A systematic review and repeatability study on the use of deep learning for classifying and detecting tuberculosis bacilli in microscopic images.

Tuberculosis (TB) is among the leading causes of death worldwide from a single infectious agent. This disease usually affects the lungs (pulmonary TB) and can be cured in most cases with a quick diagnosis and proper treatment. Microscopic sputum smear is widely used to diagnose and manage pulmonary TB. Despite being relatively fast and low cost, it can be exhausting because it depends on manually counting TB bacilli (Mycobacterium tuberculosis) in microscope images. In this context, different Deep Learning (DL) techniques are proposed in the literature to assist in performing smear microscopy. This article presents a systematic review based on the PRISMA procedure, which investigates which DL techniques can contribute to classifying TB bacilli in microscopic images of sputum smears using the Ziehl-Nielsen method. After an extensive search and a careful inclusion/exclusion procedure, 28 papers were selected from a total of 400 papers retrieved from nine databases. Based on these articles, the DL techniques are presented as possible solutions to improve smear microscopy. The main concepts necessary to understand how such techniques are proposed and used are also presented. In addition, replication work is also carried out, verifying reproducibility and comparing different works in the literature. In this review, we look at how DL techniques can be a partner to make sputum smear microscopy faster and more efficient. We also identify some gaps in the literature that can guide which issues can be addressed in other works to contribute to the practical use of these methods in laboratories.

PANCREATODUODENECTOMY IN PATIENT WITH VON HIPPEL-LINDAU DISEASE: A LITERATURE REVIEW.

BACKGROUND: The von Hippel-Lindau disease is a highly penetrant autosomal dominant syndrome characterized by tumor predisposition in different organs. AIM: This study aimed to describe a case of a pancreatoduodenectomy for a 30-year-old male patient with von Hippel-Lindau disease. METHODS: We present a case study and the literature review aiming at the state-of-the-art management of a patient with pheochromocytoma, capillary hemangioblastoma in the peripheral retina, and two neuroendocrine tumors in the pancreas. RESULTS: A larger pancreatic lesion was located in the uncinate process, measuring 31 mm. The smaller lesion was located in the proximal pancreas and was detected only on the positron emission tomography-computed tomography scan with DOTATOC-68Ga. Genetic investigation revealed a mutation in the locus NM_000551.3 c.482G>A (p.Arg161Gln) of the Von Hippel-Lindau Human Suppressor gene. The uncinate process tumor was larger than 30 mm and the patient had a mutation on exon 3; therefore, we indicated a pancreatoduodenectomy involving the proximal pancreas to resect both tumors en bloc. During the postoperative period, the patient presented a peripancreatic fluid collection, which was treated as a grade B pancreatic fistula with clinical resolution of the complication. On postoperative day 21, he was discharged home. CONCLUSION: The management of patients with von Hippel-Lindau disease and pancreatic neuroendocrine tumors is complex and must be centered on tertiary institutions with a large volume of pancreatic surgery. Although the current literature assists in decision-making in most situations, each step of the treatment requires analysis and discussion between different medical specialties, including surgeons, clinicians, radiologists, and anesthesiologists.

RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors.

Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes.

Laparoscopic Pancreatectomy in Rats: The Development of an Experimental Model.

INTRODUCTION: several pancreatectomy techniques in rats have been described and utilized for research concerning the pancreas endocrine and exocrine functions. However, we did not find a description of any kind of laparoscopic pancreatectomy in rats in the consulted databases. The objective of this study is to describe a laparoscopic splenic lobe pancreatectomy in rats. METHODS: ten Wistars rats weighting more then 300 g were operated for standardizing the laparoscopic pancreatosplenectomy technique, aided by previous descriptions of laparoscopic splenectomy and open pancreatectomy in rats. Adjustments have been progressively adopted for technical refinement. RESULTS: In five animals a low-cost rat laparoscopic set was used. In other five animals we used a standard laparoscopic set. Three rats died early due to different causes: transection of the gastroesophageal junction, hemorrhagic shock and inadvertent colonic injury. The postoperative period of the other seven rats was uneventful until the seventh postoperative day. DISCUSSION: laparoscopic distal pancreatectomy and splenectomy in rats is feasible and safe, even with a low-cost set, in which the results were alike the standard laparoscopic set.

Pancreatoduodenectomy in patient with von hippel-lindau disease: a literature review / Pancreaticoduodenectomia em paciente com doença de von hippel-lindau - revisão da literatura

ABSTRACT BACKGROUND: The von Hippel-Lindau disease is a highly penetrant autosomal dominant syndrome characterized by tumor predisposition in different organs. AIM: This study aimed to describe a case of a pancreatoduodenectomy for a 30-year-old male patient with von Hippel-Lindau disease. METHODS: We present a case study and the literature review aiming at the state-of-the-art management of a patient with pheochromocytoma, capillary hemangioblastoma in the peripheral retina, and two neuroendocrine tumors in the pancreas. RESULTS: A larger pancreatic lesion was located in the uncinate process, measuring 31 mm. The smaller lesion was located in the proximal pancreas and was detected only on the positron emission tomography-computed tomography scan with DOTATOC-68Ga. Genetic investigation revealed a mutation in the locus NM_000551.3 c.482G>A (p.Arg161Gln) of the Von Hippel-Lindau Human Suppressor gene. The uncinate process tumor was larger than 30 mm and the patient had a mutation on exon 3; therefore, we indicated a pancreatoduodenectomy involving the proximal pancreas to resect both tumors en bloc. During the postoperative period, the patient presented a peripancreatic fluid collection, which was treated as a grade B pancreatic fistula with clinical resolution of the complication. On postoperative day 21, he was discharged home. CONCLUSION: The management of patients with von Hippel-Lindau disease and pancreatic neuroendocrine tumors is complex and must be centered on tertiary institutions with a large volume of pancreatic surgery. Although the current literature assists in decision-making in most situations, each step of the treatment requires analysis and discussion between different medical specialties, including surgeons, clinicians, radiologists, and anesthesiologists.

RESUMO RACIONAL: A doença de von Hippel Lindau é uma síndrome autossômica dominante que se caracteriza por maior incidência de tumores em diferentes órgãos. OBJETIVO: Descrever um caso de pancreatoduodenectomia em paciente do sexo masculino de 30 anos com von Hippel Lindau. MÉTODO: Apresentamos o caso e a revisão da literatura realizada para otimizar o manejo do paciente, que apresentava feocromocitoma, hemangioblastoma capilar na retina periférica e dois tumores neuroendócrinos no pâncreas. RESULTADOS: O maior tumor pancreático localizava-se no processo uncinado medindo 31 mm. A lesão menor estava localizada no corpo proximal do pâncreas e foi detectada apenas na tomografia computadorizada por emissão de pósitrons com DOTATOC-68Ga. A investigação genética revelou uma mutação no locus NM_000551.3 c.482G>A (p.Arg161Gln) do gene supressor humano de Von Hippel-Lindau. O tumor no processo era maior que 30mm e o paciente apresentava mutação no exon 3. Indicamos pancreatoduodenectomia envolvendo o corpo proximal do pâncreas para ressecar em bloco ambos os tumores. No pós-operatório o paciente apresentou coleção líquida peripancreática que foi tratada como fístula pancreática grau B, com resolução clínica da complicação. Ele recebeu alta hospitalar no vigésimo primeiro dia pós-operatório. CONCLUSÕES: o manejo de pacientes com doença de von Hippel Lindau e tumores neuroendócrinos pancreáticos é complexo e deve ser centrado em instituições terciárias com grande volume de cirurgia pancreática. Embora a literatura atual auxilie na tomada de decisão na maioria das situações, cada etapa do tratamento requer análise e discussão entre diferentes especialidades médicas, incluindo cirurgiões, clínicos, radiologistas e anestesiologistas.

