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1.
Homeopathy ; 2024 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-38986484

RESUMO

BACKGROUND: Coronavirus disease 2019 (COVID-19), a disease caused by the SARS-CoV-2 coronavirus, was declared a pandemic in March 2020, posing significant challenges globally. Homeopathy has historical relevance in epidemic management. In response, the government of the state of Santa Catarina, Brazil, distributed Camphora 1M as a potential prophylactic intervention for COVID-19. OBJECTIVE: This study aimed to investigate the possible effects of Camphora 1M as an adjunctive prophylactic measure in managing COVID-19, focusing on mortality and hospitalization rates, during the period April 28 to July 31, 2020, within designated COVID-19 in-patient units in Santa Catarina. METHODS: An ecological study design was applied to this epidemiological research. Five case municipalities (Itajaí, Atalanta, Entre Rios, Rio do Campo, Trombudo Central) were compared with five control municipalities (São José, Galvão, Pedras Grandes, Grão-Pará, Ascurra). RESULTS: No statistically significant differences were observed in predictor variables between municipalities that received Camphora 1M and the respective controls. Similarly, no statistically significant differences were observed in outcomes: deaths (p = 0.879), hospitalized cases (p = 0.537), daily ward admissions (p = 0.730) and ICU admissions (p = 0.072). CONCLUSION: For the first wave of the pandemic in the state of Santa Catarina, Brazil, city-wide distribution of Camphora 1M was not associated with reduced numbers, severity or mortality among the population hospitalized in designated public hospitals for COVID-19.

2.
Ann Oncol ; 2024 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-38906254

RESUMO

BACKGROUND: After surgical resection of pancreatic ductal adenocarcinoma (PDAC), patients are predominantly treated with adjuvant chemotherapy, commonly consisting of gemcitabine-based regimens or the modified FOLFIRINOX regimen (mFFX). While mFFX has been shown to be more effective than gemcitabine-based regimens, it is also associated with higher toxicity. Current treatment decisions are based on patient performance status rather than on the molecular characteristics of the tumor. To address this gap, the goal of this study was to develop drug-specific transcriptomic signatures for personalized chemotherapy treatment. PATIENTS AND METHODS: We used PDAC datasets from preclinical models, encompassing chemotherapy response profiles for the mFFX-regimen components. From them we identified specific gene transcripts associated with chemotherapy response. Three transcriptomic AI-signatures were obtained by combining Independent Component Analysis, Least Absolute Shrinkage and the Selection Operator-Random Forest approach. We integrated a previously developed gemcitabine signature with three newly developed ones. The machine learning strategy employed to enhance these signatures incorporates transcriptomic features from the tumor microenvironment, leading to the development of the Pancreas-View tool ultimately clinically validated in a cohort of 343 patients from the PRODIGE-24/CCTG PA6 trial. RESULTS: Patients who were predicted to be sensitive to the administered drugs (n=164; 47.8%) had longer disease-free survival (DFS) than the other patients. The median DFS in the mFFX sensitive group treated with mFFX was 50.0 months (stratified HR: 0.31; 95% CI, 0.21-0.44; p<0.001) and 33.7 months (stratified HR: 0.40; 95% CI, 0.17-0.59; p<0.001) in the gemcitabine sensitive group when treated with gemcitabine. Comparatively patients with signature predictions unmatched with the treatments (n=86; 25.1%) or those resistant to all drugs (n=93; 27.1%) had shorter DFS (10.6 and 10.8 months, respectively). CONCLUSIONS: This study presents a transcriptome-based tool that was developed using preclinical models and machine learning to accurately predict sensitivity to mFFX and gemcitabine.

