Quantifying the Benefits of Imputation over QSAR Methods in Toxicology Data Modeling.

Imputation machine learning (ML) surpasses traditional approaches in modeling toxicity data. The method was tested on an open-source data set comprising approximately 2500 ingredients with limited in vitro and in vivo data obtained from the OECD QSAR Toolbox. By leveraging the relationships between different toxicological end points, imputation extracts more valuable information from each data point compared to well-established single end point methods, such as ML-based Quantitative Structure Activity Relationship (QSAR) approaches, providing a final improvement of up to around 0.2 in the coefficient of determination. A significant aspect of this methodology is its resilience to the inclusion of extraneous chemical or experimental data. While additional data typically introduces a considerable level of noise and can hinder performance of single end point QSAR modeling, imputation models remain unaffected. This implies a reduction in the need for laborious manual preprocessing tasks such as feature selection, thereby making data preparation for ML analysis more efficient. This successful test, conducted on open-source data, validates the efficacy of imputation approaches in toxicity data analysis. This work opens the way for applying similar methods to other types of sparse toxicological data matrices, and so we discuss the development of regulatory authority guidelines to accept imputation models, a key aspect for the wider adoption of these methods.

Key Challenges and Recommendations for In Vitro Testing of Tobacco Products for Regulatory Applications: Consideration of Test Materials and Exposure Parameters.

The Institute for In Vitro Sciences (IIVS) is sponsoring a series of workshops to identify, discuss and develop recommendations for optimal scientific and technical approaches for conducting in vitro assays, to assess potential toxicity within and across tobacco and various next generation nicotine and tobacco products (NGPs), including heated tobacco products (HTPs) and electronic nicotine delivery systems (ENDS). The third workshop (24-26 February 2020) summarised the key challenges and made recommendations concerning appropriate methods of test article generation and cell exposure from combustible cigarettes, HTPs and ENDS. Expert speakers provided their research, perspectives and recommendations for the three basic types of tobacco-related test articles: i) pad-collected material (PCM); ii) gas vapour phase (GVP); and iii) whole smoke/aerosol. These three types of samples can be tested individually, or the PCM and GVP can be combined. Whole smoke/aerosol can be bubbled through media or applied directly to cells at the air-liquid interface. Summaries of the speaker presentations and the recommendations developed by the workgroup are presented. Following discussion, the workshop concluded the following: that there needs to be greater standardisation in aerosol generation and collection processes; that methods for testing the NGPs need to be developed and/or optimised, since simply mirroring cigarette smoke testing approaches may be insufficient; that understanding and quantitating the applied dose is fundamental to the interpretation of data and conclusions from each study; and that whole smoke/aerosol approaches must be contextualised with regard to key information, including appropriate experimental controls, environmental conditioning, analytical monitoring, verification and performance criteria.

In vitro evaluation of mutagenic, cytotoxic, genotoxic and oral irritation potential of nicotine pouch products.

Non-clinical in vitro studies were conducted to investigate the characteristics of extracts from tobacco free nicotine pouches alongside a reference snus product and/or 1R6F reference cigarette. In vitro investigations were conducted in the Neutral Red Uptake (NRU) cytotoxicity assay, Bacterial Reverse Mutation (Ames) assay, and in vitro Mammalian Cell Micronucleus (ivMN) assay. These products were also investigated for their oral irritation potential in the EpiGingival™ 3D tissue model. Results from the Ames, in vitro Micronucleus and NRU assays indicated that the tested products were non-mutagenic, non-genotoxic and non-cytotoxic in contrast to results obtained for the 1R6F reference cigarette. Results from Complete Artificial Saliva (CAS) extracts from these products also failed to be classified as irritants (as measured using the MTT assay), in the EpiGingival™ 3D tissue model.

Review of Clinical Performance of Serology Based Commercial Diagnostic Assays for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, which caused the coronavirus disease 2019 (COVID-19) pandemic as declared by the World Health Organization, has created havoc worldwide. The highly transmissible infection can be contained only by accurate diagnosis, quarantining, and exercising social distancing. Therefore, quick and massive deployment of SARS-CoV-2 testing plays a crucial role in the identification and isolation of infected patients. Reverse transcription-polymerase chain reaction is the gold standard for COVID-19 detection; however, it needs expertise, facilities, and time. Hence, for the ease of population-wide screening, serology-based diagnostic assays were introduced. These can help determine the prevalence of infection, understand the epidemiology of the disease, and assist in suitable public health interventions while being user-friendly and less time consuming. Although serological testing kits in markets soared, their sensitivity and specificity were questioned in reports from different parts of the world. In this article, we have reviewed 40 Food and Drug Administration (FDA) and CE-approved clinically evaluated serological kits (8 enzyme-linked immunosorbent assay [ELISA] kits, 10 chemiluminescent immunoassay [CLIA] kits, and 22 lateral flow immunoassay [LFIA] kits) for their sensitivity and specificity and discussed the apparent reasons behind their performance. We observed appreciable sensitivity in the kits detecting total antibodies compared to the kits targeting single isotype antibodies. Tests that determined antibodies against nucleocapsid protein were found to be more sensitive and those detecting antibodies against spike protein were found to have greater specificity. This study was conducted to help the decision-making while acquiring antibody kits and concurrently to be mindful of their shortcomings.

