Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.

In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.

The Initial Journey of Patients with Metastatic Pancreatic Cancer (PaCTO Project): A Nationwide Survey among Portuguese Specialist Physicians.

Introduction: We aimed to characterize the initial healthcare journey of metastatic pancreatic ductal adenocarcinoma (mPDAC) patients in Portugal, including healthcare provision and factors affecting therapeutic decisions, namely BRCA mutations testing. Methods: This is a descriptive cross-sectional, web-based survey using a convenience sampling approach. Portuguese oncologists and pathologists that routinely work with mPDAC patients from the different geographical regions and settings were invited to participate in the study via email (December 2020). Descriptive statistical analyses were performed, with categorical variables reported as absolute and relative frequencies, and continuous variables with non-normal distribution as median and interquartile range (IQR) (Stata v.15.0). Results: Seventy physicians participated in the study (43 oncologists, 27 pathologists). According to the responses, a median of 28 patients per center (IQR 12-70) was diagnosed with PDAC in the previous year; 22 of them referring (IQR 8-70) to mPDAC. The pointed median time from patients' first hospital admission until disease diagnosis/staging is between 2 and 4 weeks. Endoscopic ultrasound with fine-needle biopsy is available in most hospitals (86%). Around 50% of physicians request BRCA testing; the assessment of additional biomarkers besides BRCA is requested by 40% of professionals. Half of them stated that BRCA testing should be requested earlier-upon histological diagnosis, especially because the median time for results is of 4.0 weeks (IQR 4-8). PARP inhibitors such as olaparib, when available, would be the therapy of choice for most oncologists (71%) if no disease' progression occurs after 4 months. Treatments' selection is usually grounded on clinical criteria (e.g., performance status, liver function). Around 45% of patients use FOLFIRINOX/mFOLFIRINOX as the first-line therapy. Gemcitabine + nab-paclitaxel is used by 35% of patients as the second-line therapy. Conclusions: Physicians in Portugal support the increasing role of patient-tailored treatments in mPDAC, whose selection should be grounded on tumoral subtyping and molecular profiling. Further efforts to develop multidisciplinary teams, standardized clinical practice, and optimize the implementation of new target therapies are needed.

Introdução: Este estudo teve como objetivo caracterizar o percurso inicial dos doentes com adenocarcinoma ductal pancreático metastático (ACDPm) em Portugal, incluindo a prestação de cuidados de saúde e determinação de fatores que afetam as decisões terapêuticas, nomeadamente o teste de mutações BRCA. Métodos: Trata-se de um estudo descritivo transversal (web-based) usando uma abordagem de amostragem por conveniência. Médicos oncologistas e anatomopatologistas portugueses dedicados ao ACDPm e de diferentes regiões geográficas e instituições foram convidados a participar do estudo por email (Dez-2020). Foram realizadas análises estatísticas descritivas, com variáveis categóricas relatadas como frequências absolutas e relativas, e variáveis contínuas com distribuição não-normal como mediana e intervalo interquartil (IIQ) (Stata v.15.0). Resultados: Setenta médicos participaram do estudo (43 oncologistas, 27 patologistas). De acordo com as respostas, uma mediana de 28 doentes por centro (IIQ 12­70) foi diagnosticada com ACDP no ano anterior; 22 deles (IIQ 8­70) referentes a ACDPm. O tempo médio desde a primeira admissão hospitalar dos doentes até o diagnóstico/estadiamento da doença foi entre 2­4 semanas. A ultrassonografia endoscópica com biópsia por agulha fina é realizada pela maioria dos hospitais (86%). Aproximadamente 50% dos médicos referem solicitar o teste BRCA; a avaliação de biomarcadores adicionais além do BRCA é solicitada por 40% dos profissionais. Metade dos médicos assume que o teste BRCA deveria ser solicitado mais precocemente ­ durante o diagnóstico histológico, principalmente porque o tempo médio para obtenção do resultado é de 4,0 semanas (IIQ 4­8). Os inibidores PARP, como o olaparibe, quando disponíveis, seriam a terapia de escolha para a maioria dos oncologistas (71%) caso não haja progressão da doença após quatro meses. A seleção dos tratamentos é usualmente baseada em critérios clínicos (por exemplo, performance status, função hepática). Em cerca de 45% dos doentes é utilizado FOLFIRINOX/mFOLFIRINOX como terapia de primeira linha. Um esquema com Gemcitabina + nab-paclitaxel é usado em 35% dos doentes como terapia de segunda linha. Conclusões: Os médicos em Portugal apoiam o papel crescente do tratamento individualizado no ACDPm, cuja seleção deve ser baseada na subtipagem tumoral e no perfil molecular. São necessários mais esforços para capacitar as equipas multidisciplinares, desenvolver práticas clínicas padronizadas e otimizar a implementação de novas terapias-alvo.