3.
Clin Genet ; 105(4): 376-385, 2024 04.
Artigo em Inglês | MEDLINE | ID: mdl-38148624

RESUMO

An estimated 1 in 10 000 people are born without the ability to smell, a condition known as congenital anosmia, and about one third of those people have non-syndromic, or isolated congenital anosmia (ICA). Despite the significant impact of olfaction for our quality of life, the underlying causes of ICA remain largely unknown. Using whole exome sequencing (WES) in 10 families and 141 individuals with ICA, we identified a candidate list of 162 rare, segregating, deleterious variants in 158 genes. We confirmed the involvement of CNGA2, a previously implicated ICA gene that is an essential component of the olfactory transduction pathway. Furthermore, we found a loss-of-function variant in SREK1IP1 from the family gene candidate list, which was also observed in 5% of individuals in an additional non-family cohort with ICA. Although SREK1IP1 has not been previously associated with olfaction, its role in zinc ion binding suggests a potential influence on olfactory signaling. This study provides a more comprehensive understanding of the spectrum of genetic alterations and their etiology in ICA patients, which may improve the diagnosis, prognosis, and treatment of this disorder and lead to better understanding of the mechanisms governing basic olfactory function.


Assuntos
Transtornos do Olfato , Transtornos do Olfato/congênito , Qualidade de Vida , Humanos , Transtornos do Olfato/genética , Transtornos do Olfato/diagnóstico , Mutação , Transdução de Sinais , Olfato/genética , Canais de Cátion Regulados por Nucleotídeos Cíclicos/genética
4.
Ann Oncol ; 34(8): 703-713, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37269904

RESUMO

BACKGROUND: Mismatch repair-deficient (dMMR) tumors displaying microsatellite instability (MSI) represent a paradigm for the success of immune checkpoint inhibitor (ICI)-based immunotherapy, particularly in patients with metastatic colorectal cancer (mCRC). However, a proportion of patients with dMMR/MSI mCRC exhibit resistance to ICI. Identification of tools predicting MSI mCRC patient response to ICI is required for the design of future strategies further improving this therapy. PATIENTS AND METHODS: We combined high-throughput DNA and RNA sequencing of tumors from 116 patients with MSI mCRC treated with anti-programmed cell death protein 1 ± anti-cytotoxic T-lymphocyte-associated protein 4 of the NIPICOL phase II trial (C1, NCT03350126, discovery set) and the ImmunoMSI prospective cohort (C2, validation set). The DNA/RNA predictors whose status was significantly associated with ICI status of response in C1 were subsequently validated in C2. Primary endpoint was progression-free survival by immune RECIST (iRECIST) (iPFS). RESULTS: Analyses showed no impact of previously suggested DNA/RNA indicators of resistance to ICI, e.g. MSIsensor score, tumor mutational burden, or specific cellular and molecular tumoral contingents. By contrast, iPFS under ICI was shown in C1 and C2 to depend both on a multiplex MSI signature involving the mutations of 19 microsatellites hazard ratio cohort C2 (HRC2) = 3.63; 95% confidence interval (CI) 1.65-7.99; P = 1.4 × 10-3] and the expression of a set of 182 RNA markers with a non-epithelial transforming growth factor beta (TGFB)-related desmoplastic orientation (HRC2 = 1.75; 95% CI 1.03-2.98; P = 0.035). Both DNA and RNA signatures were independently predictive of iPFS. CONCLUSIONS: iPFS in patients with MSI mCRC can be predicted by simply analyzing the mutational status of DNA microsatellite-containing genes in epithelial tumor cells together with non-epithelial TGFB-related desmoplastic RNA markers.


Assuntos
Neoplasias do Colo , Neoplasias Colorretais , Neoplasias Retais , Humanos , Inibidores de Checkpoint Imunológico/farmacologia , Inibidores de Checkpoint Imunológico/uso terapêutico , Instabilidade de Microssatélites , Estudos Prospectivos , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , Reparo de Erro de Pareamento de DNA/genética
5.
Ther Adv Respir Dis ; 17: 17534666231162252, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37067023

RESUMO

Coronavirus-induced diseases have afflicted humanity for several decades. This scenario was aggravated by the emergence of the coronavirus disease 2019 (named COVID-19) in Wuhan, China, in December 2019. Since then, COVID-19 has killed millions of people worldwide, probably the most devastating pandemic since HIV/AIDS. This review aimed to bring together important updated aspects related to coronavirus-induced diseases and the enhanced vascular permeability observed mainly in the lungs of affected people. The dysregulated vascular permeability in the lungs is of fundamental importance for coronaviruses-caused morbidity and mortality. Thus, as described in this review, it is a target of new and old drugs.


