Patients with Spondylodiscitis following Chemoradiotherapy for Head and Neck Cancer in a Portuguese Cancer Hospital: A Case Report.

Introduction: Head and neck cancer is an umbrella term for tumor manifestations across the head and neck regions, including the oral cavity, pharynx (including the naso, oro, and hypopharynx), larynx, and sinuses. Treatment options for head and neck cancer include surgery, radiation therapy, chemotherapy, and immunotherapy, with specific treatment plans depending upon individual tumor location and staging, together with overall patient health status. Furthermore, definitive chemoradiotherapy (CRT) has emerged as a highly effective therapeutic option for locoregional advanced head and neck squamous cell cancer. However, such therapy has also been linked to the development of spondylodiscitis. Spondylodiscitis consists of an infection starting at the vertebral endplates and spreading into the intervertebral discs, typically manifesting in adults. Case Presentation and Conclusion: This case report describes our clinical team's experience in managing three separate cases of spondylodiscitis following CRT for head and neck tumors that presented at our clinic for diagnosis and treatment in order to identify predisposing factors that underlie the link between CRT and spondylodiscitis.

Factors Associated With Long Survival in Patients With Cancer Admitted to Palliative Care: An Exploratory Study.

Objective: Some patients with cancer admitted to palliative care have relatively long survivals of 1 year or more. The objective of this study was to find out factors associated with prolonged survival. Methods: Retrospective case-control study comparing the available data of patients with cancer who survived more than 1 year after admission in a palliative care service with patients with cancer who survived 6 months or less. The intended proportion was 4 controls for each case. Patients were identified through electronic records from 2012 until 2018. Results: And 1721 patients were identified. Of those patients, 111 (6.4%) survived for at least 1 year, and 363 (21.1%) were included as controls according to the established criteria. The intended proportion could not be reached; the proportion was only 3.3:1. The median survival of cases was 581 days (range: 371-2763), and the median survival of controls was 57 days (range: 1-182). In the multivariable analysis, patients with a hemoglobin ≥ 10.6 g/dL and a creatinine level >95 µmol/L had a higher probability of living more than 1 year. In contrast, patients with abnormal cognition, pain, anorexia, liver metastases, an Eastern Cooperative Oncology Group performance status >1, and a neutrophil/lymphocyte ratio ≥ 3.43 had a low probability of living more than 1 year. Conclusion: Several factors were statistically associated positively or negatively with prolonged survival. However, the data of this study should be confirmed in other studies.

Hierarchical self-assembly of a reflectin-derived peptide.

Reflectins are a family of intrinsically disordered proteins involved in cephalopod camouflage, making them an interesting source for bioinspired optical materials. Understanding reflectin assembly into higher-order structures by standard biophysical methods enables the rational design of new materials, but it is difficult due to their low solubility. To address this challenge, we aim to understand the molecular self-assembly mechanism of reflectin's basic unit-the protopeptide sequence YMDMSGYQ-as a means to understand reflectin's assembly phenomena. Protopeptide self-assembly was triggered by different environmental cues, yielding supramolecular hydrogels, and characterized by experimental and theoretical methods. Protopeptide films were also prepared to assess optical properties. Our results support the hypothesis for the protopeptide aggregation model at an atomistic level, led by hydrophilic and hydrophobic interactions mediated by tyrosine residues. Protopeptide-derived films were optically active, presenting diffuse reflectance in the visible region of the light spectrum. Hence, these results contribute to a better understanding of the protopeptide structural assembly, crucial for the design of peptide- and reflectin-based functional materials.

Identification of eight novel proteasome variants in five unrelated cases of proteasome-associated autoinflammatory syndromes (PRAAS).

Mutations in genes coding for proteasome subunits and/or proteasome assembly helpers typically cause recurring autoinflammation referred to as chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperatures (CANDLE) or proteasome-associated autoinflammatory syndrome (PRAAS). Patients with CANDLE/PRAAS present with mostly chronically elevated type I interferon scores that emerge as a consequence of increased proteotoxic stress by mechanisms that are not fully understood. Here, we report on five unrelated patients with CANDLE/PRAAS carrying novel inherited proteasome missense and/or nonsense variants. Four patients were compound heterozygous for novel pathogenic variants in the known CANDLE/PRAAS associated genes, PSMB8 and PSMB10, whereas one patient showed additive loss-of-function mutations in PSMB8. Variants in two previously not associated proteasome genes, PSMA5 and PSMC5, were found in a patient who also carried the PSMB8 founder mutation, p.T75M. All newly identified mutations substantially impact the steady-state expression of the affected proteasome subunits and/or their incorporation into mature 26S proteasomes. Our observations expand the spectrum of PRAAS-associated genetic variants and improve a molecular diagnosis and genetic counseling of patients with sterile autoinflammation.

