Multilayer Complex Network Descriptors for Color-Texture Characterization

A new method based on complex networks is proposed for color-texture analysis. The proposal consists on modeling the image as a multilayer complex network where each color channel is a layer, and each pixel (in each color channel) is represented as a network vertex. The network dynamic evolution is accessed using a set of modeling parameters (radii and thresholds), and new characterization techniques are introduced to capt information regarding within and between color channel spatial interaction. An automatic and adaptive approach for threshold selection is also proposed. We conduct classification experiments on 5 well-known datasets: Vistex, Usptex, Outex13, CURet and MBT. Results among various literature methods are compared, including deep convolutional neural networks with pre-trained architectures. The proposed method presented the highest overall performance over the 5 datasets, with 97.7 of mean accuracy against 97.0 achieved by the ResNet convolutional neural network with 50 layers.Comment: 20 pages, 7 figures and 4 table

The manifesto of pharmacoenosis: Merging hiv pharmacology into pathocoenosis and syndemics in developing countries

Pathocoenosis and syndemics theories have emerged in the last decades meeting the frequent need of better understanding interconnections and reciprocal influences that coexistent communicable and non-communicable diseases play in a specific population. Nevertheless, the attention to pharmacokinetic and pharmacodynamics interactions of co-administered drugs for co-present diseases is to date limitedly paid to alert against detrimental pharmacological combos. Low and middle-income countries are plagued by the highest burden of HIV, tuberculosis, malaria, and helminthiasis, and they are experiencing an alarming rise in non-communicable disorders. In these settings, co-infections and comorbidities are common, but no tailored prescribing nor clinical trials are used to assess and exploit existing opportunities for the simultaneous and potentially synergistic treatment of intertwined diseases. Pharmacoenosis is the set of interactions that take place within a host as well as within a population due to the compresence of two or more diseases and their respective treatments. This framework should pilot integrated health programmes and routine clinical practice to face drug–drug interaction issues, avoiding negative co-administrations but also exploiting potential favourable ones to make the best out of the worst situations; still, to date, guiding data on the latter possibility is limited. Therefore, in this narrative review, we have briefly described both detrimental and favourable physiopathological interactions between HIV and other common co-occurring pathologies (malaria, tuberculosis, helminths, and cardiovascular disorders), and we have presented examples of advantageous potential pharmacological interactions among the drugs prescribed for these diseases from a pharmacokinetics, pharmacodynamics, and pharmacogenetics standpoint

Social Interaction Layers in Complex Networks for the Dynamical Epidemic Modeling of COVID-19 in Brazil

We are currently living in a state of uncertainty due to the pandemic caused by the Sars-CoV-2 virus. There are several factors involved in the epidemic spreading such as the individual characteristics of each city/country. The true shape of the epidemic dynamics is a large, complex system such as most of the social systems. In this context, Complex networks are a great candidate to analyze these systems due to their ability to tackle structural and dynamical properties. Therefore this study presents a new approach to model the COVID-19 epidemic using a multi-layer complex network, where nodes represent people, edges are social contacts, and layers represent different social activities. The model improves the traditional SIR and it is applied to study the Brazilian epidemic by analyzing possible future actions and their consequences. The network is characterized using statistics of infection, death, and hospitalization time. To simulate isolation, social distancing, or precautionary measures we remove layers and/or reduce the intensity of social contacts. Results show that even taking various optimistic assumptions, the current isolation levels in Brazil still may lead to a critical scenario for the healthcare system and a considerable death toll (average of 149,000). If all activities return to normal, the epidemic growth may suffer a steep increase, and the demand for ICU beds may surpass 3 times the country's capacity. This would surely lead to a catastrophic scenario, as our estimation reaches an average of 212,000 deaths even considering that all cases are effectively treated. The increase of isolation (up to a lockdown) shows to be the best option to keep the situation under the healthcare system capacity, aside from ensuring a faster decrease of new case occurrences (months of difference), and a significantly smaller death toll (average of 87,000).Comment: 16 pages, 7 figures, 2 table

Carbapenemase-producing klebsiella pneumoniae colonization and infection in solid organ transplant recipients: A single-center, retrospective study