Comparative and cumulative quantitative risk assessments on a novel heated tobacco product versus the 3R4F reference cigarette.

Novel tobacco products that heat rather than burn tobacco (heated tobacco products or HTPs) have been shown to produce lower levels of harmful and potentially harmful constituents than conventional combusted cigarettes. The present study uses a quantitative risk assessment approach to compare non-cancer and cancer risk estimates for emissions generated by an HTP with smoke from a reference cigarette (3R4F). Fifty-four analytes were evaluated from the HTP aerosol and the 3R4F cigarette smoke. Emissions were generated using the ISO and the Health Canada Intense smoking regimes. The measured values were extrapolated to define a conservative exposure assumption for per day use and lifetime use based on an estimated maximum usage level of 400 puffs per day i.e., approximately 8 HTP tobacco capsules or 40 combustible cigarettes. Non-cancer and cancer risk estimates were calculated using these exposure assumptions for individual and per health outcome domains based on toxicological reference values derived by regulatory and/or public health agencies. The results of this assessment showed a reduction of non-cancer and cancer risk estimates by more than 90 % for the HTP versus the 3R4F cigarette, regardless of the smoking regime.

Correlation of chemical structure with reproductive and developmental toxicity as it relates to the use of the threshold of toxicological concern.

In the absence of toxicological data on a chemical, the threshold of toxicological concern (TTC) approach provides a system to estimate a conservative exposure below which there is a low probability of risk for adverse health effects. The original toxicology dataset underlying the TTC was based on NOELs from repeat dose studies. Subsequently there have been several efforts to assess whether or not these limits are also protective for reproductive/developmental effects. This work expands the database of chemicals with reproductive and developmental data, presents these data in a comprehensive and transparent format and groups the chemicals according to the TTC "Cramer Class" rules. Distributions of NOAELs from each of these classes were used to assess whether the previously proposed TTC values based on repeat dose data are protective for reproductive/developmental toxicity endpoints as well. The present analysis indicates that, for each Cramer Class, the reproductive and developmental endpoints would be protected at the corresponding general TTC tiers derived by Munro et al. (1996).

Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links.

The differences in efficacy and molecular mechanisms of platinum anti-cancer drugs cisplatin (CP) and oxaliplatin (OX) are thought to be partially due to the differences in the DNA conformations of the CP and OX adducts that form on adjacent guanines on DNA, which in turn influence the binding of damage-recognition proteins that control downstream effects of the adducts. Here we report a comprehensive comparison of the structural distortion of DNA caused by CP and OX adducts in the TGGT sequence context using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations. When compared to our previous studies in other sequence contexts, these structural studies help us understand the effect of the sequence context on the conformation of Pt-GG DNA adducts. We find that both the sequence context and the type of Pt-GG DNA adduct (CP vs. OX) play an important role in the conformation and the conformational dynamics of Pt-DNA adducts, possibly explaining their influence on the ability of many damage-recognition proteins to bind to Pt-DNA adducts.

Pelizaeus Merzbacher disease: morphological analysis of the vestibulo-cochlear system.

CONCLUSION: In agreement with previously published findings, our results demonstrate that Pelizaeus Merzbacher disease (PMD) does not affect the development and morphology of the peripheral vestibulo-cochlear system. OBJECTIVE: PMD is a consequence of X-linked mutation of the main central nervous system (CNS) myelin protein resulting in a complex neurological syndrome. Otorhinolaryngological symptoms include nystagmus and alterations of auditory-evoked brainstem responses. To date no histopathological analysis of the inner ear has been performed. MATERIALS AND METHODS: The temporal bone morphology of an affected fetus was examined with light microscopy and synchrotron radiation-based micro computed tomography. RESULTS: The regular structure of the vestibulo-cochlear system was shown in this multi-modular analysis.

The cochlea in fetuses with neural tube defects.

