Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification.

BACKGROUND: In recent years, researchers have made significant strides in understanding the heterogeneity of breast cancer and its various subtypes. However, the wealth of genomic and proteomic data available today necessitates efficient frameworks, instruments, and computational tools for meaningful analysis. Despite its success as a prognostic tool, the PAM50 gene signature's reliance on many genes presents challenges in terms of cost and complexity. Consequently, there is a need for more efficient methods to classify breast cancer subtypes using a reduced gene set accurately. RESULTS: This study explores the potential of achieving precise breast cancer subtype categorization using a reduced gene set derived from the PAM50 gene signature. By employing a "Few-Shot Genes Selection" method, we randomly select smaller subsets from PAM50 and evaluate their performance using metrics and a linear model, specifically the Support Vector Machine (SVM) classifier. In addition, we aim to assess whether a more compact gene set can maintain performance while simplifying the classification process. Our findings demonstrate that certain reduced gene subsets can perform comparable or superior to the full PAM50 gene signature. CONCLUSIONS: The identified gene subsets, with 36 genes, have the potential to contribute to the development of more cost-effective and streamlined diagnostic tools in breast cancer research and clinical settings.

Self-reported bruxism in patients with post-traumatic stress disorder.

OBJECTIVE: The present study aimed to investigate the association between self-reported awake/sleep bruxism, and orofacial pain with post-traumatic stress disorder (PTSD). METHODS: A case-control study with a convenience sample was designed. Participants were recruited from a university-based Trauma Ambulatory. The diagnosis of PTSD was established through a clinical interview and the Structured Clinical Interview (SCID-I/P). Thirty-eight PTSD patients and 38 controls completed the Research Diagnostic Criteria for Temporomandibular Disorders Axis-II to categorize awake/sleep bruxism and orofacial pain. Following this, we performed a short clinical examination of the temporomandibular joint and extraoral muscles. RESULTS: Adjusted logistic regression analysis showed that awake bruxism was associated with PTSD (OR = 3.38, 95% CI = 1.01-11.27, p = 0.047). Sleep bruxism was not associated with any covariate included in the model. In a Poisson regression model, PTSD (IRR = 3.01, 95% CI = 1.38-6.55, p = 0.005) and the muscle pain/discomfort (IRR = 5.12, 95% CI = 2.80-9.36, p < 0.001) were significant predictors for current orofacial pain. CONCLUSIONS: PTSD was associated with self-reported awake bruxism and low-intensity orofacial pain. These conditions were frequent outcomes in patients previously exposed to traumatic events. CLINICAL RELEVANCE: We suggest including a two-question screening for bruxism in psychiatry/psychology interviews to improve under-identification and to prevent harmful consequences at the orofacial level.

Coupling of Modes in Step-Index Plastic Optical Fibers by Using D-Shape Technique.

This article presents a technique for reducing the stabilization length of steady-state modes in step-index plastic optical fibers (POFs), which is significant for sensor networks, Internet of Things, signal processing, and data fusion in sensor systems. The results obtained with the com- putational tool developed suggest that the D-shape created in the POF effectively reduces the stabi- lization length of the modes and, by extension, minimizes the dispersion effects of the modes by filtering out high-order modes. Applying the analysis to commercial POFs, the authors experimen- tally verified a reduction in the stabilization length of modes from 27 to 10 m and from 20 m to 5 m. Reducing the mode stabilization length minimizes the bit error rate (BER) in short-length SI-POF- based optical links operating at 250 Mbp/s. A reduction from 7.6 × 10-7 to 3.7 × 10-10 was achieved.

Trophic dynamics of methylmercury and trace elements in a remote Amazonian Lake.

