Sub-picosecond photodynamics of small neutral copper oxide clusters.

The ultrafast dynamics of neutral copper oxide clusters (CunOx, n < 5) are reported using femtosecond pump probe spectroscopy in the gas phase. The transient spectra recorded for each cluster demonstrate they relax on a 100s of fs timescale followed by a long-lived (>50 ps) response. Density functional theory calculations are performed to determine the lowest energy structures and spin states. Topological descripters for the excited states are calculated (time-dependent density functional theory) to relate the measured excited state dynamics to changes in the cluster's electronic structure with increasing oxidation. Strong field ionization is demonstrated here to be a soft form of ionization and able to record transient signals for clusters previously determined to be unstable to nanosecond multiphoton ionization. The relative cluster stability is further demonstrated by signal enhancement/depreciation that is recorded through the synergy from the two laser pulses. Once the oxygen atoms exceed the number of copper atoms, a weakly bound superoxide O2 unit forms, exhibiting a higher spin state. All clusters that are not in the lowest spin configuration demonstrate fragmentation.

Unknown Metabolite Identification Using Machine Learning Collision Cross-Section Prediction and Tandem Mass Spectrometry.

Ion mobility (IM) spectrometry provides semiorthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics data sets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating de novo molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of Caenorhabditis elegans. For many of those ion features, this workflow enabled the successful filtering of candidate structures generated by in silico MS/MS predictions, though in some cases, annotations were challenged by significant hurdles in instrumentation performance and data analysis. While for 37% of differential features we were able to successfully collect both MS/MS and CCS data, fewer than half of these features benefited from a reduction in the number of possible candidate structures using CCS filtering due to poor matching of the machine learning training sets, limited accuracy of experimental and predicted CCS values, and lack of candidate structures resulting from the MS/MS data. When using a CCS error cutoff of ±3%, on average, 28% of candidate structures could be successfully filtered. Herein, we identify and describe the bottlenecks and limitations associated with the identification of unknowns in non-targeted metabolomics using IM-MS to focus and provide insights into areas requiring further improvement.

A Systematic Review of Evidence-Based High School Melanoma Prevention Curricula.

Incorporation of melanoma prevention behaviors into daily lifestyles is difficult. Data suggest that high school educational programs on skin cancer prevention can be successful and should incorporate evidence-based teaching and learning strategies to achieve greatest impact. The goal of this systematic review is to describe evidence-based educational practices for a high-school melanoma curriculum through a comprehensive review of the literature. Ovid MEDLINE, Embase, CINAHL, and PyscINFO were searched in June 2020 for all original articles published between June 18, 1946 and June 17, 2020. All studies that used an educational curriculum to promote sun safety, skin exams, and early detection to high school students were included. A total of 25 studies with 22,683 adolescent participants were analyzed. Sixteen studies showed a significant increase in knowledge, twenty-one studies showed changes in behavior, and fifteen studies showed significant changes in attitudes. Limitations of this review include the heterogeneity of implementation and outcome reporting of educational curricula. These findings support incorporating active learning strategies as key aspects of creating an effective curriculum aimed at the prevention and early detection of melanoma.

CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics.

Metabolite annotation continues to be the widely accepted bottleneck in nontargeted metabolomics workflows. Annotation of metabolites typically relies on a combination of high-resolution mass spectrometry (MS) with parent and tandem measurements, isotope cluster evaluations, and Kendrick mass defect (KMD) analysis. Chromatographic retention time matching with standards is often used at the later stages of the process, which can also be followed by metabolite isolation and structure confirmation utilizing nuclear magnetic resonance (NMR) spectroscopy. The measurement of gas-phase collision cross-section (CCS) values by ion mobility (IM) spectrometry also adds an important dimension to this workflow by generating an additional molecular parameter that can be used for filtering unlikely structures. The millisecond timescale of IM spectrometry allows the rapid measurement of CCS values and allows easy pairing with existing MS workflows. Here, we report on a highly accurate machine learning algorithm (CCSP 2.0) in an open-source Jupyter Notebook format to predict CCS values based on linear support vector regression models. This tool allows customization of the training set to the needs of the user, enabling the production of models for new adducts or previously unexplored molecular classes. CCSP produces predictions with accuracy equal to or greater than existing machine learning approaches such as CCSbase, DeepCCS, and AllCCS, while being better aligned with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Another unique aspect of CCSP 2.0 is its inclusion of a large library of 1613 molecular descriptors via the Mordred Python package, further encoding the fine aspects of isomeric molecular structures. CCS prediction accuracy was tested using CCS values in the McLean CCS Compendium with median relative errors of 1.25, 1.73, and 1.87% for the 170 [M - H]-, 155 [M + H]+, and 138 [M + Na]+ adducts tested. For superclass-matched data sets, CCS predictions via CCSP allowed filtering of 36.1% of incorrect structures while retaining a total of 100% of the correct annotations using a ΔCCS threshold of 2.8% and a mass error of 10 ppm.

