Factors of significance for the ability of fighter pilots to visually indicate the magnitude of roll tilt during simulated turns in a centrifuge

During coordinated flight and centrifugation, pilots show interindividual variability in perceived roll tilt. The study explored how this variability is related to perceptual and cognitive functions. Twelve pilots underwent three 6-min centrifugations on two occasions (G levels: 1.1G, 1.8G, and 2.5G; gondola tilts: 25°, 56°, and 66°). The subjective visual horizontal (SVH) was measured with an adjustable luminous line and the pilots gave estimates of experienced G level. Afterward, they were interrogated regarding the relationship between G level and roll tilt and adjusted the line to numerically mentioned angles. Generally, the roll tilt during centrifugation was underestimated, and there was a large interindividual variability. Both knowledge on the relationship between G level and bank angle, and ability to adjust the line according to given angles contributed to the prediction of SVH in a multiple regression model. However, in most cases, SVH was substantial smaller than predictions based on specific abilities.

Intratumor genetic heterogeneity and head and neck cancer relapse

BACKGROUND

Head and neck squamous cell carcinomas are treated by surgery, radiotherapy (RT), chemoradiotherapy (CRT) or combinations thereof, but locoregional recurrences (LRs) occur in 30-40% of treated patients. We have previously shown that in approximately half of the LRs after CRT, cancer driver mutations are not shared with the index tumor.

AIM

To investigate two possible explanations for these genetically unrelated relapses, treatment-induced genetic changes and intratumor genetic heterogeneity.

METHODS

To investigate treatment-induced clonal DNA changes, we compared copy number alterations (CNAs) and mutations between primary and recurrent xenografted tumors after treatment with (C)RT. Intratumor genetic heterogeneity was studied by multi-region sequencing on DNA from 31 biopsies of 11 surgically treated tumors.

RESULTS

Induction of clonal DNA changes by (C)RT was not observed in the xenograft models. Multi-region sequencing demonstrated variations in CNA profiles between paired biopsies of individual tumors, with copy number heterogeneity scores varying from 0.027 to 0.333. In total, 32 cancer driver mutations could be identified and were shared in all biopsies of each tumor. Remarkably, multi-clonal mutations in these same cancer driver genes were observed in 6 of 11 tumors. Genetically distinct heterogeneous cell cultures could also be established from single tumors, with different biomarker profiles and drug sensitivities.

CONCLUSION

Intratumor genetic heterogeneity at the level of the cancer driver mutations might explain the discordant mutational profiles in LRs after CRT, while there are no indications in xenograft models that these changes are induced by CRT.

Visual measures of perceived roll tilt in pilots during coordinated flight and gondola centrifugation

BACKGROUND

During a simulated coordinated turn in a gondola centrifuge, experienced pilots show a substantial inter-individual variability in visual measures of perceived roll tilt. Because of the centrifuge's small radius, the pattern of stimuli to the semicircular canals during acceleration of the centrifuge differs in certain respects from that of an aircraft entering a turn.

OBJECTIVE

To explore whether these differences may be of significance for the pilot's roll- plane orientation and whether individual characteristics revealed in the centrifuge correspond to those during real flight.

METHOD

8 fixed-wing air-force pilots were tested in a centrifuge and a high-performance aircraft. The centrifuge was accelerated to 2 G (gondola inclination 60°) within 10 s. The duration at 2 G was 6 minutes. Similar profiles were created in the aircraft. The subjective visual horizontal (SVH) was measured using an adjustable luminous line in darkness. Each pilot was tested on three occasions: centrifuge (2 runs), aircraft (2 turns), centrifuge (2 runs). For each 2-G exposure, initial and final SVH values were established via curve fitting.

RESULT

Despite a large inter-individual variability (±SD), group means were similar in the aircraft (initial: 43.0±20.6°; final: 22.5±14.8°) and centrifuge (initial: 40.6±17.0°; final: 20.5±16.0°). Further, individual peculiarities in response patterns were similar in the two conditions. For both the initial and final SVH tilt there was a high correlation between centrifuge and aircraft.

CONCLUSION

The correspondence between conditions suggests that the centrifuge is an adequate means for demonstrating the fundamental motion pattern of coordinated flight and also for establishing the individual pilot's ability to perceive an aircraft's roll attitude.Findings are discussed in connection with vestibular learning and the possibility of underlying differences between pilots in the keenness for semicircular canal and somatosensory cues.

Tritium labeling of antisense oligonucleotides via different conjugation agents

A novel approach to tritium-labeled antisense oligonucleotides (ASO) was established by conjugating N-succinimidyl propionate, as well as maleimide-derivatives, to the 3′-end of ASOs targeting metastasis-associated lung adenocarcinoma transcript 1 (Malat1) containing amino- or sulfhydryl-linkers. In vitro stability and Malat1 RNA reduction studies demonstrated that N-ethylmaleimide (NEM) could be used as a stable tag while maintaining the desired target interaction. The corresponding radioactive label conjugation using [3H]-NEM resulted in tritium-labeled ASOs with a high molar specific activity of up to 17 Ci/mmol. Single-dose in vivo studies in mice were carried out to compare [3H]-ASOs with their unlabeled counterpart ASOs, with and without conjugation to N-acetylgalactosamine (GalNAc), for tissue and plasma concentrations time profiles. Despite the structural modification of the labeled ASOs, in vitro target interaction and in vivo pharmacokinetic behaviors were similar to that of the unlabeled ASOs. In conclusion, this new method provides a powerful technique for fast and safe access to tritium-labeled oligonucleotides, e.g., for pharmacokinetic, mass balance, or autoradiography studies.

