental illness reported lower occupational balance and lower cognitive reappraisal than the healthy population. Furthermore, the higher cognitive reappraisal, the higher the occupational balance, and the higher the expressive suppression, the lower the occupational balance. Conclusion. The results provide preliminary evidence of the relationship between occupational balance and emotional regulation.

Second TURB, restaging TURB or repeat TURB in primary T1 non-muscle invasive bladder cancer: impact on prognosis?

PURPOSE: A re-transurethral resection of the bladder (re-TURB) is a well-established approach in managing non-muscle invasive bladder cancer (NMIBC) for various reasons: repeat-TURB is recommended for a macroscopically incomplete initial resection, restaging-TURB is required if the first resection was macroscopically complete but contained no detrusor muscle (DM) and second-TURB is advised for all completely resected T1-tumors with DM in the resection specimen. This study assessed the long-term outcomes after repeat-, second-, and restaging-TURB in T1-NMIBC patients. METHODS: Individual patient data with tumor characteristics of 1660 primary T1-patients (muscle-invasion at re-TURB omitted) diagnosed from 1990 to 2018 in 17 hospitals were analyzed. Time to recurrence, progression, death due to bladder cancer (BC), and all causes (OS) were visualized with cumulative incidence functions and analyzed by log-rank tests and multivariable Cox-regression models stratified by institution. RESULTS: Median follow-up was 45.3 (IQR 22.7-81.1) months. There were no differences in time to recurrence, progression, or OS between patients undergoing restaging (135 patients), second (644 patients), or repeat-TURB (84 patients), nor between patients who did or who did not undergo second or restaging-TURB. However, patients who underwent repeat-TURB had a shorter time to BC death compared to those who had second- or restaging-TURB (multivariable HR 3.58, P = 0.004). CONCLUSION: Prognosis did not significantly differ between patients who underwent restaging- or second-TURB. However, a worse prognosis in terms of death due to bladder cancer was found in patients who underwent repeat-TURB compared to second-TURB and restaging-TURB, highlighting the importance of separately evaluating different indications for re-TURB.

Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis.

BACKGROUND: In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting. METHODS: In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay. FINDINGS: WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected. INTERPRETATION: We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting. FUNDING: European Research Council and the Spanish Ministerio de Ciencia.

IgM marks persistent IgG anti-human leukocyte antigen antibodies in highly sensitized heart transplant patients.

BACKGROUND: Sensitization to human leukocyte antigens (HLA) is a persistent problem in heart transplant (HT) candidates. We sought to characterize the anti-HLA antibody and circulating B cell repertoire in a cohort of highly sensitized HT candidates. METHODS: We assessed immunoglobulin G (IgG) and immunoglobulin M (IgM) anti-HLA antibodies using Luminex single antigen bead assays in a cohort of 11 highly sensitized (HS; calculated panel reactive antibody ≥ 90%) and 3 mildly sensitized (MS) candidates. We also performed B cell receptor repertoire sequencing (BCRseq) in HS candidates and 33 non-candidate controls. HLA antibody strength was measured by mean fluorescence intensity (MFI). RESULTS: We found that IgM anti-HLA antibodies were present in all HS candidates, but with a lower breadth and strength as compared to IgG. When anti-HLA IgG specificities intersected with IgM, binding strength was higher. In contrast, there were IgM but no intersecting IgG specificities for the MS group. In four candidates in the HS group, IgG anti-HLA antibodies decreased in both breadth and strength after HT, but the decrease in strength was smaller if the IgG possessed a specificity that intersected with pre-transplant IgM. BCRseq revealed larger B cell clonotypes in HS candidates but similar diversity as compared to controls. CONCLUSIONS: IgM marks IgG anti-HLA antibodies with higher strength before HT and persistence after HT. The presence of IgM intersecting IgG for an anti-HLA specificity may be a useful approach to determine which donor HLA should be avoided for a sensitized candidate.