Information on pollutant trophodynamics can be crucial for public health, as contaminated food consumption may lead to deleterious effects. This study was performed in Puruzinho Lake, a remote body of water in the Brazilian Amazon from which a riparian human population obtains an important part of its animal protein intake. Samples from 92 individuals, comprising 13 species and four trophic guilds (iliophagous, planktivorous, omnivorous, and piscivorous fish) were analysed for the determination of trace elements (Fe, Cr, Mn, Ni, Zn, Ca, Sr, Cd, Sn, Tl and Pb) and methylmercury concentrations. Samples from the same individuals had already been analysed for stable isotope (SI) measurements (δ13C and δ15N) in a previous investigation and the SI data have been statistically treated with those generated in this study for the evaluation of trophic dynamics of contaminants. Methylmercury was the only analyte that biomagnified, presenting TMF values of 4.65 and 4.55 for total and resident ichthyofauna, respectively. Trace elements presented either trophic dilution or independence from the trophic position, constituting a behaviour that was coherent with that found in the scientific literature. The similarity between Ni behaviour through the trophic web to that of essential elements contributes to the discussion on the essentiality of this metal to fish. Considering the Non-cancer Risk Assessment, the calculated Target Hazard Quotient (THQ) values were higher than 1.0 for all analysed individuals for methylmercury, as well as for only one individual for nickel. No other analyte rendered THQ values higher than 1.0.

Trypanosoma cruzi infection induces proliferation and impairs migration of a human breast cancer cell line.

Breast cancer is considered the type of cancer that most affects women in the world. The triple negative breast cancer is considered aggressive with poor prognosis. In the 1930s Russian researchers observed that T. cruzi has tropism for tumor cells. Since then, this research field has been subject of a numerous of researches. Here, we proposed to investigate the impact of T. cruzi infection on proliferation and migration of triple negative breast cancer cell line (MDA-MB-231). T. cruzi showed high invasion and multiplication rate in MDA-MB-231 cell line. The infection promoted the multiplication of MDA-MB-231 cell, continuous cell lysis throughout of days of in vitro infection and impaired MDA-MB-231 cell migration. Taken together, these results demonstrated the high susceptibility of MDA-MB-231 cell to T. cruzi and suggested that molecules from T. cruzi may impair host cell migration with potential use to avoid metastasis.

Antileishmanial effects of γCdcPLI, a phospholipase A2 inhibitor from Crotalus durissus collilineatus snake serum, on Leishmania (Leishmania) amazonensis.

BACKGROUND: Leishmaniasis, a neglected disease caused by the parasite Leishmania, is treated with drugs associated with high toxicity and limited efficacy, in addition to constant reports of the emergence of resistant parasites. In this context, snake serums emerge as good candidates since they are natural sources with the potential to yield novel drugs. OBJECTIVES: We aimed to show the antileishmanial effects of γCdcPLI, a phospholipase A2 inhibitor from Crotalus durissus collilineatus snake serum, against Leishmania (Leishmania) amazonensis. METHODS: Promastigotes forms were exposed to γCdcPLI, and we assessed the parasite viability and cell cycle, as well as invasion and proliferation assays. FINDINGS: Despite the low cytotoxicity effect on macrophages, our data indicate that γCdcPLI has a direct effect on parasites promoting an arrest in the G1 phase and reduction in the G2/M phase at the highest dose tested. Moreover, this PLA2 inhibitor reduced the parasite infectivity when promastigotes were pre-treated. Also, we demonstrated that the γCdcPLI treatment modulated the host cell environment impairing early and late steps of the parasitism. MAIN CONCLUSIONS: γCdcPLI is an interesting tool for the discovery of new essential targets on the parasite, as well as an alternative compound to improve the effectiveness of the leishmaniasis treatment.

Imputation of precipitation data in northeast Brazil.

This article evaluates four statistical methods of multiple imputation to fill in the missing data of daily precipitation in Northeast Brazil (NEB). We used a daily database collected by 94 rain gauges distributed in NEB from January 1, 1986 to December 31, 2015. The methods were: random sampling from the observed values; predictive mean matching, Bayesian linear regression; and bootstrap expectation maximization algorithm (BootEm). To compare these methods, missing data from the original series were initially excluded. The next step was to create three scenarios for each method, in which 10\%, 20\% and 30\% of the data were removed at random. The BootEM method presented the best statistical results. With the average bias between the complete series and the imputed series values ranging between -0.91 and 1.30 mm/day. The values of the Pearson correlation ranging between 0.96, 0.91 and 0.86 respectively for 10\%, 20\% and 30\% missing data. We conclude that this is an adequate method for the reconstruction of historical precipitation data in NEB.