Cytokine profiling of samples positive for Chlamydia trachomatis and Human papillomavirus.

Persistent human papillomavirus (HPV) infection is closely associated with cervical carcinoma. Co-infection in the endocervical environment with other microorganisms, such as Chlamydia trachomatis, may increase the risk of HPV infection and neoplastic progression. While in some individuals, Chlamydia trachomatis infection is resolved with the activation of Th1/IFN-γ-mediated immune response, others develop a chronic infection marked by Th2-mediated immune response, resulting in intracellular persistence of the bacterium and increasing the risk of HPV infection. This work aimed to quantify cytokines of the Th1/Th2/Th17 profile in exfoliated cervix cells (ECC) and peripheral blood (PB) of patients positive for Chlamydia trachomatis DNA, patients positive for Papillomavirus DNA, and healthy patients. Cytokine levels were quantified by flow cytometry in ECC and PB samples from patients positive for C. trachomatis DNA (n = 18), patients positive for HPV DNA (n = 30), and healthy patients (n = 17) treated at the Hospital de Amor, Campo Grande-MS. After analysis, a higher concentration of IL-17, IL-6, and IL-4 (p <0.05) in ECC; INF-γ and IL-10 (p <0.05) in PB was found in samples from patients positive for C. trachomatis DNA compared to samples from healthy patients. When comparing samples from patients positive for HPV DNA, there was a higher concentration of cytokines IL-17, IL-10, IL-6, and IL-4 (p <0.05) in ECC and IL-4 and IL-2 (p <0.05) in PB of patients positive for C. trachomatis DNA. These results suggest that induction of Th2- and Th17 mediated immune response occurs in patients positive for C. trachomatis DNA, indicating chronic infection. Our results also demonstrate a high concentration of pro-inflammatory cytokines in ECC of patients positive for C. trachomatis DNA.

Histopathological features of human mpox: Report of two cases and review of the literature.

Human monkeypox is an emerging zoonosis with epidemic potential. Although it usually causes a mild disease, some patients are at risk for complications, including death. In face of the current outbreak of monkeypox in non-endemic areas, awareness is paramount to diagnose it timely, prompting an early break of the transmission chain. Histopathologic findings in vesiculopustular lesions of monkeypox are distinctive, consisting of ballooning and reticular degeneration of keratinocytes, necrosis, especially of the upper portions of the epithelium, multinucleation of keratinocytes, nuclear enlargement showing a "basophilic halo" around a "ground glass" eosinophilic center, the orthopoxvirus-specific cytoplasmic eosinophilic Guarnieri-type inclusions (in the pustular stage especially), and a dense mixed inflammatory cell infiltrate with prominent neutrophil exocytosis. The diagnosis of human monkeypox requires a high index of suspicion. In correlation with clinical information, histopathological findings allow for a presumptive diagnosis of monkeypox if polymerase chain reaction testing is not available. Both clinicians and pathologists can optimize diagnostic sensitivity, respectively, by considering the epidemiological context, sampling pustular lesions and providing data for clinicopathological correlation, and by intentionally searching the tell-tale eosinophilic inclusions in genital, anal and oral lesions with reticular and ballooning degenerescence.

Liver fat accumulation more than fibrosis causes early liver dynamic dysfunction in patients with non-alcoholic fatty liver disease.

INTRODUCTION: In Non-Alcoholic Fatty Liver Disease (NAFLD), events driving early hepatic dysfunction with respect to specific metabolic pathways are still poorly known. METHODS: We enrolled 84 subjects with obesity and/or type 2 diabetes (T2D). FibroScan® served to assess NAFLD by controlled attenuation parameter (CAP), and fibrosis by liver stiffness (LS). Patients with LS above 7 kPa were excluded. APRI and FIB-4 were used as additional serum biomarkers of fibrosis. The stable-isotope dynamic breath test was used to assess the hepatic efficiency of portal extraction (as DOB15) and microsomal metabolization (as cPDR30) of orally-administered (13C)-methacetin. RESULTS: NAFLD occurred in 45%, 65.9%, and 91.3% of normal weight, overweight, and obese subjects, respectively. Biomarkers of liver fibrosis were comparable across subgroups, and LS was higher in obese, than in normal weight subjects. DOB15 was 23.2 ± 1.5‰ in normal weight subjects, tended to decrease in overweight (19.9 ± 1.0‰) and decreased significantly in obese subjects (16.9 ± 1.3, P = 0.008 vs. normal weight). Subjects with NAFLD had lower DOB15 (18.7 ± 0.9 vs. 22.1 ± 1.2, P = 0.03) but higher LS (4.7 ± 0.1 vs. 4.0 ± 0.2 kPa, P = 0.0003) than subjects without NAFLD, irrespective of fibrosis. DOB15 (but not cPDR30) decreased with increasing degree of NAFLD (R = -0.26; P = 0.01) and LS (R = -0.23, P = 0.03). Patients with T2D showed increased rate of NAFLD than those without T2D but similar LS, DOB15 and cPDR30. CONCLUSIONS: Overweight, obesity and liver fat accumulation manifest with deranged portal extraction efficiency of methacetin into the steatotic hepatocyte. This functional alteration occurs early, and irrespective of significant fibrosis and presence of T2D.

