Integrated image and location analysis for wound classification: a deep learning approach.

The global burden of acute and chronic wounds presents a compelling case for enhancing wound classification methods, a vital step in diagnosing and determining optimal treatments. Recognizing this need, we introduce an innovative multi-modal network based on a deep convolutional neural network for categorizing wounds into four categories: diabetic, pressure, surgical, and venous ulcers. Our multi-modal network uses wound images and their corresponding body locations for more precise classification. A unique aspect of our methodology is incorporating a body map system that facilitates accurate wound location tagging, improving upon traditional wound image classification techniques. A distinctive feature of our approach is the integration of models such as VGG16, ResNet152, and EfficientNet within a novel architecture. This architecture includes elements like spatial and channel-wise Squeeze-and-Excitation modules, Axial Attention, and an Adaptive Gated Multi-Layer Perceptron, providing a robust foundation for classification. Our multi-modal network was trained and evaluated on two distinct datasets comprising relevant images and corresponding location information. Notably, our proposed network outperformed traditional methods, reaching an accuracy range of 74.79-100% for Region of Interest (ROI) without location classifications, 73.98-100% for ROI with location classifications, and 78.10-100% for whole image classifications. This marks a significant enhancement over previously reported performance metrics in the literature. Our results indicate the potential of our multi-modal network as an effective decision-support tool for wound image classification, paving the way for its application in various clinical contexts.

Degraders in epigenetic therapy: PROTACs and beyond.

Epigenetics refers to the reversible process through which changes in gene expression occur without changing the nucleotide sequence of DNA. The process is currently gaining prominence as a pivotal objective in the treatment of cancers and other ailments. Numerous drugs that target epigenetic mechanisms have obtained approval from the Food and Drug Administration (FDA) for the therapeutic intervention of diverse diseases; many have drawbacks, such as limited applicability, toxicity, and resistance. Since the discovery of the first proteolysis-targeting chimeras (PROTACs) in 2001, studies on targeted protein degradation (TPD)-encompassing PROTACs, molecular glue (MG), hydrophobic tagging (HyT), degradation TAG (dTAG), Trim-Away, a specific and non-genetic inhibitor of apoptosis protein (IAP)-dependent protein eraser (SNIPER), antibody-PROTACs (Ab-PROTACs), and other lysosome-based strategies-have achieved remarkable progress. In this review, we comprehensively highlight the small-molecule degraders beyond PROTACs that could achieve the degradation of epigenetic proteins (including bromodomain-containing protein-related targets, histone acetylation/deacetylation-related targets, histone methylation/demethylation related targets, and other epigenetic targets) via proteasomal or lysosomal pathways. The present difficulties and forthcoming prospects in this domain are also deliberated upon, which may be valuable for medicinal chemists when developing more potent, selective, and drug-like epigenetic drugs for clinical applications.

Improved Solubility and Stability of a Thermostable Carbonic Anhydrase via Fusion with Marine-Derived Intrinsically Disordered Solubility Enhancers.

Carbonic anhydrase (CA), an enzyme catalyzing the reversible hydration reaction of carbon dioxide (CO2), is considered a promising biocatalyst for CO2 reduction. The α-CA of Thermovibrio ammonificans (taCA) has emerged as a compelling candidate due to its high thermostability, a critical factor for industrial applications. However, the low-level expression and poor in vitro solubility have hampered further utilization of taCA. Recently, these limitations have been addressed through the fusion of the NEXT tag, a marine-derived, intrinsically disordered small peptide that enhances protein expression and solubility. In this study, the solubility and stability of NEXT-taCA were further investigated. When the linker length between the NEXT tag and the taCA was shortened, the expression level decreased without compromising solubility-enhancing performance. A comparison between the NEXT tag and the NT11 tag demonstrated the NEXT tag's superiority in improving both the expression and solubility of taCA. While the thermostability of taCA was lower than that of the extensively engineered DvCA10, the NEXT-tagged taCA exhibited a 30% improvement in long-term thermostability compared to the untagged taCA, suggesting that enhanced solubility can contribute to enzyme thermostability. Furthermore, the bioprospecting of two intrinsically disordered peptides (Hcr and Hku tags) as novel solubility-enhancing fusion tags was explored, demonstrating their performance in improving the expression and solubility of taCA. These efforts will advance the practical application of taCA and provide tools and insights for enzyme biochemistry and bioengineering.

The Relationship between Clock Genes, Sirtuin 1, and Mitochondrial Activity in Head and Neck Squamous Cell Cancer: Effects of Melatonin Treatment.