Cluster effect for SNP-SNP interaction pairs for predicting complex traits.

Single nucleotide polymorphism (SNP) interactions are the key to improving polygenic risk scores. Previous studies reported several significant SNP-SNP interaction pairs that shared a common SNP to form a cluster, but some identified pairs might be false positives. This study aims to identify factors associated with the cluster effect of false positivity and develop strategies to enhance the accuracy of SNP-SNP interactions. The results showed the cluster effect is a major cause of false-positive findings of SNP-SNP interactions. This cluster effect is due to high correlations between a causal pair and null pairs in a cluster. The clusters with a hub SNP with a significant main effect and a large minor allele frequency (MAF) tended to have a higher false-positive rate. In addition, peripheral null SNPs in a cluster with a small MAF tended to enhance false positivity. We also demonstrated that using the modified significance criterion based on the 3 p-value rules and the bootstrap approach (3pRule + bootstrap) can reduce false positivity and maintain high true positivity. In addition, our results also showed that a pair without a significant main effect tends to have weak or no interaction. This study identified the cluster effect and suggested using the 3pRule + bootstrap approach to enhance SNP-SNP interaction detection accuracy.

Exploring volatile compounds and microbial dynamics: Kluyveromyces marxianus and Hanseniaspora opuntiae reduce Forastero cocoa fermentation time.

Traditional cocoa bean fermentation is a spontaneous process and can result in heterogeneous sensory quality. For this reason, yeast-integrated starter cultures may be an option for creating consistent organoleptic profiles. This study proposes the mixture of Hanseniaspora opuntiae and Kluyveromyces marxianus (from non-cocoa fermentation) as starter culture candidates. The microorganisms and volatile compounds were analyzed during the cocoa fermentation process, and the most abundant were correlated with predominant microorganisms. Results showed that Kluyveromyces marxianus, isolated from mezcal fermentation, was identified as the dominant yeast by high-throughput DNA sequencing. A total of 63 volatile compounds identified by HS-SPME-GC-MS were correlated with the more abundant bacteria and yeast using Principal Component Analysis and Agglomerative Hierarchical Clustering. This study demonstrates that yeasts from other fermentative processes can be used as starter cultures in cocoa fermentation and lead to the formation of more aromatic esters, decrease the acetic acid content.

BUB1B monoallelic germline variants contribute to prostate cancer predisposition by triggering chromosomal instability.

BACKGROUND: Prostate cancer (PrCa) is the most frequently diagnosed cancer in men. Variants in known moderate- to high-penetrance genes explain less than 5% of the cases arising at early-onset (< 56 years) and/or with familial aggregation of the disease. Considering that BubR1 is an essential component of the mitotic spindle assembly checkpoint, we hypothesized that monoallelic BUB1B variants could be sufficient to fuel chromosomal instability (CIN), potentially triggering (prostate) carcinogenesis. METHODS: To unveil BUB1B as a new PrCa predisposing gene, we performed targeted next-generation sequencing in germline DNA from 462 early-onset/familial PrCa patients and 1,416 cancer patients fulfilling criteria for genetic testing for other hereditary cancer syndromes. To explore the pan-cancer role of BUB1B, we used in silico BubR1 molecular modeling, in vitro gene-editing, and ex vivo patients' tumors and peripheral blood lymphocytes. RESULTS: Rare BUB1B variants were found in ~ 1.9% of the early-onset/familial PrCa cases and in ~ 0.6% of other cancer patients fulfilling criteria for hereditary disease. We further show that BUB1B variants lead to decreased BubR1 expression and/or stability, which promotes increased premature chromatid separation and, consequently, triggers CIN, driving resistance to Taxol-based therapies. CONCLUSIONS: Our study shows that different BUB1B variants may uncover a trigger for CIN-driven carcinogenesis, supporting the role of BUB1B as a (pan)-cancer predisposing gene with potential impact on genetic counseling and treatment decision-making.