Historical overview, current research, and emerging bioethical guidelines in researching the New York African burial ground.

OBJECTIVES: The issues addressed in this article are those related to the bioethical actions and decisions surrounding the excavation of the New York African Burial Ground (NYABG) in the 1990s, the significance of conducting research on historical African/African American remains, and the eminence of protecting newly discovered African American burial sites in the future for research purposes. MATERIALS AND METHODS: Skeletal (n = 419, at the time of excavation) and soil (n = 92) remains of the 17th and 18th century New York African Burial Ground were used to discuss the necessity of research on historical African/African American remains. DISCUSSION: Studying the remains of enslaved Africans is critical to understanding the biological processes and existence of all people. Researching the NYABG site, the oldest and largest burial site of free and enslaved Africans, illuminates the necessity and significance of scientific research on other historical African/African American cemeteries throughout the nation. The results of future research will provide a more profound sense of identity for a group of people who were forcefully severed from their genetic and cultural origins. This research will increase the representation of African descended people in genomic, anthropological, and cultural research, and ultimately help researchers to learn more about the origins of all humans.

Perioperative management of pyoderma gangrenosum.

Pyoderma gangrenosum (PG) classically presents with an acute inflammatory stage, characterized by rapid evolution of painful ulcerations. The pathergy associated with PG lesions complicates disease management. Although PG is commonly treated with immunosuppression, some patients have refractory noninflammatory ulcers. In this subpopulation, there are case reports of successful surgical treatment. However, there is no consensus on optimal perioperative treatment for patients with PG undergoing surgery of any kind, PG related or otherwise. Therefore, we conducted a comprehensive literature review describing perioperative management practices and risk factors that may predict response to surgical intervention. We identified 126 cases of surgical intervention in patients with active PG; among these, only 16.7% experienced postoperative disease progression. No perioperative treatments or clinical risk factors were identified as statistically significant predictors of disease recurrence. Although limited by case series design and publication bias, this study is a valuable means of hypothesis generation for this rare condition.

Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains.

Understanding the mechanism(s) underpinning drug resistance could lead to novel treatments to reverse the increased tolerance of a pathogen. In this study, paromomycin (PMM) resistance (PMMr) was induced in three Nepalese clinical strains of Leishmania donovani with different inherent susceptibilities to antimony (Sb) drugs by stepwise exposure of promastigotes to PMM. Exposure to PMM resulted in the production of mixed populations of parasites, even though a single cloned population was used at the start of selection. PMM 50% inhibitory concentration (IC50) values for PMMr parasites varied between 104 and 481 µM at the promastigote stage and 32 and 195 µM at the intracellular amastigote stage. PMM resistance was associated with increased resistance to nitric oxide at the amastigote stage but not the promastigote stage (P < 0.05). This effect was most marked in the Sb-resistant (Sbr) PMMr clone, in which PMM resistance was associated with a significant upregulation of glutathione compared to that in its wild type (P < 0.05), although there was no change in the regulation of trypanothione (detected in its oxidized form). Interestingly, PMMr strains showed an increase in either the keto acid derivative of isoleucine (Sb intermediate PMMr) or the 2-hydroxy acids derived from arginine and tyrosine (Sb susceptible PMMr and Sbr PMMr). These results are consistent with the recent finding that the upregulation of the branched-chain amino acid aminotransferase and d-lactate dehydrogenase is linked to PMMr In addition, we found that PMMr is associated with a significant increase in aneuploidy during PMM selection in all the strains, which could allow the rapid selection of genetic changes that confer a survival advantage.

Aluminum granuloma in a child secondary to DTaP-IPV vaccination: A case report.