Graphical abstract

Detecting cocoa plantations in Côte d'Ivoire and Ghana and their implications on protected areas

Côte d'Ivoire and Ghana are the largest producers of cocoa in the world. In recent decades the cultivation of this crop has led to the loss of vast tracts of forest areas in both countries. Efficient and accurate methods for remotely identifying cocoa plantations are essential to the implementation of sustainable cocoa practices and for the periodic and effective monitoring of forests. In this study, a method for cocoa plantation identification was developed based on a multi-temporal stack of Sentinel-1 and Sentinel-2 images and a multi-feature Random Forest (RF) algorithm. The Normalized Difference Vegetation Index (NDVI) and second-order texture features were assessed for their importance in an RF classification, and their optimal combination was used as input variables for the RF model to identify cocoa plantations in both countries. The RF model-based cocoa map achieved 82.89% producer's and 62.22% user's accuracy, detecting 3.69 million hectares (Mha) and 2.15 Mha of cocoa plantations for Côte d'Ivoire and Ghana, respectively. The results demonstrate that a combination of an RF model and multi-feature classification can distinguish cocoa plantations from other land cover/use, effectively reducing feature dimensions and improving classification efficiency. The results also highlight that cocoa farms largely encroach into protected areas (PAs), as 20% of the detected cocoa plantation area is located in PAs and almost 70% of the PAs in the study area house cocoa plantations.

In vitro and clinical investigations to determine the drug-drug interaction potential of entrectinib, a small molecule inhibitor of neurotrophic tyrosine receptor kinase (NTRK)

Background Entrectinib is a CNS-active, potent inhibitor of tyrosine receptor kinases A/B/C, ROS1 and anaplastic lymphoma kinase approved for use in patients with solid tumors. We describe the in vitro and clinical studies investigating potential entrectinib drug-drug interactions. Methods In vitro studies with human biomaterials assessed the enzymes involved in entrectinib metabolism, and whether entrectinib modulates the activity of the major cytochrome P450 (CYP) enzymes or drug transporter P-glycoprotein. Clinical studies investigated the effect of a strong CYP3A4 inhibitor (itraconazole) and inducer (rifampin) on single-dose entrectinib pharmacokinetics. The effect of entrectinib on sensitive probe substrates for CYP3A4 (midazolam) and P-glycoprotein (digoxin) were also investigated. Results Entrectinib is primarily metabolized by CYP3A4. In vitro, entrectinib is a CYP3A4/5 inhibitor (IC₅₀ 2 μM) and a weak CYP3A4 inducer. Entrectinib inhibited P-glycoprotein (IC₅₀ 1.33 μM) but is a poor substrate. In healthy subjects, itraconazole increased entrectinib C_max and AUC by 73% and 504%, respectively, and rifampin decreased entrectinib C_max and AUC by 56% and 77%, respectively. Single dose entrectinib did not affect midazolam AUC, although C_max decreased by 34%. Multiple dose entrectinib increased midazolam AUC by 50% and decreased C_max by 21%. Single dose entrectinib increased digoxin AUC and C_max by 18% and 28%, respectively, but did not affect digoxin renal clearance. Conclusions Entrectinib is a CYP3A4 substrate and is sensitive to the effects of coadministered moderate/strong CYP3A4 inhibitors and strong inducers, and requires dose adjustment. Entrectinib is a weak inhibitor of CYP3A4 and P-glycoprotein and no dose adjustments are required with CYP3A4/P- glycoprotein substrates.

Registration Number (Study 2) NCT03330990 (first posted online November 6, 2017) As studies 1 and 3 are phase 1 trials in healthy subjects, they are not required to be registered.

Multiorgan Crystal Deposition of an Amphoteric Drug in Rats Due to Lysosomal Accumulation and Conversion to a Poorly Soluble Hydrochloride Salt

Poor solubility of drug candidates mainly affects bioavailability, but poor solubility of drugs and metabolites can also lead to precipitation within tissues, particularly when high doses are tested. RO0728617 is an amphoteric compound bearing basic and acidic moieties that has previously demonstrated good solubility at physiological pH but underwent widespread crystal deposition in multiple tissues in rat toxicity studies. The aim of our investigation was to better characterize these findings and their underlying mechanism(s), and to identify possible screening methods in the drug development process. Main microscopic features observed in rat RO0728617 toxicity studies were extensive infiltrates of crystal-containing macrophages in multiple organs. Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry revealed that these crystals contained the orally administered parent compound, and locality was confirmed to be intracytoplasmic and partly intralysosomal by electron microscopic examination. Crystal formation was explained by lysosomal accumulation of the compound followed by precipitation of the hydrochloride salt under physiological conditions in the lysosomes, which have a lower pH and higher chloride concentration in comparison to the cytosol. This study demonstrates that risk of drug precipitation can be assessed by comparing the estimated lysosomal drug concentration at a given dose with the solubility of the compound at lysosomal conditions.