In this study different malformations of the cochlea could be demonstrated. Nevertheless, we could not delineate a distinct malformation of the inner ear, that can be linked to a neural tube defect. Neural tube defects are a frequent and heterogeneous group of malformations, ranging from the survivable spina bifida to fatal anencephaly. In multiple animal models an involvement of the vestibulocochlear system has been demonstrated. In this article human fetal temporal bones of neural tube defects were analysed in a multimodular work-up. The morphologic study was performed with light microscopy, transmission electron microscopy and synchrotron radiation-based microcomputed tomography. Immunohistochemistry for different neuronal markers such as peripherin, beta-III-tubulin and vimentin helped to evaluate ontogenetic tissue development. Eight fetal temporal bones with neural tube defects and five control temporal bones were included into the morphologic study. The morphologic results of the neural tube defect temporal bones showed six regularly developed cochleas and two with only a single cochlear turn. Three of the neural tube defect temporal bones were further examined with immunohistochemical analysis. No differences in the staining pattern for peripherin, beta-III-tubulin and vimentin were detected.

Development of an ultraperformance liquid chromatography/mass spectrometry method to quantify cisplatin 1,2 intrastrand guanine-guanine adducts.

Platinum chemotherapeutic agents have been widely used in the treatment of cancer. Cisplatin was the first of the platinum-based chemotherapeutic agents and therefore has been extensively studied as an antitumor agent since the late 1960s. Because this agent forms several DNA adducts, a highly sensitive and specific quantitative assay is needed to correlate the molecular dose of individual adducts with the effects of treatment. An ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay for quantification of 1,2 guanine-guanine intrastrand cisplatin adducts [CP-d(GpG)], using (15)N(10) CP-d(GpG) as an internal standard, was developed. The internal standard was characterized by MS/MS, and its concentration was validated by inductively coupled plasma mass spectrometry. Samples containing CP-d(GpG) in DNA were purified by enzyme hydrolysis, centrifugal filtration, and HPLC with fraction collection prior to quantification by UPLC-MS/MS in the selective reaction monitoring mode [m/z 412.5-->248.1 for CP-d(GpG); m/z 417.5-->253.1 for [(15)N(10)] CP-d(GpG)]. The recovery of standards was >90%, and quantification was unaffected by increasing concentrations of calf thymus DNA. This method utilizes 25 mug of DNA per injection. The limit of quantification was 3 fmol or 3.7 adducts per 10(8) nucleotides, which approaches the sensitivity of the (32)P postlabeling method for this adduct. These data suggested that this method is suitable for in vitro and in vivo assessment of CP-d(GpG) adducts formed by cisplatin and carboplatin. Subsequently, the method was applied to studies using ovarian carcinoma cell lines and C57/BL6 mice to illustrate that this method is capable of quantifying CP-d(GpG) adducts using biologically relevant systems and doses. The development of biomarkers to determine tissue-specific molecular dosimetry during treatment will lead to a more complete understanding of both therapeutic and adverse effects of cisplatin and carboplatin. This will support the refinement of therapeutic regimes and appropriate individualized treatment protocols.

Does perinatal asphyxia induce apoptosis in the inner ear?

Pre- and perinatal asphyxia is known to be an important risk factor in the development of neonatal hearing impairment. This study aims to evaluate the role of apoptosis, which is known to play an essential role in the development of the inner ear structures, in the development of neonatal hearing loss caused by pre- and perinatal asphyxia. Eight temporal bones of six different newborns were included. We performed a morphologic analysis by both light microscopy, and transmission electron microscopy, as well as immunohistochemical staining to detect the cleaved form of caspase 3 as apoptosis marker and Bcl 2 as anti-apoptotic marker. Early and late phases of apoptosis were evidenced by condensation of chromatin (electron-dense, black structure along nuclear membrane) and fragmentation of the nucleus, respectively. Changes in nuclear morphology during apoptosis correlate with cleavage by caspase 3 located downstream of Bcl 2 action. The immunohistochemistry for cleaved caspase 3 showed a particular predilection for the inner and outer hair cells, spiral ganglion cells and the marginal cells of the stria vascularis. The brain of all examined cases did not show signs of apoptosis. In summary, this investigation suggests that apoptosis takes place before brain tissue apoptosis and is probably an earlier event than thought. Apoptosis of the cochlea is known to play an essential role in the development of the inner ear. Additionally, this study shows that apoptosis may play an important role in the development of hearing impairment, caused by pre- and perinatal asphyxia.

Morphology studies of the human fetal cochlea in turner syndrome.