Assuntos
COVID-19 , Humanos , SARS-CoV-2 , Permeabilidade Capilar , Pulmão , Permeabilidade
6.
Clin Res Hepatol Gastroenterol ; 47(4): 102108, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36878461

RESUMO

BACKGROUND: Trop-2 is overexpressed in tumor cells of various cancers, including pancreatic ductal adenocarcinoma (PDAC), and has emerged as a potent therapeutic target. We evaluated Trop-2 expression both at the transcriptomic and protein levels, and its correlation with tumor features and patients' outcomes in a large cohort of PDAC. METHODS: We included patients undergoing pancreatic resection for PDAC in 5 academic hospitals in France and Belgium. Transcriptomic profiles were obtained from FFPE tissue samples, with paired primary -25and metastatic lesions when available. Protein expression was evaluated by immunohistochemistry (IHC) using tissue micro-arrays. RESULTS: 495 patients (male 54%, median age 63 years) were included between 1996 and 2012. Trop-2 mRNA expression was significantly associated to tumor cellularity, but no association with survival nor with any clinical or pathological features was observed, with tumor cells showing an overall high expression among every subgroup. Trop-2 mRNA expression was maintained between primary and metastatic lesion in all 26 paired samples evaluated. In 50 tumors assessed by IHC, 30%, 68% and 2% harbored a high, medium, or low Trop-2 expression score, respectively. Trop-2 staining was significantly associated to mRNA expression, but not to survival or any pathological features. CONCLUSIONS: Our results suggest Trop-2 overexpression as a ubiquitous marker of PDAC tumor cells and thus a promising therapeutic target to evaluate in these patients.


Assuntos
Adenocarcinoma , Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Humanos , Masculino , Pessoa de Meia-Idade , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/patologia , Adenocarcinoma/genética , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/patologia , RNA Mensageiro/genética , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Prognóstico , Neoplasias Pancreáticas
7.
Rev Neurol (Paris) ; 179(1-2): 90-105, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36517287

RESUMO

Gene therapy, i.e., any therapeutic approach involving the use of genetic material as a drug and more largely altering the transcription or translation of one or more genes, covers a wide range of innovative methods for treating diseases, including neurological disorders. Although they share common principles, the numerous gene therapy approaches differ greatly in their mechanisms of action. They also differ in their maturity for some are already used in clinical practice while others have never been used in humans. The aim of this review is to present the whole range of gene therapy techniques through the example of Duchenne muscular dystrophy (DMD). DMD is a severe myopathy caused by mutations in the dystrophin gene leading to the lack of functional dystrophin protein. It is a disease known to all neurologists and in which almost all gene therapy methods were applied. Here we discuss the mechanisms of gene transfer techniques with or without viral vectors, DNA editing with or without matrix repair and those acting at the RNA level (RNA editing, exon skipping and STOP-codon readthrough). For each method, we present the results obtained in DMD with a particular focus on clinical data. This review aims also to outline the advantages, limitations and risks of gene therapy related to the approach used.


Assuntos
Distrofia Muscular de Duchenne , Humanos , Distrofia Muscular de Duchenne/genética , Distrofia Muscular de Duchenne/terapia , Distrofia Muscular de Duchenne/metabolismo , Distrofina/genética , Distrofina/metabolismo , Terapia Genética/métodos , Mutação , Éxons
8.
Transl Oncol ; 16: 101315, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-34906890