Safety, Tissue Distribution, and Metabolism of LNA-Containing Antisense Oligonucleotides in Rats

Antisense oligonucleotides (ASOs) are chemically modified nucleic acids with therapeutic potential, some of which have been approved for marketing. We performed a study in rats to investigate mechanisms of toxicity after administration of 3 tool locked nucleic acid (LNA)-containing ASOs with differing established safety profiles. Four male rats per group were dosed once, 3, or 6 times subcutaneously, with 7 days between dosing, and sacrificed 3 days after the last dose. These ASOs were either unconjugated (naked) or conjugated with N-acetylgalactosamine for hepatocyte-targeted delivery. The main readouts were in-life monitoring, clinical and anatomic pathology, exposure assessment and metabolite identification in liver and kidney by liquid chromatography coupled to tandem mass spectrometry, ASO detection in liver and kidney by immunohistochemistry, in situ hybridization, immune electron microscopy, and matrix-assisted laser desorption/ionization mass spectrometry imaging. The highly toxic compounds showed the greatest amount of metabolites and a low degree of tissue accumulation. This study reveals different patterns of cell death associated with toxicity in liver (apoptosis and necrosis) and kidney (necrosis only) and provides new ultrastructural insights on the tissue accumulation of ASOs. We observed that the immunostimulatory properties of ASOs can be either primary from sequence-dependent properties or secondary to cell necrosis.

The Association between Tumour Markers and Meta-iodobenzylguanidine Scans in South African Children with High-risk Neuroblastoma

AIMS

Diagnostic and post-induction ¹²³I-meta-iodobenzylguanidine (¹²³I-mIBG) scans have prognostic significance in the treatment of neuroblastoma, but data from low- and middle-income countries are limited due to resource constraints. The aim of this study was to determine the association between neuroblastoma-associated tumour markers (lactate dehydrogenase [LDH], ferritin and MYCN amplification) and ¹²³I-mIBG scans (modified Curie scores and metastatic disease patterns) in predicting complete metastatic response rates (mCR) and overall survival.

MATERIALS AND METHODS

Two hundred and ninety patients diagnosed with high-risk neuroblastoma in South Africa between January 2000 and May 2018 and a subanalysis of 78 patients with diagnostic ¹²³I-mIBG scans were included. Data collection included LDH, ferritin and MYCN amplification at diagnosis. Two nuclear physicians independently determined the modified Curie scores and pattern of distribution for each diagnostic and post-induction ¹²³I-mIBG scans with high inter-rater agreement (r = 0.952) and reliability (K = 0.805). The cut-off values for the diagnostic and post-induction modified Curie scores of ≥7.0 (P = 0.026) and 3 (P = 0.009), respectively, were generated. The association between the tumour markers and the modified Curie score of the ¹²³I-mIBG scans was determined using post-induction mCR and 2-year overall survival.

RESULTS

Diagnostic LDH (P < 0.001), ferritin (P < 0.001) and the diagnostic modified Curie scores (P = 0.019) significantly predicted mCR. Only ferritin correlated with diagnostic modified Curie scores (P = 0.003) but had a low correlation coefficient of 0.353. On multivariable analysis, the only significant covariate for 2-year overall survival at diagnosis was LDH <750 U/l (P = 0.024). A post-induction chemotherapy modified Curie score ≤3.0 had a 2-year overall survival of 46.2% compared with 30.8% for a score >3.0 (P = 0.484).

CONCLUSION

LDH, ferritin and the diagnostic ¹²³I-mIBG scans significantly predicted mCR, but only LDH predicted 2-year overall survival. Ferritin and the modified Curie scores correlated with each other. MYCN amplification neither correlated with any aspect of the ¹²³I-mIBG scans nor significantly predicted mCR or 2-year overall survival. LDH and ferritin are therefore appropriate neuroblastoma tumour markers to be used in low- and middle-income countries with limited or no access to mIBG scans and/or MYCN amplification studies.

Characterization of the pharmacokinetics of entrectinib and its active M5 metabolite in healthy volunteers and patients with solid tumors

BACKGROUND

Entrectinib is an oral, CNS-active, potent inhibitor of tyrosine receptor kinases A/B/C, tyrosine kinase ROS proto-oncogene 1, and anaplastic lymphoma kinase approved for use in patients with solid tumors. We describe 3 clinical studies, including one investigating the single/multiple dose pharmacokinetics of entrectinib in patients and two studies in healthy volunteers investigating the absorption/distribution/metabolism/excretion (ADME) of entrectinib, its relative bioavailability, and effect of food on pharmacokinetics.

METHODS

The patient study is open-label with dose-escalation and expansion phases. Volunteers received entrectinib (100-400 mg/m², and 600-800 mg) once daily with food in continuous 28-day cycles. In the ADME study, volunteers received a single oral dose of [¹⁴C]entrectinib 600 mg. In the third study, volunteers received single doses of entrectinib 600 mg as the research and marketed formulations in the fasted state (Part 1), and the marketed formulation in the fed and fasted states (Part 2). Entrectinib and its major active metabolite M5 were assessed in all studies.

RESULTS

Entrectinib was absorbed in a dose-dependent manner with maximum concentrations at ~4 h postdose and an elimination half-life of ~20 h. Entrectinib was cleared mainly through metabolism and both entrectinib and metabolites were eliminated mainly in feces (minimal renal excretion). At steady-state, the M5-to-entrectinib AUC ratio was 0.5 (with 600 mg entrectinib research formulation in patients). The research and marketed formulations were bioequivalent and food had no relevant effect on pharmacokinetics.

