The Montreal Protocol protects the terrestrial carbon sink.

The control of the production of ozone-depleting substances through the Montreal Protocol means that the stratospheric ozone layer is recovering1 and that consequent increases in harmful surface ultraviolet radiation are being avoided2,3. The Montreal Protocol has co-benefits for climate change mitigation, because ozone-depleting substances are potent greenhouse gases4-7. The avoided ultraviolet radiation and climate change also have co-benefits for plants and their capacity to store carbon through photosynthesis8, but this has not previously been investigated. Here, using a modelling framework that couples ozone depletion, climate change, damage to plants by ultraviolet radiation and the carbon cycle, we explore the benefits of avoided increases in ultraviolet radiation and changes in climate on the terrestrial biosphere and its capacity as a carbon sink. Considering a range of strengths for the effect of ultraviolet radiation on plant growth8-12, we estimate that there could have been 325-690 billion tonnes less carbon held in plants and soils by the end of this century (2080-2099) without the Montreal Protocol (as compared to climate projections with controls on ozone-depleting substances). This change could have resulted in an additional 115-235 parts per million of atmospheric carbon dioxide, which might have led to additional warming of global-mean surface temperature by 0.50-1.0 degrees. Our findings suggest that the Montreal Protocol may also be helping to mitigate climate change through avoided decreases in the land carbon sink.

Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms.

MOTIVATION: Algorithms for classifying chromosomes, like convolutional deep neural networks (CNNs), show promise to augment cytogeneticists' workflows; however, a critical limitation is their inability to accurately classify various structural chromosomal abnormalities. In hematopathology, recurrent structural cytogenetic abnormalities herald diagnostic, prognostic and therapeutic implications, but are laborious for expert cytogeneticists to identify. Non-recurrent cytogenetic abnormalities also occur frequently cancerous cells. Here, we demonstrate the feasibility of using CNNs to accurately classify many recurrent cytogenetic abnormalities while being able to reliably detect non-recurrent, spurious abnormal chromosomes, as well as provide insights into dataset assembly, model selection and training methodology that improve overall generalizability and performance for chromosome classification. RESULTS: Our top-performing model achieved a mean weighted F1 score of 96.86% on the validation set and 94.03% on the test set. Gradient class activation maps indicated that our model learned biologically meaningful feature maps, reinforcing the clinical utility of our proposed approach. Altogether, this work: proposes a new dataset framework for training chromosome classifiers for use in a clinical environment, reveals that residual CNNs and cyclical learning rates confer superior performance, and demonstrates the feasibility of using this approach to automatically screen for many recurrent cytogenetic abnormalities while adeptly classifying non-recurrent abnormal chromosomes. AVAILABILITY AND IMPLEMENTATION: Software is freely available at https://github.com/DaehwanKimLab/Chromosome-ReAd. The data underlying this article cannot be shared publicly due to it being protected patient information. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

On transient climate change at the Cretaceous-Paleogene boundary due to atmospheric soot injections.

Climate simulations that consider injection into the atmosphere of 15,000 Tg of soot, the amount estimated to be present at the Cretaceous-Paleogene boundary, produce what might have been one of the largest episodes of transient climate change in Earth history. The observed soot is believed to originate from global wildfires ignited after the impact of a 10-km-diameter asteroid on the Yucatán Peninsula 66 million y ago. Following injection into the atmosphere, the soot is heated by sunlight and lofted to great heights, resulting in a worldwide soot aerosol layer that lasts several years. As a result, little or no sunlight reaches the surface for over a year, such that photosynthesis is impossible and continents and oceans cool by as much as 28 °C and 11 °C, respectively. The absorption of light by the soot heats the upper atmosphere by hundreds of degrees. These high temperatures, together with a massive injection of water, which is a source of odd-hydrogen radicals, destroy the stratospheric ozone layer, such that Earth's surface receives high doses of UV radiation for about a year once the soot clears, five years after the impact. Temperatures remain above freezing in the oceans, coastal areas, and parts of the Tropics, but photosynthesis is severely inhibited for the first 1 y to 2 y, and freezing temperatures persist at middle latitudes for 3 y to 4 y. Refugia from these effects would have been very limited. The transient climate perturbation ends abruptly as the stratosphere cools and becomes supersaturated, causing rapid dehydration that removes all remaining soot via wet deposition.