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) patients are frequently treated by chemotherapy. Even if personalized therapy based on molecular analysis can be performed for some tumors, PDAC regimens selection is still mainly based on patients' performance status and expected efficacy. Therefore, the establishment of molecular predictors of chemotherapeutic efficacy could potentially improve prognosis by tailoring treatments. We have recently developed an RNA-based signature that predicts the efficacy of adjuvant gemcitabine using 38 PDAC primary cell cultures. While demonstrated its efficiency, a significant association with the classical/basal-like PDAC spectrum was observed. We hypothesized that this flaw was due to the basal-like biased phenotype of cellular models used in our strategy. To overcome this limitation, we generated a prospective cohort of 27 consecutive biopsied derived pancreatic organoids (BDPO) and include them in the signature identification strategy. As BDPO's do not have the same biased phenotype as primary cell cultures we expect they can compensate one with each other and cover a broader range of molecular phenotypes. We then obtained an improved signature predicting gemcitabine sensibility that was validated in a cohort of 300 resected PDAC patients that have or have not received adjuvant gemcitabine. We demonstrated a significant association between the improved signature and the overall and disease-free survival in patients predicted as sensitive and treated with adjuvant gemcitabine. We propose then that including BDPO along primary cell cultures represent a powerful strategy that helps to overcome primary cell cultures limitations producing unbiased RNA-based signatures predictive of adjuvant treatments in PDAC.

9.
Nat Commun ; 12(1): 3044, 2021 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-34031415

RESUMO

Unlike other malignancies, therapeutic options in pancreatic ductal adenocarcinoma (PDAC) are largely limited to cytotoxic chemotherapy without the benefit of molecular markers predicting response. Here we report tumor-cell-intrinsic chromatin accessibility patterns of treatment-naïve surgically resected PDAC tumors that were subsequently treated with (Gem)/Abraxane adjuvant chemotherapy. By ATAC-seq analyses of EpCAM+ PDAC malignant epithelial cells sorted from 54 freshly resected human tumors, we show here the discovery of a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identify two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further develop a chromatin accessibility microarray methodology termed "ATAC-array", an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validate ATAC-array technology in both the original ATAC-seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a low-cost, clinically feasible technology for assessing chromatin accessibility profiles.


Assuntos
Sequenciamento de Cromatina por Imunoprecipitação/métodos , Cromatina , Neoplasias Pancreáticas/diagnóstico , Neoplasias Pancreáticas/genética , Biomarcadores Tumorais , Carcinoma Ductal Pancreático/diagnóstico , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/metabolismo , Núcleo Celular , Fator 1-beta Nuclear de Hepatócito/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Fatores de Transcrição Kruppel-Like/genética , Neoplasias Pancreáticas/metabolismo , Prognóstico , Fatores de Transcrição , Transcriptoma , Neoplasias Pancreáticas
10.
Ann Oncol ; 32(2): 250-260, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33188873

RESUMO

BACKGROUND: Chemotherapy is the only systemic treatment approved for pancreatic ductal adenocarcinoma (PDAC), with a selection of regimens based on patients' performance status and expected efficacy. The establishment of a potent stratification associated with chemotherapeutic efficacy could potentially improve prognosis by tailoring treatments. PATIENTS AND METHODS: Concomitant chemosensitivity and genome-wide RNA profiles were carried out on preclinical models (primary cell cultures and patient-derived xenografts) derived from patients with PDAC included in the PaCaOmics program (NCT01692873). The RNA-based stratification was tested in a monocentric cohort and validated in a multicentric cohort, both retrospectively collected from resected PDAC samples (67 and 368 patients, respectively). Forty-three (65%) and 203 (55%) patients received adjuvant gemcitabine in the monocentric and the multicentric cohorts, respectively. The relationships between predicted gemcitabine sensitivity and patients' overall survival (OS) and disease-free survival were investigated. RESULTS: The GemPred RNA signature was derived from preclinical models, defining gemcitabine sensitive PDAC as GemPred+. Among the patients who received gemcitabine in the test and validation cohorts, the GemPred+ patients had a higher OS than GemPred- (P = 0.046 and P = 0.00216). In both cohorts, the GemPred stratification was not associated with OS among patients who did not receive gemcitabine. Among gemcitabine-treated patients, GemPred+ patients had significantly higher OS than the GemPred-: 91.3 months [95% confidence interval (CI): 61.2-not reached] versus 33 months (95% CI: 24-35.2); hazard ratio 0.403 (95% CI: 0.221-0.735, P = 0.00216). The interaction test for gemcitabine and GemPred+ stratification was significant (P = 0.0245). Multivariate analysis in the gemcitabine-treated population retained an independent predictive value. CONCLUSION: The RNA-based GemPred stratification predicts the benefit of adjuvant gemcitabine in PDAC patients.