Association between Insulin use and Infective Endocarditis: An Observational Study

Abstract Background: The association between Diabetes Mellitus (DM) and Infective Endocarditis (IE) is controversial in the literature, since many controversial results have been published. However, when evaluating specifically the evidence on IE and individuals with DM using insulin, we found only two observational studies that considered this variable, with discordant results regarding the prognosis and prevalence of Staphylococcus sp in insulin users compared to non-users. Despite the lack of evidence, in clinical practice the insulin use could be interpreted as minor criteria "injection drug use", using the modified Duke criteria for IE diagnosis. Objectives: To compare the microbiological and valvar profile, as well as the outcome of non-diabetic and diabetic patients with IE who were insulin users or not. Methods: This was an observational, analytical and retrospective study of patients diagnosed with IE between 2003 and 2015 in three tertiary care centers. A total of 211 patients were included, of which 17 were diabetics and 9 were insulin users. Patients were compared using the Shapiro-Wilk normality test and Fisher's exact test, with a significance level of 5%. Results: The mortality from IE in diabetic individuals was higher than that of non-diabetic patients, but with no statistical significance (35.29% vs. 21.1%; p = 0.221), even when the groups were divided into insulin-user diabetic, non-insulin user diabetic and non-diabetic patients (33.3% vs. 37.5% vs. 21.1%, p = 0.229). There was a difference regarding the prevalence of IE caused by S. aureus (57.1% vs. 14.3% vs. 17.4%, p = 0.029) and the involvement of the tricuspid valve (33.3% vs. 0.00% vs. 10.0%, p = 0.034) among insulin users. Conclusion: In our sample, insulin use or the presence of DM did not mean higher in-hospital mortality from IE. It is not possible to generalize the microbiological and valvar findings due to the lack of studies evaluating insulin users in IE; however, particularities have been previously reported and may indicate a different behavior of IE in these patients. New studies considering the insulin use variable are required to elucidate the association between DM and IE.

A technical note on low cost rat laparoscopy an initial experience.

PURPOSE: To evaluate a novel and adapted low-cost set model for laparoscopic surgery in rats. METHODS: Nine Wistar rats underwent two different laparoscopic procedures, splenectomy (n=3) and distal pancreatectomy with splenectomy (n = 6), after assembling a low-cost set replacing the conventional one (monitor, micro camera, image processor, light source, laparoscope and insufflator). The new set included an Android Tablet 10.5 ", a 5mm USB Endoscope and semiautomatic sphygmomanometer monitor. RESULTS: The same surgeon performed the laparoscopic procedures. Total surgical time ranged from 36 to 60 minutes with a mean of 45.8 minutes. Three rats died during the distal pancreatic and splenectomy procedure (33.3%), due to respiratory failure (n = 1), uncontrolled abdominal hemorrhage (n=1) and iatrogenic gastric perforation (n = 1). We followed the other six rats (66.6%) for seven days with no further evidence of complications. CONCLUSIONS: The laparoscopic partial pancreatectomy and splenectomy can be performed with the novel low-cost set assembled in the present experimental study. Both specific training and skills development are required to validate more advanced laparoscopic procedures and achieve a desirable outcome.

A technical note on low cost rat laparoscopy an initial experience

Abstract Purpose: To evaluate a novel and adapted low-cost set model for laparoscopic surgery in rats. Methods: Nine Wistar rats underwent two different laparoscopic procedures, splenectomy (n=3) and distal pancreatectomy with splenectomy (n = 6), after assembling a low-cost set replacing the conventional one (monitor, micro camera, image processor, light source, laparoscope and insufflator). The new set included an Android Tablet 10.5 ", a 5mm USB Endoscope and semiautomatic sphygmomanometer monitor. Results: The same surgeon performed the laparoscopic procedures. Total surgical time ranged from 36 to 60 minutes with a mean of 45.8 minutes. Three rats died during the distal pancreatic and splenectomy procedure (33.3%), due to respiratory failure (n = 1), uncontrolled abdominal hemorrhage (n=1) and iatrogenic gastric perforation (n = 1). We followed the other six rats (66.6%) for seven days with no further evidence of complications. Conclusions: The laparoscopic partial pancreatectomy and splenectomy can be performed with the novel low-cost set assembled in the present experimental study. Both specific training and skills development are required to validate more advanced laparoscopic procedures and achieve a desirable outcome.

Rama: a machine learning approach for ribosomal protein prediction in plants.

Ribosomal proteins (RPs) play a fundamental role within all type of cells, as they are major components of ribosomes, which are essential for translation of mRNAs. Furthermore, these proteins are involved in various physiological and pathological processes. The intrinsic biological relevance of RPs motivated advanced studies for the identification of unrevealed RPs. In this work, we propose a new computational method, termed Rama, for the prediction of RPs, based on machine learning techniques, with a particular interest in plants. To perform an effective classification, Rama uses a set of fundamental attributes of the amino acid side chains and applies a two-step procedure to classify proteins with unknown function as RPs. The evaluation of the resultant predictive models showed that Rama could achieve mean sensitivity, precision, and specificity of 0.91, 0.91, and 0.82, respectively. Furthermore, a list of proteins that have no annotation in Phytozome v.10, and are annotated as RPs in Phytozome v.12, were correctly classified by our models. Additional computational experiments have also shown that Rama presents high accuracy to differentiate ribosomal proteins from RNA-binding proteins. Finally, two novel proteins of Arabidopsis thaliana were validated in biological experiments. Rama is freely available at http://inctipp.bioagro.ufv.br:8080/Rama .

Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae.

BACKGROUND: Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species. As a result, determining the nomenclature and taxonomically classifying geminiviruses turned into complex tasks. In addition, the gene responsible for viral replication (particularly, the viruses belonging to the genus Mastrevirus) may be spliced due to the use of the transcriptional/splicing machinery in the host cells. However, the current tools have limitations concerning the identification of introns. RESULTS: This study proposes a new method, designated Fangorn Forest (F2), based on machine learning approaches to classify genera using an ab initio approach, i.e., using only the genomic sequence, as well as to predict and classify genes in the family Geminiviridae. In this investigation, nine genera of the family Geminiviridae and their related satellite DNAs were selected. We obtained two training sets, one for genus classification, containing attributes extracted from the complete genome of geminiviruses, while the other was made up to classify geminivirus genes, containing attributes extracted from ORFs taken from the complete genomes cited above. Three ML algorithms were applied on those datasets to build the predictive models: support vector machines, using the sequential minimal optimization training approach, random forest (RF), and multilayer perceptron. RF demonstrated a very high predictive power, achieving 0.966, 0.964, and 0.995 of precision, recall, and area under the curve (AUC), respectively, for genus classification. For gene classification, RF could reach 0.983, 0.983, and 0.998 of precision, recall, and AUC, respectively. CONCLUSIONS: Therefore, Fangorn Forest is proven to be an efficient method for classifying genera of the family Geminiviridae with high precision and effective gene prediction and classification. The method is freely accessible at www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp .

Geminivirus data warehouse: a database enriched with machine learning approaches.

BACKGROUND: The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. RESULTS: Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. CONCLUSIONS: The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses.

Ischemia-reperfusion rat model of acute pancreatitis: protein carbonyl as a putative early biomarker of pancreatic injury.

Acute pancreatitis (AP) is an inflammatory disorder that can affect adjacent and/or remote organs. Some evidence indicates that the production of reactive oxygen species is able to induce AP. Protein carbonyl (PC) derivatives, which can also be generated through oxidative cleavage mechanisms, have been implicated in several diseases, but there is little or no information on this biomarker in AP. We investigated the association between some inflammatory mediators and PC, with the severity of ischemia-reperfusion AP. Wistar rats (n = 56) were randomly assigned in the following groups : control; sham, 15- or 180-min clamping of splenic artery, with 24 or 72 h of follow-up. The relationships between serum level of PC and thiobarbituric acid reactive species (TBARS) to myeloperoxidase (MPO) activity in tissue homogenates and to cytokines in culture supernatants of pancreatic samples were analyzed. MPO activity was related to the histology scores and increased in all clamping groups. Tumor necrosis factor-alpha (TNF-α), interleukin 1 beta (IL-1ß), and interleukin-6 were higher in the 180-min groups. Significant correlations were found between MPO activity and the concentrations of TNF-α and IL-1ß. PC levels increased in the 15-min to 24-h group. TBARS levels were not altered substantially. MPO activity and TNF-α and IL-1ß concentrations in pancreatic tissue are correlated with AP severity. Serum levels of PC appear to begin to rise early in the course of the ischemia-reperfusion AP and are no longer detected at later stages in the absence of severe pancreatitis. These data suggest that PC can be an efficient tool for the diagnosis of early stages of AP.

A toxicomania como paradigma do entorpecimento pulsional / Drug addiction as a paradigm of the numbness by drive / La toxicomanie comme paradigme de l’engourdissement pulsionnel

No trabalho clínico com pacientes toxicômanos, somos colocados constantemente diante de impasses que comprometem o progresso do tratamento, como, por exemplo, a indiferença frente aos riscos de morte, pouquíssima aderência ao tratamento e a prevalência do ato em detrimento às palavras. Para além de tais manifestações, escolhemos, como objeto deste artigo, a relação autoerótica do sujeito toxicômano com o corpo, tomando-a como paradigma da estrutura viciante própria da pulsão. Assim, o crescente número de casos de adições compulsivas, especificamente as toxicomanias, apresenta-se em nossa contemporaneidade marcado pela permissividade ao gozo desmedido como um paradigma do caráter entorpecente e extasiante próprio da pulsão(AU)

In clinical work with addicted patients, many impasses arise that might compromise the progress of treatment, for example, the indifference to the risk of death, very little treatment compliance and preference for act instead of the words. Beyond these manifestations, we chose as the subject of this article, the autoerotic relation of the junkie subject with its body, taking it as a paradigm of the addictive structure which is characteristic of drive itself. Thus, the growing number of cases of compulsive addictions, specifically to drugs presents itself in our contemporary world marked by excessive permissiveness to enjoyment as a paradigm of the numbing and exhilarating character of drive(AU)

Dans le travail clinique avec les patients toxicomanes, nous sommes placés en permanence devant les impasses qui compromettent les progrès du traitement, par exemple, l'indifférence au risque de la mort, très peu d’observance du traitement et la prévalence de l’acte en detriment des mots. Au delà de ces manifestations, nous avons choisi comme sujet de cet article, la relation de l'auto-érotique du junkie sujet avec le corps, en le prenant comme un paradigme de la structure addictive de la pulsion elle même. Ainsi, le nombre croissant de cas d'additions compulsives, toxicomanies spécifiquement, présent dans notre monde contemporain marqué par la permissivité excessive à la jouissance démesurée comme un paradigme Du charactère engourdissant et extasiant propre de la pulsion(AU)

A toxicomania como paradigma do entorpecimento pulsional / Drug addiction as a paradigm of the numbness by drive / La toxicomanie comme paradigme de l’engourdissement pulsionnel

No trabalho clínico com pacientes toxicômanos, somos colocados constantemente diante de impasses que comprometem o progresso do tratamento, como, por exemplo, a indiferença frente aos riscos de morte, pouquíssima aderência ao tratamento e a prevalência do ato em detrimento às palavras. Para além de tais manifestações, escolhemos, como objeto deste artigo, a relação autoerótica do sujeito toxicômano com o corpo, tomando-a como paradigma da estrutura viciante própria da pulsão. Assim, o crescente número de casos de adições compulsivas, especificamente as toxicomanias, apresenta-se em nossa contemporaneidade marcado pela permissividade ao gozo desmedido como um paradigma do caráter entorpecente e extasiante próprio da pulsão.

In clinical work with addicted patients, many impasses arise that might compromise the progress of treatment, for example, the indifference to the risk of death, very little treatment compliance and preference for act instead of the words. Beyond these manifestations, we chose as the subject of this article, the autoerotic relation of the junkie subject with its body, taking it as a paradigm of the addictive structure which is characteristic of drive itself. Thus, the growing number of cases of compulsive addictions, specifically to drugs presents itself in our contemporary world marked by excessive permissiveness to enjoyment as a paradigm of the numbing and exhilarating character of drive.

Dans le travail clinique avec les patients toxicomanes, nous sommes placés en permanence devant les impasses qui compromettent les progrès du traitement, par exemple, l'indifférence au risque de la mort, très peu d’observance du traitement et la prévalence de l’acte en detriment des mots. Au delà de ces manifestations, nous avons choisi comme sujet de cet article, la relation de l'auto-érotique du junkie sujet avec le corps, en le prenant comme un paradigme de la structure addictive de la pulsion elle même. Ainsi, le nombre croissant de cas d'additions compulsives, toxicomanies spécifiquement, présent dans notre monde contemporain marqué par la permissivité excessive à la jouissance démesurée comme un paradigme Du charactère engourdissant et extasiant propre de la pulsion.