StreetAware: A High-Resolution Synchronized Multimodal Urban Scene Dataset.

Access to high-quality data is an important barrier in the digital analysis of urban settings, including applications within computer vision and urban design. Diverse forms of data collected from sensors in areas of high activity in the urban environment, particularly at street intersections, are valuable resources for researchers interpreting the dynamics between vehicles, pedestrians, and the built environment. In this paper, we present a high-resolution audio, video, and LiDAR dataset of three urban intersections in Brooklyn, New York, totaling almost 8 unique hours. The data were collected with custom Reconfigurable Environmental Intelligence Platform (REIP) sensors that were designed with the ability to accurately synchronize multiple video and audio inputs. The resulting data are novel in that they are inclusively multimodal, multi-angular, high-resolution, and synchronized. We demonstrate four ways the data could be utilized - (1) to discover and locate occluded objects using multiple sensors and modalities, (2) to associate audio events with their respective visual representations using both video and audio modes, (3) to track the amount of each type of object in a scene over time, and (4) to measure pedestrian speed using multiple synchronized camera views. In addition to these use cases, our data are available for other researchers to carry out analyses related to applying machine learning to understanding the urban environment (in which existing datasets may be inadequate), such as pedestrian-vehicle interaction modeling and pedestrian attribute recognition. Such analyses can help inform decisions made in the context of urban sensing and smart cities, including accessibility-aware urban design and Vision Zero initiatives.

Cellular dormancy: A widespread phenomenon that perpetuates infectious diseases.

Under adverse environmental conditions, microorganisms are able to enter a state of cellular dormancy which consists of cell cycle arrest and interruption of multiplication. This process ensures their perpetuation in the infected host organism and enables the spread of disease. Throughout biological evolution, dormancy allowed microorganisms to persist in a harsh niche until favorable conditions for their reactivation were re-established. Here, we propose to discuss the dormancy of bacteria and protozoa pathogens focusing on the potential mechanisms and components associated with dormancy.

Insights into the Serum Metabolic Adaptations in Response to Inspiratory Muscle Training: A Metabolomic Approach Based on 1H NMR and UHPLC-HRMS/MS.

Inspiratory muscle training (IMT) is known to promote physiological benefits and improve physical performance in endurance sports activities. However, the metabolic adaptations promoted by different IMT prescribing strategies remain unclear. In this work, a longitudinal, randomized, double-blind, sham-controlled, parallel trial was performed to investigate the effects of 11 weeks (3 days·week-1) of IMT at different exercise intensities on the serum metabolomics profile and its main regulated metabolic pathways. Twenty-eight healthy male recreational cyclists (30.4 ± 6.5 years) were randomized into three groups: sham (6 cm·H2O of inspiratory pressure, n = 7), moderate-intensity (MI group, 60% maximal inspiratory pressure (MIP), n = 11) and high-intensity (HI group, 85-90% MIP, n = 10). Blood serum samples were collected before and after 11 weeks of IMT and analyzed by 1H NMR and UHPLC-HRMS/MS. Data were analyzed using linear mixed models and metabolite set enrichment analysis. The 1H NMR and UHPLC-HRMS/MS techniques resulted in 46 and 200 compounds, respectively. These results showed that ketone body metabolism, fatty acid biosynthesis, and aminoacyl-tRNA biosynthesis were upregulated after IMT, while alpha linolenic acid and linoleic acid metabolism as well as biosynthesis of unsaturated fatty acids were downregulated. The MI group presented higher MIP, Tryptophan, and Valine levels but decreased 2-Hydroxybutyrate levels when compared to the other two studied groups. These results suggest an increase in the oxidative metabolic processes after IMT at different intensities with additional evidence for the upregulation of essential amino acid metabolism in the MI group accompanied by greater improvement in respiratory muscle strength.