Assuntos
Adenocarcinoma , Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Adenocarcinoma/tratamento farmacológico , Adenocarcinoma/genética , Carcinoma Ductal Pancreático/tratamento farmacológico , Carcinoma Ductal Pancreático/genética , Quimioterapia Adjuvante , Desoxicitidina/análogos & derivados , Humanos , Neoplasias Pancreáticas/tratamento farmacológico , Neoplasias Pancreáticas/genética , Estudos Retrospectivos , Transcriptoma , Gencitabina
11.
Ann Oncol ; 30(9): 1428-1436, 2019 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-31161208

RESUMO

BACKGROUND: Different histological and molecular subtypes of pancreatic ductal adenocarcinoma (PDAC), with different molecular composition and survival statistics, have recently been recognised. MATERIALS AND METHODS: This review describes the currently available studies regarding molecular and histological subtypes in PDAC. Studies from major cohorts such as International Cancer Genome Consortium as well as smaller cohorts are reviewed. We discuss where the described subtypes overlap, where the discrepancies are and which paths forward could be taken regarding diagnosis, ontogeny and therapy. RESULTS: Four molecular subtypes with strong overlap among the different studies can be found, next to a list of mixed findings. Two of the four subtypes (epithelial classical and mesenchymal basal-like) were represented in every study and were often discriminated in other solid tumours as well. These two subtypes differ substantially in prognosis. One biomarker has been discovered, only discriminating these two subtypes, and insights into subtype-specific therapeutic vulnerabilities are scarce. CONCLUSION: Subtypes can be reproducibly detected in cohorts of PDAC patients and two of them directly relate with prognosis. A consensus on the subtypes is warranted. Further discovery and validation studies are needed to identify strong biomarkers, to comprehend subtype ontogeny and to define strategies for precision medicine.


Assuntos
Adenocarcinoma/genética , Biomarcadores Tumorais/genética , Carcinoma Ductal Pancreático/genética , Transcriptoma/genética , Adenocarcinoma/classificação , Adenocarcinoma/patologia , Carcinoma Ductal Pancreático/classificação , Carcinoma Ductal Pancreático/patologia , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Medicina de Precisão/tendências , Prognóstico
12.
Proc Natl Acad Sci U S A ; 116(19): 9598-9603, 2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-31000595

RESUMO

In color vision, the quantitative rules for mixing lights to make a target color are well understood. By contrast, the rules for mixing odorants to make a target odor remain elusive. A solution to this problem in vision relied on characterizing receptor responses to different wavelengths of light and subsequently relating these responses to perception. In olfaction, experimentally measuring receptor responses to a representative set of complex mixtures is intractable due to the vast number of possibilities. To meet this challenge, we develop a biophysical model that predicts mammalian receptor responses to complex mixtures using responses to single odorants. The dominant nonlinearity in our model is competitive binding (CB): Only one odorant molecule can attach to a receptor binding site at a time. This simple framework predicts receptor responses to mixtures of up to 12 monomolecular odorants to within 15% of experimental observations and provides a powerful method for leveraging limited experimental data. Simple extensions of our model describe phenomena such as synergy, overshadowing, and inhibition. We demonstrate that the presence of such interactions can be identified via systematic deviations from the competitive-binding model.