CONCLUSIONS

Entrectinib is well absorbed, with linear PK that is suitable for once-daily dosing, and can be taken with or without food.

Prediction admission in the older population in the Emergency Department: the CLEARED tool

BACKGROUND

Length of stay (LOS) in the Emergency Department (ED) is correlated with an extended in-hospital LOS and may even increase 30-day mortality. Older patients represent a growing population in the ED and they are especially at risk of adverse outcomes. Screening tools that adequately predict admission could help reduce waiting times in the ED and reduce time to treatment. We aimed to develop and validate a clinical prediction tool for admission, applicable to the aged patient population in the ED.

METHODS

Data from 7,606 ED visits of patients aged 70 years and older between 2012 and 2014 were used to develop the CLEARED tool. Model performance was assessed with discrimination using logistic regression and calibration. The model was internally validated by bootstrap resampling in Erasmus Medical Center and externally validated at two other hospitals, Medisch Spectrum Twente (MST) and Leiden University Medical Centre (LUMC).

RESULTS

CLEARED contains 10 predictors: body temperature, heart rate, diastolic blood pressure, systolic blood pressure, oxygen saturation, respiratory rate, referral status, the Manchester Triage System category, and the need for laboratory or radiology testing. The internally validated area under the curve (AUC) was 0.766 (95% CI [0.759;0.781]). External validation in MST showed an AUC of 0.797 and in LUMC, an AUC of 0.725.

CONCLUSIONS

The developed CLEARED tool reliably predicts admission in elderly patients visiting the ED. It is a promising prompt, although further research is needed to implement the tool and to investigate the benefits in terms of reduction of crowding and LOS in the ED.

Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease

BACKGROUND

The roles of asymptomatic hyperuricemia or uric acid (UA) crystals in CKD progression are unknown. Hypotheses to explain links between UA deposition and progression of CKD include that (1) asymptomatic hyperuricemia does not promote CKD progression unless UA crystallizes in the kidney; (2) UA crystal granulomas may form due to pre-existing CKD; and (3) proinflammatory granuloma-related M1-like macrophages may drive UA crystal-induced CKD progression.

METHODS

MALDI-FTICR mass spectrometry, immunohistochemistry, 3D confocal microscopy, and flow cytometry were used to characterize a novel mouse model of hyperuricemia and chronic UA crystal nephropathy with granulomatous nephritis. Interventional studies probed the role of crystal-induced inflammation and macrophages in the pathology of progressive CKD.

RESULTS

Asymptomatic hyperuricemia alone did not cause CKD or drive the progression of aristolochic acid I-induced CKD. Only hyperuricemia with UA crystalluria due to urinary acidification caused tubular obstruction, inflammation, and interstitial fibrosis. UA crystal granulomas surrounded by proinflammatory M1-like macrophages developed late in this process of chronic UA crystal nephropathy and contributed to the progression of pre-existing CKD. Suppressing M1-like macrophages with adenosine attenuated granulomatous nephritis and the progressive decline in GFR. In contrast, inhibiting the JAK/STAT inflammatory pathway with tofacitinib was not renoprotective.

CONCLUSIONS

Asymptomatic hyperuricemia does not affect CKD progression unless UA crystallizes in the kidney. UA crystal granulomas develop late in chronic UA crystal nephropathy and contribute to CKD progression because UA crystals trigger M1-like macrophage-related interstitial inflammation and fibrosis. Targeting proinflammatory macrophages, but not JAK/STAT signaling, can attenuate granulomatous interstitial nephritis.

Identification and Preclinical Development of a 2,5,6-Trisubstituted Fluorinated Pyridine Derivative as a Radioligand for the Positron Emission Tomography Imaging of Cannabinoid Type 2 Receptors

Despite the broad implications of the cannabinoid type 2 receptor (CB2) in neuroinflammatory processes, a suitable CB2-targeted probe is currently lacking in clinical routine. In this work, we synthesized 15 fluorinated pyridine derivatives and tested their binding affinities toward CB2 and CB1. With a sub-nanomolar affinity (K_i for CB2) of 0.8 nM and a remarkable selectivity factor of >12,000 over CB1, RoSMA-18-d₆ exhibited outstanding in vitro performance characteristics and was radiofluorinated with an average radiochemical yield of 10.6 ± 3.8% (n = 16) and molar activities ranging from 52 to 65 GBq/μmol (radiochemical purity > 99%). [¹⁸F]RoSMA-18-d₆ showed exceptional CB2 attributes as demonstrated by in vitro autoradiography, ex vivo biodistribution, and positron emission tomography (PET). Further, [¹⁸F]RoSMA-18-d₆ was used to detect CB2 upregulation on postmortem human ALS spinal cord tissues. Overall, these results suggest that [¹⁸F]RoSMA-18-d₆ is a promising CB2 PET radioligand for clinical translation.