Aspen Plus simulation for effluent reuse in thermomechanical pulp mills.

The objective of this study was to evaluate the closing of the water circuit and reusing the treated effluent in the production of TMP, using simulations performed with the Aspen Plus®. The treated effluent was reused to replace 50, 75 and 100% of the well water. An adaptation of the Aspen Plus® program simulating the TMP production process and a dynamic simulation test to verify the accumulation of non-process elements (NPEs) in industrial processes at different proportions of reuse were evaluated. The quality of the final product was assessed in laboratory bleaching tests for pulp brightness and brightness reversion. The concentrations of the NPE were 0.00097, 0.00122 and 0.00145 kmol/h for Mn2+, 0.012929, 0.018368 and 0.023595 kmol/h for Fe2+ and 0.000542, 0.000722 and 0.000948 kmol/h for Cu2+, with the recycling of the treated effluent of 50, 75 and 100%, respectively. The brightness and brightness reversion of the pulp were similar with the different proportions of effluent reuse and with the use of fresh industrial water, with values ranging from 83.37 to 83.97% ISO and 5.43 to 6.38 ISO units, respectively. The use of treated effluent did not affect the pulp quality, which could diminish the water use a pulp mil.

Pentachloropseudilin Treatment Impairs Host Cell Invasion by Trypanosoma cruzi.

Pentachloropseudilin (PClP) is a reversible and allosteric inhibitor of type 1 myosin. Here, we addressed the impact of PClP treatment of Trypanosoma cruzi and mammalian host cell on the parasite migration, cell adhesion and invasion. We observed that PClP was not toxic to either T. cruzi or host cell. Moreover, treatment of T. cruzi with PClP inhabited parasite motility, host cell adhesion and invasion. Treatment of host cell with PClP also impaired parasite invasion probably by decreasing lysosome migration to the entry site of the parasite. Therefore, PClP treatment impaired fundamental processes necessary for a successful T. cruzi infection.

Evaluation of HPV and EBV in OSCC and the expression of p53, p16, E-cadherin, COX-2, MYC, and MLH1.

OBJECTIVE: This study aimed to evaluate the presence of human papillomavirus (HPV) and Epstein-Barr virus (EBV) and the expression of p53, p16, E-cadherin, COX-2, MLH1, and MYC in oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS: One hundred OSCC specimens were submitted to in situ hybridization for HPV and EBV, and immunohistochemistry for detection of the human proteins. RESULTS: Thirty-one cases showed HPV in tumor tissue. EBV was not detected in any case investigated. The HPV(+) group demonstrated an increase of staining scores for nuclear p16 (p = .047), cytoplasmic MYC (p = .002), while a decrease for nuclear MLH1 (p = .048), suggesting that HPV may upregulate the expression of the first two proteins and down-regulate the latter. CONCLUSION: Our findings reinforce the hypothesis of the HPV-related oral carcinogenesis involving the expression of p16 and MYC, and MLH1 suppression. Exclusively cytoplasmic stainings for p16, MLH1, and MYC were also associated with more advanced tumors. Finally, in view of the lack of studies correlating the HPV or EBV infection to the expression of oncoproteins, more researches assessing a broader panel of markers and employing different approaches are still necessary in order to understand the role of these viruses as well as the molecular mechanisms involved in the development and progression of oral carcinomas.

REIP: A Reconfigurable Environmental Intelligence Platform and Software Framework for Fast Sensor Network Prototyping.