The circadian clock is a regulatory system, with a periodicity of approximately 24 h, which generates rhythmic changes in many physiological processes, including mitochondrial activity. Increasing evidence links chronodisruption with aberrant functionality in clock gene expression, resulting in multiple diseases such as cancer. Melatonin, whose production and secretion oscillates according to the light-dark cycle, is the principal regulator of clock gene expression. In addition, the oncostatic effects of melatonin correlate with an increase in mitochondrial activity. However, the direct links between circadian clock gene expression, mitochondrial activity, and the antiproliferative effects of melatonin in cancers, including head and neck squamous cell carcinoma (HNSCC), remain largely unknown. In this study, we analyzed the effects of melatonin on HNSCC cell lines (Cal-27 and SCC9), which were treated with 500 and 1000 µM melatonin. We found that the antiproliferative effect of melatonin is not mediated by the Bmal1 clock gene. Additionally, high doses of melatonin were observed to result in resynchronization of oscillatory circadian rhythm genes (Per2 and Sirt1). Surprisingly, the resynchronizing effect of melatonin on Per2 and Sirt1 did not produce alterations in the oscillation of mitochondrial respiratory activity. These results increase our understanding of the possible antiproliferative mechanisms in melatonin in the treatment of head and neck squamous cell carcinoma and suggest that its antiproliferative effects are independent of clock genes but are directly related to mitochondrial activity.

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.

The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer indexing strategy for comparative analysis across multiple assemblies, including the pangenome reference, GRCh38, and CHM13, a telomere-to-telomere reference assembly. Our k-mer indexing approach enabled us to identify a valuable collection of universally conserved sequences across all assemblies, referred to as "pan-conserved segment tags" (PSTs). By examining intervals between these segments, we discerned highly conserved genomic segments and those with structurally related polymorphisms. We found 60,764 polymorphic intervals with unique geo-ethnic features in the pangenome reference. In this study, we utilized ultra-conserved sequences (PSTs) to forge a link between human pangenome assemblies and reference genomes. This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework.

A remote sensing approach for exploring the dynamics of jellyfish, relative to the water current.

Drifting in large numbers, jellyfish often interfere in the operation of nearshore electrical plants, cause disturbances to marine recreational activity, encroach upon local fish populations, and impact food webs. Understanding the dynamic mechanisms behind jellyfish behavior is of importance in order to create migration models. In this work, we focus on the small-scale dynamics of jellyfish and offer a novel method to accurately track the trajectory of individual jellyfish with respect to the water current. The existing approaches for similar tasks usually involve a surface float tied to the jellyfish for location reference. This operation may induce drag on the jellyfish, thereby affecting its motion. Instead, we propose to attach an acoustic tag to the jellyfish's bell and then track its geographical location using acoustic beacons, which detect the tag's emissions, decode its ID and depth, and calculate the tag's position via time-difference-of-arrival acoustic localization. To observe the jellyfish's motion relative to the water current, we use a submerged floater that is deployed together with the released tagged jellyfish. Being Lagrangian on the horizontal plane while maintaining an on-demand depth, the floater drifts with the water current; thus, its trajectory serves as a reference for the current's velocity field. Using an acoustic modem and a hydrophone mounted to the floater, the operator from the deploying boat remotely changes the depth of the floater on-the-fly, to align it with that of the tagged jellyfish (as reported by the jellyfish's acoustic tag), thereby serving as a reference for the jellyfish's 3D motion with respect to the water current. We performed a proof-of-concept to demonstrate our approach over three jellyfish caught and tagged in Haifa Bay, and three corresponding floaters. The results present different dynamics for the three jellyfish, and show how they can move with, and even against, the water current.

A highly efficient scheme for library preparation from single-stranded DNA.

Although methods for sequencing library preparation from double-stranded DNA are well established, those from single-stranded DNA (ssDNA) have not been well studied. Further, the existing methods have limitations in efficiency and yield. Therefore, we developed a highly efficient procedure for sequencing library preparation from ssDNA. In this method, the first adaptor tagging of ssDNA is performed using terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated ssDNA (TACS) ligation, which we reported recently. After complementary strand synthesis using the adaptor-tagged ssDNA, second adaptor tagging via Vaccinia virus topoisomerase I (VTopoI or TOPO)-based adaptor ligation is performed. With additional steps for degradation, repression, and removal of the adaptor dimer, the proposed TACS-TOPO scheme realizes adaptor dimer-free sequencing library preparation from ssDNA samples of 24 pg. The TACS-TOPO scheme was successfully applied to cell-free DNA analysis with amplification-free library preparation from 50 µL of human serum. A modified TACS-TOPO scheme was also applied to DNA extracted from ancient human bones, bringing two to eight times more library yields than those using a conventional library preparation protocol. The procedures for preparing VTopoI and its complex with a double-stranded oligonucleotide adaptor are also described. Overall, the proposed TACS-TOPO scheme can facilitate practical and sensitive sequencing analysis of ssDNA.