Prompt treatment with uridine triacetate improves survival and reduces toxicity due to fluorouracil and capecitabine overdose or dihydropyrimidine dehydrogenase deficiency.

Uridine triacetate has been shown to be an effective antidote against mortality and toxicity caused by either overdoses or exaggerated susceptibility to the widely used anticancer agents 5-fluorouracil (5-FU) and capecitabine. However, a direct assessment of efficacy based on when emergency treatment was initiated was not clinically feasible. In this study we used mouse models of 5-FU overdose and of dihydropyrimidine dehydrogenase (DPD) deficiency to compare the efficacy of uridine triacetate in reducing toxicity and mortality when treatment was initiated at time points from 4 to 144 h after administration of 5-FU. We found that uridine triacetate was effective both in the 5-FU overdose and DPD deficiency models. Starting treatment within 24 h was most effective at reducing toxicity and mortality in both models, while treatment starting more than 96 to 120 h after 5-FU was far less effective. Uridine triacetate also reduced mortality in the DPD deficiency model when mice were treated with the 5-FU prodrug capecitabine. The results of this study are supportive of clinical observations and practice, indicating that efficacy declined progressively with later and later treatment initiation. Prompt treatment with uridine triacetate, within 24 h, conferred the greatest protection against 5-FU overexposure.

Investigating the Conformation of the Bridged Monosaccharide Levoglucosan.

Levoglucosan is one of the main products of the thermal degradation of glucose and cellulose and is commonly used as a tracer for biomass burning. Herein we report a conformational analysis of levoglucosan under isolation conditions, by means of microwave spectroscopy coupled with ultrafast laser vaporization in supersonic expansions. We observed three different conformations of levoglucosan in the gas phase. They all share a common heavy atom rigid bicyclic structure. The difference between the three of them lies in the network of intramolecular hydrogen bonds that arises from the OH groups at positions 2, 3 and 4. The different combinations of H-bonds give richness to the conformational landscape of levoglucosan. The gas phase conformers obtained in this work are compared to the crystal structure of levoglucosan previously reported. Although the heavy atom frame remains unchanged, there are significant differences in the positions of the H-atoms. In addition, the levoglucosan structure can be compared to the related glucose, for which gas phase conformational studies exist in the literature. In this case, in going from glucose to levoglucosan, there is an inversion in the chair conformation of the pyranose ring. This forces the OH groups to adopt axial positions (instead of the more favorable equatorial positions in glucose) and completely changes the pattern of intramolecular H-bonds.

Large amplitude motions within molecules trapped in solid parahydrogen.

Molecules of the ß-diketone and ß-dialdehyde families were trapped in solid parahydrogen (pH2) to investigate the vibrational behavior of systems containing an intramolecular hydrogen bond (IHB). In the simplest ß-diketone, acetylacetone (AcAc), H transfer related to the IHB is coupled with methyl torsions. In pH2, the study of nuclear spin conversion (NSC) in methyl groups allows the characterisation of the influence of these large amplitude motions on the vibrational modes. The deuteration of the OH group involved in the IHB has important consequences on the vibrational spectrum of the molecule and evidence of NSC in methyl groups is difficult to obtain. In the chlorine derivative (3-chloroacetylacetone), the H-transfer is no longer coupled with methyl torsion, and NSC has undetectable effects on the IR spectrum. A search of H tunnelling splitting in the IR spectra of ß-dialdehydes trapped in pH2 was performed. A few modes of 2-chloromalonaldehyde appear as doublets and were assigned to tunnelling levels. The spectroscopic results related to large amplitude motions are detailed and discussed, highlighting puzzling effects.