OBJECTIVES: Turner syndrome (TS) is the most frequent sex chromosome abnormality, and sensorineural hearing loss is common. We aimed to determine whether there are consistent morphologic cochlear abnormalities during gestational development that could be associated with TS. DESIGN: The histology of nine fetal temporal bones of TS autopsied after spontaneous abortion was studied. RESULTS: Gross morphologic examination of the TS cochleae failed to reveal a pattern of structural abnormalities that would explain the development of sensorineural hearing loss. Mondini-like cochlear dysplasia was observed in one 13-wk-old TS fetus. CONCLUSION: We could not demonstrate a consistent pattern of cochlear malformations.

Pilot study: volatile organic compounds as a diagnostic marker for head and neck tumors.

BACKGROUND: In the last decade, the analysis of volatile organic compounds (VOC) has undergone a rapid development. In this pilot study, patients with HNSCC were tested with a proton transfer reaction-mass spectrometry in order to establish a minimal invasive screening method. METHODS: Overall in a period of 2 years, 22 carcinoma patients were recruited for the study. All patients had a newly diagnosed histologically secured squamous cell carcinoma of the upper aerodigestive tract. These results were statistically compared with 3 control groups: healthy controls, high-risk, and posttherapy patients. RESULTS: Two hundred nine different masses were measured; 188 of these were evaluated. The statistical workup of the 4 study groups produced 42 different masses, which showed a statistically significant difference from the carcinoma group compared with the control groups. CONCLUSION: A screening method for HNSCC using VOC seems to be possible, but further investigation is necessary.

Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link.

Proteins that discriminate between cisplatin-DNA adducts and oxaliplatin-DNA adducts are thought to be responsible for the differences in tumor range, toxicity, and mutagenicity of these two important chemotherapeutic agents. However, the structural basis for differential protein recognition of these adducts has not been determined and could be important for the design of more effective platinum anticancer agents. We have determined high-resolution NMR structures for cisplatin-GG and undamaged DNA dodecamers in the AGGC sequence context and have compared these structures with the oxaliplatin-GG structure in the same sequence context determined previously in our laboratory. This structural study allows the first direct comparison of cisplatin-GG DNA and oxaliplatin-GG DNA solution structures referenced to undamaged DNA in the same sequence context. Non-hydrogen atom rmsds of 0.81 and 1.21 were determined for the 15 lowest-energy structures for cisplatin-GG DNA and undamaged DNA, respectively, indicating good structural convergence. The theoretical NOESY spectra obtained by back-calculation from the final average structures showed excellent agreement with the experimental data, indicating that the final structures are consistent with the NMR data. Several significant conformational differences were observed between the cisplatin-GG adduct and the oxaliplatin-GG adduct, including buckle at the 5' G6.C19 base pair, opening at the 3' G7.C18 base pair, twist at the A5G6.T20C19 base pair step, slide, twist, and roll at the G6G7.C19C18 base pair step, slide at the G7C8.C18G17 base pair step, G6G7 dihedral angle, and overall bend angle. We hypothesize that these conformational differences may be related to the ability of various DNA repair proteins, DNA binding proteins, and DNA polymerases to discriminate between cisplatin-GG and oxaliplatin-GG adducts.

Middle ear pressure changes during anesthesia with or without nitrous oxide are similar among airway devices.

We tested the hypothesis that middle ear pressure (MEP) is influenced by the choice of airway device during anesthesia with or without nitrous oxide (N2O) in the gas mixture. Eighty consecutive anesthetized, paralyzed ventilated patients (ASA physical status I-II, 18-65 yr) were randomly allocated for airway management with the orally inserted tracheal tube, classic laryngeal mask airway, ProSeal laryngeal mask airway, or laryngeal tube suction with or without N2O 66% in the gas mixture. MEP was measured from both ears in random order by a blinded observer before induction of anesthesia and every 10 min for 70 min. In the N2O groups, N2O was changed to air after 40 min. There were no differences in MEP among the airway devices in the N2O or air groups. MEP was unchanged in the air groups but increased in the N2O groups with N2O (P < 0.0001) and decreased with air (P < 0.02). Baseline values for MEP were similar, but MEP was always higher for the N2O groups (P < 0.001). We conclude that the choice of airway device does not influence MEP among orally inserted tracheal tube, classic laryngeal mask airway, ProSeal laryngeal mask airway, and laryngeal tube suction during anesthesia with or without N2O in the gas mixture.

Increase in postprandial serum insulin levels in epileptic patients with valproic acid therapy.