Mitral valve replacement in young patients: review and current challenges.

Mitral valve repair is the ideal intervention for mitral valve disease with excellent long-term survival comparable to the age-matched general population. When the mitral valve is not repairable, mechanical prostheses may be associated with improved survival as compared with biological prostheses. Newer mechanical and biological valve prostheses have the potential to improve outcomes following mitral valve replacement in young patients. Patients presenting for mitral valve surgery after failed transcatheter mitral valve-in-valve have high rates of postoperative mortality and morbidity, exceeding those seen with reoperative mitral valve surgery, which poses issues in young patients who have a higher cumulative incidence of reintervention.

Patients presenting with mitral valve disease, the most common type of heart valve disease, have a survival advantage when they undergo mitral valve repair as opposed to replacement, and this is particularly true for young patients. When the mitral valve is not repairable, mechanical prostheses (prosthetic implants) may be associated with improved survival as compared with biological prostheses, and this difference is mostly observed until the age of 70 years. Newer techniques of treating mitral valve disease without requiring open heart surgery have not yet been shown to be superior or even equivalent to traditional open heart surgery in the general population. Patients presenting for mitral valve surgery after failure of these newer techniques have high rates of death, exceeding those seen with mitral valve reoperation, which has important implications for young patients with mitral valve disease.

Erratum: The cognitive adaptability and resiliency employment screener (CARES): tool development and testing.

[This corrects the article DOI: 10.3389/fpsyt.2023.1254147.].

Speech and music recruit frequency-specific distributed and overlapping cortical networks.

To what extent does speech and music processing rely on domain-specific and domain-general neural networks? Using whole-brain intracranial EEG recordings in 18 epilepsy patients listening to natural, continuous speech or music, we investigated the presence of frequency-specific and network-level brain activity. We combined it with a statistical approach in which a clear operational distinction is made between shared, preferred, and domain-selective neural responses. We show that the majority of focal and network-level neural activity is shared between speech and music processing. Our data also reveal an absence of anatomical regional selectivity. Instead, domain-selective neural responses are restricted to distributed and frequency-specific coherent oscillations, typical of spectral fingerprints. Our work highlights the importance of considering natural stimuli and brain dynamics in their full complexity to map cognitive and brain functions.

Fascitis nodular como causa de tumor lateral de cuello / Nodular fasciitis as cause of lateral neck tumor

RESUMEN La fascitis nodular es una neoplasia infrecuente y benigna que puede presentarse en los tejidos blandos de cualquier región del cuerpo y requerir tratamiento quirúrgico. Se describe aquí el caso de una mujer de 41 años con un tumor lateral de cuello que creció hasta 74,7 por 32,5 mm durante dos años. Bajo anestesia general se realizó la resección completa del tumor. El informe patológico informó una proliferación de miofibroblastos, compatible con fascitis nodular. La paciente evolucionó con un síndrome de Claude Bernard Horner homolateral, sin complicaciones locales y con una leve debilidad del brazo homolateral que recuperó luego de 60 días con kinesioterapia. Esta entidad debería ser considerada entre los diagnósticos diferenciales de un tumor lateral de cuello.

ABSTRACT Nodular fasciitis is a rare and benign neoplasm of the soft tissues that can occur in any region of the body and require surgical treatment. We report the case of a 41-year-old female patient with a lateral neck tumor which reached a size of 74.7 × 32.5 mm after two years. The tumor was completely removed under general anesthesia. The pathological examination reported proliferation of myofibroblasts, suggestive of nodular fasciitis. The patient evolved homolateral Claude Bernard Syndrome, without local complications and mild weakness of the ipsilateral arm which improved after 60 days with kinesiotherapy. This condition should be considered among the differential diagnoses of lateral neck tumors.