Sensor networks have dynamically expanded our ability to monitor and study the world. Their presence and need keep increasing, and new hardware configurations expand the range of physical stimuli that can be accurately recorded. Sensors are also no longer simply recording the data, they process it and transform into something useful before uploading to the cloud. However, building sensor networks is costly and very time consuming. It is difficult to build upon other people's work and there are only a few open-source solutions for integrating different devices and sensing modalities. We introduce REIP, a Reconfigurable Environmental Intelligence Platform for fast sensor network prototyping. REIP's first and most central tool, implemented in this work, is an open-source software framework, an SDK, with a flexible modular API for data collection and analysis using multiple sensing modalities. REIP is developed with the aim of being user-friendly, device-agnostic, and easily extensible, allowing for fast prototyping of heterogeneous sensor networks. Furthermore, our software framework is implemented in Python to reduce the entrance barrier for future contributions. We demonstrate the potential and versatility of REIP in real world applications, along with performance studies and benchmark REIP SDK against similar systems.

Influence of diet and red wine exposure on the velocity of at home bleaching: A randomized controlled clinical trial.

PURPOSE: To evaluate the influence of diet and exposure to red wine on the treatment velocity, clinical results, postoperative tooth sensitivity, and patient satisfaction after tooth bleaching. METHODS: 45 subjects undergoing home bleaching with 16% carbamide peroxide (CP) were randomly separated into three groups, depending on the restriction of colored food and the use of a red wine mouthwash. Shades of teeth 11 and 21 were assessed using a digital spectrophotometer (VITA Easy Shade) at T0 (before treatment), T7 (7 days after treatment), T15 (15 days after treatment), and T30 (30 days after treatment). The assessments were verified using the CIELab system (values of L*, a*, and b*) and the change in shade was calculated (ΔE, ΔL, Δa, and Δb). RESULTS: No statistically significant differences in ΔE, ΔL, Δa, and Δb were found between the groups. However, at T7, the group restricted from colored foods without red wine mouthwash had meaningful variations in L*, a*, and b*. Statistically, there was no difference in tooth sensitivity between the groups in the 7- and 15-day periods. Patients in the restricted colored foods without red wine mouthwash group were more satisfied after the end of treatment. CLINICAL SIGNIFICANCE: Tooth bleaching with 16% carbamide peroxide may be performed in subjects with colorant-rich diets without influencing the clinical outcome.

Echoes of Global Silence: Is there protection and safety for Venezuelan children and adolescents?

As the crisis in Venezuela deepens, an increasing number of children urgently needs shelter, protection, and access to basic services, including food, medicine, clean water, and sanitation. Children and young people in transit are particularly at risk of criminal activity or being separated from their families. The consequences of the humanitarian crisis for children could be devastating for the country's future. The child labor problem was fueled by a mass migration of more than five million Venezuelans that turned many children into livelihoods for their families. The pandemic has aggravated risk factors for child labor. The work ranges from working in dumps to agricultural fields, adding that children in rural areas are more likely to depend on public assistance and are at greater risk of being recruited by gangs. Some Venezuelan women and girls are traveling for hours or days to cross the Colombian border and earn money as sex workers. The complex and multifaceted reality of international migration reveals enormous challenges that directly affect the lives of children and adolescents, especially the most vulnerable, and demand urgent responses from the constituted powers and civil society in the face of countless human rights violations those people experience.

Characteristics and treatment of Brazilian pulp and paper mill effluents: a review.

Pulp and paper industries are very important for developing the Brazilian economy. During production processes, many effluents are generated with high polluting potential. The objective of this study is to conduct an extensive literature review on the characteristics of effluents and treatment forms adopted by Brazilian mills in this industrial sector. Most consulted studies address raw (without treatment) and secondary (after biological treatment) effluents, considering their main characteristics like pH, chemical and biochemical oxygen demands (COD and BOD, respectively), color, solids, organochlorines, toxicity, estrogenic activity, and phenols. Raw effluents differ considerably in composition, depending on the type of paper produced, the pulping process employed, and other steps, like pulp bleaching. Raw effluent characteristics indicate that this effluent cannot be directly disposed of into water bodies, because it does not comply with federal and state disposal standards. Secondary effluents normally comply with Brazilian legislations, although some studies have reported COD and total phenol concentrations higher than disposal standards, suggesting that additional treatments are necessary. Treated effluent reuse was verified in some Brazilian mills, while its disposal in eucalyptus plantations has been considered a promising alternative for irrigation purposes.