Assuntos
Modelos Biológicos , Odorantes , Receptores Odorantes/metabolismo , Linhagem Celular , Humanos , Receptores Odorantes/genética
13.
Elife ; 62017 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-28438259

RESUMO

The mouse olfactory sensory neuron (OSN) repertoire is composed of 10 million cells and each expresses one olfactory receptor (OR) gene from a pool of over 1000. Thus, the nose is sub-stratified into more than a thousand OSN subtypes. Here, we employ and validate an RNA-sequencing-based method to quantify the abundance of all OSN subtypes in parallel, and investigate the genetic and environmental factors that contribute to neuronal diversity. We find that the OSN subtype distribution is stereotyped in genetically identical mice, but varies extensively between different strains. Further, we identify cis-acting genetic variation as the greatest component influencing OSN composition and demonstrate independence from OR function. However, we show that olfactory stimulation with particular odorants results in modulation of dozens of OSN subtypes in a subtle but reproducible, specific and time-dependent manner. Together, these mechanisms generate a highly individualized olfactory sensory system by promoting neuronal diversity.


Assuntos
Variação Genética , Condutos Olfatórios/fisiologia , Neurônios Receptores Olfatórios/classificação , Receptores Odorantes/genética , Animais , Perfilação da Expressão Gênica , Camundongos , Neurônios Receptores Olfatórios/fisiologia , Análise de Sequência de RNA
14.
Bioinformatics ; 30(23): 3419-20, 2014 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-25138169

RESUMO

UNLABELLED: We introduce Pepper (Protein complex Expansion using Protein-Protein intERactions), a Cytoscape app designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network. Comparisons based on gold standard yeast and human datasets showed Pepper's integrative approach as superior to standard protein complex discovery methods. The visualization and interpretation of the results are facilitated by an automated post-processing pipeline based on topological analysis and data integration about the predicted complex proteins. Pepper is a user-friendly tool that can be used to analyse any list of proteins. AVAILABILITY: Pepper is available from the Cytoscape plug-in manager or online (http://apps.cytoscape.org/apps/pepper) and released under GNU General Public License version 3.


Assuntos
Mapeamento de Interação de Proteínas/métodos , Software , Algoritmos , Humanos , Proteômica
15.
IEEE Trans Nanobioscience ; 13(2): 97-103, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24771593

RESUMO

Reconstruction of large scale gene regulatory networks (GRNs in the following) is an important step for understanding the complex regulatory mechanisms within the cell. Many modeling approaches have been introduced to find the causal relationship between genes using expression data. However, they have been suffering from high dimensionality-large number of genes but a small number of samples, overfitting, heavy computation time and low interpretability. We have previously proposed an original Data Mining algorithm Licorn, that infers cooperative regulation network from expression datasets. In this work, we present an extension of Licorn to a hybrid inference method h-Licorn that uses search in both discrete and real valued spaces. Licorn's algorithm, using the discrete space to find cooperative regulation relationships fitting the target gene expression, has been shown to be powerful in identifying cooperative regulation relationships that are out of the scope of most GRN inference methods. Still, as many of related GRN inference techniques, Licorn suffers from a large number of false positives. We propose here an extension of Licorn with a numerical selection step, expressed as a linear regression problem, that effectively complements the discrete search of Licorn. We evaluate a bootstrapped version of h-Licorn on the in silico Dream5 dataset and show that h-Licorn has significantly higher performance than Licorn, and is competitive or outperforms state of the art GRN inference algorithms, especially when operating on small data sets. We also applied h-Licorn on a real dataset of human bladder cancer and show that it performs better than other methods in finding candidate regulatory interactions. In particular, solely based on gene expression data, h-Licorn is able to identify experimentally validated regulator cooperative relationships involved in cancer.