Corrigendum: Evaluation of PIK3CA mutations in advanced ER+/HER2-breast cancer in Portugal - U-PIK Project.

[This corrects the article DOI: 10.3389/fmolb.2023.1082915.].

Heart rate variability and stroke or systemic embolism in patients with atrial fibrillation.

BACKGROUND: Stroke remains one of the most serious complications in atrial fibrillation (AF) patients and has been linked to disturbances of the autonomic nervous system. OBJECTIVE: The purpose of this study was to test the hypothesis that impaired cardiac autonomic function might be associated with an enhanced stroke risk in AF patients. METHODS: A total of 1922 AF patients who were in either sinus rhythm (SR group; n = 1121) or AF (AF group; n = 801) on a 5-minute resting electrocardiographic (ECG) recording were enrolled in the study. Heart rate variability triangular index (HRVI), standard deviation of normal-to-normal intervals, root mean square root of successive differences of normal-to-normal intervals, mean heart rate, 5-minute total power, and power in the high-frequency, low-frequency, and very-low-frequency ranges were calculated. Cox regression models were constructed to examine the association of heart rate variability (HRV) parameters with the composite endpoint of stroke or systemic embolism. RESULTS: Mean age was 71 ± 8 years in the SR group and 75 ± 8 years in the AF group. Thirty-seven patients in the SR group (3.4%) and 60 patients in the AF group (8.0%) experienced a stroke or systemic embolism during follow-up of 5 years. In patients with SR, HRVI <15 was the strongest HRV parameter to be associated with stroke or systemic embolism (hazard ratio 3.04; 95% confidence interval 1.3-7.0; P = .009) after adjustment for multiple confounders. In the AF group, no HRV parameter was found to be associated with the composite endpoint. CONCLUSION: HRVI measured during SR on a single 5-minute ECG recording is independently associated with stroke or systemic embolism in AF patients. HRV analysis in SR may help to improve risk stratification in AF patients.

Twiddler's Syndrome Causing Lead Fracture in Sacral Neuromodulation: A Case Report.

Twiddler's syndrome is the voluntary or involuntary manipulation of an implanted device, most described in cardiac literature. Lead coiling may result in device malfunction due to lead migration or, less commonly, lead fracture. There are few but increasing reports of Twiddler's syndrome resulting in lead migration in sacral neuromodulation, but lead fracture has not yet been described. A 57-year-old Latina female presented with fecal incontinence and refractory overactive bladder. She underwent successful implantation of a sacral neuromodulation device with the resolution of symptoms. Following significant weight loss and two falls, she developed a recurrence of symptoms and was found to have lead migration on pelvic radiographs. At the time of surgical intervention, radiographs demonstrated worsened Twiddler's syndrome with complete lead fracture despite no further trauma. She subsequently underwent partial lead removal and replacement with additional measures to prevent Twiddler's syndrome and its sequelae. Twiddler's syndrome resulting in lead fracture can occur in sacral neuromodulation. Preventive techniques may be applied for patients with known risk factors for Twiddler's syndrome, especially generator anchoring and lead replacement.

Removal of Spinal Instrumentation Is Not Required to Successfully Treat Postoperative Wound Infections in Most Cases.

INTRODUCTION: Controversy exists regarding whether spinal implants need to be removed to treat postoperative deep wound infections (DWIs). This retrospective study aimed to determine whether the removal or retention of implants impacts the successful treatment of a DWI after spine surgery. METHODS: Postoperative spine surgery patients presenting with signs of infection who underwent irrigation and debridement (I&D) at Twin Cities Spine Surgeons at Abbott Northwestern Hospital, Minnesota, USA, were studied. First, the persistence of infection when implants were retained or removed was assessed. Second, we analyzed the persistence of infection with respect to the number of I&D, the use of vacuum-assisted closure (VAC) treatment, pseudoarthrosis status, and functional outcomes. RESULTS: One hundred thirty-five patients were included. Treatment of infection with retention of implants occurred in 64% (87/135); of these, 7% (6/87) had a persistent infection. Of patients with implant removal (36%, 48/135), 6% (3/48) had a persistent infection. Thus, we observed no difference between treatment with implants present compared to implants removed (p = 1.0). Fifty of the 135 patients (37%) received I&D and primary wound closure, and 85 (63%) patients received I&D and VAC treatment. There was no statistical difference between primary wound closure and VAC treatment (p = 0.15) with respect to persistence. Repeat I&D with VAC (three or more times) had a significantly lower rate of recurrence than those with two I&Ds. Pseudoarthrosis and persistent infection were unrelated. At minimum one-year follow-up, achieving a minimum clinically important difference in functional outcome was independent of persistent infection status. CONCLUSION: Persistent infection was unrelated to the retention of implants. When VAC treatment was deemed necessary, more than two I&Ds resulted in a significantly better cure for infection. Those with a persistent infection were no more likely to exhibit pseudoarthrosis than those with no persistent infection. All patients showed improvement in functional outcomes at minimum one-year follow-up.

Feature Extraction Based on Local Histogram with Unequal Bins and a Recurrent Neural Network for the Diagnosis of Kidney Diseases from CT Images.

Kidney disease remains one of the most common ailments worldwide, with cancer being one of its most common forms. Early diagnosis can significantly increase the good prognosis for the patient. The development of an artificial intelligence-based system to assist in kidney cancer diagnosis is crucial because kidney illness is a global health concern, and there are limited nephrologists qualified to evaluate kidney cancer. Diagnosing and categorising different forms of renal failure presents the biggest treatment hurdle for kidney cancer. Thus, this article presents a novel method for detecting and classifying kidney cancer subgroups in Computed Tomography (CT) images based on an asymmetric local statistical pixel distribution. In the first step, the input image is non-overlapping windowed, and a statistical distribution of its pixels in each cancer type is built. Then, the method builds the asymmetric statistical distribution of the image's gradient pixels. Finally, the cancer type is identified by applying the two built statistical distributions to a Deep Neural Network (DNN). The proposed method was evaluated using a dataset collected and authorised by the Dhaka Central International Medical Hospital in Bangladesh, which includes 12,446 CT images of the whole abdomen and urogram, acquired with and without contrast. Based on the results, it is possible to confirm that the proposed method outperformed state-of-the-art methods in terms of the usual correctness criteria. The accuracy of the proposed method for all kidney cancer subtypes presented in the dataset was 99.89%, which is promising.

Molecular crosstalk between MUC1 and STAT3 influences the anti-proliferative effect of Napabucasin in epithelial cancers.

MUC1 is a transmembrane glycoprotein that is overexpressed and aberrantly glycosylated in epithelial cancers. The cytoplasmic tail of MUC1 (MUC1 CT) aids in tumorigenesis by upregulating the expression of multiple oncogenes. Signal transducer and activator of transcription 3 (STAT3) plays a crucial role in several cellular processes and is aberrantly activated in many cancers. In this study, we focus on recent evidence suggesting that STAT3 and MUC1 regulate each other's expression in cancer cells in an auto-inductive loop and found that their interaction plays a prominent role in mediating epithelial-to-mesenchymal transition (EMT) and drug resistance. The STAT3 inhibitor Napabucasin was in clinical trials but was discontinued due to futility. We found that higher expression of MUC1 increased the sensitivity of cancer cells to Napabucasin. Therefore, high-MUC1 tumors may have a better outcome to Napabucasin therapy. We report how MUC1 regulates STAT3 activity and provide a new perspective on repurposing the STAT3-inhibitor Napabucasin to improve clinical outcome of epithelial cancer treatment.

Corrigendum: Antimicrobial resistance in the COVID-19 landscape: is there an opportunity for anti-infective antibodies and antimicrobial peptides?

[This corrects the article DOI: 10.3389/fimmu.2022.921483.].

Lipid-Lowering Therapy and Risk of Hemorrhagic Stroke: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

BACKGROUND: There is debate over whether statins increase risk of hemorrhagic stroke, so we assessed current evidence, including data from new statin trials and trials of nonstatin low-density lipoprotein-cholesterol (LDL-C)- and triglyceride-lowering therapies. METHODS AND RESULTS: We performed a systematic review of large randomized clinical trials (≥1000 patients with ≥2 years follow-up) of LDL-C-lowering therapy (statin, ezetimibe, and PCSK-9 [proprotein convertase subtilisin/kexin type 9] inhibitor) and triglyceride-lowering therapy (omega-3 supplements and fibrate) that reported hemorrhagic stroke as an outcome. We searched MEDLINE, Embase, and Cochrane Library up to July 2, 2021 and updated a meta-analysis of cardiovascular statin trials published in 2012. Among our several subgroup analyses, we looked at difference depending on stroke status and also depending on age. We identified 37 trials for LDL-C lowering (284 301 participants) and 11 for triglyceride lowering (120 984 participants). Overall, we found a higher risk of hemorrhagic stroke for LDL-C lowering, risk ratio (RR) 1.16 (95% CI, 1.01-1.32, P=0.03). For statins (33 trials, 216 258 participants), RR=1.17 (95% CI, 1.01-1.36); for PCSK-9 inhibitors (2 trials, 46 488 participants), RR=0.86 (95% CI, 0.43-1.74); and for ezetimibe (2 trials, 21 555 participants), RR=1.14 (95% CI, 0.64-2.03). In statin trials of patients with previous stroke/transient ischemic attack, RR was 1.46 (95% CI, 1.05-2.04), and in trials with mean age ≥65 years old, RR=1.34 (95% CI, 1.04-1.73) (Pint=0.14 and Pint=0.23 respectively); for triglyceride lowering (11 trials, 120 984 participants), RR=1.05 (95% CI, 0.86-1.30). CONCLUSIONS: We found evidence for a small increased risk of hemorrhagic stroke events with LDL-C-lowering therapies but no clear evidence for triglyceride-lowering therapies. REGISTRATION: URL: https://www.crd.york.ac.uk/prospero; Unique identifier: CRD42021275363.

Is there a shift from cardiovascular to cancer death in lipid-lowering trials? A systematic review and meta-analysis.

BACKGROUND: Lipid-lowering therapy (LLT) reduces cardiovascular (CV) events, but data are conflicting on all-cause mortality, especially among older adults. Though LLT does not induce cancer, some randomized clinical trials (RCTs) found a pattern of increased cancer death under LLT. Our objective was to assess a possible shift from CV to cancer death in LLT trials (i.e. an increase in cancer and decrease in CV death) and to investigate potential subgroups at risk. METHODS: We performed a systematic review and meta-analysis. We retrieved RCTs from MEDLINE, Embase, and Cochrane Central until 08/2023. We extracted the number of CV and cancer deaths in the treatment vs. in the control arm, calculated the relative risk (RR) by dividing the risk of death in the treatment over the risk of death in the control group and then pooled them using random-effect meta-analysis. We performed subgroup analyses on primary and secondary prevention, and according to different age cut-offs. RESULTS: We included 27 trials with 188'259 participants (23 statin; 4 ezetimibe trials). The trials reported 4056 cancer deaths, 2061 under LLT and 1995 in control groups. Overall, there was no increased risk of cancer mortality (RR 1.03, 95% confidence interval 0.97-1.10), with no difference between primary and secondary prevention. In the subgroup analyses for RCTs with ≥15% of participants aged ≥75 years, the RR of cancer death was 1.11 (1.00-1.23), while the RR for CV death was 0.96 (0.91-1.01). For RCTs with a mean age ≥ 70 years, the RR for cancer death was 1.21 (0.99-1.47). CONCLUSION: LLT does not lead to a shift from CV to cancer death. However, there might be a possible shift with a pattern of increased cancer deaths in trials with more older adults, particularly ≥75 years. Individual participant data from LLT trials should be made public to allow further investigations. PROSPERO REGISTRATION: CRD42021271658.