Carbapenemase-KPC producing Klebsiella pneumoniae (CP-Kp) infection represents a serious threat to solid organ transplant (SOT). All patients admitted between 1 May 2011 and 31 August 2014 undergoing SOT were included in the retrospective study. The primary outcomes included a description of the association of enteric colonization and invasive infections by CP-Kp with one-year mortality. Secondary outcomes were the study of risk factors for colonization and invasive infections by CP-Kp. Results: A total of 5.4% (45/828) of SOT recipients had at least one positive rectal swab for CP-Kp, with most (88.9%) occurring after transplantation. 4.5% (35/828) of patients developed a CP-Kp-related invasive infection, with 68.6% (24/35) being previously colonized. The 1-year mortality was 31.1% in patients with enteric colonization with CP-Kp and, it was 51.4% among patients with CP-Kp-related invasive infections. At univariate analysis, colonization, invasive infections, sepsis, severe sepsis, and septic shock were significantly associated with 1-year mortality. At multivariate analysis, only invasive infections and the combination of sepsis, severe sepsis, or septic shock were significantly associated with 1-year mortality, whereas gastrointestinal colonization was significantly associated with survival. In this population, the 1-year mortality was significantly associated with invasive infections; otherwise, gastrointestinal colonization was not associated with increased 1-year mortality

The critical view of safety during laparoscopic cholecystectomy: Strasberg Yes or No? An Italian Multicentre study

Background: Laparoscopic cholecystectomy is considered the gold standard for the treatment of gallbladder lithiasis; nevertheless, the incidence of bile duct injuries (BDI) is still high (0.3–0.8%) compared to open cholecystectomy (0.2%). In 1995, Strasberg introduced the "Critical View of Safety" (CVS) to reduce the risk of BDI. Despite its widespread use, the scientific evidence supporting this technique to prevent BDI is controversial. Methods: Between March 2017 and March 2019, the data of patients submitted to laparoscopic cholecystectomy in 30 Italian surgical departments were collected on a national database. A survey was submitted to all members of Italian Digestive Pathology Society to obtain data on the preoperative workup, the surgical and postoperative management of patients and to judge, at the end of the procedure, if the isolation of the elements was performed according to the CVS. In the case of a declared critical view, iconographic documentation was obtained, finally reviewed by an external auditor. Results: Data from 604 patients were analysed. The study population was divided into two groups according to the evidence (Group A; n = 11) or absence (Group B; N = 593) of BDI and perioperative bleeding. The non-use of CVS was found in 54.6% of procedures in the Group A, and 25.8% in the Group B, and evaluating the operator-related variables the execution of CVS was associated with a significantly lower incidence of BDI and intraoperative bleeding. Conclusions: The CVS confirmed to be the safest technique to recognize the elements of the Calot triangle and, if correctly performed, it significantly impacted on preventing intraoperative complications. Additional educational programs on the correct application of CVS in clinical practice would be desirable to avoid extreme conditions that may require additional procedures

Clinico-pathological associations and concomitant mutations of the RAS/RAF pathway in metastatic colorectal cancer

Background: Over the past few years, next-generation sequencing (NGS) has become reliable and cost-effective, and its use in clinical practice has become a reality. A relevant role for NGS is the prediction of response to anti-EGFR agents in metastatic colorectal cancer (mCRC), where multiple exons from KRAS, NRAS, and BRAF must be sequenced simultaneously. Methods: We optimized a 14-amplicon NGS panel to assess, in a consecutive cohort of 219 patients affected by mCRC, the presence and clinico-pathological associations of mutations in the KRAS, NRAS, BRAF, and PIK3CA genes from formalin-fixed, paraffin-embedded specimens collected for diagnostics and research at the time of diagnosis. Results: We observed a statistically significant association of RAS mutations with sex, young age, and tumor site. We demonstrated that concomitant mutations in the RAS/RAF pathway are not infrequent in mCRC, and as anticipated by whole-genome studies, RAS and PIK3CA tend to be concurrently mutated. We corroborated the association of BRAF mutations in right mCRC tumors with microsatellite instability. We established tumor side as prognostic parameter independently of mutational status. Conclusions: To our knowledge, this is the first monocentric, consecutively accrued clinical mCRC cancer cohort tested by NGS in a real-world context for KRAS, NRAS, BRAF, and PIK3CA. Our study has highlighted in clinical practice findings such as the concomitance of mutations in the RAS/RAF pathway, the presence of multiple mutations in single gene, the co-occurrence of RAS and PIK3CA mutations, the prognostic value of tumor side and possible associations of sex with specific mutations