Impacto de la COVID-19 en los enfermos con diagnóstico de cáncer de pulmón en el Hospital Universitario General Calixto García / Impact of COVID-19 on Ill Patients Diagnosed with Lung Cancer at Hospital Universitario General Calixto García

Introducción: En enero de 2020 la Organización Mundial de la Salud declara el estado de pandemia por COVID-19. Los enfermos con cáncer de pulmón tienen gran vulnerabilidad ante esta enfermedad. Objetivo: Evaluar el impacto de la COVID-19 en los enfermos con diagnóstico de cáncer de pulmón. Método: Se realizó un estudio descriptivo, retrospectivo y longitudinal en 273 enfermos con cáncer de pulmón, discutidos en el Grupo Multidisciplinario de Tórax del Hospital Universitario General Calixto García desde el 2019 hasta el 2021. Se analizaron diferentes variables y se aplicaron análisis estadísticos, tales como porcentaje, desviación estándar y media. Resultados: El mayor número de enfermos operados discutidos en el grupo multidisciplinario fue durante el 2019 (21 para un 19,45 porciento). La etapa clínica II predominó en el año 2019, en 10 pacientes. La lobectomía fue la técnica más empleada y predominó en el 2019 en 16 enfermos (76,2 porciento), mientras que durante el 2020-2021 fueron 7. En estos años se diagnosticaron con COVID-19 un total de 17 individuos no operados y fallecieron 11. Conclusiones: Durante el período 2020-2021 disminuyó el número de casos discutidos por cáncer de pulmón en el Grupo Multidisciplinario de Tórax del Hospital Universitario General Calixto García. La mayoría no tuvo criterio de cirugía. La lobectomía fue la técnica quirúrgica más empleada, aunque se redujo su realización durante el 2020-2021. La mayoría de los enfermos que contrajeron COVID-19 no fueron operados y más de la mitad de ellos fallecieron(AU)

Introduction: In January 2020, the World Health Organization declares a pandemic status due to the COVID-19. Lung cancer patients are highly vulnerable to this disease. Objective: To evaluate the impact of COVID-19 in patients diagnosed with lung cancer. Methods: A descriptive, retrospective and longitudinal study was carried out in 273 patients with lung cancer, discussed in the multidisciplinary thorax group at Hospital Universitario General Calixto García from 2019 to 2021. Different variables were analyzed and statistical analyses were applied, such as percentage, standard deviation and mean. Results: The highest number of operated patients discussed in the multidisciplinary group was reported during 2019 (21, accounting for 19.45 percent). The clinical stage II predominated in 2019, with 10 patients. Lobectomy was the most used technique and the predominant in 2019, with 16 patients (76.2 percent), while 7 were reported during 2020-2021. A total of 17 nonoperated individuals were diagnosed with COVID-19 in these years and 11 died. Conclusions: During 2020-2021, there was a decrease in the number of lung cancer cases discussed in the multidisciplinary thorax group at Hospital Universitario General Calixto García decreased. Most of them did not have surgery criteria. Lobectomy was the most used surgical technique, although its realization was reduced during 2020-2021. Most of the patients who contracted COVID-19 were not operated and over half of them died(AU)

Tick infestation in spur-thighed tortoise population: a pilot study for unraveling epidemiological patterns and demographic consequences.