Structure-Activity Relationship Studies of Pyridine-Based Ligands and Identification of a Fluorinated Derivative for Positron Emission Tomography Imaging of Cannabinoid Type 2 Receptors

The cannabinoid type 2 (CB2) receptor has emerged as a valuable target for therapy and imaging of immune-mediated pathologies. With the aim to find a suitable radiofluorinated analogue of the previously reported CB2 positron emission tomography (PET) radioligand [¹¹C]RSR-056, 38 fluorinated derivatives were synthesized and tested by in vitro binding assays. With a K_i (hCB2) of 6 nM and a selectivity factor of nearly 700 over cannabinoid type 1 receptors, target compound 3 exhibited optimal in vitro properties and was selected for evaluation as a PET radioligand. [¹⁸F]3 was obtained in an average radiochemical yield of 11 ± 4% and molar activities between 33 and 114 GBq/μmol. Specific binding of [¹⁸F]3 to CB2 was demonstrated by in vitro autoradiography and in vivo PET experiments using the CB2 ligand GW-405 833. Metabolite analysis revealed only intact [¹⁸F]3 in the rat brain. [¹⁸F]3 detected CB2 upregulation in human amyotrophic lateral sclerosis spinal cord tissue and may thus become a candidate for diagnostic use in humans.

Prediction models for mortality in adult patients visiting the Emergency Department: a systematic review

We provide a systematic overview of literature on prediction models for mortality in the Emergency Department (ED). We searched various databases for observational studies in the ED or similar setting describing prediction models for short-term mortality (up to 30 days or in-hospital mortality) in a non-trauma population. We used the CHARMS-checklist for quality assessment. We found a total of 14.768 articles and included 17 articles, describing 22 models. Model performance ranged from AUC 0.63-0.93. Most articles had a moderate risk of bias in one or more domains. The full model and PARIS model performed best, but are not yet ready for implementation. There is a need for validation studies to compare multiple prediction models and to evaluate their accuracy.

Drug-induced Obstructive and Retrograde Nephropathy Associated with α2u-globulin in Male Rats

The chemically induced accumulation of α2u-globulin protein in male rats causes specific renal lesions and subsequent nephropathy. Herein, we report additional parallel findings in the kidney of male rats consistent with obstructive and retrograde nephropathy. Kidney and urinary bladder samples were evaluated from Wistar rats treated with RG7129 for 2 week and 8 week and from an 8-week mechanistic study using females, intact and castrated males. Histopathological findings were present in intact males in all studies, including hyaline droplet accumulation and granular casts consistent with α2u-globulin nephropathy. In addition, tubular degeneration and regeneration, tubular changes extending from papilla to cortex, tubular dilation, and interstitial and luminal inflammation were observed consistent with retrograde and obstructive nephropathy. Renal and urinary lesions and their severity increased in a time- and dose-dependent manner. Urinalysis findings, including increases in leukocytes, protein, and in kidney biomarkers, kidney injury molecule 1 and clusterin, were present only in intact males. No treatment-related changes were observed in female rats or in castrated males. These results indicate that RG7129 induces α2u-globulin nephropathy, associated with retrograde and obstructive nephropathy secondary to precipitation in intact male rats only, constituting a species- and sex-specific syndrome that is not expected to occur in humans or other species.

Correction: Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry

[This corrects the article DOI: 10.1371/journal.pone.0186461.].

Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry

Interest in using peptide molecules as therapeutic agents due to high selectivity and efficacy is increasing within the pharmaceutical industry. However, most peptide-derived drugs cannot be administered orally because of low bioavailability and instability in the gastrointestinal tract due to protease activity. Therefore, structural modifications peptides are required to improve their stability. For this purpose, several in-silico software tools have been developed such as PeptideCutter or PoPS, which aim to predict peptide cleavage sites for different proteases. Moreover, several databases exist where this information is collected and stored from public sources such as MEROPS and ExPASy ENZYME databases. These tools can help design a peptide drug with increased stability against proteolysis, though they are limited to natural amino acids or cannot process cyclic peptides, for example. We worked to develop a new methodology to analyze peptide structure and amide bond metabolic stability based on the peptide structure (linear/cyclic, natural/unnatural amino acids). This approach used liquid chromatography / high resolution, mass spectrometry to obtain the analytical data from in vitro incubations. We collected experimental data for a set (linear/cyclic, natural/unnatural amino acids) of fourteen peptide drugs and four substrate peptides incubated with different proteolytic media: trypsin, chymotrypsin, pepsin, pancreatic elastase, dipeptidyl peptidase-4 and neprilysin. Mass spectrometry data was analyzed to find metabolites and determine their structures, then all the results were stored in a chemically aware manner, which allows us to compute the peptide bond susceptibility by using a frequency analysis of the metabolic-liable bonds. In total 132 metabolites were found from the various in vitro conditions tested resulting in 77 distinct cleavage sites. The most frequent observed cleavage sites agreed with those reported in the literature. The main advantages of the developed approach are the abilities to elucidate metabolite structure of cyclic peptides and those containing unnatural amino acids, store processed information in a searchable format within a database leading to frequency analysis of the labile sites for the analyzed peptides. The presented algorithm may be useful to optimize peptide drug properties with regards to cleavage sites, stability, metabolism and degradation products in drug discovery.

