A proof of concept reinforcement learning based tool for non parametric population pharmacokinetics workflow optimization.

The building of population pharmacokinetic models can be described as an iterative process in which given a model and a dataset, the pharmacometrician introduces some changes to the model specification, then perform an evaluation and based on the predictions obtained performs further optimization. This process (perform an action, witness a result, optimize your knowledge) is a perfect scenario for the implementation of Reinforcement Learning algorithms. In this paper we present the conceptual background and a implementation of one of those algorithms aiming to show pharmacometricians how to automate (to a certain point) the iterative model building process.We present the selected discretization for the action and the state space. SARSA (State-Action-Reward-State-Action) was selected as the RL algorithm to use, configured with a window of 1000 episodes with and a limit of 30 actions per episode. SARSA was configured to control an interface to the Non-Parametric Optimal Design algorithm, that was actually performing the parameter optimization.The Reinforcement Learning (RL) based agent managed to obtain the same likelihood and number of support points, with a distribution similar to the reported in the original paper. The total amount of time used by the train the agent was 5.5 h although we think this time can be further improved. It is possible to automatically find the structural model that maximizes the final likelihood for an specific pharmacokinetic dataset by using RL algorithm. The framework provided could allow the integration of even more actions i.e: add/remove covariates, non-linear compartments or the execution of secondary analysis. Many limitations were found while performing this study but we hope to address them all in future studies.

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii.

BACKGROUND: Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. RESULTS: In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. CONCLUSIONS: Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied.

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana).

Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.

Powder and compaction characteristics of pregelatinized starches.

Pregelatinized starch is widely used as a pharmaceutical aid, especially as a filler-binder. It is known that the tableting performance of excipients could be affected by their source. The aim of this study was to evaluate the powder and tableting properties of pregelatinized starches obtained from yucca, corn and rice and compare those properties with those of Starch 1500. This material had the lowest particle size, and porosity and largest density and best flow. However, yucca starch and corn starch showed an irregular granule morphology, better compactibility and compressibility than Starch 1500. Their onset of plastic deformation and their strain rate sensitivity was comparable to that of Starch 1500. These two materials showed compact disintegration slower that Starch 1500. Conversely, rice starch showed a high elasticity, and friability, low compactibility, which are undesirable for direct compression. This study demonstrated the potential use of pregelatinized starches, especially those obtained from yucca and corn as direct compression filler-binders.

The Rice DNA-Binding Protein ZBED Controls Stress Regulators and Maintains Disease Resistance After a Mild Drought.

BACKGROUND: Identifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive. RESULTS: Using Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress. CONCLUSIONS: Together our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.

Characterization of Phytophthora infestans populations in Colombia: first report of the A2 mating type.

Phytophthora infestans, the causal agent of late blight in crops of the Solanaceae family, is one of the most important plant pathogens in Colombia. Not only are Solanum lycopersicum, and S. tuberosum at risk, but also several other solanaceous hosts (Physalis peruviana, S. betaceum, S. phureja, and S. quitoense) that have recently gained importance as new crops in Colombia may be at risk. Because little is known about the population structure of Phytophthora infestans in Colombia, we report here the phenotypic and molecular characterization of 97 isolates collected from these six different solanaceous plants in Colombia. All the isolates were analyzed for mating type, mitochondrial haplotypes, genotype for several microsatellites, and sequence of the internal transcribed spacer (ITS) region. This characterization identified a single individual of A2 mating type (from Physalis peruviana) for the first time in Colombia. All isolates had an ITS sequence that was at least 97% identical to the consensus sequence. Of the 97 isolates, 96 were mitochondrial haplotype IIa, with the single A2 isolate being Ia. All isolates were invariant for the microsatellites. Additionally, isolates collected from S. tuberosum and P. peruviana (64 isolates) were tested for: aggressiveness on both hosts, genotype for the isozymes (glucose-6-phosphate isomerase and peptidase), and restriction fragment length polymorphism fingerprint pattern as detected by RG57. Isolates from S. tuberosum were preferentially pathogenic on S. tuberosum, and isolates from P. peruviana were preferentially pathogenic on P. peruviana. The population from these two hosts was dominated by a single clonal lineage (59 of 64 individuals assayed), previously identified from Ecuador and Peru as EC-1. This lineage was mating type A1, IIa for mitochondrial DNA, invariant for two microsatellites, and invariant for both isozymes. The remaining four A1 isolates were in lineages very closely related to EC-1 (named EC-1.1, CO-1, and CO-2). The remaining lineage (the A2 mating type) had characteristics of the US-8 lineage (previously identified in Mexico, the United States, and Canada). These results have important epidemiological implications for the production of these two crops in Colombia.