Big data and machine learning to tackle diabetes management.

BACKGROUND: Type 2 Diabetes (T2D) diagnosis is based solely on glycaemia, even though it is an endpoint of numerous dysmetabolic pathways. Type 2 Diabetes complexity is challenging in a real-world scenario; thus, dissecting T2D heterogeneity is a priority. Cluster analysis, which identifies natural clusters within multidimensional data based on similarity measures, poses a promising tool to unravel Diabetes complexity. METHODS: In this review, we scrutinize and integrate the results obtained in most of the works up to date on cluster analysis and T2D. RESULTS: To correctly stratify subjects and to differentiate and individualize a preventive or therapeutic approach to Diabetes management, cluster analysis should be informed with more parameters than the traditional ones, such as etiological factors, pathophysiological mechanisms, other dysmetabolic co-morbidities, and biochemical factors, that is the millieu. Ultimately, the above-mentioned factors may impact on Diabetes and its complications. Lastly, we propose another theoretical model, which we named the Integrative Model. We differentiate three types of components: etiological factors, mechanisms and millieu. Each component encompasses several factors to be projected in separate 2D planes allowing an holistic interpretation of the individual pathology. CONCLUSION: Fully profiling the individuals, considering genomic and environmental factors, and exposure time, will allow the drive to precision medicine and prevention of complications.

Deep Learning Assisted Diagnosis of Onychomycosis on Whole-Slide Images.

BACKGROUND: Onychomycosis numbers among the most common fungal infections in humans affecting finger- or toenails. Histology remains a frequently applied screening technique to diagnose onychomycosis. Screening slides for fungal elements can be time-consuming for pathologists, and sensitivity in cases with low amounts of fungi remains a concern. Convolutional neural networks (CNNs) have revolutionized image classification in recent years. The goal of our project was to evaluate if a U-NET-based segmentation approach as a subcategory of CNNs can be applied to detect fungal elements on digitized histologic sections of human nail specimens and to compare it with the performance of 11 board-certified dermatopathologists. METHODS: In total, 664 corresponding H&E- and PAS-stained histologic whole-slide images (WSIs) of human nail plates from four different laboratories were digitized. Histologic structures were manually annotated. A U-NET image segmentation model was trained for binary segmentation on the dataset generated by annotated slides. RESULTS: The U-NET algorithm detected 90.5% of WSIs with fungi, demonstrating a comparable sensitivity with that of the 11 board-certified dermatopathologists (sensitivity of 89.2%). CONCLUSIONS: Our results demonstrate that machine-learning-based algorithms applied to real-world clinical cases can produce comparable sensitivities to human pathologists. Our established U-NET may be used as a supportive diagnostic tool to preselect possible slides with fungal elements. Slides where fungal elements are indicated by our U-NET should be reevaluated by the pathologist to confirm or refute the diagnosis of onychomycosis.

Fibrosis nonalcoholic steatohepatitis index validation and applicability considering glycaemic severity and T2D duration.

Nonalcoholic fatty liver disease (NAFLD) diagnosis without using invasive methods is extremely challenging, highlighting the need for simple indexes for this end. Recently, the fibrotic nonalcoholic steatohepatitis index (FNI) was developed and proposed as an affordable non-invasive score calculated with aspartate aminotransferase, high-density lipoprotein cholesterol and haemoglobin A1c. Herein, and given the link between NAFLD and diabetes, we aimed at validating FNI in a population with type 2 diabetes (T2D), also considering diabetes duration and glycaemic severity. The performance of FNI was higher than FIB-4 (AUROC = 0.89 vs 0.67, respectively). Additionally, using 0.1 as the rule-out cut-off of FNI, the sensitivity was 0.99 and the positive predictive value was 0.19. Both duration of diabetes and A1c did not impact FNI performance. In sum, FNI is a valuable score for predicting fibrotic nonalcoholic steatohepatitis not only for primary care units but also for diabetes specialized care.