Molecular Recognition by a Short Partial Peptide of the Adrenergic Receptor: A Bottom-Up Approach.

Receptor-neurotransmitter molecular recognition is key for neurotransmission. Although crystal structures of the receptors are known, the mechanism for recognition is not clear. Reported here is the ultraviolet (UV) and infrared (IR) spectra of complexes between a partial peptide (SIVSF), mimicking the binding motif of a catechol ring in the adrenergic receptor, and various ligands. The UV spectra show that two isomers coexist in the complex of SIVSF with properly recognized ligands, such as protonated adrenaline (adrenalineH+ ). From IR spectra, they are assigned to catechol- and amino-bound structures. The catechol-bound structure is not observed when the ligand is replaced by nonproper molecules, such as noradrenalineH+ . The results suggest that SIVSF not only recognizes the catechol ring but can distinguish differences in the amine side chain. The method provides a new possibility for screening molecules as potential therapeutics for activating the receptor.

Cytogenetic and Cytogenomic Microarray Characterization of Chromothripsis in Chromosome 8 Affecting MOZ/NCOA2 (TIF2), FGFR1, RUNX1T1, and RUNX1 in a Pediatric Acute Myeloid Leukemia.

Concurrent perturbations in different driver genes have been reported primarily in lymphoma. In acute myeloid leukemia (AML), cases with concurrent alterations in 2 driver genes are infrequently reported. In contrast to pathogenetic pathways in lymphoma with concurrently perturbed genes, the initial gene alteration in AML arrests maturation and the alteration in the second gene promote self-renewal of the blasts. Here, we report a unique case of infantile leukemia in which chromothripsis in chromosome 8 completely altered the G-band structure and resulted in concurrent changes in MOZ/NCOA2, FGFR1, RUNX1T1, and RUNX1. These multiple-hit abnormalities in AML have not been reported previously.

Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy.

Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level.

Hg-Xe exciplex formation in mixed Xe/Ar matrices: molecular dynamics and luminescence study.

Luminescence of Hg((3)P1) atoms trapped in mixed Ar/Xe matrices containing a small amount of Xe is reported. Broad emission bands, strongly red-shifted from absorption are recorded which are assigned to strong complexes formed between the excited mercury Hg* and xenon atoms. Molecular dynamics calculations are performed on simulated Xe/Ar samples doped with Hg to follow the behavior of Hg* in the mixed rare gas matrices leading to exciplex formation. The role of Xe atoms in the first solvation shell (SS1) around Hg was investigated in detail, revealing the formation of two kinds of triatomic exciplexes; namely, Xe-Hg*-Xe and Ar-Hg*-Xe. The first species exists only when two xenon atoms are present in SS1 with specific geometries allowing the formation of a linear or quasi-linear exciplex. In the other geometries, or in the presence of only one Xe in SS1, a linear Ar-Hg*-Xe exciplex is formed. The two kinds of exciplexes have different emission bands, the most red-shifted being that involving two Xe atoms, whose emission is very close to that observed in pure Xe matrices. Simulations give a direct access to the analysis of the experimental absorption, emission, and excitation spectra, together with the dynamics of exciplexes formation.

Evaluation of impingement behaviour in lumbar spinal disc arthroplasty.