Mixed epithelial and stromal tumour of the kidney with luteinised ovarian stroma.

We report a case of a 9-cm mixed epithelial and stromal tumour of the kidney in an obese 70-year-old woman with diabetes. The ovarian-type stroma had a spindle cell component that was positive for progesterone receptors and had the hitherto unreported presence of abundant foci of luteinised stromal cells with characteristic immunohistochemical positivity to alpha-inhibin, calretinin, aromatase and gonadotropin-releasing hormone (GnRH) receptors. We conclude that the stromal component is identical to ovarian cortical stroma. We believe that ovarian-type stroma occurs in extragenital tumours as a result of an epithelial-stromal interaction in an environment of hormonal hyperstimulation.

Pure testicular carcinoid associated with intratubular germ cell neoplasia.

This case report describes for the first time a case of pure testicular carcinoid pre-aortic lymph node metastases in a 25 year old patient with carcinoid syndrome. The simultaneous occurrence of intratubular germ cell neoplasia in the surrounding testicular tissue was identified by OCT4 and placental-like alkaline phosphatase positivity. This confirmed that the tumour had a germ cell origin in the testis, rather than being a metastasis from an extragenital carcinoid.

Optimal fluorescence excitation wavelengths for detection of squamous intra-epithelial neoplasia: results from an animal model.

Using the hamster cheek pouch carcinogenesis model, we explore which fluorescence excitation wavelengths are useful for the detection of neoplasia. 42 hamsters were treated with DMBA to induce carcinogenesis, and 20 control animals were treated only with mineral oil. Fluorescence excitation emission matrices were measured from the cheek pouches of the hamsters weekly. Results showed increased fluorescence near 350-370 nm and 410 nm excitation and decreased fluorescence near 450-470 nm excitation with neoplasia. The optimal diagnostic excitation wavelengths identified using this model - 350-370 nm excitation and 400-450 nm excitation - are similar to those identified for detection of human oral cavity neoplasia.

Optimal excitation wavelengths for in vivo detection of oral neoplasia using fluorescence spectroscopy.

There is no satisfactory mechanism to detect premalignant lesions in the upper aero-digestive tract. Fluorescence spectroscopy has potential to bridge the gap between clinical examination and invasive biopsy; however, optimal excitation wavelengths have not yet been determined. The goals of this study were to determine optimal excitation-emission wavelength combinations to discriminate normal and precancerous/cancerous tissue, and estimate the performance of algorithms based on fluorescence. Fluorescence excitation-emission matrices (EEM) were measured in vivo from 62 sites in nine normal volunteers and 11 patients with a known or suspected premalignant or malignant oral cavity lesion. Using these data as a training set, algorithms were developed based on combinations of emission spectra at various excitation wavelengths to determine which excitation wavelengths contained the most diagnostic information. A second validation set of fluorescence EEM was measured in vivo from 281 sites in 56 normal volunteers and three patients with a known or suspected premalignant or malignant oral cavity lesion. Algorithms developed in the training set were applied without change to data from the validation set to obtain an unbiased estimate of algorithm performance. Optimal excitation wavelengths for detection of oral neoplasia were 350, 380 and 400 nm. Using only a single emission wavelength of 472 nm, and 350 and 400 nm excitation, algorithm performance in the training set was 90% sensitivity and 88% specificity and in the validation set was 100% sensitivity, 98% specificity. These results suggest that fluorescence spectroscopy can provide a simple, objective tool to improve in vivo identification of oral cavity neoplasia.

Papillary serous carcinoma of the tunica vaginalis testis.

This is a case report of a testicular papillary serous carcinoma of ovarian type (PSCOT) diagnosed in a 50-year-old man. The tumor presented in the form of multiple papillary exophytic excrescencies on the visceral tunica vaginalis testis lining the inner surface of a hydrocele sac. The tumor was histologically a papillary serous carcinoma with numerous psammoma bodies, indistinguishable from similar tumors arising on the surface of the ovary. Following the tumor's surgical removal, the patient was treated with the same drugs used to treat ovarian serous carcinomas, and he is alive two years after the initial diagnosis. PSCOT must be distinguished from mesothelioma of the tunica vaginalis testis, a tumor with a most unfavorable prognosis. As shown here, immunohistochemical findings can be useful for formulating the correct diagnosis of PSCOT.

Amikacin concentration in the cerebrospinal fluid of children with acute bacterial meningitis.