Identification of GalNAc-Conjugated Antisense Oligonucleotide Metabolites Using an Untargeted and Generic Approach Based on High Resolution Mass Spectrometry

Antisense oligonucleotides linked by phosphorothioates are an important class of therapeutics under investigation in various pharmaceutical companies. Antisense oligonucleotides may be coupled to high-affinity ligands (triantennary N-acetyl galactosamine = GalNAc) for hepatocyte-specific asialoglycoprotein receptors (ASGPR) to enhance uptake to hepatocytes and to increase potency. Since disposition and biotransformation of GalNAc-conjugated oligonucleotides is different from unconjugated oligonucleotides, appropriate analytical methods are required to identify main cleavage sites and degradation products of GalNAc conjugated and unconjugated oligonucleotides in target cells. A highly sensitive method was developed to identify metabolites of oligonucleotides using capillary flow liquid chromatography with column switching coupled to a high resolution Orbitrap Fusion mass spectrometer. Detection of GalNAc-conjugated oligonucleotides and their metabolites was achieved by combining full scan MS with two parallel MS² experiments, one data-dependent scan and an untargeted MS² experiment (all ion fragmentation) applying high collision energy. In the all ion fragmentation scan, a diagnostic fragment originating from the phosphorothioate backbone (O₂PS-: m/z 94.936) was formed efficiently upon collisional activation. Based on this fragment an accurate determination of metabolites of oligonucleotides was achieved, independent of their sequence or conjugation in an untargeted but highly selective manner. The method was effectively applied to investigate uptake and metabolism of GalNAc-conjugated oligonucleotides in incubations of primary rat hepatocytes; the elucidation of expected and unexpected degradation products was achieved in subnanomolar range.

Software-aided cytochrome P450 reaction phenotyping and kinetic analysis in early drug discovery

RATIONALE

Cytochrome P450 (CYP450) reaction phenotyping (CRP) and kinetic studies are essential in early drug discovery to determine which metabolic enzymes react with new drug entities. A new semi-automated computer-assisted workflow for CRP is introduced in this work. This workflow provides not only information regarding parent disappearance, but also metabolite identification and relative metabolite formation rates for kinetic analysis.

METHODS

Time-course experiments based on incubating six probe substrates (dextromethorphan, imipramine, buspirone, midazolam, ethoxyresorufin and diclofenac) with recombinant human enzymes (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) and human liver microsomes (HLM) were performed. Liquid chromatography/high-resolution mass spectrometry (LC/HRMS) analysis was conducted with an internal standard to obtain high-resolution full-scan and MS/MS data. Data were analyzed using Mass-MetaSite software. A server application (WebMetabase) was used for data visualization and review.

RESULTS

CRP experiments were performed, and the data were analyzed using a software-aided approach. This automated-evaluation approach led to (1) the detection of the CYP450 enzymes responsible for both substrate depletion and metabolite formation, (2) the identification of specific biotransformations, (3) the elucidation of metabolite structures based on MS/MS fragment analysis, and (4) the determination of the initial relative formation rates of major metabolites by CYP450 enzymes.

CONCLUSIONS

This largely automated workflow enabled the efficient analysis of HRMS data, allowing rapid evaluation of the involvement of the main CYP450 enzymes in the metabolism of new molecules during drug discovery.

Post-acquisition analysis of untargeted accurate mass quadrupole time-of-flight MS(E) data for multiple collision-induced neutral losses and fragment ions of glutathione conjugates

RATIONALE

Analytical methods to assess glutathione (GSH) conjugate formation based on mass spectrometry usually take advantage of the specific fragmentation behavior of the glutathione moiety. However, most methods used for GSH adduct screening monitor only one specific neutral loss or one fragment ion, even though the peptide moiety of GSH adducts shows a number of other specific neutral fragments and fragment ions which can be used for identification.

METHODS

Nine reference drugs well known to form GSH adducts were incubated with human liver microsomes. Mass spectrometric analysis was performed with a quadrupole time-of-flight mass spectrometer in untargeted accurate mass MS(E) mode. The data analysis and evaluation was achieved in an automated approach with software to extract and identify GSH conjugates based on the presence of multiple collision-induced neutral losses and fragment ions specific for glutathione conjugates in the high-energy MS spectra.

RESULTS

In total 42 GSH adducts were identified. Eight (18%) adducts did not show the neutral loss of 129 but were identified based on the appearance of other GSH-specific neutral losses or fragment ions. In high-energy MS(E) spectra the GSH-specific fragment ions of m/z 308 and 179 as well as the neutral loss of 275 Da were complementary to the commonly used neutral loss of 129 Da. Further, one abundant (yet unpublished) GSH conjugate of troglitazone formed in human liver microsomes was found.

CONCLUSIONS

A software-aided approach was developed to reliably retrieve GSH adduct formation data out of untargeted complex full scan QTOFMS(E) data in a fast and efficient way. The present approach to detect and analyze multiple collision-induced neutral losses and fragment ions of glutathione conjugates in untargeted MS(E) data might be applicable to higher throughput to assess reactive metabolite formation in drug discovery.