Assuntos
Algoritmos , Redes Reguladoras de Genes , Neoplasias da Bexiga Urinária/genética , Biologia Computacional , Regulação Neoplásica da Expressão Gênica , Humanos
16.
Radiat Res ; 179(1): 76-88, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23216524

RESUMO

Spinal cord injury is a devastating condition with no effective treatment. The physiological processes that impede recovery include potentially detrimental immune responses and the production of reactive astrocytes. Previous work suggested that radiation treatment might be beneficial in spinal cord injury, although the method carries risk of radiation-induced damage. To overcome this obstacle we used arrays of parallel, synchrotron-generated X-ray microbeams (230 µm with 150 µm gaps between them) to irradiate an established model of rat spinal cord contusion injury. This technique is known to have a remarkable sparing effect in tissue, including the central nervous system. Injury was induced in adult female Long-Evans rats at the level of the thoracic vertebrae T9-T10 using 25 mm rod drop on an NYU Impactor. Microbeam irradiation was given to groups of 6-8 rats each, at either Day 10 (50 or 60 Gy in-beam entrance doses) or Day 14 (50, 60 or 70 Gy). The control group was comprised of two subgroups: one studied three months before the irradiation experiment (n = 9) and one at the time of the irradiations (n = 7). Hind-limb function was blindly scored with the Basso, Beattie and Bresnahan (BBB) rating scale on a nearly weekly basis. The scores for the rats irradiated at Day 14 post-injury, when using t test with 7-day data-averaging time bins, showed statistically significant improvement at 28-42 days post-injury (P < 0.038). H&E staining, tissue volume measurements and immunohistochemistry at day ≈ 110 post-injury did not reveal obvious differences between the irradiated and nonirradiated injured rats. The same microbeam irradiation of normal rats at 70 Gy in-beam entrance dose caused no behavioral deficits and no histological effects other than minor microglia activation at 110 days. Functional improvement in the 14-day irradiated group might be due to a reduction in populations of immune cells and/or reactive astrocytes, while the Day 10/Day 14 differences may indicate time-sensitive changes in these cells and their populations. With optimizations, including those of the irradiation time(s), microbeam pattern, dose, and perhaps concomitant treatments such as immunological intervention this method may ultimately reach clinical use.


Assuntos
Contusões/complicações , Membro Posterior/fisiopatologia , Membro Posterior/efeitos da radiação , Traumatismos da Medula Espinal/complicações , Traumatismos da Medula Espinal/radioterapia , Terapia por Raios X/métodos , Animais , Feminino , Método de Monte Carlo , Dosagem Radioterapêutica , Ratos , Ratos Long-Evans , Traumatismos da Medula Espinal/patologia , Traumatismos da Medula Espinal/fisiopatologia , Síncrotrons , Fatores de Tempo , Terapia por Raios X/instrumentação
17.
Int J Radiat Oncol Biol Phys ; 84(2): 514-9, 2012 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-22342299

RESUMO

PURPOSE: To evaluate the efficacy of "interleaved carbon minibeams" for ablating a 6.5-mm target in a rabbit brain with little damage to the surrounding brain. The method is based on the well-established tissue-sparing effect of arrays of thin planes of radiation. METHODS AND MATERIALS: Broad carbon beams from the National Aeronautics and Space Agency Space Radiation Facility at Brookhaven National Laboratory were segmented into arrays of parallel, horizontal, 0.3-mm-thick planar beams (minibeams). The minibeams' gradual broadening in tissues resulted in 0.525-mm beam thickness at the target's proximal side in the spread-out Bragg peak. Interleaving was therefore implemented by choosing a 1.05 mm beam spacing on-center. The anesthetized rabbit, positioned vertically on a stage capable of rotating about a vertical axis, was exposed to arrays from four 90° angles, with the stage moving up by 0.525 mm in between. This produced a solid radiation field at the target while exposing the nontargeted tissues to single minibeam arrays. The target "physical" absorbed dose was 40.2 Gy. RESULTS: The rabbit behaved normally during the 6-month observation period. Contrast magnetic resonance imaging and hematoxylin and eosin histology at 6 months showed substantial focal target damage with little damage to the surrounding brain. CONCLUSION: We plan to evaluate the method's therapeutic efficacy by comparing it with broad-beam carbon therapy in animal models. The method's merits would combine those of carbon therapy (i.e., tight target dose because of the carbon's Bragg-peak, sharp dose falloff, and high relative biological effectiveness at the target), together with the method's low impact on the nontargeted tissues. The method's smaller impact on the nontargeted brain might allow carbon therapy at higher target doses and/or lower normal tissue impact, thus leading to a more effective treatment of radioresistant tumors. It should also make the method more amenable to administration in either a single dose fraction or in a small number of fractions.