Penetration of the aminoglycoside, amikacin, into the cerebrospinal fluid (CSF) of twenty children with acute bacterial meningitis was studied at various times after intramuscular administration and at various stages of therapy. Six of the patients were evaluated during therapy with amikacin at 7.5 mg/kg (intramuscularly) every 12 hours plus ampicillin every 6 hours at 300 mg/kg/day (intravenously); thirteen of the remaining fourteen patients were treated with ampicillin alone, but were given a single intramuscular dose of 7.5 mg/kg of amikacin for evaluation of CSF concentration. Amikacin concentration in CSF with respect to time after administration followed essentially the same pattern as in serum. A minimum concentration of 2 microgram/ml was found in 76% of the CSF samples obtained between 0.5 and 7 hours after administration. A mean amikacin serum/CSF ratio of 3:1 was demonstrated up to 7 hours after dose in all patients who underwent clinical improvement. Patient response was predictable by a correlation of in vitro MIC values with in vivo CSF concentration in three of the six patients who received amikacin therapy.

Amikacin in gram-negative paediatric infections.

Amikacin was used in the treatment of various Gram-negative infections in sixty-six children ranging in age from two days to thirteen years. Over 72% of the infections treated were classified as severe and the remainder were moderate. Among infections in which the site of origin was the urinary or gastro-intestinal tract, amikacin achieved thirty-eight (95%) complete or partial cures in forty patients. In respiratory tract infections, amikacin completely or partially cured six (75%) out of eight patients. The remaining eighteen infections involved skin, soft tissue and other miscellaneous categories in which amikacin therapy resulted in seventeen (94%) complete or partial cures. Overall, amikacin achieved fifty-four complete cures and seven clinical or bacteriological cures in sixty-six patients, which represents an 82% complete cure rate and 10% partial cure rate for all the patients in the study.

[Epidemiology of urologic pediatric emergencies in our hospital, 1990]. / Epidemiologiá de las urgencias urológicas pediátricas en nuestro hospital, 1990.

The article's objective is to study the epidemiological patterns which define the paediatric urological emergencies within the area of influence of our hospital. To this end, 187 protocols of the paediatric emergencies attended by the urologist in 1990 were retrospectively reviewed. The most frequently observed pathologies were balanitis-phimosis, acute scrotum and genito-urinary injuries. A clear relationship of the type of disease to the patient's age and treatment, as well as some time-related variations were observed. About 40% of all cases could had been treated at a non-emergency outpatient clinic.

[Antimicrobial prophylaxis in urethrocystoscopy. Comparative study]. / Profilaxis antimicrobiana en uretrocistoscopias. Estudio comparativo.

Instrumentation of lower urinary tract is a predisposing factor for the development of urinary infection. Incidence of infective complications following urethrocystoscopy has been evaluated in a multicenter, prospective, comparative and randomized study in 2,284 patients, who had a previous negative urine culture. Patients were randomized into two groups: one to be used as control and the other one to received antimicrobial prophylaxis prior to instrumentation (ceftriazone, 1 gr intramuscular). Clinical and microbiological responses were evaluated at 48-72 hours and 4 weeks after cystoscopy. Symptomatic bacteriuria was observed in 10.2% of patients in the control group and in 2.5% in the prophylaxis group (p < 0.000); asymptomatic bacteriuria in 3.02% and 1.52% (p > 0.05) and irritative syndrome with sterile urine in 2.93% and 2.60% (p > 0.05), respectively. Thus, the use of prophylaxis reduced the incidence of infective complications in these patients.

Novel plant inputs influencing Ralstonia solanacearum during infection.

Ralstonia solanacearum is a soil and water-borne pathogen that can infect a wide range of plants and cause the devastating bacterial wilt disease. To successfully colonize a host, R. solanacearum requires the type III secretion system (T3SS), which delivers bacterial effector proteins inside the plant cells. HrpG is a central transcriptional regulator that drives the expression of the T3SS and other virulence determinants. hrpG transcription is highly induced upon plant cell contact and its product is also post-transcriptionally activated by metabolic signals present when bacteria are grown in minimal medium (MM). Here, we describe a transcriptional induction of hrpG at early stages of bacterial co-culture with plant cells that caused overexpression of the downstream T3SS effector genes. This induction was maintained in a strain devoid of prhA, the outer membrane receptor that senses bacterial contact with plant cells, demonstrating that this is a response to an unknown signal. Induction was unaffected after disruption of the known R. solanacearum pathogenicity regulators, indicating that it is controlled by a non-described system. Moreover, plant contact-independent signals are also important in planta, as shown by the hrpG induction triggered by apoplastic and xylem extracts. We also found that none of the amino acids or sugars present in the apoplast and xylem saps studied correlated with hrpG induction. This suggests that a small molecule or an environmental condition is responsible for the T3SS gene expression inside the plants. Our results also highlight the abundance and diversity of possible carbon, nitrogen and energy sources likely used by R. solanacearum during growth in planta.