Impact of radiation dose on patient-reported acute taste alteration in a prospective observational study cohort in head and neck squamous cell cancer (HNSCC).

PURPOSE: Taste alteration (TA) is a frequent acute side effect of radiation treatment in HNSCC patients. Principal aim of our study was to investigate dosimetric parameters in relation to patient-assessed taste impairment in a prospective cohort treated with intensity-modulated radiotherapy. METHODS: All patients with locally advanced HNSCC and amenable to radical treatment were included. Chemotherapy-induced taste alteration scale (CITAS), EORTC QLQ-C30 and QLQ-HN43 questionnaires at baseline (T0), 3 weeks (T1) and 3 months (T2) after radiotherapy conclusion were used to assess taste impairment. Base of tongue, submandibular glands (SG), parotid glands (PG) and taste buds, along with anterior and medium third of the tongue, were considered as organs at risk and thus delineated according to consensus guidelines. The mean dose to the above-mentioned structures was correlated with patient-reported outcomes. RESULTS: Between September 2019 and November 2020, 33 patients were recruited, 31 of which analyzed. 71% had oropharyngeal carcinoma, mostly HPV-related (60%). All were treated with tomotherapy. 77.4% had concurrent cisplatin. Mean scores of general taste alterations, global health status and dry mouth and sticky saliva were assessed. The mean doses to the anterior third, medium third and base of the tongue were 23.85, 35.50 and 47.67 Gy, respectively. Taste buds received 32.72 Gy; right and left parotid 25 and 23 Gy; right and left submandibular glands 47.8 and 39.4 Gy. At univariate analysis, dysgeusia correlated with SG mean dose (95% CI 0-0.02 p = 0.05) and PG mean dose (95% CI 0-0.02 p = 0.05); dry mouth with mean dose to anterior (95% CI 0.03-1.47 p = 0.04) and medium third (95% CI 0.02-0.93 p = 0.04) of the tongue, to taste buds (95% CI 0.06-0.96 p = 0.03) and to SGs (95% CI 0.06-0.63 p = 0.02); pain mouth with mean dose to taste buds (95% CI 0-0.02 p = 0.04), to SGs (95% CI 0-0.03 p = 0.03) and to base tongue (95% CI 0-0.02 p = 0.02). CONCLUSIONS: Our analysis supports the influence of dose distribution on the development of TA in HNSCC patients. The contribution of dose to taste buds and tongue subvolumes remains unclear and worthy of further investigation.

Marathi translation, linguistic validation, and cross-cultural adaptation of M.D. Anderson dysphagia inventory in patients of head and neck squamous cell cancer.

Background: Self-reported treatment outcome is a better way to measure patient's quality of life (QOL). This study was undertaken to translate dysphagia-specific QOL questionnaire M. D. Anderson Dysphagia Inventory (MDADI) in Marathi language, its linguistic validation, and cross-cultural adaptation in patients of head and neck squamous cell cancer (HNSCC). Methods: After Institutional ethics committee approval, MDADI was translated into Marathi with prior permission from the author of original English questionnaire (AOEQ). The translation procedure included - two forward translations (English to Marathi), formation of first intermediate Marathi translation (FIMT), two back translations (BT) (Marathi to English) of FIMT and interim Marathi translation (IMT) formation. Second intermediate Marathi translation (SIMT) was prepared after face validation of IMT by Marathi subject expert. Pretesting of SIMT was done in 10 patients of HNSCC for linguistic validation and cross-cultural adaptation. After incorporating the patients' suggestions, final Marathi translation was formulated and forwarded to primary author for approval. Results: The grammatically acceptable and conceptually equivalent face-validated SIMT was prepared and given to HNSCC patients. The questionnaire was well understood and unobjectionable reflecting its linguistic validity and cross-cultural adaptation. Some of the patients suggested changes in a few words which were then rectified, rechecked with BT, and the final Marathi translated questionnaire was prepared. The credit statement for AOEQ was used as a footnote in the translated questionnaire. Conclusion: Marathi translation of MDADI is well accepted and comprehensible. It can be used for future studies.

Molecular and biological factors in the prognosis of head and neck squamous cell cancer.

The objective of the review is to summarize available literary data on the role and prognostic value of molecular biological markers p53, UBE2C, CD147, STAT3, VEGF in the carcinogenesis of head and neck squamous cell carcinoma (HNSCC). To date, researches have been studying HNSCC molecular and genetic characteristics and obtaining information about new molecular biological markers that have different functional significance in tumor progression. This review presents current data on protein molecules involved in the HNSCC development, as well as in the formation of drug resistance mechanisms in tumors. The considered markers can be used not only for prognosis but also for developing a new approach to treatment, including patients resistant to therapy or recurrent HNSCC. However, the introduction of these markers into practice requires further examination of their functions and larger-scale studies.

Inter-nesting, migration, and foraging behaviors of green turtles (Chelonia mydas) in the central-southern Red Sea.

Sea turtles are migratory with nesting and foraging areas in distinct and often widely separated habitats. Telemetry has been a vital tool for tracking sea turtle migrations between these areas, but tagging efforts are often focused on only a few large rookeries in a given region. For instance, turtle tagging in the Red Sea has been focused in the north of the basin. We tagged five green turtles (Chelonia mydas) at a nesting site in the central-southern Red Sea and tracked them for 72-243 days. During the inter-nesting period, the turtles showed high site-fidelity, with a maximum home range of 161 km2. After the nesting season, the turtles migrated up to 1100 km to five distinct foraging locations in three countries (Saudi Arabia, Sudan, and Eritrea). Movements within foraging habitats were more wide-ranging compared to inter-nesting movements, with home ranges varying between 1.19 and 931 km2. The tracking data revealed that the creation of a relatively small marine reserve could protect the critical inter-nesting habitat in the Farasan Banks. The results also highlight the need for multinational collaboration to protect migratory corridors and foraging sites of this endangered species.

HSF1 expression in tumor-associated macrophages promotes tumor cell proliferation and indicates poor prognosis in esophageal squamous cell carcinoma

Purpose Tumor-associated macrophages (TAMs), are crucial for the survival and development of tumor cells. Heat shock factor 1 (HSF1) is a potent, complex carcinogenesis modulator, and esophageal cancer (EC) patients have a bad prognosis when HSF1 is highly expressed. HSF1's clinical importance and biological role in TAMs are still unknown. Methods The HSF1 expression profile and patient survival information were analyzed from the TCGA database. The infiltration of different types of immune cells in EC was evaluated based on HSF1 gene expression by Sangerbox 3.0. Immunochemistry was employed to assess HSF1 protein expression in 134 individuals with esophageal squamous cell carcinoma (ESCC), proceeded by association with clinicopathological variables. The role of macrophage-driven HSF1 were observed using HSF1-knockdown THP1 cells. Results High level of HSF1 have a poorer prognosis in individuals with EC. The expressing level of HSF1 was positively related to infiltration of M2 macrophages (P < 0.05). The expression of HSF1 in macrophages was an independent factor for DFS (P = 0.002) and OS (P = 0.002) in ESCC cases. HSF1 was up-regulated in IL-4 stimulation THP1 cells in a time-dependent manner. Under the heat stimulation condition, THP1-derived macrophages were more sensitive than tumor cells. Compared to IL-4 induced-THP1 cells control, the HSF1 knockdown in THP1 cell inhibited the growth and proliferation of ESCC cells. Conclusions The up-regulation of HSF1 was more rapid and could affect the proliferation of tumor cells in IL4-induced macrophages. The expression of HSF1 in TAMs can also serve as a marker for ESCC prognosis (AU)

Subjective and perceptive assessment of speech/voice and swallowing function before and after radiation therapy in patients of head-and-neck squamous cell cancer.