Ectoparasites, such as ticks, modulate host population dynamics by impacting demographic traits. They transmit infectious agents among their hosts, posing a critical threat to animal and public health. This study aimed to characterize and analyze the Hyalomma aegyptium infestation on one of its main hosts, the spur-thighed tortoise, its effects on demographic traits, and to determine the diversity of infectious agents present in both ticks and tortoises in the Maamora forest (northwestern Morocco). Our results show that 100% of the tortoises were parasitized by adult ticks in spring, an infestation intensity of 4 ticks/tortoise (5.1 and 3.6 ticks/tortoise in males and females, respectively; 4.2 and 3.3 ticks/tortoise in gravid and non-gravid females, respectively) and an abundance ranging from 1 to 12. Although without significant differences, male tortoises had higher tick abundances than females. The interaction of tortoise sex and body condition was significantly related to tick abundance, male body condition decreased with higher tick abundance in contrast to females. Nevertheless, the interaction of body condition and reproductive stage of females was not significantly related to tick abundance. Gravid females were significantly associated with tick abundance, showing a slightly higher infestation than non-gravid females. Molecular analysis of pooled tick samples revealed the presence of Ehrlichia ewingii, Candidatus Midichloria mitochondrii, and Rickettsia africae, with a minimum infection rate of 0.61 to 1.84%. However, blood sample analysis of the tortoises was infectious agent-free, pinpointing a lack of significant health problems. Given the possible effect on the transmission of zoonotic diseases by spur-thighed tortoises associated with their frequent collection as pets, it should be surveyed to control possible human health problems. In conservation terms, as a long-lived species, the role of tick infestation in demographic traits might be included in the management and conservation programs of spur-thighed tortoises.

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.

Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), has been shown to be of critical importance for immune responses to pathogens and vaccines. In recent years, B cell and T cell receptor repertoire sequencing (Rep-Seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci in different populations. Here we present a novel algorithm for extra-sensitive and specific variable (V) and joining (J) gene allele inference and genotyping allowing reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput genotyping and novel allele discovery from a wide variety of existing datasets. The developed algorithm is a part of the MiXCR software ( https://mixcr.com ) and can be incorporated into any pipeline utilizing upstream processing with MiXCR. We demonstrate the accuracy of this approach using Rep-Seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) Rep-Seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA; TRB) Rep-Seq dataset, representing 134 individuals. This allowed us to assess the genetic diversity of genes within the IGH, TRA and TRB loci in different populations and demonstrate the connection between antibody repertoire gene usage and the number of allelic variants present in the population. Finally we established a database of allelic variants of V and J genes inferred from Rep-Seq data and their population frequencies with free public access at https://vdj.online .

SeQual-Stream: approaching stream processing to quality control of NGS datasets.

BACKGROUND: Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have the complete genetic dataset before processing can even begin. This limitation clearly hinders quality control performance in those scenarios where the dataset must be downloaded from a remote repository and/or copied to a distributed file system for its parallel processing. RESULTS: In this paper we present SeQual-Stream, a streaming tool that allows performing multiple quality control operations on genomic datasets in a fast, distributed and scalable way. To do so, our approach relies on the Apache Spark framework and the Hadoop Distributed File System (HDFS) to fully exploit the stream paradigm and accelerate the preprocessing of large datasets as they are being downloaded and/or copied to HDFS. The experimental results have shown significant improvements in the execution times of SeQual-Stream when compared to a batch processing tool with similar quality control features, providing a maximum speedup of 2.7[Formula: see text] when processing a dataset with more than 250 million DNA sequences, while also demonstrating good scalability features. CONCLUSION: Our solution provides a more scalable and higher performance way to carry out quality control of large genomic datasets by taking advantage of stream processing features. The tool is distributed as free open-source software released under the GNU AGPLv3 license and is publicly available to download at https://github.com/UDC-GAC/SeQual-Stream .

Case report: Endovascular stent-graft repair of aortic penetrating trauma, literature review, and case report.

Penetrating aortic injuries are infrequent. Its incidence is unknown because most patients die of hemorrhage even before they receive adequate treatment. Aortic wounds generally require conventional thoracotomy/laparotomy repair and are related to high mortality rates. Recently with the advent of endovascular techniques, most authors prefer endovascular management when feasible due to better (still poor) outcomes. The short- and mid-term results of immediate endovascular repair of traumatic aortic injuries are promising, especially when compared with open surgical treatment, indicating that endovascular therapy is preferable in patients with multi-trauma and traumatic ruptures of the thoracic aorta. Here we present the diagnosis and treatment of a 30 years-old male patient with multiple traumatic stab wounds, including anterior aortic laceration with a grade II aortic lesion successfully managed with an endovascular stent graft.