Determination of tropical deforestation rates and related carbon losses from 1990 to 2010

We estimate changes in forest cover (deforestation and forest regrowth) in the tropics for the two last decades (1990-2000 and 2000-2010) based on a sample of 4000 units of 10 ×10 km size. Forest cover is interpreted from satellite imagery at 30 × 30 m resolution. Forest cover changes are then combined with pan-tropical biomass maps to estimate carbon losses. We show that there was a gross loss of tropical forests of 8.0 million ha yr(-1) in the 1990s and 7.6 million ha yr(-1) in the 2000s (0.49% annual rate), with no statistically significant difference. Humid forests account for 64% of the total forest cover in 2010 and 54% of the net forest loss during second study decade. Losses of forest cover and Other Wooded Land (OWL) cover result in estimates of carbon losses which are similar for 1990s and 2000s at 887 MtC yr(-1) (range: 646-1238) and 880 MtC yr(-1) (range: 602-1237) respectively, with humid regions contributing two-thirds. The estimates of forest area changes have small statistical standard errors due to large sample size. We also reduce uncertainties of previous estimates of carbon losses and removals. Our estimates of forest area change are significantly lower as compared to national survey data. We reconcile recent low estimates of carbon emissions from tropical deforestation for early 2000s and show that carbon loss rates did not change between the two last decades. Carbon losses from deforestation represent circa 10% of Carbon emissions from fossil fuel combustion and cement production during the last decade (2000-2010). Our estimates of annual removals of carbon from forest regrowth at 115 MtC yr(-1) (range: 61-168) and 97 MtC yr(-1) (53-141) for the 1990s and 2000s respectively are five to fifteen times lower than earlier published estimates.

The role of limb perfusion studies in the paediatric ischaemic limb

OBJECTIVES

To study the use of limb perfusion scans in children with limb-threatening ischaemia and determine whether such scans are helpful in making clinical decisions.

METHODS

This retrospective study compared the clinical, scan and surgical findings in children who had limb perfusion scans for critical limb ischaemia at Red Cross War Memorial Children's Hospital, Cape Town, South Africa, from July 2001 to December 2010. Records were reviewed and the data analysed for aetiology, clinical findings, limb perfusion results, operative findings and outcome.

RESULTS

There were complete clinical and scan records for 20/22 patients, aged 1 month to 12 years. The causes of limb ischaemia were meningococcal septicaemia (n = 9), septic shock (n = 6), hypovolaemic shock due to gastroenteritis (n = 4), and electrical burns (n = 1). The clinical, scan and surgical findings correlated in 40/48 imaged limbs. In one leg the findings did not correlate, but the perfusion scan results predicted the outcome. In the remaining seven cases the exact correlation was uncertain owing to technical difficulties or absent operative notes.

CONCLUSION

This study describes a method for performing limb perfusion studies in children. Limb perfusion studies correlated well with surgical findings. These studies were useful in treatment decisions, parent and patient counselling and surgical planning. They supplemented clinical examination in assessment of the children.

State and evolution of the African rainforests between 1990 and 2010

This paper presents a map of Africa's rainforests for 2005. Derived from moderate resolution imaging spectroradiometer data at a spatial resolution of 250 m and with an overall accuracy of 84%, this map provides new levels of spatial and thematic detail. The map is accompanied by measurements of deforestation between 1990, 2000 and 2010 for West Africa, Central Africa and Madagascar derived from a systematic sample of Landsat images-imagery from equivalent platforms is used to fill gaps in the Landsat record. Net deforestation is estimated at 0.28% yr(-1) for the period 1990-2000 and 0.14% yr(-1) for the period 2000-2010. West Africa and Madagascar exhibit a much higher deforestation rate than the Congo Basin, for example, three times higher for West Africa and nine times higher for Madagascar. Analysis of variance over the Congo Basin is then used to show that expanding agriculture and increasing fuelwood demands are key drivers of deforestation in the region, whereas well-controlled timber exploitation programmes have little or no direct influence on forest-cover reduction at present. Rural and urban population concentrations and fluxes are also identified as strong underlying causes of deforestation in this study.

Software aided approaches to structure-based metabolite identification in drug discovery and development

Technological advances in mass spectrometry (MS) such as accurate mass high resolution instrumentation have fundamentally changed the approach to systematic metabolite identification over the past decade. Despite technological break-through on the instrumental side, metabolite identification still requires tedious manual data inspection and interpretation of huge analytical datasets. The process of metabolite identification has become largely facilitated and partly automated by cheminformatics approaches such as knowledge base metabolite prediction using, for example, Meteor, MetaDrug, MetaSite and StarDrop that are typically applied pre-acquisition. Likewise, emerging new technologies in postacquisition data analysis like mass defect filtering (MDF) have moved the technology driven analytical methodology to metabolite identification toward generic, structure-based workflows. The biggest challenge for automation however remains the structural assignment of drug metabolites. Software-guided approaches for the unsupervised metabolite identification still cannot compete with expert user manual data interpretation yet. Recently MassMetaSite has been introduced for the automated ranked output of metabolite structures based on the combination of metabolite prediction and interrogation of analytical mass spectrometric data. This approach and others are promising milestones toward an unsupervised process to metabolite identification and structural characterization moving away from a sample focused per-compound approach to a structure-driven generic workflow.

Tetra-μ(3)-hydroxido-tetra-kis-[tricarbonyl-rhenium(I)] pyridine tetra-solvate

The title compound, [Re(4)(μ(3)-OH)(4)(CO)(12)]·4C(5)H(5)N, crystallizes with one tetranuclear rhenium(I) cubane-like molecule and four pyridine mol-ecules in the asymmetric unit. The coordination environment of each Re(I) atom is distorted octahedral. Four intra-molecular O-H⋯N and four inter-molecular C-H⋯O hydrogen-bond inter-actions are observed. Relatively strong hydrogen bonds are found between the hydrogen-bond donor (μ(3)-OH) and acceptor (basic N atom of pyridine), with N⋯O distances between 2.586 (10) and 2.628 (10) Å. Inter-cube distances of 9.873 (2) and 12.376 (3) Å are observed.