Galectin-3 plays a protective role in Leishmania (Leishmania) amazonensis infection.

Leishmania (L.) amazonensis is one of the species responsible for the development of cutaneous leishmaniasis in South America. After entering the vertebrate host, L. (L.) amazonensis invades mainly neutrophils, macrophages and dendritic cells. Studies have shown that gal-3 acts as a pattern recognition receptor. However, the role of this protein in the context of L. (L.) amazonensis infection remains unclear. Here, we investigated the impact of gal-3 expression on experimental infection by L. (L.) amazonensis. Our data showed that gal-3 plays a role in controlling parasite invasion, replication and the formation of endocytic vesicles. Moreover, mice with gal-3 deficiency showed an exacerbated inflammatory response. Taken together, our data shed light to a critical role of gal-3 in the host response to infection by L. (L.) amazonensis.

Optimizing phase variability threshold for automated synchrogram analysis of cardiorespiratory interactions in amateur cyclists.

We propose a procedure suitable for automated synchrogram analysis for setting the threshold below which phase variability between two marker event series is of such a negligible amount that the null hypothesis of phase desynchronization can be rejected. The procedure exploits the principle of maximizing the likelihood of detecting phase synchronization epochs and it is grounded on a surrogate data approach testing the null hypothesis of phase uncoupling. The approach was applied to assess cardiorespiratory phase interactions between heartbeat and inspiratory onset in amateur cyclists before and after 11-week inspiratory muscle training (IMT) at different intensities and compared to a more traditional approach to set phase variability threshold. The proposed procedure was able to detect the decrease in cardiorespiratory phase locking strength during vagal withdrawal induced by the modification of posture from supine to standing. IMT had very limited effects on cardiorespiratory phase synchronization strength and this result held regardless of the training intensity. In amateur athletes training, the inspiratory muscles did not limit the decrease in cardiorespiratory phase synchronization observed in the upright position as a likely consequence of the modest impact of this respiratory exercise, regardless of its intensity, on cardiac vagal control. This article is part of the theme issue 'Advanced computation in cardiovascular physiology: new challenges and opportunities'.

A randomized clinical trial to assess the efficacy of trial-based cognitive therapy compared to prolonged exposure for post-traumatic stress disorder: preliminary findings.

BACKGROUND: Post-traumatic stress disorder (PTSD) is a prevalent mental health condition that is often associated with psychiatric comorbidities and changes in quality of life. Prolonged exposure therapy (PE) is considered the gold standard psychological treatment for PTSD, but treatment resistance and relapse rates are high. Trial-based cognitive therapy (TBCT) is an effective treatment for depression and social anxiety disorder, and its structure seems particularly promising for PTSD. Therefore, we evaluated the efficacy of TBCT compared to PE in patients with PTSD. METHODS: Ninety-five patients (77.6% females) who met Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision, criteria for PTSD were randomly assigned to receive either TBCT (n = 44) or PE (n = 51). Patients were evaluated before and after treatment, and at follow-up 3 months after treatment. The primary outcome was improvement in PTSD symptoms as assessed by the Davidson Trauma Scale (DTS). Secondary outcomes were depression, anxiety, and dysfunctional attitudes assessed by the Beck Depression/Anxiety Inventories and Dysfunctional Attitudes Scale, as well as the dropout rate. RESULTS: A significant reduction in DTS scores was observed in both arms, but no significant difference between treatments. Regarding the secondary outcomes, we found significant differences in depressive symptoms in favor of TBCT, and the dropout rate was lower in the TBCT group than the PE group. CONCLUSION: Our preliminary results suggest that TBCT may be an effective alternative for treating PTSD. Further research is needed to better understand its role and the mechanisms of change in the treatment of this disorder.