INTRODUCTION: The objective of our in vitro study was to introduce a test method to evaluate impingement in lumbar spinal disc arthroplasty in terms of wear, contact pattern, metal ion concentration and particle release. MATERIAL AND METHOD: Impingement wear simulation was performed on a 6-station spinal wear simulator (Endolab, Germany) on a lumbar spinal disc system (activ L Aesculap AG, Germany) using four different protocols specific to impingement in flexion, in extension, in lateral bending and in combined flexion bending. Impingement contact stress is intentionally created by applying an angular displacement of +2° in addition to the intended range of motion in the impingement direction, whereas a bending moment of 8 Nm remains constant during the impingement phase (plateau). RESULTS: An average volumetric wear rate of 0.67 mm(3)/million cycles was measured by impingement under flexion, of 0.21 mm(3)/million cycles under extension, of 0.06 mm(3)/million cycles under lateral bending and of 1.44 mm(3)/million cycles under combined flexion bending. The particle size distribution of the cobalt-chromium wear particles released by impingement in flexion (anterior), extension (posterior), lateral bending (lateral) and combined flexion bending (antero-lateral) revealed that most of the detected cobalt-chromium particles were in a size range between 0.2 and 2 µm. CONCLUSION: The impingement wear simulation introduced here proved to be suitable to predict in vivo impingement behaviour in regard to contact pattern seen on retrieved devices of the activ L lumbar disc arthroplasty design in a pre-clinical test.

Automated prediction of acute promyelocytic leukemia from flow cytometry data using a graph neural network pipeline.

OBJECTIVES: Our study aimed to develop a machine learning (ML) model to accurately classify acute promyelocytic leukemia (APL) from other types of acute myeloid leukemia (other AML) using multicolor flow cytometry (MFC) data. Multicolor flow cytometry is used to determine immunophenotypes that serve as disease signatures for diagnosis. METHODS: We used a data set of MFC files from 27 patients with APL and 41 patients with other AML, including those with uncommon immunophenotypes. Our ML pipeline involved training a graph neural network (GNN) to output graph-level labels and identifying the most crucial MFC parameters and cells for predictions using an input perturbation method. RESULTS: The top-performing GNN achieved 100% accuracy on the training/validation and test sets on classifying APL from other AML and used MFC parameters similarly to expert pathologists. Pipeline performance is amenable to use in a clinical decision support system, and our deep learning architecture readily enables prediction explanations. CONCLUSIONS: Our ML pipeline shows robust performance on predicting APL and could be used to screen for APL using MFC data. It also allowed for intuitive interrogation of the model's predictions by clinicians.

RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies.

Background: Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods: Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results: For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions: These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.

Evaluation of metric and representation learning approaches: Effects of representations driven by relative distance on the performance.

Several deep neural network architectures have emerged recently for metric learning. We asked which architecture is the most effective in measuring the similarity or dissimilarity among images. To this end, we evaluated six networks on a standard image set. We evaluated variational autoencoders, Siamese networks, triplet networks, and variational auto-encoders combined with Siamese or triplet networks. These networks were compared to a baseline network consisting of multiple separable convolutional layers. Our study revealed the following: (i) the triplet architecture proved the most effective one due to learning a relative distance - not an absolute distance; (ii) combining auto-encoders with networks that learn metrics (e.g., Siamese or triplet networks) is unwarranted; and (iii) an architecture based on separable convolutional layers is a reasonable simple alternative to triplet networks. These results can potentially impact our field by encouraging architects to develop advanced networks that take advantage of separable convolution and relative distance.

EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networks.

Motivation: Transcriptional enhancers - unlike promoters - are unrestrained by distance or strand orientation with respect to their target genes, making their computational identification a challenge. Further, there are insufficient numbers of confirmed enhancers for many cell types, preventing robust training of machine-learning-based models for enhancer prediction for such cell types. Results: We present EnhancerTracker , a novel tool that leverages an ensemble of deep separable convolutional neural networks to identify cell-type-specific enhancers with the need of only two confirmed enhancers. EnhancerTracker is trained, validated, and tested on 52,789 putative enhancers obtained from the FANTOM5 Project and control sequences derived from the human genome. Unlike available tools, which accept one sequence at a time, the input to our tool is three sequences; the first two are enhancers active in the same cell type. EnhancerTracker outputs 1 if the third sequence is an enhancer active in the same cell type(s) where the first two enhancers are active. It outputs 0 otherwise. On a held-out set (15%), EnhancerTracker achieved an accuracy of 64%, a specificity of 93%, a recall of 35%, a precision of 84%, and an F1 score of 49%. Availability and implementation: https://github.com/BioinformaticsToolsmith/EnhancerTracker. Contact: hani.girgis@tamuk.edu.