Reports detailing the acute formation of aluminum granulomas, which can cause persistent, intensely pruritic nodules secondary to the administration of aluminum-containing vaccines, are infrequently described in medical literature. To our knowledge, this is the first report describing the development of an aluminum granuloma causing a persistent, pruritic nodule at the injection site following the administration of the DTaP-IPV vaccine. We present the case of a 6-year-old girl who developed a severely pruritic subcutaneous nodule on her anterior right thigh at the injection site three weeks after the administration of the aluminum-containing DTaP-IPV (Kinrix) vaccine. The nodule was eventually excised 14 months after its initial appearance, after which her symptoms resolved. Histologic inspection demonstrated a dense, deep dermal and subcutaneous nodular mixed infiltrate of lymphocytes, histiocytes, and eosinophils, with germinal center formation. The bluish, amphophilic granular cytoplasm found in most of the histiocytes is a characteristic feature of "aluminum granulomas." This adverse reaction should be considered in any patient presenting with similar findings in the weeks following a DTaP-IPV vaccination or other aluminum-containing vaccines. Furthermore, the self-limiting tendency of these nodules should not preclude affected patients from any future vaccinations, though vaccines without aluminum should be preferentially selected when possible.

In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization.

In this study, we followed the genomic, lipidomic and metabolomic changes associated with the selection of miltefosine (MIL) resistance in two clinically derived Leishmania donovani strains with different inherent resistance to antimonial drugs (antimony sensitive strain Sb-S; and antimony resistant Sb-R). MIL-R was easily induced in both strains using the promastigote-stage, but a significant increase in MIL-R in the intracellular amastigote compared to the corresponding wild-type did not occur until promastigotes had adapted to 12.2 µM MIL. A variety of common and strain-specific genetic changes were discovered in MIL-adapted parasites, including deletions at the LdMT transporter gene, single-base mutations and changes in somy. The most obvious lipid changes in MIL-R promastigotes occurred to phosphatidylcholines and lysophosphatidylcholines and results indicate that the Kennedy pathway is involved in MIL resistance. The inherent Sb resistance of the parasite had an impact on the changes that occurred in MIL-R parasites, with more genetic changes occurring in Sb-R compared with Sb-S parasites. Initial interpretation of the changes identified in this study does not support synergies with Sb-R in the mechanisms of MIL resistance, though this requires an enhanced understanding of the parasite's biochemical pathways and how they are genetically regulated to be verified fully.

Autism risk associated with parental age and with increasing difference in age between the parents.

Advancing paternal and maternal age have both been associated with risk for autism spectrum disorders (ASD). However, the shape of the association remains unclear, and results on the joint associations is lacking. This study tests if advancing paternal and maternal ages are independently associated with ASD risk and estimates the functional form of the associations. In a population-based cohort study from five countries (Denmark, Israel, Norway, Sweden and Western Australia) comprising 5 766 794 children born 1985-2004 and followed up to the end of 2004-2009, the relative risk (RR) of ASD was estimated by using logistic regression and splines. Our analyses included 30 902 cases of ASD. Advancing paternal and maternal age were each associated with increased RR of ASD after adjusting for confounding and the other parent's age (mothers 40-49 years vs 20-29 years, RR=1.15 (95% confidence interval (CI): 1.06-1.24), P-value<0.001; fathers⩾50 years vs 20-29 years, RR=1.66 (95% CI: 1.49-1.85), P-value<0.001). Younger maternal age was also associated with increased risk for ASD (mothers <20 years vs 20-29 years, RR=1.18 (95% CI: 1.08-1.29), P-value<0.001). There was a joint effect of maternal and paternal age with increasing risk of ASD for couples with increasing differences in parental ages. We did not find any support for a modifying effect by the sex of the offspring. In conclusion, as shown in multiple geographic regions, increases in ASD was not only limited to advancing paternal or maternal age alone but also to differences parental age including younger or older similarly aged parents as well as disparately aged parents.

What happened at Vienna's Allgemeines Krankenhaus after Semmelweis's contract as Assistant in the First Maternity Division was terminated?

Ignác Fülöp Semmelweis is famous for dramatically reducing puerperal mortality while he was an Assistant in Vienna's largest hospital, the Allgemeines Krankenhaus; he did this, mainly, by requiring medical personnel to disinfect their hands by washing in a chlorine solution. But Semmelweis was soon removed from his post as assistant. The conventional view, which is suggested by Semmelweis's own account, is that his contemporaries were skeptical of his results, that he was marginalized and that once he was no longer directly responsible for caring for maternity patients, puerperal mortality returned to its former high levels. In fact, the situation appears to have been quite different. In this paper, we calculate and discuss the number of deaths at the Allgemeines maternity clinic after Semmelweis was removed from his position. As we will see, his successors maintained a relatively low mortality rate roughly consistent with the rate Semmelweis himself achieved. This suggests that the chlorine washings were probably still used conscientiously after he left and that the opposition he encountered had other sources than doubts about the effectiveness of the chlorine washings.

Characterization of large deletions in the DHCR7 gene.

Pathogenic variants in the DHCR7 gene cause Smith-Lemli-Opitz syndrome (SLOS), a defect of cholesterol biosynthesis resulting in an autosomal recessive congenital metabolic malformation disorder. In approximately 4% of patients, the second mutation remains unidentified. In this study, 12 SLOS patients diagnosed clinically and/or by elevated 7-dehydrocholesterol (7-DHC) have been investigated by customized multiplex ligation-dependent probe amplification (MLPA) analysis, because only one DHCR7 sequence variant has been detected. Two unrelated patients of this cohort carry different large deletions in the DHCR7 gene. One patient showed a deletion of exons 3-6. The second patient has a deletion of exons 1 and 2 (non-coding) and lacks the major part of the promoter. These two patients show typical clinical and biochemical phenotypes of SLOS. Second disease-causing mutations are p.(Arg352Trp) and p.(Thr93Met), respectively. Deletion breakpoints were characterized successfully in both cases. Such large deletions are rare in the DHCR7 gene but will resolve some of the patients in whom a second mutation has not been detected.

Triboelectric Nanogenerators for the Masses: A Low-Cost Do-It-Yourself Pulsed Ion Source for Sample-Limited Applications.

Triboelectric nanogenerators (TENG) are useful devices for converting mechanical motion into electric current using readily available materials. Though the applications for these devices span across many fields, TENG can be leveraged for mass spectrometry (MS) as inexpensive and effective power supplies for pulsed nanoelectrospray ionization (nESI). The inherently discontinuous spray provided by TENG is particularly useful in scenarios where high sample economy is imperative, as in the case of ultraprecious samples. Previous work has shown the utility of TENG MS as a highly sensitive technique capable of yielding quality spectra from only a few microliters of sample at low micromolar concentrations. As the field of miniaturized, fieldable mass spectrometers grows, it remains critical to develop advanced ion sources with similarly small power requirements and footprints. Here, we present a redesigned TENG ion source with a sub-1000 USD material cost, lower power consumption, reduced footprint, and improved capabilities. We validate the performance of this new device for a diverse set of applications, including lipid double bond localization and native protein analysis.

Size onset of metallic behavior in neutral aluminum clusters.

The excited state lifetimes of neutral (Al)n clusters up to ∼1 nm in diameter in size, where n ≤ 43, are systematically measured with femtosecond time-resolved mass spectrometry. The onset of metallic behavior is identified as a distinct change in the relaxation behavior initiated with single ultraviolet (400 nm) photon excitation. The experimentally measured excited state lifetimes gradually decrease with size for small molecular scale clusters (n < 10) before becoming indistinguishable for larger clusters (n > 9), where the measurements are comparable to electron-lattice relaxation time of bulk Al (∼300 fs). Particularly intense, or magic, Aln clusters do not exhibit any significant excited state lifetime behavior. Time-dependent density functional theory quantify the excited state properties and are presented to show that dynamics are strongly tied to the excited state charge carrier distributions and overlap, rather than detailed changes related to changes in the cluster's electronic and geometric structure. The consistency in excited state lifetimes for clusters larger than n = 9 is attributed to the hybridization of the s- and p-orbitals as well as increasing delocalization. Al3 exhibits unique temporal delay in its transient behavior that is attributed to a transition from triangular ground state to linear structure upon excitation.

Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in Synovial Sarcoma.

Synovial Sarcoma (SS) is driven by the SS18::SSX fusion oncoprotein and is ultimately refractory to therapeutic approaches. SS18::SSX alters ATP-dependent chromatin remodeling BAF (mammalian SWI/SNF) complexes, leading to the degradation of canonical (cBAF) complex and amplified presence of an SS18::SSX-containing non-canonical BAF (ncBAF or GBAF) that drives an SS-specific transcription program and tumorigenesis. We demonstrate that SS18::SSX activates the SUMOylation program and SSs are sensitive to the small molecule SAE1/2 inhibitor, TAK-981. Mechanistically, TAK-981 de-SUMOylates the cBAF subunit SMARCE1, stabilizing and restoring cBAF on chromatin, shifting away from SS18::SSX-ncBAF-driven transcription, associated with DNA damage and cell death and resulting in tumor inhibition across both human and mouse SS tumor models. TAK-981 synergized with cytotoxic chemotherapy through increased DNA damage, leading to tumor regression. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, positioning the in-clinic TAK-981 to treat SS.

Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in Synovial Sarcoma.