Comparison of oncolytic adenoviruses for selective eradication of oral cancer and pre-cancerous lesions

Oncolytic adenoviruses are being investigated as potential anti-cancer agents. Selective lytic replication in cancer cells is essential for an effective and safe treatment. In this study, we compared 11 oncolytic adenoviruses in relevant cell cultures to assess their use for treating oral cancer and pre-cancerous lesions. We determined the cytotoxicity of oncolytic adenovirus infection and calculated selectivity indices for cytotoxicity to cancer cells compared with normal oral keratinocytes and fibroblasts. Keratinocytes were very sensitive to wild-type adenovirus serotype 5 (Ad5); 1- to 3-log more than head and neck squamous cell carcinoma (HNSCC) cells. The potencies of oncolytic adenoviruses to kill HNSCC cells within 7 days after infection ranged from approximately 10 times less potent to approximately 10 times more potent than Ad5. The selectivity indices determined on fibroblasts and keratinocytes differed markedly. Two oncolytic adenoviruses were more selective than Ad5 for HNSCC cells compared with fibroblasts; and five viruses showed selective replication on HNSCC cells compared with keratinocytes. Overall, CRAd-S.RGD with E1A driven by the survivin promoter and an infectivity-enhancing capsid modification showed the most favourable cytotoxicity pattern; being very potent in killing HNSCC cells, only slightly less effective than Ad5 in killing pre-neoplastic keratinocytes and the least toxic to normal keratinocytes.

Biological significance of DNA adducts: comparison of increments over background for various biomarkers of genotoxicity in L5178Y tk(+/-) mouse lymphoma cells treated with hydrogen peroxide and cumene hydroperoxide

DNA is affected by background damage of the order of one lesion per one hundred thousand nucleotides, with depurination and oxidative damage accounting for a major part. This damage contributes to spontaneous mutation and cancer. DNA adducts can be measured with high sensitivity, with limits of detection lower than one adduct per one billion nucleotides. Minute exposures to an exogenous DNA-reactive agent may therefore result in measurable adduct formation, although, as an increment over total DNA damage, a small increment in mutation cannot be measured and would be considered negligible. Here, we investigated whether this discrepancy also holds for adducts that are present as background induced by oxidative stress. L5178Y tk(+/-) mouse lymphoma cells were incubated for 4h with hydrogen peroxide (0, 0.8, 4, 20, 100, 500muM) or cumene hydroperoxide (0, 0.37, 1.1, 3.3, 10muM). Five endpoints of genotoxicity were measured in parallel from aliquots of three replicates of large batches of cells: Two DNA adducts, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 1,N(6)-etheno-2'-deoxyadenosine (varepsilondAdo) measured by LC-MS/MS, as well as strand breaks assessed with the comet assay and in vitro micronucleus test, and gene mutation as assessed using the thymidine kinase gene mutation assay. Background measures of 8-oxodGuo and varepsilondAdo were 500-1000 and 50-90 adducts per 10(9) nucleotides. Upon treatment, neither hydrogen peroxide nor cumene hydroperoxide significantly increased the DNA adduct levels above control. In contrast, dose-related increases above background were observed with both oxidants in the comet assay, the micronucleus test and the gene mutation assay. Differences in sensitivity of the assays were quantified by estimating the concentration of oxidant that resulted in a doubling of the background measure. We conclude that the increase in DNA breakage and mutation induced by hydrogen peroxide and cumene hydroperoxide observed in our in vitro experimental set-up was no direct consequence of the measured DNA adducts. In comparison with data obtained with the methylating agent methyl methanesulfonate we further conclude that the assumption of DNA adducts being oversensitive biomarkers is adduct-specific.

Homocysteine exerts genotoxic and antioxidative effects in vitro

INTRODUCTION

Patients with end-stage renal disease suffer from increased genomic damage and cancer incidence. One possible reason is the accumulation of uremic toxins such as homocysteine (Hcy). Elevated Hcy levels--usually indicative of cardiovascular events--correlated with the genomic damage in cross-sectional studies. Therefore we investigated the genotoxic effects of Hcy in vitro.

METHODS

To analyse the genomic damage, micronucleus tests and the comet-assay were performed in L5178Y and HL60 cells. Additionally, the influence of Hcy on cell cycle progression, DNA-cytosine-methylation, oxidative stress levels and on the cellular glutathione content were determined.

RESULTS

Low millimolar concentrations of Hcy-induced micronuclei in both cell lines but did not enhance the DNA damage observed with the comet-assay. Cell cycle progression was inhibited in S-phase, while DNA-cytosine-methylation remained unchanged. Furthermore, Hcy protected cells challenged with H(2)O(2) from oxidative stress. This was accompanied by an increased cellular glutathione level.

CONCLUSION

Since the genotoxic effect was limited to high Hcy concentrations, a contribution of Hcy to the enhanced genomic damage in end-stage renal disease patients would only be conceivable upon local Hcy accumulation. Whether the detected antioxidant capacity of Hcy is relevant for any situation in patients remains to be elucidated.