Computational Spectroscopy and Reaction Dynamics

Physico- and bio-chemical processes on the femto- to picosecond time scale are ideally suited to be investigated with all-atom simulations. They include, amongst others, vibrational relaxation, ligand migration in sterically demanding environments (proteins, ices), or vibrational spectra. By comparing with experimental data, the results can be used to obtain an understanding of the mechanisms underlying the observations. Furthermore, most of these processes are sensitive to the intermolecular interactions. Therefore, detailed refinement of such interaction potentials is possible

A Survey for Infall Motions toward Starless Cores. II. CS(2−1)CS (2-1) and N2H+(1−0)N_2H^+ (1-0) Mapping Observations

We present the results of an extensive mapping survey of 53 `starless' cores in the optically thick line of CS 2-1 and the optically thin lines of N2H+ 1-0 and C18O 1-0. The purpose of this survey was to search for signatures of extended inward motions. This study finds 10 `strong' and 9 `probable' infall candidates, based on $\delta V_{CS}$ analysis and on the spectral shapes of CS lines. From our analysis of the blue-skewed CS spectra and the $\delta V_{CS}$ parameter, we find typical infall radii of 0.06-0.14 pc. Also, using a simple two layer radiative transfer model to fit the profiles, we derive one-dimensional infall speeds, half of whose values lie in the range of 0.05-0.09 km s$^{-1}$. These values are similar to those found in L1544 by Tafalla et al., and this result confirms that infall speeds in starless cores are generally faster than expected from ambipolar diffusion in a strongly sub-critical core. In addition, the observed infall regions are too extended to be consistent with the `inside-out' collapse model applied to a very low-mass star. In the largest cores, the spatial extent of the CS spectra with infall asymmetry is larger than the extent of the $\rm N_2H^+$ core by a factor of 2-3. All these results suggest that extended inward motions are a common feature in starless cores, and that they could represent a necessary stage in the condensation of a star-forming dense core.Comment: Two tex files for manuscript and tables, and 38 figures. To appear in ApJ

Robust orienting to protofacial stimuli in autism

Newborn infants exhibit a remarkable tendency to orient to faces. This behavior is thought to be mediated by a subcortical mechanism tuned to the protoface stimulus: a face-like configuration comprising three dark areas on a lighter background. When this unique stimulus translates across their visual field, neurotypical infants will change their gaze or head direction to track the protoface [1–3] . Orienting to this low spatial frequency pattern is thought to encourage infants to attend to faces, despite their poor visual acuity [2,3] . By biasing the input into the newborn’s visual system, this primitive instinct may serve to ‘canalize’ the development of more sophisticated face representation. Leading accounts attribute deficits of face perception associated with Autism Spectrum Disorders (ASD) [4] to abnormalities within this orienting mechanism. If infants who are later diagnosed with ASD exhibit reduced protoface orienting, this may compromise the emergence of perceptual expertise for faces [5] . Here we report a novel effect that confirms that the protoface stimulus captures adults’ attention via an involuntary, exogenous process (Experiment 1). Contrary to leading developmental accounts of face perception deficits in ASD, we go on to show that this orienting response is intact in autistic individuals (Experiment 2)

Suicide associated with COVID-19 infection: an immunological point of view

OBJECTIVE: Coronavirus disease 2019 (COVID-19) is a pandemic and leading cause of death. Beyond the deaths directly caused by the virus and the suicides related to the psychological response to the dramatic changes as socioeconomic related to the pandemic, there might also be suicides related to the inflammatory responses of the infection. Infection induces inflammation as a cytokine storm, and there is an increasing number of studies that report a relationship between infection and suicide. MATERIALS AND METHODS: We searched the World Health Organization status report and the PubMed database for keywords (COVID-19, suicide, infection, inflammation, cytokines), and reviewed five cytokine pathways between suicide and inflammation using two meta-analyses and two observational studies starting from November 31, 2020, focusing on the relationship between suicide and inflammation by infection. First, we discussed existing evidence explaining the relationship between suicidal behaviors and inflammation. Second, we summarized the inflammatory features found in COVID-19 patients. Finally, we highlight the potential for these factors to affect the risk of suicide in COVID-19 patients. RESULTS: Patients infected with COVID-19 have high amounts of IL-1β, IFN-γ, IP10, and MCP1, which may lead to Th1 cell response activation. Also, Th2 cytokines (e.g., IL-4 and IL-10) were increased in COVID-19 infection. In COVID-19 patients, neurological conditions, like headache, dizziness, ataxia, seizures, and others have been observed. CONCLUSIONS: COVID-19 pandemic can serve as a significant environmental factor contributing directly to increased suicide risk; the role of inflammation by an infection should not be overlooked

Empirical assessment of biases in cerebrospinal fluid biomarkers of Alzheimer's disease: an umbrella review and re-analysis of data from meta-analyses

OBJECTIVE: Alzheimer’s disease (AD) is a leading cause of years lived with disability in older age, and several cerebrospinal fluid (CSF) markers have been proposed in individual meta-analyses to be associated with AD but field-wide evaluation and scrutiny of the literature is not available. MATERIALS AND METHODS: We performed an umbrella review for the reported associations between CSF biomarkers and AD. Data from available meta-analyses were reanalyzed using both random and fixed effects models. We also estimated between-study heterogeneity, small-study effects, excess significance, and prediction interval. RESULTS: A total of 38 meta-analyses on CSF markers from 11 eligible articles were identified and reanalyzed. In 14 (36%) of the meta-analyses, the summary estimate and the results of the largest study showed non-concordant results in terms of statistical significance. Large heterogeneity (I2≥75%) was observed in 73% and small-study effects under Egger’s test were shown in 28% of CSF biomarkers. CONCLUSIONS: Our results suggest that there is an excess of statistically significant results and significant biases in the literature of CSF biomarkers for AD. Therefore, the results of CSF biomarkers should be interpreted with caution

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment