Diverse nearest neighbors queries using linear skylines

k-nearest neighbor (k-NN) queries are well-known and widely used in a plethora of applications. However, in the original definition of k-NN queries there is no concern regarding diversity of the answer set with respect to the user’s interests. For instance, travelers may be looking for touristic sites that are close to where they are, but that would also lead them to see different parts of the city. Likewise, if one is looking for restaurants close by, it may be more interesting to learn about restaurants of different categories or ethnicities which are nonetheless relatively close. The interesting novel aspect of this type of query is that there are two competing criteria to be optimized: closeness and diversity. We propose two approaches that leverage the notion of linear skyline queries in order to find the k diverse nearest neighbors within a radius r from a given query point, or (k, r)-DNNs for short. Our proposed approaches return a relatively small set containing all optimal solutions for any linear combination of the weights a user could give to the two competing criteria, and we consider three different notions of diversity: spatial, categorical and angular. Our experiments, varying a number of parameters and exploring synthetic and real datasets, in both Euclidean space and road networks, respectively, show that our approaches are several orders of magnitude faster than a straightforward approach.     

Therapeutic Vaccines for HPV-Associated Oropharyngeal and Cervical Cancer: The Next De-Intensification Strategy?

The rise in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) has prompted a quest for further understanding of the role of high-risk HPV in tumor initiation and progression. Patients with HPV-positive OPSCC (HPV+ OPSCC) have better prognoses than their HPV-negative counterparts; however, current therapeutic strategies for HPV+ OPSCC are overly aggressive and leave patients with life-long sequalae and poor quality of life. This highlights a need for customized treatment. Several clinical trials of treatment de-intensification to reduce acute and late toxicity without compromising efficacy have been conducted. This article reviews the differences and similarities in the pathogenesis and progression of HPV-related OPSCC compared to cervical cancer, with emphasis on the role of prophylactic and therapeutic vaccines as a potential de-intensification treatment strategy. Overall, the future development of novel and effective therapeutic agents for HPV-associated head and neck tumors promises to meet the challenges posed by this growing epidemic.     

Anatomical Laser Microdissection of the Ileum Reveals mtDNA Depletion Recovery in A Mitochondrial Neuro-Gastrointestinal Encephalomyopathy (MNGIE) Patient Receiving Liver Transplant

mitochondrial neuro-gastrointestinal encephalomyopathy (MNGIE) is a rare genetic disorder characterized by thymidine phosphorylase (TP) enzyme defect. The absence of TP activity induces the imbalance of mitochondrial nucleotide pool, leading to impaired mitochondrial DNA (mtDNA) replication and depletion. Since mtDNA is required to ensure oxidative phosphorylation, metabolically active tissues may not achieve sufficient energy production. The only effective life-saving approach in MNGIE has been the permanent replacement of TP via allogeneic hematopoietic stem cell or liver transplantation. However, the follow-up of transplanted patients showed that gut tissue changes do not revert and fatal complications, such as massive gastrointestinal bleeding, can occur. The purpose of this study was to clarify whether the reintroduction of TP after transplant can recover mtDNA copy number in a normal range. Using laser capture microdissection and droplet-digital-PCR, we assessed the mtDNA copy number in each layer of full-thickness ileal samples of a naive MNGIE cohort vs. controls and in a patient pre- and post-TP replacement. The treatment led to a significant recovery of gut tissue mtDNA amount, thus showing its efficacy. Our results indicate that a timely TP replacement is needed to maximize therapeutic success before irreversible degenerative tissue changes occur in MNGIE.     

Prediction of Drug Synergism between Peptides and Antineoplastic Drugs Paclitaxel, 5-Fluorouracil,and Doxorubicin Using In Silico Approaches

Chemotherapy is the main treatment for most early-stage cancers; nevertheless, its efficacy is usually limited by drug resistance, toxicity, and tumor heterogeneity. Cell-penetrating peptides (CPPs) are small peptide sequences that can be used to increase the delivery rate of chemotherapeutic drugs to the tumor site, therefore contributing to overcoming these problems and enhancing the efficacy of chemotherapy. The drug combination is another promising strategy to overcome the aforementioned problems since the combined drugs can synergize through interconnected biological processes and target different pathways simultaneously. Here, we hypothesized that different peptides (P1–P4) could be used to enhance the delivery of chemotherapeutic agents into three different cancer cells (HT-29, MCF-7, and PC-3). In silico studies were performed to simulate the pharmacokinetic (PK) parameters of each peptide and antineoplastic agent to help predict synergistic interactions in vitro. These simulations predicted peptides P2–P4 to have higher bioavailability and lower T_max, as well as the chemotherapeutic agent 5-fluorouracil (5-FU) to have enhanced permeability properties over other antineoplastic agents, with P3 having prominent accumulation in the colon. In vitro studies were then performed to evaluate the combination of each peptide with the chemotherapeutic agents as well as to assess the nature of drug interactions through the quantification of the Combination Index (CI). Our findings in MCF-7 and PC-3 cancer cells demonstrated that the combination of these peptides with paclitaxel (PTX) and doxorubicin (DOXO), respectively, is not advantageous over a single treatment with the chemotherapeutic agent. In the case of HT-29 colorectal cancer cells, the combination of P2–P4 with 5-FU resulted in synergistic cytotoxic effects, as predicted by the in silico simulations. Taken together, these findings demonstrate that these CPP6-conjugates can be used as adjuvant agents to increase the delivery of 5-FU into HT-29 colorectal cancer cells. Moreover, these results support the use of in silico approaches for the prediction of the interaction between drugs in combination therapy for cancer.     

Antibacterial and Antibiofilm Properties of Self-Assembled Dipeptide Nanotubes

Over recent decades, multidrug-resistant pathogens have become a global concern, with WHO even considering it one of the biggest threats to global health, food security, and development today, which led to the search for alternative antibacterial agents. A special class is formed by peptides composed by the diphenylalanine motif whose antibacterial properties result from their supramolecular arrangement into nanotubes. However, several other dipeptides that also form nanotubes have been largely overlooked. Here, we present the antibacterial activity of four dipeptide nanotubes. The results point to diverse mechanisms through which dipeptide nanotubes exert their effect against bacteria. Antibacterial activity was similar for dipeptide nanotubes sufficiently wide to allow water flux while dipeptides displaying smaller channels were inactive. This suggests that two of the tested dipeptides, L-Phe-L-Phe (FF, diphenylalanine) and L-Leu-L-Ser (LS), are pore forming structures able to induce membrane permeation and affect cellular hydration and integrity. Of these two dipeptides, only FF demonstrated potential to inhibit biofilm formation. The amyloid-like nature and hydrophobicity of diphenylalanine assemblies are probably responsible for their adhesion to cell surfaces preventing biofilm formation and bacteria attachment.     

Chitosan biobased and intelligent films: Monitoring pH variations

Many factors can influence the shelf-life product, such as pH, water activity, nutrient levels available oxygen, etc. Variations in food pH could occur due to microorganism growth and chemical reactions that may impact flavour, consistency and shelf-life. The objective of this paper was to obtain and characterize the fast pH-colourimetric indicator device, applying a simple manufacturing technique, using food grade and biodegradable materials. The intelligent film was based on natural compounds as chitosan and anthocyanin (pH-colourimetric indicator). Chitosan intelligent films (C-ATH, 2.0 g/100 g) were obtained incorporating anthocyanin (1.0 g/100 g) in matrix films. Initially, a dark violet colour was observed in chitosan films dried. When immersed in different pH buffers, the colour range of the films varied from pink (in acid pH) to bluish-green (in neutral pH) and to violet (in basic pH). The water solubility and water vapour transmission rate of C-ATH were decreased to 60% and 48%, respectively, as compared to control film (CF, without indicator). The mechanical properties such as tensile strength and rigidity were maintained, and the elongation at break was reduced to 47% compared to CF. The advantages of this system were the simple manufacturing process, biodegradability and usage of natural and safe compounds.     

Characterisation of Staphylococcus aureus strains from milk and goat cheese and evaluation of their inhibition by gallic acid,nisin and velame of the Brazilian caatinga

Twenty isolates from milk and goat cheese were confirmed as Staphylococcus aureus. These isolates were characterised for phenotypic properties related to cell adhesion and for the presence of enterotoxin production, intercellular adhesion and β‐lactam resistance genes. Staphylococcus aureus L47 showed cell adhesion ability and positivity for the sec, sed, icaD, mecA and blaZ genes. Three antimicrobial compounds were tested singly or in pairs for growth control of strain L47: gallic acid (GA), nisin and essential oil (EO) of Croton heliotropiifolius (velame). At 24 h, EO and EO + nisin showed higher inhibitory activity against S. aureus L47 in goat milk.     

Methicillin‐Resistant Staphylococcus aureus in Raw Meats and Prepared Foods in Public Hospitals in Salvador,Bahia, Brazil

This study investigated the presence of methicillin‐resistant Staphylococcus aureus (MRSA) in raw meat and fish and foods prepared from them for patient consumption in public hospitals in Salvador, Bahia, in northeastern Brazil. A total of 114 samples of raw meat and fish (chicken, n = 30; beef, n = 30; pork, n = 24; and fish, n = 30) and 63 samples of prepared foods (made with chicken, n = 15; beef, n = 15; pork, n = 15; and fish, n = 18) were collected from the kitchens of 10 different hospitals. Of the 114 investigated raw meat and fish samples, 28.1% were positive for MRSA, which comprised 23.3% beef, 23.3% chicken, 37.5% pork, and 30% fish samples. Of the prepared foods, 9.5% were positive for MRSA, which comprised 5.6% chicken products, 6.7% pork products, and 22.2% fish products. MRSA contamination was not detected in prepared beef dishes. A statistical analysis showed no association between the presence of MRSA and the type of raw food (P > 0.05). The high prevalence of MRSA among the raw foods tested and the presence of the microorganism in prepared foods emphasizes the necessity of enforcing hygienic practices within hospital kitchens.