Aim: To prospectively assess subjective and perceptive speech/voice and swallowing function before and after radiation therapy (RT) in patients of head-and-neck squamous cell cancer (HNSCC). Materials and Methods: The study cohort comprised eligible consecutive HNSCC patients planned for curative RT from April 2018 to July 2018 who consented for the study. Prospective evaluation of speech/voice and swallowing function was done before and after RT. For subjective and perceptive evaluation of speech/voice, speech handicap index (SHI) and Grade, Roughness, Asthenia, Breathiness, and Strain (GRABS) Scale was used, respectively. For subjective and perceptive evaluation of swallowing, M D Anderson Dysphagia Inventory (MDADI) and Performance Status Scale for head and neck (PSSHN) were used, respectively. All patients were taught speech/voice and swallowing exercises before RT. Statistical analysis was performed using SYSTAT version-12 (Cranes software, Bengaluru). Results: The study cohort comprised 30 patients of HNSCC with a median age of 57 years and male-to-female ratio of 4:1. The most common subsite was the oral cavity (43.33%) and a majority (76.66%) presented in the locally advanced stage. Post-RT there was significant improvement in speech/voice function (SHI P = 0.0006, GRABS score P = 0.003). Perceptive assessment of swallowing function by PSSHN showed significant improvement (P = 0.0032), but subjective assessment by MDADI showed no significant (P = 0.394) improvement until the first follow-up. Conclusion: Speech/voice function improved significantly after radiotherapy when combined with rehabilitation exercises. Swallowing function did not improve till the first follow-up. Future studies with the large number of patients and long-term follow-up are needed to document the changes in organ function.

Salvage transoral laser microsurgery for early local recurrence of glottic squamous cell cancer.

BACKGROUND: For recurrent laryngeal cancer, the feasibility of salvage transoral laser microsurgery (TLM) remains controversial. This study compared the efficacy of TLM and open partial laryngectomy (OPL) for treatment of early local recurrence of glottic squamous cell cancer (GSCC) and confirm the effectiveness of salvage TLM as a treatment option. METHODS: This retrospective study involved 55 patients with early local recurrent GSCC treated with TLM, and the oncologic outcomes, functional outcomes, hospitalization time and complications were compared with a group of 40 recurrent GSCC patients matched for clinical variables of TLM group, treated by OPL by the same team of surgeons. RESULTS: The 5-year overall survival and disease-specific survival rates were 65.8% and 91.5%, respectively, for 55 patients with rTis-rT2 stage treated by TLM and 77.1% and 94.7%, respectively, for 40 patients with rTis-rT2 stage treated by OPL (OPL group). In the TLM and OPL groups, the local control rates after 5 years were 77.5% and 79.3%, respectively, and the laryngeal preservation rates were 94.4% and 83.6%, respectively (p > 0.05). Compared with the OPL group, the complication rate (1.82%) and hospitalization duration (5.42 ± 2.26 days) were significantly lower in the TLM group (p < 0.05). Compared with the OPL group, postsurgical health-related quality of life and quality of voice were significantly better in the TLM group (p < 0.001). CONCLUSION: Salvage TLM can be used as an effective treatment option for suitable patients after a full, comprehensive, and careful assessment of the characteristics of early locally recurrent glottic carcinoma.

Circulating tumour DNA kinetics in recurrent/metastatic head and neck squamous cell cancer patients.

PURPOSE: Immune checkpoint blockade (ICB) has become a standard of care in the treatment of recurrent/metastatic head and neck squamous cell cancer (R/M HNSCC). However, only a subset of patients benefit from treatment. Quantification of plasma circulating tumour DNA (ctDNA) levels and on-treatment kinetics may permit real-time assessment of disease burden under selective pressures of treatment. PATIENTS AND METHODS: R/M HNSCC patients treated with systemic therapy, platinum-based chemotherapy (CT) or ICB, underwent serial liquid biopsy sampling. Biomarkers tested included ctDNA measured by CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) and markers of host inflammation measured by neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR). RESULTS: Among 53 eligible patients, 16 (30%) received CT, 30 (57%) ICB [anti-PD1/L1] monotherapy and 7 (13%) combination immunotherapy (IO). Median progression-free survival (PFS) and overall survival (OS) were 2.8 months (95% CI, 1.3-4.3) and 8.2 months (95% CI, 5.6-10.8), respectively. Seven (13%) patients experienced a partial response and 21 (40%) derived clinical benefit. At baseline, median ctDNA variant allele frequency (VAF) was 4.3%. Baseline ctDNA abundance was not associated with OS (p = 0.56) nor PFS (p = 0.54). However, a change in ctDNA VAF after one cycle of treatment (ΔVAF (T1-2)) was predictive of both PFS (p< 0.01) and OS (p< 0.01). Additionally, decrease in ΔVAF identified patients with longer OS despite early radiological progression, 8.2 vs 4.6 months, hazard ratio 0.44 (95% CI, 0.19-0.87) p = 0.03. After incorporating NLR and PLR into multivariable Cox models, ctDNA ∆VAF retained an association with OS. CONCLUSIONS: Early dynamic changes in ctDNA abundance, after one cycle of treatment, compared to baseline predicted both OS and PFS in R/M HNSCC patients on systemic therapy.

Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA.

The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.