Synovial Sarcoma (SS) is driven by the SS18::SSX fusion oncoprotein. and is ultimately refractory to therapeutic approaches. SS18::SSX alters ATP-dependent chromatin remodeling BAF (mammalian SWI/SNF) complexes, leading to the degradation of canonical (cBAF) complex and amplified presence of an SS18::SSX-containing non-canonical BAF (ncBAF or GBAF) that drives an SS-specific transcription program and tumorigenesis. We demonstrate that SS18::SSX activates the SUMOylation program and SSs are sensitive to the small molecule SAE1/2 inhibitor, TAK-981. Mechanistically, TAK-981 de-SUMOylates the cBAF subunit SMARCE1, stabilizing and restoring cBAF on chromatin, shifting away from SS18::SSX-ncBAF-driven transcription, associated with DNA damage and cell death and resulting in tumor inhibition across both human and mouse SS tumor models. TAK-981 synergized with cytotoxic chemotherapy through increased DNA damage, leading to tumor regression. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, positioning the in-clinic TAK-981 to treat SS.

Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia.

In a previous study, we detected a 6p25-p24 region linked to schizophrenia in families with high composite cognitive deficit (CD) scores, a quantitative trait integrating multiple cognitive measures. Association mapping of a 10 Mb interval identified a 260 kb region with a cluster of single-nucleotide polymorphisms (SNPs) significantly associated with CD scores and memory performance. The region contains two colocalising genes, LYRM4 and FARS2, both encoding mitochondrial proteins. The two tagging SNPs with strongest evidence of association were located around the overlapping putative promoters, with rs2224391 predicted to alter a transcription factor binding site (TFBS). Sequencing the promoter region identified 22 SNPs, many predicted to affect TFBSs, in a tight linkage disequilibrium block. Luciferase reporter assays confirmed promoter activity in the predicted promoter region, and demonstrated marked downregulation of expression in the LYRM4 direction under the haplotype comprising the minor alleles of promoter SNPs, which however is not driven by rs2224391. Experimental evidence from LYRM4 expression in lymphoblasts, gel-shift assays and modelling of DNA breathing dynamics pointed to two adjacent promoter SNPs, rs7752203-rs4141761, as the functional variants affecting expression. Their C-G alleles were associated with higher transcriptional activity and preferential binding of nuclear proteins, whereas the G-A combination had opposite effects and was associated with poor memory and high CD scores. LYRM4 is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters, essential cofactors in multiple processes, including oxidative phosphorylation. LYRM4 downregulation may be one of the mechanisms involved in inefficient oxidative phosphorylation and oxidative stress, increasingly recognised as contributors to schizophrenia pathogenesis.

Ultrafast Proton Transfer and Contact Ion-Pair Formation in Formic Acid Clusters.

The ultrafast proton transfer dynamics of homogeneous formic acid clusters (FA)n, n < 10, are investigated with femtosecond time-resolved mass spectrometry. We monitor the proton transfer pathway following Rydberg state electronic relaxation and find that successful ion pair formation increases logarithmically with cluster size. Ab initio calculations demonstrate similar excitation/relaxation behavior for each cluster, revealing a contact ion pair forms between two molecules composing the cluster before finally a formate anion (HCOO-) is dissociated by the probe pulse. The sub-ps time scale for rearrangement and proton transfer increases almost linearly with cluster size, requiring ∼67 fs per additional formic acid molecule and ranging from 213 ± 51 fs for the trimer to 667 ± 116 fs for FA9. The near-linear trends measured for both rearrangement lifetime and ion pair formation suggest that proton transfer is unlikely in the formic acid dimer but becomes prominent in small clusters.

Nonadiabatic Photodissociation and Dehydrogenation Dynamics of n-Butyl Bromide Following p-Rydberg Excitation.

Femtosecond time-resolved mass spectrometry, correlation mapping, and density functional theory calculations are employed to reveal the mechanism of C═C and C≡C formation (and related H2 production) following excitation to the p-Rydberg states of n-butyl bromide. Ultrafast pump-probe mass spectrometry shows that nonadiabatic relaxation operates as a multistep process reaching an intermediate state within ∼500 fs followed by relaxation to a final state within 10 ps of photoexcitation. Absorption of three ultraviolet photons accesses the dense p-Rydberg state manifold, which is further excited by the probe beam for C─C bond dissociation and dehydrogenation reactions. Rapid internal conversion deactivates the dehydrogenation pathways, while activating carbon backbone dissociation pathways. Thus, unsaturated carbon fragments decay with the lifetime of p-Rydberg (∼500 fs), matching the growth recorded in saturated hydrocarbon fragments. The saturated hydrocarbon signals subsequently decay on the picosecond time scale as the molecule relaxes below the Rydberg states and into halogen release channels.