Assuntos
Neoplasias Encefálicas/cirurgia , Encéfalo/efeitos da radiação , Carbono/uso terapêutico , Órgãos em Risco/efeitos da radiação , Radiocirurgia/métodos , Animais , Comportamento Animal/efeitos da radiação , Encéfalo/patologia , Neoplasias Encefálicas/patologia , Imageamento por Ressonância Magnética , Método de Monte Carlo , Posicionamento do Paciente/métodos , Coelhos , Lesões Experimentais por Radiação/prevenção & controle , Dosagem Radioterapêutica , Eficiência Biológica Relativa
18.
ASAIO Trans ; 37(4): 653-7, 1991.
Artigo em Inglês | MEDLINE | ID: mdl-1768505

RESUMO

In the past few years, dialyzer reuse has gained increased clinical acceptance. This has been due both to the availability of automated reconditioning machines and powerful chemical cleaning and disinfecting agents. In this study the authors evaluated the effectiveness of a newly available peroxyacetic acid solution (PAS) (Dialox) as the dual cleaning and disinfecting agent in the reuse of highly permeable dialyzers. An in vivo study was conducted with ten patients already involved in our center's reuse program using the Renatron reprocessing machine and PAS at various dilutions. One hundred forty dialyzers of three different brands and membrane types (HF80 used for hemodiafiltration [HDF], Filtral 16 used for hemodialysis [HD], and FH88 used for hemofiltration [HF]) were employed for a total of 1182 treatments, giving an average 8.4 uses per module. Significantly more uses were obtained with the HF80 and Filtral 16 dialyzers (9.7 and 9.4, respectively) than for the FH88 modules used by the HF patients (6.7 uses per module). Compromised cleaning by backfiltration due to the lack of a second dialysate port on the FH88 may be a possible explanation. Greater membrane plugging due to higher ultrafiltration rates in HF may be another factor. Patient variability was found to be another factor in dialyzer reuse. The cleaning effectiveness of various dilutions of PAS was also tested in this study. The number of uses achieved was not found to vary significantly with PAS strength; however, a greater frequency of second or third reprocessing was required with more dilute cleaning solution. The authors found the dilution achieved on the Renatron reprocessing machine using the currently marketed PAS concentrate to be the most cost effective.


Assuntos
Desinfecção , Equipamentos Descartáveis , Rins Artificiais , Membranas Artificiais , Ácido Peracético , Estudos de Avaliação como Assunto , Feminino , Hemofiltração/instrumentação , Humanos , Masculino , Diálise Renal/instrumentação
19.
Nephrol Dial Transplant ; 4(11): 1000-2, 1989.
Artigo em Inglês | MEDLINE | ID: mdl-2516880

RESUMO

In this study we evaluate the effectiveness of a newly available peroxyacetic acid solution (Dialox) as a disinfecting agent in the re-use of highly permeable dialysers. The germicidal properties of Dialox were tested in an in vitro trial on previously used haemodiafilters (HF80, Fresenius) highly contaminated with Pseudomonas aeruginosa, Mycobacterium smegmatis or sporulated Bacillus cereus. Complete freedom from bacterial contamination was observed 5 min after the reprocessing treatment on a Renatron reprocessing machine, using the currently marketed Dialox concentrate.


Assuntos
Acetatos/farmacologia , Desinfetantes , Rins Artificiais , Membranas Artificiais , Ácido Peracético/farmacologia , Bacillus cereus/efeitos dos fármacos , Equipamentos Descartáveis , Técnicas In Vitro , Mycobacterium/efeitos dos fármacos , Pseudomonas aeruginosa/efeitos dos fármacos
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