A significant weight gain and increase in serum leptin levels in the course of antiepileptic treatment with valproic acid (VPA) has been described in several clinical studies. With respect to the long treatment period in antiepileptic therapy, these side effects might increase insulin resistance and metabolic risk factors. We have studied clinical and laboratory effects of VPA treatment in a cohort of female patients (n = 22) and in patients treated with carbamazepine (CBZ) or lamotrigine monotherapy (n = 21). All study participants underwent an oral glucose tolerance test (OGTT) with 75 g glucose. Body mass index (BMI) in the VPA group was higher (28.1 +/- 3.6 kg/m(2)) than in the control group (23.9 +/- 3.7 kg/m(2)) (P <.039). While plasma glucose, serum leptin, insulin, and C-peptide levels did not differ significantly between the study groups in the fasting state, postprandial (pp) insulin and proinsulin levels were found to be significantly higher in the VPA than in the control group. In the course of the OGTT, serum insulin levels reached their peak values 1 hour postprandially with 68.8 +/- 10.0 microU/mL in the VPA group and 49.8 +/- 11.2 microU/mL in the control group (P <.042). After 2 hours, the corresponding serum insulin levels were 48.5 +/- 25.2 microU/mL and 34.1 +/- 17.2 microU/mL (P <.048) and the proinsulin levels 52.5 +/- 30.2 pmol/L and 29.5 +/- 12.0 pmol/L (P <.017). While BMI values in the non-VPA group showed a significant correlation only with the fasting values of insulin, proinsulin, and C-peptide, the BMI values of the VPA-treated group were also positively related to the 2-hour pp levels of insulin (R =.690; P <.001), proinsulin (R =.667; P <.001) and C-peptide (R =.502; P <.017). VPA is a fatty acid derivative, competes with free fatty acids (FFA) for albumin binding, and acts as a gamma aminobutyric acid (GABA)-ergic agonist, mechanisms, which are known to be involved in pancreatic beta-cell regulation and insulin secretion. Therefore, it might be suspected that VPA therapy is associated with increased glucose stimulated pancreatic secretion and thus a higher body weight in the VPA group.

Polycystic ovaries, obesity and insulin resistance in women with epilepsy. A comparative study of carbamazepine and valproic acid in 105 women.

In order to investigate the possible role of valproic acid therapy in the development of obesity, hyperinsulinism and polycystic ovaries (PCOs), we have studied metabolic parameters and ovarian morphology in epileptic women. A total of 105 women, who were treated for at least 2 years with valproate (n = 52) or carbamazepine monotherapy (n = 53), were included in the examination. Menstrual disturbances were reported by 29 (28 %) of the women, 12 (11 %) of the VPA treated women, and 17 (16 %) in the CBZ group. On ultrasound scan polycystic ovaries were found in 28 patients (27 %) of the whole study population, of whom 13 (12 %) received VPA and 15 (14 %) CBZ. The mean body mass index (BMI) was significantly higher in the VPA group (24.4 kg/m(2) +/- 4.1) than in CBZ treated patients (22.9 kg/m(2) +/- 2.4;p < 0.022), and serum triglycerides tended to be increased, while total cholesterol values (178.9 +/- 30.5) and LDL-cholesterol values (92.6 +/- 27.4) were significantly lower in the valproate group, than in the carbamazepine group (207.1 +/- 43.0 vs 115.1 +/- 42.0; p < 0.001). Postprandial insulin, C-peptide and proinsulin levels were significantly higher in VPA treated patients compared with those treated with CBZ, while no differences could be found in the fasting state. In conclusion we could thus demonstrate that the frequency of PCOs in 27 % of epileptic women seems to be similar to that in the general population with a frequency of 20-30 %. The development of PCOs did not reveal a difference with the administration of VPA or CBZ. With respect to the metabolic side-effects of VPA therapy our data indicate that VPA increases glucose stimulated pancreatic insulin secretion, which might be followed by an increase in body weight.

Retention of the differentiated state by larvalXenopus liver cells in primary culture.

Electron microscopic analysis of primary cultures derived from larvalXenopus liver has shown that these cells, although they form only two-dimensional aggregates, retain and presumably also develop structural characteristics typical of liver parenchyma cells, such as bile canaliculi with microvilli and epithelial junctional complexes. As judged from structural criteria, primary cultures contain 80-90% hepatocytes. In contrast to the intact tissue, primary cultures showed excessive development of microfilaments, however.Incorporation of labeled amino acids has revealed further that the capacity for protein synthesis is maintained in culture and that synthesis of liverspecific protein albumin is maintained in vitro, even in liver cultures derived from thyrostatic tadpoles. This latter result suggests that initiation of albumin synthesis in the larval liver is probably not dependent upon thyroid hormones but rather reflects the protodifferentiated state of this tissue.