Rhabdomyosarcoma With Epithelioid Features And NSD3::FOXO1 Fusion: Evidence For Reconsideration Of Previously Reported FOXO1::FGFR1 Fusion.

Epithelioid rhabdomyosarcoma is a rare rhabdomyosarcoma variant for which no diagnostic recurrent driver genetic events have been identified. Here we report a rapidly progressive and widely metastatic rhabdomyosarcoma with epithelioid features that arose in the thigh of a male infant. Conventional cytogenetics revealed a t(8;13)(p11.2;q14) translocation. Fluorescence in situ hybridization studies showed rearrangement of FOXO1 and amplification of its 3" end, and rearrangement of NSD3 and amplification of its 5` end. Next generation sequencing identified a NSD3::FOXO1 fusion, which is a previously unreported gene fusion. We also review the historic report of a FOXO1::FGFR1 fusion in a solid variant of alveolar rhabdomyosarcoma and propose that NSD3::FOXO1 fusion may have been the more appropriate interpretation of the data presented in that report.

Recombinant chromosome 7 in a mosaic 45,X/47,XXX patient.

Individuals with pericentric inversions are at risk for producing offspring with chromosomal gains and losses, while those carrying paracentric inversions usually produce unviable gametes [Madan, 1995]. In this current study, we present a newborn with dysmorphic features and malformations, whose karyotype showed an abnormal copy of chromomosome 7 described at first as add(7)(q32) as well as mos 45,X/47,XXX. Array comparative genomic hybridization (CGH) revealed an interstitial deletion in the long arm of chromosome 7 involving bands q35 to q36.3 but retaining the 7q subtelomere. The patient's deletion is believed to be due to meiotic recombination in the inversion loop in the phenotypically normal father who seems to carry two paracentric inversions in the long arm of chromosome 7, which was described as rec(7)(7pter- > q35::q36.3- > 7qter)pat. The abnormal copy of chromosome 7 in the father has been described as: der(7)(7pter- > q22.1::q36.3- > q35::q22.1- > q35::q36.3- > 7qter). This is a unique karyotype that to our knowledge has not been previously reported in the literature and predisposes to meiotic recombination that can result in deletions or duplications of 7q35-36.

Photochemistry of acetylacetone isolated in parahydrogen matrices upon 266 nm irradiation.

The photochemistry of the chelated enol form of acetylacetone (AcAc) was investigated by UV excitation of the S(2) state at 266 nm in parahydrogen matrices, complemented by experiments in neon and normal hydrogen matrices. Infrared (IR) spectroscopy, combined with theoretical calculations, was used to identify the photoproducts. Isomerization towards various non-chelated forms (no intramolecular H-bond) of AcAc is the dominant channel whereas fragmentation is very minor. The isomerization kinetics is monitored by IR spectroscopy. Among the seven non-chelated conformers of AcAc, only three are formed in parahydrogen matrices, whereas four are observed in normal hydrogen matrices. This difference suggests that an active tunnelling process between conformers occurs in parahydrogen but is quenched in normal hydrogen where guest-host interactions are stronger. Fragmentation and isomerization of excited AcAc are discussed in the light of these new data. The role of the intermediate triplet state in the S(2)→ S(0) relaxation is confirmed, as the importance of phonons in the condensed phase.

Nuclear spin conversion to probe the methyl rotation effect on hydrogen-bond and vibrational dynamics.

A noteworthy example of a molecule with coupled large-amplitude motions is provided by acetylacetone (methyl group torsions and intramolecular hydrogen bonds). The molecule was trapped in solid parahydrogen to investigate the complex proton tunneling processes. Nuclear spin conversion in methyl groups is observed and, combined with IR spectra, documents the coupling between high frequency modes and large amplitude motions.