Exploiting Peptide Self-Assembly for the Development of Minimalistic Viral Mimetics.

Viruses are natural supramolecular nanostructures that form spontaneously by molecular self-assembly of complex biomolecules. Peptide self-assembly is a versatile tool that allows mimicking viruses by creating their simplified versions through the design of functional, supramolecular materials with modularity, tunability, and responsiveness to chemical and physical stimuli. The main challenge in the design and fabrication of peptide materials is related to the precise control between the peptide sequence and its resulting supramolecular morphology. We provide an overview of existing sequence patterns employed for the development of spherical and fibrillar peptide assemblies that can act as viral mimetics, offering the opportunity to tackle the challenges of viral infections.

The Impact of Metabolic Scion-Rootstock Interactions in Different Grapevine Tissues and Phloem Exudates.

In viticulture, grafting is used to propagate Phylloxera-susceptible European grapevines, thereby using resistant American rootstocks. Although scion-rootstock reciprocal signaling is essential for the formation of a proper vascular union and for coordinated growth, our knowledge of graft partner interactions is very limited. In order to elucidate the scale and the content of scion-rootstock metabolic interactions, we profiled the metabolome of eleven graft combination in leaves, stems, and phloem exudate from both above and below the graft union 5-6 months after grafting. We compared the metabolome of scions vs. rootstocks of homografts vs. heterografts and investigated the reciprocal effect of the rootstock on the scion metabolome. This approach revealed that (1) grafting has a minor impact on the metabolome of grafted grapevines when tissues and genotypes were compared, (2) heterografting affects rootstocks more than scions, (3) the presence of a heterologous grafting partner increases defense-related compounds in both scion and rootstocks in shorter and longer distances from the graft, and (4) leaves were revealed as the best tissue to search for grafting-related metabolic markers. These results will provide a valuable metabolomics resource for scion-rootstock interaction studies and will facilitate future efforts on the identification of metabolic markers for important agronomic traits in grafted grapevines.

Biochemical Characterization and Differential Expression of PAL Genes Associated With "Translocated" Peach/Plum Graft-Incompatibility.

Grafting is an ancient plant propagation technique widely used in horticultural crops, particularly in fruit trees. However, the involvement of two different species in grafting may lead to lack of affinity and severe disorders between the graft components, known as graft-incompatibility. This complex agronomic trait is traditionally classified into two categories: "localized" (weak graft unions with breaks in cambial and vascular continuity at the graft interface and absence of visual symptoms in scion leaves and shoots) and "translocated" (degeneration of the sieve tubes and phloem companion cells at the graft interface causing translocation problems in neighboring tissues, and reddening/yellowing of scion leaves). Over the decades, more attention has been given to the different mechanisms underlying the "localized" type of graft-incompatibility; whereas the phenylpropanoid-derived compounds and the differential gene expression associated with the "translocated" graft-incompatibility remain unstudied. Therefore, the aim of this study was to shed light on the biochemical and molecular mechanisms involved in the typical "translocated" graft-incompatibility of peach/plum graft-combinations. In this study, the "Summergrand" (SG) nectarine cultivar was budded on two plum rootstocks: "Adara" and "Damas GF 1869". "Translocated" symptoms of incompatibility were shown and biochemically characterized in the case of "SG/Damas GF 1869" graft-combination, 3 years after grafting. Non-structural carbohydrates (soluble sugars and starch), phenolic compounds and antioxidant activity, were significantly enhanced in the incompatible graft-combination scion. Similarly, the enzymatic activities of the antioxidant enzyme peroxidase, the phenylalanine ammonia-lyase (PAL) and polyphenol oxidase involved in the phenylpropanoid pathway were significantly affected by the incompatible rootstock "Damas GF 1869", inducing higher activities in the scion than those induced by the compatible rootstock "Adara". In addition, a positive and strong correlation was obtained between total phenol content, antioxidant capacity and the expression of the key genes involved in the phenylpropanoid pathway, PAL1 and PAL2. Regarding the "SG/Adara" graft-combination, there were neither external symptoms of "translocated" incompatibility nor significant differences in the biochemical and molecular parameters between scion and rootstock, proving it to be a compatible combination. The differential expression of PAL genes together with the biochemical factors cited above could be good markers for the "translocated" peach/plum graft-incompatibility.

Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot (Prunus armeniaca L.).

Graft incompatibility (GI) between the most popular Prunus rootstocks and apricot cultivars is one of the major problems for rootstock usage and improvement. Failure in producing long-leaving healthy grafts greatly affects the range of available Prunus rootstocks for apricot cultivation. Despite recent advances related to the molecular mechanisms of a graft-union formation between rootstock and scion, information on genetic control of this trait in woody plants is essentially missing because of a lack of hybrid crosses, segregating for the trait. In this study, we have employed the next-generation sequencing technology to generate the single-nucleotide polymorphism (SNP) markers and construct parental linkage maps for an apricot F1 population "Moniqui (Mo)" × "Paviot (Pa)" segregating for ability to form successful grafts with universal Prunus rootstock "Marianna 2624". To localize genomic regions associated with this trait, we genotyped 138 individuals from the "Mo × Pa" cross and constructed medium-saturated genetic maps. The female "Mo" and male "Pa" maps were composed of 557 and 501 SNPs and organized in eight linkage groups that covered 780.2 and 690.4 cM of genetic distance, respectively. Parental maps were aligned to the Prunus persica v2.0 genome and revealed a high colinearity with the Prunus reference map. Two-year phenotypic data for characters associated with unsuccessful grafting such as necrotic line (NL), bark and wood discontinuities (BD and WD), and an overall estimate of graft (in)compatibility (GI) were collected for mapping quantitative trait loci (QTLs) on both parental maps. On the map of the graft-compatible parent "Pa", two genomic regions on LG5 (44.9-60.8 cM) and LG8 (33.2-39.2 cM) were associated with graft (in)compatibility characters at different significance level, depending on phenotypic dataset. Of these, the LG8 QTL interval was most consistent between the years and supported by two significant and two putative QTLs. To our best knowledge, this is the first report on QTLs for graft (in)compatibility in woody plants. Results of this work will provide a valuable genomic resource for apricot breeding programs and facilitate future efforts focused on candidate genes discovery for graft (in)compatibility in apricot and other Prunus species.

Artificial enzymes bringing together computational design and directed evolution.

Enzymes are proteins that catalyse chemical reactions and, as such, have been widely used to facilitate a variety of natural and industrial processes, dating back to ancient times. In fact, the global enzymes market is projected to reach $10.5 billion in 2024. The development of computational and DNA editing tools boosted the creation of artificial enzymes (de novo enzymes) - synthetic or organic molecules created to present abiological catalytic functions. These novel catalysts seek to expand the catalytic power offered by nature through new functions and properties. In this manuscript, we discuss the advantages of combining computational design with directed evolution for the development of artificial enzymes and how this strategy allows to fill in the gaps that these methods present individually by providing key insights about the sequence-function relationship. We also review examples, and respective strategies, where this approach has enabled the creation of artificial enzymes with promising catalytic activity. Such key enabling technologies are opening new windows of opportunity in a variety of industries, including pharmaceutical, chemical, biofuels, and food, contributing towards a more sustainable development.

Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity.

We demonstrate phage-display screening on self-assembled ligands that enables the identification of oligopeptides that selectively bind dynamic supramolecular targets over their unassembled counterparts. The concept is demonstrated through panning of a phage-display oligopeptide library against supramolecular tyrosine-phosphate ligands using 9-fluorenylmethoxycarbonyl-phenylalanine-tyrosine-phosphate (Fmoc-FpY) micellar aggregates as targets. The 14 selected peptides showed no sequence consensus but were enriched in cationic and proline residues. The lead peptide, KVYFSIPWRVPM-NH2 (P7) was found to bind to the Fmoc-FpY ligand exclusively in its self-assembled state with K D = 74 ± 3 µM. Circular dichroism, NMR and molecular dynamics simulations revealed that the peptide interacts with Fmoc-FpY through the KVYF terminus and this binding event disrupts the assembled structure. In absence of the target micellar aggregate, P7 was further found to dynamically alternate between multiple conformations, with a preferred hairpin-like conformation that was shown to contribute to supramolecular ligand binding. Three identified phages presented appreciable binding, and two showed to catalyze the hydrolysis of a model para-nitro phenol phosphate substrate, with P7 demonstrating conformation-dependent activity with a modest k cat/K M = 4 ± 0.3 × 10-4 M-1 s-1.

Affinity Tags in Protein Purification and Peptide Enrichment: An Overview.

The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific toward particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications in proteins and peptides widen the application of affinity ligand-tag receptors pairs toward universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely the affinity tags and receptors employed on the production of recombinant fusion proteins, and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.